Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

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Documentation for package ‘scaRabee’ version 1.1-4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.

Help Pages

scaRabee-package	scaRabee toolkit
bound.parameters	Forces parameter estimates between defined boundaries.
compute.secondary	Computes secondary parameter values
convert.infusion	Process Infusion Information
create.intervals	Utility Functions for Ordinary Differential Equation Systems
dde.lags	Utility Functions for Delay Differential Equation Systems
dde.model	Delay Differential Equations
dde.syst	Utility Functions for Delay Differential Equation Systems
de.output	Utility Functions for Ordinary Differential Equation Systems
derived.parms	Utility Functions for Ordinary Differential Equation Systems
estimation.plot	Create Summary Estimation Plots
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.
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
init.cond	Utility Functions for Ordinary Differential Equation Systems
init.update	Utility Functions for Ordinary Differential Equation Systems
initialize.report	Initialize Report Files
input.scaling	Utility Functions for Ordinary Differential Equation Systems
make.dosing	Utility Functions for Ordinary Differential Equation Systems
ode.model	Ordinary Differential Equations
ode.syst	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	scaRabee toolkit
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.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