R/mice.impute.2l.zinb.R
In kkleinke/countimp: Multiple Imputation of incomplete count data
#' Multiple Imputation of Zero-Inflated Two-Level Count Data
#'
#' The functions impute zero-inflated multilevel count data based on a two-level Poisson or negative binomial zero-inflation model, either using a Bayesian regression or a bootstrap regression approach (appendix: ``\code{.boot}''). The \code{.noint} variants treat the intercept only as a fixed, but \emph{not} as a random effect. It may be specified, if the intercept is excluded from the random part of the zero model (``\code{.noint.zero}''), the count model (``\code{.noint.count}''), or both models (``\code{.noint.both}''). Zero-inflation models are mixture models and consist of two model components: the zero model (a binomial generalized linear mixed effects model), determining, if the observational unit belongs to zero-inflation process (certain zeros) or to the count process, and the count model (a two-level Poisson or NB model), determining, what count (zero or non-zero) the observational unit has.
#'
#' Model specification details:
#' \itemize{
#' \item -2 = class variable (only one class variable is allowed!)
#' \item 0 = variable not included in imputation model
#' \item 1 = variable will be included as a fixed effect (zero \emph{and} count model)
#' \item 2 = variable will be included as a fixed \emph{and} random effect (zero \emph{and} count model)
#' \item 3 = variable will be included as a fixed effect (count model only)
#' \item 4 = variable will be included as a fixed \emph{and} random effect (count model only)
#' \item 5 = variable will be included as a fixed effect (zero model only)
#' \item 6 = variable will be included as a fixed \emph{and} random effect (zero model only)
#' }
#' The Bayesian regression variants (see Rubin 1987, p. 169-170) consist of the following steps:
#' \enumerate{
#' \item Fit the zero model (a two-level binomial generalized linear mixed effects model), using the \code{glmmTMB} function from package \pkg{glmmTMB}; find bhat, the posterior mean, and V(bhat), the posterior variance of model parameters b
#' \item Draw b* from N(bhat,V(bhat))
#' \item Compute predicted probabilities for having a zero vs. non-zero count
#' \item Draw imputations (zeros and ones) from a binomial distribution with the respective individual probabilities obtained from step 3.
#' \item Fit the count model (a two-level Poisson or NB model) using the \code{glmmTMB} function from package \pkg{glmmTMB}; find bhat, the posterior mean, and V(bhat), the posterior variance of model parameters b.
#' \item Draw b* from N(bhat,V(bhat))
#' \item Compute predicted values using parameters b* and replace non-zero imputations (from step 4) by a draw from a zero-truncated NB distribution with mean parameter mu being the count predicted for the respective incomplete case.
#' }
#' The bootstrap functions draw a bootstrap sample from \code{y[ry]} and \code{x[ry,]} (Note: we resample clusters rather than individual cases) and consist of the following steps:
#' \enumerate{
#' \item Fit the zero model to the bootstrap sample
#' \item Compute predicted probabilities for having a zero vs. non-zero count
#' \item Draw imputations from a binomial distribution.
#' \item Fit the count model to the boostrap sample
#' \item Compute predicted counts and draw non-zero imputations (from step 3) from a zero-truncated Poisson or NB distribution.
#' }
#' @param y Numeric vector with incomplete data in long format (i.e. the groups are stacked upon each other)
#' @param ry Response pattern of \code{y} (\code{TRUE}=observed, \code{FALSE}=missing)
#' @param x matrix with \code{length(y)} rows containing complete covariates; also in long format
#' @param type vector of length \code{ncol(x)} identifying fixed, random, and class variables; \code{type} is automatically extracted from the \code{predictorMatrix}; see \pkg{mice}'s user's manual for details about how to specify the imputation model; see also section ``details''.
#' @param intercept.c \code{TRUE}: model will include intercept as a random effect in the count model; \code{FALSE}: count model intercept will be treated as fixed.
#' @param intercept.z \code{TRUE}: model will include intercept as a random effect in the zero model; \code{FALSE}: zero model intercept will be treated as fixed.
