From 19ef9d72c4f2cb9d5974ae718dad70fe70c12f64 Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Fri, 17 May 2019 20:26:41 -0500 Subject: [PATCH] Closing v0_3_8 --- DESCRIPTION | 4 +- NEWS.md | 3 ++ R/AHerringChile.R | 4 +- R/AlewifeLH.R | 4 +- R/AnchovetaChile.R | 4 +- R/BGHRfish.R | 2 +- R/BGHRsample.R | 2 +- R/BSkateGB.R | 5 +- R/BassFL.R | 5 +- R/BlackDrum2001.R | 4 +- R/BloaterLH.R | 5 +- R/BlueCatfish.R | 5 +- R/BlueCrab.R | 11 +++-- R/BluefishAge.R | 4 +- R/BluegillIL.R | 6 ++- R/BluegillLM.R | 4 +- R/BluntnoseIL1.R | 5 +- R/Bonito.R | 4 +- R/BrookTroutNC.R | 5 +- R/BrookTroutNEWP.R | 6 ++- R/BrookTroutNEWP1.R | 6 ++- R/BrookTroutOnt.R | 8 +++- R/BrownTroutVC1.R | 8 +++- R/BullTroutRML1.R | 5 +- R/BullTroutRML2.R | 5 +- R/BullTroutTC.R | 5 +- R/CCatfishNB.R | 5 +- R/Cabezon.R | 6 ++- R/Casselman1990.R | 2 +- R/ChinookKR.R | 3 +- R/CiscoTL.R | 3 +- R/CrappieARMS.R | 5 +- R/CreekChub.R | 5 +- R/CreelMN.R | 5 +- R/Croaker1.R | 4 +- R/Croaker2.R | 3 +- R/CutthroatALf.R | 9 +++- R/DarterMahon.R | 11 +++-- R/DarterOnt.R | 3 +- R/Deckeretal1999.R | 6 ++- R/EuroPerchTJ.R | 5 +- R/FHCatfish.R | 5 +- R/FHCatfishATL.R | 5 +- R/FWDrumLE1.R | 5 +- R/FWDrumLE2.R | 2 +- R/Ghats.R | 2 +- R/GreensCreekMine.R | 6 ++- R/Hake.R | 5 +- R/HalibutPAC.R | 5 +- R/Herman.R | 4 +- R/HerringBWE.R | 5 +- R/HerringISS.R | 5 +- R/HumpbackWFCR.R | 11 +++-- R/InchLake1.R | 4 +- R/InchLake2.R | 4 +- R/JobfishSIO.R | 11 +++-- R/JonesStockwell.R | 6 ++- R/Jonubi1.R | 5 +- R/Jonubi2.R | 2 +- R/KingCrabAK.R | 5 +- R/LJCisco.R | 5 +- R/LMBassBL.R | 6 ++- R/LMBassLCB.R | 6 ++- R/LakeTroutALTER.R | 9 +++- R/LakeTroutEggs.R | 2 +- R/LakeTroutGIS.R | 5 +- R/LakeTroutMI.R | 5 +- R/Lizardfish.R | 5 +- R/LobsterHI.R | 11 +++-- R/LobsterPEI.R | 7 ++- R/Menhaden1.R | 5 +- R/Morwong1.R | 6 ++- R/Morwong2.R | 6 ++- R/Morwong3.R | 6 ++- R/Morwong4.R | 5 +- R/Morwong4a.R | 2 +- R/Mosquitofish.R | 4 +- R/MulletBS.R | 6 ++- R/MuskieSLR.R | 6 ++- R/MuskieWI06MR.R | 6 ++- R/PSalmonAK.R | 5 +- R/Pallid.R | 5 +- R/Pathfinder.R | 9 +++- R/PikeHL.R | 11 +++-- R/PikeIL.R | 11 +++-- R/PikeNYPartial2.R | 11 +++-- R/PikeWindermere.R | 7 +-- R/PygmyWFBC.R | 7 ++- R/RBSmeltErie.R | 4 +- R/RBSmeltLM.R | 5 +- R/RBTroutKenai.R | 6 ++- R/RBTroutUNSP.R | 11 +++-- R/RWhitefishAI.R | 5 +- R/RWhitefishIR.R | 5 +- R/RedDrum.R | 5 +- R/Riffleshell.R | 8 +++- R/RockBassCL.R | 3 +- R/RockBassL01.R | 5 +- R/RockBassL02.R | 2 +- R/RuffeSLRH92.R | 6 ++- R/RuffeTL89.R | 3 +- R/SLampreyGL.R | 8 ++-- R/SalmonADP.R | 57 ++++++++++++---------- R/SalmonidsMCCA.R | 6 ++- R/SardineChile.R | 66 +++++++++++++------------ R/SardineLK.R | 5 +- R/SardinesPacific.R | 5 +- R/SculpinALTER.R | 8 +++- R/ShadCR.R | 4 +- R/ShrimpGuam.R | 11 +++-- R/SimonsonLyons.R | 69 +++++++++++++++------------ R/SiscowetMI2004.R | 3 +- R/Snapper.R | 10 ++-- R/SnapperHG1.R | 6 +-- R/SnapperHG2.R | 2 +- R/SockeyeKL.R | 12 +++-- R/SockeyeSR.R | 11 +++-- R/SpotVA2.R | 2 +- R/SpottedSucker1.R | 5 +- R/StripedBass1.R | 8 ++-- R/StripedBass2.R | 7 +-- R/StripedBass3.R | 6 +-- R/StripedBass4.R | 8 ++-- R/StripedBass5.R | 8 ++-- R/StripedBass6.R | 8 ++-- R/SturgeonBL.R | 10 ++-- R/SturgeonGB.R | 2 +- R/SunfishIN.R | 18 +++---- R/SunfishLP.R | 5 +- R/TPrawnsEG.R | 5 +- R/TroutADP.R | 6 ++- R/TroutBR.R | 5 +- R/TroutperchLM1.R | 5 +- R/TroutperchLM2.R | 5 +- R/TroutperchLM3.R | 4 +- R/VendaceLP.R | 5 +- R/VendaceLP2.R | 5 +- R/WShrimpGA.R | 5 +- R/WalleyeConsumption.R | 2 +- R/WalleyeEL.R | 5 +- R/WalleyeErie.R | 2 +- R/WalleyeErie2.R | 39 ++++++++++----- R/WalleyeKS.R | 5 +- R/WalleyeML.R | 20 +++++--- R/WalleyeMN06a.R | 5 +- R/WalleyeMN06b.R | 8 +++- R/WalleyePL.R | 8 +++- R/WalleyePS.R | 6 ++- R/WalleyeRL.R | 5 +- R/WalleyeWad.R | 5 +- R/WalleyeWyrlng.R | 5 +- R/WhiteGrunt1.R | 5 +- R/WhiteGrunt2.R | 5 +- R/WhitefishGSL.R | 5 +- R/WhitefishMB.R | 6 ++- R/WhitefishTB.R | 5 +- R/YERockfish.R | 6 ++- R/YPerchCB1.R | 5 +- R/YPerchCB2.R | 5 +- R/YPerchGB.R | 2 +- R/YPerchGL.R | 5 +- R/YPerchRL.R | 2 +- R/YPerchSB.R | 5 +- R/YPerchSB1.R | 6 ++- R/YPerchTL.R | 5 +- R/YTFlounder.R | 6 ++- cran-comments/cran-comments_v0_3_8.md | 9 ++++ man/AHerringChile.Rd | 4 +- man/AlewifeLH.Rd | 4 +- man/AnchovetaChile.Rd | 4 +- man/BGHRfish.Rd | 2 +- man/BGHRsample.Rd | 2 +- man/BSkateGB.Rd | 5 +- man/BassFL.Rd | 5 +- man/BlackDrum2001.Rd | 4 +- man/BloaterLH.Rd | 5 +- man/BlueCatfish.Rd | 5 +- man/BlueCrab.Rd | 9 +++- man/BluefishAge.Rd | 4 +- man/BluegillIL.Rd | 6 ++- man/BluegillLM.Rd | 4 +- man/BluntnoseIL1.Rd | 5 +- man/Bonito.Rd | 4 +- man/BrookTroutNC.Rd | 5 +- man/BrookTroutNEWP.Rd | 6 ++- man/BrookTroutNEWP1.Rd | 6 ++- man/BrookTroutOnt.rd | 8 +++- man/BrownTroutVC1.Rd | 8 +++- man/BullTroutRML1.Rd | 5 +- man/BullTroutRML2.Rd | 5 +- man/BullTroutTC.Rd | 5 +- man/CCatfishNB.Rd | 5 +- man/Cabezon.rd | 6 ++- man/Casselman1990.Rd | 2 +- man/ChinookKR.Rd | 3 +- man/CiscoTL.Rd | 3 +- man/CrappieARMS.Rd | 5 +- man/CreekChub.Rd | 5 +- man/CreelMN.rd | 5 +- man/Croaker1.Rd | 4 +- man/Croaker2.Rd | 3 +- man/CutthroatALf.Rd | 9 +++- man/DarterMahon.Rd | 9 +++- man/DarterOnt.Rd | 3 +- man/Deckeretal1999.Rd | 6 ++- man/EuroPerchTJ.Rd | 5 +- man/FHCatfish.Rd | 5 +- man/FHCatfishATL.Rd | 5 +- man/FWDrumLE1.Rd | 5 +- man/FWDrumLE2.Rd | 2 +- man/Ghats.Rd | 2 +- man/GreensCreekMine.Rd | 6 ++- man/Hake.Rd | 5 +- man/HalibutPAC.Rd | 5 +- man/Herman.Rd | 4 +- man/HerringBWE.Rd | 5 +- man/HerringISS.Rd | 5 +- man/HumpbackWFCR.Rd | 9 +++- man/InchLake1.rd | 4 +- man/InchLake2.rd | 4 +- man/JobfishSIO.Rd | 9 +++- man/JonesStockwell.Rd | 6 ++- man/Jonubi1.Rd | 5 +- man/Jonubi2.Rd | 2 +- man/KingCrabAK.Rd | 5 +- man/LJCisco.Rd | 5 +- man/LMBassBL.Rd | 6 ++- man/LMBassLCB.Rd | 6 ++- man/LakeTroutALTER.Rd | 9 +++- man/LakeTroutEggs.Rd | 2 +- man/LakeTroutGIS.Rd | 5 +- man/LakeTroutMI.Rd | 5 +- man/Lizardfish.Rd | 5 +- man/LobsterHI.Rd | 9 +++- man/LobsterPEI.Rd | 7 ++- man/Menhaden1.Rd | 8 ++-- man/Morwong1.Rd | 6 ++- man/Morwong2.Rd | 6 ++- man/Morwong3.Rd | 6 ++- man/Morwong4.Rd | 5 +- man/Morwong4a.Rd | 2 +- man/Mosquitofish.Rd | 4 +- man/MulletBS.Rd | 6 ++- man/MuskieSLR.Rd | 6 ++- man/MuskieWI06MR.rd | 6 ++- man/PSalmonAK.Rd | 5 +- man/Pallid.Rd | 5 +- man/Pathfinder.Rd | 9 +++- man/PikeHL.Rd | 9 +++- man/PikeIL.Rd | 9 +++- man/PikeNYPartial2.Rd | 9 +++- man/PikeWindermere.Rd | 7 +-- man/PygmyWFBC.Rd | 7 ++- man/RBSmeltErie.Rd | 3 +- man/RBSmeltLM.Rd | 5 +- man/RBTroutKenai.Rd | 6 ++- man/RBTroutUNSP.Rd | 9 +++- man/RWhitefishAI.Rd | 5 +- man/RWhitefishIR.Rd | 5 +- man/RedDrum.Rd | 5 +- man/Riffleshell.Rd | 8 +++- man/RockBassCL.Rd | 3 +- man/RockBassLO1.Rd | 5 +- man/RockBassLO2.Rd | 2 +- man/RuffeSLRH92.Rd | 6 ++- man/RuffeTL89.Rd | 3 +- man/SLampreyGL.Rd | 3 +- man/SalmonADP.Rd | 21 ++++---- man/SalmonidsMCCA.Rd | 6 ++- man/SardineChile.rd | 33 +++++++------ man/SardineLK.Rd | 5 +- man/SardinesPacific.Rd | 5 +- man/SculpinALTER.Rd | 8 +++- man/ShadCR.Rd | 4 +- man/ShrimpGuam.Rd | 9 +++- man/SimonsonLyons.Rd | 33 ++++++------- man/SiscowetMI2004.Rd | 3 +- man/Snapper.Rd | 5 +- man/SnapperHG1.Rd | 6 +-- man/SnapperHG2.Rd | 2 +- man/SockeyeKL.Rd | 5 +- man/SockeyeSR.Rd | 5 +- man/SpotVA2.Rd | 2 +- man/SpottedSucker1.Rd | 5 +- man/StripedBass1.Rd | 4 +- man/StripedBass2.Rd | 3 +- man/StripedBass3.Rd | 2 +- man/StripedBass4.Rd | 4 +- man/StripedBass5.Rd | 4 +- man/StripedBass6.Rd | 4 +- man/SturgeonBL.Rd | 6 ++- man/SturgeonGB.Rd | 2 +- man/SunfishIN.Rd | 18 +++---- man/SunfishLP.Rd | 5 +- man/TPrawnsEG.rd | 5 +- man/TroutADP.Rd | 6 ++- man/TroutBR.Rd | 5 +- man/TroutperchLM1.Rd | 5 +- man/TroutperchLM2.Rd | 5 +- man/TroutperchLM3.Rd | 4 +- man/VendaceLP.Rd | 5 +- man/VendaceLP2.Rd | 5 +- man/WShrimpGA.Rd | 5 +- man/WalleyeConsumption.Rd | 2 +- man/WalleyeEL.Rd | 5 +- man/WalleyeErie.Rd | 2 +- man/WalleyeErie2.Rd | 32 ++++++++----- man/WalleyeKS.Rd | 5 +- man/WalleyeML.Rd | 13 +++-- man/WalleyeMN06a.Rd | 5 +- man/WalleyeMN06b.Rd | 8 +++- man/WalleyePL.Rd | 8 +++- man/WalleyePS.Rd | 6 ++- man/WalleyeRL.Rd | 5 +- man/WalleyeWad.Rd | 5 +- man/WalleyeWyrlng.Rd | 5 +- man/WhiteGrunt1.Rd | 5 +- man/WhiteGrunt2.Rd | 5 +- man/WhitefishGSL.Rd | 5 +- man/WhitefishMB.Rd | 6 ++- man/WhitefishTB.Rd | 5 +- man/YERockfish.rd | 6 ++- man/YPerchCB1.Rd | 5 +- man/YPerchCB2.Rd | 5 +- man/YPerchGB.Rd | 2 +- man/YPerchGL.Rd | 5 +- man/YPerchRL.Rd | 2 +- man/YPerchSB.Rd | 5 +- man/YPerchSB1.Rd | 6 ++- man/YPerchTL.Rd | 5 +- man/YTFlounder.Rd | 6 ++- 331 files changed, 1353 insertions(+), 763 deletions(-) create mode 100644 cran-comments/cran-comments_v0_3_8.md diff --git a/DESCRIPTION b/DESCRIPTION index a14a0aa..06f5307 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: FSAdata Title: Data to Support Fish Stock Assessment ('FSA') Package -Version: 0.3.7 -Date: 2019-03-24 +Version: 0.3.8 +Date: 2019-05-17 Description: The datasets to support the Fish Stock Assessment ('FSA') package. Authors@R: person("Derek","Ogle", email="derek@derekogle.com", diff --git a/NEWS.md b/NEWS.md index f502420..3f83d79 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +# 0.3.8 17-May-19 +* Corrected misues of `\concept` in Rd files per CRAN request. + # 0.3.7 24-Mar-19 * Added `Encoding: UTF-8` to DESCRIPTION. * `PygmyWFBC`: Modified. Added the 2000 data (thought they were there but they were not). diff --git a/R/AHerringChile.R b/R/AHerringChile.R index d40b7f0..f3964e3 100644 --- a/R/AHerringChile.R +++ b/R/AHerringChile.R @@ -20,7 +20,9 @@ #' \item Somers model #' } #' -#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers +#' @concept Seasonal Growth +#' @concept von Bertalanffy +#' @concept Somers #' #' @source From figure 9 of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling? Aquatic Living Resources, 14:115-124. #' diff --git a/R/AlewifeLH.R b/R/AlewifeLH.R index 302c9ea..8d7e4b4 100644 --- a/R/AlewifeLH.R +++ b/R/AlewifeLH.R @@ -20,7 +20,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @source From Table 1A of Hoenig, J.M., M.J. Morgan, and C.A. Brown. 1995. Analysing differences between two age determination methods by tests of symmetry. Canadian Journal of Fisheries And Aquatic Systems, 52:364-368. Originally from O'Gorman, R., D.H. Barwick, and C.A. Bowen. 1987. Discrepancies between ages determined from scales and otoliths for alewives from the Great Lakes. pp. 203-210 In. Summerfelt, R.C. and G.E. Hall (Eds.) Age and Growth of Fish. Iowa State University Press, Ames, IA. #' diff --git a/R/AnchovetaChile.R b/R/AnchovetaChile.R index 8f8faa2..8a4d337 100644 --- a/R/AnchovetaChile.R +++ b/R/AnchovetaChile.R @@ -21,7 +21,9 @@ #' \item Somers model #' } #' -#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers +#' @concept Seasonal Growth +#' @concept von Bertalanffy +#' @concept Somers #' #' @source Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling? Aquatic Living Resources, 14:115-124. Data were in Figure 9. #' diff --git a/R/BGHRfish.R b/R/BGHRfish.R index 7759e4c..cd04bf4 100644 --- a/R/BGHRfish.R +++ b/R/BGHRfish.R @@ -21,7 +21,7 @@ #' \item Data Manipulation #' } #' -#' @concept 'Data Manipulation' +#' @concept Data Manipulation #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/BGHRsample.R b/R/BGHRsample.R index d2b1c84..bc88957 100644 --- a/R/BGHRsample.R +++ b/R/BGHRsample.R @@ -19,7 +19,7 @@ #' \item Data Manipulation #' } #' -#' @concept 'Data Manipulation' +#' @concept Data Manipulation #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/BSkateGB.R b/R/BSkateGB.R index e3bcfd9..1c1567e 100644 --- a/R/BSkateGB.R +++ b/R/BSkateGB.R @@ -22,9 +22,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick. 2009. Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank. North American Journal of Fisheries Management 29:512-526. +#' @source Estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick. 2009. Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank. North American Journal of Fisheries Management 29:512-526. #' #' @keywords datasets #' diff --git a/R/BassFL.R b/R/BassFL.R index e494fdd..8c676ef 100644 --- a/R/BassFL.R +++ b/R/BassFL.R @@ -21,9 +21,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux. 2005. Relative Abundance, Growth, and Mortality of Suwannee Bass in Four Florida Rivers. North American Journal of Fisheries Management 25:275-283. [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.] +#' @source From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux. 2005. Relative Abundance, Growth, and Mortality of Suwannee Bass in Four Florida Rivers. North American Journal of Fisheries Management 25:275-283. [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.] #' #' @keywords datasets #' diff --git a/R/BlackDrum2001.R b/R/BlackDrum2001.R index 5ecc7e4..34af5ca 100644 --- a/R/BlackDrum2001.R +++ b/R/BlackDrum2001.R @@ -26,7 +26,9 @@ #' \item Weight-Length #' } #' -#' @concept Growth 'von Bertalanffy' 'Weight-Length' +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Weight-Length #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/BloaterLH.R b/R/BloaterLH.R index 897db94..49ca5bb 100644 --- a/R/BloaterLH.R +++ b/R/BloaterLH.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 7 of Schaeffer, J.S. 2004. Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998. Ann Zool Fennici. 41:271-279. +#' @source From (approximately) Figure 7 of Schaeffer, J.S. 2004. Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998. Ann Zool Fennici. 41:271-279. #' #' @keywords datasets #' diff --git a/R/BlueCatfish.R b/R/BlueCatfish.R index 67baa17..5afc8c8 100644 --- a/R/BlueCatfish.R +++ b/R/BlueCatfish.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From (approximately) Figure 2 of Maceina, M.J. 2007. Use of piecewise nonlinear models to estimate variable size-related mortality rates. North American Journal of Fisheries Management, 27:971-977. +#' @source From (approximately) Figure 2 of Maceina, M.J. 2007. Use of piecewise nonlinear models to estimate variable size-related mortality rates. North American Journal of Fisheries Management, 27:971-977. #' #' @keywords datasets #' diff --git a/R/BlueCrab.R b/R/BlueCrab.R index 40b2cef..dc2a5a0 100644 --- a/R/BlueCrab.R +++ b/R/BlueCrab.R @@ -22,9 +22,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Fischler, K.J. 1965. The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs. Transactions of the American Fisheries Society, 94:287-310. +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Fischler, K.J. 1965. The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs. Transactions of the American Fisheries Society, 94:287-310. #' #' @keywords datasets #' diff --git a/R/BluefishAge.R b/R/BluefishAge.R index 9d73c82..e1e9b53 100644 --- a/R/BluefishAge.R +++ b/R/BluefishAge.R @@ -18,7 +18,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @source From Figure 2 in Chapter 3 (Bluefish) of the VMRC Final Report on Finfish Ageing, 2003 by the Center for Quantitative Fisheries Ecology at Old Dominion University. #' diff --git a/R/BluegillIL.R b/R/BluegillIL.R index edc05ad..6ea0bd9 100644 --- a/R/BluegillIL.R +++ b/R/BluegillIL.R @@ -22,9 +22,11 @@ #' \item Fabens method #' } #' -#' @concept Growth 'von Bertalanffy' Fabens +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Fabens #' -#' @source These unpublished data are from Derek H. Ogle, Northland College. \bold{Do not use for other than educational purposes without permission from the source.} +#' @source These unpublished data are from Derek H. Ogle, Northland College. \bold{Do not use for other than educational purposes without permission from the source.} #' #' @keywords datasets #' diff --git a/R/BluegillLM.R b/R/BluegillLM.R index b7f85ec..6a5ac56 100644 --- a/R/BluegillLM.R +++ b/R/BluegillLM.R @@ -22,7 +22,9 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' 'Length Conversion' 'Length Frequency' +#' @concept Weight-Length +#' @concept Length Conversion +#' @concept Length Frequency #' #' @keywords datasets #' diff --git a/R/BluntnoseIL1.R b/R/BluntnoseIL1.R index d3a2e32..6abfb9b 100644 --- a/R/BluntnoseIL1.R +++ b/R/BluntnoseIL1.R @@ -21,7 +21,10 @@ #' \item PSD #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD 'Length Expansion' +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD +#' @concept Length Expansion #' #' @seealso \code{\link{InchLake1}}, \code{\link{InchLake2}}. #' diff --git a/R/Bonito.R b/R/Bonito.R index 6bb5e04..95c9369 100644 --- a/R/Bonito.R +++ b/R/Bonito.R @@ -21,7 +21,9 @@ #' \item Somers model #' } #' -#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers +#' @concept Seasonal Growth +#' @concept von Bertalanffy +#' @concept Somers #' #' @source From figure 3 of Stewart, J., W. Robbins, K. Rowling, A. Hegarty, and A. Gould. 2013. A multifaceted approach to modelling growth of the Australian bonito, \emph{Sarda australis} (Family Scombridae), with some observations on its reproductive biology. Marine and Freshwater Research 64:671-678. #' diff --git a/R/BrookTroutNC.R b/R/BrookTroutNC.R index 5ef6e1d..265e355 100644 --- a/R/BrookTroutNC.R +++ b/R/BrookTroutNC.R @@ -20,9 +20,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty. 2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream. Freshwater Biology 55:1494-1508. +#' @source From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty. 2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream. Freshwater Biology 55:1494-1508. #' #' @keywords datasets #' diff --git a/R/BrookTroutNEWP.R b/R/BrookTroutNEWP.R index 5f91c19..9f49326 100644 --- a/R/BrookTroutNEWP.R +++ b/R/BrookTroutNEWP.R @@ -24,9 +24,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Table 1 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. +#' @source From Table 1 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. #' #' @seealso See \code{\link{BrookTroutNEWP1}} for these data AND the results from Schnute (1983). #' diff --git a/R/BrookTroutNEWP1.R b/R/BrookTroutNEWP1.R index 6ee5063..026cfcd 100644 --- a/R/BrookTroutNEWP1.R +++ b/R/BrookTroutNEWP1.R @@ -37,9 +37,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Tables 1-3 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. +#' @source From Tables 1-3 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. #' #' @seealso See \code{\link{BrookTroutNEWP}} for only the data (note the results from Schnute (1983)). #' diff --git a/R/BrookTroutOnt.R b/R/BrookTroutOnt.R index cb677f1..2225b5f 100644 --- a/R/BrookTroutOnt.R +++ b/R/BrookTroutOnt.R @@ -24,9 +24,13 @@ #' \item Petersen #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen #' -#' @source From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan. 2003. Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout. North American Journal of Fisheries Management 23:35-47. +#' @source From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan. 2003. Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout. North American Journal of Fisheries Management 23:35-47. #' #' @keywords datasets #' diff --git a/R/BrownTroutVC1.R b/R/BrownTroutVC1.R index 83c55f9..83a534b 100644 --- a/R/BrownTroutVC1.R +++ b/R/BrownTroutVC1.R @@ -22,9 +22,13 @@ #' \item Petersen #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen #' -#' @source Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society, 126:35-48. +#' @source Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society, 126:35-48. #' #' @keywords datasets #' diff --git a/R/BullTroutRML1.R b/R/BullTroutRML1.R index 5d57061..be5428f 100644 --- a/R/BullTroutRML1.R +++ b/R/BullTroutRML1.R @@ -21,9 +21,10 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' 'Length Frequency' +#' @concept Weight-Length +#' @concept Length Frequency #' -#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] +#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] #' #' @keywords datasets #' diff --git a/R/BullTroutRML2.R b/R/BullTroutRML2.R index 6b47e95..eb36c2e 100644 --- a/R/BullTroutRML2.R +++ b/R/BullTroutRML2.R @@ -22,9 +22,10 @@ #' \item Von Bertalanffy growth model #' } #' -#' @concept Growth 'Von Bertalanffy' +#' @concept Growth +#' @concept Von Bertalanffy #' -#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] +#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] #' #' @keywords datasets #' diff --git a/R/BullTroutTC.R b/R/BullTroutTC.R index 045c3be..ae4e6c1 100644 --- a/R/BullTroutTC.R +++ b/R/BullTroutTC.R @@ -18,9 +18,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho. North American Journal of Fisheries Management 26:190-200. +#' @source From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho. North American Journal of Fisheries Management 26:190-200. #' #' @keywords datasets #' diff --git a/R/CCatfishNB.R b/R/CCatfishNB.R index b801abc..acfdcfa 100644 --- a/R/CCatfishNB.R +++ b/R/CCatfishNB.R @@ -19,11 +19,12 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' -#' @source From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska. Master's thesis, University of Nebraska, Lincoln, NE. [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.] +#' @source From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska. Master's thesis, University of Nebraska, Lincoln, NE. [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.] #' #' @keywords datasets #' diff --git a/R/Cabezon.R b/R/Cabezon.R index b7bc92b..a203479 100644 --- a/R/Cabezon.R +++ b/R/Cabezon.R @@ -22,9 +22,11 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' Maturity +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Maturity #' -#' @source Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.] +#' @source Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.] #' #' @keywords datasets #' diff --git a/R/Casselman1990.R b/R/Casselman1990.R index bf0b4ff..39a6057 100644 --- a/R/Casselman1990.R +++ b/R/Casselman1990.R @@ -21,7 +21,7 @@ #' #' @concept Other #' -#' @source From Figure 8 of Casselman, J.M. 1990. Growth and relative size of calcified structures of fish. Transactions of the American Fisheries Society. 119:673-688. +#' @source From Figure 8 of Casselman, J.M. 1990. Growth and relative size of calcified structures of fish. Transactions of the American Fisheries Society. 119:673-688. #' #' @keywords datasets #' diff --git a/R/ChinookKR.R b/R/ChinookKR.R index b8c053f..8fab55d 100644 --- a/R/ChinookKR.R +++ b/R/ChinookKR.R @@ -19,7 +19,8 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' #' @source Was (is?) from http://www.pcouncil.org/bb/2006/0406/age2a_supp_att3.pdf. #' diff --git a/R/CiscoTL.R b/R/CiscoTL.R index 0e7015d..d85ed54 100644 --- a/R/CiscoTL.R +++ b/R/CiscoTL.R @@ -24,7 +24,8 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' 'Length Frequency' +#' @concept Weight-Length +#' @concept Length Frequency #' #' @source Was (is?) available for download from http://www.limnology.wisc.edu/. #' diff --git a/R/CrappieARMS.R b/R/CrappieARMS.R index 2bd9298..742881a 100644 --- a/R/CrappieARMS.R +++ b/R/CrappieARMS.R @@ -18,9 +18,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda. 1998. An age-structured model for erratic crappie fisheries. Ecological Modeling 107:289-303. +#' @source From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda. 1998. An age-structured model for erratic crappie fisheries. Ecological Modeling 107:289-303. #' #' @keywords datasets #' diff --git a/R/CreekChub.R b/R/CreekChub.R index f21fd79..5b0900b 100644 --- a/R/CreekChub.R +++ b/R/CreekChub.R @@ -20,11 +20,12 @@ #' \item Growth #' } #' -#' @concept 'Age-Length Key' 'Growth' +#' @concept Age-Length Key +#' @concept Growth #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' -#' @source Recreated (andom digits were added to construct mm lengths from the cm length bins) from information in Box 15.2 of Quist, M.C., Pegg, M.A., and DeVries, D.R. 2012. Age and growth. In Zale, A.V., Parrish, D.L., and Sutton, T.M., editors. Fisheries Techniques, Third Edition, chapter 15, pages 677-731. American Fisheries Society, Bethesda, MD. +#' @source Recreated (random digits were added to construct mm lengths from the cm length bins) from information in Box 15.2 of Quist, M.C., Pegg, M.A., and DeVries, D.R. 2012. Age and growth. In Zale, A.V., Parrish, D.L., and Sutton, T.M., editors. Fisheries Techniques, Third Edition, chapter 15, pages 677-731. American Fisheries Society, Bethesda, MD. #' #' @keywords datasets #' diff --git a/R/CreelMN.R b/R/CreelMN.R index e57d91f..1856d88 100644 --- a/R/CreelMN.R +++ b/R/CreelMN.R @@ -19,7 +19,7 @@ #' #' @concept Other #' -#' @source From tables in Cook, M.F., T.J. Goeman, P.J. Radomski, J.A. Younk, and P.C. Jacobson. 2001. Creel limits in Minnesota: A proposal for change. Fisheries 26:19-26. +#' @source From tables in Cook, M.F., T.J. Goeman, P.J. Radomski, J.A. Younk, and P.C. Jacobson. 2001. Creel limits in Minnesota: A proposal for change. Fisheries 26:19-26. #' #' @keywords datasets #' @@ -32,7 +32,7 @@ #' ## ONLY RUN IN INTERACTIVE MODE #' \dontrun{ #' require(FSA) -#' wae <- Subset(CreelMN,species=="WAE") +#' wae <- filterD(CreelMN,species=="WAE") #' ( waetbl <- table(wae$harvest) ) #' ( waeptbl <- prop.table(waetbl)*100 ) #' ( waercum <- rcumsum(waeptbl) ) @@ -50,7 +50,6 @@ #' xtabs(~svd1,data=wae) #' ( svd1 <- sum(wae$svd1[wae$svd1>0]) ) #' round(svd1/ttlwae*100,1) -#' #' } #' NULL \ No newline at end of file diff --git a/R/Croaker1.R b/R/Croaker1.R index 94e2687..8387c7b 100644 --- a/R/Croaker1.R +++ b/R/Croaker1.R @@ -19,7 +19,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @source From Figure 2 in Chapter 1 (Atlantic Croaker) of the VMRC Final Report on Finfish Ageing, 1999 by the Center for Quantitative Fisheries Ecology at Old Dominion University. #' diff --git a/R/Croaker2.R b/R/Croaker2.R index 9a6ce47..843a6f9 100644 --- a/R/Croaker2.R +++ b/R/Croaker2.R @@ -19,7 +19,8 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @source From Figure 4 in Chapter 1 (Atlantic Croaker) of the VMRC Final Report on Finfish Ageing, 1999 by the Center for Quantitative Fisheries Ecology at Old Dominion University. #' diff --git a/R/CutthroatALf.R b/R/CutthroatALf.R index 1b19308..93cf050 100644 --- a/R/CutthroatALf.R +++ b/R/CutthroatALf.R @@ -22,9 +22,14 @@ #' \item Capture History #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Jolly-Seber' 'Capture History' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Jolly-Seber +#' @concept Capture History #' -#' @source Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. Accessed from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf. +#' @source Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. Accessed from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf. #' #' @seealso See \code{CutthroatAL} for the same data in \dQuote{individual} fish format (i.e., the data in this file were converted using \code{capHistConvert} from \pkg{FSA}). See \code{mrOpen} from \pkg{FSA} for an example analysis. #' diff --git a/R/DarterMahon.R b/R/DarterMahon.R index c69759a..7416e0f 100644 --- a/R/DarterMahon.R +++ b/R/DarterMahon.R @@ -26,9 +26,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Mahon, R. 1980. Accuracy of catch-effort methods for estimating fish density and biomass in streams. Environmental Biology of Fishes. 4:343-363. +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Mahon, R. 1980. Accuracy of catch-effort methods for estimating fish density and biomass in streams. Environmental Biology of Fishes. 4:343-363. #' #' @keywords datasets #' diff --git a/R/DarterOnt.R b/R/DarterOnt.R index 31ad397..fec370d 100644 --- a/R/DarterOnt.R +++ b/R/DarterOnt.R @@ -21,7 +21,8 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @source From Figure 2 of Reid, S.M. Age estimates and length distributions of Ontario channel darter (\emph{Percina copelandi}) populations. Journal of Freshwater Ecology 19:441-444. #' diff --git a/R/Deckeretal1999.R b/R/Deckeretal1999.R index e51ffc0..d37d777 100644 --- a/R/Deckeretal1999.R +++ b/R/Deckeretal1999.R @@ -27,9 +27,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Appendix 2a and 2b in Decker, A.S., J.M. Bratty, S.C. Riley, and J. Korman. 1999. Estimating standing stock of juvenile coho salmon (\emph{Oncorhynchus kisutch}) and cutthroat trout (\emph{Oncorhynchus clarki}) in a small stream: a comparison of sampling designs. Canadian Technical Report of Fisheries and Aquatic Sciences 2282. 24 pp. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/239481.pdf.] +#' @source From Appendix 2a and 2b in Decker, A.S., J.M. Bratty, S.C. Riley, and J. Korman. 1999. Estimating standing stock of juvenile coho salmon (\emph{Oncorhynchus kisutch}) and cutthroat trout (\emph{Oncorhynchus clarki}) in a small stream: a comparison of sampling designs. Canadian Technical Report of Fisheries and Aquatic Sciences 2282. 24 pp.[Was (is?) from http://www.dfo-mpo.gc.ca/Library/239481.pdf.] #' #' @keywords datasets #' diff --git a/R/EuroPerchTJ.R b/R/EuroPerchTJ.R index 1aa640b..5d7af03 100644 --- a/R/EuroPerchTJ.R +++ b/R/EuroPerchTJ.R @@ -19,9 +19,10 @@ #' \item fon Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From (approximately) Figure 2 in Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society, 128:483-490. +#' @source From (approximately) Figure 2 in Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society, 128:483-490. #' #' @keywords datasets #' diff --git a/R/FHCatfish.R b/R/FHCatfish.R index 0c66aee..4323165 100644 --- a/R/FHCatfish.R +++ b/R/FHCatfish.R @@ -19,9 +19,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From (approximately) Figure 3 in Sakaris, P.C., E.R. Irwin, J.C. Jolley, and D. Harrison. 2006. Comparison of Native and Introduced Flathead Catfish Populations in Alabama and Georgia: Growth, Mortality, and Management. North American Journal of Fisheries Management 26:867-874. +#' @source From (approximately) Figure 3 in Sakaris, P.C., E.R. Irwin, J.C. Jolley, and D. Harrison. 2006.Comparison of Native and Introduced Flathead Catfish Populations in Alabama and Georgia: Growth, Mortality, and Management. North American Journal of Fisheries Management 26:867-874. #' #' @keywords datasets #' diff --git a/R/FHCatfishATL.R b/R/FHCatfishATL.R index c1b1745..73f76d8 100644 --- a/R/FHCatfishATL.R +++ b/R/FHCatfishATL.R @@ -19,9 +19,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From (approximately) Figure 2 in Kwak, T.J., W.E. Pine III, and D.S. Waters. 2006. Age, growth, and mortality of introduced flathead catfish in Atlantic rivers and a review of other populations. North American Journal of Fisheries Management 26:73-87. +#' @source From (approximately) Figure 2 in Kwak, T.J., W.E. Pine III, and D.S. Waters. 2006. Age, growth, and mortality of introduced flathead catfish in Atlantic rivers and a review of other populations. North American Journal of Fisheries Management 26:73-87. #' #' @keywords datasets #' diff --git a/R/FWDrumLE1.R b/R/FWDrumLE1.R index cbd8716..b23b870 100644 --- a/R/FWDrumLE1.R +++ b/R/FWDrumLE1.R @@ -18,11 +18,12 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @seealso \code{\link{FWDrumLE2}}. #' -#' @source Simulated from Table 3 of Bur, M.T. 1984. Growth, reproduction, mortality, distribution, and biomass of freshwater drum in Lake Erie. Journal of Great Lakes Research. 