inst/doc/longitudinal-and-repeating.R

In REDCapR: Interaction Between R and REDCap

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

knit_print.data.frame <- function(x, ...) {
  # See https://cran.r-project.org/package=knitr/vignettes/knit_print.html
  . <- NULL # Avoid lintr check
  x %>%
    # rmarkdown::print.paged_df() %>%
    kable(
      col.names = gsub("_", "<br>", colnames(.)),
      # col.names = paste0("<code>", gsub("_", "<br>", colnames(.)), "</code>"),
      # col.names = gsub("_", " ", colnames(.)),
      escape = FALSE,
      format = "html"
    ) %>%
    kableExtra::kable_styling(
      bootstrap_options = c("striped", "hover", "condensed", "responsive"),
      full_width        = FALSE
    ) %>%
    c("", "", .) %>%
    paste(collapse = "\n") %>%
    asis_output()
}

# register the method
registerS3method("knit_print", "data.frame", knit_print.data.frame)

## ----retrieve-credential------------------------------------------------------
# Support pipes
library(magrittr)

# Retrieve token
path_credential <- system.file("misc/example.credentials", package = "REDCapR")
credential  <- REDCapR::retrieve_credential_local(
  path_credential = path_credential,
  project_id      = 3181
)

## ----redcapr-intake-----------------------------------------------------------
col_types_intake <-
  readr::cols_only(
    record_id                 = readr::col_integer(),
    height                    = readr::col_double(),
    weight                    = readr::col_double(),
    bmi                       = readr::col_double()
  )

ds_intake <-
  REDCapR::redcap_read(
    redcap_uri  = credential$redcap_uri, # From the previous code snippet.
    token       = credential$token,
    forms       = c("intake"),
    col_types   = col_types_intake,
    verbose     = FALSE,
  )$data

ds_intake

## ----redcapr-repeating--------------------------------------------------------
col_types_blood_pressure <-
  readr::cols(
    record_id                 = readr::col_integer(),
    redcap_repeat_instrument  = readr::col_character(),
    redcap_repeat_instance    = readr::col_integer(),
    sbp                       = readr::col_double(),
    dbp                       = readr::col_double(),
    blood_pressure_complete   = readr::col_integer()
  )

ds_blood_pressure <-
  REDCapR::redcap_read(
    redcap_uri  = credential$redcap_uri,
    token       = credential$token,
    forms       = c("blood_pressure"),
    col_types   = col_types_blood_pressure,
    verbose     = FALSE
  )$data

ds_blood_pressure %>%
  tidyr::drop_na(redcap_repeat_instrument)

col_types_laboratory  <-
  readr::cols(
    record_id                 = readr::col_integer(),
    redcap_repeat_instrument  = readr::col_character(),
    redcap_repeat_instance    = readr::col_integer(),
    lab                       = readr::col_character(),
    conc                      = readr::col_character(),
    laboratory_complete       = readr::col_integer()
  )

ds_laboratory  <-
  REDCapR::redcap_read(
    redcap_uri  = credential$redcap_uri,
    token       = credential$token,
    forms       = c("laboratory"),
    col_types   = col_types_laboratory,
    verbose     = FALSE
  )$data

ds_laboratory %>%
  tidyr::drop_na(redcap_repeat_instrument)

## ----redcapr-block------------------------------------------------------------
ds_block <-
  REDCapR::redcap_read(
    redcap_uri  = credential$redcap_uri,
    token       = credential$token,
    col_types   = readr::cols(.default = readr::col_character()),
    verbose     = FALSE,
  )$data

ds_block

## ----session-info, echo=FALSE-------------------------------------------------
if (requireNamespace("sessioninfo", quietly = TRUE)) {
  sessioninfo::session_info()
} else {
  sessionInfo()
}