environmentalinformatics-marburg · fdetsch · Jun 9, 2022 · Jun 9, 2022 · Jun 9, 2022 · Jun 9, 2022
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,14 @@
 Package: GSODTools
 Title: R Functions to Select, Download, and Process GSOD Data
-Version: 1.0.5
+Version: 1.0.5.9003
 Author: Florian Detsch
 Maintainer: Florian Detsch <fdetsch@web.de>
 Description: R functions to select, download, and process GSOD data.
 License: MIT + file LICENSE
 Depends: 
     R (>= 4.1)
 Imports: 
-    rworldmap,
     gmt,
-    dplyr,
     zoo,
     Rssa,
     reshape2,
@@ -26,6 +24,6 @@ Suggests:
     checkmate,
     tinytest
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/NAMESPACE b/NAMESPACE
@@ -28,12 +28,10 @@ import(utils)
 importFrom(Rssa,nsigma)
 importFrom(Rssa,ssa)
 importFrom(TSA,harmonic)
-importFrom(dplyr,arrange)
 importFrom(forecast,forecast)
 importFrom(gmt,geodist)
 importFrom(graphics,points)
 importFrom(reshape2,melt)
-importFrom(rworldmap,mapGriddedData)
 importFrom(sf,st_as_sf)
 importFrom(zoo,as.yearmon)
 importFrom(zoo,read.zoo)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,16 @@
+# GSODTools 1.0.5.9003 (2024-07-19)
+
+#### ✨ features and improvements
+
+#### 🐛 bug fixes
+
+#### 💬 documentation etc
+
+#### 🍬 miscellaneous
+
+  * Eliminates {dplyr} and {rworldmap} dependencies (#12)
+
+
 # GSODTools 1.0.5 (2022-06-08)
 
 #### 🍬 miscellaneous

diff --git a/R/GSODTools-package.R b/R/GSODTools-package.R
@@ -3,7 +3,6 @@
 #' R functions to select, download, and process GSOD data.
 #'
 #' @name GSODTools-package
-#' @docType package
 #' @title R Functions to Select, Download, and Process GSOD Data
 #' @author Florian Detsch \cr
 #' \cr
@@ -12,5 +11,4 @@
 #' @import methods stats utils
 #'
 #' @keywords package
-#'
-NULL
+"_PACKAGE"
diff --git a/R/as.ki.data.R b/R/as.ki.data.R
@@ -1,7 +1,7 @@
 #' Convert data set to ki.data object
 #' 
 #' @param input_filepath Needs documentation.
-#' @param start.column [\code{integer}] Defaults to \code{9L}.
+#' @param start.column \[`integer`\] Defaults to `9L`.
 #' @param ... Currently not used.
 #' 
 #' @importFrom reshape2 melt

diff --git a/R/data.R b/R/data.R
@@ -3,7 +3,7 @@
 #' A data set containing the full Global Summary of the Day (GSOD) station list.
 #' 
 #' @seealso Integrated Surface Database Station History, May 2022. Available 
-#'   online: <https://www.ncei.noaa.gov/pub/data/noaa/isd-history.txt> (last
+#'   online: <https://www.ncei.noaa.gov/pub/data/noaa/isd-history.csv> (last
 #'   accessed 2023-12-12).
 #' 
 #' @format A `data.table` with 29640 rows and 11 columns:
@@ -12,7 +12,7 @@
 #' * `"WBAN"`: \[`character`\] NCDC WBAN number.
 #' * `"STATION NAME"`: \[`character`\] Station name.
 #' * `"CTRY"`: \[`character`\] FIPS country ID, see also 
-#'   <https://www.ncei.noaa.gov/data/global-summary-of-the-day/doc/country-list.txt>.
+#'   <https://www.ncei.noaa.gov/pub/data/noaa/country-list.txt>.
 #' * `"STATE"`: \[`character`\] State for US stations.
 #' * `"ICAO"`: \[`character`\] ICAO ID.
 #' * `"LAT, LON"`: \[`numeric`\] Latitude, longitude in thousandths of decimal 
@@ -32,14 +32,12 @@
 #'   imputed based on singular spectrum analysis (SSA).
 #' 
 #' @format A \code{data.table} with 30684 rows and 6 columns:
-#' \itemize{
-#'   \item{"PlotId": }{[\code{factor}] Station name (\code{"kil"}: Kilimanjaro, 
-#'     \code{"jom"}: Nairobi)}
-#'   \item{"Status": }{[\code{factor}] Preprocess level (\code{"cleansed"}: 
-#'     outliers removed, \code{"filled"}: gaps filled via SSA)}
-#'   \item{"Datetime": }{[\code{POSIXct}] Time in Eastern Africa Time}
-#'   \item{"TEMP,MIN,MAX": }{[\code{numeric}] Mean, minimum, maximum air 
-#'     temperature in degC}
-#' }
+#' * `"PlotId"`: \[`factor`\] Station name (\code{"kil"}: Kilimanjaro, 
+#'   \code{"jom"}: Nairobi);
+#' * `"Status"`: \[`factor`\] Preprocess level (\code{"cleansed"}: outliers 
+#'   removed, \code{"filled"}: gaps filled via SSA);
+#' * `"Datetime"`: \[`POSIXct`\] Time in Eastern Africa Time;
+#' * `"TEMP, MIN, MAX"`: \[`numeric\] Mean, minimum, maximum air temperature in 
+#'   degC.
 #' 
 "eastafrica"
diff --git a/R/stationFromCoords.R b/R/stationFromCoords.R
@@ -29,10 +29,6 @@
 #'                               y = -3.065053, 
 #'                               width = 100)
 #'
-#' rworldmap::mapGriddedData(mapRegion = "africa", plotData = FALSE, borderCol = "black", 
-#'                addLegend = FALSE)
-#' points(sf::st_coordinates(gsod_shp), col = "red", pch = 20, cex = 2)
-#'  
 #' # Alternatively
 #' gsod_shp <- stationFromCoords(x = c(37.359031, -3.065053), 
 #'                               width = 100)
@@ -50,8 +46,6 @@
 #' gsod_shp <- stationFromCoords(x = kibo, 
 #'                               width = 100)
 #' 
-#' @importFrom dplyr arrange
-#' 
 #' @export
 stationFromCoords <- function(x, 
                               y = NULL, 
@@ -69,6 +63,7 @@ stationFromCoords <- function(x,
   }
 
