Merge pull request #6 from degauss-org/4.0.1-updates

4.0.1 updates

.gitignore

@@ -1,4 +1,5 @@
 .Rproj.user
+.Rproj
 .Rhistory
 .RData
 .Ruserdata

Dockerfile

@@ -1,7 +1,9 @@
-FROM rocker/verse:4.0.3
+FROM rocker/verse:4.1.2
 
 # install a newer-ish version of renv, but the specific version we want will be restored from the renv lockfile
 RUN R --quiet -e "install.packages('renv', repos = 'https://cran.rstudio.com')"
+ENV RENV_VERSION 0.15.2
+RUN R --quiet -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
 
 WORKDIR /app
 
@@ -15,13 +17,14 @@ RUN apt-get update \
   && apt-get clean
 
 COPY renv.lock .
-RUN R --quiet -e "renv::restore(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))"
-#RUN R --quiet -e "renv::restore(repos = c(CRAN = 'https://cran.rstudio.com'))"
+#RUN R --quiet -e "renv::restore(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))"
+RUN R --quiet -e "renv::restore(repos = c(CRAN = 'https://cran.rstudio.com'))"
 
 COPY tract_to_neighborhood.rds .
 COPY ham_neighborhoods_dep_index_shp.rds .
 COPY weekly_data_report.R .
+COPY entrypoint.R .
 
 WORKDIR /tmp
 
-ENTRYPOINT ["/app/weekly_data_report.R"]
+ENTRYPOINT ["/app/entrypoint.R"]

Makefile

@@ -9,7 +9,7 @@ build:
 	docker build -t $(IMAGE) .
 
 test:
-	docker run --rm -v "${PWD}/test":/tmp $(IMAGE) simulated_jfs_data_geocoded.csv
+	docker run --rm -v "${PWD}/test":/tmp $(IMAGE) simulated_jfs_data_geocoded_all_years.csv
 
 shell:
 	docker run --rm -it --entrypoint=/bin/bash -v "${PWD}/test":/tmp $(IMAGE)

entrypoint.R

@@ -15,6 +15,7 @@ args <- parse_args(p)
 # ALLEGATION_ADDRESS, formatted in a string without punctuation, it includes city, state, and zip code
 
 suppressPackageStartupMessages(library(readr))
+suppressPackageStartupMessages(library(tidyverse))
 d <- read_csv(args$file_name,
               col_types = cols(INTAKE_ID = col_character(),
                                SCREENING_DECISION = col_character(),
@@ -44,20 +45,10 @@ d <- read_csv(args$file_name,
                                ))
 d <- dplyr::mutate(d, DECISION_DATE = dht::check_dates(DECISION_DATE))
 
+tract_to_neighborhood <- readRDS('/app/tract_to_neighborhood.rds')
+
 message("\nNeighborhood repsonses with < 5 instances have been censored for privacy purposes\n")
 
-rmarkdown::render(input = '/app/aggregate_data_report.rmd',
+rmarkdown::render(input = '/app/weekly_data_report.R',
                   params = list(d = d),
                   envir = new.env())
-
-
-# rmarkdown::render(input = '/app/acv_level_report.rmd',
-#                   params = list(d = d),
-#                   envir = new.env(),
-#                   output_file = fs::path("/tmp", paste0(gsub('.csv', '', args$file_name, fixed=TRUE), '_acv_level_report.html')))
-
-# rmarkdown::render(input = '/app/intake_level_report.rmd',
-#                   params = list(d = d),
-#                   envir = new.env(),
-#                   output_file = fs::path("/tmp", paste0(gsub('.csv', '', args$file_name, fixed=TRUE), '_intake_level_report.html')))
-