initial commit

R/pagasa_cyclones.R

@@ -0,0 +1,49 @@
+#'
+#' Retrieve download links for yearly cyclones reports
+#' 
+#' @param url
+#' 
+#' @returns A vector of URL links to the yearly cyclones reports
+#' 
+#'
+
+cyclones_get_report_links <- function(url = "https://www.pagasa.dost.gov.ph/tropical-cyclone/publications/annual-report") {
+  httr::config(ssl_verifypeer = 0L) |>
+    httr::set_config()
+
+  url_session <- rvest::session(url)
+
+  url_session |>
+    rvest::html_elements(css = ".panel .panel-body li a") |>
+    rvest::html_attr(name = "href")
+}
+
+
+#'
+#' Download cyclones reports
+#' 
+#' @param url_link
+#' @param directory
+#'
+#' @returns File downloaded to specified path (invisible). A character value for
+#'   path to downloaded file
+#'
+
+cyclones_download_report <- function(url_link, directory) {
+  ## Check if directory exists; if not create ----
+  if (!dir.exists(directory))
+    dir.create(directory, showWarnings = FALSE, recursive = TRUE)
+
+  ## Create file path to download ----
+  path <- file.path(directory, basename(url_link))
+
+  ## Download file/s ----
+  Map(
+    f = download.file,
+    url = as.list(url_link),
+    destfile = as.list(path)
+  )
+
+  ## Return path/s ----
+  path
+}

README.Rmd

@@ -11,7 +11,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# A template R workflow for general data analysis
+# pagasa_db:
 
 <!-- badges: start -->
 <!-- badges: end -->
@@ -20,14 +20,12 @@ This repository is a template for a [`docker`](https://www.docker.com/get-starte
 
