# Graphical Independence Networks

## Documentation for package ‘gRain’ version 1.3.13

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

## Help Pages

A B C E F G I L M N O P Q R S U V

## -- A --

absorbEvidence | Set, update and remove evidence.
andtab | Conditional probability tables based on logical dependencies
andtable | Conditional probability tables based on logical dependencies
as.data.frame.grain_evidence | Evidence objects

## -- B --

booltab | Conditional probability tables based on logical dependencies

## -- C --

chest | Chest clinic example
chest_cpt | Chest clinic example
compile.cpt_grain | Compile a graphical independence network (a Bayesian network)
compile.grain | Compile a graphical independence network (a Bayesian network)
compile.pot_grain | Compile a graphical independence network (a Bayesian network)
compileCPT | Compile conditional probability tables / cliques potentials.
compilePOT | Compile conditional probability tables / cliques potentials.
components_extract | Extract conditional probabilities and clique potentials from data.
components_gather | Compile conditional probability tables / cliques potentials.
compute_p_evidence | Propagate a graphical independence network (a Bayesian network)
cpt | Create conditional probability table CPT.
cptable | Create conditional probability tables (CPTs)

## -- E --

evidence | Set, update and remove evidence.
evidence.grain | Set, update and remove evidence.
evidence<- | Set, update and remove evidence.
evidence<-.grain | Set, update and remove evidence.
evidence_object | Evidence objects
extractCPT | Extract conditional probabilities and clique potentials from data.
extractMARG | Extract conditional probabilities and clique potentials from data.
extractPOT | Extract conditional probabilities and clique potentials from data.

## -- F --

finding | Set, retrieve, and retract finding in Bayesian network.

## -- G --

generics | gRain generics
getEvidence | Set, update and remove evidence.
getFinding | Set, retrieve, and retract finding in Bayesian network.
get_superset_list | Get superset for each element in a list
grain | Graphical Independence Network
grain-main | Graphical Independence Network
grain-simulate | Simulate from an independence network
grain.CPTspec | Graphical Independence Network
grain.cpt_spec | Graphical Independence Network
grain.dModel | Graphical Independence Network
grain.graphNEL | Graphical Independence Network
grain.pot_spec | Graphical Independence Network
grain_compile | Compile a graphical independence network (a Bayesian network)
grain_evidence | Set, update and remove evidence.
grain_joint_evidence | Set joint evidence in grain objects
grain_predict | Make predictions from a probabilistic network
grain_propagate | Propagate a graphical independence network (a Bayesian network)
grass | Wet grass example
grass_cpt | Wet grass example

## -- I --

is.null_evi | Evidence objects
isCompiled | gRain generics
isCompiled<- | gRain generics
isPropagated | gRain generics
isPropagated<- | gRain generics

## -- L --

load-save-hugin | Load and save Hugin net files
loadHuginNet | Load and save Hugin net files
logical | Conditional probability tables based on logical dependencies

## -- M --

marg2pot | Extract conditional probabilities and clique potentials from data.
mendel | Mendelian segregation

## -- N --

new_evi | Evidence objects
new_jev | Set joint evidence in grain objects
nodeNames | gRain generics
nodeNames.grain | gRain generics
nodeStates | gRain generics
nodeStates.grain | gRain generics

## -- O --

ortab | Conditional probability tables based on logical dependencies
ortable | Conditional probability tables based on logical dependencies

## -- P --

parse_cpt | Compile conditional probability tables / cliques potentials.
parse_cpt, | Compile conditional probability tables / cliques potentials.
parse_cpt.default | Compile conditional probability tables / cliques potentials.
parse_cpt.xtabs,parse_cpt.cptable_class, | Compile conditional probability tables / cliques potentials.
pEvidence | Set, update and remove evidence.
pFinding | Set, retrieve, and retract finding in Bayesian network.
pot2marg | Extract conditional probabilities and clique potentials from data.
predict.grain | Make predictions from a probabilistic network
print.grain_evidence | Evidence objects
print.grain_joint_evidence | Set joint evidence in grain objects
propagate.grain | Propagate a graphical independence network (a Bayesian network)
propagateLS | Propagate a graphical independence network (a Bayesian network)
propagateLS__ | Propagate a graphical independence network (a Bayesian network)

## -- Q --

qgrain | Query a network
querygrain | Query a network
querygrain.grain | Query a network

## -- R --

repeatPattern | Create repeated patterns in Bayesian networks
replace-cpt | Replace CPTs in Bayesian network
replaceCPT | Replace CPTs in Bayesian network
replaceCPT.cpt_grain | Replace CPTs in Bayesian network
retractEvidence | Set, update and remove evidence.
retractFinding | Set, retrieve, and retract finding in Bayesian network.
retractJEvidence | Set joint evidence in grain objects
rip.grain | gRain generics

## -- S --

saveHuginNet | Load and save Hugin net files
setdiff_evi | Evidence objects
setEvidence | Set, update and remove evidence.
setFinding | Set, retrieve, and retract finding in Bayesian network.
setJEvidence | Set joint evidence in grain objects
simplify_query | Simplify output query to a Bayesian network
simulate.grain | Simulate from an independence network
subset.grain_evidence | Evidence objects

## -- U --

union_evi | Evidence objects
universe | gRain generics
universe.grain | gRain generics

## -- V --

varNames.grainEvidence_ | gRain generics
varNames.grain_evidence | Evidence objects
vpar.cpt_grain | gRain generics
vpar.cpt_spec | gRain generics