ordicoeno: Coenoclines for an Ordination Axis

Description Usage Arguments Details Value Author(s) References Examples

Description

A graph is produced that summarizes (through GAM as implemented by gam) how the abundance of all species of the community data set change along an ordination axis (based on the position of sites along the axis and the information from the community data set).

Usage

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ordicoeno(x, ordiplot, axis = 1, legend = FALSE, cex = 0.8, ncol = 4, ...)

Arguments

x

Community data frame with sites as rows, species as columns and species abundance as cell values.

ordiplot

Ordination plot created by ordiplot.

axis

Axis of the ordination graph (1: horizontal, 2: vertical).

legend

if TRUE, then add a legend to the plot.

cex

the amount by which plotting text and symbols should be magnified relative to the default; see also par

ncol

the number of columns in which to set the legend items; see also legend

...

Other arguments passed to functions plot and points.

Details

This functions investigates the relationship between the species vectors and the position of sites on an ordination axis. A GAM (gam) investigates the relationship by using the species abundances of each species as response variable, and the site position as the explanatory variable. The graph shows how the abundance of each species changes over the gradient of the ordination axis.

Value

The function plots coenoclines and provides the expected degrees of freedom (complexity of the relationship) estimated for each species by GAM.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

Examples

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library(vegan)
library(mgcv)
data(dune)
Ordination.model1 <- rda(dune)
plot1 <- ordiplot(Ordination.model1, choices=c(1,2), scaling=1)
ordicoeno(dune, ordiplot=plot1, legend=TRUE)

Example output

Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
BiodiversityR 2.11-1: Use command BiodiversityRGUI() to launch the Graphical User Interface; 
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)

Warning message:
no DISPLAY variable so Tk is not available 
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
edfs from GAM models for each species...
Achimill Agrostol Airaprae Alopgeni Anthodor Bellpere Bromhord Chenalbu 
2.471313 1.000000 1.620946 6.785975 3.682010 1.000000 1.543822 1.000000 
Cirsarve Comapalu Eleopalu Elymrepe Empenigr Hyporadi Juncarti Juncbufo 
1.000000 8.968935 2.459064 2.327898 1.000000 1.473894 1.000000 1.427246 
Lolipere Planlanc  Poaprat  Poatriv Ranuflam Rumeacet Sagiproc Salirepe 
1.000000 1.849688 1.342248 1.000000 2.794590 1.800620 2.344303 1.000000 
Scorautu Trifprat Trifrepe Vicilath Bracruta Callcusp 
1.000000 2.260650 3.346612 1.000000 1.199549 2.025276 

BiodiversityR documentation built on April 20, 2021, 5:07 p.m.