# Multi-state Path-Dependent Models in Discrete Time

## Documentation for package ‘mspath’ version 0.9-9

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

A B C D E F I J L M N O P Q R S T U W

## -- A --

activeCases | Calculator for Multi-State Path Models
activeCases-method | Calculator for Multi-State Path Models
activeCases<- | Calculator for Multi-State Path Models
activeCases<--method | Calculator for Multi-State Path Models
activeCases<--methods | Calculator for Multi-State Path Models
addResult | Add a Job Run's Results to the Analyzer
addResult-method | Class "runTime"
alldone | Distributed Calculation Shut-Down

## -- B --

bitMask | Class "readingError"
bitMask-method | Class "readingError"
boolMask | Class "readingError"
boolMask-method | Class "readingError"

## -- C --

calculate | calculate
calculate-method | calculate
calculate-methods | calculate
checkpoint | Checkpointing and progress information
coef-method | Results of a multi-state path calculation
coef-method | Class "mspathCoefficients"
coef-method | mspathEstimatedCoefficients
coef-method | Class "readingError"
cpuTime | Class "runTime"
cpuTime-method | Class "runTime"

## -- D --

deltamethod | The delta method
done | Finished with a Calculator
done-method | Finished with a Calculator
done-methods | Finished with a Calculator
doTrials | Run trials until told to stop

## -- E --

e2 | Allowed Misclassifications: e2
effort | Get measures of effort to perform a calculation
effort-method | Get measures of effort to perform a calculation
effort-methods | Get measures of effort to perform a calculation
endTime | Class "runTime"
endTime-method | Class "runTime"
estimateWork | Estimate Amount of Work for Computations
estimateWork-method | Estimate Amount of Work for Computations
estimateWork-methods | Estimate Amount of Work for Computations
expit | Inverse logit function

## -- F --

fixedSchedule | fixedSchedule

## -- I --

isAllFixed | Test for fixed objects
isAllFixed-method | Test for fixed objects
isAllFixed-method | Class "mspathCoefficients"
isAllFixed-methods | Test for fixed objects

## -- J --

job | Class "runTime"
job-method | Class "runTime"

## -- L --

logit | Logit function

## -- M --

master | Start Multi-State Path Model Distributed Calculations on Master Node
matrixCoef | Class "mspathCoefficients"
matrixCoef-method | Results of a multi-state path calculation
matrixCoef-method | Class "mspathCoefficients"
matrixCoef-methods | Class "mspathCoefficients"
MatrixExp | Matrix exponential
mean-method | Class "readingError"
minus2loglik | Retrieve Multi-State Path Model Likelihood
minus2loglik-method | Retrieve Multi-State Path Model Likelihood
minus2loglik-method | Results of a multi-state path calculation
minus2loglik-methods | Retrieve Multi-State Path Model Likelihood
mpirank | Class "runTime"
mpirank-method | Class "runTime"
mpirank<- | Class "runTime"
mpirank<--method | Class "runTime"
mspath | Multi-state Path-Dependent Models
mspath-class | Results of a multi-state path calculation
mspath.subset | subset a dataset based on estimated work
mspathAbstractCalculator-class | Calculator for Multi-State Path Models
mspathCalculator | Constructors for mspathCalculator Objects
mspathCalculator-class | Calculator for Multi-State Path Models
mspathCalculatorFromArgs | Constructors for mspathCalculator Objects
mspathCoefficients | Class "mspathCoefficients"
mspathCoefficients-class | Class "mspathCoefficients"
mspathDistributedCalculator | Constructors for mspathCalculator Objects
mspathDistributedCalculator-class | Distributed Calculator for Multi-State Path Models
mspathDistributedCalculatorFactory | Make a Constructor for mspathCalculator Objects
mspathEstimatedCoefficients | mspathEstimatedCoefficients
mspathEstimatedCoefficients-class | mspathEstimatedCoefficients
mspathFull-class | Results of a multi-state path calculation

