diff --git a/DESCRIPTION b/DESCRIPTION index 1aec7623..3296e30d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FSA -Version: 0.8.32.9000 -Date: 2021-6-1 +Version: 0.9.0 +Date: 2021-6-8 Title: Simple Fisheries Stock Assessment Methods Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website . diff --git a/NEWS.md b/NEWS.md index a18b9763..eb49abf8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,28 +1,29 @@ -# FSA 0.9.0 ongoing +# FSA 0.9.0 8-Jun-21 +* Make note of the several **removed** (now defunct) and **deprecated** (soon to be defunct) functions listed below. * Added Jason Doll as an `AUThor`. * Moved `plyr` from Imports to Suggests. * `alkPlot()`: Modified. Removed use of `chooseColors()` (see below). * `binCI()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). -* `bootCase()`: REMOVED. Users can use `car::Boot()`, which partially addresses [#65](https://github.com/droglenc/FSA/issues/65). - * `plot.boot()`: REMOVED. Conflicted with `boot::plot.boot()` which caused an error with CRAN. Same functionality is available with `pairs($t)`. +* `bootCase()`: **REMOVED**. Users can use `car::Boot()`, which partially addresses [#65](https://github.com/droglenc/FSA/issues/65). + * `plot.boot()`: **REMOVED**. Conflicted with `boot::plot.boot()` which caused an error with CRAN. Same functionality is available with `pairs($t)`. * `catchCurve()`: Modified. Removed hard-coding of `ylim=` for `plot.catchCurve()` (this addresses [#70](https://github.com/droglenc/FSA/issues/70) ... Thanks to Brendan Runde). Added `round.est=` so that the user can control the decimals on mortality estimate values. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). * `chapmanRobson()`: Modified. Removed hard-coding of `ylim=` for `plot.chapmanRobson()`. Added `round.est=` so that the user can control the decimals on mortality and survival estimate values. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). -* `chooseColors()`: REMOVED. This was an exported function that should have been internal. Regardless, where it was used has been removed and the user is now allowed to provide their own vector of colors. See `iCheckMultColors()`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). -* `compIntercepts()`: REMOVED (to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). -* `compSlopes()`: REMOVED (to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `chooseColors()`: **REMOVED**. This was an exported function that should have been internal. Regardless, where it was used has been removed and the user is now allowed to provide their own vector of colors. See `iCheckMultColors()`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `compIntercepts()`: **REMOVED** (to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `compSlopes()`: **REMOVED** (to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). * `depletion()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). -* `filterD()`: DEPRECATED (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). -* `fitPlot()`: DEPRECATED (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). Prior to that removed use of `chooseColors()` (see above). -* `diags()`: REMOVED (moved to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). -* `hoCoef()`: REMOVED (moved to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `filterD()`: **DEPRECATED** (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). +* `fitPlot()`: **DEPRECATED** (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). Prior to that removed use of `chooseColors()` (see above). +* `diags()`: **REMOVED** (moved to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `hoCoef()`: **REMOVED** (moved to `FSAmisc`). Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). * `hyperCI()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). * `iCheckConfLevel()`: Added (internal to address [#66](https://github.com/droglenc/FSA/issues/66)). * `iCheckMultColors()`: Added (internal). Part of removing `chooseColors()` and `paletteChoices()`. -* `iRichColors()`: REMOVED (as part of removing `chooseColors()`). -* `mapvalues()`: REMOVED. Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `iRichColors()`: **REMOVED** (as part of removing `chooseColors()`). +* `mapvalues()`: **REMOVED**. Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). * `mrClosed()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). * `mrOpen()`: Modified. Added a warning for when r==0, which causes the SE of M and thus N to be `Infinity` (this addresses [#69](https://github.com/droglenc/FSA/issues/69)). Added a similar warning for when R==0 (but not the last time period). Added tests for the warning messages. Changed one use of `apply()` to `rowSums()` for ease of reading. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). -* `paletteChoices()`: REMOVED. See `chooseColors()` above. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `paletteChoices()`: **REMOVED**. See `chooseColors()` above. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). * `poiCI()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). * `psdAdd()`: Modified. Changed a `levels()` in `iPSDlitCheck()` to `unique()` because `species` is no longer a factor due to updating `PSDlit` (i.e., rdata file changed with new `read.csv()`). * `psdCalc()`: Modified. Added a catch for when "tibble"s are sent in `data=` (addresses [#75](https://github.com/droglenc/FSA/issues/75)). Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). @@ -30,8 +31,8 @@ * `PSDlit`: Modified. Added length categories for Shoal Bass and Pallid Sturgeon. Added Striped Bass (Hybrid) and Striped Bass x White Bass; though these are the same as the existing Palmetto Bass. Added "source"s for each entry. * `psdVal()`: Modified. Changed a `levels()` in `iPSDlitCheck()` and `iListSpecies()` to `unique()` because `species` is no longer a factor due to updating `PSDlit` (i.e., rdata file changed with new `read.csv()`). Added a `showJustSource=` argument that will show the source info (if `TRUE`) or not (if `FALSE`; default), which partially addresses [#76](https://github.com/droglenc/FSA/issues/76). * `removal()`: Modified. Added check and then warning if non-whole numbers are in `catch=` (addresses [#60](https://github.com/droglenc/FSA/issues/60)). Also modified checks of data integrity to be more robust (e.g., if a character vector is sent). Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)). -* `residPlot()`: DEPRECATED (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). Prior to that removed use of `chooseColors()` (see above). -* `Subset()`: REMOVED. Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). +* `residPlot()`: **DEPRECATED** (partially addresses [#65](https://github.com/droglenc/FSA/issues/65)). Prior to that removed use of `chooseColors()` (see above). +* `Subset()`: **REMOVED**. Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65). * `wrAdd()`: Modified. Changed a `levels()` in `iwsLitCheck()` to `unique()` because `species` is no longer a factor due to updating `WSlit` (i.e., rdata file changed with new `read.csv()`). * `WSlit`: Modified. Addresses [#68](https://github.com/droglenc/FSA/issues/68). * Corrected capitalization of "Cavedano Chub", "European Chub", "Lake Herring" (metric), and "Pursak Chub". diff --git a/cran-comments/cran-comments-v0_9_0.md b/cran-comments/cran-comments-v0_9_0.md new file mode 100644 index 00000000..c3333ca5 --- /dev/null +++ b/cran-comments/cran-comments-v0_9_0.md @@ -0,0 +1,9 @@ +* This updates the existing FSA package on CRAN. + +## Notes +* There may be a note about "fishR" being misspelled in the description. This is not a misspelling. +* On [CRAN](https://cran.r-project.org/web/checks/check_results_FSA.html), there is a note in the previous version about a missing `RMark` package for the "r-patched-solaris-x86" flavor. Again (as with previous versions), I am not sure what to do about this note. + +## Testing Environments +* My Windows machine. +* Win Builder -- old-release, release, and development. diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index aca5b842..3dcb67cf 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -79,7 +79,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/authors.html b/docs/authors.html index dbdf79c1..df06c679 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -79,7 +79,7 @@ FSA - 0.8.32.9000 + 0.9.0 @@ -122,12 +122,12 @@

