Prepare next release

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: resourcecode
 Title: Access to the 'RESOURCECODE' Hindcast Database
-Version: 0.5.3.9000
+Version: 0.5.4
 Authors@R: 
     person("Nicolas", "Raillard", , "nicolas.raillard@ifremer.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3385-5104"))
@@ -13,7 +13,6 @@ Description: Utility functions to download data from the 'RESOURCECODE'
     surface elevation variance spectral density.
 License: GPL (>= 3)
 URL: https://github.com/Resourcecode-project/r-resourcecode,
-    https://resourcecode-project.github.io/r-resourcecode/,
     https://resourcecode-project.r-universe.dev/resourcecode
 BugReports: https://github.com/Resourcecode-project/r-resourcecode/issues
 Depends: 
@@ -47,10 +46,10 @@ LinkingTo:
     RcppArmadillo
 VignetteBuilder: 
     knitr
+Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3

NEWS.md

@@ -1,4 +1,4 @@
-# resourcecode (development version)
+# resourcecode 0.5.4
 
 - `get_parameters` now correctly handles `Date` format as inputs by spanning on the right period;
 - Update `rscd_casandra_end_date` with new data availability: 2025-12-31 23:00:00.

R/data.R

@@ -1,27 +1,3 @@
-#' Resourcecode frequency vector of 1D and 2D spectra
-#'
-#' The wave spectrum discretization considers 36 frequencies, starting from
-#' 0.0339 Hz up to 0.9526 Hz with a frequency increment factor of 1.1
-#'
-#' @format ## `rscd_freq`
-#' An array 36 elements with the frequencies values
-#'
-#' @source User Manual of the RESOURCECODE database
-#' <https://archimer.ifremer.fr/doc/00751/86306/>
-"rscd_freq"
-
-#' Resourcecode directional bins
-#'
-# In terms of directional discretization, 36 directions were used
-#' (equivalent to a directional resolution of 10°;
-#'
-#' @format ## `rscd_dir`
-#' An array of length 36 with the directionnal bins
-#'
-#' @source User Manual of the RESOURCECODE database
-#' <https://archimer.ifremer.fr/doc/00751/86306/>
-"rscd_dir"
-
 #' Resourcecode data extract
 #'
 #' An extract of the Resourcecode Hindcast database, at node 123456, spanning from

R/orbital_speed.R

@@ -16,7 +16,7 @@
 #' S <- t(sapply(1:10, function(h) {
 #'   jonswap(h)$spec
 #' }))
-#' orb_speeds <- compute_orbital_speeds(S, rscd_freq, depth = 100, z = 10)
+#' orb_speeds <- compute_orbital_speeds(S, resourcecodedata::rscd_freq, depth = 100, z = 10)
 #' plot(1:10, orb_speeds[, 1],
 #'   type = "l",
 #'   ylim = range(orb_speeds),
@@ -25,11 +25,12 @@
 #' )
 #' lines(1:10, orb_speeds[, 2], type = "l", col = "red")
 compute_orbital_speeds <- function(
-    spec,
-    freq,
-    z = 0,
-    depth = Inf,
-    output_speeds = FALSE) {
+  spec,
+  freq,
+  z = 0,
+  depth = Inf,
+  output_speeds = FALSE
+) {
   # z: distance above sea floor
 
   dims <- dim(spec)
@@ -69,8 +70,8 @@ compute_orbital_speeds <- function(
 
   if (output_speeds) {
     out <- array(NA, dim = c(dim(spectral_u_component), 2))
-    out[, , 1] <- spectral_u_component
-    out[, , 2] <- spectral_v_component
+    out[,, 1] <- spectral_u_component
+    out[,, 2] <- spectral_v_component
     out
   } else {
     u_rms <- sqrt(2 * resourcecode::fastTrapz(freq, spectral_u_component, 2))

R/plots.R

@@ -17,12 +17,13 @@
 #' rscd_mapplot(resourcecodedata::rscd_field$depth)
 #'
 rscd_mapplot <- function(
-    z,
-    name = "Depth (m)",
-    zlim = NULL,
-    palette = "YlOrRd",
-    direction = 1,
-    transform = "identity") {
+  z,
+  name = "Depth (m)",
+  zlim = NULL,
+  palette = "YlOrRd",
+  direction = 1,
+  transform = "identity"
+) {
   xyzgz <- tibble::tibble(
     x = resourcecodedata::rscd_field$longitude[
       resourcecodedata::rscd_triangles

