## Selected R packages useful for geological sciences | Packages | References | | ------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | [aqp](https://cran.r-project.org/package=aqp): Algorithms for Quantitative Pedology | Beaudette, D.E., Roudier, P. and O’Geen, A.T., 2013. Algorithms for quantitative pedology: A toolkit for soil scientists. Computers & Geosciences, 52, 258–268. [DOI](http://dx.doi.org/10.1016/j.cageo.2012.10.020) | | [analogue](http://CRAN.R-project.org/package=analogue): Analogue and Weighted Averaging Methods for Palaeoecology | Simpson, G.L., 2007. Analogue Methods in Palaeoecology: Using the analogue Package. Journal of Statistical Software, 22/2, 29 pp. [DOI](http://dx.doi.org/10.18637/jss.v022.i02) | | [ArArRedux](http://CRAN.R-project.org/package=ArArRedux): Rigorous Data Reduction and Error Propagation of Ar40/Ar39 Data | Vermeesch, P., 2015. Revised error propagation of 40Ar/39Ar data, including covariances. Geochimica et Cosmochimica Acta, 171, 325–337. [DOI](https://doi.org/10.1016/j.gca.2015.09.008) | | [astrochron](http://CRAN.R-project.org/package=astrochron): A Computational Tool for Astrochronology | Meyers, S.R., 2019. Cyclostratigraphy and the problem of astrochronologic testing. Earth-Science Reviews 190, 190–223. [DOI](https://doi-org.uaccess.univie.ac.at/10.1016/j.earscirev.2018.11.015) | | [ClamR](http://cran.r-project.org/package=ClamR): Time Series Modeling for Climate Change Proxies | Wang, T., Surge, D. and Lees, J.M., 2015. ClamR: A statistical evaluation of isotopic and temperature records in sclerochronologic studies. Palaeogeography, Palaeoclimatology, Palaeoecology, 437, 26–32. [DOI](http://dx.doi.org/10.1016/j.palaeo.2015.07.008) | | [CoinCalc](https://github.com/JonatanSiegmund/CoinCalc): Event Coincidence Analysis | Siegmund, J.F., Siegmund, N. and Donner, R.V., 2017. CoinCalc—A new R package for quantifying simultaneities of event series. Computers & Geosciences, 98, 64–72. [DOI](http://dx.doi.org/10.1016/j.cageo.2016.10.004) | | [compositions](https://CRAN.R-project.org/package=compositions): Compositional Data Analysis | | | [detzrcr](https://CRAN.R-project.org/package=detzrcr): Compare Detrital Zircon Suites | | | [ElementR](https://cran.r-project.org/package=elementR): A Set of R6 Classes & a Shiny Application for Reducing Elemental LA-ICPMS Data from Solid Structures | Sirot, C., Ferraton, F., Panfili, J., Childs, A.-R., Guilhaumon, F. and Darnaude, A.M., 2017. elementr: An R package for reducing elemental data from LA-ICPMS analysis of biological calcified structures. Methods in Ecology and Evolution. [DOI](https://doi.org/10.1111/2041-210X.12822) | | [EMMAgeo](http://CRAN.R-project.org/package=EMMAgeo): End-Member Modelling of Grain-Size Data | Dietze, E., and Dietze, M., 2019, Grain-size distribution unmixing using the R package EMMAgeo. E&G Quaternary Science Journal, 68, 29–46. [DOI](https://doi.org/10.5194/egqsj-68-29-2019 ) | | [eseis](https://CRAN.R-project.org/package=eseis): Environmental Seismology Toolbox | Dietze, M., 2018. The R package “eseis” - a comprehensive software toolbox for environmental seismology. Earth Surface Dynamics Discussions, 6, 669-686. [DOI](https://doi.org/10.5194/esurf-6-669-2018) | | [FactoMineR](https://cran.r-project.org/package=FactoMineR): Multivariate Exploratory Data Analysis and Data Mining | Lê, S., Josse, J. and Husson, F., 2008. FactoMineR: An R Package for Multivariate Analysis. Journal of Statistical Software, 25, 1–18. | | [forams](http://CRAN.R-project.org/package=forams): Foraminifera and Community Ecology Analyses | | | [fossil](http://CRAN.R-project.org/package=fossil): Palaeoecological and Palaeogeographical Analysis Tools | Vavrek, M.J., 2011. fossil: Palaeoecological and palaeogeographical analysis tools. Palaeontologia Electronica, 14, 1T, 16 pp. [DOI](http://www.palaeo-electronica.org/2011_1/238/index.html) | | [G2Sd](https://CRAN.R-project.org/package=G2Sd): Grain-Size