Avoiding CRAN warnings

Author: gustavdelius

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mizer
 Title: Dynamic Multi-Species Size Spectrum Modelling
-Date: 2024-03-08
+Date: 2024-11-13
 Type: Package
 Description: A set of classes and methods to set up and run multi-species, trait
     based and community size spectrum ecological models, focused on the marine

R/calibrate.R

@@ -120,9 +120,9 @@ calibrateNumber <- function(params) {
 #' `r lifecycle::badge("deprecated")`
 #' 
 #' This function has been deprecated and will be removed in the future unless
-#' you have a usecase for it. If you do have a usecase for it, please let the
+#' you have a use case for it. If you do have a usecase for it, please let the
 #' developers know by creating an issue at
-#' <https://github.com/sizespectrum/mizerExperimental/issues>.
+#' <https://github.com/sizespectrum/mizer/issues>.
 #' 
 #' Given a MizerParams object `params` for which yield observations are
 #' available for at least some species via the `yield_observed` column in the
@@ -154,7 +154,7 @@ calibrateNumber <- function(params) {
 calibrateYield <- function(params) {
     lifecycle::deprecate_warn(
         "2.6.0", "calibrateYield()",
-        details = "This function has not proven useful. If you do have a use case for it, please let the developers know by creating an issue at https://github.com/sizespectrum/mizerExperimental/issues"
+        details = "This function has not proven useful. If you do have a use case for it, please let the developers know by creating an issue at https://github.com/sizespectrum/mizer/issues"
     )
     if ((!("yield_observed" %in% names(params@species_params))) ||
         all(is.na(params@species_params$yield_observed))) {

R/match.R

@@ -130,13 +130,14 @@ matchNumbers <- function(params, species = NULL) {
 #' 
 #' `r lifecycle::badge("deprecated")`
 #' This function has been deprecated and will be removed in the future unless
-#' you have a usecase for it. If you do have a usecase for it, please let the
+#' you have a usecase for it. If you do have a use case for it, please let the
 #' developers know by creating an issue at
-#' <https://github.com/sizespectrum/mizerExperimental/issues>.
+#' <https://github.com/sizespectrum/mizer/issues>.
 #' 
 #' If you want to match the yields to observations, you should use the
-#' `mizerExperimental::matchYield()` function instead, which adjusts the
-#' catchability to match the yield rather than by adjusting the biomass.
+#' matchYield() function from the mizerExperimental package instead, which
+#' adjusts the catchability to match the yield rather than by adjusting the
+#' biomass.
 #' 
 #' The function adjusts the abundances of the species in the model so that their
 #' yearly yields under the given fishing mortalities match with observations.
@@ -174,7 +175,7 @@ matchNumbers <- function(params, species = NULL) {
 matchYields <- function(params, species = NULL) {
     lifecycle::deprecate_warn(
         "2.6.0", "matchYields()", "mizerExperimental::matchYield()",
-        details = "This function has not proven useful. If you do have a usecase for it, please let the developers know by creating an issue at https://github.com/sizespectrum/mizerExperimental/issues"
+        details = "This function has not proven useful. If you do have a use case for it, please let the developers know by creating an issue at https://github.com/sizespectrum/mizer/issues"
     )
     if (!("yield_observed" %in% names(params@species_params))) {
         return(params)

R/selectivity_funcs.R

@@ -129,8 +129,8 @@ knife_edge <- function(w, knife_edge_size, ...) {
 #' Weight based sigmoidal selectivity function
 #'
 #' A sigmoidal selectivity function with 50% selectivity at
-#' weight `sigmoidal_weight` and width `sigmoidal_sigma`.
-#' \deqn{S(w) = \left(1 + \left(\frac{w}{\text{sigmoidal_weight}}\right)^{-\text{sigmoidal_sigma}}\right)^{-1}}{S(w) = (1 + (w/sigmoidal_weight)^{-sigmoidal_sigma})^{-1}}
+#' weight `sigmoidal_weight` \eqn{=w_{\text{sigmoid}}} and width `sigmoidal_sigma` \eqn{=\sigma}.
+#' \deqn{S(w) = \left(1 + \left(\frac{w}{w_{\text{sigmoid}}}\right)^{-\sigma}\right)^{-1}}{S(w) = (1 + (w/sigmoidal_weight)^{-sigmoidal_sigma})^{-1}}
 #'
 #' @param w Vector of sizes.
 #' @param sigmoidal_weight The weight at which the knife-edge operates.

R/setFishing.R

@@ -287,8 +287,7 @@ setFishing <- function(params, selectivity = NULL, catchability = NULL,
 #' For the details see [setFishing()]. 
 #' 
 #' There can optionally also be a column `yield_observed` that allows you to
-#' specify for each gear and species the total annual fisheries yield. This is
-#' used by [mizerExperimental::matchYield()].
+#' specify for each gear and species the total annual fisheries yield. 
 #' 
 #' The fishing effort, which is also needed to determine the fishing mortality
 #' exerted by a gear is not set via the `gear_params` data frame but is set