added or improved usage to function documentation

Author: marlonecobos

R/organize_for_projection.R

@@ -9,17 +9,15 @@
 #' making the variables properly organized for modeling projections.
 #' See **Details** for more information.
 #'
-#' @usage organize_for_projection(output_dir, models = NULL,
-#'                                variable_names = NULL,
-#'                                categorical_variables = NULL,
-#'                                present_file = NULL,
-#'                                past_files = NULL, past_period = NULL,
-#'                                past_gcm = NULL, future_files = NULL,
-#'                                future_period = NULL, future_pscen = NULL,
-#'                                future_gcm = NULL, static_variables = NULL,
-#'                                check_extent = TRUE,
-#'                                resample_to_present = TRUE, mask = NULL,
-#'                                overwrite = FALSE)
+#' @usage
+#' organize_for_projection(output_dir, models = NULL, variable_names = NULL,
+#'                         categorical_variables = NULL, present_file = NULL,
+#'                         past_files = NULL, past_period = NULL,
+#'                         past_gcm = NULL, future_files = NULL,
+#'                         future_period = NULL, future_pscen = NULL,
+#'                         future_gcm = NULL, static_variables = NULL,
+#'                         check_extent = TRUE, resample_to_present = TRUE,
+#'                         mask = NULL, overwrite = FALSE)
 #'
 #' @param output_dir (character) path to the folder where the organized data
 #' will be saved.

R/prediction_changes.R

@@ -1,4 +1,14 @@
-#' Compute changes of suitable areas between scenarios (single scenario / GCM)
+#' Compute changes of suitable areas in other scenarios (single scenario / GCM)
+#'
+#' @usage
+#' prediction_changes(current_predictions, new_predictions,
+#'                    predicted_to = "future", fitted_models = NULL,
+#'                    consensus = "mean", user_threshold = NULL,
+#'                    force_resample = FALSE, gain_color = "#009E73",
+#'                    loss_color = "#D55E00", stable_suitable = "#0072B2",
+#'                    stable_unsuitable = "grey", write_results = FALSE,
+#'                    output_dir = NULL, overwrite = FALSE,
+#'                    write_bin_models = FALSE)
 #'
 #' @param current_predictions (SpatRaster) A `SpatRaster` object returned by
 #'  `predict_selected()` with suitability predicted under current conditions.
@@ -99,6 +109,7 @@
 #'                                 predicted_to = "future")
 #' # Plot result
 #' terra::plot(p_changes)
+
 prediction_changes <- function(current_predictions,
                                new_predictions,
                                predicted_to = "future",
@@ -113,7 +124,7 @@ prediction_changes <- function(current_predictions,
                                write_results = FALSE,
                                output_dir = NULL,
                                overwrite = FALSE,
-                               write_bin_models = FALSE){
+                               write_bin_models = FALSE) {
   #### Check data ####
   if (missing(current_predictions)) {
     stop("Argument 'current_predictions' must be defined.")

R/single_mop.R

@@ -5,6 +5,16 @@
 #' represent dissimilarities and non-analogous conditions when comparing a set
 #' of reference conditions (M) against another set of scenario conditions (G).
 #'
+#' @usage
+#' single_mop(data, new_variables, subset_variables = FALSE,
+#'            mask = NULL, type = "basic", na_in_range = TRUE,
+#'            calculate_distance = FALSE, where_distance = "in_range",
+#'            distance = "euclidean", scale = FALSE, center = FALSE,
+#'            fix_NA = TRUE, percentage = 1, comp_each = 2000, tol = NULL,
+#'            rescale_distance = FALSE, parallel = FALSE, ncores = NULL,
+#'            progress_bar = TRUE, write_files = FALSE, out_dir = NULL,
+#'            overwrite = FALSE)
+#'
 #' @param data an object of class `fitted_models` returned by the
 #' [fit_selected()] function, an object of class `prepared_data` returned by
 #' the [prepare_data()] function, or an object of class `calibration_results`
@@ -160,7 +170,7 @@
 #' # Run MOP
 #' sm <- single_mop(data = fitted_model_maxnet, new_variables = future_scenario,
 #'                  type = "detailed")
-#'
+
 single_mop <- function(data,
                        new_variables,
                        subset_variables = FALSE,
@@ -182,7 +192,7 @@ single_mop <- function(data,
                        progress_bar = TRUE,
                        write_files = FALSE,
                        out_dir = NULL,
-                       overwrite = FALSE){
+                       overwrite = FALSE) {
 
   #Check data
   if (missing(data)) {