wetlands: Data on species richness in constructed wetlands at...

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

Description

Data are the number of species observed in a 0.25 m^2 plot. The original data include the number of stems and percentage cover of each species within the sampling plot. Data collected by Gerry Koza ([e-mail]) in the summer 2017.

Usage

wetlands

Format

A data frame with 78 rows and 5 variables:

site

Gameland

wetland

Wetland number. Can be 1 2 or3

plot

Transect and plot designations

water.depth

depth of water within sapling plot

spp.richness

The number of species observed within the sampling plot

Examples

## Load packages

library(ggplot2)
library(ggpubr)

## Set wetland as a factor
wetlands$wetland <- factor(wetlands$wetland)

## Not run: 
## Explore data graphically

### Plot boxplots
ggpubr::ggboxplot(data = wetlands,
          y = "spp.richness",
          x = "wetland",
          fill = "wetland")

### Plot histograms
ggpubr::gghistogram(data = wetlands,
          x = "spp.richness",
          title = "All data")


ggpubr::gghistogram(data = wetlands,
          x = "spp.richness",
          facet.by = "wetland",
          fill = "wetland",
          title = "Faceted by wetland")

## Plot means with 95% confidence intervals
ggpubr::ggerrorplot(wetlands,
  x = "wetland",
  y = "spp.richness",
  desc_stat = "mean_ci",
  add = "mean")

## End(Not run)

## 1-way ANOVA

### null model
model.null <- lm(spp.richness ~ 1, data = wetlands)

### model of interest
model.alt <- lm(spp.richness ~ wetland, data = wetlands)

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

## Pairwise comparisons after 1-way ANOVA
### no corrections for multiple comparisons
pairwise.t.test(x = wetlands$spp.richness, g = wetlands$wetland,
      p.adjust.method = "none")

### Bonferonni correction
pairwise.t.test(x = wetlands$spp.richness, g = wetlands$wetland,
      p.adjust.method = "bonferroni")

## Tukey test

### re-fit model with aov()
model.alt.aov <- aov(spp.richness ~ wetland, data = wetlands)

### 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.