Tag: data preparation

Note: The R and CSV files exported from REDCap must be located in the same directory.

If the REDCap project is longitudinal (contains more than one event) then a third element should be specified with the correspondence of each event with each form of the project. This csv file can be downloaded in the REDCap of the project following these steps: Project Setup < Designate Instruments for My Events < Download instrument-event mappings (CSV).

dataset <- redcap_data(data_path="C:/Users/username/example.r",
                       dic_path="C:/Users/username/example_dictionary.csv",
                       event_path="C:/Users/username/events.csv")

Note: if the project is longitudinal and the event-form file is not provided using the event_path argument, some steps of the processment can not be performed.

Another way to read data exported from a REDCap project is using an API connection. To do this, we can use the arguments uri and token which respectively refer to the uniform resource identifier of the REDCap project and the user-specific string that serves as the password:

dataset_api <- redcap_data(uri ="https://redcap.idibell.cat/api/",
                           token = "55E5C3D1E83213ADA2182A4BFDEA")

In this case, there is no need to specify the event-form file since the function will download it automatically using the API connection, if the project is longitudinal.

Remember that the token would give anyone access to all the project’s information. You should be careful about who you give this information to.

This function returns a list with 3 elements (imported data, dictionary and event-form mapping) which can then be used for further analysis or visualization.

The main function involved in the processing of the data is rd_transform. This function is used to process the REDCap data read into R using the redcap_data, as described above. Using the arguments of the function we can perform different type of transformations of our data.

As previously stated, we will use the built-in dataset covican as an example.

The only necessary elements that must be provided are the dataset to be transformed and the corresponding dictionary. If the project is longitudinal, as in the case of covican, also the event-form dataset should be specified. These elements can be specified directly using the output of the redcap_data function or separately in different arguments.

#Option A: list object 
covican_transformed <- rd_transform(covican)

#Option B: separately with different arguments
covican_transformed <- rd_transform(data = covican$data, 
                                    dic = covican$dictionary, 
                                    event_form = covican$event_form)

#Print the results of the transformation
covican_transformed$results

1. Recalculating calculated fields and saving them as '[field_name]_recalc'

| Total calculated fields | Non-transcribed fields | Recalculated different fields |
|:-----------------:|:----------------:|:-----------------------:|
|         2         |      0 (0%)      |         1 (50%)         |


|     field_name      | Transcribed? | Is equal? |
|:-------------------:|:------------:|:---------:|
|         age         |     Yes      |   FALSE   |
| screening_fail_crit |     Yes      |   TRUE    |

2. Transforming checkboxes: changing their values to No/Yes and changing their names to the names of its options. For checkboxes that have a branching logic, when the logic is missing their values will be set to missing

Table: Checkbox variables advisable to be reviewed

| Variables without any branching logic |
|:-------------------------------------:|
|        type_underlying_disease        |

3. Replacing original variables for their factor version

4. Deleting variables that contain some patterns

This function will return a list with the transformed dataset, dictionary and the output of the results of the transformation.

As we can see, there are 4 steps in the transformation and they are briefly explained in the output of the function. This four steps are:

1. 1. 1. 1. Recalculation of REDCap calculated fields

         2. Checkbox transformation

         3. Replacement of the original variable by its factor version

         4. Elimination of variables containing some pattern

In addition, we can change the final structure of the transformed dataset by specifying in the final_format argument whether we want our data to be split by event or by form.

For more examples and information on extra arguments, see the vignette.

rd_query

The rd_query function allows users to generate queries by using a specific expression. It can be used to identify missing values, values that fall outside the lower and upper limit of a variable and other types of inconsistencies.

example <- rd_query(covican_transformed,
                    variables = c("copd", "age"),
                    expression = c("%in%NA", "%in%NA"),
                    event = "baseline_visit_arm_1")

# Printing results
example$results

example <- rd_query(variables="age",
                    expression=">70",
                    event="baseline_visit_arm_1",
                    dic=covican_transformed$dictionary,
                    data=covican_transformed$data)

# Printing results
example$results

check_queries

Once the process of identifying queries is complete, the typical approach would be to adress them by modifying the original dataset in REDCap and re-run the query identification process generating a new query dataset.

The check_queries function compares the previous query dataset with the new one by using the arguments old and new, respectively. The output remains a list with 2 items, but the data frame containing the information for each query will now have an additional column (“Modification”) indicating which queries are new, which have been modified, which have been corrected, and which remain pending. Besides, the summary will show the number of queries in each one of these categories:

check <- check_queries(old = example$queries, 
                       new = new_example$queries)

# Print results
check$results

There are 7 pending queries, 3 solved queries, 1 miscorrected query, and 1 new query between the previous and the new query dataset.

Note: The “Miscorrected” category includes queries that belong to the same combination of record identifier and variable in both the old and new reports, but with a different reason. For instance, if a variable had a missing value in the old report, but in the new report shows a value outside the established range, it would be classified as “Miscorrected”.

Query control output: