Closing out v0.8.24

fishR-Core-Team · May 18, 2019 · 1238ab3 · 1238ab3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: FSA
-Version: 0.8.23.9000
-Date: 2019-5-1
+Version: 0.8.24
+Date: 2019-5-17
 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
@@ -1,4 +1,5 @@
-# FSA 0.8.24 ongoing
+# FSA 0.8.24 17-May-19
+* Corrected misues of `\concept` in Rd files per CRAN request.
 
 # FSA 0.8.23 1-May-19
 * Reorganized `testthat` folder as suggested in `testthat` release notes.

diff --git a/R/BluegillJL.R b/R/BluegillJL.R
@@ -22,9 +22,14 @@
 #'    \item Capture History
 #'  }
 #' 
-#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Petersen 'Capture History'
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Mark-Recapture
+#' @concept Capture-Recapture
+#' @concept Petersen
+#' @concept Capture History
 #' 
-#' @source From example 8.1 in Schneider, J.C. 1998.  Lake fish population estimates by mark-and-recapture methods.  Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor.  [Was (is?) from http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf.]
+#' @source From example 8.1 in Schneider, J.C. 1998. Lake fish population estimates by mark-and-recapture methods. Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor. [Was (is?) from http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf.]
 #' 
 #' @seealso Used in \code{\link{mrClosed}} examples.
 #' 

diff --git a/R/BrookTroutTH.R b/R/BrookTroutTH.R
@@ -19,9 +19,10 @@
 #'    \item Chapman-Robson 
 #'  }
 #' 
-#' @concept Mortality 'Catch Curve'
+#' @concept Mortality
+#' @concept Catch Curve
 #' 
-#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999.  [Was (is?) from http://www.fws.gov/midwest/ashland/brook/biochar/biolchar.html.]
+#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999. [Was (is?) from http://www.fws.gov/midwest/ashland/brook/biochar/biolchar.html.]
 #'  
 #' @seealso Used in \code{\link{catchCurve}} and \code{\link{chapmanRobson}} examples.
 #' 

diff --git a/R/ChinookArg.R b/R/ChinookArg.R
@@ -18,9 +18,9 @@
 #'    \item Weight-Length 
 #'  }
 #' 
-#' @concept 'Weight-Length'
+#' @concept Weight-Length
 #' 
-#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara.  2007.  Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications.  Revista Chilena d Historia Natural, 80:81-98.  [Was (is?) from http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf.]
+#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara. 2007. Establishment of Chinook Salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications. Revista Chilena d Historia Natural, 80:81-98. [Was (is?) from http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf.]
 #' 
 #' @seealso Used in \code{\link{lwCompPreds}} examples.
 #' 

diff --git a/R/CodNorwegian.R b/R/CodNorwegian.R
@@ -19,9 +19,10 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #' 
-#' @source From Garrod, D.J. 1967.  Population dynamics of the Arcto-Norwegian cod.  Journal of the Fisheries Research Board of Canada, 24:145-190.
+#' @source From Garrod, D.J. 1967. Population dynamics of the Arcto-Norwegian Cod. Journal of the Fisheries Research Board of Canada, 24:145-190.
 #' 
 #' @seealso Used in \code{\link{srStarts}}, \code{\link{srFuns}}, and \code{\link{nlsTracePlot}} examples.
 #' 

diff --git a/R/CutthroatAL.R b/R/CutthroatAL.R
@@ -30,9 +30,14 @@
 #'    \item Capture History 
 #'  }
 #' 
-#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Jolly-Seber' 'Capture History'
-#' 
-#' @source 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.  [Was (is?) from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf.]
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Mark-Recapture
+#' @concept Capture-Recapture
+#' @concept Jolly-Seber
+#' @concept Capture History
+#' 
+#' @source 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. [Was (is?) from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf.]
 #' 
 #' @note Entered into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}
 #' 

