added code of conduct

.Rbuildignore

@@ -17,3 +17,5 @@
 ^CRAN-SUBMISSION$
 drafting
 app
+^\.lintr$
+^CODE_OF_CONDUCT\.md$

.lintr

@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+    commented_code_linter = NULL
+  )
+encoding: "UTF-8"
+exclusions: list(
+    "drafting/"
+  )

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at andreas@gdamsbo.dk. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -30,14 +30,10 @@ Suggests:
     gt,
     usethis,
     ggplot2,
-    haven,
     here,
     styler,
     devtools,
     roxygen2,
-    openxlsx2,
-    rsconnect,
-    shiny,
     spelling
 License: GPL (>= 3)
 Encoding: UTF-8
@@ -53,7 +49,11 @@ Imports:
     keyring,
     purrr,
     readr,
-    stats
+    stats,
+    shiny,
+    openxlsx2,
+    rsconnect,
+    haven
 Collate: 
     'utils.r'
     'process_user_input.r'

R/REDCap_split.r

@@ -26,17 +26,17 @@
 #' records <- postForm(
 #'   uri = api_url, # Supply your site-specific URI
 #'   token = api_token, # Supply your own API token
-#'   content = 'record',
+#'   content = "record",
-#'   format = 'json',
+#'   format = "json",
-#'   returnFormat = 'json'
+#'   returnFormat = "json"
 #' )
 #'
 #' # Get the metadata
 #' metadata <- postForm(
 #'   uri = api_url, # Supply your site-specific URI
 #'   token = api_token, # Supply your own API token
-#'   content = 'metadata',
+#'   content = "metadata",
-#'   format = 'json'
+#'   format = "json"
 #' )
 #'
 #' # Convert exported JSON strings into a list of data.frames
@@ -49,7 +49,8 @@
 #'
 #' # Get the metadata
 #' metadata <- read.csv(
-#' "/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv")
+#'   "/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv"
+#' )
 #'
 #' # Split the tables
 #' REDCapRITS::REDCap_split(records, metadata)
@@ -86,7 +87,6 @@ REDCap_split <- function(records,
                          metadata,
                          primary_table_name = "",
                          forms = c("repeating", "all")) {
-
   # Process user input
   records <- process_user_input(records)
   metadata <-
@@ -97,7 +97,8 @@ REDCap_split <- function(records,
 
   # Process repeat instrument names to match the redcap naming
   if (is_repeated_longitudinal(records)) {
-  records$redcap_repeat_instrument <- clean_redcap_name(records$redcap_repeat_instrument)
+    records$redcap_repeat_instrument <-
+      clean_redcap_name(records$redcap_repeat_instrument)
 
     # Match arg for forms
     forms <- match.arg(forms, c("repeating", "all"))
@@ -145,7 +146,8 @@ REDCap_split <- function(records,
     # Variables to be at the beginning of each repeating instrument
     repeat_instrument_fields <- grep("^redcap_repeat.*",
       vars_in_data,
-                                     value = TRUE)
+      value = TRUE
+    )
 
     # Identify the subtables in the data
     subtables <- unique(records$redcap_repeat_instrument)
@@ -169,35 +171,36 @@ REDCap_split <- function(records,
     # Delete the variables that are not relevant
     for (i in names(out)) {
       if (i == primary_table_name) {
-        out_fields <- which(vars_in_data %in% c(universal_fields,
+        out_fields <- which(vars_in_data %in% c(
+          universal_fields,
           fields[!fields[, 2] %in%
-                                                         subtables, 1]))
+            subtables, 1]
+        ))
         out[[primary_table_index]] <-
           out[[primary_table_index]][out_fields]
-
       } else {
-        out_fields <- which(vars_in_data %in% c(universal_fields,
+        out_fields <- which(vars_in_data %in% c(
+          universal_fields,
           repeat_instrument_fields,
-                                                fields[fields[, 2] == i, 1]))
+          fields[fields[, 2] == i, 1]
+        ))
         out[[i]] <- out[[i]][out_fields]
-
       }
-
     }
 
     if (forms == "all") {
-      out <- c(split_non_repeating_forms(out[[primary_table_index]],
+      out <- c(
+        split_non_repeating_forms(
+          out[[primary_table_index]],
           universal_fields,
-                                         fields[!fields[, 2] %in% subtables, ]),
+          fields[!fields[, 2] %in% subtables, ]
-               out[-primary_table_index])
+        ),
-
+        out[-primary_table_index]
+      )
     }
-
   } else {
     out <- split_non_repeating_forms(records, universal_fields, fields)
-
   }
 
   out
 }
-

R/ds2dd.R

@@ -41,7 +41,7 @@ ds2dd <-
     dd <- data.frame(matrix(ncol = length(metadata), nrow = ncol(ds)))
     colnames(dd) <- metadata
 
-    if (is.character(record.id) & !record.id %in% colnames(ds)) {
+    if (is.character(record.id) && !record.id %in% colnames(ds)) {
       stop("Provided record.id is not a variable name in provided data set.")
     }
 
@@ -59,7 +59,7 @@ ds2dd <-
     dd[, "field_name"] <-
       c(field.name[colsel], field.name[!colsel])
 
-    if (length(form.name) > 1 & length(form.name) != ncol(ds)) {
+    if (length(form.name) > 1 && length(form.name) != ncol(ds)) {
       stop(
         "Provided form.name should be of length 1 (value is reused) or equal
         length as number of variables in data set."
@@ -67,7 +67,7 @@ ds2dd <-
     }
     dd[, "form_name"] <- form.name
 
-    if (length(field.type) > 1 & length(field.type) != ncol(ds)) {
+    if (length(field.type) > 1 && length(field.type) != ncol(ds)) {
       stop(
         "Provided field.type should be of length 1 (value is reused) or equal
         length as number of variables in data set."

