eem_parafac: Runs a PARAFAC analysis on EEM data

In jakehosen/stardom_aqualog: PARAFAC Analysis of EEMs from DOM

Description

One or more PARAFAC models can be calculated depending on the number of components. The idea is to compare the different models to get the most suitable. B-mode is emmission wavelengths, C-mode is excitation wavelengths and, A-mode is the loadings of the samples. The calculation is done with parafac, please see details there.

Usage

eem_parafac(eem_list, comps, maxit = 500, normalise = TRUE,
  const = c("nonneg", "nonneg", "nonneg"), nstart = 10, ctol = 10^-4,
  cores = parallel::detectCores(logical = FALSE), verbose = FALSE, ...)

Arguments

eem_list	object of class eem
comps	vector containing the desired numbers of components. For each of these numbers one model is calculated
maxit	maximum iterations for PARAFAC algorithm
normalise	state whether EEM data should be normalised in advance
const	constraints of PARAFAC analysis. Default is non-negative ("nonneg"), alternatively smooth and non-negative ("smonon") might be interesting for an EEM analysis.
nstart	number of random starts
ctol	Convergence tolerance (R^2 change)
cores	number of parallel calculations (e.g. number of physical cores in CPU)
verbose	print infos
...	additional parameters that are passed on to parafac

Value

object of class parafac

See Also

parafac

Examples

data(eem_list)

dim_min <- 3 # minimum number of components
dim_max <- 7 # maximum number of components
nstart <- 10 # random starts for PARAFAC analysis, models built simulanuously, best selected
cores <- parallel::detectCores(logical=FALSE) # use all cores but do not use all threads
maxit = 1000
ctol <- 10^-5 # tolerance for parafac

pfres_comps <- eem_parafac(eem_list,comps=seq(dim_min,dim_max),
    normalise = TRUE,maxit=10000,nstart=nstart,ctol=ctol,cores=cores)

jakehosen/stardom_aqualog documentation built on May 14, 2019, 3:06 a.m.