#' \code{lqm} fits linear quantile regression model
#'
#' Function using JAGS to estimate the linear quantile regression model assuming asymmetric Laplace
#' distribution for residual error.
#'
#' @param formula formula for the quantile regression including response variable
#' @param data dataset of observed variables
#' @param tau the quantile(s) to be estimated. This must be a number between 0 and 1, otherwise the execution is stopped. If more than one quantile is specified, rounding off to the 4th decimal must give non–duplicated values of \code{tau}, otherwise the execution is stopped.
#' @param n.chains the number of parallel chains for the model; default is 1.
#' @param n.iter integer specifying the total number of iterations; default is 10000
#' @param n.burnin integer specifying how many of n.iter to discard as burn-in ; default is 5000
#' @param n.thin integer specifying the thinning of the chains; default is 1
#' @param n.adapt integer specifying the number of iterations to use for adaptation; default is NULL
#' @param save_jagsUI If TRUE (is FALSE by default), the output of jagsUI package is return by the function
#' @param parallel see jagsUI::jags() function
#'
#' @return A \code{BQt} object which is a list with the following elements:
#' \describe{
#' \item{\code{mean}}{list of posterior mean for each parameter}
#' \item{\code{median}}{list of posterior median for each parameter}
#' \item{\code{modes}}{list of posterior mode for each parameter}
#' \item{\code{StErr}}{list of standard error for each parameter}
#' \item{\code{StDev}}{list of standard deviation for each parameter}
#' \item{\code{Rhat}}{Gelman and Rubin diagnostic for all parameters}
#' \item{\code{ICs}}{list of the credibility interval at 0.95 for each parameters excepted for covariance parameters in covariance matrix of random effects. Otherwise, use save_jagsUI=TRUE to have the associated quantiles.}
#' \item{\code{data}}{data included in argument}
#' \item{\code{sims.list}}{list of the MCMC chains of the parameters and random effects}
#' \item{\code{control}}{list of arguments giving details about the estimation}
#' \item{\code{W}}{list including both posterior mean and posterior standard deviation of subject-specific random varaible W}
#' \item{\code{out_jagsUI}}{only if \code{save_jagsUI=TRUE} in argument: list including posterior mean, median, quantiles (2.5%, 25%, 50%, 75%, 97.5%), standart deviation for each parameter and each random effect.
#' Moreover, this list also returns the MCMC draws, the Gelman and Rubin diagnostics (see output of jagsUI objects)}
#' }
#'
#' @author Antoine Barbieri
#'
#' @import jagsUI
#' @export
#'
#' @examples
#' #---- Use data
#' data(wave)
#'
#' #---- Fit regression model for the first quartile
#' lqm_025 <- lqm(formula = h110d~vent_vit_moy,
#' data = wave,
#' n.iter = 1000,
#' n.burnin = 500,
#' tau = 0.25)
#'
#' #---- Get the posterior mean of parameters
#' lqm_025$mean
#'
#' #---- Summary of output
#' summary(lqm_025)
#'
lqm <- function(formula,
data,
tau = 0.5,
n.chains = 3,
n.iter = 10000,
n.burnin = 5000,
n.thin = 1,
n.adapt = NULL,
save_jagsUI = FALSE,
parallel = FALSE){
# data
tmp <- data[c(all.vars(formula))]
tmp <- unique(tmp)
I <- nrow(tmp)
# design matrices
y <- data[all.vars(formula)][,1]
