version 1.0.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: track2KBA
 Title: Identifying Important Areas from Animal Tracking Data
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
-    person("Martin", "Beal", email = "martinbeal88@gmail.com", role = "cre", comment = c(ORCID = "0000-0003-1654-1410")),
+    person("Martin", "Beal", email = "martinbeal88@gmail.com", role = c("aut","cre"), comment = c(ORCID = "0000-0003-1654-1410")),
     person("Steffen", "Oppel", email = "steffen.oppel@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-1654-1410")),
     person("Maria", "Dias", email = "maria.dias@birdlife.org", role = "aut", comment = c(ORCID = "0000-0002-7281-4391")),
     person("Mark", "Miller", email = "mark.gr.miller@gmail.com", role = "ctb"),
@@ -17,23 +17,23 @@ Description: Functions for preparing and analyzing animal tracking data,
     the population level and therefore of conservation interest. Areas identified 
     using this package may be checked against global or regionally-defined criteria,
     such as those set by the Key Biodiversity Area program. The method
-    published herein is an optimized and updated version of the method described in Lascelles
-    et al. 2016 <doi:10.1111/ddi.12411>.
+    published herein is described in full in Beal et al. 2021 <doi:10.1111/2041-210X.13713>.
 Depends: R (>= 2.10)
 License: LGPL-3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1
 BugReports: https://github.com/BirdLifeInternational/track2kba/issues
-Suggests: adehabitatLT, doParallel, knitr, maps, Matching, move,
-        parallel, rmarkdown, tinytest, rgeos, rgdal (>= 1.5-0)
+Suggests: adehabitatLT, doParallel, knitr, parallel, rmarkdown,
+        tinytest
 VignetteBuilder: knitr
 Imports: adehabitatHR, dplyr, foreach, geosphere, ggplot2, lubridate,
-        magrittr, maptools, methods, purrr, raster, rlang, sf (>=
-        0.7-4), sp (>= 1.4-1), tidyr
+        magrittr, maps, maptools, Matching, methods, move, purrr,
+        raster, rgdal (>= 1.5-0), rgeos, rlang, sf (>= 0.7-4), sp (>=
+        1.4-1), tidyr
 NeedsCompilation: no
-Packaged: 2021-08-07 15:19:36 UTC; Martim Bill
-Author: Martin Beal [cre] (<https://orcid.org/0000-0003-1654-1410>),
+Packaged: 2022-04-26 14:58:38 UTC; Martim Bill
+Author: Martin Beal [aut, cre] (<https://orcid.org/0000-0003-1654-1410>),
   Steffen Oppel [aut] (<https://orcid.org/0000-0003-1654-1410>),
   Maria Dias [aut] (<https://orcid.org/0000-0002-7281-4391>),
   Mark Miller [ctb],
@@ -44,4 +44,4 @@ Author: Martin Beal [cre] (<https://orcid.org/0000-0003-1654-1410>),
   Ben Lascelles [ctb]
 Maintainer: Martin Beal <martinbeal88@gmail.com>
 Repository: CRAN
-Date/Publication: 2021-08-07 23:10:01 UTC
+Date/Publication: 2022-04-26 16:00:02 UTC

