Function for performing data.table operations on an object of class treedata.table
Source: R/treedata.table.R
sub-.treedata.table.RdThis function can be used to subset rows, select and compute on columns data.table.
Value
A new object of class treedata.table with $dat and $phy
corresponding with the changes set to $dat using
data.table's structure.
Examples
data(anolis)
anolis2 <- anolis$phy
anolis2$tip.label[1] <- "NAA"
anolis1 <- anolis$phy
anolis1$tip.label[1] <- "NAA"
trees <- list(anolis1, anolis2)
class(trees) <- "multiPhylo"
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"
# A phylo object that fully matches the data
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
#> Tip labels detected in column: X
#> Phylo object detected
#> All tips from original tree/dataset were preserved
td <- as.treedata.table(anolis$phy, anolis$dat)
#> Tip labels detected in column: X
#> Phylo object detected
#> All tips from original tree/dataset were preserved
td[, SVL]
#> $phy
#>
#> Phylogenetic tree with 100 tips and 99 internal nodes.
#>
#> Tip labels:
#> ahli, allogus, rubribarbus, imias, sagrei, bremeri, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> SVL
#> <num>
#> 1: 4.039125
#> 2: 4.040138
#> 3: 4.078469
#> 4: 4.099687
#> 5: 4.067162
#> 6: 4.113371
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
#> $phy
#>
#> Phylogenetic tree with 12 tips and 11 internal nodes.
#>
#> Tip labels:
#> ahli, allogus, rubribarbus, imias, sagrei, bremeri, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> ecomorph island SVL
#> <char> <char> <num>
#> 1: TG Cuba 4.039125
#> 2: TG Cuba 4.040138
#> 3: TG Cuba 4.078469
#> 4: TG Cuba 4.099687
#> 5: TG Cuba 4.067162
#> 6: TG Cuba 4.113371
td[, utils::head(.SD, 1), by = .(ecomorph, island)]
#> $phy
#>
#> Phylogenetic tree with 23 tips and 22 internal nodes.
#>
#> Tip labels:
#> ahli, ophiolepis, garmani, opalinus, grahami, valencienni, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> ecomorph island tip.label SVL PCI_limbs PCII_head
#> <char> <char> <char> <num> <num> <num>
#> 1: TG Cuba ahli 4.039125 -3.2482860 0.3722519
#> 2: GB Cuba ophiolepis 3.637962 0.7915117 1.4585760
#> 3: CG Puerto Rico garmani 4.769473 -0.7735264 0.9371249
#> 4: TC Jamaica opalinus 3.838376 -1.7794371 -0.3245381
#> 5: TC Puerto Rico grahami 4.154274 -2.3056535 -1.9139369
#> 6: TW Jamaica valencienni 4.321524 2.9424139 -0.8846007
#> PCIII_padwidth_vs_tail PCIV_lamella_num awesomeness hostility attitude
#> <num> <num> <num> <num> <num>
#> 1: -1.0422187 -2.4147423 -0.24165170 -0.17347691 0.6443771
#> 2: -1.3152005 -2.2377514 0.35441877 0.05366142 -0.0938953
#> 3: 0.2594994 0.1051149 0.16779131 0.67675600 -0.6946008
#> 4: 1.5569939 0.9366501 1.48302162 -0.90826653 0.7261348
#> 5: 1.6852579 1.0144193 0.41064280 -0.11746257 0.7022959
#> 6: 1.8543308 0.1288233 -0.08837008 0.46528679 -0.5675490
# A multiphylo object that fully matches the data
td <- as.treedata.table(tree = treesFM, data = anolis$dat)
#> Tip labels detected in column: X
#> Multiphylo object detected
#> All tips from original tree/dataset were preserved
td <- as.treedata.table(treesFM, anolis$dat)
#> Tip labels detected in column: X
#> Multiphylo object detected
#> All tips from original tree/dataset were preserved
td[, SVL]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> SVL
#> <num>
#> 1: 4.039125
#> 2: 4.040138
#> 3: 4.078469
#> 4: 4.099687
#> 5: 4.067162
#> 6: 4.113371
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> ecomorph island SVL
#> <char> <char> <num>
#> 1: TG Cuba 4.039125
#> 2: TG Cuba 4.040138
#> 3: TG Cuba 4.078469
#> 4: TG Cuba 4.099687
#> 5: TG Cuba 4.067162
#> 6: TG Cuba 4.113371
td[, utils::head(.SD, 1), by = .(ecomorph, island)]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> ecomorph island tip.label SVL PCI_limbs PCII_head
#> <char> <char> <char> <num> <num> <num>
#> 1: TG Cuba ahli 4.039125 -3.2482860 0.3722519
#> 2: GB Cuba ophiolepis 3.637962 0.7915117 1.4585760
#> 3: CG Puerto Rico garmani 4.769473 -0.7735264 0.9371249
#> 4: TC Jamaica opalinus 3.838376 -1.7794371 -0.3245381
#> 5: TC Puerto Rico grahami 4.154274 -2.3056535 -1.9139369
#> 6: TW Jamaica valencienni 4.321524 2.9424139 -0.8846007
#> PCIII_padwidth_vs_tail PCIV_lamella_num awesomeness hostility attitude
#> <num> <num> <num> <num> <num>
#> 1: -1.0422187 -2.4147423 -0.24165170 -0.17347691 0.6443771
#> 2: -1.3152005 -2.2377514 0.35441877 0.05366142 -0.0938953
#> 3: 0.2594994 0.1051149 0.16779131 0.67675600 -0.6946008
#> 4: 1.5569939 0.9366501 1.48302162 -0.90826653 0.7261348
#> 5: 1.6852579 1.0144193 0.41064280 -0.11746257 0.7022959
#> 6: 1.8543308 0.1288233 -0.08837008 0.46528679 -0.5675490
# A phylo object that partially matches the data
td <- as.treedata.table(tree = anolis1, data = anolis$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
td <- as.treedata.table(anolis1, 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
td[, SVL]
#> $phy
#>
#> Phylogenetic tree with 99 tips and 98 internal nodes.
