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augPred.R
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augPred.R
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.augPredIpredModel <- function(fit) {
.ipredModel <- .getSimModel(fit, hideIpred=FALSE,tad=FALSE)
eval(as.call(list(quote(`rxModelVars`), .ipredModel[[-1]])))
}
.augPredExpandData <- function(fit, covsInterpolation = c("locf", "nocb", "linear", "midpoint"),
minimum = NULL, maximum = NULL, length.out = 51L) {
.origData <- rxode2::etTrans(fit$dataSav, .augPredIpredModel(fit), addCmt=TRUE, keepDosingOnly=TRUE, allTimeVar=TRUE,
addlKeepsCov = fit$control$rxControl$addlKeepsCov,
addlDropSs = fit$control$rxControl$addlDropSs,
ssAtDoseTime = fit$control$rxControl$ssAtDoseTime)
.predDf <- fit$ui$predDf
.range <- range(.origData$TIME)
.covs <- fit$ui$allCovs
.obsData <- .origData[.origData$EVID %in% c(0, 2), ]
.allCmt <- unique(.obsData$CMT)
.idLvl <- attr(class(.origData), ".rxode2.lst")$idLvl
if (is.null(minimum)) {
minimum <- .range[1]
}
if (is.null(maximum)) {
maximum <- .range[2]
}
.fs <- c(locf = 0, nocb = 1, midpoint = 0.5, linear = 0)
.base <- expand.grid(TIME=seq(minimum, maximum, length.out=length.out),
EVID=2, AMT=NA_real_, II=NA_real_, DV=NA_real_, CMT=.allCmt)
.covsi <- match.arg(covsInterpolation)
.ret0 <- c(list(as.data.frame(.origData)),
lapply(seq_along(.idLvl), function(id) {
.cur <- .origData[.origData$ID == id, ]
if (length(.covs) > 0) {
cbind(data.frame(ID=id, .base),
setNames(data.frame(lapply(.covs, function(cov){
suppressWarnings({
.fun <- stats::approxfun(.cur$TIME, .cur[[cov]],
method = ifelse(.covsi == "linear", "linear", "constant"),
rule = 2,
f = .fs[.covsi])
.fun(.base$TIME)
})
})), .covs))
} else {
data.frame(ID=id, .base)
}
}))
.u <- unique(unlist(lapply(.ret0, function(x){
names(x)
})))
.ret0 <- lapply(.ret0, function(x) {
.d <- setdiff(.u, names(x))
if (any(.d == "CENS")) {
x$CENS <- 0
}
if (any(.d == "LIMIT")) {
x$LIMIT <- NA_real_
}
.d <- setdiff(.d, c("CENS", "LIMIT"))
for (.c in .d) {
x[[.c]] <- NA_real_
}
x
})
.ret <- do.call("rbind", .ret0)
attr(.ret$ID, "levels") <- .idLvl
class(.ret$ID) <- "factor"
.ret <- .ret[order(.ret$ID, .ret$TIME), ]
.ret
}
#' Augmented Prediction for nlmixr2 fit
#'
#' @param fit Nlmixr2 fit object
#' @inheritParams nlme::augPred
#' @inheritParams rxode2::rxSolve
#' @return Stacked data.frame with observations, individual/population predictions.
#' @author Matthew L. Fidler
#' @export
nlmixr2AugPredSolve <- function(fit, covsInterpolation = c("locf", "nocb", "linear", "midpoint"),
minimum = NULL, maximum = NULL, length.out = 51L, ...) {
.si <- fit$simInfo
.rx <- .getSimModel(fit, hideIpred=TRUE)
.rx <- eval(.rx)
.sigma <- .si$sigma
.omega <- .si$omega
if (is.null(.omega)) {
.params <- data.frame(t(fit$theta),
t(setNames(rep(0, dim(.sigma)[1]), dimnames(.sigma)[[2]])))
.params <- setNames(as.numeric(.params), names(.params))
} else {
.params <- data.frame(t(fit$theta),fit$eta[, -1, drop = FALSE],
t(setNames(rep(0, dim(.sigma)[1]), dimnames(.sigma)[[2]])))
}
.events <- .augPredExpandData(fit, covsInterpolation = covsInterpolation,
minimum = minimum, maximum = maximum,
length.out = length.out)
# ipred
.sim <- rxode2::rxSolve(object=.rx, .params, .events,
keep=c("DV", "CMT"), returnType="data.frame")
# now do pred
if (is.null(.omega)) {
names(.sim) <- sub("sim", "pred", names(.sim))
.stk <- stack(.sim[, c("pred", "DV")])
} else {
names(.sim) <- sub("sim", "ipred", names(.sim))
.params <- c(t(fit$theta),t(rep(0, dim(.omega)[1])),
t(rep(0, dim(.sigma)[1])))
.params <- setNames(.params, c(names(fit$theta),
dimnames(.omega)[[2]],
dimnames(.sigma)[[2]]))
.sim2 <- rxode2::rxSolve(object=.rx, params=.params, events=.events,
returnType="data.frame")
.sim$pred <- .sim2$sim
.stk <- stack(.sim[, c("ipred", "pred", "DV")])
}
.stk$id <- .sim$id
.stk$time <- .sim$time
.stk$cmt <- as.integer(.sim$CMT)
.ipredModel <- .augPredIpredModel(fit)
.lvl <- c(.ipredModel$state, .ipredModel$stateExtra)
if (length(.lvl) == 1L && .lvl == "rxLinCmt") {
if (rxModelVars(fit)$flags["ka"] == c(ka=1L)) {
.lvl <- c("depot", "central")
} else {
.lvl <- "central"
}
}
levels(.stk$cmt) <- .lvl
class(.stk$cmt) <- "factor"
.stk <- .stk[!is.na(.stk$values), ]
class(.stk) <- c("nlmixr2AugPred", "data.frame")
if (is.null(.omega)) {
levels(.stk$ind) <- sub("pred", "Population",
sub("DV", "Observed", levels(.stk$ind)))
} else {
levels(.stk$ind) <- sub("pred", "Population",
sub("ipred", "Individual",
sub("DV", "Observed", levels(.stk$ind))))
}
.stk$Endpoint <- factor(paste(.stk$cmt))
.stk <- .stk[, names(.stk) != "cmt"]
class(.stk) <- c("nlmixr2AugPred", "data.frame")
.stk
}
#' @rdname nlmixr2AugPredSolve
#' @export
augPred.nlmixr2FitData <- function(object, primary = NULL, minimum = NULL, maximum = NULL,
length.out = 51, ...) {
nlmixr2AugPredSolve(
fit=object, minimum = minimum, maximum = maximum,
length.out = length.out, ...
)
}