scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

Share:

scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based application. It 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.

Author
Sebastien Bihorel
Date of publication
2014-08-22 08:26:44
Maintainer
Sebastien Bihorel <sb.pmlab@gmail.com>
License
GPL-3
Version
1.1-3

View on CRAN

Man pages

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

Files in this package

scaRabee
scaRabee/inst
scaRabee/inst/doc
scaRabee/inst/doc/scaRabee.R
scaRabee/inst/doc/scaRabee.pdf
scaRabee/inst/doc/scaRabee.Rnw
scaRabee/NAMESPACE
scaRabee/demo
scaRabee/demo/example5.R
scaRabee/demo/example4.R
scaRabee/demo/example3.R
scaRabee/demo/example8.R
scaRabee/demo/example1.R
scaRabee/demo/00Index
scaRabee/demo/example7.R
scaRabee/demo/example2.R
scaRabee/demo/example6.R
scaRabee/data
scaRabee/data/example8.data.rda
scaRabee/data/example3.initials.rda
scaRabee/data/example2.initials.rda
scaRabee/data/example2.data.rda
scaRabee/data/example8.initials.rda
scaRabee/data/example1.initials.rda
scaRabee/data/example4.data.rda
scaRabee/data/example1.data.rda
scaRabee/data/example6.data.rda
scaRabee/data/example6.initials.rda
scaRabee/data/example4.initials.rda
scaRabee/data/example3.data.rda
scaRabee/Changelog
scaRabee/R
scaRabee/R/derived.parms.R
scaRabee/R/scarabee.analysis.R
scaRabee/R/get.layout.R
scaRabee/R/init.update.R
scaRabee/R/ode.model.R
scaRabee/R/bound.parameters.R
scaRabee/R/input.scaling.R
scaRabee/R/order.parms.list.R
scaRabee/R/compute.secondary.R
scaRabee/R/create.intervals.R
scaRabee/R/weighting.R
scaRabee/R/fitmle.cov.R
scaRabee/R/convert.infusion.R
scaRabee/R/scarabee.read.model.R
scaRabee/R/scarabee.check.model.R
scaRabee/R/dde.model.R
scaRabee/R/dde.lags.R
scaRabee/R/estimation.plot.R
scaRabee/R/ode.syst.R
scaRabee/R/scarabee.read.data.R
scaRabee/R/make.dosing.R
scaRabee/R/fitmle.R
scaRabee/R/scarabee.new.R
scaRabee/R/initialize.report.R
scaRabee/R/get.parms.data.R
scaRabee/R/pder.R
scaRabee/R/get.secondary.R
scaRabee/R/problem.eval.R
scaRabee/R/get.events.R
scaRabee/R/explicit.model.R
scaRabee/R/scarabee.gridsearch.R
scaRabee/R/scarabee.read.parms.R
scaRabee/R/init.cond.R
scaRabee/R/dde.syst.R
scaRabee/R/get.cov.matrix.R
scaRabee/R/finalize.report.R
scaRabee/R/scarabee.directory.R
scaRabee/R/scarabee.check.reserved.R
scaRabee/R/simulation.plot.R
scaRabee/R/de.output.R
scaRabee/R/finalize.grid.report.R
scaRabee/R/simulation.report.R
scaRabee/R/scarabee.clean.R
scaRabee/R/residual.report.R
scaRabee/vignettes
scaRabee/vignettes/ode.utils.tex
scaRabee/vignettes/convert.infusion.tex
scaRabee/vignettes/Rd2latex.sh
scaRabee/vignettes/scarabee.read.model.tex
scaRabee/vignettes/dde.model.tex
scaRabee/vignettes/simulation.plot.tex
scaRabee/vignettes/simulation.report.tex
