Permutation Analysis of Similarity (anosim) for Censored Data

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

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))
#> Warning: Input > 80% censored -- Results are tenuous.
PbHeron.low <- data.frame(PbHeron.low)
PbHeron.low$DosageGroup <- "Low"

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

# ANOSIM analysis
library(vegan)
#> Warning: package 'vegan' was built under R version 4.1.3
#> Loading required package: permute
#> Warning: package 'permute' was built under R version 4.1.3
#> Loading required package: lattice
#> This is vegan 2.6-4
#> 
#> Attaching package: 'vegan'
#> The following object is masked from 'package:EnvStats':
#> 
#>     calibrate
PbHeron.anosim <- with(PbHeron.ros,anosim(modeled,DosageGroup))
summary(PbHeron.anosim)
#> 
#> Call:
#> anosim(x = modeled, grouping = DosageGroup) 
#> Dissimilarity: bray 
#> 
#> ANOSIM statistic R: 0.1205 
#>       Significance: 0.017 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Upper quantiles of permutations (null model):
#>    90%    95%  97.5%    99% 
#> 0.0569 0.0820 0.1087 0.1303 
#> 
#> Dissimilarity ranks between and within classes:
#>         0%    25%   50%    75% 100%   N
#> Between  1  99.25 198.5 275.75  348 182
#> High     4 173.50 252.5 299.50  351  78
#> Low      8  60.00 108.0 160.50  242  91
#> 

# Plot
anosimPlot(PbHeron.anosim)