Check data column classes against REDCap expectations
Source:R/REDCap_coltype_check.R
REDCap_coltype_check.RdUses REDCap codebook metadata to infer expected classes and compares these to
classes in data.
Usage
REDCap_coltype_check(
codebook,
indicator_POSIXct = "datetime_dmy",
indicator_date = "Date",
indicator_time = "time",
indicator_logical = "yesno",
indicator_numeric.val_col = c("number", "integer"),
indicator_numeric.type_col = c("radio", "dropdown"),
label_col = `Field Label`,
name_col = `Variable / Field Name`,
type_col = `Field Type`,
val_col = `Text Validation Type OR Show Slider Number`,
data
)Arguments
- codebook
REDCap data dictionary.
- indicator_POSIXct
Indicator in
val_colidentifying datetime fields.- indicator_date
Pattern used in labels to identify date variables.
- indicator_time
Indicator in
val_colidentifying time-only fields.- indicator_logical
Indicator in
type_colidentifying logical fields.- indicator_numeric.val_col
Indicators in
val_colfor numeric fields.- indicator_numeric.type_col
Indicators in
type_colfor numeric fields.- label_col
Unquoted codebook label column.
- name_col
Unquoted codebook variable-name column.
- type_col
Unquoted codebook field-type column.
- val_col
Unquoted codebook validation/type-hint column.
- data
Data frame to validate.
Examples
library(gt)
dict_path <- system.file("ext", "DataDictionary_sleepdiary.csv",
package = "melidosData"
)
dict <- utils::read.csv(dict_path, check.names = FALSE)
coltype_check <- REDCap_coltype_check(dict, data = REDCap_example_sleep)
coltype_check$ok
#> [1] TRUE
coltype_check$summary
#> $missing
#> character(0)
#>
#> $missing_by_expected
#> # A tibble: 0 × 2
#> # ℹ 2 variables: expected <chr>, cols <list>
#>
#> $wrong_type
#> # A tibble: 0 × 3
#> # ℹ 3 variables: col <chr>, expected_type <chr>, actual_type <chr>
#>
#> $ok
#> [1] "bedtime" "sleep" "offset" "out_ofbed"
#> [5] "sleepdelay" "awakenings" "awake_duration" "sleepquality"
#> [9] "daytype2" "status" "scheduledate" "record_id"
#> [13] "comments" "uuid" "supplementaldata" "serializedresult"
#>
coltype_check$details |> gt()
col
expected
present
actual
type_ok
issue
dict_path <- system.file("ext", "DataDictionary_chronotype.csv",
package = "melidosData"
)
dict <- utils::read.csv(dict_path, check.names = FALSE)
dict <- REDCap_codebook_prepare(dict, form.filter = "mctq")
coltype_check <- REDCap_coltype_check(dict, data = REDCap_example_chronotype)
coltype_check$ok
#> [1] FALSE
coltype_check$summary
#> $missing
#> [1] "mctq_desctext_1" "mctq_sleep_cycle_pic" "mctq_desctext_2"
#> [4] "mctq_desctext_3" "mctq_desctext_4" "mctq_reason"
#> [7] "mctq_desctext_5" "mctq_commute" "mctq_desctext_6"
#> [10] "mctq_outdoor" "mctq_desctext_7"
#>
#> $missing_by_expected
#> # A tibble: 1 × 2
#> expected cols
#> <chr> <list>
#> 1 character <chr [11]>
#>
#> $wrong_type
#> # A tibble: 10 × 3
#> col expected_type actual_type
#> <chr> <chr> <chr>
#> 1 mctq_outdoor_work_min numeric character
#> 2 mctq_outdoor_free_min numeric character
#> 3 mctq_regular_work logical numeric
#> 4 mctq_alarm_work logical numeric
#> 5 mctq_wake_alarm logical numeric
#> 6 mctq_alarm_free logical numeric
#> 7 mctq_choose_sleep_free logical numeric
#> 8 mctq_shift_work logical numeric
#> 9 mctq_outdoor_work_calc character numeric
#> 10 mctq_outdoor_free_calc character numeric
#>
#> $ok
#> [1] "mctq_nr_workdays" "mctq_fall_sleep_work" "mctq_get_up_work"
#> [4] "mctq_fall_sleep_free" "mctq_get_up_free" "mctq_work_flex"
#> [7] "mctq_work_travel" "mctq_com_to_work_h" "mctq_com_to_work_min"
#> [10] "mctq_com_from_work_h" "mctq_com_from_work_min" "mctq_outdoor_work_h"
#> [13] "mctq_outdoor_free_h" "mctq_stim_cigar" "mctq_stim_beer"
#> [16] "mctq_stim_wine" "mctq_stim_liquor" "mctq_stim_coffee"
#> [19] "mctq_stim_tea" "mctq_stim_caf_drink" "mctq_stim_sleep_med"
#> [22] "mctq_nr_cigar" "mctq_nr_beer" "mctq_nr_wine"
#> [25] "mctq_nr_liquor" "mctq_nr_coffee" "mctq_nr_tea"
#> [28] "mctq_nr_caf_drink" "mctq_nr_sleep_med" "mctq_bedtime_work"
#> [31] "mctq_ready_sleep_work" "mctq_wake_time_work" "mctq_bedtime_free"
#> [34] "mctq_ready_sleep_free" "mctq_wake_time_free" "mctq_work_start"
#> [37] "mctq_work_end" "record_id" "mctq_reason_spec"
#>
coltype_check$details
#> # A tibble: 60 × 6
#> col expected present actual type_ok issue
#> <chr> <chr> <lgl> <chr> <lgl> <chr>
#> 1 mctq_nr_workdays numeric TRUE numeric TRUE ok
#> 2 mctq_fall_sleep_work numeric TRUE numeric TRUE ok
#> 3 mctq_get_up_work numeric TRUE numeric TRUE ok
#> 4 mctq_fall_sleep_free numeric TRUE numeric TRUE ok
#> 5 mctq_get_up_free numeric TRUE numeric TRUE ok
#> 6 mctq_work_flex numeric TRUE numeric TRUE ok
#> 7 mctq_work_travel numeric TRUE numeric TRUE ok
#> 8 mctq_com_to_work_h numeric TRUE numeric TRUE ok
#> 9 mctq_com_to_work_min numeric TRUE numeric TRUE ok
#> 10 mctq_com_from_work_h numeric TRUE numeric TRUE ok
#> # ℹ 50 more rows