Citation

Source: inst/CITATION -

Ogle, D.H., P. Wheeler, and A. Dinno. 2021. FSA: Fisheries Stock Analysis. R package version 0.8.32.9000, https://github.com/droglenc/FSA.

+

Ogle, D.H., P. Wheeler, and A. Dinno. 2021. FSA: Fisheries Stock Analysis. R package version 0.9.0, https://github.com/droglenc/FSA.

@Manual{,
   title = {FSA: Fisheries Stock Analysis},
   author = {Derek H. Ogle and Powell Wheeler and Alexis Dinno},
   year = {2021},
-  note = {R package version 0.8.32.9000},
+  note = {R package version 0.9.0},
   url = {https://github.com/droglenc/FSA},
 }
diff --git a/docs/index.html b/docs/index.html index 18124bb5..35a66366 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a3a7d21a..a6c5c154 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.11.4 pkgdown: 1.6.1 pkgdown_sha: ~ articles: {} -last_built: 2021-06-01T21:47Z +last_built: 2021-06-09T14:46Z urls: reference: http://derekogle.com/FSA/reference article: http://derekogle.com/FSA/articles diff --git a/docs/reference/BluegillJL.html b/docs/reference/BluegillJL.html index 9aaca305..7b6f8e84 100644 --- a/docs/reference/BluegillJL.html +++ b/docs/reference/BluegillJL.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/BrookTroutTH.html b/docs/reference/BrookTroutTH.html index b4acf33d..c1801408 100644 --- a/docs/reference/BrookTroutTH.html +++ b/docs/reference/BrookTroutTH.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html index 2fc2c295..93e83fa3 100644 --- a/docs/reference/ChinookArg.html +++ b/docs/reference/ChinookArg.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html index 8db8f9c8..78c0188f 100644 --- a/docs/reference/CodNorwegian.html +++ b/docs/reference/CodNorwegian.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html index e04a4901..15b733e5 100644 --- a/docs/reference/CutthroatAL.html +++ b/docs/reference/CutthroatAL.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html index 6eb73cd2..f3207409 100644 --- a/docs/reference/Ecoli.html +++ b/docs/reference/Ecoli.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html index dff22914..ae701c42 100644 --- a/docs/reference/FSA-internals.html +++ b/docs/reference/FSA-internals.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html index 251fc44a..2d0e04b5 100644 --- a/docs/reference/FSA.html +++ b/docs/reference/FSA.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html index 67cbeb55..9060bfea 100644 --- a/docs/reference/Mirex.html +++ b/docs/reference/Mirex.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html index 0bc5d22a..0c09ff06 100644 --- a/docs/reference/PSDlit.html +++ b/docs/reference/PSDlit.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html index 4b2f0edb..a8176e7f 100644 --- a/docs/reference/PikeNY.html +++ b/docs/reference/PikeNY.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html index 03a66741..f2d053de 100644 --- a/docs/reference/PikeNYPartial1.html +++ b/docs/reference/PikeNYPartial1.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html index ade527ae..1d35b608 100644 --- a/docs/reference/SMBassLS.html +++ b/docs/reference/SMBassLS.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html index aaf8a14d..565ef18d 100644 --- a/docs/reference/SMBassWB.html +++ b/docs/reference/SMBassWB.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html index cb4135e8..6e2389e7 100644 --- a/docs/reference/Schnute.html +++ b/docs/reference/Schnute.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html index 7fa82e50..90f9c48f 100644 --- a/docs/reference/SpotVA1.html +++ b/docs/reference/SpotVA1.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html index 69f95b0d..19dc0b8a 100644 --- a/docs/reference/Summarize.html +++ b/docs/reference/Summarize.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html index 4a6b77f7..3a30acec 100644 --- a/docs/reference/WR79.html +++ b/docs/reference/WR79.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html index 9191df28..108a60af 100644 --- a/docs/reference/WSlit.html +++ b/docs/reference/WSlit.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html index 9f4cfd1f..619e157e 100644 --- a/docs/reference/WhitefishLC.html +++ b/docs/reference/WhitefishLC.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html index 29680b48..98b1df63 100644 --- a/docs/reference/addZeroCatch.html +++ b/docs/reference/addZeroCatch.