partvar: Variance partitioning accross nested scales

In cati: Community Assembly by Traits: Individuals and Beyond

Variance partitioning accross nested scales

Description

Variance partitioning accross nested scales using a decomposition (varcomp function) of variance on restricted maximum likelihood (REML) method (lme function). See Messier et al. 2010 for more information. barPartvar and piePartvar are associated plotting functions.

Usage

	partvar(traits, factors, printprogress = TRUE)
	barPartvar(partvar, col.bar = NA, ...)
	piePartvar(partvar, col.pie = NA, ...)

Arguments

traits	Matrix of traits with traits in column
factors	A matrix of factors with the first column corresponds to the higher level factor, the second row the second higher level factor and so on.
printprogress	Logical value; print progress during the calculation or not.
partvar	The result of the partvar function.
col.bar	Vector of colors of bars
...	Any additional arguments are passed to the pie function.
col.pie	Vector of color for pie.

Value

An object of class "partvar" corresponding to a matrix of variance values with traits in rows and nested factors in column.

Author(s)

Adrien Taudiere Julie Messier

References

Messier, Julie, Brian J. McGill, et Martin J. Lechowicz. 2010. How do traits vary across ecological scales? A case for trait-based ecology: How do traits vary across ecological scales? Ecology Letters 13(7): 838-848. doi:10.1111/j.1461-0248.2010.01476.x.

See Also

piePartvar; barPartvar

Examples

	data(finch.ind)
	## Not run: 
	cond<-seq(1,length(sp.finch)*2, by = 2)
	genus <- as.vector(unlist(strsplit(as.vector(sp.finch),"_"))[cond])

	res.partvar.finch <- partvar(traits = traits.finch, 
	factors = cbind(sites = as.factor(as.vector(ind.plot.finch)), 
	species = as.factor(as.vector(sp.finch)), genus = as.factor(genus)))
	
	res.partvar.finch
	
	oldpar<-par()
	par(mfrow = c(2,2), mai = c(0.2,0.2,0.2,0.2))
	piePartvar(res.partvar.finch)
	par(oldpar)
	
	barPartvar(res.partvar.finch)
	
## End(Not run)

cati documentation built on March 18, 2022, 5:43 p.m.