R/ds2dd_detailed.R

@@ -1,4 +1,9 @@
-utils::globalVariables(c(  "stats::setNames",  "field_name",  "field_type",  "select_choices_or_calculations"))
+utils::globalVariables(c(
+  "stats::setNames",
+  "field_name",
+  "field_type",
+  "select_choices_or_calculations"
+))
 #' Try at determining which are true time only variables
 #'
 #' @description
@@ -18,8 +23,13 @@ utils::globalVariables(c(  "stats::setNames",  "field_name",  "field_type",  "se
 #' @examples
 #' data <- redcapcast_data
 #' data |> guess_time_only_filter()
-#' data |> guess_time_only_filter(validate = TRUE) |> lapply(head)
+#' data |>
-guess_time_only_filter <- function(data, validate = FALSE, sel.pos = "[Tt]i[d(me)]", sel.neg = "[Dd]at[eo]") {
+#'   guess_time_only_filter(validate = TRUE) |>
+#'   lapply(head)
+guess_time_only_filter <- function(data,
+                                   validate = FALSE,
+                                   sel.pos = "[Tt]i[d(me)]",
+                                   sel.neg = "[Dd]at[eo]") {
   datetime_nms <- data |>
     lapply(\(x) any(c("POSIXct", "hms") %in% class(x))) |>
     (\(x) names(data)[do.call(c, x)])()
@@ -42,12 +52,8 @@ guess_time_only_filter <- function(data, validate = FALSE, sel.pos = "[Tt]i[d(me
   }
 }
 
-#' Correction based on time_only_filter function. Introduces new class for easier
+#' Correction based on time_only_filter function
-#' validation labelling.
 #'
-#' @description
-#' Dependens on the data class "hms" introduced with
-#' `guess_time_only_filter()` and converts these
 #'
 #' @param data data set
 #' @param ... arguments passed on to `guess_time_only_filter()`
@@ -119,8 +125,8 @@ hms2character <- function(data) {
 #' data set (imported .dta file with `haven::read_dta()`. Default is "label"
 #' @param field.validation manually specify field validation(s). Vector of
 #' length 1 or ncol(data). Default is NULL and `levels()` are used for factors
-#' or attribute `factor.labels.attr` for haven_labelled data set (imported .dta file with
+#' or attribute `factor.labels.attr` for haven_labelled data set (imported .dta
-#' `haven::read_dta()`).
+#' file with `haven::read_dta()`).
 #' @param metadata redcap metadata headings. Default is
 #' REDCapCAST:::metadata_names.
 #' @param validate.time Flag to validate guessed time columns
@@ -164,7 +170,8 @@ ds2dd_detailed <- function(data,
   }
 
   if (lapply(data, haven::is.labelled) |> (\(x)do.call(c, x))() |> any()) {
-    message("Data seems to be imported with haven from a Stata (.dta) file and will be treated as such.")
+    message("Data seems to be imported with haven from a Stata (.dta) file and
+            will be treated as such.")
     data.source <- "dta"
   } else {
     data.source <- ""
@@ -172,18 +179,25 @@ ds2dd_detailed <- function(data,
 
   ## data classes
 
-  ### Only keeps the first class, as time fields (POSIXct/POSIXt) has two classes
+  ### Only keeps the first class, as time fields (POSIXct/POSIXt) has two
+  ### classes
   if (data.source == "dta") {
     data_classes <-
       data |>
       haven::as_factor() |>
-      time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
+      time_only_correction(
+        sel.pos = time.var.sel.pos,
+        sel.neg = time.var.sel.neg
+      ) |>
       lapply(\(x)class(x)[1]) |>
       (\(x)do.call(c, x))()
   } else {
     data_classes <-
       data |>
-      time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
+      time_only_correction(
+        sel.pos = time.var.sel.pos,
+        sel.neg = time.var.sel.neg
+      ) |>
       lapply(\(x)class(x)[1]) |>
       (\(x)do.call(c, x))()
   }
@@ -204,7 +218,7 @@ ds2dd_detailed <- function(data,
   if (is.null(form.name)) {
     dd$form_name <- "data"
   } else {
-    if (length(form.name) == 1 | length(form.name) == nrow(dd)) {
+    if (length(form.name) == 1 || length(form.name) == nrow(dd)) {
       dd$form_name <- form.name
     } else {
       stop("Length of supplied 'form.name' has to be one (1) or ncol(data).")
@@ -229,9 +243,11 @@ ds2dd_detailed <- function(data,
     }
 
     dd <-
-      dd |> dplyr::mutate(field_label = dplyr::if_else(is.na(label), field_name, label))
+      dd |> dplyr::mutate(field_label = dplyr::if_else(is.na(label),
+        field_name, label
+      ))
   } else {
-    if (length(field.label) == 1 | length(field.label) == nrow(dd)) {
+    if (length(field.label) == 1 || length(field.label) == nrow(dd)) {
       dd$field_label <- field.label
     } else {
       stop("Length of supplied 'field.label' has to be one (1) or ncol(data).")
@@ -245,9 +261,11 @@ ds2dd_detailed <- function(data,
     dd$field_type <- "text"
 
     dd <-
-      dd |> dplyr::mutate(field_type = dplyr::if_else(data_classes == "factor", "radio", field_type))
+      dd |> dplyr::mutate(field_type = dplyr::if_else(data_classes == "factor",
+        "radio", field_type
+      ))
   } else {
-    if (length(field.type) == 1 | length(field.type) == nrow(dd)) {
+    if (length(field.type) == 1 || length(field.type) == nrow(dd)) {
       dd$field_type <- field.type
     } else {
       stop("Length of supplied 'field.type' has to be one (1) or ncol(data).")
@@ -271,10 +289,11 @@ ds2dd_detailed <- function(data,
         )
       )
   } else {
-    if (length(field.validation) == 1 | length(field.validation) == nrow(dd)) {
+    if (length(field.validation) == 1 || length(field.validation) == nrow(dd)) {
       dd$text_validation_type_or_show_slider_number <- field.validation
     } else {
-      stop("Length of supplied 'field.validation' has to be one (1) or ncol(data).")
+      stop("Length of supplied 'field.validation'
+           has to be one (1) or ncol(data).")
     }
   }
 