MD5

@@ -1,27 +1,28 @@
-858b9e434a7acfb65d8ba87cb3000833 *DESCRIPTION
-e17809e2754787d9009a2b5b3372ffbb *NAMESPACE
-5e0cab40fbb59a2cb6706e035694695c *NEWS.md
+18e4bbaf9b46e65fecc7473861e4f7bb *DESCRIPTION
+93e3b9916b77a848ae93ebc3c11542bd *NAMESPACE
+83e568f7597ce837e83b2d83dc87eb4e *NEWS.md
 5afb06434961b0be419fbe9735f7b859 *R/data.R
-ab012c486074aba8d04797c85309d4c8 *R/estSpaceUse.r
-e29ac7667e9c1c76479e4dea81ba8892 *R/findScale.R
+6103697a1209ac99d60ebf5e8443cfb0 *R/estSpaceUse.r
+ec39b7061af0d398a8c72e55933e8a43 *R/findScale.R
 9b572462a47ddcf629dcefc35a23f337 *R/findSite.R
 634f7dfde76b4a888af6058b5787ea46 *R/formatFields.R
-e8f2b82858933e8f67a71c0c3abf271e *R/indEffectTest.R
-23ba043ce4205dc3887cfa2825065d1d *R/mapKDE.R
-ac3297c0ddfe8866153d16ebe13bad4a *R/mapSite.R
+f02218e46dce91e91031424a90ba5730 *R/indEffectTest.R
+ab8463d85fd6da48fe7dcf472b9c3936 *R/mapKDE.R
+4c5697fee9ec3f9fe8ef63b982d6ef7e *R/mapSite.R
 df17739628efa1556aeb7870d9f3b08d *R/mapTrips.R
-2d3d8cb67283eafc41ac9bec26500bd4 *R/move2KBA.r
+7fea76ab1d809a59775d86ef93da0fc5 *R/move2KBA.r
 c7bfad1743d262db2f2754ae3e6468a5 *R/projectTracks.R
-1ce1db6e154414a1511540d5855c4eb8 *R/repAssess.r
+02cd2377fe5221bfc8978e1d12273f27 *R/repAssess.r
 05e2ee19cab1a56b2c136d5376a3bee5 *R/tripSplit.r
-27498d41c37adff06f4c6a15f25c9fbd *R/tripSummary.r
-976c4ab79dc5cabf9046e920a2c7e152 *README.md
-4602b9b161e6b7fc2f788a283f713486 *build/vignette.rds
+39c6d854a52914f0d575f9bdff5b3074 *R/tripSummary.r
+c0c01deda993b653a950260bfc824ec9 *README.md
+b5ce74432b1e2cfb81bd9e24075ebcb4 *build/vignette.rds
 0ec0d3e2720c25cf1f2928f2c4771bbc *data/KDE_example.rda
 6aa6e7e87ffbef6b951ff18d494cd295 *data/boobies.rda
-621677aa1dd7f1e23280e18e9dc99611 *inst/doc/track2kba_workflow.R
-2c607f035bcd97147ae4a55df5c78ed4 *inst/doc/track2kba_workflow.Rmd
-42c4efa857473900a370cce8ef2a42fa *inst/doc/track2kba_workflow.html
+31384b8205170d4954fb5c09392d600f *inst/CITATION
+89ee74ee7a77e77fa2245026eb15b91c *inst/doc/track2kba_workflow.R
+aa690e44704a2fb3c36a3dce4d88730b *inst/doc/track2kba_workflow.Rmd
+92ba28cf12e7e1d69307391b7a8871ce *inst/doc/track2kba_workflow.html
 6456da43b40fbc0072f215c4c59dd47f *inst/tinytest/boobies_testdata.csv
 3a641a98f789ced53371662e8fb83095 *inst/tinytest/movebank_testdata.csv
 b372cfe93ecfed0c206c9b2c97bd88b1 *inst/tinytest/test_estSpaceUse.R
@@ -43,14 +44,14 @@ c0e9741aa986d789d90538626267ae51 *man/estSpaceUse.Rd
 c2d3fd4403b3fd2888df52181ff194db *man/figures/KBA_sp_plot.png
 ec999a2da8b41eb76aedaafba10fee5c *man/figures/estSpaceUse-1.png
 c44395cf03534ac7a36d15954ca1f96b *man/figures/findScale-1.png
-a0089c638427bf6e500fbf540dd9c7a3 *man/figures/logo.png
+52df063d44f5bca0f54ff3211953ce11 *man/figures/logo.png
 5eaaa0d51bca3db52c7a69117bd21f55 *man/figures/plot_KBA_sf.png
 bf7a5d90d020baf91712aba59960d8f8 *man/figures/repAssess-1.png
 96c8090440db043fc6ec40e557b19e69 *man/figures/tripSplit-chunk-3-1.png
 b454598cf37e2eada7bd9d3da1920220 *man/findScale.Rd
 c51a0dee672082acef6d752f3797b77d *man/findSite.Rd
 bd34091a71c6da3da369a49d264535c2 *man/formatFields.Rd
-8ef1cfbd51cd57f94fa47443b536aa19 *man/indEffectTest.Rd
+c144bb694e1693f4641dd5355cd1e593 *man/indEffectTest.Rd
 b7347953469348e572ec48fdca79d171 *man/mapKDE.Rd
 7821abc97cc970fd04b5964408574dc5 *man/mapSite.Rd
 dcc9da9d8d4d9f974a9d623a6229c3d2 *man/mapTrips.Rd
@@ -65,5 +66,5 @@ ec999a2da8b41eb76aedaafba10fee5c *vignettes/estSpaceUse-1.png
 c44395cf03534ac7a36d15954ca1f96b *vignettes/findScale-1.png
 5eaaa0d51bca3db52c7a69117bd21f55 *vignettes/plot_KBA_sf.png
 bf7a5d90d020baf91712aba59960d8f8 *vignettes/repAssess-1.png
-2c607f035bcd97147ae4a55df5c78ed4 *vignettes/track2kba_workflow.Rmd
+aa690e44704a2fb3c36a3dce4d88730b *vignettes/track2kba_workflow.Rmd
 96c8090440db043fc6ec40e557b19e69 *vignettes/tripSplit-chunk-3-1.png

