From 69f3fff0dd4af389cc22bf6c7c685c35874e840a Mon Sep 17 00:00:00 2001 From: agdamsbo <43278243+agdamsbo@users.noreply.github.com> Date: Tue, 27 Feb 2024 11:56:38 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20agdamsbo?= =?UTF-8?q?/REDCapCAST@cff0977fb95e5ceebd3ac460a76cb10b06c87ca1=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 + LICENSE.html | 2 + articles/Database-creation.html | 187 ++++++++++++++++++++ articles/Introduction.html | 214 ++++++++++++----------- articles/Shiny-app.html | 127 ++++++++++++++ articles/index.html | 8 +- authors.html | 2 + index.html | 31 ++-- news/index.html | 2 + pkgdown.yml | 4 +- reference/REDCap_split.html | 2 + reference/clean_redcap_name.html | 2 + reference/d2w.html | 2 + reference/deploy_shiny.html | 108 ++++++++++++ reference/ds2dd.html | 2 + reference/ds2dd_detailed.html | 2 + reference/easy_redcap.html | 2 + reference/file_extension.html | 2 + reference/focused_metadata.html | 2 + reference/get_api_key.html | 2 + reference/get_id_name.html | 2 + reference/guess_time_only_filter.html | 2 + reference/hms2character.html | 2 + reference/index.html | 12 ++ reference/is_repeated_longitudinal.html | 2 + reference/mark_complete.html | 2 + reference/match_fields_to_form.html | 2 + reference/mtcars_redcap.html | 129 ++++++++++++++ reference/read_input.html | 2 + reference/read_redcap_instrument.html | 2 + reference/read_redcap_tables.html | 2 + reference/redcap_wider.html | 2 + reference/redcapcast_data.html | 2 + reference/redcapcast_meta.html | 2 + reference/sanitize_split.html | 2 + reference/server_factory.html | 2 + reference/shiny_cast.html | 2 + reference/split_non_repeating_forms.html | 2 + reference/strsplitx.html | 2 + reference/time_only_correction.html | 2 + reference/ui_factory.html | 2 + search.json | 2 +- sitemap.xml | 12 ++ 43 files changed, 774 insertions(+), 124 deletions(-) create mode 100644 articles/Database-creation.html create mode 100644 articles/Shiny-app.html create mode 100644 reference/deploy_shiny.html create mode 100644 reference/mtcars_redcap.html diff --git a/404.html b/404.html index 0e5d6ab..c7349d1 100644 --- a/404.html +++ b/404.html @@ -46,7 +46,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/LICENSE.html b/LICENSE.html index 1b38f5a..39276bb 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/articles/Database-creation.html b/articles/Database-creation.html new file mode 100644 index 0000000..0410d64 --- /dev/null +++ b/articles/Database-creation.html @@ -0,0 +1,187 @@ + + + + + + + + +Database-creation • REDCapCAST + + + + + + + + + + + + + + + + + Skip to contents + + +
    + + + + +
    +
    +

    Database-creation

    + + + Source: vignettes/Database-creation.Rmd +
    Database-creation.Rmd
    +
    + + + + +
    +

    Easy data set to data base workflow +

    +

    THe first iteration of a dataset to data dictionary function is the +ds2dd(), which creates a very basic data dictionary with +all variables stored as text. This is sufficient for just storing old +datasets/spreadsheets securely in REDCap.

    +
    +mtcars |>
+  dplyr::mutate(record_id = seq_len(dplyr::n())) |>
+  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.

    +

    The dataset should be correctly formatted for the data dictionary to +preserve as much information as possible.

    +
    +dd_ls <- mtcars |>
+  dplyr::mutate(record_id = seq_len(dplyr::n())) |>
+  dplyr::select(record_id, dplyr::everything()) |>
+  ds2dd_detailed()
+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.

    +
    +

    Step 3 - Meta data upload +

    +

    Now the DataDictionary can be exported as a spreadsheet and uploaded +or it can be uploaded using the REDCapR package (only +projects with “Development” status).

    +

    Use one of the two approaches below:

    +
    +

    Manual upload +

    +
    +write.csv(dd_ls$meta, "datadictionary.csv")
    +
    +
    +

    Upload with REDCapR +

    +
    +REDCapR::redcap_metadata_write(
+  dd_ls$meta,
+  redcap_uri = keyring::key_get("DB_URI"),
+  token = keyring::key_get("DB_TOKEN")
+)
    +

    In the “REDCap R +Handbook” more is written on interfacing with REDCap in R using the +library(keyring)to store credentials in chapter +1.1.

