From b92cf99d70e1f8a6fe1d7846b631d0f3b89ea501 Mon Sep 17 00:00:00 2001 From: July Pilowsky Date: Fri, 20 Sep 2024 14:43:02 -0400 Subject: [PATCH] Updated poems links All references to poems objects link properly now. --- DESCRIPTION | 1 + R/PaleoPopModel.R | 17 +++++++++++++---- R/PaleoPopResults.R | 4 ++-- R/paleopop-package.R | 2 +- R/paleopop_simulator.R | 9 +++++++-- cran-comments.md | 14 +++++++------- man/PaleoPopModel.Rd | 17 +++++++++++++---- man/PaleoPopResults.Rd | 4 ++-- man/paleopop.Rd | 2 +- man/paleopop_simulator.Rd | 9 +++++++-- 10 files changed, 54 insertions(+), 25 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1abec07..4484222 100644 --- a/DESCRIPTION +++ b/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: diff --git a/R/PaleoPopModel.R b/R/PaleoPopModel.R index 126b9b9..94e6024 100644 --- a/R/PaleoPopModel.R +++ b/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$sample_attributes) { if (missing(value)) { diff --git a/R/PaleoPopResults.R b/R/PaleoPopResults.R index 72685b2..0fb165b 100644 --- a/R/PaleoPopResults.R +++ b/R/PaleoPopResults.R @@ -3,7 +3,7 @@ #' @description #' \code{\link[R6:R6Class]{R6}} class for encapsulating and dynamically generating #' spatially-explicit \code{\link{paleopop_simulator}} results, as well as optional -#' re-generated \code{\link{Generator}} for niche carrying capacity and/or human +#' re-generated \code{\link[poems:Generator]{Generator}} for niche carrying capacity and/or human #' density. #' #' @examples @@ -138,7 +138,7 @@ PaleoPopResults <- R6Class("PaleoPopResults", } }, - #' @field region A \code{\link{Region}} (or inherited class) object specifying the study region. + #' @field region A \code{\link[poems:Region]{Region}} (or inherited class) object specifying the study region. region = function(value) { # inherited if (missing(value)) { super$region diff --git a/R/paleopop-package.R b/R/paleopop-package.R index 00cfa65..b717398 100644 --- a/R/paleopop-package.R +++ b/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. #' } diff --git a/R/paleopop_simulator.R b/R/paleopop_simulator.R index fbfa7a5..9998d88 100644 --- a/R/paleopop_simulator.R +++ b/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.} diff --git a/cran-comments.md b/cran-comments.md index 488ebdb..048589f 100644 --- a/cran-comments.md +++ b/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 diff --git a/man/PaleoPopModel.Rd b/man/PaleoPopModel.Rd index af660ef..c2ffc18 100644 --- a/man/PaleoPopModel.Rd +++ b/man/PaleoPopModel.Rd @@ -6,7 +6,7 @@ \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 @@ -52,7 +52,7 @@ template_model#is_consistent() # however, the attributes that are filled in are \item{\code{model_attributes}}{A vector of model attribute names.} -\item{\code{region}}{A \code{\link{Region}} (or inherited class) object specifying the study region.} +\item{\code{region}}{A \code{\link[poems:Region]{Region}} (or inherited class) object specifying the study region.} \item{\code{coordinates}}{Data frame (or matrix) of X-Y population coordinates (WGS84) in longitude (degrees West) and latitude (degrees North).} @@ -70,7 +70,12 @@ template_model#is_consistent() # however, the attributes that are filled in are \item{\code{standard_deviation}}{Standard deviation (numeric) for applying environmental stochasticity 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}}{Array (or matrix) of carrying capacity values at each population cell (across time).} @@ -78,7 +83,11 @@ template_model#is_consistent() # however, the attributes that are filled in are \item{\code{growth_rate_max}}{Maximum growth rate (utilized by density dependence processes).} -\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.} diff --git a/man/PaleoPopResults.Rd b/man/PaleoPopResults.Rd index f7f784b..3266e61 100644 --- a/man/PaleoPopResults.Rd +++ b/man/PaleoPopResults.Rd @@ -6,7 +6,7 @@ \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{ @@ -67,7 +67,7 @@ results_model$ema # expected minimum abundance \describe{ \item{\code{model_attributes}}{A vector of model attribute names.} -\item{\code{region}}{A \code{\link{Region}} (or inherited class) object specifying the study region.} +\item{\code{region}}{A \code{\link[poems:Region]{Region}} (or inherited class) object specifying the study region.} \item{\code{coordinates}}{Data frame (or matrix) of X-Y population coordinates (WGS84) in longitude (degrees West) and latitude (degrees North).} diff --git a/man/paleopop.Rd b/man/paleopop.Rd index c15f3d6..ef41671 100644 --- a/man/paleopop.Rd +++ b/man/paleopop.Rd @@ -21,7 +21,7 @@ functionality for modeling populations over paleo time scales. \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. } diff --git a/man/paleopop_simulator.Rd b/man/paleopop_simulator.Rd index b54595a..ca627d9 100644 --- a/man/paleopop_simulator.Rd +++ b/man/paleopop_simulator.Rd @@ -16,7 +16,12 @@ paleopop_simulator(inputs) \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).} @@ -26,7 +31,7 @@ paleopop_simulator(inputs) \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.}