R/ageRatioTest.R

In ernestguevarra/nipnTK: National Information Platforms for Nutrition Anthropometric Data Toolkit

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#
#' Age ratio test
#'
#' Age ratio test is an age-related test of survey and data quality. In this
#' test, the ratio of the number of children aged from 6 to 29 months to the
#' number of children aged from 30 to 59 months is calculated. This ratio is
#' then compared to an expected ratio (usually set at 0.85). The difference
#' of the observed ratio to the expected ratio is then compared statistically
#' using Chi-squared test.
#'
#' @param x A vector of ages. Should either be in whole months (integer) or in
#'   calculated decimal months (numeric).
#' @param ratio Expected age ratio. Default is 0.85.
#'
#' @returns A lit of class `"ageRatioTest"` with:
#'
#' | **Variable** | **Description** |
#' | :--- | :--- |
#' | *expectedR* | Expected sex ratio |
#' | *expectedP* | Expected proportion aged 6:29 months |
#' | *observedR* | Observed sex ratio |
#' | *observedP* | Observed proportion aged 6:29 months |
#' | *X2* | Chi-squared test statistic |
#' | *df* | Degrees of freedom for Chi-squared test |
#' | *p* | `p-value` for Chi-squared test |
#'
#' @examples
#' # Age-ratio test on survey dataset from Kabul, Afghanistan (`dp.ex02`)
#' # with an age ratio of 0.85
#' svy <- dp.ex02
#' ageRatioTest(svy$age, ratio = 0.85)
#'
#' # The age ratio test applied to data for each sex separately
#' by(svy$age, svy$sex, ageRatioTest, ratio = 0.85)
#'
#' @export
#'
#
################################################################################

ageRatioTest <- function(x, ratio = 0.85) {
  ## If x is numeric ----
  if (is.numeric(x)) x <- floor(x)

  ## If x is not numeric or integer ----
  if (!is.numeric(x) & !is.integer(x))
    stop("Age should be of class integer or numeric. Try again.")

  ## Calculate age ratio ----
  g <- ifelse(x < 30, 1, 2)
  expectedP <- ratio / (ratio + 1)
  observedP <- sum(g == 1, na.rm = TRUE)/ sum(table(g))
  observedR <- observedP / (1 - observedP)
  X2 <- prop.test(sum(g == 1, na.rm = TRUE), sum(table(g)), p = expectedP)
  result <- list(expectedR = ratio,
                 expectedP = expectedP,
                 observedR = observedR,
                 observedP = observedP,
                 X2 = X2$statistic,
                 df = X2$parameter,
                 p = X2$p.value)
  class(result) <- "ageRatioTest"
  return(result)
}


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#
#' [print()] helper function for [ageRatioTest()] function
#'
#' @param x Object resulting from applying [ageRatioTest()] function
#' @param ... Additional [print()] arguments
#'
#' @returns Printed output of [ageRatioTest()] function
#'
#' @examples
#' # Print age-ratio test results for survey dataset from Kabul, Afghanistan
#' svy <- dp.ex02
#' print(ageRatioTest(svy$age, ratio = 0.85))
#'
#' @export
#'
#
################################################################################

print.ageRatioTest <- function(x, ...) {
  cat("\n\t\tAge Ratio Test (children\'s data)\n\n", sep = "")
  cat("                    Expected age ratio = ",
      formatC(x$expectedR, format = "f", width = 6), "\n", sep = "")
  cat("Expected proportion aged 6 - 29 months = ",
      formatC(x$expectedP, format = "f", width = 6), "\n\n", sep = "")
  cat("                    Observed age ratio = ",
      formatC(x$observedR, format = "f", width = 6), "\n", sep = "")
  cat("Observed proportion aged 6 - 29 months = ",
      formatC(x$observedP, format = "f", width = 6), "\n\n", sep = "")
  cat("X-squared = ", formatC(x$X2, format = "f", width = 6),
      ", p = ", formatC(x$p, format = "f", width = 6), "\n\n", sep = "")
}