-easy_redcap(uri = "YOUR URI",
- project.name = "MY_PROJECT",
- widen.data = TRUE,
- fields = c("record_id", "OTHER FIELDS"))easy_redcap(
+ uri = "YOUR URI",
+ project.name = "MY_PROJECT",
+ widen.data = TRUE,
+ fields = c("record_id", "OTHER FIELDS")
+)
To save the metadata as labels in the dataset, we can save field labels and the choices from radio buttons and dropdown features:
-labelled_data <-
- apply_field_label(data=redcapcast_data,
- meta=redcapcast_meta) |>
- apply_factor_labels(meta=redcapcast_meta)labelled_data <-
+ apply_field_label(
+ data = redcapcast_data,
+ meta = redcapcast_meta
+ ) |>
+ apply_factor_labels(meta = redcapcast_meta)The REDCap_split function splits the data set into a
list of data.frames.
@@ -2244,7 +2248,7 @@ list of data.frames. records = labelled_data, metadata = redcapcast_meta, forms = "all" - ) |> + ) |> # Next steps cleans up and removes generic columns sanitize_split() str(list) @@ -2315,127 +2319,133 @@ widen the data, by transforming the list of data.frames to a single data.frame with one row for each subject/record_id (wide data format):+#> $ new_event_complete____2____follow1: chr [1:6] NA NA "Incomplete" "Complete" ... +#> $ new_event_complete____2____follow2: chr [1:6] NA NA "Incomplete" "Incomplete" ... +#> $ new_event_complete____3____follow1: chr [1:6] NA NA NA NA ... +#> $ new_event_complete____3____follow2: chr [1:6] NA NA "Incomplete" "Complete" ...-wide_data <- redcap_wider(list) +wide_data <- redcap_wider(list, + event.glue = "{.value}____{redcap_event_name}", + inst.glue = "{.value}____{redcap_repeat_instance}" +) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` wide_data |> str() #> tibble [6 × 49] (S3: tbl_df/tbl/data.frame) -#> $ record_id : num [1:6] 1 2 3 4 5 6 +#> $ record_id : num [1:6] 1 2 3 4 5 6 #> ..- attr(*, "label")= chr "ID" -#> $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ... +#> $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ... #> ..- attr(*, "label")= chr "CPR (Danish civil registration number)" -#> $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ... -#> $ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... +#> $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ... +#> $ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... #> ..- attr(*, "units")= chr "secs" -#> $ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ... -#> $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ... +#> $ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ... +#> $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ... #> ..- attr(*, "label")= chr "Age\r\nNote: Apparently, the build in datediff() function does not handle counting whole years. This results in"| __truncated__ -#> $ age_integer : num [1:6] 83 89 66 117 126 91 +#> $ age_integer : num [1:6] 83 89 66 117 126 91 #> ..- attr(*, "label")= chr "Age integer\r\nNote: as opposed to the build in datediff() this handles counting years as integers very well. C"| __truncated__ -#> $ sex : chr [1:6] "female" "male" "male" "female" ... +#> $ sex : chr [1:6] "female" "male" "male" "female" ... #> ..- attr(*, "label")= chr "Legal sex" -#> $ cohabitation : 'labelled' chr [1:6] "Yes" "Yes" "No" NA ... +#> $ cohabitation : 'labelled' chr [1:6] "Yes" "Yes" "No" NA ... #> ..- attr(*, "label")= chr "Cohabitation" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ hypertension : 'labelled' chr [1:6] "No" "No" "Yes" NA ... +#> $ hypertension : 'labelled' chr [1:6] "No" "No" "Yes" NA ... #> ..- attr(*, "label")= chr "Hypertension" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ diabetes : 'labelled' chr [1:6] "Yes" "No" "Yes" NA ... +#> $ diabetes : 'labelled' chr [1:6] "Yes" "No" "Yes" NA ... #> ..- attr(*, "label")= chr "Diabetes" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ region : 'labelled' chr [1:6] "East" "South" "North" NA ... +#> $ region : 'labelled' chr [1:6] "East" "South" "North" NA ... #> ..- attr(*, "label")= chr "Region" #> ..- attr(*, "labels")= Named chr [1:4] "1" "2" "3" "4" #> .. ..- attr(*, "names")= chr [1:4] "North" "East" "South" "West" -#> $ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ... -#> $ mrs_assessed_inclusion : 'labelled' chr [1:6] "Yes" "Yes" NA NA ... +#> $ baseline_data_start_complete : chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ... +#> $ mrs_assessed____inclusion : 'labelled' chr [1:6] "Yes" "Yes" NA NA ... #> ..- attr(*, "label")= chr "Assesed" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ mrs_assessed_follow1 : 'labelled' chr [1:6] NA "Yes" "Yes" NA ... +#> $ mrs_assessed____follow1 : 'labelled' chr [1:6] NA "Yes" "Yes" NA ... #> ..- attr(*, "label")= chr "Assesed" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ mrs_assessed_follow2 : 'labelled' chr [1:6] NA NA "Yes" NA ... +#> $ mrs_assessed____follow2 : 'labelled' chr [1:6] NA NA "Yes" NA ... #> ..- attr(*, "label")= chr "Assesed" #> ..- attr(*, "labels")= Named chr [1:2] "1" "2" #> .. ..- attr(*, "names")= chr [1:2] "Yes" "No" -#> $ mrs_date_inclusion : Date[1:6], format: "2023-03-13" "2023-03-07" ... -#> $ mrs_date_follow1 : Date[1:6], format: NA "2023-03-09" ... -#> $ mrs_date_follow2 : Date[1:6], format: NA NA ... -#> $ mrs_score_inclusion : 'labelled' num [1:6] 1 1 NA NA NA NA +#> $ mrs_date____inclusion : Date[1:6], format: "2023-03-13" "2023-03-07" ... +#> $ mrs_date____follow1 : Date[1:6], format: NA "2023-03-09" ... +#> $ mrs_date____follow2 : Date[1:6], format: NA NA ... +#> $ mrs_score____inclusion : 'labelled' num [1:6] 1 1 NA NA NA NA #> ..