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html index dc788301..ba0b066e 100644 --- a/docs/reference/ageBias.html +++ b/docs/reference/ageBias.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html index 9c0ee65a..d2c23601 100644 --- a/docs/reference/agePrecision.html +++ b/docs/reference/agePrecision.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html index 2fbaaebb..cfe10933 100644 --- a/docs/reference/alkAgeDist.html +++ b/docs/reference/alkAgeDist.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html index dd05ed44..fa406e4d 100644 --- a/docs/reference/alkIndivAge.html +++ b/docs/reference/alkIndivAge.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/alkMeanVar.html b/docs/reference/alkMeanVar.html index 75fbcc82..c65a5bb8 100644 --- a/docs/reference/alkMeanVar.html +++ b/docs/reference/alkMeanVar.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/alkPlot.html b/docs/reference/alkPlot.html index 4b0370b9..adfc10b9 100644 --- a/docs/reference/alkPlot.html +++ b/docs/reference/alkPlot.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/binCI.html b/docs/reference/binCI.html index 3cdb4e02..b462fdb9 100644 --- a/docs/reference/binCI.html +++ b/docs/reference/binCI.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/capHistConvert.html b/docs/reference/capHistConvert.html index 153bd4c4..87dee295 100644 --- a/docs/reference/capHistConvert.html +++ b/docs/reference/capHistConvert.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/capHistSum.html b/docs/reference/capHistSum.html index 124a7fbb..c147fa39 100644 --- a/docs/reference/capHistSum.html +++ b/docs/reference/capHistSum.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/catchCurve.html b/docs/reference/catchCurve.html index a9a749b9..f86d91c3 100644 --- a/docs/reference/catchCurve.html +++ b/docs/reference/catchCurve.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/chapmanRobson.html b/docs/reference/chapmanRobson.html index e2235459..2a2ac179 100644 --- a/docs/reference/chapmanRobson.html +++ b/docs/reference/chapmanRobson.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/col2rgbt.html b/docs/reference/col2rgbt.html index 004538b6..c2e9f26a 100644 --- a/docs/reference/col2rgbt.html +++ b/docs/reference/col2rgbt.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/depletion.html b/docs/reference/depletion.html index 0c04aefe..3bc29f08 100644 --- a/docs/reference/depletion.html +++ b/docs/reference/depletion.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/dunnTest.html b/docs/reference/dunnTest.html index d3814288..b096a83b 100644 --- a/docs/reference/dunnTest.html +++ b/docs/reference/dunnTest.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/expandCounts.html b/docs/reference/expandCounts.html index ec9e78bc..9ea45d12 100644 --- a/docs/reference/expandCounts.html +++ b/docs/reference/expandCounts.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/expandLenFreq.html b/docs/reference/expandLenFreq.html index d70e3109..455004ca 100644 --- a/docs/reference/expandLenFreq.html +++ b/docs/reference/expandLenFreq.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/extraTests.html b/docs/reference/extraTests.html index 3a168960..6271f01a 100644 --- a/docs/reference/extraTests.html +++ b/docs/reference/extraTests.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/fact2num.html b/docs/reference/fact2num.html index e693e643..669ceb00 100644 --- a/docs/reference/fact2num.html +++ b/docs/reference/fact2num.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/fishR.html b/docs/reference/fishR.html index c517a661..f0447eb7 100644 --- a/docs/reference/fishR.html +++ b/docs/reference/fishR.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/fitPlot.html b/docs/reference/fitPlot.html index c1319026..17d7a0a6 100644 --- a/docs/reference/fitPlot.html +++ b/docs/reference/fitPlot.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/fsaNews.html b/docs/reference/fsaNews.html index 94a2154d..4fea641e 100644 --- a/docs/reference/fsaNews.html +++ b/docs/reference/fsaNews.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 6f034fa3..75659385 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 diff --git a/docs/reference/growthModels.html b/docs/reference/growthModels.html index a3a09825..471ca0b1 100644 --- a/docs/reference/growthModels.html +++ b/docs/reference/growthModels.html @@ -80,7 +80,7 @@ FSA - 0.8.32.9000 + 0.9.0 @@ -265,232 +265,174 @@