10:48-58. +#' @source Simulated from Table 3 of Bur, M.T. 1984. Growth, reproduction, mortality, distribution, and biomass of freshwater drum in Lake Erie. Journal of Great Lakes Research. 10:48-58. #' #' @keywords datasets #' diff --git a/R/FWDrumLE2.R b/R/FWDrumLE2.R index b929ad5..cf0b310 100644 --- a/R/FWDrumLE2.R +++ b/R/FWDrumLE2.R @@ -17,7 +17,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{\link{FWDrumLE1}}. #' diff --git a/R/Ghats.R b/R/Ghats.R index 36380c7..848ca75 100644 --- a/R/Ghats.R +++ b/R/Ghats.R @@ -19,7 +19,7 @@ #' #' @concept Other #' -#' @source From (approximately) Figure 1 in Dahanukar, N., R. Raut, and A. Bhat. 2004. Distribution, endemism and threat status of freshwater fishes in the Western Ghats of India. Journal of Biogeography 31:123-126. +#' @source From (approximately) Figure 1 in Dahanukar, N., R. Raut, and A. Bhat. 2004. Distribution, endemism and threat status of freshwater fishes in the Western Ghats of India. Journal of Biogeography 31:123-126. #' #' @keywords datasets #' diff --git a/R/GreensCreekMine.R b/R/GreensCreekMine.R index a70969c..ecf081b 100644 --- a/R/GreensCreekMine.R +++ b/R/GreensCreekMine.R @@ -27,9 +27,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Appendix C1 of Kanouse, K.M. and B.P. Brewster. 2012. Aquatic Biomonitoring at Greens Creek Mine, 2012. Alaska Department of Fish and Game Technical Report No. 12-11. [Was (is?) from http://dnr.alaska.gov/mlw/mining/largemine/greenscreek/pdf/gc2012bio.pdf.] +#' @source From Appendix C1 of Kanouse, K.M. and B.P. Brewster. 2012. Aquatic Biomonitoring at Greens Creek Mine, 2012. Alaska Department of Fish and Game Technical Report No. 12-11. [Was (is?) from http://dnr.alaska.gov/mlw/mining/largemine/greenscreek/pdf/gc2012bio.pdf.] #' #' @keywords datasets #' diff --git a/R/Hake.R b/R/Hake.R index ba75ab8..c2ac509 100644 --- a/R/Hake.R +++ b/R/Hake.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source Cadima, E. 2003. Fish Stock Assessment Manual, FAO Fisheries Department. 131 pp. +#' @source Cadima, E. 2003. Fish Stock Assessment Manual, FAO Fisheries Department. 131 pp. #' #' @keywords datasets #' diff --git a/R/HalibutPAC.R b/R/HalibutPAC.R index 790e18a..3eac6da 100644 --- a/R/HalibutPAC.R +++ b/R/HalibutPAC.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Anonymous. 1989. International Pacific Halibut Commission. Annual Report 1989.; Myhre, Gordon, Peltonen, Stpierre, Skud, and Walden. International Pacific halibut Commission. Technical Report No. 14.; Pers. Comm. with Pat Sullivan. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Anonymous. 1989. International Pacific Halibut Commission. Annual Report 1989.; Myhre, Gordon, Peltonen, Stpierre, Skud, and Walden. International Pacific halibut Commission. Technical Report No. 14.; Pers. Comm. with Pat Sullivan. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/Herman.R b/R/Herman.R index b96d551..6f1d3c8 100644 --- a/R/Herman.R +++ b/R/Herman.R @@ -22,7 +22,9 @@ #' \item PSD #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' #' @source From a South Dakota Fish and Game report that was (does not appear to be there (or anywhere) now) at http://www.sdgfp.info/Wildlife/fishing/SELakes/Herman05.pdf. #' diff --git a/R/HerringBWE.R b/R/HerringBWE.R index 53478ae..d8e8f8f 100644 --- a/R/HerringBWE.R +++ b/R/HerringBWE.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Fox, C.J. 2001. Recent trends in stock-recruitment of Blackwater herring (\emph{Clupea harengus} L.) in relation to larval production. ICES Journal of Marine Science, 58:750-762. +#' @source From Fox, C.J. 2001. Recent trends in stock-recruitment of Blackwater herring (\emph{Clupea harengus} L.) in relation to larval production. ICES Journal of Marine Science, 58:750-762. #' #' @keywords datasets #' diff --git a/R/HerringISS.R b/R/HerringISS.R index e56df2e..12b6c8d 100644 --- a/R/HerringISS.R +++ b/R/HerringISS.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From the Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1995. Assess: 9.; Anon. 1986. Report of the herring assessment working group for the area south of 62 degrees N. ICES Doc. C.M. 1986. Assess: 19.; Anon. 1991. Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1991. Assess: 17.; State of marine stocks and environmental conditions in Icelandic waters 1989 Fishing prospects 1990, August 1990. Hafranns\'oknastofnun Fj\"olrit NR. 19. Marine Research Institute, Iceland. Mon Jun 20, 1988.; Report of the Northern Pelagic and Blue Whiting Fisheries Working Group. ICES Doc. C.M. 1997. Assess:14. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From the Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1995. Assess: 9.; Anon. 1986. Report of the herring assessment working group for the area south of 62 degrees N. ICES Doc. C.M. 1986. Assess: 19.; Anon. 1991. Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1991. Assess: 17.; State of marine stocks and environmental conditions in Icelandic waters 1989 Fishing prospects 1990, August 1990. Hafranns\'oknastofnun Fj\"olrit NR. 19. Marine Research Institute, Iceland. Mon Jun 20, 1988.; Report of the Northern Pelagic and Blue Whiting Fisheries Working Group. ICES Doc. C.M. 1997. Assess:14. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/HumpbackWFCR.R b/R/HumpbackWFCR.R index 0090560..933390c 100644 --- a/R/HumpbackWFCR.R +++ b/R/HumpbackWFCR.R @@ -24,9 +24,14 @@ #' \item Capture History #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History' -#' -#' @source From Table 10 in Gryska, A.D. 2014. Stock assessment of humpback whitefish in the Chatanika River, 2012. Alaska Department of Fish and Game, Fishery Data Series No. 14-12, Anchorage. Available from https://www.cf.adfg.state.ak.us/FedAidPDFs/FDS14-12.pdf. +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen +#' @concept Capture History +#' +#' @source From Table 10 in Gryska, A.D. 2014. Stock assessment of humpback whitefish in the Chatanika River, 2012. Alaska Department of Fish and Game, Fishery Data Series No. 14-12, Anchorage. Was (is?) at https://www.cf.adfg.state.ak.us/FedAidPDFs/FDS14-12.pdf. #' #' @keywords datasets #' @examples diff --git a/R/InchLake1.R b/R/InchLake1.R index 76fe85d..f77eb7e 100644 --- a/R/InchLake1.R +++ b/R/InchLake1.R @@ -22,7 +22,9 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' #' @seealso See \code{\link{InchLake2}} for a subsample that include weights. #' diff --git a/R/InchLake2.R b/R/InchLake2.R index 24fe6c5..e69100e 100644 --- a/R/InchLake2.R +++ b/R/InchLake2.R @@ -23,7 +23,9 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' Condition 'Length Frequency' +#' @concept Weight-Length +#' @concept Condition +#' @concept Length Frequency #' #' @seealso See \code{\link{InchLake1}} for the entire sample, but without weights. #' diff --git a/R/JobfishSIO.R b/R/JobfishSIO.R index 758bd29..780e7f1 100644 --- a/R/JobfishSIO.R +++ b/R/JobfishSIO.R @@ -22,9 +22,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Table 2 of Grandcourt, E.M. 2003. The effect of intensive line fishing on the virgin biomass of a tropical deepwater snapper, the crimson jobfish (\emph{Pristipomoides filamentosus}). Fisheries Bulletin, 101:305-311. [Was (is?) from http://fishbull.noaa.gov/1012/08grandc.pdf.] +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Table 2 of Grandcourt, E.M. 2003. The effect of intensive line fishing on the virgin biomass of a tropical deepwater snapper, the crimson jobfish (\emph{Pristipomoides filamentosus}). Fisheries Bulletin, 101:305-311. [Was (is?) from http://fishbull.noaa.gov/1012/08grandc.pdf.] #' #' @keywords datasets #' diff --git a/R/JonesStockwell.R b/R/JonesStockwell.R index 9187ba0..a5df904 100644 --- a/R/JonesStockwell.R +++ b/R/JonesStockwell.R @@ -27,9 +27,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Table 1 in Jones, M.L. and J.D. Stockwell. 1995. A rapid assessment procedure for enumeration of salmonine populations in streams. North American Journal of Fisheries Management, 15:551-562. +#' @source From Table 1 in Jones, M.L. and J.D. Stockwell. 1995. A rapid assessment procedure for enumeration of salmonine populations in streams. North American Journal of Fisheries Management, 15:551-562. #' #' @keywords datasets #' diff --git a/R/Jonubi1.R b/R/Jonubi1.R index f1aff83..d513b36 100644 --- a/R/Jonubi1.R +++ b/R/Jonubi1.R @@ -18,11 +18,12 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @seealso \code{\link{Jonubi2}}. #' -#' @source Simulated from table 2 of Yildirim, A., H.U. Haluloulu, M. Turkmen, and O. Erdouan. 2003. Age and growth characteristics of \emph{Chalcalburnus mossulensis} (Heckel, 1843) living in Karasu River (Erzurum-Turkey). Turkish Journal of Veterinary and Animal Science. 27: 1091-1096. +#' @source Simulated from table 2 of Yildirim, A., H.U. Haluloulu, M. Turkmen, and O. Erdouan. 2003. Age and growth characteristics of \emph{Chalcalburnus mossulensis} (Heckel, 1843) living in Karasu River (Erzurum-Turkey). Turkish Journal of Veterinary and Animal Science. 27: 1091-1096. #' #' @keywords datasets #' diff --git a/R/Jonubi2.R b/R/Jonubi2.R index d306b66..98e98c3 100644 --- a/R/Jonubi2.R +++ b/R/Jonubi2.R @@ -19,7 +19,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{\link{Jonubi1}}. #' diff --git a/R/KingCrabAK.R b/R/KingCrabAK.R index 1553c39..61f4cec 100644 --- a/R/KingCrabAK.R +++ b/R/KingCrabAK.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From table 1 in Bechtol W.R. and G.H. Kruse. 2009. Analysis of a stock-recruit relationship for red king crab off Kodiak Island Alaska. Marine and Coastal Fisheries: Dynamics Management and Ecosystem Science 1:29-44. +#' @source From table 1 in Bechtol W.R. and G.H. Kruse. 2009. Analysis of a stock-recruit relationship for Red King Crab off Kodiak Island Alaska. Marine and Coastal Fisheries: Dynamics Management and Ecosystem Science 1:29-44. #' #' @keywords datasets #' diff --git a/R/LJCisco.R b/R/LJCisco.R index c6f385f..7b93fda 100644 --- a/R/LJCisco.R +++ b/R/LJCisco.R @@ -19,9 +19,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source Simulated from age-length data provided in tables 2 and 3 of Jobes, F.W. 1946. The age, growth, and distribution of the longjaw cisco, \emph{Leucichthys alpenae} Koelz, in Lake Michigan. Transactions of the American Fisheries Society. 76:215-247. +#' @source Simulated from age-length data provided in tables 2 and 3 of Jobes, F.W. 1946. The age, growth, and distribution of the longjaw cisco, \emph{Leucichthys alpenae} Koelz, in Lake Michigan. Transactions of the American Fisheries Society. 76:215-247. #' #' @keywords datasets #' diff --git a/R/LMBassBL.R b/R/LMBassBL.R index e08e240..b5014e3 100644 --- a/R/LMBassBL.R +++ b/R/LMBassBL.R @@ -18,9 +18,11 @@ #' \item PSD #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' -#' @source From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +#' @source From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. #' #' @keywords datasets #' diff --git a/R/LMBassLCB.R b/R/LMBassLCB.R index f45b8aa..3b4191e 100644 --- a/R/LMBassLCB.R +++ b/R/LMBassLCB.R @@ -18,9 +18,11 @@ #' \item PSD #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' -#' @source From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +#' @source From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. #' #' @keywords datasets #' diff --git a/R/LakeTroutALTER.R b/R/LakeTroutALTER.R index ed10744..bc45036 100644 --- a/R/LakeTroutALTER.R +++ b/R/LakeTroutALTER.R @@ -38,9 +38,14 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Weight-Length' 'Growth' 'von Bertalanffy' 'Size Structure' 'Length Conversion' +#' @concept Length Frequency +#' @concept Weight-Length +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Size Structure +#' @concept Length Conversion #' -#' @source Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89mcne12.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. +#' @source Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89mcne12.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. #' #' @keywords datasets #' diff --git a/R/LakeTroutEggs.R b/R/LakeTroutEggs.R index 2d50845..1435fa3 100644 --- a/R/LakeTroutEggs.R +++ b/R/LakeTroutEggs.R @@ -19,7 +19,7 @@ #' #' @concept Other #' -#' @source From (approximately) Figure 2 of Schram, S.T. 1993. Fecundity and egg deposition of a wild Lake Superior Lake Trout stock. Wisconsin Department of Natural Resources, Fisheries Management Report no. 149. +#' @source From (approximately) Figure 2 of Schram, S.T. 1993. Fecundity and egg deposition of a wild Lake Superior Lake Trout stock. Wisconsin Department of Natural Resources, Fisheries Management Report no. 149. #' #' @keywords datasets #' diff --git a/R/LakeTroutGIS.R b/R/LakeTroutGIS.R index 96e5b4d..79cffa3 100644 --- a/R/LakeTroutGIS.R +++ b/R/LakeTroutGIS.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Schram, S.T., J.H. Selgeby, C.R. Bronte, and B.L. Swanson. 1995. Population recovery and natural recruitment of Lake Trout at Gull Island Shoal, Lake Superior, 1964-1992. Journal of Great Lakes Research. 21(supp.1):225-232. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Schram, S.T., J.H. Selgeby, C.R. Bronte, and B.L. Swanson. 1995. Population recovery and natural recruitment of Lake Trout at Gull Island Shoal, Lake Superior, 1964-1992. Journal of Great Lakes Research. 21(supp.1):225-232. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/LakeTroutMI.R b/R/LakeTroutMI.R index a6dcd7f..4749e95 100644 --- a/R/LakeTroutMI.R +++ b/R/LakeTroutMI.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) figures in Richards, J.M., M.J. Hansen, C.R. Bronte, and S.P. Sitar. 2004. Recruitment dynamics of the 1971-1991 year-classes of Lake Trout in Michigan waters of Lake Superior. North American Journal of Fisheries Management. 24:475-489. +#' @source From (approximately) figures in Richards, J.M., M.J. Hansen, C.R. Bronte, and S.P. Sitar. 2004. Recruitment dynamics of the 1971-1991 year-classes of Lake Trout in Michigan waters of Lake Superior. North American Journal of Fisheries Management. 24:475-489. #' #' @keywords datasets #' diff --git a/R/Lizardfish.R b/R/Lizardfish.R index edf1585..fbd0b0f 100644 --- a/R/Lizardfish.R +++ b/R/Lizardfish.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source VIsually estimated from Figure 7.12 (p. 267) of Hilborn, R. and C.J. Walters. 1992. Quantitative Fisheries Stock Assessment: Choice, Dynamics, and Uncertainty. Chapman and Hall, New York. 570 p. +#' @source Visually estimated from Figure 7.12 (p. 267) of Hilborn, R. and C.J. Walters. 1992. Quantitative Fisheries Stock Assessment: Choice, Dynamics, and Uncertainty. Chapman and Hall, New York. 570 p. #' #' @keywords datasets #' diff --git a/R/LobsterHI.R b/R/LobsterHI.R index 90d0491..093625c 100644 --- a/R/LobsterHI.R +++ b/R/LobsterHI.R @@ -30,9 +30,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Table 1 of Clarke, R.P., and S.S. Yoshimoto. 1990. Application of the Leslie model to commercial catch and effort of the slipper lobster, \emph{Scyllarides squammosus}, fishery in the northwestern hawaiian islands. Marine Fisheries Review, 52(2):1-7. +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Table 1 of Clarke, R.P., and S.S. Yoshimoto. 1990. Application of the Leslie model to commercial catch and effort of the slipper lobster, \emph{Scyllarides squammosus}, fishery in the northwestern hawaiian islands. Marine Fisheries Review, 52(2):1-7. #' #' @keywords datasets #' diff --git a/R/LobsterPEI.R b/R/LobsterPEI.R index 4eefb83..792aef0 100644 --- a/R/LobsterPEI.R +++ b/R/LobsterPEI.R @@ -25,7 +25,12 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability #' #' @source From Table 1 of DeLury, D.B. 1947. On the estimation of biological populations. Biometrics 3:145-167. #' diff --git a/R/Menhaden1.R b/R/Menhaden1.R index 2ecbbdd..a123b57 100644 --- a/R/Menhaden1.R +++ b/R/Menhaden1.R @@ -24,9 +24,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Table 2 in Vaughan, D.S., K.W. Shertzer, and J.W. Smith. 2007. Gulf menhaden (\emph{Brevoortia patronus}) in the U.S. Gulf of Mexico: Fishery characteristics and biological reference points for management. Fisheries Research 83:263-275. [Was (is?) from http://menhaden.gsmfc.org/FishRes_Vaughan_etal_2007-GM.pdf.] +#' @source From Table 2 in Vaughan, D.S., K.W. Shertzer, and J.W. Smith. 2007. Gulf menhaden (\emph{Brevoortia patronus}) in the U.S. Gulf of Mexico: Fishery characteristics and biological reference points for management. Fisheries Research 83:263-275. #' #' @keywords datasets #' diff --git a/R/Morwong1.R b/R/Morwong1.R index ae029f5..f3beffa 100644 --- a/R/Morwong1.R +++ b/R/Morwong1.R @@ -20,9 +20,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Table 5 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +#' @source From Table 5 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. #' #' @keywords datasets #' diff --git a/R/Morwong2.R b/R/Morwong2.R index 12815a0..4e4be5d 100644 --- a/R/Morwong2.R +++ b/R/Morwong2.R @@ -20,9 +20,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Table 6 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +#' @source From Table 6 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. #' #' @keywords datasets #' diff --git a/R/Morwong3.R b/R/Morwong3.R index 0fa940d..7be4398 100644 --- a/R/Morwong3.R +++ b/R/Morwong3.R @@ -20,9 +20,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Table 7 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +#' @source From Table 7 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. #' #' @keywords datasets #' diff --git a/R/Morwong4.R b/R/Morwong4.R index 252d4bb..2576273 100644 --- a/R/Morwong4.R +++ b/R/Morwong4.R @@ -18,11 +18,12 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @seealso \code{\link{Morwong4a}}. #' -#' @source Ffrom appendix 1 of of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +#' @source Ffrom appendix 1 of of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. #' #' @keywords datasets #' diff --git a/R/Morwong4a.R b/R/Morwong4a.R index 4b8fe1d..8737c90 100644 --- a/R/Morwong4a.R +++ b/R/Morwong4a.R @@ -17,7 +17,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{\link{Morwong4}}. #' diff --git a/R/Mosquitofish.R b/R/Mosquitofish.R index e6b2a0c..2ab7040 100644 --- a/R/Mosquitofish.R +++ b/R/Mosquitofish.R @@ -26,7 +26,9 @@ #' \item Somers model #' } #' -#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers +#' @concept Seasonal Growth +#' @concept von Bertalanffy +#' @concept Somers #' #' @source From figure 3 of Carmona-Catot, G., A.F.G.N. Santos, P.A. Tedesco, and E. Garcia-Berthou. 2014. Quantifying seasonality along a latitudinal gradient: From stream temperature to growth of invasive mosquitofish. Ecosphere 5:134. #' diff --git a/R/MulletBS.R b/R/MulletBS.R index c09c559..a78a11d 100644 --- a/R/MulletBS.R +++ b/R/MulletBS.R @@ -20,9 +20,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Figure 3 of Polat, N., D. Bostanci, S. Yilmaz. 2005. Differences between whole otolith and broken-burnt otolith ages of red mullet (\emph{Mullus barbatus ponticus} Essipov, 1927) sampled from the Black Sea (Samsun, Turkey). Turkish Journal of Veterinary and Animal Science 29:429-433. +#' @source From Figure 3 of Polat, N., D. Bostanci, S. Yilmaz. 2005. Differences between whole otolith and broken-burnt otolith ages of red mullet (\emph{Mullus barbatus ponticus} Essipov, 1927) sampled from the Black Sea (Samsun, Turkey). Turkish Journal of Veterinary and Animal Science 29:429-433. #' #' @keywords datasets #' diff --git a/R/MuskieSLR.R b/R/MuskieSLR.R index 51b9391..3c6481a 100644 --- a/R/MuskieSLR.R +++ b/R/MuskieSLR.R @@ -20,9 +20,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Figure 3 in Casselman,J.M. 1983. Age and growth assessment of fish from their calcified structures - techniques and tools. In E.D. Prince and L.M. Pulos, editors, Proceedings of the international workshop on age determination of oceanic pelagic fishes: Tunas, billfishes, and sharks, volume NOAA Technical Report, NMFS 8:1-17. +#' @source From Figure 3 in Casselman,J.M. 1983. Age and growth assessment of fish from their calcified structures - techniques and tools. In E.D. Prince and L.M. Pulos, editors, Proceedings of the international workshop on age determination of oceanic pelagic fishes: Tunas, billfishes, and sharks, volume NOAA Technical Report, NMFS 8:1-17. #' #' @keywords datasets #' diff --git a/R/MuskieWI06MR.R b/R/MuskieWI06MR.R index 5f5eec6..5e9b895 100644 --- a/R/MuskieWI06MR.R +++ b/R/MuskieWI06MR.R @@ -25,7 +25,11 @@ #' \item Petersen #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen #' #' @source Wisconsin Department of Natural Resources. #' diff --git a/R/PSalmonAK.R b/R/PSalmonAK.R index ab2deb3..8e3e102 100644 --- a/R/PSalmonAK.R +++ b/R/PSalmonAK.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Table 3.1 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. +#' @source From Table 3.1 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. #' #' @keywords datasets #' diff --git a/R/Pallid.R b/R/Pallid.R index c3aed57..5f503bb 100644 --- a/R/Pallid.R +++ b/R/Pallid.R @@ -23,9 +23,10 @@ #' \item Length Conversion #' } #' -#' @concept 'Weight-Length' 'Length Conversion' +#' @concept Weight-Length +#' @concept Length Conversion #' -#' @source From Table 1 in Keenlyne, K.D. and S.J. Maxwell. 1993. Length conversions and length-weight relations for pallid sturgeon. North American Journal of Fisheries Management. 13:395-397. +#' @source From Table 1 in Keenlyne, K.D. and S.J. Maxwell. 1993. Length conversions and length-weight relations for pallid sturgeon. North American Journal of Fisheries Management. 13:395-397. #' #' @keywords datasets #' diff --git a/R/Pathfinder.R b/R/Pathfinder.R index b70a768..2dc467f 100644 --- a/R/Pathfinder.R +++ b/R/Pathfinder.R @@ -25,9 +25,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability #' -#' @source From Table 3 of Polovina, J.J. 1985. A variable catchability version of the Leslie model with application to an intensive fishing experiment on a multispecies stock. Fishery Bulletin 84:423-428. [Was (is?) from https://swfsc.noaa.gov/publications/CR/1986/8679.PDF.] +#' @source From Table 3 of Polovina, J.J. 1985. A variable catchability version of the Leslie model with application to an intensive fishing experiment on a multispecies stock. Fishery Bulletin 84:423-428. [Was (is?) from https://swfsc.noaa.gov/publications/CR/1986/8679.PDF.] #' #' @keywords datasets #' diff --git a/R/PikeHL.R b/R/PikeHL.R index 4417d8e..871f7ec 100644 --- a/R/PikeHL.R +++ b/R/PikeHL.R @@ -25,9 +25,14 @@ #' \item Capture History #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History' -#' -#' @source Capture histories simulated from summarzed data in table 2 and text of Burkholder, A. 1991. Abundance and composition of northern pike, Harding Lake, 1990. Fishery Data Series 91-9, Alaksa Department of Fish and Game. Accessed from http://www.sf.adfg.state.ak.us/FedAidpdfs/Fds91-09.pdf +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen +#' @concept Capture History +#' +#' @source Capture histories simulated from summarzed data in table 2 and text of Burkholder, A. 1991. Abundance and composition of northern pike, Harding Lake, 1990. Fishery Data Series 91-9, Alaksa Department of Fish and Game. Was (is?) from http://www.sf.adfg.state.ak.us/FedAidpdfs/Fds91-09.pdf #' #' @keywords datasets #' diff --git a/R/PikeIL.R b/R/PikeIL.R index c2e9270..bec01a9 100644 --- a/R/PikeIL.R +++ b/R/PikeIL.R @@ -23,9 +23,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Table 1 of Peterson, J., M. Taylor, and A. Hanson. 1980. Leslie population estimate for a large lake. Transactions of the American Fisheries Society, 109:329-331. +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Table 1 of Peterson, J., M. Taylor, and A. Hanson. 1980. Leslie population estimate for a large lake. Transactions of the American Fisheries Society, 109:329-331. #' #' @keywords datasets #' diff --git a/R/PikeNYPartial2.R b/R/PikeNYPartial2.R index bb809d7..ebf012f 100644 --- a/R/PikeNYPartial2.R +++ b/R/PikeNYPartial2.R @@ -25,9 +25,14 @@ #' \item Capture History #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' 'Capture History' -#' -#' @source Simulated from summary data in Table C-1 of New York Power Authority. 2004. Use of buckhorn marsh and grand island tributaries by northern pike for spawning and as a nursery. Technical report, New York Power Authority, January 2004. Niagara Power Project (FERC No. 2216). +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel +#' @concept Capture History +#' +#' @source Simulated from summary data in Table C-1 of New York Power Authority. 2004. Use of Buckhorn Marsh and Grand Island tributaries by Northern Pike for spawning and as a nursery. Technical report, New York Power Authority, January 2004. Niagara Power Project (FERC No. 2216). #' #' @keywords datasets #' diff --git a/R/PikeWindermere.R b/R/PikeWindermere.R index 194fb2a..84c540b 100644 --- a/R/PikeWindermere.R +++ b/R/PikeWindermere.R @@ -15,7 +15,7 @@ #' \item{tdd14}{Temperature degree-days over 14C} #' } #' -#' @note Stock values were originally reported in 1000s of kgs and recruits were originally recorded in tens of numbers. Thus, plots look very discrete. +#' @note Stock values were originally reported in 1000s of kgs and recruits were originally recorded in tens of numbers. Thus, plots look very discrete. #' #' @section Topic(s): #' \itemize{ @@ -23,9 +23,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From table 3 in Kipling, C. 1983. Changes in the population of pike (\emph{Esox lucius}) in Windermere from 1944 to 1981. Journal of Animal Ecology 52:989-999. +#' @source From table 3 in Kipling, C. 1983. Changes in the population of pike (\emph{Esox lucius}) in Windermere from 1944 to 1981. Journal of Animal Ecology 52:989-999. #' #' @keywords datasets #' diff --git a/R/PygmyWFBC.R b/R/PygmyWFBC.R index 37fd937..e390993 100644 --- a/R/PygmyWFBC.R +++ b/R/PygmyWFBC.R @@ -33,9 +33,12 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' 'Age Comparison' Condition 'Length Frequency' +#' @concept Weight-Length +#' @concept Age Comparison +#' @concept Condition +#' @concept Length Frequency #' -#' @source 2000 data from Appendix 9 of J. D. McPhail and R. J. Zemlak. October 2001. Pygmy whitefish studies on Dina Lake #1, 2000. Peace/Williston Fish and Wildlife Compensation Program, Report No. 245. 36pp plus appendices. [Was (is?) from https://www.bchydro.com/pwcp/pdfs/reports/pwfwcp_report_no_245.pdf.] +#' @source 2000 data from Appendix 9 of J. D. McPhail and R. J. Zemlak. October 2001. Pygmy Whitefish studies on Dina Lake #1, 2000. Peace/Williston Fish and Wildlife Compensation Program, Report No. 245. 36pp plus appendices. [Was (is?) from https://www.bchydro.com/pwcp/pdfs/reports/pwfwcp_report_no_245.pdf.] #' #' 2001 data from Appendix 14 of Zemlak, R.J. and J.D. McPhail. 2003. Pygmy Whitefish studies on Dina Lake #1, 2001. Peace/Williston Fish and Wildlife Compensation Program Report No. 279. 35pp plus appendices. [Was (is?) from http://a100.gov.bc.ca/appsdata/acat/documents/r39503/pwfwcp_report_no_279_1383686631923_d6d1b25e3156cee45e442c5b3f756a6a7b4bb7ad7753efb1c51dc23ac997a9a6.pdf.] #' diff --git a/R/RBSmeltErie.R b/R/RBSmeltErie.R index faab8a9..4e16115 100644 --- a/R/RBSmeltErie.R +++ b/R/RBSmeltErie.R @@ -20,8 +20,8 @@ #' } #' #' @concept Recruitment -#' @source From Ontario Ministry of Natural Resources, Fish and Wildlife Branch, 1997. Lake Erie fisheries report 1996. Lake Erie Committee Meeting, -#' Great Lakes Fishery Commission, Ann Arbor, Michigan. pp 26. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' +#' @source From Ontario Ministry of Natural Resources, Fish and Wildlife Branch, 1997. Lake Erie fisheries report 1996. Lake Erie Committee Meeting, Great Lakes Fishery Commission, Ann Arbor, Michigan. pp 26. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/RBSmeltLM.R b/R/RBSmeltLM.R index 7bc2758..22f5f4c 100644 --- a/R/RBSmeltLM.R +++ b/R/RBSmeltLM.R @@ -17,9 +17,10 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' +#' @concept Length Frequency +#' @concept Size Structure #' -#' @source From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +#' @source From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. #' #' @keywords datasets #' diff --git a/R/RBTroutKenai.R b/R/RBTroutKenai.R index 8b266c8..92454a2 100644 --- a/R/RBTroutKenai.R +++ b/R/RBTroutKenai.R @@ -20,9 +20,11 @@ #' \item Fabens method #' } #' -#' @concept Growth 'von Bertalanffy' Fabens +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Fabens #' -#' @source From Table 4.10 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press. 560 pages. This table is a 1/3rd subsample of the actual data presented in Baker, T.T., R. Lafferty, and T.J. Quinn II. 1991. A general growth model for mark-recapture data. Fisheries Research 11:257-281. +#' @source From Table 4.10 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press. 560 pages. This table is a 1/3rd subsample of the actual data presented in Baker, T.T., R. Lafferty, and T.J. Quinn II. 1991. A general growth model for mark-recapture data. Fisheries Research 11:257-281. #' #' @keywords datasets #' diff --git a/R/RBTroutUNSP.R b/R/RBTroutUNSP.R index 0b175fe..59b5115 100644 --- a/R/RBTroutUNSP.R +++ b/R/RBTroutUNSP.R @@ -22,9 +22,14 @@ #' \item Capture History #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History' -#' -#' @source Simulated from Table 10 in of Warren, C.D., K.A. Frank, and F.E. Partridge. 2004. Federal aid in fish restoration - 2000 job performance report. Idaho Department of Fish and Game. +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Petersen +#' @concept Capture History +#' +#' @source Simulated from Table 10 in of Warren, C.D., K.A. Frank, and F.E. Partridge. 2004. Federal Aid in Fish Restoration - 2000 job performance report. Idaho Department of Fish and Game. #' #' @keywords datasets #' diff --git a/R/RWhitefishAI.R b/R/RWhitefishAI.R index 4ead517..c5e3eb3 100644 --- a/R/RWhitefishAI.R +++ b/R/RWhitefishAI.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From Table 3 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] +#' @source From Table 3 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of Round Whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] #' #' @keywords datasets #' diff --git a/R/RWhitefishIR.R b/R/RWhitefishIR.R index 93f0c04..9e3cc11 100644 --- a/R/RWhitefishIR.R +++ b/R/RWhitefishIR.