Package: eprscope 0.1.17

Ján Tarábek

eprscope: Processing and Analysis of Electron Paramagnetic Resonance Data and Spectra in Chemistry

Processing, analysis and plottting of Electron Paramagnetic Resonance (EPR) spectra in chemistry. Even though the main emphasis is on continuous wave (CW) EPR/ENDOR, many functions may be also used for the integrated forms of 1D PULSED EPR spectra. The primary goal is to find the most important spectral characteristics like g-factor, linewidth, maximum of derivative or integral intensities and single/double integrals. This is especially important in spectral (time) series, consisting of many EPR spectra like during variable temperature experiments, electrochemical or photochemical radical generation and/or decay. Therefore, processing of data/spectra for the analytical (quantitative) purposes belongs to the package core. The aim is to evaluate rate constants, considering different kinetic models, to describe the radical reactions. Following the 'reading' of EPR spectral data (also providing automatic procedures for the most common spectrometers/acquisition softwares) a transformation into the universal R 'data frame' format is supported. Subsequently, all the EPR spectra can be visualized and are fully consistent either with the 'ggplot2' package or with the interactive formats based on 'plotly'. Package also covers simulations and fitting of the isotropic (solution) EPR spectra. In addition, the advanced simulation parameters obtained by the MATLAB-EasySpin toolbox and results from the quantum chemical calculations like g-factor and hyperfine splitting/coupling constants (a/A) can be compared and summarized in table-form in order to analyze the EPR spectra by the most effective way. Reproducible reports of the entire data processing and analysis can be created by the quarto publishing system, resulting in various formats like '.pdf','.docx','.html'.

Authors:Ján Tarábek [aut, cre]

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 |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
eprscope/json (API)

# Install 'eprscope' in R:
install.packages('eprscope', repos = c('https://jatanrt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jatanrt/eprscope/issues

Pkgdown/docs site:https://jatanrt.github.io

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • isotopes_ds - Nuclear Isotope Data Frame (Dataset) with ENDOR Frequencies
  • solvents_ds - Solvent Properties Data Frame (Dataset) for EPR/ENDOR

On CRAN:

Conda:

chemistrydata-analysisdata-visualizationepresrfittingoptimizationprogramming-languagereproducible-researchscientific-plottingspectroscopyopenjdk

4.68 score 1 stars 11 scripts 62 exports 101 dependencies

Last updated from:a40b428ea1. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK317
source / vignettesERROR437
linux-release-x86_64OK301
macos-release-arm64OK356
macos-oldrel-arm64OK339
windows-develOK335
windows-releaseOK276
windows-oldrelOK310
wasm-releaseOK183

Exports:%>%convert_A_MHz_2aconvert_a_mT_2Aconvert_Bconvert_time2varcorrect_time_Exp_Specscreate_qmdReport_projdraw_molecule_by_rcdkeval_ABIC_forFiteval_DeltaXpp_Speceval_ECh_QNe_chronoampeval_extremeX_Speceval_FWHMx_Speceval_gFactoreval_gFactor_QCHcompeval_gFactor_Speceval_integ_EPR_Speceval_interval_cnfd_tVeceval_kinR_EPR_modelFiteval_kinR_Eyring_GHSeval_kinR_ODE_modeleval_nu_ENDOReval_peakPick_Speceval_sim_EPR_isoeval_sim_EPR_iso_comboeval_sim_EPR_isoFiteval_sim_EPR_isoFit_spaceload_data_exampleoptim_for_EPR_fitnessplot_ECh_VoC_amperogramplot_EPR_present_interactplot_EPR_Specsplot_EPR_Specs_integplot_EPR_Specs2D_interactplot_EPR_Specs3D_interactplot_eval_EPRtheo_mltipletplot_eval_ExpSim_appplot_eval_RA_forFitplot_labels_xyzplot_layout2D_interactplot_theme_In_ticksplot_theme_NoY_ticksplot_theme_Out_tickspresent_EPR_Sim_Specquantify_EPR_Absquantify_EPR_Norm_constquantify_EPR_Sim_seriesreadEPR_Exp_SpecsreadEPR_Exp_Specs_kinreadEPR_Exp_Specs_multifreadEPR_param_slctreadEPR_params_slct_kinreadEPR_params_slct_quantreadEPR_params_slct_simreadEPR_params_tabsreadEPR_Sim_SpecreadEPR_solvent_propsreadMAT_params_filerearrange_aAiso_QCHcomprearrange_aAiso_QCHorgausmooth_EPR_Spec_by_npregtransform_dfs_2tidyDF

