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@@ -10,6 +10,11 @@ | |
| *.zip | ||
| site | ||
| !inst/testdata/*.csv | ||
| report/*.html | ||
| report/*.pdf | ||
| report/*.txt | ||
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| # env file | ||
| *.env | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,7 +1,7 @@ | ||
| Package: redcapcustodian | ||
| Type: Package | ||
| Title: Data automation for R-centric workflows with a nod towards REDCap | ||
| Version: 1.14.1 | ||
| Version: 1.26.2 | ||
| Authors@R: c( | ||
| person("Philip", "Chase", | ||
| email = "[email protected]", | ||
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@@ -23,6 +23,10 @@ Authors@R: c( | |
| email = "[email protected]", | ||
| role = "aut", | ||
| comment=c(ORCID = "0000-0002-5790-4268")), | ||
| person("Sai Pavan", "Kamma", | ||
| email = "[email protected]", | ||
| role = "aut", | ||
| comment=c(ORCID = "0009-0004-4619-0409")), | ||
| person("Christopher", "Barnes", | ||
| email = "[email protected]", | ||
| role = "ctb", | ||
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@@ -55,17 +59,22 @@ Imports: | |
| tibble, | ||
| tidyr, | ||
| vctrs, | ||
| jsonlite | ||
| jsonlite, | ||
| openxlsx, | ||
| quarto | ||
| Suggests: | ||
| RSQLite, | ||
| digest, | ||
| dotenv, | ||
| duckdb, | ||
| fs, | ||
| kableExtra, | ||
| knitr (>= 1.18), | ||
| rmarkdown (>= 2.0), | ||
| testthat (>= 3.0.0) | ||
| testthat (>= 3.0.0), | ||
| tidyverse | ||
| VignetteBuilder: knitr | ||
| Config/testthat/edition: 3 | ||
| RoxygenNote: 7.2.1 | ||
| RoxygenNote: 7.3.2 | ||
| Depends: | ||
| R (>= 2.10) | ||
| R (>= 3.5.0) | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,72 @@ | ||
| #' Create a REDCap data dictionary from a dataframe | ||
| #' | ||
| #' @param df the dataframe to generate the data dictionary for | ||
| #' @param form_name the form name to display in REDCap | ||
| #' @param record_id_col a column in the dataframe that uniquely identifies each record | ||
| #' | ||
| #' @return A redcap data dictionary | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' | ||
| #' df <- data.frame( | ||
| #' pk_col = c("a1", "a2", "a3"), | ||
| #' integer_col = c(1, 2, 3), | ||
| #' numeric_col = 5.9, | ||
| #' character_col = c("a", "b", "c"), | ||
| #' date_col = as.Date("2011-03-07"), | ||
| #' date_time_col = as.POSIXct(strptime("2011-03-27 01:30:00", "%Y-%m-%d %H:%M:%S")), | ||
| #' email_col = c("[email protected]", "[email protected]", "[email protected]") | ||
| #' ) | ||
| #' | ||
| #' redcap_data_dictionary <- dataframe_to_redcap_dictionary(df, "test_form") | ||
| #' redcap_data_dictionary <- dataframe_to_redcap_dictionary(df, "test_form", "character_col") | ||
| #' } | ||
| dataframe_to_redcap_dictionary <- function(df, | ||
| form_name, | ||
| record_id_col = NULL) { | ||
| contains_emails <- function(col) { | ||
| email_pattern <- "^[A-Za-z0-9._%-]+@[A-Za-z0-9.-]+\\.[A-Za-z]{2,4}$" | ||
| return(any(grepl(email_pattern, col))) | ||
| } | ||
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| get_validation_type <- function(col) { | ||
| if (contains_emails(col)) { | ||
| return("email") | ||
| } | ||
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| col_type <- class(col)[1] | ||
| switch( | ||
| col_type, | ||
| "numeric" = "number", | ||
| "integer" = "number", | ||
| "Date" = "datetime_ymd", | ||
| "POSIXct" = "datetime_seconds_ymd", | ||
| as.character(NA) | ||
| ) | ||
| } | ||
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| # Rearrange the dataframe if a record_id_col is provided | ||
| if (!is.null(record_id_col)) { | ||
| ordered_df <- df |> | ||
| dplyr::select(record_id_col, dplyr::everything()) | ||
| } else { | ||
| ordered_df <- df | ||
| } | ||
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| redcap_data_dictionary <- data.frame( | ||
| field_name = names(ordered_df), | ||
| form_name = form_name, | ||
| section_header = as.character(NA), | ||
| field_type = "text", | ||
| field_label = names(ordered_df), | ||
| select_choices_or_calculations = as.character(NA), | ||
| field_note = as.character(NA), | ||
| text_validation_type_or_show_slider_number = sapply(ordered_df, get_validation_type) | ||
| ) | ||
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| rownames(redcap_data_dictionary) <- NULL | ||
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| return(redcap_data_dictionary) | ||
| } |
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