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Changelog

Source: NEWS.md

eprscope 0.1.12

2024-12-05

Bug Fixes/Critical Updates

  • README documentation → fixed/updated, because it did not contain the information about the JDK installation as well as that about the essential R packages + couple of learning or tutorial resources and comments were added

  • several fixes and/or updates in documentation (functions + vignettes)

  • the default intensity multiplication coefficient (parameter) boundaries within the eval_sim_EPR_isoFit function are fixed and correctly set up + extended default boundaries for hyperfine coupling constants (A) added

  • fixed visualization of an EPR spectrum fit within the eval_sim_EPR_isoFit + the initial simulation (see updates) also includes a baseline correction (it should also work for the consecutive optim.method (vector))

  • increased decimal places of the magnetic flux density (B) and intensity by the reading of ASCII files, using the read_EPR_Specs and related functions

  • fixed issue with the origin argument definition (regarding the spectrometer software labels/names) in reading functions

  • initial qvars for the "(a=1)A + (r=1)R --> [k1] B" model reaction (see also updates) are now correctly set up

  • the minimum sum of residual squares (RSS) value argument was renamed (min.LSQ.sum → min.rss) and unified in all relevant fitting functions

  • tube diameter within the quantify_EPR_Abs is now correctly defined

  • fixed issue with the integral scale within the eval_integ_EPR_Spec

Updates

  • code in several functions → cleaned up in order to be more readable, this also includes renaming of several arguments in those functions + messages and stops added on couple of places, within the code, for the sake of interactivity/awareness of operations

  • reorganization of files and folders related to vignettes

  • code for the integration of EPR spectra (see the eval_integ_EPR_Spec function) was simplified and supplemented with the option to integrate spectra having the [B] = T units, this also applies to the quantify_EPR_Sim_series function

  • the initial simulated EPR spectrum was added to output graphics of the eval_sim_EPR_isoFit value/list (for the case of check.fit.plot = TRUE) in order to compare it with the final/best fit as well as with the experimental EPR spectrum

  • number of letters in kinetic reaction schemes were decreased in order to be more readable + the last scheme (see also bug fixes above) as well as the time duration and resolution were simplified in order to better work with the numeric ODE integration (by the deSolve::ode function)

  • option to select a method for the numeric ODE integration (argument solve.ode.method) was added to both key functions analyzing the radical kinetics

  • added option to select a specific implementation of the pswarm (“particle swarm”) optimization algorithm/method, within the optim_for_EPR_fitness → either “SPSO2007” (for small particle spaces and swarm sizes) or “SPSO2011” (for larger ones) can be set up + internal function updated (not provided as a user option), the number of “informants” (related to particles) was slightly increased by the corresponding exponent, k = 6 (see also documentation for the pso::psoptim)

  • value/output list of the eval_sim_EPR_isoFit was extended to exclusively include vector of the optimized parameters (together with the min.rss) and data frame of the best EPR simulation fit in order to be ready for the new fitting function (currently under development)

  • simple residual analysis (plots) added to the eval_kinR_EPR_modelFit output/value list, including the Q-Q (“quantile-quantile”) plot (to check weather residuals are normally distributed) as well as the Residual plot (residuals vs predicted/fitted qvarRs, e.g. concentration) in order to check the kinetic model fit and precision of the optimized kinetic parameters

New Functions/Files/Vignettes

  • create_qmdReport_proj → create file-folder structure of an EPR project to create a reproducible Quarto report (please, also refer to the https://quarto.org/ website)

  • peak picking in EPR/ENDOR spectrum: eval_peakPick_Spec, with the selection of positive or negative intensity peaks for both derivative as well as integrated forms of an EPR/ENDOR spectrum

  • evaluate activation parameters of an elementary radical reaction, obtained by the “Eyring fit” of the experimental k vs T dependence, based on the essential transition state theory (TST) → eval_kinR_Eyring_GHS

eprscope 0.1.11 (1st public release)

2024-08-29

Bug Fixes/Critical Updates

  • fixed reading of spectral time series within the readEPR_Exp_Specs function

  • reading parameter strings from ‘parameter’ files within the readEPR_param_slct function fixed

  • the g-value scale on x-axis within the plotting functions is now properly displayed

  • if the related time(series) unit is converted in relevant data frames, the corresponding column is renamed in order to inherit the new unit (like time_s) accordingly

  • now, the elements in names argument, within the readEPR_Exp_Specs_multif, can also contain characters like c("a","b","c"), not just numbers, e.g. c("250","260","270")

  • fixed visualization of legend labels within the plot_EPR_Specs function

  • natural abundance of interacting nuclei to calculate the intensities within the eval_sim_EPR_iso and related functions/examples

Updates

  • polynomial to fit the distribution of (B1,Bm) within the cavity was extended in quantify_EPR_Abs. Now, the degrees from 5 to 12 are available

