Rev Language Reference
fnInvASRV - fnInvASRV
Add an invariable-sites component to a site model.
Usage
fnInvASRV(SiteMixtureModel submodel, RealPos pInv)
Arguments
| submodel : | SiteMixtureModel (pass by const reference) |
| Sub-rate matrix. | |
| pInv : | RealPos (pass by const reference) |
| The fraction of invariable sites. |
Return Type
Details
This model specifies that some fraction pInv of sites are invariable.
If the site model parameter is a mixture model with m components, this function will return a model with
m+1 components.
Example
# fnInvASRV( ) creates a mixture model by adding invariant sites to an underlying site model.
for (i in 1:10) { taxa[i] = taxon("T"+i) }
psi ~ dnBDP(lambda=1, rootAge=1, taxa=taxa)
p_inv ~ dnUniform(0,1)
M := fnInvASRV( fnJC(4), p_inv)
seq ~ dnPhyloCTMC(psi, M, type="DNA", nSites=10)
# As an alternative approach, models can be built up iteratively using pipes.
M := fnJC(4) |> fnInv(p_inv)
M := fnJC(4) |> fnGammaASRV(alpha, 4) |> fnInvASRV(p_inv) # This has 5 (4+1) components - faster.
M := fnJC(4) |> fnInvASRV(p_inv) |> fnGammaASRV(alpha, 4) # This has 8 (4*2) components - slower.
# Not recommended -- illustration only. 3 components.
M := fnJC(4) |> fnInv(p1) |> fnInv(p2) # Fraction of invariable sites is p2 + (1-p2)*p1
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