@@ -300,7 +319,13 @@ ds2dd_detailed <- function(data,
           ## Re-factors to avoid confusion with missing levels
           ## Assumes alle relevant levels are represented in the data
           re_fac <- factor(x)
-          paste(paste(unique(as.numeric(re_fac)), levels(re_fac), sep = ", "), collapse = " | ")
+          paste(
+            paste(unique(as.numeric(re_fac)),
+              levels(re_fac),
+              sep = ", "
+            ),
+            collapse = " | "
+          )
         } else {
           NA
         }
@@ -319,7 +344,10 @@ ds2dd_detailed <- function(data,
 
   list(
     data = data |>
-      time_only_correction(sel.pos = time.var.sel.pos, sel.neg = time.var.sel.neg) |>
+      time_only_correction(
+        sel.pos = time.var.sel.pos,
+        sel.neg = time.var.sel.neg
+      ) |>
       hms2character() |>
       (\(x)stats::setNames(x, tolower(names(x))))(),
     meta = dd
@@ -337,7 +365,12 @@ mark_complete <- function(upload, ls){
   data <- ls$data
   meta <- ls$meta
   forms <- unique(meta$form_name)
-  cbind(data[[1]][data[[1]] %in% upload$affected_ids],
+  cbind(
-        data.frame(matrix(2,ncol=length(forms),nrow=upload$records_affected_count))) |>
+    data[[1]][data[[1]] %in% upload$affected_ids],
+    data.frame(matrix(2,
+      ncol = length(forms),
+      nrow = upload$records_affected_count
+    ))
+  ) |>
     stats::setNames(c(names(data)[1], paste0(forms, "_complete")))
 }

R/easy_redcap.R

@@ -1,4 +1,3 @@
-
 #' Retrieve project API key if stored, if not, set and retrieve
 #'
 #' @param key.name character vector of key name

R/mtcars_redcap.R

@@ -20,4 +20,3 @@
 #' }
 #' @usage data(mtcars_redcap)
 "mtcars_redcap"
-

R/process_user_input.r

@@ -30,10 +30,8 @@ process_user_input.character <- function(x, ...) {
   }
 
   jsonlite::fromJSON(x)
-
 }
 
 process_user_input.response <- function(x, ...) {
   process_user_input(rawToChar(x$content))
-
 }

R/read_redcap_instrument.R

@@ -1,11 +1,13 @@
-#' Convenience function to download complete instrument, using token storage in keyring.
+#' 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 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".
-#' @param records specify the records to download. Index numbers. Numeric vector.
+#' @param records specify the records to download. Index numbers.
+#' Numeric vector.
 #'
 #' @return data.frame
 #' @export

R/read_redcap_tables.R

@@ -38,7 +38,8 @@ read_redcap_tables <- function(uri,
     fields_test <- fields %in% unique(m$field_name)
 
     if (any(!fields_test)) {
-      print(paste0("The following field names are invalid: ", paste(fields[!fields_test], collapse = ", "), "."))
+      print(paste0("The following field names are invalid: ",
+                   paste(fields[!fields_test], collapse = ", "), "."))
       stop("Not all supplied field names are valid")
     }
   }
@@ -48,7 +49,8 @@ read_redcap_tables <- function(uri,
     forms_test <- forms %in% unique(m$form_name)
 
     if (any(!forms_test)) {
-      print(paste0("The following form names are invalid: ", paste(forms[!forms_test], collapse = ", "), "."))
+      print(paste0("The following form names are invalid: ",
+                   paste(forms[!forms_test], collapse = ", "), "."))
       stop("Not all supplied form names are valid")
     }
   }
@@ -62,7 +64,8 @@ read_redcap_tables <- function(uri,
     event_test <- events %in% unique(arm_event_inst$data$unique_event_name)
 
     if (any(!event_test)) {
-      print(paste0("The following event names are invalid: ", paste(events[!event_test], collapse = ", "), "."))
+      print(paste0("The following event names are invalid: ",
+                   paste(events[!event_test], collapse = ", "), "."))
       stop("Not all supplied event names are valid")
     }
   }
@@ -97,7 +100,4 @@ read_redcap_tables <- function(uri,
   )
 
   sanitize_split(out)
-
 }
-
-

R/redcap_wider.R

@@ -1,6 +1,8 @@
-utils::globalVariables(c("redcap_wider",
+utils::globalVariables(c(
+  "redcap_wider",
   "event.glue",
-"inst.glue"))
+  "inst.glue"
+))
 
 #' @title Redcap Wider
 #' @description Converts a list of REDCap data frames from long to wide format.
@@ -16,42 +18,65 @@ utils::globalVariables(c("redcap_wider",
 #'
 #' @examples
 #' # Longitudinal
-#' list1 <- list(data.frame(record_id = c(1,2,1,2),
+#' list1 <- list(
+#'   data.frame(
+#'     record_id = c(1, 2, 1, 2),
 #'     redcap_event_name = c("baseline", "baseline", "followup", "followup"),
-#' age = c(25,26,27,28)),
+#'     age = c(25, 26, 27, 28)
-#' data.frame(record_id = c(1,2),
+#'   ),
+#'   data.frame(
+#'     record_id = c(1, 2),
 #'     redcap_event_name = c("baseline", "baseline"),
-#' gender = c("male", "female")))
+#'     gender = c("male", "female")
+#'   )
+#' )
 #' redcap_wider(list1)
 #' # Simpel with two instruments
-#' list2 <- list(data.frame(record_id = c(1,2),
+#' list2 <- list(
-#' age = c(25,26)),
+#'   data.frame(
-#' data.frame(record_id = c(1,2),
+#'     record_id = c(1, 2),
-#' gender = c("male", "female")))
+#'     age = c(25, 26)
+#'   ),
+#'   data.frame(
+#'     record_id = c(1, 2),
+#'     gender = c("male", "female")
+#'   )
+#' )
 #' redcap_wider(list2)
 #' # Simple with single instrument
-#' list3 <- list(data.frame(record_id = c(1,2),
+#' list3 <- list(data.frame(
-#' age = c(25,26)))
+#'   record_id = c(1, 2),
+#'   age = c(25, 26)
+#' ))
 #' redcap_wider(list3)
 #' # Longitudinal with repeatable instruments
-#' list4 <- list(data.frame(record_id = c(1,2,1,2),
+#' list4 <- list(
+#'   data.frame(
+#'     record_id = c(1, 2, 1, 2),
 #'     redcap_event_name = c("baseline", "baseline", "followup", "followup"),
-#' age = c(25,26,27,28)),
+#'     age = c(25, 26, 27, 28)
-#' data.frame(record_id = c(1,1,1,1,2,2,2,2),
+#'   ),
-#' redcap_event_name = c("baseline", "baseline", "followup", "followup",
+#'   data.frame(
-#' "baseline", "baseline", "followup", "followup"),
+#'     record_id = c(1, 1, 1, 1, 2, 2, 2, 2),
+#'     redcap_event_name = c(
+#'       "baseline", "baseline", "followup", "followup",
+#'       "baseline", "baseline", "followup", "followup"
+#'     ),
 #'     redcap_repeat_instrument = "walk",
 #'     redcap_repeat_instance = c(1, 2, 1, 2, 1, 2, 1, 2),
-#' dist = c(40, 32, 25, 33, 28, 24, 23, 36)),
+#'     dist = c(40, 32, 25, 33, 28, 24, 23, 36)
-#' data.frame(record_id = c(1,2),
+#'   ),
+#'   data.frame(
+#'     record_id = c(1, 2),
 #'     redcap_event_name = c("baseline", "baseline"),
-#' gender = c("male", "female")))
+#'     gender = c("male", "female")
+#'   )
+#' )
 #' redcap_wider(list4)
 redcap_wider <-
   function(data,
            event.glue = "{.value}_{redcap_event_name}",
            inst.glue = "{.value}_{redcap_repeat_instance}") {
-
     if (!is_repeated_longitudinal(data)) {
       if (is.list(data)) {
         if (length(data) == 1) {
@@ -62,10 +87,7 @@ redcap_wider <-
       } else if (is.data.frame(data)) {
         out <- data
       }
-
-
     } else {
-
       id.name <- do.call(c, lapply(data, names))[[1]]
 
