inst/doc/workflow-read.R

In REDCapR: Interaction Between R and REDCap

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  tidy    = FALSE
)

## ----pre-req------------------------------------------------------------------
requireNamespace("REDCapR")

# If this fails, run `install.packages("REDCapR")` or `remotes::install_github(repo="OuhscBbmc/REDCapR")`

## ----retrieve-credential------------------------------------------------------
path_credential <- system.file("misc/example.credentials", package = "REDCapR")
credential  <- REDCapR::retrieve_credential_local(
  path_credential = path_credential, 
  project_id      = 153
)

credential

## ----unstructured-1-----------------------------------------------------------
ds_1 <- 
  REDCapR::redcap_read(
    redcap_uri  = credential$redcap_uri, 
    token       = credential$token
  )$data

## ----unstructured-2-----------------------------------------------------------
ds_1

hist(ds_1$weight)

summary(ds_1)

summary(lm(age ~ 1 + sex + bmi, data = ds_1))

## ----choose-records-----------------------------------------------------------
# Return only records with IDs of 1 and 4
desired_records <- c(1, 4)
REDCapR::redcap_read(
  redcap_uri  = credential$redcap_uri,
  token       = credential$token,
  records     = desired_records,
  verbose     = FALSE
)$data

## ----choose-records-filter----------------------------------------------------
# Return only records with a birth date after January 2003
REDCapR::redcap_read(
  redcap_uri    = credential$redcap_uri,
  token         = credential$token,
  filter_logic  = "'2003-01-01' < [dob]",
  verbose       = FALSE
)$data

## ----choose-fields------------------------------------------------------------
# Return only the fields record_id, name_first, and age
desired_fields <- c("record_id", "name_first", "age")
REDCapR::redcap_read(
  redcap_uri  = credential$redcap_uri,
  token       = credential$token,
  fields      = desired_fields,
  verbose     = FALSE
)$data

## ----col_types----------------------------------------------------------------
# Specify the column types.
desired_fields <- c("record_id", "race")
col_types <- readr::cols(
  record_id  = readr::col_integer(),
  race___1   = readr::col_logical(),
  race___2   = readr::col_logical(),
  race___3   = readr::col_logical(),
  race___4   = readr::col_logical(),
  race___5   = readr::col_logical(),
  race___6   = readr::col_logical()
)
REDCapR::redcap_read(
  redcap_uri  = credential$redcap_uri,
  token       = credential$token,
  fields      = desired_fields,
  verbose     = FALSE,
  col_types   = col_types
)$data

## ----col_types-string---------------------------------------------------------
# Specify the column types.
desired_fields <- c("record_id", "race")
col_types <- readr::cols(.default = readr::col_character())
REDCapR::redcap_read(
  redcap_uri  = credential$redcap_uri,
  token       = credential$token,
  fields      = desired_fields,
  verbose     = FALSE,
  col_types   = col_types
)$data