I'm not sure if this is the best place to make a bug report, but I thought others might be interested.
I was trying to replicate, with geiger, a demonstration of estimating lambda with measurement error from Liam's blog: http://phytools.blogspot.com/2011/11/including-measurement-error-in.html Replicating this with fitContinuous, I received the following error: > fitContinuous(tree,xe,model="lambda",meserr=se) Error in meserr[o, ] : incorrect number of dimensions The problem is related to this bit of code in fitContinuous, used to determine whether meserr is a single value, a vector, or a matrix: else if (is.vector(meserr)) { if (!is.null(names(meserr))) { o <- match(rownames(td$data), names(meserr)) if (length(o) != ntax) stop("meserr is missing some taxa from the tree") meserr <- as.matrix(meserr[o,]) Removing the comma from the final line fixed the problem. The values I receive from geiger after removing the comma are identical to the values I get from phytools::phylosig for the same data, so I am assuming I haven't broken anything important. The full code I used is at the end of this message, for those interested. Best, Matt Johnson > library(geiger) Loading required package: ape Loading required package: MASS Loading required package: mvtnorm Loading required package: msm Loading required package: ouch Loading required package: subplex > library(phytools) Loading required package: mnormt Loading required package: phangorn Loading required package: quadprog Loading required package: igraph Loading required package: rgl > source("mjContinuous.R") #fitContinuous with offending comma removed > set.seed(2) > gen.lambda=0.7 > tree = drop.tip(birthdeath.tree(b=1,d=0,taxa.stop=501),"501") > se = sqrt(rchisq(n=500,df=2)) > names(se) = tree$tip.label > > x= fastBM(lambdaTree(tree,gen.lambda),sig2=1) > e = rnorm(n=500,sd=se) > xe=x+e > > fitContinuous(tree,x,model="lambda") Fitting lambda model: $Trait1 $Trait1$lnl [1] -1031.783 $Trait1$beta [1] 1.221674 $Trait1$lambda [1] 0.7613218 $Trait1$aic [1] 2069.567 $Trait1$aicc [1] 2069.615 $Trait1$k [1] 3 > fitContinuous(tree,xe,model="lambda") Fitting lambda model: $Trait1 $Trait1$lnl [1] -1154.987 $Trait1$beta [1] 1.412728 $Trait1$lambda [1] 0.5495113 $Trait1$aic [1] 2315.975 $Trait1$aicc [1] 2316.023 $Trait1$k [1] 3 > fitContinuous(tree,xe,model="lambda",meserr=se) Error in meserr[o, ] : incorrect number of dimensions > > mjContinuous(tree,xe,model="lambda",meserr=se) #with problematic comma removed Fitting lambda model: $Trait1 $Trait1$lnl [1] -1141.14 $Trait1$beta [1] 1.170196 $Trait1$lambda [1] 0.7484273 $Trait1$aic [1] 2288.281 $Trait1$aicc [1] 2288.329 $Trait1$k [1] 3 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
