redcapAPI (version 2.7.1)

fieldCastingFunctions: Functions for Casting Fields After Export (Post Processing)

Description

The functions provided here allow for recasting fields after records have been exported. They generally have a similar interface to the casting strategy of exportRecordsTyped, though they may not each offer all the same options.

Usage

recastRecords(data, rcon, fields, cast = list(), suffix = "")
castForImport(
  data,
  rcon,
  fields = NULL,
  na = list(),
  validation = list(),
  cast = list()
)
guessCast(
  data,
  rcon,
  na = isNAorBlank,
  validation,
  cast,
  quiet = FALSE,
  threshold = 0.8
)
guessDate(
  data,
  rcon,
  na = isNAorBlank,
  validation = valRx("^[0-9]{1,4}-(0?[1-9]|1[012])-(0?[1-9]|[12][0-9]|3[01])$"),
  cast = function(x, ...) as.POSIXct(x, format = "%Y-%m-%d"),
  quiet = FALSE,
  threshold = 0.8
)
mChoiceCast(data, rcon, style = "labelled")

Arguments

data

data.frame with the data fields to be recoded.

rcon

recapConnection object.

fields

character/logical/integerish. A vector for identifying which fields to recode. When logical, the length must match the number of columns in data (i.e., recycling not permitted). A message is printed if any of the indicated fields are not a multiple choice field; no action will be taken on such fields. For this function, yes/no and true/false fields are considered multiple choice fields. Fields of class mChoice are quietly skipped.

cast

A named list of user specified class casting functions. Keys must correspond to a truncated REDCap field type, i.e. date_, datetime_, datetime_seconds_, time_mm_ss, time_hh_mm_ss, time, float, number, calc, int, integer, select, radio, dropdown, yesno, truefalse, checkbox, form_complete, sql. The function will be provided the variables (x, field_name, coding). See fieldValidationAndCasting

suffix

character(1). An optional suffix to provide if the recoded variables should be returned as new columns. For example, if recoding a field forklift_brand and suffix = "_labelled", the result will have one column with the coded values (forklift_brand) and one column with the labelled values (forklift_brand_labelled).

na

A named list of user specified functions to determine if the data is NA. This is useful when data is loaded that has coding for NA, e.g. -5 is NA. Keys must correspond to a truncated REDCap field type, i.e. date_, datetime_, datetime_seconds_, time_mm_ss, time_hh_mm_ss, time, float, number, calc, int, integer, select, radio, dropdown, yesno, truefalse, checkbox, form_complete, sql. The function will be provided the variables (x, field_name, coding). The function must return a vector of logicals matching the input. It defaults to isNAorBlank for all entries.

validation

A named list of user specified validation functions. The same named keys are supported as the na argument. The function will be provided the variables (x, field_name, coding). The function must return a vector of logical matching the input length. Helper functions to construct these are valRx and valChoice. Only fields that are not identified as NA will be passed to validation functions.

quiet

Print no messages if triggered, Default=FALSE.

threshold

numeric(1). The threshold of non-NA data to trigger casting.

style

character. One of "labelled" or "coded". Default is "labelled"

Details

recastRecords is a post-processing function motivated initially by the need to switch between codes and labels in multiple choice fields. Field types for which no casting function is specified will be returned with no changes. It will not attempt to validate the content of fields; fields that can not be successfully cast will be quietly returned as missing values.

castForImport is written with defaults that will return data in a format ready to be imported to a project via importRecords. All fields are returned as character vectors. If any values fail to validation check, are report is returned as an attribute named invalid. These are then set to NA, which will be imported as blanks through the API.

guessCast is a helper function to make a guess at casting uncast columns. It will do a type cast if a validation is met above a threshold ratio of non-NA records. It modifies the existing invalid attribute to reflect the cast. guessDate is a special cast of guessCast that has defaults set for casting a date field.

mChoiceCast is a helper function that adds the Hmisc::mChoice multiple choice class. It adds a column for a multiple choice checkbox that is cast to the Hmisc::mChoice class. Requires Hmisc to be loaded.

Examples

if (FALSE) {
# Using guessCast
recs <- exportRecordsTyped(rcon, 
                           cast = raw_cast) |> 
  guessCast(rcon, 
            validation=valRx("^[0-9]{1,4}-(0?[1-9]|1[012])-(0?[1-9]|[12][0-9]|3[01])$"), 
            cast=as.Date,
            threshold=0.6)

# Using mChoiceCast            
recs <- exportRecordsTyped(rcon) |> mChoiceCast(rcon)
}