Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- echo=FALSE--------------------------------------------------------------
data.table::setDTthreads(2)
## ----setup--------------------------------------------------------------------
suppressPackageStartupMessages(library(tidyvpc, quietly = TRUE))
library(nlmixr2, quietly = TRUE)
library(magrittr)
## ----model-estimate-----------------------------------------------------------
one_compartment <- function() {
ini({
tka <- log(1.57); label("Ka")
tcl <- log(2.72); label("Cl")
tv <- log(31.5); label("V")
eta_ka ~ 0.6
eta_cl ~ 0.3
eta_v ~ 0.1
add_sd <- 0.7
})
# and a model block with the error specification and model specification
model({
ka <- exp(tka + eta_ka)
cl <- exp(tcl + eta_cl)
v <- exp(tv + eta_v)
d/dt(depot) <- -ka * depot
d/dt(center) <- ka * depot - cl / v * center
cp <- center / v
cp ~ add(add_sd)
})
}
data_model <- theo_sd
data_model$WTSTRATA <- ifelse(data_model$WT < median(data_model$WT), "Low weight", "High weight")
fit <- nlmixr2(one_compartment, data_model, est="saem", saemControl(print=0))
## ----vpcsim-------------------------------------------------------------------
fit_vpcsim <- vpcSim(object = fit, keep = "WTSTRATA")
## ----vpc-std-setup------------------------------------------------------------
obs_data <- data_model[data_model$EVID == 0,]
vpc <-
observed(obs_data, x=TIME, y=DV) %>%
simulated(fit_vpcsim, x=time, y=sim) %>%
stratify(~ WTSTRATA) %>%
binning(bin = "jenks") %>%
vpcstats()
## ----vpc-std-plot-------------------------------------------------------------
plot(vpc)
## ----vpc-predcorr-setup-------------------------------------------------------
# Add PRED to observed data
data_pred <- data_model[data_model$EVID == 0, ]
data_pred$PRED <- fit$PRED
vpc_predcorr <-
observed(data_pred, x=TIME, y=DV) %>%
simulated(fit_vpcsim, x=time, y=sim) %>%
stratify(~ WTSTRATA) %>%
binning(bin = "jenks") %>%
predcorrect(pred=PRED) %>%
vpcstats()
## ----vpc-predcorr-plot--------------------------------------------------------
plot(vpc_predcorr)
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