{
  "_id": "6a1edab6b401979e7340f64b",
  "Package": "staRdom",
  "Type": "Package",
  "Title": "PARAFAC Analysis of EEMs from DOM",
  "Version": "1.1.32",
  "Date": "2026-02-19",
  "Authors@R": "c(person(\"Matthias\", \"Pucher\", email = \"matthias.pucher@ecosight.at\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Daniel\", \"Graeber\", email = \"daniel.graeber@ufz.de\",\nrole = c(\"aut\", \"ctb\")),\nperson(\"Stefan\", \"Preiner\", email = \"stefan.preiner@boku.ac.at\",\nrole = c(\"ctb\")),\nperson(\"Renata\", \"Pinto\", email = \"renatamspinto@sapo.pt\",\nrole = c(\"ctb\")))",
  "Description": "'This is a user-friendly way to run a parallel factor\n(PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on\nexcitation emission matrix (EEM) data from dissolved organic\nmatter (DOM) samples (Murphy et al., 2013)\n<doi:10.1039/c3ay41160e>. The analysis includes profound\nmethods for model validation. Some additional functions allow\nthe calculation of absorbance slope parameters and create\nbeautiful plots.'",
  "License": "AGPL-3",
  "Encoding": "UTF-8",
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  "BugReports": "https://github.com/MatthiasPucher/staRdom/issues",
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  "Repository": "https://matthiaspucher.r-universe.dev",
  "Date/Publication": "2026-02-19 13:37:06 UTC",
  "RemoteUrl": "https://github.com/matthiaspucher/stardom",
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    "User": "root"
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  "Author": "Matthias Pucher [aut, cre],\nDaniel Graeber [aut, ctb],\nStefan Preiner [ctb],\nRenata Pinto [ctb]",
  "Maintainer": "Matthias Pucher <matthias.pucher@ecosight.at>",
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  "_exports": [
    "A_missing",
    "abs_blcor",
    "abs_fit_slope",
    "abs_parms",
    "absorbance_read",
    "eem_absdil",
    "eem_apply",
    "eem_checkdata",
    "eem_checksize",
    "eem_corrections",
    "eem_csv",
    "eem_csv2",
    "eem_dilcorr",
    "eem_dilution",
    "eem_duplicates",
    "eem_easy",
    "eem_eemdil",
    "eem_exclude",
    "eem_export",
    "eem_extend2largest",
    "eem_getextreme",
    "eem_hitachi",
    "eem_ife_correction",
    "eem_import_dir",
    "eem_interp",
    "eem_is.na",
    "eem_load_dreem",
    "eem_matmult",
    "eem_metatemplate",
    "eem_name_replace",
    "eem_overview_plot",
    "eem_parafac",
    "eem_raman_area",
    "eem_raman_normalisation2",
    "eem_range",
    "eem_read_csv",
    "eem_red2smallest",
    "eem_rem_scat",
    "eem_scale_ext",
    "eem_setNA",
    "eem_smooth",
    "eem_spectral_cor",
    "eem_write_csv",
    "eem2array",
    "eempf_bindxc",
    "eempf_comp_load_plot",
    "eempf_comp_mat",
    "eempf_comp_names",
    "eempf_comp_names<-",
    "eempf_compare",
    "eempf_comps3D",
    "eempf_convergence",
    "eempf_corcondia",
    "eempf_corplot",
    "eempf_cortable",
    "eempf_eemqual",
    "eempf_excomp",
    "eempf_export",
    "eempf_fits",
    "eempf_leverage",
    "eempf_leverage_data",
    "eempf_leverage_ident",
    "eempf_leverage_plot",
    "eempf_load_plot",
    "eempf_mleverage",
    "eempf_OF_upload",
    "eempf_openfluor",
    "eempf_plot_comps",
    "eempf_plot_ssccheck",
    "eempf_reorder",
    "eempf_report",
    "eempf_rescaleBC",
    "eempf_residuals",
    "eempf_residuals_metrics",
    "eempf_residuals_plot",
    "eempf_ssc",
    "eempf_ssccheck",
    "eempf_varimp",
    "eempf4analysis",
    "geom_eempeakloc",
    "geom_eemregions",
    "geom_eemscatter",
    "ggeem",
    "ggeem_overlay",
    "list_join",
    "maxlines",
    "norm_array",
    "norm2A",
    "parafac_conv",
    "splithalf",
    "splithalf_plot",
    "splithalf_splits",
    "splithalf_tcc",
    "ssc",
    "ssc_max",
    "tcc",
    "tcc_find_pairs"
  ],
  "_datasets": [
    {
      "name": "eem_list",
      "title": "15 fluorescence samples from drEEM used for examples.",
      "object": "eem_list",
      "class": [
