DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 24.2.1
+Version: 24.1.2
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -34,9 +34,7 @@ Suggests:
     ggplot2,
     haven,
     here,
-    styler,
+    styler
-    devtools,
-    roxygen2
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
@@ -51,17 +49,13 @@ Imports:
     keyring,
     purrr,
     readr,
-    stats,
+    stats
-    calendar,
-    lubridate,
-    glue
 Collate: 
     'utils.r'
     'process_user_input.r'
     'REDCap_split.r'
     'ds2dd.R'
     'ds2dd_detailed.R'
-    'ds2ical.R'
     'easy_redcap.R'
     'read_redcap_instrument.R'
     'read_redcap_tables.R'

NAMESPACE

@@ -5,7 +5,6 @@ export(clean_redcap_name)
 export(d2w)
 export(ds2dd)
 export(ds2dd_detailed)
-export(ds2ical)
 export(easy_redcap)
 export(focused_metadata)
 export(get_api_key)

NEWS.md

@@ -1,17 +1,13 @@
-# REDCapCAST 24.2.1
+# REDCapCAST 24.1.2
 
 ### Functions
 
 * Fix: `ds2dd()`: uses correct default dd column names. Will be deprecated.
 
-* Fix: `easy_redcap()`: fixed to actually allow project naming. also specifically asks for uri.
-
 * NEW: `ds2dd_detailed()`: extension of the `ds2dd()`, which serves to preserve as much metadata as possible automatically. Depends on a group of helper functions also introduced. Of special note is the `guess_time_only_filter()`, which will try to guess which columns/variables should be formatted as time only formats. Supports hms time format. DETAILED INSTRUCTION AND VIGNETTE IS PENDING.
 
 * NEW: `read_redcap_instrument()` convenience function to retrieve complete instrument. Goes a little against the focused approach. DETAILED INSTRUCTION IS PENDING.
 
-* NEW: `ds2ical()` converts data set to ical format with easy glue string for summary and description. Export ics file with `calendar::ic_write()`.
-
 ### Other
 
 I believe `renv` has now been added and runs correctly. After clone, do `renv::restore()` to install all necessary package to modify the package.

R/ds2ical.R

@@ -1,59 +0,0 @@
-utils::globalVariables(c("DTSTART"))
-
-#' Convert data set to ical file
-#'
-#' @param data data set
-#' @param start event start column
-#' @param location event location column
-#' @param event.length use lubridate functions to generate "Period" class
-#' element (default is lubridate::hours(2))
-#' @param summary.glue.string character string to pass to glue::glue() for event
-#' name (summary). Can take any column from data set.
-#' @param description.glue.string character string to pass to glue::glue() for
-#' event description. Can take any column from data set.
-#'
-#' @return tibble of class "ical"
-#' @export
-#'
-#' @examples
-#' df <- dplyr::tibble(start = c(Sys.time(), Sys.time() + lubridate::days(2)),
-#' id = c("1", 3), assessor = "A", location = "111", note = c(NA, "OBS"))
-#' df |> ds2ical(start, location)
-#' df |> ds2ical(start, location,
-#' summary.glue.string = "ID {id} [{assessor}] {note}")
-#' # Export .ics file: (not run)
-#' ical <- df |> ds2ical(start, location, description.glue.string = "{note}")
-#' # ical |> calendar::ic_write(file=here::here("calendar.ics"))
-ds2ical <- function(data,
-                   start,
-                   location,
-                   summary.glue.string = "ID {id} [{assessor}]",
-                   description.glue.string = NULL,
-                   event.length = lubridate::hours(2)) {
-  ds <- data |>
-    dplyr::transmute(
-      SUMMARY = glue::glue(summary.glue.string, .na = ""),
-      DTSTART = lubridate::ymd_hms({{ start }}, tz = "CET"),
-      DTEND = DTSTART + event.length,
-      LOCATION = {{ location }}
-    )
-
-  if (!is.null(description.glue.string)){
-    ds <- dplyr::tibble(ds,
-                        dplyr::transmute(data,
-                                         DESCRIPTION = glue::glue(
-                                           description.glue.string,
-                                           .na = ""
-                                           )
-                                         )
-                        )
-  }
-
-  ds |>
-    (\(x){
-      x |>
-        dplyr::mutate(UID = replicate(nrow(x), calendar::ic_guid()))
-    })() |>
-    dplyr::filter(!is.na(DTSTART)) |>
-    calendar::ical()
-}

R/easy_redcap.R

@@ -21,19 +21,19 @@ get_api_key <- function(key.name) {
 #' @param project.name The name of the current project (for key storage with
 #' `keyring::key_set()`)
 #' @param widen.data argument to widen the exported data
-#' @param uri REDCap database API uri
 #' @param ... arguments passed on to `REDCapCAST::read_redcap_tables()`
 #'
 #' @return data.frame or list depending on widen.data
 #' @importFrom purrr reduce
 #' @importFrom dplyr left_join
 #' @export
-easy_redcap <- function(project.name, widen.data = TRUE, uri, ...) {
+easy_redcap <- function(project.name, widen.data = TRUE, ...) {
+  project.name <- "ENIGMA"
+
   key <- get_api_key(key.name = paste0(project.name, "_REDCAP_API"))
 
   out <- read_redcap_tables(
     token = key,
-    uri = uri,
     ...
   )
 

