R/cat_localmean_prop.R

In spsurvey: Spatial Sampling Design and Analysis

################################################################################
# Function: cat_localmean_prop (not exported)
# Programmer: Tom Kincaid
# Date: July 23, 2020
# Revised: October 23, 2020 to correct a coding error when calculating
#          proportion estimates for a stratum
# Revised: January 28, 2021 to replace "pcfactor.ind" with "pcfactor_ind"
# Revised: April 27, 2021 to check whether the local mean variance estimator
#          produced negative estimates and to use the SRS variance estimator
#          when that situation occurs
# Revised: June 8, 2021 to eliminate use of the finite population correction
#          factor with the local mean variance estimator
#
#' Local Mean Variance Estimates of Estimated Proportions for Categorical Data
#'
#' This function organizes input and output for calculation of the local mean
#' variance estimator for estimated proportions for categorical data.
#'
#' @param itype Character value that identifies a factor variable in the design
#'   argument containing subpopulation (domain) values.
#'
#' @param lev_itype Character vector that provides levels of the subpopulation
#'   variable.
#'
#' @param nlev_itype Numeric value that provides the number of levels of the
#'   subpopulation variable.
#'
#' @param ivar Character value that identifies a factor variable in the design
#'   argument containing categorical response values.
#'
#' @param lev_ivar Character vector that provides levels of the categorical
#'   response variable.
#'
#' @param nlev_ivar Numeric value that provides the number of levels of the
#'   categorical response variable.
#'
#' @param design Object of class \code{survey.design} that specifies a complex
#'   survey design.
#'
#' @param design_names Character vector that provides names of survey design
#'   variables in the design argument.
#'
#' @param rslt_P Data frame that provides proportion estimates for the
#'   categorical response variable.
#'
#' @param mult Numeric value that provides the Normal distribution confidence
#'   bound multiplier.
#'
#' @param warn_ind Logical value that indicates whether warning messages were
#'   generated.
#'
#' @param warn_df Data frame for storing warning messages.
#'
#' @return A list containing the following objects:
#'   \itemize{
#'     \item{\code{stderr_P}}{data frame containing standard error estimates}
#'     \item{\code{confval_P}}{data frame containing confidence bound estimates}
#'     \item{\code{warn_ind}}{logical variable that indicates whether warning
#'       messages were generated}
#'     \item{\code{warn_df}}{data frame for storing warning messages}
#'   }
#'
#' @author Tom Kincaid \email{Kincaid.Tom@@epa.gov}
#'
#' @keywords survey
#'
#' @noRd
################################################################################

cat_localmean_prop <- function(itype, lev_itype, nlev_itype, ivar, lev_ivar,
                               nlev_ivar, design, design_names, rslt_P,
                               mult, warn_ind, warn_df) {

  # Assign a value to the function name variable

  fname <- "cat_localmean_prop"

  # For variables that exist in the design$variables data frame, assign survey
  # design variables

  dframe <- design$variables
  for (i in names(design_names)) {
    if (is.null(design_names[[i]])) {
      eval(parse(text = paste0(i, " <- NULL")))
    } else {
      eval(parse(text = paste0(i, " <- dframe[, \"", design_names[[i]], "\"]")))
    }
  }

  # Assign values to the categorical response variable vector, catvar

  catvar <- dframe[, ivar]

  # Assign a value to the indicator variable for a two-stage sample

  cluster_ind <- !is.null(clusterID)

  # Assign values to weight variables

  if (cluster_ind) {
    wgt1 <- dframe$wgt1
    wgt2 <- dframe$wgt2
  } else {
    wgt <- dframe$wgt
  }

