EcoCommons attribution

New EcoCommons citation

EcoCommons Australia 2024. EcoCommons Australia – a collaborative commons for ecological and environmental modelling, EcoCommons, Queensland Cyber Infrastructure Foundation, Brisbane, Queensland. Available: https://data–explorer.app.ecocommons.org.au/ (Accessed: Date[ e.g., January 30, 2024]). https://doi.org/10.47486/PL108

EcoCommons citation for usage 2020-2022

EcoCommons Australia 2022. EcoCommons Australia – the platform of choice for ecological and environmental modelling, EcoCommons, Griffith University, Nathan, Queensland. Available: https://data–explorer.app.ecocommons.org.au/ (Accessed: Date[ e.g., January 19, 2022]). https://doi.org/10.47486/PL108

Acknowledgement

EcoCommons Australia is a partnership of nine organisations including NCRIS-funded Australian Research Data Commons (ARDC), the Atlas of Living Australia (ALA), CEBRA at the University of Melbourne, CSIRO’s Land and Water unit, Griffith University, Macquarie University, QCIF, TERN, and the University of NSW. It also involves an investment from the Queensland Government’s Research Infrastructure Co-investment Fund (RICF) (edited)

Recommended citation of R & main packages as well as Python and main libraries

EcoCommons would not exist without the considerable work on packages by many developers. Please cite both the language and the packages you used in your work. Find a full list of current citation information for using R and our R packages and some of the Python citations below.

To get the latest R citation to use the function below from the R.

citation()

To get citation information for any R package you can use this function in R.

citation(package = "here")

Citation for R:
R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.Statistical

DISMO R package citation:

Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith (2021). dismo: Species Distribution Modeling. R package version 1.3-
5. https://CRAN.R-project.org/package=dismo

Biomod2 citation:

Wilfried Thuiller, Damien Georges, Maya Gueguen, Robin Engler and Frank Breiner (2021). biomod2: Ensemble Platform for Species Distribution Modeling. R package
version 3.5.1. https://CRAN.R-project.org/package=biomod2

Python citation:

Van Rossum, G., & Drake Jr, F. L. (1995). Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam.

citation for NumPy library:

Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2. (Publisher link).

Citations for R packages used within the EcoCommons platform:

