# Ternary Network Estimation

## Documentation for package ‘ternarynet’ version 1.38.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I M N P R S T X

## -- A --

attractorSummary | Summarize Attractors

## -- B --

backupStage | Ternary Network Fitting Parameters
backupStage-method | Ternary Network Fitting Parameters
backupStage<- | Ternary Network Fitting Parameters
backupStage<--method | Ternary Network Fitting Parameters
beta0 | Ternary Network Fitting Parameters
beta0-method | Ternary Network Fitting Parameters
beta0<- | Ternary Network Fitting Parameters
beta0<--method | Ternary Network Fitting Parameters

## -- C --

chi0 | Ternary Network Fitting Parameters
chi0-method | Ternary Network Fitting Parameters
chi0<- | Ternary Network Fitting Parameters
chi0<--method | Ternary Network Fitting Parameters
class:ternaryFit | Ternary Network Fit
class:ternaryFitParameters | Ternary Network Fitting Parameters
class:ternaryPost | Ternary Network Posterior

## -- D --

degreeObjMin | Ternary Network Fit
degreeObjMin-method | Ternary Network Fit
degreeObjMin<- | Ternary Network Fit
degreeObjMin<--method | Ternary Network Fit
degreeObjs | Ternary Network Posterior
degreeObjs-method | Ternary Network Posterior
degreeObjs<- | Ternary Network Posterior
degreeObjs<--method | Ternary Network Posterior
delta | Ternary Network Fitting Parameters
delta-method | Ternary Network Fitting Parameters
delta<- | Ternary Network Fitting Parameters
delta<--method | Ternary Network Fitting Parameters
dim-method | Ternary Network Fit
dim-method | Ternary Network Posterior

## -- E --

edgePenalty | Ternary Network Fitting Parameters
edgePenalty-method | Ternary Network Fitting Parameters
edgePenalty<- | Ternary Network Fitting Parameters
edgePenalty<--method | Ternary Network Fitting Parameters
epsilon | Ternary Network Fitting Parameters
epsilon-method | Ternary Network Fitting Parameters
epsilon<- | Ternary Network Fitting Parameters
epsilon<--method | Ternary Network Fitting Parameters
experimentNames | Ternary Network Fit
experimentNames-method | Ternary Network Fit
experimentNames-method | Ternary Network Posterior
experimentNames<- | Ternary Network Fit
experimentNames<--method | Ternary Network Fit
experimentNames<--method | Ternary Network Posterior

## -- F --

finalTemperature | Ternary Network Fit
finalTemperature-method | Ternary Network Fit
finalTemperature<- | Ternary Network Fit
finalTemperature<--method | Ternary Network Fit

## -- G --

geneNames | Ternary Network Fit
geneNames-method | Ternary Network Fit
geneNames-method | Ternary Network Posterior
geneNames<- | Ternary Network Fit
geneNames<--method | Ternary Network Fit
geneNames<--method | Ternary Network Posterior
graphObjMin | Ternary Network Fit
graphObjMin-method | Ternary Network Fit
graphObjMin<- | Ternary Network Fit
graphObjMin<--method | Ternary Network Fit
graphObjs | Ternary Network Posterior
graphObjs-method | Ternary Network Posterior
graphObjs<- | Ternary Network Posterior
graphObjs<--method | Ternary Network Posterior
graphPosterior | Network Topology

## -- I --

initialize-method | Ternary Network Fit
initialize-method | Ternary Network Fitting Parameters
initialize-method | Ternary Network Posterior
inputParams | Ternary Network Fit
inputParams-method | Ternary Network Fit
inputParams-method | Ternary Network Posterior
inputParams<- | Ternary Network Fit
inputParams<--method | Ternary Network Fit
inputParams<--method | Ternary Network Posterior

## -- M --

m0 | Ternary Network Fitting Parameters
m0-method | Ternary Network Fitting Parameters
m0<- | Ternary Network Fitting Parameters
m0<--method | Ternary Network Fitting Parameters
maxDegree | Ternary Network Fitting Parameters
maxDegree-method | Ternary Network Fitting Parameters
maxDegree<- | Ternary Network Fitting Parameters
maxDegree<--method | Ternary Network Fitting Parameters
maxStage | Ternary Network Fitting Parameters
maxStage-method | Ternary Network Fitting Parameters
maxStage<- | Ternary Network Fitting Parameters
maxStage<--method | Ternary Network Fitting Parameters
maxTransition | Ternary Network Fitting Parameters
maxTransition-method | Ternary Network Fitting Parameters
maxTransition<- | Ternary Network Fitting Parameters
maxTransition<--method | Ternary Network Fitting Parameters
minScore | Ternary Network Fit
minScore-method | Ternary Network Fit
minScore<- | Ternary Network Fit
minScore<--method | Ternary Network Fit