 ## About the Project
 
-
-
 ## Repository Structure
 
 The project repository is structured as follows:
 
 ```
-sc-policy-review
+pagasa_db
     |-- .github/
       |-- workflows/
     |-- data/

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# A template R workflow for general data analysis
+# pagasa_db:
 
 <!-- badges: start -->
 <!-- badges: end -->
@@ -18,7 +18,7 @@ This repository is a template for a
 
 The project repository is structured as follows:
 
-    sc-policy-review
+    pagasa_db
         |-- .github/
           |-- workflows/
         |-- data/

_targets.yaml

@@ -0,0 +1,6 @@
+cyclones:
+  script: _targets_cyclones.R
+  store: _targets_cyclones
+heat:
+  script: _targets_heat.R
+  store: _targets_heat

_targets_cyclones.R

@@ -0,0 +1,68 @@
+################################################################################
+#
+# General Targets Workflow
+#
+################################################################################
+
+## Load libraries and custom functions -----------------------------------------
+suppressPackageStartupMessages(source("packages.R"))
+for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
+
+## Create targets --------------------------------------------------------------
+
+### Download targets ----
+
+download_targets <- tar_plan(
+  tar_target(
+    name = cyclone_reports_links,
+    command = cyclones_get_report_links()
+  ),
+  tar_target(
+    name = cyclone_reports_download_files,
+    command = cyclones_download_report(
+      url_link = cyclone_reports_links,
+      directory = "data-raw/cyclones"
+    ),
+    pattern = map(cyclone_reports_links),
+    format = "file"
+  )
+)
+
+### Data targets
+data_targets <- tar_plan(
+
+)
+
+
+### Processing targets
+processing_targets <- tar_plan(
+
+)
+
+
+### Analysis targets
+analysis_targets <- tar_plan(
+
+)
+
+
+### Output targets
+output_targets <- tar_plan(
+
+)
+
+
+### Reporting targets
+report_targets <- tar_plan(
+
+)
+
+
+### Deploy targets
+deploy_targets <- tar_plan(
+
+)
+
+
+## List targets ----------------------------------------------------------------
+all_targets()

_targets_cyclones/.gitignore

@@ -0,0 +1,5 @@
+*
+!.gitignore
+!meta
+meta/*
+!meta/meta

_targets_cyclones/meta/meta

@@ -0,0 +1,20 @@
+name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error
+.Random.seed|object|1617e1b0d9b19ac3|||||||||||||||
+all_targets|function|b6dd8c08c18a0132|||||||||||||||
+analysis_targets|object|ef46db3751d8e999|||||||||||||||
+cyclone_reports_download_files|pattern|0aba2b50cff34e6a|f6ca15f19248c12f||1643365027||||50315072|file|local|vector||cyclone_reports_download_files_1342b9b0*cyclone_reports_download_files_3de468d2*cyclone_reports_download_files_1f710163*cyclone_reports_download_files_3a21c11c|111.33||
+cyclone_reports_download_files_1342b9b0|branch|60729b809d91b79c|f6ca15f19248c12f|06035e6aa816dd5c|1498400784|data-raw/cyclones/PAGASA_ARTC_2017.pdf|t19818.7964824806s|5313c5a66b4edadc|5460545|file|local|vector|cyclone_reports_download_files||31.722||
+cyclone_reports_download_files_1f710163|branch|de688a74a6ff77fd|f6ca15f19248c12f|06035e6aa816dd5c|226425042|data-raw/cyclones/PAGASA_ARTC_2019.pdf|t19818.7971196276s|65928e670053fd1b|12015407|file|local|vector|cyclone_reports_download_files||26.517||
+cyclone_reports_download_files_3a21c11c|branch|db3ea6470ddc52b2|f6ca15f19248c12f|06035e6aa816dd5c|-825356566|data-raw/cyclones/PAGASA_ARTC_2020.pdf|t19818.7974045428s|a566e253d0d1ff29|15191585|file|local|vector|cyclone_reports_download_files||24.597||
+cyclone_reports_download_files_3de468d2|branch|bc6d333cb1096ac5|f6ca15f19248c12f|06035e6aa816dd5c|1448407431|data-raw/cyclones/PAGASA_ARTC_2018.pdf|t19818.7968125359s|dab08093bc4d0be0|17647535|file|local|vector|cyclone_reports_download_files||28.494||
+cyclone_reports_links|stem|976139e21c1457e1|50c3fa41d6ec29a2|3c2674030d3a4120|-147333770||t19818.7875375608s|4859fc503e8e9e17|155|rds|local|vector|||4.655||
+cyclones_download_report|function|cb072b709121376a|||||||||||||||
+cyclones_get_report_links|function|4ae6238e54fa5d98|||||||||||||||
+data_targets|object|ef46db3751d8e999|||||||||||||||
+deploy_targets|object|ef46db3751d8e999|||||||||||||||
+download_targets|object|d135cd3318e807a0|||||||||||||||
+f|object|2cca7bbc806ca10a|||||||||||||||
+get_cyclone_report_links|function|4ae6238e54fa5d98|||||||||||||||
+output_targets|object|ef46db3751d8e999|||||||||||||||
+processing_targets|object|ef46db3751d8e999|||||||||||||||
+report_targets|object|ef46db3751d8e999|||||||||||||||

_targets_heat.R

@@ -0,0 +1,50 @@
+################################################################################
+#
+# General Targets Workflow
+#
+################################################################################
+
+## Load libraries and custom functions -----------------------------------------
+suppressPackageStartupMessages(source("packages.R"))
+for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
+
+## Create targets and list targets objects -------------------------------------
+
+### Data targets
+data_targets <- tar_plan(
+
+)
+
+
+### Processing targets
+processing_targets <- tar_plan(
+
+)
+
+
+### Analysis targets
+analysis_targets <- tar_plan(
+
+)
+
+
+### Output targets
+output_targets <- tar_plan(
+
+)
+
+
+### Reporting targets
+report_targets <- tar_plan(
+
+)
+
+
+### Deploy targets
+deploy_targets <- tar_plan(
+
+)
+
+
+## List targets
+all_targets()

renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.1",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -193,13 +193,13 @@
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.4.6",
+      "Version": "0.4.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "707fae4bbf73697ec8d85f9d7076c061"
+      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
     },
     "curl": {
       "Package": "curl",
@@ -498,7 +498,7 @@
     },
     "igraph": {
       "Package": "igraph",
-      "Version": "1.5.1",
+      "Version": "2.0.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -514,9 +514,10 @@
         "pkgconfig",
         "rlang",
         "stats",
-        "utils"
+        "utils",
+        "vctrs"
       ],
-      "Hash": "80401cb5ec513e8ddc56764d03f63669"
+      "Hash": "c3b7d801d722e26e4cd888e042bf9af5"
     },
     "isoband": {
       "Package": "isoband",
@@ -944,6 +945,16 @@
       ],
       "Hash": "906cb23d2f1c5680b8ce439b44c6fa63"
     },
+    "secretbase": {
+      "Package": "secretbase",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "e9591ffb6d5adcc9284213e496ed7fe9"
+    },
     "selectr": {
       "Package": "selectr",
       "Version": "0.4-2",
@@ -1042,7 +1053,7 @@
     },
     "targets": {
       "Package": "targets",
-      "Version": "1.3.0",
+      "Version": "1.6.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1056,7 +1067,9 @@
         "digest",
         "igraph",
         "knitr",
+        "ps",
         "rlang",
+        "secretbase",
         "stats",
         "tibble",
         "tidyselect",
@@ -1065,7 +1078,7 @@
         "vctrs",
         "yaml"
       ],
-      "Hash": "da40edff48c5c900c369d16564b51af1"
+      "Hash": "35b83348e5cf547715687c93ce5c2126"
     },
     "tibble": {
       "Package": "tibble",