eempf_report: Create a html report of a PARAFAC analysis

In staRdom: PARAFAC Analysis of EEMs from DOM

Create a html report of a PARAFAC analysis

Description

Create a html report of a PARAFAC analysis

Usage

eempf_report(
  pfmodel,
  export,
  eem_list = NULL,
  absorbance = NULL,
  meta = NULL,
  metacolumns = NULL,
  splithalf = FALSE,
  shmodel = NULL,
  performance = FALSE,
  residuals = FALSE,
  spp = 5,
  cores = parallel::detectCores(logical = FALSE),
  ...
)

Arguments

pfmodel	PARAFAC model
export	path to exported html file
eem_list	optional EEM data
absorbance	optional absorbance data
meta	optional meta data table
metacolumns	optional column names of metadata table
splithalf	optional logical, states whether split-half analysis should be included
shmodel	optional results from split-half analysis. If this data is not supplied but EEM data is available the split-half analysis is calculated on the creation of the report. Calculating the split-half analysis takes some time!
performance	calculating model performance: eempf_eemqual
residuals	logical, whether residuals are plotted in the report
spp	plots per page for loadgins and residuals plot
cores	cores to be used for the calculation
...	arguments to or from other functions

Value

TRUE if report was created

Examples

folder <- system.file("extdata/EEMs", package = "staRdom") # load example data
eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv)

abs_folder <- system.file("extdata/absorbance", package = "staRdom") # load example data
absorbance <- absorbance_read(abs_folder, cores = 2)

metatable <- system.file("extdata/metatable_dreem.csv",package = "staRdom")
meta <- read.table(metatable, header = TRUE, sep = ",", dec = ".", row.names = 1)

checked <- eem_checkdata(eem_list, absorbance, metadata = meta,
metacolumns = "dilution", error = FALSE)

eem_names(eem_list)
pfm <- A_missing(eem_list,pf4[[1]], cores = 2)
eempf_report(pfm, export = file.path(tempdir(),"pf_report.html"), eem_list = eem_list,
             absorbance = absorbance, meta = metatable, metacolumns = "dilution", cores = 2)

staRdom documentation built on July 9, 2023, 5:57 p.m.