Dependencies:askpassbackportsbase64encbroombslibcachemclicodetoolscommonmarkconstantscpp11crosstalkcurldata.tabledeSolvedigestdplyrDTerrorsevaluatefarverfastmapfingerprintfontawesomefsfuturefuture.applygenericsggplot2globalsgluegsignalgtablehighrhtmltoolshtmlwidgetshttpuvhttrisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglaterlazyevallifecyclelistenvmagrittrMASSmemoisemimeminpack.lmnloptrnpregopensslotelparallellypatchworkpillarpkgconfigplotlypngpracmaprogressrpromisespsopurrrR.matlabR.methodsS3R.ooR.utilsR6rappdirsrcdkrcdklibsRColorBrewerRcpprJavarlangrmarkdownS7sassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml

Basic Functionality
Introduction | Drawing of Molecular Structures | Reading Files and Writing Data Frames | Visualizations of Spectral Data | Static Plots by | Interactive Plots by | Basic EPR Spectral Characteristics | Finding the g~iso~-Value | Linewidth, 𝚫B~pp~ Determination | Hyperfine (HF) Structure and Simulations | Integration of the EPR Spectrum | both integrals are presented separately | with their corresponding intensities automatically | scaled onto the y-axis (defined by "free_y") | References
Rendered fromfunctionality.Rmdusingknitr::rmarkdown

Last update: 2026-04-26
Started: 2023-05-21

First Steps with R Language
Variable/Function Names and Assignment | Functions and Packages | Vectors and Matrices | Data Frames and the Pipe Operator | Operations with Columns and Rows | Descriptive Statistics of Data Frames | The Pipe Operator | Tidy and Messy Data | Processing and Analysis of Kinetic Data | Lists | References
Rendered fromfirstSteps.Rmdusingknitr::rmarkdown

Last update: 2026-04-08
Started: 2025-05-10

Introduction
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2023-05-15

Package Datasets
Built-In Datasets | Nuclear Isotope Data Frame | Solvent Properties | Datasets for Examples and Tests
Rendered fromdatasets.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2024-02-03

