corrtest: Detect autocorrelated rates.
In cathyqqtao/RRF: Relative Rate Framework in R

Description Usage Arguments Value Author(s) References Examples

View source: R/corrtest.R

This function tests the hypothesis of independence of evolutionary rates among branches in a phylogeny.

corrtest(
  tree.name = "",
  outgroup = "",
  sister.resample = 0,
  anchor.node = 0,
  anchor.time = 0,
  filename = ""
)

`tree.name`	a file name of the branch length tree that is in the Newick format.
`outgroup`	a character list containing names of tips belonging to the rooting outgroup, which will be removed in the calculation. If outgroup = "" (the default), the input tree must be rooted and no tips will be removed.
`sister.resample`	an integer indicating the number of resampling of sister rate pairs. A large value (>50) is recommended for reliable calculation of the correlation of sister lineage rates when the tree is small (<50 tips). The default value is 0.
`anchor.node`	an ingeter corresponding to the ID of a node with user-provide node time. The user-provide value is used to convert relative rates to absolute rates. If anchor.node = 0 (the default), rates will not be converted and are still relative rates.
`anchor.time`	a numeric value specifying to the node time of anchor.node. When anchor.node = 0, anchor.time will be ingnored.
`filename`	a file name specified for the output file.

CorrScore and the P-value for testing the null hypothesis of rate independence (<filename>_corrtest.txt). If non-zero anchor.node and anchor.time are specified, the mean and standard deviation of rates will be provided.

Qiqing Tao (qiqing.tao@temple.edu) and Sudhir Kumar

Q. Tao et al. Mol. Biol. Evol. (2019) 36:811-824. doi:10.1093/molbev/msz014.

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# Please download the "example.nwk" from https://github.com/cathyqqtao/RRF/tree/main/data.

corrtest(tree.name = "data/example.nwk", outgroup = c("Ornithorhynchus_anatinus", "Zaglossus_bruijni", "Tachyglossus_aculeatus"), sister.resample = 50, anchor.node = 0, anchor.time = 0, filename = "data/example")