R/resourcecode-package.R

@@ -3,7 +3,7 @@
 
 ## usethis namespace: start
 #' @importFrom ggplot2 ggplot aes geom_path coord_sf theme_void geom_polygon scale_fill_distiller
-#'                     scale_color_distiller theme margin element_rect element_blank geom_rect
+#' @importFrom ggplot2 scale_color_distiller theme margin element_rect element_blank geom_rect
 #' @importFrom Rcpp sourceCpp evalCpp
 #' @importFrom rlang .data
 #' @useDynLib resourcecode, .registration = TRUE

R/specta_data_ploting.R

@@ -13,8 +13,8 @@
 #' @examples
 #' plot_2d_specta(resourcecodedata::rscd_2d_spectra, 1)
 #' @importFrom ggplot2 ggplot geom_rect scale_x_continuous scale_y_continuous
-#'                     theme_linedraw coord_polar scale_color_distiller scale_fill_distiller
-#'                     labs expansion
+#' @importFrom ggplot2 theme_linedraw coord_polar scale_color_distiller scale_fill_distiller
+#' @importFrom ggplot2 labs expansion
 plot_2d_specta <- function(
   spec,
   time = 1L,
@@ -36,7 +36,7 @@ plot_2d_specta <- function(
   df_freq$frequency2 <- spec$frequency2[df_freq$frequency1]
   df_freq$frequency1 <- spec$frequency1[df_freq$frequency1]
 
-  df <- tibble::tibble(df_freq, ef = c(spec$efth[, , time]))
+  df <- tibble::tibble(df_freq, ef = c(spec$efth[,, time]))
 
   legend_text <- "Power spectrum\n(m^2.s)"
 
@@ -116,8 +116,7 @@ plot_2d_specta <- function(
 #' @examples
 #' plot_1d_specta(resourcecodedata::rscd_1d_spectra, 1)
 #' @importFrom ggplot2 ggplot geom_line scale_x_continuous scale_y_continuous
-#'                     theme_linedraw
-#'                     labs expansion
+#' @importFrom ggplot2 theme_linedraw labs expansion
 plot_1d_specta <- function(
   spec,
   time = 1L,
@@ -136,7 +135,7 @@ plot_1d_specta <- function(
     warning(
       "Frequency vector not provided: using the default Resourcecode frequency vector."
     )
-    freq_plot <- rscd_freq
+    freq_plot <- resourcecodedata::rscd_freq
   } else {
     freq_plot <- spec$freq
   }

R/utils.R

@@ -235,7 +235,13 @@ metconv2zmcomp <- function(speed, direction, names = c("uwnd", "vwnd")) {
 #' plot(S1, type = "l", ylim = c(0, 72))
 #' lines(S2, col = "red")
 #' abline(v = 1 / 15)
-jonswap <- function(hs = 5, tp = 15, fmax = rscd_freq, df = NULL, gam = 3.3) {
+jonswap <- function(
+  hs = 5,
+  tp = 15,
+  fmax = resourcecodedata::rscd_freq,
+  df = NULL,
+  gam = 3.3
+) {
   if (length(fmax) > 1) {
     # Case when the frequency vector if given
     freq <- fmax

R/weather_windows.R

@@ -12,7 +12,12 @@
 #'
 #' @return POSIXct vector of detected window start times.
 #' @export
-weather_windows <- function(valid_periods, window_length, allow_overlap = TRUE, time_step = 3600) {
+weather_windows <- function(
+  valid_periods,
+  window_length,
+  allow_overlap = TRUE,
+  time_step = 3600
+) {
   if ("time" %nin% names(valid_periods)) {
     stop("'valid_periods' must be a data frame with a 'time' column (POSIXct)")
   }