NAMESPACE

@@ -13,8 +13,10 @@ export(projectTracks)
 export(repAssess)
 export(tripSplit)
 export(tripSummary)
-import(dplyr)
+import(rgdal)
+import(rgeos)
 import(sp)
+importFrom(Matching,ks.boot)
 importFrom(adehabitatHR,estUDm2spixdf)
 importFrom(adehabitatHR,getverticeshr)
 importFrom(adehabitatHR,kernelUD)
@@ -24,6 +26,7 @@ importFrom(dplyr,filter)
 importFrom(dplyr,first)
 importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
+importFrom(dplyr,lag)
 importFrom(dplyr,last)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -63,8 +66,13 @@ importFrom(graphics,points)
 importFrom(graphics,polygon)
 importFrom(graphics,text)
 importFrom(magrittr,"%>%")
+importFrom(maps,map)
 importFrom(maptools,spRbind)
 importFrom(methods,as)
+importFrom(move,getMovebank)
+importFrom(move,getMovebankData)
+importFrom(move,getMovebankID)
+importFrom(move,movebankLogin)
 importFrom(rlang,.data)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)

NEWS.md

@@ -1,3 +1,5 @@
+# Version 1.0.1.9000
+
 # Version 1.0.1
 
 Fixing CRAN checks.

R/estSpaceUse.r

@@ -68,6 +68,7 @@
 #'KDE <- estSpaceUse(tracks, scale=10, levelUD = 50)
 #'
 #' @export
+#' @import rgdal
 #' @importFrom stats na.omit quantile sd var
 #' @importFrom methods as
 #' @importFrom adehabitatHR getverticeshr kernelUD

R/findScale.R

@@ -124,7 +124,7 @@
 #'  h_vals <- findScale(tracks_prj, sumTrips = sumTrips, scaleARS = FALSE)
 #'
 #' @export
-#' @import dplyr
+#' @importFrom dplyr lag
 #' @import sp
 #' @importFrom stats setNames
 

R/indEffectTest.R

@@ -108,21 +108,17 @@
 #' 
 #' @export
 #' @importFrom ggplot2 aes geom_boxplot
+#' @importFrom Matching ks.boot
 #' @import sp
 
 indEffectTest <- function(
   tracks, tripID, groupVar, plot=TRUE, 
   method = c("HR", "PHR", "VI", "BA", "UDOI", "HD"), 
   conditional = TRUE, levelUD=50, scale, grid = 500, iterations = 1000) {
 
-  if (!requireNamespace("Matching", quietly = TRUE)) {
-    stop("Package \"Matching\" needed for  function to work. Please install.",
-      call. = FALSE)  }
-
   if (!(tripID) %in% names(tracks)) stop("Within-group field does not exist")
   if (!groupVar %in% names(tracks)) stop("Group field does not exist")
 
-
   tracks@data <- tracks@data %>% 
     dplyr::select({{groupVar}}, {{tripID}}, .data$Latitude, .data$Longitude)
 

R/mapKDE.R

@@ -40,19 +40,18 @@
 #'mapKDE(KDE)
 #'
 #' @export
+#' @importFrom maps map
 #' @importFrom sf st_bbox
 #' @importFrom ggplot2 geom_sf coord_sf borders ggplot theme element_rect
 #' @importFrom ggplot2 theme element_rect ylab xlab
 #' @importFrom graphics image
 
 mapKDE <- function(KDE, colony=NULL, show=TRUE) {
   ### Polygon data ###
-  if (class(KDE)[1] == "sf") {
-    if (!requireNamespace("maps", quietly = TRUE)) { stop(
-    "Packages \"maps\"is needed. Please install it.", call. = FALSE)
-    }
+  if (inherits(KDE, "sf")) {
+
     coordsets <- sf::st_bbox(KDE)
-    UDPLOT <- ggplot(KDE) + geom_sf(data = KDE, aes(col = id), fill = NA) +
+    UDPLOT <- ggplot(KDE) + geom_sf(data = KDE, aes(col = .data$id), fill = NA) +
       coord_sf(
         xlim = c(coordsets$xmin, coordsets$xmax),
         ylim = c(coordsets$ymin, coordsets$ymax), expand = TRUE) +

