Update site and remove private functions

R/utils.R

@@ -318,6 +318,8 @@ averageTimeSeries = function(mdl, var, n_years = 10){
 #'
 #' @return Plain data frame without tibble attributes
 #'
+#' @noRd
+#'
 untibble <- function (tibble) {
   data.frame(unclass(tibble), check.names = FALSE, stringsAsFactors = FALSE)
 }  ## escape the nonsense

R/zoomss_mvf.R

@@ -1,31 +1,31 @@
 #' McKendrick-von Foerster Equation Solver (Base R Implementation)
 #'
 #' @title Solve McKendrick-von Foerster equation for size-structured populations
-#' @description Solves the McKendrick-von Foerster (MvF) partial differential equation 
+#' @description Solves the McKendrick-von Foerster (MvF) partial differential equation
 #'   for size-structured population dynamics using a finite difference approach in base R.
-#' @details This function implements the numerical solution to the McKendrick-von Foerster 
+#' @details This function implements the numerical solution to the McKendrick-von Foerster
 #'   equation, which describes how populations change across size classes over time.
 #'   The equation is solved using an upwind finite difference scheme that handles:
 #'   - Growth through size classes (advection term)
-#'   - Diffusion between adjacent size classes  
+#'   - Diffusion between adjacent size classes
 #'   - Source and sink terms from feeding and mortality
-#'   
+#'
 #'   The function processes each functional group separately and applies boundary conditions
 #'   appropriate for size-structured models. The last size class is set to zero abundance
 #'   to represent maximum size limits.
-#'   
+#'
 #'   This is a core computational component of ZooMSS that updates population abundances
 #'   at each time step based on growth, mortality, and reproduction processes.
 #'
 #' @param ngrps Number of functional groups in the model
 #' @param curr_min_size Vector of minimum size class indices for each group
-#' @param curr_max_size Vector of maximum size class indices for each group  
+#' @param curr_max_size Vector of maximum size class indices for each group
 #' @param A_iter Matrix of advection coefficients for current iteration
 #' @param C_iter Matrix of diagonal coefficients for current iteration
 #' @param Nb_iter Matrix to store updated abundances for current iteration
 #' @param S_iter Matrix of source terms for current iteration
 #' @param A Matrix of advection coefficients
-#' @param B Matrix of diffusion coefficients  
+#' @param B Matrix of diffusion coefficients
 #' @param C Matrix of diagonal coefficients
 #' @param Nb Matrix of abundances to be updated
 #' @param S Matrix of source terms
@@ -40,19 +40,21 @@
 #' ngrid <- 100
 #' curr_min_size <- c(1, 10, 20, 30, 40, 50, 60, 70, 80)
 #' curr_max_size <- c(30, 40, 50, 60, 70, 80, 90, 95, 100)
-#' 
+#'
 #' # Initialize coefficient matrices
 #' A <- matrix(0, nrow = ngrps, ncol = ngrid)
-#' B <- matrix(0, nrow = ngrps, ncol = ngrid) 
+#' B <- matrix(0, nrow = ngrps, ncol = ngrid)
 #' C <- matrix(1, nrow = ngrps, ncol = ngrid)
 #' S <- matrix(0, nrow = ngrps, ncol = ngrid)
 #' Nb <- matrix(0.1, nrow = ngrps, ncol = ngrid)
-#' 
+#'
 #' # Run MvF solver
 #' updated_abundances <- zoomss_mvf(ngrps, curr_min_size, curr_max_size,
 #'                                        A, C, Nb, S, A, B, C, Nb, S)
 #' }
 #'
+#' @noRd
+#'
 zoomss_mvf <- function(ngrps, curr_min_size, curr_max_size, A_iter, C_iter, Nb_iter, S_iter, A, B, C, Nb, S){
 
   for(i in 1:ngrps){

R/zoomss_params.R

@@ -53,6 +53,8 @@
 #' params <- zoomss_params(Groups, input_params, isave = 50)
 #' }
 #'
+#' @noRd
+#'
 zoomss_params <- function(Groups, input_params, isave){
 
   # Calculate dt and tmax from time column in input_params

R/zoomss_run.R

@@ -54,6 +54,8 @@
 #' final_abundances <- results$N[dim(results$N)[1],,]
 #' }
 #'
+#' @noRd
+#'
 zoomss_run <- function(model){
 
   # Pull out some useful parameters - just a shortcut

R/zoomss_setup.R

@@ -57,6 +57,8 @@
 #' results <- zoomss_run(model)
 #' }
 #'
+#' @noRd
+#'
 zoomss_setup <- function(param){
 
   ## Dynamic prey availability matrix: dim1 is predators, dim2 is predator size classes,

_pkgdown.yml

@@ -4,7 +4,7 @@ template:
   bslib:
     toc: true
     toc-expand: 3
-  bootswatch: flatly
+  bootswatch: cerulean
 reference:
 - title: Data
   desc: Data related functions and datasets
@@ -30,10 +30,6 @@ reference:
   - starts_with("extract")
   - starts_with("get")
   - starts_with("reduce")
-- title: Private functions
-  desc: Functions to be unexported
-- contents:
-  - untibble
 navbar:
   structure:
     right: [github, search]

docs/pkgdown.yml

@@ -3,4 +3,4 @@ pkgdown: 2.1.3
 pkgdown_sha: ~
 articles:
   zoomss: zoomss.html
-last_built: 2025-08-25T00:06Z
+last_built: 2025-08-25T00:52Z