# bootstrap: Bootstrapping for uncertainty quantification In ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

 bootstrap R Documentation

## Bootstrapping for uncertainty quantification

### Description

Parametric bootstrapping for ouch models.

### Usage

``````## S4 method for signature 'missing'
bootstrap(object, ...)

## S4 method for signature 'ANY'
bootstrap(object, ...)

## S4 method for signature 'hansentree'
bootstrap(object, nboot = 200, seed = NULL, ...)

## S4 method for signature 'browntree'
bootstrap(object, nboot = 200, seed = NULL, ...)
``````

### Arguments

 `object` A fitted model object. `...` Additional arguments are passed to `update`. `nboot` integer; number of bootstrap replicates. `seed` integer; setting `seed` to a non-`NULL` value allows one to fix the random seed (see simulate).

### Details

`bootstrap` performs a parametric bootstrap for estimation of confidence intervals.

Other methods for ouch trees: `as_data_frame`, `coef()`, `logLik`, `ouch-package`, `paint()`, `plot()`, `print()`, `simulate()`, `summary()`, `update()`

### Examples

``````## Not run:
## Fit BM and a 5-regime OU model to the A. bimaculatus data
tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species))

h1 <- brown(
data=log(bimac['size']),
tree=tree
)

h5 <- hansen(
data=log(bimac['size']),
tree=tree,
regimes=bimac['OU.LP'],
sqrt.alpha=1,
sigma=1,
reltol=1e-11,
parscale=c(0.1,0.1),
hessian=TRUE
)

## What are appropriate AIC.c cutoffs?
simdat <- simulate(h1,nsim=100,seed=92759587)
b1 <- sapply(simdat,function(x)summary(update(h1,data=x))\$aic.c)
tic <- Sys.time()
b5 <- sapply(simdat,function(x)summary(update(h5,data=x))\$aic.c)
toc <- Sys.time()
print(toc-tic)
cat("approximate 95% AIC.c cutoff",signif(quantile(b1-b5,0.95),digits=3),"\n")

## Bootstrap confidence intervals
boots.h1 <- bootstrap(h1,nboot=200,seed=92759587)
cat("bootstrap 95% confidence intervals for h1:\n")
print(t(sapply(boots.h1,quantile,probs=c(0.025,0.975))),digits=3)

boots.h5 <- bootstrap(h5,nboot=200,seed=92759587)
cat("bootstrap 95% confidence intervals for h5:\n")
print(t(sapply(boots.h5,quantile,probs=c(0.025,0.975))),digits=3)

## End(Not run)

``````

ouch documentation built on April 25, 2023, 9:10 a.m.