Statistics and Description of Sediment | Fournier, J., Gallon, R.K. and Paris, R., 2014. G2Sd: a new R package for the statistical analysis of unconsolidated sediments. Géomorphologie: relief, processus, environnement, 1, 73–78. [DOI](http://dx.doi.org/10.4000/geomorphologie.10513) | | [GcClust](https://pubs.er.usgs.gov/publication/tm7C13): Clustering of regional geochemical data | Ellefsen, K.J. and Smith, D.B., 2016. User’s guide for GcClust—An R package for clustering of regional geochemical data. U.S. Geological Survey report Techniques and Methods 7–C13, 21 p. [DOI](https://doi.org/10.3133/tm7C13) | | [geoknife](https://cran.r-project.org/package=geoknife): Web-Processing of Large Gridded Datasets | Read, J.S., Walker, J.I., Appling, A.P., Blodgett, D.L., Read, E.K. and Winslow, L.A., 2016. geoknife: reproducible web-processing of large gridded datasets. Ecography, 39, 354–360. [DOI](https://doi.org/10.1111/ecog.01880) | | [geomorph](https://CRAN.R-project.org/package=geomorph): Geometric Morphometric Analyses of 2D/3D Landmark Data | Adams, D.C. and Otárola-Castillo, E., 2013. geomorph: an r package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution, 4, 393–399. [DOI](http://dx.doi.org/10.1111/2041-210X.12035) | | [geoscale](http://CRAN.R-project.org/package=geoscale): Geological Time Scale Plotting | | | [geotech](https://CRAN.R-project.org/package=geotech): Geotechnical Engineering | | | [ggfortify](https://CRAN.R-project.org/package=ggfortify): Data Visualization Tools for Statistical Analysis Results | Yuan Tang, Masaaki Horikoshi, and Wenxuan Li., 2016. ggfortify: Unified Interface to Visualize Statistical Result of Popular R Packages. The R Journal, 8/2, 474-485. | | [ggmap](https://cran.r-project.org/package=ggmap): Spatial Visualization with ggplot2 | Kahle, D. and Wickham, H., 2013. ggmap: Spatial visualization with ggplot2. R Journal, 5, 144–161. | | [ggtern](http://CRAN.R-project.org/package=ggtern): An Extension to \'ggplot2\', for the Creation of Ternary Diagrams | | | [GrapheR](https://cran.r-project.org/package=GrapheR): A Multi-Platform GUI for Drawing Customizable Graphs in R | Hervé, M., 2011. GrapheR: a Multiplatform GUI for Drawing Customizable Graphs in R. The R Journal, 3, 45–53. | | [hydrogeo](http://CRAN.R-project.org/package=hydrogeo): Groundwater data presentation and interpretation | | | [IsoplotR](http://cran.r-project.org/package=IsoplotR): Statistical Toolbox for Radiometric Geochronology | Vermeesch, P., 2018. IsoplotR: A free and open toolbox for geochronology. Geoscience Frontiers, 9, 1479–1493. [DOI](https://doi.org/10.1016/j.gsf.2018.04.001) | | [Isoreader](https://cran.r-project.org/package=isoreader): Read Stable Isotope Data Files | | | [KarsTS](https://cran.r-project.org/package=KarsTS): An Interface for Microclimate Time Series Analysis | Sáez, M., C. Pla, S. Cuezva, und D. Benavente. 2019. „KarsTS: An R Package for Microclimate Time Series Analysis“. Earth Science Informatics, published online 06 July 2019. [DOI](https://doi.org/10.1007/s12145-019-00393-0) | | [LAND-SE](https://github.com/maurorossi/LAND-SE): LANDslide Susceptibility Evaluation | Rossi, M. and Reichenbach, P., 2016. LAND-SE: a software for statistically based landslide susceptibility zonation, version 1.0. Geoscientific Model Development, 9, 3533–3543. [DOI](http://dx.doi.org/10.5194/gmd-9-3533-2016) | | [Luminescence](http://CRAN.R-project.org/package=Luminescence): Comprehensive Luminescence Dating Data Analysis | Kreutzer, S. , Schmidt, C. , Fuchs, M. C. , Dietze, M. , Fischer, M. and Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30, 1-8. [hdl](http://hdl.handle.net/10013/epic.44194.d001) | | [MALDIquant](http://strimmerlab.org/software/maldiquant/): Quantitative Analysis of Mass Spectrometry Data | Gibb, S. and Strimmer, K., 2012. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics, 28(17):2270–2271. [DOI](https://doi.org/10.1093/bioinformatics/bts447) | | [matlab](http://CRAN.R-project.org/package=matlab): MATLAB emulation package | | | [marmap](https://CRAN.R-project.org/package=marmap): Import, Plot and Analyze Bathymetric and Topographic Data | Pante, E. and Simon-Bouhet, B., 2013. marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS ONE, 8, e73051. [DOI](http://dx.doi.org/10.1371/journal.pone.0073051) | | [measuRing](https://CRAN.R-project.org/package=measuRing): Detection and Control of Tree-Ring Widths on Scanned Image Sections | Lara, W., Bravo, F. and Sierra, C.A., 2015. measuRing: An R package to measure tree-ring widths from scanned images. Dendrochronologia, 34, 43–50. [DOI](http://dx.doi.org/10.1016/j.dendro.2015.04.002) | | [paleobioDB](https://CRAN.R-project.org/package=paleobioDB): Download and Process Data from the Paleobiology Database | Varela, S., González-Hernández, J., Sgarbi, L.F., Marshall, C., Uhen, M.D., Peters, S. and McClennen, M., 2015. paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. Ecography, 38, 419–425. [DOI](http://dx.doi.org/10.1111/ecog.01154) | | [paleofire](https://CRAN.R-project.org/package=paleofire): Analysis of Charcoal Records from the Global Charcoal Database | Blarquez, O., Vannière, B., Marlon, J.R., Daniau, A.-L., Power, M.J., Brewer, S. and Bartlein, P.J., 2014. paleofire: An R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning. Computers & Geosciences, 72, 255–261. [DOI](http://dx.doi.org/10.1016/j.cageo.2014.07.020) | | [paleoMAS](https://CRAN.R-project.org/package=paleoMAS): Paleoecological Analysis | | | [paleotree](http://CRAN.R-project.org/package=paleotree): Paleontological and Phylogenetic Analyses of Evolution | Bapst, D.W., 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3, 803–807. [DOI](http://dx.doi.org/10.1111/j.2041-210X.2012.00223.x) | | [paleoTS](https://CRAN.R-project.org/package=paleoTS): Analyze Paleontological Time-Series | | | [palinsol](http://CRAN.R-project.org/package=palinsol): Insolation for palaeoclimate studies | | | [phylogram](https://cran.r-project.org/package=phylogram): Dendrograms for Evolutionary Analysis | Wilkinson, S.P. and Davy, S.K., 2018\. phylogram: an R package for phylogenetic analysis with nested lists. Journal of Open Source Software, 3, 790. [DOI](https://doi.org/10.21105/joss.00790) | | [provenance](http://CRAN.R-project.org/package=provenance): Statistical Toolbox for Sedimentary Provenance Analysis | Vermeesch, P., Resentini, A. and Garzanti, E., 2016. An R package for statistical provenance analysis. Sedimentary Geology, 336, 14–25. [DOI](http://dx.doi.org/10.1016/j.sedgeo.2016.01.009) | | [rioja](https://CRAN.R-project.org/package=rioja): Analysis of Quaternary Science Data | | | [R.matlab](https://CRAN.R-project.org/package=R.matlab): Read and Write MAT Files and Call MATLAB from within R | | | [RNetCDF](https://CRAN.R-project.org/package=RNetCDF): Interface to NetCDF Datasets | Michna, P. and Woods, M., 2013. RNetCDF - A Package for Reading and Writing NetCDF Datasets. The R Journal, 5/2, [29-36](https://journal.r-project.org/archive/2013-2/michna-woods.pdf). | | [robCompositions](https://CRAN.R-project.org/package=robCompositions): Robust Estimation for Compositional Data | Templ, M., Hron, K. and Filzmoser, P., 2011. robCompositions: An R-package for Robust Statistical Analysis of Compositional Data. Pp. 341–355 in: Compositional Data Analysis (V. Pawlowsky-Glahn and A. Buccianti, editors). John Wiley & Sons, Ltd. | | [RockFab](http://CRAN.R-project.org/package=RockFab): Rock fabric and strain analysis tools | | | [SDAR](https://cran.r-project.org/package=SDAR): Stratigraphic Data Analysis | Jaramillo, Carlos; Ortiz, John (2020): SDAR. Smithsonian Tropical Research