Package	R Reference
abind	Tony Plate and Richard Heiberger (2016). abind: Combine Multidimensional Arrays. R package version 1.4-5. https://CRAN.R-project.org/package=abind
Acepack	Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley, Shawn Garbett and Jonathan Baron (2016). acepack: ACE and AVAS for Selecting Multiple Regression Transformations. R package version 1.4.1. https://CRAN.R-project.org/package=acepack
Ade4	Dray S, Dufour A (2007). “The ade4 Package: Implementing the Duality Diagram for Ecologists.” _Journal of Statistical Software_, 22(4), 1-20. doi: 10.18637/jss.v022.i04 (URL: https://doi.org/10.18637/jss.v022.i04). Bougeard S, Dray S (2018). “Supervised Multiblock Analysis in R with the de4Package.” _Journal of Statistical Software_, 86(1), 1-17. doi: 10.18637/jss.v086.i01 (URL: https://doi.org/10.18637/jss.v086.i01). Chessel D, Dufour A, Thioulouse J (2004). “The ade4 Package – I: One-Table Methods.” _R News_, 4(1), 5-10. <URL: https://cran.r project.org/doc/Rnews/>. Dray S, Dufour A, Chessel D (2007). “The ade4 Package – II: Two-Table and K-Table Methods.” _R News_, 7(2), 47-52. <URL: https://cran.r-project.org/doc/Rnews/>. Thioulouse J, Dray S, Dufour A, Siberchicot A, Jombart T, Pavoine S (2018).Multivariate Analysis of Ecological Data with ade4_. Springer. doi: 10.1007/978-1-4939-8850-1 (URL: https://doi.org/10.1007/978-1-4939-8850-1).
adehabitatHR	Calenge, C. (2006) The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 516-519
adehabitatLT	Calenge, C. (2006) The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 516-519
adehabitatMA	Calenge, C. (2006) The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 516-519
alphahull	Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal and . (2019). alphahull: Generalization of the Convex Hull of a Sample of Points in the Plane. R package version 2.2. https://CRAN.R-project.org/package=alphahull
Ape	Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
Askpass	Jeroen Ooms (2019). askpass: Safe Password Entry for R, Git, and SSH. R package version 1.1. https://CRAN.R-project.org/package=askpass
Assertthat	Hadley Wickham (2019). assertthat: Easy Pre and Post Assertions. R package version 0.2.1. https://CRAN.R-project.org/package=assertthat
Backports	Michel Lang and R Core Team (2021). backports: Reimplementations of Functions Introduced Since R-3.0.0. R package version 1.4.1. https://CRAN.R-project.org/package=backports
base	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Base64enc	Simon Urbanek (2015). base64enc: Tools for base64 encoding. R package version 0.1-3. https://CRAN.R-project.org/package=base64enc
BH	Dirk Eddelbuettel, John W. Emerson and Michael J. Kane (2021). BH: Boost C++ Header Files. R package version 1.78.0-0. https://CRAN.R-project.org/package=BH
BiocManager	Martin Morgan (2021). BiocManager: Access the Bioconductor Project Package Repository. R package version 1.30.16. https://CRAN.R-project.org/package=BiocManager
Biomod2	Wilfried Thuiller, Damien Georges, Maya Gueguen, Robin Engler and Frank Breiner (2021). biomod2: Ensemble Platform for Species Distribution Modeling.R package version 3.5.1. https://CRAN.R-project.org/package=biomod2
Bit	Jens Oehlschlägel and Brian Ripley (2020). bit: Classes and Methods for Fast Memory-Efficient Boolean Selections. R package version 4.0.4. https://CRAN.R-project.org/package=bit
Bit64	Jens Oehlschlägel and Leonardo Silvestri (2020). bit64: A S3 Class for Vectors of 64bit Integers. R package version 4.0.5. https://CRAN.R-project.org/package=bit64
Bitops	S original by Steve Dutky initial R port, extensions by Martin Maechler; revised and modified by Steve Dutky (2021). bitops: Bitwise Operations. R package version 1.0-7. https://CRAN.R-project.org/package=bitops
Blob	Hadley Wickham (2021). blob: A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’). R package version 1.2.2. https://CRAN.R-project.org/package=blob
boot	Angelo Canty and Brian Ripley (2021). boot: Bootstrap R (S-Plus) Functions. R package version 1.3-28. Davison, A. C. & Hinkley, D. V. (1997) Bootstrap Methods and Their Applications. Cambridge University Press, Cambridge. ISBN 0-521-57391-2
Brew	Jeffrey Horner and Greg Hunt (2022). brew: Templating Framework for Report Generation. R package version 1.0-7. https://CRAN.R-project.org/package=brew
brio	Jim Hester and Gábor Csárdi (2021). brio: Basic R Input Output. R package version 1.1.3. https://CRAN.R-project.org/package=brio
Broom	David Robinson, Alex Hayes and Simon Couch (2022). broom: Convert Statistical Objects into Tidy Tibbles. R package version 0.7.12. https://CRAN.R-project.org/package=broom
bslib	Carson Sievert and Joe Cheng (2021). bslib: Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’. R package version 0.3.1. https://CRAN.R-project.org/package=bslib
cachem	Winston Chang (2021). cachem: Cache R Objects with Automatic Pruning. R package version 1.0.6. https://CRAN.R-project.org/package=cachem
Callr	Gábor Csárdi and Winston Chang (2021). callr: Call R from R. R package version 3.7.0. https://CRAN.R-project.org/package=callr
car	John Fox and Sanford Weisberg (2019). An {R} Companion to Applied Regression, Third Edition. Thousand Oaks CA: Sage. URL: https://socialsciences.mcmaster.ca/jfox/Books/Companion/
carData	John Fox, Sanford Weisberg and Brad Price (2022). carData: Companion to Applied Regression Data Sets. R package version 3.0-5. https://CRAN.R-project.org/package=carData
Caret	Max Kuhn (2021). caret: Classification and Regression Training. R package version 6.0-90. https://CRAN.R-project.org/package=caret
cellranger	Jennifer Bryan (2016). cellranger: Translate Spreadsheet Cell Ranges to Rows and Columns. R package version 1.1.0. https://CRAN.R-project.org/package=cellranger
Checkmate	Lang M (2017). “checkmate: Fast Argument Checks for Defensive R Programming.”The R Journal_, 9(1), 437-445. <URL: https://journal.r-project.org/archive/2017/RJ-2017-028/index.html>.
CircStats	S-plus original by Ulric Lund and R port by Claudio Agostinelli (2018). CircStats: Circular Statistics, from “Topics in Circular Statistics” (2001). R package version 0.2-6. https://CRAN.R-project.org/package=CircStats
class	Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
classInt	Roger Bivand (2020). classInt: Choose Univariate Class Intervals. R package version 0.4-3. https://CRAN.R-project.org/package=classInt
Cli	Gábor Csárdi (2022). cli: Helpers for Developing Command Line Interfaces. R package version 3.1.1. https://CRAN.R-project.org/package=cli
Clipr	Matthew Lincoln (2020). clipr: Read and Write from the System Clipboard. R package version 0.7.1. https://CRAN.R-project.org/package=clipr
Clisymbols	Gábor Csárdi and Sindre Sorhus (2017). clisymbols: Unicode Symbols at the R Prompt. R package version 1.2.0. https://CRAN.R-project.org/package=clisymbols
cluster	Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K.(2022). cluster: Cluster Analysis Basics and Extensions. R package version 2.1.3.
codetools	Luke Tierney (2020). codetools: Code Analysis Tools for R. R package version 0.2-18. https://CRAN.R-project.org/package=codetools
Colorspace	Zeileis A, Fisher JC, Hornik K, Ihaka R, McWhite CD, Murrell P, Stauffer R, Wilke CO (2020). “colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes.” _Journal of Statistical Software_, 96(1), 1-49. doi:10.18637/jss.v096.i01 (URL: dttps://doi.org/10.18637/jss.v096.i01).
colourvalues	David Cooley (2020). colourvalues: Assigns Colours to Values. R package version 0.3.7. https://CRAN.R-project.org/package=colourvalues
Commonmark	Jeroen Ooms (2018). commonmark: High Performance CommonMark and Github Markdown Rendering in R. R package version 1.7. https://CRAN.R-project.org/package=commonmark
compiler	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
conditionz	Scott Chamberlain (2019). conditionz: Control How Many Times Conditions are Thrown. R package version 0.1.0. https://CRAN.R-project.org/package=conditionz
conflicted	Hadley Wickham (2021). conflicted: An Alternative Conflict Resolution Strategy. R package version 1.1.0. https://CRAN.R-project.org/package=conflicted
conquer	Xuming He, Xiaoou Pan, Kean Ming Tan and Wen-Xin Zhou (2022). conquer: Convolution-Type Smoothed Quantile Regression. R package version 1.3.0. https://CRAN.R-project.org/package=conquer
ConR	Gilles Dauby (2020). ConR: Computation of Parameters Used in Preliminary Assessment of Conservation Status. R package version 1.3.0. https://CRAN.R-project.org/package=ConR
Covr	Jim Hester (2020). covr: Test Coverage for Packages. R package version 3.5.1. https://CRAN.R-project.org/package=covr
cpp11	Jim Hester and Romain François (2021). cpp11: A C++11 Interface for R’s C Interface. R package version 0.4.2. https://CRAN.R-project.org/package=cpp11
Crayon	Gábor Csárdi (2021). crayon: Colored Terminal Output. R package version 1.4.2. https://CRAN.R-project.org/package=crayon
credentials	Jeroen Ooms (2021). credentials: Tools for Managing SSH and Git Credentials. R package version 1.3.2. https://CRAN.R-project.org/package=credentials
Crosstalk	oe Cheng and Carson Sievert (2021). crosstalk: Inter-Widget Interactivity for HTML Widgets. R package version 1.2.0. https://CRAN.R-project.org/package=crosstalk
crul	Scott Chamberlain (2021). crul: HTTP Client. R package version 1.2.0. https://CRAN.R-project.org/package=crul
Curl	Jeroen Ooms (2021). curl: A Modern and Flexible Web Client for R. R package version 4.3.2. https://CRAN.R-project.org/package=curl
Cyclocomp	Gabor Csardi (2016). cyclocomp: Cyclomatic Complexity of R Code. R package version 1.1.0. https://CRAN.R-project.org/package=cyclocomp data.table
Data.table	Matt Dowle and Arun Srinivasan (2021). data.table: Extension of `data.frame`. R package version 1.14.2. https://CRAN.R-project.org/package=data.table
datasets	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
DBI	R Special Interest Group on Databases (R-SIG-DB), Hadley Wickham and Kirill Müller (2021). DBI: R Database Interface. R package version 1.1.2. https://CRAN.R-project.org/package=DBI
Dbplyr	Hadley Wickham, Maximilian Girlich and Edgar Ruiz (2021). dbplyr: A ‘dplyr’ Back End for Databases. R package version 2.1.1. https://CRAN.R-project.org/package=dbplyr
deldir	Rolf Turner (2021). deldir: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation. R package version 1.0-6. https://CRAN.R-project.org/package=deldir