   # Calculate distance from point of interest to supplied stations
+  # TODO: what happens if there are 2+ points in input
   stations <- gsodstations
   x.to.stations <- gmt::geodist(
     Nfrom = y
@@ -78,8 +73,16 @@ stationFromCoords <- function(x,
   # Add calculated distances to stations
   stations$DIST <- round(x.to.stations, ...)
 
-  # Identify and return GSOD stations that lie within the given buffer width
-  stations <- stations |> subset(DIST <= width) |> dplyr::arrange(DIST) |> gsodDf2Sp()
+  # Find stations that lie within the given buffer width and convert to spatial
+  stations = stations |> 
+    subset(
+      DIST <= width
+    ) |> 
+    gsodDf2Sp()
 
-  return(stations)
+  # Sort by distance and return
+  stations[
+    order(stations$DIST)
+    ,
+  ]
 }
diff --git a/R/stationFromExtent.R b/R/stationFromExtent.R
@@ -23,12 +23,6 @@
 #' kili <- sf::st_bbox(c(xmin = 37, xmax = 37.72, ymin = -3.4, ymax = -2.84))
 #' gsod_shp_kili <- stationFromExtent(bb = kili)
 #' 
-#' rworldmap::mapGriddedData(mapRegion = "africa", plotData = FALSE, borderCol = "black", 
-#'                addLegend = FALSE)
-#' points(sf::st_coordinates(gsod_shp_kili), col = "red")
-#' 
-#' @importFrom rworldmap mapGriddedData
-#' 
 #' @export
 stationFromExtent <- function(bb, 
                              ...) {

diff --git a/README.md b/README.md
@@ -73,20 +73,18 @@ numerics. For instance, let’s search for GSOD stations in a circle of
 500 km around Kibo summit, Mt. Kilimanjaro, Tanzania. The referring
 coordinates are `c(37.359031, -3.065053)`.
 
+    library(mapview)
+
     shp_kibo <- stationFromCoords(x = 37.359031, y = -3.065053, width = 500)
     # or: stationFromCoords(x = c(37.359031, -3.065053), width = 500)
     # or: stationFromCoords(x = SpatialPoints(data.frame(x = 37.359031, 
     #                                                    y = -3.065053), 
     #                                         proj4string = CRS("+init=epsg:4326")), 
     #                       width = 500)
 
-    rworldmap::mapGriddedData(
-      mapRegion = "africa"
-      , plotData = FALSE
-      , borderCol = "black"
-      , addLegend = FALSE
+    mapview(
+      shp_kibo
     )
-    points(sf::st_coordinates(shp_kibo), col = "red", pch = 20, cex = 2)
 
 ![](figure/stationFromCoords-1.png)
 
@@ -115,13 +113,9 @@ automatically disabled.
     )
     shp_kili_south <- stationFromExtent(bb = bbox_kibo_south)
 
-    rworldmap::mapGriddedData(
-      mapRegion = "africa"
-      , plotData = FALSE
-      , borderCol = "black"
-      , addLegend = FALSE
+    mapview(
+      shp_kili_south
     )
-    points(sf::st_coordinates(shp_kili_south), col = "red", pch = 20, cex = 2)
 
