Essa é uma revisão anterior do documento!

# R Stuff

Some R-codes, class notes and tutorials produced by our team and collaborators. Hopefully part of them will become R-packages and printed publications in a near future.

Meanwhile we are glad to share them as they are, of course without any warranty that they are all running properly.

## Species Abundance Distributions

These codes are part of an ongoing research project on developing a protocol to fit by maximum likelihood and to compare by model selection different SAD models.

### Fisher Logseries

The original numerical recipe proposed by Fisher et al. (1943) to fit the Fisher logseries to abundance data is a maximum likelihood method (Alonso et al 2008). Above functions to fit the logseries which return the likelihood and AIC. Also funtions for ploting the predicted abundances in a rank-abundance plot, and for the PDF (original discrete form and the continuous approximation by Green & Plotkin 2007) and CDF of the logseries.

### Lognormal

Codes to CDFs and PDFs of the truncated lognormal and their resulting random sampling model, the Poisson-Lognormal (Bulmer 1974), which takes advantage of the poilog R package (Grøtan & Engen, 2008).

### Niche-Partitioning models

Currently just simple functions for the expected abundances for the i-th species in a rank-abundance plot for the Geometric (Motomura 1932) and Broken-Stick (MacArthur 1960) models.

### Rank-abundance Plots

These functions plot rank-abundance plots and allow to compare visually the fit of the four classical models.

### Supporting Documentation

The R package vegan has functions for individual-based permutation tests of additive diversity partitioning (sensu Crist et al. 2003).

Here we provide a code for the sample-based tests (Crist et al. 2003), where sample units of a given level are shuffled within units of the level above.

This code is an improved version of those used by Ribeiro et al. (2008). Apart code fine-tuning, the main change is that the average diversity indexes are not weighted (see Crist et al. 2003).

## References

[2008, article | www]
Alonso, D., Ostling, A., & Etienne, R. S. (2008). The implicit assumption of symmetry and the species abundance distribution. Ecology Letters, 11, 93-105.
[1974, article]
Bulmer, M. G. (1974). On fitting the Poisson lognormal distribution to species abundance data. Biometrics, 30, 651-660.
[2003, article]
Crist, T. O., Veech, J. A., Gering, J. C., & Summerville, K. S. (2003). Partitioning species diversity across landscapes and regions: a hierarchical analysis of $$\alpha$$, $$\beta$$, and $$\gamma$$ diversity. The American Naturalist, 162, 734-743.
[1943, article]
Fisher, R. A., Corbet, A. S., & Williams, C. B. (1943). The relation between the number of the species and the number of individuals in a random sample from animal population. Journal of Animal Ecology, 12, 42-58.
[2007, article | www]
Green, J. L., & Plotkin, J. B. (2007). A statistical theory for sampling species abundances. Ecology Letters, 10, 1037-1045.
[2008, manual | www]
Grøtan, V., & Engen, S. (2008). Poilog: Poisson lognormal and bivariate Poisson lognormal distribution.
[1960, article]
MacArthur, R. H. (1960). On the relative abundance of species. American Naturalist, 94, 25-36.
[1932, article]
Motomura, I. (1932). On the statistical treatment of communities. Zoological Magazine, Tokyo, 44, 379-383.
[2009, article]
Pardini, R., Faria, D., Accacio, G. M., Laps, R. R., Mariano-Neto, E., & Paciencia, M. L. B., et al. (2009). The challenge of maintaining Atlantic forest biodiversity: A multi-taxa conservation assessment of specialist and generalist species in an agro-forestry mosaic in southern Bahia. Biological Conservation, 142(6), 1178-1190.
[2008, article | ribeiro2008.pdf]
Ribeiro, D. B., Prado, P. I., Brown Jr, K. S., & Freitas, A. V. L. (2008). Additive partitioning of butterfly diversity in a fragmented landscape: importance of scale and implications for conservation. Diversity and Distributions, 14(6), 961-968.

watch movies
apoio.1289661276.txt.gz · Última modificação: 2011/08/24 08:27 (edição externa)
Alterações recentes · Índice · Mostrar código fonte · Autenticar-se