Desc	Gábor Csárdi, Kirill Müller and Jim Hester (2021). desc: Manipulate DESCRIPTION Files. R package version 1.4.0. https://CRAN.R-project.org/package=desc
Devtools	Hadley Wickham, Jim Hester, Winston Chang and Jennifer Bryan (2021). devtools: Tools to Make Developing R Packages Easier. R package version 2.4.3. https://CRAN.R-project.org/package=devtools
dials	Max Kuhn and Hannah Frick (2022). dials: Tools for Creating Tuning Parameter Values. R package version 0.1.1. https://CRAN.R-project.org/package=dials
DiceDesign	Delphine Dupuy, Celine Helbert, Jessica Franco (2015). DiceDesign and DiceEval: Two R Packages for Design and Analysis of Computer Experiments. Journal of Statistical Software, 65(11), 1-38. URL https://www.jstatsoft.org/v65/i11/
dichromat	Thomas Lumley (2022). dichromat: Color Schemes for Dichromats. R package version 2.0-0.1. https://CRAN.R-project.org/package=dichromat
Diffobj	Brodie Gaslam (2021). diffobj: Diffs for R Objects. R package version 0.3.5. https://CRAN.R-project.org/package=diffobj
Digest	Dirk Eddelbuettel with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell, Matthew de Queljoe, Ion Suruceanu, Bill Denney, Dirk Schumacher and and Winston Chang. (2021). digest: Create Compact Hash Digests of R Objects. R package version 0.6.29. https://CRAN.R-project.org/package=digest
Dismo	Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith (2021). dismo: Species Distribution Modeling. R package version 1.3-5. https://CRAN.R-project.org/package=dismo
doParallel	Microsoft Corporation and Steve Weston (2022). doParallel: Foreach Parallel Adaptor for the ‘parallel’ Package. R package version 1.0.17. https://CRAN.R-project.org/package=doParallel
doSNOW	Microsoft Corporation and Stephen Weston (2022). doSNOW: Foreach Parallel Adaptor for the ‘snow’ Package. R package version 1.0.20. https://CRAN.R-project.org/package=doSNOW
dotCall64	F. Gerber, K. Moesinger, R. Furrer (2018), dotCall64: An R package providing an efficient interface to compiled C, C++, and Fortran code supporting long vectors, SoftwareX 7, 217-221, https://doi.org/10.1016/j.softx.2018.06.002. F. Gerber, K. Moesinger, R. Furrer (2017), Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data, Computer & Geoscience 104, 109-119, https://doi.org/10.1016/j.cageo.2016.11.015.
Dplyr	Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr
DT	Yihui Xie, Joe Cheng and Xianying Tan (2021). DT: A Wrapper of the JavaScript Library ‘DataTables’. R package version 0.20. https://CRAN.R-project.org/package=DT
Dtpylr	Hadley Wickham, Maximilian Girlich, Mark Fairbanks and Ryan Dickerson (2022). dtplyr: Data Table Back-End for ‘dplyr’. R package version 1.2.1. https://CRAN.R-project.org/package=dtplyr
E1071	David Meyer, Evgenia Dimitriadou, Kurt Hornik, Andreas Weingessel and Friedrich Leisch (2021). e1071: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. R package version 1.7-9. https://CRAN.R-project.org/package=e1071
Earth	Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller’s Fortran utilities with Thomas Lumley’s leaps wrapper. (2021). earth: Multivariate Adaptive Regression Splines. R package version 5.3.1. https://CRAN.R-project.org/package=earth
ecospat	Goslee, S.C. and Urban, D.L. 2007. The ecodist package for dissimilarity-based analysis of ecological data. Journal of Statistical Software 22(7):1-19.
Ellipsis	Hadley Wickham (2021). ellipsis: Tools for Working with …. R package version 0.3.2. https://CRAN.R-project.org/package=ellipsis
ENMeval	Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C. L., Pinilla-Buitrago, G. E., Boria, R. A., Soley-Guardia, M., and R. P. Anderson (2021). ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13628
Evaluate	Hadley Wickham and Yihui Xie (2019). evaluate: Parsing and Evaluation Tools that Provide More Details than the Default. R package version 0.14. https://CRAN.R-project.org/package=evaluate
Fansi	Brodie Gaslam (2022). fansi: ANSI Control Sequence Aware String Functions. R package version 1.0.2. https://CRAN.R-project.org/package=fansi
Farver	Thomas Lin Pedersen, Berendea Nicolae and Romain François (2021). farver: High Performance Colour Space Manipulation. R package version 2.1.0. https://CRAN.R-project.org/package=farver
Fastmap	Winston Chang (2021). fastmap: Fast Data Structures. R package version 1.1.0. https://CRAN.R-project.org/package=fastmap
Fields	Douglas Nychka, Reinhard Furrer, John Paige, Stephan Sain (2021). “fields: Tools for spatial data.” R package version 13.3, <URL: https://github.com/dnychka/fieldsRPackage>.
Filehash	Peng RD (2006). “Interacting with data using the filehash package,” R News, 6 (4), 19–24.
FNN	Alina Beygelzimer, Sham Kakadet, John Langford, Sunil Arya, David Mount and Shengqiao Li (2019). FNN: Fast Nearest Neighbor Search Algorithms and Applications. R package version 1.1.3. https://CRAN.R-project.org/package=FNN
Foghorn	Francois Michonneau (2021). foghorn: Summarize CRAN Check Results in the Terminal. R package version 1.4.2. https://CRAN.Rproject.org/package=foghorn
fontawesome	Richard Iannone (2021). fontawesome: Easily Work with ‘Font Awesome’ Icons. R package version 0.2.2. https://CRAN.R-project.org/package=fontawesome
fontBitstreamVera	Lionel Henry (2017). fontBitstreamVera: Fonts with ‘Bitstream Vera Fonts’ License. R package version 0.1.1. https://CRAN.R-project.org/package=fontBitstreamVera
fontLiberation	Pravin Satpute and Steve Matteson (2016). fontLiberation: Liberation Fonts. R package version 0.1.0. https://CRAN.R-project.org/package=fontLiberation
fontquiver	Lionel Henry (2017). fontquiver: Set of Installed Fonts. R package version 0.2.1. https://CRAN.R-project.org/package=fontquiver
forcats	Hadley Wickham (2021). forcats: Tools for Working with Categorical Variables (Factors). R package version 0.5.1. https://CRAN.R-project.org/package=forcats
Foreach	Microsoft and Steve Weston (2022). foreach: Provides Foreach Looping Construct. R package version 1.5.2. https://CRAN.R-project.org/package=foreach
forecast	Hyndman R, Athanasopoulos G, Bergmeir C, Caceres G, Chhay L, O’Hara-Wild M, Petropoulos F, Razbash S, Wang E, Yasmeen F (2022). _forecast: Forecasting functions for time series and linear models_. R package version 8.16, <URL: https://pkg.robjhyndman.com/forecast/>. Hyndman RJ, Khandakar Y (2008). “Automatic time series forecasting: the forecast package for R.” _Journal of Statistical Software_, 26(3), 1-22. doi: 10.18637/jss.v027.i03 (URL: https://doi.org/10.18637/jss.v027.i03).
foreign	R Core Team (2022). foreign: Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …. R package version 0.8-82. https://CRAN.R-project.org/package=foreign
