powdR
packagepowdR
is an open source implementation of the full pattern summation approach to quantitative mineralogy from X-ray powder diffraction data (Chipera and Bish 2002, 2013; Eberl 2003), written in the R
programming language. It seeks to make quantitative phase analysis from XRPD data a faster and more user-friendly procedure.
This short tutorial explains the installation and basic use of powdR
, which requires a prior installation of R. A more detailed tutorial of the package is provided in the pacakge Vignette, and video tutorials of the powdR
web application can be found on the powdR YouTube channel.
The stable version of powdR
is on CRAN:
install.packages("powdR")
Alternatively, the development version can be downloaded from GitHub
#Install devtools if you don't already have it on your machine
install.packages("devtools")
devtools::install_github('benmbutler/powdR')
library(powdR)
#> powdR: Full Pattern Summation of X-Ray Powder Diffraction Data
#Load some soils to quantify
data(soils)
#Load a powdRlib reference library of pure patterns
data(minerals)
#Quantify a sample
q <- fps(lib = minerals,
smpl = soils$sandstone,
refs = minerals$phases$phase_id,
std = "QUA.1")
#>
#> -Aligning sample to the internal standard
#> -Interpolating library to same 2theta scale as aligned sample
#> -Optimising...
#> -Removing negative coefficients and reoptimising...
#> -Computing phase concentrations
#> -Internal standard concentration unknown. Assuming phases sum to 100 %
#> ***Full pattern summation complete***
#Inspect the phase concentrations (summarised by name)
q$phases_grouped
#> phase_name phase_percent
#> 1 Quartz 53.6918
#> 2 K-feldspar 1.3184
#> 3 Plagioclase 1.1637
#> 4 Illite 1.3515
#> 5 Kaolinite 1.3697
#> 6 Organic-Matter 41.1049
#Inspect the quantification
plot(q, wavelength = "Cu")
Alternatively, plot(q, wavelength = "Cu", interactive = TRUE)
provides an interactive plot for better inspection of the fit.
powdR
Shiny appTo run powdR
via the Shiny web applicationp, use run_powdR()
. This loads the application in your default web browser. The application has eight tabs:
powdRlib
reference library from two .csv files: one for the XRPD measurements, and the other for the ID, name and reference intensity ratio of each pattern.powdRlib
reference library.powdRlib
reference library .powdRfps
and powdRafps
objects to be edited via addition or removal of reference patterns to the fitting process.powdR
Shiny application.