R/mapSite.R

@@ -39,16 +39,15 @@
 #' mapSite(pot_site)
 #' 
 #' @export
+#' @import rgeos
 #' @importFrom sf st_bbox
 #' @importFrom ggplot2 geom_sf coord_sf borders ggplot theme element_rect
 #' @importFrom ggplot2 ylab xlab scale_fill_continuous scale_colour_continuous
 #' @importFrom ggplot2 geom_point guides aes element_line
 
 mapSite <- function(Site, colony=NULL, show=TRUE) {
-  if (class(Site)[1] == "sf") {
-    if (!requireNamespace("maps", quietly = TRUE)) { stop(
-      "Packages \"maps\"is needed. Please install it.", call. = FALSE)
-    }
+  if (inherits(Site, "sf")) {
+
     coordsets <- sf::st_bbox(Site)
 
     csf <- ggplot2::coord_sf(
@@ -102,7 +101,7 @@ mapSite <- function(Site, colony=NULL, show=TRUE) {
       print(denseplot)
     } else { return(denseplot) }
 
-  } else if (class(Site) == "SpatialPixelsDataFrame") {
+  } else if (inherits(Site,"SpatialPixelsDataFrame")) {
     plot(Site[Site$N_IND > 0, ])
   } else { stop("'Site' is not an sf nor SpatialPixelsDataFrame object") }
 

R/move2KBA.r

@@ -36,13 +36,11 @@
 #'}
 #'
 #' @export
+#' @importFrom move movebankLogin getMovebankID getMovebankData getMovebank
 #' @importFrom magrittr %>%
 #' @importFrom dplyr select rename arrange
 
 move2KBA <- function(movebankID=NULL, user=NULL, password=NULL, filename=NULL) {
-  if (!requireNamespace("move", quietly = TRUE)) {
-    stop("Package \"move\" needed. Please install.", call. = FALSE)
-  }
 
   ### IMPORT FROM MOVEBANK IF CREDENTIALS SUPPLIED ----------------------------
   if (any(!is.null(movebankID), !is.null(user), !is.null(password))) {

R/repAssess.r

@@ -131,13 +131,13 @@ repAssess <- function(
   if (is.null(KDE)) {
     stop("No Utilization Distributions supplied to KDE argument.
       See track2KBA::estSpaceUse()")
-  } else if (class(KDE) == "estUDm") {
+  } else if (inherits(KDE, "estUDm")) {
     KDEraster <- raster::stack(lapply(KDE, function(x) {
       raster::raster(as(x, "SpatialPixelsDataFrame"), values = TRUE)
       }))
-  } else if (class(KDE) == "SpatialPixelsDataFrame") {
+  } else if (inherits(KDE, "SpatialPixelsDataFrame")) {
     KDEraster <- raster::stack(KDE)
-  } else if (class(KDE) == "RasterStack") {
+  } else if (inherits(KDE, "RasterStack")) {
     KDEraster <- KDE
   }
 

R/tripSummary.r

@@ -71,7 +71,7 @@ tripSummary <- function(trips, colony=NULL, nests=FALSE, extraDist=FALSE)
   ### helper function to calculate distance unless no previous location -------
   poss_dist <- purrr::possibly(geosphere::distm, otherwise = NA)
 
-  if(class(trips) == "SpatialPointsDataFrame") {
+  if(inherits(trips, "SpatialPointsDataFrame")) {
     trips <- as.data.frame(trips@data)
   } else { trips <- trips }
 

README.md

@@ -7,16 +7,16 @@
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/BirdLifeInternational/track2kba/workflows/R-CMD-check/badge.svg)](https://github.com/BirdLifeInternational/track2kba/actions)
 [![Coverage
-Status](https://codecov.io/gh/BirdLifeInternational/track2kba/branch/master/graph/badge.svg)](https://codecov.io/gh/BirdLifeInternational/track2kba/)
-[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/track2KBA)](https://cran.r-project.org/package=track2KBA)
+Status](https://codecov.io/gh/BirdLifeInternational/track2kba/branch/master/graph/badge.svg)](https://app.codecov.io/gh/BirdLifeInternational/track2kba)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/track2KBA)](https://cran.r-project.org/package=track2KBA)
+[![CRAN_Status_Badge](https://cranlogs.r-pkg.org/badges/track2KBA)](https://cran.r-project.org/package=track2KBA)
 <!-- badges: end -->
 
