change n1_map to integer (#9) and update docs

Author: katarzynam-165

DESCRIPTION

@@ -35,7 +35,7 @@ Suggests:
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))
 Depends: 
     R (>= 3.5.0)

R/disp.R

@@ -234,7 +234,7 @@ dists_tab <- function(N_pos, kernel, dist_resolution) {
 
 #' Dispersal From Non-Empty Grid Cells
 #'
-#' This function calls [sq_disp_calc] with arguments passed from [disp] or
+#' This function calls `sq_disp_calc` with arguments passed from [disp] or
 #' without them (in case of parallel computations).
 #'
 #' Arguments for parallel computation are exported to clusters in [sim].
@@ -273,7 +273,7 @@ sq_disp <- function(
 #' Calculate Dispersal From Non-Empty Grid Cells
 #'
 #' This function calculates more possible target cells available
-#' from source cell `i` (if needed). Then, it uses [one_dist_sq_disp] function
+#' from source cell `i` (if needed). Then, it uses `one_dist_sq_disp` function
 #' to find cells that individuals will emigrate to.
 #'
 #' @param i integer vector of length 1; number of current source cell

R/initialise.R

@@ -373,7 +373,11 @@ initialise <- function(
 
   # output list ---------------------------------------------
   out <- list(
-    n1_map = as.matrix(n1_map, wide = TRUE),
+    n1_map = matrix(
+      data = as.integer(values(n1_map)),
+      nrow = nrow(n1_map),
+      ncol = ncol(n1_map),
+      byrow = TRUE),
     id = wrap(id),
     dist_bin = dist_bin,
     dist_resolution = dist_resolution,
@@ -454,7 +458,7 @@ K_n1_map_check <- function(K_map, n1_map, changing_env) {
 
 #' Get Carrying Capacity For The First Time Step
 #'
-#' [K_get_init_values] returns all values from map of carrying capacity
+#' `K_get_init_values` returns all values from map of carrying capacity
 #' in the first time step.
 #'
 #' @inheritParams K_n1_map_check
@@ -484,19 +488,19 @@ K_get_init_values <- function(K_map, changing_env) {
 
 #' Check For Precalculating Target Cells
 #'
-#' [calc_dist] checks if target cells should be precalculated
-#' and if so calls [dist_list].
+#' `calc_dist` checks if target cells should be precalculated
+#' and if so calls `dist_list`.
 #'
 #' @param id [`SpatRaster`][terra::SpatRaster-class]; contains all cells ids
 #' @param data_table matrix; contains information about all cells in current
 #' time points
 #' @param dist_resolution integer vector of length 1; dimension of one side of
 #' one cell of `id`; in case of an irregular grid or lon/lat raster it is calculated during [`initialisation`][`initialise`]
-#' calculated by [`calculate_dist_params`]
+#' calculated by `calculate_dist_params`
 #' @param dist_bin numeric vector of length 1 with value `>= 0`; in case of an irregular grid or lon/lat raster it is
-#' calculated by [`calculate_dist_params`]
+#' calculated by `calculate_dist_params`
 #' is equal to 0 if  input maps are planar raster; if input maps are lon/lat it is calculated by
-#' rasters, `dist_bin` is calculated by [`calculate_dist_params`]
+#' rasters, `dist_bin` is calculated by `calculate_dist_params`
 #' @param id_within numeric vector; ids of cells inside the study area
 #' @inheritParams initialise
 #'
@@ -538,7 +542,7 @@ calc_dist <- function(
 #' Precalculating Target Cells For Dispersal
 #'
 #' `dist_list` prepares data for precalculation of target cells ids
-#' and then uses [`target_ids`] for calculation
+#' and then uses `target_ids` for calculation
 #'
 #' @inheritParams calc_dist
 #'
@@ -651,7 +655,7 @@ calculate_dist_params <- function(id, id_within, data_table, progress_bar, quiet
 #' from any cells of template `r`. It takes raster's dist_resolution into account.
 #'
 #' @param template template [`SpatRaster`][terra::SpatRaster-class] object
-#' @param dist_resolution parameter calculated by [`calculate_dist_params`] function
+#' @param dist_resolution parameter calculated by `calculate_dist_params` function
 #'
 #' @return numeric vector; numbers of target cells on every possible distance
 #' range

R/target_ids.R

@@ -1,13 +1,13 @@
 
 #' Get Indexes Of Target Cells
 #'
-#' [target_ids] finds all target cells available from given focal cell,
+#' `target_ids` finds all target cells available from given focal cell,
 #' that lie within the maximum distance threshold (`max_dist`).
 #'
 #' @param idx integer vector of length 1; id of cell
-#' @param data integer matrix; necessary data (defined in [dist_list])
+#' @param data integer matrix; necessary data (defined in `dist_list`)
 #' @param id_within integer vector; indexes of cells inside study area
-#' (defined in [dist_list])
+#' (defined in `dist_list`)
 #' @inheritParams dist_list
 #'
 #' @return List of target cells for each distance or `NULL` if there isn't any
@@ -95,7 +95,7 @@ get_vect_from_xy <- function(template, xy_cell, idx = NULL) {
 #' @param xy_vect [`SpatVector`][terra::SpatVector-class] object; represents current cell
 #' @param dist_resolution integer vector of length 1; dimension of one side of
 #' one cell of `id`; in case of an irregular grid or lon/lat raster it is
-#' calculated by [`calculate_dist_params`]
+#' calculated by `calculate_dist_params`
 #' @param min_dist_scaled integer vector of length 1; minimum distance to calculate target cell scaled by `dist_resolution`
 #' @param max_dist_scaled integer vector of length 1; maximum distance to calculate target cell scaled by `dist_resolution`
 #'
@@ -129,7 +129,7 @@ get_ds <- function(template, xy_vect, id_within, dist_resolution,
   ids <- id_within[in_range]
   ds <- d_within[in_range]
 
-  return(matrix(c(ids, ds), ncol = 2))
+  return(matrix(as.integer(c(ids, ds)), ncol = 2))
 }