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

In brouwern/compbio4all: Datasets and helpful functions for learning bioinformatics and computational biology

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)
## Not run: 
## Explore data graphically

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

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

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

## Plot means with 95% confidence intervals
ggpubr::ggerrorplot(trillium,
  x = "site",
  y = "length.stem.cm",
  desc_stat = "mean_ci",
  add = "mean")
 
## End(Not run)

## 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/compbio4all documentation built on Dec. 19, 2021, 11:47 a.m.