labdsv: dematrify – R documentation

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dematrify

Create Three Column Database Form Data Frame from Sparse Data Frames

Description

Takes a sparse matrix data frame (typical of ecological abundance data) and converts it into three column database format.

Usage

dematrify(comm, filename, sep = ",", thresh = 0)

Arguments

`comm`	a sparse data.frame or matrix, with samples as rows and comm as columns
`filename`	the name of the filename to produce
`sep`	the separator to use in separating columns
`thresh`	the minimum abundance to be included in the output

Details

The routine is pure R code to convert data from sparse matrix form to three column database form for export or reduced storage

Value

a data.frame with the first column the sample ID, the second column the taxon ID, and the third column the abundance.

Note

Typically, large ecological data sets are characterized by sparse matrices of taxon abundance in samples with many zeros in the matrix. Because these datasets may be many columns wide, they are difficult to work with in text editors or spreadsheets, and require excessive amount of space for storage. The reduced three column form is suitable for input to databases, and more easily edited.

Author(s)

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

Examples

library(labdsv)
data(bryceveg)
x <- dematrify(bryceveg)

labdsv

Ordination and Multivariate Analysis for Ecology

v2.0-1

GPL (>= 2)

Authors

David W. Roberts <droberts@montana.edu>

Initial release