Formula	Zeileis A, Croissant Y (2010). “Extended Model Formulas in R: Multiple Parts and Multiple Responses.” _Journal of Statistical Software_, 34(1), 1-13. doi: 10.18637/jss.v034.i01 (URL: https://doi.org/10.18637/jss.v034.i01).
fracdiff	Martin Maechler (2020). fracdiff: Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models. R package version 1.5-1. https://CRAN.R-project.org/package=fracdiff
freetypeharfbuzz	Error in citation(package = “freetypeharfbuzz”) : there is no package called ‘freetypeharfbuzz’
Fs	Jim Hester, Hadley Wickham and Gábor Csárdi (2021). fs: Cross-Platform File System Operations Based on ‘libuv’. R package version 1.5.2. https://CRAN.R-project.org/package=fs
furrr	Davis Vaughan and Matt Dancho (2022). furrr: Apply Mapping Functions in Parallel using Futures. R package version 0.3.0. https://CRAN.R-project.org/package=furrr
future	Henrik Bengtsson, A Unifying Framework for Parallel and Distributed Processing in R using Futures, The R Journal (2021) 13:2, pages 208-227, doi:10.32614/RJ-2021-048
future.apply	Henrik Bengtsson, A Unifying Framework for Parallel and Distributed Processing in R using Futures, The R Journal (2021) 13:2, pages 208-227, doi:10.32614/RJ-2021-048
Gam	Trevor Hastie (2020). gam: Generalized Additive Models. R package version 1.20. https://CRAN.R-project.org/package=gam
Gargle	Jennifer Bryan, Craig Citro and Hadley Wickham (2021). gargle: Utilities for working with Google APIs. R package version 1.2.0. https://CRAN.R-project.org/package=gargle
Gbm	Brandon Greenwell, Bradley Boehmke, Jay Cunningham and GBM Developers (2020). gbm: Generalized Boosted Regression Models. R package version 2.1.8. https://CRAN.R-project.org/package=gbm
gdalUtils	Jonathan Asher Greenberg and Matteo Mattiuzzi (2020). gdalUtils: Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities. R package version 2.0.3.2. https://CRAN.R-project.org/package=gdalUtils
Gdata	Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni Magnusson, Jim Rogers and others (2017). gdata: Various R Programming Tools for Data Manipulation. R package version 2.18.0. https://CRAN.R-project.org/package=gdata
Gdtools	David Gohel, Hadley Wickham, Lionel Henry and Jeroen Ooms (2021). gdtools: “Utilities for Graphical Rendering. R package version 0.2.3. Utilities for Graphical Rendering. R package version 0.2.3. https://CRAN.R-project.org/package=gdtools “
generics	Hadley Wickham, Max Kuhn and Davis Vaughan (2022). generics: Common S3 Generics not Provided by Base R Methods Related to Model Fitting. R package version 0.1.2. https://CRAN.R-project.org/package=generics
geojsonsf	David Cooley (2022). geojsonsf: GeoJSON to Simple Feature Converter. R package version 2.0.2. https://CRAN.R-project.org/package=geojsonsf
geometries	David Cooley (2020). geometries: Convert Between R Objects and Geometric Structures. R package version 0.2.0. https://CRAN.R-project.org/package=geometries
geosphere	Robert J. Hijmans (2021). geosphere: Spherical Trigonometry. R package version 1.5-14. https://CRAN.R-project.org/package=geosphere
gert	Jeroen Ooms (2022). gert: Simple Git Client for R. R package version 1.6.0. https://CRAN.R-project.org/package=gert
ggdendro	Andrie de Vries and Brian D. Ripley (2022). ggdendro: Create Dendrograms and Tree Diagrams Using ‘ggplot2’. R package version 0.1.23. https://CRAN.R-project.org/package=ggdendro
ggmap	D. Kahle and H. Wickham. ggmap: Spatial Visualization with ggplot2. The R Journal, 5(1), 144-161. URL http://journal.r-project.org/archive/2013-1/kahle-wickham.pdf
ggplot2	H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
ggplot2movies	Hadley Wickham (2015). ggplot2movies: Movies Data. R package version 0.0.1. https://CRAN.R-project.org/package=ggplot2movies
gh	Jennifer Bryan and Hadley Wickham (2021). gh: ‘GitHub’ ‘API’. R package version 1.3.0. https://CRAN.R-project.org/package=gh
Git2r	Widgren, S., et al. (2020) git2r: Provides Access to Git Repositories. R package version 0.27.1. URL https://CRAN.R-project.org/package=git2r.
gitcreds	Gábor Csárdi (2020). gitcreds: Query ‘git’ Credentials from ‘R’. R package version 0.1.1. https://CRAN.R-project.org/package=gitcreds
glmnet	Jerome Friedman, Trevor Hastie, Robert Tibshirani (2010). Regularization Paths for Generalized Linear Models via Coordinate Descent. Journal of Statistical Software, 33(1), 1-22. URL https://www.jstatsoft.org/v33/i01/.
globals	Henrik Bengtsson (2022). globals: Identify Global Objects in R Expressions. R package version 0.15.0. https://CRAN.R-project.org/package=globals
Glue	Jim Hester and Jennifer Bryan (2022). glue: Interpreted String Literals. R package version 1.6.1. https://CRAN.R-project.org/package=glue
glue	Jim Hester and Jennifer Bryan (2022). glue: Interpreted String Literals. R package version 1.6.2. https://CRAN.R-project.org/package=glue
Gmailr	Jim Hester and Jennifer Bryan (2021). gmailr: Access the ‘Gmail’ ‘RESTful’ API. R package version 1.0.1. https://CRAN.R-project.org/package=gmailr
Gmodels	Gregory R. Warnes, Ben Bolker, Thomas Lumley, Randall C Johnson. Contributions from Randall C. Johnson are Copyright SAIC-Frederick, Inc. Funded by the Intramural Research Program, of the NIH, National Cancer Institute and Center for Cancer Research under NCI Contract NO1-CO-12400. (2018). gmodels: Various R Programming Tools for Model Fitting. R package version 2.18.1. https://CRAN.R-project.org/package=gmodels
Goftest	Julian Faraway, George Marsaglia, John Marsaglia and Adrian Baddeley (2021). goftest: Classical Goodness-of-Fit Tests for Univariate Distributions. R package version 1.2-3. https://CRAN.R-project.org/package=goftest
googledrive	Lucy D’Agostino McGowan and Jennifer Bryan (2021). googledrive: An Interface to Google Drive. R package version 2.0.0. https://CRAN.R-project.org/package=googledrive
googlePolylines	David Cooley (2020). googlePolylines: Encoding Coordinates into ‘Google’ Polylines. R package version 0.8.2. https://CRAN.R-project.org/package=googlePolylines
googlesheets4	Jennifer Bryan (2021). googlesheets4: Access Google Sheets using the Sheets API V4. R package version 1.0.0. https://CRAN.R-project.org/package=googlesheets4
gower	Mark van der Loo (2022). gower: Gower’s Distance. R package version 1.0.0. https://CRAN.R-project.org/package=gower
GPfit	Blake MacDonald, Pritam Ranjan, Hugh Chipman (2015). GPfit: An R Package for Fitting a Gaussian Process Model to Deterministic Simulator Outputs. Journal of Statistical Software, 64(12), 1-23. URL http://www.jstatsoft.org/v64/i12/.
graphics	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
grDevices	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