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From Table 4 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] +#' @source From Table 4 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] #' #' @keywords datasets #' diff --git a/R/RedDrum.R b/R/RedDrum.R index 195d90e..13ad6d0 100644 --- a/R/RedDrum.R +++ b/R/RedDrum.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From (approximately) Figure 27 in Vaughan, D.S. and T.E. Helser. 1990. Status of the red drum stock of the Atlantic Coast: Stock assessment report for 1989. NOAA Technical Memorandum, NMFS-SEFC-263. +#' @source From (approximately) Figure 27 in Vaughan, D.S. and T.E. Helser. 1990. Status of the red drum stock of the Atlantic Coast: Stock assessment report for 1989. NOAA Technical Memorandum, NMFS-SEFC-263. #' #' @keywords datasets #' diff --git a/R/Riffleshell.R b/R/Riffleshell.R index ff5b583..98059dd 100644 --- a/R/Riffleshell.R +++ b/R/Riffleshell.R @@ -26,9 +26,13 @@ #' \item Schumacher-Eschmeyer #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel #' -#' @source From Table 1-2 of Rogers, S.O. 1999. Population biology of the tan fiffleshell (\emph{Epioblasma florentina walkeri}) and the effects of substratum and light on juvenile mussel propagation. Virginia Tech M.S. Thesis. +#' @source From Table 1-2 of Rogers, S.O. 1999. Population biology of the Tan Riffleshell (\emph{Epioblasma florentina walkeri}) and the effects of substratum and light on juvenile mussel propagation. Virginia Tech M.S. Thesis. #' #' @keywords datasets #' diff --git a/R/RockBassCL.R b/R/RockBassCL.R index eb3d1d5..9388e3a 100644 --- a/R/RockBassCL.R +++ b/R/RockBassCL.R @@ -18,7 +18,8 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' #' @source D.S. Robson and D.G. Chapman. 1961. Catch curves and mortality rates. Transactions of the American Fisheries Society. 90:181-189. #' diff --git a/R/RockBassL01.R b/R/RockBassL01.R index eb0a161..a256578 100644 --- a/R/RockBassL01.R +++ b/R/RockBassL01.R @@ -18,11 +18,12 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @seealso \code{\link{RockBassLO2}}. #' -#' @source Simulated from Table 1 of Wolfert, D.R. 1980. Age and growth of rock bass in Eastern Lake Ontario. New York Fish and Game Journal, 27:88:90. +#' @source Simulated from Table 1 of Wolfert, D.R. 1980. Age and growth of Rock Bass in Eastern Lake Ontario. New York Fish and Game Journal, 27:88:90. #' #' @keywords datasets #' diff --git a/R/RockBassL02.R b/R/RockBassL02.R index b91c6dd..cd19f52 100644 --- a/R/RockBassL02.R +++ b/R/RockBassL02.R @@ -19,7 +19,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{\link{RockBassLO1}}. #' diff --git a/R/RuffeSLRH92.R b/R/RuffeSLRH92.R index fc03889..9acc4b7 100644 --- a/R/RuffeSLRH92.R +++ b/R/RuffeSLRH92.R @@ -31,7 +31,11 @@ #' \item Maturity #' } #' -#' @concept Growth 'von Bertalanffy' 'Length Frequency' 'Weight-Length' Maturity +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Length Frequency +#' @concept Weight-Length +#' @concept Maturity #' #' @source personal collection by the United States Geological Survey, Lake Superior Biological Station, Ashland, WI. #' diff --git a/R/RuffeTL89.R b/R/RuffeTL89.R index 77b7bc9..b130b99 100644 --- a/R/RuffeTL89.R +++ b/R/RuffeTL89.R @@ -17,7 +17,8 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' +#' @concept Length Frequency +#' @concept Size Structure #' #' @source personal collection by the United States Geological Survey, Lake Superior Biological Station, Ashland, WI. #' diff --git a/R/SLampreyGL.R b/R/SLampreyGL.R index 5b29b46..0fcd175 100644 --- a/R/SLampreyGL.R +++ b/R/SLampreyGL.R @@ -1,8 +1,9 @@ -#' Stock and recruitment data for Sea Lamprey in the Great Lakes, 1997-2007. +#' @title Stock and recruitment data for Sea Lamprey in the Great Lakes, 1997-2007. #' -#' Stock and recruitment data for Sea Lamprey (\emph{Petromyzon marinus}) in the Great Lakes, 1997-2007 from 37 streams. +#' @description Stock and recruitment data for Sea Lamprey (\emph{Petromyzon marinus}) in the Great Lakes, 1997-2007 from 37 streams. #' #' @name SLampreyGL +#' #' @docType data #' #' @format A data frame of 76 observations on the following two variables: @@ -17,7 +18,8 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' #' @source From (approximately) Figures 2a and 2b in Dawson, H.A. and M.L. Jones. 2009. Factors affecting recruiting dynamics of Great Lakes sea lamprey (\emph{Petromyzon marinus}) populations. Journal of Great Lakes Research 35:353-360. #' diff --git a/R/SalmonADP.R b/R/SalmonADP.R index f65933f..0f8d2ac 100644 --- a/R/SalmonADP.R +++ b/R/SalmonADP.R @@ -1,27 +1,34 @@ -#'Catches in removal events of salmon parr. -#' -#'Catches in removal events of salmon parr from the Afon Dulas at Pentre, 19Jun79. -#' -#'@name SalmonADP -#'@docType data -#'@format A data frame with 5 observations on the following 2 variables: -#'\describe{ -#' \item{catch}{Removal event.} -#' \item{caught}{Number of fish captured and removed.} -#'} -#'@section Topic(s): \itemize{ -#' \item Population size -#' \item Abundance -#' \item Removal -#'} -#'@concept Abundance 'Population Size' Removal -#'@seealso \link{TroutADP} -#'@source From Table 2 in Cowx, I.G. 1983. Review of the methods for estimating -#'fish population size from survey removal data. Fisheries Management, 14:67-82. -#'@keywords datasets -#'@examples -#'data(SalmonADP) -#'str(SalmonADP) -#'SalmonADP +#' Catches in removal events of salmon parr. +#' +#' Catches in removal events of salmon parr from the Afon Dulas at Pentre, 19Jun79. +#' +#' @name SalmonADP +#' @docType data +#' @format A data frame with 5 observations on the following 2 variables: +#' \describe{ +#' \item{catch}{Removal event.} +#' \item{caught}{Number of fish captured and removed.} +#' } +#' +#' @section Topic(s): \itemize{ +#' \item Population size +#' \item Abundance +#' \item Removal +#' } +#' +#' @concept Abundance +#' @concept Population Size +#' @concept Removal +#' +#' @seealso \link{TroutADP} +#' +#' @source From Table 2 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. +#' +#' @keywords datasets +#' +#' @examples +#' data(SalmonADP) +#' str(SalmonADP) +#' SalmonADP #' NULL \ No newline at end of file diff --git a/R/SalmonidsMCCA.R b/R/SalmonidsMCCA.R index d24e888..9641bdb 100644 --- a/R/SalmonidsMCCA.R +++ b/R/SalmonidsMCCA.R @@ -24,9 +24,11 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' -#' @source From Table 2 of Voight, H. 1999. Assessment of juvenile salmonid populations in two index reaches of McGarvey Creek, a tributary to the lower Klamath River. First Year of Investigations - 1998. [Was (is?) from http://www.krisweb.com/biblio/klamath_yuroktfp_voight_1999_7.pdf.] +#' @source From Table 2 of Voight, H. 1999. Assessment of juvenile salmonid populations in two index reaches of McGarvey Creek, a tributary to the lower Klamath River. First Year of Investigations - 1998. [Was (is?) from http://www.krisweb.com/biblio/klamath_yuroktfp_voight_1999_7.pdf.] #' #' @keywords datasets #' diff --git a/R/SardineChile.R b/R/SardineChile.R index aba1896..2237bba 100644 --- a/R/SardineChile.R +++ b/R/SardineChile.R @@ -1,34 +1,40 @@ -#'Ages and lengths of two year-classes of Sardine from Chilean waters. +#' @title Ages and lengths of two year-classes of Sardine from Chilean waters. #' -#'Ages (in months) and total lengths of two year-classes of Sardine -#'(\emph{Strangomera bentincki}) from central Chilean waters. +#' @description Ages (in months) and total lengths of two year-classes of Sardine (\emph{Strangomera bentincki}) from central Chilean waters. #' -#'@name SardineChile -#'@docType data -#'@format A data frame with 196 observations of the following 3 variables: -#'\describe{ -#' \item{age.mon}{Age in months.} -#' \item{tl.cm}{Total length (cm).} -#' \item{cohort}{Year-class.} -#'} -#'@section Topic(s): \itemize{ -#' \item Growth -#' \item Seasonal Growth -#' \item von Bertalanffy -#' \item Somers model -#'} -#'@concept Growth 'von Bertalanffy' Somers 'Seasonal Growth' -#'@source Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. -#'Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off -#'Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to -#'seasonal upwelling? Aquatic Living Resources, 14:115-124. Data were in -#'Figure 9. -#'@keywords datasets -#'@examples -#'data(SardineChile) -#'str(SardineChile) -#'head(SardineChile) -#'SardineChile$age <- SardineChile$age.mon/12 -#'plot(tl.cm~age,data=SardineChile) +#' @name SardineChile +#' +#' @docType data +#' +#' @format A data frame with 196 observations of the following 3 variables: +#' \describe{ +#' \item{age.mon}{Age in months.} +#' \item{tl.cm}{Total length (cm).} +#' \item{cohort}{Year-class.} +#' } +#' +#' @section Topic(s): +#' \itemize{ +#' \item Growth +#' \item Seasonal Growth +#' \item von Bertalanffy +#' \item Somers model +#' } +#' +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Somers +#' @concept Seasonal Growth +#' +#' @source Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling? Aquatic Living Resources, 14:115-124. Data were in Figure 9. +#' +#' @keywords datasets +#' +#' @examples +#' data(SardineChile) +#' str(SardineChile) +#' head(SardineChile) +#' SardineChile$age <- SardineChile$age.mon/12 +#' plot(tl.cm~age,data=SardineChile) #' NULL \ No newline at end of file diff --git a/R/SardineLK.R b/R/SardineLK.R index 4b3c83f..e485752 100644 --- a/R/SardineLK.R +++ b/R/SardineLK.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From (approximately) Figure 3 of Mtsambiwa, M.Z. 1992. Fitting a von Bertalanffy growth model to length at age data for larval \emph{Limnothrissa miodon} from Lake Kariba. Paper presented at the Symposium on biology, stock assessment, and exploitation of small pelagic fish species in the African Great Lakes region. [Was (is?) from http://www.fao.org/docrep/005/v2648e/V2648E06.htm.] +#' @source From (approximately) Figure 3 of Mtsambiwa, M.Z. 1992. Fitting a von Bertalanffy growth model to length at age data for larval \emph{Limnothrissa miodon} from Lake Kariba. Paper presented at the Symposium on biology, stock assessment, and exploitation of small pelagic fish species in the African Great Lakes region. [Was (is?) from http://www.fao.org/docrep/005/v2648e/V2648E06.htm.] #' #' @keywords datasets #' diff --git a/R/SardinesPacific.R b/R/SardinesPacific.R index 766ec89..a2e56b7 100644 --- a/R/SardinesPacific.R +++ b/R/SardinesPacific.R @@ -18,9 +18,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Jacobson, L.D. and A.D. MacCall. 1995. Stock-recruitment models for Pacific sardine (\emph{Sardinops sagax}). Canadian Journal of Fisheries and Aquatic Sciences. 52:566-577. +#' @source From Jacobson, L.D. and A.D. MacCall. 1995. Stock-recruitment models for Pacific Sardine (\emph{Sardinops sagax}). Canadian Journal of Fisheries and Aquatic Sciences. 52:566-577. #' #' @keywords datasets #' diff --git a/R/SculpinALTER.R b/R/SculpinALTER.R index 4f36220..587a38e 100644 --- a/R/SculpinALTER.R +++ b/R/SculpinALTER.R @@ -24,9 +24,13 @@ #' \item Size Structure #' } #' -#' @concept Growth 'von Bertalanffy' 'Length Frequency' 'Weight-Length' 'Size Structure' +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Length Frequency +#' @concept Weight-Length +#' @concept Size Structure #' -#' @source Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89hes6ag.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. +#' @source Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89hes6ag.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. #' #' @keywords datasets #' diff --git a/R/ShadCR.R b/R/ShadCR.R index b087629..99d0e5c 100644 --- a/R/ShadCR.R +++ b/R/ShadCR.R @@ -26,7 +26,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/ShrimpGuam.R b/R/ShrimpGuam.R index ad7736c..f545ec4 100644 --- a/R/ShrimpGuam.R +++ b/R/ShrimpGuam.R @@ -28,9 +28,14 @@ #' \item Catchability #' } #' -#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability -#' -#' @source From Table 1 of Ralson, S. 1986. An intensive fishing experiment for the Caridean Shrimp, \emph{Heterocarpus laevigatus}, at Alamagn Island in the Mariana Archipelago. Fishery Bulletin 84:927-934. [Was (is?) from http://fishbull.noaa.gov/844/ralston.pdf.] +#' @concept Abundance +#' @concept Population Size +#' @concept Leslie +#' @concept DeLury +#' @concept Depletion +#' @concept Catchability +#' +#' @source From Table 1 of Ralson, S. 1986. An intensive fishing experiment for the Caridean Shrimp, \emph{Heterocarpus laevigatus}, at Alamagn Island in the Mariana Archipelago. Fishery Bulletin 84:927-934. [Was (is?) from http://fishbull.noaa.gov/844/ralston.pdf.] #' #' @keywords datasets #' diff --git a/R/SimonsonLyons.R b/R/SimonsonLyons.R index 3b3258e..5114c13 100644 --- a/R/SimonsonLyons.R +++ b/R/SimonsonLyons.R @@ -1,35 +1,44 @@ -#'Catches in removal events of trout at various locations. +#' @title Catches in removal events of trout at various locations. #' -#'Catches of various species in consecutive removal events at various locations. +#' @description Catches of various species in consecutive removal events at various locations. #' -#'@name SimonsonLyons -#'@docType data -#'@format A data frame of 58 observations on the following 7 variables: -#'\describe{ -#' \item{species}{Species of fish.} -#' \item{stream}{Stream name.} -#' \item{first}{Catch on the first removal pass.} -#' \item{second}{Catch on the second removal pass.} -#' \item{third}{Catch on the third removal pass.} -#' \item{fourth}{Catch on the fourth removal pass.} -#' \item{pop.cs}{Population estimate by Carle-Strub method.} -#'} -#'@section Topic(s): \itemize{ -#' \item Population size -#' \item Abundance -#' \item Removal -#'} -#'@concept Abundance 'Population Size' Removal -#'@source From Appendix in Simonson, T.D. and J. Lyons. 1995. Comparison of -#'catch per effort and removal procedures for sampling stream fish assemblages. -#'North American Journal of Fisheries Management, 15:419-427. -#'@keywords datasets -#'@examples -#'data(SimonsonLyons) -#'str(SimonsonLyons) -#'head(SimonsonLyons) +#' @name SimonsonLyons +#' +#' @docType data +#' +#' @format A data frame of 58 observations on the following 7 variables: +#' \describe{ +#' \item{species}{Species of fish.} +#' \item{stream}{Stream name.} +#' \item{first}{Catch on the first removal pass.} +#' \item{second}{Catch on the second removal pass.} +#' \item{third}{Catch on the third removal pass.} +#' \item{fourth}{Catch on the fourth removal pass.} +#' \item{pop.cs}{Population estimate by Carle-Strub method.} +#' } +#' #' -#'## extract data for one species and stream (e.g., 3rd row) -#'SimonsonLyons[3,] +#' @section Topic(s): +#' \itemize{ +#' \item Population size +#' \item Abundance +#' \item Removal +#' } +#' +#' @concept Abundance +#' @concept Population Size +#' @concept Removal +#' +#' @source From Appendix in Simonson, T.D. and J. Lyons. 1995. Comparison of catch per effort and removal procedures for sampling stream fish assemblages. North American Journal of Fisheries Management, 15:419-427. +#' +#' @keywords datasets +#' +#' @examples +#' data(SimonsonLyons) +#' str(SimonsonLyons) +#' head(SimonsonLyons) +#' +#' ## extract data for one species and stream (e.g., 3rd row) +#' SimonsonLyons[3,] #' NULL \ No newline at end of file diff --git a/R/SiscowetMI2004.R b/R/SiscowetMI2004.R index 99ea107..721b7d1 100644 --- a/R/SiscowetMI2004.R +++ b/R/SiscowetMI2004.R @@ -24,7 +24,8 @@ #' \item Growth #' } #' -#' @concept 'Age-Length Key' 'Growth' +#' @concept Age-Length Key +#' @concept Growth #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/Snapper.R b/R/Snapper.R index ff6ccf8..cbbaa53 100644 --- a/R/Snapper.R +++ b/R/Snapper.R @@ -1,8 +1,9 @@ -#' Lengths for Snapper from Australia. +#' @title Lengths for Snapper from Australia. #' -#' Lengths of Australian Snapper (\emph{Chrysophrys auratus}) taken by trawl. +#' @description Lengths of Australian Snapper (\emph{Chrysophrys auratus}) taken by trawl. #' #' @name Snapper +#' #' @docType data #' #' @format A data frame of 256 observations on the following 1 variable: @@ -16,9 +17,10 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' +#' @concept Length Frequency +#' @concept Size Structure #' -#' @source Simulated from length frequency summaries found in \code{data(cassie)} of the \pkg{mixdist} package. Data originally from Cassie, R.M. 1954. Some uses of probability paper in the analysis of size frequency distributions. Australian Journal of Marine and Freshwater Research. 5:513-522. +#' @source Simulated from length frequency summaries found in \code{data(cassie)} of the \pkg{mixdist} package. Data originally from Cassie, R.M. 1954. Some uses of probability paper in the analysis of size frequency distributions. Australian Journal of Marine and Freshwater Research. 5:513-522. #' #' @keywords datasets #' diff --git a/R/SnapperHG1.R b/R/SnapperHG1.R index d237dfb..9182b75 100644 --- a/R/SnapperHG1.R +++ b/R/SnapperHG1.R @@ -18,11 +18,11 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' -#' @note the unaged fish were simulated from Table 5 assuming that the total number of fish was large enough that at least one fish was observed in each cell where a proportion was listed. +#' @note The unaged fish were simulated from Table 5 assuming that the total number of fish was large enough that at least one fish was observed in each cell where a proportion was listed. #' -#' @source Recreated from Tables 2, 3, and 5 in Davies, N.M. and C. Walsh. 2002. Snapper age and length samples from Kaharoa research trawl surveys KAH8810 and KAH0012 of the Hauraki Gulf. Final Research Report for Ministry of Fisheries Research Project SNA2000/01. National Institute of Water and Atmospheric Research. [Was (is?) from http://fs.fish.govt.nz/Page.aspx?pk=113&dk=22516.] +#' @source Recreated from Tables 2, 3, and 5 in Davies, N.M. and C. Walsh. 2002. Snapper age and length samples from Kaharoa research trawl surveys KAH8810 and KAH0012 of the Hauraki Gulf. Final Research Report for Ministry of Fisheries Research Project SNA2000/01. National Institute of Water and Atmospheric Research. [Was (is?) from http://fs.fish.govt.nz/Page.aspx?pk=113&dk=22516.] #' #' @keywords datasets #' diff --git a/R/SnapperHG2.R b/R/SnapperHG2.R index 6dfb823..a1121cc 100644 --- a/R/SnapperHG2.R +++ b/R/SnapperHG2.R @@ -17,7 +17,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @source Recreated from summarized results in Table 8.3 of Quinn, T. J. and R. B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, NY. 542 p. #' diff --git a/R/SockeyeKL.R b/R/SockeyeKL.R index ba53ff7..58907ad 100644 --- a/R/SockeyeKL.R +++ b/R/SockeyeKL.R @@ -1,8 +1,9 @@ -#' Stock and recruitment data for Sockeye Salmon from Karluk Lake, AK, 1921-1948. +#' @title Stock and recruitment data for Sockeye Salmon from Karluk Lake, AK, 1921-1948. #' -#' Sockeye Salmon (\emph{Oncorhynchus nerka}) stock and recruitment in Karluk Lake, AK, by year, 1921-1948. +#' @description Sockeye Salmon (\emph{Oncorhynchus nerka}) stock and recruitment in Karluk Lake, AK, by year, 1921-1948. #' #' @name SockeyeKL +#' #' @docType data #' #' @format A data frame of 28 observations on the following 3 variables: @@ -18,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Gulland, J.A. 1983. Fish stock assessment: A manual of basic methods. John Wiley and Sons, New York, NY. 223 p. +#' @source From Gulland, J.A. 1983. Fish stock assessment: A manual of basic methods. John Wiley and Sons, New York, NY. 223 p. #' #' @keywords datasets #' @@ -33,4 +35,4 @@ #' plot(recruits~stock,data=SockeyeKL) #' par(op) #' -NULL \ No newline at end of file +NULL diff --git a/R/SockeyeSR.R b/R/SockeyeSR.R index 57f10f6..4501211 100644 --- a/R/SockeyeSR.R +++ b/R/SockeyeSR.R @@ -1,8 +1,6 @@ -#' Stock and recruitment data for Skeena River Sockeye Salmon, 1940-1967. +#' @title Stock and recruitment data for Skeena River Sockeye Salmon, 1940-1967. #' -#' Stock and recruitment data for Skeena River Sockeye Salmon (\emph{Oncorhynchus nerka}), 1940-1967. -#' -#' The dataset is usually analysed without case 12 because a rockslide occurred that year. +#' @description Stock and recruitment data for Skeena River Sockeye Salmon (\emph{Oncorhynchus nerka}), 1940-1967. #' #' @name SockeyeSR #' @@ -21,7 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @note The dataset is usually analysed without case 12 because a rockslide occurred that year. +#' +#' @concept Stock-Recruit +#' @concept Recruitment #' #' @source Carroll, R. J. and Ruppert, D. 1988. Transformation and Weighting in Regression. Chapman and Hall, New York. 140 pp. #' diff --git a/R/SpotVA2.R b/R/SpotVA2.R index 3d1a1ef..c43ffb5 100644 --- a/R/SpotVA2.R +++ b/R/SpotVA2.R @@ -17,7 +17,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{SpotVA1} in \pkg{FSA}. #' diff --git a/R/SpottedSucker1.R b/R/SpottedSucker1.R index 4890619..3306983 100644 --- a/R/SpottedSucker1.R +++ b/R/SpottedSucker1.R @@ -18,9 +18,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From Box 5.4 in Iseley, J.J. and T.B. Grabowski. 2007. Age and Growth in Guy, C.S. and M.L. Brown, editors. Analysis and Interpretation of Freshwater Fisheries Data. American Fisheries Society. Likely originally from Grabowski, T.B., S.P. Young, J.J. Isely, and P.C. Ely. Age, growth, and reproductive biology of three catostomids from the Apalachicola River, Florida. Journal of Fish and Wildlife Management 3:223-237. [Was (is?) from http://www.fwspubs.org/doi/pdf/10.3996/012012-JFWM-008.] +#' @source From Box 5.4 in Iseley, J.J. and T.B. Grabowski. 2007. Age and Growth in Guy, C.S. and M.L. Brown, editors. Analysis and Interpretation of Freshwater Fisheries Data. American Fisheries Society. Likely originally from Grabowski, T.B., S.P. Young, J.J. Isely, and P.C. Ely. Age, growth, and reproductive biology of three catostomids from the Apalachicola River, Florida. Journal of Fish and Wildlife Management 3:223-237. [Was (is?) from http://www.fwspubs.org/doi/pdf/10.3996/012012-JFWM-008.] #' #' @keywords datasets #' diff --git a/R/StripedBass1.R b/R/StripedBass1.R index 62c80c0..4f166d8 100644 --- a/R/StripedBass1.R +++ b/R/StripedBass1.R @@ -1,6 +1,6 @@ -#' Ages of Striped Bass assigned from scales and otoliths. +#' @title Ages of Striped Bass assigned from scales and otoliths. #' -#' Ages of Striped Bass (\emph{Morone saxatilis}) assessed from heat-pressed scales and cracked-and-burnt otoliths. +#' @description Ages of Striped Bass (\emph{Morone saxatilis}) assessed from heat-pressed scales and cracked-and-burnt otoliths. #' #' @name StripedBass1 #' @@ -20,7 +20,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @source From Figure 6 in Chapter 10 (Striped Bass) of the VMRC Final Report on Finfish Ageing, 2000 by the Center for Quantitative Fisheries Ecology at Old Dominion University. #' diff --git a/R/StripedBass2.R b/R/StripedBass2.R index a186236..1400d52 100644 --- a/R/StripedBass2.R +++ b/R/StripedBass2.R @@ -1,6 +1,6 @@ -#' Ages and lengths of Atlantic Ocean Striped Bass. +#' @title Ages and lengths of Atlantic Ocean Striped Bass. #' -#' Assigned ages (from otoliths) and measured total lengths for each of 1201 Striped Bass (\emph{Morone saxatilis}) from the Atlantic Ocean. +#' @description Assigned ages (from otoliths) and measured total lengths for each of 1201 Striped Bass (\emph{Morone saxatilis}) from the Atlantic Ocean. #' #' @name StripedBass2 #' @@ -18,7 +18,8 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' #' @seealso \code{\link{StripedBass3}}. #' diff --git a/R/StripedBass3.R b/R/StripedBass3.R index 2322146..bee4ec3 100644 --- a/R/StripedBass3.R +++ b/R/StripedBass3.R @@ -1,6 +1,6 @@ -#' Ages (subsample) and lengths (all fish) for Striped Bass. +#' @title Ages (subsample) and lengths (all fish) for Striped Bass. #' -#' As many as 10 fish per 1-inch total length intervals from the \code{StripedBass2} data frame were obtained for age assignment. The remaining fish in the file were only measured for length (i.e., the ages were deleted). This data file can be used to demonstrate the use of age-length keys. +#' @description As many as 10 fish per 1-inch total length intervals from the \code{StripedBass2} data frame were obtained for age assignment. The remaining fish in the file were only measured for length (i.e., the ages were deleted). This data file can be used to demonstrate the use of age-length keys. #' #' @name StripedBass3 #' @@ -17,7 +17,7 @@ #' \item Age-Length Key #' } #' -#' @concept 'Age-Length Key' +#' @concept Age-Length Key #' #' @seealso \code{\link{StripedBass2}}. #' diff --git a/R/StripedBass4.R b/R/StripedBass4.R index 5d17b04..f0fd2ef 100644 --- a/R/StripedBass4.R +++ b/R/StripedBass4.R @@ -1,6 +1,6 @@ -#' Ages of Striped Bass assigned from scales by two readers. +#' @title Ages of Striped Bass assigned from scales by two readers. #' -#' Ages assigned by two different readers to the scales of Striped Bass (\emph{Morone saxatilis}). +#' @description Ages assigned by two different readers to the scales of Striped Bass (\emph{Morone saxatilis}). #' #' @name StripedBass4 #' @@ -20,7 +20,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @seealso \code{\link{StripedBass5}} and \code{\link{StripedBass6}}. #' diff --git a/R/StripedBass5.R b/R/StripedBass5.R index 4379ff6..7080bd2 100644 --- a/R/StripedBass5.R +++ b/R/StripedBass5.R @@ -1,6 +1,6 @@ -#' Ages of Striped Bass assigned from otoliths by two readers. +#' @title Ages of Striped Bass assigned from otoliths by two readers. #' -#' Ages assigned by two different readers to the otoliths of Striped Bass (\emph{Morone saxatilis}). +#' @description Ages assigned by two different readers to the otoliths of Striped Bass (\emph{Morone saxatilis}). #' #' @name StripedBass5 #' @@ -20,7 +20,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @seealso \code{\link{StripedBass4}} and \code{\link{StripedBass6}}. #' diff --git a/R/StripedBass6.R b/R/StripedBass6.R index 696f6bf..e6ab2c0 100644 --- a/R/StripedBass6.R +++ b/R/StripedBass6.R @@ -1,6 +1,6 @@ -#' Ages of Striped Bass assigned from scales and otoliths. +#' @title Ages of Striped Bass assigned from scales and otoliths. #' -#' Ages assigned to the scales and otoliths of Striped Bass (\emph{Morone saxatilis}). +#' @description Ages assigned to the scales and otoliths of Striped Bass (\emph{Morone saxatilis}). #' #' @name StripedBass6 #' @@ -20,7 +20,9 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' #' @seealso \code{\link{StripedBass4}} and \code{\link{StripedBass5}}. #' diff --git a/R/SturgeonBL.R b/R/SturgeonBL.R index 16a909c..86d25da 100644 --- a/R/SturgeonBL.R +++ b/R/SturgeonBL.R @@ -1,6 +1,6 @@ -#' Summarized multiple mark-recapture data for Lake Sturgeon. +#' @title Summarized multiple mark-recapture data for Lake Sturgeon. #' -#' The number of Lake Sturgeon (\emph{Acipenser fulvescens}) caught in multiple samples from Black Lake, MI in 1997. The caught fish were examined for previous marks, marked (if previously unmarked), and then returned to the population. +#' @description The number of Lake Sturgeon (\emph{Acipenser fulvescens}) caught in multiple samples from Black Lake, MI in 1997. The caught fish were examined for previous marks, marked (if previously unmarked), and then returned to the population. #' #' @name SturgeonBL #' @docType data @@ -23,7 +23,11 @@ #' \item Schumacher-Eschmeyer #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Schnabel +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel #' #' @source From Table 1 in Baker, E.A. and D.J. Borgeson. 1999. Lake sturgeon abundance and harvest in Black Lake, Michigan, 1975-1999. North American Journal of Fisheries Management. 19:1080-1088. #' diff --git a/R/SturgeonGB.R b/R/SturgeonGB.R index 88fd650..e029f4f 100644 --- a/R/SturgeonGB.R +++ b/R/SturgeonGB.R @@ -17,7 +17,7 @@ #' \item Year-class Strength #' } #' -#' @concept 'Year-class Strength' +#' @concept Year-class Strength #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' diff --git a/R/SunfishIN.R b/R/SunfishIN.R index 9a5b330..c16d57b 100644 --- a/R/SunfishIN.R +++ b/R/SunfishIN.R @@ -24,19 +24,13 @@ #' \item Schumacher-Eschmeyer #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Schnabel +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel #' -#' @source Originally from -#' -#' Gerking, S.D. 1953. Vital statistics of the fish population of Gordy Lake, Indiana. Transactions of the American Fisheries Society. 82:48-67. -#' -#' But also found in Table 2.4 of -#' -#' Krebs, C.J. 1999. Ecological Methodology. Addison-Welsey Educational Publishing, second edition. -#' -#' and Table 4.4 of -#' -#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada +#' @source Originally from Gerking, S.D. 1953. Vital statistics of the fish population of Gordy Lake, Indiana. Transactions of the American Fisheries Society. 82:48-67. But also found in Table 2.4 of Krebs, C.J. 1999. Ecological Methodology. Addison-Welsey Educational Publishing, second edition and Table 4.4 of Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. #' #' @keywords datasets #' diff --git a/R/SunfishLP.R b/R/SunfishLP.R index 09e73a6..f53aed6 100644 --- a/R/SunfishLP.R +++ b/R/SunfishLP.R @@ -18,9 +18,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From (approximately) Figure 2 in Crawford, S. and M.S. Allen. 2006. Fishing and natural mortality of bluegills and redear sunfish at Lake Panasoffkee, Florida: Implications for size limits. North American Journal of Fisheries Management 26:42-51. Note that I added a percentage for age-1 fish (the difference in percentages from Fig. 2). +#' @source From (approximately) Figure 2 in Crawford, S. and M.S. Allen. 2006. Fishing and natural mortality of Bluegills and Redear Sunfish at Lake Panasoffkee, Florida: Implications for size limits. North American Journal of Fisheries Management 26:42-51. Note that I added a percentage for age-1 fish (the difference in percentages from Fig. 2). #' #' @keywords datasets #' diff --git a/R/TPrawnsEG.R b/R/TPrawnsEG.R index 976d874..dce63b6 100644 --- a/R/TPrawnsEG.R +++ b/R/TPrawnsEG.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From table 9.1 in Haddon, M. 2000. Modeling and Quantitative Methods in Fisheries, CRC Press. Originally from Penn, J. W., and Caputi, N. 1986. Spawning stock-recruitment relationships and environmental influences on the tiger prawn (\emph{Penaeus esculentus}) fishery in Exmouth Gulf, Western Australia. Australian Journal of Marine and Freslzwater Research 37:491-505. +#' @source From table 9.1 in Haddon, M. 2000. Modeling and Quantitative Methods in Fisheries, CRC Press. Originally from Penn, J. W., and Caputi, N. 1986. Spawning stock-recruitment relationships and environmental influences on the Tiger Prawn (\emph{Penaeus esculentus}) fishery in Exmouth Gulf, Western Australia. Australian Journal of Marine and Freslzwater Research 37:491-505. #' #' @keywords datasets #' diff --git a/R/TroutADP.R b/R/TroutADP.R index 8d5ef60..d41cd00 100644 --- a/R/TroutADP.R +++ b/R/TroutADP.R @@ -19,11 +19,13 @@ #' \item Removal #' } #' -#' @concept Abundance 'Population Size' Removal +#' @concept Abundance +#' @concept Population Size +#' @concept Removal #' #' @seealso \link{SalmonADP} #' -#' @source From Table 1 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. +#' @source From Table 1 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. #' #' @keywords datasets #' diff --git a/R/TroutBR.R b/R/TroutBR.R index 10c2c3a..44b7c5f 100644 --- a/R/TroutBR.R +++ b/R/TroutBR.R @@ -19,9 +19,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From tables 18 and 19 of Scholl, D.K., P.J. Peeters, and S.T. Schram. 