# Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

## Documentation for package ‘scaRabee’ version 1.1-3

- 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