  # Create the output data frames for standard error estimates and confidence
  # bound estimates

  stderr_P <- data.frame(array(0, c(nlev_itype, nlev_ivar + 1)))
  dimnames(stderr_P) <- list(lev_itype, c(lev_ivar, "Total"))
  temp <- nlev_ivar + 1
  confval_P <- data.frame(array(0, c(nlev_itype * temp, 2)))
  confval_P[seq(temp, by = temp, length = nlev_itype), ] <- c(1.0, 1.0)
  dimnames(confval_P) <- list(
    paste(rep(lev_itype, rep(temp, nlev_itype)),
      rep(c(lev_ivar, "Total"), nlev_itype),
      sep = ":"
    ),
    c("LCB", "UCB")
  )

  # Loop through all subpopulations

  for (isubpop in 1:nlev_itype) {
    tst <- !is.na(dframe[, ivar]) &
      (dframe[, itype] %in% lev_itype[isubpop])

    # Assign values to the vector of category proportion estimates, prop

    prop <- unlist(rslt_P[isubpop, 1:nlev_ivar])
    prop_names <- lev_ivar

    # Assign values to the warn_vec vector

    warn_vec <- c(itype, lev_itype[isubpop], ivar)

    # Assign a value to the indicator variable for a stratified sample

    stratum_ind <- !is.null(stratumID)

    # For a stratified design, determine whether the subpopulation contains a
    # single stratum

    if (stratum_ind) {
      stratum <- factor(stratumID[tst])
      stratum_levels <- levels(stratum)
      nstrata <- length(stratum_levels)
      if (nstrata == 1) {
        stratum_ind <- FALSE
      }
    }

    # Branch for a stratified sample

    if (stratum_ind) {

      # Calculate values required for weighting strata

      if (cluster_ind) {
        popsize_hat <- tapply(wgt1[tst] * wgt2[tst], stratum, sum)
        sum_popsize_hat <- sum(wgt1[tst] * wgt2[tst])
      } else {
        popsize_hat <- tapply(wgt[tst], stratum, sum)
        sum_popsize_hat <- sum(wgt[tst])
      }

      # Begin the subsection for individual strata

      for (i in 1:nstrata) {

        # Calculate proportion estimates for the stratum

        stratum_i <- tst & stratumID == stratum_levels[i]
        prop_st <- t(as.data.frame(svymean(make.formula(ivar),
          design = subset(design, stratum_i), na.rm = TRUE
        ))[1])

        # Calculate variance estimates

        if (cluster_ind) {
          temp <- catvar_prop(
            factor(catvar[stratum_i]), wgt2[stratum_i],
            xcoord[stratum_i], ycoord[stratum_i], prop_st, prop_names,
            stratum_ind, stratum_levels[i], cluster_ind, clusterID[stratum_i],
            wgt1[stratum_i], xcoord1[stratum_i], ycoord1[stratum_i],
            warn_ind, warn_df, warn_vec
          )
        } else {
          temp <- catvar_prop(factor(catvar[stratum_i]), wgt[stratum_i],
            xcoord[stratum_i], ycoord[stratum_i], prop_st, prop_names,
            stratum_ind, stratum_levels[i], cluster_ind,
            warn_ind = warn_ind, warn_df = warn_df, warn_vec = warn_vec
          )
        }
        warn_ind <- temp$warn_ind
        warn_df <- temp$warn_df
        if (any(temp$varest < 0)) {
          temp$vartype <- "SRS"
          warn_ind <- TRUE
          act <- "The simple random sampling variance estimator for an infinite population was used.\n"
          warn <- paste0("The local mean variance estimator produced one or more  negative variance estimates in \nstratum \"", stratum_levels[i], "\", the simple random sampling variance estimator for an infinite \npopulation was used to calculate variance of the category proportion estimates.\n")
          warn_df <-
            rbind(
              warn_df,
              data.frame(
                func = I(fname), subpoptype = warn_vec[1], subpop = warn_vec[2],
                indicator = warn_vec[3], stratum = I(stratum_levels[i]),
                warning = I(warn), action = I(act)
              )
            )
        }
        if (temp$vartype == "SRS") {
          rslt_svy <- svymean(make.formula(ivar),
            design = subset(design, stratum_i), na.rm = TRUE
          )
          varest <- SE(rslt_svy)^2
          names(varest) <- prop_names
        } else {
          varest <- temp$varest
        }