        "eemlist"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "eem_list_outliers",
      "title": "2 fluorescence samples from drEEM that were excluded as outliers from the PARAFAC model.",
      "object": "eem_list_outliers",
      "class": [
        "eemlist"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "peaks",
      "title": "data.frame containing common EEM peaks with the wavelengths and possible deviations",
      "object": "peaks",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "name",
        "ex",
        "em",
        "ex_max",
        "em_max",
        "ex_min",
        "em_min",
        "value"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "pf1",
      "title": "PARAFAC model, see vignette, unconstrained",
      "object": "pf_models",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pf1n",
      "title": "PARAFAC model, see vignette, non-negative constraints",
      "object": "pf_models",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pf2",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised",
      "object": "pf_models",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pf3",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed",
      "object": "pf_models",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pf4",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcy",
      "object": "pf_models",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sh",
      "title": "result from PARAFAC split-half analysis, periodic data split",
      "object": "sh",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-eem_csv",
      "title": "Import EEMs from generic csv files.",
      "topics": [
        ".eem_csv"
      ]
    },
    {
      "page": "dot-trans_parafac",
      "title": "Add data of a PARAFAC model derived from multiway from EEMs",
      "topics": [
        ".trans_parafac"
      ]
    },
    {
      "page": "A_missing",
      "title": "Calculate the sample loadings for samples not involved in model building",
      "topics": [
        "A_missing"
      ]
    },
    {
      "page": "abs_blcor",
      "title": "Baseline correction for absorbance data",
      "topics": [
        "abs_blcor"
      ]
    },
    {
      "page": "abs_fit_slope",
      "title": "Fit absorbance data to exponential curve. 'drm' is used for the fitting process.",
      "topics": [
        "abs_fit_slope"
      ]
    },
    {
      "page": "abs_parms",
      "title": "Calculating slopes and slope ratios of a data frame of absorbance data.",
      "topics": [
        "abs_parms"
      ]
    },
    {
      "page": "absorbance_read",
      "title": "Reading absorbance data from txt and csv files.",
      "topics": [
        "absorbance_read"
      ]
    },
    {
      "page": "as.data.frame.eem",
      "title": "Converting EEM data from class eem to data.frame.",
      "topics": [
        "as.data.frame.eem"
      ]
    },
    {
      "page": "eem_absdil",
      "title": "Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.",
      "topics": [
        "eem_absdil"
      ]
    },
    {
      "page": "eem_apply",
      "title": "Applying functions on EEMs",
      "topics": [
        "eem_apply"
      ]
    },
    {
      "page": "eem_checkdata",
      "title": "Check your EEM, absorption and metadata before processing",
      "topics": [
        "eem_checkdata"
      ]
    },
    {
      "page": "eem_checksize",
      "title": "Check size of EEMs",
      "topics": [
        "eem_checksize"
      ]
    },
    {
      "page": "eem_corrections",
      "title": "Return names of samples where certain corrections are missing.",
      "topics": [
        "eem_corrections"
      ]
    },
    {
      "page": "eem_csv",
      "title": "Importer function for generic csv files to be used with eem_read().",
      "topics": [
        "eem_csv"
      ]
    },
    {
      "page": "eem_csv2",
      "title": "Importer function for generic csv files to be used with eem_read().",
      "topics": [
        "eem_csv2"
      ]
    },
    {
      "page": "eem_dilcorr",
