const: Constancy Table

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/const.R

Description

For a classified set of vegetation samples, lists for each species the fraction of samples in each class the species occurs in.

Usage

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const(taxa, clustering, minval = 0, show = minval, digits = 2, 
             sort = FALSE, spcord = NULL)

Arguments

taxa

a data.frame of species abundances with samples as rows and species as columns

clustering

(1) an object of class ‘clustering’, class ‘partana’, or class ‘partition’, (2) a vector of numeric cluster memberships, (3) a factor vector, or (4) a character vector.

minval

the minimum constancy a species must have in at least one class to be included in the output

show

the minimum constancy a species must have to show a printed value

digits

the number of digits to report in the table

sort

a switch to control interactive re-ordering of the output table

spcord

a vector of integers to specify the order in which species should be listed in the table

Details

Produces a table with species as rows, and species constancy in clusters as columns.

The ‘clustering’ vector represents a classification of the samples that the table summarizes. It may result from a cluster analysis, partitioning an ordination, subjective partitioning of a vegetation table, or other source.

The ‘minval’ argument is used to emphasize the dominant species and suppress the rare species. Vegetation tables are often very sparse, and this argument simplifies making them more compact.

The ‘digits’ argument limits the reported precision of the calculations. Generally, relatively low precision is adequate and perhaps more realistic.

The ‘spcord’ argument specifies the order species are listed in a table. You can use the reverse of the number of occurrences to get dominant species at the top to rarer at the bottom, use fidelity values for the ordered clusters, or possibly the order of species centroids in an ordination.

Value

a data.frame with species as rows, classes as columns, with fraction of occurrence of species in classes.

Note

Constancy tables are often used in vegetation classification to calculate or present characteristic species for specific classes or types. ‘const’ may be combined with ‘importance’ and ‘vegtab’ to achieve a vegetation table-oriented analysis.

Author(s)

David W. Roberts [email protected]

References

http://ecology.msu.montana.edu/labdsv/R/labs/lab3/lab3.html

See Also

importance, vegtab, vegemite

Examples

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data(bryceveg) # returns a data.frame called bryceveg
class <- sample(1:10,nrow(bryceveg),replace=TRUE)
const(bryceveg,class,minval=0.25)

Example output

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-25. For overview type 'help("mgcv-package")'.
Loading required package: MASS
Loading required package: cluster

Attaching package: 'labdsv'

The following object is masked from 'package:stats':

    density

          1    2    3    4    5    6    7    8    9   10
ameuta  .    .   0.40  .    .    .    .    .    .    .  
arcpat 0.47 0.44 0.60 0.36 0.54 0.50 0.46 0.44 0.38 0.41
arttri  .    .    .    .    .    .    .    .   0.38  .  
ceamar 0.40 0.44 0.47  .   0.46 0.42 0.31 0.28 0.38 0.29
cermon  .    .    .   0.36  .   0.25  .   0.28  .    .  
chrvis  .   0.31 0.27 0.29 0.33  .    .   0.28 0.25 0.29
juncom  .   0.31 0.33  .   0.25 0.33  .    .   0.25  .  
pacmyr 0.27 0.31 0.47  .   0.25 0.33 0.31 0.28 0.38  .  
purtri 0.33 0.44  .   0.43 0.54 0.58  .   0.39 0.31 0.47
ribcer  .   0.25 0.27  .    .   0.25  .    .    .    .  
symore 0.60 0.50 0.53 0.29 0.50 0.50 0.54 0.56 0.44 0.59
artarb  .   0.25  .   0.29 0.25 0.25  .   0.28  .   0.29
berrep 0.47 0.50 0.53  .   0.38 0.42 0.62 0.50 0.38 0.29
tetcan 0.27  .    .    .    .   0.33  .    .    .   0.41
carrss 0.53 0.62 0.53 0.29 0.54 0.67 0.77 0.56 0.50 0.47
koenit  .   0.31  .    .    .    .    .    .    .   0.29
oryhym 0.33  .    .   0.43 0.29  .    .    .   0.56  .  
poafen 0.27  .    .    .   0.25  .    .   0.28  .    .  
sithys 0.27 0.31 0.33 0.36 0.42 0.33  .   0.28 0.31  .  
sticom  .   0.25  .   0.29 0.25  .    .    .    .   0.29
achmil  .   0.25  .    .    .   0.25  .    .   0.25  .  
astmis  .    .   0.33  .    .    .    .    .    .    .  
calnut  .    .    .    .   0.25  .    .   0.28  .    .  
caschr  .    .    .    .   0.25  .    .    .    .    .  
caslin  .   0.31  .    .    .   0.25  .    .   0.25  .  
corkin  .    .    .   0.29  .    .    .    .    .    .  
drasub  .    .   0.27  .    .    .    .    .    .    .  
eriala  .    .    .    .    .   0.33  .    .    .    .  
erirac  .   0.25 0.27  .    .   0.25  .   0.28  .   0.29
euplur  .    .    .    .   0.25 0.33  .    .    .    .  
hymaca  .    .    .    .    .   0.25  .    .    .    .  
hymfil  .    .   0.27  .    .   0.33  .    .    .    .  
hymric  .    .    .    .   0.25 0.42  .    .    .    .  
lesint  .    .    .    .    .   0.33  .    .    .    .  
linlew  .    .    .    .    .    .    .    .    .   0.29
litmul 0.27  .    .    .    .    .    .    .    .    .  
lotuta  .   0.31  .    .    .    .    .    .    .    .  
macgri  .    .    .    .    .   0.25  .    .    .    .  
opueri  .    .    .    .    .    .    .    .   0.25  .  
pedcan  .    .    .    .   0.29 0.33  .   0.33  .   0.29
pencae 0.33  .    .    .    .    .    .    .    .    .  
senmul 0.53 0.69 0.40 0.36 0.54 0.67  .   0.56 0.31 0.41
swerad  .   0.25 0.40  .    .    .   0.31  .    .    .  

labdsv documentation built on May 30, 2017, 12:46 a.m.