foodweb (version 1-0)

analyse.seq: Calculate Network Parameters from Multiple, Binary, Predator-prey Matrices Contained in Files That Are Named Sequentially

Description

Calculates species richness, connectance, total number of links, link density, number of trophic positions, prey:predator ratio, and fraction of cannibals, herbivores, top species and intermediate species. If asymmetrical matrices are provided for analysis, they will be made symmetrical if species names have been provided in the first row and column. Absence of a species from the columns of a matrix is taken to mean that it does not consume any species. Absence of a species from the rows is taken to mean that it is not consumed by any species.

Usage

analyse.seq(prefix, suffix, first, last, maxlevels=8, 
sp.names = c("FALSE", "TRUE"), sym = c("FALSE", "TRUE"), 
output="Results.csv", problem="Problem.csv", separator=",")

Arguments

prefix

Text preceding the number that forms the sequence of files to be read. For example, for files named Web1.csv, Web2.csv, Web3.csv, the prefix is Web

suffix

Text following the number that forms the sequence of files to be read. For example, for files named Web1.csv, Web2.csv, Web3.csv, the suffix is .csv

first

An integer. The first number in the sequence of files to be read.

last

An integer. Last number in the sequence of files to be read.

maxlevels

Optional. An integer indicating the maximum number of trophic levels expected to be represented in the food web matrix provided. Defaults to 8. Decreasing this number may make calculation faster.

sym

If TRUE, the matrix used for calculations is generated as output. This may be useful when the matrix provided was not symmetrical. The symmetrical matrix will be provided in a .csv file. Its name is that of the original matrix, followed by the suffix "-sym".

output

Optional. The full name of the output file in which results will be written. Defaults to Results.csv.

problem

Optional. The full name of the output file in which the names of food web matrix files with data other than zeroes and ones will be written. Defaults to Problem.csv.

separator

Optional. The character that separates values in the food web matrices provided. Defaults to comma. If separator="" is specified, the separator is 'white space', that is: one or more spaces, tabs, newlines or carriage returns separate the values. The matrices are imported via read.table(). Therefore, if you are having trouble, check that your matrices are read correctly by that function.

sp.names

Should be set to TRUE if species names are provided in the matrix files.

Value

A .csv file with the calculated network parameters of all the adequately formated matrices provided

Where problems in the matrices were found, a file with the name of the problematic matrix(ces) listed.

Optionally, binary, symmetrical, predator:prey matrices of each file provided can be generated as output.

References

Perdomo G., Sunnucks P. and Thompson R.M. (submitted). food web: an open-source program for the visualisation and analysis of compilations of complex food webs. Environmental Modelling and Software.

See Also

analyse.single analyse.list plotweb mat.2.list

Examples

## Not run: 
# data(moss)
# write.table(moss,file="Web1.csv", append=FALSE,sep=",", row.names=FALSE, col.names=FALSE)
# write.table(moss[-(2:4), -(8:10)],file="Web2.csv", append=FALSE,sep=",", 
# row.names=FALSE, col.names=FALSE)
# analyse.seq(prefix="Web", suffix=".csv", first=1, last=2, maxlevels=4, sp.names="FALSE")
# ## End(Not run)