        # Add estimates to the stderr_P data frame

        ind <- prop_names %in% names(varest)
        indx <- (1:nlev_ivar)[ind]
        stderr_P[isubpop, indx] <- stderr_P[isubpop, indx] +
          ((popsize_hat[i] / sum_popsize_hat)^2) * varest

        # End the subsection for individual strata
      }

      # Begin the subsection for all strata combined

      # Add estimates to the data frames for results

      names_sdest <- names(stderr_P)[stderr_P[isubpop, ] > 0]
      ind <- prop_names %in% names_sdest
      indx <- (1:nlev_ivar)[ind]
      stderr_P[isubpop, indx] <- sqrt(stderr_P[isubpop, indx])
      lbound <- unlist(pmax(prop[ind] - mult * stderr_P[isubpop, indx], 0))
      ubound <- unlist(pmin(prop[ind] + mult * stderr_P[isubpop, indx], 1))
      temp <- paste(rep(lev_itype[isubpop], length(names_sdest)), names_sdest,
        sep = ":"
      )
      ind <- rownames(confval_P) %in% temp
      confval_P[ind, ] <- cbind(lbound, ubound)

      # End the subsection for all strata combined

      # Branch for an unstratified sample
    } else {

      # Calculate the standard error estimates

      if (cluster_ind) {
        temp <- catvar_prop(
          factor(catvar[tst]), wgt2[tst], xcoord[tst],
          ycoord[tst], prop, prop_names, stratum_ind, NULL, cluster_ind,
          clusterID[tst], wgt1[tst], xcoord1[tst], ycoord1[tst], warn_ind,
          warn_df, warn_vec
        )
      } else {
        temp <- catvar_prop(factor(catvar[tst]), wgt[tst], xcoord[tst],
          ycoord[tst], prop, prop_names, stratum_ind, NULL, cluster_ind,
          warn_ind = warn_ind, warn_df = warn_df, warn_vec = warn_vec
        )
      }
      warn_ind <- temp$warn_ind
      warn_df <- temp$warn_df
      if (any(temp$varest < 0)) {
        temp$vartype <- "SRS"
        warn_ind <- TRUE
        act <- "The simple random sampling variance estimator for an infinite population was used.\n"
        warn <- paste0("The local mean variance estimator produced one or more  negative variance estimates, the \nsimple random sampling variance estimator for an infinite population was used to \ncalculate variance of the category proportion estimates.\n")
        warn_df <-
          rbind(
            warn_df,
            data.frame(
              func = I(fname), subpoptype = warn_vec[1], subpop = warn_vec[2],
              indicator = warn_vec[3], stratum = NA, warning = I(warn),
              action = I(act)
            )
          )
      }
      if (temp$vartype == "SRS") {
        rslt_svy <- svymean(make.formula(ivar),
          design = subset(design, tst),
          na.rm = TRUE
        )
        sdest <- SE(rslt_svy)
        names(sdest) <- prop_names
      } else {
        sdest <- sqrt(temp$varest)
      }

      # Calculate confidence bounds

      names_sdest <- names(sdest)
      ind <- prop_names %in% names_sdest
      lbound <- pmax(prop[ind] - mult * sdest, 0)
      ubound <- pmin(prop[ind] + mult * sdest, 1)

      # Add estimates to the data frames for results

      indx <- (1:nlev_ivar)[ind]
      stderr_P[isubpop, indx] <- sdest
      temp <- paste(rep(lev_itype[isubpop], length(names_sdest)), names_sdest,
        sep = ":"
      )
      ind <- rownames(confval_P) %in% temp
      confval_P[ind, ] <- cbind(lbound, ubound)
    }
  }

  # Return results

  list(
    stderr_P = stderr_P,
    confval_P = confval_P,
    warn_ind = warn_ind,
    warn_df = warn_df
  )
}