1984. Migratory brown trout and rainbow trout populations of the Brule River, Wisconsin. Wisconsin Department of Natural Resources, Fish Management Report No. 123. +#' @source From tables 18 and 19 of Scholl, D.K., P.J. Peeters, and S.T. Schram. 1984. Migratory brown trout and rainbow trout populations of the Brule River, Wisconsin. Wisconsin Department of Natural Resources, Fish Management Report No. 123. #' #' @keywords datasets #' diff --git a/R/TroutperchLM1.R b/R/TroutperchLM1.R index 5e9ff57..fab2cbe 100644 --- a/R/TroutperchLM1.R +++ b/R/TroutperchLM1.R @@ -19,9 +19,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source Simulated from the age-length data provided in Table 1 of House, R., and L. Wells. 1973. Age, growth, spawning season, and fecundity of the trout-perch (\emph{Percopsis omsicomaycus}) in southeastern Lake Michigan. Journal of the Fisheries Research Board of Canada. 30:1221-1225. +#' @source Simulated from the age-length data provided in Table 1 of House, R., and L. Wells. 1973. Age, growth, spawning season, and fecundity of the trout-perch (\emph{Percopsis omsicomaycus}) in southeastern Lake Michigan. Journal of the Fisheries Research Board of Canada. 30:1221-1225. #' #' @keywords datasets #' diff --git a/R/TroutperchLM2.R b/R/TroutperchLM2.R index 04abacf..d9ccd1c 100644 --- a/R/TroutperchLM2.R +++ b/R/TroutperchLM2.R @@ -17,9 +17,10 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' +#' @concept Length Frequency +#' @concept Size Structure #' -#' @source From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +#' @source From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. #' #' @keywords datasets #' diff --git a/R/TroutperchLM3.R b/R/TroutperchLM3.R index 3b2defc..8e8025d 100644 --- a/R/TroutperchLM3.R +++ b/R/TroutperchLM3.R @@ -20,7 +20,9 @@ #' \item Size Structure #' } #' -#' @concept 'Length Frequency' 'Size Structure' 'Length Expansion' +#' @concept Length Frequency +#' @concept Size Structure +#' @concept Length Expansion #' #' @seealso \code{\link{TroutperchLM2}}. #' diff --git a/R/VendaceLP.R b/R/VendaceLP.R index 1c206e4..814dcf5 100644 --- a/R/VendaceLP.R +++ b/R/VendaceLP.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 1 and 2 of Marjomaki, T.J. 2004. Analysis of the spawning stock-recruitment relationship of vendace (\emph{Coregonus albula} (L.)) with evaluation of alternative models, additional variables, biases and errors. Ecology of Freshwater Fish 13:46-60. +#' @source From (approximately) Figure 1 and 2 of Marjomaki, T.J. 2004. Analysis of the spawning stock-recruitment relationship of vendace (\emph{Coregonus albula} (L.)) with evaluation of alternative models, additional variables, biases and errors. Ecology of Freshwater Fish 13:46-60. #' #' @keywords datasets #' diff --git a/R/VendaceLP2.R b/R/VendaceLP2.R index 19411b9..de97390 100644 --- a/R/VendaceLP2.R +++ b/R/VendaceLP2.R @@ -20,9 +20,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 6 in Helminen, H. and J. Sarvala. 1994. Population regulation of vendance (\emph{Coregonus albula}) in Lake Pyhajarvi, southwest Finland. Journal of Fish Biology 45:387-400. +#' @source From (approximately) Figure 6 in Helminen, H. and J. Sarvala. 1994. Population regulation of vendance (\emph{Coregonus albula}) in Lake Pyhajarvi, southwest Finland. Journal of Fish Biology 45:387-400. #' #' @keywords datasets #' diff --git a/R/WShrimpGA.R b/R/WShrimpGA.R index d157169..75ec236 100644 --- a/R/WShrimpGA.R +++ b/R/WShrimpGA.R @@ -22,9 +22,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figures 2 and 3 of Belcher, C.N., and C.A. Jennings. 2004. Evaluation of stock-recruitment curves for white shrimp in Georgia. North American Journal of Fisheries Management. 24:654-661. +#' @source From (approximately) Figures 2 and 3 of Belcher, C.N., and C.A. Jennings. 2004. Evaluation of stock-recruitment curves for white shrimp in Georgia. North American Journal of Fisheries Management. 24:654-661. #' #' @keywords datasets #' diff --git a/R/WalleyeConsumption.R b/R/WalleyeConsumption.R index ed2489d..aa57f89 100644 --- a/R/WalleyeConsumption.R +++ b/R/WalleyeConsumption.R @@ -17,7 +17,7 @@ #' \item Nonlinear modeling #' } #' -#' @source From Figure 3 in Madenjian, C.P., and S.R. Carpenter. 1991. Individual-based model for growth of young-of-the-year walleye: A piece of the recruitment puzzle. Ecological Applications. 1:268-279. Data were originally from Swenson, W. A. 1977. Food consumptions of walleye (\emph{Stizostedion vitreum vitreum}) and sauger (\emph{S. canadense}) in relation to food availability and physical conditions in Lake of the Woods, Minnesota, Shagawa Lake, and western Lake Superior. Journal of the Fisheries Research Board of Canada 34:1643-1654. [Madenjian et al. (1991) was (is?) from http://www.esajournals.org/doi/abs/10.2307/1941756. Swenson (1977) was (is?) from http://www.nrcresearchpress.com/doi/abs/10.1139/f77-229?journalCode=jfrbc.] +#' @source From Figure 3 in Madenjian, C.P., and S.R. Carpenter. 1991. Individual-based model for growth of young-of-the-year walleye: A piece of the recruitment puzzle. Ecological Applications. 1:268-279. Data were originally from Swenson, W. A. 1977. Food consumptions of walleye (\emph{Stizostedion vitreum vitreum}) and sauger (\emph{S. canadense}) in relation to food availability and physical conditions in Lake of the Woods, Minnesota, Shagawa Lake, and western Lake Superior. Journal of the Fisheries Research Board of Canada 34:1643-1654. [Madenjian et al. (1991) was (is?) from http://www.esajournals.org/doi/abs/10.2307/1941756. Swenson (1977) was (is?) from http://www.nrcresearchpress.com/doi/abs/10.1139/f77-229?journalCode=jfrbc.] #' #' @keywords datasets #' diff --git a/R/WalleyeEL.R b/R/WalleyeEL.R index c90aacd..c64ec62 100644 --- a/R/WalleyeEL.R +++ b/R/WalleyeEL.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source Hansen, M. J., M. A. Bozek, J. R. Newby, S. P. Newman, and M. D. Staggs. 1998. Factors affecting recruitment of walleyes in Escanaba Lake, Wisconsin, 1958-1995. North American Journal of Fisheries Management 18:764-774. +#' @source Hansen, M. J., M. A. Bozek, J. R. Newby, S. P. Newman, and M. D. Staggs. 1998. Factors affecting recruitment of walleyes in Escanaba Lake, Wisconsin, 1958-1995. North American Journal of Fisheries Management 18:764-774. #' #' @keywords datasets #' diff --git a/R/WalleyeErie.R b/R/WalleyeErie.R index 72ec47b..fe93bdf 100644 --- a/R/WalleyeErie.R +++ b/R/WalleyeErie.R @@ -17,7 +17,7 @@ #' #' @concept Recruitment #' -#' @source From Wolfert, D. R. 1981. The commercial fishery for walleyes in New York waters of Lake Erie, 1959-1978. North American Journal of Fisheries Management 1: 112-126. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Wolfert, D. R. 1981. The commercial fishery for walleyes in New York waters of Lake Erie, 1959-1978. North American Journal of Fisheries Management 1: 112-126. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/WalleyeErie2.R b/R/WalleyeErie2.R index ec64f91..385b4e3 100644 --- a/R/WalleyeErie2.R +++ b/R/WalleyeErie2.R @@ -3,7 +3,9 @@ #' @description Walleye (\emph{Sander vitreus}) biological data (length, weight, sex, maturity, and age) from several locations in Lake Erie, October-November of 2003-2014. #' #' @name WalleyeErie2 +#' #' @docType data +#' #' @format A data frame of 33734 observations on the following 10 variables: #' \describe{ #' \item{setID}{Unique gear (multifilament gill net kegged 6 ft below surface) set identification number.} @@ -16,19 +18,30 @@ #' \item{mat}{Maturity (immature, mature).} #' \item{age}{Age (yrs) from otoliths.} #' } -#' @section Topic(s): \itemize{ -#' \item Growth -#' \item von Bertalanffy -#' \item Weight-Length -#' \item Catch curve -#' \item Mortality -#' \item Maturity -#' \item Size Structure -#' \item Length Frequency -#' \item Condition -#' } -#' @concept 'Growth' 'Weight-Length' 'Catch curve' 'Mortality' 'Maturity' 'Size Structure' 'Condition' 'Length Frequency' -#' @source These unpublished data are from the Ohio Department of Natural Resources, Division of Wildlife (via Christopher Vandergoot). \bold{Do not use for other than educational purposes without permission from the source.} +#' +#' @section Topic(s): +#' \itemize{ +#' \item Growth +#' \item von Bertalanffy +#' \item Weight-Length +#' \item Catch curve +#' \item Mortality +#' \item Maturity +#' \item Size Structure +#' \item Length Frequency +#' \item Condition +#' } +#' +#' @concept Growth +#' @concept Weight-Length +#' @concept Catch curve +#' @concept Mortality +#' @concept Maturity +#' @concept Size Structure +#' @concept Condition +#' @concept Length Frequency +#' +#' @source These unpublished data are from the Ohio Department of Natural Resources, Division of Wildlife (via Christopher Vandergoot). \bold{Do not use for other than educational purposes without permission from the source.} #' #' @keywords datasets #' diff --git a/R/WalleyeKS.R b/R/WalleyeKS.R index 3a350f1..359317f 100644 --- a/R/WalleyeKS.R +++ b/R/WalleyeKS.R @@ -21,9 +21,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Figure 2 of Quist, M.C., J.L. Stephen, C.S. Guy, and R.D. Schultz. 2004. Age structure and mortality of Walleyes in Kansas reservoirs: Use of mortality caps to establish realistic management objectives. North American Journal of Fisheries Management 24:990-1002. +#' @source From Figure 2 of Quist, M.C., J.L. Stephen, C.S. Guy, and R.D. Schultz. 2004. Age structure and mortality of Walleyes in Kansas reservoirs: Use of mortality caps to establish realistic management objectives. North American Journal of Fisheries Management 24:990-1002. #' #' @keywords datasets #' diff --git a/R/WalleyeML.R b/R/WalleyeML.R index c5cb884..8bf2fe8 100644 --- a/R/WalleyeML.R +++ b/R/WalleyeML.R @@ -3,7 +3,9 @@ #' @description Back-calculated lengths-at-age for Walleye (\emph{Sander vitreus}) from Lake Mille Lacs. Walleye were captured by Minnesota Department of Natural Resources personnel in fishery-independent gillnets (five multifilament nylon mesh panels with each panel measuring 15.2 m wide and 1.8 m high; bar-measure mesh sizes of the panels were 19.1, 25.4, 31.7, 38.1, and 50.8 mm) set in the fall (mid September to early October) from 2000 to 2011. #' #' @name WalleyeML +#' #' @docType data +#' #' @format A data frame of 14583 observations on the following 9 variables: #' \describe{ #' \item{ID}{A unique fish identification number.} @@ -16,12 +18,18 @@ #' \item{BC.Age}{Annulus or previous age.} #' \item{BC.Len}{Back-calculated length at \code{BC.Age}. Lengths were back-calculated using the \emph{Scale-Proportional Hypothesis} method.} #' } -#' @section Topic(s): \itemize{ -#' \item Growth -#' \item von Bertalanffy -#' \item Back-calculation -#' } -#' @concept 'Growth' 'von Bertalanffy' 'Back-calculation' +#' +#' @section Topic(s): +#' \itemize{ +#' \item Growth +#' \item von Bertalanffy +#' \item Back-calculation +#' } +#' +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Back-calculation +#' #' @source These unpublished data are from the Minnesota Department of Natural Resources, Section of Fisheries (via Melissa Treml). \bold{Do not use for other than educational purposes without permission from the source.} #' #' @keywords datasets diff --git a/R/WalleyeMN06a.R b/R/WalleyeMN06a.R index 84abfab..29eb5be 100644 --- a/R/WalleyeMN06a.R +++ b/R/WalleyeMN06a.R @@ -19,9 +19,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From various tables in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] +#' @source From various tables in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] #' #' @keywords datasets #' diff --git a/R/WalleyeMN06b.R b/R/WalleyeMN06b.R index fad5af6..449a655 100644 --- a/R/WalleyeMN06b.R +++ b/R/WalleyeMN06b.R @@ -25,9 +25,13 @@ #' \item Schumacher-Eschmeyer #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel #' -#' @source From appendix 2 in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] +#' @source From appendix 2 in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] #' #' @keywords datasets #' diff --git a/R/WalleyePL.R b/R/WalleyePL.R index db182c0..eac8c25 100644 --- a/R/WalleyePL.R +++ b/R/WalleyePL.R @@ -25,9 +25,13 @@ #' \item Schumacher-Eschmeyer #' } #' -#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' +#' @concept Abundance +#' @concept Population Size +#' @concept Mark-Recapture +#' @concept Capture-Recapture +#' @concept Schnabel #' -#' @source From table 3 of Mraz, D. 1968. Recruitment, growth, exploitation, and management of walleyes in a southeastern Wisconsin lake. Wisconsin Department of Natural Resources Technical Bulletin 40. 38 pages. +#' @source From table 3 of Mraz, D. 1968. Recruitment, growth, exploitation, and management of walleyes in a southeastern Wisconsin lake. Wisconsin Department of Natural Resources Technical Bulletin 40. 38 pages. #' #' @keywords datasets #' diff --git a/R/WalleyePS.R b/R/WalleyePS.R index e7596b5..132513d 100644 --- a/R/WalleyePS.R +++ b/R/WalleyePS.R @@ -24,9 +24,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From Figure 2 in Kocovsky, P.M., and R.M. Carline. 2000. A comparison of methods for estimating ages of unexploited walleyes. North American Journal of Fisheries Management 20:1044-1048. +#' @source From Figure 2 in Kocovsky, P.M., and R.M. Carline. 2000. A comparison of methods for estimating ages of unexploited walleyes. North American Journal of Fisheries Management 20:1044-1048. #' #' @keywords datasets #' diff --git a/R/WalleyeRL.R b/R/WalleyeRL.R index b0ffd13..21cbf51 100644 --- a/R/WalleyeRL.R +++ b/R/WalleyeRL.R @@ -31,9 +31,10 @@ #' \item Weisberg linear growth model #' } #' -#' @concept Growth Weisberg LGM +#' @concept Growth +#' @concept Weisberg LGM #' -#' @source Cyterski, M.J. and G.R. Spangler. 1996. A tool for age determination. North American Journal of Fisheries Management, 16:403-412. +#' @source Cyterski, M.J. and G.R. Spangler. 1996. A tool for age determination. North American Journal of Fisheries Management, 16:403-412. #' #' @keywords datasets #' diff --git a/R/WalleyeWad.R b/R/WalleyeWad.R index 2e2b525..6437e3d 100644 --- a/R/WalleyeWad.R +++ b/R/WalleyeWad.R @@ -21,11 +21,12 @@ #' \item Catch Curve #' } #' -#' @concept 'Catch Curve' Mortality +#' @concept Catch Curve +#' @concept Mortality #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' -#' @source From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. +#' @source From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. #' #' @keywords datasets #' diff --git a/R/WalleyeWyrlng.R b/R/WalleyeWyrlng.R index 4acfa8a..4e26d1f 100644 --- a/R/WalleyeWyrlng.R +++ b/R/WalleyeWyrlng.R @@ -22,11 +22,12 @@ #' \item Recruitment #' } #' -#' @concept 'Year-class Strength' Recruitment +#' @concept Year-class Strength +#' @concept Recruitment #' #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' -#' @source From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. +#' @source From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. #' #' @keywords datasets #' diff --git a/R/WhiteGrunt1.R b/R/WhiteGrunt1.R index f4f9dba..93acadb 100644 --- a/R/WhiteGrunt1.R +++ b/R/WhiteGrunt1.R @@ -18,9 +18,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Figure 7 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. +#' @source From Figure 7 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. #' #' @keywords datasets #' diff --git a/R/WhiteGrunt2.R b/R/WhiteGrunt2.R index 0549424..88fbb74 100644 --- a/R/WhiteGrunt2.R +++ b/R/WhiteGrunt2.R @@ -19,9 +19,10 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' +#' @concept Growth +#' @concept von Bertalanffy #' -#' @source From (approximately) Figure 6 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. +#' @source From (approximately) Figure 6 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. #' #' @keywords datasets #' diff --git a/R/WhitefishGSL.R b/R/WhitefishGSL.R index f477341..4f80bb2 100644 --- a/R/WhitefishGSL.R +++ b/R/WhitefishGSL.R @@ -24,9 +24,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Table 19 of Mosenko, R.W., and G. Low. 1980. Data from the commercial fishery for lake whitefish \emph{Coregonus clupeaformis} (Mitchill), on Great Slave Lake, Northwest Territories, 1979. Canadian Data Report of Fisheries And Aquatic Sciences, No. 194. +#' @source From Table 19 of Mosenko, R.W., and G. Low. 1980. Data from the commercial fishery for lake whitefish \emph{Coregonus clupeaformis} (Mitchill), on Great Slave Lake, Northwest Territories, 1979. Canadian Data Report of Fisheries And Aquatic Sciences, No. 194. #' #' @keywords datasets #' diff --git a/R/WhitefishMB.R b/R/WhitefishMB.R index 5b9db2a..1b1510c 100644 --- a/R/WhitefishMB.R +++ b/R/WhitefishMB.R @@ -21,9 +21,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From (approximately) Figure 1 of Mills, K.H., and R.J. Beamish. 1980. Comparison of fin-ray and scale age determinations for lake whitefish (\emph{Coregonus clupeaformis}) and their implications for estimates of growth and annual survival. Canadian Journal of Fisheries and Aquatic Sciences, 37:534-544. +#' @source From (approximately) Figure 1 of Mills, K.H., and R.J. Beamish. 1980. Comparison of fin-ray and scale age determinations for lake whitefish (\emph{Coregonus clupeaformis}) and their implications for estimates of growth and annual survival. Canadian Journal of Fisheries and Aquatic Sciences, 37:534-544. #' #' @keywords datasets #' diff --git a/R/WhitefishTB.R b/R/WhitefishTB.R index d9503ed..13d217d 100644 --- a/R/WhitefishTB.R +++ b/R/WhitefishTB.R @@ -21,9 +21,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Petzold, M. 1995. An historical analysis of the Lake Whitefish fisheries of Thunder Bay (Zone 1) and Whitefish Bay (Zone 34), Lake Superior. Ontario Min. of Nat. Res. unpubl. manuscript. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Petzold, M. 1995. An historical analysis of the Lake Whitefish fisheries of Thunder Bay (Zone 1) and Whitefish Bay (Zone 34), Lake Superior. Ontario Min. of Nat. Res. unpubl. manuscript. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/YERockfish.R b/R/YERockfish.R index 818101e..2c10f3f 100644 --- a/R/YERockfish.R +++ b/R/YERockfish.R @@ -22,9 +22,11 @@ #' \item von Bertalanffy #' } #' -#' @concept Growth 'von Bertalanffy' 'Maturity' +#' @concept Growth +#' @concept von Bertalanffy +#' @concept Maturity #' -#' @source Obtained directly (from Bob Hannah). Date were used in Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf] +#' @source Obtained directly (from Bob Hannah). Data were used in Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf] #' #' @keywords datasets #' diff --git a/R/YPerchCB1.R b/R/YPerchCB1.R index e49d19a..fc121ed 100644 --- a/R/YPerchCB1.R +++ b/R/YPerchCB1.R @@ -33,9 +33,10 @@ #' \item Catch curve #' } #' -#' @concept Mortality 'Catch Curve' +#' @concept Mortality +#' @concept Catch Curve #' -#' @source From Table 1 in Bronte, C.R., J.H. Selgeby, D.V.Swedberg. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management 13:511-523. +#' @source From Table 1 in Bronte, C.R., J.H. Selgeby, D.V.Swedberg. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management 13:511-523. #' #' @keywords datasets #' diff --git a/R/YPerchCB2.R b/R/YPerchCB2.R index 851b408..a4e44b9 100644 --- a/R/YPerchCB2.R +++ b/R/YPerchCB2.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From (approximately) Figure 7 in Bronte et al. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management. 13:511-523. +#' @source From (approximately) Figure 7 in Bronte et al. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management. 13:511-523. #' #' @keywords datasets #' diff --git a/R/YPerchGB.R b/R/YPerchGB.R index 6b72951..0670008 100644 --- a/R/YPerchGB.R +++ b/R/YPerchGB.R @@ -19,7 +19,7 @@ #' #' @concept Recruitment #' -#' @source From Walters, C., and A. Punt. 1994. Placing odds on sustainable catch virtual population analysis and survey data. Canadian Journal of Fisheries and Aquatic Sciences, 51:946-958. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Walters, C., and A. Punt. 1994. Placing odds on sustainable catch virtual population analysis and survey data. Canadian Journal of Fisheries and Aquatic Sciences, 51:946-958. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/YPerchGL.R b/R/YPerchGL.R index 73bf176..bc2d9bb 100644 --- a/R/YPerchGL.R +++ b/R/YPerchGL.R @@ -19,9 +19,10 @@ #' \item Length Frequency #' } #' -#' @concept 'Weight-Length' 'Length Frequency' +#' @concept Weight-Length +#' @concept Length Frequency #' -#' @source From (approximately) Figure 3 in Brylinsky, M. 2001. An evaluation of changes in the yellow perch (\emph{Perca flavescens}) population of Grafton Lake, Kejimkujik National Park, after dam removal. Technical Report Publication No. 59, Acadia Centre for Estuarine Research. 2001. +#' @source From (approximately) Figure 3 in Brylinsky, M. 2001. An evaluation of changes in the yellow perch (\emph{Perca flavescens}) population of Grafton Lake, Kejimkujik National Park, after dam removal. Technical Report Publication No. 59, Acadia Centre for Estuarine Research. #' #' @keywords datasets #' diff --git a/R/YPerchRL.R b/R/YPerchRL.R index 6505f1a..416abdb 100644 --- a/R/YPerchRL.R +++ b/R/YPerchRL.R @@ -19,7 +19,7 @@ #' #' @concept Recruitment #' -#' @source From Smith, L. L. Jr. 1977. Walleye (\emph{Stizostedion vitreum}) and yellow perch (\emph{Perca flavescens}) populations and fisheries of the Red Lakes, Minnesota, 1930-75. J. Fish. Res. Board Can. 34: 1774-1783. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Smith, L.L. Jr. 1977. Walleye (\emph{Stizostedion vitreum}) and yellow perch (\emph{Perca flavescens}) populations and fisheries of the Red Lakes, Minnesota, 1930-75. J. Fish. Res. Board Can. 34: 1774-1783. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/YPerchSB.R b/R/YPerchSB.R index a4550a4..93c46d5 100644 --- a/R/YPerchSB.R +++ b/R/YPerchSB.R @@ -19,9 +19,10 @@ #' \item Recruitment #' } #' -#' @concept 'Stock-Recruit' Recruitment +#' @concept Stock-Recruit +#' @concept Recruitment #' -#' @source From Henderson, B.A. 1985. Factors affecting growth and recruitment of yellow perch, \emph{Perca flavescens} Mitchill, in South Bay, Lake Huron. Journal of Fisheries Biology 26:449-458. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +#' @source From Henderson, B.A. 1985. Factors affecting growth and recruitment of yellow perch, \emph{Perca flavescens} Mitchill, in South Bay, Lake Huron. Journal of Fisheries Biology 26:449-458. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. #' #' @keywords datasets #' diff --git a/R/YPerchSB1.R b/R/YPerchSB1.R index 96ca545..1572886 100644 --- a/R/YPerchSB1.R +++ b/R/YPerchSB1.R @@ -19,9 +19,11 @@ #' \item PSD #' } #' -#' @concept 'Length Frequency' 'Size Structure' PSD +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' -#' @source Simulated (uniform distribution of values within length bin) from summarized length frequencies in Figure 2 (top) in Diana, J.S. and R. Salz. 1990. Energy storage, growth, and maturation of yellow perch from different locations in Saginaw Bay, Michigan. Transactions of the American Fisheries Society 119:976-984. +#' @source Simulated (uniform distribution of values within length bin) from summarized length frequencies in Figure 2 (top) in Diana, J.S. and R. Salz. 1990. Energy storage, growth, and maturation of yellow perch from different locations in Saginaw Bay, Michigan. Transactions of the American Fisheries Society 119:976-984. #' #' @keywords datasets #' diff --git a/R/YPerchTL.R b/R/YPerchTL.R index f266f00..082226e 100644 --- a/R/YPerchTL.R +++ b/R/YPerchTL.R @@ -25,7 +25,10 @@ #' \item PSD #' } #' -#' @concept 'Weight-Length' 'Length Frequency' 'Size Structure' PSD +#' @concept Weight-Length +#' @concept Length Frequency +#' @concept Size Structure +#' @concept PSD #' #' @source From a query to the North Temperate Lakes Long Term Ecological Research, Fish Lengths and Weights Database which was (is?) at https://lter.limnology.wisc.edu/dataset/north-temperate-lakes-lter-fish-lengths-and-weights-1981-current. #' diff --git a/R/YTFlounder.R b/R/YTFlounder.R index 63c8b1b..78d60aa 100644 --- a/R/YTFlounder.R +++ b/R/YTFlounder.R @@ -21,9 +21,11 @@ #' \item Ageing Error #' } #' -#' @concept Age Precision Bias 'Age Comparison' +#' @concept Age Precision +#' @concept Age Bias +#' @concept Age Comparison #' -#' @source From tables in Annex 3 of Walsh, S.J. and J. Burnett. 2002. The Canada-United States yellowtail flounder age reading workshop: 28-30 November2000, St. John's, Newfoundland. North Atlantic Fisheries Organization. Scientific Council Studies 35:1-59. +#' @source From tables in Annex 3 of Walsh, S.J. and J. Burnett. 2002. The Canada-United States yellowtail flounder age reading workshop: 28-30 November 2000, St. John's, Newfoundland. North Atlantic Fisheries Organization. Scientific Council Studies 35:1-59. #' #' @keywords datasets #' diff --git a/cran-comments/cran-comments_v0_3_8.md b/cran-comments/cran-comments_v0_3_8.md new file mode 100644 index 0000000..b0e5b2b --- /dev/null +++ b/cran-comments/cran-comments_v0_3_8.md @@ -0,0 +1,9 @@ +* This updates the existing FSAdata package on CRAN with corrections, largely to the use of \concept(), as directed by CRAN (per e-mail from Kurt Hornik on 17-May-19). + +## Notes +* There may be a note about "datasets" being misspelled in the description. I do not consider "datasets" to be misspelled. + +## Testing Environments +* My Windows machine. +* Win Builder -- current and development. +* Travis-CI. \ No newline at end of file diff --git a/man/AHerringChile.Rd b/man/AHerringChile.Rd index 1680964..ed71dd6 100644 --- a/man/AHerringChile.Rd +++ b/man/AHerringChile.Rd @@ -32,5 +32,7 @@ head(AHerringChile) plot(len~age,data=AHerringChile) } -\concept{'Seasonal Growth' 'von Bertalanffy' Somers} +\concept{Seasonal Growth} +\concept{Somers} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/AlewifeLH.Rd b/man/AlewifeLH.Rd index c588430..51fa5dd 100644 --- a/man/AlewifeLH.Rd +++ b/man/AlewifeLH.Rd @@ -33,5 +33,7 @@ plot(scales~otoliths,data=AlewifeLH) xtabs(~otoliths+scales,data=AlewifeLH) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/AnchovetaChile.Rd b/man/AnchovetaChile.Rd index add1bcc..8fcd82e 100644 --- a/man/AnchovetaChile.Rd +++ b/man/AnchovetaChile.Rd @@ -34,5 +34,7 @@ AnchovetaChile$age <- AnchovetaChile$age.mon/12 plot(tl.cm~age,data=AnchovetaChile) } -\concept{'Seasonal Growth' 'von Bertalanffy' Somers} +\concept{Seasonal Growth} +\concept{Somers} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/BGHRfish.Rd b/man/BGHRfish.Rd index d4f95ec..89bd247 100644 --- a/man/BGHRfish.Rd +++ b/man/BGHRfish.Rd @@ -38,5 +38,5 @@ head(BGHRfish) \seealso{ See \code{\link{BGHRfish}} for individual fish collected in these samples. } -\concept{'Data Manipulation'} +\concept{Data Manipulation} \keyword{datasets} diff --git a/man/BGHRsample.Rd b/man/BGHRsample.Rd index fcd0af2..a34eb0c 100644 --- a/man/BGHRsample.Rd +++ b/man/BGHRsample.Rd @@ -36,5 +36,5 @@ head(BGHRsample) \seealso{ See \code{\link{BGHRfish}} for individual fish collected in these samples. } -\concept{'Data Manipulation'} +\concept{Data Manipulation} \keyword{datasets} diff --git a/man/BSkateGB.Rd b/man/BSkateGB.Rd index ed007ad..dfe9c8e 100644 --- a/man/BSkateGB.Rd +++ b/man/BSkateGB.Rd @@ -12,7 +12,7 @@ \item{season}{a factor containing the season of capture (fall, spring, winter)} }} \source{ -estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick. 2009. Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank. North American Journal of Fisheries Management 29:512-526. +Estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick. 2009. Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank. North American Journal of Fisheries Management 29:512-526. } \description{ Stock and recruitment data for Barndoor Skate (\emph{Dipturus laevis}) from Georges Bank for three seasons. @@ -42,5 +42,6 @@ plot(recruits~spawners,data=BSkateGB,subset=season=="winter",main="winter") par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/BassFL.Rd b/man/BassFL.Rd index 01fb7bd..fe18e0a 100644 --- a/man/BassFL.Rd +++ b/man/BassFL.Rd @@ -13,7 +13,7 @@ \item{age}{Age of fish at capture} }} \source{ -From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux. 2005. Relative Abundance, Growth, and Mortality of Suwannee Bass in Four Florida Rivers. North American Journal of Fisheries Management 25:275-283. [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.] +From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux. 2005. Relative Abundance, Growth, and Mortality of Suwannee Bass in Four Florida Rivers. North American Journal of Fisheries Management 25:275-283. [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.] } \description{ Catch-at-age for Suwanee (\emph{Micropterus notius}) and Largemouth Bass (\emph{Micropterus salmoides}) collected from several lakes in Florida, 2001-2002. @@ -52,5 +52,6 @@ legend("topright",legend=c("2001","2002"),col=c("black","red"),pch=19) par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/BlackDrum2001.Rd b/man/BlackDrum2001.Rd index c75a7cd..c1cb5ad 100644 --- a/man/BlackDrum2001.Rd +++ b/man/BlackDrum2001.Rd @@ -41,5 +41,7 @@ head(BlackDrum2001) plot(tl~otoage,data=BlackDrum2001) } -\concept{Growth 'von Bertalanffy' 'Weight-Length'} +\concept{Growth} +\concept{Weight-Length} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/BloaterLH.Rd b/man/BloaterLH.Rd index f32192c..5964872 100644 --- a/man/BloaterLH.Rd +++ b/man/BloaterLH.Rd @@ -11,7 +11,7 @@ \item{age3}{Relative abundance of age-3 fish} }} \source{ -From (approximately) Figure 7 of Schaeffer, J.S. 2004. Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998. Ann Zool Fennici. 41:271-279. +From (approximately) Figure 7 of Schaeffer, J.S. 2004. Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998. Ann Zool Fennici. 