importance: Importance Table

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

Description

For a classified set of vegetation samples, a importance table lists for each species the average or typical abundance of each species in each class.

Usage

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importance(comm,clustering,minval=0,digits=2,show=minval,
       sort=FALSE,typical=TRUE,spcord,dots=TRUE)

Arguments

comm

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

clustering

a vector of (integer) class memberships, or an object of class ‘clustering’, class ‘partana’, of class partition

minval

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

digits

the number of digits to report in the table

show

the minimum value a species must have to print a value

sort

a switch to control interactive re-ordering

typical

a switch to control how mean abundance is calculated. Typical=TRUE divides the sum of species abundance by the number of plots in which it occurs; typical=FALSE divides by the number of plots in the type

spcord

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

dots

a switch to control substituting dots for small values

Value

a data.frame with species as rows, classes as columns, with average abundance of species in classes.

Note

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

Author(s)

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

References

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

See Also

const, vegtab, concov

Examples

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data(bryceveg) # returns a data.frame called bryceveg
data(brycesite)
class <- cut(brycesite$elev,10,labels=FALSE)
importance(bryceveg,class,minval=0.25)

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

            1    2    3    4    5    6    7    8    9   10
junost   0.50  .    .    .    .   0.50  .    .    .    .  
ameuta    .   0.50  .   0.50 1.00 0.50 0.50 0.50 0.50 0.50
arcpat    .   1.88 1.50 3.00 3.70 3.40 2.62 2.96 2.01 1.58
arttri   1.82 1.33  .    .    .   0.50  .    .    .    .  
atrcan   1.35 0.83  .    .    .    .    .    .    .    .  
berfre   0.50 0.50  .    .    .    .    .    .    .    .  
ceamar    .   1.00 0.50 0.75 0.83 0.60 0.70 0.68 0.62 0.83
cerled    .   0.50  .    .   1.00 0.50  .   0.50  .    .  
cermon   0.75 0.89 0.79 1.00 0.50 0.67 0.50  .    .    .  
chrdep    .    .    .    .   0.50  .    .    .    .    .  
chrnau   0.50  .    .    .    .   0.50  .    .    .    .  
chrpar    .    .    .    .   2.00 0.90  .    .   0.50  .  
chrvis   0.50 0.50  .    .   0.81 0.75  .    .    .    .  
eurlan   0.50 1.67  .    .    .    .    .    .    .    .  
juncom    .    .    .    .    .   0.50 0.62 0.83 0.89 0.81
pacmyr    .    .    .    .    .   0.50 0.50 0.50 0.50 0.50
pruvir    .    .    .    .    .    .    .    .   0.50 0.50
purtri   0.50 0.92 0.88 0.71 0.78 0.50 1.33 0.83 0.55 0.67
quegam   0.50 0.83 0.80 2.33 2.00 0.67 0.50 0.50  .    .  
rhutri    .    .   0.50  .    .    .    .    .    .    .  
ribcer    .    .    .    .    .    .   0.50 0.57 0.50 0.50
roswoo    .    .    .    .    .   0.50  .   0.50 0.50  .  
samcoe    .    .    .   0.50 0.50 0.75 0.50 0.50 0.50  .  
shearg    .    .   0.50  .    .    .    .    .    .    .  
sherot   0.50 0.75 0.50 0.67  .    .    .    .    .    .  
symore    .   0.50 0.50 0.50 0.50 0.50 0.55 0.56 0.62 0.67
arcuva    .   1.00  .    .    .    .    .    .    .    .  
artarb    .   0.50  .    .   2.08 1.97  .    .    .    .  
artfri    .    .    .    .    .   0.71  .    .    .    .  
artpyg    .    .    .    .   0.75  .    .    .    .    .  
atrcon   0.50  .    .    .    .    .    .    .    .    .  
berrep    .   0.50 0.50 0.50 0.50 0.50 0.64 0.65 0.69 1.12
ericor   2.00 0.75  .    .    .    .    .    .    .    .  
gutsar    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
tetcan    .    .   0.50  .   0.50 0.65 0.62 0.75 0.50  .  
agrcri   0.50  .    .    .    .    .    .    .    .    .  