## -- N --

nActiveCases | Calculator for Multi-State Path Models
nActiveCases-method | Calculator for Multi-State Path Models
nActiveCases-methods | Calculator for Multi-State Path Models
nBadNodes | Results of a multi-state path calculation
nBadNodes-method | Results of a multi-state path calculation
nBadNodes-method | Calculator for Multi-State Path Models
nBadNodes-methods | Results of a multi-state path calculation
nCases | Results of a multi-state path calculation
nCases-method | Results of a multi-state path calculation
nCases-method | Calculator for Multi-State Path Models
nCases-methods | Results of a multi-state path calculation
newRun | Class to Analyze Runtimes
newRun-method | Class to Analyze Runtimes
nGoodNodes | Results of a multi-state path calculation
nGoodNodes-method | Results of a multi-state path calculation
nGoodNodes-method | Calculator for Multi-State Path Models
nGoodNodes-methods | Results of a multi-state path calculation
nGoodPathNodes | Results of a multi-state path calculation
nGoodPathNodes-method | Results of a multi-state path calculation
nGoodPathNodes-method | Calculator for Multi-State Path Models
nGoodPathNodes-methods | Results of a multi-state path calculation
nGoodPaths | Results of a multi-state path calculation
nGoodPaths-method | Results of a multi-state path calculation
nGoodPaths-method | Calculator for Multi-State Path Models
nGoodPaths-methods | Results of a multi-state path calculation

## -- O --

optimizeWork | Calculator for Multi-State Path Models
optimizeWork-method | Calculator for Multi-State Path Models
optimizeWork-methods | Calculator for Multi-State Path Models
optresults | Results of a multi-state path calculation
optresults-method | Results of a multi-state path calculation
optresults-methods | Results of a multi-state path calculation
optresults<- | Results of a multi-state path calculation
optresults<--method | Results of a multi-state path calculation
optresults<--methods | Results of a multi-state path calculation

## -- P --

params<- | Calculator for Multi-State Path Models
params<--method | Calculator for Multi-State Path Models
params<--method | Distributed Calculator for Multi-State Path Models
params<--methods | Calculator for Multi-State Path Models
print-method | Results of a multi-state path calculation
print-method | Class "mspathCoefficients"
print-method | mspathEstimatedCoefficients
printFooter | Results of a multi-state path calculation
printFooter-method | Results of a multi-state path calculation
printFooter-methods | Results of a multi-state path calculation

## -- Q --

q2 | Allowed Transitions: q2

## -- R --

readingError | Class "readingError"
readingError-class | Class "readingError"
remoteTime<- | Class "runTime"
remoteTime<--method | Class "runTime"
results | Retrieve Results of Multi-State Path Calculation
results-method | Retrieve Results of Multi-State Path Calculation
results-methods | Retrieve Results of Multi-State Path Calculation
runAnalyzer | Class to Analyze Runtimes
runAnalyzer-class | Class to Analyze Runtimes
runeverywhere | Top Level of Distributed Calculation for Multi-State Path Model
runTime | runTime constructor
runTime-class | Class "runTime"

## -- S --

sd-method | Results of a multi-state path calculation
sd-method | Class "mspathCoefficients"
sd-method | mspathEstimatedCoefficients
show-method | Results of a multi-state path calculation
show-method | Class "mspathCoefficients"
show-method | mspathEstimatedCoefficients
sim1 | HCV Progression after liver transplant
sim2 | HCV Progression after liver transplant
sim3 | HCV Progression after liver transplant
simulateObservations | Calculator for Multi-State Path Models
simulateObservations-method | Calculator for Multi-State Path Models
simulateObservations-methods | Calculator for Multi-State Path Models
slave | Prepare for Distributed Multi-State Path Model Computations on Slaves
smoosh | Analyze Runtime Estimates and Actual Values
smoosh-method | Class to Analyze Runtimes
startTime | Class "runTime"
startTime-method | Class "runTime"

## -- T --

trial | Class "trial"
trial-class | Class "trial"

## -- U --

useActualTimes | Calculator for Multi-State Path Models
useActualTimes-method | Calculator for Multi-State Path Models
useActualTimes-methods | Calculator for Multi-State Path Models

## -- W --

waitTime | Class "runTime"
waitTime-method | Class "runTime"
wallTime | Class "runTime"
wallTime-method | Class "runTime"