I am learning popPK through books. So, I wanted to get tangible examples for the practice.
I found NLMIXR2 library ( https://cran.r-project.org/web/packages/nlmixr2/index.html ), and I got a problem executing the reference example code on the manual.
I was using R 4.2.3 on RStudio, Windows 11.
An example code is below:
library(nlmixr2)
library(nlmixr2data) #### MIN-SOO KIM: I think I need to define theo_sd on the line 27
## The basic model consiss of an ini block that has initial estimates
one.compartment <- function() {
ini({
tka <- 0.45 # Log Ka
tcl <- 1 # Log Cl
tv <- 3.45 # Log V
eta.ka ~ 0.6
eta.cl ~ 0.3
eta.v ~ 0.1
add.sd <- 0.7
})
# and a model block with the error sppecification 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)
})
}
## The fit is performed by the function nlmixr/nlmix2 specifying the model, data and estimate
fit <- nlmixr2(one.compartment, theo_sd, est="saem", saemControl(print=0))
print(fit)
And I goe an error message as below:
> fit <- nlmixr2(one.compartment, theo_sd, est="saem", saemControl(print=0))ℹ parameter labels from comments will be replaced by 'label()'Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :arguments imply differing number of rows: 1, 0Error: arguments imply differing number of rows: 1, 0
Since I had no idea what I needed to do next, I checked if there were some mistakes in the installation. I ran 'nlmixr2CheckInstall' method (below).
I could not resolve the error, and I sent an email to Matthew Fidler who was the maintainer of the project ( https://github.com/nlmixr2/nlmixr2/ ).
Matthew replied that some of the packages on CRAN were out of sync, and gave me a code. According to the reply from Matthew, I reinstall them using the code below:
install.packages(c("dparser", "nlmixr2data", "lotri", "rxode2ll",
"rxode2parse", "rxode2random", "rxode2et",
"rxode2", "nlmixr2est", "nlmixr2extra", "nlmixr2plot",
"nlmixr2"),
repos = c('https://nlmixr2.r-universe.dev',
And, solved!!