grid	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Gridextra	Baptiste Auguie (2017). gridExtra: Miscellaneous Functions for “Grid” Graphics. R package version2.3. https://CRAN.R-project.org/package=gridExtra
gtable	Hadley Wickham and Thomas Lin Pedersen (2019). gtable: Arrange ‘Grobs’ in Tables. R package version 0.3.0. https://CRAN.R-project.org/package=gtable
gtools	Gregory R. Warnes, Ben Bolker and Thomas Lumley (2021). gtools: Various R Programming Tools. R package version 3.9.2. https://CRAN.R-project.org/package=gtools
hardhat	Davis Vaughan and Max Kuhn (2022). hardhat: Construct Modeling Packages. R package version 0.2.0. https://CRAN.R-project.org/package=hardhat
haven	Hadley Wickham, Evan Miller and Danny Smith (2022). haven: Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files. R package version 2.5.0. https://CRAN.R-project.org/package=haven
hexbin	Dan Carr, ported by Nicholas Lewin-Koh, Martin Maechler and contains copies of lattice functions written by Deepayan Sarkar (2021). hexbin: Hexagonal Binning Routines. R package version 1.28.2. https://CRAN.R-project.org/package=hexbin
highlight	Romain Francois (2019). highlight: Syntax Highlighter. R package version 0.5.0. https://CRAN.R-project.org/package=highlight
highr	Yihui Xie and Yixuan Qiu (2021). highr: Syntax Highlighting for R Source Code. R package version 0.9. https://CRAN.R-project.org/package=highr
Hmisc	Frank E Harrell Jr (2021). Hmisc: Harrell Miscellaneous. R package version 4.6-0. https://CRAN.R-project.org/package=Hmisc
hms	Kirill Müller (2021). hms: Pretty Time of Day. R package version 1.1.1. https://CRAN.R-project.org/package=hms
htmlTable	Max Gordon, Stephen Gragg and Peter Konings (2022). htmlTable: Advanced Tables for Markdown/HTML. R package version 2.4.0. https://CRAN.R-project.org/package=htmlTable
htmltools	Joe Cheng, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie and Jeff Allen (2021). htmltools: Tools for HTML. R package version 0.5.2. https://CRAN.R-project.org/package=htmltools
htmlwidgets	Ramnath Vaidyanathan, Yihui Xie, JJ Allaire, Joe Cheng, Carson Sievert and Kenton Russell (2021). htmlwidgets: HTML Widgets for R. R package version 1.5.4. https://CRAN.R-project.org/package=htmlwidgets
httpcode	Scott Chamberlain (2020). httpcode: ‘HTTP’ Status Code Helper. R package version 0.3.0. https://CRAN.R-project.org/package=httpcode
httpuv	Joe Cheng and Winston Chang (2022). httpuv: HTTP and WebSocket Server Library. R package version 1.6.5. https://CRAN.R-project.org/package=httpuv
httr	Hadley Wickham (2020). httr: Tools for Working with URLs and HTTP. R package version 1.4.2.https://CRAN.R-project.org/package=httr
hunspell	Jeroen Ooms (2020). hunspell: High-Performance Stemmer, Tokenizer, and Spell Checker. R package version 3.0.1. https://CRAN.R-project.org/package=hunspell
ids	Rich FitzJohn (2017). ids: Generate Random Identifiers. R package version 1.0.1. https://CRAN.R-project.org/package=ids
igraph	Jeroen Ooms (2020). hunspell: High-Performance Stemmer, Tokenizer, and Spell Checker. R package version 3.0.1. https://CRAN.R-project.org/package=hunspell
infer	Andrew Bray, Chester Ismay, Evgeni Chasnovski, Simon Couch, Ben Baumer and Mine Cetinkaya-Rundel (2021). infer: Tidy Statistical Inference. R package version 1.0.0. https://CRAN.R-project.org/package=infer
ini	David Valentim Dias (2018). ini: Read and Write ‘.ini’ Files. R package version 0.3.1. https://CRAN.R-project.org/package=ini
intervals	Richard Bourgon (2020). intervals: Tools for Working with Points and Intervals. R package version 0.15.2. https://CRAN.R-project.org/package=intervals
ipred	Andrea Peters and Torsten Hothorn (2021). ipred: Improved Predictors. R package version 0.9-12. https://CRAN.R-project.org/package=ipred
IRdisplay	Thomas Kluyver, Philipp Angerer and Jan Schulz (2022). IRdisplay: ‘Jupyter’ Display Machinery. R package version 1.1. https://CRAN.R-project.org/package=Irdisplay
IRkernel	Thomas Kluyver, Philipp Angerer, Jan Schulz and Karthik Ram (2022). IRkernel: Native R Kernel for the ‘Jupyter Notebook’. R package version 1.3. https://CRAN.R-project.org/package=Irkernel
isoband	Claus O. Wilke and Thomas Lin Pedersen (2021). isoband: Generate Isolines and Isobands from Regularly Spaced Elevation Grids. R package version 0.2.5. https://CRAN.R-project.org/package=isoband
iterators	Revolution Analytics and Steve Weston (2022). iterators: Provides Iterator Construct. R package version 1.0.14. https://CRAN.R-project.org/package=iterators
jpeg	Simon Urbanek (2021). jpeg: Read and write JPEG images. R package version 0.1-9. https://CRAN.R-project.org/package=jpeg
jquerylib	Carson Sievert and Joe Cheng (2021). jquerylib: Obtain ‘jQuery’ as an HTML Dependency Object. R package version 0.1.4. https://CRAN.R-project.org/package=jquerylib
jsonify	David Cooley (2020). jsonify: Convert Between ‘R’ Objects and Javascript Object Notation (JSON). R package version 1.2.1. https://CRAN.R-project.org/package=jsonify
jsonlite	Jeroen Ooms (2014). The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects. arXiv:1403.2805 [stat.CO] URL https://arxiv.org/abs/1403.2805.
kernlab	Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis (2004). kernlab – An S4 Package for Kernel Methods in R. Journal of Statistical Software 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/
KernSmooth	Matt Wand (2021). KernSmooth: Functions for Kernel Smoothing Supporting Wand & Jones (1995). R package version 2.23-20. https://CRAN.R-project.org/package=KernSmooth
knitr	Yihui Xie (2021). knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.37. Yihui Xie (2015) Dynamic Documents with R and knitr. 2nd edition. Chapman and Hall/CRC. ISBN 978-1498716963 Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible Research in R. In Victoria Stodden, Friedrich Leisch and Roger D. Peng, editors, Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595
ks	Tarn Duong (2021). ks: Kernel Smoothing. R package version 1.13.3. https://CRAN.R-project.org/package=ks
labeling	Justin Talbot, (2020). labeling: Axis Labeling. R package version 0.4.2. https://CRAN.R-project.org/package=labeling
Lahman	Michael Friendly, Chris Dalzell, Martin Monkman and Dennis Murphy (2021). Lahman: Sean ‘Lahman’ Baseball Database. R package version 9.0-0. https://CRAN.R-project.org/package=Lahman
later	Winston Chang and Joe Cheng (2021). later: Utilities for Scheduling Functions to Execute Later with Event Loops. R package version 1.3.0. https://CRAN.R-project.org/package=later
lattice	Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
