Develop (#14)

* Added docker file
* Added commands to run Dockerfile
* Added Dockefile to .Buildignore
* #13 Deprecated function
  - decompress_gz
  - import_geff_data_from_tar
  - mean_percs
  - stack_netcdf_files
* Fixed tests and updated description
* removed linters
* Fixed message in deprecated functions

Author: cvitolo

.Rbuildignore

@@ -11,3 +11,4 @@
 ^NOTICE$
 ^docs$
 ^_pkgdown\.yml$
+^Dockerfile$

.travis.yml

@@ -6,14 +6,16 @@ dist: xenial
 
 addons:
   apt:
+    sources:
+      - sourceline: 'ppa:ubuntugis/ubuntugis-unstable'
     packages:
-    - libssl-dev
-    - libnetcdf-dev
-    - netcdf-bin
-    - libhdf5-dev
-    - libproj-dev
-    - libgdal-dev
-    - gdal-bin
+      - libssl-dev
+      - libproj-dev
+      - libgeos-dev
+      - libhdf4-alt-dev
+      - libhdf5-serial-dev
+      - libgdal-dev
+      - libnetcdf-dev
 
 r_github_packages:
   - jimhester/lintr

DESCRIPTION

@@ -43,6 +43,6 @@ Suggests:
     lintr
 VignetteBuilder: knitr
 Encoding: UTF-8
-SystemRequirements: GDAL binaries, PROJ.4, netcdf4, hdf5, openssl
+SystemRequirements: GDAL with HDF4&5 support, PROJ.4, netcdf4, hdf5, openssl
 License:  Apache License 2.0
 RoxygenNote: 6.1.1

Dockerfile

@@ -0,0 +1,16 @@
+FROM s22s/geo-swak
+
+RUN set -eux \
+	&& apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+	&& add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu cosmic-cran35/' \
+	&& apt-get update --yes
+
+RUN set -eux \
+	&& env DEBIAN_FRONTEND=noninteractive \
+		apt install --yes \
+		libssl-dev \
+		r-base-dev
+
+RUN set -eux \
+	&& R -e 'install.packages("devtools")' \
+	&& R -e 'devtools::install_github("ecmwf/caliver")'

NAMESPACE

@@ -3,6 +3,7 @@
 export(anomaly)
 export(classify_index)
 export(daily_clima)
+export(decompress_gz)
 export(firegram)
 export(forecast_summary)
 export(forecast_summary_clima)
@@ -11,8 +12,10 @@ export(get_fire_season)
 export(get_gfed4)
 export(get_perc_risk_index)
 export(get_percentile_raster)
+export(import_geff_data_from_tar)
 export(mask_crop_subset)
 export(mask_with_fuelmodel)
+export(mean_percs)
 export(plot_anomaly)
 export(plot_classified_index)
 export(plot_fire_pdf)

R/anomaly.R

@@ -22,8 +22,6 @@
 
 anomaly <- function(r, clima){
 
-  options(warn = -1)
-
   if (round(r@extent@xmin, 0) == 0) {
 
     # Rotate a Raster* object that has x coordinates (longitude) from 0 to 360,
@@ -46,7 +44,6 @@ anomaly <- function(r, clima){
 
   anomaly_map_cat <- r
   for (i in 1:raster::nlayers(r)){
-    print(i)
     rx <- r[[i]]
     # Get the forecast dates
     forecast_date <- substr(x = names(rx), start = 7, stop = 11)