      "title": "Create table how samples should be corrected because of dilution",
      "topics": [
        "eem_dilcorr"
      ]
    },
    {
      "page": "eem_dilution",
      "title": "Modifying fluorescence data according to dilution.",
      "topics": [
        "eem_dilution"
      ]
    },
    {
      "page": "eem_duplicates",
      "title": "Check for duplicate sample names",
      "topics": [
        "eem_duplicates",
        "eem_duplicates.data.frame",
        "eem_duplicates.default",
        "eem_duplicates.eemlist"
      ]
    },
    {
      "page": "eem_easy",
      "title": "Opens an R markdown template for an easy and userfriendly analysis of EEM data.",
      "topics": [
        "eem_easy"
      ]
    },
    {
      "page": "eem_eemdil",
      "title": "Correct names of EEM samples to match undiluted absorbance data.",
      "topics": [
        "eem_eemdil"
      ]
    },
    {
      "page": "eem_exclude",
      "title": "Exclude complete wavelengths or samples form data set",
      "topics": [
        "eem_exclude"
      ]
    },
    {
      "page": "eem_export",
      "title": "Export all samples of an eem_list",
      "topics": [
        "eem_export"
      ]
    },
    {
      "page": "eem_extend2largest",
      "title": "EEM sample data is extended to include all wavelengths in all samples",
      "topics": [
        "eem_extend2largest"
      ]
    },
    {
      "page": "eem_getextreme",
      "title": "Determines the the biggest range of EEM spectrum where data is available from each sample.",
      "topics": [
        "eem_getextreme"
      ]
    },
    {
      "page": "eem_hitachi",
      "title": "Importer function for Hitachi F-7000 txt files to be used with eem_read().",
      "topics": [
        "eem_hitachi"
      ]
    },
    {
      "page": "eem_ife_correction",
      "title": "Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths.",
      "topics": [
        "eem_ife_correction"
      ]
    },
    {
      "page": "eem_import_dir",
      "title": "Load all eemlist obects saved in different Rdata or RDa files in a folder.",
      "topics": [
        "eem_import_dir"
      ]
    },
    {
      "page": "eem_interp",
      "title": "Missing values are interpolated within EEM data",
      "topics": [
        "eem_interp"
      ]
    },
    {
      "page": "eem_is.na",
      "title": "Check for NAs in EEM data",
      "topics": [
        "eem_is.na"
      ]
    },
    {
      "page": "eem_list",
      "title": "15 fluorescence samples from drEEM used for examples.",
      "topics": [
        "eem_list"
      ]
    },
    {
      "page": "eem_list_outliers",
      "title": "2 fluorescence samples from drEEM that were excluded as outliers from the PARAFAC model.",
      "topics": [
        "eem_list_outliers"
      ]
    },
    {
      "page": "eem_load_dreem",
      "title": "Load original data from the drEEM tutorial and return it as eemlist",
      "topics": [
        "eem_load_dreem"
      ]
    },
    {
      "page": "eem_matmult",
      "title": "Multiply all EEMs with a matrix",
      "topics": [
        "eem_matmult"
      ]
    },
    {
      "page": "eem_metatemplate",
      "title": "Create table that contains sample names and locations of files.",
      "topics": [
        "eem_metatemplate"
      ]
    },
    {
      "page": "eem_name_replace",
      "title": "Replace matched patterns in sample names",
      "topics": [
        "eem_name_replace"
      ]
    },
    {
      "page": "eem_overview_plot",
      "title": "Plot fluorescence data from several samples split into several plots.",
      "topics": [
        "eem_overview_plot"
      ]
    },
    {
      "page": "eem_parafac",
      "title": "Runs a PARAFAC analysis on EEM data",
      "topics": [
        "eem_parafac"
      ]
    },
    {
      "page": "eem_raman_area",
      "title": "Calculate raman area of EEM samples",
      "topics": [
        "eem_raman_area"
      ]
    },
    {
      "page": "eem_raman_normalisation2",
      "title": "Wrapper function to eem_raman_normalisation (eemR).",
