View source: R/constrainMuSSE.R
constrainMuSSE | R Documentation |
Returns a likelihood function that has been constrained to match an MuSSE model of chromosome evolution yielding essentially the original chromevol model.
constrainMuSSE(data, lik, hyper = T,
polyploidy = F, s.lambda = T, s.mu = T,
verbose = F, constrain)
data |
This is the data matrix created by running |
lik |
This is a likelihood function created with make.MuSSE |
hyper |
If |
polyploidy |
If |
s.lambda |
If |
s.mu |
If |
verbose |
If |
constrain |
a list capable of carrying additional model constraints these include see details for specifications. |
If the rate identity matrix is returned rates are indicated by the numbers:
rate1 ascending aneuploidy - diploid or state 1 of hypertrait
rate2 descending aneuploidy - diploid or state 1 of hypertrait
rate3 ascending aneuploidy - polyploid or state 2 of hypertrait
rate4 descending aneuploidy - polyploid or state 2 of hypertrait
rate5 polyploidization of a diploid or state 1 of hypertrait
rate6 polploidization of a polyploid or state 2 of hypertrait
rate7 rediploidization of a polyploid
rate8 transitions from state 1 to 2 of hypertrait
rate9 transitions from state 2 to 1 of hypertrait
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.
constrained likelihood function is returned
Heath Blackmon
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