Merge pull request #103 from fishR-Core-Team/dev

Moving dev to master in preparation for releasing v0.9.4 to CRAN

Author: droglenc

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 

.github/workflows/test-coverage.yaml

@@ -1,48 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,14 +1,18 @@
 Package: FSA
-Version: 0.9.3.9000
-Date: 2022-2-15
+Version: 0.9.4
+Date: 2023-2-1
 Title: Simple Fisheries Stock Assessment Methods
 Description: A variety of simple fish stock assessment methods.
 Authors@R: c(
-    person("Derek", "Ogle", email="derek@derekogle.com", role=c("aut","cre"),
+    person(c("Derek","H."), "Ogle", email="DerekOgle51@gmail.com",
+           role=c("aut","cre"),
            comment=c(ORCID="0000-0002-0370-9299")),
-    person("Jason", "Doll", email="jason.doll@fmarion.edu", role=c("aut")),
-    person("Powell", "Wheeler", email="powell.wheeler@gmail.com", role="aut"),
-    person("Alexis", "Dinno", email="alexis.dinno@pdx.edu", role="aut",
+    person(c("Jason","C."), "Doll", email="jason.doll@fmarion.edu",
+           role=c("aut")),
+    person(c("A.","Powell"), "Wheeler", email="powell.wheeler@gmail.com",
+           role="aut"),
+    person("Alexis", "Dinno", email="alexis.dinno@pdx.edu",
+           role="aut",
            comment="Provided base functionality of dunnTest()")
     )
 URL: https://fishr-core-team.github.io/FSA/
@@ -46,4 +50,4 @@ Suggests:
     tibble,
     covr
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

NEWS.md

@@ -29,7 +29,7 @@
 #' @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.] \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/BluegillJL.csv}{CSV file}
 #' 
 #' @seealso Used in \code{\link{mrClosed}} examples.
 #' 

R/BluegillJL.R

@@ -22,7 +22,7 @@
 #' @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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/BrookTroutTH.csv}{CSV file}
 #'  
 #' @seealso Used in \code{\link{catchCurve}} and \code{\link{chapmanRobson}} examples.
 #' 

R/BrookTroutTH.R

@@ -20,7 +20,7 @@
 #' 
 #' @return A #x2 matrix that contains the lower and upper confidence interval bounds as columns and, if \code{verbose=TRUE} \code{x}, \code{n}, and \code{x/n} .
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}, though this is largely based on \code{binom.exact}, \code{binom.wilson}, and \code{binom.approx} from the old epitools package.
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}, though this is largely based on \code{binom.exact}, \code{binom.wilson}, and \code{binom.approx} from the old epitools package.
 #'
 #' @seealso See \code{\link{binom.test}}; \code{binconf} in \pkg{Hmisc}; and functions in \pkg{binom}.
 #'
@@ -138,7 +138,7 @@ binCI <- function(x,n,conf.level=0.95,type=c("wilson","exact","asymptotic"),
 #'
 #' @return A #x2 matrix that contains the lower and upper confidence interval bounds as columns and, if \code{verbose=TRUE} \code{x}.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}, though this is largely based on \code{pois.exact}, \code{pois.daly}, \code{pois.byar}, and \code{pois.approx} from the old epitools package.
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}, though this is largely based on \code{pois.exact}, \code{pois.daly}, \code{pois.byar}, and \code{pois.approx} from the old epitools package.
 #'
 #' @keywords htest
 #'
@@ -270,7 +270,7 @@ poiCI <- function(x,conf.level=0.95,type=c("exact","daly","byar","asymptotic"),
 #'
 #' @return A 1x2 matrix that contains the lower and upper confidence interval bounds.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #'
 #' @keywords htest
 #'

R/CIDists.R

@@ -20,7 +20,7 @@
 #' 
 #' @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.] \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/ChinookArg.csv}{CSV file}
 #' 
 #' @seealso Used in \code{\link{lwCompPreds}} examples.
 #' 

R/ChinookArg.R

@@ -22,7 +22,7 @@
 #' @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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/CodNorwegian.csv}{CSV file}
 #' 
 #' @seealso Used in \code{\link{srStarts}}, \code{\link{srFuns}}, and \code{\link{nlsTracePlot}} examples.
 #' 

R/CodNorwegian.R

@@ -37,7 +37,7 @@
 #' @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.]
+#' @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.] \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/CutthroatAL.csv}{CSV file}
 #' 
 #' @note Entered into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}
 #' 

R/CutthroatAL.R

@@ -21,7 +21,7 @@
 #' @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. \href{https://raw.githubusercontent.com/fishR-Core-Team/FSA/master/data-raw/Ecoli.csv}{CSV file}
 #' 
 #' @keywords datasets
 NULL

R/Ecoli.R

@@ -2,7 +2,7 @@
 #' 
 #' @description Functions to support basic fisheries stock assessment methods.
 #'
-#' @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")}.
+#' @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 Introductory Fisheries Analysis with R book (Ogle 2016) (see \code{fishR("IFAR")}). 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/fishR-Core-Team/FSA/issues/}{GitHub FSA Issues page}.
 #' 
@@ -13,10 +13,10 @@
 #'   \item The \href{https://github.com/droglenc/FSAWs/}{FSAWs package} contains functions for developing and validating standard weight equations.
 #' }
 #'
-#' @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{https://fishr-core-team.github.io/fishR/pages/books.html#introductory-fisheries-analyses-with-r}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' @docType package
 #' 
 #' @name FSA
 #' 
-NULL
+NULL