fix merge conflicts

Author: M3nin0

NAMESPACE

@@ -494,6 +494,7 @@ export(sits_smooth)
 export(sits_som_clean_samples)
 export(sits_som_evaluate_cluster)
 export(sits_som_map)
+export(sits_som_remove_samples)
 export(sits_stats)
 export(sits_stratified_sampling)
 export(sits_svm)

R/api_conf.R

@@ -547,24 +547,24 @@
 #' @param source        Data source
 #'
 #' @return              Called for side effects.
-.conf_list_source <- function(s){
-    cat(paste0(s, ":\n"))
-    collections <- .source_collections(source = s)
-    purrr::map(collections, function(c) {
-        cat(paste0("- ", c))
+.conf_list_source <- function(source){
+    cat(paste0(source, ":\n"))
+    collections <- .source_collections(source)
+    purrr::map(collections, function(col) {
+        cat(paste0("- ", col))
         cat(paste0(
-            " (", .source_collection_satellite(s, c),
-            "/", .source_collection_sensor(s, c), ")\n",
-            "- grid system: ", .source_collection_grid_system(s, c), "\n"
+            " (", .source_collection_satellite(source, col),
+            "/", .source_collection_sensor(source, col), ")\n",
+            "- grid system: ", .source_collection_grid_system(source, col), "\n"
         ))
         cat("- bands: ")
-        cat(.source_bands(s, c))
+        cat(.source_bands(source, col))
         cat("\n")
-        if (.source_collection_open_data(source = s, collection = c)) {
+        if (.source_collection_open_data(source, col)) {
             cat("- opendata collection ")
             if (.source_collection_open_data(
-                source = s,
-                collection = c,
+                source = source,
+                collection = col,
                 token = TRUE
             )) {
                 cat("(requires access token)")

R/api_plot_raster.R

@@ -266,7 +266,7 @@
                             dimension = "band",
                             maxColorValue = max_value,
                             use_alpha = FALSE,
-                            probs = c(fst_quant, las_quant),
+                            probs = c(fst_quant, lst_quant),
                             stretch = TRUE
     )
     # tmap params

R/sits_config.R

@@ -64,8 +64,6 @@ sits_config <- function(config_user_file = NULL) {
 }
 #' @title Show current sits configuration
 #' @name sits_config_show
-#' @param source                 Data source (character vector).
-#' @param collection             Collection (character vector).
 #'
 #' @description
 #' Prints the current sits configuration options.
@@ -94,7 +92,7 @@ sits_config_show <- function() {
     config_view <- sits_env[["config"]][["view"]]
     .conf_list_params(config_view)
 
-    cat("User sits_config_user_file() to create a user configuration file")
+    cat("Use sits_config_user_file() to create a user configuration file")
     return(invisible(NULL))
 }
 
@@ -138,12 +136,14 @@ sits_list_collections <- function(source = NULL) {
 #' @title List the cloud collections supported by sits
 #' @name sits_config_user_file
 #' @param  file_path file to store the user configuration file
+#' @param  overwrite replace current configurarion file?
 #' @description
 #' Creates a user configuration file.
 #'
 #' @return Called for side effects
 #' @examples
-#' sits_config_user_file(tempdir(), "my_config_file.yml")
+#' user_file <- paste0(tempdir(), "/my_config_file.yml")
+#' sits_config_user_file(user_file)
 #' @export
 sits_config_user_file <- function(file_path, overwrite = FALSE){
     # get default user configuration file
@@ -181,7 +181,7 @@ sits_config_user_file <- function(file_path, overwrite = FALSE){
 
     if (update)
         warning(.conf("messages", "sits_config_user_file_updated"))
-    else if (newfile)
+    else if (new_file)
         warning(.conf("messages", "sits_config_user_file_new_file"))
     else
         warning(.conf("messages", "sits_config_user_file_no_update"))

R/sits_som.R

@@ -371,3 +371,42 @@ sits_som_evaluate_cluster <- function(som_map) {
     )
     return(purity_by_cluster)
 }
+#' @title Evaluate cluster
+#' @name sits_som_remove_samples
+#' @description
+#' Remove samples from a given class inside a neuron of another class
+#' @param som_map   A SOM map produced by the som_map() function
+#' @param som_eval  An evaluation produced by the som_eval() function
+#' @param class_cluster Dominant class of a set of neurons
+#' @param class_remove  Class to be removed from the neurons of the "class_cluster"
+#' @return A new set of samples with the desired class neurons remove
+#' @examples
+#' if (sits_run_examples()) {
+#'     # create a som map
+#'     som_map <- sits_som_map(samples_modis_ndvi)
+#'     # evaluate the som map and create clusters
+#'     som_eval <- sits_som_evaluate_cluster(som_map)
+#'     # clean the samples
+#'     new_samples <- sits_som_remove_samples(som_map, som_eval, "Pasture", "Cerrado")
+#' }
+#' @export
+sits_som_remove_samples <- function(som_map, som_eval, class_cluster, class_remove){
+
+    # get the samples with id_neuron
+    data <- som_map$data
+    # get the samples by neurons
+    neurons <- som_map$labelled_neurons
+
+    neurons_class_1 <- dplyr::filter(neurons, .data[["label_samples"]] == class_cluster
+                                     & .data[["prior_prob"]] > 0.50)
+    id_neurons_class_1 <- neurons_class_1[["id_neuron"]]
+    # find samples of class2 in neurons of class1
+    samples_remove <- dplyr::filter(data, .data[["label"]] == class_remove &
+                                        .data[["id_neuron"]] %in% id_neurons_class_1)
+    # get the id of the samples to be removed
+    id_samples_remove <- samples_remove[["id_sample"]]
+    # obtain the new samples
+    new_samples <- dplyr::filter(data, !(.data[["id_sample"]] %in% id_samples_remove))
+    # return the new samples
+    return(new_samples)
+}