lights updates on the documentations of the functions + adding the cli package for messages when verbose

Author: ptaconet

R/mf_download_data.R

@@ -12,7 +12,6 @@
 #' @param parallel boolean. Parallelize the download ? Default to FALSE
 #' @param num_workers integer. Number of workers in case of parallel download. Default to number of workers available in the machine minus one.
 #' @param min_filesize integer. Minimum file size expected (in bites) for one file downloaded. If files downloaded are less that this value, the files will be downloaded again. Default 5000.
-#' @param ... not used
 #'
 #' @return a data.frame with the same structure of the input data.frame \code{df_to_dl} + columns providing details of the data downloaded. The additional columns are :
 #' \describe{
@@ -73,7 +72,7 @@
 #' ### Plot the data
 #' terra::plot(modis_ts)
 #' }
-mf_download_data <- function(df_to_dl, path = tempfile("modisfast_"), parallel = FALSE, num_workers = parallel::detectCores() - 1, credentials = NULL, verbose = TRUE, min_filesize = 5000, ...) {
+mf_download_data <- function(df_to_dl, path = tempfile("modisfast_"), parallel = FALSE, num_workers = parallel::detectCores() - 1, credentials = NULL, verbose = TRUE, min_filesize = 5000) {
   fileSize <- destfile <- fileDl <- folders <- readme_files <- source <- NULL
 
   source <- "earthdata"
@@ -189,16 +188,16 @@ mf_download_data <- function(df_to_dl, path = tempfile("modisfast_"), parallel =
 
   if (!(identical(data_dl, data_downloaded))) {
     if (verbose) {
-      cli_alert_warning("Only part of the data has been downloaded. Downloading the remaining datasets one by one...\n")
+      cli::cli_alert_warning("Only part of the data has been downloaded. Downloading the remaining datasets one by one...\n")
     }
     mf_download_data(df_to_dl = df_to_dl, path = path, parallel = FALSE, credentials = credentials) # ,source=source)
   } else {
     # 1 : download ok
     # 2 : download error
     # 3 : data already existing in output folder
     if (verbose) {
-      cli_alert_success("\nData were all properly downloaded under the folder(s) ", paste(as.character(unique(dirname(df_to_dl$destfile))), collapse = " and "))
-      cli_alert_info("\nTo import the data in R, use the function modisfast::mf_import_data() rather than terra::rast() or stars::read_stars(). More info at help(mf_import_data)\n")
+      cli::cli_alert_success("\nData were all properly downloaded under the folder(s) ", paste(as.character(unique(dirname(df_to_dl$destfile))), collapse = " and "))
+      cli::cli_alert_info("\nTo import the data in R, use the function modisfast::mf_import_data() rather than terra::rast() or stars::read_stars(). More info at help(mf_import_data)\n")
     }
   }
 

R/mf_get_url.R

@@ -13,7 +13,6 @@
 #' @param opt_param list of optional arguments. optional. (see details).
 #' @param credentials vector string of length 2 with username and password. optional if the function \link{mf_login} was previously executed.
 #' @param verbose boolean. optional. Verbose (default TRUE)
-#' @param ... not used
 #'
 #' @return a data.frame with one row for each dataset to download and 5 columns :
 #'  \describe{
@@ -43,6 +42,7 @@
 #'
 #' @importFrom stringr str_replace
 #' @importFrom stats ave
+#' @importFrom cli cli_alert_success
 #' @import dplyr
 #'
 #' @examples
@@ -97,8 +97,7 @@ mf_get_url <- function(collection,
                        single_netcdf = TRUE,
                        opt_param = NULL,
                        credentials = NULL,
-                       verbose = TRUE,
-                       ...) {
+                       verbose = TRUE) {
   existing_variables <- odap_coll_info <- odap_timeDimName <- odap_lonDimName <- odap_latDimName <- . <- name <- destfile <- roi_id <- NULL
 
   ## tests :
@@ -142,7 +141,7 @@ mf_get_url <- function(collection,
 
   # test variables
   # if(verbose){cat("Checking if specified variables exist for the collection specified...\n")}
-  available_variables <- opt_param$availableVariables$name[which(opt_param$availableVariables$extractable_w_opendapr == "extractable")]
+  available_variables <- opt_param$availableVariables$name[which(opt_param$availableVariables$extractable_with_modisfast == "extractable")]
   if (is.null(variables)) {
     variables <- available_variables
   } else {
@@ -172,7 +171,7 @@ mf_get_url <- function(collection,
     dplyr::rename(time_start = date, id_roi = roi_id)
 
   if (verbose) {
-    cat("OK\n")
+    cli::cli_alert_success("URL(s) built\n")
   }
 
   return(table_urls)