Examp 
###########################################################
 ## Simple Examples -- Von B
 ( vb1 <- vbFuns() )
-
#> function (t, Linf, K = NULL, t0 = NULL) 
-#> {
-#>     if (length(Linf) == 3) {
-#>         K <- Linf[[2]]
-#>         t0 <- Linf[[3]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * (1 - exp(-K * (t - t0)))
-#> }
-#> <bytecode: 0x00000000061d4800>
-#> <environment: 0x000000001ca69a38>
ages <- 0:20
+
#> function(t,Linf,K=NULL,t0=NULL) {
+#>   if (length(Linf)==3) { K <- Linf[[2]]
+#>                          t0 <- Linf[[3]]
+#>                          Linf <- Linf[[1]] }
+#>   Linf*(1-exp(-K*(t-t0)))
+#>   }
+#> <bytecode: 0x000000001eb6d9b8>
+#> <environment: 0x000000001f64bb58>
ages <- 0:20
 plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19)
 
( vb2 <- vbFuns("Francis") )
-
#> function (t, L1, L2 = NULL, L3 = NULL, t1, t3 = NULL) 
-#> {
-#>     if (length(L1) == 3) {
-#>         L2 <- L1[[2]]
-#>         L3 <- L1[[3]]
-#>         L1 <- L1[[1]]
-#>     }
-#>     if (length(t1) == 2) {
-#>         t3 <- t1[[2]]
-#>         t1 <- t1[[1]]
-#>     }
-#>     r <- (L3 - L2)/(L2 - L1)
-#>     L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - 
-#>         r^2))
-#> }
-#> <bytecode: 0x000000001ce4bdf0>
-#> <environment: 0x00000000061a2de8>
plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
+
#> function(t,L1,L2=NULL,L3=NULL,t1,t3=NULL) {
+#>   if (length(L1)==3) { L2 <- L1[[2]]; L3 <- L1[[3]]; L1 <- L1[[1]] }
+#>   if (length(t1)==2) { t3 <- t1[[2]]; t1 <- t1[[1]] }
+#>   r <- (L3-L2)/(L2-L1)
+#>   L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2))
+#>   }
+#> <bytecode: 0x000000001e796f88>
+#> <environment: 0x000000001c6d4438>
plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
 
( vb2c <- vbFuns("Francis",simple=TRUE) )   # compare to vb2
-
#> function (t, L1, L2, L3, t1, t3) 
-#> {
-#>     r <- (L3 - L2)/(L2 - L1)
-#>     L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - 
-#>         r^2))
-#> }
-#> <bytecode: 0x000000001ce49d10>
-#> <environment: 0x000000001c6defd0>

