Full pattern summation of X-ray powder diffraction data as
described in Chipera and Bish (2002)
powdR is an implementation of the full pattern summation approach to quantitative mineralogy from X-ray powder diffraction data (Chipera and Bish 2002; Chipera and Bish 2013; Eberl 2003). Version 0.1.0 contains functionality for a standardless approach, which assumes all phases within a sample can be identified, and thus they sum to 100 %. Future versions of
powdR seek to add functionality for samples prepared with an internal standard.
powdR has several advantages over the excel based implementations of full pattern summation such as FULLPAT (Chipera and Bish 2002) and ROCKJOCK (Eberl 2003). First, computation is faster and, when quantifying multiple samples, can be used in combination with other packages (e.g
foreach) for parralel processing. Secondly, powdR can be run via a
shiny web application, which offers a user friendly interface for fast and iterative mineral quantification. Lastly, R represents a powerful tool for data manipulation, allowing users to creatively adapt, pre-treat and visualise their XRPD data.
devtools::install_github('benmbutler/powdR')#alternatively, an installation that builds the vignettedevtools::install_github('benmbutler/powdR', build_vignettes = TRUE)
library(powdR)#> powdR: full pattern summation of X-ray powder diffraction data#Load some soils to quantifydata(soils)#Load a reference library of pure patternsdata(minerals)#Quantify a sampleq <- fps(lib = minerals,smpl = soils$sandstone,refs = minerals$phases$phase_id,std = "QUA.1")#Inspect the phase concentrations (summarised by name)q$phases_summary#> phase_name phase_percent#> 1 Illite 1.237556#> 2 K-feldspar 1.250870#> 3 Kaolinite 1.390756#> 4 Organic-Matter 39.805850#> 5 Plagioclase 1.159294#> 6 Quartz 55.155674#Inspect the quantificationplot(q)
plot(q, interactive = TRUE) provides an interative plot for better inspection of the fit. More detailed usage instructions are provided in the package vignette.
powdR via the shiny app, use
run_powdR(). This loads the application in your default web browser. The application has four tabs:
Chipera, Steve J., and David L. Bish. 2002. “FULLPAT: A full-pattern quantitative analysis program for X-ray powder diffraction using measured and calculated patterns.” Journal of Applied Crystallography 35 (6): 744–49. doi:10.1107/S0021889802017405.
———. 2013. “Fitting Full X-Ray Diffraction Patterns for Quantitative Analysis: A Method for Readily Quantifying Crystalline and Disordered Phases.” Advances in Materials Physics and Chemistry 03 (01): 47–53. doi:10.4236/ampc.2013.31A007.
Eberl, D. D. 2003. “User’s guide to ROCKJOCK - A program for determining quantitative mineralogy from powder X-ray diffraction data.” Boulder, CA: USGS.