![]() ![]() R-devel: Rarefy_1.1.1.zip, r-release: Rarefy_1.1.1.zip, r-oldrel: Rarefy_1.1.1.zip You are correct that when you rarify your OTU table it is likely that low abundance OTUs will be removed from the table, and that these lower abundance OTUs may. These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study. KableExtra, knitr, phyloregion, picante, phytools, raster, rmarkdown, sfĪ quick introduction to rarefaction analisys using Rarefy ![]() Version:Īde4, adiv, ape, dplyr, geiger, methods, stats, vegan (2016) Bacaro, G., Rocchini, D., Ghisla, A., Marcantonio, M., Neteler, M., & Chiarucci, A. (2019) Bacaro, G., Altobelli, A., Cameletti, M., Ciccarelli, D., Martellos, S., Palmer, M. The application of amplicon sequencing in water research provides a rapid and sensitive technique for microbial community analysis in a variety of environments ranging from freshwater lakes to water and wastewater treatment plants. The user can also rarefy any biodiversity metric as provided by a self-written function (or an already existent one) that gives as output a vector with the values of a certain index of biodiversity calculated per plot (Ricotta, C., Acosta, A., Bacaro, G., Carboni, M., Chiarucci, A., Rocchini, D., Pavoine, S. Includes functions for the calculation of spatially and non-spatially explicit rarefaction curves using different indices of taxonomic, functional and phylogenetic diversity. ![]()
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