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This vignette covers the included functions and basic functionality.
A dataset and a meta data file are provided with the package for demonstration of the functions.
| record_id | redcap_event_name | redcap_repeat_instrument | redcap_repeat_instance | cpr | inclusion | inclusion_time | dob | age | age_integer | sex | cohabitation | hypertension | diabetes | region | baseline_data_start_complete | mrs_assessed | mrs_date | mrs_score | mrs_complete | event_datetime | event_age | event_type | new_event_complete |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | inclusion | NA | NA | 1203401OB4 | 2023-03-13 | 12:38:49 | 1940-03-12 | 83.00239 | 83 | female | Yes | No | Yes | East | Incomplete | Yes | 2023-03-13 | 1 | Incomplete | NA | NA | NA | NA |
| 2 | inclusion | NA | NA | 0102342303 | 2023-03-01 | 10:38:57 | 1934-02-01 | 89.07780 | 89 | male | Yes | No | No | South | Incomplete | Yes | 2023-03-07 | 1 | Incomplete | NA | NA | NA | NA |
| 2 | follow1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Yes | 2023-03-09 | 3 | Incomplete | NA | NA | NA | NA |
| 2 | follow1 | New Event (?) | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:49:42 | NA | TIA | Incomplete |
| 3 | inclusion | NA | NA | 2301569823 | 2022-03-08 | 12:01:07 | 1956-01-23 | 66.12319 | 66 | male | No | Yes | Yes | North | Incomplete | NA | NA | NA | Incomplete | NA | NA | NA | NA |
| 3 | follow1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Yes | 2022-08-16 | 2 | Incomplete | NA | NA | NA | NA |
| 3 | follow2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Yes | 2023-03-13 | 1 | Incomplete | NA | NA | NA | NA |
| 3 | follow1 | New Event (?) | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:49:58 | NA | AIS | Incomplete |
| 3 | follow1 | New Event (?) | 2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:01 | NA | ICH | Incomplete |
| 3 | follow2 | New Event (?) | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:05 | NA | ICH | Incomplete |
| 3 | follow2 | New Event (?) | 2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:07 | NA | TIA | Incomplete |
| 3 | follow2 | New Event (?) | 3 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:09 | NA | AIS | Incomplete |
| 4 | inclusion | NA | NA | 0204051342 | 2023-03-14 | 20:39:19 | 1905-04-02 | 117.94903 | 117 | female | NA | NA | NA | NA | Incomplete | NA | NA | NA | Incomplete | NA | NA | NA | NA |
| 4 | follow2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Incomplete | NA | NA | NA | NA |
| 4 | follow2 | New Event (?) | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:19 | NA | AIS | Complete |
| 4 | follow2 | New Event (?) | 2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:22 | NA | ICH | Incomplete |
| 4 | follow2 | New Event (?) | 3 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 2024-01-18 12:50:24 | NA | Unknown | Complete |
| 5 | inclusion | NA | NA | 0201976043 | 2023-03-23 | 08:50:31 | 1897-01-02 | 126.21751 | 126 | male | No | Yes | Yes | East | Complete | NA | NA | NA | Incomplete | NA | NA | NA | NA |
| 6 | inclusion | NA | NA | 1202320122 | 2024-01-25 | 08:49:28 | 1932-02-12 | 91.95261 | 91 | female | No | Yes | No | East | Complete | NA | NA | NA | Incomplete | NA | NA | NA | NA |
| field_name | form_name | section_header | field_type | field_label | select_choices_or_calculations | field_note | text_validation_type_or_show_slider_number | text_validation_min | text_validation_max | identifier | branching_logic | required_field | custom_alignment | question_number | matrix_group_name | matrix_ranking | field_annotation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| record_id | baseline_data_start | NA | text | ID | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| cpr | baseline_data_start | NA | text | CPR (Danish civil registration number) | NA | ddmmyyxxxx | NA | NA | NA | y | NA | y | NA | NA | NA | NA | NA |
