xpose.xtras (version 0.2.2)

nlmixr_example: Generate example xp_xtras objects from nlmixr2 fits

Description

Runs an nlmixr2 fit on demand and returns the result as a ready-to-use xp_xtras object. nlmixr2_example is an alias.

Usage

nlmixr_example(name)
nlmixr2_example(name)

Value

An xp_xtras object with the nlmixr2 fit attached.

Arguments

name

<character> Name of the example to generate. One of "xpdb_nlmixr2", "xpdb_nlmixr2_saem", "nlmixr2_warfarin", "nlmixr2_m3", "xpdb_nlmixr2_nocov".

Details

Available examples:

"xpdb_nlmixr2"

One-compartment FOCEI fit to the theophylline dataset. The basic introductory example from the nlmixr2 documentation. See Theoph.

"xpdb_nlmixr2_saem"

The same one-compartment theophylline model fit with SAEM instead of FOCEI.

"nlmixr2_warfarin"

Multiple-endpoint warfarin PK/PD model with a four-compartment PK and turnover PD. Provides categorical covariate data useful for eta diagnostic examples.

"nlmixr2_m3"

Theophylline one-compartment model with censoring applied to provoke M3 likelihood handling. Includes a BLQLIKE output variable for use as a categorical DV example with catdv_vs_dvprobs().

"xpdb_nlmixr2_nocov"

The same one-compartment theophylline FOCEI fit as "xpdb_nlmixr2", but with the covariance step skipped (covMethod = ""). Useful for exercising code paths that depend on parameter uncertainty, such as get_cov_matrix(), when it is not available.

References

Fidler M (2025). nlmixr2: Nonlinear Mixed Effects Models in Population PK/PD. tools:::Rd_expr_doi("doi:10.32614/CRAN.package.nlmixr2"), R package version 3.0.2, https://CRAN.R-project.org/package=nlmixr2.

Fidler M, Wilkins J, Hooijmaijers R, Post T, Schoemaker R, Trame M, Xiong Y, Wang W (2019). "Nonlinear Mixed-Effects Model Development and Simulation Using nlmixr and Related R Open-Source Packages." CPT: Pharmacometrics & Systems Pharmacology, 8(9), 621-633. tools:::Rd_expr_doi("doi:10.1002/psp4.12445").

Schoemaker R, Fidler M, Laveille C, Wilkins J, Hooijmaijers R, Post T, Trame M, Xiong Y, Wang W (2019). "Performance of the SAEM and FOCEI Algorithms in the Open-Source, Nonlinear Mixed Effect Modeling Tool nlmixr." CPT: Pharmacometrics & Systems Pharmacology, 8(12), 923-930. tools:::Rd_expr_doi("doi:10.1002/psp4.12471").

Beal, S.L. Ways to Fit a PK Model with Some Data Below the Quantification Limit. J Pharmacokinet Pharmacodyn 28, 481-504 (2001). tools:::Rd_expr_doi("doi:10.1023/A:1012299115260")

See Also

nlmixr2_as_xtra(), catdv_vs_dvprobs()

Examples

if (FALSE) {
xpdb_nlmixr2 <- nlmixr_example("xpdb_nlmixr2")

nlmixr2_m3 <- nlmixr_example("nlmixr2_m3")
nlmixr2_m3 %>%
  set_var_types(catdv = CENS, dvprobs = BLQLIKE) %>%
  set_dv_probs(1, 1 ~ BLQLIKE, .dv_var = CENS) %>%
  set_var_levels(1, CENS = lvl_bin()) %>%
  catdv_vs_dvprobs(xlab = "basic", quiet = TRUE)
}