latticeExtra	Deepayan Sarkar and Felix Andrews (2019). latticeExtra: Extra Graphical Utilities Based on Lattice. R package version 0.6-29. https://CRAN.R-project.org/package=latticeExtra
lava	Klaus K. Holst and Esben Budtz-Joergensen (2013). Linear Latent Variable Models: The lava-package. Computational Statistics, 28 (4), pp. 1385-1452. doi: 10.1007/s00180-012-0344-y. Klaus K. Holst and Esben Budtz-Joergensen (2020). A two-stage estimation procedure for non-linear structural equation models. Biostatistics, 21 (4), pp. 676-691. doi: 10.1093/biostatistics/kxy082.
lazyeval	Hadley Wickham (2019). lazyeval: Lazy (Non-Standard) Evaluation. R package version 0.2.2. https://CRAN.R-project.org/package=lazyeval
leafem	Tim Appelhans (2022). leafem: ‘leaflet’ Extensions for ‘mapview’. R package version 0.2.0. https://CRAN.R-project.org/package=leafem
leaflet	Joe Cheng, Bhaskar Karambelkar and Yihui Xie (2022). leaflet: Create Interactive Web Maps with the JavaScript ‘Leaflet’ Library. R package version 2.1.1. https://CRAN.R-project.org/package=leaflet
leaflet.providers	Leslie Huang (2019). leaflet.providers: Leaflet Providers. R package version 1.9.0. https://CRAN.R-project.org/package=leaflet.providers
leafsync	Tim Appelhans and Kenton Russell (2019). leafsync: Small Multiples for Leaflet Web Maps. R package version 0.1.0. https://CRAN.R-project.org/package=leafsync
lhs	Rob Carnell (2022). lhs: Latin Hypercube Samples. R package version 1.1.5. https://CRAN.R-project.org/package=lhs
lifecycle	Lionel Henry and Hadley Wickham (2021). lifecycle: Manage the Life Cycle of your Package Functions. R package version 1.0.1. https://CRAN.R-project.org/package=lifecycle
lintr	Jim Hester, Florent Angly and Russ Hyde (2020). lintr: A ‘Linter’ for R Code. R package version 2.0.1. https://CRAN.R-project.org/package=lintr
listenv	Henrik Bengtsson (2019). listenv: Environments Behaving (Almost) as Lists. R package version 0.8.0. https://CRAN.R-project.org/package=listenv
lme4	Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1),1-48. doi:10.18637/jss.v067.i01.
lmtest	Achim Zeileis, Torsten Hothorn (2002). Diagnostic Checking in Regression Relationships. R News 2(3), 7-10. URL https://CRAN.R-project.org/doc/Rnews/
loggcondens	Lutz Duembgen, Kaspar Rufibach (2011). logcondens: Computations Related to Univariate Log-Concave Density Estimation. Journal of Statistical Software, 39(6), 1-28. DOI https://doi.org/10.18637/jss.v039.i06.
lubridate	Garrett Grolemund, Hadley Wickham (2011). Dates and Times Made Easy with lubridate. Journal of Statistical Software, 40(3), 1-25. URL https://www.jstatsoft.org/v40/i03/.
lwgeom	Edzer Pebesma (2021). lwgeom: Bindings to Selected ‘liblwgeom’ Functions for Simple Features. R package version 0.2-8. https://CRAN.R-project.org/package=lwgeom
magrittr	Stefan Milton Bache and Hadley Wickham (2022). rmagrittr: A Forward-Pipe Operator for R. R package version 2.0.2. https://CRAN.R-project.org/package=magrittr
mapdata	Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg. (2018). mapdata: Extra Map Databases. R package version 2.3.0. https://CRAN.R-project.org/package=mapdata
mapdeck	David Cooley (2020). mapdeck: Interactive Maps Using ‘Mapbox GL JS’ and ‘Deck.gl’. R package version 0.3.4. https://CRAN.R-project.org/package=mapdeck
mapproj	Doug McIlroy. Packaged for R by Ray Brownrigg, Thomas P Minka and transition to Plan 9 codebase by Roger Bivand. (2022). mapproj: Map Projections. R package version 1.2.8. https://CRAN.R-project.org/package=mapproj
maps	Original S code by Richard A. Becker, Allan R. Wilks. R version by Ray Brownrigg. Enhancements by Thomas P Minka and Alex Deckmyn. (2021). maps: Draw Geographical Maps. R package version 3.4.0. https://CRAN.R-project.org/package=maps
maptools	Roger Bivand and Nicholas Lewin-Koh (2021). maptools: Tools for Handling Spatial Objects. R package version 1.1-2. https://CRAN.R-project.org/package=maptools
markdown	JJ Allaire, Jeffrey Horner, Yihui Xie, Vicent Marti and Natacha Porte (2019). Markdown: Render Markdown with the C Library ‘Sundown’. R package version 1.1. https://CRAN.R-project.org/package=markdown
MASS	Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
Matrix	Douglas Bates, Martin Maechler and Mikael Jagan (2022). Matrix: Sparse and Dense Matrix Classes and Methods. R package version 1.4-1. https://CRAN.R-project.org/package=Matrix
MatrixModels	Douglas Bates and Martin Maechler (2021). MatrixModels: Modelling with Sparse and Dense Matrices. R package version 0.5-0. https://CRAN.R-project.org/package=MatrixModels
matrixStats	Henrik Bengtsson (2022). matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors). R package version 0.62.0. https://CRAN.R-project.org/package=matrixStats
maxnet	Steven Phillips (2021). maxnet: Fitting ‘Maxent’ Species Distribution Models with ‘glmnet’. R package version 0.1.4. https://CRAN.R-project.org/package=maxnet
mclust	Scrucca L., Fop M., Murphy T. B. and Raftery A. E. (2016) mclust 5: clustering, classification and density estimation using Gaussian finite mixture models The R Journal 8/1, pp. 289-317
mda	S original by Trevor Hastie & Robert Tibshirani. Original R port by Friedrich Leisch, Kurt Hornik and Brian D. Ripley. Balasubramanian Narasimhan has contributed to the upgrading of the code. (2020). mda: Mixture and Flexible Discriminant Analysis. R package version 0.5-2. https://CRAN.R-project.org/package=mda
memoise	Hadley Wickham, Jim Hester, Winston Chang, Kirill Müller and Daniel Cook (2021). memoise: ‘Memoisation’ of Functions. R package version 2.0.1. https://CRAN.R-project.org/package=memoise
methods	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
mgcv	Wood, S.N. (2011) Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. Journal of the Royal Statistical Society (B) 73(1):3-36 Wood S.N., N. Pya and B. Saefken (2016) Smoothing parameter and model selection for general smooth models (with discussion). Journal of the American Statistical Association 111:1548-1575. Wood, S.N. (2004) Stable and efficient multiple smoothing parameter estimation for generalized additive models. Journal of the American Statistical Association. 99:673-686. Wood, S.N. (2017) Generalized Additive Models: An Introduction with R (2nd edition). Chapman and Hall/CRC. Wood, S.N. (2003) Thin-plate regression splines. Journal of the Royal Statistical Society (B) 65(1):95-114.
microbenchmark	Olaf Mersmann (2021). microbenchmark: Accurate Timing Functions. R package version 1.4.9. https://CRAN.R-project.org/package=microbenchmark
MigClim	Warning in install.packages : package ‘MigClim’ is not available for this version of R
mime	Yihui Xie (2021). mime: Map Filenames to MIME Types. R package version 0.12. https://CRAN.R-project.org/package=mime