41:271-279. } \description{ Egg deposition and relative abundance of age-3 Lake Huron Bloaters (\emph{Coregonus hoyi}) by year, 1981-1996. @@ -34,5 +34,6 @@ plot(eggs~age3,data=BloaterLH) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/BlueCatfish.Rd b/man/BlueCatfish.Rd index d0e2334..fecb617 100644 --- a/man/BlueCatfish.Rd +++ b/man/BlueCatfish.Rd @@ -10,7 +10,7 @@ \item{tl}{Total length (mm)} }} \source{ -From (approximately) Figure 2 of Maceina, M.J. 2007. Use of piecewise nonlinear models to estimate variable size-related mortality rates. North American Journal of Fisheries Management, 27:971-977. +From (approximately) Figure 2 of Maceina, M.J. 2007. Use of piecewise nonlinear models to estimate variable size-related mortality rates. North American Journal of Fisheries Management, 27:971-977. } \description{ Ages and total lengths of Blue Catfish (\emph{Ictalurus furcatus}) collected form the Wilson Reservoir on the Tennessee River, AL. @@ -30,5 +30,6 @@ head(BlueCatfish) plot(tl~age,data=BlueCatfish) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/BlueCrab.Rd b/man/BlueCrab.Rd index 0c99da5..4b1b2d5 100644 --- a/man/BlueCrab.Rd +++ b/man/BlueCrab.Rd @@ -10,7 +10,7 @@ \item{effort}{A numeric vector of lines used per day to catch Blue Crab.} }} \source{ -From Fischler, K.J. 1965. The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs. Transactions of the American Fisheries Society, 94:287-310. +From Fischler, K.J. 1965. The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs. Transactions of the American Fisheries Society, 94:287-310. } \description{ Catch and effort data for a population of male Blue Crabs (\emph{Callinectes sapidus}) for a 12-week period. @@ -33,5 +33,10 @@ str(BlueCrab) BlueCrab } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/BluefishAge.Rd b/man/BluefishAge.Rd index 8738f13..6df455c 100644 --- a/man/BluefishAge.Rd +++ b/man/BluefishAge.Rd @@ -31,5 +31,7 @@ head(BluefishAge) plot(r1~r2,data=BluefishAge) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/BluegillIL.Rd b/man/BluegillIL.Rd index dbfc3b5..24ccad3 100644 --- a/man/BluegillIL.Rd +++ b/man/BluegillIL.Rd @@ -13,7 +13,7 @@ \item{deltaTime}{Time-at-large (yrs).} }} \source{ -These unpublished data are from Derek H. Ogle, Northland College. \bold{Do not use for other than educational purposes without permission from the source.} +These unpublished data are from Derek H. Ogle, Northland College. \bold{Do not use for other than educational purposes without permission from the source.} } \description{ Length-at-marking and recapture and time-at-large for Bluegill (\emph{Lepomis macrochirus}) originally captured in Spring 2010 from Inch Lake, Wisconsin. @@ -34,5 +34,7 @@ head(BluegillIL) plot((lenRecap-lenMark)~deltaTime,data=BluegillIL) } -\concept{Growth 'von Bertalanffy' Fabens} +\concept{Fabens} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/BluegillLM.Rd b/man/BluegillLM.Rd index f5ad0ee..9ba704b 100644 --- a/man/BluegillLM.Rd +++ b/man/BluegillLM.Rd @@ -40,5 +40,7 @@ par(op) \seealso{ \code{lakemary} in \pkg{alr3} for a different sample of Bluegill from Lake Mary that has length and age. } -\concept{'Weight-Length' 'Length Conversion' 'Length Frequency'} +\concept{Length Conversion} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/BluntnoseIL1.Rd b/man/BluntnoseIL1.Rd index 3c88d79..ef97f54 100644 --- a/man/BluntnoseIL1.Rd +++ b/man/BluntnoseIL1.Rd @@ -35,5 +35,8 @@ head(BluntnoseIL1) \seealso{ \code{\link{InchLake1}}, \code{\link{InchLake2}}. } -\concept{'Length Frequency' 'Size Structure' PSD 'Length Expansion'} +\concept{Length Expansion} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/Bonito.Rd b/man/Bonito.Rd index 820bbc4..de1fc1c 100644 --- a/man/Bonito.Rd +++ b/man/Bonito.Rd @@ -33,5 +33,7 @@ head(Bonito) plot(fl~age,data=Bonito) } -\concept{'Seasonal Growth' 'von Bertalanffy' Somers} +\concept{Seasonal Growth} +\concept{Somers} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/BrookTroutNC.Rd b/man/BrookTroutNC.Rd index c706786..8898fe0 100644 --- a/man/BrookTroutNC.Rd +++ b/man/BrookTroutNC.Rd @@ -10,7 +10,7 @@ \item{yoy}{a numeric vector giving autumn YOY density (number per square meter) in following year} }} \source{ -From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty. 2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream. Freshwater Biology 55:1494-1508. +From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty. 2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream. Freshwater Biology 55:1494-1508. } \description{ Stock and recruitment data for Brook Trout (\emph{Salvelinus fontinalis}) from Ball Creek, NC, 1991-2004. @@ -33,5 +33,6 @@ head(BrookTroutNC) plot(adult~yoy,data=BrookTroutNC) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/BrookTroutNEWP.Rd b/man/BrookTroutNEWP.Rd index 6879056..66c10bc 100644 --- a/man/BrookTroutNEWP.Rd +++ b/man/BrookTroutNEWP.Rd @@ -15,7 +15,7 @@ \item{fourth}{Catch on the fourth removal pass.} }} \source{ -From Table 1 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. +From Table 1 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. } \description{ Catches in removal events for Brook Trout (\emph{Salvelinus fontinalis}) in two streams in the the Nashwaak Experimental Watersheds Project on multiple dates. @@ -39,5 +39,7 @@ BrookTroutNEWP[3,] \seealso{ See \code{\link{BrookTroutNEWP1}} for these data AND the results from Schnute (1983). } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/BrookTroutNEWP1.Rd b/man/BrookTroutNEWP1.Rd index 5bc814f..cc61643 100644 --- a/man/BrookTroutNEWP1.Rd +++ b/man/BrookTroutNEWP1.Rd @@ -28,7 +28,7 @@ \item{ChiSq}{Schnute (1983) chi-square from likelihood ratio comparison of Moran and Schnute methods.} }} \source{ -From Tables 1-3 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. +From Tables 1-3 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169. } \description{ Catches in removal events for Brook Trout (\emph{Salvelinus fontinalis}) in two streams in the the Nashwaak Experimental Watersheds Project on multiple dates. Includes results from Schnute (1983). @@ -52,5 +52,7 @@ BrookTroutNEWP1[3,] \seealso{ See \code{\link{BrookTroutNEWP}} for only the data (note the results from Schnute (1983)). } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/BrookTroutOnt.rd b/man/BrookTroutOnt.rd index e6c9309..f278823 100644 --- a/man/BrookTroutOnt.rd +++ b/man/BrookTroutOnt.rd @@ -13,7 +13,7 @@ \item{correction}{Number of age-1 fish to be added to final estimated based on mark-recapture to correct for gear selectivity of age-1 fish} }} \source{ -From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan. 2003. Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout. North American Journal of Fisheries Management 23:35-47. +From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan. 2003. Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout. North American Journal of Fisheries Management 23:35-47. } \description{ The number of Brook Trout (\emph{Salvelinus fontinalis}) marked, captured, and recaptured for several years on Meach Lake in central Ontario. @@ -35,5 +35,9 @@ str(BrookTroutOnt) head(BrookTroutOnt) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/BrownTroutVC1.Rd b/man/BrownTroutVC1.Rd index 4f18502..a928610 100644 --- a/man/BrownTroutVC1.Rd +++ b/man/BrownTroutVC1.Rd @@ -11,7 +11,7 @@ \item{recap}{A factor variable representing whether the fish was a \dQuote{recap}ture in the second sample (\code{YES}) or not (\code{NO})} }} \source{ -Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society, 126:35-48. +Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society, 126:35-48. } \description{ Single censuse mark-recapture data for Brown Trout (\emph{Salmo trutta}) from Valley Creek, MN captured in April, 1988. Length of trout was recorded so that abundance estimated can be made by length categories. @@ -34,5 +34,9 @@ head(BrownTroutVC1) hist(BrownTroutVC1$len,main="") } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/BullTroutRML1.Rd b/man/BullTroutRML1.Rd index d9bcf74..c42df7a 100644 --- a/man/BullTroutRML1.Rd +++ b/man/BullTroutRML1.Rd @@ -11,7 +11,7 @@ \item{era}{Era of collection (\code{1977-79} and \code{2001})} }} \source{ -From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] +From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] } \description{ Lengths and weights of Bull Trout (\emph{Salvelinus confluentis}) from two Rocky Mountain lakes in Alberta, CAN and two eras. @@ -37,5 +37,6 @@ plot(mass~fl,data=BullTroutRML1,subset=era=="2001",main="2001") par(op) } -\concept{'Weight-Length' 'Length Frequency'} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/BullTroutRML2.Rd b/man/BullTroutRML2.Rd index 269488f..bc1e12b 100644 --- a/man/BullTroutRML2.Rd +++ b/man/BullTroutRML2.Rd @@ -12,7 +12,7 @@ \item{era}{Era of collection (\code{1977-80} and \code{1997-01}). See details.} }} \source{ -From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] +From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.] } \description{ Assigned ages (from otoliths) and fork lengths of Bull Trout (\emph{Salvelinus confluentis}) from two Rocky Mountain lakes in Alberta, CAN before and after a regulation change. @@ -40,5 +40,6 @@ plot(fl~age,data=BullTroutRML2,subset=lake=="Osprey" & era=="1997-01",main="Ospr par(op) } -\concept{Growth 'Von Bertalanffy'} +\concept{Growth} +\concept{Von Bertalanffy} \keyword{datasets} diff --git a/man/BullTroutTC.Rd b/man/BullTroutTC.Rd index 74d5db3..c71dbde 100644 --- a/man/BullTroutTC.Rd +++ b/man/BullTroutTC.Rd @@ -10,7 +10,7 @@ \item{carcasses}{A numeric vector of number of carcasses found in and along Trestle Creek.} }} \source{ -From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho. North American Journal of Fisheries Management 26:190-200. +From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho. North American Journal of Fisheries Management 26:190-200. } \description{ Catch-at-age (actually carcasses-at-age) for Bull Trout (\emph{Salvelinus confluentis}) in Trestle Creek, ID. @@ -30,5 +30,6 @@ head(BullTroutTC) plot(log(carcasses)~age,data=BullTroutTC) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/CCatfishNB.Rd b/man/CCatfishNB.Rd index 4ac9136..c068687 100644 --- a/man/CCatfishNB.Rd +++ b/man/CCatfishNB.Rd @@ -11,7 +11,7 @@ \item{loc}{Location of collection (\code{Central} and \code{Lower})} }} \source{ -From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska. Master's thesis, University of Nebraska, Lincoln, NE. [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.] +From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska. Master's thesis, University of Nebraska, Lincoln, NE. [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.] } \description{ Catch-at-age of Channel Catfish (\emph{Ictalurs puncatatus}) from two sections of the Platte River, NB, in 2007 and 2008. @@ -37,5 +37,6 @@ plot(log(catch)~age,data=CCatfishNB,subset=loc=="Lower",main="Lower") par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/Cabezon.rd b/man/Cabezon.rd index 83b78a4..3457fb2 100644 --- a/man/Cabezon.rd +++ b/man/Cabezon.rd @@ -13,7 +13,7 @@ \item{stage}{Stage of maturity (\code{1}:Immature, \code{2}:Maturing, \code{3}:Mature, \code{4}:Fertilized, \code{5}:Ripe, \code{6}:Spent, \code{7}:Resting)} }} \source{ -Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.] +Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.] } \description{ Ages, lengths, and maturity for female Cabezon (\emph{Scorpaenichthys marmoratus}) from Newport and Depoe Bay, Oregon. @@ -43,5 +43,7 @@ plot(ptbl2[,2]~as.numeric(row.names(ptbl2)),type="l",xlab="Length",ylab="Proport par(op) } -\concept{Growth 'von Bertalanffy' Maturity} +\concept{Growth} +\concept{Maturity} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/Casselman1990.Rd b/man/Casselman1990.Rd index 12d0d48..3f3b436 100644 --- a/man/Casselman1990.Rd +++ b/man/Casselman1990.Rd @@ -12,7 +12,7 @@ \item{scale}{A numeric vector of instantaneous growth rates (percent change per day) for scales.} }} \source{ -From Figure 8 of Casselman, J.M. 1990. Growth and relative size of calcified structures of fish. Transactions of the American Fisheries Society. 119:673-688. +From Figure 8 of Casselman, J.M. 1990. Growth and relative size of calcified structures of fish. Transactions of the American Fisheries Society. 119:673-688. } \description{ Instantaneous growth rates (percent change per day) for body growth and two calcified ageing structures from age 1-4 female Northern Pike (\emph{Esox lucius}) from Wickett Lake, Ontario. diff --git a/man/ChinookKR.Rd b/man/ChinookKR.Rd index 584651d..212263f 100644 --- a/man/ChinookKR.Rd +++ b/man/ChinookKR.Rd @@ -34,5 +34,6 @@ plot(recruits~spawners,data=ChinookKR) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/CiscoTL.Rd b/man/CiscoTL.Rd index 4364dca..090a086 100644 --- a/man/CiscoTL.Rd +++ b/man/CiscoTL.Rd @@ -40,5 +40,6 @@ plot(weight~length,data=CiscoTL,subset=sex=="I",main="Immature") par(op) } -\concept{'Weight-Length' 'Length Frequency'} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/CrappieARMS.Rd b/man/CrappieARMS.Rd index 004110e..f44da6c 100644 --- a/man/CrappieARMS.Rd +++ b/man/CrappieARMS.Rd @@ -11,7 +11,7 @@ \item{recruits}{Number of age-0 fish per hectare} }} \source{ -From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda. 1998. An age-structured model for erratic crappie fisheries. Ecological Modeling 107:289-303. +From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda. 1998. An age-structured model for erratic crappie fisheries. Ecological Modeling 107:289-303. } \description{ Stock and recruitment data for Crappies from four reservoirs in Arkansas and Mississippi, USA. @@ -36,5 +36,6 @@ plot(recruits~stock,data=CrappieARMS,subset=(reservoir=="Ross.Barnett"),main="Ro par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/CreekChub.Rd b/man/CreekChub.Rd index 4ad2b55..4d0af41 100644 --- a/man/CreekChub.Rd +++ b/man/CreekChub.Rd @@ -10,7 +10,7 @@ \item{age}{Assigned ages (yrs; from scales)} }} \source{ -Recreated (andom digits were added to construct mm lengths from the cm length bins) from information in Box 15.2 of Quist, M.C., Pegg, M.A., and DeVries, D.R. 2012. Age and growth. In Zale, A.V., Parrish, D.L., and Sutton, T.M., editors. Fisheries Techniques, Third Edition, chapter 15, pages 677-731. American Fisheries Society, Bethesda, MD. +Recreated (random digits were added to construct mm lengths from the cm length bins) from information in Box 15.2 of Quist, M.C., Pegg, M.A., and DeVries, D.R. 2012. Age and growth. In Zale, A.V., Parrish, D.L., and Sutton, T.M., editors. Fisheries Techniques, Third Edition, chapter 15, pages 677-731. American Fisheries Society, Bethesda, MD. } \description{ Ages (subsample) and lengths (all fish) for Creek Chub (\emph{Semotilus atromaculatus}). @@ -37,5 +37,6 @@ xtabs(~age,data=CreekChub) plot(len~age,data=CreekChub) } -\concept{'Age-Length Key' 'Growth'} +\concept{Age-Length Key} +\concept{Growth} \keyword{datasets} diff --git a/man/CreelMN.rd b/man/CreelMN.rd index f9f76f7..600bd79 100644 --- a/man/CreelMN.rd +++ b/man/CreelMN.rd @@ -10,7 +10,7 @@ \item{harvest}{number of fish of that species harvested by one angler.} }} \source{ -From tables in Cook, M.F., T.J. Goeman, P.J. Radomski, J.A. Younk, and P.C. Jacobson. 2001. Creel limits in Minnesota: A proposal for change. Fisheries 26:19-26. +From tables in Cook, M.F., T.J. Goeman, P.J. Radomski, J.A. Younk, and P.C. Jacobson. 2001. Creel limits in Minnesota: A proposal for change. Fisheries 26:19-26. } \description{ The species targeted, number of fish harvested, and number of individuals harvesting that number of that species of fish from a large number of surveys on Minnesota Lakes, 1980-1996. @@ -31,7 +31,7 @@ levels(CreelMN$species) ## ONLY RUN IN INTERACTIVE MODE \dontrun{ require(FSA) - wae <- Subset(CreelMN,species=="WAE") + wae <- filterD(CreelMN,species=="WAE") ( waetbl <- table(wae$harvest) ) ( waeptbl <- prop.table(waetbl)*100 ) ( waercum <- rcumsum(waeptbl) ) @@ -49,7 +49,6 @@ levels(CreelMN$species) xtabs(~svd1,data=wae) ( svd1 <- sum(wae$svd1[wae$svd1>0]) ) round(svd1/ttlwae*100,1) - } } diff --git a/man/Croaker1.Rd b/man/Croaker1.Rd index e3a3aec..f30c065 100644 --- a/man/Croaker1.Rd +++ b/man/Croaker1.Rd @@ -33,5 +33,7 @@ plot(reader2~reader1,data=Croaker1) xtabs(~reader1+reader2,data=Croaker1) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/Croaker2.Rd b/man/Croaker2.Rd index 8d1c584..a3d6006 100644 --- a/man/Croaker2.Rd +++ b/man/Croaker2.Rd @@ -34,5 +34,6 @@ plot(tl~age,data=Croaker2,subset=sex=="M",main="Male") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/CutthroatALf.Rd b/man/CutthroatALf.Rd index f260f50..8139fea 100644 --- a/man/CutthroatALf.Rd +++ b/man/CutthroatALf.Rd @@ -10,7 +10,7 @@ \item{freq}{Frequency of fish with that capture history} }} \source{ -Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. Accessed from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf. +Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. Accessed from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf. } \description{ Summarized (\dQuote{RMark} format) capture histories of Cutthroat Trout (\emph{Oncorhynchus clarki}) in Auke Lake, Alaska, from samples taken in 1998-2006. @@ -36,5 +36,10 @@ head(CutthroatALf) \seealso{ See \code{CutthroatAL} for the same data in \dQuote{individual} fish format (i.e., the data in this file were converted using \code{capHistConvert} from \pkg{FSA}). See \code{mrOpen} from \pkg{FSA} for an example analysis. } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Jolly-Seber' 'Capture History'} +\concept{Abundance} +\concept{Capture History} +\concept{Capture-Recapture} +\concept{Jolly-Seber} +\concept{Mark-Recapture} +\concept{Population Size} \keyword{datasets} diff --git a/man/DarterMahon.Rd b/man/DarterMahon.Rd index ee72b85..a801ff5 100644 --- a/man/DarterMahon.Rd +++ b/man/DarterMahon.Rd @@ -10,7 +10,7 @@ \item{effort}{Constant electrofishing effort.} }} \source{ -From Mahon, R. 1980. Accuracy of catch-effort methods for estimating fish density and biomass in streams. Environmental Biology of Fishes. 4:343-363. +From Mahon, R. 1980. Accuracy of catch-effort methods for estimating fish density and biomass in streams. Environmental Biology of Fishes. 4:343-363. } \description{ Catch and effort data for Fantail Darter (\emph{Etheostoma flabellare}) from seven removal events conducted by Mahon (1980). @@ -38,5 +38,10 @@ str(DarterMahon) head(DarterMahon) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/DarterOnt.Rd b/man/DarterOnt.Rd index dbdefa6..be537eb 100644 --- a/man/DarterOnt.Rd +++ b/man/DarterOnt.Rd @@ -37,5 +37,6 @@ plot(tl~age,data=DarterOnt,subset=river=="Trent",main="Trent R.") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/Deckeretal1999.Rd b/man/Deckeretal1999.Rd index 46d371d..0b95bd1 100644 --- a/man/Deckeretal1999.Rd +++ b/man/Deckeretal1999.Rd @@ -18,7 +18,7 @@ \item{cutt3}{Cutthroat Trout removed on the third pass.} }} \source{ -From Appendix 2a and 2b in Decker, A.S., J.M. Bratty, S.C. Riley, and J. Korman. 1999. Estimating standing stock of juvenile coho salmon (\emph{Oncorhynchus kisutch}) and cutthroat trout (\emph{Oncorhynchus clarki}) in a small stream: a comparison of sampling designs. Canadian Technical Report of Fisheries and Aquatic Sciences 2282. 24 pp. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/239481.pdf.] +From Appendix 2a and 2b in Decker, A.S., J.M. Bratty, S.C. Riley, and J. Korman. 1999. Estimating standing stock of juvenile coho salmon (\emph{Oncorhynchus kisutch}) and cutthroat trout (\emph{Oncorhynchus clarki}) in a small stream: a comparison of sampling designs. Canadian Technical Report of Fisheries and Aquatic Sciences 2282. 24 pp.[Was (is?) from http://www.dfo-mpo.gc.ca/Library/239481.pdf.] } \description{ Catches of Coho Salmon (\emph{Oncorhynchus kisutch}) and Cutthroat Trout (\emph{Oncorhynchus clarki}) in consecutive removal events at various locations in Little Stawamus Creek (British Columbia, Canada) in 1997. @@ -41,5 +41,7 @@ head(Deckeretal1999) Deckeretal1999[3,] } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/EuroPerchTJ.Rd b/man/EuroPerchTJ.Rd index c05c1de..55a9f8b 100644 --- a/man/EuroPerchTJ.Rd +++ b/man/EuroPerchTJ.Rd @@ -11,7 +11,7 @@ \item{sex}{Sex (female, male).} }} \source{ -From (approximately) Figure 2 in Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society, 128:483-490. +From (approximately) Figure 2 in Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society, 128:483-490. } \description{ Assigned ages, measured fork lengths, and observed sexes for European Perch (\emph{Perca fluviatilis}) from Lake Tjuekemeer (The Netherlands). @@ -34,5 +34,6 @@ plot(fl~age,data=EuroPerchTJ,subset=sex=="male",main="Male") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/FHCatfish.Rd b/man/FHCatfish.Rd index cb28dd8..63e0e94 100644 --- a/man/FHCatfish.Rd +++ b/man/FHCatfish.Rd @@ -11,7 +11,7 @@ \item{abundance}{Number of captured fish with boat electrofishing} }} \source{ -From (approximately) Figure 3 in Sakaris, P.C., E.R. Irwin, J.C. Jolley, and D. Harrison. 2006. Comparison of Native and Introduced Flathead Catfish Populations in Alabama and Georgia: Growth, Mortality, and Management. North American Journal of Fisheries Management 26:867-874. +From (approximately) Figure 3 in Sakaris, P.C., E.R. Irwin, J.C. Jolley, and D. Harrison. 2006.Comparison of Native and Introduced Flathead Catfish Populations in Alabama and Georgia: Growth, Mortality, and Management. North American Journal of Fisheries Management 26:867-874. } \description{ Numbers of Flathead Catfish (\emph{Pylodictis olivaris}) captured by electrofishing in three rivers -- Coosa River, AL; Ocmulgee River, GA; and Satilla River, GA. @@ -35,5 +35,6 @@ plot(log(abundance)~age,data=FHCatfish,subset=river=="Satilla",main="Satilla") par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/FHCatfishATL.Rd b/man/FHCatfishATL.Rd index d66a496..4cde577 100644 --- a/man/FHCatfishATL.Rd +++ b/man/FHCatfishATL.Rd @@ -11,7 +11,7 @@ \item{number}{Number of captured fish.} }} \source{ -From (approximately) Figure 2 in Kwak, T.J., W.E. Pine III, and D.S. Waters. 2006. Age, growth, and mortality of introduced flathead catfish in Atlantic rivers and a review of other populations. North American Journal of Fisheries Management 26:73-87. +From (approximately) Figure 2 in Kwak, T.J., W.E. Pine III, and D.S. Waters. 2006. Age, growth, and mortality of introduced flathead catfish in Atlantic rivers and a review of other populations. North American Journal of Fisheries Management 26:73-87. } \description{ Catch-at-age of Flathead Catfish (\emph{Pylodictis olivaris}) from three populations of Atlantic rivers -- Lumber River, Northeast Cape Fear River (NCF), and Neuse River. @@ -35,5 +35,6 @@ plot(log(number)~age,data=FHCatfishATL,subset=river=="Neuse",main="Neuse") par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/FWDrumLE1.Rd b/man/FWDrumLE1.Rd index 080a849..40bd528 100644 --- a/man/FWDrumLE1.Rd +++ b/man/FWDrumLE1.Rd @@ -10,7 +10,7 @@ \item{tl}{Measured total lengths (mm).} }} \source{ -Simulated from Table 3 of Bur, M.T. 1984. Growth, reproduction, mortality, distribution, and biomass of freshwater drum in Lake Erie. Journal of Great Lakes Research. 10:48-58. +Simulated from Table 3 of Bur, M.T. 1984. Growth, reproduction, mortality, distribution, and biomass of freshwater drum in Lake Erie. Journal of Great Lakes Research. 10:48-58. } \description{ Assigned ages (from scales) and measured total lengths for each of 1577 Freshwater Drum (\emph{Aplodinotus grunniens}) from Lake Erie. @@ -33,5 +33,6 @@ plot(tl~age,data=FWDrumLE1) \seealso{ \code{\link{FWDrumLE2}}. } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/FWDrumLE2.Rd b/man/FWDrumLE2.Rd index 615f945..8f33cb7 100644 --- a/man/FWDrumLE2.Rd +++ b/man/FWDrumLE2.Rd @@ -34,5 +34,5 @@ str(FWD.length) \seealso{ \code{\link{FWDrumLE1}}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/Ghats.Rd b/man/Ghats.Rd index 3dafc66..ab828cd 100644 --- a/man/Ghats.Rd +++ b/man/Ghats.Rd @@ -10,7 +10,7 @@ \item{cumspec}{cumulative number of species described in the reviewed manuscripts.} }} \source{ -From (approximately) Figure 1 in Dahanukar, N., R. Raut, and A. Bhat. 2004. Distribution, endemism and threat status of freshwater fishes in the Western Ghats of India. Journal of Biogeography 31:123-126. +From (approximately) Figure 1 in Dahanukar, N., R. Raut, and A. Bhat. 2004. Distribution, endemism and threat status of freshwater fishes in the Western Ghats of India. Journal of Biogeography 31:123-126. } \description{ Species accumulation data for fish of the Western Ghats of India derived from nine random samples of publications. diff --git a/man/GreensCreekMine.Rd b/man/GreensCreekMine.Rd index c679f4d..0164c5e 100644 --- a/man/GreensCreekMine.Rd +++ b/man/GreensCreekMine.Rd @@ -16,7 +16,7 @@ \item{max.FL}{Maximum observed fork length.} }} \source{ -From Appendix C1 of Kanouse, K.M. and B.P. Brewster. 2012. Aquatic Biomonitoring at Greens Creek Mine, 2012. Alaska Department of Fish and Game Technical Report No. 12-11. [Was (is?) from http://dnr.alaska.gov/mlw/mining/largemine/greenscreek/pdf/gc2012bio.pdf.] +From Appendix C1 of Kanouse, K.M. and B.P. Brewster. 2012. Aquatic Biomonitoring at Greens Creek Mine, 2012. Alaska Department of Fish and Game Technical Report No. 12-11. [Was (is?) from http://dnr.alaska.gov/mlw/mining/largemine/greenscreek/pdf/gc2012bio.pdf.] } \description{ Catches in removal events of Coho Salmon (\emph{Oncorhynchus kisutch}) and Dolly Varden Char (\emph{Salvelinus malma}) at various locations near the Greens Creek (AK) Mine site. @@ -42,5 +42,7 @@ head(GreensCreekMine) GreensCreekMine[3,] } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/Hake.Rd b/man/Hake.Rd index 9a138fc..75633b2 100644 --- a/man/Hake.Rd +++ b/man/Hake.Rd @@ -11,7 +11,7 @@ \item{spawn.biomass}{a numeric vector of spawning biomass in thousand tonnes} }} \source{ -Cadima, E. 2003. Fish Stock Assessment Manual, FAO Fisheries Department. 131 pp. +Cadima, E. 2003. Fish Stock Assessment Manual, FAO Fisheries Department. 131 pp. } \description{ Stock and recruitment data for Hake (\emph{Merluccius merluccius}), 1982-1996. @@ -34,5 +34,6 @@ plot(recruits~spawn.biomass,data=Hake) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/HalibutPAC.Rd b/man/HalibutPAC.Rd index b1bcef8..e55f4f0 100644 --- a/man/HalibutPAC.Rd +++ b/man/HalibutPAC.Rd @@ -13,7 +13,7 @@ \item{fmort}{Fishing related mortality} }} \source{ -From Anonymous. 1989. International Pacific Halibut Commission. Annual Report 1989.; Myhre, Gordon, Peltonen, Stpierre, Skud, and Walden. International Pacific halibut Commission. Technical Report No. 14.; Pers. Comm. with Pat Sullivan. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Anonymous. 1989. International Pacific Halibut Commission. Annual Report 1989.; Myhre, Gordon, Peltonen, Stpierre, Skud, and Walden. International Pacific halibut Commission. Technical Report No. 14.; Pers. Comm. with Pat Sullivan. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Pacific Halibut (\emph{Hippoglossus stenolepis}) stock, recruitment, landings, and fishing mortality by year, 1929-1991. @@ -36,5 +36,6 @@ plot(rec~ssb,data=HalibutPAC) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/Herman.Rd b/man/Herman.Rd index 10f59ea..dddbb9e 100644 --- a/man/Herman.Rd +++ b/man/Herman.Rd @@ -41,5 +41,7 @@ with(subset(Herman,spec=="wae" & yr==1999),hist(tl,main="Walleye, 1999")) par(op) } -\concept{'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/HerringBWE.Rd b/man/HerringBWE.Rd index 65ed3a1..5d250cb 100644 --- a/man/HerringBWE.Rd +++ b/man/HerringBWE.Rd @@ -11,7 +11,7 @@ \item{recruits}{a numeric vector containing the number of recruits} }} \source{ -From Fox, C.J. 2001. Recent trends in stock-recruitment of Blackwater herring (\emph{Clupea harengus} L.) in relation to larval production. ICES Journal of Marine Science, 58:750-762. +From Fox, C.J. 2001. Recent trends in stock-recruitment of Blackwater herring (\emph{Clupea harengus} L.) in relation to larval production. ICES Journal of Marine Science, 58:750-762. } \description{ Stock and recruitment data for Blackwater Estuary Herring (\emph{Clupea harengus}), 1962-1997 spawning years. @@ -34,5 +34,6 @@ plot(recruits~ssb,data=HerringBWE) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/HerringISS.Rd b/man/HerringISS.Rd index d6df9df..7aeae77 100644 --- a/man/HerringISS.Rd +++ b/man/HerringISS.Rd @@ -13,7 +13,7 @@ \item{fmort}{Fishing related mortality} }} \source{ -From the Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1995. Assess: 9.; Anon. 1986. Report of the herring assessment working group for the area south of 62 degrees N. ICES Doc. C.M. 1986. Assess: 19.; Anon. 1991. Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1991. Assess: 17.; State of marine stocks and environmental conditions in Icelandic waters 1989 Fishing prospects 1990, August 1990. Hafranns\'oknastofnun Fj\"olrit NR. 19. Marine Research Institute, Iceland. Mon Jun 20, 1988.; Report of the Northern Pelagic and Blue Whiting Fisheries Working Group. ICES Doc. C.M. 1997. Assess:14. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From the Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1995. Assess: 9.; Anon. 1986. Report of the herring assessment working group for the area south of 62 degrees N. ICES Doc. C.M. 1986. Assess: 19.; Anon. 1991. Report of the Atlanto-Scandian Herring and Capelin Working Group. ICES Doc. C.M. 1991. Assess: 17.; State of marine stocks and environmental conditions in Icelandic waters 1989 Fishing prospects 1990, August 1990. Hafranns\'oknastofnun Fj\"olrit NR. 19. Marine Research Institute, Iceland. Mon Jun 20, 1988.; Report of the Northern Pelagic and Blue Whiting Fisheries Working Group. ICES Doc. C.M. 1997. Assess:14. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Icelandic summer spawning Herring (\emph{Clupeaformis harengus}) stock, recruitment, landings, and fishing mortality by year, 1946-1996. @@ -36,5 +36,6 @@ plot(rec~ssb,data=HerringISS) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/HumpbackWFCR.Rd b/man/HumpbackWFCR.Rd index 7ded0fc..263281e 100644 --- a/man/HumpbackWFCR.Rd +++ b/man/HumpbackWFCR.Rd @@ -12,7 +12,7 @@ \item{sectRrun}{Section where the fish was captured on the recapture run} }} \source{ -From Table 10 in Gryska, A.D. 2014. Stock assessment of humpback whitefish in the Chatanika River, 2012. Alaska Department of Fish and Game, Fishery Data Series No. 14-12, Anchorage. Available from https://www.cf.adfg.state.ak.us/FedAidPDFs/FDS14-12.pdf. +From Table 10 in Gryska, A.D. 2014. Stock assessment of humpback whitefish in the Chatanika River, 2012. Alaska Department of Fish and Game, Fishery Data Series No. 14-12, Anchorage. Was (is?) at https://www.cf.adfg.state.ak.us/FedAidPDFs/FDS14-12.pdf. } \description{ Capture histories for Humpback Whitefish (\emph{Coregonus pidschian}) greater than 360 mm in the Chatanika River, AK in 2012. @@ -35,5 +35,10 @@ str(HumpbackWFCR) head(HumpbackWFCR) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History'} +\concept{Abundance} +\concept{Capture History} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/InchLake1.rd b/man/InchLake1.rd index 7374ba9..2b22421 100644 --- a/man/InchLake1.rd +++ b/man/InchLake1.rd @@ -45,5 +45,7 @@ seine.il <- subset(InchLake1,netType=="seine") \seealso{ See \code{\link{InchLake2}} for a subsample that include weights. } -\concept{'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/InchLake2.rd b/man/InchLake2.rd index 4d90695..35b26b7 100644 --- a/man/InchLake2.rd +++ b/man/InchLake2.rd @@ -43,5 +43,7 @@ lmb7.il <- subset(InchLake2,species=="Largemouth Bass" & year==2007) \seealso{ See \code{\link{InchLake1}} for the entire sample, but without weights. } -\concept{'Weight-Length' Condition 'Length Frequency'} +\concept{Condition} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/JobfishSIO.Rd b/man/JobfishSIO.Rd index 7fdb5ab..8a7af6f 100644 --- a/man/JobfishSIO.Rd +++ b/man/JobfishSIO.Rd @@ -10,7 +10,7 @@ \item{effort}{Effort (man-hours).} }} \source{ -From Table 2 of Grandcourt, E.M. 2003. The effect of intensive line fishing on the virgin biomass of a tropical deepwater snapper, the crimson jobfish (\emph{Pristipomoides filamentosus}). Fisheries Bulletin, 101:305-311. [Was (is?) from http://fishbull.noaa.gov/1012/08grandc.pdf.] +From Table 2 of Grandcourt, E.M. 2003. The effect of intensive line fishing on the virgin biomass of a tropical deepwater snapper, the crimson jobfish (\emph{Pristipomoides filamentosus}). Fisheries Bulletin, 101:305-311. [Was (is?) from http://fishbull.noaa.gov/1012/08grandc.pdf.] } \description{ Catch and effort data for Jobfish (\emph{Pristipomoides filamentosus}) from the South Indian Ocean. @@ -33,5 +33,10 @@ str(JobfishSIO) head(JobfishSIO) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/JonesStockwell.Rd b/man/JonesStockwell.Rd index 6ad53b0..4bb30f5 100644 --- a/man/JonesStockwell.Rd +++ b/man/JonesStockwell.Rd @@ -18,7 +18,7 @@ \item{rejected}{Logical is \code{TRUE} if Schnute method rejected the population estimate because the standard error was too large.} }} \source{ -From Table 1 in Jones, M.L. and J.D. Stockwell. 1995. A rapid assessment procedure for enumeration of salmonine populations in streams. North American Journal of Fisheries Management, 15:551-562. +From Table 1 in Jones, M.L. and J.D. Stockwell. 1995. A rapid assessment procedure for enumeration of salmonine populations in streams. North American Journal of Fisheries Management, 15:551-562. } \description{ Catches of Brown (\emph{Salmo trutta}) and Rainbow Trout (\emph{Oncorhynchus mykiss}) in consecutive removal events at various locations. @@ -41,5 +41,7 @@ head(JonesStockwell) JonesStockwell[3,] } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/Jonubi1.Rd b/man/Jonubi1.Rd index c7e1012..ba52eda 100644 --- a/man/Jonubi1.Rd +++ b/man/Jonubi1.Rd @@ -10,7 +10,7 @@ \item{age}{Assigned ages (years).} }} \source{ -Simulated from table 2 of Yildirim, A., H.U. Haluloulu, M. Turkmen, and O. Erdouan. 2003. Age and growth characteristics of \emph{Chalcalburnus mossulensis} (Heckel, 1843) living in Karasu River (Erzurum-Turkey). Turkish Journal of Veterinary and Animal Science. 27: 1091-1096. +Simulated from table 2 of Yildirim, A., H.U. Haluloulu, M. Turkmen, and O. Erdouan. 2003. Age and growth characteristics of \emph{Chalcalburnus mossulensis} (Heckel, 1843) living in Karasu River (Erzurum-Turkey). Turkish Journal of Veterinary and Animal Science. 27: 1091-1096. } \description{ Assigned ages and measured fork lengths for male Jonubi (\emph{Chalcalburnus mossulensis}) from the Karasu River (Turkey). @@ -33,5 +33,6 @@ plot(fl~age,data=Jonubi1) \seealso{ \code{\link{Jonubi2}}. } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/Jonubi2.Rd b/man/Jonubi2.Rd index 9f0a9f7..c936425 100644 --- a/man/Jonubi2.Rd +++ b/man/Jonubi2.Rd @@ -32,5 +32,5 @@ plot(fl~age,data=Jonubi2) \seealso{ \code{\link{Jonubi1}}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/KingCrabAK.Rd b/man/KingCrabAK.Rd index d942b9b..e619d47 100644 --- a/man/KingCrabAK.Rd +++ b/man/KingCrabAK.Rd @@ -11,7 +11,7 @@ \item{adults}{abundance (thousands) legal (>=145 mm carapace length) males} }} \source{ -From table 1 in Bechtol W.R. and G.H. Kruse. 2009. Analysis of a stock-recruit relationship for red king crab off Kodiak Island Alaska. Marine and Coastal Fisheries: Dynamics Management and Ecosystem Science 1:29-44. +From table 1 in Bechtol W.R. and G.H. Kruse. 2009. Analysis of a stock-recruit relationship for Red King Crab off Kodiak Island Alaska. Marine and Coastal Fisheries: Dynamics Management and Ecosystem Science 1:29-44. } \description{ Stock and recruitment data for Red King Crab (\emph{Paralithodes camtschaticus}) from the northern Gulf of Alaska around Kodiak Island by brood year, 1960-2004. @@ -34,5 +34,6 @@ plot(recruits~adults,data=KingCrabAK) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/LJCisco.Rd b/man/LJCisco.Rd index 03838ca..9edbba1 100644 --- a/man/LJCisco.Rd +++ b/man/LJCisco.Rd @@ -11,7 +11,7 @@ \item{loc}{Capture location (\code{NE}=northeast and \code{S}=south).} }} \source{ -Simulated from age-length data provided in tables 2 and 3 of Jobes, F.W. 1946. The age, growth, and distribution of the longjaw cisco, \emph{Leucichthys alpenae} Koelz, in Lake Michigan. Transactions of the American Fisheries Society. 76:215-247. +Simulated from age-length data provided in tables 2 and 3 of Jobes, F.W. 1946. The age, growth, and distribution of the longjaw cisco, \emph{Leucichthys alpenae} Koelz, in Lake Michigan. Transactions of the American Fisheries Society. 76:215-247. } \description{ Assigned age (by scales) and total length of Longjaw Cisco (\emph{Leucichthys alpenae}) captured at two locations in Lake Michigan. @@ -34,5 +34,6 @@ plot(tl~age,data=LJCisco,subset=loc=="S",main="south") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/LMBassBL.Rd b/man/LMBassBL.Rd index a1a1c45..4c03370 100644 --- a/man/LMBassBL.Rd +++ b/man/LMBassBL.Rd @@ -9,7 +9,7 @@ \item{tl}{measured total length (cm)} }} \source{ -From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. } \description{ Length measurements of Largemouth Bass (\emph{Micropterus salmoides}) from Boomer Lake, Oklahoma, in 1974. @@ -30,5 +30,7 @@ head(LMBassBL) hist(LMBassBL$tl,main="") } -\concept{'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/LMBassLCB.Rd b/man/LMBassLCB.Rd index 13c9915..31965ae 100644 --- a/man/LMBassLCB.Rd +++ b/man/LMBassLCB.Rd @@ -9,7 +9,7 @@ \item{tl}{Measured total length (cm).} }} \source{ -From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +From McNew, R.W. and R.C. Summerfelt. 1978. Evaluation of a maximum-likelihood estimator for analysis of length-frequency distributions. Transactions of the American Fisheries Society 107:730-736. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. } \description{ Lengthsfor Largemouth Bass (\emph{Micropterus salmoides}) from Lake Carl Blackwell, Oklahoma, in 1973. @@ -30,5 +30,7 @@ head(LMBassLCB) hist(LMBassLCB$tl,main="") } -\concept{'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/LakeTroutALTER.Rd b/man/LakeTroutALTER.Rd index a72796d..947808e 100644 --- a/man/LakeTroutALTER.Rd +++ b/man/LakeTroutALTER.Rd @@ -16,7 +16,7 @@ \item{sex}{Sex of the fish (\code{F}=female and \code{M}=male).} }} \source{ -Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89mcne12.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. +Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89mcne12.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. } \description{ Biological data (lengths, weight, age, and sex) of Lake Trout (\emph{Salvelinus namaycush}) sampled from Lake NE12 of the Arctic Long Term Ecological Research location. @@ -57,5 +57,10 @@ plot(tl~age,data=LakeTroutALTER) par(op) } -\concept{'Length Frequency' 'Weight-Length' 'Growth' 'von Bertalanffy' 'Size Structure' 'Length Conversion'} +\concept{Growth} +\concept{Length Conversion} +\concept{Length Frequency} +\concept{Size Structure} +\concept{Weight-Length} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/LakeTroutEggs.Rd b/man/LakeTroutEggs.Rd index bef5b59..dd6135e 100644 --- a/man/LakeTroutEggs.Rd +++ b/man/LakeTroutEggs.Rd @@ -10,7 +10,7 @@ \item{eggs}{Estimated number of eggs.} }} \source{ -From (approximately) Figure 2 of Schram, S.T. 1993. Fecundity and egg deposition of a wild Lake Superior Lake Trout stock. Wisconsin Department of Natural Resources, Fisheries Management Report no. 149. +From (approximately) Figure 2 of Schram, S.T. 1993. Fecundity and egg deposition of a wild Lake Superior Lake Trout stock. Wisconsin Department of Natural Resources, Fisheries Management Report no. 149. } \description{ Length and egg deposition of Lake Superior Lake Trout (\emph{Salvelinus namaycush}). diff --git a/man/LakeTroutGIS.Rd b/man/LakeTroutGIS.Rd index 4d80af0..b22250e 100644 --- a/man/LakeTroutGIS.Rd +++ b/man/LakeTroutGIS.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recruits (number of age-0 fish per ha) captured the following fall in bottom trawls} }} \source{ -From Schram, S.T., J.H. Selgeby, C.R. Bronte, and B.L. Swanson. 1995. Population recovery and natural recruitment of Lake Trout at Gull Island Shoal, Lake Superior, 1964-1992. Journal of Great Lakes Research. 21(supp.1):225-232. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Schram, S.T., J.H. Selgeby, C.R. Bronte, and B.L. Swanson. 1995. Population recovery and natural recruitment of Lake Trout at Gull Island Shoal, Lake Superior, 1964-1992. Journal of Great Lakes Research. 21(supp.1):225-232. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Lake trout (\emph{Salvelinus namaycush}) stock and recruitment by year at Gull Island Shoal, Lake Superior, 1964-1991. @@ -34,5 +34,6 @@ plot(recruits~stock,data=LakeTroutGIS) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/LakeTroutMI.Rd b/man/LakeTroutMI.Rd index 269664d..8fc2ac1 100644 --- a/man/LakeTroutMI.Rd +++ b/man/LakeTroutMI.Rd @@ -13,7 +13,7 @@ \item{area}{Lake Superior management unit} }} \source{ -From (approximately) figures in Richards, J.M., M.J. Hansen, C.R. Bronte, and S.P. Sitar. 2004. Recruitment dynamics of the 1971-1991 year-classes of Lake Trout in Michigan waters of Lake Superior. North American Journal of Fisheries Management. 24:475-489. +From (approximately) figures in Richards, J.M., M.J. Hansen, C.R. Bronte, and S.P. Sitar. 2004. Recruitment dynamics of the 1971-1991 year-classes of Lake Trout in Michigan waters of Lake Superior. North American Journal of Fisheries Management. 24:475-489. } \description{ Stock and recruitment data for the 1971-1991 year-classes of Lake Trout (\emph{Salvelinus namaycush}) in Michigan waters of Lake Superior. @@ -45,5 +45,6 @@ plot(recruits~stock,data=LakeTroutMI,subset=area=="MI7",col="yellow",main="MI7") par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/Lizardfish.Rd b/man/Lizardfish.Rd index 7360d75..84c465a 100644 --- a/man/Lizardfish.Rd +++ b/man/Lizardfish.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recruits (in hundred thousands)} }} \source{ -VIsually estimated from Figure 7.12 (p. 267) of Hilborn, R. and C.J. Walters. 1992. Quantitative Fisheries Stock Assessment: Choice, Dynamics, and Uncertainty. Chapman and Hall, New York. 570 p. +Visually estimated from Figure 7.12 (p. 267) of Hilborn, R. and C.J. Walters. 1992. Quantitative Fisheries Stock Assessment: Choice, Dynamics, and Uncertainty. Chapman and Hall, New York. 570 p. } \description{ Greater Lizardfish (\emph{Saurida tumbil}) stock and recruitment by year, 1955-1964. @@ -34,5 +34,6 @@ plot(recruits~stock,data=Lizardfish) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/LobsterHI.Rd b/man/LobsterHI.Rd index a7c6ef6..0cd0303 100644 --- a/man/LobsterHI.Rd +++ b/man/LobsterHI.Rd @@ -14,7 +14,7 @@ \item{effort}{Total daily effort expended.} }} \source{ -From Table 1 of Clarke, R.P., and S.S. Yoshimoto. 1990. Application of the Leslie model to commercial catch and effort of the slipper lobster, \emph{Scyllarides squammosus}, fishery in the northwestern hawaiian islands. Marine Fisheries Review, 52(2):1-7. +From Table 1 of Clarke, R.P., and S.S. Yoshimoto. 1990. Application of the Leslie model to commercial catch and effort of the slipper lobster, \emph{Scyllarides squammosus}, fishery in the northwestern hawaiian islands. Marine Fisheries Review, 52(2):1-7. } \description{ Catches of Slipper Lobster (\emph{Scyllarides squammosus}) in three categories from the vicinity of Laysan Bank, Hawaiian Islands on 34 consecutive days in 1986. @@ -42,5 +42,10 @@ str(LobsterHI) head(LobsterHI) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/LobsterPEI.Rd b/man/LobsterPEI.Rd index bc42339..0523f41 100644 --- a/man/LobsterPEI.Rd +++ b/man/LobsterPEI.Rd @@ -37,5 +37,10 @@ str(LobsterPEI) head(LobsterPEI) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/Menhaden1.Rd b/man/Menhaden1.Rd index 1eca4e1..223f9fc 100644 --- a/man/Menhaden1.Rd +++ b/man/Menhaden1.Rd @@ -15,6 +15,9 @@ \item{age5}{Estimated catch (millions) of age-5 fish.} \item{age6}{Estimated catch (millions) of age-6 fish.} }} +\source{ +From Table 2 in Vaughan, D.S., K.W. Shertzer, and J.W. Smith. 2007. Gulf menhaden (\emph{Brevoortia patronus}) in the U.S. Gulf of Mexico: Fishery characteristics and biological reference points for management. Fisheries Research 83:263-275. +} \description{ Estimated catch-at-age for Gulf Menhaden (\emph{Brevoortia patronus}), 1964-2004 from thereduction fishery in the U.S. Gulf of Mexico. } @@ -36,7 +39,6 @@ ct <- t(Menhaden1[Menhaden1$year==1974,-1]) plot(ct~ages,pch=16,type="b",xlab="Age",ylab="Est. Catch (Millions)",main="year==1974") } -\concept{Mortality 'Catch Curve' - - @source From Table 2 in Vaughan, D.S., K.W. Shertzer, and J.W. Smith. 2007. Gulf menhaden (\emph{Brevoortia patronus}) in the U.S. Gulf of Mexico: Fishery characteristics and biological reference points for management. Fisheries Research 83:263-275. [Was (is?) from http://menhaden.gsmfc.org/FishRes_Vaughan_etal_2007-GM.pdf.]} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/Morwong1.Rd b/man/Morwong1.Rd index 109a5e7..5bae142 100644 --- a/man/Morwong1.Rd +++ b/man/Morwong1.Rd @@ -10,7 +10,7 @@ \item{second}{Ages assigned on the second reading} }} \source{ -From Table 5 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +From Table 5 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. } \description{ Ages assigned at two different times by Reader A to the otoliths of Jackass Morwong (\emph{Nemadactylus macropterus}). @@ -33,5 +33,7 @@ plot(second~first,data=Morwong1) xtabs(~first+second,data=Morwong1) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/Morwong2.Rd b/man/Morwong2.Rd index 97b6caf..15262dc 100644 --- a/man/Morwong2.Rd +++ b/man/Morwong2.Rd @@ -10,7 +10,7 @@ \item{second}{Ages assigned on the second reading} }} \source{ -From Table 6 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +From Table 6 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. } \description{ Ages assigned at two different times by Reader B to the otoliths of Jackass Morwong (\emph{Nemadactylus macropterus}). @@ -33,5 +33,7 @@ plot(second~first,data=Morwong2) xtabs(~first+second,data=Morwong2) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/Morwong3.Rd b/man/Morwong3.Rd index 10900d2..8503195 100644 --- a/man/Morwong3.Rd +++ b/man/Morwong3.Rd @@ -10,7 +10,7 @@ \item{readerB}{Ages assigned by Reader B} }} \source{ -From Table 7 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +From Table 7 of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. } \description{ Ages assigned by two different readers to the otoliths of Jackass Morwong (\emph{Nemadactylus macropterus}). @@ -33,5 +33,7 @@ plot(readerB~readerA,data=Morwong3) with(Morwong3,table(readerA,readerB)) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/Morwong4.Rd b/man/Morwong4.Rd index e592754..04d2bc0 100644 --- a/man/Morwong4.Rd +++ b/man/Morwong4.Rd @@ -10,7 +10,7 @@ \item{age}{Assigned ages (from otoliths).} }} \source{ -Ffrom appendix 1 of of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. +Ffrom appendix 1 of of Restall, J.E., and K. Krusic-Golub. 2004. Development of jackass morwong age-length keys for 2000-2002. Final report to Australian Fisheries Management Authority. 13 pp. Primary Industries Research Victoria, Queenscliff. Was (is?) available at http://web-test.afma.gov.au/wp-content/uploads/2010/07/r03_1724b.pdf. } \description{ Assigned ages (from otoliths) and fork lengths of Jackass Morwong (\emph{Nemadactylus macropterus}) from the Eastern portion of the Southern and Eastern Scalefish and Shark Fishery (SESSF) in 2000. @@ -33,5 +33,6 @@ plot(fl~age,data=Morwong4) \seealso{ \code{\link{Morwong4a}}. } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/Morwong4a.Rd b/man/Morwong4a.Rd index c7a3eef..1647cc0 100644 --- a/man/Morwong4a.Rd +++ b/man/Morwong4a.Rd @@ -36,5 +36,5 @@ str(m4a.length) \seealso{ \code{\link{Morwong4}}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/Mosquitofish.Rd b/man/Mosquitofish.Rd index 7ac42d9..06796c7 100644 --- a/man/Mosquitofish.Rd +++ b/man/Mosquitofish.Rd @@ -38,5 +38,7 @@ head(Mosquitofish) plot(sl~age2,data=Mosquitofish) } -\concept{'Seasonal Growth' 'von Bertalanffy' Somers} +\concept{Seasonal Growth} +\concept{Somers} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/MulletBS.Rd b/man/MulletBS.Rd index 7d25a18..81e6c9b 100644 --- a/man/MulletBS.Rd +++ b/man/MulletBS.Rd @@ -10,7 +10,7 @@ \item{bb}{Ages assigned from broken/burnt otoliths} }} \source{ -From Figure 3 of Polat, N., D. Bostanci, S. Yilmaz. 2005. Differences between whole otolith and broken-burnt otolith ages of red mullet (\emph{Mullus barbatus ponticus} Essipov, 1927) sampled from the Black Sea (Samsun, Turkey). Turkish Journal of Veterinary and Animal Science 29:429-433. +From Figure 3 of Polat, N., D. Bostanci, S. Yilmaz. 2005. Differences between whole otolith and broken-burnt otolith ages of red mullet (\emph{Mullus barbatus ponticus} Essipov, 1927) sampled from the Black Sea (Samsun, Turkey). Turkish Journal of Veterinary and Animal Science 29:429-433. } \description{ Ages assigned to whole and broken-burnt otoliths of Red Mullet (\emph{Mullus barbatus ponticus}) sampled from the Black Sea (Samsun, Turkey). @@ -33,5 +33,7 @@ plot(whole~bb,data=MulletBS) xtabs(~bb+whole,data=MulletBS) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/MuskieSLR.Rd b/man/MuskieSLR.Rd index b57ac4a..73b7821 100644 --- a/man/MuskieSLR.Rd +++ b/man/MuskieSLR.Rd @@ -10,7 +10,7 @@ \item{ageS}{Age assigned from examination of scales} }} \source{ -From Figure 3 in Casselman,J.M. 1983. Age and growth assessment of fish from their calcified structures - techniques and tools. In E.D. Prince and L.M. Pulos, editors, Proceedings of the international workshop on age determination of oceanic pelagic fishes: Tunas, billfishes, and sharks, volume NOAA Technical Report, NMFS 8:1-17. +From Figure 3 in Casselman,J.M. 1983. Age and growth assessment of fish from their calcified structures - techniques and tools. In E.D. Prince and L.M. Pulos, editors, Proceedings of the international workshop on age determination of oceanic pelagic fishes: Tunas, billfishes, and sharks, volume NOAA Technical Report, NMFS 8:1-17. } \description{ Ages of St. Lawrence River, ONT, Muskellunge (\emph{Esox masquinongy}) assessed from scales and cleithra. @@ -33,5 +33,7 @@ plot(ageS~ageC,data=MuskieSLR) xtabs(~ageC+ageS,data=MuskieSLR) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/MuskieWI06MR.rd b/man/MuskieWI06MR.rd index 1998608..51b2744 100644 --- a/man/MuskieWI06MR.rd +++ b/man/MuskieWI06MR.rd @@ -36,5 +36,9 @@ str(MuskieWI06MR) head(MuskieWI06MR) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/PSalmonAK.Rd b/man/PSalmonAK.Rd index 9d40128..76a55f7 100644 --- a/man/PSalmonAK.Rd +++ b/man/PSalmonAK.Rd @@ -13,7 +13,7 @@ \item{SST}{Average sea surface temperature (C) between June and November off Sitka, AK from one year latter (lagging is for matching when the salmon are actually in the ocean)} }} \source{ -From Table 3.1 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. +From Table 3.1 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. } \description{ Harvest, escapement, and return of northern Southeast Alaska Pink Salmon (\emph{Oncorhynchus gorbuscha}), 1960-1991, and average sea surface temperature between June and November off Sitka, Alaska, 1960-1990. @@ -36,5 +36,6 @@ plot(return~escapement,data=PSalmonAK) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/Pallid.Rd b/man/Pallid.Rd index 34186d3..3a1512f 100644 --- a/man/Pallid.Rd +++ b/man/Pallid.Rd @@ -15,7 +15,7 @@ \item{loc}{Location of fish collection (\code{NB}=Nebraska, \code{SD}=South Dakota, \code{ND}=North Dakota, \code{MT}=Montana)} }} \source{ -From Table 1 in Keenlyne, K.D. and S.J. Maxwell. 1993. Length conversions and length-weight relations for pallid sturgeon. North American Journal of Fisheries Management. 13:395-397. +From Table 1 in Keenlyne, K.D. and S.J. Maxwell. 1993. Length conversions and length-weight relations for pallid sturgeon. North American Journal of Fisheries Management. 13:395-397. } \description{ Lengths (standard, fork, and total) and weights for Pallid Sturgion (\emph{Scaphirhynchus albus}) collected at four locations in the Missouri River drainage. @@ -41,5 +41,6 @@ plot(w~tl,data=Pallid,subset=loc=="MT",main="Montana") par(op) } -\concept{'Weight-Length' 'Length Conversion'} +\concept{Length Conversion} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/Pathfinder.Rd b/man/Pathfinder.Rd index 6977de4..e7ac555 100644 --- a/man/Pathfinder.Rd +++ b/man/Pathfinder.Rd @@ -13,7 +13,7 @@ \item{Ecarbunculus}{Catch of \emph{Etelis carbunculUs}} }} \source{ -From Table 3 of Polovina, J.J. 1985. A variable catchability version of the Leslie model with application to an intensive fishing experiment on a multispecies stock. Fishery Bulletin 84:423-428. [Was (is?) from https://swfsc.noaa.gov/publications/CR/1986/8679.PDF.] +From Table 3 of Polovina, J.J. 1985. A variable catchability version of the Leslie model with application to an intensive fishing experiment on a multispecies stock. Fishery Bulletin 84:423-428. [Was (is?) from https://swfsc.noaa.gov/publications/CR/1986/8679.PDF.] } \description{ Catch and effort for three Snapper species (\emph{Pristipomoides zonatus}, \emph{Pristipomoides auricilla}, and \emph{Etelis carbunculUs}) in a depletion experiment around Pathfinder Reef in the Mariana Archipelago. @@ -35,5 +35,10 @@ data(Pathfinder) str(Pathfinder) head(Pathfinder) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/PikeHL.Rd b/man/PikeHL.Rd index 9da7aa0..df25bf5 100644 --- a/man/PikeHL.Rd +++ b/man/PikeHL.Rd @@ -11,7 +11,7 @@ \item{second}{a numeric vector of indicator variables for the second sample (1=captured)} }} \source{ -Capture histories simulated from summarzed data in table 2 and text of Burkholder, A. 1991. Abundance and composition of northern pike, Harding Lake, 1990. Fishery Data Series 91-9, Alaksa Department of Fish and Game. Accessed from http://www.sf.adfg.state.ak.us/FedAidpdfs/Fds91-09.pdf +Capture histories simulated from summarzed data in table 2 and text of Burkholder, A. 1991. Abundance and composition of northern pike, Harding Lake, 1990. Fishery Data Series 91-9, Alaksa Department of Fish and Game. Was (is?) from http://www.sf.adfg.state.ak.us/FedAidpdfs/Fds91-09.pdf } \description{ Capture histories for Northern Pike (\emph{Esox lucius}) captured from Harding Lake, 1990. @@ -37,5 +37,10 @@ str(PikeHL) head(PikeHL) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History'} +\concept{Abundance} +\concept{Capture History} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/PikeIL.Rd b/man/PikeIL.Rd index 78627be..7e19353 100644 --- a/man/PikeIL.Rd +++ b/man/PikeIL.Rd @@ -11,7 +11,7 @@ \item{catch}{Number of captured and removed pike.} }} \source{ -From Table 1 of Peterson, J., M. Taylor, and A. Hanson. 1980. Leslie population estimate for a large lake. Transactions of the American Fisheries Society, 109:329-331. +From Table 1 of Peterson, J., M. Taylor, and A. Hanson. 1980. Leslie population estimate for a large lake. Transactions of the American Fisheries Society, 109:329-331. } \description{ Catch and effort data for nine removal events of Northern Pike (\emph{Esox lucius}) from Island Lake, NB. @@ -34,5 +34,10 @@ str(PikeIL) head(PikeIL) } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/PikeNYPartial2.Rd b/man/PikeNYPartial2.Rd index 23ed208..fa161ea 100644 --- a/man/PikeNYPartial2.Rd +++ b/man/PikeNYPartial2.Rd @@ -10,7 +10,7 @@ \item{id}{Unique fish identification numbers} }} \source{ -Simulated from summary data in Table C-1 of New York Power Authority. 2004. Use of buckhorn marsh and grand island tributaries by northern pike for spawning and as a nursery. Technical report, New York Power Authority, January 2004. Niagara Power Project (FERC No. 2216). +Simulated from summary data in Table C-1 of New York Power Authority. 2004. Use of Buckhorn Marsh and Grand Island tributaries by Northern Pike for spawning and as a nursery. Technical report, New York Power Authority, January 2004. Niagara Power Project (FERC No. 2216). } \description{ Capture histories (4 samples), in capture-by-date format, of a subset of Northern Pike from Buckthorn Marsh. @@ -37,5 +37,10 @@ str(PikeNYPartial2) head(PikeNYPartial2) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' 'Capture History'} +\concept{Abundance} +\concept{Capture History} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/PikeWindermere.Rd b/man/PikeWindermere.Rd index a4e806d..37fa306 100644 --- a/man/PikeWindermere.Rd +++ b/man/PikeWindermere.Rd @@ -13,13 +13,13 @@ \item{tdd14}{Temperature degree-days over 14C} }} \source{ -From table 3 in Kipling, C. 1983. Changes in the population of pike (\emph{Esox lucius}) in Windermere from 1944 to 1981. Journal of Animal Ecology 52:989-999. +From table 3 in Kipling, C. 1983. Changes in the population of pike (\emph{Esox lucius}) in Windermere from 1944 to 1981. Journal of Animal Ecology 52:989-999. } \description{ Stock and recruitment data for Northern Pike (\emph{Esox lucius}) from Lake Windermere, 1944-1981. } \note{ -Stock values were originally reported in 1000s of kgs and recruits were originally recorded in tens of numbers. Thus, plots look very discrete. +Stock values were originally reported in 1000s of kgs and recruits were originally recorded in tens of numbers. Thus, plots look very discrete. } \section{Topic(s)}{ @@ -42,5 +42,6 @@ par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/PygmyWFBC.Rd b/man/PygmyWFBC.Rd index 799a203..9f7e4bd 100644 --- a/man/PygmyWFBC.Rd +++ b/man/PygmyWFBC.Rd @@ -21,7 +21,7 @@ \item{USE}{Should the individual be used for analyses.} }} \source{ -2000 data from Appendix 9 of J. D. McPhail and R. J. Zemlak. October 2001. Pygmy whitefish studies on Dina Lake #1, 2000. Peace/Williston Fish and Wildlife Compensation Program, Report No. 245. 36pp plus appendices. [Was (is?) from https://www.bchydro.com/pwcp/pdfs/reports/pwfwcp_report_no_245.pdf.] +2000 data from Appendix 9 of J. D. McPhail and R. J. Zemlak. October 2001. Pygmy Whitefish studies on Dina Lake #1, 2000. Peace/Williston Fish and Wildlife Compensation Program, Report No. 245. 36pp plus appendices. [Was (is?) from https://www.bchydro.com/pwcp/pdfs/reports/pwfwcp_report_no_245.pdf.] 2001 data from Appendix 14 of Zemlak, R.J. and J.D. McPhail. 2003. Pygmy Whitefish studies on Dina Lake #1, 2001. Peace/Williston Fish and Wildlife Compensation Program Report No. 279. 35pp plus appendices. [Was (is?) from http://a100.gov.bc.ca/appsdata/acat/documents/r39503/pwfwcp_report_no_279_1383686631923_d6d1b25e3156cee45e442c5b3f756a6a7b4bb7ad7753efb1c51dc23ac997a9a6.pdf.] } @@ -47,5 +47,8 @@ str(PygmyWFBC) head(PygmyWFBC) } -\concept{'Weight-Length' 'Age Comparison' Condition 'Length Frequency'} +\concept{Age Comparison} +\concept{Condition} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/RBSmeltErie.Rd b/man/RBSmeltErie.Rd index 65870b6..4e62819 100644 --- a/man/RBSmeltErie.Rd +++ b/man/RBSmeltErie.Rd @@ -10,8 +10,7 @@ \item{recruits}{Number of recruits (per hour).} }} \source{ -From Ontario Ministry of Natural Resources, Fish and Wildlife Branch, 1997. Lake Erie fisheries report 1996. Lake Erie Committee Meeting, -Great Lakes Fishery Commission, Ann Arbor, Michigan. pp 26. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Ontario Ministry of Natural Resources, Fish and Wildlife Branch, 1997. Lake Erie fisheries report 1996. Lake Erie Committee Meeting, Great Lakes Fishery Commission, Ann Arbor, Michigan. pp 26. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Rainbow Smelt (\emph{Osmerus mordax}) recruitment time series for Lake Erie, 1977-1996. diff --git a/man/RBSmeltLM.Rd b/man/RBSmeltLM.Rd index 634d7bc..d5af5e4 100644 --- a/man/RBSmeltLM.Rd +++ b/man/RBSmeltLM.Rd @@ -9,7 +9,7 @@ \item{fl}{Fork length (mm)} }} \source{ -From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. } \description{ Rainbow Smelt (\emph{Osmerus mordax}) fork lengths from near Grand Haven, Lake Michigan, 1977. @@ -29,5 +29,6 @@ head(RBSmeltLM) hist(RBSmeltLM$fl,main="") } -\concept{'Length Frequency' 'Size Structure'} +\concept{Length Frequency} +\concept{Size Structure} \keyword{datasets} diff --git a/man/RBTroutKenai.Rd b/man/RBTroutKenai.Rd index 0bb7644..14993f2 100644 --- a/man/RBTroutKenai.Rd +++ b/man/RBTroutKenai.Rd @@ -11,7 +11,7 @@ \item{dt}{Time-at-large (yrs).} }} \source{ -From Table 4.10 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press. 560 pages. This table is a 1/3rd subsample of the actual data presented in Baker, T.T., R. Lafferty, and T.J. Quinn II. 1991. A general growth model for mark-recapture data. Fisheries Research 11:257-281. +From Table 4.10 in Quinn, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press. 560 pages. This table is a 1/3rd subsample of the actual data presented in Baker, T.T., R. Lafferty, and T.J. Quinn II. 1991. A general growth model for mark-recapture data. Fisheries Research 11:257-281. } \description{ Length-at-marking and recapture and time-at-large for Rainbow Trout (\emph{Oncorhynchus mykiss}) from the Kenai River, Alaska. @@ -32,5 +32,7 @@ head(RBTroutKenai) plot((Lr-Lm)~dt,data=RBTroutKenai) } -\concept{Growth 'von Bertalanffy' Fabens} +\concept{Fabens} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/RBTroutUNSP.Rd b/man/RBTroutUNSP.Rd index 46e6341..ef6fd59 100644 --- a/man/RBTroutUNSP.Rd +++ b/man/RBTroutUNSP.Rd @@ -10,7 +10,7 @@ \item{second}{Indicator variable for the second sample (1=captured)} }} \source{ -Simulated from Table 10 in of Warren, C.D., K.A. Frank, and F.E. Partridge. 