R/admort.R

In DHS.rates: Calculates Demographic Indicators

#' Calculates adult and maternal mortality indicators based on survey data.
#'
#' \code{admort} returns adult mortality indicators such as the Age Specific Mortality Rate (ASMR),
#' Age Adjusted Mortality Rate (AAMR), Age Specific Maternal Mortality Rate (ASMMR),
#' Age Adjusted Maternal Mortality Rate (AAMMR), Age Specific Pregnancy Related Mortality Rate (ASPRMR),
#' Age Adjusted Pregnancy Related Mortality Rate (AAPRMR), Maternal Mortality Ratio (MMR) and Pregnancy Related Mortality Ratio (PRMR).
#' \code{admort} returns the Standard Error (SE), exposure (N), weighted exposure (WN),
#' Design Effect (DEFT), Relative Standard Error (RSE), and Confidence Interval (CI).
#'
#' @author Mahmoud Elkasabi.
#'
#' @param Data.Name The DHS women (IR) dataset or data from other survey with the same format.
#'
#' @param Indicator Type of indicator to be calculated ("asmr", "aamr", "asmmr", "aammr", "asprmr", "aaprmr", "mmr", "prmr", "aagfr").
#'
#' @param JK "Yes" to estimate Jackknife SE for AAMR, AAMMR, AAPRMR, MMR and PRMR.
#'
#' @param CL Confidence level to calculate the Confidence Coefficient Z of the Confidence Intervals; default if 95.
#'
#' @param Strata Stratification variable if other than "v022".
#'
#' @param Cluster Sample cluster variable if other than "v021".
#'
#' @param Weight Survey weight variable if other than "v005".
#'
#' @param Date_of_interview Date of Interview (CMC) variable if other than "v008".
#'
#' @param PeriodEnd The end of the exposure period in YYYY-MM format; default is the date of the survey.
#'
#' @param Period The study period for fertility in months; default is 36 months (3 years).
#'
#' @return Mortality indicators (ASMR, AAMR, ASMMR, AAMMR, ASPRMR, AAPRMR, MMR, PRMR and AAGFR), and precision indicators (SE, DEFT, RSE, and CI).
#'
#' @importFrom dplyr %>% summarise
#'
#' @export
admort <- function(Data.Name, Indicator, JK = NULL, CL = NULL, Strata = NULL, Cluster = NULL, Weight = NULL,
                 Date_of_interview = NULL, PeriodEnd = NULL, Period = NULL){

  if (!Indicator %in% c("asmr", "aamr", "asmmr", "aammr", "asprmr", "aaprmr", "prmr", "mmr", "aagfr"))
    stop("Please specify a valid adult mortality indicator, such as asmr, aamr, asmmr, aammr, asprmr, mmr, prmr or aagfr")

  if (!is.null(Strata)){
    Data.Name$strata = Data.Name[[Strata]]
    Data.Name$v022 = NULL
    names(Data.Name)[names(Data.Name) == c("strata")] <- c("v022")
  }

  if (!is.null(Cluster)){
    Data.Name$cluster = Data.Name[[Cluster]]
    Data.Name$v021 = NULL
    names(Data.Name)[names(Data.Name) == c("cluster")] <- c("v021")
  }

  if (!is.null(Weight)){
    Data.Name$weight = Data.Name[[Weight]]
    Data.Name$v005 = NULL
    names(Data.Name)[names(Data.Name) == c("weight")] <- c("v005")
  }

    if (!is.null(Date_of_interview)){
    Data.Name$DOI = Data.Name[[Date_of_interview]]
    Data.Name$v008 = NULL
    names(Data.Name)[names(Data.Name) == c("DOI")] <- c("v008")
  }

  if (!("v021" %in% names(Data.Name))) stop({message("Error: v021/Primary-sampling-unit is missing")})
  if (!("v005" %in% names(Data.Name))) stop({message("Error: v005/Sample-weight is missing")})
  if (!("v008" %in% names(Data.Name))) stop({message("Error: v008/Date-of-Interview is missing")})
  if (!("v022" %in% names(Data.Name))) stop({message("Error: v022/Sample-strata is missing")})

