Performs checks on the estimated divergence times.
Source:R/inferDivergenceTimes.R
checkDivergenceTimeEstimates.RdThis function performs two different checks:
Checks where ancestral nodes without TimeTree information occur most often along the tree path: (a) near the root, (b) in the middle, or (c) near the tips.
Checks the accuracy of different models for extrapolating the TimeTree information, by "erasing" some known points and comparing the estimates with the true values.
Usage
checkDivergenceTimeEstimates(
tree,
timelines = NULL,
cladeName = NULL,
models = c("t_gamdec", "t_lin", "t_scam", "t_exp", "t_gam", "t_iso", "t_power")
)Arguments
- tree
A
ConvenientTblTreeobject.- timelines
An optional named list of data frames, where each name corresponds to an NCBI ID. Each element in the list is a data frame containing the timeline from the specified taxon to the last common ancestor of all cellular organisms. Each row of the dataframe represents one ancestral node. This list is computed by this function and returned in
timeTreeTimelines, but because computation can take time, a previously computed list can also be given as an optional argument.- cladeName
An optional parameter with the name of the analyzed clade.
- models
An optional parameter defining which models will be used for extrapolating the data from TimeTree. Models must be listed in order of preference. The first model is preferred for setting the divergence time. If there is insufficient information to use a model, the next model is tried, and so on. Available options:
t_gam(Generalized Additive Model),t_scam(Shape Constrained Additive Model),t_gamdec(Generalized Additive Model with a decreasing monotonicity constraint),t_iso(Isotonic regression),t_lin(Linear interpolation),t_exp(Exponential model),t_power(Power-law model).