2004. Federal aid in fish restoration - 2000 job performance report. Idaho Department of Fish and Game. +Simulated from Table 10 in of Warren, C.D., K.A. Frank, and F.E. Partridge. 2004. Federal Aid in Fish Restoration - 2000 job performance report. Idaho Department of Fish and Game. } \description{ Capture histories for Rainbow Trout (\emph{Oncorhynchus mykiss}) in Upper Niagara Springs pond. @@ -33,5 +33,10 @@ str(RBTroutUNSP) head(RBTroutUNSP) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen' 'Capture History'} +\concept{Abundance} +\concept{Capture History} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Petersen} +\concept{Population Size} \keyword{datasets} diff --git a/man/RWhitefishAI.Rd b/man/RWhitefishAI.Rd index f55579c..e1a127e 100644 --- a/man/RWhitefishAI.Rd +++ b/man/RWhitefishAI.Rd @@ -10,7 +10,7 @@ \item{age}{Age (from scales).} }} \source{ -From Table 3 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] +From Table 3 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of Round Whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] } \description{ Ages and total lengths of Round Whitefish (\emph{Prosopium cylindraceum}) collected from the Apostles Islands, Lake Superior. @@ -30,5 +30,6 @@ head(RWhitefishAI) plot(tl~age,data=RWhitefishAI) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/RWhitefishIR.Rd b/man/RWhitefishIR.Rd index 701859a..841d826 100644 --- a/man/RWhitefishIR.Rd +++ b/man/RWhitefishIR.Rd @@ -10,7 +10,7 @@ \item{age}{Age (from scales).} }} \source{ -From Table 4 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] +From Table 4 (a random tenths digit was added to the TL) in Bailey, M.M. 1963. Age, growth, and maturity of round whitefish of the Apostle Islands and Isle Royale Regions, Lake Superior. Fishery Bulletin, 63:63-75. [Was (is?) from http://fishbull.noaa.gov/63-1/bailey.pdf.] } \description{ Ages and total lengths of Round Whitefish (\emph{Prosopium cylindraceum}) collected from Isle Royale, Lake Superior. @@ -30,5 +30,6 @@ head(RWhitefishIR) plot(tl~age,data=RWhitefishIR) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/RedDrum.Rd b/man/RedDrum.Rd index 71e6b6e..d3a1d1a 100644 --- a/man/RedDrum.Rd +++ b/man/RedDrum.Rd @@ -10,7 +10,7 @@ \item{fl}{Fork length (mm)} }} \source{ -From (approximately) Figure 27 in Vaughan, D.S. and T.E. Helser. 1990. Status of the red drum stock of the Atlantic Coast: Stock assessment report for 1989. NOAA Technical Memorandum, NMFS-SEFC-263. +From (approximately) Figure 27 in Vaughan, D.S. and T.E. Helser. 1990. Status of the red drum stock of the Atlantic Coast: Stock assessment report for 1989. NOAA Technical Memorandum, NMFS-SEFC-263. } \description{ Assigned ages (from otoliths) and fork lengths of Red Drum (\emph{Sciaenops ocellatus}) from various areas of the Atlantic Coast, 1981-1988. @@ -30,5 +30,6 @@ head(RedDrum) plot(fl~age,data=RedDrum) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/Riffleshell.Rd b/man/Riffleshell.Rd index 3feee19..0f24f39 100644 --- a/man/Riffleshell.Rd +++ b/man/Riffleshell.Rd @@ -12,7 +12,7 @@ \item{retmarks}{Number of marked fish returned to the population} }} \source{ -From Table 1-2 of Rogers, S.O. 1999. Population biology of the tan fiffleshell (\emph{Epioblasma florentina walkeri}) and the effects of substratum and light on juvenile mussel propagation. Virginia Tech M.S. Thesis. +From Table 1-2 of Rogers, S.O. 1999. Population biology of the Tan Riffleshell (\emph{Epioblasma florentina walkeri}) and the effects of substratum and light on juvenile mussel propagation. Virginia Tech M.S. Thesis. } \description{ Summarized multiple mark-recapture data for Tan Riffleshell. @@ -38,5 +38,9 @@ str(Riffleshell) head(Riffleshell) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/RockBassCL.Rd b/man/RockBassCL.Rd index 5ba2513..2c985d1 100644 --- a/man/RockBassCL.Rd +++ b/man/RockBassCL.Rd @@ -30,5 +30,6 @@ RockBassCL plot(log(catch)~age,data=RockBassCL) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/RockBassLO1.Rd b/man/RockBassLO1.Rd index 5dc2180..9ba133f 100644 --- a/man/RockBassLO1.Rd +++ b/man/RockBassLO1.Rd @@ -10,7 +10,7 @@ \item{tl}{Measured total lengths (mm).} }} \source{ -Simulated from Table 1 of Wolfert, D.R. 1980. Age and growth of rock bass in Eastern Lake Ontario. New York Fish and Game Journal, 27:88:90. +Simulated from Table 1 of Wolfert, D.R. 1980. Age and growth of Rock Bass in Eastern Lake Ontario. New York Fish and Game Journal, 27:88:90. } \description{ Assigned ages (from scales) and measured total lengths for each of 1288 Rock Bass (\emph{Ambloplites rupestris}) from Lake Ontario. @@ -33,5 +33,6 @@ plot(tl~age,data=RockBassLO1) \seealso{ \code{\link{RockBassLO2}}. } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/RockBassLO2.Rd b/man/RockBassLO2.Rd index 03328b7..f60bf2e 100644 --- a/man/RockBassLO2.Rd +++ b/man/RockBassLO2.Rd @@ -37,5 +37,5 @@ rb.length <- subset(RockBassLO2,is.na(age)) \seealso{ \code{\link{RockBassLO1}}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/RuffeSLRH92.Rd b/man/RuffeSLRH92.Rd index 9a4b394..735095a 100644 --- a/man/RuffeSLRH92.Rd +++ b/man/RuffeSLRH92.Rd @@ -55,5 +55,9 @@ xtabs(~maturity,data=RuffeSLRH92) xtabs(~maturity+month+sex,data=RuffeSLRH92) } -\concept{Growth 'von Bertalanffy' 'Length Frequency' 'Weight-Length' Maturity} +\concept{Growth} +\concept{Length Frequency} +\concept{Maturity} +\concept{Weight-Length} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/RuffeTL89.Rd b/man/RuffeTL89.Rd index c0e0e6a..30ebfe7 100644 --- a/man/RuffeTL89.Rd +++ b/man/RuffeTL89.Rd @@ -29,5 +29,6 @@ head(RuffeTL89) hist(RuffeTL89$tl,main="") } -\concept{'Length Frequency' 'Size Structure'} +\concept{Length Frequency} +\concept{Size Structure} \keyword{datasets} diff --git a/man/SLampreyGL.Rd b/man/SLampreyGL.Rd index fbf4da9..190c260 100644 --- a/man/SLampreyGL.Rd +++ b/man/SLampreyGL.Rd @@ -30,5 +30,6 @@ head(SLampreyGL) plot(recruits~stock,data=SLampreyGL) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/SalmonADP.Rd b/man/SalmonADP.Rd index 7c28bcf..7ae4a69 100644 --- a/man/SalmonADP.Rd +++ b/man/SalmonADP.Rd @@ -5,22 +5,21 @@ \alias{SalmonADP} \title{Catches in removal events of salmon parr.} \format{A data frame with 5 observations on the following 2 variables: -\describe{ -\item{catch}{Removal event.} -\item{caught}{Number of fish captured and removed.} -}} + \describe{ + \item{catch}{Removal event.} + \item{caught}{Number of fish captured and removed.} + }} \source{ -From Table 2 in Cowx, I.G. 1983. Review of the methods for estimating -fish population size from survey removal data. Fisheries Management, 14:67-82. +From Table 2 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. } \description{ Catches in removal events of salmon parr from the Afon Dulas at Pentre, 19Jun79. } \section{Topic(s)}{ \itemize{ -\item Population size -\item Abundance -\item Removal + \item Population size + \item Abundance + \item Removal } } @@ -33,5 +32,7 @@ SalmonADP \seealso{ \link{TroutADP} } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/SalmonidsMCCA.Rd b/man/SalmonidsMCCA.Rd index e6fd409..1f8cea0 100644 --- a/man/SalmonidsMCCA.Rd +++ b/man/SalmonidsMCCA.Rd @@ -13,7 +13,7 @@ \item{pass3}{Catch on the third removal pass.} }} \source{ -From Table 2 of Voight, H. 1999. Assessment of juvenile salmonid populations in two index reaches of McGarvey Creek, a tributary to the lower Klamath River. First Year of Investigations - 1998. [Was (is?) from http://www.krisweb.com/biblio/klamath_yuroktfp_voight_1999_7.pdf.] +From Table 2 of Voight, H. 1999. Assessment of juvenile salmonid populations in two index reaches of McGarvey Creek, a tributary to the lower Klamath River. First Year of Investigations - 1998. [Was (is?) from http://www.krisweb.com/biblio/klamath_yuroktfp_voight_1999_7.pdf.] } \description{ Catches in removal events of Cutthroate Trout (\emph{Oncorhynchus clarki}) and Steelhead (\emph{Oncorhynchus mykiss}) of various sizes in two reaches of McGarvey Creek (CA). @@ -39,5 +39,7 @@ head(SalmonidsMCCA) SalmonidsMCCA[3,] } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/SardineChile.rd b/man/SardineChile.rd index 7ebbda1..2e26b8d 100644 --- a/man/SardineChile.rd +++ b/man/SardineChile.rd @@ -5,28 +5,24 @@ \alias{SardineChile} \title{Ages and lengths of two year-classes of Sardine from Chilean waters.} \format{A data frame with 196 observations of the following 3 variables: -\describe{ -\item{age.mon}{Age in months.} -\item{tl.cm}{Total length (cm).} -\item{cohort}{Year-class.} -}} + \describe{ + \item{age.mon}{Age in months.} + \item{tl.cm}{Total length (cm).} + \item{cohort}{Year-class.} + }} \source{ -Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. -Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off -Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to -seasonal upwelling? Aquatic Living Resources, 14:115-124. Data were in -Figure 9. +Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa. 2001. Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling? Aquatic Living Resources, 14:115-124. Data were in Figure 9. } \description{ -Ages (in months) and total lengths of two year-classes of Sardine -(\emph{Strangomera bentincki}) from central Chilean waters. +Ages (in months) and total lengths of two year-classes of Sardine (\emph{Strangomera bentincki}) from central Chilean waters. } \section{Topic(s)}{ + \itemize{ -\item Growth -\item Seasonal Growth -\item von Bertalanffy -\item Somers model + \item Growth + \item Seasonal Growth + \item von Bertalanffy + \item Somers model } } @@ -38,5 +34,8 @@ SardineChile$age <- SardineChile$age.mon/12 plot(tl.cm~age,data=SardineChile) } -\concept{Growth 'von Bertalanffy' Somers 'Seasonal Growth'} +\concept{Growth} +\concept{Seasonal Growth} +\concept{Somers} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/SardineLK.Rd b/man/SardineLK.Rd index 40ac111..667626a 100644 --- a/man/SardineLK.Rd +++ b/man/SardineLK.Rd @@ -10,7 +10,7 @@ \item{tl}{Total length (mm within 0.1).} }} \source{ -From (approximately) Figure 3 of Mtsambiwa, M.Z. 1992. Fitting a von Bertalanffy growth model to length at age data for larval \emph{Limnothrissa miodon} from Lake Kariba. Paper presented at the Symposium on biology, stock assessment, and exploitation of small pelagic fish species in the African Great Lakes region. [Was (is?) from http://www.fao.org/docrep/005/v2648e/V2648E06.htm.] +From (approximately) Figure 3 of Mtsambiwa, M.Z. 1992. Fitting a von Bertalanffy growth model to length at age data for larval \emph{Limnothrissa miodon} from Lake Kariba. Paper presented at the Symposium on biology, stock assessment, and exploitation of small pelagic fish species in the African Great Lakes region. [Was (is?) from http://www.fao.org/docrep/005/v2648e/V2648E06.htm.] } \description{ Ages (days) and total lengths of larval Lake Tanganyika Sardine (\emph{Limnothrissa miodon}) from Lake Kariba. @@ -30,5 +30,6 @@ head(SardineLK) plot(tl~days,data=SardineLK) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/SardinesPacific.Rd b/man/SardinesPacific.Rd index adca2a4..9ff9f4c 100644 --- a/man/SardinesPacific.Rd +++ b/man/SardinesPacific.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recruitment index -- millions of fish} }} \source{ -From Jacobson, L.D. and A.D. MacCall. 1995. Stock-recruitment models for Pacific sardine (\emph{Sardinops sagax}). Canadian Journal of Fisheries and Aquatic Sciences. 52:566-577. +From Jacobson, L.D. and A.D. MacCall. 1995. Stock-recruitment models for Pacific Sardine (\emph{Sardinops sagax}). Canadian Journal of Fisheries and Aquatic Sciences. 52:566-577. } \description{ Pacific Sardine (\emph{Sardinops sagax}) stock and recruitment by year, 1935-1990. @@ -34,5 +34,6 @@ plot(recruits~ssb,data=SardinesPacific) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/SculpinALTER.Rd b/man/SculpinALTER.Rd index b928e16..b9fb486 100644 --- a/man/SculpinALTER.Rd +++ b/man/SculpinALTER.Rd @@ -11,7 +11,7 @@ \item{age}{Age (completed growing seasons from otoliths) at capture} }} \source{ -Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89hes6ag.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. +Was (does not appear to be available there now) from http://ecosystems.mbl.edu/ARC/lakes/fish/89hes6ag.html. It seems like it should still be available from the Arctic LTER site at http://ecosystems.mbl.edu/ARC/lakes/fish/index.shtml. } \description{ Biological data (length, weight, and age) for Slimy Sculpin (\emph{Cottus cognatus}) sampled from Lake S-6 of the Arctic Long Term Ecological Research location. @@ -42,5 +42,9 @@ plot(tl~age,data=SculpinALTER) par(op) } -\concept{Growth 'von Bertalanffy' 'Length Frequency' 'Weight-Length' 'Size Structure'} +\concept{Growth} +\concept{Length Frequency} +\concept{Size Structure} +\concept{Weight-Length} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/ShadCR.Rd b/man/ShadCR.Rd index 474f461..e19ccd4 100644 --- a/man/ShadCR.Rd +++ b/man/ShadCR.Rd @@ -47,5 +47,7 @@ plot(agerC1~agerC2,data=ShadCR) plot(agerA1~agerB1,data=ShadCR) par(op) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/ShrimpGuam.Rd b/man/ShrimpGuam.Rd index 69713f6..bcdb71a 100644 --- a/man/ShrimpGuam.Rd +++ b/man/ShrimpGuam.Rd @@ -12,7 +12,7 @@ \item{effort}{Total effort (trap-nights) for the standard traps.} }} \source{ -From Table 1 of Ralson, S. 1986. An intensive fishing experiment for the Caridean Shrimp, \emph{Heterocarpus laevigatus}, at Alamagn Island in the Mariana Archipelago. Fishery Bulletin 84:927-934. [Was (is?) from http://fishbull.noaa.gov/844/ralston.pdf.] +From Table 1 of Ralson, S. 1986. An intensive fishing experiment for the Caridean Shrimp, \emph{Heterocarpus laevigatus}, at Alamagn Island in the Mariana Archipelago. Fishery Bulletin 84:927-934. [Was (is?) from http://fishbull.noaa.gov/844/ralston.pdf.] } \description{ Catch and effort data for Deepwater Caridean Shrimp (\emph{Heterocarpus laevigatus}) from 15 days in 1984 from near Alamagan Islan in the Marian Archipelago (near Guam). @@ -48,5 +48,10 @@ ShrimpGuam$total <- ShrimpGuam$standard+ShrimpGuam$pyramid ShrimpGuam$cumCatch <- cumsum(ShrimpGuam$total)-ShrimpGuam$total/2 } -\concept{Abundance 'Population Size' Leslie DeLury Depletion Catchability} +\concept{Abundance} +\concept{Catchability} +\concept{DeLury} +\concept{Depletion} +\concept{Leslie} +\concept{Population Size} \keyword{datasets} diff --git a/man/SimonsonLyons.Rd b/man/SimonsonLyons.Rd index 5e6f3a3..bc5692e 100644 --- a/man/SimonsonLyons.Rd +++ b/man/SimonsonLyons.Rd @@ -5,28 +5,27 @@ \alias{SimonsonLyons} \title{Catches in removal events of trout at various locations.} \format{A data frame of 58 observations on the following 7 variables: -\describe{ -\item{species}{Species of fish.} -\item{stream}{Stream name.} -\item{first}{Catch on the first removal pass.} -\item{second}{Catch on the second removal pass.} -\item{third}{Catch on the third removal pass.} -\item{fourth}{Catch on the fourth removal pass.} -\item{pop.cs}{Population estimate by Carle-Strub method.} -}} + \describe{ + \item{species}{Species of fish.} + \item{stream}{Stream name.} + \item{first}{Catch on the first removal pass.} + \item{second}{Catch on the second removal pass.} + \item{third}{Catch on the third removal pass.} + \item{fourth}{Catch on the fourth removal pass.} + \item{pop.cs}{Population estimate by Carle-Strub method.} + }} \source{ -From Appendix in Simonson, T.D. and J. Lyons. 1995. Comparison of -catch per effort and removal procedures for sampling stream fish assemblages. -North American Journal of Fisheries Management, 15:419-427. +From Appendix in Simonson, T.D. and J. Lyons. 1995. Comparison of catch per effort and removal procedures for sampling stream fish assemblages. North American Journal of Fisheries Management, 15:419-427. } \description{ Catches of various species in consecutive removal events at various locations. } \section{Topic(s)}{ + \itemize{ -\item Population size -\item Abundance -\item Removal + \item Population size + \item Abundance + \item Removal } } @@ -39,5 +38,7 @@ head(SimonsonLyons) SimonsonLyons[3,] } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/SiscowetMI2004.Rd b/man/SiscowetMI2004.Rd index 94cf1a3..7c0abca 100644 --- a/man/SiscowetMI2004.Rd +++ b/man/SiscowetMI2004.Rd @@ -44,5 +44,6 @@ plot(len~age,data=SiscowetMI2004,subset=locID=="Little Lake Harbor",main="Little par(op) } -\concept{'Age-Length Key' 'Growth'} +\concept{Age-Length Key} +\concept{Growth} \keyword{datasets} diff --git a/man/Snapper.Rd b/man/Snapper.Rd index 8ba871f..8b97c98 100644 --- a/man/Snapper.Rd +++ b/man/Snapper.Rd @@ -9,7 +9,7 @@ \item{len}{Length in inches} }} \source{ -Simulated from length frequency summaries found in \code{data(cassie)} of the \pkg{mixdist} package. Data originally from Cassie, R.M. 1954. Some uses of probability paper in the analysis of size frequency distributions. Australian Journal of Marine and Freshwater Research. 5:513-522. +Simulated from length frequency summaries found in \code{data(cassie)} of the \pkg{mixdist} package. Data originally from Cassie, R.M. 1954. Some uses of probability paper in the analysis of size frequency distributions. Australian Journal of Marine and Freshwater Research. 5:513-522. } \description{ Lengths of Australian Snapper (\emph{Chrysophrys auratus}) taken by trawl. @@ -29,5 +29,6 @@ head(Snapper) hist(Snapper$len,main="") } -\concept{'Length Frequency' 'Size Structure'} +\concept{Length Frequency} +\concept{Size Structure} \keyword{datasets} diff --git a/man/SnapperHG1.Rd b/man/SnapperHG1.Rd index 08ba3af..c7f6f31 100644 --- a/man/SnapperHG1.Rd +++ b/man/SnapperHG1.Rd @@ -11,13 +11,13 @@ \item{survey}{Survey location (\code{KAH8810} or \code{KAH0012})} }} \source{ -Recreated from Tables 2, 3, and 5 in Davies, N.M. and C. Walsh. 2002. Snapper age and length samples from Kaharoa research trawl surveys KAH8810 and KAH0012 of the Hauraki Gulf. Final Research Report for Ministry of Fisheries Research Project SNA2000/01. National Institute of Water and Atmospheric Research. [Was (is?) from http://fs.fish.govt.nz/Page.aspx?pk=113&dk=22516.] +Recreated from Tables 2, 3, and 5 in Davies, N.M. and C. Walsh. 2002. Snapper age and length samples from Kaharoa research trawl surveys KAH8810 and KAH0012 of the Hauraki Gulf. Final Research Report for Ministry of Fisheries Research Project SNA2000/01. National Institute of Water and Atmospheric Research. [Was (is?) from http://fs.fish.govt.nz/Page.aspx?pk=113&dk=22516.] } \description{ A large sample (not random or proportional) of Snapper (\emph{Pagrus auratus}) were aged from otoliths, with the remainder of the fish just measured for length. Note that age-20 is actually age 19+. } \note{ -the unaged fish were simulated from Table 5 assuming that the total number of fish was large enough that at least one fish was observed in each cell where a proportion was listed. +The unaged fish were simulated from Table 5 assuming that the total number of fish was large enough that at least one fish was observed in each cell where a proportion was listed. } \section{Topic(s)}{ @@ -43,5 +43,5 @@ sn1.length <- subset(sn1,is.na(age)) str(sn1.length) } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/SnapperHG2.Rd b/man/SnapperHG2.Rd index 87c3414..592871f 100644 --- a/man/SnapperHG2.Rd +++ b/man/SnapperHG2.Rd @@ -39,5 +39,5 @@ str(sn2.length) \seealso{ See the same data in summarized format as \code{alkdata} in \pkg{fishmethods}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/SockeyeKL.Rd b/man/SockeyeKL.Rd index b8ca189..5436a2f 100644 --- a/man/SockeyeKL.Rd +++ b/man/SockeyeKL.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recruits.} }} \source{ -From Gulland, J.A. 1983. Fish stock assessment: A manual of basic methods. John Wiley and Sons, New York, NY. 223 p. +From Gulland, J.A. 1983. Fish stock assessment: A manual of basic methods. John Wiley and Sons, New York, NY. 223 p. } \description{ Sockeye Salmon (\emph{Oncorhynchus nerka}) stock and recruitment in Karluk Lake, AK, by year, 1921-1948. @@ -34,5 +34,6 @@ plot(recruits~stock,data=SockeyeKL) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/SockeyeSR.Rd b/man/SockeyeSR.Rd index 033c076..04f419d 100644 --- a/man/SockeyeSR.Rd +++ b/man/SockeyeSR.Rd @@ -16,7 +16,7 @@ Carroll, R. J. and Ruppert, D. 1988. Transformation and Weighting in Regression \description{ Stock and recruitment data for Skeena River Sockeye Salmon (\emph{Oncorhynchus nerka}), 1940-1967. } -\details{ +\note{ The dataset is usually analysed without case 12 because a rockslide occurred that year. } \section{Topic(s)}{ @@ -38,5 +38,6 @@ plot(recruits~spawners,data=SockeyeSR1) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/SpotVA2.Rd b/man/SpotVA2.Rd index 990a163..8da5ffd 100644 --- a/man/SpotVA2.Rd +++ b/man/SpotVA2.Rd @@ -39,5 +39,5 @@ str(spot.length) \seealso{ \code{SpotVA1} in \pkg{FSA}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/SpottedSucker1.Rd b/man/SpottedSucker1.Rd index ca36c01..529445f 100644 --- a/man/SpottedSucker1.Rd +++ b/man/SpottedSucker1.Rd @@ -10,7 +10,7 @@ \item{age}{Age (from scales).} }} \source{ -From Box 5.4 in Iseley, J.J. and T.B. Grabowski. 2007. Age and Growth in Guy, C.S. and M.L. Brown, editors. Analysis and Interpretation of Freshwater Fisheries Data. American Fisheries Society. Likely originally from Grabowski, T.B., S.P. Young, J.J. Isely, and P.C. Ely. Age, growth, and reproductive biology of three catostomids from the Apalachicola River, Florida. Journal of Fish and Wildlife Management 3:223-237. [Was (is?) from http://www.fwspubs.org/doi/pdf/10.3996/012012-JFWM-008.] +From Box 5.4 in Iseley, J.J. and T.B. Grabowski. 2007. Age and Growth in Guy, C.S. and M.L. Brown, editors. Analysis and Interpretation of Freshwater Fisheries Data. American Fisheries Society. Likely originally from Grabowski, T.B., S.P. Young, J.J. Isely, and P.C. Ely. Age, growth, and reproductive biology of three catostomids from the Apalachicola River, Florida. Journal of Fish and Wildlife Management 3:223-237. [Was (is?) from http://www.fwspubs.org/doi/pdf/10.3996/012012-JFWM-008.] } \description{ Ages and total lengths of Spotted Sucker (\emph{Minytrema melanops}) collected from the Apalachicola River, Florida. @@ -30,5 +30,6 @@ head(SpottedSucker1) plot(tl~age,data=SpottedSucker1) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/StripedBass1.Rd b/man/StripedBass1.Rd index 416aca1..b9777b1 100644 --- a/man/StripedBass1.Rd +++ b/man/StripedBass1.Rd @@ -33,5 +33,7 @@ plot(ageS~ageO,data=StripedBass1) xtabs(~ageO+ageS,data=StripedBass1) } -\concept{Age Precision Bias} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/StripedBass2.Rd b/man/StripedBass2.Rd index 2e06341..f785d73 100644 --- a/man/StripedBass2.Rd +++ b/man/StripedBass2.Rd @@ -33,5 +33,6 @@ plot(tl~age,data=StripedBass2) \seealso{ \code{\link{StripedBass3}}. } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/StripedBass3.Rd b/man/StripedBass3.Rd index f9ee573..80700af 100644 --- a/man/StripedBass3.Rd +++ b/man/StripedBass3.Rd @@ -36,5 +36,5 @@ str(sb.length) \seealso{ \code{\link{StripedBass2}}. } -\concept{'Age-Length Key'} +\concept{Age-Length Key} \keyword{datasets} diff --git a/man/StripedBass4.Rd b/man/StripedBass4.Rd index b36cad2..922e671 100644 --- a/man/StripedBass4.Rd +++ b/man/StripedBass4.Rd @@ -36,5 +36,7 @@ xtabs(~reader1+reader2,data=StripedBass4) \seealso{ \code{\link{StripedBass5}} and \code{\link{StripedBass6}}. } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/StripedBass5.Rd b/man/StripedBass5.Rd index 7583852..a172b30 100644 --- a/man/StripedBass5.Rd +++ b/man/StripedBass5.Rd @@ -36,5 +36,7 @@ xtabs(~reader1+reader2,data=StripedBass5) \seealso{ \code{\link{StripedBass4}} and \code{\link{StripedBass6}}. } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/StripedBass6.Rd b/man/StripedBass6.Rd index 0cd276c..8c3743c 100644 --- a/man/StripedBass6.Rd +++ b/man/StripedBass6.Rd @@ -36,5 +36,7 @@ xtabs(~otolith+scale,data=StripedBass6) \seealso{ \code{\link{StripedBass4}} and \code{\link{StripedBass5}}. } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/SturgeonBL.Rd b/man/SturgeonBL.Rd index c9073ec..2d8a116 100644 --- a/man/SturgeonBL.Rd +++ b/man/SturgeonBL.Rd @@ -35,5 +35,9 @@ str(SturgeonBL) head(SturgeonBL) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Schnabel} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/SturgeonGB.Rd b/man/SturgeonGB.Rd index f306abc..b9868f0 100644 --- a/man/SturgeonGB.Rd +++ b/man/SturgeonGB.Rd @@ -32,5 +32,5 @@ head(SturgeonGB) plot(age~year,data=SturgeonGB) } -\concept{'Year-class Strength'} +\concept{Year-class Strength} \keyword{datasets} diff --git a/man/SunfishIN.Rd b/man/SunfishIN.Rd index 4f13986..e1e19d6 100644 --- a/man/SunfishIN.Rd +++ b/man/SunfishIN.Rd @@ -12,17 +12,7 @@ \item{retmarks}{Number of marked fish returned to the population} }} \source{ -Originally from - -Gerking, S.D. 1953. Vital statistics of the fish population of Gordy Lake, Indiana. Transactions of the American Fisheries Society. 82:48-67. - -But also found in Table 2.4 of - -Krebs, C.J. 1999. Ecological Methodology. Addison-Welsey Educational Publishing, second edition. - -and Table 4.4 of - -Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada +Originally from Gerking, S.D. 1953. Vital statistics of the fish population of Gordy Lake, Indiana. Transactions of the American Fisheries Society. 82:48-67. But also found in Table 2.4 of Krebs, C.J. 1999. Ecological Methodology. Addison-Welsey Educational Publishing, second edition and Table 4.4 of Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. } \description{ The number of Redear Sunfish (\emph{Lepomis microlophus}) caught in multiple samples from Gordy Lake, IN. The caught fish were examined for previous marks, marked (if previously unmarked), and then returned to the population. @@ -44,5 +34,9 @@ data(SunfishIN) str(SunfishIN) SunfishIN } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Schnabel} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/SunfishLP.Rd b/man/SunfishLP.Rd index 06f11ce..2ff7a39 100644 --- a/man/SunfishLP.Rd +++ b/man/SunfishLP.Rd @@ -11,7 +11,7 @@ \item{perc.freq}{Percent frequency of fish collected in 1998} }} \source{ -From (approximately) Figure 2 in Crawford, S. and M.S. Allen. 2006. Fishing and natural mortality of bluegills and redear sunfish at Lake Panasoffkee, Florida: Implications for size limits. North American Journal of Fisheries Management 26:42-51. Note that I added a percentage for age-1 fish (the difference in percentages from Fig. 2). +From (approximately) Figure 2 in Crawford, S. and M.S. Allen. 2006. Fishing and natural mortality of Bluegills and Redear Sunfish at Lake Panasoffkee, Florida: Implications for size limits. North American Journal of Fisheries Management 26:42-51. Note that I added a percentage for age-1 fish (the difference in percentages from Fig. 2). } \description{ The percent frequency of of Bluegill (\emph{Lepomis macrochirus}) and Redear Sunfish (\emph{Lepomis microlophus}) caught in Lake Panasoffkee, FL. @@ -30,5 +30,6 @@ head(SunfishLP) plot(log(perc.freq)~age,data=SunfishLP) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/TPrawnsEG.rd b/man/TPrawnsEG.rd index 3f816cd..4d02115 100644 --- a/man/TPrawnsEG.rd +++ b/man/TPrawnsEG.rd @@ -13,7 +13,7 @@ \item{cycloneFeb}{a numeric vector containing the relative rainfal in February as an index of cyclonic activity} }} \source{ -From table 9.1 in Haddon, M. 2000. Modeling and Quantitative Methods in Fisheries, CRC Press. Originally from Penn, J. W., and Caputi, N. 1986. Spawning stock-recruitment relationships and environmental influences on the tiger prawn (\emph{Penaeus esculentus}) fishery in Exmouth Gulf, Western Australia. Australian Journal of Marine and Freslzwater Research 37:491-505. +From table 9.1 in Haddon, M. 2000. Modeling and Quantitative Methods in Fisheries, CRC Press. Originally from Penn, J. W., and Caputi, N. 1986. Spawning stock-recruitment relationships and environmental influences on the Tiger Prawn (\emph{Penaeus esculentus}) fishery in Exmouth Gulf, Western Australia. Australian Journal of Marine and Freslzwater Research 37:491-505. } \description{ Stock and recruitment data for Exmouth Gulf Tiger Prawn (\emph{Panaeus esculentus}), 1970-1983. @@ -37,5 +37,6 @@ par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/TroutADP.Rd b/man/TroutADP.Rd index 2c7165c..842efea 100644 --- a/man/TroutADP.Rd +++ b/man/TroutADP.Rd @@ -10,7 +10,7 @@ \item{caught}{Number of fish captured and removed.} }} \source{ -From Table 1 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. +From Table 1 in Cowx, I.G. 1983. Review of the methods for estimating fish population size from survey removal data. Fisheries Management, 14:67-82. } \description{ Catches of trout on five successive removal events from the Afon Dulas at Pentre, 19Jun79. @@ -33,5 +33,7 @@ TroutADP \seealso{ \link{SalmonADP} } -\concept{Abundance 'Population Size' Removal} +\concept{Abundance} +\concept{Population Size} +\concept{Removal} \keyword{datasets} diff --git a/man/TroutBR.Rd b/man/TroutBR.Rd index 2234e65..82eab36 100644 --- a/man/TroutBR.Rd +++ b/man/TroutBR.Rd @@ -11,7 +11,7 @@ \item{species}{Species (\code{Brown} and \code{Rainbow}).} }} \source{ -From tables 18 and 19 of Scholl, D.K., P.J. Peeters, and S.T. Schram. 1984. Migratory brown trout and rainbow trout populations of the Brule River, Wisconsin. Wisconsin Department of Natural Resources, Fish Management Report No. 123. +From tables 18 and 19 of Scholl, D.K., P.J. Peeters, and S.T. Schram. 1984. Migratory brown trout and rainbow trout populations of the Brule River, Wisconsin. Wisconsin Department of Natural Resources, Fish Management Report No. 123. } \description{ Total lengths (inches) and ages (from scales) of Brown Trout (\emph{Salmo trutta}) and Rainbow Trout (\emph{Oncorhynchus mykiss}) migrating upstream on the Bois Brule River, WI in 1978 and 1979. @@ -34,5 +34,6 @@ plot(tl~age,data=TroutBR,subset=species=="Rainbow",main="Rainbow Trout") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/TroutperchLM1.Rd b/man/TroutperchLM1.Rd index 5bc6251..c7a6eb3 100644 --- a/man/TroutperchLM1.Rd +++ b/man/TroutperchLM1.Rd @@ -11,7 +11,7 @@ \item{sex}{Sex (\code{f}=female and \code{m}=male).} }} \source{ -Simulated from the age-length data provided in Table 1 of House, R., and L. Wells. 1973. Age, growth, spawning season, and fecundity of the trout-perch (\emph{Percopsis omsicomaycus}) in southeastern Lake Michigan. Journal of the Fisheries Research Board of Canada. 