isamic: Indicator Species Analysis Minimizing Intermediate...

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

Description

Calculates the degree to which species are either always present or always absent within clusters or types.

Usage

1
isamic(comm,clustering,sort=FALSE)

Arguments

comm

a matrix or data.frame of samples, species as columns, samples as rows

clustering

a vector of numeric cluster memberships for samples, or a classification object returned from pam, partana, or slice

sort

if TRUE, return in order of highest value to lowest rather than input order

Details

Calculates the constancy (fractional occurrence of each species in every type), and then calculates twice the the sum of the absolute values of the constancy - 0.5, normalized to the number of clusters (columns).

Value

A data.frame of species indicator values

Author(s)

David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/droberts/droberts.html

References

Aho, K., D.W. Roberts, and T.W. Weaver. 2008. Using geometric and non-geometric internal evaluators to compare eight vegetation classification methods. J. Veg. Sci. 19(4):549-562.

See Also

indval

Examples

1
2
3
4

Example output

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. 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

  junost   ameuta   arcpat   arttri   atrcan   berfre   ceamar   cerled 
   0.956    0.712    0.468    0.800    0.820    0.908    0.576    0.952 
  cermon   chrdep   chrnau   chrpar   chrvis   eurlan   juncom   pacmyr 
   0.768    0.992    0.980    0.944    0.760    0.916    0.716    0.756 
  pruvir   purtri   quegam   rhutri   ribcer   roswoo   samcoe   shearg 
   0.976    0.352    0.624    0.952    0.720    0.968    0.888    0.976 
  sherot   symore   arcuva   artarb   artfri   artpyg   atrcon   berrep 
   0.860    0.712    0.988    0.860    0.896    0.984    0.988    0.668 
  ericor   gutsar   tetcan   agrcri   agrdas   agrscr   agrsmi   bougra 
   0.916    0.840    0.672    0.960    0.912    0.992    0.872    0.816 
  broano   brocil   broine   carrss   elysal   fesovi   hiljam   junbal 
   0.916    0.956    0.976    0.560    0.908    0.972    0.972    0.948 
  koenit   muhmon   muhric   oryhym   orymic   phlpra   poacom   poafen 
   0.780    0.940    0.984    0.556    0.940    0.988    0.984    0.672 
  poanev   poapra   sithys   sticom   stilet   stipin   achmil   agogla 
   0.948    0.956    0.500    0.828    0.980    0.916    0.696    0.880 
  anemul   antros antros.1   apoand   arahol   arapen   arefen   artcar 
   0.988    0.984    0.944    0.936    0.976    0.976    0.984    0.992 
  artlud   astagr   astchi   astcon   asthum   astken   astmeg   astmis 
   0.948    0.968    0.992    0.800    0.924    0.964    0.876    0.720 
  astten   balsag   calnut   caschr   caslin   chadou   cirneo   compal 
   0.988    0.976    0.768    0.884    0.744    0.864    0.932    0.964 
  corkin   creint   crycon   cympur   dessop   drasub   echtri   eriala 
   0.832    0.980    0.856    0.964    0.992    0.688    0.988    0.664 
  erican   erieat   erifla   eripan   eripum   erirac   erisub   eriumb 
   0.964    0.988    0.924    0.952    0.928    0.676    0.988    0.924 
  eupfen   euplur   euprob   fraves   genaff   gerfre   gerric   gilcon 
   0.864    0.672    0.936    0.976    0.992    0.908    0.992    0.844 
  haparm   heddru   hymaca   hymfil   hymric   ipoagg   irimis   ivesab 
   0.848    0.988    0.788    0.780    0.580    0.976    0.984    0.988 
  leppun   lesint   leueri   ligpor   linkin   linlew   litinc   litmul 
   0.832    0.800    0.988    0.988    0.864    0.776    0.988    0.828 
  lotuta   lupkin   lupser   lyggra   lygspi   macgri   molpar   oenbra 
   0.716    0.968    0.956    0.964    0.992    0.660    0.944    0.888 
  oencae   oencor   oenfla   oenlav   opueri   orofas   pedcan   pedsim 
   0.884    0.964    0.992    0.820    0.784    0.976    0.532    0.972 
  pencae   pencom   penlei   penuta   phllon   phycha   potcon   potcri 
   0.804    0.884    0.988    0.988    0.964    0.924    0.980    0.968 
  potgra   pteand   pyrvir   salibe   sclwhi   senmul   sphcoc   stapin 
   0.968    0.920    0.988    0.988    0.948    0.404    0.844    0.988 
  steten   strcor   swerad   taroff   thafen   towmin   tradub   valacu 
   0.936    0.976    0.704    0.964    0.972    0.980    0.908    0.988 
  vicame 
   0.988 

labdsv documentation built on Aug. 4, 2019, 5:03 p.m.

Related to isamic in labdsv...