entrypoint.R

#!/usr/local/bin/Rscript

dht::greeting()

## load libraries without messages or warnings
withr::with_message_sink("/dev/null", library(dplyr))
withr::with_message_sink("/dev/null", library(tidyr))
withr::with_message_sink("/dev/null", library(sf))

doc <- "
      Usage:
      entrypoint.R <filename> <site>
      "

opt <- docopt::docopt(doc)

## for interactive testing
## opt <- docopt::docopt(doc, args = c('my_address_file_geocoded.csv', 'cchmc'))

centers <- readr::read_csv('/app/center_addresses.csv')
selected_site <- opt$site

if (!selected_site %in% centers$abbreviation) {
  stop(
    'site argument is invalid or missing; please consult documentation for details',
    call. = FALSE
  )
}

message("reading input file...")
d <- dht::read_lat_lon_csv(
  opt$filename,
  nest_df = T,
  sf = T,
  project_to_crs = 5072
)

dht::check_for_column(d$raw_data, "lat", d$raw_data$lat)
dht::check_for_column(d$raw_data, "lon", d$raw_data$lon)

message('loading isochrone shape file...')
isochrones <- readRDS(glue::glue(
  "/app/isochrones/{selected_site}_isochrones.rds"
)) # 5072 projection

## add code here to calculate geomarkers
message('finding drive time for each point...')
d$d <- suppressWarnings(st_join(d$d, isochrones, largest = TRUE)) %>%
  mutate(
    drive_time = ifelse(!is.na(drive_time), as.character(drive_time), "> 60")
  )

message('finding distance (m) for each point...')

centers <- centers %>%
  filter(abbreviation == selected_site) %>%
  st_as_sf(coords = c('lon', 'lat'), crs = 4326) %>%
  st_transform(5072)

d$d$distance <-
  st_distance(centers, d$d) |>
  as.numeric()

## merge back on .row after unnesting .rows into .row
dht::write_geomarker_file(
  d = d$d,
  raw_data = d$raw_data,
  filename = opt$filename,
  argument = opt$site
)