Dear Philp,
You may also want to have a look at the open-source R package campsis
(https://calvagone.github.io/).
Below is some R-code that illustrates how you can easily simulate individual
profiles taking the ETAs from a NONMEM output table.
Best regards, Andreas.
---------------------------------------------------------------------------------------------------------------------------
library(tidyverse)
library(campsis)
# Load a standard model from the library
# you can also set-up a custom model using the free online simulator
e-campsis.com)
model <- model_library$advan2_trans2
# set the parameter values
model <- model %>% replace(Theta("V", value=20))
model <- model %>% replace(Theta("CL", value=5))
model <- model %>% replace(Omega("V", value=0.1,type = 'var'))
model <- model %>% replace(Omega("CL", value=0.1,type = 'var'))
model <- model %>% replace(Sigma("PROP", value=0.02,type = 'var'))
# Have a look at the model
model
# load NONMEM output table containing the ETAS (and covariates if you have)
ETA.tab <- read_table("patab001",skip = 1) %>%
group_by(ID) %>% slice(1) %>% # take only the first record of each subject
rename(ETA_CL=ETA1,ETA_V=ETA2) # you may need to rename variables to match
with the model code
# set-up the simulation schedule; the number of subject must equal that of
ETA.tab
dataset <- Dataset(subjects = n_distinct(ETA.tab$ID)) %>%
add(Bolus(time=0, amount=1000, ii=12, addl=2)) %>%
add(Observations(times=seq(0, 36, by=0.5)))
# add the ETAs by using the bootstrap functionality
dataset <- dataset %>%
add(Bootstrap(data= ETA.tab, id="ID", replacement=FALSE, random=FALSE,
export_id=TRUE))
# we need to discard the random IIV as the ETAs are taken from the dataset
model@parameters@list <- model@parameters@list %>% purrr::discard(.p=~is(.x,
"omega"))
# run the simulation
results <- model %>% simulate(dataset=dataset,outvars = c('BS_ID')) # BS_ID is
the original ID in the ETA.tab
# plot the results
spaghettiPlot(results,'OBS_CP')
-----Original Message-----
From: [email protected] <[email protected]> On Behalf Of
Philip Harder Delff
Sent: Sunday, October 8, 2023 9:30 PM
To: [email protected]
Subject: [NMusers] Simulate with ETAs from .phi and residual variability
Dear all,
I want to simulate subjects with ETAs estimated. I use the .phi file using a
$ETAS statement like:
$ETAS FILE=file.phi FORMAT=s1pE15.8 TBLN=1
As far as I understand that has to be accompanied by a $ESTIMATION step that
specifies FNLETA=2 like this:
$ESTIMATION MAXEVAL=0 NOABORT METHOD=1 INTERACTION FNLETA=2
$SIM ONLYSIM does not work with $ESTIMATION so instead I just do:
$SIMULATION (220412)
This however means that in the following from $ERROR we don't get the
ERR(1) and ERR(2) simulated and so Y=IPRED.
Y=F+F*ERR(1)+ERR(2)
I need to be able to edit the phi file to only simulate a subset of the
patients so I can't use msf based solutions. Can I somehow use $ETAS without
$ESTIMATION? Or how else can I get it to simulate the residual variability?
Thank you,
Philip
