fit_OU_mean_var {ShiVa} | R Documentation |
Fit OU Model with Shifts in Mean and Variance
Description
Fits an Ornstein-Uhlenbeck (OU) model with user-specified shifts in both optimal trait values (mean) and evolutionary variance along a phylogeny. The method uses numerical optimization to estimate shift magnitudes, base variance, and intercept, and can optionally incorporate measurement error in trait values.
Usage
fit_OU_mean_var(
tree,
Y,
alpha,
shifts_mean,
shifts_var,
max.steps = 1000,
t = 0.01,
thres = 0.01,
measurement_error = FALSE,
max.num.shifts = Inf
)
Arguments
tree |
A phylogenetic tree of class |
Y |
A numeric vector of continuous trait values at the tips of the tree. |
alpha |
A non-negative numeric value specifying the strength of selection in the OU process. |
shifts_mean |
An integer vector indicating the indices of branches where shifts in the optimal trait value occur. |
shifts_var |
An integer vector indicating the indices of branches where shifts in evolutionary variance occur. |
max.steps |
Maximum number of optimization steps. Default is 1000. |
t |
Step size for the optimizer. Default is 0.01. |
thres |
Convergence threshold for change in log-likelihood. Default is 0.01. |
measurement_error |
Logical. If |
max.num.shifts |
Maximum allowed number of shifts (combined for mean and variance). Default is |
Value
A list containing:
tree |
The phylogenetic tree. |
Y |
The trait values. |
shifts_mean |
Indices of branches with non-zero shifts in optimal trait value. |
shifts_var |
Indices of branches with non-zero shifts in evolutionary variance. |
beta |
Estimated shift magnitudes for optima values. |
gamma |
Estimated shift magnitudes for variance. |
sigma2 |
Estimated base evolutionary variance. |
b0 |
Estimated intercept (ancestral trait value). |
sigma2_error |
Estimated measurement error variance (only returned if |
loglik |
Log-likelihood of the fitted model. |
BIC |
BBIC for model selection. |
mBIC |
mBIC for accounting shift sparsity and shared support. |
pBIC |
pBIC incorporating determinant of projected design matrix. |
fitted.values |
Fitted trait values based on the estimated model. |
Sigma |
Estimated trait covariance matrix under the fitted model. |