Closing out v0.8.31

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FSA
-Version: 0.8.30.9000
-Date: 2020-5-27
+Version: 0.8.31
+Date: 2020-11-7
 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/>.
@@ -42,7 +42,8 @@ Suggests:
     pkgdown,
     psych,
     Rcapture,
+    rmarkdown,
     testthat,
-    rmarkdown
+    tibble
 Encoding: UTF-8
 RoxygenNote: 7.1.1

NEWS.md

@@ -1,6 +1,9 @@
-# FSA 0.8.31 ongoing
+# FSA 0.8.31 7-Nov20
 * Now using roxygen v7.1.1.
+* Added `tibble` to suggests (see comment about `headtail()` below).
 * Cleaned up the documentation of parameters for `RichardsFuns()` (documentation did not change when parameter letters were changed for the Age and Growth book).
+* Changed example in `headtail()` to use `as_tibble()` from `tibble` package rather than `tbl_df()` from `dplyr` package. Required adding `tibble` to suggests.
+* `nlsTracePlot()`: Modified. Created a conditional catch depending on the version of R as the results of `nls(*,trace=TRUE)` are changing in v4.1.0 (per e-mail from Martin Maechler on 2-Nov-20).
 
 # FSA 0.8.30 9-Mar-20
 * Started using `rhub::check_for_cran()` for checking before sending to CRAN.
@@ -1033,7 +1036,7 @@
 # FSA 0.4.11 May14
 
 * Removed Roxygen directives in DESCRIPTION (with changes to roxygen2 4.0.1).
-* Changed `@S3method` and `@method` to `@export` in the following files according to changes in ROxygen2 as [described here](http://stackoverflow.com/questions/7198758/roxygen2-how-to-properly-document-s3-methods/7199577#7199577), among several other places: `ageBias`, `agePrecision`, `bootCase`, `catchCurve`, `chapmanRobson`, `confint.nlsboot`, `depletion`, `dietOverlap`, `fitPlot`, `hist.formula`, `htest.nlsBoot`, `ks2d1`, `ks2d1p`, `ks2d2`, `ks2d2p`, `ksTest`, `lencat`, `mrClosed`, `mrOpen`, `plotBinResp`, `predict.nlsBoot`, `removal`, `residPlot`, `srStarts`, `Subset`, `Summarize`, `sumTable`, `vbStarts`, and `walfordChapmanPlot`.
+* Changed `@S3method` and `@method` to `@export` in the following files according to changes in ROxygen2 as [described here](https://stackoverflow.com/questions/7198758/roxygen2-how-to-properly-document-s3-methods/7199577/), among several other places: `ageBias`, `agePrecision`, `bootCase`, `catchCurve`, `chapmanRobson`, `confint.nlsboot`, `depletion`, `dietOverlap`, `fitPlot`, `hist.formula`, `htest.nlsBoot`, `ks2d1`, `ks2d1p`, `ks2d2`, `ks2d2p`, `ksTest`, `lencat`, `mrClosed`, `mrOpen`, `plotBinResp`, `predict.nlsBoot`, `removal`, `residPlot`, `srStarts`, `Subset`, `Summarize`, `sumTable`, `vbStarts`, and `walfordChapmanPlot`.
 
 * `addZeroCatch()`: Modified.  Added a catch for the situation where no zeros need to be added to the data.frame.  Cleaned-up the help file, modified the examples, and added another example.  Thanks to Ben Neely for bringing this bug (handling where zeros are not needed) to my attention.
 * `capHistSum()`: Modified.  Cleaned up the code (no changes in functionality).

R/FSA.R

@@ -4,16 +4,16 @@
 #'
 #' @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/droglenc/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/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.
+#'   \item The \href{https://github.com/droglenc/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.
 #' }
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' @docType package
 #' 

R/FSAUtils.R

@@ -186,7 +186,7 @@ col2rgbt <- function(col,transp=1) {
 #'
 #' @return A data.frame with one variable that contains the values from the chosen diagonal of \code{x} and, optionally, a second variable that contains the chosen labels for those values.
 #'
-#' @author Derek H. Ogle, \email{derek@@derekogle.com}, but relied heavily on \url{http://stackoverflow.com/a/27935808/1123933}.
+#' @author Derek H. Ogle, \email{derek@@derekogle.com}, but relied heavily on \url{https://stackoverflow.com/a/27935808/1123933/}.
 #'
 #' @keywords manip
 #'
@@ -235,7 +235,7 @@ diags <- function(x,which=0,incl.labels=c("none","row","column"),
   if (nrow(x)==1 | ncol(x)==1)
     STOP("'x' must have more than 1 row and more than 1 column.")
   ## find indices of diagonals for the matrix
-  ## idea from http://stackoverflow.com/a/27935808/1123933
+  ## idea from https://stackoverflow.com/a/27935808/1123933/
   ind <- row(x)-col(x)
   if (is.null(which)) { # nocov start
     ## Simply show the matrix of indices
@@ -421,14 +421,14 @@ FSANews <- function () {
 #' headtail(miris,addrownums=FALSE)
 #' headtail(miris,10,which=2:4)
 #'
-#' ## Make a tbl_df type from dplyr ... note how headtail()
+#' ## Make a tbl_df type from tibble ... note how headtail()
 #' ## is not limited by the tbl_df restriction on number of
 #' ## rows to show (but head() is).
-#' if (require(dplyr)) {
-#'   iris2 <- tbl_df(iris)
+#' if (require(tibble)) {
+#'   iris2 <- as_tibble(iris)
 #'   class(iris2)
 #'   headtail(iris2,n=15)
-#'   head(iris2,n=30)
+#'   head(iris2,n=15)
 #' }
 #' @export
 headtail <- function(x,n=3L,which=NULL,addrownums=TRUE,...) {