R/mf_import_data.R

@@ -8,6 +8,7 @@
 #' @param proj_epsg numeric. EPSG of the desired projection for the output raster (default : source projection of the data).
 #' @param roi_mask \code{SpatRaster} or \code{SpatVector} or \code{sf}. Area beyond which data will be masked. Typically, the input ROI of \link{mf_get_url} (default : NULL (no mask))
 #' @param vrt boolean. Import virtual raster instead of SpatRaster. Useful for very large files. (default : FALSE)
+#' @param verbose boolean. optional. Verbose (default TRUE)
 #' @inheritParams mf_get_url
 #' @param ... not used
 #'
@@ -28,6 +29,7 @@
 #' @import purrr
 #' @importFrom terra rast t merge flip
 #' @importFrom magrittr %>%
+#' @importFrom cli cli_alert_success
 #' @export
 #'
 #' @examples
@@ -74,6 +76,7 @@ mf_import_data <- function(path,
                            proj_epsg = NULL,
                            roi_mask = NULL,
                            vrt = FALSE,
+                           verbose = TRUE,
                            ...) {
   rasts <- NULL
 
@@ -89,11 +92,19 @@ mf_import_data <- function(path,
     stop("paramater 'output_class' must be SpatRaster.")
   }
 
+  if (verbose) {
+    cat("Importing the dataset as a",output_class,"object...\n")
+  }
+
   if (odap_coll_info$source %in% c("MODIS", "VIIRS")) {
     rasts <- .import_modis_viirs(path, output_class, proj_epsg, roi_mask, vrt)
   } else if (odap_coll_info$source == "GPM") {
     rasts <- .import_gpm(path, output_class, proj_epsg, roi_mask)
   }
 
+  if (verbose) {
+    cli_alert_success("Dataset imported")
+  }
+
   return(rasts)
 }

R/mf_list_variables.R

@@ -6,7 +6,7 @@
 #' @inheritParams mf_get_url
 #'
 #' @return A data.frame with the variables available for the collection, and a set of related information for each variable.
-#' The variables marked as "extractable" in the column "extractable_w_opendapr" can be provided as input parameter \code{variables} of the function \link{mf_get_url}
+#' The variables marked as "extractable" in the column "extractable_with_modisfast" can be provided as input parameter \code{variables} of the function \link{mf_get_url}
 #'
 #' @export
 #'
@@ -83,20 +83,20 @@ mf_list_variables <- function(collection, credentials = NULL) { # for a given co
   dim_proj <- opendapMetadata$dim_proj
 
   tab <- tab %>%
-    dplyr::mutate(extractable_w_opendapr = dplyr::case_when(
+    dplyr::mutate(extractable_with_modisfast = dplyr::case_when(
       name %in% c(dim_lon, dim_lat, dim_time, dim_proj) ~ "automatically extracted",
       grepl(dim_lon, tab$indices) & grepl(dim_lat, tab$indices) & grepl(dim_time, tab$indices) & !is.na(dim_time) ~ "extractable",
       grepl(dim_lon, tab$indices) & grepl(dim_lat, tab$indices) & is.na(dim_time) ~ "extractable"
     ))
 
-  tab$extractable_w_opendapr[which(is.na(tab$extractable_w_opendapr))] <- "not extractable"
+  tab$extractable_with_modisfast[which(is.na(tab$extractable_with_modisfast))] <- "not extractable"
 
   if (opendapMetadata$source == "SMAP") {
-    tab$extractable_w_opendapr[which(tab$extractable_w_opendapr == "not extractable")] <- "extractable"
+    tab$extractable_with_modisfast[which(tab$extractable_with_modisfast == "not extractable")] <- "extractable"
   }
 
 
-  tab <- tab[c("name", "long_name", "units", "indices", "all_info", "extractable_w_opendapr")]
+  tab <- tab[c("name", "long_name", "units", "indices", "all_info", "extractable_with_modisfast")]
 
   return(tab)
 }

R/mf_login.R

@@ -4,6 +4,8 @@
 #'
 #' @inheritParams mf_get_url
 #'
+#' @importFrom cli cli_alert_success
+#'
 #' @return None.
 #' @export
 #'
@@ -39,6 +41,6 @@ mf_login <- function(credentials, verbose = TRUE) {
   # }
   # if(verbose){cat("Successfull login to",source,"\n")}
   if (verbose) {
-    cat("Successfull login to Earthdata\n")
+    cli::cli_alert_success("Successfull login to Earthdata\n")
   }
 }