Partially Matching of Trait Data and Tree(s) in treedata.table

Josef Uyeda, Cristian Roman-Palacios, April Wright

08/08/2020

Partially matching trait data and tree(s)

The as.treedata.table function enables users to match a tree (or multiple trees) against a single trait database. We first load the sample dataset.

library(ape)
library(treedata.table)

##          Thank you for using the {treedata.table} R package!   
## 
##                         🙂Happy coding!!🙂

# Load example data
data(anolis)
#Create treedata.table object with as.treedata.table
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)

## Tip labels detected in column: X

## Phylo object detected

## All tips from original tree/dataset were preserved

Tips that are not common between the tree (or trees) and dataset are dropped from the resulting treedata.table object. For instance, below I have modified the original anole phylogeny such that A. ahli (ahli) is replaced for a label that is not present in the dataset (NAA).

anolis_newtip<-anolis$phy
anolis_newtip$tip.label[1]<-'NAA'
anolis_newtip

## 
## Phylogenetic tree with 100 tips and 99 internal nodes.
## 
## Tip labels:
##   NAA, allogus, rubribarbus, imias, sagrei, bremeri, ...
## 
## Rooted; includes branch lengths.

We then use this modified tree to fit a treedata.table object using the as.treedata.table function:

td <- as.treedata.table(tree=anolis_newtip, data=anolis$dat)

## Tip labels detected in column: X

## Phylo object detected

## 1 tip(s) dropped from the original tree
## 1 row(s) dropped from the original dataset

Note that as.treedata.table drops all non-overlapping tips (NAA [present in the tree but not in the trait data] and ahi [present in the database but not in tree] in this case) and returns a treedata.table object with fully matching phy and data objects.

td

## $phy 
## 
## Phylogenetic tree with 99 tips and 98 internal nodes.
## 
## Tip labels:
##   allogus, rubribarbus, imias, sagrei, bremeri, quadriocellifer, ...
## 
## Rooted; includes branch lengths.
## 
## $dat 
##          tip.label      SVL PCI_limbs PCII_head PCIII_padwidth_vs_tail
##             <char>    <num>     <num>     <num>                  <num>
## 1:         allogus 4.040138 -2.845570 0.6001134             -1.0253056
## 2:     rubribarbus 4.078469 -2.238349 1.1199779             -1.1929572
## 3:           imias 4.099687 -3.048917 2.3320349              0.1616442
## 4:          sagrei 4.067162 -1.741055 2.0228243              0.1693635
## 5:         bremeri 4.113371 -1.813611 2.6067501              0.6399320
## 6: quadriocellifer 3.901619 -2.267894 0.9909208              0.3553405
##    PCIV_lamella_num awesomeness  hostility   attitude ecomorph island
##               <num>       <num>      <num>      <num>   <char> <char>
## 1:        -2.463311   0.6244689 -0.5000962  0.7128910       TG   Cuba
## 2:        -2.087433  -0.4277574  0.4800445 -0.9674263       TG   Cuba
## 3:        -2.112606   0.1694260 -0.4108123  0.1963580       TG   Cuba
## 4:        -1.375769  -0.6304338  0.7193130 -1.2228276       TG   Cuba
## 5:        -1.626299  -1.7543006  1.4127184  0.1832345       TG   Cuba
## 6:        -2.105059  -0.2576389  0.4627081 -0.2712794       TG   Cuba

Fully-matching matrix and trees are also returned in treedata.table objects with multiPhylo objects in their phy component. See the example below.

We first construct a multiPhylo object that partially overlaps the original trait database by using NAA instead of ahi.

anolis2<-anolis$phy
anolis2$tip.label[1]<-'NAA'
anolis1<-anolis$phy
anolis1$tip.label[1]<-'NAA'
trees<-list(anolis1,anolis2)
class(trees) <- "multiPhylo"
trees

## 2 phylogenetic trees

Next, we fit the treedata.table object using the relevant multiPhylo object and the original trait database.

td <- as.treedata.table(tree=trees, data=anolis$dat)

## Tip labels detected in column: X

## Multiphylo object detected

## 1 tip(s) dropped from 2 trees
## 1 row(s) dropped from the original dataset

Note that 1 tip was dropped for all trees in the multiPhylo object and a single row was deleted from the data.table object in the treedata.table object.

td

## $phy 
## 2 phylogenetic trees
## 
## $dat 
##          tip.label      SVL PCI_limbs PCII_head PCIII_padwidth_vs_tail
##             <char>    <num>     <num>     <num>                  <num>
## 1:         allogus 4.040138 -2.845570 0.6001134             -1.0253056
## 2:     rubribarbus 4.078469 -2.238349 1.1199779             -1.1929572
## 3:           imias 4.099687 -3.048917 2.3320349              0.1616442
## 4:          sagrei 4.067162 -1.741055 2.0228243              0.1693635
## 5:         bremeri 4.113371 -1.813611 2.6067501              0.6399320
## 6: quadriocellifer 3.901619 -2.267894 0.9909208              0.3553405
##    PCIV_lamella_num awesomeness  hostility   attitude ecomorph island
##               <num>       <num>      <num>      <num>   <char> <char>
## 1:        -2.463311   0.6244689 -0.5000962  0.7128910       TG   Cuba
## 2:        -2.087433  -0.4277574  0.4800445 -0.9674263       TG   Cuba
## 3:        -2.112606   0.1694260 -0.4108123  0.1963580       TG   Cuba
## 4:        -1.375769  -0.6304338  0.7193130 -1.2228276       TG   Cuba
## 5:        -1.626299  -1.7543006  1.4127184  0.1832345       TG   Cuba
## 6:        -2.105059  -0.2576389  0.4627081 -0.2712794       TG   Cuba