[R] Function for translation of a list into a matrix as used by ordination?

Billy_Schweiger at nps.gov Billy_Schweiger at nps.gov
Fri Jan 25 22:29:48 CET 2008


Does anyone know of an existing function that takes a list in the form of:

Plot1 Species1    Abundance1
Plot1 Species2    Abundance2
Plot2 Species1    Abundance1
Plot2 Species3    Abundance3
PlotN SpeciesN    AbundanceN

and translates into a matrix in the form of

      Species1    Species2....      SpeciesN
Plot1 Abundance1  Abundance2...     AbundanceN
Plot2 Abundance1  Abundance2...     AbundanceN

PlotN AbundanceN  AbundanceN...     AbundanceN

This is a basic operation used in the initial stages of ordination etc of
ecological data (vegetation or other species) that is usually stored in a
database or flatfile in the list format above. It is similar to a cross
tabulation like the function xtabs(), however its useful to be able to
control whether a measured abundance for a taxa is included or a boolean
(presence/absence) for the taxa in a given plot.

Im new to such analyses in R, but before writing it myself hope or suspect
that such a function or library is out there (although I dont see it after
some quick searching in things like Vegan or BiodivesityR or labdsv).


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