R/PSDlit.R

@@ -36,7 +36,7 @@
 #'
 #' @seealso See \code{\link{psdVal}}, \code{\link{psdCalc}}, \code{\link{psdPlot}}, \code{\link{psdAdd}}, and \code{\link{tictactoe}} for related functionality.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #'
 #' @source Original summary table from Dr. Michael Hansen, University of Wisconsin-Stevens Point. Additional species have been added by the package author from the literature.
 #'

R/WSlit.R

@@ -40,7 +40,7 @@
 #'
 #' @section IFAR Chapter: 8-Condition.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #'
 #' @source Most of these equations can be found in Neumann, R.M., C.S. Guy, and D.W. Willis. 2012. Length, Weight, and Associated Indices. Chapter 14 in Zale, A.V., D.L. Parrish, and T.M. Sutton, editors. Fisheries Techniques. American Fisheries Society, Bethesda, MD.
 #' 

R/addZeroCatch.R

@@ -25,7 +25,7 @@
 #' 
 #' @seealso \code{complete} in \pkg{tidyr} package.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' @keywords manip
 #'

R/ageComparisons.R

@@ -19,10 +19,10 @@
 #'   \item R Number of age estimates given in \code{formula}.
 #'   \item PercAgree The percentage of fish for which all age estimates perfectly agree.
 #'   \item ASD The average (across all fish) standard deviation of ages within a fish.
-#'   \item ACV The average (across all fish) coefficient of variation of ages within a fish using the \bold{mean} as the divisor. See the \href{http://derekogle.com/IFAR}{IFAR chapter} for calculation details.
+#'   \item ACV The average (across all fish) coefficient of variation of ages within a fish using the \bold{mean} as the divisor. See the \href{http://derekogle.com/IFAR/}{IFAR chapter} for calculation details.
 #'   \item ACV2 The average (across all fish) coefficient of variation of ages within a fish using the \bold{median} as the divisor. This will only be shown if R>2 or \code{show.prec2=TRUE}.
 #'   \item AAD The average (across all fish) absolute deviation of ages within a fish.
-#'   \item APE The average (across all fish) percent error of ages within a fish using the \bold{mean} as the divisor. See the \href{http://derekogle.com/IFAR}{IFAR chapter} for calculation details.
+#'   \item APE The average (across all fish) percent error of ages within a fish using the \bold{mean} as the divisor. See the \href{http://derekogle.com/IFAR/}{IFAR chapter} for calculation details.
 #'   \item APE2 The average (across all fish) percent error of ages within a fish using the \bold{median} as the divisor. This will only be shown if R>2 or \code{show.prec2=TRUE}.
 #'   \item AD The average (across all fish) index of precision (D).
 #' }
@@ -63,7 +63,7 @@
 #'
 #' @seealso See \code{\link{ageBias}} for computation of the full age agreement table, along with tests and plots of age bias.
 #' 
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Beamish, R.J. and D.A. Fournier. 1981. A method for comparing the precision of a set of age determinations. Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. [Was (is?) available from http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf.]
 #'
@@ -420,7 +420,7 @@ summary.agePrec <- function(object,what=c("precision","difference",
 #'
 #' @section IFAR Chapter: 4-Age Comparisons. \bold{Note that \code{plot} has changed since IFAR was published. Some of the original functionality is in \code{\link{plotAB}}.}
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.]
 #'

R/alkIndivAge.R

@@ -13,7 +13,7 @@
 #' @param key A numeric matrix that contains the age-length key. The format of this matrix is important. See details.
 #' @param formula A formula of the form \code{age~length} where \code{age} generically represents the variable that will contain the estimated ages once the key is applied (i.e., should currently contain no values) and \code{length} generically represents the variable that contains the known length measurements. If only \code{~length} is used, then a new variable called \dQuote{age} will be created in the resulting data frame.
 #' @param data A data.frame that minimally contains the length measurements and possibly contains a variable that will receive the age assignments as given in \code{formula}.
-#' @param type A string that indicates whether to use the semi-random (\code{type="SR"}, default) or completely-random (\code{type="CR"}) methods for assigning ages to individual fish. See the \href{http://derekogle.com/IFAR}{IFAR chapter} for more details.
+#' @param type A string that indicates whether to use the semi-random (\code{type="SR"}, default) or completely-random (\code{type="CR"}) methods for assigning ages to individual fish. See the \href{http://derekogle.com/IFAR/}{IFAR chapter} for more details.
 #' @param breaks A numeric vector of lower values that define the length intervals. See details.
 #' @param seed A single numeric that is given to \code{set.seed} to set the random seed. This allows repeatability of results.
 #' 
@@ -27,7 +27,7 @@
 #'
 #' @seealso  See \code{\link{alkAgeDist}} and \code{\link{alkMeanVar}} for alternative methods to derived age distributions and mean (and SD) values for each age. See \code{\link{alkPlot}} for methods to visualize age-length keys.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Isermann, D.A. and C.T. Knight. 2005. A computer program for age-length keys incorporating age assignment to individual fish. North American Journal of Fisheries Management, 25:1153-1160. [Was (is?) from http://www.tandfonline.com/doi/abs/10.1577/M04-130.1.]
 #'

