Rev Language Reference

fnScale - fnScale

Scale a vector of SiteMixtureModels

Usage

fnScale(SiteMixtureModel model, RealPos rate)

Arguments

model : SiteMixtureModel (pass by const reference)
The mixture model to scale.
rate : RealPos (pass by const reference)
The factor by which to scale the speed.

Return Type

SiteMixtureModel

Details

This function has two forms. The first form takes a SiteMixtureModel `model` and scales it by a rate `rate`. This form returns SiteMixtureModel. The second form takes SiteMixtureModel[] `models` and RealPos[] `rates`, and scales `models[i]` by `rates[i]`. This form returns SiteMixtureModel[]. As a shortcut, if the second argument `rates` is a vector but the first element `model` is not, then the first argument will be automatically replaced with a vector of SiteMixtureModels of the same length as `rates`, where each element is identical to `model`.

Example

Q = fnJC(4)                    # The rate of Q is 1

# Operating on SiteMixtureModel
Q2 = fnScale(Q,2)              # The rate of Q2 is 2

# Operating on SiteMixtureModel[]
Qs = fnScale([Q,Q],[1,2])      # Qs[1] and Qs[2] have rates 1 and 2
Qs = fnScale(Q,    [1,2])      # An abbreviation for the above.

# We can build up models iteratively using pipes
Qs = Q |> fnScale([1,2])       # A shorter abbreviation.

# A JC+LogNormal[4] ASRV model
site_rates := dnLognormal(0,lsigma) |> fnDiscretizeDistribution(4)
MM := fnJC(4) |> fnScale(site_rates) |> fnMixtureASRV()
M := fnScale(MM, 1/MM.rate())

# A FreeRates[5] ASRV model
rates ~ dnDirichlet( [1,1,1,1,1] )
weights ~ dnDirichlet( [2,2,2,2,2] )
MM := fnJC(4) |> fnScale(rates) |> fnMixtureASRV(weights)
M := fnScale(MM, 1/MM.rate())

See Also

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