Getting Ready for v0.2.7

fishR-Core-Team · Dec 19, 2023 · 2f89963 · 2f89963
1 parent aae912b
commit 2f89963
Show file tree

Hide file tree

Showing 56 changed files with 332 additions and 63 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,5 @@
-# RFishBC 0.2.7 18-Dec-2023
-* Updated my e-mail address.
+# RFishBC 0.2.7
+* Updated my (DHO) e-mail address in description and all `@author` tags in the documentation files.
 * Removed use of `captioner` package in vignettes as it is no longer available on CRAN (address [#54](https://github.com/fishR-Core-Team/RFishBC/issues/54)).
 * Removed `itemize()` in `@return` section of `digitizeRadii()` documentation (addresses note in R-devel CRAN check).
 * Replaced `itemize()` with `describe()` in `@details` section of `RFBCoptions()` documentation (addresses note in R-devel CRAN check).
@@ -10,7 +10,7 @@
 * `saveDigitizedImage()`: Added (address [#44](https://github.com/fishR-Core-Team/RFishBC/issues/44)).
 * `showDigitizedImage()`: Added `Encoding()` to unicode "arrows" for plotting to address an issue in the upcoming R v4.4.0 (will address [#59](https://github.com/fishR-Core-Team/RFishBC/issues/59)).
 
-# RFishBC 0.2.6 28-Aug-2023
+# RFishBC 0.2.6
 * Updated `test-coverage.yaml` to [latest version](https://github.com/r-lib/actions/blob/v2/examples/test-coverage.yaml).
 * Updated `pkgdown.yaml` to [latest version](https://github.com/r-lib/actions/blob/v2/examples/pkgdown.yaml).
 * `listFiles()`: Corrected URL errors in documentation.

diff --git a/R/RFBCoptions.R b/R/RFBCoptions.R
@@ -60,7 +60,7 @@
 #' 
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{showDigitizedImage}}
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/aStandard.R b/R/aStandard.R
@@ -5,7 +5,7 @@
 #' @param species A string that contains the species name for which to find teh standard intercept value.
 #' @return A single value from \code{\link{StdIntLit}} that is the standard intercept value (a; mm) for the species provided in \code{species}.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #'
 #' @seealso \code{\link{StdIntLit}}
 #' 

diff --git a/R/addFindNotes.R b/R/addFindNotes.R
@@ -9,7 +9,7 @@
 #' 
 #' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'
@@ -42,7 +42,7 @@ addNote <- function(nms,note) {
 #' 
 #' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/backCalc.R b/R/backCalc.R
@@ -7,7 +7,7 @@
 #' @param BCM A single numeric between 1 and 22 or a string that indicates which model to use (based on numbers and names in Vigliola and Meekan (2009)). See Details in \code{\link{bcFuns}} for the list of available models.
 #' @param a The fish length when the structure first forms as used in the Fraser-Lee model (i.e., \code{BCM=1} or \code{BCM="FRALE"}). If this is missing then \code{a} will be estimated as the intercept from the fish length on structure radius linear regression.
 #' @param L0p The length at the \dQuote{Biological Intercept} point. Only used in the \dQuote{Biological Intercept} (\code{BCM=3}), \dQuote{Watanabe and Kuroki} (\code{BCM=12}), and \dQuote{Modified Fry} (\code{BCM=14}) models.
-#' @param R0p The stucture radius at the \dQuote{Biological Intercept} point. Only used in the \dQuote{Biological Intercept} (\code{BCM=3}), \dQuote{Watanabe and Kuroki} (\code{BCM=12}), and \dQuote{Modified Fry} (\code{BCM=14}) models.
+#' @param R0p The structure radius at the \dQuote{Biological Intercept} point. Only used in the \dQuote{Biological Intercept} (\code{BCM=3}), \dQuote{Watanabe and Kuroki} (\code{BCM=12}), and \dQuote{Modified Fry} (\code{BCM=14}) models.
 #' @param L0 The length at the arbitrarily selected point in the \dQuote{Fry} (\code{BCM=13}) model.
 #' @param R0 The structure radius at the arbitrarily selected point in the \dQuote{Fry} (\code{BCM=13}) model.
 #' @param inFormat The format of the data in \code{dat}. The two choices are \code{"long"} with one radial measurement per line (and all radial measurements for a fish in separate rows) and \code{"wide"} with one fish per line (and all radial measurements in separate variables). Defaults to \code{"long"}.
@@ -17,6 +17,10 @@
 #'
 #' @return A data.frame similar to \code{dat} but with the radial measurements replaced by back-calculated lengths at previous ages.
 #'
+#' @author Derek H. Ogle, \email{[email protected]}
+#' 
+#' @keywords manip
+#'
 #' @examples
 #' ## Get some data
 #' data(SMBassWB1,package="RFishBC") ## fish data

diff --git a/R/bcFuns.R b/R/bcFuns.R
@@ -33,7 +33,7 @@
 #' }
 #' @return A function that can be used to predict length at previous age (Li) given length-at-capture (Lcap), hard-part radius-at-age i (Ri), and hard-part radius-at-capture (Rcap). In addition, some functions/models may require the previous age (agei) and the age-at-capture (agec), certain parameters related to the biological intercept (R0p & L0p), or certain parameters estimated from various regression models (a,b,c,A,B,C). See source for more information.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #'
 #' @section IFAR Supplement: \url{https://derekogle.com/IFAR/supplements/backcalculation.html}
 #'