diff --git a/R/Ecoli.R b/R/Ecoli.R
@@ -18,9 +18,10 @@
 #'    \item Other
 #'  }
 #'  
-#' @concept 'Nonlinear Model' Other
+#' @concept Nonlinear Model
+#' @concept Other
 #' 
-#' @source McKendrick, A.G. and M. Kesava Pai. 1911. The Rate of Multiplication of Micro-Organisms: a Mathematical Study. Proceedings of the Royal Society of Edinburgh. 31: 649-655.
+#' @source McKendrick, A.G. and M. Kesava Pai. 1911. The Rate of Multiplication of Micro-Organisms: a Mathematical Study. Proceedings of the Royal Society of Edinburgh. 31:649-655.
 #' 
 #' @seealso Used in \code{\link{bootCase}} and \code{\link{fitPlot}} examples.
 #' 

diff --git a/R/Mirex.R b/R/Mirex.R
@@ -22,9 +22,10 @@
 #'    \item Other
 #'  }
 #'  
-#' @concept 'Linear Models' Other
+#' @concept Linear Models
+#' @concept Other
 #'
-#' @source From (actual data) Makarewicz, J.C., E.Damaske, T.W. Lewis, and M. Merner.  2003.  Trend analysis reveals a recent reduction in mirex concentrations in coho (\emph{Oncorhynchus kisutch}) and chinook (\emph{O. tshawytscha}) salmon from Lake Ontario.  Environmental Science and Technology, 37:1521-1527.
+#' @source From (actual data) Makarewicz, J.C., E.Damaske, T.W. Lewis, and M. Merner. 2003. Trend analysis reveals a recent reduction in mirex concentrations in Coho (\emph{Oncorhynchus kisutch}) and Chinook (\emph{O. tshawytscha}) Salmon from Lake Ontario. Environmental Science and Technology, 37:1521-1527.
 #'
 #' @seealso Used in \code{\link{fitPlot}}, \code{\link{residPlot}}, \code{\link{compSlopes}}, \code{\link{compIntercepts}}, \code{\link{hoCoef}}, and \code{\link{rSquared}} examples.
 #' 

diff --git a/R/PSDlit.R b/R/PSDlit.R
@@ -29,7 +29,8 @@
 #'    \item Proportional stock density
 #'  }
 #'
-#' @concept 'Size Structure' PSD
+#' @concept Size Structure
+#' @concept PSD
 #' 
 #' @section IFAR Chapter: 6-Size Structure.
 #'

diff --git a/R/PikeNY.R b/R/PikeNY.R
@@ -24,7 +24,11 @@
 #'    \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 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).
 #'

diff --git a/R/PikeNYPartial1.R b/R/PikeNYPartial1.R
@@ -26,7 +26,12 @@
 #'    \item Capture History
 #'  }
 #'
-#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Schnabel' 'Capture History'
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Mark-Recapture
+#' @concept Capture-Recapture
+#' @concept Schnabel
+#' @concept Capture History
 #'
 #' @source Summary values taken from 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).
 #'

diff --git a/R/SMBassLS.R b/R/SMBassLS.R
@@ -23,7 +23,12 @@
 #'    \item Catchability
 #'  }
 #'
-#' @concept Abundance 'Population Size' Depletion Leslie DeLury Catchability
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Depletion
+#' @concept Leslie
+#' @concept DeLury
+#' @concept Catchability
 #'
 #' @source From Omand, D.N. 1951. A study of populations of fish based on catch-effort statistics. Journal of Wildlife Management, 15:88-98.
 #'

diff --git a/R/SMBassWB.R b/R/SMBassWB.R
@@ -39,7 +39,10 @@
 #'    \item Back-Calculation
 #'  }
 #'
-#' @concept Growth 'Increment Analysis' 'Weisberg LGM' 'Back-Calculation'
+#' @concept Growth
+#' @concept Increment Analysis
+#' @concept Weisberg LGM
+#' @concept Back-Calculation
 #'
 #' @source Data from the linear growth modeling software distributed in support of Weisberg, S. 1993. Using hard-part increment data to estimate age and environmental effects. Canadian Journal of Fisheries and Aquatic Sciences 50:1229-1237.
 #'

