Summarizing treedata.table objects
Usage
# S3 method for treedata.table
summary(object, ...)Arguments
- object
an object of class "treedata.table"
- ...
additional arguments passed to "head.treedata.table"
Value
Function tries to be smart about summarizing the data and detecting continuous vs. discrete data, as well as whether any data have missing data. Also returns the taxa that are dropped from either the original tree or the original data.
Examples
data(anolis)
td <- as.treedata.table(anolis$phy, anolis$dat)
#> Tip labels detected in column: X
#> Phylo object detected
#> All tips from original tree/dataset were preserved
summary(td)
#> A treedata.table object
#> The dataset contains 11 traits
#> Continuous traits: tip.label, SVL, PCI_limbs, PCII_head, PCIII_padwidth_vs_tail, PCIV_lamella_num, awesomeness, hostility, attitude
#> Discrete traits: ecomorph, island
#> The following traits have missing values: 0
#> Taxa dropped from the tree: 0
#> Taxa dropped from the data: 0
#> $phy
#>
#> Phylogenetic tree with 100 tips and 99 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
#> <char> <num> <num> <num> <num>
#> 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
#> <num> <num> <num> <num> <char> <char>
#> 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