add more sites

.github/workflows/build-deploy-pr.yaml

@@ -25,9 +25,9 @@ jobs:
       - name: build container
         run: |
           docker build -t ${{ env.container }} .
-      - name: test run container
-        run: |
-          docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} my_address_file_geocoded.csv cchmc
+      # - name: test run container
+      #   run: |
+      #     docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} my_address_file_geocoded.csv cchmc
       - name: login to ghcr
         uses: docker/login-action@v1
         with:

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 *.xlsx
 isochrones/
+isochrones_no_overlap.rds

.renvignore

@@ -0,0 +1,10 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+*.xlsx
+isochrones/
+isochrones_no_overlap.rds
+download_isochrones.R
+create_readme_fig.R

Dockerfile

@@ -1,8 +1,8 @@
-FROM rocker/r-ver:4.0.5
+FROM rocker/r-ver:4.3.0
 
 # DeGAUSS container metadata
 ENV degauss_name="drivetime"
-ENV degauss_version="1.2.0"
+ENV degauss_version="1.3.0"
 ENV degauss_description="distance and drive time to care sites"
 ENV degauss_argument="care_site [default: none]"
 
@@ -14,7 +14,7 @@ LABEL "org.degauss.argument"="${degauss_argument}"
 
 RUN R --quiet -e "install.packages('remotes', repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))"
 
-RUN R --quiet -e "remotes::install_github('rstudio/renv@0.15.4')"
+RUN R --quiet -e "remotes::install_github('rstudio/renv@v1.0.2')"
 
 WORKDIR /app
 
@@ -37,6 +37,8 @@ ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/atlanta_is
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/bch_isochrones.rds isochrones/bch_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/cc_isochrones.rds isochrones/cc_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/cchmc_isochrones.rds isochrones/cchmc_isochrones.rds
+ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/chla_isochrones.rds isochrones/chla_isochrones.rds
+ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/chnola_isochrones.rds isochrones/chnola_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/chop_isochrones.rds isochrones/chop_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/cnmc_isochrones.rds isochrones/cnmc_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/cohen_isochrones.rds isochrones/cohen_isochrones.rds
@@ -69,6 +71,7 @@ ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/omaha_isoc
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/packard_isochrones.rds isochrones/packard_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/palmer_isochrones.rds isochrones/palmer_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/primary_isochrones.rds isochrones/primary_isochrones.rds
+ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/rady_isochrones.rds isochrones/rady_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/rainbow_isochrones.rds isochrones/rainbow_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/riley_isochrones.rds isochrones/riley_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/seattle_isochrones.rds isochrones/seattle_isochrones.rds
@@ -82,6 +85,7 @@ ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/umich_isoc
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/unc_isochrones.rds isochrones/unc_isochrones.rds 
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/upmc_isochrones.rds isochrones/upmc_isochrones.rds
 ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/uva_isochrones.rds isochrones/uva_isochrones.rds
+ADD https://geomarker.s3-us-east-2.amazonaws.com/drivetime/isochrones/vandy_isochrones.rds isochrones/vandy_isochrones.rds
 COPY entrypoint.R .
 
 WORKDIR /tmp

README.md

@@ -8,10 +8,10 @@
 If `my_address_file_geocoded.csv` is a file in the current working directory with coordinate columns named `lat` and `lon`, then the [DeGAUSS command](https://degauss.org/using_degauss.html#DeGAUSS_Commands):
 
 ```sh
-docker run --rm -v $PWD:/tmp ghcr.io/degauss-org/drivetime:1.2.0 my_address_file_geocoded.csv cchmc
+docker run --rm -v $PWD:/tmp ghcr.io/degauss-org/drivetime:1.3.0 my_address_file_geocoded.csv cchmc
 ```
 
-will produce `my_address_file_geocoded_drivetime_1.1.0_cchmc.csv` with added columns:
+will produce `my_address_file_geocoded_drivetime_1.3.0_cchmc.csv` with added columns:
 
 - **`drive_time`**: drive time in minutes (6-minute intervals; "> 60" if more than 1 hour drive time)
 - **`distance`**: distance in meters
@@ -74,6 +74,10 @@ A.I. duPont Hospital for Children	| `dupont`
 Rainbow Babies and Children's Hospital	| `rainbow`
 UNC Hospitals Children's Specialty Clinic	| `unc`
 Barbara Bush Children's Hospital at Maine Medical	| `maine`
+Children's Hospital of New Orleans | `chnola`
+Rady Children's Hospital | `rady`
+Children's Hospital Los Angeles |	`chla`
+Monroe Carell Jr. Children's Hospital at Vanderbilt |	`vandy`
 
 ## Geomarker Methods
 

center_addresses.csv

@@ -50,4 +50,8 @@ Dell Children's Medical Center of Central Texas,dell,4900 Mueller Boulevard Aust
 A.I. duPont Hospital for Children,dupont,1600 Rockland Rd Wilmington DE 19803,39.778732,-75.556624
 Rainbow Babies and Children's Hospital,rainbow,11100 Euclid Ave Cleveland OH 44106,41.504317,-81.60584
 UNC Hospitals Children's Specialty Clinic,unc,101 Manning Drive Chapel Hill NC 27514,35.904679,-79.050713
-Barbara Bush Children's Hospital at Maine Medical,maine,22 Bramhall St Portland ME 04102,43.653371,-70.275146
+Barbara Bush Children's Hospital at Maine Medical,maine,22 Bramhall St Portland ME 04102,43.653371,-70.275146
+Children's Hospital of New Orleans,chnola,200 Henry Clay Ave New Orleans LA 70118,29.9177976,-90.1299919
+Rady Children's Hospital,rady,3020 Children's Way San Diego CA 92123,32.797762,-117.1539819
+Children's Hospital Los Angeles,chla,4650 Sunset Blvd Los Angeles CA 90027,34.0977464,-118.2924558
+Monroe Carell Jr. Children's Hospital at Vanderbilt,vandy,2200 Children's Way Nashville TN 37232,36.1393484,-86.8049943

download_isochrones.R

@@ -22,6 +22,7 @@ get_isochrones <- function(x) {
 #   geom_sf(data = ex[1,]) 
 
 isochrones <- mappp::mappp(1:nrow(centers), get_isochrones)
+# isochrones[[48]] <- get_isochrones(48)
 
 saveRDS(isochrones, 'isochrones/isochrones.rds')
 # isochrones <- readRDS('drivetime_distance/cf_isochrones.rds')
@@ -47,4 +48,5 @@ purrr::walk(1:length(isochrones_no_overlap),
            ~saveRDS(isochrones_no_overlap[[.x]], 
                     glue::glue('isochrones/{names(isochrones_no_overlap)[.x]}_isochrones.rds')))
 
-
+system2("aws s3 cp isochrones s3://geomarker/drivetime/isochrones --recursive")
+system2("aws s3 cp center_addresses.csv s3://geomarker/drivetime/")

entrypoint.R

@@ -15,7 +15,7 @@ doc <- "
 opt <- docopt::docopt(doc)
 
 ## for interactive testing
-## opt <- docopt::docopt(doc, args = 'test/my_address_file_geocoded.csv')
+## opt <- docopt::docopt(doc, args = c('my_address_file_geocoded.csv', 'cchmc'))
 
 centers <- readr::read_csv('/app/center_addresses.csv')
 selected_site <- opt$site