Merge pull request #76 from bczernecki/dev

climate 1.0.5

.Rbuildignore

@@ -11,3 +11,4 @@
 ^vignettes/articles$
 ^\.github$
 ^\.Rhistory$
+^\.lintr$

.github/workflows/R-CMD-check.yaml

@@ -80,6 +80,8 @@ jobs:
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+          remotes::install_cran("covr")
+          remotes::install_cran("xml2")
         shell: Rscript {0}
 
       - name: Session info
@@ -88,7 +90,7 @@ jobs:
           pkgs <- installed.packages()[, "Package"]
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
-
+        
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
@@ -106,3 +108,7 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -8,3 +8,5 @@ inst/doc
 .README.md.swp
 climate.Rproj
 .DS_Store
+covr_report.html
+lib

.lintr

@@ -0,0 +1,10 @@
+linters: with_defaults(
+   line_length_linter = line_length_linter(120),
+   commented_code_linter = NULL,
+   absolute_path_linter(),
+   object_name_linter = NULL,
+   object_length_linter(length = 50L),
+   object_usage_linter(source_file = NULL),
+   cyclocomp_linter(complexity_limit = 33L),
+   assignment_linter = NULL
+ )

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: climate
 Title: Interface to Download Meteorological (and Hydrological) Datasets
-Version: 1.0.4
+Version: 1.0.5
 Authors@R: c(person(given = "Bartosz",
            family = "Czernecki",
            role = c("aut", "cre"),
@@ -22,7 +22,7 @@ Description: Automatize downloading of meteorological and hydrological data from
     University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
     Polish Institute of Meterology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
     and National Oceanic & Atmospheric Administration (NOAA).
-    This package also allows for adding geographical coordinates for each observation.
+    This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

NEWS.md

@@ -1,3 +1,11 @@
+# climate 1.0.5
+
+* `meteo_imgw` family of functions supports multiple names as argument - bug fix
+* unit tests and code coverage computed with CI/CD
+* units added to column labels for `nearest_stations_` set of functions instead of column names for easier processing (e.g. [km] are visible now only as attributes)
+* new functions follow lintr settings
+
+
 # climate 1.0.4
 
 * Function `spheroid_dist` added to improve accuracy of calculations between points, but also avoid installing GIS dependencies (thanks to @kadyb)

R/check_locale.R

@@ -1,21 +1,23 @@
 #' Check locale
 #'
-#' This is an extra check for some systems that make use of "C.UTF-8" or any iso-like encoding recognized as causing potential problems; 
-#' The provided list of checked encoding cannot parse properly characters used in the Polish metservice's repository and therefore will be forced to use ASCII//TRANSLIT
+#' This is an extra check for some systems that make use of "C.UTF-8" or any
+#' iso-like encoding recognized as causing potential problems;
+#' The provided list of checked encoding cannot parse properly characters used
+#' in the Polish metservice's repository and therefore will be forced to
+#' use ASCII//TRANSLIT
 #' @noRd
 
-check_locale = function(){
-  
+check_locale = function() {
+
   if (Sys.getlocale("LC_CTYPE") %in% c("C.UTF-8", "en_US.iso885915")) {
     locale = Sys.getlocale("LC_CTYPE")
-    message(paste0("    Your system locale is: " , locale," which may cause trouble. 
-    Please consider changing it manually while working with climate, e.g.: 
+    message(paste0("    Your system locale is: ", locale, " which may cause trouble.
+    Please consider changing it manually while working with climate, e.g.:
     Sys.setlocale(category = 'LC_ALL', locale = 'en_US.UTF-8') "))
     Sys.sleep(4)
     return(1)
   } else {
     return(0)
   }
-
-}
 
+}

R/clean_metadata_hydro.R

@@ -5,19 +5,18 @@
 #' @param interval temporal interval
 #' @importFrom utils read.fwf
 #' @keywords internal
-clean_metadata_hydro = function(address, interval){
-
+clean_metadata_hydro = function(address, interval) {
   temp = tempfile()
-  
+
   test_url(link = address, output = temp)
   a = readLines(temp, warn = FALSE)
-  
+
   a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT") # usuwamy polskie znaki, bo to robi spore "kuku"
   a = gsub(a, pattern = "\\?", replacement = "") # usuwamy znaki zapytania powstale po konwersji
-  
+
   # additional workarounds for mac os but not only...
-  a = gsub(x = a, pattern="'", replacement = "")
-  a = gsub(x = a, pattern="\\^", replacement = "")
+  a = gsub(x = a, pattern = "'", replacement = "")
+  a = gsub(x = a, pattern = "\\^", replacement = "")
 
   if (interval == "monthly") {
     b = list(data.frame(parameters = a[3:12])) # sklad danych jeszcze nie wiem jak ominąć problem kontroli

