This function can be used to remove species from an object of class treedata.table. The resulting treedata.table will include fully matching $dat and $phy elements. The user should confirm the changes before they are processed.

droptreedata.table(tdObject, taxa)

Arguments

tdObject

An object of class treedata.table

taxa

A vector class character containing all taxa that needs to be dropped from the original treedata.table object

Value

An object of class treedata.table with matching $dat and $phy elements based on whether taxa were dropped or not.

Examples

data(anolis) # With a multiphylo object in the treedata.table object td <- as.treedata.table(anolis$phy, anolis$dat)
#> Tip labels detected in column: X
#> Phylo object detected
#> No tips were dropped from the original tree/dataset
droptreedata.table( tdObject = td, taxa = c("chamaeleonides", "eugenegrahami") )
#> 2 taxa were dropped from the treedata.table object
#> $phy #> #> Phylogenetic tree with 98 tips and 97 internal nodes. #> #> Tip labels: #> ahli, allogus, rubribarbus, imias, sagrei, bremeri, ... #> #> Rooted; includes branch lengths. #> #> $dat #> tip.label SVL PCI_limbs PCII_head PCIII_padwidth_vs_tail #> 1: ahli 4.039125 -3.248286 0.3722519 -1.0422187 #> 2: allogus 4.040138 -2.845570 0.6001134 -1.0253056 #> 3: rubribarbus 4.078469 -2.238349 1.1199779 -1.1929572 #> 4: imias 4.099687 -3.048917 2.3320349 0.1616442 #> 5: sagrei 4.067162 -1.741055 2.0228243 0.1693635 #> 6: bremeri 4.113371 -1.813611 2.6067501 0.6399320 #> PCIV_lamella_num awesomeness hostility attitude ecomorph island #> 1: -2.414742 -0.2416517 -0.1734769 0.6443771 TG Cuba #> 2: -2.463311 0.6244689 -0.5000962 0.7128910 TG Cuba #> 3: -2.087433 -0.4277574 0.4800445 -0.9674263 TG Cuba #> 4: -2.112606 0.1694260 -0.4108123 0.1963580 TG Cuba #> 5: -1.375769 -0.6304338 0.7193130 -1.2228276 TG Cuba #> 6: -1.626299 -1.7543006 1.4127184 0.1832345 TG Cuba
# With a multiphylo object in the treedata.table object treesFM <- list(anolis$phy, anolis$phy) class(treesFM) <- "multiPhylo" td <- as.treedata.table(treesFM, anolis$dat)
#> Tip labels detected in column: X
#> Multiphylo object detected
#> No tips were dropped from the original trees/dataset
droptreedata.table( tdObject = td, taxa = c("chamaeleonides", "eugenegrahami") )
#> 2 taxa were dropped from the treedata.table object
#> $phy #> 2 phylogenetic trees #> #> $dat #> tip.label SVL PCI_limbs PCII_head PCIII_padwidth_vs_tail #> 1: ahli 4.039125 -3.248286 0.3722519 -1.0422187 #> 2: allogus 4.040138 -2.845570 0.6001134 -1.0253056 #> 3: rubribarbus 4.078469 -2.238349 1.1199779 -1.1929572 #> 4: imias 4.099687 -3.048917 2.3320349 0.1616442 #> 5: sagrei 4.067162 -1.741055 2.0228243 0.1693635 #> 6: bremeri 4.113371 -1.813611 2.6067501 0.6399320 #> PCIV_lamella_num awesomeness hostility attitude ecomorph island #> 1: -2.414742 -0.2416517 -0.1734769 0.6443771 TG Cuba #> 2: -2.463311 0.6244689 -0.5000962 0.7128910 TG Cuba #> 3: -2.087433 -0.4277574 0.4800445 -0.9674263 TG Cuba #> 4: -2.112606 0.1694260 -0.4108123 0.1963580 TG Cuba #> 5: -1.375769 -0.6304338 0.7193130 -1.2228276 TG Cuba #> 6: -1.626299 -1.7543006 1.4127184 0.1832345 TG Cuba