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Check data format

Source: R/checkDataFormat.R
checkDataFormat.Rd

This function checks if a data.frame object conforms with the Metapsy data standard.

Usage

checkDataFormat(data,
                must.contain = c("study", "condition_arm1",
                                 "condition_arm2", 
                                 "multi_arm1", 
                                 "multi_arm2",
                                 "outcome_type", "instrument",
                                 "time", "time_weeks",
                                 "rating", "mean_arm1", "mean_arm2",
                                 "sd_arm1", "sd_arm2",
                                 "n_arm1", "n_arm2",
                                 "event_arm1", "event_arm2",
                                 "totaln_arm1", "totaln_arm2"),
                variable.class = list("study" = "character", 
                                      "condition_arm1" = "character",
                                      "condition_arm2" = "character", 
                                      "multi_arm1" = "character", 
                                      "multi_arm2" = "character",
                                      "outcome_type" = "character", 
                                      "instrument" = "character",
                                      "time" = "character", 
                                      "time_weeks" = "numeric",
                                      "rating" = "character", 
                                      "mean_arm1" = "numeric", 
                                      "mean_arm2" = "numeric",
                                      "sd_arm1" = "numeric", 
                                      "sd_arm2" = "numeric",
                                      "n_arm1" = "numeric", 
                                      "n_arm2" = "numeric",
                                      "event_arm1" = "numeric", 
                                      "event_arm2" = "numeric",
                                      "totaln_arm1" = "numeric", 
                                      "totaln_arm2" = "numeric"))

Arguments

data

A data.frame containint meta-analysis data.

must.contain

character vector, containing all the variable names the data set should contain. Defaults correspond with the Metapsy data standard.

variable.class

list, defining the required class for some or all variables. If the class differs in data, the function will try to convert the variable to the desired class. Defaults correspond with the Metapsy data standard.

Value

checkDataFormat returns messages that specify if input variables, values and classes of the variables are as defined.

If default settings are used, checkDataFormat() can be used in combination with checkConflicts() to determine if a dataset follows the Metapsy data standard. Datasets that are formatted using this standard can be directly used in the analysis module in metapsyTools; for example the runMetaAnalysis() function.

Details

The function checks if:

  • the data set contains all relevant variables and

  • variables have the desired class (if not, it tries to convert).

See also

expandMultiarmTrials

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: Check with default arguments
checkDataFormat(depressionPsyCtr)

#Example 2: Check for non-default arguments
checkDataFormat(depressionPsyCtr,
                must.contain = c("study", "condition",
                                 "primary", "year"),
                variable.class = list(study = "character",
                                      no.arms = "numeric"))
}