R code for illustrating morphological null model analysis, guild proportionality analysis, and morphological and guild proportionality analysis.
Ecological Archives M080-003-S1.
File list (downloads)
Rogerio R. Silva
Museu de Zoologia da Universidade de São Paulo
Avenida Nazaré, 481, 04263-000, São Paulo, SP173 Mulford #3114, Berkeley CA 94720-3114
These code illustrates in detail the R scripts used in morphological null model and guild proportionality analysis. For the morphological null model analysis, the code provided here uses the R function sample in the R-package base to build a null distribution of species traits and tests if the morphological structure of the assemblage is more variable (significant divergence) or more uniform (significant aggregation) than expected from assemblages that are comprised of random samples drawn from a pool of potential colonizers. For the guild proportionality analysis, the code provided here uses random matrices of species co-occurrences generate by EcoSim software (Gotelli and Entsminger 2005) to calculate the observed Variance Relative Index (Watkins and Wilson 2003). This index has a range of +1 to -1; assuming value equal to 0 when the observed variance in guild proportion is equal to that expected under the null model, and value smaller than 0 when there is guild proportionality (Alpha guilds). A value > 0 indicates disproportionality (Beta guilds structuring).
MNND_Analysis_supplement_Code.R contains annotated code for morphological null model analysis.
Guild_Proportionality_Analysis_supplement_Code.R contains annotated code for guild proportionality analysis.
Morphological_and_Guild_Analysis_supplement_Code.R contains annotated code used in morphological null models analysis and guild proportionality analysis.
Gotelli, N. J., and G. L. Entsminger. 2005. EcoSim: Null models software for ecology. Version 7. Acquired Intelligence Inc. & Kesey-Bear, Jericho, Vermont. <http://homepages.together.net/~gentsmin/ecosim.htm>.
Watkins, A. J., and J. B. Wilson. 2003. Local texture convergence: a new approach to seeking assembly rules. Oikos 102:525–532.
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