#' @param wy Logical vector of length \code{length(y)}. A \code{TRUE} value indicates locations in \code{y} for which imputations are created. Default is \code{!ry}
#' @param EV should automatic outlier handling of imputed values be enabled? Default is \code{TRUE}: extreme imputations will be identified. These values will be replaced by imputations obtained by predictive mean matching (function \code{mice.impute.midastouch()})
#' @return Numeric vector of length \code{sum(!ry)} with imputations
#' @export
#' @import glmmTMB stats
#' @importFrom stats as.formula na.pass predict rbinom rnorm vcov
#' @aliases mice.impute.2l.zinb mice.impute.2l.zinb.boot mice.impute.2l.zinb.noint.both mice.impute.2l.zinb.noint.both.boot mice.impute.2l.zinb.noint.zero mice.impute.2l.zinb.noint.zero.boot mice.impute.2l.zinb.noint.count mice.impute.2l.zinb.noint.count.boot
#' @aliases mice.impute.2l.zip mice.impute.2l.zip.boot mice.impute.2l.zip.noint.both mice.impute.2l.zip.noint.both.boot mice.impute.2l.zip.noint.zero mice.impute.2l.zip.noint.zero.boot mice.impute.2l.zip.noint.count mice.impute.2l.zip.noint.count.boot
#' @author Kristian Kleinke
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; random intercepts
mice.impute.2l.zinb <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values<-im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; random intercepts
mice.impute.2l.zinb.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercepts
mice.impute.2l.zinb.noint.both.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercepts
mice.impute.2l.zinb.noint.both <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercept in count model
mice.impute.2l.zinb.noint.count.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in count model
mice.impute.2l.zinb.noint.count <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed interceot in zero model
mice.impute.2l.zinb.noint.zero.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in zero model
mice.impute.2l.zinb.noint.zero <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
### new 2018-04-28
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; random intercepts
mice.impute.2l.zip <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values<-im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; random intercepts
mice.impute.2l.zip.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercepts
mice.impute.2l.zip.noint.both.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercepts
mice.impute.2l.zip.noint.both <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercept in count model
mice.impute.2l.zip.noint.count.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in count model
mice.impute.2l.zip.noint.count <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed interceot in zero model
mice.impute.2l.zip.noint.zero.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in zero model
mice.impute.2l.zip.noint.zero <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
kkleinke/countimp documentation built on Nov. 5, 2024, 11:51 a.m.
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#' Multiple Imputation of Zero-Inflated Two-Level Count Data
#'
#' The functions impute zero-inflated multilevel count data based on a two-level Poisson or negative binomial zero-inflation model, either using a Bayesian regression or a bootstrap regression approach (appendix: ``\code{.boot}''). The \code{.noint} variants treat the intercept only as a fixed, but \emph{not} as a random effect. It may be specified, if the intercept is excluded from the random part of the zero model (``\code{.noint.zero}''), the count model (``\code{.noint.count}''), or both models (``\code{.noint.both}''). Zero-inflation models are mixture models and consist of two model components: the zero model (a binomial generalized linear mixed effects model), determining, if the observational unit belongs to zero-inflation process (certain zeros) or to the count process, and the count model (a two-level Poisson or NB model), determining, what count (zero or non-zero) the observational unit has.
#'
#' Model specification details:
#' \itemize{
#' \item -2 = class variable (only one class variable is allowed!)
#' \item 0 = variable not included in imputation model
#' \item 1 = variable will be included as a fixed effect (zero \emph{and} count model)
#' \item 2 = variable will be included as a fixed \emph{and} random effect (zero \emph{and} count model)
#' \item 3 = variable will be included as a fixed effect (count model only)
#' \item 4 = variable will be included as a fixed \emph{and} random effect (count model only)
#' \item 5 = variable will be included as a fixed effect (zero model only)
#' \item 6 = variable will be included as a fixed \emph{and} random effect (zero model only)
#' }
#' The Bayesian regression variants (see Rubin 1987, p. 169-170) consist of the following steps:
#' \enumerate{
#' \item Fit the zero model (a two-level binomial generalized linear mixed effects model), using the \code{glmmTMB} function from package \pkg{glmmTMB}; find bhat, the posterior mean, and V(bhat), the posterior variance of model parameters b
#' \item Draw b* from N(bhat,V(bhat))
#' \item Compute predicted probabilities for having a zero vs. non-zero count
#' \item Draw imputations (zeros and ones) from a binomial distribution with the respective individual probabilities obtained from step 3.
