From 817126bef5c91ef3bc69f8f5d4d1a3483b61531d Mon Sep 17 00:00:00 2001
From: syounkin <syounkin@wisc.edu>
Date: Tue, 29 Oct 2024 10:39:05 -0500
Subject: [PATCH] Run Markdown Script with make

Created a Makefile to be used to run R markdown scripts. See README for more info. Also created R and html subdirectories. The repo should contain the html subdirectory but not the files in it.
---
 .gitignore                                    | 15 ++++++-
 Makefile                                      | 15 +++++++
 route_analysis.R => R/route_analysis.Rmd      | 43 ++++++++++++++++---
 .../route_analysis.Rproj                      |  0
 html/.gitignore                               |  4 ++
 5 files changed, 68 insertions(+), 9 deletions(-)
 create mode 100644 Makefile
 rename route_analysis.R => R/route_analysis.Rmd (91%)
 rename route_analysis.Rproj => R/route_analysis.Rproj (100%)
 create mode 100644 html/.gitignore

diff --git a/.gitignore b/.gitignore
index 599f426..b349772 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,19 @@
 .Rproj*
-
 data/addresses/*
 api_keys/*
 figures/*
-
 .Rhistory
 .Rproj.user
+*.md
+.DS_Store
+!README.md
+.Rhistory
+*\.\#*
+data
+!data/
+.RData
+data-bkup/
+data-bkup
+*.R
+*.bak
+archive/
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..70d7bb1
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,15 @@
+route_analysis: R/route_analysis.Rmd
+	R -e 'library("rmarkdown"); old_path <- Sys.getenv("PATH"); Sys.setenv(PATH = paste(old_path, "/usr/local/bin", sep = ":")); rmarkdown::render(knit_root_dir = "~/route_analysis/", output_dir = "~/route_analysis/html", input = "./R/route_analysis.Rmd", output_file = "./html/route_analysis.html")'
+
+clean: clean-data clean-figure clean-script
+
+clean-data:
+	rm -vf ./R/data/*.rds
+
+clean-script:
+	rm -rvf ./*.md
+
+clean-figure:
+	rm -rvf ./figure/
+
+.PHONY: data
diff --git a/route_analysis.R b/R/route_analysis.Rmd
similarity index 91%
rename from route_analysis.R
rename to R/route_analysis.Rmd
index 24ad135..dfe65bc 100644
--- a/route_analysis.R
+++ b/R/route_analysis.Rmd
@@ -1,3 +1,17 @@
+---
+title: "Route Analysis"
+output:
+  html_document:
+    toc: true
+    toc_depth: 5
+    toc_float:
+      collapsed: false
+      smooth_scroll: true
+---
+
+```{r libs, eval = TRUE, echo = TRUE, results = "show", warning = FALSE, error = TRUE, message = FALSE}
+date()
+rm(list=ls())
 library(tidyverse)
 library(ggmap)
 library(sf)
@@ -5,8 +19,13 @@ library(osrm)
 library(smoothr)
 library(magick)
 library(ggnewscale)
+fig.height <- 6
+set.seed(1)
+```
 
+# Main R script
 
+```{r Rscript, eval = FALSE, echo = TRUE, results = "show", warning = FALSE, error = FALSE, message = FALSE}
 ## school focus
 school_focus <- data.frame(name = c("East High School"), NCES_CODE = c("550852000925"))
 
@@ -17,7 +36,7 @@ walk_boundary_m <- 1.5 * 1609
 WI_schools <- st_read(dsn = "data/Schools/WI_schools.gpkg")
 
 ## load addresses
-addresses <- read_csv(file="data/addresses/Addresses_Students_EastHS_2024_GeocodeResults.csv") %>% 
+addresses <- read_csv(file="data/addresses/Addresses_Students_EastHS_2024_GeocodeResults.csv") %>%
   filter(lat > 0) %>%
   st_as_sf(coords=c("lon","lat"), crs=4326) # remember x=lon and y=lat
 
@@ -71,9 +90,9 @@ school_symbol <- image_read_svg(path = "other/school_FILL0_wght400_GRAD0_opsz24.
 
 
 bbox <- st_bbox(st_transform(st_buffer(addresses_near, dist = 500), crs = 4326))
-bbox <- c(left = as.double(bbox[1]), 
-          bottom = as.double(bbox[2]), 
-          right = as.double(bbox[3]), 
+bbox <- c(left = as.double(bbox[1]),
+          bottom = as.double(bbox[2]),
+          right = as.double(bbox[3]),
           top = as.double(bbox[4]))
 
 #get basemap
@@ -118,7 +137,7 @@ ggmap(basemap) +
                 size = 2)
 
 ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+                     school_focus %>% pull(name),
                      " Routes.pdf"),
        title = paste0(school_focus %>% pull(name), " Walking Routes"),
        device = pdf,
@@ -165,7 +184,7 @@ ggmap(basemap) +
                 label.size = 0.04,
                 size = 2)
 ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+                     school_focus %>% pull(name),
                      " Routes - Traffic Stress.pdf"),
        title = paste0(school_focus %>% pull(name), " Walking Routes - Traffic Stress"),
        device = pdf,
@@ -209,7 +228,7 @@ ggmap(basemap) +
                 label.size = 0.04,
                 size = 2)
 ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+                     school_focus %>% pull(name),
                      " Addresses.pdf"),
        title = paste0(school_focus %>% pull(name), " Addresses"),
        device = pdf,
@@ -217,3 +236,13 @@ ggsave(file = paste0("figures/",
        width = 11,
        units = "in",
        create.dir = TRUE)
+
+
+```
+
+# Appendix
+
+```{r chunklast, eval = TRUE, echo = TRUE, results = "show", warning = TRUE, error = TRUE, message = TRUE}
+date()
+sessionInfo()
+```
diff --git a/route_analysis.Rproj b/R/route_analysis.Rproj
similarity index 100%
rename from route_analysis.Rproj
rename to R/route_analysis.Rproj
diff --git a/html/.gitignore b/html/.gitignore
new file mode 100644
index 0000000..5e7d273
--- /dev/null
+++ b/html/.gitignore
@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore