Use of aptg
The aptg package is used to generate phylogenetic trees from a vector of species names or a tree of a taxon down to whatever taxon that is included in the first one. The phylogenetic tree are generated from brranching::phylomatic based on the program of the same name accessible there : http://phylodiversity.net/phylomatic/.
When the tree is generated from a vector of species names, distance matrices are given.
taxa.tree
The function needs list of species name as an input and will give phylogenetic trees and distance matrices as an output. Let’s do an example with a mixed list of mammal and angiosperm species.
taxa.tree(c("Canis lupus", "Canis latrans", "Acer saccharum", "Castor canadensis", "Alces alces", "Acer rubrum", "Vulpes vulpes", "Salix babylonica", "Odocoileus virginianus", "Betula alleghaniensis", "Rangifer tarandus","Juniperus occidentalis", "Pinus strobus"))## # A tibble: 2 × 4
## tsn target commonNames nameUsage
## <chr> <chr> <chr> <chr>
## 1 22503 Salix babylonica weeping willow not accepted
## 2 837788 Salix babylonica weeping willow accepted
## Castor_canadensis Alces_alces
## Castor_canadensis 0.0 197.8
## Alces_alces 197.8 0.0
## Odocoileus_virginianus 197.8 37.0
## Rangifer_tarandus 197.8 37.0
## Canis_lupus 197.8 177.0
## Canis_latrans 197.8 177.0
## Vulpes_vulpes 197.8 177.0
## Odocoileus_virginianus Rangifer_tarandus
## Castor_canadensis 197.8 197.8
## Alces_alces 37.0 37.0
## Odocoileus_virginianus 0.0 28.4
## Rangifer_tarandus 28.4 0.0
## Canis_lupus 177.0 177.0
## Canis_latrans 177.0 177.0
## Vulpes_vulpes 177.0 177.0
## Canis_lupus Canis_latrans Vulpes_vulpes
## Castor_canadensis 197.8 197.8 197.8
## Alces_alces 177.0 177.0 177.0
## Odocoileus_virginianus 177.0 177.0 177.0
## Rangifer_tarandus 177.0 177.0 177.0
## Canis_lupus 0.0 2.8 14.8
## Canis_latrans 2.8 0.0 14.8
## Vulpes_vulpes 14.8 14.8 0.0
## Pinus_strobus Juniperus_occidentalis Acer_rubrum
## Pinus_strobus 0.0000 533.4320 704.4692
## Juniperus_occidentalis 533.4320 0.0000 704.4692
## Acer_rubrum 704.4692 704.4692 0.0000
## Acer_saccharum 704.4692 704.4692 20.0674
## Salix_babylonica 704.4696 704.4696 235.0698
## Betula_alleghaniensis 704.4696 704.4696 235.0698
## Acer_saccharum Salix_babylonica
## Pinus_strobus 704.4692 704.4696
## Juniperus_occidentalis 704.4692 704.4696
## Acer_rubrum 20.0674 235.0698
## Acer_saccharum 0.0000 235.0698
## Salix_babylonica 235.0698 0.0000
## Betula_alleghaniensis 235.0698 226.5180
## Betula_alleghaniensis
## Pinus_strobus 704.4696
## Juniperus_occidentalis 704.4696
## Acer_rubrum 235.0698
## Acer_saccharum 235.0698
## Salix_babylonica 226.5180
## Betula_alleghaniensis 0.0000Here, Salix babylonica have required an input to choose the good TSN number, if we omit it it is not include in the plot. As you can see the taxa have been sorted by reference trees; mammals and angiosperms. The distance matrices are also an output.
downto.tree
This function creates a phylogenetic tree from a taxon down to another one. For now, only the input species gives a result, but any higher taxon can be choosed.
downto.tree("Canidae", "species")
When running the code, this message would have appeared:
NOTE: 10 taxa not matched: canidae/canis/canis_anthus, canidae/canis/canis_lupaster, canidae/dusicyon/dusicyon_australis, canidae/lycalopex/lycalopex_culpaeus, canidae/lycalopex/lycalopex_fulvipes, canidae/lycalopex/lycalopex_gymnocercus, canidae/lycalopex/lycalopex_sechurae, canidae/lycalopex/lycalopex_vetulus, canidae/vulpes/vulpes_lagopus, canidae/vulpes/vulpes_macrotis, ];For esthetic purposes we omitted all the messages of the function, but when creating the tree, certain inputs from functions included in downto.tree are not recognized in the reference supertrees.