From de78eeef3b1e9196f58a7615f993ddd68caa1040 Mon Sep 17 00:00:00 2001
From: elmeraa <eazadpour@usgs.gov>
Date: Mon, 18 Dec 2023 11:15:19 -0800
Subject: [PATCH] set up repo and read in vulnerability indicators data
---
.gitignore | 27 +++++++++++++++++++++++++++
1_fetch.R | 23 +++++++++++++++++++++++
1_fetch/in/.empty | 0
1_fetch/out/.empty | 0
1_fetch/src/.empty | 0
2_process.R | 7 +++++++
2_process/in/.empty | 0
2_process/out/.empty | 0
2_process/src/.empty | 0
3_visualize.R | 6 ++++++
3_visualize/.empty | 0
3_visualize/in/.empty | 0
3_visualize/out/.empty | 0
_targets.R | 24 ++++++++++++++++++++++++
vulnerability-indicators.Rproj | 13 +++++++++++++
15 files changed, 100 insertions(+)
create mode 100644 .gitignore
create mode 100644 1_fetch.R
create mode 100644 1_fetch/in/.empty
create mode 100644 1_fetch/out/.empty
create mode 100644 1_fetch/src/.empty
create mode 100644 2_process.R
create mode 100644 2_process/in/.empty
create mode 100644 2_process/out/.empty
create mode 100644 2_process/src/.empty
create mode 100644 3_visualize.R
create mode 100644 3_visualize/.empty
create mode 100644 3_visualize/in/.empty
create mode 100644 3_visualize/out/.empty
create mode 100644 _targets.R
create mode 100644 vulnerability-indicators.Rproj
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..a9962c4
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,27 @@
+.Rproj.user
+.Rproj.user/
+.Rhistory
+.RData
+.Ruserdata
+.RProfile
+.Renvironment
+.DS_Store
+1_fetch/out/*
+1_fetch/in/*
+1_fetch/src/*
+2_process/in/*
+2_process/src/*
+2_process/out/*
+3_visualize/in/*
+3_visualize/src/*
+3_visualize/out/*
+!1_fetch/in/.empty
+!1_fetch/src/.empty
+!1_fetch/out/.empty
+!2_process/in/.empty
+!2_process/src/.empty
+!2_process/out/.empty
+!3_visualize/in/.empty
+!3_visualize/src/.empty
+!3_visualize/out/.empty
+_targets/
diff --git a/1_fetch.R b/1_fetch.R
new file mode 100644
index 0000000..feff5e3
--- /dev/null
+++ b/1_fetch.R
@@ -0,0 +1,23 @@
+source("1_fetch/src/fetch_utils.R")
+
+p1_targets <- list(
+ ##### Vulnerability indicators data #####
+ tar_target(p1_sb_id,
+ '63f79d49d34e4f7eda456572'),
+ ##### Vulnerability indicators metadata #####
+ tar_target(p1_vul_ind_xml,
+ download_from_sb(sb_id = p1_sb_id,
+ filename = 'Uncertainty_Summary.xml',
+ dest_dir = '1_fetch/out'),
+ format = 'file'),
+ ##### Uncertainty statistics for the indicators #####
+ tar_target(p1_unc_stats_csv,
+ download_from_sb(sb_id = p1_sb_id,
+ filename = 'Uncertainty_Summary.csv',
+ dest_dir = '1_fetch/out'),
+ format = 'file'),
+ tar_target(p1_unc_stats,
+ readr::read_csv(p1_unc_stats_csv) |>
+ janitor::clean_names()
+ )
+ )
\ No newline at end of file
diff --git a/1_fetch/in/.empty b/1_fetch/in/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/1_fetch/out/.empty b/1_fetch/out/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/1_fetch/src/.empty b/1_fetch/src/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/2_process.R b/2_process.R
new file mode 100644
index 0000000..69c9e99
--- /dev/null
+++ b/2_process.R
@@ -0,0 +1,7 @@
+# source('1_fetch/src/file_utils.R')
+# source('2_process/src/spatial_utils.R')
+# source('2_process/src/data_utils.R')
+
+p2_targets <- list(
+
+)
\ No newline at end of file
diff --git a/2_process/in/.empty b/2_process/in/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/2_process/out/.empty b/2_process/out/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/2_process/src/.empty b/2_process/src/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/3_visualize.R b/3_visualize.R
new file mode 100644
index 0000000..6a4f6c4
--- /dev/null
+++ b/3_visualize.R
@@ -0,0 +1,6 @@
+# source('1_fetch/src/file_utils.R')
+# source('3_visualize/src/plot_utils.R')
+
+p3_targets <- list(
+
+)
\ No newline at end of file
diff --git a/3_visualize/.empty b/3_visualize/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/3_visualize/in/.empty b/3_visualize/in/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/3_visualize/out/.empty b/3_visualize/out/.empty
new file mode 100644
index 0000000..e69de29
diff --git a/_targets.R b/_targets.R
new file mode 100644
index 0000000..ef873ec
--- /dev/null
+++ b/_targets.R
@@ -0,0 +1,24 @@
+library(targets)
+library(tarchetypes) # need version >= 0.6.0.9000
+
+options(tidyverse.quiet = TRUE, timeout = 800)
+tar_option_set(packages = c('tidyverse',
+ 'sf',
+ 'terra',
+ 'rmapshaper',
+ 'purrr',
+ 'raster',
+ 'magick',
+ 'janitor',
+ 'sbtools'))
+
+# Phase target makefiles
+source("1_fetch.R")
+source("2_process.R")
+source("3_visualize.R")
+
+# Combined list of target outputs
+c(p1_targets,
+ p2_targets,
+ p3_targets
+)
\ No newline at end of file
diff --git a/vulnerability-indicators.Rproj b/vulnerability-indicators.Rproj
new file mode 100644
index 0000000..8e3c2eb
--- /dev/null
+++ b/vulnerability-indicators.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
--
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