    +
    +
    +
    +

    Step 4 - Data upload +

    +

    The same two options are available for data upload as meta data +upload: manual or through REDCapR.

    +

    Only the latter is shown here.

    +
    +REDCapR::redcap_write(
+  dd_ls$data,
+  redcap_uri = keyring::key_get("DB_URI"),
+  token = keyring::key_get("DB_TOKEN")
+)
    +
    +
    +
    +
    + + + + +
    + + + + + + + diff --git a/articles/Introduction.html b/articles/Introduction.html index 95c8407..b04b6e4 100644 --- a/articles/Introduction.html +++ b/articles/Introduction.html @@ -48,7 +48,9 @@
  • + Database-creation Introduction + Shiny-app
  • @@ -98,23 +100,23 @@ demonstration of the functions.

     redcapcast_data |> gt::gt()
    -
    - @@ -1065,23 +1067,23 @@ demonstration of the functions.

     redcapcast_meta |> gt::gt()
    -
    - diff --git a/articles/Shiny-app.html b/articles/Shiny-app.html new file mode 100644 index 0000000..508db9b --- /dev/null +++ b/articles/Shiny-app.html @@ -0,0 +1,127 @@ + + + + + + + + +Shiny-app • REDCapCAST + + + + + + + + + + + + + + + + + Skip to contents + + +
    + + + + +
    +
    +

    Shiny-app

    + + + Source: vignettes/Shiny-app.Rmd +
    Shiny-app.Rmd
    +
    + + + + +

    To make the easiest possible transistion from spreadsheet/dataset to +REDCap, I have created a small Shiny app, which adds a graphical +interface to the casting of a data dictionary and data upload. Install +the package and run the app as follows:

    + +

    The app will launch in a new window and the interface should be +fairly self-explanatory. The app only provides the most basic +functionality, but might be extended in the future.

    +
    +
    + + + + +
    + + + + + + + diff --git a/articles/index.html b/articles/index.html index e22fe81..6d267e3 100644 --- a/articles/index.html +++ b/articles/index.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • @@ -53,7 +55,11 @@

    All vignettes

    -
    Introduction
    +
    Database-creation
    +
    +
    Introduction
    +
    +
    Shiny-app
    diff --git a/authors.html b/authors.html index ec02683..8fc816c 100644 --- a/authors.html +++ b/authors.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/index.html b/index.html index 12b371d..e280a24 100644 --- a/index.html +++ b/index.html @@ -7,10 +7,9 @@
    + Database-creation Introduction + Shiny-app
  • @@ -105,25 +105,26 @@

    REDCapCAST package

    -

    REDCap Castellated data handling when using repeated instruments.

    +

    REDCap database casting and handling of castellated data when using repeated instruments and longitudinal projects.

    This package is a fork of pegeler/REDCapRITS. The REDCapRITS represents great and extensive work to handle castellated REDCap data in different programming languages. This fork is purely minded on R usage and includes a few implementations of the main REDCap_split function.

    -

    The main goal for this project was to allow for a “minimal data” approach by allowing to filter records, instruments and variables in the export to only download data needed. I think this approach is desireable for handling sensitive, clinical data. No similar functionality is available from similar tools (like REDCapR or REDCapTidieR). Please refer to REDCap-Tools for other great tools.

    +

    This package is very much to be seen as an attempt at a R-to-REDCap-to-R foundry for handling both the transition from dataset/variable list to database and the other way, from REDCap database to a tidy dataset. The goal was also to allow for a “minimal data” approach by allowing to filter records, instruments and variables in the export to only download data needed. I think this approach is desirable for handling sensitive, clinical data. Please refer to REDCap-Tools for other great tools for working with REDCap in R.

    Use and immprovements

    -

    This package is primarily relevant for working with longitudinal projects and/or projects using repeated instruments. Here is just a short descirption of the main functions:

    +

    Here is just a short description of the main functions:

    • REDcap_split(): Works largely as the original REDCapRITS::REDCap_split(). It takes a REDCap dataset and metadata (data dictionary) to split the data set into a list of dataframes of instruments.

      • -

    • read_redcap_tables(): wraps the use of REDCapR::redcap_read() with REDCap_split() to ease the export of REDCap data.

      • -

    • redcap_wider(): pivots each data frame with repeated instruments to a wide format utilizing the tidyr::pivot_wider() from the tidyverse.

      • +

    • read_redcap_tables(): wraps the use of REDCapR::redcap_read() with REDCap_split() to ease the export of REDCap data. Default output is a list of data frames with one data frame for each REDCap instrument.

      • +

    • redcap_wider(): joins and pivots a list of data frames with repeated instruments to a wide format utilizing the tidyr::pivot_wider() from the tidyverse.