diff --git a/R/SpotVA1.R b/R/SpotVA1.R
@@ -20,7 +20,8 @@
 #'    \item von Bertalanffy
 #'  }
 #'
-#' @concept Growth 'von Bertalanffy'
+#' @concept Growth
+#' @concept von Bertalanffy
 #'
 #' @seealso Used in \code{\link{vbFuns}}, \code{\link{vbStarts}}, and \code{\link{nlsTracePlot}} examples. Also see \code{\link[FSAdata]{SpotVA2}} in \pkg{FSAdata} for related data.
 #'

diff --git a/R/WR79.R b/R/WR79.R
@@ -20,7 +20,7 @@
 #'    \item Age-Length Key
 #'  }
 #'
-#' @concept 'Age-Length Key'
+#' @concept Age-Length Key
 #'
 #' @source Simulated from Table 2A in Westerheim, S.J. and W.E. Ricker. 1979. Bias in using age-length key to estimate age-frequency distributions. Journal of the Fisheries Research Board of Canada. 35:184-189.
 #'

diff --git a/R/WSlit.R b/R/WSlit.R
@@ -32,15 +32,17 @@
 #'    \item Condition
 #'  }
 #'
-#' @concept Condition 'Relative Weight' 'Standard Weight'
+#' @concept Condition
+#' @concept Relative Weight
+#' @concept Standard Weight
 #'
 #' @seealso See \code{\link{wsVal}} and \code{\link{wrAdd}} for related functionality.
 #'
 #' @section IFAR Chapter: 8-Condition.
 #'
-#' @references Ogle, D.H.  2016.  \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}.  Chapman & Hall/CRC, Boca Raton, FL.
+#' @references Ogle, D.H. 2016. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #'
-#' @source Most of these equations can be found in Neumann, R.M., C.S. Guy, and D.W. Willis.  2012.  Length, Weight, and Associated Indices.  Chapter 14 in Zale, A.V., D.L. Parrish, and T.M. Sutton, editors.  Fisheries Techniques.  American Fisheries Society, Bethesda, MD.
+#' @source Most of these equations can be found in Neumann, R.M., C.S. Guy, and D.W. Willis. 2012. Length, Weight, and Associated Indices. Chapter 14 in Zale, A.V., D.L. Parrish, and T.M. Sutton, editors. Fisheries Techniques. American Fisheries Society, Bethesda, MD.
 #' 
 #' Some species were not in Neumann et al (2012) and are noted as such in the \code{comments} variable.
 #'

diff --git a/R/WhitefishLC.R b/R/WhitefishLC.R
@@ -30,7 +30,10 @@
 #'    \item Age Comparisons
 #'  }
 #'
-#' @concept Age Precision Bias 'Ageing Error' 'Age Comparisons'
+#' @concept Age Precision
+#' @concept Age Bias
+#' @concept Ageing Error
+#' @concept Age Comparisons
 #'
 #' @source Data from Herbst, S.J. and J.E. Marsden.  2011.  Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain.  Journal of Great Lakes Research.  37:386-389.  Contributed by Seth Herbst.  \bold{Do not use for other than educational purposes without permission from the author.}  [Was (is?) from http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf.]
 #'

diff --git a/cran-comments/cran-comments-v0_8_24.md b/cran-comments/cran-comments-v0_8_24.md
@@ -0,0 +1,9 @@
+* This updates the existing FSA 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 "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/man/BluegillJL.Rd b/man/BluegillJL.Rd
diff --git a/man/BrookTroutTH.Rd b/man/BrookTroutTH.Rd
diff --git a/man/ChinookArg.Rd b/man/ChinookArg.Rd
diff --git a/man/CodNorwegian.Rd b/man/CodNorwegian.Rd
diff --git a/man/CutthroatAL.Rd b/man/CutthroatAL.Rd
diff --git a/man/Ecoli.Rd b/man/Ecoli.Rd
diff --git a/man/Mirex.Rd b/man/Mirex.Rd
diff --git a/man/PSDlit.Rd b/man/PSDlit.Rd