From 254bbf4bfdf61cdadc319d951a914eb74b8dc26e Mon Sep 17 00:00:00 2001
From: Insang Song <insang.song@nih.gov>
Date: Wed, 13 Sep 2023 17:39:32 -0400
Subject: [PATCH] isong update - tidying (09132023) - PR #27: shiny app sources
 are moved to /tools     - /tools is included in .Rbuildignore for package
 building - EPA data download rmarkdown was moved to /vignettes - Reference:
 https://r-pkgs.org/misc.html

---
 .Rbuildignore                                 |   1 +
 R/.DS_Store                                   | Bin 6148 -> 6148 bytes
 R/{ => vignettes}/epa_download.Rmd            |   8 ++++++--
 R/{ => vignettes}/epa_download.html           |   0
 tools/.DS_Store                               | Bin 0 -> 6148 bytes
 {R => tools}/shiny_explore_pm/data/.DS_Store  | Bin
 .../shiny_explore_pm/data/STFDF_pm25.rds      | Bin
 .../shiny_explore_pm/data/STFDF_pm25_site.rds | Bin
 .../data/STVariogram_pm25.rds                 | Bin
 .../data/STVariogram_pm25_site.rds            | Bin
 .../shiny_explore_pm/data/SharedData_sf.gpkg  | Bin
 .../data/SharedLongData.parquet               | Bin
 .../data/Site_missingrate.gpkg                | Bin
 .../data/States_NMonitors.gpkg                | Bin
 .../shiny_explore_pm/data/aqs_monitors.rds    | Bin
 .../shiny_explore_pm/data/aqs_sites.csv       |   0
 .../shiny_explore_pm/data/daily/no2.rds       | Bin
 .../shiny_explore_pm/data/daily/pm25_FRM.rds  | Bin
 .../shiny_explore_pm/data/gadm41_USA_1.json   |   0
 .../shiny_explore_pm/data/monitors.rds        | Bin
 .../shiny_explore_pm/data/state_fips.csv      |   0
 ...issingness_exploration_pm_quarto_shiny.qmd |   0
 22 files changed, 7 insertions(+), 2 deletions(-)
 rename R/{ => vignettes}/epa_download.Rmd (95%)
 rename R/{ => vignettes}/epa_download.html (100%)
 create mode 100644 tools/.DS_Store
 rename {R => tools}/shiny_explore_pm/data/.DS_Store (100%)
 rename {R => tools}/shiny_explore_pm/data/STFDF_pm25.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/STFDF_pm25_site.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/STVariogram_pm25.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/STVariogram_pm25_site.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/SharedData_sf.gpkg (100%)
 rename {R => tools}/shiny_explore_pm/data/SharedLongData.parquet (100%)
 rename {R => tools}/shiny_explore_pm/data/Site_missingrate.gpkg (100%)
 rename {R => tools}/shiny_explore_pm/data/States_NMonitors.gpkg (100%)
 rename {R => tools}/shiny_explore_pm/data/aqs_monitors.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/aqs_sites.csv (100%)
 rename {R => tools}/shiny_explore_pm/data/daily/no2.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/daily/pm25_FRM.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/gadm41_USA_1.json (100%)
 rename {R => tools}/shiny_explore_pm/data/monitors.rds (100%)
 rename {R => tools}/shiny_explore_pm/data/state_fips.csv (100%)
 rename {R => tools}/shiny_explore_pm/missingness_exploration_pm_quarto_shiny.qmd (100%)

diff --git a/.Rbuildignore b/.Rbuildignore
index c503c4f6..13d4f111 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1,2 @@
 ^\.github$
+tools/
\ No newline at end of file
diff --git a/R/.DS_Store b/R/.DS_Store
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diff --git a/R/epa_download.Rmd b/R/vignettes/epa_download.Rmd
similarity index 95%
rename from R/epa_download.Rmd
rename to R/vignettes/epa_download.Rmd
index b23c7608..1e736444 100644
--- a/R/epa_download.Rmd
+++ b/R/vignettes/epa_download.Rmd
@@ -1,6 +1,10 @@
 ---
-title: "EPA_data_download"
-output: html_document
+title: "Downloading EPA Daily Data"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{epa_download}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 date: "2023-08-21"
 author: "Mariana Alifa"
 ---
diff --git a/R/epa_download.html b/R/vignettes/epa_download.html
similarity index 100%
rename from R/epa_download.html
rename to R/vignettes/epa_download.html
diff --git a/tools/.DS_Store b/tools/.DS_Store
new file mode 100644