    • easy_redcap(): combines secure API key storage with the keyring-package, focused data retrieval and optional widening. This is the recommended approach for easy data access and analysis.

      • +

    • ds2dd_detailed(): Converts a data set to a data dictionary for upload to a new REDCap database. Variables (fields) and instruments in a REDCap data base are defined by this data dictionary.

      • +

    • shiny_cast(): Shiny application to ease the process of converting a spreadsheet/data set to a REDCap database. The app runs locally and data is transferred securely. You can just create and upload the data dictionary, but you can also transfer the given data in the same process.

    -

    Compared to the original REDCapRITS, all matching functions are improved to accept column naming of REDCap data from manual download or API export.

    Future

    -

    The plan with this package is to be bundled with a Handbook on working with REDCap from R. I plan to also include functionality to assist in casting (yes, pun intended) the initial REDCap database.

    +

    The plan with this package is to be bundled with a Handbook on working with REDCap from R. This work is in progress but is limited by the time available. Please feel free to contact me or create and issue with ideas for future additions.

    Installation diff --git a/news/index.html b/news/index.html index 9bc4842..da16b08 100644 --- a/news/index.html +++ b/news/index.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/pkgdown.yml b/pkgdown.yml index b45ea11..e02baa0 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,8 +2,10 @@ pandoc: 2.19.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: + Database-creation: Database-creation.html Introduction: Introduction.html -last_built: 2024-02-26T20:10Z + Shiny-app: Shiny-app.html +last_built: 2024-02-27T11:56Z urls: reference: https://agdamsbo.github.io/REDCapCAST/reference article: https://agdamsbo.github.io/REDCapCAST/articles diff --git a/reference/REDCap_split.html b/reference/REDCap_split.html index 3bf030b..c4b09e7 100644 --- a/reference/REDCap_split.html +++ b/reference/REDCap_split.html @@ -28,7 +28,9 @@ is used to determine which fields should be included in each resultant table."><
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/clean_redcap_name.html b/reference/clean_redcap_name.html index dfc61eb..e4345f1 100644 --- a/reference/clean_redcap_name.html +++ b/reference/clean_redcap_name.html @@ -28,7 +28,9 @@ Trying to make up for different naming conventions.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/d2w.html b/reference/d2w.html index 28023e3..4c8d34b 100644 --- a/reference/d2w.html +++ b/reference/d2w.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/deploy_shiny.html b/reference/deploy_shiny.html new file mode 100644 index 0000000..c5e8f40 --- /dev/null +++ b/reference/deploy_shiny.html @@ -0,0 +1,108 @@ + +Deploy the Shiny app with rsconnect — deploy_shiny • REDCapCAST + Skip to contents + + +
    +
    +
    +

    Deploy the Shiny app with rsconnect

    + Source: R/shiny_cast.R +
    deploy_shiny.Rd
    +
    + +
    +

    Deploy the Shiny app with rsconnect

    +
    + +
    +

    Usage

    + 
    deploy_shiny(path = here::here("app/"), name.app = "shiny_cast")
    +
    + +
    +

    Arguments

    +
    path
    +

    app folder path

    + + +
    name.app
    +

    name of deployed app

    + +
    +
    +

    Value

    + + +

    deploy

    +
    + +
    +

    Examples

    + 
    # deploy_shiny
+
+
+
    +
    +
    + + +
    +

    Developed by Andreas Gammelgaard Damsbo, Paul Egeler.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + diff --git a/reference/ds2dd.html b/reference/ds2dd.html index d96d2b4..0ccfae5 100644 --- a/reference/ds2dd.html +++ b/reference/ds2dd.html @@ -26,7 +26,9 @@ for a more advanced function.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/ds2dd_detailed.html b/reference/ds2dd_detailed.html index 4f84b4f..0f0ff15 100644 --- a/reference/ds2dd_detailed.html +++ b/reference/ds2dd_detailed.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/easy_redcap.html b/reference/easy_redcap.html index 978913d..6dba5db 100644 --- a/reference/easy_redcap.html +++ b/reference/easy_redcap.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/file_extension.html b/reference/file_extension.html index 17acea2..5538c86 100644 --- a/reference/file_extension.html +++ b/reference/file_extension.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/focused_metadata.html b/reference/focused_metadata.html index 56b7bd1..c7a0dd2 100644 --- a/reference/focused_metadata.html +++ b/reference/focused_metadata.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/get_api_key.html b/reference/get_api_key.html index 3806088..3d7f45c 100644 --- a/reference/get_api_key.html +++ b/reference/get_api_key.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/get_id_name.html b/reference/get_id_name.html index b1d4bb4..d98df53 100644 --- a/reference/get_id_name.html +++ b/reference/get_id_name.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/guess_time_only_filter.html b/reference/guess_time_only_filter.html index bf3ee6c..f47bcbe 100644 --- a/reference/guess_time_only_filter.html +++ b/reference/guess_time_only_filter.html @@ -30,7 +30,9 @@ has to be converted to character class before REDCap upload.'>
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/hms2character.html b/reference/hms2character.html index 07402f9..0edc309 100644 --- a/reference/hms2character.html +++ b/reference/hms2character.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/index.html b/reference/index.html index c28a8ff..6113bd7 100644 --- a/reference/index.html +++ b/reference/index.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • @@ -77,6 +79,11 @@
    Convert single digits to words