agrdas   1.00 0.50  .    .   1.00 0.60  .    .    .    .  
agrscr    .    .    .    .    .   0.50  .    .    .    .  
agrsmi   1.00 0.75  .    .   0.50 1.17  .    .    .    .  
bougra   0.50 1.25  .   0.50 0.50 0.50  .    .    .    .  
broano    .    .    .    .    .   0.82  .    .    .    .  
brocil    .    .    .    .   0.50  .   0.50  .   0.50  .  
broine    .    .    .    .    .   0.50  .    .    .    .  
carrss    .   0.90 0.62 0.50 0.62 1.19 0.64 0.53 0.52 0.56
elysal   1.00 0.50  .    .   1.50  .    .    .    .    .  
fesovi    .    .    .    .    .   0.50 0.50  .    .    .  
hiljam   0.50  .    .    .    .    .    .    .    .    .  
junbal    .    .    .    .   0.50 1.08  .    .    .    .  
koenit    .   0.50  .    .   0.64 0.52 0.50  .    .    .  
muhmon    .    .    .    .    .   1.06  .    .    .    .  
muhric    .    .    .    .    .   1.25  .    .    .    .  
oryhym   0.50 0.58 0.50 0.50 0.58 0.50 0.50 0.50 0.50 0.50
orymic    .   0.50 0.50  .   0.50  .    .    .    .    .  
phlpra    .    .    .    .    .    .   0.50  .    .    .  
poacom    .    .    .    .   0.50 1.00  .    .    .    .  
poafen   0.50 0.50  .   0.75 0.75 0.78  .    .   0.50  .  
poanev    .    .    .    .    .   1.29  .    .    .    .  
poapra    .    .    .    .    .   1.33  .    .    .    .  
sithys   1.45 0.75  .    .   0.50 0.50 0.50 0.50 0.50 0.50
sticom    .   0.50  .    .   1.50 1.43  .    .    .    .  
stilet    .    .    .    .    .   0.50  .   0.50  .    .  
stipin    .    .    .    .   0.50 0.57  .    .    .    .  
achmil    .    .    .    .    .   0.50 0.50 0.50 0.50 0.50
agogla    .    .    .    .    .   0.50  .    .    .    .  
anemul    .    .    .    .    .    .   0.50  .    .    .  
antros    .    .    .    .   0.50 0.50  .    .    .    .  
antros.1  .    .    .    .   0.50 0.50  .   0.50  .    .  
apoand    .    .    .    .    .   0.50  .   0.50 0.50 0.50
arahol    .    .    .    .   0.50  .    .    .    .    .  
arapen    .    .    .    .    .    .    .    .   0.50  .  
arefen    .    .    .    .    .   0.50  .    .    .    .  
artcar    .    .    .    .    .   0.50  .    .    .    .  
artlud    .    .    .    .   0.50 0.50  .   0.50 0.50  .  
astagr    .    .    .    .   0.50 0.50  .    .    .    .  
astchi    .    .    .    .    .   0.50  .    .    .    .  
astcon    .    .    .   0.50  .   0.50 0.50 0.50 0.50  .  
asthum    .    .    .    .   0.50 0.50  .    .    .    .  
astken    .    .    .    .   0.50 0.50  .    .    .    .  
astmeg    .    .    .    .    .   0.50 0.50 0.50 0.50 0.50
astmis    .    .    .    .    .    .   0.50 0.50 0.50 0.50
astten    .    .    .    .    .    .    .   0.50  .    .  
balsag    .    .    .    .    .    .    .    .   0.75  .  
calnut   0.50 0.50  .    .   0.50 0.50  .    .    .    .  
caschr   0.50  .    .    .   0.50  .    .    .    .    .  
caslin   0.50 0.50 0.50  .   0.50 0.50 0.50 0.50 0.50  .  
chadou    .    .    .   0.50  .   0.50 0.50 0.50 0.50  .  
cirneo   0.50 0.50  .    .    .    .    .    .    .    .  
compal    .    .    .    .   0.50  .    .    .    .    .  
corkin   0.50 0.50 0.50  .   0.50 0.50  .    .    .    .  
creint   0.50  .    .    .   0.50  .    .    .    .    .  
crycon   0.50 0.50 0.50 0.50  .    .    .    .    .    .  
cympur    .    .    .   0.50  .    .   0.50  .    .    .  
dessop    .    .    .    .    .   0.50  .    .    .    .  
drasub    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
echtri    .   0.50  .    .    .    .    .    .    .    .  
eriala    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50  .  
erican    .    .    .    .   0.50 0.50  .   0.50  .    .  
erieat    .    .    .    .    .    .    .   0.50  .    .  
erifla    .    .    .    .    .   0.50  .    .    .    .  
eripan    .   0.50  .    .    .   0.50  .    .    .    .  
eripum   0.50  .    .    .   0.50  .    .    .    .    .  
erirac    .   0.50  .    .   0.50 0.50 0.50 0.50 0.50 0.50
erisub   0.50  .    .    .    .    .    .    .    .    .  
eriumb    .    .    .    .   0.50 0.50  .    .    .    .  
