openVA (version 1.2.0)

prepCalibration: Convert the assigned causes to the format expected by vacalibration::vacalibration().

Description

This function prepares the output from codeVA (using the InSilicoVA or InterVA5 algorithms) and/or EAVA for the vacalibration function. The output is a named list, with each element consisting of a data frame with columns for the death ID ("ID") and the assigned CoD ("cause"). The name of each element is the algorithm used to assign the CoD -- "insilicova", "interva", or "eava". If the

Usage

prepCalibration(fit, ...)

Value

a list with each element being a Data Frames that contains variables "ID" and "cause", and the element's name (in the list) is the algorithm name used to assign causes of death (either "insilicova", "interva", or "eava")

Arguments

fit

a fitted object from codeVA using either InSilicoVA, InterVA5, or output from EAVA::codEAVA. The EAVA algorithm is assumed if the the argument is a Data Frame (with columns "ID" and "cause").

...

more fitted objects from codeVA using either InSilicoVA or InterVA5, or from EAVA::codEAVA.

Examples

if (FALSE) {
data(NeonatesVA5)
fit_insilico <- codeVA(NeonatesVA5)
insilico_prep <- prepCalibration(fit_insilico)
calib_insilico = vacalibration::vacalibration(va_data = insilico_prep,
                                              age_group = "neonate",
                                              country = "Mozambique")
summary(calib_insilico)

fit_interva <- codeVA(NeonatesVA5, model = "InterVA", version = "5", write = FALSE)
interva_prep <- prepCalibration(fit_interva)
calib_interva = vacalibration::vacalibration(va_data = interva_prep,
                                             age_group = "neonate",
                                             country = "Mozambique")
summary(calib_interva)

two_fits <- prepCalibration(fit_insilico, fit_interva)
calib_ensemble = vacalibration::vacalibration(va_data = two_fits,
                                              age_group = "neonate",
                                              country = "Mozambique")
summary(calib_ensemble)

}