devtools_history.R

@@ -28,6 +28,7 @@ rscd_data_example = resourcecode::get_parameters(
   parameters = c("hs", "tp", "dp", "uwnd", "vwnd", "dpt")
 )
 usethis::use_data(rscd_data_example, version = 3, overwrite = TRUE)
+tools::resaveRdaFiles("data/")
 
 rcd_cassandra_url = "https://resourcecode-datacharts.ifremer.fr/"
 rscd_hindcast_start_date = as.POSIXct("1994-01-01 00:00:00", tz = 'UTC')
@@ -36,9 +37,6 @@ rscd_hindcast_end_date = as.POSIXct("2024-12-31 23:00:00", tz = 'UTC')
 rscd_casandra_start_date = as.POSIXct("1994-01-01 00:00:00", tz = 'UTC')
 rscd_casandra_end_date = as.POSIXct("2025-12-31 23:00:00", tz = 'UTC')
 
-rscd_freq <- array(0.0339 * 1.1^(0:35))
-rscd_dir <- array(seq(from = 0, to = 350, by = 10))
-
 usethis::use_data(
   rcd_cassandra_url,
   rscd_hindcast_start_date,
@@ -51,7 +49,8 @@ usethis::use_data(
   version = 3,
   overwrite = TRUE
 )
-tools::resaveRdaFiles("data/")
+tools::resaveRdaFiles("R/")
+
 
 #set up automatic "check" on several plateforms
 usethis::use_github_action()
@@ -135,7 +134,7 @@ devtools::check_mac_release()
 
 
 # Upgrade version number
-usethis::use_version(which = c("patch", "minor", "major", "dev")[3])
+usethis::use_version(which = c("patch", "minor", "major", "dev")[1])
 
 usethis::use_release_issue()
 

tests/testthat/test-test_closest_point.R

@@ -2,7 +2,6 @@
 # Test Suite 1: Input Validation
 # ==============================================================================
 
-
 test_that("Input validation works correctly", {
   # Test ill-formed coordinates input
   expect_error(
@@ -52,14 +51,16 @@ test_that("Unique node selection works", {
     node_test
   )
   expect_equal(closest_point_spec(point_test)$point, spec_test)
-  expect_equal(closest_point_spec(point_test[1], point_test[2])$point, spec_test)
+  expect_equal(
+    closest_point_spec(point_test[1], point_test[2])$point,
+    spec_test
+  )
 })
 
 # ==============================================================================
 # Test Suite 3: Multiple nodes selection
 # ==============================================================================
 
-
 test_that("Multiple nodes selection works", {
   skip_if(!requireNamespace("resourcecodedata", quietly = TRUE))
 
@@ -73,7 +74,6 @@ test_that("Multiple nodes selection works", {
   node_test <- matrix(c(100, 1000), ncol = 2)
   spec_test <- matrix(c(23045, 22274), ncol = 2)
 
-
   output <- closest_point_field(point_test)
   expect_named(output, c("points", "distances"))
   expect_identical(dim(output$points), c(1L, 2L))
@@ -98,7 +98,6 @@ test_that("Multiple nodes selection works", {
 # Test Suite 4: Several closest points selection
 # ==============================================================================
 
-
 test_that("List of closest nodes selection works", {
   skip_if(!requireNamespace("resourcecodedata", quietly = TRUE))
 
@@ -119,14 +118,22 @@ test_that("List of closest nodes selection works", {
   expect_equal(output$point, node_test)
   expect_true(all(output$distance[, 1] == 0))
 
-  output2 <- closest_point_field(point_test[, 1], point_test[, 2], closest = closest)
+  output2 <- closest_point_field(
+    point_test[, 1],
+    point_test[, 2],
+    closest = closest
+  )
   expect_equal(output2, output)
 
   output_spec <- closest_point_spec(point_test, closest = 3)
   expect_named(output_spec, c("points", "distances"))
   expect_identical(dim(output_spec$points), c(2L, 3L))
   expect_identical(dim(output_spec$distances), c(2L, 3L))
 
-  output2_spec <- closest_point_spec(point_test[, 1], point_test[, 2], closest = 3)
+  output2_spec <- closest_point_spec(
+    point_test[, 1],
+    point_test[, 2],
+    closest = 3
+  )
   expect_equal(output2_spec, output_spec)
 })