I am trying to clean up my fluorescence data using staRdom package (script below), but I keep getting this error: Error in eem_raman_normalisation2(eem_list, blank = "Blank_correction") : ***
*** First argument must be of class eemlist, second argument must be 'blank' for a blank correction, a number for correction with this number or a vector with a number for each sample
This script was working perfectly in my previous runs but now it is not working anymore and I don't know what is going on.
I really appreciate your help!
library("staRdom")
cores <- detectCores(logical = FALSE)
folder <- "D:/PhD US/Research/Wetlands/Fall 2023/11082023 Aminoacids/Repetition at lower pH/FL/FL for processing"
eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv)
absorbance_path = "D:/PhD US/Research/Wetlands/Fall 2023/11082023 Aminoacids/Repetition at lower pH/UV/Absorbance for processing"
absorbance <- absorbance_read(absorbance_path, cores = cores)
problem <- eem_checkdata(eem_list,absorbance,error=FALSE)
absorbance <- abs_blcor(absorbance,wlrange = c(680,700))
ex_range <- c(210, 300)
em_range <- c(230,350 )
eem_list <- eem_range(eem_list, ex_range, em_range)
eem_list <- eem_extend2largest(eem_list, interpolation = 20, extend = FALSE, cores = cores, resolution = 4)
eem_list <- eem_ife_correction(eem_list,absorbance, cuvl = 1)
eem_list <- eem_remove_blank(eem_list)
eem_list <- eem_raman_normalisation2(eem_list, blank = "Blank_correction")
eem_list <- eem_extract(eem_list, c("nano", "miliq", "milliq", "mq", "Blank"),ignore_case = TRUE)
absorbance <- dplyr::select(absorbance, -matches("nano|miliq|milliq|mq|blank", ignore.case = TRUE))
remove_scatter <- c(TRUE, TRUE, TRUE, TRUE)
remove_scatter_width <- c(50,50,50,50)
eem_list <- eem_rem_scat(eem_list, remove_scatter = remove_scatter, remove_scatter_width = remove_scatter_width)
eem_list <- eem_interp(eem_list, cores = cores, type = 1, extend = FALSE)
eem_overview_plot(eem_list, spp=6, contour = TRUE)