update documentation

OuhscBbmc · Jul 20, 2021 · c5bce6a · c5bce6a
1 parent 67a32f3
commit c5bce6a
Show file tree

Hide file tree

Showing 6 changed files with 17 additions and 19 deletions.
diff --git a/R/redcap-read-oneshot.R b/R/redcap-read-oneshot.R
@@ -93,9 +93,9 @@
 #' viewable by executing [httr::httr_options()].  The `httr` package and
 #' documentation is available at https://cran.r-project.org/package=httr.
 #'
-#' If you do not pass in this export_data_access_groups value, it will default
-#' to `FALSE`. The following is from the API help page for version 5.2.3:
-#' This flag is only viable if the user whose token is being used to make the
+#' If you do not pass in this `export_data_access_groups` value, it will default
+#' to `FALSE`. The following is from the API help page for version 10.5.1:
+#' >This flag is only viable if the user whose token is being used to make the
 #' API request is *not* in a data access group. If the user is in a group,
 #' then this flag will revert to its default value.
 #'

diff --git a/R/redcap-read.R b/R/redcap-read.R
@@ -102,7 +102,7 @@
 #' * `elapsed_seconds`: The duration of the function.
 #'
 #' @details
-#' Specifically, it internally uses multiple calls to [redcap_read_oneshot()]
+#' [redcap_read()] internally uses multiple calls to [redcap_read_oneshot()]
 #' to select and return data.  Initially, only the primary key is queried
 #' through the REDCap API.  The long list is then subsetted into batches,
 #' whose sizes are determined by the `batch_size` parameter.  REDCap is then
@@ -117,7 +117,7 @@
 #' A second benefit is less RAM is required on the webserver.  Because
 #' each batch is smaller than the entire dataset, the webserver
 #' tackles more manageably sized objects in memory.  Consider batching
-#' if you encounter the error
+#' if you encounter the error:
 #'
 #' ```
 #' ERROR: REDCap ran out of server memory. The request cannot be processed.

diff --git a/man/redcap_read.Rd b/man/redcap_read.Rd
diff --git a/man/redcap_read_oneshot.Rd b/man/redcap_read_oneshot.Rd
diff --git a/utility/refresh.R b/utility/refresh.R
@@ -9,6 +9,7 @@ devtools::build_vignettes()
 
 checks_to_exclude <- c(
   "covr",
+  "cyclocomp",
   "lintr_line_length_linter"
 )
 gp <-

diff --git a/vignettes/workflow-read.Rmd b/vignettes/workflow-read.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Typical REDCap Workflow for a Data Analyst"
-author: Will Beasley & Geneva Marshall, [Biomedical & Behavior Methodology Core](https://ouhsc.edu/bbmc/team/), OUHSC Pediatrics
+author: Will Beasley, Geneva Marshall, & Thomas Wilson, [Biomedical & Behavior Methodology Core](https://ouhsc.edu/bbmc/team/), OUHSC Pediatrics
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Typical REDCap Workflow for a Data Analyst}
@@ -41,7 +41,7 @@ Check with your institution's REDCap administrator to ensure you have
 
 This might be the first time you've ever needed to request a token, and your institution may have a formal process for API approval.  Your REDCap admin can help.
 
-For this vignette, we'll use a fake dataset hosted at "https://ou.edu/redcap/api/" and accessible with the token "9A81268476645C4E5F03428B8AC3AA7B".
+For this vignette, we'll use a fake dataset hosted at "https://bbmc.ouhsc.edu/redcap/api/" and accessible with the token "9A81268476645C4E5F03428B8AC3AA7B".
 
 Note to REDCap Admins:
 
@@ -80,9 +80,9 @@ The [`retrieve_credential_local()`](https://ouhscbbmc.github.io/REDCapR/referenc
 
 ```csv
 redcap_uri,username,project_id,token,comment
-"https://ou.edu/redcap/api/","myusername",153,9A81268476645C4E5F03428B8AC3AA7B,"simple"
-"https://ou.edu/redcap/api/","myusername",212,0434F0E9CF53ED0587847AB6E51DE762,"longitudinal"
-"https://ou.edu/redcap/api/","myusername",213,D70F9ACD1EDD6F151C6EA78683944E98,"write data"
+"https://bbmc.ouhsc.edu/redcap/api/","myusername",153,9A81268476645C4E5F03428B8AC3AA7B,"simple"
+"https://bbmc.ouhsc.edu/redcap/api/","myusername",212,0434F0E9CF53ED0587847AB6E51DE762,"longitudinal"
+"https://bbmc.ouhsc.edu/redcap/api/","myusername",213,D70F9ACD1EDD6F151C6EA78683944E98,"write data"
 ```
 
 To retrieve the credentials for the first project listed above, pass the value of "153" to `project_id`.
@@ -260,7 +260,7 @@ Part 6 - Next Steps
 Other REDCapR Resources
 -------------------------
 
-In addition to documentation [for each function](https://ouhscbbmc.github.io/REDCapR/reference) the REDCapR package contains a handful of [vignettes](https://ouhscbbmc.github.io/REDCapR/articles) including a troubleshooting guide.
+In addition to documentation [for each function](https://ouhscbbmc.github.io/REDCapR/reference) the REDCapR package contains a handful of [vignettes](https://ouhscbbmc.github.io/REDCapR/articles) including a [troubleshooting guide](https://ouhscbbmc.github.io/REDCapR/articles/TroubleshootingApiCalls.html).
 
 Create an Arch for Reuse
 -------------------------
@@ -277,7 +277,7 @@ Once the dataset is in R, take advantage of all the reproducible research tools
 Batching
 -------------------------
 
-By default, `REDCapR::redcap_read()` requests datasets of 100 patients as a time, and stacks the resulting subsets together before returning a data.frame.  This can be adjusted to improve performance; see the 'Details' section of [`REDCapR::redcap_read()`](https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html).
+By default, `REDCapR::redcap_read()` requests datasets of 100 patients as a time, and stacks the resulting subsets together before returning a data.frame.  This can be adjusted to improve performance; the 'Details' section of [`REDCapR::redcap_read()`](https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html#details) discusses the trade offs.
 
 Writing to the Server
 -------------------------
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,6 +9,7 @@ devtools::build_vignettes() @@
     checks_to_exclude <- c(
       "covr",
+      "cyclocomp",
       "lintr_line_length_linter"
     )
     gp <-
@@ Expand Down @@