    else{

    if (("TRUE" %in% (!(paste("mm1_0", 1:9, sep = "") %in% names(Data.Name)))) |
        ("TRUE" %in% (!(paste("mm1_", 10:20, sep = "") %in% names(Data.Name)))))
    {warning("Siblings variables mm1_01:mm1_20 are not complete; the missing variables were created")}

      if (("TRUE" %in% (!(paste("mm2_0", 1:9, sep = "") %in% names(Data.Name)))) |
          ("TRUE" %in% (!(paste("mm2_", 10:20, sep = "") %in% names(Data.Name)))))
      {warning("Siblings variables mm2_01:mm2_20 are not complete; the missing variables were created")}

      if (("TRUE" %in% (!(paste("mm4_0", 1:9, sep = "") %in% names(Data.Name)))) |
          ("TRUE" %in% (!(paste("mm4_", 10:20, sep = "") %in% names(Data.Name)))))
      {warning("Siblings variables mm4_01:mm4_20 are not complete; the missing variables were created")}

      if (("TRUE" %in% (!(paste("mm8_0", 1:9, sep = "") %in% names(Data.Name)))) |
          ("TRUE" %in% (!(paste("mm8_", 10:20, sep = "") %in% names(Data.Name)))))
      {warning("Siblings variables mm8_01:mm8_20 are not complete; the missing variables were created")}

      if (("TRUE" %in% (!(paste("mm9_0", 1:9, sep = "") %in% names(Data.Name)))) |
          ("TRUE" %in% (!(paste("mm9_", 10:20, sep = "") %in% names(Data.Name)))))
      {warning("Siblings variables mm9_01:mm9_20 are not complete; the missing variables were created")}

      if (("TRUE" %in% (!(paste("mm12_0", 1:9, sep = "") %in% names(Data.Name)))) |
          ("TRUE" %in% (!(paste("mm12_", 10:20, sep = "") %in% names(Data.Name)))))
      {warning("Siblings variables mm12_01:mm12_20 are not complete; the missing variables were created")}

  }

  for (i in 1:9){
    if ("TRUE" %in% (!(paste("mm1_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm1_0", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm2_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm2_0", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm4_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm4_0", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm8_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm8_0", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm9_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm9_0", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm12_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm12_0", i, sep = "")]] <- NA

    # Flag data with no data for MMR
    if ("TRUE" %in% (!(paste("mm16_0", i, sep = "") %in% names(Data.Name))))
      Data.Name$PRMMRT <- NA
    if ("TRUE" %in% (!(paste("mm16_0", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm16_0", i, sep = "")]] <- NA
  }

  for (i in 10:20){
    if ("TRUE" %in% (!(paste("mm1_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm1_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm2_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm2_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm4_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm4_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm8_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm8_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm9_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm9_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm12_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm12_", i, sep = "")]] <- NA

    if ("TRUE" %in% (!(paste("mm16_", i, sep = "") %in% names(Data.Name))))
      Data.Name[[paste("mm16_", i, sep = "")]] <- NA
  }

  Data.Name <- as.data.frame(Data.Name)

  if (Indicator == "asmr"){
    ASMR(Data.Name, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "aamr"){
    AAMR(Data.Name, JK, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "asmmr"){
    ASMMR(Data.Name, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "aammr"){
    AAMMR(Data.Name, JK, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "asprmr"){
    ASPRMR(Data.Name, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "aaprmr"){
    AAPRMR(Data.Name, JK, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "prmr"){
    PRMR(Data.Name, JK, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "mmr"){
    MMR(Data.Name, JK, CL, PeriodEnd, Period)[[1]]

  }
  else if (Indicator == "aagfr"){
    AAGFR(Data.Name, PeriodEnd, Period)[[1]]

  }
}