R/read_redcap_instrument.R

@@ -1,7 +1,7 @@
 #' Convenience function to download complete instrument, using token storage in keyring.
 #'
 #' @param key key name in standard keyring for token retrieval.
-#' @param uri REDCap database API uri
+#' @param uri redcap api url
 #' @param instrument instrument name
 #' @param raw_or_label raw or label passed to `REDCapR::redcap_read()`
 #' @param id_name id variable name. Default is "record_id".
@@ -11,7 +11,7 @@
 #' @export
 read_redcap_instrument <- function(key,
                             uri,
-                            instrument,
+                            instrument = "rbans",
                             raw_or_label = "raw",
                             id_name = "record_id",
                             records = NULL) {

R/read_redcap_tables.R

@@ -5,7 +5,7 @@
 #' events using the built-in focused_metadata including some clean-up.
 #' Works with classical and longitudinal projects with or without repeating
 #' instruments.
-#' @param uri REDCap database API uri
+#' @param uri REDCap database uri
 #' @param token API token
 #' @param records records to download
 #' @param fields fields to download

man/ds2ical.Rd

@@ -1,47 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ds2ical.R
-\name{ds2ical}
-\alias{ds2ical}
-\title{Convert data set to ical file}
-\usage{
-ds2ical(
-  data,
-  start,
-  location,
-  summary.glue.string = "ID {id} [{assessor}]",
-  description.glue.string = NULL,
-  event.length = lubridate::hours(2)
-)
-}
-\arguments{
-\item{data}{data set}
-
-\item{start}{event start column}
-
-\item{location}{event location column}
-
-\item{summary.glue.string}{character string to pass to glue::glue() for event
-name (summary). Can take any column from data set.}
-
-\item{description.glue.string}{character string to pass to glue::glue() for
-event description. Can take any column from data set.}
-
-\item{event.length}{use lubridate functions to generate "Period" class
-element (default is lubridate::hours(2))}
-}
-\value{
-tibble of class "ical"
-}
-\description{
-Convert data set to ical file
-}
-\examples{
-df <- dplyr::tibble(start = c(Sys.time(), Sys.time() + lubridate::days(2)),
-id = c("1", 3), assessor = "A", location = "111", note = c(NA, "OBS"))
-df |> ds2ical(start, location)
-df |> ds2ical(start, location,
-summary.glue.string = "ID {id} [{assessor}] {note}")
-# Export .ics file: (not run)
-ical <- df |> ds2ical(start, location, description.glue.string = "{note}")
-# ical |> calendar::ic_write(file=here::here("calendar.ics"))
-}

man/easy_redcap.Rd

@@ -4,7 +4,7 @@
 \alias{easy_redcap}
 \title{Secure API key storage and data acquisition in one}
 \usage{
-easy_redcap(project.name, widen.data = TRUE, uri, ...)
+easy_redcap(project.name, widen.data = TRUE, ...)
 }
 \arguments{
 \item{project.name}{The name of the current project (for key storage with
@@ -12,8 +12,6 @@ easy_redcap(project.name, widen.data = TRUE, uri, ...)
 
 \item{widen.data}{argument to widen the exported data}
 
-\item{uri}{REDCap database API uri}
-
 \item{...}{arguments passed on to `REDCapCAST::read_redcap_tables()`}
 }
 \value{

man/read_redcap_instrument.Rd

@@ -7,7 +7,7 @@
 read_redcap_instrument(
   key,
   uri,
-  instrument,
+  instrument = "rbans",
   raw_or_label = "raw",
   id_name = "record_id",
   records = NULL
@@ -16,7 +16,7 @@ read_redcap_instrument(
 \arguments{
 \item{key}{key name in standard keyring for token retrieval.}
 
-\item{uri}{REDCap database API uri}
+\item{uri}{redcap api url}
 
 \item{instrument}{instrument name}
 

man/read_redcap_tables.Rd

@@ -18,7 +18,7 @@ read_redcap_tables(
 )
 }
 \arguments{
-\item{uri}{REDCap database API uri}
+\item{uri}{REDCap database uri}
 
 \item{token}{API token}
 

renv.lock

@@ -93,19 +93,6 @@
       ],
       "Hash": "9fe98599ca456d6552421db0d6772d8f"
     },
-    "calendar": {
-      "Package": "calendar",
-      "Version": "0.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "lubridate",
-        "methods",
-        "tibble"
-      ],
-      "Hash": "ab478f470a5203ff9990e42d916005b0"
-    },
     "checkmate": {
       "Package": "checkmate",
       "Version": "2.3.1",
@@ -310,19 +297,6 @@
       ],
       "Hash": "b8552d117e1b808b09a832f589b79035"
     },
-    "lubridate": {
-      "Package": "lubridate",
-      "Version": "1.9.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "generics",
-        "methods",
-        "timechange"
-      ],
-      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
-    },
     "magrittr": {
       "Package": "magrittr",
       "Version": "2.0.3",
@@ -575,17 +549,6 @@
       ],
       "Hash": "79540e5fcd9e0435af547d885f184fd5"
     },
-    "timechange": {
-      "Package": "timechange",
-      "Version": "0.3.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
-    },
     "tzdb": {
       "Package": "tzdb",
       "Version": "0.4.0",