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Check for (potential) data format conflicts

Source: R/checkConflicts.R
checkConflicts.Rd

This function checks for potential data formatting conflicts that may produce errors or incorrect results when applying the calculateEffectSizes() or runMetaAnalysis() function later on.

Usage

checkConflicts(.data,
               vars.for.id = c("study", "outcome_type",
                               "instrument", "time",
                               "time_weeks",
                               "rating"),
               .condition = "condition",
               .condition.specification = "multi",
               .groups.column.indicator = c("_arm1", "_arm2"))

Arguments

.data

Meta-analysis data stored as a data.frame, to be checked by the function.

vars.for.id

character vector, containing column names of all variables used to construct unique comparison IDs.

.condition

character. The prefix of the two variables in data in which the conditions (e.g. "guided iCBT", "waitlist") of the trial arm comparison are stored.

.condition.specification

character, name of the column containing the specific condition in each trial arm. For multiarm trials, these conditions must be distinct (e.g. "cbt-guided" and "cbt-unguided").

.groups.column.indicator

character. A character vector with two elements, representing the suffix used to differentiate between the first and second arm in a comparison.

Value

The type of data returned by checkConflicts depends on the outcome of the evaluation. When no problems have been detected, the function simply returns the data set provided in .data.

When (potential) formatting formatting issues have been detected, the function throws a message and returns the affected studies/data.frame columns. In particular, results are provided within a list of three objects:

  • allConflicts, a data.frame containing all affected rows, regardless of conflict type.

  • idConflicts, a data.frame containing rows with ID/number of arms conflicts.

  • cgConflicts, a data.frame containing rows with reference arm conflicts (there must be a unique control/reference group for each comparison).

The returned list has class checkConflicts.

See also

checkDataFormat

Author

Mathias Harrer mathias.h.harrer@gmail.com, Paula Kuper paula.r.kuper@gmail.com, Pim Cuijpers p.cuijpers@vu.nl

Examples

if (FALSE) {
data("depressionPsyCtr")

# Example 1: Use defaults and simply run checks
depressionPsyCtr %>%
  checkDataFormat() %>%
  checkConflicts() -> res

# Example 2: Overrule defaults; this will produce a conflict
depressionPsyCtr %>%
  checkDataFormat() %>%
  checkConflicts(vars.for.id = "study") -> res

}