Package: sisters 0.0.0.9000
Brian OMeara
sisters: Runs various sister group comparisons to test hypotheses about diversification
Sister groups are pairs of clades that differ in a key character. If that character leads to higher diversification rate, then clades with that trait should have more species than their sisters. There are several tests to see if this is the case, ranging from a basic sign test to more complex ones (many implemented in the ape package). This package can identify sister groups that differ in a binary trait and perform all the relevant tests. It can also discretize a continuous trait into a binary "high" vs "low" state.
Authors:
sisters_0.0.0.9000.tar.gz
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sisters_0.0.0.9000.tgz(r-4.4-any)sisters_0.0.0.9000.tgz(r-4.3-any)
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sisters.pdf |sisters.html✨
sisters/json (API)
| # Install 'sisters' in R: |
| install.packages('sisters', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bomeara/sisters/issues
Last updated 1 years agofrom:219ba29741. Checks:OK: 1 NOTE: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 23 2024 |
| R-4.5-win | NOTE | Oct 23 2024 |
| R-4.5-linux | NOTE | Oct 23 2024 |
| R-4.4-win | NOTE | Oct 23 2024 |
| R-4.4-mac | NOTE | Oct 23 2024 |
| R-4.3-win | NOTE | Oct 23 2024 |
| R-4.3-mac | NOTE | Oct 23 2024 |
Exports:sis_cleansis_discretizesis_format_comparisonsis_format_simpifiedsis_get_sister_pairsis_get_sisterssis_iteratesis_test
Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmforeachgeigergenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelpbapplyphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clean up trait and tree | sis_clean |
| Discretize continuous trait data | sis_discretize |
| Is the taxon in one of the sister groups | sis_find_taxon |
| Get comparison format | sis_format_comparison |
| Get simplified comparison format suitable for passing into other functions | sis_format_simpified |
| Get monomorphic trait | sis_get_monomorphic |
| Get sister groups for a node | sis_get_sister_pair |
| Get sister groups for all internal nodes | sis_get_sisters |
| Get trait values for tip numbers | sis_get_trait_values |
| Iterate tests trying a variety of cutoff values | sis_iterate |
| Do a test with a single cutoff value | sis_iterate_single_run |
| Compute multiple tests based on sister group comparisons | sis_test |
| Try but returns NA rather than error | tryNA |
