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reference/ds2dd_detailed.md
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reference/ds2dd_detailed.md
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# Extract data from stata file for data dictionary
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Extract data from stata file for data dictionary
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## Usage
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``` r
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ds2dd_detailed(
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data,
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add.auto.id = FALSE,
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date.format = "dmy",
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form.name = NULL,
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form.sep = NULL,
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form.prefix = TRUE,
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field.type = NULL,
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field.label = NULL,
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field.label.attr = "label",
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field.validation = NULL,
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metadata = names(REDCapCAST::redcapcast_meta),
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convert.logicals = FALSE
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)
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```
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## Arguments
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- data:
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data frame
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- add.auto.id:
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flag to add id column
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- date.format:
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date format, character string. ymd/dmy/mdy. dafault is dmy.
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- form.name:
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manually specify form name(s). Vector of length 1 or ncol(data).
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Default is NULL and "data" is used.
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- form.sep:
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If supplied dataset has form names as suffix or prefix to the
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column/variable names, the seperator can be specified. If supplied,
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the form.name is ignored. Default is NULL.
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- form.prefix:
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Flag to set if form is prefix (TRUE) or suffix (FALSE) to the column
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names. Assumes all columns have pre- or suffix if specified.
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- field.type:
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manually specify field type(s). Vector of length 1 or ncol(data).
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Default is NULL and "text" is used for everything but factors, which
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wil get "radio".
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- field.label:
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manually specify field label(s). Vector of length 1 or ncol(data).
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Default is NULL and colnames(data) is used or attribute
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\`field.label.attr\` for haven_labelled data set (imported .dta file
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with \`haven::read_dta()\`).
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- field.label.attr:
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attribute name for named labels for haven_labelled data set (imported
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.dta file with \`haven::read_dta()\`. Default is "label"
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- field.validation:
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manually specify field validation(s). Vector of length 1 or
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ncol(data). Default is NULL and \`levels()\` are used for factors or
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attribute \`factor.labels.attr\` for haven_labelled data set (imported
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.dta file with \`haven::read_dta()\`).
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- metadata:
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redcap metadata headings. Default is
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names(REDCapCAST::redcapcast_meta).
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- convert.logicals:
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convert logicals to factor. Default is TRUE.
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## Value
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list of length 2
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## Details
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This function is a natural development of the ds2dd() function. It
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assumes that the first column is the ID-column. No checks. Please, do
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always inspect the data dictionary before upload.
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Ensure, that the data set is formatted with as much information as
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possible.
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\`field.type\` can be supplied
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## Examples
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``` r
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## Basic parsing with default options
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requireNamespace("REDCapCAST")
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redcapcast_data |>
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dplyr::select(-dplyr::starts_with("redcap_")) |>
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ds2dd_detailed()
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#> $data
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#> # A tibble: 25 × 24
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#> record_id cpr inclusion inclusion_time dob age age_integer sex
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#> <dbl> <chr> <date> <chr> <date> <dbl> <dbl> <chr>
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#> 1 1 12034… 2023-03-13 12:38:49 1940-03-12 83.0 83 fema…
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#> 2 2 01023… 2023-03-01 10:38:57 1934-02-01 89.1 89 male
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#> 3 2 NA NA NA NA NA NA NA
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#> 4 2 NA NA NA NA NA NA NA
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#> 5 3 23015… 2022-03-08 12:01:07 1956-01-23 66.1 66 male
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#> 6 3 NA NA NA NA NA NA NA
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#> 7 3 NA NA NA NA NA NA NA
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#> 8 3 NA NA NA NA NA NA NA
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#> 9 3 NA NA NA NA NA NA NA
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#> 10 3 NA NA NA NA NA NA NA
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#> # ℹ 15 more rows