#' \item Fit the count model (a two-level Poisson or NB model) using the \code{glmmTMB} function from package \pkg{glmmTMB}; find bhat, the posterior mean, and V(bhat), the posterior variance of model parameters b.
#' \item Draw b* from N(bhat,V(bhat))
#' \item Compute predicted values using parameters b* and replace non-zero imputations (from step 4) by a draw from a zero-truncated NB distribution with mean parameter mu being the count predicted for the respective incomplete case.
#' }
#' The bootstrap functions draw a bootstrap sample from \code{y[ry]} and \code{x[ry,]} (Note: we resample clusters rather than individual cases) and consist of the following steps:
#' \enumerate{
#' \item Fit the zero model to the bootstrap sample
#' \item Compute predicted probabilities for having a zero vs. non-zero count
#' \item Draw imputations from a binomial distribution.
#' \item Fit the count model to the boostrap sample
#' \item Compute predicted counts and draw non-zero imputations (from step 3) from a zero-truncated Poisson or NB distribution.
#' }
#' @param y Numeric vector with incomplete data in long format (i.e. the groups are stacked upon each other)
#' @param ry Response pattern of \code{y} (\code{TRUE}=observed, \code{FALSE}=missing)
#' @param x matrix with \code{length(y)} rows containing complete covariates; also in long format
#' @param type vector of length \code{ncol(x)} identifying fixed, random, and class variables; \code{type} is automatically extracted from the \code{predictorMatrix}; see \pkg{mice}'s user's manual for details about how to specify the imputation model; see also section ``details''.
#' @param intercept.c \code{TRUE}: model will include intercept as a random effect in the count model; \code{FALSE}: count model intercept will be treated as fixed.
#' @param intercept.z \code{TRUE}: model will include intercept as a random effect in the zero model; \code{FALSE}: zero model intercept will be treated as fixed.
#' @param wy Logical vector of length \code{length(y)}. A \code{TRUE} value indicates locations in \code{y} for which imputations are created. Default is \code{!ry}
#' @param EV should automatic outlier handling of imputed values be enabled? Default is \code{TRUE}: extreme imputations will be identified. These values will be replaced by imputations obtained by predictive mean matching (function \code{mice.impute.midastouch()})
#' @return Numeric vector of length \code{sum(!ry)} with imputations
#' @export
#' @import glmmTMB stats
#' @importFrom stats as.formula na.pass predict rbinom rnorm vcov
#' @aliases mice.impute.2l.zinb mice.impute.2l.zinb.boot mice.impute.2l.zinb.noint.both mice.impute.2l.zinb.noint.both.boot mice.impute.2l.zinb.noint.zero mice.impute.2l.zinb.noint.zero.boot mice.impute.2l.zinb.noint.count mice.impute.2l.zinb.noint.count.boot
#' @aliases mice.impute.2l.zip mice.impute.2l.zip.boot mice.impute.2l.zip.noint.both mice.impute.2l.zip.noint.both.boot mice.impute.2l.zip.noint.zero mice.impute.2l.zip.noint.zero.boot mice.impute.2l.zip.noint.count mice.impute.2l.zip.noint.count.boot
#' @author Kristian Kleinke
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; random intercepts
mice.impute.2l.zinb <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values<-im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; random intercepts
mice.impute.2l.zinb.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercepts
mice.impute.2l.zinb.noint.both.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercepts
mice.impute.2l.zinb.noint.both <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercept in count model
mice.impute.2l.zinb.noint.count.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in count model
mice.impute.2l.zinb.noint.count <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed interceot in zero model
mice.impute.2l.zinb.noint.zero.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in zero model
mice.impute.2l.zinb.noint.zero <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="nbinom2",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = stats::rnbinom(n=length(p), size = fit.sum$sigma, mu = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
### new 2018-04-28
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; random intercepts
mice.impute.2l.zip <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values<-im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; random intercepts
mice.impute.2l.zip.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercepts
mice.impute.2l.zip.noint.both.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercepts
mice.impute.2l.zip.noint.both <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed intercept in count model
mice.impute.2l.zip.noint.count.boot<-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in count model
mice.impute.2l.zip.noint.count <-
function (y, ry, x, type, intercept.c = FALSE, intercept.z = TRUE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb bootstrap regression variant; fixed interceot in zero model
mice.impute.2l.zip.noint.zero.boot<-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
GRPnam=nam[grp]
colnames(dat)[colnames(dat)%in%nam[grp]]<-"GRP"
cls <- sample(unique(dat$GRP),replace=TRUE)
cls.col <- data.frame(GRP=cls)
dat <- merge(cls.col,dat,by="GRP")
colnames(dat)[colnames(dat)=="GRP"] <- GRPnam
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fit, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
#' @export
#' @describeIn mice.impute.2l.zinb Bayesian regression variant; fixed intercept in zero model
mice.impute.2l.zip.noint.zero <-
function (y, ry, x, type, intercept.c = TRUE, intercept.z = FALSE, wy = NULL, EV=TRUE)
{
if (is.null(wy))
wy <- !ry
if (sum(type == -2) > 1) {
stop("only one class allowed!")
