constrainMkn | R Documentation |
Returns a likelihood function that has been constrained to match an mkn model of chromosome evolution yielding essentially the original chromevol model.
constrainMkn(data, lik, hyper, polyploidy, verbose, oneway, constrain)
data |
This is the data matrix created by running |
lik |
This is a likelihood function created with make.mkn |
hyper |
|
polyploidy |
|
verbose |
If |
oneway |
Default is |
constrain |
Takes a list that can include up to 6 items to create different types of constrained models. Options are explained below in the details section. |
If the rate identity matrix is returned rates are indicated by the numbers:
rate1 ascending aneuploidy - state1
rate2 descending aneuploidy - state1
rate3 ascending aneuploidy - state2
rate4 descending aneuploidy - state2
rate5 polyploidization of state1
rate6 polploidization of state2
rate7 rediploidization of a state2
rate8 transitions from 1 to 2 for hyperstate
rate9 transitions from 2 to 1 for hyperstate
rate10 demipolyploidy for state1 - even
rate11 demipolyploidy for state1 - odd
rate12 demipolyploidy for state2 - even
rate13 demipolyploidy for state2 - odd
rate14 sex chromosome - autosome fusions (transitions from hyperstate 1 to 2)
rate15 Ro transitions (transitions from hyperstate 2 to 1)
The argument constrain
can contain any of the items listed below. The default state is shown.
drop.poly=F
Sets polyploidy rate to zero
drop.demi=F
Sets demiploidy rate to zero
symmetric=F
Sets all chromosome change rates to be symmetric
nometa=F
Drops metastate from analysis
meta="ARD"
Can be set as either "ARD"
or "SYM"
these have the same meanings as ace
in the APE package.
saf.model=F
Models transitions between hyperstates as sex chromosome-autosome fusions (1 -> 2) and Ro transitions (2 -> 1). Follows model described in Anderson et al. 2020.
sym.hyperstates=F
If TRUE
, sets one ascendeing and descending transition rate for hyperstates one and two.
constrained likelihood function is returned
Heath Blackmon
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