Updated poems links

All references to poems objects link properly now.

DESCRIPTION

@@ -20,6 +20,7 @@ Description: This extension of the poems pattern-oriented modeling (POM) framewo
 Depends: R (>= 3.6.0)
 License: GPL (>= 3)
 Encoding: UTF-8
+Language: en_AU
 LazyData: true
 RoxygenNote: 7.3.1
 Imports:

R/PaleoPopModel.R

@@ -2,7 +2,7 @@
 #'
 #' @description \code{\link[R6:R6Class]{R6}} class representing a
 #' spatially-explicit demographic-based population model. It extends the
-#' \code{\link{SimulationModel}} class with parameters for the
+#' \code{\link[poems:SimulationModel]{poems}} class with parameters for the
 #' \code{\link{paleopop_simulator}}. It inherits functionality for creating a
 #' nested model, whereby a nested template model with fixed parameters is
 #' maintained when a model is cloned for various sampled parameters. Also
@@ -289,7 +289,7 @@ PaleoPopModel <- R6Class("PaleoPopModel",
       }
     },
 
-    #' @field region A \code{\link{Region}} (or inherited class) object specifying the study region.
+    #' @field region A \code{\link[poems:Region]{Region}} (or inherited class) object specifying the study region.
     region = function(value) { # inherited
       if (missing(value)) {
         super$region
@@ -416,7 +416,12 @@ PaleoPopModel <- R6Class("PaleoPopModel",
       }
     },
 
-    #' @field compact_decomposition List containing a compact transposed (Cholesky) decomposition \emph{matrix} (t_decomposition_compact_matrix) and a corresponding \emph{map} of population indices (t_decomposition_compact_map), as per \code{\link{SpatialCorrelation}} class attributes.
+    #' @field compact_decomposition List containing a compact transposed 
+    #' (Cholesky) decomposition \emph{matrix} (t_decomposition_compact_matrix) 
+    #' and a corresponding \emph{map} of population indices 
+    #' (t_decomposition_compact_map), as per 
+    #' \code{\link[poems:SpatialCorrelation]{SpatialCorrelation}} class 
+    #' attributes.
     compact_decomposition = function(value) {
       if (is.null(self$template_model) || "compact_decomposition" %in% self$sample_attributes) {
         if (missing(value)) {
@@ -487,7 +492,11 @@ PaleoPopModel <- R6Class("PaleoPopModel",
       }
     },
 
-    #' @field dispersal_data List of data frames of non-zero dispersal rates and indices for constructing a compact dispersal matrix, and optional changing rates over time, as per class \code{\link{DispersalGenerator}} \emph{dispersal_data} attribute.
+    #' @field dispersal_data List of data frames of non-zero dispersal rates and
+    #'  indices for constructing a compact dispersal matrix, and optional 
+    #'  changing rates over time, as per class 
+    #'  \code{\link[poems:DispersalGenerator]{DispersalGenerator}} 
+    #'  \emph{dispersal_data} attribute.
     dispersal_data = function(value) {
       if (is.null(self$template_model) || "dispersal_data" %in% self$sample_attributes) {
         if (missing(value)) {

R/PaleoPopResults.R

@@ -3,7 +3,7 @@
 #' @description
 #' \code{\link[R6:R6Class]{R6}} class for encapsulating and dynamically generating
 #' spatially-explicit \code{\link{paleopop_simulator}} results, as well as optional
-#' re-generated \code{\link{Generator}} for niche carrying capacity and/or human
+#' re-generated \code{\link[poems:Generator]{Generator}} for niche carrying capacity and/or human
 #' density.
 #' 
 #' @examples 
@@ -138,7 +138,7 @@ PaleoPopResults <- R6Class("PaleoPopResults",
       }
     },
 
-    #' @field region A \code{\link{Region}} (or inherited class) object specifying the study region.
+    #' @field region A \code{\link[poems:Region]{Region}} (or inherited class) object specifying the study region.
     region = function(value) { # inherited
       if (missing(value)) {
         super$region