       l <- lapply(data, function(i) {
@@ -124,4 +146,3 @@ redcap_wider <-
 
     out
   }
-

R/redcapcast_data.R

@@ -33,5 +33,3 @@
 #' }
 #' @usage data(redcapcast_data)
 "redcapcast_data"
-
-

R/redcapcast_meta.R

@@ -25,5 +25,3 @@
 #' }
 #' @usage data(redcapcast_meta)
 "redcapcast_meta"
-
-

R/shiny_cast.R

@@ -15,7 +15,6 @@ server_factory <- function() {
 ui_factory <- function() {
   # require(ggplot2)
   source(here::here("app/ui.R"))
-
 }
 
 #' Launch the included Shiny-app for database casting and upload

R/utils.r

@@ -128,9 +128,11 @@ sanitize_split <- function(l,
                              "redcap_repeat_instrument",
                              "redcap_repeat_instance"
                            )) {
-  generic.names <- c(get_id_name(l),
+  generic.names <- c(
+    get_id_name(l),
     generic.names,
-                     paste0(names(l), "_complete"))
+    paste0(names(l), "_complete")
+  )
 
   lapply(l, function(i) {
     if (ncol(i) > 2) {
@@ -334,7 +336,8 @@ split_non_repeating_forms <-
 #' @export
 #'
 #' @examples
-#' test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
+#' test <- c("12 months follow-up", "3 steps", "mRS 6 weeks",
+#' "Counting to 231 now")
 #' strsplitx(test, "[0-9]", type = "around")
 strsplitx <- function(x,
                       split,
@@ -403,7 +406,8 @@ d2w <- function(x, lang = "en", neutrum = FALSE, everything = FALSE) {
   # In Danish the written 1 depends on the counted word
   if (neutrum) nt <- "t" else nt <- "n"
 
-  # A sapply() call with nested lapply() to handle vectors, data.frames and lists
+  # A sapply() call with nested lapply() to handle vectors, data.frames
+  # and lists
   convert <- function(x, lang, neutrum) {
     zero_nine <- data.frame(
       num = 0:9,
@@ -503,7 +507,9 @@ is_repeated_longitudinal <- function(data, generics = c(
 #' @examples
 #' file_extension(list.files(here::here(""))[[2]])[[1]]
 file_extension <- function(filenames) {
-  sub(pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "", filenames, perl = TRUE)
+  sub(pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
+      filenames,
+      perl = TRUE)
 }
 
 #' Flexible file import based on extension
@@ -517,7 +523,6 @@ file_extension <- function(filenames) {
 #' @examples
 #' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
 read_input <- function(file, consider.na = c("NA", '""', "")) {
-
   ext <- file_extension(file)
 
