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powdR: An R package for quantitative mineralogy using full pattern summation of X-ray powder diffraction data
Computers & Geosciences ( IF 4.2 ) Pub Date : 2021-02-01 , DOI: 10.1016/j.cageo.2020.104662
Benjamin M. Butler , Stephen Hillier

Abstract X-ray powder diffraction (XRPD) is consistently found to be the most accurate analytical technique for qualitative and quantitative mineralogy. For environmental samples such as rocks, sediments and soils that can contain a range of crystalline, disordered and amorphous components, quantitative XRPD methods implemented in Excel-based programs such as FULLPAT and RockJock have proved particularly appropriate. Such programs quantify phase concentrations in complex mixtures by treating the diffractogram of a given mixture as the sum of contributions from individual components. Thus, using this full pattern summation (FPS) approach, an observed diffractogram of a sample can be modelled by scaling the contributions of the diffractograms for all pure phases within it and then phase concentrations computed using reference intensity ratios. Here the principles implemented in FULLPAT, RockJock and an in-house application for FPS have together been used to create the powdR package for R. The powdR package advances on previous implementations of FPS in terms of functionality, speed (parallel computation) and adaptability (via use of bespoke R code), and includes a Shiny web application for user-friendly analysis. powdR can be used to quantify samples prepared either with or without an internal standard, and includes the public domain RockJock library of 169 pure diffractograms that cover a wide range of phases that may be encountered in soil and rock samples. Furthermore, powdR contains functionality for automated phase quantification, which can select appropriate phases from a comprehensive reference library (e.g., RockJock). Here the FPS functions implemented in powdR and their use are described in detail.

中文翻译:

powdR:使用 X 射线粉末衍射数据的全图求和进行定量矿物学的 R 包

摘要 X 射线粉末衍射 (XRPD) 一直被认为是用于定性和定量矿物学的最准确的分析技术。对于岩石、沉积物和土壤等环境样品,这些样品可能包含一系列结晶、无序和无定形成分,在 FULLPAT 和 RockJock 等基于 Excel 的程序中实施的定量 XRPD 方法已证明特别合适。这些程序通过将给定混合物的衍射图作为单个组分贡献的总和来量化复杂混合物中的相浓度。因此,使用这种全模式求和 (FPS) 方法,可以通过缩放其中所有纯相的衍射图的贡献,然后使用参考强度比计算相浓度来模拟观察到的样品衍射图。在这里,FULLPAT、RockJock 和 FPS 的内部应用程序中实现的原则一起用于创建 R 的 powdR 包。 powdR 包在功能、速度(并行计算)和适应性方面比以前的 FPS 实现有所进步(通过使用定制的 R 代码),并包括一个用于用户友好分析的 Shiny Web 应用程序。powdR 可用于量化使用或不使用内标制备的样品,并包括公共领域的 RockJock 库,其中包含 169 个纯衍射图,涵盖土壤和岩石样品中可能遇到的各种相。此外,powdR 包含自动相位量化功能,可以从综合参考库(例如 RockJock)中选择合适的相位。
更新日期:2021-02-01
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