R/paleopop-package.R

@@ -18,7 +18,7 @@
 #'     \code{\link[poems:SimulationModel]{SimulationModel}}, this class encapsulates the input parameters
 #'     utilized by the \code{\link{paleopop_simulator}}.
 #'   \item \code{\link{PaleoPopResults}} class: Inherited from
-#'     \code{\link{SimulationResults}}, this class encapsulates the results generated
+#'     \code{\link[poems:SimulationResults]{SimulationResults}}, this class encapsulates the results generated
 #'     by the \code{\link{paleopop_simulator}}, as well as dynamically generating
 #'     additional derived results.
 #' }

R/paleopop_simulator.R

@@ -21,7 +21,12 @@
 #'     \item{\code{initial_abundance}}{Array of initial abundances for each population.}
 #'     \item{\code{transition_rate}}{Rate of transition (or fecundity) between generations.}
 #'     \item{\code{standard_deviation}}{Standard deviation applied to transition rates.}
-#'     \item{\code{compact_decomposition}}{List containing a compact transposed (Cholesky) decomposition \emph{matrix} (t_decomposition_compact_matrix) and a corresponding \emph{map} of population indices (t_decomposition_compact_map), as per \code{\link{SpatialCorrelation}} class attributes.}
+#'     \item{\code{compact_decomposition}}{List containing a compact transposed 
+#'     (Cholesky) decomposition \emph{matrix} (t_decomposition_compact_matrix) 
+#'     and a corresponding \emph{map} of population indices 
+#'     (t_decomposition_compact_map), as per 
+#'     \code{\link[poems:SpatialCorrelation]{SpatialCorrelation}} class 
+#'     attributes.}
 #'     \item{\code{carrying_capacity}}{Matrix of carrying capacities (\emph{populations} rows by \emph{time_steps} columns).}
 #'     \item{\code{density_dependence}}{Density dependence type ("competition", "logistic", or "ceiling").}
 #'     \item{\code{growth_rate_max}}{Maximum growth rate (for "competition" or "logistic" density dependence).}
@@ -31,7 +36,7 @@
 #'     \item{\code{harvest_z}}{The \emph{Z} parameter in the harvest function.}
 #'     \item{\code{harvest_max_n}}{Maximum density per grid cell.}
 #'     \item{\code{human_density}}{Matrix of human density (fraction) (\emph{populations} rows by \emph{time_steps} columns).}
-#'     \item{\code{dispersal_data}}{List of data frames of non-zero dispersal rates and indices for constructing a compact dispersal matrix, and optional changing rates over time, as per class \code{\link{DispersalGenerator}} \emph{dispersal_data} attribute.}
+#'     \item{\code{dispersal_data}}{List of data frames of non-zero dispersal rates and indices for constructing a compact dispersal matrix, and optional changing rates over time, as per class \code{\link[poems:DispersalGenerator]{DispersalGenerator}} \emph{dispersal_data} attribute.}
 #'     \item{\code{dispersal_target_k}}{Target population carrying capacity threshold for density dependent dispersal.}
 #'     \item{\code{abundance_threshold}}{Abundance threshold (that needs to be exceeded) for each population to persist.}
 #'     \item{\code{occupancy_threshold}}{Threshold for the number of populations occupied (that needs to be exceeded) for all populations to persist.}

cran-comments.md

@@ -1,12 +1,12 @@
 # Test environments
 
-- Local R 4.4.1 installation on macOS 14.0 (intel chip)
-- Windows, R-devel (via win-builder)
-- Apple Silicon, R 4.4.1 (via mac-builder)
+- Local R 4.4.1 installation on macOS 15.0 (intel chip)
+- macOS 14.6.1, R 4.4.1 (via Github Actions)
+- Microsoft Windows Server 2022, R 4.4.1 (via Github Actions)
+- Ubuntu 22.04.5, R-devel (via Github Actions)
+- Ubuntu 22.04.5, R 4.4.1 (via Github Actions)
+- Ubuntu 22.04.5, R 4.3.3 (via Github Actions)
 
 # R CMD check results
 
-0 errors ✔ \| 0 warnings ✔ \| 1 note
-
-# Comments on check results
-
+0 errors ✔ \| 0 warnings ✔ \| 0 notes