      "topics": [
        "eem_raman_normalisation2"
      ]
    },
    {
      "page": "eem_range",
      "title": "Cut EEM data matching a given wavelength range",
      "topics": [
        "eem_range"
      ]
    },
    {
      "page": "eem_read_csv",
      "title": "Import EEMs from generic csv tables (deprecated)",
      "topics": [
        "eem_read_csv"
      ]
    },
    {
      "page": "eem_red2smallest",
      "title": "Remove wavelengths, that are missing in at least one sample form the whole set.",
      "topics": [
        "eem_red2smallest"
      ]
    },
    {
      "page": "eem_rem_scat",
      "title": "Remove Raman and Rayleigh scattering in fluorescence data",
      "topics": [
        "eem_rem_scat"
      ]
    },
    {
      "page": "eem_scale_ext",
      "title": "Determine the range of fluorescence values in a set of samples",
      "topics": [
        "eem_scale_ext"
      ]
    },
    {
      "page": "eem_setNA",
      "title": "set parts of specific samples to NA and optionally interpolate these parts",
      "topics": [
        "eem_setNA"
      ]
    },
    {
      "page": "eem_smooth",
      "title": "Smooth fluorescence data by calculating rolling mean along excitation wavelengths.",
      "topics": [
        "eem_smooth"
      ]
    },
    {
      "page": "eem_spectral_cor",
      "title": "Multiply EEMs with spectral correction vectors (Emission and Excitation)",
      "topics": [
        "eem_spectral_cor"
      ]
    },
    {
      "page": "eem_write_csv",
      "title": "Export samples in an EEM list to a single csv files",
      "topics": [
        "eem_write_csv"
      ]
    },
    {
      "page": "eem2array",
      "title": "Data from an eemlist is transformed into an array",
      "topics": [
        "eem2array"
      ]
    },
    {
      "page": "eempf_bindxc",
      "title": "Combining extracted components of PARAFAC models",
      "topics": [
        "eempf_bindxc"
      ]
    },
    {
      "page": "eempf_comp_load_plot",
      "title": "Plot components from a PARAFAC model",
      "topics": [
        "eempf_comp_load_plot"
      ]
    },
    {
      "page": "eempf_comp_mat",
      "title": "Extract EEM matrix for single components determined in the PARAFAC analysis",
      "topics": [
        "eempf_comp_mat"
      ]
    },
    {
      "page": "eempf_comp_names",
      "title": "Extract names from PARAFAC model components",
      "topics": [
        "eempf_comp_names"
      ]
    },
    {
      "page": "eempf_comp_names-set",
      "title": "Set names of PARAFAC components",
      "topics": [
        "eempf_comp_names<-"
      ]
    },
    {
      "page": "eempf_compare",
      "title": "Plot a set of PARAFAC models to compare the single components",
      "topics": [
        "eempf_compare"
      ]
    },
    {
      "page": "eempf_comps3D",
      "title": "3D plots of PARAFAC components",
      "topics": [
        "eempf_comps3D"
      ]
    },
    {
      "page": "eempf_convergence",
      "title": "Extract modelling information from a PARAFAC model.",
      "topics": [
        "eempf_convergence"
      ]
    },
    {
      "page": "eempf_corcondia",
      "title": "Calculate the core consistancy of an EEM PARAFAC model",
      "topics": [
        "eempf_corcondia"
      ]
    },
    {
      "page": "eempf_corplot",
      "title": "Plot correlations of components in samples",
      "topics": [
        "eempf_corplot"
      ]
    },
    {
      "page": "eempf_cortable",
      "title": "Calculating correlations between the component loadings in all samples (C-Modes).",
      "topics": [
        "eempf_cortable"
      ]
    },
    {
      "page": "eempf_eemqual",
      "title": "Calculating EEMqual which is an indicator of a PARAFAC model's quality",
      "topics": [
        "eempf_eemqual"
      ]
    },
    {
      "page": "eempf_excomp",
      "title": "Extracting components of a PARAFAC model",
      "topics": [
        "eempf_excomp"
      ]
    },
    {
      "page": "eempf_export",
