Creating a compartive object in R from two dataframes for comparitive phylogenetics

Question

I'm trying to read in two dataframes into a comparitive object so I can plot them using pgls.

I'm not sure what the error being returned means, and how to go about getting rid of it.

My code:

library(ape)
library(geiger)
library(caper)

taxatree <- read.nexus("taxonomyforzeldospecies.nex")
LWEVIYRcombodata <- read.csv("LWEVIYR.csv")


LWEVIYRcombodataPGLS <-data.frame(LWEVIYRcombodata$Sum.of.percentage,OGT=LWEVIYRcombodata$OGT, Species=LWEVIYRcombodata$Species)

comp.dat <- comparative.data(taxatree, LWEVIYRcombodataPGLS, "Species")

Returns error:

> comp.dat <- comparative.data(taxatree, LWEVIYRcombodataPGLS, 'Species')
Error in if (tabulate(phy$edge[, 1])[ntips + 1] > 2) FALSE else TRUE : 
  missing value where TRUE/FALSE needed

Check the `?comparative.data` help page. The first parameter must be a phylogeny (an object of class "phylo"), not a data.frame. Those errors are because you are passing in the wrong type of object. — MrFlick, Jun 12 '18 at 15:26
Nexus files are phylogenies, maybe it just doesn't accept that filetype though? — Biomage, Jun 12 '18 at 15:34
You are right. I misread that. Sorry. It would be easier to say what's going in for sure with a [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) so we can run the code to see what's going on. Right not since we don't have the input files we just have to guess. — MrFlick, Jun 12 '18 at 15:36

score 0 · Answer 1 · answered Jun 13 '18 at 01:17

This might come from your data set and your phylogeny having some discrepancies that comparative.data struggles to handle (by the look of the error message).

You can try cleaning both the data set and the tree using dispRity::clean.data:

library(dispRity)

## Reading the data
taxatree <- read.nexus("taxonomyforzeldospecies.nex")
LWEVIYRcombodata <- read.csv("LWEVIYR.csv")
LWEVIYRcombodataPGLS <- data.frame(LWEVIYRcombodata$Sum.of.percentage,OGT=LWEVIYRcombodata$OGT, Species=LWEVIYRcombodata$Species)

## Cleaning the data
cleaned_data <- clean.data(LWEVIYRcombodataPGLS, taxatree)

## Preparing the comparative data object
comp.dat <- comparative.data(cleaned_data$tree, cleaned_data$data, "Species")

However, as @MrFlick suggests, it's hard to know if that solves the problem without a reproducible example.

When trying to run this, I get : `Error in comparative.data(cleaned_data$tree, cleaned_data$data, "Species")` `:` `'cleaned_data$tree' not of class 'phylo'` Although that happens even if I use a newick tree, which does work with my original code, not sure what's going on here! — Biomage, Jun 13 '18 at 08:31
You might have multiple trees in your newick file. Did you try `class(taxatree)` and `class(cleaned_data$tree)`? If they are `multiPhylo` you might want to select only the one tree (`one_tree <- cleaned_data$tree[[1]]`) or use a multiple tree approach (e.g. [mulTree](https://github.com/TGuillerme/mulTree)). — Thomas Guillerme, Jun 13 '18 at 23:58

score 0 · Accepted Answer · answered Jun 13 '18 at 08:29

0

The error here is that I was using a nexus file, although ?comparitive.data does not specify which phylo objects it should use, newick trees seem to work fine, whereas nexus files do not.

answered Jun 13 '18 at 08:29

Biomage

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Creating a compartive object in R from two dataframes for comparitive phylogenetics

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