R/clean_metadata_meteo.R

@@ -16,38 +16,32 @@
 #' }
 #'
 
-clean_metadata_meteo = function(address, rank = "synop", interval = "hourly"){
-  
+clean_metadata_meteo = function(address, rank = "synop", interval = "hourly") {
+
   temp = tempfile()
-
-
   test_url(link = address, output = temp)
   a = readLines(temp, warn = FALSE)
-  
+
   a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT") # usuwamy polskie znaki, bo to robi spore "kuku"
   a = gsub(a, pattern = "\\?", replacement = "") # usuwamy znaki zapytania powstale po konwersji
-
-  # additional workarounds for mac os but not only...
-  a = gsub(x = a, pattern="'", replacement = "")
-  a = gsub(x = a, pattern="\\^0", replacement = "")
-
 
+  # additional workarounds for mac os but not only...
+  a = gsub(x = a, pattern = "'", replacement = "")
+  a = gsub(x = a, pattern = "\\^0", replacement = "")
   a = data.frame(V1 = a[nchar(a) > 0], stringsAsFactors = FALSE)
-
-  # to nie dziala na windowsie:
+  # this one does not work on windows
   # a = suppressWarnings(na.omit(read.fwf(address, widths = c(1000),
   #                                        fileEncoding = "CP1250", stringsAsFactors = FALSE)))
-
   length_char = max(nchar(a$V1), na.rm = TRUE)
 
-  if(rank == "precip" && interval == "hourly") length_char = 40 # wyjatek dla precipow
-  if(rank == "precip" && interval == "daily") length_char = 40 # wyjatek dla precipow dobowych
-  if(rank == "synop" && interval == "hourly") length_char = 60 # wyjatek dla synopow terminowych
-  if(rank == "climate" && interval == "monthly") length_char = 52 # wyjatek dla synopow terminowych
+  if (rank == "precip" && interval == "hourly") length_char = 40 # wyjatek dla precipow
+  if (rank == "precip" && interval == "daily") length_char = 40 # wyjatek dla precipow dobowych
+  if (rank == "synop" && interval == "hourly") length_char = 60 # wyjatek dla synopow terminowych
+  if (rank == "climate" && interval == "monthly") length_char = 52 # wyjatek dla synopow terminowych
 
   field = substr(a$V1, length_char - 3, length_char)
 
-  if(rank == "synop" && interval == "monthly") {
+  if (rank == "synop" && interval == "monthly") {
     length_char = as.numeric(names(sort(table(nchar(a$V1)), decreasing = TRUE)[1])) + 2
     field = substr(a$V1, length_char - 3, length_char + 2)
   }
@@ -56,11 +50,10 @@ clean_metadata_meteo = function(address, rank = "synop", interval = "hourly"){
   a$field2 = suppressWarnings(as.numeric(unlist(lapply(strsplit(field, "/"), function(x) x[2]))))
 
   a$V1 = trimws(substr(a$V1, 1, nchar(a$V1) - 3))
-  
+
   strsplit(x = a$V1, split = "/")
-
-  #a = a[nchar(a$V1)>2,] # usuwamy puste lub prawie puste wiersze dodatkowo...
-  a = a[!(is.na(a$field1) & is.na(a$field2)), ] # usuwanie info o statusach
+  #a = a[nchar(a$V1)>2,] # remove empty or almost empty rows
+  a = a[!(is.na(a$field1) & is.na(a$field2)), ] # remove info about status
   colnames(a)[1] = "parameters"
-  a
+  return(a)
 }

R/co2_demo.R

@@ -1,9 +1,7 @@
 #' @name co2_demo
-#' @title Examplary CO2 dataset from Mauna Loa Observatory (NOAA dataset) 
-#'
+#' @title Examplary CO2 dataset from Mauna Loa Observatory (NOAA dataset)
 #' @description The object contains pre-downloaded CO2 dataset from Mauna Loa observatory
 #' The snapshot was taken 2020/05/05.
-#' 
 #' @importFrom utils data
 #'
 #' @docType data