- attr(*, "label")= chr "mRS score" #> ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ... #> .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ... -#> $ mrs_score_follow1 : 'labelled' num [1:6] NA 3 2 NA NA NA +#> $ mrs_score____follow1 : 'labelled' num [1:6] NA 3 2 NA NA NA #> ..- attr(*, "label")= chr "mRS score" #> ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ... #> .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ... -#> $ mrs_score_follow2 : 'labelled' num [1:6] NA NA 1 NA NA NA +#> $ mrs_score____follow2 : 'labelled' num [1:6] NA NA 1 NA NA NA #> ..- attr(*, "label")= chr "mRS score" #> ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ... #> .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ... -#> $ mrs_complete_inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ... -#> $ mrs_complete_follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ... -#> $ mrs_complete_follow2 : chr [1:6] NA NA "Incomplete" NA ... -#> $ event_datetime_1_follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ... -#> $ event_datetime_1_follow2 : POSIXct[1:6], format: NA NA ... -#> $ event_age_1_follow1 : num [1:6] NA NA NA 96 127 NA +#> $ mrs_complete____inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ... +#> $ mrs_complete____follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ... +#> $ mrs_complete____follow2 : chr [1:6] NA NA "Incomplete" NA ... +#> $ event_datetime____1____follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ... +#> $ event_datetime____1____follow2 : POSIXct[1:6], format: NA NA ... +#> $ event_age____1____follow1 : num [1:6] NA NA NA 96 127 NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_age_1_follow2 : num [1:6] NA NA NA 118 NA NA +#> $ event_age____1____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_type_1_follow1 : 'labelled' chr [1:6] NA "TIA" "AIS" "TIA" ... +#> $ event_type____1____follow1 : 'labelled' chr [1:6] NA "TIA" "AIS" "TIA" ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ event_type_1_follow2 : 'labelled' chr [1:6] NA NA "ICH" "AIS" ... +#> $ event_type____1____follow2 : 'labelled' chr [1:6] NA NA "ICH" "AIS" ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ new_event_complete_1_follow1: chr [1:6] NA "Incomplete" "Incomplete" "Complete" ... -#> $ new_event_complete_1_follow2: chr [1:6] NA NA "Incomplete" "Complete" ... -#> $ event_datetime_2_follow1 : POSIXct[1:6], format: NA NA ... -#> $ event_datetime_2_follow2 : POSIXct[1:6], format: NA NA ... -#> $ event_datetime_3_follow1 : POSIXct[1:6], format: NA NA ... -#> $ event_datetime_3_follow2 : POSIXct[1:6], format: NA NA ... -#> $ event_age_2_follow1 : num [1:6] NA NA NA 105 127 NA +#> $ new_event_complete____1____follow1: chr [1:6] NA "Incomplete" "Incomplete" "Complete" ... +#> $ new_event_complete____1____follow2: chr [1:6] NA NA "Incomplete" "Complete" ... +#> $ event_datetime____2____follow1 : POSIXct[1:6], format: NA NA ... +#> $ event_datetime____2____follow2 : POSIXct[1:6], format: NA NA ... +#> $ event_datetime____3____follow1 : POSIXct[1:6], format: NA NA ... +#> $ event_datetime____3____follow2 : POSIXct[1:6], format: NA NA ... +#> $ event_age____2____follow1 : num [1:6] NA NA NA 105 127 NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_age_2_follow2 : num [1:6] NA NA NA 118 NA NA +#> $ event_age____2____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_age_3_follow1 : num [1:6] NA NA NA NA NA NA +#> $ event_age____3____follow1 : num [1:6] NA NA NA NA NA NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_age_3_follow2 : num [1:6] NA NA NA 118 NA NA +#> $ event_age____3____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, "label")= chr "Age at event" -#> $ event_type_2_follow1 : 'labelled' chr [1:6] NA NA "ICH" "TIA" ... +#> $ event_type____2____follow1 : 'labelled' chr [1:6] NA NA "ICH" "TIA" ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ event_type_2_follow2 : 'labelled' chr [1:6] NA NA "TIA" "ICH" ... +#> $ event_type____2____follow2 : 'labelled' chr [1:6] NA NA "TIA" "ICH" ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ event_type_3_follow1 : 'labelled' chr [1:6] NA NA NA NA ... +#> $ event_type____3____follow1 : 'labelled' chr [1:6] NA NA NA NA ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ event_type_3_follow2 : 'labelled' chr [1:6] NA NA "AIS" "Unknown" ... +#> $ event_type____3____follow2 : 'labelled' chr [1:6] NA NA "AIS" "Unknown" ... #> ..- attr(*, "label")= chr "Neurovascular event" #> ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ... #> .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ... -#> $ new_event_complete_2_follow1: chr [1:6] NA NA "Incomplete" "Complete" ... -#> $ new_event_complete_2_follow2: chr [1:6] NA NA "Incomplete" "Incomplete" ... -#> $ new_event_complete_3_follow1: chr [1:6] NA NA NA NA ... -#> $ new_event_complete_3_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...
Transfer suffixes to labels:
+
+wide_data_suffixes <- wide_data |> suffix2label()
-wide_data |>
- dplyr::select(sex,hypertension, diabetes) |>
+
+wide_data_suffixes |>
+ dplyr::select(sex, hypertension, diabetes,mrs_score____follow2) |>
gtsummary::tbl_summary()