Readme and manuals

Help Manual

Help pageTopics
Convert Coupling Constants into Splitting Ones.convert_A_MHz_2a
Convert Splitting Constants into Coupling Ones.convert_a_mT_2A
Conversion of Magnetic Flux Densityconvert_B
Convert Time t into Variable Linearly Depending on t.convert_time2var
Time Correction for the Experimental CW EPR Time Series.correct_time_Exp_Specs
Basic Quarto Reproducible Project File/Folder Structure for EPR Reportscreate_qmdReport_proj
Draw Molecule by '{rcdk}' Defined by SMILES or SDFdraw_molecule_by_rcdk
General Ranking of Models/Fits Using the AIC and BIC Metricseval_ABIC_forFit
Calculation of EPR/ENDOR Spectrum Linewidth ( e.g. Delta B_{pp})eval_DeltaXpp_Spec
Transferred Charge and Number of Electrons from Chronoamperogrameval_ECh_QNe_chronoamp
Find Intensity Extremes within the EPR/ENDOR Spectrumeval_extremeX_Spec
Evaluating Full Width at Half-Maximum (FWHM) from the Integrated EPR Spectrumeval_FWHMx_Spec
Basic Calculation of g-Factoreval_gFactor
Calculation of g-factor from the Quantum Chemical Computational Outputeval_gFactor_QCHcomp
Calculation of g-factor ("Position") from the EPR Spectrum/Dataeval_gFactor_Spec
Integration of EPR Spectrum/Data for Quantitative Analysiseval_integ_EPR_Spec
Confidence Interval of a Vector or Data Frame Columneval_interval_cnfd_tVec
Radical Kinetic Models Fitted onto Experimental Dataeval_kinR_EPR_modelFit
Reaction Activation Parameters Obtained by the Essential Transition State Theoryeval_kinR_Eyring_GHS
Quantitative EPR Kinetic Model Profiles by Numeric Solution of the ODE.eval_kinR_ODE_model
ENDOR/Larmor Frequency of Specific Nucleieval_nu_ENDOR
Peak Picking of EPR/ENDOR Spectraeval_peakPick_Spec
Simulation of Isotropic EPR Spectraeval_sim_EPR_iso
Simulation of Isotropic EPR Spectra Consisting of Several Componentseval_sim_EPR_iso_combo
Least-Squares Fitting of Isotropic EPR Spectra by Simulationseval_sim_EPR_isoFit
Explore the Hyperspace of Initial EPR Simulation Parameters (Searching for the Best Fit)eval_sim_EPR_isoFit_space
Nuclear Isotope Data Frame (Dataset) with ENDOR Frequenciesisotopes_ds
Loading the Built-In Data Files for Package Examplesload_data_example
General Function for Non-Linear Optimization/Fitting of EPR Parameters/Dataoptim_for_EPR_fitness
Plot Voltammogram or Chronoamperogram from the (Spectro)Electrochemical Experimentplot_ECh_VoC_amperogram
Present/Save Interactive Plot for Publication in '.html','.pdf' or '.docx'plot_EPR_present_interact
Essential Plots of EPR/ENDOR Spectrum/Spectraplot_EPR_Specs
Plotting Integrated Forms of EPR Spectra Acquired by the 'eval_integ_EPR_Spec'plot_EPR_Specs_integ
Interactive Plot (incl. Zooming, Data Reading...etc) of EPR Spectraplot_EPR_Specs2D_interact
Interactive 3D Surface and 2D Contour Plots for the Series of EPR Spectraplot_EPR_Specs3D_interact
EPR Intensity Multiplet Prediction for Interactions of Electron with Selected Nucleus/Nucleiplot_eval_EPRtheo_mltiplet
Interactive Application to Plot and Evaluate CW Isotropic EPR Spectraplot_eval_ExpSim_app
General Diagnostics for Models/Fits by Simple Residual Analysisplot_eval_RA_forFit
Labels for Various Plots (Spectroscopy, EPR, Voltammetry,...etc)plot_labels_xyz
Additional Layout for the Interactive 2D Plotsplot_layout2D_interact
Custom 'ggplot2' Theme with Axis Ticks Oriented Inside the Panelplot_theme_In_ticks
Custom 'ggplot2' Theme without 'Y' Axis Ticksplot_theme_NoY_ticks
Custom 'ggplot2' Theme with Axis Ticks Oriented Outside the Panelplot_theme_Out_ticks
A Comparison of the Experimental and Simulated Forms of EPR Spectrapresent_EPR_Sim_Spec
Absolute Quantification of Radicals/Spinsquantify_EPR_Abs
Normalization Constant Calculation for the Quantitative EPR Analysisquantify_EPR_Norm_const
Quantify EPR Simulated Spectral Components in the Experimental Seriesquantify_EPR_Sim_series
Reading of the Experimental ASCII or Binary EPR Spectra/Data.readEPR_Exp_Specs
Read and Process CW EPR Time Series ExperimentsreadEPR_Exp_Specs_kin
Load Several/Multiple EPR Data/Spectra Files SimultaneouslyreadEPR_Exp_Specs_multif
Read the Selected EPR Instrumental Parameters and InformationreadEPR_param_slct
Read the Selected Instrumental Parameters of EPR Time Series ExperimentreadEPR_params_slct_kin
Read the Selected Instrumental Parameters Relevant to EPR Quantitative AnalysisreadEPR_params_slct_quant
Read the Selected Instrumental Parameters Required for EPR SimulationsreadEPR_params_slct_sim
Read the EPR Instrumental Parameters and Information for Tabular OutputsreadEPR_params_tabs
Read the ASCII Data of a Simulated EPR SpectrumreadEPR_Sim_Spec
Reading Solvent Properties from the 'solvents_ds' DatasetreadEPR_solvent_props
Reading EPR Simulation Parameters and Information from the _MATLAB_ '.mat' FilereadMAT_params_file
Rearrangement of A_{iso}/a_{iso} from the Quantum Chemical (QCH) Computationsrearrange_aAiso_QCHcomp
Rearrangement of A_{iso}/a_{iso} from the Gaussian & ORCA Computationsrearrange_aAiso_QCHorgau
Smoothing and Fitting of an EPR Spectrum by Splinessmooth_EPR_Spec_by_npreg
Solvent Properties Data Frame (Dataset) for EPR/ENDORsolvents_ds
Transformation of Several Data Frame Objects/Variables into one Tidy (Long Table) Formtransform_dfs_2tidyDF