NEWS.md

In benmbutler/powdR: Full Pattern Summation of X-Ray Powder Diffraction Data

powdR 1.3.0.999

Bug fixes

• Bug that stopped fps() from running properly when only one pattern was supplied now fixed.

New features

• Added to tabulate_lod() function with methods of powdRfps and powdRafps objects. Tabulates limit of detection estimates for all quantified phases in a given sample.
• The afps() function now accepts a logical skip_nnls argument. When skip_nnls = TRUE, the non-negative least squares part of phase selection is skipped.

powdR 1.3.0

New features

• Vignettes updated to account for all new features detailed below.
• Twenty one additional reference patterns associated for soils from the Africa Soil Information Service XRPD database now added as afsis data. The phase IDs in the data have been modified for clarity, and the originals are found in afsis_codes data that is also included with the package.
• Regrouping data for the rockjock and afsis reference libraries now provided in rockjock_regroup and afsis_regroup, respectively.
• plot methods for powdRfps and powdRafps objects now accept a logical group argument. When TRUE this results in reference patterns being plotted grouped and summed by phase name.
• A background fitting shiny app is now included that is loaded via run_bkg()
• as_xy() added, which creates XY objects from data frames that contain two columns denoting 2theta and counts.
• as_multi_xy() added, which creates a multiXY objects from a list of `XY data frames or a data frame containing data from multiple samples. multiXY objects can easily be plotted using the new plot.multiXY method, whilst XY objects can be plotted using the plot.XY method.
• align_xy() added with associated S3 methods for aligning XRPD data within XY and multiXY objects to a chosen standard.
• multi_xy_to_df() added, which converts multiXY objects to data frames.
• interpolate() added, which contains methods for interpolating XY, multiXY and powdRlib objects onto a new 2theta scale.
• merge() method added for powdRlib objects, which allows two powdRlib objects to be merged into a single powdRlib object.
• extract_xy() added, which is a wrapper for read_xyData() from the rxylib package. This function extracts any number of xy data frames from various proprietary formats of X-ray powder diffraction data.
• read_xy() added, which reads any number of ASCII XY files.
• fps() and afps() now accept omit_std and closed arguments which are used to specify how the phase concentrations are adjusted based on the internal standard.
• The normalise argument of fps() and afps() is now deprecated and replaced with closed.
• The new omit_std() methods for powdRfps and powdRafps objects allows for the internal standard concentration to be omitted from the output and phase concentrations re-computed.
• The new close_quant() methods for powdRfps and powdRafps objects allows for the quantitative composition to be closed so that it sums to 100 percent.
• Objective functions Delta, R and Rwp are now implemented in functions delta(), r() and rwp, respectively.
• powdRfps and powdRafps objects, derived from fps() and afps(), respectively, now include data for the full 2theta range, even when discrete limits are set using the tth_fps argument.
• Methods plot.powdRfps and plot.powdRafps now include grey boxes for areas that were excluded from the fitting process via the tth_fps argument. These boxes can be turned off by setting the show_excluded argument to FALSE.
• fps_lm() added that facilitates non-quantitative full-pattern summation by linear regression, yielding a powdRlm object. Derived coefficients may be either positive or negative, making the function particularly suitable for fitting the loadings from principal component analysis.
• plot method for powdRlm objects added.
• xrpd_pca() facilitates principal component analysis of XRPD patterns. The derived loading for each dimension can be fitted to patterns within a powdRlib reference library using fps_lm().

powdR 1.2.5

New features

• fps() and afps() now accept diffraction data that has negative values for count intensities. In such cases Rwp cannot be used as the objective function and R will be used as the default instead.
• The rwp item in the outputs from fps() and afps() has been renamed obj, which contains a named vector of the values for three objective parameters: Rwp, R and Delta.
• summarise_mineralogy now accepts two additional arguments: r and delta which are logical parameters used to specify whether the R and Delta objective parameters, respectively,are included in the summary table.

powdR 1.2.4

New features

• powdRlib() now accepts a logical check_names argument. If TRUE (the default) then the names of the variables are checked to ensure that they are syntactically valid and are not duplicated.

Bug fixes

• Default value for the normalise argument in fps() and afps() is now supplied (FALSE)
• powdRlib() now ensures that the phases object is a dataframe.

powdR 1.2.3

New features

• New function regroup() allows for an alternative mineral grouping structure to be applied to powdRfps and powdRafps objects.
• New function tth_transform() allows 2theta transformation between different monochromatic X-ray wavelengths.
• fps() and afps() now accept a logical normalise argument, which allows the internal standard concentration to be omitted and phase concentrations subsequently normalised to sum to 100 %.

powdR 1.2.2

New features

• fps() now accepts the force argument, forcing phases to remain in the final output even if their coefficients are negative.
• fps() and afps() will now stop if any of the phases specified in the refs argument are not in the library.
• Warning messages now generally do not include the call.
• Progress bar now included in the Shiny app when computing fps() and afps().
• summarise_mineralogy() now accepts single samples (i.e. a list of 1 powdRfps or powdRafps object).

