spaa (version 0.1.2)

spaa-package: Species Association Analysis and Niche Overlap

Description

Package for species association analysis and niche overlap

Details

ll{ Package: spaa Type: Package Version: 0.1.2 Date: 2010-08-11 License: GPL-2 LazyLoad: yes } This package will be used in examining species association. add.col adds information from one dataframe to another. data2mat converts field data record to species matrix. freq.calc returns the relative frequency for each species. plotlowertri plots the semimatrix using setted types of points. plotnetwork plots the simple correlation network. sp.assoc gives the total species association results. sp.pair calculates species association between each pair of species. sub.sp.matrix obtains the subset of a standard species matrix, according to species relative frequency. niche.overlap calculates species niche overlap. niche.overlap.boot bootstrap the spcies niche overlap niche.width calculates species niche width.

References

Zhang Qiaoying, Peng Shaolin, Zhang Sumei, Zhang Yunchun, Hou Yuping. (2008). Association of dominant species in Guia hill Municipal Park of Macao. Ecology and Environment. 17:1541-1547 Guo Zhongling, Ma Yuandan, Zheng Jiping, Liu Wande, Jin Zefeng. (2004). Biodiversity of tree species, their populations'spatial distribution pattern and interspecific association in mixed deciduous broadleaved forest in Changbai Mountains Chinese Journal of Applied Ecology. 15:2013-2018 Shi Zuomin, Liu Shirong, Cheng Ruimei, Jiang Youxu. (2001). Interspecific association of plant populations in deciduous broad leaved forest in Baotianman. Scientia Silvae Sinicae. 37:30-35 Zhou XY, Wang BS, Li MG, Zan QJ. (2000). An analysis of interspecific associations in secondary succession forest communities in Heishiding Nature Reserve, Guangdong Province. Acta Phytoecologica Sinica. 24:332-339 JIAN Minfei, LIU qijing, ZHU du, YOU hai. (2009). Inter-specific correlations among dorminant populations of tree layer species in evergreen broad-leaved forest in Jiulianshan Mountain of subtropical China. Chinese Journal of Plant Ecology. 33:672-680 Zhang Jin-tun,(2004 ) Quantitative Ecology, Science Press, Beijing Nicholas J. Gotelli. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606-2621. http://esapubs.org/archive/ecol/E081/022/EcoSim

Examples

data(testdata)
testdata
data(splist)
splist

## adding information
## add genera from dataframe B to dataframe A.
add.col(inputA = testdata, inputB = splist, add = "genera",
according = "species")
## add family from dataframe B to dataframe A.
add.col(inputA = testdata, inputB = splist, add = "family", 
according = "species")


### data tranformation
(spmatrix <- data2mat(testdata))
#Species association
sp.assoc(spmatrix)


# Species association between each pair of species
(result <- sp.pair(spmatrix))

# simple network with positive lines in red and negative lines 
# in blue
plotnetwork(result$Pearson)
title("Pearson Correlation Network")

# The lower matrix plot illustrating Pearson's correlation 
# between each pair of species Note the triangle didn't appeared
# in the plots, but have been added to the legend. This is due 
# to the distribution of data. Be carefull in seletion of intervals.

plotlowertri(result$Pearson, int = 0.5, cex=3, interval = 4, 
pchlist = c(19, 17, 15, 1, 5), size = TRUE)
title("Pearson Correlation Lower Matrix Plot")

## plot lower matrix
## Using BCI data for lower matrix plot
library(vegan)
data(BCI)
## select the top 30 species according to relative frequeny.
sub <- sub.sp.matrix(BCI, common = 30)
## Set the digits to 1
plotlowertri(cor(sub), size = TRUE, cex = 3, digits = 1)

#### Niche width and niche overlap
data(datasample)
niche.overlap.boot(datasample[,1:3], method = "levins")
niche.overlap(datasample, method = "levins")
niche.width(datasample[,1:3], method = "shannon")