In uva-bi-sdad/dc.webmd.primcare: Social Data Commons: Health, Behavior, Diet: Primary Care Access Scores

knitr::opts_chunk$set(echo = TRUE)

Get dataset DOI

dataset_doi <- readLines(here::here("data/dataset_doi"))[1]

Code you used to create dataset - LIST BELOW

dc_health_behavior_diet.va_hdcttrbg_webmd_2021_access_scores_primcare: prepare_data.Rmd and catchment_scores.Rmd for VA

# Ex database_table_name: "va_hd_vdoe_2019_2021_3rd_grade_mean_median_read_score"
table_names = c("va_hdcttrbg_webmd_2021_access_scores_primcare") 

con <- get_db_conn()

dat_file_name <- table_names[1]
db_schema_name <- "dc_health_behavior_diet"  # Ex database schema_name: dc_education_training
all_geos_dat <- DBI::dbReadTable(con, c(db_schema_name, dat_file_name))  

if (length(table_names) > 1)
{
  for (i in 2:length(table_names))
  { 
    dat_file_name <- table_names[i]
    dat <- DBI::dbReadTable(con, c(db_schema_name, dat_file_name)) 

    all_geos_dat <- rbind(all_geos_dat, dat)  
  }
}

DBI::dbDisconnect(con)

all_geos_file_name <- "va_hdcttrbg_webmd_2021_access_scores_primcare"  #Ex: "va_vdoe_2019_2021_3rd_grade_mean_median_read_score"
assign(all_geos_file_name, all_geos_dat)

Write to compressed file

dat_file_path <- here::here(paste0("data/", all_geos_file_name, ".csv.xz"))

readr::write_csv(get(all_geos_file_name),
                 xzfile(dat_file_path, compression = 9))

Upload Files to Dataverse Dataset

# check if file already exists

file_names <- dataverse::dataset_files(
    dataset = dataset_doi,
    version = ":latest",
    key = Sys.getenv("DATAVERSE_KEY"),
    server = Sys.getenv("DATAVERSE_SERVER")
)

names <- c()

if (length(file_names) > 0)
{
  for(i in 1:length(file_names))
  {
    names <- c(names, file_names[[i]]$dataFile$filename)
  }

} else
{
  names <- file_names
}


if (paste0(all_geos_file_name, ".csv.xz") %in% names) # file already exists, so we update it
{
   idx = which(names == paste0(all_geos_file_name, ".csv.xz"))

   dataverse::update_dataset_file(
     file = dat_file_path,
     dataset = dataset_doi,
     id = file_names[[idx]]$dataFile$id,
     key = Sys.getenv("DATAVERSE_KEY"),
     server   = Sys.getenv("DATAVERSE_SERVER"),
     description = all_geos_file_name
   )

} else  # file doesn't exist, so we add it to the dataset
{
   dataverse::add_dataset_file(
     file = dat_file_path,
     dataset = dataset_doi,
     key = Sys.getenv("DATAVERSE_KEY"),
     server   = Sys.getenv("DATAVERSE_SERVER"),
     description = all_geos_file_name
   )
}

uva-bi-sdad/dc.webmd.primcare documentation built on June 18, 2022, 7 a.m.