Closing out v0.9.0

fishR-Core-Team · Jun 9, 2021 · 910d4a5 · 910d4a5
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diff --git 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 <http://derekogle.com/fishR/>.

diff --git a/NEWS.md b/NEWS.md
@@ -1,37 +1,38 @@
-# 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(<boot object>$t)`.
+* `bootCase()`: **REMOVED**. Users can use `car::Boot()`, which partially addresses [#65](https://github.com/droglenc/FSA/issues/65).
+  * `plot.boot()`: **REMOVED**. Conflicted with `boot::plot.boot()` which caused an error with CRAN. Same functionality is available with `pairs(<boot object>$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)).
 * `psdCI()`: Modified. Changed to use `iCheckConfLevel()` (which addresses [#66](https://github.com/droglenc/FSA/issues/66)).
 * `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
@@ -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
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git 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
diff --git a/docs/reference/BrookTroutTH.html b/docs/reference/BrookTroutTH.html
diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html
diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html
diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html
diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html
diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html
diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html
diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html
diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html
diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html
diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html
diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html
diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html
diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html
diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html
diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html
diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html
diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html
diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html