mfX <- model.frame(formula, data = tmp)
X <- model.matrix(formula, mfX)
ncX <- ncol(X)
# use lm function to initiated values
lm_tmp <- stats::lm(formula,
data = tmp)
# prior beta parameters
priorMean.beta <- as.numeric(lm_tmp$coefficients)
# priorTau.beta <- diag(1/c(1,smcure_out$beta_var)/100)
# list of data jags
jags.data <- list(y = y,
X = X,
tau = tau,
ncX = ncX,
I = I
# ,
# priorMean.beta = priorMean.beta,
# priorTau.beta = priorTau.beta,
# priorA.shape = 1/100,
# priorB.shape = 1/100
)
#---- write jags model in txt from R function
working.directory = getwd()
write.model.jags(model = jags_lqm,
name_model = "jags_lqm",
intitled = file.path(working.directory,"JagsModel.txt"),
Data = jags.data)
# jags argument
parms_to_save <- c("beta", "sigma", "va1")
#---- use JAGS sampler
# if (!require("rjags"))
# stop("'rjags' is required.\n")
# using jagsUI
out_jags = jagsUI::jags(data = jags.data,
parameters.to.save = parms_to_save,
model.file = "JagsModel.txt",
n.chains = n.chains,
parallel = parallel,
n.adapt = n.adapt,
n.iter = n.iter,
n.burnin = n.burnin,
n.thin = n.thin,
DIC = F)
file.remove(file.path(working.directory, "JagsModel.txt"))
#---- output
out <- list(data = data)
out$control <- list(formula = formula,
tau = tau,
call_function = "lqm",
n.chains = n.chains,
parallel = parallel,
n.adapt = n.adapt,
n.iter = n.iter,
n.burnin = n.burnin,
n.thin = n.thin)
#- other outputs
# sims.list output
out$sims.list <- out_jags$sims.list
out$sims.list$va1 <- NULL
# Random variable W esponentially distributed
out$W <- list(postMeans = out_jags$mean$va1,
postSd = out_jags$sd$va1)
# median : Posterior median of parameters (if mean, you can use mean instead of q50)
out$median <- out_jags$q50
out$median$va1 <- NULL
# mean : Posterior mean of parameters (if mean, you can use mean instead of q50)
out$mean <- out_jags$mean
out$mean$va1 <- NULL
# modes of parameters
out$modes <- lapply(out$sims.list, function(x) {
m <- function(x) {
d <- density(x, bw = "nrd", adjust = 3, n = 1000)
d$x[which.max(d$y)]
}
if (is.matrix(x))
as.array(apply(x, 2, m))
else{
if(is.array(x))
apply(x, c(2,3), m)
else m(x)
}
})
# standard error of parameters
out$StErr <- lapply(out$sims.list, function(x) {
f <- function(x) {
acf.x <- drop(acf(x, lag.max = 0.4 * length(x), plot = FALSE)$acf)[-1]
acf.x <- acf.x[seq_len(rle(acf.x > 0)$lengths[1])]
ess <- length(x)/(1 + 2 * sum(acf.x))
sqrt(var(x)/ess)
}
if (is.matrix(x))
as.array(apply(x, 2, f))
else{
if(is.array(x))
apply(x, c(2,3), f)
else f(x)
}
})
# standard deviation of parameters
out$StDev <- out_jags$sd
out$StDev$va1 <- NULL
# Rhat : Gelman & Rubin diagnostic
out$Rhat <- out_jags$Rhat
out$Rhat$va1 <- NULL
# names
names(out$mean$beta) <-
names(out$median$beta) <-
names(out$Rhat$beta) <-
names(out$modes$beta) <-
names(out$StErr$beta) <-
names(out$StDev$beta) <- colnames(X)
# credible intervalles
out$CIs$beta <- cbind(as.vector(t(out_jags$q2.5$beta)),
as.vector(t(out_jags$q97.5$beta)))
rownames(out$CIs$beta) <- colnames(X)
colnames(out$CIs$beta) <- c("2.5%", "97.5%")
out$CIs$sigma <- c(out_jags$q2.5$sigma,
out_jags$q97.5$sigma)
names(out$CIs$sigma) <- c("2.5%", "97.5%")
# save jags output if requires
if(save_jagsUI)
out$out_jagsUI <- out_jags
# End of function
class(out) <- "BQt"
out
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.