cati: an R package using functional traits to detect and quantify multi-level community assembly processes

Abstract

Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null-model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses. Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T-statistics. More generally, the cati package 1) calculates a variety of single-trait and multi-trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non-random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions. The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.