30:1221-1225. +Simulated from the age-length data provided in Table 1 of House, R., and L. Wells. 1973. Age, growth, spawning season, and fecundity of the trout-perch (\emph{Percopsis omsicomaycus}) in southeastern Lake Michigan. Journal of the Fisheries Research Board of Canada. 30:1221-1225. } \description{ The assigned ages (by scales), total lengths (mm), and sexes of Troutperch (\emph{Percopsis omsicomaycus}) captured in southeastern Lake Michigan. @@ -34,5 +34,6 @@ plot(tl~age,data=TroutperchLM1,subset=sex=="m",main="male") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/TroutperchLM2.Rd b/man/TroutperchLM2.Rd index c6018fd..3db826b 100644 --- a/man/TroutperchLM2.Rd +++ b/man/TroutperchLM2.Rd @@ -9,7 +9,7 @@ \item{fl}{fork length (mm)} }} \source{ -From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. +From Brandt, S.B., J.J. Magnuson, and L.B. Crowder. 1980. Thermal habitat partitioning by fishes in Lake Michigan. Canadian Journal of Fisheries and Aquatic Sciences. 37:1557-1564. Data was simulated (uniform distribution of values within length bin) from summarized length frequencies in http://fishbase.org/. } \description{ Troutperch (\emph{Percopsis omiscomaycus}) fork lengths from near Grand Haven, Lake Michigan, 1977. @@ -29,5 +29,6 @@ head(TroutperchLM2) hist(TroutperchLM2$fl,main="") } -\concept{'Length Frequency' 'Size Structure'} +\concept{Length Frequency} +\concept{Size Structure} \keyword{datasets} diff --git a/man/TroutperchLM3.Rd b/man/TroutperchLM3.Rd index bca3393..f4467a0 100644 --- a/man/TroutperchLM3.Rd +++ b/man/TroutperchLM3.Rd @@ -32,5 +32,7 @@ head(TroutperchLM3) \seealso{ \code{\link{TroutperchLM2}}. } -\concept{'Length Frequency' 'Size Structure' 'Length Expansion'} +\concept{Length Expansion} +\concept{Length Frequency} +\concept{Size Structure} \keyword{datasets} diff --git a/man/VendaceLP.Rd b/man/VendaceLP.Rd index 1ec6d7b..fff0166 100644 --- a/man/VendaceLP.Rd +++ b/man/VendaceLP.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recuit index -- density (indivs/ha) of age-0+ fish in first autumn} }} \source{ -From (approximately) Figure 1 and 2 of Marjomaki, T.J. 2004. Analysis of the spawning stock-recruitment relationship of vendace (\emph{Coregonus albula} (L.)) with evaluation of alternative models, additional variables, biases and errors. Ecology of Freshwater Fish 13:46-60. +From (approximately) Figure 1 and 2 of Marjomaki, T.J. 2004. Analysis of the spawning stock-recruitment relationship of vendace (\emph{Coregonus albula} (L.)) with evaluation of alternative models, additional variables, biases and errors. Ecology of Freshwater Fish 13:46-60. } \description{ Vendace (\emph{Coregonus albula}) recruitment by year in Lake Puulavesi, 1982-1996. @@ -34,5 +34,6 @@ plot(recruits~stock,data=VendaceLP) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/VendaceLP2.Rd b/man/VendaceLP2.Rd index dabb1fc..c9bc72a 100644 --- a/man/VendaceLP2.Rd +++ b/man/VendaceLP2.Rd @@ -10,7 +10,7 @@ \item{recruits}{Number of recruits (10^6 fish) in Autumn after hatching} }} \source{ -From (approximately) Figure 6 in Helminen, H. and J. Sarvala. 1994. Population regulation of vendance (\emph{Coregonus albula}) in Lake Pyhajarvi, southwest Finland. Journal of Fish Biology 45:387-400. +From (approximately) Figure 6 in Helminen, H. and J. Sarvala. 1994. Population regulation of vendance (\emph{Coregonus albula}) in Lake Pyhajarvi, southwest Finland. Journal of Fish Biology 45:387-400. } \description{ Vendace (\emph{Coregonus albula}) recruitment in Lake Pyhajarvi. @@ -33,5 +33,6 @@ head(VendaceLP2) plot(recruits~fecundity,data=VendaceLP2) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/WShrimpGA.Rd b/man/WShrimpGA.Rd index f0b8ffb..ed9b693 100644 --- a/man/WShrimpGA.Rd +++ b/man/WShrimpGA.Rd @@ -12,7 +12,7 @@ \item{yrconf}{A code of confidence for whether or not the stock value is known to come from the year shown (see the note)} }} \source{ -From (approximately) Figures 2 and 3 of Belcher, C.N., and C.A. Jennings. 2004. Evaluation of stock-recruitment curves for white shrimp in Georgia. North American Journal of Fisheries Management. 24:654-661. +From (approximately) Figures 2 and 3 of Belcher, C.N., and C.A. Jennings. 2004. Evaluation of stock-recruitment curves for white shrimp in Georgia. North American Journal of Fisheries Management. 24:654-661. } \description{ White Shrimp (\emph{Litopenaeus setiferus}) stock and recruitment data from off the coast of Georgia (USA), 1979-2000. @@ -38,5 +38,6 @@ plot(recruits~stock,data=WShrimpGA) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/WalleyeConsumption.Rd b/man/WalleyeConsumption.Rd index 051927a..90dd9d0 100644 --- a/man/WalleyeConsumption.Rd +++ b/man/WalleyeConsumption.Rd @@ -10,7 +10,7 @@ \item{FoodConsump}{Food consumption by predator (mg per cubic meter)} }} \source{ -From Figure 3 in Madenjian, C.P., and S.R. Carpenter. 1991. Individual-based model for growth of young-of-the-year walleye: A piece of the recruitment puzzle. Ecological Applications. 1:268-279. Data were originally from Swenson, W. A. 1977. Food consumptions of walleye (\emph{Stizostedion vitreum vitreum}) and sauger (\emph{S. canadense}) in relation to food availability and physical conditions in Lake of the Woods, Minnesota, Shagawa Lake, and western Lake Superior. Journal of the Fisheries Research Board of Canada 34:1643-1654. [Madenjian et al. (1991) was (is?) from http://www.esajournals.org/doi/abs/10.2307/1941756. Swenson (1977) was (is?) from http://www.nrcresearchpress.com/doi/abs/10.1139/f77-229?journalCode=jfrbc.] +From Figure 3 in Madenjian, C.P., and S.R. Carpenter. 1991. Individual-based model for growth of young-of-the-year walleye: A piece of the recruitment puzzle. Ecological Applications. 1:268-279. Data were originally from Swenson, W. A. 1977. Food consumptions of walleye (\emph{Stizostedion vitreum vitreum}) and sauger (\emph{S. canadense}) in relation to food availability and physical conditions in Lake of the Woods, Minnesota, Shagawa Lake, and western Lake Superior. Journal of the Fisheries Research Board of Canada 34:1643-1654. [Madenjian et al. (1991) was (is?) from http://www.esajournals.org/doi/abs/10.2307/1941756. Swenson (1977) was (is?) from http://www.nrcresearchpress.com/doi/abs/10.1139/f77-229?journalCode=jfrbc.] } \description{ Consumption of prey by Walleye (\emph{Sander vitreus}) at different prey densities. diff --git a/man/WalleyeEL.Rd b/man/WalleyeEL.Rd index 011fcf8..296494d 100644 --- a/man/WalleyeEL.Rd +++ b/man/WalleyeEL.Rd @@ -13,7 +13,7 @@ \item{yep}{Abundance of adult (larger than 152.4 mm) Yellow Perch} }} \source{ -Hansen, M. J., M. A. Bozek, J. R. Newby, S. P. Newman, and M. D. Staggs. 1998. Factors affecting recruitment of walleyes in Escanaba Lake, Wisconsin, 1958-1995. North American Journal of Fisheries Management 18:764-774. +Hansen, M. J., M. A. Bozek, J. R. Newby, S. P. Newman, and M. D. Staggs. 1998. Factors affecting recruitment of walleyes in Escanaba Lake, Wisconsin, 1958-1995. North American Journal of Fisheries Management 18:764-774. } \description{ Abundance of age-0 and age-5 and older Walleye (\emph{Sander vitreus}), abundance of adult Yellow Perch (\emph{Perca flavescens}), and coefficient of variation of May temperatures for Escanaba Lake, WI, 1958-1992. @@ -36,5 +36,6 @@ plot(age0~age5,data=WalleyeEL) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/WalleyeErie.Rd b/man/WalleyeErie.Rd index 3ae8c8e..e1df3e5 100644 --- a/man/WalleyeErie.Rd +++ b/man/WalleyeErie.Rd @@ -10,7 +10,7 @@ \item{recruits}{Number of recruits (per 1000 ft of net).} }} \source{ -From Wolfert, D. R. 1981. The commercial fishery for walleyes in New York waters of Lake Erie, 1959-1978. North American Journal of Fisheries Management 1: 112-126. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Wolfert, D. R. 1981. The commercial fishery for walleyes in New York waters of Lake Erie, 1959-1978. North American Journal of Fisheries Management 1: 112-126. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Walleye (\emph{Sander vitreus}) recruitment time-series for Lake Erie, 1959-1972. diff --git a/man/WalleyeErie2.Rd b/man/WalleyeErie2.Rd index 2d7aea8..e65ebb1 100644 --- a/man/WalleyeErie2.Rd +++ b/man/WalleyeErie2.Rd @@ -17,23 +17,24 @@ \item{age}{Age (yrs) from otoliths.} }} \source{ -These unpublished data are from the Ohio Department of Natural Resources, Division of Wildlife (via Christopher Vandergoot). \bold{Do not use for other than educational purposes without permission from the source.} +These unpublished data are from the Ohio Department of Natural Resources, Division of Wildlife (via Christopher Vandergoot). \bold{Do not use for other than educational purposes without permission from the source.} } \description{ Walleye (\emph{Sander vitreus}) biological data (length, weight, sex, maturity, and age) from several locations in Lake Erie, October-November of 2003-2014. } \section{Topic(s)}{ + \itemize{ - \item Growth - \item von Bertalanffy - \item Weight-Length - \item Catch curve - \item Mortality - \item Maturity - \item Size Structure - \item Length Frequency - \item Condition -} + \item Growth + \item von Bertalanffy + \item Weight-Length + \item Catch curve + \item Mortality + \item Maturity + \item Size Structure + \item Length Frequency + \item Condition + } } \examples{ @@ -43,5 +44,12 @@ head(WalleyeErie2) xtabs(~year+loc+sex,data=WalleyeErie2) } -\concept{'Growth' 'Weight-Length' 'Catch curve' 'Mortality' 'Maturity' 'Size Structure' 'Condition' 'Length Frequency'} +\concept{Catch curve} +\concept{Condition} +\concept{Growth} +\concept{Length Frequency} +\concept{Maturity} +\concept{Mortality} +\concept{Size Structure} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/WalleyeKS.Rd b/man/WalleyeKS.Rd index fb41a5f..c75f9e1 100644 --- a/man/WalleyeKS.Rd +++ b/man/WalleyeKS.Rd @@ -11,7 +11,7 @@ \item{catch}{Number of fish captured} }} \source{ -From Figure 2 of Quist, M.C., J.L. Stephen, C.S. Guy, and R.D. Schultz. 2004. Age structure and mortality of Walleyes in Kansas reservoirs: Use of mortality caps to establish realistic management objectives. North American Journal of Fisheries Management 24:990-1002. +From Figure 2 of Quist, M.C., J.L. Stephen, C.S. Guy, and R.D. Schultz. 2004. Age structure and mortality of Walleyes in Kansas reservoirs: Use of mortality caps to establish realistic management objectives. North American Journal of Fisheries Management 24:990-1002. } \description{ Catch-at-age for Walleye (\emph{Sander vitreus}) from eight Kansas reservoirs during 1991-1999. @@ -43,5 +43,6 @@ plot(log(catch)~age,data=WalleyeKS,subset=(reservoir=="Wilson"),main="Wilson") par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/WalleyeML.Rd b/man/WalleyeML.Rd index fb1652e..c0e693b 100644 --- a/man/WalleyeML.Rd +++ b/man/WalleyeML.Rd @@ -23,11 +23,12 @@ These unpublished data are from the Minnesota Department of Natural Resources, S Back-calculated lengths-at-age for Walleye (\emph{Sander vitreus}) from Lake Mille Lacs. Walleye were captured by Minnesota Department of Natural Resources personnel in fishery-independent gillnets (five multifilament nylon mesh panels with each panel measuring 15.2 m wide and 1.8 m high; bar-measure mesh sizes of the panels were 19.1, 25.4, 31.7, 38.1, and 50.8 mm) set in the fall (mid September to early October) from 2000 to 2011. } \section{Topic(s)}{ + \itemize{ - \item Growth - \item von Bertalanffy - \item Back-calculation -} + \item Growth + \item von Bertalanffy + \item Back-calculation + } } \examples{ @@ -37,5 +38,7 @@ head(WalleyeML) xtabs(~Year+Est.Age+Sex,data=WalleyeML) } -\concept{'Growth' 'von Bertalanffy' 'Back-calculation'} +\concept{Back-calculation} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/WalleyeMN06a.Rd b/man/WalleyeMN06a.Rd index 675c16d..8e09435 100644 --- a/man/WalleyeMN06a.Rd +++ b/man/WalleyeMN06a.Rd @@ -11,7 +11,7 @@ \item{number}{A numeric vector of number of fish} }} \source{ -From various tables in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] +From various tables in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] } \description{ Catch-at-age for Walleye (\emph{Sander vitreus}) collected from four lakes in Northern Minnesota, USA. @@ -36,5 +36,6 @@ plot(log(number)~age,data=WalleyeMN06a,subset=lake=="Tom") par(op) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/WalleyeMN06b.Rd b/man/WalleyeMN06b.Rd index 83823e9..63167e4 100644 --- a/man/WalleyeMN06b.Rd +++ b/man/WalleyeMN06b.Rd @@ -13,7 +13,7 @@ \item{retMark}{Marked fish returned to the population} }} \source{ -From appendix 2 in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] +From appendix 2 in Borkholder, B.D., A.J. Edwards, and C. Olson. 2007. Spring adult and fall juvenile walleye popluation surveys within the 1854 ceded territory of Minnesota, 2006. Fond du Lac Division of Resource Management, Technical Report 41. [Was (is?) from http://www.1854treatyauthority.org/cms/files/REP\%20Fish\%20Walleye\%20Survey\%202006.pdf.] } \description{ Summary results of capture histories (number captured, number of recaptured fish, and number of unmarked fish that were marked) for Walleye (\emph{Sander vitreus}) collected from four lakes in Northern Minnesota, USA. @@ -36,5 +36,9 @@ str(WalleyeMN06b) head(WalleyeMN06b) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/WalleyePL.Rd b/man/WalleyePL.Rd index c6bd0f8..3c00b7e 100644 --- a/man/WalleyePL.Rd +++ b/man/WalleyePL.Rd @@ -13,7 +13,7 @@ \item{newmarks}{Number of unmarked walleyes that were captured, marked, and returned to the population} }} \source{ -From table 3 of Mraz, D. 1968. Recruitment, growth, exploitation, and management of walleyes in a southeastern Wisconsin lake. Wisconsin Department of Natural Resources Technical Bulletin 40. 38 pages. +From table 3 of Mraz, D. 1968. Recruitment, growth, exploitation, and management of walleyes in a southeastern Wisconsin lake. Wisconsin Department of Natural Resources Technical Bulletin 40. 38 pages. } \description{ The numbers of young-of-year walleye (\emph{Sander vitreus}) that were captured, found to have previous marks (i.e., recaptured), and were newly marked on several sampling occasions in 1959, 1960, 1961, and 1962 in Pike Lake, Wisconsin. @@ -37,5 +37,9 @@ WalleyePL subset(WalleyePL,year==1960) } -\concept{Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel'} +\concept{Abundance} +\concept{Capture-Recapture} +\concept{Mark-Recapture} +\concept{Population Size} +\concept{Schnabel} \keyword{datasets} diff --git a/man/WalleyePS.Rd b/man/WalleyePS.Rd index 8f2552a..c1d728e 100644 --- a/man/WalleyePS.Rd +++ b/man/WalleyePS.Rd @@ -12,7 +12,7 @@ \item{sex}{Sex of fish (\code{female} and \code{male})} }} \source{ -From Figure 2 in Kocovsky, P.M., and R.M. Carline. 2000. A comparison of methods for estimating ages of unexploited walleyes. North American Journal of Fisheries Management 20:1044-1048. +From Figure 2 in Kocovsky, P.M., and R.M. Carline. 2000. A comparison of methods for estimating ages of unexploited walleyes. North American Journal of Fisheries Management 20:1044-1048. } \description{ Age of Pymatuning Sanctuary (PA) Walleye (\emph{Sander vitreus}) assessed from three calcified structures -- sectioned otoliths, sectioned dorsal spines, and scale impressions. @@ -44,5 +44,7 @@ plot(spine~otolith,data=WalleyePS,subset=sex=="male",main="Male") par(op) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/WalleyeRL.Rd b/man/WalleyeRL.Rd index 3910a7d..b7ea5c1 100644 --- a/man/WalleyeRL.Rd +++ b/man/WalleyeRL.Rd @@ -21,7 +21,7 @@ \item{radcap}{Scale radius at time of capture} }} \source{ -Cyterski, M.J. and G.R. Spangler. 1996. A tool for age determination. North American Journal of Fisheries Management, 16:403-412. +Cyterski, M.J. and G.R. Spangler. 1996. A tool for age determination. North American Journal of Fisheries Management, 16:403-412. } \description{ Growth increment data for Red Lakes Walleye (\emph{Sander vitreus}) in one-fish-per-line format. @@ -43,5 +43,6 @@ str(WalleyeRL) head(WalleyeRL) } -\concept{Growth Weisberg LGM} +\concept{Growth} +\concept{Weisberg LGM} \keyword{datasets} diff --git a/man/WalleyeWad.Rd b/man/WalleyeWad.Rd index 2792087..94e802f 100644 --- a/man/WalleyeWad.Rd +++ b/man/WalleyeWad.Rd @@ -11,7 +11,7 @@ \item{numM}{Number of captured males} }} \source{ -From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. +From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. } \description{ Catches-at-age for male and female Walleye from Lake Winnebago, WI, 2010. @@ -38,5 +38,6 @@ plot(numF~age,data=WalleyeWad) points(numM~age,data=WalleyeWad,pch=19) } -\concept{'Catch Curve' Mortality} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/WalleyeWyrlng.Rd b/man/WalleyeWyrlng.Rd index 59f5e4e..b628f14 100644 --- a/man/WalleyeWyrlng.Rd +++ b/man/WalleyeWyrlng.Rd @@ -12,7 +12,7 @@ \item{yrclass}{Year-class of the captured yearlings (capture year minus 1)} }} \source{ -From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. +From Koenigs, R.P., Bruch, R.M., Stelzer, R.S., and Kamke, K.K. 2015. Validation of otolith ages for Walleye (\emph{Sander vitreus}) in the Winnebago System. Fisheries Research, 167:13-21. Obtained directly from Ryan Koenigs. } \description{ Annual catches of yearling Walleye (\emph{Sander vitreus}) in bottom trawls from Lake Winnebago, WI, 1986-2010. @@ -38,5 +38,6 @@ head(WalleyeWyrlng) plot(yearlings~yrclass,data=WalleyeWyrlng) } -\concept{'Year-class Strength' Recruitment} +\concept{Recruitment} +\concept{Year-class Strength} \keyword{datasets} diff --git a/man/WhiteGrunt1.Rd b/man/WhiteGrunt1.Rd index a338c33..090acf3 100644 --- a/man/WhiteGrunt1.Rd +++ b/man/WhiteGrunt1.Rd @@ -10,7 +10,7 @@ \item{catch}{A numeric vector of number of fish.} }} \source{ -From Figure 7 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. +From Figure 7 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. } \description{ Catch-at-age for White Grunt (\emph{Haemulon plumierii}) collected from the central coast of Brazil. @@ -30,5 +30,6 @@ head(WhiteGrunt1) plot(log(catch)~age,data=WhiteGrunt1) } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/WhiteGrunt2.Rd b/man/WhiteGrunt2.Rd index 405908b..f8d97c9 100644 --- a/man/WhiteGrunt2.Rd +++ b/man/WhiteGrunt2.Rd @@ -11,7 +11,7 @@ \item{sex}{Sex (\code{male} and \code{female})} }} \source{ -From (approximately) Figure 6 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. +From (approximately) Figure 6 of Araujo, J.N. and A.S. Martins. 2007. Age, growth and mortality of white grunt (\emph{Haemulon plumierii}) from the central coast of Brazil. Scientia Marina 71:793-800. } \description{ Ages, lengths, and sexes of White Grunt (\emph{Haemulon plumierii}) collected from the central coast of Brazil @@ -34,5 +34,6 @@ plot(tl~age,data=WhiteGrunt2,subset=sex=="male",main="Male") par(op) } -\concept{Growth 'von Bertalanffy'} +\concept{Growth} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/WhitefishGSL.Rd b/man/WhitefishGSL.Rd index 611c5a4..eb8cb5f 100644 --- a/man/WhitefishGSL.Rd +++ b/man/WhitefishGSL.Rd @@ -14,7 +14,7 @@ \item{area.IW}{Catches for area IW.} }} \source{ -From Table 19 of Mosenko, R.W., and G. Low. 1980. Data from the commercial fishery for lake whitefish \emph{Coregonus clupeaformis} (Mitchill), on Great Slave Lake, Northwest Territories, 1979. Canadian Data Report of Fisheries And Aquatic Sciences, No. 194. +From Table 19 of Mosenko, R.W., and G. Low. 1980. Data from the commercial fishery for lake whitefish \emph{Coregonus clupeaformis} (Mitchill), on Great Slave Lake, Northwest Territories, 1979. Canadian Data Report of Fisheries And Aquatic Sciences, No. 194. } \description{ Age composition of commercial Whitefish (\emph{Coregonus clupeaformis}) catches for five areas of Great Slave Lake. @@ -50,5 +50,6 @@ names(WhitefishGSL1) <- c("age","area","number") } } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/WhitefishMB.Rd b/man/WhitefishMB.Rd index 3ffa435..b68b7e5 100644 --- a/man/WhitefishMB.Rd +++ b/man/WhitefishMB.Rd @@ -11,7 +11,7 @@ \item{lake}{Lake from which the fish was captured (\code{L122}, \code{L226}, \code{Huron}, or \code{Dezadeash})} }} \source{ -From (approximately) Figure 1 of Mills, K.H., and R.J. Beamish. 1980. Comparison of fin-ray and scale age determinations for lake whitefish (\emph{Coregonus clupeaformis}) and their implications for estimates of growth and annual survival. Canadian Journal of Fisheries and Aquatic Sciences, 37:534-544. +From (approximately) Figure 1 of Mills, K.H., and R.J. Beamish. 1980. Comparison of fin-ray and scale age determinations for lake whitefish (\emph{Coregonus clupeaformis}) and their implications for estimates of growth and annual survival. Canadian Journal of Fisheries and Aquatic Sciences, 37:534-544. } \description{ Ages of Lake Whitefish (\emph{Coregonus clupeaformis}) from four lakes as determined by scales and fin-rays. @@ -38,5 +38,7 @@ plot(scale~fin,data=WhitefishMB,subset=lake=="Dezadeash",main="Dezadeash") par(op) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets} diff --git a/man/WhitefishTB.Rd b/man/WhitefishTB.Rd index fd85364..82c6f67 100644 --- a/man/WhitefishTB.Rd +++ b/man/WhitefishTB.Rd @@ -13,7 +13,7 @@ \item{fmort}{Fishing related mortality (natural mortality was assumed to be 0.3)} }} \source{ -From Petzold, M. 1995. An historical analysis of the Lake Whitefish fisheries of Thunder Bay (Zone 1) and Whitefish Bay (Zone 34), Lake Superior. Ontario Min. of Nat. Res. unpubl. manuscript. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Petzold, M. 1995. An historical analysis of the Lake Whitefish fisheries of Thunder Bay (Zone 1) and Whitefish Bay (Zone 34), Lake Superior. Ontario Min. of Nat. Res. unpubl. manuscript. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Lake Whitefish (\emph{Coregonus clupeaformis}) stock, recruitment, landings, and fishing mortality by year, 1975-1988. @@ -36,5 +36,6 @@ plot(rec~ssb,data=WhitefishTB) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/YERockfish.rd b/man/YERockfish.rd index 7670bc9..6c29d2b 100644 --- a/man/YERockfish.rd +++ b/man/YERockfish.rd @@ -13,7 +13,7 @@ \item{stage}{Stage of maturity (\code{1}:Immature, \code{2}:Maturing, \code{3}:Mature, \code{4}:Fertilized, \code{5}:Ripe, \code{6}:Spent, \code{7}:Resting)} }} \source{ -Obtained directly (from Bob Hannah). Date were used in Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf] +Obtained directly (from Bob Hannah). Data were used in Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf] } \description{ Ages, lengths, and maturity for female Yelloweye Rockfish (\emph{Sebastes rubberimus}) from Oregon. @@ -43,5 +43,7 @@ plot(ptbl2[,2]~as.numeric(row.names(ptbl2)),type="l",xlab="Age",ylab="Proportion par(op) } -\concept{Growth 'von Bertalanffy' 'Maturity'} +\concept{Growth} +\concept{Maturity} +\concept{von Bertalanffy} \keyword{datasets} diff --git a/man/YPerchCB1.Rd b/man/YPerchCB1.Rd index 0314b73..49934c3 100644 --- a/man/YPerchCB1.Rd +++ b/man/YPerchCB1.Rd @@ -25,7 +25,7 @@ \item{year88}{Number of fish at each age in capture year 1988.} }} \source{ -From Table 1 in Bronte, C.R., J.H. Selgeby, D.V.Swedberg. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management 13:511-523. +From Table 1 in Bronte, C.R., J.H. Selgeby, D.V.Swedberg. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management 13:511-523. } \description{ Catch-at-age for Yellow Perch (\emph{Perca flavescens}) from Chequamegon Bay, Lake Superior, 1973-1988. @@ -71,5 +71,6 @@ yc82 <- diag(as.matrix(YPerchCB1[1:7,11:17])) plot(log(yc82)~YPerchCB1$age[1:7],main="1982 Year-Class") } -\concept{Mortality 'Catch Curve'} +\concept{Catch Curve} +\concept{Mortality} \keyword{datasets} diff --git a/man/YPerchCB2.Rd b/man/YPerchCB2.Rd index 61b3ef6..22fc388 100644 --- a/man/YPerchCB2.Rd +++ b/man/YPerchCB2.Rd @@ -11,7 +11,7 @@ \item{recruits}{Catches of age-2 fish (when the year-class is formed)} }} \source{ -From (approximately) Figure 7 in Bronte et al. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management. 13:511-523. +From (approximately) Figure 7 in Bronte et al. 1993. Dynamics of a yellow perch population in Western Lake Superior. North American Journal of Fisheries Management. 13:511-523. } \description{ Yellow Perch (\emph{Perca flavescens}) stock-recruitment by year-class in Chequamegon Bay, 1975-1986. @@ -34,5 +34,6 @@ plot(recruits~stock,data=YPerchCB2) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/YPerchGB.Rd b/man/YPerchGB.Rd index f04ba44..cd23f5d 100644 --- a/man/YPerchGB.Rd +++ b/man/YPerchGB.Rd @@ -10,7 +10,7 @@ \item{recruits}{Number of recruits (thousands per hour).} }} \source{ -From Walters, C., and A. Punt. 1994. Placing odds on sustainable catch virtual population analysis and survey data. Canadian Journal of Fisheries and Aquatic Sciences, 51:946-958. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Walters, C., and A. Punt. 1994. Placing odds on sustainable catch virtual population analysis and survey data. Canadian Journal of Fisheries and Aquatic Sciences, 51:946-958. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Yellow Perch (\emph{Perca flavescens}) recruitment time-series for Green Bay, 1978-1992. diff --git a/man/YPerchGL.Rd b/man/YPerchGL.Rd index ce2c2eb..a10241e 100644 --- a/man/YPerchGL.Rd +++ b/man/YPerchGL.Rd @@ -11,7 +11,7 @@ \item{year}{Year of capture (\code{1994} or \code{2000})} }} \source{ -From (approximately) Figure 3 in Brylinsky, M. 2001. An evaluation of changes in the yellow perch (\emph{Perca flavescens}) population of Grafton Lake, Kejimkujik National Park, after dam removal. Technical Report Publication No. 59, Acadia Centre for Estuarine Research. 2001. +From (approximately) Figure 3 in Brylinsky, M. 2001. An evaluation of changes in the yellow perch (\emph{Perca flavescens}) population of Grafton Lake, Kejimkujik National Park, after dam removal. Technical Report Publication No. 59, Acadia Centre for Estuarine Research. } \description{ Yellow Perch (\emph{Perca flavescens}) fork lengths and weights seperated by year. @@ -34,5 +34,6 @@ plot(w~fl,data=YPerchGL,subset=year==2000,main="2000") par(op) } -\concept{'Weight-Length' 'Length Frequency'} +\concept{Length Frequency} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/YPerchRL.Rd b/man/YPerchRL.Rd index 3bfb6d4..cfd2918 100644 --- a/man/YPerchRL.Rd +++ b/man/YPerchRL.Rd @@ -10,7 +10,7 @@ \item{recruits}{CPUE of recruits (relative to a mean).} }} \source{ -From Smith, L. L. Jr. 1977. Walleye (\emph{Stizostedion vitreum}) and yellow perch (\emph{Perca flavescens}) populations and fisheries of the Red Lakes, Minnesota, 1930-75. J. Fish. Res. Board Can. 34: 1774-1783. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Smith, L.L. Jr. 1977. Walleye (\emph{Stizostedion vitreum}) and yellow perch (\emph{Perca flavescens}) populations and fisheries of the Red Lakes, Minnesota, 1930-75. J. Fish. Res. Board Can. 34: 1774-1783. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Yellow Perch (\emph{Perca flavescens}) recruitment time-series for Red Lakes, MN, 1942-1960. diff --git a/man/YPerchSB.Rd b/man/YPerchSB.Rd index 786437d..2d62fa1 100644 --- a/man/YPerchSB.Rd +++ b/man/YPerchSB.Rd @@ -11,7 +11,7 @@ \item{recruits}{Recruits (number per set)} }} \source{ -From Henderson, B.A. 1985. Factors affecting growth and recruitment of yellow perch, \emph{Perca flavescens} Mitchill, in South Bay, Lake Huron. Journal of Fisheries Biology 26:449-458. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. +From Henderson, B.A. 1985. Factors affecting growth and recruitment of yellow perch, \emph{Perca flavescens} Mitchill, in South Bay, Lake Huron. Journal of Fisheries Biology 26:449-458. Obtained from Ransom Myers online database which was (is?) at http://ram.biology.dal.ca/~myers/data.html. } \description{ Yellow Perch (\emph{Perca flavescens}) stock and recruitment by year in South Bay, Lake Huron, 1950-1983. @@ -34,5 +34,6 @@ plot(recruits~stock,data=YPerchSB) par(op) } -\concept{'Stock-Recruit' Recruitment} +\concept{Recruitment} +\concept{Stock-Recruit} \keyword{datasets} diff --git a/man/YPerchSB1.Rd b/man/YPerchSB1.Rd index ef3d91e..f6275a3 100644 --- a/man/YPerchSB1.Rd +++ b/man/YPerchSB1.Rd @@ -10,7 +10,7 @@ \item{loc}{Location of capture (\code{inner} or \code{outer}).} }} \source{ -Simulated (uniform distribution of values within length bin) from summarized length frequencies in Figure 2 (top) in Diana, J.S. and R. Salz. 1990. Energy storage, growth, and maturation of yellow perch from different locations in Saginaw Bay, Michigan. Transactions of the American Fisheries Society 119:976-984. +Simulated (uniform distribution of values within length bin) from summarized length frequencies in Figure 2 (top) in Diana, J.S. and R. Salz. 1990. Energy storage, growth, and maturation of yellow perch from different locations in Saginaw Bay, Michigan. Transactions of the American Fisheries Society 119:976-984. } \description{ Length measurements for Yellow Perch (\emph{Perca flavescens}) from two locations -- inner and outer bay -- in Saginaw Bay, Lake Michigan. @@ -34,5 +34,7 @@ with(subset(YPerchSB1,loc=="outer"),hist(tl,main="Outer")) par(op) } -\concept{'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} \keyword{datasets} diff --git a/man/YPerchTL.Rd b/man/YPerchTL.Rd index 0e76628..058e221 100644 --- a/man/YPerchTL.Rd +++ b/man/YPerchTL.Rd @@ -37,5 +37,8 @@ head(YPerchTL) plot(weight~length,data=YPerchTL) } -\concept{'Weight-Length' 'Length Frequency' 'Size Structure' PSD} +\concept{Length Frequency} +\concept{PSD} +\concept{Size Structure} +\concept{Weight-Length} \keyword{datasets} diff --git a/man/YTFlounder.Rd b/man/YTFlounder.Rd index 5c259ae..e84f967 100644 --- a/man/YTFlounder.Rd +++ b/man/YTFlounder.Rd @@ -11,7 +11,7 @@ \item{cross}{Ages assigned from cross-sections of otoliths} }} \source{ -From tables in Annex 3 of Walsh, S.J. and J. Burnett. 2002. The Canada-United States yellowtail flounder age reading workshop: 28-30 November2000, St. John's, Newfoundland. North Atlantic Fisheries Organization. Scientific Council Studies 35:1-59. +From tables in Annex 3 of Walsh, S.J. and J. Burnett. 2002. The Canada-United States yellowtail flounder age reading workshop: 28-30 November 2000, St. John's, Newfoundland. North Atlantic Fisheries Organization. Scientific Council Studies 35:1-59. } \description{ Ages of commercially caught Georges Bank Yellowtail Flounder (\emph{Limanda ferruginea}) as determined by scales, whole otoliths, or otolith cross-sections. @@ -37,5 +37,7 @@ plot(whole~cross,data=YTFlounder) par(op) } -\concept{Age Precision Bias 'Age Comparison'} +\concept{Age Bias} +\concept{Age Comparison} +\concept{Age Precision} \keyword{datasets}