Description Usage Arguments Details Value
This function fits a Bayesian version of Ridge regression on edge paths, producing a phylogenetically smoothed estimate of trait evolution rates along a phylogeny's branches. Shrinkage limits how much change in rates can occur at each split of the phylogeny.
1 2 3 4 |
x |
Object of class |
family |
a character vector specifying the statistical families to be used for each trait. If named, names will be used to match the family to a column in the traits data, otherwise they will be used in order. If the length of the vector is less than the number of traits, it will be recycled with a warning. |
method |
Method to use. Currently the only option is "Ridge". This is mainly for compatibility
with |
tree |
A phylogeny of class |
regularise_first_split |
Should the edges beginning at the first split in the phylogeny be regularised? If not, these are treated like a a set of 'intercepts' for evolutionary rates, and every subsequent change in these rates along the tree are regularised (penalised). |
n_samples |
Number of MCMC samples to draw during the fitting process. |
thin |
Thinning rate for MCMC samples. |
warmup |
Number of iteration to use for warmup of the MCMC sampling process. |
chains |
Number of replicate MCMC chains to run. |
n_cores |
Number of CPU cores to use for sampling. |
... |
Any other parameters to pass to the underlying fitting function (in this case |
Test equations:
1 2 3 4 5 6 7 8 9 10 11 | yi ~ f(μ, φ)
===
\
g(μ) = α + / βj
===
j
βj ~ Normal(0, τ)
τ ~ InvGamma(1, 1)
|
Object of class phurl
, containing a fitted model in the model
slot, and a
tibble in the results
slot containing estimates of rates along each edge, estimates of
rate changes at each node, and ancestral character estimates (ACEs), including samples from the full
posterior distribution.
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