    • + deploy_shiny() +
    +
    Deploy the Shiny app with rsconnect
    +
    + ds2dd()
    (DEPRECATED) Data set to data dictionary function
    @@ -137,6 +144,11 @@
    Match fields to forms
    + mtcars_redcap +
    +
    mtcars dataset slightly modified to use for Shiny app upload demonstration
    +
    + read_input()
    Flexible file import based on extension
    diff --git a/reference/is_repeated_longitudinal.html b/reference/is_repeated_longitudinal.html index 10de80a..34bc60f 100644 --- a/reference/is_repeated_longitudinal.html +++ b/reference/is_repeated_longitudinal.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/mark_complete.html b/reference/mark_complete.html index 3b092bd..b320965 100644 --- a/reference/mark_complete.html +++ b/reference/mark_complete.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/match_fields_to_form.html b/reference/match_fields_to_form.html index 3649898..01afbdb 100644 --- a/reference/match_fields_to_form.html +++ b/reference/match_fields_to_form.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/mtcars_redcap.html b/reference/mtcars_redcap.html new file mode 100644 index 0000000..7ab64fa --- /dev/null +++ b/reference/mtcars_redcap.html @@ -0,0 +1,129 @@ + +mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap • REDCapCAST + Skip to contents + + +
    +
    +
    +

    mtcars dataset slightly modified to use for Shiny app upload demonstration

    + Source: R/mtcars_redcap.R +
    mtcars_redcap.Rd
    +
    + +
    +

    mtcars dataset slightly modified to use for Shiny app upload demonstration

    +
    + +
    +

    Usage

    + 
    data(mtcars_redcap)
    +
    + +
    +

    Format

    +

    A data frame with 13 variables:

