Merge pull request #17 from fishR-Core-Team/dev

Merge Dev to main to create v0.4.1 (for CRAN)
fishR-Core-Team · Aug 24, 2023 · 3f00d60 · 3f00d60
2 parents 64c5772 + 963fd78
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diff --git 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="[email protected]",
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
+NULL
diff --git 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.
 #' 
@@ -36,11 +36,12 @@
 #' @docType package
 #' 
 #' @name FSAdata
+#' @aliases FSAdata-package
 #' 
 #' @export
 FSAdataTopics <- c("Length Expansion","Length Conversion",
                    "Age Comparison","Age-Length Key","Back-Calculation",
                    "Weight-Length","Length Frequency","Size Structure",
                    "Capture-Recapture","Depletion","Removal",
                    "Mortality","Growth","Recruitment","Maturity",
-                   "Other")
+                   "Other")
diff --git 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
+NULL
diff --git 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
+NULL
diff --git 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
+NULL
diff --git 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
+NULL
diff --git 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
+NULL
diff --git a/cran-comments/cran-comments_v0_4_1.md 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)
diff --git a/docs/404.html b/docs/404.html