| inclusion | baseline_data_start | NA | text | Inclusion date | NA | NA | date_ymd | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| dob | baseline_data_start | NA | text | Date of birth (From CPR) | NA | NA | date_ymd | NA | NA | NA | NA | NA | NA | NA | NA | NA | @CALCTEXT(if([cpr]!="", concat(if(mid([cpr], 7, 1)>=0 and mid([cpr], 7, 1)<=3,19, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=36 and mid([cpr], 7, 1)>=4 and mid([cpr], 7, 1)<=4,20, if(mid([cpr], 5, 2)>=37 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=4 and mid([cpr], 7, 1)<=4,19, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=57 and mid([cpr], 7, 1)>=5 and mid([cpr], 7, 1)<=5,20, if(mid([cpr], 5, 2)>=58 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=5 and mid([cpr], 7, 1)<=5,18, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=57 and mid([cpr], 7, 1)>=6 and mid([cpr], 7, 1)<=6,20, if(mid([cpr], 5, 2)>=58 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=6 and mid([cpr], 7, 1)<=6,18, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=57 and mid([cpr], 7, 1)>=7 and mid([cpr], 7, 1)<=7,20, if(mid([cpr], 5, 2)>=58 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=7 and mid([cpr], 7, 1)<=7,18, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=57 and mid([cpr], 7, 1)>=8 and mid([cpr], 7, 1)<=8,20, if(mid([cpr], 5, 2)>=58 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=8 and mid([cpr], 7, 1)<=8,18, if(mid([cpr], 5, 2)>=0 and mid([cpr], 5, 2)<=36 and mid([cpr], 7, 1)>=9 and mid([cpr], 7, 1)<=9,20, if(mid([cpr], 5, 2)>=37 and mid([cpr], 5, 2)<=99 and mid([cpr], 7, 1)>=9 and mid([cpr], 7, 1)<=9,19,17))))))))))))), mid([cpr], 5, 2), "-",mid([cpr],3, 2), "-", left([cpr], 2) ), "")) |
| age | baseline_data_start | NA | calc | Age Note: Apparently, the build in datediff() function does not handle counting whole years. This results in wrongly counting age higher around the date of birth. | if([cpr]!="" and [inclusion]!="", datediff([dob], [inclusion], 'y'), "") | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| age_integer | baseline_data_start | NA | calc | Age integer Note: as opposed to the build in datediff() this handles counting years as integers very well. Calculate decimal years in statistical programming software. In R you can use with(ds, stRoke::age_calc(dob, inclusion)). | if([cpr]!="", left([inclusion], 4)-left([dob], 4) - if(mid([dob], 6, 2) < mid([inclusion], 6, 2) or (mid([dob], 6, 2) = mid([inclusion], 6, 2) and mid([dob], 9, 2) <= mid([inclusion], 9, 2)), 0, 1),"") | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sex | baseline_data_start | NA | text | Legal sex | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | @CALCTEXT(if([cpr]!="",if((right([cpr],1)=1 or right([cpr],1)=3 or right([cpr],1)=5 or right([cpr],1)=7 or right([cpr],1)=9),"male","female"),"")) |
| cohabitation | baseline_data_start | History and social | radio | Cohabitation | 1, Yes | 2, No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| hypertension | baseline_data_start | NA | radio | Hypertension | 1, Yes | 2, No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| diabetes | baseline_data_start | NA | radio | Diabetes | 1, Yes | 2, No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| region | baseline_data_start | Area | dropdown | Region | 1, North | 2, East | 3, South | 4, West | NA | autocomplete | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| mrs_assessed | mrs | NA | radio | Assesed | 1, Yes | 2, No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| mrs_date | mrs | NA | text | Assessment date | NA | NA | date_dmy | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| mrs_score | mrs | NA | radio | mRS score | 0, 0 | 1, 1 | 2, 2 | 3, 3 | 4, 4 | 5, 5 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| event_date | new_event | NA | text | Date of event | NA | NA | date_dmy | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| event_type | new_event | NA | radio | Neurovascular event | 1, TIA | 2, AIS | 3, ICH | 4, SAH | 99, Unknown | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
list <-
REDCap_split(
records = redcapcast_data,
metadata = redcapcast_meta,
forms = "repeating"
) |>
sanitize_split()
str(list)
#> List of 2
#> $ : tibble [10 × 17] (S3: tbl_df/tbl/data.frame)
#> ..$ record_id : num [1:10] 1 2 2 3 3 3 4 4 5 6
#> ..$ redcap_event_name : chr [1:10] "inclusion" "inclusion" "follow1" "inclusion" ...
