README.md
In cathyqqtao/RRF: Relative Rate Framework in R

RRF

An R package for molecular dates, rates, and priors using the relative rate framework.

# Install via remotes.
# install.packages("remotes")
remotes::install_github("cathyqqtao/RRF")

# Alternatively, install via devtools. Note that manually installation of "Rtools" package may be required for successful use of devtools.  
# install.packages("devtools")
devtools::install_github("cathyqqtao/RRF")

If you encounter an error messge saying that '.../library/RRF/R/RRF.rdb' is corrupt, please restart R or R session.

rrf.rates(tree.name = "", outgroup = "", filename = "") estimates relative lineage rates from a branch length tree using the relative rate framework (RRF). It outputs a table of relative lineage rates (\<filename>_RRF_rates.csv).

rrf.times(tree.name = "", outgroup = "", filename = "") estimates relative node times from a branch length tree using RRF. It outputs a table of relative node times (\<filename>_RRF_times.csv).

rrf.rates.times(tree.name = "", outgroup = "", filename = "", plot = TRUE) estimates relative node times from a branch length tree using RRF. It outputs a table of relative lineage rates and node times (\<filename>_RRF_table.csv) and a timetree with relative rates labelled (\<filename>_RRF_timetree.nexus). It also plots the timetree with branches colored by the relative rates, if plot=TRUE.

corrtest(tree.name = "", outgroup = "", sister.resample = 0, anchor.node = 0, anchor.time = 0, filename = "") tests the hypothesis of independence of evolutionary rates among branches in a phylogeny. It outputs a 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.

ddbd(tree.name = "", outgroup = "", sampling.frac = 0, anchor.node = 0, anchor.time = 1, measure = c("SSE","KL"), filename = "", plot = TRUE) estiamtes the values of parameters of Borth-Death speciation tree prior for downstream Bayesian dating analysis from a branch length tree. It outputs estiamted values of parameters in Birth-Death speciation model (\<filename>_ddbd.txt). If the sampling.fraction is specified, only birth rate and death rate will be estimated. Otherwise, all three parameters will be estimated. A histogram of node times and a density curve of the estimated parameters of Birth-Death model will be plotted, if plot=TRUE.