Package: eprscope 0.1.11

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 package is mainly focused on continuous wave (CW) EPR/ENDOR, many functions may be also used for the integrated forms of 1D PULSED EPR spectra. It is able 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. Package also enables to process data/spectra for the analytical (quantitative) purposes. Namely, how many radicals or paramagnetic centers can be found in the analyte/sample. The goal is to evaluate rate constants, considering different kinetic models, to describe the radical reactions. The key feature of the package resides in processing of the universal ASCII text formats (such as '.txt', '.csv' or '.asc') from scratch. No proprietary formats are used (except the MATLAB EasySpin outputs) and in such respect the package is in accordance with the FAIR data principles. Upon 'reading' (also providing automatic procedures for the most common EPR spectrometers) the spectral data are transformed into the universal R 'data frame' format. Subsequently, the EPR spectra can be visualized and are fully consistent either with the 'ggplot2' package or with the interactive formats based on 'plotly'. Additionally, simulations and fitting of the isotropic EPR spectra are also included in the package. Advanced simulation parameters provided 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-format in order to analyze the EPR spectra by the most effective way.

Authors:Ján Tarábek [aut, cre]

eprscope_0.1.11.tar.gz
eprscope_0.1.11.zip(r-4.5)eprscope_0.1.11.zip(r-4.4)eprscope_0.1.11.zip(r-4.3)
eprscope_0.1.11.tgz(r-4.4-any)eprscope_0.1.11.tgz(r-4.3-any)
eprscope_0.1.11.tar.gz(r-4.5-noble)eprscope_0.1.11.tar.gz(r-4.4-noble)
eprscope_0.1.11.tgz(r-4.4-emscripten)eprscope_0.1.11.tgz(r-4.3-emscripten)
 |eprscope.html✨
eprscope/json (API)
NEWS

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

Peer review:

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

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:

4.83 score 7 scripts 55 exports 90 dependencies

Last updated 15 hours agofrom:b8e6717a3e. Checks:ERROR: 1 OK: 2 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macNOTENov 22 2024

Exports:%>%convert_A_MHz_2aconvert_a_mT_2Aconvert_Bconvert_time2varcorrect_time_Exp_Specscreate_qmdReport_projdraw_molecule_by_rcdkeval_DeltaXpp_Speceval_ECh_QNe_chronoampeval_extremeX_Speceval_FWHMx_Speceval_gFactoreval_gFactor_QCHcompeval_gFactor_Speceval_integ_EPR_Speceval_interval_cnfd_tVeceval_kinR_EPR_modelFiteval_kinR_ODE_modeleval_nu_ENDOReval_peakPick_Speceval_sim_EPR_isoeval_sim_EPR_iso_comboeval_sim_EPR_isoFitload_data_exampleoptim_for_EPR_fitnessplot_ECh_VoC_amperogramplot_EPR_present_interactplot_EPR_Specsplot_EPR_Specs_integplot_EPR_Specs2D_interactplot_EPR_Specs3D_interactplot_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_npreg

Dependencies:askpassbackportsbase64encbroombslibcachemclicolorspaceconstantscpp11crosstalkcurldata.tabledeSolvedigestdplyrerrorsevaluatefansifarverfastmapfingerprintfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimeminpack.lmmunsellnlmenloptropensslpillarpkgconfigplotlypngpracmapromisespsopurrrR.matlabR.methodsS3R.ooR.utilsR6rappdirsrcdkrcdklibsRColorBrewerRcpprJavarlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Basic Functionality

Rendered fromfunctionality.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-26
Started: 2023-05-21

Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-26
Started: 2023-05-15

Package Datasets

Rendered fromdatasets.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-18
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 the EPR Reportscreate_qmdReport_proj
Draw Molecule by '{rcdk}' Defined by SMILES or SDFdraw_molecule_by_rcdk
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 Integrated EPR Spectrumeval_FWHMx_Spec
Basic Calculation of g-factoreval_gFactor
Calculation of g-factor from Quantum Chemical Computational Outputeval_gFactor_QCHcomp
Calculation of g-factor ("Position") from 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
Quantitative EPR Kinetic Model Profiles by Numeric Solution of the ODE.eval_kinR_ODE_model
ENDOR/Larmor Frequency of Specific Nucleuseval_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
Nuclear Isotope Data Frame (Dataset) with ENDOR Frequenciesisotopes_ds
Loading 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 Plotting of EPR/ENDOR Spectrum/Spectraplot_EPR_Specs
Plotting Integrated Forms of EPR Spectra Acquired by '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
Labels for Various Plots (Spectroscopy, EPR, Voltammetry,...etc)plot_labels_xyz
Additional Layout for 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 EPR Spectra Between Experimental and Simulated Formpresent_EPR_Sim_Spec
Absolute Quantification of Radicals/Spinsquantify_EPR_Abs
Normalization Constant Calculation for Quantitative EPR Analysisquantify_EPR_Norm_const
Quantify (Components) Areas of Series of Simulated EPR Spectraquantify_EPR_Sim_series
Read the Experimental ASCII or other Text-Based EPR Data.readEPR_Exp_Specs
Read and Process Spectral Data of Time Dependent CW EPR ExperimentsreadEPR_Exp_Specs_kin
Load Several/Multiple EPR Data/Spectra Files SimultaneouslyreadEPR_Exp_Specs_multif
Read 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 EPR Instrumental Parameters and Information into TablesreadEPR_params_tabs
Read Simulated ASCII EPR SpectrumreadEPR_Sim_Spec
Reading Solvent Properties from 'solvents_ds' DatasetreadEPR_solvent_props
Read EPR Simulation Parameters and Information from _MATLAB_ '.mat' FilereadMAT_params_file
Rearrangement of A_{iso}/a_{iso} from Quantum Chemical (QCH) Computationsrearrange_aAiso_QCHcomp
Rearrangement of A_{iso}/a_{iso} from 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