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#' At-risk-of-poverty threshold
#'
#' The standard definition is to use 60\% of the median income.
#'
#' @param formula a formula specifying the income variable
#' @param design a design object of class \code{survey.design} or class \code{svyrep.design} from the \code{survey} library.
#' @param quantiles income quantile quantiles, usually .50 (median)
#' @param percent fraction of the quantile, usually .60
#' @param na.rm Should cases with missing values be dropped?
#' @param ... arguments passed on to `survey::oldsvyquantile`
#'
#' @details you must run the \code{convey_prep} function on your survey design object immediately after creating it with the \code{svydesign} or \code{svrepdesign} function.
#'
#' @return Object of class "\code{cvystat}", which are vectors with a "\code{var}" attribute giving the variance and a "\code{statistic}" attribute giving the name of the statistic.
#'
#' @author Djalma Pessoa and Anthony Damico
#'
#' @seealso \code{\link{svyarpr}}
#'
#' @references Guillaume Osier (2009). Variance estimation for complex indicators
#' of poverty and inequality. \emph{Journal of the European Survey Research
#' Association}, Vol.3, No.3, pp. 167-195,
#' ISSN 1864-3361, URL \url{https://ojs.ub.uni-konstanz.de/srm/article/view/369}.
#'
#' Jean-Claude Deville (1999). Variance estimation for complex statistics and estimators:
#' linearization and residual techniques. Survey Methodology, 25, 193-203,
#' URL \url{https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X19990024882}.
#'
#' @keywords survey
#'
#' @examples
#'
#' library(survey)
#' library(laeken)
#' data(eusilc) ; names( eusilc ) <- tolower( names( eusilc ) )
#'
#' # linearized design
#'
#' des_eusilc <- svydesign( ids = ~rb030 , strata = ~db040 , weights = ~rb050 , data = eusilc )
#' des_eusilc <- convey_prep( des_eusilc )
#' svyarpt( ~eqincome , design = des_eusilc )
#'
#' # replicate-weighted design
#' des_eusilc_rep <- as.svrepdesign( des_eusilc , type = "bootstrap" )
#' des_eusilc_rep <- convey_prep( des_eusilc_rep )
#' svyarpt( ~eqincome , design = des_eusilc_rep )
#'
#' \dontrun{
#'
#' # linearized design using a variable with missings
#' svyarpt( ~ py010n , design = des_eusilc )
#' svyarpt( ~ py010n , design = des_eusilc , na.rm = TRUE )
#' # replicate-weighted design using a variable with missings
#' svyarpt( ~ py010n , design = des_eusilc_rep )
#' svyarpt( ~ py010n , design = des_eusilc_rep , na.rm = TRUE )
#'
#'
#' # database-backed design
#' library(RSQLite)
#' library(DBI)
#' dbfile <- tempfile()
#' conn <- dbConnect( RSQLite::SQLite() , dbfile )
#' dbWriteTable( conn , 'eusilc' , eusilc )
#'
#' dbd_eusilc <-
#' svydesign(
#' ids = ~rb030 ,
#' strata = ~db040 ,
#' weights = ~rb050 ,
#' data="eusilc",
#' dbname=dbfile,
#' dbtype="SQLite"
#' )
#'
#' dbd_eusilc <- convey_prep( dbd_eusilc )
#'
#' svyarpt( ~ eqincome , design = dbd_eusilc )
#'
#' dbRemoveTable( conn , 'eusilc' )
#'
#' dbDisconnect( conn , shutdown = TRUE )
#'
#' }
#'
#' @export
svyarpt <-
function(formula, design, ...) {
if( length( attr( terms.formula( formula ) , "term.labels" ) ) > 1 ) stop( "convey package functions currently only support one variable in the `formula=` argument" )
UseMethod("svyarpt", design)
}
#' @rdname svyarpt
#' @export
svyarpt.survey.design <-
function(formula, design, quantiles = 0.5, percent = 0.6, na.rm = FALSE,...) {
if (is.null(attr(design, "full_design"))) stop("you must run the ?convey_prep function on your linearized survey design object immediately after creating it with the svydesign() function.")
