Merge pull request #83 from droglenc/rd-work

Rd work

R/FSA-defunct.R

@@ -1,4 +1,4 @@
-#' @title Defunct functions.
+#' @title DEFUNCT functions.
 #' @description These functions were once part of FSA but have now been removed.
 #' @param \dots Additional arguments to pass through.
 #' @name FSA-defunct

R/FSAUtils.R

@@ -1,5 +1,3 @@
-#' @name FSAUtils
-#' 
 #' @title Capitalizes the first letter of first or all words in a string.
 #' 
 #' @description Capitalizes the first letter of first or all words in a string.
@@ -196,7 +194,8 @@ fishR <- function(where=c("home","IFAR","general","books",
   invisible(tmp)
 }
 
-
+#' @name fsaNews
+#' 
 #' @title Read news and changes for the 'FSA' package.
 #'
 #' @description Opens up the \href{https://github.com/droglenc/FSA/blob/master/NEWS.md}{News.md GitHub file} for the \sQuote{FSA} package in an external browser.
@@ -404,7 +403,7 @@ logbtcf <- function(obj,base=exp(1)) {
 }
 
 
-#' @name oddeven
+#' @name is.odd
 #' 
 #' @title Determine if a number is odd or even.
 #' 
@@ -418,6 +417,8 @@ logbtcf <- function(obj,base=exp(1)) {
 #' 
 #' @keywords manip
 #' 
+#' @aliases is.odd is.even
+#' 
 #' @examples
 #' ## Individual values
 #' is.odd(1)
@@ -430,11 +431,11 @@ logbtcf <- function(obj,base=exp(1)) {
 #' data.frame(d,odd=is.odd(d),even=is.even(d))
 NULL
 
-#' @rdname oddeven
+#' @rdname is.odd
 #' @export
 is.odd <- function (x) iOddEven(x,1)
 
-#' @rdname oddeven
+#' @rdname is.odd
 #' @export
 is.even <- function(x) iOddEven(x,0)
 
@@ -866,7 +867,7 @@ se <- function (x,na.rm=TRUE) {
 #' levels(iris.set3$Species)
 #' xtabs(~Species,data=iris.set3)
 #' 
-#' @rdname filterD-deprecated
+#' @rdname filterD
 #' @export
 filterD <- function(x,...,except=NULL) {
   .Deprecated(msg="'filter' is deprecated and will soon be removed from 'FSA'; please use 'droplevels' after 'subset' or 'dplyr::filter' for the same result (see fishR post from 26-May-2021).")

R/bootstrap.R

@@ -1,5 +1,3 @@
-#' @name bootstrap
-#' 
 #' @title Associated S3 methods for bootstrap results from car::Boot.
 #'
 #' @description S3 methods are provided to construct non-parametric bootstrap confidence intervals, predictions with non-parametric confidence intervals, hypothesis tests, and plots of the parameter estimates for objects returned from \code{\link[car]{Boot}} from \pkg{car}.
@@ -188,7 +186,7 @@ hist.boot <- function(x,same.ylim=TRUE,ymax=NULL,
 #'
 #' @seealso \code{\link[car]{Boot}} and related methods in \pkg{car} and \code{summary.\link[nlstools]{nlsBoot}} in \pkg{nlstools}.
 #'
-#' @aliases confint.nlsboot htest.nlsboot predict.nlsbooot
+#' @aliases confint.nlsBoot htest.nlsBoot predict.nlsBoot
 #'
 #' @keywords htest
 #'

R/deprecated_fitPlot.R

@@ -118,15 +118,15 @@
 #' fitPlot(glm1)
 #' fitPlot(glm1,yaxis1.ticks=c(0,1),yaxis1.lbls=c(0,1))
 #'
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot <- function (object, ...) {
   if ("lm" %in% class(object)) ## This is a hack so no double deprecation warning
     .Deprecated(msg="'fitPlot' is deprecated and will soon be removed from 'FSA'; see fishR post from 25-May-2021 for alternative methods.")
   UseMethod("fitPlot") 
 }
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.lm <- function(object, ...) {
   object <- iTypeoflm(object)
@@ -137,7 +137,7 @@ fitPlot.lm <- function(object, ...) {
   fitPlot(object,...)
 }
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.SLR <- function(object,plot.pts=TRUE,pch=16,col.pt="black",
                         col.mdl="red",lwd=3,lty=1,
@@ -196,7 +196,7 @@ fitPlot.SLR <- function(object,plot.pts=TRUE,pch=16,col.pt="black",
 }
 
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.IVR <- function(object,...) {
   ## Do some checks
@@ -369,14 +369,14 @@ iFitPlotIVR2 <- function(object,plot.pts=TRUE,pch=c(16,21,15,22,17,24,c(3:14)),
   }  # nocov end
 }
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.POLY <- function(object,...) {
   fitPlot.SLR(object,...)
 }
 
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.ONEWAY <- function (object,
                             xlab=object$Enames[1],ylab=object$Rname,main="",
@@ -410,7 +410,7 @@ fitPlot.ONEWAY <- function (object,
 } # nocov end
 
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.TWOWAY <- function(object,which,change.order=FALSE,
                            xlab=object$Enames[ord[1]],ylab=object$Rname,
@@ -465,7 +465,7 @@ fitPlot.TWOWAY <- function(object,which,change.order=FALSE,
 }
 
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.nls <- function(object,d,
                         pch=c(19,1),col.pt=c("black","red"),col.mdl=col.pt,
@@ -544,7 +544,7 @@ fitPlot.nls <- function(object,d,
   }
 }  # nocov end
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.glm <- function(object, ...) {
   if (object$family$family=="binomial" & object$family$link=="logit")
@@ -553,7 +553,7 @@ fitPlot.glm <- function(object, ...) {
     STOP("Currently only logistic regression GLM models are supported by fitPlot.")
 }
 
-#' @rdname fitPlot-deprecated
+#' @rdname fitPlot
 #' @export
 fitPlot.logreg <- function(object,
                            xlab=names(object$model)[2],ylab=names(object$model)[1],

R/stockRecruitment.R

@@ -1,4 +1,4 @@
-#' @name stockRecruitment
+#' @name srFuns
 #' 
 #' @title Creates a function for a specific parameterization of a common stock-recruitment function .
 #'
@@ -37,6 +37,8 @@
 #' 
 #' @keywords manip
 #' 
+#' @aliases srFuns srFunShow
+#' 
 #' @examples
 #' ## See the formulae
 #' ## Simple Examples
@@ -105,7 +107,7 @@
 
 NULL
 
-#' @rdname stockRecruitment
+#' @rdname srFuns
 #' @export
 srFuns <- function(type=c("BevertonHolt","Ricker","Shepherd",
                           "SailaLorda","independence"),
@@ -239,7 +241,7 @@ srFuns <- function(type=c("BevertonHolt","Ricker","Shepherd",
   get(type)
 }
 
-#' @rdname stockRecruitment
+#' @rdname srFuns
 #' @export
 srFunShow <- function(type=c("BevertonHolt","Ricker","Shepherd","SailaLorda"),
                       param=1,plot=FALSE,...) {

_pkgdown.yml

@@ -90,7 +90,7 @@ reference:
       - binCI
       - hyperCI
       - poiCI
-      - bootstrap
+      - boot
       - dunnTest
       - extraSS
       - geomean
@@ -100,6 +100,7 @@ reference:
       - ksTest
       - logbtcf
       - lrt
+      - nlsBoot
       - nlsTracePlot
       - pcumsum
       - rSquared