diff --git a/R/combineData.R b/R/combineData.R
@@ -11,7 +11,7 @@
 #' 
 #' @details A detailed description of its use is in \href{https://fishr-core-team.github.io/RFishBC/articles/collectRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}. The list of R data file names may be efficiently created with \code{\link{listFiles}} as described in that vignette. The R data file names may also be selected from a dialog box if using Windows.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/digitizeRadii.R b/R/digitizeRadii.R
@@ -60,7 +60,7 @@
 #' 
 #' @seealso \code{\link{showDigitizedImage}} and \code{\link{RFBCoptions}}.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}.
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}.
 #' 
 #' @export
 #'

diff --git a/R/findScalingFactor.R b/R/findScalingFactor.R
@@ -19,7 +19,7 @@
 #'
 #' @return A single numeric that is the scaling factor (a multiplier that is used to convert image lengths to actual lengths).
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/getID.R b/R/getID.R
@@ -19,7 +19,7 @@
 #'
 #' @return Character vector.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/growthDataUtils.R b/R/growthDataUtils.R
@@ -16,7 +16,7 @@
 #'
 #' The newly computed data will be labeled with a prefix the same as \code{out.type=} (i.e., \code{"rad"} or \code{"inc"}) unless \code{out.pre=} is set by the user. For example, if the data are converted to radial measurements, then the output variables will be \dQuote{rad1}, \dQuote{rad2}, etc. unless \code{out.pre=} was changed from the default. This function assumes that the measurements start with age-1.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #'
 #' @seealso See \code{\link{addRadCap}} for related functionality.
 #'
@@ -92,7 +92,7 @@ gConvert<-function(df,in.pre=NULL,in.var=NULL,
 #'
 #' @seealso See \code{\link{gConvert}} for related functionality.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #'
 #' @keywords manip
 #'
@@ -147,4 +147,4 @@ bcUtilChecker <- function(df,in.pre,in.var) {
   }
   ## Return in.var
   in.var
-}
+}
diff --git a/R/listFiles.R b/R/listFiles.R
@@ -14,7 +14,7 @@
 #'
 #' @return Character vector.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/saveDigitizedImage.R b/R/saveDigitizedImage.R
@@ -28,7 +28,7 @@
 #'
 #' @seealso \code{\link{showDigitizedImage}}, \code{\link{digitizeRadii}}, \code{\link{RFBCoptions}}, and \code{\link{jpeg}}, \code{\link{png}}, and \code{\link{pdf}}.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/R/showDigitizedImage.R b/R/showDigitizedImage.R
@@ -26,7 +26,7 @@
 #'
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{RFBCoptions}}.
 #' 
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#' @author Derek H. Ogle, \email{DerekOgle51@gmail.com}
 #' 
 #' @export
 #'

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -20,6 +20,7 @@ reference:
       - RFBCoptions
       - digitizeRadii
       - showDigitizedImage
+      - saveDigitizedImage
       - combineData
       - findScalingFactor
   - title: Back-calculation

diff --git a/cran-comments/cran-comments-v0_2_7.md b/cran-comments/cran-comments-v0_2_7.md
@@ -0,0 +1,9 @@
+* This updates the RFishBC package that was archived earlier this month. This fixes all errors and notes that caused the archive, and includes some other updates. Importantly my e-mail address has been updated throughout (this may be why I did not receive notice from CRAN about the errors that caused the archiving).
+
+## Notes
+* If there is a note about "fishBC" being misspelled in the description, then note that this is not a misspelling.
+
+## Testing Environments
+* My Windows machine.
+* Win Builder -- old-release, release, and development.
+* GitHub Action (R-CMD-check.yaml)
diff --git a/docs/articles/BCCalc.html b/docs/articles/BCCalc.html
diff --git a/docs/articles/BCIntro.html b/docs/articles/BCIntro.html
diff --git a/docs/articles/BCWorkflow.html b/docs/articles/BCWorkflow.html
diff --git a/docs/articles/Other.html b/docs/articles/Other.html
diff --git a/docs/articles/collectRadiiData.html b/docs/articles/collectRadiiData.html
diff --git a/docs/articles/seeRadiiData.html b/docs/articles/seeRadiiData.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   collectRadiiData: collectRadiiData.html
   Other: Other.html
   seeRadiiData: seeRadiiData.html
-last_built: 2023-12-18T13:52Z
+last_built: 2023-12-19T13:51Z
 urls:
   reference: https://fishr-core-team.github.io/RFishBC/reference
   article: https://fishr-core-team.github.io/RFishBC/articles

diff --git a/docs/reference/RFBCoptions.html b/docs/reference/RFBCoptions.html
diff --git a/docs/reference/aStandard.html b/docs/reference/aStandard.html
diff --git a/docs/reference/addNote.html b/docs/reference/addNote.html
diff --git a/docs/reference/addRadCap.html b/docs/reference/addRadCap.html
diff --git a/docs/reference/backCalc.html b/docs/reference/backCalc.html