eem_apply: Applying functions on EEMs

In staRdom: PARAFAC Analysis of EEMs from DOM

Applying functions on EEMs

Description

Applying functions on EEMs

Usage

eem_apply(data, func, return = c("eemlist", "value"), ...)

Arguments

data	eemlist to be modified
func	a function to be applied on the data.
return	either "eemlist" or "value"
...	additional arguments passed on to func

Details

The EEMs are passed on as first argument to func. Additionally, the vector of excitation wavelengths is passed on as ex and the emission wavelengths as em. Therefore, the supplied function has to allow these arguments. The easiest way would be ... (see example).

Value

eemlist or list

Examples

## define a function, that would divide a matrix by its maximum
# more general, if you want to return a valid eemlist (see below),
# a matrix of the same size has to be returned
# ... is used as a placeholder for any argument, important: em and
# ex wavelengths are passed on, so the function needs to take them as arguments,
# even if they are not used
norm_max <- function(x, ...){
  x/max(x)
}

# load example data
data("eem_list")

# normalise eems by the function defined above
norm_eems <- eem_apply(eem_list,norm_max,"eemlist")

# plot the results to see the difference
ggeem(norm_eems)

# define another function. what values were used to
# multiply the eems with?
norm_fac <- function(x, ...){
  1/max(x)
}

# return a list of factors used for normalisation
norm_factors <- eem_apply(eem_list,norm_fac,"value")

unlist(norm_factors)

# return list of em vectors.
# important: x needs to be in the first position, but
# is not used later!
extr_em <- function(x,em,...){
  em
}

em_vectors <- eem_apply(eem_list,extr_em,"value")

em_vectors

staRdom documentation built on Sept. 9, 2025, 5:53 p.m.