Running examples in ‘betaper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis_pertables
> ### Title: Function to assess the efects of taxonomic uncertainty on
> ###   permutational multivariate analysis of variance using distance
> ###   matrices
> ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables
> ### Keywords: multivariate
> 
> ### ** Examples
> 
>  
> 
> 
> data(Amazonia)
> data(soils)
> 
> # Define a new index that includes the terms used in the \code{Amazonia} dataset to define
> # undetermined taxa at different taxonomic levels
> 
> index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")
> 
> # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
> # uncertainty)
>  ## Not run: 
> ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)
> ##D 
> ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:
> ##D 
> ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
> ##D 
> ##D Amazonia.adonis
> ##D 
> ##D plot(Amazonia.adonis)
> ## End(Not run)
> # Fast example for Rcheck
> 
> Amazonia_subset <- Amazonia[1:50,]
> Amazonia4.p2<- pertables.p2(Amazonia_subset, index=index.Amazon, nsim=4, ncl=2)
> 
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2  ~ Ca + K + Mg + Na, data=soils)
> 
> Amazonia.adonis
Permutation tests for multivariate analysis of variance using distance matrices 

Call:
adonis_pertables(formula = Amazonia4.p2 ~ Ca + K + Mg + Na, data = soils) 

Permutation: free
Number of permutations: 5

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model      R2  Pr(>F)   Pr(tax)    
Ca         1   0.40368 0.40368  1.3171 0.13150 0.66667 < 2.2e-16 ***
K          1   0.71782 0.71782  2.3420 0.23382 0.33333 < 2.2e-16 ***
Mg         1   0.31974 0.31974  1.0432 0.10415 0.50000 < 2.2e-16 ***
Na         1   0.40264 0.40264  1.3137 0.13116 0.33333 < 2.2e-16 ***
Residuals  4   1.22602 0.30650         0.39937                      
Total      8   3.06990                 1.00000                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


Confidence intervals of R-squared under different taxonomic scenarios 

             Ca         K         Mg        Na
0%    0.1124643 0.1793658 0.07831701 0.1105672
0.5%  0.1124757 0.1795483 0.07848216 0.1106236
2.5%  0.1125214 0.1802787 0.07914274 0.1108490
50%   0.1152612 0.1974331 0.08987673 0.1160851
97.5% 0.1205642 0.2033955 0.10676312 0.1192461
99.5% 0.1207761 0.2033999 0.10782278 0.1193370
100%  0.1208290 0.2034010 0.10808769 0.1193597


Confidence intervals of p-values under different taxonomic scenarios 

             Ca         K        Mg        Na
0%    0.6666667 0.1666667 0.5000000 0.5000000
0.5%  0.6666667 0.1666667 0.5000000 0.5025000
2.5%  0.6666667 0.1666667 0.5000000 0.5125000
50%   0.6666667 0.1666667 0.6666667 0.6666667
97.5% 0.8208333 0.1666667 0.9875000 0.6666667
99.5% 0.8308333 0.1666667 0.9975000 0.6666667
100%  0.8333333 0.1666667 1.0000000 0.6666667
> 
> plot(Amazonia.adonis)
Error in hist.default(z, plot = FALSE, breaks = seq(min(z), max(z), by = diff.z/30)) : 
  invalid number of 'breaks'
Calls: plot -> plot.adonis_pertables -> hist -> hist.default
Execution halted