scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models
Version 1.1-3

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.

AuthorSebastien Bihorel
Date of publication2014-08-22 08:26:44
MaintainerSebastien Bihorel <sb.pmlab@gmail.com>
LicenseGPL-3
Version1.1-3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("scaRabee")

Getting started

Package overview

Popular man pages

dde.utils: Utility Functions for Delay Differential Equation Systems
examples.data: Datasets for scaRabee demo.
explicit.model: Explicit Equations
fitmle: Maximum Likelihood Estimator
fitmle.cov: Computation of the Covariance Matrix
get.secondary: Computation of Secondary Parameter Estimates
initialize.report: Initialize Report Files
See all...

All man pages Function index File listing

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

Functions

bound.parameters Man page Source code
compute.secondary Man page Source code
convert.infusion Man page Source code
create.intervals Man page Source code
dde.lags Man page Source code
dde.model Man page Source code
dde.syst Man page Source code
de.output Man page Source code
derived.parms Man page Source code
estimation.plot Man page Source code
example1.data Man page
example1.initials Man page
example2.data Man page
example2.initials Man page
example3.data Man page
example3.initials Man page
example4.data Man page
example4.initials Man page
example6.data Man page
example6.initials Man page
example8.data Man page
example8.initials Man page
explicit.model Man page Source code
finalize.grid.report Man page Source code
finalize.report Man page Source code
fitmle Man page Source code
fitmle.cov Man page Source code
get.cov.matrix Man page Source code
get.events Man page Source code
get.layout Man page Source code
get.parms.data Man page Source code
get.secondary Man page Source code
init.cond Man page Source code
init.update Man page Source code
initialize.report Man page Source code
input.scaling Man page Source code
make.dosing Man page Source code
ode.model Man page Source code
ode.syst Man page Source code
order.parms.list Man page Source code
pder Man page Source code
problem.eval Man page Source code
residual.report Man page Source code
scaRabee Man page
scaRabee-package Man page
scarabee.analysis Man page Source code
scarabee.check.model Man page Source code
scarabee.check.reserved Man page Source code
scarabee.clean Man page Source code
scarabee.directory Man page Source code
scarabee.gridsearch Man page Source code
scarabee.new Man page Source code
scarabee.read.data Man page Source code
scarabee.read.model Man page Source code
scarabee.read.parms Man page Source code
simulation.plot Man page Source code
simulation.report Man page Source code
weighting Man page Source code

Files

inst
inst/doc
inst/doc/scaRabee.R
inst/doc/scaRabee.pdf
inst/doc/scaRabee.Rnw
NAMESPACE
demo
demo/example5.R
demo/example4.R
demo/example3.R
demo/example8.R
demo/example1.R
demo/00Index
demo/example7.R
demo/example2.R
demo/example6.R
data
data/example8.data.rda
data/example3.initials.rda
data/example2.initials.rda
data/example2.data.rda
data/example8.initials.rda
data/example1.initials.rda
data/example4.data.rda
data/example1.data.rda
data/example6.data.rda
data/example6.initials.rda
data/example4.initials.rda
data/example3.data.rda
Changelog
R
R/derived.parms.R
R/scarabee.analysis.R
R/get.layout.R
R/init.update.R
R/ode.model.R
R/bound.parameters.R
R/input.scaling.R
R/order.parms.list.R
R/compute.secondary.R
R/create.intervals.R
R/weighting.R
R/fitmle.cov.R
R/convert.infusion.R
R/scarabee.read.model.R
R/scarabee.check.model.R
R/dde.model.R
R/dde.lags.R
R/estimation.plot.R
R/ode.syst.R
R/scarabee.read.data.R
R/make.dosing.R
R/fitmle.R
R/scarabee.new.R
R/initialize.report.R
R/get.parms.data.R
R/pder.R
R/get.secondary.R
R/problem.eval.R
R/get.events.R
R/explicit.model.R
R/scarabee.gridsearch.R
R/scarabee.read.parms.R
R/init.cond.R
R/dde.syst.R
R/get.cov.matrix.R
R/finalize.report.R
R/scarabee.directory.R
R/scarabee.check.reserved.R
R/simulation.plot.R
R/de.output.R
R/finalize.grid.report.R
R/simulation.report.R
R/scarabee.clean.R
R/residual.report.R
vignettes
vignettes/ode.utils.tex
vignettes/convert.infusion.tex
vignettes/Rd2latex.sh
vignettes/scarabee.read.model.tex
vignettes/dde.model.tex
vignettes/simulation.plot.tex
vignettes/simulation.report.tex
vignettes/estimation.plot.tex
vignettes/pder.tex
vignettes/leuko.pdf
vignettes/get.secondary.tex
vignettes/explicit.model.tex
vignettes/bound.parameters.tex
vignettes/problem.eval.tex
vignettes/order.parms.list.tex
vignettes/get.parms.data.tex
vignettes/finalize.grid.report.tex
vignettes/dde.utils.tex
vignettes/scaRabee.Rnw
vignettes/compute.secondary.tex
vignettes/scarabee.check.model.tex
vignettes/residual.report.tex
vignettes/finalize.report.tex
vignettes/examples.data.tex
vignettes/scarabee_R.pdf
vignettes/fitmle.tex
vignettes/ode.model.tex
vignettes/deinputs.png
vignettes/scarabee.clean.tex
vignettes/precursor.pdf
vignettes/scarabee.read.data.tex
vignettes/get.layout.tex
vignettes/get.events.tex
vignettes/scarabee.analysis.tex
vignettes/tmdd.pdf
vignettes/get.cov.matrix.tex
vignettes/scarabee.gridsearch.tex
vignettes/scaRabee_network_2.pdf
vignettes/initialize.report.tex
vignettes/scaRabee_network_1.pdf
vignettes/scaRabee.bib
vignettes/scaRabee-package.tex
vignettes/scarabee.check.reserved.tex
vignettes/scarabee.new.tex
vignettes/fitmle.cov.tex
vignettes/scarabee.directory.tex
vignettes/weighting.tex
vignettes/scarabee.read.parms.tex
MD5
build
build/vignette.rds
DESCRIPTION
man
man/scarabee.analysis.Rd
man/scarabee.gridsearch.Rd
man/convert.infusion.Rd
man/get.cov.matrix.Rd
man/residual.report.Rd
man/fitmle.cov.Rd
man/bound.parameters.Rd
man/order.parms.list.Rd
man/explicit.model.Rd
man/get.layout.Rd
man/scarabee.check.model.Rd
man/ode.utils.Rd
man/scarabee.clean.Rd
man/finalize.grid.report.Rd
man/scarabee.directory.Rd
man/estimation.plot.Rd
man/dde.model.Rd
man/examples.data.Rd
man/finalize.report.Rd
man/initialize.report.Rd
man/simulation.plot.Rd
man/get.secondary.Rd
man/scarabee.read.data.Rd
man/scaRabee-package.Rd
man/weighting.Rd
man/scarabee.check.reserved.Rd
man/dde.utils.Rd
man/scarabee.read.model.Rd
man/fitmle.Rd
man/pder.Rd
man/compute.secondary.Rd
man/scarabee.new.Rd
man/problem.eval.Rd
man/scarabee.read.parms.Rd
man/get.events.Rd
man/simulation.report.Rd
man/get.parms.data.Rd
man/ode.model.Rd
scaRabee documentation built on May 19, 2017, 8:32 a.m.

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