add basemaps chapter and references

Author: Sara Altman

_bookdown.yml

@@ -2,7 +2,9 @@ new_session: true
 delete_merged_file: true
 
 rmd_files: [
-  "index.Rmd"
+  "index.Rmd",
+  "basemaps.Rmd",
+  "references.Rmd"
 ]
 
 before_chapter_script: "_common.R"

basemaps.Rmd

@@ -0,0 +1,52 @@
+# Downloads and unzips Snow's cholera data
+# Creates two geojson files: one for pumps and one for deaths
+
+# Author: Sara Altman, Bill Behrman
+# Version: 2019-02-27
+
+# Libraries
+library(tidyverse)
+library(sf)
+
+# Parameters
+url_data <- "http://rtwilson.com/downloads/SnowGIS_KML.zip"
+# Output files
+file_out_deaths <- "cholera_deaths.geojson"
+file_out_pumps <- "cholera_pumps.geojson"
+#===============================================================================
+
+# Create temporary directory
+dir_tmp <- str_glue("/tmp/{Sys.time() %>% as.integer()}")
+if (!file.exists(dir_tmp)) {
+  dir.create(dir_tmp, recursive = TRUE)
+}
+
+file_zip <- str_glue("{dir_tmp}/SnowGIS_KML.zip")
+
+if (download.file(url = url_data, destfile = file_zip, quiet = TRUE)) {
+  stop("Error: Download failed")
+}
+
+unzip(zipfile = file_zip, exdir = dir_tmp)
+
+str_glue("{dir_tmp}/SnowGIS_KML/cholera_deaths.kml") %>% 
+  read_sf() %>% 
+  transmute(
+    deaths = str_extract(Description, "\\d+") %>% as.integer(),
+    geometry = geometry
+  ) %>% 
+  arrange(desc(deaths)) %>% 
+  st_write(file_out_deaths, delete_dsn = TRUE)
+  
+str_glue("{dir_tmp}/SnowGIS_KML/pumps.kml") %>% 
+  read_sf() %>%  
+  select(geometry) %>% 
+  st_write(file_out_pumps, delete_dsn = TRUE)
+
+# Remove temporary directory
+if (unlink(dir_tmp, recursive = TRUE, force = TRUE)) {
+  print("Error: Remove temporary directory failed")
+}
+
+
+

data/cholera/cholera_deaths.geojson

@@ -0,0 +1,41 @@
+# 
+
+# Author: Sara Altman, Bill Behrman
+# Version: 2019-02-27
+
+# Libraries
+library(tidyverse)
+library(sf)
+
+# Parameters
+url_data <- "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/50m/cultural/ne_50m_admin_0_countries.zip"
+# Output files
+file_out_africa <- "africa.geojson"
+#===============================================================================
+
+# Create temporary directory
+dir_tmp <- str_glue("/tmp/{Sys.time() %>% as.integer()}")
+
+if (!file.exists(dir_tmp)) {
+  dir.create(dir_tmp, recursive = TRUE)
+}
+
+file_zip <- str_glue("{dir_tmp}/ne_50m_admin_0_countries.zip")
+
+if (download.file(url = url_data, destfile = file_zip, quiet = TRUE)) {
+  stop("Error: Download failed")
+}
+
+unzip(zipfile = file_zip, exdir = dir_tmp)
+
+str_glue("{dir_tmp}/ne_50m_admin_0_countries.shp") %>% 
+  read_sf() %>% 
+  rename_all(str_to_lower) %>% 
+  filter(continent == "Africa") %>% 
+  select(name, population = pop_est, geometry) %>% 
+  st_write(file_out_africa)
+  
+# Remove temporary directory
+if (unlink(dir_tmp, recursive = TRUE, force = TRUE)) {
+  print("Error: Remove temporary directory failed")
+}

data/cholera/cholera_pumps.geojson

@@ -8,7 +8,7 @@ url: 'https\://datalab.stanford.edu/dcl-docs/geo-vis'
 github-repo: dcl-docs/geo-vis
 site: bookdown::bookdown_site
 documentclass: book
-#bibliography: references.bib
+bibliography: references.bib
 link-citations: true
 ---
 

data/cholera/data.R

@@ -0,0 +1 @@
+`r if (knitr:::is_html_output()) "# References {-}"`

data/countries/africa.geojson

@@ -0,0 +1,8 @@
+@book{snow-1855,
+  author    = {John Snow},
+  title     = {On the Mode of Communication of Cholera},
+  publisher = {John Churchill},
+  year      = 1855,
+  address   = {London},
+  edition   = 2
+}