tree_phyglm {sensiPhy} | R Documentation |
Phylogenetic uncertainty - Phylogenetic Logistic Regression
Description
Performs Phylogenetic logistic regression evaluating uncertainty in trees topology.
Usage
tree_phyglm(formula, data, phy, n.tree = 2, btol = 50, track = TRUE, ...)
Arguments
formula |
The model formula |
data |
Data frame containing species traits with species as row names. |
phy |
A phylogeny (class 'multiPhylo', see ? |
n.tree |
Number of times to repeat the analysis with n different trees picked
randomly in the multiPhylo file.
If NULL, |
btol |
Bound on searching space. For details see |
track |
Print a report tracking function progress (default = TRUE) |
... |
Further arguments to be passed to |
Details
This function fits a phylogenetic logistic regression model using phyloglm
to n trees, randomly picked in a multiPhylo file.
Currently, this function can only implement simple logistic models (i.e. trait~
predictor
). In the future we will implement more complex models.
Output can be visualised using sensi_plot
.
Value
The function tree_phyglm
returns a list with the following
components:
formula
: The formula
data
: Original full dataset
sensi.estimates
: Coefficients, aic and the optimised
value of the phylogenetic parameter (e.g. lambda
) for each regression with a
different phylogenetic tree.
N.obs
: Size of the dataset after matching it with tree tips and removing NA's.
stats
: Main statistics for model parameters.CI_low
and CI_high
are the lower
and upper limits of the 95
all.stats
: Complete statistics for model parameters. sd_intra
is the standard deviation
due to intraspecific variation. CI_low
and CI_high
are the lower and upper limits
of the 95
Author(s)
Caterina Penone & Pablo Ariel Martinez
References
Paterno, G. B., Penone, C. Werner, G. D. A. sensiPhy: An r-package for sensitivity analysis in phylogenetic comparative methods. Methods in Ecology and Evolution 2018, 9(6):1461-1467
Donoghue, M.J. & Ackerly, D.D. (1996). Phylogenetic Uncertainties and Sensitivity Analyses in Comparative Biology. Philosophical Transactions: Biological Sciences, pp. 1241-1249.
Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.
See Also
phyloglm
, sensi_plot
,tree_phylm
Examples
### Simulating Data:
set.seed(6987)
mphy = rmtree(150, N = 30)
x = rTrait(n=1,phy=mphy[[1]])
X = cbind(rep(1,150),x)
y = rbinTrait(n=1,phy=mphy[[1]], beta=c(-1,0.5), alpha=.7 ,X=X)
dat = data.frame(y, x)
# Run sensitivity analysis:
tree <- tree_phyglm(y ~ x, data = dat, phy = mphy, n.tree = 30)
# summary results:
summary(tree)
# Visual diagnostics for phylogenetic uncertainty:
sensi_plot(tree)