Summarizing multi-level pattern analysis

This is a summary function for multipatt objects.

# S3 method for multipatt
summary(
  object,
  alpha = 0.05,
  minstat = NULL,
  At = NULL,
  Bt = NULL,
  indvalcomp = FALSE,
  ...
)

Arguments

object

An object returned by function multipatt.

alpha

Significance level for selecting species in the summary.

minstat

Minimum value of the statistic for selecting species in the summary.

At

Minimum value of positive predictive value (A) for selecting indicators. This argument is effective only if multipatt function was executed using func = "IndVal" or func = "IndVal.g".

Bt

Minimum value for sensitivity (B) for selecting indicators. This argument is effective only if multipatt function was executed using func = "IndVal" or func = "IndVal.g".

indvalcomp

Logical flag used to report components "A" (or "A.g") and "B" of indicator values. This argument is effective only if multipatt function was executed using func = "IndVal" or func = "IndVal.g".

...

Additional arguments of the summary function.

Details

The summary function for multipatt objects presents the results of the analysis by grouping species following their associated site group combination. Only significantly associated species are listed for each combination. The user can limit the species shown by setting a significance level and the minimum value for the strength of the association.

See also

strassoc, signassoc, multipatt

Author

Miquel De Cáceres Ainsa, EMF-CREAF

Examples

library(stats)

## Loads species data
data(wetland) 

## Creates three clusters using kmeans
wetkm <- kmeans(wetland, centers=3) 

## Runs the combination analysis using IndVal.g as statistic
wetpt <- multipatt(wetland, wetkm$cluster) 

## Lists those species with significant association to one combination
summary(wetpt) 
#> 
#>  Multilevel pattern analysis
#>  ---------------------------
#> 
#>  Association function: IndVal.g
#>  Significance level (alpha): 0.05
#> 
#>  Total number of species: 33
#>  Selected number of species: 6 
#>  Number of species associated to 1 group: 3 
#>  Number of species associated to 2 groups: 3 
#> 
#>  List of species associated to each combination: 
#> 
#>  Group 1  #sps.  2 
#>         stat p.value   
#> Psespi 0.894   0.005 **
#> Ipoaqu 0.595   0.040 * 
#> 
#>  Group 3  #sps.  1 
#>         stat p.value   
#> Phynod 0.764    0.01 **
#> 
#>  Group 1+2  #sps.  2 
#>         stat p.value   
#> Orysp. 0.962   0.005 **
#> Ludads 0.882   0.005 **
#> 
#>  Group 2+3  #sps.  1 
#>         stat p.value   
#> Melcor 0.818    0.01 **
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

## Lists those species with significant association to one combination, 
## including indval components
summary(wetpt, indvalcomp=TRUE) 
#> 
#>  Multilevel pattern analysis
#>  ---------------------------
#> 
#>  Association function: IndVal.g
#>  Significance level (alpha): 0.05
#> 
#>  Total number of species: 33
#>  Selected number of species: 6 
#>  Number of species associated to 1 group: 3 
#>  Number of species associated to 2 groups: 3 
#> 
#>  List of species associated to each combination: 
#> 
#>  Group 1  #sps.  2 
#>             A      B  stat p.value   
#> Psespi 0.9318 0.8571 0.894   0.005 **
#> Ipoaqu 0.6190 0.5714 0.595   0.040 * 
#> 
#>  Group 3  #sps.  1 
#>             A      B  stat p.value   
#> Phynod 0.8959 0.6522 0.764    0.01 **
#> 
#>  Group 1+2  #sps.  2 
#>             A      B  stat p.value   
#> Orysp. 0.9245 1.0000 0.962   0.005 **
#> Ludads 1.0000 0.7778 0.882   0.005 **
#> 
#>  Group 2+3  #sps.  1 
#>             A      B  stat p.value   
#> Melcor 0.9106 0.7353 0.818    0.01 **
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1