    record_id
    +

    ID, numeric

    + +
    mpg
    +

    ID, numeric

    + +
    cyl
    +

    ID, numeric

    + +
    disp
    +

    ID, numeric

    + +
    hp
    +

    ID, numeric

    + +
    drat
    +

    ID, numeric

    + +
    wt
    +

    ID, numeric

    + +
    qsec
    +

    ID, numeric

    + +
    vs
    +

    ID, numeric

    + +
    am
    +

    ID, numeric

    + +
    gear
    +

    ID, numeric

    + +
    carb
    +

    ID, numeric

    + +
    name
    +

    original rownames, charater

    + + + +
    + +
    + + +
    +

    Developed by Andreas Gammelgaard Damsbo, Paul Egeler.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + diff --git a/reference/read_input.html b/reference/read_input.html index a357439..84ce6fc 100644 --- a/reference/read_input.html +++ b/reference/read_input.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/read_redcap_instrument.html b/reference/read_redcap_instrument.html index 68a2395..180e459 100644 --- a/reference/read_redcap_instrument.html +++ b/reference/read_redcap_instrument.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/read_redcap_tables.html b/reference/read_redcap_tables.html index 009b80b..0d8d6a2 100644 --- a/reference/read_redcap_tables.html +++ b/reference/read_redcap_tables.html @@ -32,7 +32,9 @@ instruments.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/redcap_wider.html b/reference/redcap_wider.html index 7b46a95..3f51288 100644 --- a/reference/redcap_wider.html +++ b/reference/redcap_wider.html @@ -26,7 +26,9 @@ Handles longitudinal projects, but not yet repeated instruments.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/redcapcast_data.html b/reference/redcapcast_data.html index dc1b6b3..4e96622 100644 --- a/reference/redcapcast_data.html +++ b/reference/redcapcast_data.html @@ -26,7 +26,9 @@ Contains only synthetic data.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/redcapcast_meta.html b/reference/redcapcast_meta.html index 9430b6a..08ccaf0 100644 --- a/reference/redcapcast_meta.html +++ b/reference/redcapcast_meta.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/sanitize_split.html b/reference/sanitize_split.html index 8d82d72..18645b4 100644 --- a/reference/sanitize_split.html +++ b/reference/sanitize_split.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/server_factory.html b/reference/server_factory.html index e4d0fdf..5ab7f44 100644 --- a/reference/server_factory.html +++ b/reference/server_factory.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/shiny_cast.html b/reference/shiny_cast.html index c38941a..467281e 100644 --- a/reference/shiny_cast.html +++ b/reference/shiny_cast.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/split_non_repeating_forms.html b/reference/split_non_repeating_forms.html index 36bbac5..48be70b 100644 --- a/reference/split_non_repeating_forms.html +++ b/reference/split_non_repeating_forms.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/reference/strsplitx.html b/reference/strsplitx.html index 98eb2e4..58567e5 100644 --- a/reference/strsplitx.html +++ b/reference/strsplitx.html @@ -26,7 +26,9 @@ easing the split around the defined delimiter, see example.">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/time_only_correction.html b/reference/time_only_correction.html index ff90ad7..5f180dd 100644 --- a/reference/time_only_correction.html +++ b/reference/time_only_correction.html @@ -28,7 +28,9 @@ validation labelling. — time_only_correction">
    + Database-creation Introduction + Shiny-app
  • diff --git a/reference/ui_factory.html b/reference/ui_factory.html index 9d36595..0cd8349 100644 --- a/reference/ui_factory.html +++ b/reference/ui_factory.html @@ -24,7 +24,9 @@
  • + Database-creation Introduction + Shiny-app
  • diff --git a/search.json b/search.json index 659e1f2..3f8f0e2 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"Introduction","text":"","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() list <- REDCap_split(records = redcapcast_data, metadata = redcapcast_meta, forms = \"repeating\")|> sanitize_split() str(list) #> List of 2 #> $ : tibble [10 × 17] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:10] 1 2 2 3 3 3 4 4 5 6 #> ..$ redcap_event_name : chr [1:10] \"inclusion\" \"inclusion\" \"follow1\" \"inclusion\" ... #> ..$ cpr : chr [1:10] \"1203401OB4\" \"0102342303\" NA \"2301569823\" ... #> ..$ inclusion : Date[1:10], format: \"2023-03-13\" \"2023-03-01\" ... #> ..$ dob : Date[1:10], format: \"1940-03-12\" \"1934-02-01\" ... #> ..$ age : num [1:10] 83 89.1 NA 66.1 NA ... #> ..$ age_integer : num [1:10] 83 89 NA 66 NA NA 117 NA 126 91 #> ..$ sex : chr [1:10] \"female\" \"male\" NA \"male\" ... #> ..$ cohabitation : chr [1:10] \"Yes\" \"Yes\" NA \"No\" ... #> ..$ hypertension : chr [1:10] \"No\" \"No\" NA \"Yes\" ... #> ..$ diabetes : chr [1:10] \"Yes\" \"No\" NA \"Yes\" ... #> ..$ region : chr [1:10] \"East\" \"South\" NA \"North\" ... #> ..