Modified alkPlot() documentation

Author: droglenc

NEWS.md

@@ -9,13 +9,14 @@
   * Moved all `require()` in individual files to `testthat.R`. This removed many `require()` that were not needed.
 * Fixed four minor errors in documentation from legacy uses of `\R{}` rather than `\code{}`.
 
-* `catchCurve()`: Added `as.df=` to extractor functions and `incl.est=` to `confint.catchCurve()` to match functionality added to `depletion()`.
-* `chapmanRobson()`: Added `as.df=` to extractor functions and `incl.est=` to `confint.chapmanRobson()` to match functionality added to `depletion()`.
+* `alkPlot()`: Modified. Added note in documentation pointing to a fishR blog post on using `ggplot2` to make similar plots.
+* `catchCurve()`: Modified. Added `as.df=` to extractor functions and `incl.est=` to `confint.catchCurve()` to match functionality added to `depletion()`.
+* `chapmanRobson()`: Modified. Added `as.df=` to extractor functions and `incl.est=` to `confint.chapmanRobson()` to match functionality added to `depletion()`.
 * `depletion()`: Modified to address [#111](https://github.com/fishR-Core-Team/FSA/issues/111).
   * Added formula notation such that `depletion()` wash changed to a method call and `depletion.default()` and `depletion.formula()` were added. Tests for the formula were included.
   * Added `as.df=` to `coef.depletion()`, `confint.depletion()`, and `summary.depletion()` so that the result is returned as a data.frame when set to `TRUE` (default is `FALSE` to maintain backward compatability).
   * Added `incl.est=` to `confint.depletion()` to make it easier to get away from the clunky `cbind("Est"=coef(),confint())` code.
-* `GompertzFuns()`: Accepted pull request related to [#112](https://github.com/fishR-Core-Team/FSA/issues/112) that fixed several typos and dead links in the documentation ... thanks Arni. Corrected the erroneous reference to t* (should have been t0) in the documentation for the Gompertz function (fixes [#113](https://github.com/fishR-Core-Team/FSA/issues/113) ... thanks again to Arni).
+* `GompertzFuns()`: Modified. Accepted pull request related to [#112](https://github.com/fishR-Core-Team/FSA/issues/112) that fixed several typos and dead links in the documentation ... thanks Arni. Corrected the erroneous reference to t* (should have been t0) in the documentation for the Gompertz function (fixes [#113](https://github.com/fishR-Core-Team/FSA/issues/113) ... thanks again to Arni).
 * `metaM()`: Modified to address [#114](https://github.com/fishR-Core-Team/FSA/issues/114).
   * Returns data.frame rather than list.
   * Added conditional mortality rate (cm) to returned data.frame (for use with `rFAMS`).

R/alkPlot.R

@@ -10,8 +10,11 @@
 #'   \item A plot with (differently colored) lines, as estimated by loess splines, that connect the proportions of ages within each length interval is constructed with \code{type="splines"}.
 #'   \item A \dQuote{bubble} plot where circles whose size is proportional to the proportion of fish of each age in each length interval is constructed with \code{type="bubble"}. The color of the bubbles can be controlled with \code{col=} and an underlying grid for ease of seeing the age and length interval for each bubble can be controlled with \code{grid=}. Bubbles from a second age-length key can be overlaid on an already constructed bubble plot by using \code{add=TRUE} in a second call to \code{alkPlot}.
 #' }
+#' 
 #' Note that all plots are \dQuote{vertically conditional} -- i.e., each represents the proportional ages WITHIN each length interval.
 #' 
+#' @note These plots are used primarily to explore the structure of an age-length key. While some may find them of "publication-quality", that level of quality and overall control of aspects of the plot are not the primary purpose of this function. Publication-quality plots can be readily made using \code{ggplot2} as demonstrated \href{https://fishr-core-team.github.io/fishR/blog/posts/2025-1-5_ALKPlots_GGplot/}{in this fishR post}.
+#' 
 #' @param key A numeric matrix that contains the age-length key.
 #' @param type A string that indicates the type of plot to construct. See details.
 #' @param xlab,ylab A string that contains the label for the x- or y-axis.