R/get.critical.results.E.R

In agaye/ESPRESSO.E: Power Analysis and Sample Size Calculation for a model with a main effect environmental exposure

#' 
#' @title Provides a summary of the main results
#' @description Gets the number of cases and controls or subjects and the 
#' empirical and theoretical power under each model and prints a summary on 
#' the screen.
#' @param scenario scenario number.
#' @param pheno.model outcome type; binary=0 and quantitative=1.
#' @param env.model model of the exposure: binary=0, quantitative-normal=1, quantitative-uniform=2.
#' @param sample.sizes.required number of cases and controls or number of subjects 
#' required to achieve the desired power.
#' @param empirical.power estimated empirical power.
#' @param modelled.power calculated theoretical power.
#' @param mean.beta mean beta value of each of the determinants.
#' @return a list that contains the sample size required to achieve the desired power and the
#' estimated modelled and theoretical power.
#' @keywords internal
#' @author Gaye A.
#'
get.critical.results.E <- function (scenario = 1, pheno.model = 0, env.model = 0, sample.sizes.required = NULL, 
    empirical.power = 0.8, modelled.power = 0.8, mean.beta = NULL) 
{
    if (is.null(sample.sizes.required)) {
        cat("\n\n ALERT!\n")
        cat(" The sample size required may have not been computed.\n")
        cat(" Check the output of the function 'samplsize.calc'.\n")
        stop(" End of process!\n\n", call. = FALSE)
    }
    if (is.null(mean.beta)) {
        cat("\n\n ALERT!\n")
        cat(" The argument 'mean.beta' is empty.\n")
        cat(" This argument should average beta value'.\n")
        stop(" End of process!\n\n", call. = FALSE)
    }
    if (env.model == 0) {
        e.model <- "binary"
    }
    else {
        if (env.model == 1) {
            e.model <- "normal distribution"
        }
        else {
            e.model <- "uniform distribution"
        }
    }
    if (pheno.model == 0) {
        numcases <- sample.sizes.required[[1]]
        numcontrols <- sample.sizes.required[[2]]
    }
    else {
        numsubjects <- sample.sizes.required[[1]]
    }
    if (pheno.model == 0) {
        estimated.OR <- exp(mean.beta)
        estimated.effect <- "NA"
        cat("\n---- SUMMARY OF SCENARIO", scenario, "----\n")
        cat("\nModels\n")
        cat("------\n")
        cat("  Outcome: binary \n")
        cat("  Environmental determinant: ", e.model)
        cat("\n\nNumber of cases required\n")
        cat("------------------------\n")
        cat(" ", numcases)
        cat("\n\nNumber of controls required\n")
        cat("---------------------------\n")
        cat(" ", numcontrols)
        cat("\n\nEmpirical power\n")
        cat("---------------\n")
        cat(" ", empirical.power)
        cat("\n\nModel power\n")
        cat("-----------\n")
        cat(" ", round(modelled.power, 2))
        cat("\n\nEstimated OR\n")
        cat("-----------\n")
        cat(" ", round(estimated.OR, 2))
        cat("\n\n---- END OF SUMMARY ----\n")
        crit.res <- c(e.model, numcases, numcontrols, round(empirical.power, 
            2), round(modelled.power, 2), round(estimated.OR, 2), estimated.effect)
        return(list(environment.model = crit.res[1], number.of.cases.required = crit.res[2], 
            number.of.controls.required = crit.res[3], empirical.power = crit.res[4], 
            modelled.power = crit.res[5], estimated.OR = crit.res[6], estimated.effect = crit.res[7]))
    }
    else {
        estimated.OR <- "NA"
        estimated.effect <- mean.beta
        cat("\n---- SUMMARY OF SCENARIO", scenario, "----\n")
        cat("\nModels\n")
        cat("------\n")
        cat(" Outcome: quantitative \n")
        cat(" Environmental determinant: ", e.model)
        cat("\n\nNumber of subjects required\n")
        cat("------------------------\n")
        cat(" ", numsubjects)
        cat("\n\nEmpirical power\n")
        cat("---------------\n")
        cat(" ", empirical.power)
        cat("\n\nModel power\n")
        cat("-----------\n")
        cat(" ", round(modelled.power, 2))
        cat("\n\nEstimated effect\n")
        cat("-----------\n")
        cat(" ", estimated.effect)
        cat("\n\n---- END OF SUMMARY ----\n")
        crit.res <- c(e.model, numsubjects, round(empirical.power, 
            2), round(modelled.power, 2), estimated.OR, round(estimated.effect,2))
        return(list(environment.model = crit.res[1], number.of.subjects.required = crit.res[2], 
            empirical.power = crit.res[3], modelled.power = crit.res[4], 
            estimated.OR = crit.res[5], estimated.effect = crit.res[6]))
    }
}