Package: scaRabee 1.1-4

Sebastien Bihorel

scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

A port of the Scarabee toolkit originally written as a Matlab-based application. scaRabee provides a framework for simulation and optimization of pharmacokinetic-pharmacodynamic models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.

Authors:Sebastien Bihorel [aut, cre]

scaRabee_1.1-4.tar.gz
scaRabee_1.1-4.tar.gz(r-4.5-noble)scaRabee_1.1-4.tar.gz(r-4.4-noble)
scaRabee_1.1-4.tgz(r-4.4-emscripten)scaRabee_1.1-4.tgz(r-4.3-emscripten)
scaRabee.pdf |scaRabee.html✨
scaRabee/json (API)

# Install 'scaRabee' in R:

install.packages('scaRabee', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example1.data - Datasets for scaRabee demo.
example1.initials - Datasets for scaRabee demo.
example2.data - Datasets for scaRabee demo.
example2.initials - Datasets for scaRabee demo.
example3.data - Datasets for scaRabee demo.
example3.initials - Datasets for scaRabee demo.
example4.data - Datasets for scaRabee demo.
example4.initials - Datasets for scaRabee demo.
example6.data - Datasets for scaRabee demo.
example6.initials - Datasets for scaRabee demo.
example8.data - Datasets for scaRabee demo.
example8.initials - Datasets for scaRabee demo.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 279 downloads 44 exports 6 dependencies

Last updated 3 years agofrom:c329982527. Checks:1 OK, 2 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 17 2025
R-4.5-linux	NOTE	Mar 17 2025
R-4.4-linux	NOTE	Mar 17 2025

Exports:bound.parameters compute.secondary convert.infusion create.intervals dde.lags dde.model dde.syst de.output derived.parms estimation.plot explicit.model finalize.grid.report finalize.report fitmle fitmle.cov get.cov.matrix get.events get.layout get.parms.data get.secondary init.cond init.update initialize.report input.scaling make.dosing ode.model ode.syst order.parms.list pder problem.eval residual.report scarabee.analysis scarabee.check.model scarabee.check.reserved scarabee.clean scarabee.directory scarabee.gridsearch scarabee.new scarabee.read.data scarabee.read.model scarabee.read.parms simulation.plot simulation.report weighting

Dependencies:deSolve lattice Matrix neldermead optimbase optimsimplex

scaRabee: An R-based Tool for Model Simulation and Optimization in Pharmacometrics

Sebastien Bihorel

Rendered frommanual.Rmdusingknitr::rmarkdownon Mar 17 2025.

Last update: 2022-02-04
Started: 2022-02-04

Citation

To cite package ‘scaRabee’ in publications use:

Bihorel S (2022). scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models. R package version 1.1-4, https://CRAN.R-project.org/package=scaRabee.

Corresponding BibTeX entry:

  @Manual{,
    title = {scaRabee: Optimization Toolkit for
      Pharmacokinetic-Pharmacodynamic Models},
    author = {Sebastien Bihorel},
    year = {2022},
    note = {R package version 1.1-4},
    url = {https://CRAN.R-project.org/package=scaRabee},
  }

Readme and manuals

scaRabee: Optimization toolkit for pharmacometric models

scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based application. It provides a framework for simulation and optimization of pharmacometric models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.

Help Manual

Help page	Topics
scaRabee toolkit	scaRabee-package scaRabee
Forces parameter estimates between defined boundaries.	bound.parameters
Computes secondary parameter values	compute.secondary
Process Infusion Information	convert.infusion
Delay Differential Equations	dde.model
Utility Functions for Delay Differential Equation Systems	dde.lags dde.syst
Create Summary Estimation Plots	estimation.plot
Datasets for scaRabee demo.	example1.data example1.initials example2.data example2.initials example3.data example3.initials example4.data example4.initials example6.data example6.initials example8.data example8.initials
Explicit Equations	explicit.model
Finalize Direct Grid Search Report	finalize.grid.report
Finalize Estimation Report	finalize.report
Maximum Likelihood Estimator	fitmle
Computation of the Covariance Matrix	fitmle.cov
Computation of the Covariance Matrix	get.cov.matrix
Create events from bolus dosing records.	get.events
Layout for Lattice Functions	get.layout
Extract data from scaRabee parameter table	get.parms.data
Computation of Secondary Parameter Estimates	get.secondary
Initialize Report Files	initialize.report
Ordinary Differential Equations	ode.model
Utility Functions for Ordinary Differential Equation Systems	create.intervals de.output derived.parms init.cond init.update input.scaling make.dosing ode.syst
Sort a scaRabee parameter table	order.parms.list
Compute Matrix of Partial Derivatives	pder
Evaluation of structural and residual variability models	problem.eval
Creation of Prediction & Residual Report	residual.report
Run a scaRabee Analysis	scarabee.analysis
Check scaRabee Models	scarabee.check.model
Check for Reserved Variable Names	scarabee.check.reserved
Cleaning of the Run Directory	scarabee.clean
Creation of the Run Directory	scarabee.directory
Direct Grid Search Utility	scarabee.gridsearch
Create a scaRabee Analysis Folder	scarabee.new
Read scaRabee Data File	scarabee.read.data
Read scaRabee Model File	scarabee.read.model
Read scaRabee Parameter File	scarabee.read.parms
Create Simulation Plots	simulation.plot
Simulations	simulation.report
Residual Variability	weighting