small changes

Author: elgabbas

R/DWF_IAS_distribution.R

@@ -244,15 +244,16 @@ IAS_distribution <- function(
 
   IASDT.R::cat_time(
     paste0("There are ", length(Countries2Exclude), " countries to exclude:"),
-    level = 2, time = FALSE)
+    level = 2, cat_timestamp = FALSE)
 
   # Mask grid to exclude countries - `TRUE` for grid cells to be considered as
   # presence if present in any of the data source; `FALSE` for grid cells need
   # to be masked as 0 in species distribution maps (1 becomes 0)
   if (length(Countries2Exclude) > 0) {
 
     IASDT.R::cat_time(
-      paste(sort(Countries2Exclude), collapse = " + "), level = 3, time = FALSE)
+      paste(sort(Countries2Exclude), collapse = " + "),
+      level = 3, cat_timestamp = FALSE)
 
     Mask_Keep <- Grid_10_CNT %>%
       dplyr::mutate(Keep = !(Country %in% Countries2Exclude)) %>%

R/DWF_IAS_process.R

@@ -194,7 +194,8 @@ IAS_process <- function(env_file = ".env", n_cores = 6L, overwrite = TRUE) {
 
   IASDT.R::cat_diff(
     init_time = .StartTimeDist,
-    prefix = "Processing Species-specific data took ", n_lines = 1, level = 2)
+    prefix = "Processing Species-specific data took ",
+    msg_n_lines = 1, level = 2)
 
   # # ..................................................................... ###
 

R/DWF_bioreg.R

@@ -113,7 +113,7 @@ bioreg_process <- function(env_file = ".env") {
       "Download link extraction failed. Found: ", length(BioReg_URL2),
       call. = FALSE)
   }
-  IASDT.R::cat_time(BioReg_URL2, level = 2, time = FALSE)
+  IASDT.R::cat_time(BioReg_URL2, level = 2, cat_timestamp = FALSE)
 
   # # |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ##
 
@@ -122,11 +122,12 @@ bioreg_process <- function(env_file = ".env") {
   Zip_file <- IASDT.R::path(Path_Raw, ZipFileName)
   DownCommand <- stringr::str_glue(
     'curl -J --create-dirs --output-dir {Path_Raw} -o\\
-    "{ZipFileName}" -L {BioReg_URL2} --silent --max-time 300')
+    "{ZipFileName}" -L {BioReg_URL2} --silent --max-cat_time 300')
 
   attempt <- 1
   repeat {
-    IASDT.R::cat_time(paste0("Attempt ", attempt), level = 2, time = FALSE)
+    IASDT.R::cat_time(
+      paste0("Attempt ", attempt), level = 2, cat_timestamp = FALSE)
 
     invisible(IASDT.R::system_command(DownCommand))
 
@@ -239,7 +240,7 @@ bioreg_process <- function(env_file = ".env") {
   # Saving processed data ----
   IASDT.R::cat_time("Saving processed data")
 
-  IASDT.R::cat_time("tiff", level = 1, time = FALSE)
+  IASDT.R::cat_time("tiff", level = 1, cat_timestamp = FALSE)
   terra::writeRaster(
     x = BioReg_R, overwrite = TRUE,
     filename = file.path(Path_BioReg, "BioReg_R.tif"))
@@ -250,12 +251,12 @@ bioreg_process <- function(env_file = ".env") {
       file = file.path(Path_BioReg, "BioReg_R.tif.vat.dbf"),
       factor2char = TRUE, max_nchar = 254)
 
-  IASDT.R::cat_time("RData - raster object", level = 1, time = FALSE)
+  IASDT.R::cat_time("RData - raster object", level = 1, cat_timestamp = FALSE)
   IASDT.R::save_as(
     object = terra::wrap(BioReg_R), object_name = "BioReg_R",
     out_path = file.path(Path_BioReg, "BioReg_R.RData"))
 
-  IASDT.R::cat_time("RData - sf object", level = 1, time = FALSE)
+  IASDT.R::cat_time("RData - sf object", level = 1, cat_timestamp = FALSE)
   save(BioReg_sf, file = file.path(Path_BioReg, "BioReg_sf.RData"))
 
   # # ..................................................................... ###

R/DWF_railway_intensity.R

@@ -238,7 +238,7 @@ railway_intensity <- function(
     file = IASDT.R::path(Path_Railways, "Railways_Links.RData"))
 
