diff --git a/DESCRIPTION b/DESCRIPTION index aed0343..2eb77df 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: FSAdata Title: Data to Support Fish Stock Assessment ('FSA') Package -Version: 0.4.0 -Date: 2022-12-10 +Version: 0.4.1 +Date: 2023-8-23 Description: The datasets to support the Fish Stock Assessment ('FSA') package. Authors@R: person("Derek","Ogle", email="derekogle51@gmail.com", @@ -22,4 +22,4 @@ Suggests: readxl, rmarkdown Encoding: UTF-8 -RoxygenNote: 7.2.2 +RoxygenNote: 7.2.3 diff --git a/NEWS.md b/NEWS.md index 81e4ed1..351f906 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# FSAdata 0.4.1 +* Fixed FSAdata-package `\alias` problem using the "manual approach" (i.e., adding a specific `@aliases FSAdata-package` line to `FSAdata.R`) suggested in an e-mail from Kurt Hornik on 19-Aug-2023. +* Changed all `http://derekogle.com/` URLs to `https://derekogle.com/`. +* Updated `CITATION` file to meet CRAN requirements. + # FSAdata 0.4.0 * Changed my (DHO) email in `DESCRIPTION`. * Added Code of Conduct diff --git a/R/BGHRfish.R b/R/BGHRfish.R index c43f70e..d1c1dab 100644 --- a/R/BGHRfish.R +++ b/R/BGHRfish.R @@ -23,7 +23,7 @@ #' #' @concept Data Manipulation #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source Obtained directly from Ben Neely. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/BGHRfish.csv}{CSV file} #' diff --git a/R/BGHRsample.R b/R/BGHRsample.R index 1441274..296784a 100644 --- a/R/BGHRsample.R +++ b/R/BGHRsample.R @@ -21,7 +21,7 @@ #' #' @concept Data Manipulation #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source Obtained directly from Ben Neely. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/BGHRsample.csv}{CSV file} #' diff --git a/R/BlackDrum2001.R b/R/BlackDrum2001.R index bec2808..0b23979 100644 --- a/R/BlackDrum2001.R +++ b/R/BlackDrum2001.R @@ -30,7 +30,7 @@ #' @concept von Bertalanffy #' @concept Weight-Length #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source Obtained directly from the Virginia Marine Resources Commission via Hank Liao. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/BlackDrum2001.csv}{CSV file} #' diff --git a/R/CCatfishNB.R b/R/CCatfishNB.R index f7955e1..313234f 100644 --- a/R/CCatfishNB.R +++ b/R/CCatfishNB.R @@ -22,7 +22,7 @@ #' @concept Mortality #' @concept Catch Curve #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/CCatfishNB.csv}{CSV file} #' diff --git a/R/CreekChub.R b/R/CreekChub.R index 7859c63..6f9d151 100644 --- a/R/CreekChub.R +++ b/R/CreekChub.R @@ -23,7 +23,7 @@ #' @concept Age-Length Key #' @concept Growth #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/CreekChub.csv}{CSV file} #' @@ -36,4 +36,4 @@ #' xtabs(~age,data=CreekChub) #' plot(len~age,data=CreekChub) #' -NULL \ No newline at end of file +NULL diff --git a/R/FSAdata.R b/R/FSAdata.R index c628e87..26f552f 100644 --- a/R/FSAdata.R +++ b/R/FSAdata.R @@ -2,7 +2,7 @@ #' #' @description This package contains data to support the FSA package. #' -#' @details This package contains additional data files that can be used for common fisheries stock assessment methods described in the \pkg{FSA} package and on the \href{http://derekogle.com/fishR/}{fishR website}. +#' @details This package contains additional data files that can be used for common fisheries stock assessment methods described in the \pkg{FSA} package and on the \href{https://derekogle.com/fishR/}{fishR website}. #' #' The help files for these datasets are embedded with topics that can be searched to find data files that can be analyzed with those topics. For example, use the following commands to find data files for the corresponding topics. #' @@ -36,6 +36,7 @@ #' @docType package #' #' @name FSAdata +#' @aliases FSAdata-package #' #' @export FSAdataTopics <- c("Length Expansion","Length Conversion", @@ -43,4 +44,4 @@ FSAdataTopics <- c("Length Expansion","Length Conversion", "Weight-Length","Length Frequency","Size Structure", "Capture-Recapture","Depletion","Removal", "Mortality","Growth","Recruitment","Maturity", - "Other") \ No newline at end of file + "Other") diff --git a/R/ShadCR.R b/R/ShadCR.R index 1ed22d0..947ceaf 100644 --- a/R/ShadCR.R +++ b/R/ShadCR.R @@ -30,7 +30,7 @@ #' @concept Age Bias #' @concept Age Comparison #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source From McBride, R.S., Hendricks, M.L., and Olney, J.E. 2005. Testing the validity of Cating's (1953) method for age determination of American Shad using scales. Fisheries, 30:10-18. Obtained directly from Rich McBride. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/ShadCR.csv}{CSV file} #' @@ -46,4 +46,4 @@ #' plot(agerC1~agerC2,data=ShadCR) #' plot(agerA1~agerB1,data=ShadCR) #' par(op) -NULL \ No newline at end of file +NULL diff --git a/R/SiscowetMI2004.R b/R/SiscowetMI2004.R index fdfe6c3..5cd10d4 100644 --- a/R/SiscowetMI2004.R +++ b/R/SiscowetMI2004.R @@ -27,7 +27,7 @@ #' @concept Age-Length Key #' @concept Growth #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source Obtained directly from the U.S. Fish and Wildlife Service via Michael Seider. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/SiscowetMI2004.csv}{CSV file} #' @@ -44,4 +44,4 @@ #' plot(len~age,data=SiscowetMI2004,subset=locID=="Little Lake Harbor",main="Little Lake Harbor") #' par(op) #' -NULL \ No newline at end of file +NULL diff --git a/R/SturgeonGB.R b/R/SturgeonGB.R index fd50731..f1fcdf2 100644 --- a/R/SturgeonGB.R +++ b/R/SturgeonGB.R @@ -19,7 +19,7 @@ #' #' @concept Year-class Strength #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. #' #' @source From Pratt, T.C., Gardner, W.M., Pearce, J., Greenwood, S., and Chong, S.C. 2014. Identification of a robust Lake Sturgeon (\emph{Acipenser fulvescens} Rafinesque, 1917) population in Goulais Bay, Lake Superior. Journal of Applied Ichthyology 30:1328-1334. Obtained directly from Tom Pratt. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/SturgeonGB.csv}{CSV file} #' @@ -31,4 +31,4 @@ #' head(SturgeonGB) #' plot(age~year,data=SturgeonGB) #' -NULL \ No newline at end of file +NULL diff --git a/R/WalleyeWad.R b/R/WalleyeWad.R index db70857..06b69c6 100644 --- a/R/WalleyeWad.R +++ b/R/WalleyeWad.R @@ -24,7 +24,7 @@ #' @concept Catch Curve #' @concept Mortality #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/WalleyeWad.csv}{CSV file} #' @@ -37,4 +37,4 @@ #' plot(numF~age,data=WalleyeWad) #' points(numM~age,data=WalleyeWad,pch=19) #' -NULL \ No newline at end of file +NULL diff --git a/R/WalleyeWyrlng.R b/R/WalleyeWyrlng.R index 4663443..dde9f46 100644 --- a/R/WalleyeWyrlng.R +++ b/R/WalleyeWyrlng.R @@ -25,7 +25,7 @@ #' @concept Year-class Strength #' @concept Recruitment #' -#' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book. +#' @note Used in the \href{https://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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSAdata/main/data-raw/WalleyeWyrlng.csv}{CSV file} #' @@ -37,4 +37,4 @@ #' head(WalleyeWyrlng) #' plot(yearlings~yrclass,data=WalleyeWyrlng) #' -NULL \ No newline at end of file +NULL diff --git a/cran-comments/cran-comments_v0_4_1.md b/cran-comments/cran-comments_v0_4_1.md new file mode 100644 index 0000000..ccca699 --- /dev/null +++ b/cran-comments/cran-comments_v0_4_1.md @@ -0,0 +1,10 @@ +* This updates the existing FSAdata package on CRAN by fixing FSAdata-package `\alias` problem with the "manual approach" (i.e., adding a specific `@aliases FSAdata-package` line to `FSAdata.R`) suggested in an e-mail from Kurt Hornik on 19-Aug-2023. + +## Notes +* There may be a note about a change in maintainers that stems from me (Derek Ogle) updating to a new e-mail address. +* 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, development, and old-release. +* GitHub Action (R-CMD-check.yaml) \ No newline at end of file diff --git a/docs/404.html b/docs/404.html index d78e01a..e09e195 100644 --- a/docs/404.html +++ b/docs/404.html @@ -7,10 +7,10 @@ Page not found (404) • FSAdata - - + + - + Contributor Covenant Code of Conduct • FSAdataContributor Covenant Code of Conduct • FSAdata @@ -10,7 +10,7 @@ FSAdata - 0.4.0 + 0.4.1