Package: treestartr 0.1.0
April Wright
treestartr: Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.
Authors:
treestartr_0.1.0.tar.gz
treestartr_0.1.0.zip(r-4.5)treestartr_0.1.0.zip(r-4.4)treestartr_0.1.0.zip(r-4.3)
treestartr_0.1.0.tgz(r-4.4-any)treestartr_0.1.0.tgz(r-4.3-any)
treestartr_0.1.0.tar.gz(r-4.5-noble)treestartr_0.1.0.tar.gz(r-4.4-noble)
treestartr_0.1.0.tgz(r-4.4-emscripten)treestartr_0.1.0.tgz(r-4.3-emscripten)
treestartr.pdf |treestartr.html✨
treestartr/json (API)
| # Install 'treestartr' in R: |
| install.packages('treestartr', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/treestartr/issues
- absent_list - Bears
- bears - Bears
- mrca_df - Bears
- tax_frame - Bears
- tree - Bears
Last updated 5 years agofrom:b0535afdd7 (on master)
Exports:absent_tipprdataf_parsrecho_rbecho_subtreegenera_stripprpresent_tipprrand_absent_tipprtext_placr
Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add tips to tree via user input | absent_tippr |
| bears | absent_list bears mrca_df tax_frame tree |
| Detect file format of taxon file | dataf_parsr |
| Print RevBayes-formatted clade constriants. | echo_rb |
| Print subtrees with tips added. | echo_subtree |
| Utility function to check if file is a csv or tsv. | fileformat |
| Check if tip is on tree | genera_strippr |
| Get dataframe of tips that do not have congeners on tree. | get_found |
| Determine if a tip is present on a tree | get_lost |
| Determine which tips are not on the tree, and get their genera. | make_absentdf |
| Determine which tips are on the tree, and get their genera. | make_treedf |
| Add tips to the tree based on taxonomy. | present_tippr |
| Random addition of taxa | rand_absent_tippr |
| Utility function to check taxon_names in parsed data file | taxon_testr |
| Add tips to tree via taxon list | text_placr |
| treestartr: A package for generating reasonable starting trees for phylogenetic analysis. | treestartr-package treestartr |