Bug fixes

• utils no longer in imports (hence fixing associated note in CRAN checks).

powdR 1.2.1

New features

• plot() methods for powdRfps and powdRafps objects now include mode and xlim arguments, allowing for different plot types and x-axis adjustment.

Bug fixes

• Dependency on packages DT and shinyWidgets now defined in namespace.
• Bug stopping the shiny app working in shiny versions >1.3.2 now fixed.
• Couple of other small edits to phase selection in the shiny app that should keep things simple.
• powdRlib() no longer orders the reference patterns alphabetically, and instead retains the original order that they are supplied in.
• Negative values from natural spline interpolation now removed from data as these can prevent the optimisation routines from working.
• Phases are no longer ordered alphabetically in outputs from fps() and afps().

powdR 1.2.0

New features

• fps() and afps() no longer require the shift_res argument.
• Shifting is now calculated by optimisation of the objective function.
• Natural splines are now used instead of linear splines throughout fps() and afps().
• The Full Pattern Summation tab in the Shiny application has been updated, as has the video tutorial for it.

powdR 1.1.0

New features

• The refs argument of fps() and subset() now accepts phase names as well as phase ID's. For example, if the phase name "Quartz" in supplied, then all phase ID's associated with Quartz will be selected.

• Similarly, the force argument of afps() now accepts both phase names and phase ID's.

• summarise_mineralogy() now contains an optional rwp argument (default = FALSE). This is a logical parameter used to define whether the Rwp should be included in the summary table as a measure of the difference between the measured and fitted patterns.

• When the std_conc argument is supplied to fps() or afps(), the computed phase concentrations now include that of the internal standard.

powdR 1.0.0

New features

• Outputs from fps() and afps() (powdRfps and powdRafps objects, respectively) contain an inputs component. This provides a list of each of the arguments (including defaults) used to produce the fit.

• summarise_mineralogy() is a new function that creates a summary table from lists containing multiple powdRfps and/or powdRafps objects.

• A comprehensive reference library of pure phases from the RockJock computer software is now provided as an example powdRlib object called rockjock. This library covers most clay, non-clay and amorphous phases that may be encountered in soil samples. The library can be loaded into the global environment via data(rockjock). Data of synthetic mineral mixtures are also now provided in the rockjock_mixtures data, which can be used to test the accuracy of full pattern summation via the fps() and afps() functions.

• fps() and afps() now accept "L-BFGS-B" in the solver argument. If selected, this uses L-BFGS-B optimisation constrained so that parameters cannot be lower than zero.

• fps() now contains an optional shift argument, identical to that already implemented in afps(). This defines the 2$\theta$ range within with a grid-search algorithm can optimise the alignment of standards to the sample. If not defined in the function call it defaults to 0.

• fps() and afps() now have a shift_res argument which accepts a single integer to define the increase in resolution used during grid search shifting. Higher values facilitate finer shifts at the expense of longer computation. If not defined in the function call it defaults to 4.

• fps() and afps() now have a logical manual_align argument which specifies whether to manually align the sample to the value specified in the align argument (manual_align = TRUE), or optimise the alignment based on a maximum shift defined in the align argument (manual_align = FALSE).

• fps() and afps() now have a logical harmonise argument which specifies whether to automatically harmonise the sample and library onto the same 2$\theta$ scale via linear interpolation.

• The lod argument of afps(), now simply represents an estimate of the limit of detection of the selected internal standard defined by the std argument. The function then uses the reference intensity ratios to estimate limits of detection for all other phases.

• fps() now contains an optional remove_trace argument that allows the user to exclude phases below a small trace value that would unlikely be detected. Default = 0.

• subset() is a new function that allows simple subsetting of a powdRlib object.

• The run_powdR() shiny app now contains tabs for subsetting a powdRlib object via subset() function, editingpowdRfps and powdRafps objects, and video tutorials.

powdR 0.2.0

New features

• Suggests packages nnls (>=1.4), baseline (>= 1.2) and shinyWidgets (>= 0.4.3) in the DESCRIPTION.

• fps() now accepts "NNLS" in the solver argument. If "NNLS" (non-negative least squares) is selected, the algorithm uses non negative least squares instead of minimising an objective function. This is a much faster alternative but less accurate for samples containing amorphous phases.

• bkg() is a new function that allows for backgrounds to be fitted to XRPD data. It is a wrapper of the baseline::baseline.fillPeaks() method, and the output is a powdRbkg object.

• afps() is a new function that automates the process of full pattern summation by firstly selecting samples from the reference library (using NNLS) and then excluding those estimated to be below detection limit. The output is a powdRafps object.

• New plot() methods for powdRbkg and powdRafps objects

• The shiny application behind run_powdR() has been updated to accept "NNLS", and now includes tabs for background fitting (using bkg()) and automated full pattern summation (using afps()).

powdR 0.1.0

• Released on CRAN

benmbutler/powdR documentation built on Nov. 29, 2021, 1:05 p.m.