Adds asymmetric and symmetric SAM

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,35 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -29,4 +29,4 @@ Suggests:
     testthat (>= 2.1.0),
     tibble
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -2,6 +2,8 @@
 
 export(download_aao)
 export(download_ao)
+export(download_asymsam_daily)
+export(download_asymsam_monthly)
 export(download_dmi)
 export(download_enso)
 export(download_mei)

R/download-asymsam.R

@@ -0,0 +1,117 @@
+#' @export
+#' @title Download Asymmetric and Symmetric SAM indices
+#' 
+#' @description The Asymmetric and Symmetric SAM indices are computed as the 
+#' projection of geopotential height anomalies onto the zonally asymmetric and 
+#' zonally symmetric parts of the SAM field. 
+#' The detailed methodology can be found in Campitelli et al. (2022).
+#' The source of the data is \url{https://www.cima.fcen.uba.ar/~elio.campitelli/asymsam/}
+#' 
+#' @inheritParams download_oni
+#' @param levels atmospheric levels in hPa to download. 
+#' If \code{"all"} download all available levels. 
+#' Available levels are: 1, 2, 3, 5, 7, 10, 20, 30, 50, 70, 100, 125, 150, 175,
+#'  200, 225, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 775, 800,
+#'  825, 850, 875, 900, 925, 950, 975 and 1000.
+#' 
+#' @return 
+#' \itemize{
+#' \item Lev: Atmospheric level in hPa
+#' \item Date: Date object that uses the first of the month as a placeholder. Date formatted as date on the first of the month because R only supports one partial of date time
+#' \item Index: Type of index. Either "sam", "ssam" or "asam".
+#' \item Value: Value of the index
+#' \item Value_normalized: Value of the index normalized by the standard deviation of the index
+#' \item R.squared: The variance explained by the index (only in the daily version)
+#' }
+#' 
+#' @examples
+#' \dontrun{
+#' asymsam <- download_asymsam_monthly()
+#' }
+#'
+#' @references Campitelli, E., Díaz, L. B., & Vera, C. (2022). Assessment of zonally symmetric and asymmetric components of the Southern Annular Mode using a novel approach. Climate Dynamics, 58(1), 161–178. \url{https://doi.org/10.1007/s00382-021-05896-5}
+download_asymsam_monthly <- function(use_cache = FALSE, file = NULL) {
+  with_cache(use_cache = use_cache, file = file, 
+             memoised = download_asymsam_monthly_memoised, 
+             unmemoised = download_asymsam_monthly_unmemoised, 
+             read_function = read_asymsam_monthly)
+}
+
+download_asymsam_monthly_unmemoised = function() {
+  asymsam_monthly_link = "https://www.cima.fcen.uba.ar/~elio.campitelli/asymsam/data/sam_monthly.csv"
+
+  data <- read.csv(asymsam_monthly_link, colClasses = c("integer", "character", "Date", "numeric", "numeric"),
+                   col.names = c("Lev", "Index", "Date", "Value", "Value_normalized"))
+  data$Index <- factor(data$Index, levels = c("sam", "ssam", "asam"))
+
+  class(data) = c("tbl_df", "tbl", "data.frame") 
+  data
+}
+
+download_asymsam_monthly_memoised <- memoise::memoise(download_asymsam_monthly_unmemoised)
+
+read_asymsam_monthly <- function(file) {
+  data <- read.csv(file)
+  data$Date <- as.Date(data$Date)
+  data$Index <- factor(data$Index, levels = c("sam", "ssam", "asam"))
+  class(data) <- c("tbl_df", "tbl", "data.frame")
+  data
+}
+
+
+#' @export
+#' @rdname download_asymsam_monthly
+download_asymsam_daily <- function(levels = 700, use_cache = FALSE, file = NULL) {
+  with_cache(use_cache = use_cache, file = file, 
+             memoised = download_asymsam_monthly_memoised, 
+             unmemoised = download_asymsam_daily_unmemoised, 
+             read_function = read_asymsam_monthly, 
+             levels = levels)
+}
+
+
+download_asymsam_daily_unmemoised = function(levels = 700)  {
+    available_levels <- c(1L, 2L, 3L, 5L, 7L, 10L, 20L, 30L, 50L, 70L, 100L, 125L, 150L, 
+                          175L, 200L, 225L, 250L, 300L, 350L, 400L, 450L, 500L, 550L, 600L, 
+                          650L, 700L, 750L, 775L, 800L, 825L, 850L, 875L, 900L, 925L, 950L, 
+                          975L, 1000L)
+    if (levels[1] == "all") {
+      levels <- available_levels
+    } 
+
+    bad_levels <- !(levels %in% available_levels)
+    if (any(bad_levels)) {
+      stop(paste("Invalid levels:", paste(levels[bad_levels], collapse = ", "),
+                 "\nValid levels are:", paste(available_levels, collapse = ", ")))
+    }
+
+    root_link = "https://www.cima.fcen.uba.ar/~elio.campitelli/asymsam/data/sam_level/"
+
+    all_data <- list()
+    for (level in levels) {
+      message("Downloading level: ", level)
+      link <- paste0(root_link, "sam_", level, "hPa.csv")
+      data <- read.csv(link, colClasses = c("integer", "character", "Date", "numeric", "numeric", "numeric"),
+                       col.names = c("Lev", "Index", "Date", "Value", "R.squared", "dump"))
+      data$dump <- NULL
+      all_data <- append(all_data, list(data))
+    }
+    all_data <- do.call(rbind, all_data)
+
+    all_data$Index <- factor(all_data$Index, levels = c("sam", "ssam", "asam"))
+
+    class(all_data) = c("tbl_df", "tbl", "data.frame") 
+    all_data
+  }
+
+
+download_asymsam_monthly_memoised <- download_asymsam_monthly_unmemoised
+
+read_asymsam_daily <- function(file) {
+  data <- read.csv(file)
+  data$Date <- as.Date(data$Date)
+  data$Lev <- as.integer(data$Lev)
+  data$Index <- factor(data$Index, levels = c("sam", "ssam", "asam"))
+  class(data) <- c("tbl_df", "tbl", "data.frame")
+  data
+}

R/download-nao.R

@@ -39,7 +39,8 @@ download_nao_unmemoised <- function(){
 
   nao = read.fwf(nao_link, 
                 widths = c(4, rep(7, 12)),
-                header = FALSE, 
+                header = FALSE,
+                skip = 1, 
                 col.names = c("Year", month.abb))
 
   reshaped_list <- lapply(

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) 
-[![R-CMD-check](https://github.com/boshek/rsoi/workflows/R-CMD-check/badge.svg)](https://github.com/boshek/rsoi/actions)
+[![R-CMD-check](https://github.com/boshek/rsoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/boshek/rsoi/actions/workflows/R-CMD-check.yaml)
 
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rsoi.Rproj

@@ -15,3 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

tests/testthat/test_download_.R

@@ -1,5 +1,4 @@
-indexes <- c("oni", "ao", "nao", "soi", "mei", "npgo", "aao", "pdo", "dmi")
-
+indexes <- c("oni", "ao", "nao", "soi", "mei", "npgo", "aao", "pdo", "dmi", "asymsam_monthly", "asymsam_daily")
 context("Testing download")