   IASDT.R::cat_diff(
-    init_time = .StartTimeDown, n_lines = 1, level = 1,
+    init_time = .StartTimeDown, msg_n_lines = 1, level = 1,
     prefix = "Preparing railways download links took ")
 
   # # ..................................................................... ###
@@ -423,7 +423,7 @@ railway_intensity <- function(
 
   IASDT.R::cat_diff(
     init_time = .StartTimeProcess,
-    prefix = "Processing railway data took ", n_lines = 1, level = 1)
+    prefix = "Processing railway data took ", msg_n_lines = 1, level = 1)
 
   # # ..................................................................... ###
 

R/DWF_river_length.R

@@ -132,7 +132,7 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
 
   # Extract only the missing or outdated files
   if (length(Rivers2extract) > 0) {
-    IASDT.R::cat_time("Extracting files", level = 1, time = FALSE)
+    IASDT.R::cat_time("Extracting files", level = 1, cat_timestamp = FALSE)
     archive::archive_extract(
       Path_Rivers_Zip, dir = Path_Rivers_Interim,
       files = basename(Rivers2extract)) %>%
@@ -166,7 +166,8 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
 
           # Load data from sf file if already exists and valid
           IASDT.R::cat_time(
-            "GPKG file was already processed as sf", level = 2, time = FALSE)
+            "GPKG file was already processed as sf",
+            level = 2, cat_timestamp = FALSE)
           River_sf <- IASDT.R::load_as(File_Sf)
 
         } else {
@@ -194,7 +195,8 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
 
           if (nrow(gpkg_2_Extract) > 0) {
 
-            IASDT.R::cat_time("Extracting gpkg file", level = 2, time = FALSE)
+            IASDT.R::cat_time(
+              "Extracting gpkg file", level = 2, cat_timestamp = FALSE)
 
             # `archive::archive_extract` will always keep the file structure
             # inside of the ZIP file, which is not what needed here.
@@ -205,15 +207,16 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
           } else {
 
             IASDT.R::cat_time(
-              "gpkg file was already extracted", level = 2, time = FALSE)
+              "gpkg file was already extracted",
+              level = 2, cat_timestamp = FALSE)
 
           }
 
           # # .................................. #
 
           # Read the gpkg file as sf object
           IASDT.R::cat_time(
-            "Read the gpkg files as sf", level = 2, time = FALSE)
+            "Read the gpkg files as sf", level = 2, cat_timestamp = FALSE)
 
           River_sf <- sf::st_read(
             # Read the gpkg files
@@ -238,7 +241,7 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
 
           # Save the processed data as an sf object
           IASDT.R::cat_time(
-            "Saving processed data as sf", level = 2, time = FALSE)
+            "Saving processed data as sf", level = 2, cat_timestamp = FALSE)
           IASDT.R::save_as(
             object = River_sf, object_name = "River_sf", out_path = File_Sf)
         }
@@ -247,7 +250,7 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
         # # .................................. #
 
         # Rasterize the river network data
-        IASDT.R::cat_time("Rasterizing", level = 2, time = FALSE)
+        IASDT.R::cat_time("Rasterizing", level = 2, cat_timestamp = FALSE)
 
         River_sf %>%
           dplyr::mutate(
@@ -310,13 +313,13 @@ river_length <- function(env_file = ".env", cleanup = FALSE) {
   # # |||||||||||||||||||||||||||||||||||
 
   # Save as RData
-  IASDT.R::cat_time("Save as RData", level = 1, time = FALSE)
+  IASDT.R::cat_time("Save as RData", level = 1, cat_timestamp = FALSE)
   IASDT.R::save_as(
     object = terra::wrap(River_Lengths), object_name = "river_length",
     out_path = IASDT.R::path(Path_Rivers, "River_Lengths.RData"))
 
   # Save as tif files
-  IASDT.R::cat_time("Save as tif files", level = 1, time = FALSE)
+  IASDT.R::cat_time("Save as tif files", level = 1, cat_timestamp = FALSE)
   terra::writeRaster(
     x = River_Lengths,
     filename = IASDT.R::path(

R/general_cat_diff.R

@@ -46,7 +46,7 @@
 
 cat_diff <- function(
     init_time, chunk_text = "Session summary", prefix = "Completed in ",
-    cat_info = FALSE, level = 0L, time = FALSE, ...) {
+    cat_info = FALSE, level = 0L, cat_timestamp = FALSE, ...) {
 
   if (is.null(init_time)) {
     stop("`init_time` cannot be NULL", call. = FALSE)
@@ -57,7 +57,8 @@ cat_diff <- function(
     prefix <- paste0("\n", prefix)
   }
 