R/alkPlot.R

@@ -36,7 +36,7 @@
 #' 
 #' @seealso See \code{\link{alkIndivAge}} for using an age-length key to assign ages to individual fish.
 #' 
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' @keywords plot
 #' 

R/alkSummaries.R

@@ -27,7 +27,7 @@
 #'
 #' @seealso  See \code{\link{alkIndivAge}} and related functions for a completely different methodology. See \code{\link[fishmethods]{alkprop}} from \pkg{fishmethods} for the exact same methodology but with a different format for the inputs.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Lai, H.-L. 1987. Optimum allocation for estimating age composition using age-length key. Fishery Bulletin, 85:179-185.
 #' 
@@ -127,7 +127,7 @@ iALKAgeProp <- function(p_jgi,l_i,n_i,N) {
 #'
 #' @seealso  See \code{\link{alkIndivAge}} and related functions for a completely different methodology. See \code{\link{alkAgeDist}} for a related method of determining the proportion of fish at each age. See the \pkg{ALKr} package.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Bettoli, P. W. and Miranda, L. E. 2001. A cautionary note about estimating mean length at age with subsampled data. North American Journal of Fisheries Management, 21:425-428.
 #'  

R/capHistConvert.R

@@ -96,7 +96,7 @@
 #'
 #' @seealso See \code{\link{capHistSum}} to summarize \dQuote{individual} capture histories into a format usable in \code{\link{mrClosed}} and \code{\link{mrOpen}}. Also see \pkg{Rcapture}, \code{RMark}, or \pkg{marked} packages for handling more complex analyses.
 #' 
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' @keywords manip
 #'

R/capHistSum.R

@@ -41,7 +41,7 @@
 #'
 #' @seealso See \code{\link[Rcapture]{descriptive}} in \pkg{Rcapture} for \code{m.array} and some of the same values in \code{sum}. See \code{\link{capHistConvert}} for a descriptions of capture history data file formats and how to convert between them. See \code{\link{mrClosed}} and \code{\link{mrOpen}} for how to estimate abundance from the summarized capture history information.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Baillargeon, S. and Rivest, L.-P. (2007). Rcapture: Loglinear models for capture-recapture in R. Journal of Statistical Software, 19(5):1-31.
 #' 

R/catchCurve.R

@@ -46,7 +46,7 @@
 #' 
 #' @seealso See \code{\link[fishmethods]{agesurv}} in \pkg{fishmethods} for similar functionality. See \code{\link{chapmanRobson}} and \code{\link[fishmethods]{agesurvcl}} in \pkg{fishmethods} for alternative methods to estimate mortality rates. See \code{\link{metaM}} for empirical methods to estimate natural mortality.
 #' 
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Maceina, M.J., and P.W. Bettoli. 1998. Variation in Largemouth Bass recruitment in four mainstream impoundments on the Tennessee River. North American Journal of Fisheries Management 18:998-1003.
 #' 

R/chapmanRobson.R

@@ -46,7 +46,7 @@
 #'
 #' @seealso See \code{\link[fishmethods]{agesurv}} in \pkg{fishmethods} for similar functionality. See \code{\link{catchCurve}} and \code{\link[fishmethods]{agesurvcl}} in \pkg{fishmethods} for alternative methods. See \code{\link{metaM}} for empirical methods to estimate natural mortality.
 #' 
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Chapman, D.G. and D.S. Robson. 1960. The analysis of a catch curve. Biometrics. 16:354-368.
 #'

R/depletion.R

@@ -54,7 +54,7 @@
 #'
 #' @seealso See \code{\link{removal}} for related functionality and \code{\link[fishmethods]{deplet}} in \pkg{fishmethods} for similar functionality.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.]
 #'

R/growthModels.R

@@ -50,7 +50,7 @@
 #'
 #' @seealso See \code{\link{Schnute}} for an implementation of the Schnute (1981) model.
 #'
-#' @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{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 
 #' Campana, S.E. and C.M. Jones. 1992. Analysis of otolith microstructure data. Pages 73-100 In D.K. Stevenson and S.E. Campana, editors. Otolith microstructure examination and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/141734.pdf.]
 #'