def unrelated_model(modelWh, modelPu):
'model mom, dad, child as independent'
pstate = model.VarFilterState('Pu', modelPu)
wstate = model.VarFilterState('Wh', modelWh)
prior = model.StateGraph({'START': {pstate: 0.9, wstate: 0.1}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
pstate: {
stop: 1.
},
wstate: {
stop: 1.
},
robomendel.noneState: {
stop: 1.
}
})
dg = model.DependencyGraph({
'START': {
'mom': prior,
'dad': prior,
'child': prior
},
'mom': {
'STOP': term
},
'dad': {
'STOP': term
},
'child': {
'STOP': term
}
})
return dg
def mixture_model2(modelWh, modelPu):
'model process as single species, with mixture emission, supports multiple matingID'
mixModel = get_mix_model(modelWh, modelPu)
peaSpecies = model.VarFilterState('pea', mixModel)
prior = model.StateGraph({'START': {peaSpecies: 1.0}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
peaSpecies: {
stop: 1.
},
robomendel.noneState: {
stop: 1.
}
})
sct = robomendel.SpeciesCrossTransition()
moms = model.BranchGenerator('mom', prior, iterTag='matingID')
dads = model.BranchGenerator('dad', prior, iterTag='matingID')
dg = model.DependencyGraph(
{
'START': {
moms: {},
dads: {}
},
('mom', 'dad'): {
'child': sct
},
'child': {
'STOP': term
}
},
joinTags=('matingID', ))
return dg
def mixture_model(modelWh, modelPu):
'model process as single species, with mixture emission'
mixModel = get_mix_model(modelWh, modelPu)
peaSpecies = model.VarFilterState('pea', mixModel)
prior = model.StateGraph({'START': {peaSpecies: 1.0}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
peaSpecies: {
stop: 1.
},
robomendel.noneState: {
stop: 1.
}
})
sct = robomendel.SpeciesCrossTransition()
dg = model.DependencyGraph({
'START': {
'mom': prior,
'dad': prior
},
('mom', 'dad'): {
'child': sct
},
'child': {
'STOP': term
}
})
return dg
def multicond_setup(modelWh, modelPu, pHybrid=0.):
pstate = model.VarFilterState('Pu', modelPu)
wstate = model.VarFilterState('Wh', modelWh)
prior = model.StateGraph({'START': {pstate: 0.9, wstate: 0.1}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
pstate: {
stop: 1.
},
wstate: {
stop: 1.
},
robomendel.noneState: {
stop: 1.
}
})
sct = robomendel.SpeciesCrossTransition(pHybrid=pHybrid)
return pstate, wstate, prior, stop, term, sct
def unrelated_model2(modelWh, modelPu):
'model mom, dad, child as independent, supports multiple matingID'
pstate = model.VarFilterState('Pu', modelPu)
wstate = model.VarFilterState('Wh', modelWh)
prior = model.StateGraph({'START': {pstate: 0.9, wstate: 0.1}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
pstate: {
stop: 1.
},
wstate: {
stop: 1.
},
robomendel.noneState: {
stop: 1.
}
})
moms = model.BranchGenerator('mom', prior, iterTag='matingID')
dads = model.BranchGenerator('dad', prior, iterTag='matingID')
kids = model.BranchGenerator('child', prior, iterTag='matingID')
dg = model.DependencyGraph(
{
'START': {
moms: {},
dads: {},
kids: {}
},
'mom': {
'STOP': term
},
'dad': {
'STOP': term
},
'child': {
'STOP': term
}
},
joinTags=('matingID', ))
return dg
def environmental_model(modelWh, modelPu):
'model wh / pu as random extrinsic variable'
def filter_from_node(fromNode, *args):
return dict(var=fromNode.var.label)
pstate = model.VarFilterState('Pu', modelPu, filter_f=filter_from_node)
wstate = model.VarFilterState('Wh', modelWh, filter_f=filter_from_node)
peaSpecies = model.SilentState('pea')
prior = model.StateGraph({'START': {peaSpecies: 1.}})
extSG = model.StateGraph({peaSpecies: {pstate: 0.9, wstate: 0.1}})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({pstate: {stop: 1.}, wstate: {stop: 1.}})
sct = robomendel.SpeciesCrossTransition()
dg = model.DependencyGraph({
'START': {
'mom': prior,
'dad': prior
},
'mom': {
'ext': extSG
},
'dad': {
'ext': extSG
},
('mom', 'dad'): {
'child': sct
},
'child': {
'ext': extSG
},
'ext': {
'STOP': term
}
})
return dg
def environmental_model2(modelWh, modelPu):
'model wh / pu as random extrinsic variable, supports multiple matingID'
def filter_from_node(fromNode, *args):
return dict(var=fromNode.var.label)
pstate = model.VarFilterState('Pu', modelPu, filter_f=filter_from_node)
wstate = model.VarFilterState('Wh', modelWh, filter_f=filter_from_node)
peaSpecies = model.SilentState('pea')
prior = model.StateGraph({'START': {peaSpecies: 1.}})
noSpecies = model.SilentState('no-species')
extNone = model.VarFilterState('ext-none',
model.EmissionDict({None: 1.}),
filter_f=filter_from_node)
extSG = model.StateGraph({
peaSpecies: {
pstate: 0.9,
wstate: 0.1
},
noSpecies: {
extNone: 1.
}
})
stop = model.StopState(useObsLabel=False)
term = model.StateGraph({
pstate: {
stop: 1.
},
wstate: {
stop: 1.
},
extNone: {
stop: 1.
}
})
sct = robomendel.SpeciesCrossTransition(noneState=noSpecies)
moms = model.BranchGenerator('mom', prior, iterTag='matingID')
dads = model.BranchGenerator('dad', prior, iterTag='matingID')
dg = model.DependencyGraph(
{
'START': {
moms: {},
dads: {}
},
'mom': {
'ext': extSG
},
'dad': {
'ext': extSG
},
('mom', 'dad'): {
'child': sct
},
'child': {
'ext': extSG
},
'ext': {
'STOP': term
}
},
joinTags=('matingID', ))
return dg