# staRdom v1.0.8

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## PARAFAC Analysis of EEMs from DOM

This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.

## Functions in staRdom

Name | Description | |

A_missing | Calculate the amount of each component for samples not involved in model building | |

eempf_comps3D | 3D plots of PARAFAC components | |

eem2array | Data from an eemlist is transformed into an array | |

eempf_cortable | Calculating correlations between the component loadings in all samples (C-Modes). | |

blank | blank samples | |

eem_exclude | Exclude complete wavelengths or samples form data set | |

eem_ife_correction | Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths. | |

absorbance_read | Reading absorbance data from txt and csv files. | |

eem_import_dir | Load all eemlist obects saved in different Rdata files in folder | |

eem_range | Cut EEM data matching a given wavelength range | |

eem_interp | Missing values are interpolated within EEM data | |

eempf4analysis | Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters. | |

eem_easy | Opens an R markdown template for an easy and userfriendly analysis of EEM data. | |

eempf_rescaleBC | Rescale B and C modes of PARAFAC model | |

eem_parafac | Runs a PARAFAC analysis on EEM data | |

eem_is.na | Check for NAs in EEM data | |

eem_dilcorr | Create table how samples should be corrected because of dilution | |

eem_getextreme | Determines the the biggest range of EEM spectrum where data is available from each sample. | |

eem_red2smallest | Reduce wavelength range of EEM spectra to widest available in the whole sample set. | |

eem_raman_area | Calculate raman area of EEM samples | |

eem_list | Fluorescence data of 52 corrected samples. | |

eempf_fits | Fits vs. components of PARAFAC models are plotted | |

eempf_leverage_ident | Plot leverage of emission wavelengths, excitation wavelengths and samples. | |

eem_rem_scat | Remove Raman and Rayleigh scattering in fluorescence data | |

eem_metatemplate | Create table that contains sample names and locations of files. | |

eempf_corcondia | Calculate the core consistancy of an EEM PARAFAC model | |

eem_raman_normalisation2 | Wrapper function to eem_raman_normalisation (eemR). | |

splithalf_tcc | Extracting TCC values from a splithalf analysis | |

eempf_leverage_data | Combine leverages into one data frame and add optional labels. | |

eempf_plot_comps | Plot all components of PARAFAC models | |

eempf_eemqual | Calculating EEMqual which is an indicator of a PARAFAC model's quality | |

eem_scale_ext | Determine the range of fluorescence values in a set of samples | |

eem_smooth | Smooth fluorescence data by calculating rolling mean along excitation wavelengths. | |

eempf_corplot | Plot correlations of components in samples | |

eempf_comp_load_plot | Plot components from a PARAFAC model | |

sh | result from PARAFAC split-half analysis | |

tcc | Caluclate Tucker's Congruence Coefficient of PARAFAC components | |

ggeem | EEM spectra plotted with ggplot2 | |

eempf_export | Create one table containing the PARAFAC models factors and optionally exporting it to csv or txt | |

abs_parms | Calculating slopes and slope ratios of a data frame of absorbance data. | |

eempf_compare | Plot a set of PARAFAC models to compare the single components | |

eempf_leverage | Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC model | |

splithalf_plot | Plot results from a splithalf analysis | |

eempf_residuals | Calculate residuals of EEM data according to a certain model | |

eempf_mleverage | Calculate the leverage of each emission and excitation wavelength and each sample from a list of PARAFAC models | |

eempf_residuals_plot | Plot samples by means of whole sample, each single component and residuum | |

splithalf_splits | Extracting a list of sample names in each subsample from a splithalf analysis | |

eem_name_replace | Replace matched patterns in sample names | |

abs_fit_slope | Fit absorbance data to exponential curve. drm is used for the fitting process. | |

eempf_openfluor | Write out PARAFAC components to submit to openfluor.org. | |

tcc_find_pairs | Reorders components of different PARAFAC models according to best fit (TCC) | |

pfres_comps | PARAFAC model | |

eempf_report | Create a html report of a PARAFAC analysis | |

eem_duplicates | Check for duplicate sample names | |

eem_dilution | Modifying fluorescence data according to dilution. | |

norm2A | Compensate for normalisation in C-modes | |

eem_overview_plot | Plot fluorescence data from several samples split into several plots. | |

splithalf | Running a Split-Half analysis on a PARAFAC model | |

eempf_comp_mat | Extract EEM matrix for single components determined in the PARAFAC analysis | |

norm_array | Normalise 3-dimensional array in first and second dimension | |

list_join | Full join of a list of data frames. | |

eempf_leverage_plot | Plot leverage of emission wavelengths, excitation wavelengths and samples. | |

eempf_load_plot | Plot amount of each component in each sample as bar plot | |

maxlines | Extract data from emission and excitation wavelengths of the components of a PARAFAC model | |

pfres_comps2 | Absorption data of 7 samples | |

eem_absdil | Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used. | |

eem_checkdata | Check your EEM, absorption and metadata before processing | |

eem_eemdil | Correct names of EEM samples to match undiluted absorbance data. | |

as.data.frame.eem | Converting EEM data from class eem to data.frame. | |

eem_corrections | Return names of samples where certain corrections are missing. | |

abs_data | raw data from absorbance measurements, 5cm pathlength | |

No Results! |

## Vignettes of staRdom

Name | ||

Basic_analysis_of_DOM_samples.Rmd | ||

PARAFAC_analysis_of_EEM.Rmd | ||

staRdom384.png | ||

No Results! |

## Last month downloads

## Details

Type | Package |

Date | 2018-06-07 |

License | AGPL |

Encoding | UTF-8 |

LazyData | true |

RoxygenNote | 6.0.1 |

VignetteBuilder | knitr |

URL | https://github.com/MatthiasPucher/staRdom |

BugReports | https://github.com/MatthiasPucher/staRdom/issues |

NeedsCompilation | no |

Packaged | 2018-06-20 12:24:46 UTC; maetz |

Repository | CRAN |

Date/Publication | 2018-06-21 13:59:05 UTC |

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