eem_interp: Missing values are interpolated within EEM data

In jakehosen/stardom_aqualog: PARAFAC Analysis of EEMs from DOM

Description

Missing EEM data can be interpolated. Usually it is the result of removing scatter or other parts where noise is presumed. Different interpolation algorithms can be used (see details).

Usage

eem_interp(data, cores = parallel::detectCores(logical = FALSE),
  type = TRUE, verbose = FALSE, nonneg = TRUE, ...)

Arguments

data	object of class eemlist with spectra containing missing values
cores	specify number of cores for parallel computation
type	numeric 0 to 4 or TRUE which resembles type 1
verbose	logical, whether more information on calculation should be provided
nonneg	logical, whether negative values should be replaced by 0
...	arguments passed on to other functions (pchip, na.approx, mba.points)

Details

The types of interpolation are (0) setting all NAs to 0, (1) spline interpolation with mba.points, (2) excitation and emission wavelength-wise interpolation with pchip and subsequent mean, (3) excitation wavelength-wise interpolation with pchip and (4) linear interpolation in 2 dimensions with na.approx and again subsequent mean calculation. Calculating the mean is a way of ensuring NAs are also interpolated where missing boundary values would make that impossible. Using type = 3, extrapolation can be suppressed by adding the argument extend = FALSE.

Value

object of class eemlist with interpoleted spectra.

References

Elcoroaristizabal, S., Bro, R., García, J., Alonso, L. 2015. PARAFAC models of fluorescence data with scattering: A comparative study. Chemometrics and Intelligent Laboratory Systems, 142, 124-130 https://doi.org/10.1016/j.chemolab.2015.01.017

See Also

pchip, mba.points, na.approx

Examples

data(eem_list)
eem_list <- eem_list[1:6]
class(eem_list) <- "eemlist"

remove_scatter <- c(TRUE, TRUE, TRUE, TRUE)

remove_scatter_width = c(15,10,16,12)

eem_list <- eem_rem_scat(eem_list,remove_scatter,remove_scatter_width)

eem_list <- eem_interp(eem_list)

ggeem(eem_list)

eem_list2 <- eem_setNA(eem_list,ex=200:280,interpolate=FALSE)

ggeem(eem_list2)

eem_list3 <- eem_interp(eem_list2,type=1,extend = TRUE)

ggeem(eem_list3)

eem_list3 <- eem_interp(eem_list2,type=1,extend = FALSE)

ggeem(eem_list3)

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