cwm: Community weighted mean of species attributes
In zdealveindy/weimea: Weighted Mean Analysis

Description Usage Arguments Details Value Author(s) Examples

Function cwm calculates weighted mean of species attributes, using matrix of species composition and one or several species attributes.

cwm(com, traits, wstand = FALSE)

is.cwm(object)

## S3 method for class 'cwm'
object[i, j, drop = FALSE]

## S3 method for class 'cwm'
summary(object, long = FALSE, ...)

## S3 method for class 'cwm'
print(x, ...)

extract(x, ...)

## S3 method for class 'cwm'
extract(x, what = "traits", ...)

range_cwm(object, max = 9, recalculate = TRUE)

`com`	Matrix or data frame with species composition data (samples x species).
`traits`	Vector, matrix or data frame with species attributes (species x attributes). This can be `numeric` or `factor`.
`wstand`	Logical. Should be the values in `traits` weighted-standardized prior to calculation of CWM? Weights are column sums in community data matrix `com`.
`object, x`	Object of the class `cwm`
`i, j`	Subscripts of the matrix of the class "cwm" (rows and columns).
`drop`	Argument in the subsetting function, but currently not implemented (`[.cwm` always return data frame with at least one variable).
`long`	should summary return long output? (TRUE vs FALSE)
`...`	Other arguments passed into `as.matrix`, `summary` or `print` function. Currently not supported.
`what`	Attributes extracted from the object of class `cwm`; either `traits` for the matrix of species attributes (species x traits), or `com` for matrix of species composition (samples x species).
`max`	upper bound of the rescaled values
`recalculate`	should the mean values in `object` be recalculated?

Function [.cwm] is for extracting specified rows and columns from matrix of class cwm. As a side effect, resulting object will have concatenated the com and traits attributes to match the dimension of the resulting matrix. This function is only for extracting the parts of cwm object, not for replacing - the attempt to replace will work, but will break the inner structure of the object.

Generic function extract with argument what applied on object of class "cwm" extracts the original species composition matrix or species attribute matrix, respectively, which were used to calculate weighted means.

Function range_cwm changes the range of species attributes and recalculates the CWM values.

Object of class "cwm", which has print, summary, as.matrix and '[.' methods. Object of "cwm" class contains the matrix of calculated weighted means of species attributes for each sample (sample x weighted mean) and three attributes: com, species x sample matrix from which the weighted mean was calculated, traits, species x attributes matrix with species attributes, and wstand, logical value specifying whether traits were weighted-standardized prior to calculation of CWM (weights are column sums of com). All weighted means of species attributes must be based on the same species x sample matrix with the same number of samples.

David Zeleny (zeleny.david@gmail.com)

# Calculation of weighted mean of species Ellenberg indicator values using dataset Vltava
data (vltava)
mean.eiv <- cwm (com = vltava$spe, traits = vltava$eiv)

summary (mean.eiv)

# Extracting values from the object of cwm class
mean.eiv[,1]
mean.eiv[1:10, 2:3]