R/decompress_gz.R

@@ -0,0 +1,191 @@
+#' @title decompress_gz (DEPRECATED)
+#'
+#' @description This function decompresses all .gz files in a given folder
+#'
+#' @param input_dir directory path where all the files to read have been stored
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'   decompress_gz(input_dir = "/var/tmp/moc0/forestfire/")
+#' }
+#'
+
+decompress_gz <- function(input_dir = getwd()){
+
+  .Deprecated()
+  message(paste("NOTE: Since GEFF v2.2 this function is no longer needed.",
+                "It is now deprecated and",
+                "will be removed in the next release."))
+
+  list_of_gzfiles <- list.files(path = input_dir,
+                                pattern = "*.gz", full.names = TRUE)
+
+  # Decompress any gz files
+  for (i in seq_along(list_of_gzfiles)){
+
+    R.utils::gunzip(list_of_gzfiles[i], overwrite = TRUE)
+
+  }
+
+}
+
+
+#' @title import_geff_data_from_tar (DEPRECATED)
+#'
+#' @description This function imports GEFF data (reanalysis or realtime) from a
+#' tar file into a raster stack. Depending on the user's query to the web
+#' portal, the stack can contain different variables.
+#'
+#' @param archive file path to the tar file
+#' @param stack_ncfiles logical (TRUE by default) variable to decided wheteher
+#' decompressed nc files should be stacked or not.
+#'
+#' @export
+#'
+#' @return If \code{stack_ncfiles} is TRUE, the function returns a RasterBrick.
+#' If \code{stack_ncfiles} is FALSE, it returns the list of uncompressed files.
+#'
+#' @examples
+#' \dontrun{
+#'   s <- import_geff_data_from_tar(archive = "test.tar")
+#' }
+#'
+
+import_geff_data_from_tar <- function(archive, stack_ncfiles = TRUE){
+
+  .Deprecated()
+  message(paste("NOTE: Since GEFF v2.2 this function is no longer needed.",
+                "It is now deprecated and",
+                "will be removed in the next release."))
+
+  # From .tar to .gz, and finally to .nc
+  my_temp_dir <- tempdir()
+  list_of_gzfiles <- file.path(my_temp_dir, utils::untar(tarfile = archive,
+                                                         exdir = my_temp_dir,
+                                                         list = TRUE))
+
+  # Untar files
+  utils::untar(tarfile = archive, exdir = my_temp_dir)
+
+  # Decompress any gz files
+  for (i in seq_along(list_of_gzfiles)){
+
+    R.utils::gunzip(list_of_gzfiles[i])
+
+  }
+
+  if (stack_ncfiles == TRUE){
+
+    s <- raster::stack(tools::file_path_sans_ext(list_of_gzfiles))
+
+    return(raster::brick(s))
+
+  } else {
+
+    return(tools::file_path_sans_ext(list_of_gzfiles))
+
+  }
+
+}
+
+
+#' @title mean_percs (DEPRECATED)
+#'
+#' @description Calculate average percentile
+#'
+#' @param vals is the a raster object
+#' @param perc_val is the percentile value used as a threshold
+#' @param mod defines if the values considered for the mean are above ("gt") or
+#' below ("lt") the threshold
+#'
+#' @export
+#'
+
+mean_percs <- function(vals, perc_val, mod){
+
+  .Deprecated()
+  message(paste("NOTE: Since GEFF v2.2 this function is no longer needed.",
+                "It is now deprecated and",
+                "will be removed in the next release."))
+
+  .Deprecated(msg = "This function is deprecated.")
+
+  p_val <- stats::quantile(vals, perc_val / 100, na.rm = TRUE)
+
+  if (mod == "gt") {
+
+    v_perc <- vals[vals >= p_val]
+
+  } else if (mod == "lt") {
+
+    v_perc <- vals[vals <= p_val]
+
+  } else {
+
+    stop("mod should be 'lt' or 'gt'")
+
+  }
+
+  return(mean(v_perc, na.rm = TRUE))
+
+}
+
+
+#' @title stack_netcdf_files (DEPRECATED)
+#'
+#' @description This function merges all the netcdf files in a given directory
+#' over the time dimension. It saves the merged file in the working directory.
+#'
+#' @param input_dir is the directory where all the files to read are stored
+#' @param varname name of the variable to extract
+#' @param pattern regular expression pattern to select a subset of files
+#' @param recursive logical (TRUE by default). If set to TRUE it looks in
+#' folders and subfolders
+#' @param output_file output filename (including path)
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'   # Mergetime using single variable nc files
+#'   stack_netcdf_files(input_dir = "/var/tmp/moc0/forestfire",
+#'                      varname = NULL,
+#'                      pattern = "geff_reanalysis_an_fwis_fwi_",
+#'                      recursive = TRUE,
+#'                      output_file = "outfile.nc")
+#' }
+#'
+
+stack_netcdf_files <- function(input_dir = NULL,
+                               varname = NULL,
+                               pattern = NULL,
+                               recursive = FALSE,
+                               output_file = NULL){
+
+  .Deprecated("raster::stack()")
+  message(paste("NOTE: Since GEFF v2.2 this function is no longer needed.",
+                "It is now deprecated and",
+                "will be removed in the next release."))
+
+  if (is.null(input_dir)) stop("Please specify data folder 'input_dir'!")
+
+  ifiles <- list.files(path = input_dir,
+                       pattern = pattern,
+                       recursive = recursive,
+                       full.names = TRUE)
+
+  if (is.null(output_file)) output_file <- tempfile(fileext = ".nc")
+
+  if (is.null(varname)) varname <- ""
+  s <- raster::stack(x = ifiles, varname = varname)
+
+  if (!is.null(output_file)) {
+    raster::writeRaster(s, filename = output_file,
+                        format = "CDF", overwrite = TRUE)
+  }
+
+  return(s)
+
+}