## -- N --

ne | Ternary Network Fitting Parameters
ne-method | Ternary Network Fitting Parameters
ne<- | Ternary Network Fitting Parameters
ne<--method | Ternary Network Fitting Parameters
neighborDegree | Ternary Network Fitting Parameters
neighborDegree-method | Ternary Network Fitting Parameters
neighborDegree<- | Ternary Network Fitting Parameters
neighborDegree<--method | Ternary Network Fitting Parameters
newScore | Ternary Network Fit
newScore-method | Ternary Network Fit
newScore<- | Ternary Network Fit
newScore<--method | Ternary Network Fit

## -- P --

pAddParent | Ternary Network Fitting Parameters
pAddParent-method | Ternary Network Fitting Parameters
pAddParent<- | Ternary Network Fitting Parameters
pAddParent<--method | Ternary Network Fitting Parameters
parallelFit | Fit ternary network models using parallel tempering
perturbationObj | Ternary Network Fit
perturbationObj-method | Ternary Network Fit
perturbationObj-method | Ternary Network Posterior
perturbationObj<- | Ternary Network Fit
perturbationObj<--method | Ternary Network Fit
perturbationObj<--method | Ternary Network Posterior
perturbationType | Ternary Network Fitting Parameters
perturbationType-method | Ternary Network Fitting Parameters
perturbationType<- | Ternary Network Fitting Parameters
perturbationType<--method | Ternary Network Fitting Parameters
pExchangeParent | Ternary Network Fitting Parameters
pExchangeParent-method | Ternary Network Fitting Parameters
pExchangeParent<- | Ternary Network Fitting Parameters
pExchangeParent<--method | Ternary Network Fitting Parameters
plotFit | Network Fit Plot
plotPost | Network Posterior Plot
plotTraces | Network Fit Traces
pNeighborhood | Ternary Network Fitting Parameters
pNeighborhood-method | Ternary Network Fitting Parameters
pNeighborhood<- | Ternary Network Fitting Parameters
pNeighborhood<--method | Ternary Network Fitting Parameters
predictAttractor | Predict the attractor(s) resulting from a given perturbation

## -- R --

rho | Ternary Network Fitting Parameters
rho-method | Ternary Network Fitting Parameters
rho<- | Ternary Network Fitting Parameters
rho<--method | Ternary Network Fitting Parameters

## -- S --

scores | Ternary Network Posterior
scores-method | Ternary Network Posterior
scores<- | Ternary Network Posterior
scores<--method | Ternary Network Posterior
scoreType | Ternary Network Fitting Parameters
scoreType-method | Ternary Network Fitting Parameters
scoreType<- | Ternary Network Fitting Parameters
scoreType<--method | Ternary Network Fitting Parameters
show-method | Ternary Network Fit
show-method | Ternary Network Fitting Parameters
show-method | Ternary Network Posterior
simulateSteadyState | Simulate Steady State Data
stageCount | Ternary Network Fit
stageCount-method | Ternary Network Fit
stageCount<- | Ternary Network Fit
stageCount<--method | Ternary Network Fit
steadyStateObj | Ternary Network Fit
steadyStateObj-method | Ternary Network Fit
steadyStateObj-method | Ternary Network Posterior
steadyStateObj<- | Ternary Network Fit
steadyStateObj<--method | Ternary Network Fit
steadyStateObj<--method | Ternary Network Posterior

## -- T --

tableObjMin | Ternary Network Fit
tableObjMin-method | Ternary Network Fit
tableObjMin<- | Ternary Network Fit
tableObjMin<--method | Ternary Network Fit
tableObjs | Ternary Network Posterior
tableObjs-method | Ternary Network Posterior
tableObjs<- | Ternary Network Posterior
tableObjs<--method | Ternary Network Posterior
ternaryFit | Ternary Network Fit
ternaryFit-class | Ternary Network Fit
ternaryFit-methods | Ternary Network Fit
ternaryFitParameters | Ternary Network Fitting Parameters
ternaryFitParameters-class | Ternary Network Fitting Parameters
ternaryFitParameters-methods | Ternary Network Fitting Parameters
ternaryPost | Ternary Network Posterior
ternaryPost-class | Ternary Network Posterior
ternaryPost-methods | Ternary Network Posterior
tnetfit | Ternary Network Fitting
tnetpost | Ternary Network Posterior Sampling
traces | Ternary Network Fit
traces-method | Ternary Network Fit
traces<- | Ternary Network Fit
traces<--method | Ternary Network Fit

## -- X --

xSeed | Ternary Network Fit
xSeed-method | Ternary Network Fit
xSeed<- | Ternary Network Fit
xSeed<--method | Ternary Network Fit