 This package is comprised of functions that facilitate the
 identification of areas of importance for biodiversity, such as Key
 Biodiversity Areas (KBAs), based on individual tracking data. For
 further detail concerning the method itself, please refer to this
-[paper](https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12411) by
-Lacelles et al. (2016).
+[paper](https://doi.org/10.1111/2041-210X.13713) by Beal et al. (2021).
 
 Key functions include utilities to estimate individual core use areas,
 the level of representativeness of the tracked sample, and overlay
@@ -28,7 +28,13 @@ data set, and splitting and summarizing individual foraging trips.
 
 ------------------------------------------------------------------------
 
-You can download the development version from
+You can download the stable version from CRAN with:
+
+``` r
+install.packages("track2KBA")
+```
+
+Or you can download the development version from
 [GitHub](https://github.com/) with:
 
 ``` r
@@ -55,7 +61,7 @@ fields, and an ID field (i.e. individual animal, track, or trip).
 library(track2KBA) # load package
 
 data(boobies)
-# ?boobies  # for some background on the available data set 
+# ?boobies  # for some background info on the example data set 
 
 dataGroup <- formatFields(
   dataGroup = boobies, 
@@ -308,7 +314,7 @@ This map shows the number or proportion of individual animals in the
 population overlapping in space. The red lines indicate the ‘potential
 site’; that is, the areas used by a significant proportion of the local
 population, given the representativeness of the sample of tracked
-individuals. In this case, since representativeness is &gt;90%, any area
+individuals. In this case, since representativeness is \>90%, any area
 used by 10% or more of the population is considered important (see
 Lascelles et al. 2016 for details). The orange dot is the colony
 location and the black line is the coastline.
@@ -349,29 +355,41 @@ around the breeding island.
 
 ------------------------------------------------------------------------
 
-### Reference
+### Package reference
 
 If you use any functions in this package for your work, please use the
 following citation:
 
-Martin Beal, Steffen Oppel, Jonathan Handley, Lizzie Pearmain, Virginia
-Morera-Pujol, Mark Miller, Phil Taylor, Ben Lascelles, & Maria Dias.
-(2020, May 13). *BirdLifeInternational/track2kba: First Release (Version
-0.5.0). Zenodo. <https://doi.org/10.5281/zenodo.3823902>*
+Beal, M., Oppel, S., Handley, J., Pearmain, E. J., Morera-Pujol, V.,
+Carneiro, A. P. B., Davies, T. E., Phillips, R. A., Taylor, P. R.,
+Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla,
+A., Staniland, I., Boyd, C., Catry, P., & Dias, M. P. (2021). track2KBA:
+An R package for identifying important sites for biodiversity from
+tracking data. Methods in Ecology and Evolution, n/a(n/a).
+<https://doi.org/10.1111/2041-210X.13713>
 
-### Example data
+### Example data reference
 
 Oppel, S., Beard, A., Fox, D., Mackley, E., Leat, E., Henry, L.,
 Clingham, E., Fowler, N., Sim, J., Sommerfeld, J., Weber, N., Weber, S.,
 Bolton, M., 2015. *Foraging distribution of a tropical seabird supports
 Ashmole’s hypothesis of population regulation. Behav Ecol Sociobiol 69,
 915–926. <https://doi.org/10.1007/s00265-015-1903-3>*
 
-Thanks to Annalea Beard for kindly sharing these example data for use in
-the package.
+### Other references
+
+Lascelles, B. G., Taylor, P. R., Miller, M. G. R., Dias, M. P., Oppel,
+S., Torres, L., Hedd, A., Corre, M. L., Phillips, R. A., Shaffer, S. A.,
+Weimerskirch, H., & Small, C. (2016). Applying global criteria to
+tracking data to define important areas for marine conservation.
+Diversity and Distributions, 22(4), 422–431.
+<https://doi.org/10.1111/ddi.12411>
 
 ### Acknowledgements
 
+Thanks to Annalea Beard for kindly sharing these example data for use in
+the package.
+
 This project has received funding from the European Union’s Horizon 2020
 research and innovation programme under the Marie Skłodowska-Curie grant
 agreement No 766417.