$ baseline_data_start_complete: chr [1:10] \"Incomplete\" \"Incomplete\" NA \"Incomplete\" ... #> ..$ mrs_assessed : chr [1:10] \"Yes\" \"Yes\" \"Yes\" NA ... #> ..$ mrs_date : Date[1:10], format: \"2023-03-13\" \"2023-03-07\" ... #> ..$ mrs_score : num [1:10] 1 1 3 NA 2 1 NA NA NA NA #> ..$ mrs_complete : chr [1:10] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ new_event: tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:9] 2 3 3 3 3 3 4 4 4 #> ..$ redcap_event_name : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #> ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #> ..$ redcap_repeat_instance : num [1:9] 1 1 2 1 2 3 1 2 3 #> ..$ event_type : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #> ..$ new_event_complete : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... list <- REDCap_split(records = redcapcast_data, metadata = redcapcast_meta, forms = \"all\") |> sanitize_split() str(list) #> List of 3 #> $ baseline_data_start: tibble [6 × 13] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:6] 1 2 3 4 5 6 #> ..$ redcap_event_name : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #> ..$ cpr : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #> ..$ inclusion : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #> ..$ dob : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #> ..$ age : num [1:6] 83 89.1 66.1 117.9 126.2 ... #> ..$ age_integer : num [1:6] 83 89 66 117 126 91 #> ..$ sex : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #> ..$ cohabitation : chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #> ..$ hypertension : chr [1:6] \"No\" \"No\" \"Yes\" NA ... #> ..$ diabetes : chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #> ..$ region : chr [1:6] \"East\" \"South\" \"North\" NA ... #> ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ mrs : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:5] 1 2 2 3 3 #> ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #> ..$ mrs_assessed : chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #> ..$ mrs_date : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #> ..$ mrs_score : num [1:5] 1 1 3 2 1 #> ..$ mrs_complete : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ new_event : tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:9] 2 3 3 3 3 3 4 4 4 #> ..$ redcap_event_name : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #> ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #> ..$ redcap_repeat_instance : num [1:9] 1 1 2 1 2 3 1 2 3 #> ..$ event_type : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #> ..$ new_event_complete : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"Introduction","text":"function wraps demonstrated function get dataset, metadata, apply REDCap_splitfunction bit cleaning. just cuts outs steps easier approach. function works similar REDCapR::redcap_read() allowing specify fields, events forms export instead exporting whole database filtering afterwards. believe better safer, focused approach.","code":"# read_redcap_tables(uri = \"YOUR URI\", token = \"YOUR TOKEN\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"pivotting-to-wider-format","dir":"Articles","previous_headings":"","what":"Pivotting to wider format","title":"Introduction","text":"","code":"redcap_wider(list) |> str() #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> 'data.frame': 6 obs. of 36 variables: #> $ record_id : num 1 2 3 4 5 6 #> $ cpr : chr \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #> $ inclusion : Date, format: \"2023-03-13\" \"2023-03-01\" ... #> $ dob : Date, format: \"1940-03-12\" \"1934-02-01\" ... #> $ age : num 83 89.1 66.1 117.9 126.2 ... #> $ age_integer : num 83 89 66 117 126 91 #> $ sex : chr \"female\" \"male\" \"male\" \"female\" ... #> $ cohabitation : chr \"Yes\" \"Yes\" \"No\" NA ... #> $ hypertension : chr \"No\" \"No\" \"Yes\" NA ... #> $ diabetes : chr \"Yes\" \"No\" \"Yes\" NA ... #> $ region : chr \"East\" \"South\" \"North\" NA ... #> $ baseline_data_start_complete: chr \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ mrs_assessed_inclusion : chr \"Yes\" \"Yes\" NA NA ... #> $ mrs_assessed_follow1 : chr NA \"Yes\" \"Yes\" NA ... #> $ mrs_assessed_follow2 : chr NA NA \"Yes\" NA ... #> $ mrs_date_inclusion : Date, format: \"2023-03-13\" \"2023-03-07\" ... #> $ mrs_date_follow1 : Date, format: NA \"2023-03-09\" ... #> $ mrs_date_follow2 : Date, format: NA NA ... #> $ mrs_score_inclusion : num 1 1 NA NA NA NA #> $ mrs_score_follow1 : num NA 3 2 NA NA NA #> $ mrs_score_follow2 : num NA NA 1 NA NA NA #> $ mrs_complete_inclusion : chr \"Incomplete\" \"Incomplete\" NA NA ... #> $ mrs_complete_follow1 : chr NA \"Incomplete\" \"Incomplete\" NA ... #> $ mrs_complete_follow2 : chr NA NA \"Incomplete\" NA ... #> $ event_type_1_follow1 : chr NA \"TIA\" \"AIS\" NA ... #> $ event_type_1_follow2 : chr NA NA \"ICH\" \"AIS\" ... #> $ new_event_complete_1_follow1: chr NA \"Incomplete\" \"Incomplete\" NA ... #> $ new_event_complete_1_follow2: chr NA NA \"Incomplete\" \"Complete\" ... #> $ event_type_2_follow1 : chr NA NA \"ICH\" NA ... #> $ event_type_2_follow2 : chr NA NA \"TIA\" \"ICH\" ... #> $ event_type_3_follow1 : chr NA NA NA NA ... #> $ event_type_3_follow2 : chr NA NA \"AIS\" \"Unknown\" ... #> $ new_event_complete_2_follow1: chr NA NA \"Incomplete\" NA ... #> $ new_event_complete_2_follow2: chr NA NA \"Incomplete\" \"Incomplete\" ... #> $ new_event_complete_3_follow1: chr NA NA NA NA ... #> $ new_event_complete_3_follow2: chr NA NA \"Incomplete\" \"Complete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2024). REDCapCAST: REDCap Castellated Data Handling. R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{, title = {REDCapCAST: REDCap Castellated Data Handling}, author = {Andreas Gammelgaard Damsbo and Paul Egeler}, year = {2024}, note = {R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/}, url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Castellated Data Handling","title":"REDCap Castellated Data Handling","text":"REDCap Castellated data handling using repeated instruments. package fork pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. fork purely minded R usage includes implementations main REDCap_split function. main goal project allow “minimal data” approach allowing filter records, instruments variables export download data needed. think approach desireable handling sensitive, clinical data. similar functionality available similar tools (like REDCapR REDCapTidieR). Please refer REDCap-Tools great tools.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"use-and-immprovements","dir":"","previous_headings":"","what":"Use and immprovements","title":"REDCap Castellated Data Handling","text":"package primarily relevant working longitudinal projects /projects using repeated instruments. just short descirption main functions: REDcap_split(): Works largely original REDCapRITS::REDCap_split(). takes REDCap dataset metadata (data dictionary) split data set list dataframes instruments. read_redcap_tables(): wraps use REDCapR::redcap_read() REDCap_split() ease export REDCap data. redcap_wider(): pivots data frame repeated instruments wide format utilizing tidyr::pivot_wider() tidyverse. easy_redcap(): combines secure API key storage keyring-package, focused data retrieval optional widening. recommended approach easy data access analysis. Compared original REDCapRITS, matching functions improved accept column naming REDCap data manual download API export.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. plan also include functionality assist casting (yes, pun intended) initial REDCap database.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"REDCap Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub:","code":"install.packages(\"REDCapCAST\") remotes::install_github(\"agdamsbo/REDCapCAST\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split( records, metadata, primary_table_name = \"\", forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table (described README.md). Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ depending forms option selected. 'repeating': one base table one tables repeating instrument. '': data.frame instrument, regardless whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler, M.S., GStat","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # Using an API call ------------------------------------------------------- library(RCurl) # Get the records records <- postForm( uri = api_url, # Supply your site-specific URI token = api_token, # Supply your own API token content = 'record', format = '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', format = 'json' ) # Convert exported JSON strings into a list of data.frames REDCapRITS::REDCap_split(records, metadata) # Using a raw data export ------------------------------------------------- # Get the records 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\") # Split the tables REDCapRITS::REDCap_split(records, metadata) # In conjunction with the R export script --------------------------------- # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\") # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\") # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\") # Split the tables REDCapRITS::REDCap_split(data, metadata) setwd(old) }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":null,"dir":"Reference","previous_headings":"","what":"clean_redcap_name — clean_redcap_name","title":"clean_redcap_name — clean_redcap_name","text":"Stepwise removal non-alphanumeric characters, trailing white space, substitutes spaces underscores converts lower case. Trying make different naming conventions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clean_redcap_name — clean_redcap_name","text":"","code":"clean_redcap_name(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clean_redcap_name — clean_redcap_name","text":"x vector data frame cleaning","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clean_redcap_name — clean_redcap_name","text":"vector