search for: clade

Hi Wondering if anyone knows of a package that does Nested Clade Analysis? Thanks -- View this message in context: http://www.nabble.com/Nested-Clade-Analysis-tp20637180p20637180.html Sent from the R help mailing list archive at Nabble.com.

Hi, I was recently splitting some massive phylo class objects with extract.clade() and noticed what appears to be a bug in how tip labels are copied from the full tree to the pruned tree. This possible bug was also mentioned here: http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html An example: library(ape) set.seed(5) x <- matrix(rnorm(100), ncol=10)...

...qr.fitted(Q, Xbar) : 'qr' and 'y' must have the same number of rows or cca Error in weighted.mean.default(newX[, i], ...) : 'x' and 'w' must have the same length when using a conditioning distance object instead of a variable (Clade) of the same length as the constraints ( Latitude and Longitude) I would be grateful, for any pointers on this, ie which test is the appropriate one to use ( I believe capscale since it is "similar to distance-based redundancy analysis (Legendre & Anderson 1999)") and whether th...

...m getting concerns a tree with a very clear division into two very distinct top level clusters. However on this data set the subclusters with confidence appear low down in the tree, and the very top most division gets zero significance. I'm suspicious of this given the rather clear top-level clade structure in this data set with lots of examples and not many NA's, i.e. pretty vanilla data. Also, in a related data set there seems to be a crash: pvclst bootstraps and scales happily for a while, then prints: Bootstrap (r = 1.29)... Done. Bootstrap (r = 1.29)... Done. Error in solve.default(...

...he multivariate normal density formula it uses the PCMBase (R package, see below) to obtain the value of the likelihood in linear (in number of tip species) instead of quadratic time. Furthermore, as there is no need to store the between-species-between-traits variance covariance matrix much larger clades, then previously can be handled. From the user's perspective the main changes are the interface and increased functionality: a) the phylogeny has to be now in the phylo (instead of ouch) format, b) the trait data has to be a matrix (and not a data frame), c) the package can automatically compa...

...he multivariate normal density formula it uses the PCMBase (R package, see below) to obtain the value of the likelihood in linear (in number of tip species) instead of quadratic time. Furthermore, as there is no need to store the between-species-between-traits variance covariance matrix much larger clades, then previously can be handled. From the user's perspective the main changes are the interface and increased functionality: a) the phylogeny has to be now in the phylo (instead of ouch) format, b) the trait data has to be a matrix (and not a data frame), c) the package can automatically compa...