R/Medicine 2024 part 1a

skadauke/rmedicine_2024_redcap_r_workshop#1

documentation-for-developers/r-meidicine-2024-part-1.R

@@ -0,0 +1,101 @@
+## ----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      = 3181
+)
+
+credential
+
+## ----unstructured-1-----------------------------------------------------------
+ds_1 <-
+  REDCapR::redcap_read(
+    redcap_uri  = credential$redcap_uri,
+    token       = credential$token
+  )$data
+
+View(ds_1)
+
+
+# View corresponding REDCap project in browser:
+# https://bbmc.ouhsc.edu/redcap/redcap_v14.3.13/DataEntry/record_home.php?pid=3181&arm=1&id=1
+
+
+# ---- redcap_metadata_read ----------------------------------------------------
+REDCapR::redcap_metadata_read(
+  redcap_uri  = credential$redcap_uri,
+  token       = credential$token
+)$data
+
+
+# ---- grain - 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       = "intake",
+    col_types   = col_types_intake,
+    verbose     = FALSE,
+  )$data
+
+ds_intake
+
+
+# ---- grain - bp --------------------------------------------------------------
+col_types_blood_pressure <-
+  readr::cols(
+    record_id                 = readr::col_integer(),
+    redcap_repeat_instrument  = readr::col_character(),
+    redcap_repeat_instance    = readr::col_integer(),
+    sbp                       = readr::col_double(),
+    dbp                       = readr::col_double(),
+    blood_pressure_complete   = readr::col_integer()
+  )
+
+ds_blood_pressure <-
+  REDCapR::redcap_read(
+    redcap_uri  = credential$redcap_uri,
+    token       = credential$token,
+    forms       = "blood_pressure",
+    col_types   = col_types_blood_pressure,
+    verbose     = FALSE
+  )$data
+
+ds_blood_pressure |>
+  tidyr::drop_na(redcap_repeat_instrument)
+
+# ---- grain - labs ------------------------------------------------------------
+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       = "laboratory",
+    col_types   = col_types_laboratory,
+    verbose     = FALSE
+  )$data
+
+ds_laboratory |>
+  tidyr::drop_na(redcap_repeat_instrument)

vignettes/workflow-write.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Writing to a REDCap Project"
-author: Will Beasley [Biomedical & Behavior Methodology Core](https://www.ouhsc.edu/bbmc/team/), OUHSC Pediatrics;<br>Raymond Balise, University of Miami School of Medicine
+author: Will Beasley [Biomedical & Behavior Methodology Core](https://www.ouhsc.edu/bbmc/team/), OUHSC Pediatrics;;<br>Raymond Balise, University of Miami School of Medicine<br>Stephan Kadauke, Children's Hospital of Philadelphia
 output:
   rmarkdown::html_vignette
 vignette: >
@@ -357,8 +357,10 @@ Notes
 This vignette was originally designed for the
 [2023 R/Medicine](https://events.linuxfoundation.org/r-medicine/) workshop,
 _Using REDCap and R to Rapidly Produce Biomedical Publications Cleaning Medical Data_
-with [Raymond R. Balise](https://github.com/RaymondBalise), Belén Hervera, Daniel Maya, Anna Calderon, Tyler Bartholomew, Stephan Kadauke, and João Pedro Carmezim Correia.
-The entire workshop's slides are at <https://github.com/RaymondBalise/r_med_redcap_2023_public>.
+with [Raymond R. Balise](https://github.com/RaymondBalise), Belén Hervera, Daniel Maya, Anna Calderon, Tyler Bartholomew, Stephan Kadauke, and João Pedro Carmezim Correia and the [2024 R/Medicine](https://rconsortium.github.io/RMedicine_website/Program.html) workshop, 
+_REDCap + R: Teaming Up in the Tidyverse_, with Stephan Kadauke.
+The workshop slides are for [2023](https://github.com/RaymondBalise/r_med_redcap_2023_public)
+and [2024](https://github.com/skadauke/rmedicine_2024_redcap_r_workshop).
 
 This work was made possible in part by the NIH grant [U54GM104938](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=U54GM104938&arg_ProgOfficeCode=127)
 to the [Oklahoma Shared Clinical and Translational Resource)](http://osctr.ouhsc.edu).