data frame, format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\" \"three\" \"four\" \"five\" \"six\" \"seven\" \"eight\" \"21\" d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #> X2.7 X3.8 X1 #> 1 to tre et #> 2 tre fire et #> 3 fire fem et #> 4 fem seks et #> 5 seks syv et #> 6 syv otte et ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\" \"three\" \"four\" \"five\" \"six\" \"seven\" \"eight\" #> #> [[2]] #> [1] \"two\" \"six\" \"four\" \"two three\" #> #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd( ds, record.id = \"record_id\", form.name = \"basis\", field.type = \"text\", field.label = NULL, include.column.names = FALSE, metadata = metadata_names )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included REDCapCAST::metadata_names.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names=TRUE) #> $DataDictionary #> field_name form_name section_header field_type #> 1 record_id basis NA text #> 2 redcap_event_name basis NA text #> 3 redcap_repeat_instrument basis NA text #> 4 redcap_repeat_instance basis NA text #> 5 cpr basis NA text #> 6 inclusion basis NA text #> 7 inclusion_time basis NA text #> 8 dob basis NA text #> 9 age basis NA text #> 10 age_integer basis NA text #> 11 sex basis NA text #> 12 cohabitation basis NA text #> 13 hypertension basis NA text #> 14 diabetes basis NA text #> 15 region basis NA text #> 16 baseline_data_start_complete basis NA text #> 17 mrs_assessed basis NA text #> 18 mrs_date basis NA text #> 19 mrs_score basis NA text #> 20 mrs_complete basis NA text #> 21 event_datetime basis NA text #> 22 event_age basis NA text #> 23 event_type basis NA text #> 24 new_event_complete basis NA text #> field_label select_choices_or_calculations field_note #> 1 record_id NA NA #> 2 redcap_event_name NA NA #> 3 redcap_repeat_instrument NA NA #> 4 redcap_repeat_instance NA NA #> 5 cpr NA NA #> 6 inclusion NA NA #> 7 inclusion_time NA NA #> 8 dob NA NA #> 9 age NA NA #> 10 age_integer NA NA #> 11 sex NA NA #> 12 cohabitation NA NA #> 13 hypertension NA NA #> 14 diabetes NA NA #> 15 region NA NA #> 16 baseline_data_start_complete NA NA #> 17 mrs_assessed NA NA #> 18 mrs_date NA NA #> 19 mrs_score NA NA #> 20 mrs_complete NA NA #> 21 event_datetime NA NA #> 22 event_age NA NA #> 23 event_type NA NA #> 24 new_event_complete NA NA #> text_validation_type_or_show_slider_number text_validation_min #> 1 NA NA #> 2 NA NA #> 3 NA NA #> 4 NA NA #> 5 NA NA #> 6 NA NA #> 7 NA NA #> 8 NA NA #> 9 NA NA #> 10 NA NA #> 11 NA NA #> 12 NA NA #> 13 NA NA #> 14 NA NA #> 15 NA NA #> 16 NA NA #> 17 NA NA #> 18 NA NA #> 19 NA NA #> 20 NA NA #> 21 NA NA #> 22 NA NA #> 23 NA NA #> 24 NA NA #> text_validation_max identifier branching_logic required_field #> 1 NA NA NA NA #> 2 NA NA NA NA #> 3 NA NA NA NA #> 4 NA NA NA NA #> 5 NA NA NA NA #> 6 NA NA NA NA #> 7 NA NA NA NA #> 8 NA NA NA NA #> 9 NA NA NA NA #> 10 NA NA NA NA #> 11 NA NA NA NA #> 12 NA NA NA NA #> 13 NA NA NA NA #> 14 NA NA NA NA #> 15 NA NA NA NA #> 16 NA NA NA NA #> 17 NA NA NA NA #> 18 NA NA NA NA #> 19 NA NA NA NA #> 20 NA NA NA NA #> 21 NA NA NA NA #> 22 NA NA NA NA #> 23 NA NA NA NA #> 24 NA NA NA NA #> custom_alignment question_number matrix_group_name matrix_ranking #> 1 NA NA NA NA #> 2 NA NA NA NA #> 3 NA NA NA NA #> 4 NA NA NA NA #> 5 NA NA NA NA #> 6 NA NA NA NA #> 7 NA NA NA NA #> 8 NA NA NA NA #> 9 NA NA NA NA #> 10 NA NA NA NA #> 11 NA NA NA NA #> 12 NA NA NA NA #> 13 NA NA NA NA #> 14 NA NA NA NA #> 15 NA NA NA NA #> 16 NA NA NA NA #> 17 NA NA NA NA #> 18 NA NA NA NA #> 19 NA NA NA NA #> 20 NA NA NA NA #> 21 NA NA NA NA #> 22 NA NA NA NA #> 23 NA NA NA NA #> 24 NA NA NA NA #> field_annotation #> 1 NA #> 2 NA #> 3 NA #> 4 NA #> 5 NA #> 6 NA #> 7 NA #> 8 NA #> 9 NA #> 10 NA #> 11 NA #> 12 NA #> 13 NA #> 14 NA #> 15 NA #> 16 NA #> 17 NA #> 18 NA #> 19 NA #> 20 NA #> 21 NA #> 22 NA #> 23 NA #> 24 NA #> #> $`Column names` #> [1] \"record_id\" \"redcap_event_name\" #> [3] \"redcap_repeat_instrument\" \"redcap_repeat_instance\" #> [5] \"cpr\" \"inclusion\" #> [7] \"inclusion_time\" \"dob\" #> [9] \"age\" \"age_integer\" #> [11] \"sex\" \"cohabitation\" #> [13] \"hypertension\" \"diabetes\" #> [15] \"region\" \"baseline_data_start_complete\" #> [17] \"mrs_assessed\" \"mrs_date\" #> [19] \"mrs_score\" \"mrs_complete\" #> [21] \"event_datetime\" \"event_age\" #> [23] \"event_type\" \"new_event_complete\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed( data, add.auto.id = FALSE, date.format = \"dmy\", form.name = NULL, field.type = NULL, field.label = NULL, field.label.attr = \"label\", field.validation = NULL, metadata = metadata_names, validate.time = FALSE, time.var.sel.pos = \"[Tt]i[d(me)]\", time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default REDCapCAST:::metadata_names. validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"data <- redcapcast_data data |> ds2dd_detailed(validate.time = TRUE) #> $is.POSIX #> # A tibble: 19 × 2 #> inclusion_time event_datetime #>