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#> # ℹ 16 more variables: cohabitation <chr>, hypertension <chr>, diabetes <chr>,
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#> # region <chr>, baseline_data_start_complete <chr>, mrs_assessed <chr>,
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#> # mrs_date <date>, mrs_score <dbl>, mrs_complete <chr>, con_mrs <dbl>,
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#> # con_calc <dbl>, consensus_complete <chr>, event_datetime <dttm>,
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#> # event_age <dbl>, event_type <chr>, new_event_complete <chr>
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#>
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#> $meta
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#> # A tibble: 24 × 18
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#> field_name form_name section_header field_type field_label
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#> <chr> <chr> <lgl> <chr> <chr>
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#> 1 record_id data NA text record_id
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#> 2 cpr data NA text cpr
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#> 3 inclusion data NA text inclusion
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#> 4 inclusion_time data NA text inclusion_time
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#> 5 dob data NA text dob
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#> 6 age data NA text age
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#> 7 age_integer data NA text age_integer
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#> 8 sex data NA text sex
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#> 9 cohabitation data NA text cohabitation
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#> 10 hypertension data NA text hypertension
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#> # ℹ 14 more rows
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#> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>,
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#> # text_validation_type_or_show_slider_number <chr>,
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#> # text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>,
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#> # branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>,
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#> # question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>,
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#> # field_annotation <lgl>
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#>
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#> attr(,"class")
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#> [1] "REDCapCAST" "list"
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## Adding a record_id field
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iris |> ds2dd_detailed(add.auto.id = TRUE)
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#> $data
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#> # A tibble: 150 × 6
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#> record_id sepallength sepalwidth petallength petalwidth species
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#> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 1 5.1 3.5 1.4 0.2 1
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#> 2 2 4.9 3 1.4 0.2 1
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#> 3 3 4.7 3.2 1.3 0.2 1
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#> 4 4 4.6 3.1 1.5 0.2 1
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#> 5 5 5 3.6 1.4 0.2 1
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#> 6 6 5.4 3.9 1.7 0.4 1
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#> 7 7 4.6 3.4 1.4 0.3 1
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#> 8 8 5 3.4 1.5 0.2 1
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#> 9 9 4.4 2.9 1.4 0.2 1
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#> 10 10 4.9 3.1 1.5 0.1 1
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#> # ℹ 140 more rows
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#>
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#> $meta
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#> # A tibble: 6 × 18
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#> field_name form_name section_header field_type field_label
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#> <chr> <chr> <lgl> <chr> <chr>
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#> 1 record_id data NA text record_id
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#> 2 sepallength data NA text Sepal.Length
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#> 3 sepalwidth data NA text Sepal.Width
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#> 4 petallength data NA text Petal.Length
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#> 5 petalwidth data NA text Petal.Width
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#> 6 species data NA radio Species
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#> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>,
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#> # text_validation_type_or_show_slider_number <chr>,
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#> # text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>,
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#> # branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>,
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#> # question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>,
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#> # field_annotation <lgl>
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#>
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#> attr(,"class")
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#> [1] "REDCapCAST" "list"
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## Passing form name information to function
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iris |>
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ds2dd_detailed(
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add.auto.id = TRUE,
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form.name = sample(c("b", "c"), size = 6, replace = TRUE, prob = rep(.5, 2))
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) |>
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purrr::pluck("meta")
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#> # A tibble: 6 × 18
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#> field_name form_name section_header field_type field_label
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#> <chr> <chr> <lgl> <chr> <chr>
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#> 1 record_id c NA text record_id
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#> 2 sepallength b NA text Sepal.Length
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#> 3 sepalwidth c NA text Sepal.Width
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#> 4 petallength b NA text Petal.Length
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#> 5 petalwidth c NA text Petal.Width
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#> 6 species b NA radio Species
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#> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>,
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#> # text_validation_type_or_show_slider_number <chr>,
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#> # text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>,
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#> # branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>,
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#> # question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>,
