update to ratebytree to use ginv if Hessian nearly singular

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: phytools
-Version: 0.6-26
-Date: 2017-09-18
+Version: 0.6-27
+Date: 2017-09-19
 Title: Phylogenetic Tools for Comparative Biology (and Other Things)
 Author: Liam J. Revell
 Maintainer: Liam J. Revell <liam.revell@umb.edu>
 Depends: R (>= 3.2.0), ape (>= 4.0), maps
 Imports: animation, clusterGeneration, coda, combinat, graphics, grDevices, 
-	methods, mnormt, msm, nlme, numDeriv, phangorn (>= 2.1.1), plotrix, 
+	MASS, methods, mnormt, msm, nlme, numDeriv, phangorn (>= 2.1.1), plotrix, 
 	scatterplot3d, stats, utils
 Suggests: geiger, rgl
 ZipData: no
@@ -56,6 +56,6 @@ Description: Package contains various functions for phylogenetic analysis.
 	research.
 License: GPL (>= 2)
 URL: http://github.com/liamrevell/phytools
-Packaged: 2017-09-18 12:00:00 EST
+Packaged: 2017-09-19 12:00:00 EST
 Repository: 
-Date/Publication: 2017-09-18 12:00:00 EST
+Date/Publication: 2017-09-19 12:00:00 EST

NAMESPACE

@@ -132,3 +132,4 @@ pdf, dev.off, col2rgb)
 importFrom(combinat, permn)
 importFrom(coda, HPDinterval)
 importFrom(nlme, gls, varFixed)
+importFrom(MASS, ginv)

R/ratebytree.R

@@ -233,7 +233,7 @@ rbt.cont<-function(trees,x,...){
 	## compute covariance matrix
 	H.multi<-hessian(lik.multi,fit.multi$par,trees=trees,y=x,
 		se=se,model=model,trace=FALSE)
-	Cov.multi<-solve(H.multi)
+	Cov.multi<-if(qr(H.multi)$rank!=ncol(H.multi)) ginv(H.multi) else solve(H.multi)
 	## now fit single-rate model
 	lik.onerate<-function(theta,trees,y,se,model,trace=FALSE){
 		n<-sapply(trees,Ntip)
@@ -289,7 +289,7 @@ rbt.cont<-function(trees,x,...){
 		## compute covariance matrix
 	H.onerate<-hessian(lik.onerate,fit.onerate$par,trees=trees,y=x,
 		se=se,model=model,trace=FALSE)
-	Cov.onerate<-solve(H.onerate)
+	Cov.onerate<-if(qr(H.onerate)$rank!=ncol(H.onerate)) ginv(H.onerate) else solve(H.onerate)
 	## compare models:
 	LR<-2*(-fit.multi$value+fit.onerate$value)
 	km<-2*N+if(model=="BM") 0 else if(model%in%c("OU","EB")) N

man/ratebytree.Rd

@@ -27,11 +27,13 @@ posthoc.ratebytree(x, ...)
 }
 \details{
 	At present it is not possible to specify different models to fit for the different trees - although if (for instance) character evolution on tree 1 proceeded by a strong \emph{OU} process while character evolution on tree 2 was by \emph{BM}, we would probably reject a constant-process model and tree 2 should show a very low value of \code{alpha}.
+
+	To compute the standard errors for each fitted paramater value, the function computes the negative inverse of the Hessian matrix at the MLEs; however, if this matrix is computationally singular generalized inverse (\code{\link{ginv}}) will be used instead without warning.
 
 	The function also conducts a likelihood-ratio test to compare the two models.
 }
 \value{
-	An object of class \code{"ratebytree"}.
+	An object of class \code{"ratebytree"} or an object of class \code{"posthoc.ratebytree"} in the case of the method \code{posthoc}.
 }
 \references{
 	Adams, D. C. (2012) Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood. \emph{Syst. Biol.}, \bold{62}, 181-192.