Use the lower level pakages like nlmixr2est and nlme

[mattfidler]

This will be required for the next release of nlmixr2

[mattfidler]

This isn't a large change @A2P2 if you can take a look.

[Copilot]

Pull Request Overview

This PR updates internal calls to leverage lower-level packages for NPDE, prediction augmentation, and VPC simulations, and adds necessary package suggestions.

• Switch addNpde and vpcSim calls from nlmixr2 to nlmixr2est
• Replace augPred call from nlmixr2 to nlme
• Add nlme to DESCRIPTION suggests

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
R/nlmixr.R	Updated addNpde, augPred, and vpcSim calls to use nlmixr2est and nlme
DESCRIPTION	Added nlme to the Suggests field

Comments suppressed due to low confidence (3)

R/nlmixr.R:68

• Error handling for vpcSim occurs after converting the result to a data.table. If vpcSim fails, setDT will error on a try-error object. Consider checking inherits(sim_data, "try-error") immediately after the try() call before further processing.

sim_data <- setDT(sim_data)

R/nlmixr.R:51

• The call to augPred references nlme::augPred, but this function is not provided by nlme. It should reference the correct package (e.g., nlmixr2::augPred or nlmixr2est equivalent) to avoid runtime errors.

finegrid <- try(invisible(nlme::augPred(fit)), silent = TRUE)

DESCRIPTION:65

• The code now depends on nlmixr2est, but nlmixr2est is not declared in Suggests. Please add nlmixr2est to the DESCRIPTION Suggests field to properly record this dependency.

nlme,