+
#> function(t,L1,L2,L3,t1,t3) {
+#>     r <- (L3-L2)/(L2-L1)
+#>     L1+(L3-L1)*((1-r^(2*((t-t1)/(t3-t1))))/(1-r^2))
+#>   }
+#> <bytecode: 0x000000001e8bcda8>
+#> <environment: 0x000000001ceed520>

 ## Simple Examples -- Gompertz
 ( gomp1 <- GompertzFuns() )
-
#> function (t, Linf, gi = NULL, ti = NULL) 
-#> {
-#>     if (length(Linf) == 3) {
-#>         gi <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * exp(-exp(-gi * (t - ti)))
-#> }
-#> <bytecode: 0x000000001ceb0790>
-#> <environment: 0x000000001cf32450>
plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
+
#> function(t,Linf,gi=NULL,ti=NULL) {
+#>     if (length(Linf)==3) { gi <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     Linf <- Linf[[1]] }
+#>     Linf*exp(-exp(-gi*(t-ti)))
+#>   }
+#> <bytecode: 0x000000001cc7c828>
+#> <environment: 0x000000001cb3c060>
plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
 
( gomp2 <- GompertzFuns("Ricker2") )
-
#> function (t, L0, a = NULL, gi = NULL) 
-#> {
-#>     if (length(L0) == 3) {
-#>         a <- L0[[2]]
-#>         gi <- L0[[3]]
-#>         L0 <- L0[[1]]
-#>     }
-#>     L0 * exp(a * (1 - exp(-gi * t)))
-#> }
-#> <bytecode: 0x000000001ceb52f8>
-#> <environment: 0x000000001ccfb248>
plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
+
#> function(t,L0,a=NULL,gi=NULL) {
+#>     if (length(L0)==3) { a <- L0[[2]]
+#>     gi <- L0[[3]]
+#>     L0 <- L0[[1]] }
+#>     L0*exp(a*(1-exp(-gi*t)))
+#>   }
+#> <bytecode: 0x000000001cc5dab8>
+#> <environment: 0x000000001c917b00>
plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
 
( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) )   # compare to gomp2
-
#> function (t, L0, a, gi) 
-#> {
-#>     L0 * exp(a * (1 - exp(-gi * t)))
-#> }
-#> <bytecode: 0x000000001ceb6398>
-#> <environment: 0x000000001c9f4338>
( gompT <- GompertzFuns("Troynikov1"))
-
#> function (Lm, dt, Linf, gi = NULL) 
-#> {
-#>     if (length(Linf) == 2) {
-#>         gi <- Linf[2]
-#>         Linf <- Linf[1]
-#>     }
-#>     Linf * ((Lm/Linf)^exp(-gi * dt)) - Lm
-#> }
-#> <bytecode: 0x000000001cf21880>
-#> <environment: 0x000000001c88ad88>

+
#> function(t,L0,a,gi) {
+#>     L0*exp(a*(1-exp(-gi*t)))
+#>   }
+#> <bytecode: 0x000000001cc254c8>
+#> <environment: 0x000000001c6f7440>
( gompT <- GompertzFuns("Troynikov1"))
+
#> function(Lm,dt,Linf,gi=NULL) {
+#>     if (length(Linf)==2) { gi <- Linf[2]
+#>     Linf <- Linf[1] }
+#>     Linf*((Lm/Linf)^exp(-gi*dt))-Lm
+#>   }
+#> <bytecode: 0x000000001cbb0d38>
+#> <environment: 0x000000001c606308>

 ## Simple Examples -- Richards
 ( rich1 <- RichardsFuns() )
-
#> function (t, Linf, k = NULL, a = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 4) {
-#>         k <- Linf[[2]]
-#>         a <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * (1 - a * exp(-k * t))^b
-#> }
-#> <bytecode: 0x000000001c6ad1e0>
-#> <environment: 0x000000001c670588>
plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,a=NULL,b=NULL) {
+#>     if (length(Linf)==4) { k <- Linf[[2]]
+#>     a <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Linf*(1-a*exp(-k*t))^b
+#>   }
+#> <bytecode: 0x000000001c1ff7a0>
+#> <environment: 0x000000001bf9ef38>
plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
 
( rich2 <- RichardsFuns(2) )
-
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 4) {
-#>         k <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * (1 - (1/b) * exp(-k * (t - ti)))^b
-#> }
-#> <bytecode: 0x000000001c69c4a8>
-#> <environment: 0x000000001c270148>
plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
+#>     if (length(Linf)==4) { k <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Linf*(1-(1/b)*exp(-k*(t-ti)))^b
+#>   }
+#> <bytecode: 0x000000001c1cfb28>
+#> <environment: 0x000000001b49bb30>
plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
 
