sensiPhy (version 0.8.5)

samp_phyglm: Sensitivity Analysis Species Sampling - Phylogenetic Logistic Regression

Description

Performs analyses of sensitivity to species sampling by randomly removing species and detecting the effects on parameter estimates in phylogenetic logistic regression.

Usage

samp_phyglm(
  formula,
  data,
  phy,
  n.sim = 30,
  breaks = seq(0.1, 0.5, 0.1),
  btol = 50,
  track = TRUE,
  ...
)

Arguments

formula

The model formula

data

Data frame containing species traits with row names matching tips in phy.

phy

A phylogeny (class 'phylo') matching data.

n.sim

The number of times species are randomly deleted for each break.

breaks

A vector containing the percentages of species to remove.

btol

Bound on searching space. For details see phyloglm

track

Print a report tracking function progress (default = TRUE)

...

Further arguments to be passed to phyloglm

Value

The function samp_phylm returns a list with the following components:

formula: The formula

full.model.estimates: Coefficients, aic and the optimised value of the phylogenetic parameter (e.g. lambda or kappa) for the full model without deleted species.

sensi.estimates: A data frame with all simulation estimates. Each row represents a model rerun with a given number of species n.remov removed, representing n.percent of the full dataset. Columns report the calculated regression intercept (intercept), difference between simulation intercept and full model intercept (DIFintercept), the percentage of change in intercept compared to the full model (intercept.perc) and intercept p-value (pval.intercept). All these parameters are also reported for the regression slope (DIFestimate etc.). Additionally, model aic value (AIC) and the optimised value (optpar) of the phylogenetic parameter (e.g. kappa or lambda, depending on the phylogenetic model used) are reported. Lastly we reported the standardised difference in intercept (sDIFintercept) and slope (sDIFestimate).

sign.analysis For each break (i.e. each percentage of species removed) this reports the percentage of statistically significant (at p<0.05) intercepts (perc.sign.intercept) over all repetitions as well as the percentage of statisticaly significant (at p<0.05) slopes (perc.sign.estimate).

data: Original full dataset.

Details

This function randomly removes a given percentage of species (controlled by breaks) from the full phylogenetic logistic regression, fits a phylogenetic logistic regression model without these species using phyloglm, repeats this many times (controlled by n.sim), stores the results and calculates the effects on model parameters.

Only logistic regression using the "logistic_MPLE"-method from phyloglm is implemented.

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.

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.

Werner, G.D.A., Cornwell, W.K., Sprent, J.I., Kattge, J. & Kiers, E.T. (2014). A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nature Communications, 5, 4087.

#' 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, samp_phylm, influ_phyglm, sensi_plot

Examples

# NOT RUN {
# Simulate Data:
set.seed(6987)
phy = rtree(100)
x = rTrait(n=1,phy=phy)
X = cbind(rep(1,100),x)
y = rbinTrait(n=1,phy=phy, beta=c(-1,0.5), alpha=.7 ,X=X)
dat = data.frame(y, x)
# Run sensitivity analysis:
samp <- samp_phyglm(y ~ x, data = dat, phy = phy, n.sim = 10) 
# To check summary results and most influential species:
summary(samp)
# }
# NOT RUN {
# Visual diagnostics for clade removal:
sensi_plot(samp)
# }