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#> # field_annotation <lgl>
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mtcars |>
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dplyr::mutate(unknown = NA) |>
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numchar2fct() |>
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ds2dd_detailed(add.auto.id = TRUE)
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#> $data
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#> # A tibble: 32 × 13
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#> record_id mpg cyl disp hp drat wt qsec vs am gear carb
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#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 1 21 2 160 110 3.9 2.62 16.5 1 2 2 4
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#> 2 2 21 2 160 110 3.9 2.88 17.0 1 2 2 4
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#> 3 3 22.8 1 108 93 3.85 2.32 18.6 2 2 2 1
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#> 4 4 21.4 2 258 110 3.08 3.22 19.4 2 1 1 1
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#> 5 5 18.7 3 360 175 3.15 3.44 17.0 1 1 1 2
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#> 6 6 18.1 2 225 105 2.76 3.46 20.2 2 1 1 1
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#> 7 7 14.3 3 360 245 3.21 3.57 15.8 1 1 1 4
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#> 8 8 24.4 1 147. 62 3.69 3.19 20 2 1 2 2
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#> 9 9 22.8 1 141. 95 3.92 3.15 22.9 2 1 2 2
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#> 10 10 19.2 2 168. 123 3.92 3.44 18.3 2 1 2 4
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#> # ℹ 22 more rows
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#> # ℹ 1 more variable: unknown <dbl>
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#>
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#> $meta
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#> # A tibble: 13 × 18
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#> field_name form_name section_header field_type field_label
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#> <chr> <chr> <lgl> <chr> <chr>
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#> 1 record_id data NA text record_id
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#> 2 mpg data NA text mpg
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#> 3 cyl data NA radio cyl
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#> 4 disp data NA text disp
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#> 5 hp data NA text hp
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#> 6 drat data NA text drat
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#> 7 wt data NA text wt
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#> 8 qsec data NA text qsec
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#> 9 vs data NA radio vs
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#> 10 am data NA radio am
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#> 11 gear data NA radio gear
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#> 12 carb data NA radio carb
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#> 13 unknown data NA truefalse unknown
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#> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>,
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#> # text_validation_type_or_show_slider_number <chr>,
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#> # text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>,
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#> # branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>,
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#> # question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>,
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#> # field_annotation <lgl>
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#>
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#> attr(,"class")
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#> [1] "REDCapCAST" "list"
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## Using column name suffix to carry form name
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data <- iris |>
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ds2dd_detailed(add.auto.id = TRUE) |>
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purrr::pluck("data")
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names(data) <- glue::glue("{sample(x = c('a','b'),size = length(names(data)),
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replace=TRUE,prob = rep(x=.5,2))}__{names(data)}")
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data |> ds2dd_detailed(form.sep = "__")
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#> $data
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#> # A tibble: 150 × 6
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#> record_id sepallength sepalwidth petallength petalwidth species
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#> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 1 5.1 3.5 1.4 0.2 1
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#> 2 2 4.9 3 1.4 0.2 1
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#> 3 3 4.7 3.2 1.3 0.2 1
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#> 4 4 4.6 3.1 1.5 0.2 1
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#> 5 5 5 3.6 1.4 0.2 1
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#> 6 6 5.4 3.9 1.7 0.4 1
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#> 7 7 4.6 3.4 1.4 0.3 1
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#> 8 8 5 3.4 1.5 0.2 1
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#> 9 9 4.4 2.9 1.4 0.2 1
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#> 10 10 4.9 3.1 1.5 0.1 1
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#> # ℹ 140 more rows
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#>
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#> $meta
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#> # A tibble: 6 × 18
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#> field_name form_name section_header field_type field_label
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#> <chr> <chr> <lgl> <chr> <chr>
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#> 1 record_id b NA text record_id
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#> 2 sepallength a NA text sepallength
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#> 3 sepalwidth a NA text sepalwidth
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#> 4 petallength a NA text petallength
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#> 5 petalwidth a NA text petalwidth
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#> 6 species a NA text species
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#> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>,
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#> # text_validation_type_or_show_slider_number <chr>,
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#> # text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>,
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#> # branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>,
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#> # question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>,
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#> # field_annotation <lgl>
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#>
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#> attr(,"class")
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#> [1] "REDCapCAST" "list"
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```
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