cheshire-likelihood
cheshire-likelihood
cheshire.likelihood
LikelihoodEvaluation
LikelihoodEvaluation
LikelihoodKernel
Partition
Partition
PartitionKernel
EdgeLikelihood
NodeLikelihood
PartitionKernel
TreeLikelihood
TreeLikelihood
PostOrderLeaf
PostOrderNode
PreOrderNode
PreOrderRootParent
cheshire-likelihood
/
cheshire.likelihood
/
Partition
Partition
trait
Partition
[
F
[
_
],
R
]
Companion:
object
Graph
Supertypes
class
Object
trait
Matchable
class
Any
Type members
Value members
Type members
Types
type
Clv
=
NodeClv
|
TipClv
type
Matrix
type
Model
type
NodeClv
type
Partial
=
Ppv
|
Clv
type
Ppv
type
TipClv
Value members
Abstract methods
def
backcast
(
y:
Clv
,
P:
Matrix
):
F
[
NodeClv
]
def
backcastProduct
(
y:
Clv
,
Py:
Matrix
,
z:
Clv
,
Pz:
Matrix
):
F
[
NodeClv
]
def
categoryCount
:
Int
def
edgeLikelihood
(
model:
Model
,
ppv:
Ppv
,
clv:
Clv
)(
t:
R
):
F
[
LikelihoodEvaluation
[
F
,
R
]]
def
forecast
(
x:
Ppv
,
P:
Matrix
):
F
[
Ppv
]
def
integrateProduct
(
x:
Ppv
,
y:
Clv
):
F
[
R
]
def
matrix
(
model:
Model
,
t:
R
):
F
[
Matrix
]
def
model
(
freqs:
IndexedSeq
[
R
],
params:
IndexedSeq
[
R
],
rate:
R
,
alpha:
R
):
F
[
Model
]
def
nodeLikelihood
(
model:
Model
,
ppv:
Ppv
,
parentHeight:
R
,
leftClv:
Clv
,
leftHeight:
R
,
rightClv:
Clv
,
rightHeight:
R
)(
t:
R
):
F
[
LikelihoodEvaluation
[
F
,
R
]]
@targetName
("ppvProduct")
def
product
(
x:
Ppv
,
y:
Clv
):
F
[
Ppv
]
@targetName
("clvProduct")
def
product
(
x:
Clv
,
y:
Clv
):
F
[
NodeClv
]
def
rates
(
model:
Model
):
F
[
IndexedSeq
[
R
]]
def
seed
(
model:
Model
):
F
[
Ppv
]
def
seedAndIntegrate
(
model:
Model
,
x:
Clv
):
F
[
R
]
def
tips
:
IndexedSeq
[
TipClv
]