## ----set_options--------------------------------------------------------------
report_render_start_time <- Sys.time()
report_render_duration_in_seconds <- -999 # In case the vignette isn't evaluated (on CRAN)

library(knitr)
library(magrittr)
suppressPackageStartupMessages(requireNamespace("kableExtra"))

opts_chunk$set(
  eval    = !REDCapR:::on_cran(),
  comment = "#>",
  tidy    = FALSE
)

## ----project_values-----------------------------------------------------------
# library(REDCapR) #Load the package into the current R session.
# uri                   <- "https://redcap-dev-2.ouhsc.edu/redcap/api/"
# token_simple          <- "9A068C425B1341D69E83064A2D273A70"
# token_longitudinal    <- "DA6F2BB23146BD5A7EA3408C1A44A556"

## ----retrieve-longitudinal----------------------------------------------------
# library(magrittr)
# suppressPackageStartupMessages(requireNamespace("dplyr"))
# suppressPackageStartupMessages(requireNamespace("tidyr"))
# events_to_retain  <- c("dose_1_arm_1", "visit_1_arm_1", "dose_2_arm_1", "visit_2_arm_1")
# 
# ds_long <- REDCapR::redcap_read_oneshot(redcap_uri = uri, token = token_longitudinal)$data
# ds_long %>%
#   dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4)

## ----widen-simple-------------------------------------------------------------
# ds_wide <-
#   ds_long %>%
#   dplyr::select(study_id, redcap_event_name, pmq1) %>%
#   dplyr::filter(redcap_event_name %in% events_to_retain) %>%
#   tidyr::pivot_wider(
#     id_cols     = study_id,
#     names_from  = redcap_event_name,
#     values_from = pmq1
#   )
# ds_wide

## ----widen-typical------------------------------------------------------------
# pattern <- "^(\\w+?)_arm_(\\d)$"
# ds_wide <-
#   ds_long %>%
#   dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
#   dplyr::mutate(
#     event = sub(pattern, "\\1", redcap_event_name),
#     event = dplyr::recode(event, "first_dose"="dose_1", "first_visit"="visit_1"),
#     arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
#   ) %>%
#   dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
#   dplyr::filter(!(event %in%
#     c("enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
#   )) %>%
#   tidyr::pivot_wider(
#     id_cols     = c(study_id, arm),
#     names_from  = event,
#     values_from = c(pmq1, pmq2, pmq3, pmq4)
#   )
# 
# ds_wide

## ----widen-long-first---------------------------------------------------------
# ds_eav <-
#   ds_long %>%
#   dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
#   dplyr::mutate(
#     event = sub(pattern, "\\1", redcap_event_name),
#     event = dplyr::recode(event, "first_dose" = "dose_1", "first_visit" = "visit_1"),
#     arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
#   ) %>%
#   dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
#   tidyr::pivot_longer(
#     cols      = c(pmq1, pmq2, pmq3, pmq4),
#     names_to  = "key",
#     values_to = "value"
#   ) %>%
#   # For old versions of tidyr that predate `pivot_wider()`:
#   # tidyr::gather(key=key, value=value, pmq1, pmq2, pmq3, pmq4) %>%
#   dplyr::filter(!(event %in% c(
#     "enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
#   )) %>%
#   dplyr::mutate( # Simulate correcting for mismatched names across arms:
#     key = paste0(key, "_", event)
#   ) %>%
#   dplyr::select(-event)
# 
# # Show the first 10 rows of the EAV table.
# ds_eav %>%
#   head(10)
# 
# # Spread the EAV to wide.
# ds_wide_2 <-
#   ds_eav %>%
#   tidyr::pivot_wider(
#     id_cols     = c(study_id, arm),
#     names_from  = key,
#     values_from = value
#   )
# # For old versions of tidyr that predate `pivot_wider()`:
# # tidyr::spread(key=key, value=value)
# ds_wide_2

## -----------------------------------------------------------------------------
# cert_location <- system.file("cacert.pem", package = "openssl")
# if (file.exists(cert_location)) {
#   config_options         <- list(cainfo = cert_location)
#   ds_different_cert_file <- redcap_read_oneshot(
#     redcap_uri     = uri,
#     token          = token_simple,
#     config_options = config_options
#   )$data
# }

## -----------------------------------------------------------------------------
# config_options <- list(sslversion = 3)
# ds_ssl_3 <- redcap_read_oneshot(
#   redcap_uri     = uri,
#   token          = token_simple,
#   config_options = config_options
# )$data
# 
# config_options <- list(ssl.verifypeer = FALSE)
# ds_no_ssl <- redcap_read_oneshot(
#   redcap_uri     = uri,
#   token          = token_simple,
#   config_options = config_options
# )$data

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

## ----session-duration, echo=FALSE---------------------------------------------
# report_render_duration_in_seconds <- round(as.numeric(difftime(Sys.time(), report_render_start_time, units = "secs")))