anosimPlot: Permutation Analysis of Similarity (anosim) for Censored Data

In NADA2: Data Analysis for Censored Environmental Data

Permutation Analysis of Similarity (anosim) for Censored Data

Description

Plots the permutation histogram and test statistic produced by an anosim (nonparametric multivariate) test of differences between groups.

Usage

anosimPlot(
  ano.out,
  hcol = "light blue",
  title = "Histogram of anosim permutations"
)

Arguments

ano.out	an anosim object. See details and example
hcol	color of histogram
title	title of histogram

Value

Plots a histogram of the permutation test statistics representing the null hypothesis along with the observed test statistic from the data. The p-value is the proportion of test statistics equal to or more extreme than the observed test statistic.

References

Helsel, D.R., 2011. Statistics for Censored Environmental Data using Minitab and R, 2nd ed. John Wiley & Sons, USA, N.J.

Oksanen, J., Guillaume, F., 2018. Vegan: ecological diversity. CRAN R-Project. https://cran.r-project.org/package=vegan

See Also

vegan::anosim

Examples

data(PbHeron)

# ROS model for each group
PbHeron.high <- with(subset(PbHeron,DosageGroup=="High"),NADA::ros(Blood,BloodCen))
PbHeron.high <- data.frame(PbHeron.high)
PbHeron.high$DosageGroup <- "High"

PbHeron.low <- with(subset(PbHeron,DosageGroup=="Low"),NADA::ros(Blood,BloodCen))
PbHeron.low <- data.frame(PbHeron.low)
PbHeron.low$DosageGroup <- "Low"

PbHeron.ros=rbind(PbHeron.high,PbHeron.low)

# ANOSIM analysis
library(vegan)
PbHeron.anosim <- with(PbHeron.ros,anosim(modeled,DosageGroup))
summary(PbHeron.anosim)

# Plot
anosimPlot(PbHeron.anosim)

NADA2 documentation built on Sept. 11, 2024, 8:06 p.m.