mmap	Jeffrey A. Ryan (2020). mmap: Map Pages of Memory. R package version 0.6-19. https://CRAN.R-project.org/package=mmap
mockery	Warning in install.packages : package ‘mockey’ is not available for this version of R
modeldata	Max Kuhn (2021). modeldata: Data Sets Used Useful for Modeling Packages. R package version 0.1.1. https://CRAN.R-project.org/package=modeldata
ModelMetrics	Tyler Hunt (2020). ModelMetrics: Rapid Calculation of Model Metrics. R package version 1.2.2.2. https://CRAN.R-project.org/package=ModelMetrics
modelr	Hadley Wickham (2020). modelr: Modelling Functions that Work with the Pipe. R package version 0.1.8. https://CRAN.R-project.org/package=modelr
multcomp	Torsten Hothorn, Frank Bretz and Peter Westfall (2008). Simultaneous Inference in General Parametric Models. Biometrical Journal 50(3), 346–363.
multicool	James Curran, Aaron Williams, Jerome Kelleher and Dave Barber (2021). multicool: Permutations of Multisets in Cool-Lex Order. R package version 0.1-12. https://CRAN.R-project.org/package=multicool
munsell	Charlotte Wickham (2018). munsell: Utilities for Using Munsell Colours. R package version 0.5.0. https://CRAN.R-project.org/package=munsell
mvtnorm	Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch, Fabian Scheipl, Torsten Hothorn (2021). mvtnorm: Multivariate Normal and t Distributions. R package version 1.1-3. URL http://CRAN.R-project.org/package=mvtnorm Alan Genz, Frank Bretz (2009), Computation of Multivariate Normal and t Probabilities. Lecture Notes in Statistics, Vol. 195., Springer-Verlag, Heidelberg. ISBN 978-3-642-01688-2
ncdf4	David Pierce (2021). ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. R package version 1.19. https://CRAN.R-project.org/package=ncdf4
nlme	José Pinheiro, Douglas Bates and R Core Team (2022). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-157. https://CRAN.R-project.org/package=nlme
nloptr	Steven G. Johnson, The NLopt nonlinear-optimization package, https://nlopt.readthedocs.io/en/latest/
nnet	Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
numDeriv	Paul Gilbert and Ravi Varadhan (2019). numDeriv: Accurate Numerical Derivatives. R package version 2016.8-1.1. https://CRAN.R-project.org/package=numDeriv
nycflights13	Hadley Wickham (2021). nycflights13: Flights that Departed NYC in 2013. R package version 1.0.2. https://CRAN.R-project.org/package=nycflights13
oai	Scott Chamberlain and Michal Bojanowski (2021). oai: General Purpose ‘Oai-PMH’ Services Client. R package version 0.3.2. https://CRAN.R-project.org/package=oai
openssl	Jeroen Ooms (2021). openssl: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL. R package version 1.4.6. https://CRAN.R-project.org/package=openssl
openxlsx	Philipp Schauberger and Alexander Walker (2021). openxlsx: Read, Write and Edit xlsx Files. R package version 4.2.5. https://CRAN.R-project.org/package=openxlsx
ordinal	Christensen, R. H. B. (2019). ordinal – Regression Models for Ordinal Data. R package version 2019.12-10. https://CRAN.R-project.org/package=ordinal.
parallel	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
parallelly	Henrik Bengtsson (2022). parallelly: Enhancing the ‘parallel’ Package. R package version 1.31.1. https://CRAN.R-project.org/package=parallelly
parsedate	Gábor Csárdi and Linus Torvalds (2021). parsedate: Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats. R package version 1.2.1. https://CRAN.R-project.org/package=parsedate
parsnip	Max Kuhn and Davis Vaughan (2022). parsnip: A Common API to Modeling and Analysis Functions. R package version 0.2.1. https://CRAN.R-project.org/package=parsnip
patchwork	Thomas Lin Pedersen (2020). patchwork: The Composer of Plots. R package version 1.1.1. https://CRAN.R-project.org/package=patchwork
pbdZMQ	Chen, W.-C., Schmidt, D., Heckendorf, C., and Ostrouchov, G. (2015) pbdZMQ: Programming with Big Data — Interface to ZeroMQ. R Package, URL https://cran.r-project.org/package=pbdZMQ Chen, W.-C. and Schmidt, D. (2015) A Quick Guide for the pbdZMQ Package. R Vignette, URL https://cran.r-project.org/package=pbdZMQ
pbkrtest	Ulrich Halekoh, Søren Højsgaard (2014). A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models – The R Package pbkrtest. Journal of Statistical Software, 59(9), 1-30. URL https://www.jstatsoft.org/v59/i09/.
pdp	Brandon M. Greenwell (2017). pdp: An R Package for Constructing Partial Dependence Plots. The R Journal, 9(1), 421–436. URL https://journal.r-project.org/archive/2017/RJ-2017-016/index.html.
permute	Gavin L. Simpson (2022). permute: Functions for Generating Restricted Permutations of Data. R package version 0.9-7. https://CRAN.R-project.org/package=permute
pillar	Kirill Müller and Hadley Wickham (2022). pillar: Coloured Formatting for Columns. R package version 1.7.0. https://CRAN.R-project.org/package=pillar
Pingr	Gábor Csárdi (2020). pingr: Check if a Remote Computer is Up. R package version 2.0.1. https://CRAN.R-project.org/package=pingr
pkgbuild	Hadley Wickham, Jim Hester and Gábor Csárdi (2021). pkgbuild: Find Tools Needed to Build R Packages. R package version 1.3.1. https://CRAN.R-project.org/package=pkgbuild
pkgconfig	Gábor Csárdi (2019). pkgconfig: Private Configuration for ‘R’ Packages. R package version 2.0.3. https://CRAN.R-project.org/package=pkgconfig
pkgdown	Hadley Wickham, Jay Hesselberth and Maëlle Salmon (2022). pkgdown: Make Static HTML Documentation for a Package. R package version 2.0.3. https://CRAN.R-project.org/package=pkgdown
pkgload	Hadley Wickham, Winston Chang, Jim Hester and Lionel Henry (2021). pkgload: Simulate Package Installation and Attach. R package version 1.2.4. https://CRAN.R-project.org/package=pkgload
plogr	Kirill Müller (2018). plogr: The ‘plog’ C++ Logging Library. R package version 0.2.0. https://CRAN.R-project.org/package=plogr
plotmo	Stephen Milborrow (2021). plotmo: Plot a Model’s Residuals, Response, and Partial Dependence Plots. R package version 3.6.1. https://CRAN.R-project.org/package=plotmo
plotrix	Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4): 8-12.
plyr	Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data Analysis. Journal of Statistical Software, 40(1), 1-29. URL http://www.jstatsoft.org/v40/i01/.
