data-for-regions-snapshots: Download a File from the Data for Regions REDcap Project

In jesse-smith/coviData: COVID-19 Data Munging Tools for the Shelby County Health Department

Download a File from the Data for Regions REDcap Project

Description

These functions downloads a file posted on the Data for Regions project. You'll need API access to the project (and an API token for it) to use this function.

download_nbs_snapshot() downloads the current snapshot of NBS investigation data (if posted).

download_pcr_snapshot() downloads the current snapshot of PCR testing data (if posted).

download_antigen_snapshot() downloads the current snapshot of antigen testing data (if posted).

download_serology_snapshot() downloads the current snapshot of serology testing data (if posted).

download_vaccine_snapshot() downloads the current snapshot of vaccination data (if posted). Note that this is only posted on Tues/Fri, unlike other snapshot files.

Usage

download_nbs_snapshot(
  date = Sys.Date(),
  api_token = Sys.getenv("redcap_DFR_token"),
  redcap_file = "nbs_daily_upload",
  directory = paste0("V:/EPI DATA ANALYTICS TEAM/COVID SANDBOX REDCAP DATA/",
    "Sandbox data pull Final/"),
  new_file = paste0(date, " Final Data Pull.csv"),
  force = FALSE
)

download_pcr_snapshot(
  date = Sys.Date(),
  api_token = Sys.getenv("redcap_DFR_token"),
  redcap_file = "lab_pcr",
  directory = "V:/EPI DATA ANALYTICS TEAM/COVID SANDBOX REDCAP DATA/MSR PCR/",
  new_file = paste0("MSR - All PCRs_", format(Sys.Date(), "%m%d%Y"), ".csv"),
  force = FALSE
)

download_antigen_snapshot(
  date = Sys.Date(),
  api_token = Sys.getenv("redcap_DFR_token"),
  redcap_file = "lab_antigen",
  directory = "V:/EPI DATA ANALYTICS TEAM/COVID SANDBOX REDCAP DATA/MSR ANTIGEN/",
  new_file = paste0("MSR - All Antigens_", format(Sys.Date(), "%m%d%Y"), ".csv"),
  force = FALSE
)

download_serology_snapshot(
  date = Sys.Date(),
  api_token = Sys.getenv("redcap_DFR_token"),
  redcap_file = "lab_serology",
  directory = "V:/EPI DATA ANALYTICS TEAM/COVID SANDBOX REDCAP DATA/MSR SEROLOGY/",
  new_file = paste0("MSR - All Serologies_", format(Sys.Date(), "%m%d%Y"), ".csv"),
  force = FALSE
)

download_vaccine_snapshot(
  date = Sys.Date(),
  api_token = Sys.getenv("redcap_DFR_token"),
  redcap_file = "covid_vaccine_data",
  directory = path_create("V:/EPI DATA ANALYTICS TEAM/COVID SANDBOX REDCAP DATA/",
    "COVID-19 Vaccine Reporting/data/COVID-19 Vaccine data pull/"),
  new_file = name_vac_file(date, redcap_file = redcap_file, api_token = api_token),
  force = FALSE
)

Arguments

date	A Date indicating the date of the file to download
api_token	The API token for accessing the Data for Regions REDcap project. This should be stored in an .Renviron file; see env_vars for details.
redcap_file	A string indicating the name of the file to download from REDcap
directory	A string specifying the save directory; this should usually be left alone
new_file	A string specifying the save file name; this should always end in .csv and should usually be left alone
force	A logical indicating whether to ignore any existing files matching date and directory

Value

Invisibly returns the path to the new data file

jesse-smith/coviData documentation built on Jan. 14, 2023, 11:08 a.m.