( rich3 <- RichardsFuns(3) )
-
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 4) {
-#>         k <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf/((1 + b * exp(-k * (t - ti)))^(1/b))
-#> }
-#> <bytecode: 0x000000001c69a9b0>
-#> <environment: 0x000000001bdb90a8>
plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
+#>     if (length(Linf)==4) { k <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Linf/((1+b*exp(-k*(t-ti)))^(1/b))
+#>   }
+#> <bytecode: 0x000000001c0dc800>
+#> <environment: 0x000000001b30ad00>
plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
 
( rich4 <- RichardsFuns(4) )
-
#> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 4) {
-#>         k <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - b))
-#> }
-#> <bytecode: 0x000000001c6947f0>
-#> <environment: 0x000000001b7b2b98>
plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,ti=NULL,b=NULL) {
+#>     if (length(Linf)==4) { k <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Linf*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
+#>   }
+#> <bytecode: 0x000000001c0773a8>
+#> <environment: 0x0000000009ae8090>
plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
 
lines(rich4(ages,Linf=800,k=0.5,ti=3,b=1.5)~ages,type="b",pch=19,col="blue")
 
( rich5 <- RichardsFuns(5) )
-
#> function (t, Linf, k = NULL, L0 = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 4) {
-#>         k <- Linf[[2]]
-#>         L0 <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf * (1 + (((L0/Linf)^(1 - b)) - 1) * exp(-k * t))^(1/(1 - 
-#>         b))
-#> }
-#> <bytecode: 0x000000001c67c3c8>
-#> <environment: 0x000000001b177580>
plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,L0=NULL,b=NULL) {
+#>     if (length(Linf)==4) { k <- Linf[[2]]
+#>     L0 <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Linf*(1+(((L0/Linf)^(1-b))-1)*exp(-k*t))^(1/(1-b))
+#>   }
+#> <bytecode: 0x000000001c0416b8>
+#> <environment: 0x0000000007e376e0>
plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
 
( rich6 <- RichardsFuns(6) )
-
#> function (t, Linf, k = NULL, ti = NULL, Lninf = NULL, b = NULL) 
-#> {
-#>     if (length(Linf) == 5) {
-#>         k <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         Lninf <- Linf[[3]]
-#>         b <- Linf[[4]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Lninf + (Linf - Lninf) * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - 
-#>         b))
-#> }
-#> <bytecode: 0x000000001c672b48>
-#> <environment: 0x000000000a554a68>
plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
+
#> function(t,Linf,k=NULL,ti=NULL,Lninf=NULL,b=NULL) {
+#>     if (length(Linf)==5) { k <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     Lninf <- Linf[[3]]
+#>     b <- Linf[[4]]
+#>     Linf <- Linf[[1]] }
+#>     Lninf+(Linf-Lninf)*(1+(b-1)*exp(-k*(t-ti)))^(1/(1-b))
+#>   }
+#> <bytecode: 0x000000001bfe3918>
+#> <environment: 0x0000000009182490>
plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
 
( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
-
#> function (t, Linf, k, ti, b) 
-#> {
-#>     Linf * (1 - (1/b) * exp(-k * (t - ti)))^b
-#> }
-#> <bytecode: 0x000000001c69a080>
-#> <environment: 0x00000000097ede00>

+
#> function(t,Linf,k,ti,b) {
+#>     Linf*(1-(1/b)*exp(-k*(t-ti)))^b
+#>   }
+#> <bytecode: 0x000000001c0f3428>
+#> <environment: 0x00000000061322e8>

 ## Simple Examples -- Logistic
 ( log1 <- logisticFuns() )
-
#> function (t, Linf, gninf = NULL, ti = NULL) 
-#> {
-#>     if (length(Linf) == 3) {
-#>         gninf <- Linf[[2]]
-#>         ti <- Linf[[3]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf/(1 + exp(-gninf * (t - ti)))
-#> }
-#> <bytecode: 0x0000000007f43110>
-#> <environment: 0x000000001ca98bb0>
plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
+
#> function(t,Linf,gninf=NULL,ti=NULL) {
+#>     if (length(Linf)==3) { gninf <- Linf[[2]]
+#>     ti <- Linf[[3]]
+#>     Linf <- Linf[[1]] }
+#>     Linf/(1+exp(-gninf*(t-ti)))
+#>   }
+#> <bytecode: 0x0000000021e33728>
+#> <environment: 0x0000000021c21e98>
plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
 
