labdsv (version 2.1-0)

matrify: Create Taxon Data.frames From Three Column Database Form

Description

Takes a data.frame in three column form (sample.id, taxon, abundance) and converts it into full matrix form, and then exports it as a data.frame with the appropriate row.names and column names.

Usage

matrify(data, strata=FALSE, base=100)

Value

A data.frame with samples as rows, taxa as columns, and abundance values for taxa in samples.

Arguments

data

a data.frame or matrix in three column format (or database format), where the first column is the sample ID, the second column is the taxon ID, and the third sample is the abundance of that taxon in that sample.

strata

are the species abundances recorded in multiple strata?

base

what is the numeric base relative to 1.0

Author

David W. Roberts

Details

The routine is pure R code to convert data from database form to the sparse matrix form required by multivariate analyses in packages ‘labdsv’ and ‘vegan’, as well as dist and other routines. If TRUE, the strata argument specifies calculating individual species abundances as independent overlap of strata. The base function is useful for converting percent to a fraction.

See Also

dematrify

Examples

x <- cbind(c('a','a','b','b','b','c','c'),
           c('x','y','x','z','w','y','z'),
           c(1,2,1,3,2,2,1))
matrify(x)