updated renv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 24.1.2
+Version: 24.2.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -34,7 +34,9 @@ Suggests:
     ggplot2,
     haven,
     here,
-    styler
+    styler,
+    devtools,
+    roxygen2
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
@@ -49,13 +51,17 @@ 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

@@ -5,6 +5,7 @@ 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

@@ -1,13 +1,17 @@
-# REDCapCAST 24.1.2
+# REDCapCAST 24.2.1
 
 ### 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

@@ -0,0 +1,59 @@
+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, ...) {
+easy_redcap <- function(project.name, widen.data = TRUE, uri, ...) {
-  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 api url
+#' @param uri REDCap database API uri
 #' @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 = "rbans",
+                            instrument,
                             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 uri
+#' @param uri REDCap database API uri
 #' @param token API token
 #' @param records records to download
 #' @param fields fields to download

man/ds2ical.Rd

@@ -0,0 +1,47 @@
+% 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, ...)
+easy_redcap(project.name, widen.data = TRUE, uri, ...)
 }
 \arguments{
 \item{project.name}{The name of the current project (for key storage with
@@ -12,6 +12,8 @@ easy_redcap(project.name, widen.data = TRUE, ...)
 
 \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 = "rbans",
+  instrument,
   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 api url}
+\item{uri}{REDCap database API uri}
 
 \item{instrument}{instrument name}
 

man/read_redcap_tables.Rd

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

renv.lock

@@ -93,6 +93,19 @@
       ],
       "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",
@@ -297,6 +310,19 @@
       ],
       "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",
@@ -549,6 +575,17 @@
       ],
       "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",