      "title": "Create one table containing the PARAFAC models factors and optionally exporting it to csv or txt",
      "topics": [
        "eempf_export"
      ]
    },
    {
      "page": "eempf_fits",
      "title": "Fits vs. components of PARAFAC models are plotted",
      "topics": [
        "eempf_fits"
      ]
    },
    {
      "page": "eempf_leverage",
      "title": "Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC model",
      "topics": [
        "eempf_leverage"
      ]
    },
    {
      "page": "eempf_leverage_data",
      "title": "Combine leverages into one data frame and add optional labels.",
      "topics": [
        "eempf_leverage_data"
      ]
    },
    {
      "page": "eempf_leverage_ident",
      "title": "Plot leverage of emission wavelengths, excitation wavelengths and samples.",
      "topics": [
        "eempf_leverage_ident"
      ]
    },
    {
      "page": "eempf_leverage_plot",
      "title": "Plot leverage of emission wavelengths, excitation wavelengths and samples.",
      "topics": [
        "eempf_leverage_plot"
      ]
    },
    {
      "page": "eempf_load_plot",
      "title": "Plot amount of each component in each sample as bar plot",
      "topics": [
        "eempf_load_plot"
      ]
    },
    {
      "page": "eempf_mleverage",
      "title": "Calculate the leverage of each emission and excitation wavelength and each sample from a list of PARAFAC models",
      "topics": [
        "eempf_mleverage"
      ]
    },
    {
      "page": "eempf_OF_upload",
      "title": "Upload PARAFAC models to openfluor.org",
      "topics": [
        "eempf_OF_upload"
      ]
    },
    {
      "page": "eempf_openfluor",
      "title": "Write out PARAFAC components to submit to openfluor.org.",
      "topics": [
        "eempf_openfluor"
      ]
    },
    {
      "page": "eempf_plot_comps",
      "title": "Plot all components of PARAFAC models",
      "topics": [
        "eempf_plot_comps"
      ]
    },
    {
      "page": "eempf_plot_ssccheck",
      "title": "Plot results from an SSC check",
      "topics": [
        "eempf_plot_ssccheck"
      ]
    },
    {
      "page": "eempf_reorder",
      "title": "Reorder PARAFAC components",
      "topics": [
        "eempf_reorder"
      ]
    },
    {
      "page": "eempf_report",
      "title": "Create a html report of a PARAFAC analysis",
      "topics": [
        "eempf_report"
      ]
    },
    {
      "page": "eempf_rescaleBC",
      "title": "Rescale B and C modes of PARAFAC model",
      "topics": [
        "eempf_rescaleBC"
      ]
    },
    {
      "page": "eempf_residuals",
      "title": "Calculate residuals of EEM data according to a certain model",
      "topics": [
        "eempf_residuals"
      ]
    },
    {
      "page": "eempf_residuals_metrics",
      "title": "Calculate residual metrics from a PARAFAC model",
      "topics": [
        "eempf_residuals_metrics"
      ]
    },
    {
      "page": "eempf_residuals_plot",
      "title": "Plot samples by means of whole sample, each single component and residuum",
      "topics": [
        "eempf_residuals_plot"
      ]
    },
    {
      "page": "eempf_ssc",
      "title": "Calculate the shift-and shape-sensitive congruence (SSC) between model components",
      "topics": [
        "eempf_ssc"
      ]
    },
    {
      "page": "eempf_ssccheck",
      "title": "Check SSCs between different models or initialisations of one model",
      "topics": [
        "eempf_ssccheck"
      ]
    },
    {
      "page": "eempf_varimp",
      "title": "Calculate the importance of each component.",
      "topics": [
        "eempf_varimp"
      ]
    },
    {
      "page": "eempf4analysis",
      "title": "Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters.",
      "topics": [
        "eempf4analysis"
      ]
    },
    {
      "page": "geom_eempeakloc",
      "title": "Mark common EEM peaks",
      "topics": [
        "geom_eempeakloc"
      ]
    },
    {
      "page": "geom_eemregions",