scaRabee/vignettes/estimation.plot.tex
scaRabee/vignettes/pder.tex
scaRabee/vignettes/leuko.pdf
scaRabee/vignettes/get.secondary.tex
scaRabee/vignettes/explicit.model.tex
scaRabee/vignettes/bound.parameters.tex
scaRabee/vignettes/problem.eval.tex
scaRabee/vignettes/order.parms.list.tex
scaRabee/vignettes/get.parms.data.tex
scaRabee/vignettes/finalize.grid.report.tex
scaRabee/vignettes/dde.utils.tex
scaRabee/vignettes/scaRabee.Rnw
scaRabee/vignettes/compute.secondary.tex
scaRabee/vignettes/scarabee.check.model.tex
scaRabee/vignettes/residual.report.tex
scaRabee/vignettes/finalize.report.tex
scaRabee/vignettes/examples.data.tex
scaRabee/vignettes/scarabee_R.pdf
scaRabee/vignettes/fitmle.tex
scaRabee/vignettes/ode.model.tex
scaRabee/vignettes/deinputs.png
scaRabee/vignettes/scarabee.clean.tex
scaRabee/vignettes/precursor.pdf
scaRabee/vignettes/scarabee.read.data.tex
scaRabee/vignettes/get.layout.tex
scaRabee/vignettes/get.events.tex
scaRabee/vignettes/scarabee.analysis.tex
scaRabee/vignettes/tmdd.pdf
scaRabee/vignettes/get.cov.matrix.tex
scaRabee/vignettes/scarabee.gridsearch.tex
scaRabee/vignettes/scaRabee_network_2.pdf
scaRabee/vignettes/initialize.report.tex
scaRabee/vignettes/scaRabee_network_1.pdf
scaRabee/vignettes/scaRabee.bib
scaRabee/vignettes/scaRabee-package.tex
scaRabee/vignettes/scarabee.check.reserved.tex
scaRabee/vignettes/scarabee.new.tex
scaRabee/vignettes/fitmle.cov.tex
scaRabee/vignettes/scarabee.directory.tex
scaRabee/vignettes/weighting.tex
scaRabee/vignettes/scarabee.read.parms.tex
scaRabee/MD5
scaRabee/build
scaRabee/build/vignette.rds
scaRabee/DESCRIPTION
scaRabee/man
scaRabee/man/scarabee.analysis.Rd
scaRabee/man/scarabee.gridsearch.Rd
scaRabee/man/convert.infusion.Rd
scaRabee/man/get.cov.matrix.Rd
scaRabee/man/residual.report.Rd
scaRabee/man/fitmle.cov.Rd
scaRabee/man/bound.parameters.Rd
scaRabee/man/order.parms.list.Rd
scaRabee/man/explicit.model.Rd
scaRabee/man/get.layout.Rd
scaRabee/man/scarabee.check.model.Rd
scaRabee/man/ode.utils.Rd
scaRabee/man/scarabee.clean.Rd
scaRabee/man/finalize.grid.report.Rd
scaRabee/man/scarabee.directory.Rd
scaRabee/man/estimation.plot.Rd
scaRabee/man/dde.model.Rd
scaRabee/man/examples.data.Rd
scaRabee/man/finalize.report.Rd
scaRabee/man/initialize.report.Rd
scaRabee/man/simulation.plot.Rd
scaRabee/man/get.secondary.Rd
scaRabee/man/scarabee.read.data.Rd
scaRabee/man/scaRabee-package.Rd
scaRabee/man/weighting.Rd
scaRabee/man/scarabee.check.reserved.Rd
scaRabee/man/dde.utils.Rd
scaRabee/man/scarabee.read.model.Rd
scaRabee/man/fitmle.Rd
scaRabee/man/pder.Rd
scaRabee/man/compute.secondary.Rd
scaRabee/man/scarabee.new.Rd
scaRabee/man/problem.eval.Rd
scaRabee/man/scarabee.read.parms.Rd
scaRabee/man/get.events.Rd
scaRabee/man/simulation.report.Rd
scaRabee/man/get.parms.data.Rd
scaRabee/man/ode.model.Rd