Merge pull request #4 from adamhsparks/devel

Update from level

.Rbuildignore

@@ -20,3 +20,5 @@ vignettes/figure
 ^_pkgdown\.yml$
 ^\.circleci$
 ^GSODR.code-workspace$
+^doc$
+^Meta$

.gitignore

@@ -22,3 +22,5 @@ inst/doc
 
 generate.rb
 *.code-workspace
+doc
+Meta

.travis.yml

@@ -1,3 +1,4 @@
+dist: xenial
 language: r
 cache: packages
 r_check_args: --as-cran --run-donttest
@@ -10,6 +11,15 @@ matrix:
   - os: linux
     r: devel
 
+addons:
+  apt:
+    sources:
+      - sourceline: 'ppa:ubuntugis/ppa'
+    packages:
+      - libudunits2-dev
+      - libproj-dev
+      - libgdal-dev
+
 after_failure:
   - ./pkg-build.sh dump_logs
 

DESCRIPTION

@@ -14,8 +14,6 @@ Authors@R: c(person("Adam", "Sparks", role = c("aut", "cre"),
     person("Hugh", "Parsonage", role = c("cph", "ctb"),
     email = "[email protected]",
     comment = c(ORCID = "0000-0003-4055-0835")),
-    person("Bob", "Rudis", email = "[email protected]", role = c("cph", "ctb"),
-    comment = c(ORCID = "0000-0001-5670-2640")),
     person("Gwenael", "Giboire", email = "[email protected]",
     role = "ctb",
     comment = "Several bug reports in early versions and testing feedback"),
@@ -46,6 +44,7 @@ Depends:
     R (>= 3.3.0)
 License: MIT + file LICENSE
 Imports: 
+    countrycode,
     curl,
     data.table (>= 1.11.6),
     future.apply,
@@ -56,22 +55,19 @@ Imports:
 Suggests:
     covr,
     dplyr,
-    DT,
     future,
     ggplot2,
     gridExtra,
-    ggthemes,
     knitr,
     mapproj,
     maps,
     plotKML,
-    raster,
     reshape2,
     rgdal (>= 1.1-9),
-    rgeos,
     rmarkdown,
     roxygen2 (>= 6.1.0),
     sf,
+    skimr,
     sp,
     spacetime,
     testthat,

NEWS.md

@@ -7,18 +7,22 @@ data could not be downloaded any longer
 
 ## Major changes
 
-- Corrected elevation values are no longer available from GSODR, this makes
-package updates much easier
+- Corrected elevation values are no longer available from GSODR
 
 - Objects are returned as `data.table` objects
 
 ## Minor changes
 
+- `get_inventory()` now uses https rather than FTP server
+
+- `update_station_list()` now uses https rather than FTP server
+
 - Implement better error handling when attempting to fetch station inventories
 
 - Reduced package dependencies
 
-- Improved vignettes
+- Improved vignettes that are pre-compiled for faster package installation and
+updated content with linting and error corrections
 
 - Users may now specify country by FIPS code when using `get_GSOD()`
 

R/get_GSOD.R

@@ -74,8 +74,8 @@
 #'
 #' tbar
 #'
-#' # Download data for Australia from 2010 to 2015
-#' AUS <- get_GSOD(years = 2010:2015, country = "Australia")
+#' # Download data for Australia from 2010 to 2011
+#' AUS <- get_GSOD(years = 2010:2011, country = "Australia")
 #'
 #' AUS
 #' }
@@ -94,10 +94,6 @@ get_GSOD <- function(years,
                      country = NULL,
                      max_missing = NULL,
                      agroclimatology = FALSE) {
-  # Create objects for use in retrieving files ---------------------------------
-  original_timeout <- options("timeout")[[1]]
-  options(timeout = 300)
-  on.exit(options(timeout = original_timeout))
 
   # Validate user inputs -------------------------------------------------------
   .validate_years(years)
@@ -129,6 +125,7 @@ get_GSOD <- function(years,
 
   # Load station list
   load(system.file("extdata", "isd_history.rda", package = "GSODR")) # nocov
+  setkeyv(isd_history, "STNID")
 
   # Validate user entered stations for existence in stations list from NCEI
   invisible(lapply(
@@ -152,17 +149,14 @@ get_GSOD <- function(years,
   if (!is.null(country)) {
     # Load country list
     # CRAN NOTE avoidance
-    country_list <- NULL # nocov
-    load(system.file("extdata", "country_list.rda", package = "GSODR")) # nocov
 
-    country <- .validate_country(country, country_list)
+    country <- .validate_country(country, isd_history)
 
     file_list <-
-      .subset_country_list(country,
-                           country_list,
-                           file_list,
-                           isd_history,
-                           years)
+      .subset_country_list(country = country,
+                           isd_history = isd_history,
+                           file_list = file_list,
+                           years = years)
   }
 
   # Validate stations for missing days -----------------------------------------

R/get_inventory.R

@@ -2,7 +2,7 @@
 #' Download and return a data frame of \acronym{GSOD} weather station data inventories
 #'
 #' The \acronym{NCEI} maintains a document,
-#' \url{ftp://ftp.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt}, which lists
+#' \url{https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt}, which lists
 #' the number of weather observations by station-year-month from the beginning
 #' of the stations' records.  This function retrieves that document and prints
 #' an information header displaying the last update time with a data frame of
@@ -28,21 +28,11 @@
 get_inventory <- function() {
   load(system.file("extdata", "isd_history.rda", package = "GSODR")) #nocov
 