eupfen   0.50 0.50 0.50  .   0.50 0.50 0.50  .    .    .  
euplur    .    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
euprob    .   0.50  .    .   0.50 0.50  .    .    .    .  
fraves    .    .    .    .    .    .    .    .   0.50  .  
genaff    .    .    .    .    .   0.50  .    .    .    .  
gerfre    .    .    .    .    .    .   0.50 0.50 0.50  .  
gerric    .    .    .    .    .   0.50  .    .    .    .  
gilcon    .    .    .    .   0.50 0.50  .   0.50 0.50 0.50
haparm   0.50 0.50 0.50 0.50 0.50  .    .    .    .    .  
heddru    .   0.50  .    .    .    .    .    .    .    .  
hymaca    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50  .    .  
hymfil   0.50 0.50  .   0.50 0.50 0.50 0.50 0.50 0.50  .  
hymric   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.62 0.50  .  
ipoagg    .    .    .    .    .   0.50  .    .    .    .  
irimis    .    .    .    .    .   0.50  .    .    .    .  
ivesab    .   0.50  .    .    .    .    .    .    .    .  
leppun    .    .    .    .   0.50 0.50  .    .    .    .  
lesint   0.50 0.50 0.50  .   0.50 0.50 0.50  .    .    .  
leueri    .   0.50  .    .    .    .    .    .    .    .  
ligpor    .   1.00  .    .    .    .    .    .    .    .  
linkin    .   0.62  .    .   0.50 0.50  .   0.50 0.50  .  
linlew    .   0.50 0.50  .   0.50 0.50  .   0.50 0.50 0.50
litinc    .    .    .    .    .    .    .   0.50  .    .  
litmul    .    .    .    .   0.50 0.50 0.50 0.50 0.50 0.50
lotuta    .    .    .    .   0.50 0.50 0.50 0.50 0.50 0.50
lupkin    .    .    .    .   0.50 0.50  .    .    .    .  
lupser    .    .    .    .   0.50  .    .    .    .    .  
lyggra    .    .    .    .   0.50 0.50  .    .    .    .  
lygspi    .    .    .    .   0.50  .    .    .    .    .  
macgri    .   0.50 0.50 0.50 0.50  .   0.50 0.50  .    .  
molpar   0.50  .    .    .    .    .    .    .    .    .  
oenbra    .   0.50  .    .   0.50 0.50 0.50  .    .    .  
oencae    .    .   0.50 0.50 0.50 0.50  .    .   0.50  .  
oencor    .    .    .    .   0.50 0.50  .    .    .    .  
oenfla    .    .    .    .    .   0.50  .    .    .    .  
oenlav    .   0.50  .    .   0.50 0.53  .    .    .    .  
opueri   0.50 0.50 0.50 0.50 0.50  .    .    .    .    .  
orofas    .    .    .    .   0.50 0.50  .    .    .    .  
pedcan    .   0.50  .   0.50 0.50 0.50 0.50 0.50 0.50 0.50
pedsim   0.50  .    .    .   0.50  .    .    .    .    .  
pencae    .    .   0.50  .   0.50 0.50 0.50 0.50  .    .  
pencom   0.50  .    .    .   0.50 0.50  .    .    .    .  
penlei    .    .    .    .    .    .    .    .   0.50  .  
penuta    .   0.50  .    .    .    .    .    .    .    .  
phllon    .    .    .    .   0.50 0.50  .    .    .    .  
phycha    .   0.50 0.50  .    .    .    .   0.50  .    .  
potcon    .    .    .    .    .   0.50 0.50  .    .    .  
potcri    .    .    .    .    .   0.50  .    .    .    .  
potgra    .    .    .    .   0.50 0.50  .    .    .    .  
pteand    .    .    .    .   0.50 0.50 0.50 0.50 0.50  .  
pyrvir    .    .    .    .    .    .   0.50  .    .    .  
salibe    .   0.50  .    .    .    .    .    .    .    .  
sclwhi   0.50 0.50  .   0.50  .    .    .    .    .    .  
senmul    .    .   0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
sphcoc   0.50  .    .    .   0.50  .    .    .    .    .  
stapin    .   0.50  .    .    .    .    .    .    .    .  
steten    .    .    .    .    .   0.50 0.50 0.50  .    .  
strcor    .    .   0.50  .    .    .    .    .    .    .  
swerad    .   0.50  .    .   0.50 0.50 0.50 0.50 0.50 0.50
taroff    .    .    .    .    .   0.50  .    .    .    .  
thafen    .    .    .    .    .    .   0.50 0.50  .    .  
towmin    .   0.50  .    .    .   0.50  .    .    .    .  
tradub   1.00  .    .    .   0.50 0.50  .    .    .    .  
valacu    .    .    .    .    .    .   0.50  .    .    .  
vicame    .    .    .    .    .    .    .   0.50  .    .  

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

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