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..bfc6f18
--- /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 = "./", output_dir = "./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 83%
rename from route_analysis.R
rename to R/route_analysis.Rmd
index 24ad135..f391e28 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 = TRUE, echo = TRUE, results = "show", warning = FALSE, error = TRUE, message = FALSE}
 ## school focus
 school_focus <- data.frame(name = c("East High School"), NCES_CODE = c("550852000925"))
 
@@ -14,10 +33,10 @@ school_focus <- data.frame(name = c("East High School"), NCES_CODE = c("55085200
 walk_boundary_m <- 1.5 * 1609
 
 ## load school locations
-WI_schools <- st_read(dsn = "data/Schools/WI_schools.gpkg")
+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
 
@@ -25,7 +44,7 @@ addresses <- read_csv(file="data/addresses/Addresses_Students_EastHS_2024_Geocod
 options(osrm.server = "http://127.0.0.1:5000/")
 options(osrm.profile = "walk")
 
-register_stadiamaps(key = substr(read_file(file = "api_keys/stadia_api_key"), 1, 36))
+register_stadiamaps(key = substr(read_file(file = "../api_keys/stadia_api_key"), 1, 36))
 
 ## subset addresses within 1.5 miles
 walk_boundary_poly <- fill_holes(st_make_valid(osrmIsodistance(
@@ -37,7 +56,7 @@ walk_boundary_poly <- fill_holes(st_make_valid(osrmIsodistance(
 addresses_near <- st_intersection(addresses, walk_boundary_poly)
 
 ## load bike tls
-bike_lts <- st_read("data/bike_lts/bike_lts_DANE.geojson")
+bike_lts <- st_read("../data/bike_lts/bike_lts_DANE.geojson")
 bike_lts[["lts"]] <- as.factor(bike_lts$LTS_F)
 
 bike_lts_scale <- data.frame(code = c(1, 2, 3, 4, 9),
@@ -58,7 +77,7 @@ for(i in addresses_near$number) {
 routes <- bind_rows(routes)
 
 ## combine routes
-bike_lts_buffer <- st_buffer(st_intersection(bike_lts, walk_boundary_poly), 10)
+bike_lts_buffer <- st_buffer(st_intersection(bike_lts, walk_boundary_poly), 20)
 
 bike_lts_buffer["student_use"] <- unlist(lapply(st_intersects(bike_lts_buffer, routes), length))
 
@@ -66,14 +85,14 @@ bike_lts <- st_join(bike_lts, bike_lts_buffer %>% select(OBJECTID, student_use))
 
 ## make maps
 # load logo
-logo <- image_read(path = "other/BFW_Logo_180_x_200_transparent_background.png")
-school_symbol <- image_read_svg(path = "other/school_FILL0_wght400_GRAD0_opsz24.svg")
+logo <- image_read(path = "../other/BFW_Logo_180_x_200_transparent_background.png")
+school_symbol <- image_read_svg(path = "../other/school_FILL0_wght400_GRAD0_opsz24.svg")
 
 
 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
@@ -87,7 +106,7 @@ ggmap(basemap) +
     x = NULL,
     y = NULL,
     color = NULL,
-    linewidth = "How many students can use road") +
+    linewidth = "Potential student walkers") +
   theme(axis.text=element_blank(),
         axis.ticks=element_blank(),
         plot.caption = element_text(color = "grey")) +
@@ -117,8 +136,8 @@ ggmap(basemap) +
                 label.size = 0.04,
                 size = 2)
 
-ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+ggsave(file = paste0("../figures/",
+                     school_focus %>% pull(name),
                      " Routes.pdf"),
        title = paste0(school_focus %>% pull(name), " Walking Routes"),
        device = pdf,
@@ -131,11 +150,11 @@ ggsave(file = paste0("figures/",
 ggmap(basemap) +
   labs(title = paste0("Walking routes for students at ",
                       school_focus %>% pull(name)),
-       subtitle = "only showing routes within the 1.5 walk boundary",
+       subtitle = "only showing routes within the walk boundary",
        x = NULL,
        y = NULL,
        color = NULL,
-       linewidth = "How many students can use road") +
+       linewidth = "Potential student walkers") +
   theme(axis.text=element_blank(),
         axis.ticks=element_blank(),
         plot.caption = element_text(color = "grey")) +
@@ -164,8 +183,8 @@ ggmap(basemap) +
                 nudge_y = 0.0015,
                 label.size = 0.04,
                 size = 2)
-ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+ggsave(file = paste0("../figures/",
+                     school_focus %>% pull(name),
                      " Routes - Traffic Stress.pdf"),
        title = paste0(school_focus %>% pull(name), " Walking Routes - Traffic Stress"),
        device = pdf,
@@ -208,8 +227,8 @@ ggmap(basemap) +
                 nudge_y = 0.0015,
                 label.size = 0.04,
                 size = 2)
-ggsave(file = paste0("figures/",
-                     school_focus %>% pull(name), 
+ggsave(file = paste0("../figures/",
+                     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/README.md b/README.md
index 2e4d3e9..5354ae9 100644
--- a/README.md
+++ b/README.md
@@ -15,3 +15,7 @@ This script will generate a few figures:
 
 ### A map of those routes colored by the level of traffic stress to bike
 ![example routes-lts figure](examples/example-routes-lts.png)
+
+## Using make
+The command `make route_analysis` will run *route_analysis.Rmd* which
+is an R markdown file containing the original R script *route_analysis.R*
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