( log2 <- logisticFuns("CJ2") )
-
#> function (t, Linf, gninf = NULL, a = NULL) 
-#> {
-#>     if (length(Linf) == 3) {
-#>         gninf <- Linf[[2]]
-#>         a <- Linf[[3]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     Linf/(1 + a * exp(-gninf * t))
-#> }
-#> <bytecode: 0x0000000007f44568>
-#> <environment: 0x0000000022339dc8>
plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
+
#> function(t,Linf,gninf=NULL,a=NULL) {
+#>     if (length(Linf)==3) { gninf <- Linf[[2]]
+#>     a <- Linf[[3]]
+#>     Linf <- Linf[[1]] }
+#>     Linf/(1+a*exp(-gninf*t))
+#>   }
+#> <bytecode: 0x0000000021e0d798>
+#> <environment: 0x0000000006a86c60>
plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
 
( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
-
#> function (t, Linf, gninf, a) 
-#> {
-#>     Linf/(1 + a * exp(-gninf * t))
-#> }
-#> <bytecode: 0x0000000007f3ded8>
-#> <environment: 0x00000000215ffaa0>
( log3 <- logisticFuns("Karkach") )
-
#> function (t, Linf, L0 = NULL, gninf = NULL) 
-#> {
-#>     if (length(Linf) == 3) {
-#>         L0 <- Linf[[2]]
-#>         gninf <- Linf[[3]]
-#>         Linf <- Linf[[1]]
-#>     }
-#>     L0 * Linf/(L0 + (Linf - L0) * exp(-gninf * t))
-#> }
-#> <bytecode: 0x0000000007f32390>
-#> <environment: 0x00000000228b9988>
plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
+
#> function(t,Linf,gninf,a) {
+#>     Linf/(1+a*exp(-gninf*t))
+#>   }
+#> <bytecode: 0x0000000021d80f78>
+#> <environment: 0x00000000242952c0>
( log3 <- logisticFuns("Karkach") )
+
#> function(t,Linf,L0=NULL,gninf=NULL) {
+#>     if (length(Linf)==3) { L0 <- Linf[[2]]
+#>     gninf <- Linf[[3]]
+#>     Linf <- Linf[[1]] }
+#>     L0*Linf/(L0+(Linf-L0)*exp(-gninf*t))
+#>   }
+#> <bytecode: 0x0000000021cf83b0>
+#> <environment: 0x0000000021bbefc0>
plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
 
( log4 <- logisticFuns("Haddon") )
-
#> function (Lm, dLmax, L50 = NULL, L95 = NULL) 
-#> {
-#>     if (length(dLmax) == 3) {
-#>         L50 <- dLmax[2]
-#>         L95 <- dLmax[3]
-#>         dLmax <- dLmax[1]
-#>     }
-#>     dLmax/(1 + exp(log(19) * ((Lm - L50)/(L95 - L50))))
-#> }
-#> <bytecode: 0x00000000075e59f0>
-#> <environment: 0x00000000220bdd40>

+
#> function(Lm,dLmax,L50=NULL,L95=NULL) {
+#>     if (length(dLmax)==3) { L50 <- dLmax[2]
+#>     L95 <- dLmax[3]
+#>     dLmax <- dLmax[1] }
+#>     dLmax/(1+exp(log(19)*((Lm-L50)/(L95-L50))))
+#>   }
+#> <bytecode: 0x0000000021c98318>
+#> <environment: 0x0000000021c30ec0>

 
 ###########################################################
 ## Examples of fitting
diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html
index 79dd7fd9..5890e410 100644
--- a/docs/reference/headtail.html
+++ b/docs/reference/headtail.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     