#> ..$ cpr : chr [1:10] "1203401OB4" "0102342303" NA "2301569823" ...
#> ..$ inclusion : Date[1:10], format: "2023-03-13" "2023-03-01" ...
#> ..$ dob : Date[1:10], format: "1940-03-12" "1934-02-01" ...
#> ..$ age : num [1:10] 83 89.1 NA 66.1 NA ...
#> ..$ age_integer : num [1:10] 83 89 NA 66 NA NA 117 NA 126 91
#> ..$ sex : chr [1:10] "female" "male" NA "male" ...
#> ..$ cohabitation : chr [1:10] "Yes" "Yes" NA "No" ...
#> ..$ hypertension : chr [1:10] "No" "No" NA "Yes" ...
#> ..$ diabetes : chr [1:10] "Yes" "No" NA "Yes" ...
#> ..$ region : chr [1:10] "East" "South" NA "North" ...
#> ..$ baseline_data_start_complete: chr [1:10] "Incomplete" "Incomplete" NA "Incomplete" ...
#> ..$ mrs_assessed : chr [1:10] "Yes" "Yes" "Yes" NA ...
#> ..$ mrs_date : Date[1:10], format: "2023-03-13" "2023-03-07" ...
#> ..$ mrs_score : num [1:10] 1 1 3 NA 2 1 NA NA NA NA
#> ..$ mrs_complete : chr [1:10] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...
#> $ new_event: tibble [9 × 6] (S3: tbl_df/tbl/data.frame)
#> ..$ record_id : num [1:9] 2 3 3 3 3 3 4 4 4
#> ..$ redcap_event_name : chr [1:9] "follow1" "follow1" "follow1" "follow2" ...
#> ..$ redcap_repeat_instrument: chr [1:9] "new_event" "new_event" "new_event" "new_event" ...
#> ..$ redcap_repeat_instance : num [1:9] 1 1 2 1 2 3 1 2 3
#> ..$ event_type : chr [1:9] "TIA" "AIS" "ICH" "ICH" ...
#> ..$ new_event_complete : chr [1:9] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...list <-
REDCap_split(
records = redcapcast_data,
metadata = redcapcast_meta,
forms = "all"
) |>
sanitize_split()
str(list)
#> List of 3
#> $ baseline_data_start: tibble [6 × 13] (S3: tbl_df/tbl/data.frame)
#> ..$ record_id : num [1:6] 1 2 3 4 5 6
#> ..$ redcap_event_name : chr [1:6] "inclusion" "inclusion" "inclusion" "inclusion" ...
#> ..$ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...
#> ..$ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...
#> ..$ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ...
#> ..$ age : num [1:6] 83 89.1 66.1 117.9 126.2 ...
#> ..$ age_integer : num [1:6] 83 89 66 117 126 91
#> ..$ sex : chr [1:6] "female" "male" "male" "female" ...
#> ..$ cohabitation : chr [1:6] "Yes" "Yes" "No" NA ...
#> ..$ hypertension : chr [1:6] "No" "No" "Yes" NA ...
#> ..$ diabetes : chr [1:6] "Yes" "No" "Yes" NA ...
#> ..$ region : chr [1:6] "East" "South" "North" NA ...
#> ..$ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...
#> $ mrs : tibble [5 × 6] (S3: tbl_df/tbl/data.frame)
#> ..$ record_id : num [1:5] 1 2 2 3 3
#> ..$ redcap_event_name: chr [1:5] "inclusion" "inclusion" "follow1" "follow1" ...
#> ..$ mrs_assessed : chr [1:5] "Yes" "Yes" "Yes" "Yes" ...
#> ..$ mrs_date : Date[1:5], format: "2023-03-13" "2023-03-07" ...
#> ..$ mrs_score : num [1:5] 1 1 3 2 1
#> ..$ mrs_complete : chr [1:5] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...