  • additionally, the above-corresponding (B1,Bm) theoretical distribution calculation was removed for now, and will be addressed in the future

  • intensity, B, and the time.series column indices arguments, in general reading function readEPR_Exp_Specs, were renamed (using .id) in order to clearly point to headers in col.names

  • magnettech option added to reading functions to read the EPR spectra and parameters from these instruments, additionally, the ‘general’ reading function readEPR_Exp_Specs was updated to read files, from the most common EPR instruments, more easily by adding the auxiliary data.structure argument

  • the optimization algorithms, other than diff-levenmarq, were removed from the eval_kinR_EPR_modelFit for now, additional optimization methods will be implemented later on

  • many function documentations updated + several examples added + code-cleaning (by styler package) done in many functions + README, DESCRIPTION and vignettes updated, accordingly

  • vignette to describe the EPR simulations and fitting was removed, for now (will be added later), however, the important points from that vignette are summarized in the relevant function documentations

  • stoichiometric coefficient notation as well as reaction model scheme for consecutive reactions within the eval_kinR_ODE_model updated/extended

  • option to use Tesla (T) unit, now available in all g-value evaluations

  • line.type option added to all relevant plotting functions

  • calculation of confidence interval by the eval_interval_cnfd_tVec simplified

  • to read the EPR instrumental parameters by readEPR_params_slct, added option to read several parameters simultaneously (vectorized input)

  • customized plot themes, like plot_theme_In_ticks, were simplified, now, there is no need to add opposite axis-ticks by additional theme layer, those function can now also include additional arguments from general theme() function

New Functions/Files/Vignettes

  • perinaphthenyl (PNT) ENDOR spectral data added to package database for documentation examples (in plotting and reading functions)

  • setting up the continuous integrations like R CMD check and pkgdown (in order to build the site) via github actions

  • CONTRIBUTING.md added to package/site

  • new vignette for datasets added

  • new family functions for EPR spectroelectrochemistry, including the function to plot voltammograms and chronoamperograms (plot_ECh_VoC_amperogram) as well as to calculate the transferred charge and the corresponding number of electrons from chronoamperogram (eval_ECh_QNe_chronoamp)

  • new dataset (Triarylamine_radCat_decay_a) as an example of time series experimental data + new datasets coming from magnettech instrument: AcridineDeriv_Irrad_365nm

eprscope 0.1.10

2024-01-24

Bug Fixes/Critical Updates

  • calculation of normalization constant quantify_EPR_Norm_const ⇒ number of points added to calculated norm. constant by unitless receiver gain

  • kinetic models by ODE ⇒ eval_kinR_ODE_model + eval_kinR_EPR_modelFit now consider partial reaction orders and correct formulas for rates ⇒ derivations divided by stoichiometric coefficients according to IUPAC recommendations (see also https://doi.org/10.1021/ed083p510) + additionally, now the kinetic parameters can be optimized not only by the Levenberg-Marquardt algorithm but also by those including within the optim_for_EPR_fitness (in case if the partial reaction orders are considered)

  • eval_kinR_ODE_model can now compare/plot experimental data and model in order to ‘play’ with (manually optimize) partial reaction orders and/or stoichiometric coefficients to fit the experimental data e.g. like integrals or concentrations vs. time. Additionally, the A <– R –> B kinetic model was removed (also from eval_kinR_EPR_modelFit) simply, because it “doubles” the R –> B model. The model can be added later on.

  • several bugs in quantify_EPR_Abs (e.g. like concentration calculation + default temperature definition) were fixed. The function was completely rewritten. Moreover, now the quantification possesses user’s/instrument’s defined polynomial (orders from 6 to 11) fitting of the spatial distribution of B1 and Bm as well as point sample calibration factor as arguments in order to be more flexible. Finally, the theoretical B1 and Bm distribution (see e.g. https://www.sciencedirect.com/science/article/pii/S1090780797912489) can be considered as well in order to estimate the radical concentration.

  • remedy for the Breit-Rabi calculations of energies/frequencies/Bs in simulation => now the g-value for each level is corrected and B are calculated by the fixed-point iterations (see e.g https://doi.org/10.1016/j.jmr.2005.08.013). Simulations are not limited by the number of equivalent nuclei groups anymore (6 could be used up to now). Right now any number of groups maybe used in the actual simulation functions. All simulations are also continuously checked by the package tests/examples.

