Package: powdR 1.3.0.999

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

Full pattern summation of X-ray powder diffraction data as described in Chipera and Bish (2002) <doi:10.1107/S0021889802017405> and Butler and Hillier (2021) <doi:10.1016/j.cageo.2020.104662>. Derives quantitative estimates of crystalline and amorphous phase concentrations in complex mixtures.

Authors:Benjamin Butler [aut, cre], Stephen Hillier [aut], Dylan Beaudette [ctb], Dennis Eberl [ctb]

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powdR.pdf |powdR.html✨
powdR/json (API)
NEWS

# Install 'powdR' in R:
install.packages('powdR', repos = c('https://benmbutler.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/benmbutler/powdr/issues

Datasets:
  • afsis - Africa Soil Information Service (AfSIS) XRPD reference library
  • afsis_codes - Original codes for the 'afsis' reference patterns
  • afsis_regroup - Regrouping structure for the Africa Soil Information Service (AfSIS) XRPD reference library
  • minerals - An example powdRlib reference library
  • minerals_phases - Example phases table for a reference library
  • minerals_regroup - Example regrouping structure for the 'minerals' data
  • minerals_xrd - Example xrd table for a reference library
  • rockjock - RockJock reference library
  • rockjock_mixtures - RockJock synthetic mixtures
  • rockjock_regroup - Regrouping structure for the rockjock reference library
  • rockjock_weights - Mineral concentrations of the 'rockjock_mixtures' data
  • soils - Example soil XRPD data

On CRAN:

5.54 score 12 stars 29 scripts 271 downloads 1 mentions 24 exports 132 dependencies

Last updated 3 years agofrom:1edf506de0. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:afpsalign_xyas_multi_xyas_xybkgclose_quantdeltaextract_xyfpsfps_lminterpolatemulti_xy_to_dfomit_stdpowdRlibrread_xyregrouprun_bkgrun_powdRrwpsummarise_mineralogytabulate_lodtth_transformxrpd_pca

Dependencies:abindaskpassbackportsbase64encbaselineBHbootbroombslibcachemcarcarDatacliclustercolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelimSolvelme4lpSolvemagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnnlsnumDerivopensslpbkrtestpillarpkgconfigplotlyplyrpolynompromisespurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppEigenreshapereshape2rlangrmarkdownrstatixrxylibsassscalesscatterplot3dshinyshinyWidgetssourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunxtableyaml

Full pattern summation of XRPD data

Rendered fromfull_pattern_summation.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-08-13
Started: 2021-07-14

Loading and manipulating XRPD data

Rendered fromLoading_and_manipulating.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-08-11
Started: 2021-07-14

Readme and manuals

Help Manual

Help pageTopics
Automated full pattern summationafps
Automated full pattern summationafps.powdRlib
Africa Soil Information Service (AfSIS) XRPD reference libraryafsis
Original codes for the 'afsis' reference patternsafsis_codes
Regrouping structure for the Africa Soil Information Service (AfSIS) XRPD reference libraryafsis_regroup
Align XRPD data to a given standardalign_xy
Align XRPD data in a multiXY object to a given standardalign_xy.multiXY
Align XRPD data in an XY object to a given standardalign_xy.XY
Create a multiXY objectas_multi_xy
Create a multiXY object from a list of XRPD dataas_multi_xy.data.frame
Create a multiXY object from a list of XRPD dataas_multi_xy.list
Create an XY objectas_xy
Fit a background to XRPD databkg
Close the phase concentration data within a 'powdRfps' or 'powdRafps' objectclose_quant
Close the phase concentration data within a 'powdRafps' objectclose_quant.powdRafps
Close the phase concentration data within a 'powdRfps' objectclose_quant.powdRfps
Calculate the Delta value for a fitted patterndelta
Import and extract XY data from proprietary filesextract_xy
Full pattern summationfps
Full pattern summation using linear regressionfps_lm
Full pattern summation using linear regressionfps_lm.powdRlib
Full pattern summationfps.powdRlib
Interpolate an XY, multiXY or powdRlib object to a given 2theta scale.interpolate
Interpolate a multiXY object onto a given 2theta scale.interpolate.multiXY
Interpolate a 'powdRlib' object onto a given 2theta scale.interpolate.powdRlib
Interpolate an 'XY' object onto a given 2theta scale.interpolate.XY
Merge two powdRlib objectsmerge.powdRlib
An example powdRlib reference libraryminerals
Example phases table for a reference libraryminerals_phases
Example regrouping structure for the 'minerals' dataminerals_regroup
Example xrd table for a reference libraryminerals_xrd
Convert a multiXY object to a data frame.multi_xy_to_df
Convert a multiXY object to a data frame.multi_xy_to_df.multiXY
Omit the internal standard from phase concentration data within a 'powdRfps' or 'powdRafps' objectomit_std
Omit the internal standard from phase concentration data within a 'powdRafps' objectomit_std.powdRafps
Omit the internal standard from phase concentration data within a 'powdRfps' objectomit_std.powdRfps
Plotting a multiXY objectplot.multiXY
Plotting elements of a powdRafps objectplot.powdRafps
Plotting a powdRbkg objectplot.powdRbkg
Plotting elements of a powdRfps objectplot.powdRfps
Plotting elements of a powdRlib objectplot.powdRlib
Plotting elements of a powdRlm objectplot.powdRlm
Plotting an XY objectplot.XY
powdR: Full Pattern Summation of X-Ray Powder Diffraction DatapowdR
Create an XRPD reference librarypowdRlib
Calculate the R value for a fitted patternr
Read ASCII XY dataread_xy
regroupregroup
regroupregroup.powdRafps
regroupregroup.powdRfps
RockJock reference libraryrockjock
RockJock synthetic mixturesrockjock_mixtures
Regrouping structure for the rockjock reference libraryrockjock_regroup
Mineral concentrations of the 'rockjock_mixtures' datarockjock_weights
Run the background fitting shiny apprun_bkg
Run the powdR shiny apprun_powdR
Calculate the Rwp value for a fitted patternrwp
Example soil XRPD datasoils
Subset a powdRlib objectsubset.powdRlib
Summarise the mineralogy from multiple powdRfps and powdRafps outputssummarise_mineralogy
Tabulate limit of detection estimatestabulate_lod
Tabulate limit of detection estimatestabulate_lod.powdRafps
Tabulate limit of detection estimatestabulate_lod.powdRfps
Transform a two theta axis between wavelengthstth_transform
PCA of XRPD dataxrpd_pca