   tryCatch(

README.md

@@ -52,3 +52,6 @@ Install the latest version directly from GitHub:
 remotes::install_github("agdamsbo/REDCapCAST")
 ```
 
+## Code of Conduct
+
+Please note that the REDCapCAST project is released with a [Contributor Code of Conduct](https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

data-raw/data-upload-examples.R

@@ -1,4 +1,6 @@
-mtcars_redcap <- mtcars |> dplyr::mutate(record_id=seq_len(dplyr::n()),
+mtcars_redcap <- mtcars |>
+  dplyr::mutate(
+    record_id = seq_len(dplyr::n()),
     name = rownames(mtcars)
   ) |>
   dplyr::select(record_id, dplyr::everything())

data-raw/metadata_names.R

@@ -3,11 +3,12 @@
 #   "field_label", "select_choices_or_calculations", "field_note",
 #   "text_validation_type_or_show_slider_number", "text_validation_min",
 #   "text_validation_max", "identifier", "branching_logic", "required_field",
-#   "custom_alignment", "question_number", "matrix_group_name", "matrix_ranking",
+#   "custom_alignment", "question_number", "matrix_group_name",
-#   "field_annotation"
+#   "matrix_ranking", "field_annotation"
 # )
 
-metadata_names <- REDCapR::redcap_metadata_read(redcap_uri = keyring::key_get("DB_URI"),
+metadata_names <- REDCapR::redcap_metadata_read(
+  redcap_uri = keyring::key_get("DB_URI"),
   token = keyring::key_get("cast_api")
 )$data |> names()
 

data-raw/redcapcast_data.R

@@ -1,6 +1,7 @@
 ## code to prepare `redcapcast_data` dataset goes here
 
-redcapcast_data <- REDCapR::redcap_read(redcap_uri = keyring::key_get("DB_URI"),
+redcapcast_data <- REDCapR::redcap_read(
+  redcap_uri = keyring::key_get("DB_URI"),
   token = keyring::key_get("cast_api"),
   raw_or_label = "label"
 )$data |> dplyr::tibble()

data-raw/redcapcast_meta.R

@@ -1,5 +1,6 @@
 ## code to prepare `redcapcast_meta` dataset goes here
-redcapcast_meta <- REDCapR::redcap_metadata_read(redcap_uri = keyring::key_get("DB_URI"),
+redcapcast_meta <- REDCapR::redcap_metadata_read(
+  redcap_uri = keyring::key_get("DB_URI"),
   token = keyring::key_get("cast_api")
 )$data
 

inst/WORDLIST

@@ -0,0 +1,67 @@
+Assesment
+CMD
+Codecov
+DOI
+DataDictionary
+GStat
+GithubActions
+JSON
+Lifecycle
+METACRAN
+POSIXct
+Pivotting
+README
+REDCap
+REDCapR
+REDCapRITS
+THe
+UI
+Whishes
+al
+api
+attr
+charater
+da
+dafault
+datetime
+demonstrational
+dmy
+doi
+dplyr
+ds
+dta
+et
+gues
+hms
+immprovements
+io
+jbi
+keyring
+labelled
+mRS
+matadata
+md
+mdy
+mtcars
+natively
+ncol
+og
+param
+pegeler
+perl
+pos
+readr
+rsconnect
+sel
+shinyapps
+stRoke
+stata
+strsplit
+thorugh
+tibble
+tidyverse
+transistion
+ui
+uri
+wil
+ymd

man/REDCap_split.Rd

@@ -52,17 +52,17 @@ library(RCurl)
 records <- postForm(
   uri = api_url, # Supply your site-specific URI
   token = api_token, # Supply your own API token
-  content = 'record',
+  content = "record",
-  format = 'json',
+  format = "json",
-  returnFormat = 'json'
+  returnFormat = "json"
 )
 
 # Get the metadata
 metadata <- postForm(
   uri = api_url, # Supply your site-specific URI
   token = api_token, # Supply your own API token
-  content = 'metadata',
+  content = "metadata",
-  format = 'json'
+  format = "json"
 )
 
 # Convert exported JSON strings into a list of data.frames
@@ -75,7 +75,8 @@ records <- read.csv("/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv")
 
 # Get the metadata
 metadata <- read.csv(
-"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv")
+  "/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv"
+)
 
 # Split the tables
 REDCapRITS::REDCap_split(records, metadata)

man/ds2dd_detailed.Rd

@@ -44,8 +44,8 @@ data set (imported .dta file with `haven::read_dta()`. Default is "label"}
 
 \item{field.validation}{manually specify field validation(s). Vector of
 length 1 or ncol(data). Default is NULL and `levels()` are used for factors
-or attribute `factor.labels.attr` for haven_labelled data set (imported .dta file with
+or attribute `factor.labels.attr` for haven_labelled data set (imported .dta
-`haven::read_dta()`).}
+file with `haven::read_dta()`).}
 
 \item{metadata}{redcap metadata headings. Default is
 REDCapCAST:::metadata_names.}

man/guess_time_only_filter.Rd

@@ -32,5 +32,7 @@ has to be converted to character class before REDCap upload.
 \examples{
 data <- redcapcast_data
 data |> guess_time_only_filter()
-data |> guess_time_only_filter(validate = TRUE) |> lapply(head)
+data |>
+  guess_time_only_filter(validate = TRUE) |>
+  lapply(head)
 }

man/read_redcap_instrument.Rd

@@ -2,7 +2,8 @@
 % Please edit documentation in R/read_redcap_instrument.R
 \name{read_redcap_instrument}
 \alias{read_redcap_instrument}
-\title{Convenience function to download complete instrument, using token storage in keyring.}
+\title{Convenience function to download complete instrument, using token storage
+in keyring.}
 \usage{
 read_redcap_instrument(
   key,
@@ -24,11 +25,13 @@ read_redcap_instrument(
 
 \item{id_name}{id variable name. Default is "record_id".}
 
-\item{records}{specify the records to download. Index numbers. Numeric vector.}
+\item{records}{specify the records to download. Index numbers.
+Numeric vector.}
 }
 \value{
 data.frame
 }
 \description{
-Convenience function to download complete instrument, using token storage in keyring.
+Convenience function to download complete instrument, using token storage
+in keyring.
 }

man/redcap_wider.Rd

@@ -26,35 +26,59 @@ Handles longitudinal projects, but not yet repeated instruments.
 }
 \examples{
 # Longitudinal
-list1 <- list(data.frame(record_id = c(1,2,1,2),
+list1 <- list(
+  data.frame(
+    record_id = c(1, 2, 1, 2),
     redcap_event_name = c("baseline", "baseline", "followup", "followup"),
-age = c(25,26,27,28)),
+    age = c(25, 26, 27, 28)
-data.frame(record_id = c(1,2),
+  ),
+  data.frame(
+    record_id = c(1, 2),
     redcap_event_name = c("baseline", "baseline"),
-gender = c("male", "female")))
+    gender = c("male", "female")
+  )
+)
 redcap_wider(list1)
 # Simpel with two instruments
-list2 <- list(data.frame(record_id = c(1,2),
+list2 <- list(
-age = c(25,26)),
