Precursor model no longer running

[eliotmiller]

Code that previously worked for me to run precursor models is no longer working. I'm not able to run the code in the vignette to see if the example works there, as the data file in the vignette directory appears corrupt. Suspect the example would fail too, possibly a good place to start. Am getting this error when I run the model.

Error in liks.down[root, ] <- liks.down[root, ] * root.p : number of items to replace is not a multiple of replacement length

[jboyko]

Hi,

The code still works, but the "yang" root.prior does not because the 2,R1 state is not allowed into the model. You can either specify a root.prior, use "maddfitz", or use "flat". Example code below.

require(corHMM)
require(MASS)
data(primates)
phy <- multi2di(primates[[1]])
data <- primates[[2]]

Precur_Dat <- data[,c(1,2)]

Precur_LegendAndMat <- getStateMat4Dat(Precur_Dat)
Precur_R1 <- Precur_LegendAndMat$rate.mat 
Precur_R1 <- dropStateMatPars(Precur_R1, c(1, 2)) 
Precur_R2 <- equateStateMatPars(Precur_LegendAndMat$rate.mat, c(1,2))
RateClassMat <- equateStateMatPars(getRateCatMat(2), c(1,2))

Precur_FullMat <- getFullMat(list(Precur_R1, Precur_R2), RateClassMat) 
Precur_FullMat[c(4, 2), c(2, 4)] <- 0
Precur_FullMat

Precur_res.corHMM <- corHMM(phy = phy, data = Precur_Dat, rate.cat = 2, rate.mat = Precur_FullMat, root.p = "maddfitz")

Best, James

[eliotmiller]

That does it! Thanks!