      "title": "Mark common reagions to EEMs to show molecular groups",
      "topics": [
        "geom_eemregions"
      ]
    },
    {
      "page": "geom_eemscatter",
      "title": "Mark EEM scatter bands",
      "topics": [
        "geom_eemscatter"
      ]
    },
    {
      "page": "ggeem",
      "title": "EEM spectra plotted with ggplot2",
      "topics": [
        "ggeem",
        "ggeem.data.frame",
        "ggeem.default",
        "ggeem.eem",
        "ggeem.eemlist",
        "ggeem.parafac"
      ]
    },
    {
      "page": "ggeem_overlay",
      "title": "Add layers of scatter bands, molecular regions and common peaks to EEM plots",
      "topics": [
        "ggeem_overlay"
      ]
    },
    {
      "page": "list_join",
      "title": "Full join of a list of data frames.",
      "topics": [
        "list_join"
      ]
    },
    {
      "page": "maxlines",
      "title": "Extract data from emission and excitation wavelengths of the components of a PARAFAC model (scaled B- and C-modes)",
      "topics": [
        "maxlines"
      ]
    },
    {
      "page": "norm_array",
      "title": "Normalise 3-dimensional array in first and second dimension",
      "topics": [
        "norm_array"
      ]
    },
    {
      "page": "norm2A",
      "title": "Compensate for normalisation in C-modes",
      "topics": [
        "norm2A"
      ]
    },
    {
      "page": "parafac_conv",
      "title": "Calculate a PARAFAC model similar to and using 'parafac'.",
      "topics": [
        "parafac_conv"
      ]
    },
    {
      "page": "peaks",
      "title": "data.frame containing common EEM peaks with the wavelengths and possible deviations",
      "topics": [
        "peaks"
      ]
    },
    {
      "page": "pf1",
      "title": "PARAFAC model, see vignette, unconstrained",
      "topics": [
        "pf1"
      ]
    },
    {
      "page": "pf1n",
      "title": "PARAFAC model, see vignette, non-negative constraints",
      "topics": [
        "pf1n"
      ]
    },
    {
      "page": "pf2",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised",
      "topics": [
        "pf2"
      ]
    },
    {
      "page": "pf3",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed",
      "topics": [
        "pf3"
      ]
    },
    {
      "page": "pf4",
      "title": "PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcy",
      "topics": [
        "pf4"
      ]
    },
    {
      "page": "sh",
      "title": "result from PARAFAC split-half analysis, periodic data split",
      "topics": [
        "sh"
      ]
    },
    {
      "page": "splithalf",
      "title": "Running a Split-Half analysis on a PARAFAC model",
      "topics": [
        "splithalf"
      ]
    },
    {
      "page": "splithalf_plot",
      "title": "Plot results from a splithalf analysis",
      "topics": [
        "splithalf_plot"
      ]
    },
    {
      "page": "splithalf_splits",
      "title": "Extracting a list of sample names in each subsample from a splithalf analysis",
      "topics": [
        "splithalf_splits"
      ]
    },
    {
      "page": "splithalf_tcc",
      "title": "Extracting TCC values from a splithalf analysis",
      "topics": [
        "splithalf_tcc"
      ]
    },
    {
      "page": "ssc",
      "title": "Calculate the shift-and shape-sensitive congruence (SSC) between two matrices",
      "topics": [
        "ssc"
      ]
    },
    {
      "page": "ssc_max",
      "title": "Calculate the combination of components giving the maximum of geometric mean of TCCs",
      "topics": [
        "ssc_max"
      ]
    },
    {
      "page": "tcc",
      "title": "Caluclate Tucker's Congruence Coefficient of PARAFAC components",
      "topics": [
        "tcc"
      ]
    },
    {
      "page": "tcc_find_pairs",
      "title": "Reorders components of different PARAFAC models according to best fit (TCC)",
      "topics": [
        "tcc_find_pairs"
      ]
    }
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  "_vignettes": [
    {
      "source": "Basic_analysis_of_DOM_samples.Rmd",