+  data.frame(
-data.frame(record_id = c(1,2),
+    record_id = c(1, 2),
-gender = c("male", "female")))
+    age = c(25, 26)
+  ),
+  data.frame(
+    record_id = c(1, 2),
+    gender = c("male", "female")
+  )
+)
 redcap_wider(list2)
 # Simple with single instrument
-list3 <- list(data.frame(record_id = c(1,2),
+list3 <- list(data.frame(
-age = c(25,26)))
+  record_id = c(1, 2),
+  age = c(25, 26)
+))
 redcap_wider(list3)
 # Longitudinal with repeatable instruments
-list4 <- list(data.frame(record_id = c(1,2,1,2),
+list4 <- list(
+  data.frame(
+    record_id = c(1, 2, 1, 2),
     redcap_event_name = c("baseline", "baseline", "followup", "followup"),
-age = c(25,26,27,28)),
+    age = c(25, 26, 27, 28)
-data.frame(record_id = c(1,1,1,1,2,2,2,2),
+  ),
-redcap_event_name = c("baseline", "baseline", "followup", "followup",
+  data.frame(
-"baseline", "baseline", "followup", "followup"),
+    record_id = c(1, 1, 1, 1, 2, 2, 2, 2),
+    redcap_event_name = c(
+      "baseline", "baseline", "followup", "followup",
+      "baseline", "baseline", "followup", "followup"
+    ),
     redcap_repeat_instrument = "walk",
     redcap_repeat_instance = c(1, 2, 1, 2, 1, 2, 1, 2),
-dist = c(40, 32, 25, 33, 28, 24, 23, 36)),
+    dist = c(40, 32, 25, 33, 28, 24, 23, 36)
-data.frame(record_id = c(1,2),
+  ),
+  data.frame(
+    record_id = c(1, 2),
     redcap_event_name = c("baseline", "baseline"),
-gender = c("male", "female")))
+    gender = c("male", "female")
+  )
+)
 redcap_wider(list4)
 }

man/strsplitx.Rd

@@ -25,6 +25,7 @@ Can be used as a substitute of the base function. Main claim to fame is
 easing the split around the defined delimiter, see example.
 }
 \examples{
-test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
+test <- c("12 months follow-up", "3 steps", "mRS 6 weeks",
+"Counting to 231 now")
 strsplitx(test, "[0-9]", type = "around")
 }

man/time_only_correction.Rd

@@ -2,8 +2,7 @@
 % Please edit documentation in R/ds2dd_detailed.R
 \name{time_only_correction}
 \alias{time_only_correction}
-\title{Correction based on time_only_filter function. Introduces new class for easier
+\title{Correction based on time_only_filter function}
-validation labelling.}
 \usage{
 time_only_correction(data, ...)
 }
@@ -16,8 +15,7 @@ time_only_correction(data, ...)
 tibble
 }
 \description{
-Dependens on the data class "hms" introduced with
+Correction based on time_only_filter function
-`guess_time_only_filter()` and converts these
 }
 \examples{
 data <- redcapcast_data

renv.lock

@@ -39,6 +39,17 @@
       ],
       "Hash": "e76c401b631961c865b89bb5a4ea3b97"
     },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+    },
     "askpass": {
       "Package": "askpass",
       "Version": "1.2.0",
@@ -69,6 +80,16 @@
       ],
       "Hash": "c39fbec8a30d23e721980b8afb31984c"
     },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
     "bit": {
       "Package": "bit",
       "Version": "4.0.5",
@@ -93,6 +114,38 @@
       ],
       "Hash": "9fe98599ca456d6552421db0d6772d8f"
     },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.6.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "lifecycle",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.0.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "c35768291560ce302c0a6589f92e837d"
+    },
     "checkmate": {
       "Package": "checkmate",
       "Version": "2.3.1",
@@ -126,6 +179,13 @@
       ],
       "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
     },
+    "commonmark": {
+      "Package": "commonmark",
+      "Version": "1.9.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5d8225445acb167abf7797de48b2ee3c"
+    },
     "cpp11": {
       "Package": "cpp11",
       "Version": "0.4.7",
@@ -158,6 +218,17 @@
       ],
       "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9"
     },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.34",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
+    },
     "dplyr": {
       "Package": "dplyr",
       "Version": "1.1.4",
@@ -181,6 +252,17 @@
       ],
       "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
+    "ellipsis": {
+      "Package": "ellipsis",
+      "Version": "0.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "rlang"
+      ],
+      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
+    },
     "fansi": {
       "Package": "fansi",
       "Version": "1.0.6",
@@ -193,6 +275,13 @@
       ],
       "Hash": "962174cf2aeb5b9eea581522286a911f"
     },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+    },
     "filelock": {
       "Package": "filelock",
       "Version": "1.0.3",
@@ -203,6 +292,45 @@
       ],
       "Hash": "192053c276525c8495ccfd523aa8f2d1"
     },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "forcats": {
+      "Package": "forcats",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "rlang",
+        "tibble"
+      ],
+      "Hash": "1a0a9a3d5083d0d573c4214576f1e690"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
+    },
     "generics": {
       "Package": "generics",
       "Version": "0.1.3",
@@ -225,6 +353,27 @@
       ],
       "Hash": "e0b3a53876554bd45879e596cdb10a52"
     },
+    "haven": {
+      "Package": "haven",
+      "Version": "2.5.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cli",
+        "cpp11",
+        "forcats",
+        "hms",
+        "lifecycle",
+        "methods",
+        "readr",
+        "rlang",
+        "tibble",
+        "tidyselect",
+        "vctrs"
+      ],
+      "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1"
+    },
     "hms": {
       "Package": "hms",
       "Version": "1.1.3",
@@ -239,6 +388,38 @@
       ],
       "Hash": "b59377caa7ed00fa41808342002138f9"
     },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "digest",
+        "ellipsis",
+        "fastmap",
+        "grDevices",
+        "rlang",
+        "utils"
+      ],
+      "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
+    },
+    "httpuv": {
+      "Package": "httpuv",
