R/data.R

In xpose.xtras: Extra Functionality for the 'xpose' Package

#' An example `xpose_set` object
#'
#' A set of identical `xpdb` objects to demo various features of `xpose.xtras`.
#'
#' @format ## `xpose_set`
#' An `xpose_set` object of length 4 with a single lineage.
#'
#' @source Assembled from the `xpdb_ex_pk` object in the `xpose` package.
"xpdb_set"

#' An example `xp_xtras` object
#'
#' The <[`xpdb_ex_pk`][xpose::xpdb_ex_pk]> object converted to `xp_xtras`. For examples.
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object with no extra data filled.
#'
#' @source Assembled from the `xpdb_ex_pk` object in the `xpose` package.
"xpdb_x"

#' A more complex example of `xpose_set` object
#'
#' Model-building set for the phenobarbital in neonates PK data
#' used across multiple packages.
#'
#' This is not a demonstration of high-quality model-building,
#' it is just a typical and simple example.
#'
#' @format ## `xpose_set`
#' An `xpose_set` object of length 14 with a branched lineage.
#'
#' @source https://doi.org/10.1159/000457062 and nlmixr2data::pheno_sd
"pheno_set"

#' An `xp_xtras` example of a base model
#'
#' Base model for phenobarbital in neonates.
#'
#' This is `run6` in <[`pheno_set`]>
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @source https://doi.org/10.1159/000457062 and nlmixr2data::pheno_sd
"pheno_base"

#' An `xp_xtras` example of a final model
#'
#' Final model for phenobarbital in neonates.
#'
#' This is re-parameterized from the covariate-building work, which
#' in this case did not identify a relationship with Apgar score.
#'
#' This is `run16` in <[`pheno_set`]>
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @source https://doi.org/10.1159/000457062 and nlmixr2data::pheno_sd
"pheno_final"

#' An `xp_xtras` example of a final model
#'
#' Final model for phenobarbital in neonates.
#'
#' This is the same as [`pheno_final`] but fitted with SAEM/IMP.
#'
#' Not a part of <[`pheno_set`]>
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @source https://doi.org/10.1159/000457062 and nlmixr2data::pheno_sd
"pheno_saem"

#' A tibble of mock data used for fitting vismodegib models
#'
#' The referenced work presents two alternative modeling approaches
#' for muscle spasm response to vismodegib. There is a mock
#' dataset for one person, and using the provided model a 50 participant
#' mock dataset could be generated.
#'
#'
#' @format ## `tibble`
#' An `tibble`.
#'
#' @references
#' Lu, T., Yang, Y., Jin, J.Y. and Kågedal, M. (2020),
#' Analysis of Longitudinal-Ordered Categorical Data for
#' Muscle Spasm Adverse Event of Vismodegib: Comparison
#' Between Different Pharmacometric Models. CPT
#' Pharmacometrics Syst. Pharmacol., 9: 96-105.
#' https://doi.org/10.1002/psp4.12487
#'
#' @source Generated using sup-0009 and sup-0010 from the reference.
#'
"vismodegib"

#' An `xp_xtras` example of the proportional odds categorical vismodegib model
#'
#' The referenced work presents two alternative modeling approaches
#' for muscle spasm response to vismodegib. This is a fit of the
#' provided proportional odds model to the 50 participant mock data.
#'
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @references
#' Lu, T., Yang, Y., Jin, J.Y. and Kågedal, M. (2020),
#' Analysis of Longitudinal-Ordered Categorical Data for
#' Muscle Spasm Adverse Event of Vismodegib: Comparison
#' Between Different Pharmacometric Models. CPT
#' Pharmacometrics Syst. Pharmacol., 9: 96-105.
#' https://doi.org/10.1002/psp4.12487
#'
#' @source Derived from sup-0009 and sup-0010 from the reference.
#'
"vismo_pomod"

#' An `xp_xtras` example of the discrete-time Markov model of categorical vismodegib data
#'
#' The referenced work presents two alternative modeling approaches
#' for muscle spasm response to vismodegib. This is a fit of the
#' provided discrete-time Markov model to the 50 participant mock data.
#'
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @references
#' Lu, T., Yang, Y., Jin, J.Y. and Kågedal, M. (2020),
#' Analysis of Longitudinal-Ordered Categorical Data for
#' Muscle Spasm Adverse Event of Vismodegib: Comparison
#' Between Different Pharmacometric Models. CPT
#' Pharmacometrics Syst. Pharmacol., 9: 96-105.
#' https://doi.org/10.1002/psp4.12487
#'
#' @source Derived from sup-0009 and sup-0010 from the reference.
#'
"vismo_dtmm"

#' An `xp_xtras` example of an M3 model
#'
#' A representative PK/PD model with M3 fitting applied.
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @references
#' Beal, S.L. Ways to Fit a PK Model with Some Data
#' Below the Quantification Limit. J Pharmacokinet
#' Pharmacodyn 28, 481-504 (2001).
#' https://doi.org/10.1023/A:1012299115260
#'
#' Prybylski JP. Indirect modeling of derived outcomes:
#' Are minor prediction discrepancies a cause for concern?
#' CPT Pharmacometrics Syst Pharmacol. 2024; 00: 1-9.
#' doi:10.1002/psp4.13219
#'
#' @source https://doi.org/10.1002/psp4.13219
"pkpd_m3"

#' An `xp_xtras` example of an M3 model (dataset)
#'
#' The dataset used to fit the [`pkpd_m3`] model.
#'
#' @format ## `xp_xtras`
#' An `xp_xtras` object.
#'
#' @references
#' Prybylski JP. Indirect modeling of derived outcomes:
#' Are minor prediction discrepancies a cause for concern?
#' CPT Pharmacometrics Syst Pharmacol. 2024; 00: 1-9.
#' doi:10.1002/psp4.13219
#'
#' @source https://doi.org/10.1002/psp4.13219
"pkpd_m3_df"