-  Period <- lubridate::time_length(lubridate::now(tzone = "CET") - init_time) %>%
+  Period <- lubridate::time_length(
+    lubridate::now(tzone = "CET") - init_time) %>%
     lubridate::seconds_to_period()
   Period_hours <- stringr::str_pad(
     (lubridate::hour(Period) + 24 * lubridate::day(Period)),
@@ -69,7 +70,7 @@ cat_diff <- function(
 
   paste0(Period_hours, ":", Period_minutes, ":", Period_seconds) %>%
     paste0(prefix, .) %>%
-    IASDT.R::cat_time(level = level, time = time, ...)
+    IASDT.R::cat_time(level = level, cat_timestamp = cat_timestamp, ...)
 
   return(invisible(NULL))
 }

R/general_cat_sep.R

@@ -9,13 +9,13 @@
 #' readability of console output in R scripts or during interactive sessions.
 #' @param n_separators integer; the number of separator lines to print. Default
 #'   is `1`.
-#' @param lines_before,lines_after integer; the number of extra empty lines to
-#'   print before and after the separator lines. Default is `0` and `1`,
-#'   respectively.
+#' @param sep_lines_before,sep_lines_after integer; the number of extra empty
+#'   lines to print before and after the separator lines. Default is `0` and
+#'   `1`, respectively.
 #' @param line_char character; the character used to construct the separator
 #'   line. Default is `"-"`.
-#' @param repetitions integer; the number of times the character is repeated to
-#'   form a separator line. Default is `50`.
+#' @param line_char_rep integer; the number of times the character is repeated
+#'   to form a separator line. Default is `50`.
 #' @param ... additional arguments to be passed to `cat()`.
 #' @name cat_sep
 #' @inheritParams cat_time
@@ -31,44 +31,46 @@
 #'
 #' cat_sep(2,2,3, line_char = "*")
 #'
-#' cat_sep(2,2,3, line_char = "*", repetitions = 20)
+#' cat_sep(2,2,3, line_char = "*", line_char_rep = 20)
 #' @export
 
 cat_sep <- function(
-    n_separators = 1L, lines_before = 0L, lines_after = 1L, line_char = "-",
-    repetitions = 50L, bold = FALSE, red = FALSE, ...) {
+    n_separators = 1L, sep_lines_before = 0L, sep_lines_after = 1L,
+    line_char = "-", line_char_rep = 50L, cat_bold = FALSE, cat_red = FALSE,
+    ...) {
 
   # Check input arguments
   AllArgs <- ls(envir = environment())
   AllArgs <- purrr::map(
     AllArgs,
     function(x) get(x, envir = parent.env(env = environment()))) %>%
     stats::setNames(AllArgs)
-  NumericArgs <- c("n_separators", "lines_before", "lines_after", "repetitions")
+  NumericArgs <- c(
+    "n_separators", "sep_lines_before", "sep_lines_after", "line_char_rep")
   IASDT.R::check_args(
     args_all = AllArgs, args_to_check = NumericArgs, args_type = "numeric")
   IASDT.R::check_args(
     args_all = AllArgs, args_to_check = "line_char", args_type = "character")
 
-  if (bold) {
+  if (cat_bold) {
     line_char <- crayon::bold(line_char)
   }
-  if (red) {
+  if (cat_red) {
     line_char <- crayon::red(line_char)
   }
 
-  if (lines_before > 0) {
-    cat(strrep("\n", lines_before), ...)
+  if (sep_lines_before > 0) {
+    cat(strrep("\n", sep_lines_before), ...)
   }
 
 
-  paste(rep(line_char, repetitions), collapse = "") %>%
+  paste(rep(line_char, line_char_rep), collapse = "") %>%
     rep(n_separators) %>%
-    paste0(collapse = "\n") %>%
+    paste(collapse = "\n") %>%
     cat(...)
 