  • eval_sim_EPR_isoFit now contains the option not only to fit the pseudo-Voight lines but also pure Lorentzian or pure Gaussian onto the experimental EPR spectra

Updates

  • README ⇒ pkg. badges initiated + usage examples added + DESCRIPTION + vignette demonstrating the basic functionality of the package

  • several documentations and examples

  • draw_molecule_by_rcdk ⇒ renamed and focused just on one molecule + added option to place label of the molecule onto an arbitrary position of output image + documentation + examples

  • increased accuracy of ENDOR frequencies in nuclei isotopes_ds dataset

  • couple of variables/arguments (e.g. like B <-> B.val) renamed in order to be consistent throughout the package

  • to select/remove the columns from data frame objects by dplyr the dplyr::all_of() function is now mostly applied in the package code

  • extended tolerance to find half of the max. intensity in order to evaluate FWHM

  • functions to read the EPR spectra like readEPR_Exp_Specs, readEPR_Exp_Specs_kin as well as readEPR_Exp_Specs_multif were simplified and now contain the option to take additional arguments from the essential data.table::fread() which are not predefined in those functions in order to be more flexible upon reading

New Functions/Files/Vignettes

  • added files required to run examples as well as those incl. in vignette(s) ⇒ they are related to EPR spectra of electrochemically generated tetramethyl-phenylenediamine (TMPD) radical cation

  • smoothing of EPR spectra by {npreg} package ⇒ smooth_EPR_Spec_by_npreg which is based on the evaluation of polynomial splines

  • fitting of the experimental EPR spectra by simulations ⇒ eval_sim_EPR_isoFit where several optimization methods can be applied ⇒ all incl. in optim_for_EPR_fitness + baseline correction (either “constant” or “linear” or “quadratic”) is now included in the fitting procedure

  • new tutorial vignette for simulations EPR_Simulations was initiated/set up

  • testing environment by the testthat pkg. set up and initiated + added tests for simulations and conversions

  • added files/spectral data corresponding to an EPR spectrum of aminoxyl radical for examples and testing

eprscope 0.1.9

2023-10-18

Bug Fixes

  • main function to read EPR spectral data (readEPR_Exp_Specs) is now forced to use file argument ⇒ that is data.table::fread(file = path_to_ASC)

  • conversion of time to var within a cyclic change in convert_time2var

  • changed tolerance to find intensity values around 0 in g-factor evaluation (eval_gFactor_Spec) in order to take into account different spectral data resolutions

  • general integration function (eval_integ_EPR_Spec) now includes the proper scaling of sigmoid integrals + fixed Intensity bug in vector output for the integrated form of EPR spectra

  • temperature parameter in instrumental .DSC or .par files is sometimes missing ⇒ now the readEPR_params_tabs checks whether the temperature parameter is present and creates the table accordingly (with or without the temperature)

Updates

  • README, DESCRIPTION and “Introduction”” vignette

  • documentation references set up

  • Code for the absolute quantification of paramag. centers/radicals was simplified within the quantify_EPR_abs function.

  • Function to draw molecules was rewritten to read both .sdf files and smiles characters + it was renamed to draw_molecules_by_rcdk.

  • Reading the simulated spectra (readEPR_Sim_Spec) has now the option to read ASCII data from various sources like ⇒ “easyspin”, “xenon”, “simfonia” (winepr) or “csv”.

  • Instrumental parameters (related to recording of EPR spectra, readEPR_params_tab) can be converted into interactive table based on {DT} package.

  • Both solvents and isotopes datasets were renamed to ..._ds.

  • several documentations and examples

  • The Intensity selection based on different character strings is now replaced by the lineSpecs.form argument throughout the corresponding functions.

  • The simulation section/family was renamed to Simulation and Optimization.

  • Presentation of simulated and experimental spectra (presentEPR_Sim_Spec) has now option to display overlayed spectra.

New Functions

  • read properties of solvents (from the corresponding datasets) ⇒ readEPR_solvent_props

  • convert magnetic flux density (B) values according to input-output units ⇒ convert_B

  • simulation of isotropic EPR spectra in both derivative & integrated spectral forms ⇒ eval_sim_EPR_iso

  • simulation of isotropic EPR spectra corresponding to linear combination of several components evaluated by the latter function ⇒ eval_sim_EPR_iso_combo

  • read instrumental parameters required for the simulations that is now implemented in both sim. functions ⇒ readEPR_params_slct_sim

eprscope 0.1.8

2023-05-15

  • Added functions to evaluate radical kinetics incl. fitting procedures to experimental data (integral intensities).

  • Added basic package data structure and vignettes. Package data now include the isotope database, isotope_db, to gather the basic properties of nuclei mainly for analysis in EPR/ENDOR spectroscopy. For such purpose the new function eval_nu_ENDOR was written. It provides calculation of ENDOR/Larmor frequencies for selected nuclei at specific saturation magnetic flux densities, Bsat.

  • All functions (incl. documentation) are now linked by sections/families.

eprscope 0.1.7

2023-04-25

  • First tagging after main updates in quantify_EPR_sim function. Additionally, the main reading functions, readEPR_... have been completely rewritten.