Closing v0.9.3 -- Attempted fix of CRAN notes and testing errors

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FSA
-Version: 0.9.2
-Date: 2022-2-12
+Version: 0.9.3
+Date: 2022-2-15
 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/>.
@@ -12,8 +12,8 @@ Authors@R: c(
     person("Alexis", "Dinno", email="alexis.dinno@pdx.edu", role="aut",
            comment="Provided base functionality of dunnTest()")
     )
-URL: https://github.com/droglenc/FSA
-BugReports: https://github.com/droglenc/FSA/issues
+URL: https://github.com/fishR-Core-Team/FSA
+BugReports: https://github.com/fishR-Core-Team/FSA/issues
 License: GPL (>= 2)
 LazyData: true
 Depends:
@@ -25,14 +25,13 @@ Imports:
     tools,
     utils,
     car,
-    dplyr,
     dunn.test,
     lmtest,
     plotrix,
-    sciplot,
     withr
 Suggests:
     DescTools,
+    dplyr,
     fishmethods,
     FSAdata,
     knitr,

R/FSA.R

@@ -4,11 +4,11 @@
 #'
 #' @details Functions from this package can be used to perform a variety of basic fisheries stock assessment methods. Detailed descriptions for most functions are available in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analysis with R} book (Ogle 2016). Vignettes for the boxed examples in the \dQuote{Analysis and Interpretation of Freshwater Fisheries Data} book can be viewed with \code{fishR("AIFFD")}.
 #' 
-#' Questions, comments, or suggestions should be given on the \href{https://github.com/droglenc/FSA/issues/}{GitHub FSA Issues page}.
+#' Questions, comments, or suggestions should be given on the \href{https://github.com/fishR-Core-Team/FSA/issues/}{GitHub FSA Issues page}.
 #' 
 #' Packages with related functionality by the same author are
 #' \itemize{
-#'   \item The \href{https://github.com/droglenc/FSAdata/}{FSAdata package} contains additional data sets.
+#'   \item The \href{https://github.com/fishR-Core-Team/FSAdata/}{FSAdata package} contains additional data sets.
 #'   \item The \href{https://github.com/droglenc/FSAsim/}{FSAsim package} simulation routines for various fisheries methods.
 #'   \item The \href{https://github.com/droglenc/FSAWs/}{FSAWs package} contains functions for developing and validating standard weight equations.
 #' }

R/FSAUtils.R

@@ -770,7 +770,7 @@ repeatedRows2Keep <- function(df,cols2use=NULL,cols2ignore=NULL,
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso See \code{\link[sciplot]{se}} in \pkg{sciplot} for similar functionality.
+#' @seealso See \code{se} in \pkg{sciplot} for similar functionality.
 #'
 #' @keywords manip
 #'

README.md

@@ -2,8 +2,8 @@
 [![DOI](https://zenodo.org/badge/18348400.svg)](https://zenodo.org/badge/latestdoi/18348400)
 [![CRAN Version](http://www.r-pkg.org/badges/version/FSA)](http://www.r-pkg.org/pkg/FSA)
 [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
-[![R-CMD-check](https://github.com/droglenc/FSA/workflows/R-CMD-check/badge.svg)](https://github.com/droglenc/FSA/actions)
-[![Codecov test coverage](https://codecov.io/gh/droglenc/FSA/branch/master/graph/badge.svg)](https://codecov.io/gh/droglenc/FSA?branch=master)
+[![R-CMD-check](https://github.com/fishR-Core-Team/FSA/workflows/R-CMD-check/badge.svg)](https://github.com/fishR-Core-Team/FSA/actions)
+[![Codecov test coverage](https://codecov.io/gh/fishR-Core-Team/FSA/branch/master/graph/badge.svg)](https://codecov.io/gh/droglenc/FSA?branch=master)
 [![CRAN RStudio mirror downloads rate](http://cranlogs.r-pkg.org/badges/FSA)
 ![CRAN RSTudio mirror downloads total](http://cranlogs.r-pkg.org/badges/grand-total/FSA)](http://www.r-pkg.org/pkg/FSA)
 [![Rdoc](http://www.rdocumentation.org/badges/version/FSA)](http://www.rdocumentation.org/packages/FSA)
@@ -23,19 +23,19 @@ The most recent development version (on GitHub) may be installed with
 
 ```r
 if (!require('remotes')) install.packages('remotes'); require('remotes')
-remotes::install_github('droglenc/FSA')
+remotes::install_github('fishR-Core-Team/FSA')
 ```
 
 You may need to have R Tools installed on your system to install the development version from GitHub. See the instructions for ([R Tools for Windows](https://cran.r-project.org/bin/windows/Rtools/) or [R Tools for Mac OS X](https://cran.r-project.org/bin/macosx/tools/)).
 
 
 ### Questions / Comments / Problems or Contributions
-Report questions, comments, or bug reports on the [issues page](https://github.com/droglenc/FSA/issues).
+Report questions, comments, or bug reports on the [issues page](https://github.com/fishR-Core-Team/FSA/issues).
 
 We are always looking for others to contribute to **FSA**. Please feel free to make a pull request via GitHub or to contact the maintainers.
 
 Please adhere to the [Code of Conduct](http://derekogle.com/FSA/CODE_OF_CONDUCT.html).
 
 
 ### Note about **FSA** and *Introduction to Fisheries Analysis with R* book
-Versions of **FSA** beginning with v0.9.0 may no longer work as shown in the IFAR book. Many functions have not changed from when the book was published, but some have. Thus, you will need to install an **FSA** version before v0.9.0 to be assured that functions work as described in the IFAR book.
+Versions of **FSA** beginning with v0.9.0 may no longer work as shown in the IFAR book. Many functions have not changed from when the book was published, but some have. Thus, you will need to install an **FSA** version before v0.9.0 to be assured that functions work as described in the IFAR book.

cran-comments/cran-comments-v0_9_3.md

@@ -0,0 +1,10 @@
+* This updates the existing FSA package on CRAN, fixing notes and "additional issues" (as brought to my attention by Prof. Ripley on 15-Feb-22).
+
+## Notes
+* There may be a note about "fishR" being misspelled in the description. This is not a misspelling.
+
+## Testing Environments
+* My Windows machine.
+* Win Builder -- old-release, release, and development.
+* Mac Builder
+* GitHub Action (R-CMD-check.yaml)