Institute. Software. [DOI](https://doi.org/10.25573/data.13118426.v2) | | [shapeR](http://CRAN.R-project.org/package=shapeR): Collection and Analysis of Otolith Shape Data | Libungan, L.A. and Pálsson, S., 2015. ShapeR: An R Package to Study Otolith Shape Variation among Fish Populations. PLoS ONE, 10, e0121102. [DOI](http://dx.doi.org/10.1371/journal.pone.0121102) | | [smwrGraphs](https://github.com/USGS-R/smwrGraphs): Graphical USGS water science R functions | Lorenz, D.L., and Diekoff, A.L., 2017, smwrGraphs—An R package for graphing hydrologic data, version 1.1.2: U.S. Geological Survey Open-File Report 2016–1188, 17 pp., [DOI](https://doi.org/10.3133/ofr20161188) | | [soilphysics](https://CRAN.R-project.org/package=soilphysics): Soil Physical Analysis | da Silva, A.R. and de Lima, R.P., 2015. soilphysics: An R package to determine soil preconsolidation pressure. Computers & Geosciences, 84, 54–60. [DOI](http://dx.doi.org/10.1016/j.cageo.2015.08.008) | | [spMC](http://cran.r-project.org/package=spMC): Continuous-Lag Spatial Markov Chains | Sartore, L., Fabbri, P. and Gaetan, C., 2016. spMC: an R-package for 3D lithological reconstructions based on spatial Markov chains. Computers & Geosciences, 94, 40–47. [DOI](http://dx.doi.org/10.1016/j.cageo.2016.06.001) | | [strap](http://CRAN.R-project.org/package=strap): Stratigraphic Tree Analysis for Palaeontology | Bell, M.A. and Lloyd, G.T., 2015. strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology, 58, 379–389. [DOI](http://dx.doi.org/10.1111/pala.12142) | | [StratigrapheR](https://cran.r-project.org/package=StratigrapheR): Integrated Stratigraphy | Wouters, S., Silva, A.-C.D., Boulvain, F., and Devleeschouwer, X., accepted. StratigrapheR: Concepts for Litholog Generation in R: The R Journal, [DOI](https://journal.r-project.org/archive/2021/RJ-2021-039/index.html) | | [TERMITE](https://github.com/SimonMischel/TERMITE/): Fast reduction of LA-ICPMS data and its application to trace element measurements | Mischel, S.A., Mertz-Kraus, R., Jochum, K.P. and Scholz, D., 2017. TERMITE: An R script for fast reduction of laser ablation inductively coupled plasma mass spectrometry data and its application to trace element measurements. Rapid Communications in Mass Spectrometry, 31, 1079–1087. [DOI](http://dx.doi.org/10.1002/rcm.7895) | | [tgcd](http://CRAN.R-project.org/package=tgcd): Thermoluminescence Glow Curve Deconvolution | Peng, J., Dong, Z. and Han, F., 2016. tgcd: An R package for analyzing thermoluminescence glow curves. SoftwareX, 5, 112–120. [DOI](http://dx.doi.org/10.1016/j.softx.2016.06.001) | | [treeclim](http://CRAN.R-project.org/package=treeclim): Numerical Calibration of Proxy-Climate Relationships | Zang, C. and Biondi, F., 2015. treeclim: an R package for the numerical calibration of proxy-climate relationships. Ecography, 38, 431–436. [DOI](http://dx.doi.org/10.1111/ecog.01335) | | [XLConnect](http://CRAN.R-project.org/package=XLConnect): Excel Connector for R | | | [zCompositions](https://CRAN.R-project.org/package=zCompositions): Treatment of Zeros and Nondetects in Compositional Data Sets | Palarea-Albaladejo, J. and Martín-Fernández, J.A., 2015. zCompositions — R package for multivariate imputation of left-censored data under a compositional approach. Chemometrics and Intelligent Laboratory Systems, 143, 85–96. [DOI](http://dx.doi.org/10.1016/j.chemolab.2015.02.019) | | **CRAN Task View**: | | | [Analysis of Spatial Data](https://CRAN.R-project.org/view=Spatial) | | | [Handling and Analyzing Spatio-Temporal Data](https://CRAN.R-project.org/view=SpatioTemporal) | | **([Home](https://homepage.univie.ac.at/dieter.mader/ "Home"))** ----- [University of Vienna](https://www.univie.ac.at/), [Department of Lithospheric Research](https://lithosphere.univie.ac.at/), Impact Research and Planetary Geology, UZA II, Josef-Holaubek-Platz 2, 1090 Vienna, Austria ----- [Datenschutzerklärung](https://dsba.univie.ac.at/datenschutzerklaerung)