 ![](figure/stationFromExtent-1.png)
 

diff --git a/README.rmd b/README.rmd
@@ -74,20 +74,19 @@ in a circle of 500 km around Kibo summit, Mt. Kilimanjaro, Tanzania. The referri
 coordinates are `c(37.359031, -3.065053)`.
 
 ```{r stationFromCoords}
+library(mapview)
+
 shp_kibo <- stationFromCoords(x = 37.359031, y = -3.065053, width = 500)
 # or: stationFromCoords(x = c(37.359031, -3.065053), width = 500)
 # or: stationFromCoords(x = SpatialPoints(data.frame(x = 37.359031, 
 #                                                    y = -3.065053), 
 #                                         proj4string = CRS("+init=epsg:4326")), 
 #                       width = 500)
 
-rworldmap::mapGriddedData(
-  mapRegion = "africa"
-  , plotData = FALSE
-  , borderCol = "black"
-  , addLegend = FALSE
+mapview(
+  shp_kibo
 )
-points(sf::st_coordinates(shp_kibo), col = "red", pch = 20, cex = 2)
+
 ```
 
 `stationFromExtent`, just like `stationFromCoords`, allows station selection 
@@ -111,13 +110,10 @@ bbox_kibo_south <- sf::st_bbox(
 )
 shp_kili_south <- stationFromExtent(bb = bbox_kibo_south)
 
-rworldmap::mapGriddedData(
-  mapRegion = "africa"
-  , plotData = FALSE
-  , borderCol = "black"
-  , addLegend = FALSE
+mapview(
+  shp_kili_south
 )
-points(sf::st_coordinates(shp_kili_south), col = "red", pch = 20, cex = 2)
+
 ```
 
 The third and, at the moment, final possibility to select a GSOD station is to 

diff --git a/TODO b/TODO
@@ -5,7 +5,7 @@ General
   - further details: https://roxygen2.r-lib.org/articles/markdown.html
 * add ci/cd
 * gsod --> isd
-* {dplyr}, {data.table} (built-in data object) or base
+* {data.table} (built-in data object) or base
 * re-enable (some) `\dontrun` examples
 * handle records in `gsodstations` with lon = lat = 0.0
 * find solution for `gsodstations` duplication (internal vs. external)

diff --git a/figure/stationFromCoords-1.png b/figure/stationFromCoords-1.png
diff --git a/figure/stationFromExtent-1.png b/figure/stationFromExtent-1.png
diff --git a/inst/tinytest/test_gsodPlot.R b/inst/tinytest/test_gsodPlot.R
@@ -22,15 +22,17 @@ filled_data = lst[
   )
 ]
 
-expect_inherits(
-  gsodPlot(
-    cleansed_data
-    , filled_data
-    , stations = c("NAIROBI JKIA", "KILIMANJARO INTL")
-    , type = "trends"
+for (type in c("original", "trends", "both")) {
+  expect_inherits(
+    gsodPlot(
+      cleansed_data
+      , filled_data
+      , stations = c("NAIROBI JKIA", "KILIMANJARO INTL")
+      , type = type
+    )
+    , class = "ggplot"
   )
-  , class = "ggplot"
-)
+}
 
 ## early exit: non-matching type
 expect_error(

diff --git a/inst/tinytest/test_stationFrom.R b/inst/tinytest/test_stationFrom.R
@@ -50,6 +50,11 @@ expect_true(
   , info = "in case of coords, 'DIST' column is appended to output"
 )
 
+expect_false(
+  is.unsorted(gsod_shp$DIST)
+  , info = "appended 'DIST' column is sorted"
+)
+
 
 ## `stationFromExtent()` ====
 

diff --git a/inst/tinytest/test_utils.R b/inst/tinytest/test_utils.R
@@ -0,0 +1,11 @@
+out = toCelsius(c(32, 212)) # freezing point, boiling point
+
+expect_identical(
+  out
+  , target = c(
+    0.
+    , 100.
+  )
+  , info = "output is of the same length as input and content is correct"
+)
+
diff --git a/inst/tinytest/test_vectorHarmonics.R b/inst/tinytest/test_vectorHarmonics.R
@@ -0,0 +1,36 @@
+dat = subset(
+  eastafrica
+  , PlotId == "kil" &
+    Datetime < "1984-01-01"
+)
+
+agg = aggregate(
+  dat["TEMP"]
+  , by = list(
+    YEARMO = format(
+      dat$Datetime
+      , "%Y-%m"
+    )
+  )
+  , FUN = mean
+  , na.rm = TRUE
+)
+
+out = vectorHarmonics(
+  agg$TEMP
+  , st = c(1980, 1)
+  , nd = c(1983, 12)
+)
+
+expect_inherits(
+  out
+  , class = "numeric"
+)
+
+expect_identical(
+  length(out)
+  , target = formals(
+    vectorHarmonics
+  )$frq
+  , info = "output is of the same length as input frequency"
+)
diff --git a/man/GSODTools-package.Rd b/man/GSODTools-package.Rd