#> $ new_event : tibble [9 × 6] (S3: tbl_df/tbl/data.frame)
#> ..$ record_id : num [1:9] 2 3 3 3 3 3 4 4 4
#> ..$ redcap_event_name : chr [1:9] "follow1" "follow1" "follow1" "follow2" ...
#> ..$ redcap_repeat_instrument: chr [1:9] "new_event" "new_event" "new_event" "new_event" ...
#> ..$ redcap_repeat_instance : num [1:9] 1 1 2 1 2 3 1 2 3
#> ..$ event_type : chr [1:9] "TIA" "AIS" "ICH" "ICH" ...
#> ..$ new_event_complete : chr [1:9] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...This function wraps all the above demonstrated function to get the
dataset, the metadata, apply the REDCap_splitfunction and
then a bit of cleaning. It just cuts outs all the steps for an easier
approach.
The function works very similar to the
REDCapR::redcap_read() in allowing to specify fields,
events and forms for export instead of exporting the whole database and
filtering afterwards. I believe this is a better and safer, focused
approach.
redcap_wider(list) |> str()
#> Joining with `by = join_by(record_id)`
#> Joining with `by = join_by(record_id)`
#> 'data.frame': 6 obs. of 36 variables:
#> $ record_id : num 1 2 3 4 5 6
#> $ cpr : chr "1203401OB4" "0102342303" "2301569823" "0204051342" ...
#> $ inclusion : Date, format: "2023-03-13" "2023-03-01" ...
#> $ dob : Date, format: "1940-03-12" "1934-02-01" ...
#> $ age : num 83 89.1 66.1 117.9 126.2 ...
#> $ age_integer : num 83 89 66 117 126 91
#> $ sex : chr "female" "male" "male" "female" ...
#> $ cohabitation : chr "Yes" "Yes" "No" NA ...
#> $ hypertension : chr "No" "No" "Yes" NA ...
#> $ diabetes : chr "Yes" "No" "Yes" NA ...
#> $ region : chr "East" "South" "North" NA ...
#> $ baseline_data_start_complete: chr "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...
#> $ mrs_assessed_inclusion : chr "Yes" "Yes" NA NA ...
#> $ mrs_assessed_follow1 : chr NA "Yes" "Yes" NA ...
#> $ mrs_assessed_follow2 : chr NA NA "Yes" NA ...
#> $ mrs_date_inclusion : Date, format: "2023-03-13" "2023-03-07" ...
#> $ mrs_date_follow1 : Date, format: NA "2023-03-09" ...
#> $ mrs_date_follow2 : Date, format: NA NA ...
#> $ mrs_score_inclusion : num 1 1 NA NA NA NA
#> $ mrs_score_follow1 : num NA 3 2 NA NA NA
#> $ mrs_score_follow2 : num NA NA 1 NA NA NA
#> $ mrs_complete_inclusion : chr "Incomplete" "Incomplete" NA NA ...
#> $ mrs_complete_follow1 : chr NA "Incomplete" "Incomplete" NA ...
#> $ mrs_complete_follow2 : chr NA NA "Incomplete" NA ...
#> $ event_type_1_follow1 : chr NA "TIA" "AIS" NA ...
#> $ event_type_1_follow2 : chr NA NA "ICH" "AIS" ...
#> $ new_event_complete_1_follow1: chr NA "Incomplete" "Incomplete" NA ...
#> $ new_event_complete_1_follow2: chr NA NA "Incomplete" "Complete" ...
#> $ event_type_2_follow1 : chr NA NA "ICH" NA ...
#> $ event_type_2_follow2 : chr NA NA "TIA" "ICH" ...
#> $ event_type_3_follow1 : chr NA NA NA NA ...
#> $ event_type_3_follow2 : chr NA NA "AIS" "Unknown" ...
#> $ new_event_complete_2_follow1: chr NA NA "Incomplete" NA ...
#> $ new_event_complete_2_follow2: chr NA NA "Incomplete" "Incomplete" ...
#> $ new_event_complete_3_follow1: chr NA NA NA NA ...
#> $ new_event_complete_3_follow2: chr NA NA "Incomplete" "Complete" ...These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.