+      "Version": "1.6.14",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "Rcpp",
+        "later",
+        "promises",
+        "utils"
+      ],
+      "Hash": "16abeb167dbf511f8cc0552efaf05bab"
+    },
     "httr": {
       "Package": "httr",
       "Version": "1.4.7",
@@ -254,6 +435,16 @@
       ],
       "Hash": "ac107251d9d9fd72f0ca8049988f1d7f"
     },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools"
+      ],
+      "Hash": "5aab57a3bd297eee1c1d862735972182"
+    },
     "jsonlite": {
       "Package": "jsonlite",
       "Version": "1.8.8",
@@ -284,6 +475,17 @@
       ],
       "Hash": "5cd8cfb2e90c57110b7dd1785c599aba"
     },
+    "later": {
+      "Package": "later",
+      "Version": "1.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Rcpp",
+        "rlang"
+      ],
+      "Hash": "a3e051d405326b8b0012377434c62b37"
+    },
     "lifecycle": {
       "Package": "lifecycle",
       "Version": "1.0.4",
@@ -307,6 +509,17 @@
       ],
       "Hash": "7ce2733a9826b3aeb1775d56fd305472"
     },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "cachem",
+        "rlang"
+      ],
+      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+    },
     "mime": {
       "Package": "mime",
       "Version": "0.12",
@@ -327,6 +540,35 @@
       ],
       "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5"
     },
+    "openxlsx2": {
+      "Package": "openxlsx2",
+      "Version": "1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "Rcpp",
+        "grDevices",
+        "magrittr",
+        "stringi",
+        "utils",
+        "zip"
+      ],
+      "Hash": "9fa7cdc5fbdb1c8511fdde72a944db63"
+    },
+    "packrat": {
+      "Package": "packrat",
+      "Version": "0.9.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "tools",
+        "utils"
+      ],
+      "Hash": "55ddd2d4a1959535f18393478b0c14a6"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -378,6 +620,22 @@
       ],
       "Hash": "f4625e061cb2865f111b47ff163a5ca6"
     },
+    "promises": {
+      "Package": "promises",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R6",
+        "Rcpp",
+        "fastmap",
+        "later",
+        "magrittr",
+        "rlang",
+        "stats"
+      ],
+      "Hash": "0d8a15c9d000970ada1ab21405387dee"
+    },
     "purrr": {
       "Package": "purrr",
       "Version": "1.0.2",
@@ -447,6 +705,83 @@
       ],
       "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
     },
+    "rsconnect": {
+      "Package": "rsconnect",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "curl",
+        "digest",
+        "jsonlite",
+        "lifecycle",
+        "openssl",
+        "packrat",
+        "renv",
+        "rlang",
+        "rstudioapi",
+        "tools",
+        "yaml"
+      ],
+      "Hash": "94bb3a2125b01b13dd2e4a784c2a9639"
+    },
+    "rstudioapi": {
+      "Package": "rstudioapi",
+      "Version": "0.15.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5564500e25cffad9e22244ced1379887"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
+    },
+    "shiny": {
+      "Package": "shiny",
+      "Version": "1.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "bslib",
+        "cachem",
+        "commonmark",
+        "crayon",
+        "ellipsis",
+        "fastmap",
+        "fontawesome",
+        "glue",
+        "grDevices",
+        "htmltools",
+        "httpuv",
+        "jsonlite",
+        "later",
+        "lifecycle",
+        "methods",
+        "mime",
+        "promises",
+        "rlang",
+        "sourcetools",
+        "tools",
+        "utils",
+        "withr",
+        "xtable"
+      ],
+      "Hash": "3a1f41807d648a908e3c7f0334bf85e6"
+    },
     "sodium": {
       "Package": "sodium",
       "Version": "1.3.1",
@@ -454,6 +789,16 @@
       "Repository": "CRAN",
       "Hash": "dd86d6fd2a01d4eb3777dfdee7076d56"
     },
+    "sourcetools": {
+      "Package": "sourcetools",
+      "Version": "0.1.7-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5f5a7629f956619d519205ec475fe647"
+    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.8.3",
@@ -622,12 +967,31 @@
       ],
       "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
     },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
     "yaml": {
       "Package": "yaml",
       "Version": "2.3.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "29240487a071f535f5e5d5a323b7afbd"
+    },
+    "zip": {
+      "Package": "zip",
+      "Version": "2.3.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab"
     }
   }
 }

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

tests/testthat/data/create-ref-data.R

@@ -12,17 +12,18 @@ ref_data_location <- function(x) file.path("tests","testthat","data", x)
 # RCurl -------------------------------------------------------------------
 
 REDCap_split(
-  ref_data_location("ExampleProject_records.json") %>% fromJSON,
+  ref_data_location("ExampleProject_records.json") %>% fromJSON(),
-  ref_data_location("ExampleProject_metadata.json") %>% fromJSON
+  ref_data_location("ExampleProject_metadata.json") %>% fromJSON()
-  ) %>% digest
+) %>% digest()
 
 
 # Basic CSV ---------------------------------------------------------------
 
 REDCap_split(
-  ref_data_location("ExampleProject_DATA_2018-06-07_1129.csv") %>% read.csv,
+  ref_data_location("ExampleProject_DATA_2018-06-07_1129.csv") %>% read.csv(),
-  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>% read.csv
+  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>%
-  ) %>% digest
+    read.csv()
+) %>% digest()
 
 # REDCap R Export ---------------------------------------------------------
 
@@ -30,10 +31,11 @@ source("tests/testthat/helper-ExampleProject_R_2018-06-07_1129.r")
 
 REDCap_split(
   ref_data_location("ExampleProject_DATA_2018-06-07_1129.csv") %>%
-    read.csv %>%
+    read.csv() %>%
-    REDCap_process_csv,
+    REDCap_process_csv(),
-  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>% read.csv
+  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>%
-  ) %>% digest
+    read.csv()
+) %>% digest()
 