 
diff --git a/docs/reference/hist.formula.html b/docs/reference/hist.formula.html
index dd58437f..b37ee6f2 100644
--- a/docs/reference/hist.formula.html
+++ b/docs/reference/hist.formula.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/histFromSum.html b/docs/reference/histFromSum.html
index c6274d17..831416c9 100644
--- a/docs/reference/histFromSum.html
+++ b/docs/reference/histFromSum.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/hyperCI.html b/docs/reference/hyperCI.html
index 400f09ee..70df32a8 100644
--- a/docs/reference/hyperCI.html
+++ b/docs/reference/hyperCI.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d67bbe1c..ab79a82e 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -79,7 +79,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/knitUtil.html b/docs/reference/knitUtil.html
index 92a11812..4399aed0 100644
--- a/docs/reference/knitUtil.html
+++ b/docs/reference/knitUtil.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/ksTest.html b/docs/reference/ksTest.html
index 9a5a0108..ae22c799 100644
--- a/docs/reference/ksTest.html
+++ b/docs/reference/ksTest.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/lagratio.html b/docs/reference/lagratio.html
index fd9a697a..fc8e1346 100644
--- a/docs/reference/lagratio.html
+++ b/docs/reference/lagratio.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/lencat.html b/docs/reference/lencat.html
index ffb7b441..2a7075d3 100644
--- a/docs/reference/lencat.html
+++ b/docs/reference/lencat.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/logbtcf.html b/docs/reference/logbtcf.html
index adf02bd0..e286098c 100644
--- a/docs/reference/logbtcf.html
+++ b/docs/reference/logbtcf.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/lwCompPreds.html b/docs/reference/lwCompPreds.html
index 31259849..edccd4dd 100644
--- a/docs/reference/lwCompPreds.html
+++ b/docs/reference/lwCompPreds.html
@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/metaM.html b/docs/reference/metaM.html
index fce38e70..bdb8d91a 100644
--- a/docs/reference/metaM.html
+++ b/docs/reference/metaM.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/mrClosed.html b/docs/reference/mrClosed.html
index 19856726..b9ba5006 100644
--- a/docs/reference/mrClosed.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/mrOpen.html b/docs/reference/mrOpen.html
index 2cd51aa8..9b95f22a 100644
--- a/docs/reference/mrOpen.html
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@@ -80,7 +80,7 @@
       
       
         FSA
-        0.8.32.9000
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diff --git a/docs/reference/nlsBoot.html b/docs/reference/nlsBoot.html
index 1ad8a647..c1dd6b96 100644
--- a/docs/reference/nlsBoot.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/nlsTracePlot.html b/docs/reference/nlsTracePlot.html
index 55bb4139..336e7cf8 100644
--- a/docs/reference/nlsTracePlot.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/perc.html b/docs/reference/perc.html
index 0805befd..0c4c27ca 100644
--- a/docs/reference/perc.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/plotAB.html b/docs/reference/plotAB.html
index 17026b26..ca4146c0 100644
--- a/docs/reference/plotAB.html
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         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/poiCI.html b/docs/reference/poiCI.html
index 05a81cdb..28bc102d 100644
--- a/docs/reference/poiCI.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/psdAdd.html b/docs/reference/psdAdd.html
index a0e9926c..2ab4936a 100644
--- a/docs/reference/psdAdd.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/psdCI.html b/docs/reference/psdCI.html
index bcfc0b1c..3e0c5690 100644
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         FSA
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diff --git a/docs/reference/psdCalc.html b/docs/reference/psdCalc.html
index 868aebd6..dfbebb80 100644
--- a/docs/reference/psdCalc.html
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         FSA
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diff --git a/docs/reference/psdPlot.html b/docs/reference/psdPlot.html
index a5a30dda..10b0d94a 100644
--- a/docs/reference/psdPlot.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/psdVal.html b/docs/reference/psdVal.html
index 3d864afc..2e9a471d 100644
--- a/docs/reference/psdVal.html
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         FSA
-        0.8.32.9000
+        0.9.0
       
     
 
diff --git a/docs/reference/rSquared.html b/docs/reference/rSquared.html
index efb57bc6..da441c72 100644
--- a/docs/reference/rSquared.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/rcumsum.html b/docs/reference/rcumsum.html
index 46626d95..84a13105 100644
--- a/docs/reference/rcumsum.html
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/removal.html b/docs/reference/removal.html
index 5cf7b3f0..f12fed7a 100644
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         FSA
-        0.8.32.9000
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diff --git a/docs/reference/residPlot.html b/docs/reference/residPlot.html
index 8ec3a493..06d831d3 100644
--- a/docs/reference/residPlot.html
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         FSA
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diff --git a/docs/reference/se.html b/docs/reference/se.html
index 2cda14d1..abb64adb 100644
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         FSA
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diff --git a/docs/reference/srStarts.html b/docs/reference/srStarts.html
index 00f9371f..ca6d1c57 100644
--- a/docs/reference/srStarts.html
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         FSA
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diff --git a/docs/reference/sumTable.html b/docs/reference/sumTable.html
index 6e3f037e..bc39283c 100644
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         FSA
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diff --git a/docs/reference/tictactoe.html b/docs/reference/tictactoe.html
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         FSA
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diff --git a/docs/reference/validn.html b/docs/reference/validn.html
index f2b578e2..4debc275 100644
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         FSA
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diff --git a/docs/reference/vbStarts.html b/docs/reference/vbStarts.html
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         FSA
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diff --git a/docs/reference/wrAdd.html b/docs/reference/wrAdd.html
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         FSA
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diff --git a/docs/reference/wsVal.html b/docs/reference/wsVal.html
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         FSA
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