-  ftp_handle <-
-    curl::new_handle(
-      ftp_use_epsv = FALSE,
-      crlf = TRUE,
-      ssl_verifypeer = FALSE,
-      ftp_response_timeout = 30,
-      ftp_skip_pasv_ip = TRUE
-    )
-
   tryCatch({
     curl::curl_download(
-      "ftp://ftp.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt",
+      "https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt",
       destfile = file.path(tempdir(), "inventory.txt"),
-      quiet = TRUE,
-      handle = ftp_handle
+      quiet = TRUE
     )
 
     "STNID" <- NULL #nocov

R/internal_functions.R

@@ -40,9 +40,9 @@
       paste0(station),
       " is not a valid station ID number, please check your entry.\n",
       "Valid Station IDs can be found in the isd-history.txt file\n",
-      "available from the US NCEI FTP server by combining the USAF and\n",
+      "available from the US NCEI server by combining the USAF and\n",
       "WBAN columns, e.g. '007005' '99999' is '007005-99999' from this\n",
-      "file <ftp://ftp.ncdc.noaa.gov/pub/data/noaa/isd-history.txt>\n"
+      "file <https://www1.ncdc.noaa.gov/pub/data/noaa/isd-history.txt>\n"
     )
   }
   BEGIN <-
@@ -64,43 +64,43 @@
 #' Validate Country Requests
 #'
 #' @param country User requested country name
-#' @param country_list country_list file from NCEI provided by GSODR
+#' @param isd_history Data provided from NCEI on stations' locations and years
 #' @keywords internal
 #' @return A validated country name
 #' @noRd
 
 .validate_country <-
-  function(country, country_list) {
+  function(country, isd_history) {
     if (!is.null(country)) {
       country <- toupper(trimws(country[1]))
       nc <- nchar(country)
       if (nc == 3) {
-        if (country %in% country_list$ISO3C) {
-          c <- which(country == country_list$ISO3C)
-          country <- country_list[[c, 1]]
+        if (country %in% isd_history$ISO3C) {
+          c <- which(country == isd_history$ISO3C)
+          country <- as.character(isd_history[c, "CTRY"][1])
         } else {
           stop(call. = FALSE,
-               "\nPlease provide a valid name or 2 or 3",
+               "\nPlease provide a valid name or 2 or 3 ",
                "letter ISO country code\n")
         }
       } else if (nc == 2) {
-        if (country %in% country_list$ISO2C) {
-          c <- which(country == country_list$ISO2C)
-          country <- country_list[[c, 1]]
-        } else if (country %in% country_list$FIPS) {
-          c <- which(country == country_list$FIPS)
-          country <- country_list[[c, 1]]
+        if (country %in% isd_history$ISO2C) {
+          c <- which(country == isd_history$ISO2C)
+          country <- as.character(isd_history[c, "CTRY"][1])
+        } else if (country %in% isd_history$CTRY) {
+          c <- which(country == isd_history$CTRY)
+          country <- as.character(isd_history[c, "CTRY"][1])
         } else {
           stop(call. = FALSE,
-               "\nPlease provide a valid name or 2 or 3",
+               "\nPlease provide a valid name or 2 or 3 ",
                "\nletter ISO country code")
         }
-      } else if (country %in% country_list$COUNTRY_NAME) {
-        c <- which(country == country_list$COUNTRY_NAME)
-        country <- country_list[[c, 1]]
+      } else if (country %in% isd_history$COUNTRY_NAME) {
+        c <- which(country == isd_history$COUNTRY_NAME)
+        country <- as.character(isd_history[c, "CTRY"][1])
       } else {
         stop(call. = FALSE,
-             "\nPlease provide a valid name or 2 or 3",
+             "\nPlease provide a valid name or 2 or 3 ",
              "letter ISO country code\n")
       }
     }
@@ -263,7 +263,6 @@
 #' Subset Country List
 #'
 #' @param country Country of interest to subset on
-#' @param country_list Country list file provided by NCEI as a part of GSODR
 #' @param GSOD_list List of GSOD files to be subset
 #' @param isd_history isd_history.csv file from NCEI provided by GSODR
 #' @param years Years being requested
@@ -273,7 +272,6 @@
 
 .subset_country_list <-
   function(country,
-           country_list,
            file_list,
            isd_history,
            years) {

R/process_csv.R

@@ -93,7 +93,6 @@
 
   # Add STNID col --------------------------------------------------------------
   DT[, STNID := gsub('^(.{6})(.*)$', '\\1-\\2', DT$STATION)]
-  setkey(DT, "STNID")
 
   # Add and convert date related columns ---------------------------------------
   DT[, YEARMODA := as.Date(DATE, format = "%Y-%m-%d")]
@@ -159,6 +158,7 @@
   DT[, FRSHTT := NULL]
 
   # Join with internal isd-history for CTRY column -----------------------------
+  setkey(DT, STNID)
   DT <- isd_history[DT]
 
   # drop extra cols
@@ -215,5 +215,7 @@
       "RH"
     )
   )
+  # drop extra cols before returning object
+  DT[, c("COUNTRY_NAME", "ISO2C", "ISO3C") := NULL]
   return(DT)
 }

R/reformat_GSOD.R

@@ -84,6 +84,7 @@
 reformat_GSOD <- function(dsn = NULL, file_list = NULL) {
   isd_history <- NULL # nocov
   load(system.file("extdata", "isd_history.rda", package = "GSODR")) # nocov
+  setkeyv(isd_history, "STNID")
 
   # If dsn !NULL, create a list of files to reformat
   if (!is.null(dsn)) {