This is a summary function for multipatt objects.
Usage
# S3 method for class '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
multipattfunction was executed usingfunc = "IndVal"orfunc = "IndVal.g".- Bt
Minimum value for sensitivity (B) for selecting indicators. This argument is effective only if
multipattfunction was executed usingfunc = "IndVal"orfunc = "IndVal.g".- indvalcomp
Logical flag used to report components "A" (or "A.g") and "B" of indicator values. This argument is effective only if
multipattfunction was executed usingfunc = "IndVal"orfunc = "IndVal.g".- ...
Additional arguments of the
summaryfunction.
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.
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: 12
#> Number of species associated to 1 group: 9
#> Number of species associated to 2 groups: 3
#>
#> List of species associated to each combination:
#>
#> Group 1 #sps. 4
#> stat p.value
#> Pancam 0.783 0.005 **
#> Eupvac 0.771 0.005 **
#> Cynarc 0.762 0.005 **
#> Merhed 0.548 0.020 *
#>
#> Group 2 #sps. 3
#> stat p.value
#> Ludads 0.907 0.005 **
#> Orysp. 0.856 0.005 **
#> Psespi 0.602 0.020 *
#>
#> Group 3 #sps. 2
#> stat p.value
#> Phynod 0.963 0.005 **
#> Aesind 0.538 0.050 *
#>
#> Group 1+3 #sps. 1
#> stat p.value
#> Melcor 0.876 0.005 **
#>
#> Group 2+3 #sps. 2
#> stat p.value
#> Helind 0.758 0.020 *
#> Elesp. 0.741 0.015 *
#> ---
#> 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: 12
#> Number of species associated to 1 group: 9
#> Number of species associated to 2 groups: 3
#>
#> List of species associated to each combination:
#>
#> Group 1 #sps. 4
#> A B stat p.value
#> Pancam 0.7672 0.8000 0.783 0.005 **
#> Eupvac 0.6607 0.9000 0.771 0.005 **
#> Cynarc 0.9686 0.6000 0.762 0.005 **
#> Merhed 1.0000 0.3000 0.548 0.020 *
#>
#> Group 2 #sps. 3
#> A B stat p.value
#> Ludads 1.0000 0.8235 0.907 0.005 **
#> Orysp. 0.7330 1.0000 0.856 0.005 **
#> Psespi 0.8811 0.4118 0.602 0.020 *
#>
#> Group 3 #sps. 2
#> A B stat p.value
#> Phynod 0.9278 1.0000 0.963 0.005 **
#> Aesind 0.8108 0.3571 0.538 0.050 *
#>
#> Group 1+3 #sps. 1
#> A B stat p.value
#> Melcor 0.8764 0.8750 0.876 0.005 **
#>
#> Group 2+3 #sps. 2
#> A B stat p.value
#> Helind 0.9381 0.6129 0.758 0.020 *
#> Elesp. 1.0000 0.5484 0.741 0.015 *
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1