# if the class of the full_design attribute is just a TRUE, then the design is
# already the full design. otherwise, pull the full_design from that attribute.
if ("logical" %in% class(attr(design, "full_design")))
full_design <- design else full_design <- attr(design, "full_design")
incvar <- model.frame(formula, design$variables, na.action = na.pass)[[1]]
if(na.rm){
nas<-is.na(incvar)
design<-design[!nas,]
if (length(nas) > length(design$prob))
incvar <- incvar[!nas]
else incvar[nas] <- 0
}
if( is.null( names( design$prob ) ) ) ind <- as.character( seq( length( design$prob ) ) ) else ind <- names(design$prob)
w <- 1/design$prob
incvec <- model.frame(formula, full_design$variables, na.action = na.pass)[[1]]
if(na.rm){
nas<-is.na(incvec)
full_design<-full_design[!nas,]
if (length(nas) > length(full_design$prob))
incvec <- incvec[!nas]
else incvec[nas] <- 0
}
if( is.null( names( full_design$prob ) ) ) ncom <- as.character( seq( length( full_design$prob ) ) ) else ncom <- names(full_design$prob)
wf <- 1/full_design$prob
htot <- h_fun(incvar, w)
q_alpha <- survey::oldsvyquantile(x = formula, design = design, quantiles = quantiles,
method = "constant", na.rm = na.rm,...)
q_alpha <- as.vector(q_alpha)
rval <- percent * q_alpha
Fprime <- densfun(formula = formula, design = design, q_alpha, h=htot, FUN = "F", na.rm=na.rm)
N <- sum(w)
if (sum(1/design$prob==0) > 0) ID <- 1*(1/design$prob!=0) else
ID <- 1 * ( ncom %in% ind )
linquant<- -(1/(N * Fprime)) * ID*((incvec <= q_alpha) - quantiles)
lin <- percent * linquant
variance <- survey::svyrecvar(lin/full_design$prob, full_design$cluster,
full_design$strata, full_design$fpc, postStrata = full_design$postStrata)
colnames( variance ) <- rownames( variance ) <- names( rval ) <- strsplit( as.character( formula )[[2]] , ' \\+ ' )[[1]]
class(rval) <- c( "cvystat" , "svystat" )
attr(rval, "var") <- variance
attr(rval, "statistic") <- "arpt"
attr(rval, "lin") <- lin
rval
}
#' @rdname svyarpt
#' @export
svyarpt.svyrep.design <-
function(formula, design, quantiles = 0.5, percent = 0.6, na.rm = FALSE, ...) {
if (is.null(attr(design, "full_design")))
stop("you must run the ?convey_prep function on your replicate-weighted survey design object immediately after creating it with the svrepdesign() function.")
# if the class of the full_design attribute is just a TRUE, then the design is
# already the full design. otherwise, pull the full_design from that attribute.
if ("logical" %in% class(attr(design, "full_design"))) full_design <- design else full_design <- attr(design, "full_design")
df <- model.frame(design)
incvar <- model.frame(formula, design$variables, na.action = na.pass)[[1]]
if(na.rm){
nas<-is.na(incvar)
design<-design[!nas,]
df <- model.frame(design)
incvar <- incvar[!nas]
}
w <- weights(design, "sampling")
quant_val <- computeQuantiles(incvar, w, p = quantiles)
quant_val <- as.vector(quant_val)
rval <- percent * quant_val
ww <- weights(design, "analysis")
qq <- apply(ww, 2, function(wi) 0.6 * computeQuantiles(incvar, wi, p = quantiles))
if(anyNA(qq))variance <- NA
else variance <- survey::svrVar(qq, design$scale, design$rscales, mse = design$mse, coef = rval)
variance <- as.matrix( variance )
colnames( variance ) <- rownames( variance ) <- names( rval ) <- strsplit( as.character( formula )[[2]] , ' \\+ ' )[[1]]
class(rval) <- c( "cvystat" , "svrepstat" )
attr(rval, "var") <- variance
attr(rval, "statistic") <- "arpt"
rval
}
#' @rdname svyarpt
#' @export
svyarpt.DBIsvydesign <-
function (formula, design, ...)
{
if (!( "logical" %in% class(attr(design, "full_design"))) ){
full_design <- attr( design , "full_design" )
full_design$variables <-
getvars(
formula,
attr( design , "full_design" )$db$connection,
attr( design , "full_design" )$db$tablename,
updates = attr( design , "full_design" )$updates,
subset = attr( design , "full_design" )$subset
)
attr( design , "full_design" ) <- full_design
rm( full_design )
}
design$variables <-
getvars(
formula,
design$db$connection,
design$db$tablename,
updates = design$updates,
subset = design$subset
)
NextMethod("svyarpt", design)
}
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