mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-27 23:31:54 +01:00
88 lines
2.1 KiB
Plaintext
88 lines
2.1 KiB
Plaintext
---
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title: "Shiny-app"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{Shiny-app}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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To make the easiest possible transition from spreadsheet/dataset to REDCap, I have created a small app, which adds a graphical interface to the casting of a data dictionary and data upload. Install the package and launch the app as follows:
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```{r eval=FALSE}
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REDCapCAST::shiny_cast()
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```
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The app primarily wraps one function: `ds2dd_detailed()`.
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```{r}
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library(REDCapCAST)
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ds <- REDCap_split(
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records = redcapcast_data,
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metadata = redcapcast_meta,
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forms = "all"
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) |>
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sanitize_split() |>
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redcap_wider()
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str(ds)
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```
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```{r}
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ds|>
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ds2dd_detailed(metadata = names(REDCapCAST::redcapcast_meta))|>
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purrr::pluck("data") |>
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str()
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```
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```{r}
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ds|>
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ds2dd_detailed(metadata = names(REDCapCAST::redcapcast_meta))|>
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purrr::pluck("meta") |>
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head(10)
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```
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Different data formats are accepted, which all mostly implements the `readr::col_guess()` functionality to parse column classes.
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To ensure uniformity in data import this parsing has been implemented on its own to use with `ds2dd_detailed()` or any other data set for that matter:
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```{r}
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ds_parsed <- redcapcast_data |>
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dplyr::mutate(dplyr::across(dplyr::everything(),as.character)) |>
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parse_data()
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str(ds_parsed)
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```
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It will ignore specified columns, which is neat for numeric-looking strings like cpr-with a leading 0:
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```{r}
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redcapcast_data |>
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dplyr::mutate(dplyr::across(dplyr::everything(),as.character)) |>
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parse_data(ignore.vars = c("record_id","cpr")) |>
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str()
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```
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Column classes can be passed to `parse_data()`.
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Making a few crude assumption for factorising data, `numchar2fct()` factorises numerical and character vectors based on a set threshold for unique values:
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```{r}
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mtcars |> str()
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mtcars |>
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numchar2fct(numeric.threshold = 6) |>
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str()
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```
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```{r}
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ds_parsed|>
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numchar2fct(numeric.threshold = 2) |>
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str()
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```
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