 # Longitudinal data from @pbchase; Issue #7 -------------------------------
 
@@ -41,9 +43,10 @@ file_paths <- vapply(
   c(
     records = "WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv",
     metadata = "WARRIORtestForSoftwareUpgrades_DataDictionary_2018-06-21.csv"
-  ), FUN.VALUE = "character", ref_data_location
+  ),
+  FUN.VALUE = "character", ref_data_location
 )
 
 redcap <- lapply(file_paths, read.csv, stringsAsFactors = FALSE)
 redcap[["metadata"]] <- with(redcap, metadata[metadata[, 1] > "", ])
-with(redcap, REDCap_split(records, metadata)) %>% digest
+with(redcap, REDCap_split(records, metadata)) %>% digest()

tests/testthat/test-csv-exports.R

@@ -1,5 +1,3 @@
-
-
 # Set up the path and data -------------------------------------------------
 metadata <- read.csv(
   get_data_location("ExampleProject_DataDictionary_2018-06-07.csv"),
@@ -8,7 +6,8 @@ metadata <- read.csv(
 
 records <-
   read.csv(get_data_location("ExampleProject_DATA_2018-06-07_1129.csv"),
-           stringsAsFactors = TRUE)
+    stringsAsFactors = TRUE
+  )
 
 redcap_output_csv1 <- REDCap_split(records, metadata)
 
@@ -19,18 +18,19 @@ test_that("CSV export matches reference", {
 
 # Test that REDCap_split can handle a focused dataset
 
-records_red <- records[!records$redcap_repeat_instrument == "sale",
+records_red <- records[
+  !records$redcap_repeat_instrument == "sale",
   !names(records) %in%
     metadata$field_name[metadata$form_name == "sale"] &
-                         !names(records) == "sale_complete"]
+    !names(records) == "sale_complete"
+]
 records_red$redcap_repeat_instrument <-
   as.character(records_red$redcap_repeat_instrument)
 
 redcap_output_red <- REDCap_split(records_red, metadata)
 
 
-test_that("REDCap_split handles subset dataset",
+test_that("REDCap_split handles subset dataset", {
-          {
   testthat::expect_length(redcap_output_red, 1)
 })
 
@@ -47,35 +47,40 @@ if (requireNamespace("Hmisc", quietly = TRUE)) {
 
 
 if (requireNamespace("readr", quietly = TRUE)) {
-
   metadata <-
     readr::read_csv(get_data_location(
-      "ExampleProject_DataDictionary_2018-06-07.csv"))
+      "ExampleProject_DataDictionary_2018-06-07.csv"
+    ))
 
   records <-
     readr::read_csv(get_data_location(
-      "ExampleProject_DATA_2018-06-07_1129.csv"))
+      "ExampleProject_DATA_2018-06-07_1129.csv"
+    ))
 
   redcap_output_readr <- REDCap_split(records, metadata)
 
   expect_matching_elements <- function(FUN) {
     FUN <- match.fun(FUN)
-    expect_identical(lapply(redcap_output_readr, FUN),
+    expect_identical(
-                     lapply(redcap_output_csv1, FUN))
+      lapply(redcap_output_readr, FUN),
+      lapply(redcap_output_csv1, FUN)
+    )
   }
 
   test_that("Result of data read in with `readr` will
-            match result with `read.csv`",
+            match result with `read.csv`", {
-            {
     # The list itself
-              expect_identical(length(redcap_output_readr),
+    expect_identical(
-                               length(redcap_output_csv1))
+      length(redcap_output_readr),
-              expect_identical(names(redcap_output_readr),
+      length(redcap_output_csv1)
-                               names(redcap_output_csv1))
+    )
+    expect_identical(
+      names(redcap_output_readr),
+      names(redcap_output_csv1)
+    )
 
     # Each element of the list
     expect_matching_elements(names)
     expect_matching_elements(dim)
   })
-
 }

tests/testthat/test-utils.R

@@ -1,6 +1,7 @@
 test_that("strsplitx works", {
   expect_equal(2 * 2, 4)
-  test <- c("12 months follow-up", "3 steps", "mRS 6 weeks", "Counting to 231 now")
+  test <- c("12 months follow-up", "3 steps", "mRS 6 weeks",
+            "Counting to 231 now")
   expect_length(strsplitx(test, "[0-9]", type = "around")[[1]], 3)
 
   expect_equal(strsplitx(test, "[0-9]", type = "classic")[[2]][1], "")
@@ -10,11 +11,12 @@ test_that("strsplitx works", {
 })
 
 test_that("d2w works", {
-
   expect_length(d2w(c(2:8, 21)), 8)
 
-  expect_equal(d2w(data.frame(2:7,3:8,1),lang="da",
+  expect_equal(d2w(data.frame(2:7, 3:8, 1),
-                              neutrum=TRUE)[1,3],"et")
+    lang = "da",
+    neutrum = TRUE
+  )[1, 3], "et")
 
   expect_equal(d2w(list(2:8, c(2, 6, 4, 23), 2), everything = T)[[2]][4], "two three")
 })

vignettes/Database-creation.Rmd

@@ -25,7 +25,8 @@ THe first iteration of a dataset to data dictionary function is the `ds2dd()`, w
 ```{r eval=FALSE}
 mtcars |>
   dplyr::mutate(record_id = seq_len(dplyr::n())) |>
-  ds2dd() |> str()
+  ds2dd() |>
+  str()
 ```
 
 The more advanced `ds2dd_detailed()` is a natural development. It will try to apply the most common data classes for data validation and will assume that the first column is the id number. It outputs a list with the dataset with modified variable names to comply with REDCap naming conventions and a data dictionary. 
@@ -37,7 +38,8 @@ dd_ls <- mtcars |>
   dplyr::mutate(record_id = seq_len(dplyr::n())) |>
   dplyr::select(record_id, dplyr::everything()) |>
   ds2dd_detailed()
-dd_ls |> str()
+dd_ls |> 
+  str()
 ```
 
 Additional specifications to the DataDictionary can be made manually, or it can be uploaded and modified manually in the graphical user interface on the web page.

vignettes/Introduction.Rmd

@@ -33,17 +33,23 @@ redcapcast_meta |> gt::gt()
 ```
 ```{r}
 list <-
-  REDCap_split(records = redcapcast_data,
+  REDCap_split(
+    records = redcapcast_data,
     metadata = redcapcast_meta,
-                           forms = "repeating")|> sanitize_split()
+    forms = "repeating"
+  ) |> 
+  sanitize_split()
 str(list)
 ```
 
 ```{r}
 list <-
-  REDCap_split(records = redcapcast_data,
+  REDCap_split(
+    records = redcapcast_data,
     metadata = redcapcast_meta,
-                           forms = "all") |> sanitize_split()
+    forms = "all"
+  ) |> 
+  sanitize_split()
 str(list)
 ```
 
@@ -62,5 +68,3 @@ The function works very similar to the `REDCapR::redcap_read()` in allowing to s
 ```{r}
 redcap_wider(list) |> str()
 ```
-
-