trillium: Data on the size of Trillium from several sites in Crawford...

In brouwern/wildlifeR: Wildlife biology and animal ecology datasets with example analyses.

Description

The size of Trillium has been hypothesized to be correlated with the intensity of deer browse occuring on thee population.

Usage

trillium

Format

A data frame

site

site code for different forests and woodlots in NW Pennsylvania near the Pymatuning Laboratory of Ecology

spp

species. All are = T for Trillium

length.stem.cm

length from soil to leaf whorl

length.leaf.cm

length of longest leaf in cm

References

Author year.

Examples

library(ggplot2)
library(ggpubr)

## Explore data graphically

### Plot boxplots
ggboxplot(data = trillium,
          y = "length.stem.cm",
          x = "site",
          fill = "site")

### Plot histograms
gghistogram(data = trillium,
          x = "length.stem.cm",
          title = "All data")

 gghistogram(data = trillium,
          x = "length.stem.cm",
          facet.by = "site",
          fill = "site",
          title = "Faceted by site")

## Plot means with 95% confidence intervals
ggerrorplot(trillium,
  x = "site",
  y = "length.stem.cm",
  desc_stat = "mean_ci",
  add = "mean")

## 1-way ANOVA to compare sites

### null model
model.null <- lm(length.stem.cm ~ 1, data = trillium)

### model of interest
model.alt <- lm(length.stem.cm ~ site, data = trillium)

### compare models
anova(model.null, model.alt)

## Pairwise comparisons after 1-way ANOVA
### no corrections for multiple comparisons
pairwise.t.test(x = trillium$length.stem.cm, g = trillium$site,
      p.adjust.method = "none")

### Bonferonni correction
pairwise.t.test(x = trillium$length.stem.cm, g = trillium$site,
      p.adjust.method = "bonferroni")

## Tukey test

### re-fit model with aov()
model.alt.aov <- aov(length.stem.cm ~ site, data = trillium)

### TukeyHSD() on model from aov()
TukeyHSD(model.alt.aov)

### Plot effect sizes
plotTukeysHSD(TukeyHSD(model.alt.aov))

brouwern/wildlifeR documentation built on May 28, 2019, 7:13 p.m.