apm: Additive Partitioning of Net Biodiversity Effects
In BenjaminDelory/bef: Tools for Biodiversity-Ecosystem Functioning Research

Description Usage Arguments Details Value Author(s) References Examples

This function uses the two-way method of Loreau and Hector (2001) or the tripartite method of Fox (2005) to partition net biodiversity effects into complementarity and dominance/selection effects.

1	apm(mix, mono, ry=NULL, method="loreau")

`mix`	A matrix or a data frame containing the biomass of each plant species (columns) in each mixture plot (lines). Column (species) names must be provided.
`mono`	A matrix or a data frame containing the biomass of each plant species (columns) in each monoculture plot (lines). Column (species) names must be provided.
`ry`	A matrix or a data frame giving the expected relative yield of each species (columns) in each mixture plot (lines). Column (species) names must be provided. See details.
`method`	The additive partitioning method to be used. Could be either “loreau” (two-way partitioning method of Loreau and Hector (2001)) or “fox” (tripartite partitioning method of Fox (2005)).

The expected relative yield of each species growing in mixtures should be provided with the ry argument. By default (ry=NULL), all species in a given mixture are assumed to have the same expected relative yield (i.e., all species are assumed to have been sown/planted in equal proportions). If a matrix or a data frame is provided, it should exclusively contain values comprised between 0 and 1.

The two-way method of Loreau and Hector (2001) partitions net biodiversity effects into a complementarity effect and a selection effect. The tripartite method of Fox (2005), however, partitions net biodiversity effects into a dominance effect, a trait-dependent complementarity effect, and a trait-independent complementarity effect. The selection effect of Loreau and Hector (2001) is equal to the sum of the dominance and trait-dependent effects of Fox (2005), while the trait-independent complementarity effect of Fox (2005) is equal to the complementarity effect calculated by the method of Loreau and Hector (2001). With the Fox method, a total complementarity effect can be calculated by summing trait-independent and trait-dependent complementarity effects. I strongly recommend the reading of Loreau and Hector (2001) and Fox (2005) for more information about how interpreting results given by these two partitioning methods.

For each species, the monoculture biomass is calculated as the mean value of all monoculture plots.

Returns a matrix with three (Loreau method) or four (Fox method) columns.

If method="loreau", the matrix has the following columns:

NBE: net biodiversity effect
CE: complementarity effect
SE: selection effect

If method="fox", the matrix has the following columns:

NBE: net biodiversity effect
TICE: trait-independent complementarity effect
TDCE: trait-dependent complementarity effect
DE: dominance effect

Benjamin M. Delory

Loreau M., Hector A. (2001) Partitioning selection and complementarity in biodiversity experiments, Nature, DOI: 10.1038/35083573.

Fox J. (2005) Interpreting the selection effect of biodiversity on ecosystem function, Ecology Letters, DOI: 10.1111/j.1461-0248.2005.00795.x.

path<-system.file("extdata", package = "bef")
datamix<-read.table(paste(path, "datamix.txt", sep="/"), header=TRUE, sep=",")
datamono<-read.table(paste(path, "datamono.txt", sep="/"), header=TRUE, sep=",")
addpart<-apm(mix=datamix, mono=datamono, method="fox")