}
Y = y[ry]
X = x[ry, ]
X = data.frame(X)
nam = colnames(X)
grp <- which(type == -2)
dat=data.frame(Y,X)
fc <- which(type == 3)
rc <- which(type == 4)
fz <- which(type == 5)
rz <- which(type == 6)
f <- which(type == 1)
r <- which(type == 2)
ran <- c(r, rz)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 6)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fz, rz)
fix <- unique(fix)
fix <- sort(fix)
fixedeff <- paste(nam[fix], collapse = "+")
nz <- as.numeric(dat$Y == 0)
dat$nz = nz
form = as.formula(paste("nz", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = dat,
family="binomial")
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
im <- rbinom(n = length(p), size = 1, prob = 1 - p)
nonzero <- which(im == 1)
ran <- c(r, rc)
ran <- unique(ran)
ran <- sort(ran)
randeff <- paste(nam[ran], collapse = "+")
if (any(type == 2) | any(type == 4)) {
randeff = paste("+", paste(nam[ran], collapse = "+"),
sep = "")
if (!intercept.c) {
randeff = paste("(0", randeff, "|", paste(nam[grp],")"),
sep = "")
}
else {
randeff = paste("(1", randeff, "|", paste(nam[grp], ")"),
sep = "")
}
}
else {
if (!intercept.c) {
randeff <- paste("(0", "|", paste(nam[grp]),")", sep = "")
}
else {
randeff <- paste("(1", "|", paste(nam[grp]),")", sep = "")
}
}
fix <- c(f, r, fc, rc)
fix <- unique(fix)
fix <- sort(fix)
fixedeff = paste(paste(nam[-grp], collapse = "+"), sep = "")
form = as.formula(paste("Y", "~", fixedeff, "+", randeff, sep = ""))
fit <- glmmTMB::glmmTMB(formula = form, data = subset(dat,
dat[, "Y"] > 0),
family=list(family="poisson",link="log"))
fit.sum=summary(fit)
fit.sum <- summary(fit)
beta <- fixef(fit)$cond
rv <- t(chol(vcov(fit)$cond))
b.star <- beta + rv %*% rnorm(ncol(rv))
fitmis <- fit
fitmis$fit$par[names(fitmis$fit$par)=="beta"] <- b.star
newdatamis = data.frame(X = x[wy, , drop = FALSE])
colnames(newdatamis) = nam
p <- predict(fitmis, newdata = newdatamis, type = "response",
na.action = na.pass, allow.new.levels = TRUE)
imc = rpois(n=length(p), lambda = p)
im[nonzero] <- imc[nonzero]
imputed.values <- im
if(EV){
outliers <- getOutliers(imputed.values, rho = c(0.3,
0.3), FLim = c(0.15, 0.85))
nans <- which(is.nan(imputed.values))
idx <- c(outliers$iLeft, outliers$iRight, nans)
if (length(idx) != 0) {
imputed.values[idx] <- NA
y[!ry] <- imputed.values
R = ry
ry <- !is.na(y)
new.values <- mice.impute.midastouch(y, ry, x,
wy = NULL)
imputed.values[idx] <- new.values
}}
return(imputed.values)
}
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