#>
#> Tip labels:
#> allogus, rubribarbus, imias, sagrei, bremeri, quadriocellifer, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> SVL
#> <num>
#> 1: 4.040138
#> 2: 4.078469
#> 3: 4.099687
#> 4: 4.067162
#> 5: 4.113371
#> 6: 3.901619
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
#> $phy
#>
#> Phylogenetic tree with 11 tips and 10 internal nodes.
#>
#> Tip labels:
#> allogus, rubribarbus, imias, sagrei, bremeri, quadriocellifer, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> ecomorph island SVL
#> <char> <char> <num>
#> 1: TG Cuba 4.040138
#> 2: TG Cuba 4.078469
#> 3: TG Cuba 4.099687
#> 4: TG Cuba 4.067162
#> 5: TG Cuba 4.113371
#> 6: TG Cuba 3.901619
td[, utils::head(.SD, 1), by = .(ecomorph, island)]
#> $phy
#>
#> Phylogenetic tree with 23 tips and 22 internal nodes.
#>
#> Tip labels:
#> allogus, ophiolepis, garmani, opalinus, grahami, valencienni, ...
#>
#> Rooted; includes branch lengths.
#>
#> $dat
#> ecomorph island tip.label SVL PCI_limbs PCII_head
#> <char> <char> <char> <num> <num> <num>
#> 1: TG Cuba allogus 4.040138 -2.8455702 0.6001134
#> 2: GB Cuba ophiolepis 3.637962 0.7915117 1.4585760
#> 3: CG Puerto Rico garmani 4.769473 -0.7735264 0.9371249
#> 4: TC Jamaica opalinus 3.838376 -1.7794371 -0.3245381
#> 5: TC Puerto Rico grahami 4.154274 -2.3056535 -1.9139369
#> 6: TW Jamaica valencienni 4.321524 2.9424139 -0.8846007
#> PCIII_padwidth_vs_tail PCIV_lamella_num awesomeness hostility attitude
#> <num> <num> <num> <num> <num>
#> 1: -1.0253056 -2.4633111 0.62446888 -0.50009622 0.7128910
#> 2: -1.3152005 -2.2377514 0.35441877 0.05366142 -0.0938953
#> 3: 0.2594994 0.1051149 0.16779131 0.67675600 -0.6946008
#> 4: 1.5569939 0.9366501 1.48302162 -0.90826653 0.7261348
#> 5: 1.6852579 1.0144193 0.41064280 -0.11746257 0.7022959
#> 6: 1.8543308 0.1288233 -0.08837008 0.46528679 -0.5675490
# A multiphylo object that partially matches the data
td <- as.treedata.table(tree = trees, data = anolis$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
td <- as.treedata.table(trees, 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
td[, SVL]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> SVL
#> <num>
#> 1: 4.040138
#> 2: 4.078469
#> 3: 4.099687
#> 4: 4.067162
#> 5: 4.113371
#> 6: 3.901619
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> ecomorph island SVL
#> <char> <char> <num>
#> 1: TG Cuba 4.040138
#> 2: TG Cuba 4.078469
#> 3: TG Cuba 4.099687
#> 4: TG Cuba 4.067162
#> 5: TG Cuba 4.113371
#> 6: TG Cuba 3.901619
td[, utils::head(.SD, 1), by = .(ecomorph, island)]
#> $phy
#> 2 phylogenetic trees
#>
#> $dat
#> ecomorph island tip.label SVL PCI_limbs PCII_head
#> <char> <char> <char> <num> <num> <num>
#> 1: TG Cuba allogus 4.040138 -2.8455702 0.6001134
#> 2: GB Cuba ophiolepis 3.637962 0.7915117 1.4585760
#> 3: CG Puerto Rico garmani 4.769473 -0.7735264 0.9371249
#> 4: TC Jamaica opalinus 3.838376 -1.7794371 -0.3245381
#> 5: TC Puerto Rico grahami 4.154274 -2.3056535 -1.9139369
#> 6: TW Jamaica valencienni 4.321524 2.9424139 -0.8846007
#> PCIII_padwidth_vs_tail PCIV_lamella_num awesomeness hostility attitude
#> <num> <num> <num> <num> <num>
#> 1: -1.0253056 -2.4633111 0.62446888 -0.50009622 0.7128910
#> 2: -1.3152005 -2.2377514 0.35441877 0.05366142 -0.0938953
#> 3: 0.2594994 0.1051149 0.16779131 0.67675600 -0.6946008
#> 4: 1.5569939 0.9366501 1.48302162 -0.90826653 0.7261348
#> 5: 1.6852579 1.0144193 0.41064280 -0.11746257 0.7022959
#> 6: 1.8543308 0.1288233 -0.08837008 0.46528679 -0.5675490