-  if (lines_after > 0) {
-    cat(strrep("\n", lines_after), ...)
+  if (sep_lines_after > 0) {
+    cat(strrep("\n", sep_lines_after), ...)
   }
   return(invisible(NULL))
 }

R/general_cat_time.R

@@ -10,20 +10,21 @@
 #' print after the message.
 #' @param text character; the text to print before the timestamp. If empty
 #'   (default), only the timestamp is printed.
-#' @param n_lines integer; the number of newline characters to print after the
-#'   message. Default is 1.
-#' @param time logical; whether to include the time in the timestamp. Default is
-#'   `TRUE`. If `FALSE`, only the text is printed.
-#' @param date logical; whether to include the date in the timestamp. Only
+#' @param msg_n_lines integer; the number of newline characters to print after
+#'   the message. Default is 1.
+#' @param cat_timestamp logical; whether to include the time in the timestamp.
+#'   Default is `TRUE`. If `FALSE`, only the text is printed.
+#' @param cat_date logical; whether to include the date in the timestamp. Only
 #'   effective if `time` is `TRUE`. Default is `FALSE`, meaning only the time is
 #'   printed. If `TRUE`, the date is printed in the format "%d/%m/%Y %X".
 #' @param time_zone character; the time zone to use for the timestamp. Default
 #'   is `CET`.
 #' @param level integer; the level at which the message will be printed. If e.g.
 #'   level = 1, the following string will be printed at the beginning of the
 #'   message: "   >>>   ". Default is `0`.
-#' @param bold logical; whether to print the text in bold. Default is `FALSE`.
-#' @param red logical; whether to print the text in red. Default is `FALSE`.
+#' @param cat_bold logical; whether to print the text in bold. Default is
+#'   `FALSE`.
+#' @param cat_red logical; whether to print the text in red. Default is `FALSE`.
 #' @param ... additional arguments passed to `cat`.
 #' @name cat_time
 #' @author Ahmed El-Gabbas
@@ -33,15 +34,15 @@
 #' @examples
 #' cat_time()
 #'
-#' cat_time(date = TRUE)
+#' cat_time(cat_date = TRUE)
 #'
 #' cat_time("time now")
 #'
-#' cat_time("\n\nTime now", n_lines = 2L, level = 1L)
+#' cat_time("\n\nTime now", msg_n_lines = 2L, level = 1L)
 #'
 #' cat_time(
-#'   "\ntime now", date = TRUE, bold = TRUE, red = TRUE,
-#'   n_lines = 2L, level = 1L)
+#'   "\ntime now", cat_date = TRUE, cat_bold = TRUE, cat_red = TRUE,
+#'   msg_n_lines = 2L, level = 1L)
 #'
 #' # The use of levels
 #' {
@@ -52,8 +53,8 @@
 #' }
 
 cat_time <- function(
-    text = "", n_lines = 1L, time = TRUE, bold = FALSE,
-    red = FALSE, date = FALSE, time_zone = "CET", level = 0L, ...) {
+    text = "", msg_n_lines = 1L, cat_timestamp = TRUE, cat_bold = FALSE,
+    cat_red = FALSE, cat_date = FALSE, time_zone = "CET", level = 0L, ...) {
 
   # Validate inputs
   AllArgs <- ls(envir = environment())
@@ -63,23 +64,23 @@ cat_time <- function(
     stats::setNames(AllArgs)
   IASDT.R::check_args(
     args_all = AllArgs, args_type = "logical",
-    args_to_check = c("time", "bold", "red", "date"))
+    args_to_check = c("cat_timestamp", "cat_bold", "cat_red", "cat_date"))
   IASDT.R::check_args(
     args_all = AllArgs, args_type = "numeric",
-    args_to_check = c("n_lines", "level"))
+    args_to_check = c("msg_n_lines", "level"))
   rm(AllArgs, envir = environment())
 
   # Current time
   Now <- lubridate::now(tzone = time_zone)
 
   # Format date / time
-  if (date && time) {
+  if (cat_date && cat_timestamp) {
     Now <- format(Now, "%d/%m/%Y %X")
     Now2 <- paste0(" - ", Now)
-  } else if (date) {
+  } else if (cat_date) {
     Now <- format(Now, "%d/%m/%Y")
     Now2 <- paste0(" - ", Now)
-  } else if (time) {
+  } else if (cat_timestamp) {
     Now <- format(Now, "%X")
     Now2 <- paste0(" - ", Now)
   } else {
@@ -114,15 +115,15 @@ cat_time <- function(
 
   }
 
-  if (bold) {
+  if (cat_bold) {
     text <- crayon::bold(text)
   }
-  if (red) {
+  if (cat_red) {
     text <- crayon::red(text)
   }
 
   cat(text, ...)
-  cat(rep("\n", n_lines))
+  cat(rep("\n", msg_n_lines))
 
   return(invisible(NULL))
 }