R/get_coord_from_string.R

@@ -20,15 +20,14 @@ get_coord_from_string = function(txt, pattern = "Longitude") {
   tmp = trimws(substr(txt, start = start, stop = start + 8))
   tmp = strsplit(tmp, "-")[[1]]
   hemisphere = gsub("[0-9]", "", strsplit(tmp, "-")[2])
-  hemisphere = gsub(".*?(\\b[A-Za-z0-9 ]+\\b).*","\\1", hemisphere)
+  hemisphere = gsub(".*?(\\b[A-Za-z0-9 ]+\\b).*", "\\1", hemisphere)
 
   tmp = suppressWarnings(as.numeric(gsub("([0-9]+).*$", "\\1", strsplit(tmp, "-"))))
 
   wsp = suppressWarnings(as.numeric(tmp)[1] + (as.numeric(tmp)[2] * 5 / 3) / 100)
 
-  if( hemisphere %in% c("W","S") ) {
+  if (hemisphere %in% c("W", "S")) {
     wsp = wsp * -1
   }
 return(wsp)
 }
-

R/hydro_imgw.R

@@ -1,36 +1,55 @@
 #' Hydrological data from IMGW
 #'
-#' Downloading daily, and monthly hydrological data from the measurement stations available in the danepubliczne.imgw.pl collection
+#' Downloading daily, and monthly hydrological data from the measurement stations
+#' available in the danepubliczne.imgw.pl collection
 #'
-#' @param interval temporal resolution of the data ("daily" , "monthly", or "semiannual_and_annual")
+#' @param interval temporal resolution of the data ("daily" , "monthly",
+#' or "semiannual_and_annual")
 #' @param year vector of years (e.g., 1966:2000)
 #' @param coords add coordinates of the stations (logical value TRUE or FALSE)
-#' @param value type of data (can be: state - "H" (default), flow - "Q", or temperature - "T")
-#' @param station vector of hydrological stations danepubliczne.imgw.pl; can be given as station name with CAPITAL LETTERS (character)
+#' @param value type of data (can be: state - "H" (default), flow - "Q", or
+#' temperature - "T")
+#' @param station vector of hydrological stations danepubliczne.imgw.pl;
+#' can be given as station name with CAPITAL LETTERS (character)
 #' It accepts either names (characters in CAPITAL LETTERS) or stations' IDs (numeric)
-#' @param col_names three types of column names possible: "short" - default, values with shorten names, "full" - full English description, "polish" - original names in the dataset
-#' @param ... other parameters that may be passed to the 'shortening' function that shortens column names
-#' 
+#' @param col_names three types of column names possible: "short" - default,
+#' values with shorten names, "full" - full English description,
+#' "polish" - original names in the dataset
+#' @param ... other parameters that may be passed to the 'shortening'
+#' function that shortens column names
 #' @export
-#' @return A data.frame with columns describing the hydrological parameters (e.g. flow, water level) where each row represent a measurement,
-#'  depending on the interval, at a given hour, month or year. If `coords = TRUE` additional two columns with geografic coordinates are added.  
-#'
-#' @examples 
+#' @return A data.frame with columns describing the hydrological parameters
+#' (e.g. flow, water level) where each row represent a measurement,
+#' depending on the interval, at a given hour, month or year.
+#' If `coords = TRUE` additional two columns with geografic coordinates are added.
+#' @examples
 #' \donttest{
 #'   x = hydro_imgw("monthly", year = 1999)
 #'   head(x)
 #' }
-hydro_imgw = function(interval, year, coords = FALSE, value = "H", station = NULL, col_names = "short", ...){
+hydro_imgw = function(interval,
+                      year,
+                      coords = FALSE,
+                      value = "H",
+                      station = NULL,
+                      col_names = "short", ...) {
 
-  if (interval == "daily"){
+  if (interval == "daily") {
     # dobowe
     calosc = hydro_imgw_daily(year = year, coords = coords, station = station, col_names = col_names, ...)
-  } else if (interval == "monthly"){
+  } else if (interval == "monthly") {
     #miesieczne
-    calosc = hydro_imgw_monthly(year = year, coords = coords, station = station, col_names = col_names, ...)
-  } else if (interval == "semiannual_and_annual"){
+    calosc = hydro_imgw_monthly(year = year,
+                                coords = coords,
+                                station = station,
+                                col_names = col_names, ...)
+  } else if (interval == "semiannual_and_annual") {
     # polroczne_i_roczne
-    calosc = hydro_imgw_annual(year = year, coords = coords, value = value, station = station, col_names = col_names, ...)
+    calosc = hydro_imgw_annual(year = year,
+                               coords = coords,
+                               value = value,
+                               station = station,
+                               col_names = col_names, ...)
   } else{
     stop("Wrong `interval` value. It should be either 'daily', 'monthly', or 'semiannual_and_annual'.", call. = FALSE)
   }