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diff --git a/R/shiny_explore_pm/data/.DS_Store b/tools/shiny_explore_pm/data/.DS_Store
similarity index 100%
rename from R/shiny_explore_pm/data/.DS_Store
rename to tools/shiny_explore_pm/data/.DS_Store
diff --git a/R/shiny_explore_pm/data/STFDF_pm25.rds b/tools/shiny_explore_pm/data/STFDF_pm25.rds
similarity index 100%
rename from R/shiny_explore_pm/data/STFDF_pm25.rds
rename to tools/shiny_explore_pm/data/STFDF_pm25.rds
diff --git a/R/shiny_explore_pm/data/STFDF_pm25_site.rds b/tools/shiny_explore_pm/data/STFDF_pm25_site.rds
similarity index 100%
rename from R/shiny_explore_pm/data/STFDF_pm25_site.rds
rename to tools/shiny_explore_pm/data/STFDF_pm25_site.rds
diff --git a/R/shiny_explore_pm/data/STVariogram_pm25.rds b/tools/shiny_explore_pm/data/STVariogram_pm25.rds
similarity index 100%
rename from R/shiny_explore_pm/data/STVariogram_pm25.rds
rename to tools/shiny_explore_pm/data/STVariogram_pm25.rds
diff --git a/R/shiny_explore_pm/data/STVariogram_pm25_site.rds b/tools/shiny_explore_pm/data/STVariogram_pm25_site.rds
similarity index 100%
rename from R/shiny_explore_pm/data/STVariogram_pm25_site.rds
rename to tools/shiny_explore_pm/data/STVariogram_pm25_site.rds
diff --git a/R/shiny_explore_pm/data/SharedData_sf.gpkg b/tools/shiny_explore_pm/data/SharedData_sf.gpkg
similarity index 100%
rename from R/shiny_explore_pm/data/SharedData_sf.gpkg
rename to tools/shiny_explore_pm/data/SharedData_sf.gpkg
diff --git a/R/shiny_explore_pm/data/SharedLongData.parquet b/tools/shiny_explore_pm/data/SharedLongData.parquet
similarity index 100%
rename from R/shiny_explore_pm/data/SharedLongData.parquet
rename to tools/shiny_explore_pm/data/SharedLongData.parquet
diff --git a/R/shiny_explore_pm/data/Site_missingrate.gpkg b/tools/shiny_explore_pm/data/Site_missingrate.gpkg
similarity index 100%
rename from R/shiny_explore_pm/data/Site_missingrate.gpkg
rename to tools/shiny_explore_pm/data/Site_missingrate.gpkg
diff --git a/R/shiny_explore_pm/data/States_NMonitors.gpkg b/tools/shiny_explore_pm/data/States_NMonitors.gpkg
similarity index 100%
rename from R/shiny_explore_pm/data/States_NMonitors.gpkg
rename to tools/shiny_explore_pm/data/States_NMonitors.gpkg
diff --git a/R/shiny_explore_pm/data/aqs_monitors.rds b/tools/shiny_explore_pm/data/aqs_monitors.rds
similarity index 100%
rename from R/shiny_explore_pm/data/aqs_monitors.rds
rename to tools/shiny_explore_pm/data/aqs_monitors.rds
diff --git a/R/shiny_explore_pm/data/aqs_sites.csv b/tools/shiny_explore_pm/data/aqs_sites.csv
similarity index 100%
rename from R/shiny_explore_pm/data/aqs_sites.csv
rename to tools/shiny_explore_pm/data/aqs_sites.csv
diff --git a/R/shiny_explore_pm/data/daily/no2.rds b/tools/shiny_explore_pm/data/daily/no2.rds
similarity index 100%
rename from R/shiny_explore_pm/data/daily/no2.rds
rename to tools/shiny_explore_pm/data/daily/no2.rds
diff --git a/R/shiny_explore_pm/data/daily/pm25_FRM.rds b/tools/shiny_explore_pm/data/daily/pm25_FRM.rds
similarity index 100%
rename from R/shiny_explore_pm/data/daily/pm25_FRM.rds
rename to tools/shiny_explore_pm/data/daily/pm25_FRM.rds
diff --git a/R/shiny_explore_pm/data/gadm41_USA_1.json b/tools/shiny_explore_pm/data/gadm41_USA_1.json
similarity index 100%
rename from R/shiny_explore_pm/data/gadm41_USA_1.json
rename to tools/shiny_explore_pm/data/gadm41_USA_1.json
diff --git a/R/shiny_explore_pm/data/monitors.rds b/tools/shiny_explore_pm/data/monitors.rds
similarity index 100%
rename from R/shiny_explore_pm/data/monitors.rds
rename to tools/shiny_explore_pm/data/monitors.rds
diff --git a/R/shiny_explore_pm/data/state_fips.csv b/tools/shiny_explore_pm/data/state_fips.csv
similarity index 100%
rename from R/shiny_explore_pm/data/state_fips.csv
rename to tools/shiny_explore_pm/data/state_fips.csv
diff --git a/R/shiny_explore_pm/missingness_exploration_pm_quarto_shiny.qmd b/tools/shiny_explore_pm/missingness_exploration_pm_quarto_shiny.qmd
similarity index 100%
rename from R/shiny_explore_pm/missingness_exploration_pm_quarto_shiny.qmd
rename to tools/shiny_explore_pm/missingness_exploration_pm_quarto_shiny.qmd