      "filename": "Basic_analysis_of_DOM_samples.html",
      "title": "Correcting raw data, calculating peaks and indices in EEMS and absorbance (slope) parameters",
      "author": "r packageDescription('staRdom')$Maintainer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Aim  of this document",
        "Hint for beginners in R",
        "Starting the analysis using the template",
        "Output parameters",
        "Input parameters",
        "Fluorometer data (EEM)",
        "Photometer data (absorbance)",
        "Meta data",
        "Spectral correction",
        "Write out results and plots",
        "Results table",
        "Plots",
        "Save data to RData file",
        "Data correction",
        "Absorbance baseline correction",
        "Dilution",
        "EEM range reduction",
        "Blank correction",
        "Correct inner filter effects",
        "Remove and interpolate scattering",
        "Raman normalisation",
        "Smoothing",
        "Running the analysis",
        "Installation",
        "R",
        "RStudio",
        "Optional software",
        "Troubleshooting",
        "Peaks table shows NAs",
        "Only some sample plots show peaks",
        "I cannot read csv files in MS Excel",
        "I get error messages concerning my output directory",
        "References"
      ],
      "created": "2018-04-06 14:25:23",
      "modified": "2026-02-19 11:54:33",
      "commits": 19
    },
    {
      "source": "PARAFAC_analysis_of_EEM.Rmd",
      "filename": "PARAFAC_analysis_of_EEM.html",
      "title": "PARAFAC analysis of EEM data to separate DOM components in R",
      "author": "r packageDescription('staRdom')$Maintainer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Aim of this document",
        "Remark on errors and warnings",
        "Install and load staRdom",
        "Parallel processing",
        "Overview of analysis steps",
        "Example data coming with the package",
        "Raw EEM data",
        "Raw absorbance data",
        "Additional raw data",
        "Corrected EEM data",
        "PARAFAC model",
        "Import raw data",
        "Check data",
        "Data preparation and correction",
        "Sample names",
        "Absorbance baseline correction",
        "Spectral correction",
        "Blank subtraction",
        "Inner-filter effect correction",
        "Raman normalisation",
        "Remove blanks from sample set",
        "Remove and interpolate scattering",
        "Correct for dilution",
        "Smooth data",
        "Overview of samples",
        "Peak picking and indices",
        "Absorbance indices",
        "Creating a PARAFAC model",
        "Loading data",
        "Load drEEM example dataset",
        "Sample set wavelength ranges",
        "Find and remove noise in EEM data",
        "Explore dataset",
        "Check the correlation between different components",
        "Find and exclude outliers leverage",
        "Examine residuals",
        "Recalculating the model with increased accuracy",
        "Plot the resulting components and loadings",
        "Plotting samples and residuals",
        "Split-half analysis",
        "Loadings of outliers",
        "Further model validation",
        "Core consistency",
        "EEMqual",
        "Importance of components",
        "Formatting a model",
        "Naming models and components",
        "Sorting components",
        "Model export and interpretation",
        "Comparing your data using openfluor.org",
        "Comparing data using SSC",
        "Creating a report on your analysis",
        "Exporting the model",
        "Combine results and handle dilution issues",
        "Identify peaks visually",
        "Experimental(!) functions",
        "SSCs between initialisations",
        "Recombining components",
        "References"
      ],
      "created": "2018-04-06 14:25:23",
      "modified": "2026-02-19 11:54:33",
      "commits": 26
    }
  ],
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