png	Simon Urbanek (2013). png: Read and write PNG images. R package version 0.1-7. https://CRAN.R-project.org/package=png
poibin	Yili Hong and R Core Team (2020). poibin: The Poisson Binomial Distribution. R package version 1.5. https://CRAN.R-project.org/package=poibin
polspline	Charles Kooperberg (2020). polspline: Polynomial Spline Routines. R package version 1.1.19. https://CRAN.R-project.org/package=polspline
polyclip	Angus Johnson and Adrian Baddeley (2019). polyclip: Polygon Clipping. R package version 1.10-0. https://CRAN.R-project.org/package=polyclip
praise	Gabor Csardi and Sindre Sorhus (2015). praise: Praise Users. R package version 1.0.0. https://CRAN.R-project.org/package=praise
PresenceAbsence	Freeman, E. A. and Moisen, G. (2008). PresenceAbsence: An R Package for Presence-Absence Model Analysis. Journal of Statistical Software, 23(11):1-31. http://www.jstatsoft.org/v23/i11
prettyunits	Gabor Csardi (2020). prettyunits: Pretty, Human Readable Formatting of Quantities. R package version 1.1.1. https://CRAN.R-project.org/package=prettyunits
pROC	Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez and Markus Müller (2011). pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics, 12, p. 77. DOI: 10.1186/1471-2105-12-77 http://www.biomedcentral.com/1471-2105/12/77/
processx	Gábor Csárdi and Winston Chang (2021). processx: Execute and Control System Processes. R package version 3.5.2. https://CRAN.R-project.org/package=processx
prodlim	Thomas A. Gerds (2019). prodlim: Product-Limit Estimation for Censored Event History Analysis. R package version 2019.11.13. https://CRAN.R-project.org/package=prodlim
profvis	Thomas A. Gerds (2019). prodlim: Product-Limit Estimation for Censored Event History Analysis. R package version 2019.11.13. https://CRAN.R-project.org/package=prodlim
progress	Gábor Csárdi and Rich FitzJohn (2019). progress: Terminal Progress Bars. R package version 1.2.2. https://CRAN.R-project.org/package=progress
progressr	Henrik Bengtsson (2021). progressr: An Inclusive, Unifying API for Progress Updates. R package version 0.10.0. https://CRAN.R-project.org/package=progressr
promises	Joe Cheng (2021). promises: Abstractions for Promise-Based Asynchronous Programming. R package version 1.2.0.1. https://CRAN.R-project.org/package=promises
proxy	David Meyer and Christian Buchta (2021). proxy: Distance and Similarity Measures. R package version 0.4-26. https://CRAN.R-project.org/package=proxy
ps	Jay Loden, Dave Daeschler, Giampaolo Rodola’ and Gábor Csárdi (2021). ps: List, Query, Manipulate System Processes. R package version 1.6.0. https://CRAN.R-project.org/package=ps
purrr	Lionel Henry and Hadley Wickham (2020). purrr: Functional Programming Tools. R package version 0.3.4. https://CRAN.R-project.org/package=purrr
quadprog	S original by Berwin A. Turlach R port by Andreas Weingessel <Andreas.Weingessel@ci.tuwien.ac.at> Fortran contributions from Cleve Moler dpodi/LINPACK) (2019). quadprog: Functions to Solve Quadratic Programming Problems. R package version 1.5-8. https://CRAN.R-project.org/package=quadprog
quantmod	Jeffrey A. Ryan and Joshua M. Ulrich (2022). quantmod: Quantitative Financial Modelling Framework. R package version 0.4.20. https://CRAN.R-project.org/package=quantmod
quantreg	Roger Koenker (2022). quantreg: Quantile Regression. R package version 5.88. https://CRAN.R-project.org/package=quantreg
R.methodsS3	Bengtsson, H. The R.oo package – Object-Oriented Programming with References Using Standard R Code, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), ISSN 1609-395X, Hornik, K.; Leisch, F. & Zeileis, A. (ed.), 2003
R.oo	Bengtsson, H. The R.oo package – Object-Oriented Programming with References Using Standard R Code, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), ISSN 1609-395X, Hornik, K.; Leisch, F. & Zeileis, A. (ed.), 2003
R.utils	Henrik Bengtsson (2021). R.utils: Various Programming Utilities. R package version 2.11.0. https://CRAN.R-project.org/package=R.utils
R6	Winston Chang (2021). R6: Encapsulated Classes with Reference Semantics. R package version 2.5.1. https://CRAN.R-project.org/package=R6
randomForest	A. Liaw and M. Wiener (2002). Classification and Regression by randomForest. R News 2(3), 18–22.
randomForestSRC	Ishwaran H. and Kogalur U.B. (2022). Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC), R package version 3.1.0. Ishwaran H. and Kogalur U.B. (2007). Random survival forests for R. R News 7(2), 25–31. Ishwaran H., Kogalur U.B., Blackstone E.H. and Lauer M.S. (2008). Random survival forests. Ann. Appl. Statist. 2(3), 841–860.
rangeModelMetadata	Cory Merow, Brian Maitner, Hannah Owens, Jamie Kass, Brian Enquist, Rob Guralnik, Damaris Zurrell and Christian Koenig (2021). rangeModelMetadata: Provides Templates for Metadata Files Associated with Species Range Models. R package version 0.1.4. https://CRAN.R-project.org/package=rangeModelMetadata
rapidjsonr	David Cooley (2020). rapidjsonr: ‘Rapidjson’ C++ Header Files. R package version 1.2.0. https://CRAN.R-project.org/package=rapidjsonr
rappdirs	Sridhar Ratnakumar, Trent Mick and Trevor Davis (2021). rappdirs: Application Directories: Determine Where to Save Data, Caches, and Logs. R package version 0.3.3. https://CRAN.R-project.org/package=rappdirs
raster	Robert J. Hijmans (2020). raster: Geographic Data Analysis and Modeling. R package version 3.1-5. https://CRAN.Rproject.org/package=raster
rasterVis	Oscar Perpinan Lamigueiro and Robert Hijmans (2022), rasterVis. R package version 0.51.2.
rbison	Scott Chamberlain (2020). rbison: Interface to the ‘USGS’ ‘BISON’ API. R package version 1.0.0. https://CRAN.R-project.org/package=rbison
rcmdcheck	Gábor Csárdi (2021). rcmdcheck: Run ‘R CMD check’ from ‘R’ and Capture Results. R package version 1.4.0. https://CRAN.Rproject.org/package=rcmdcheck
RColorBrewer	Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://CRAN.R-project.org/package=RColorBrewer
Rcpp	Dirk Eddelbuettel and Romain Francois (2011). Rcpp: Seamless R and C++ Integration. Journal of Statistical Software, 40(8), 1-18. URL http://www.jstatsoft.org/v40/i08/. Eddelbuettel, Dirk (2013) Seamless R and C++ Integration with Rcpp. Springer, New York. ISBN 978-1-4614-6867-7. Dirk Eddelbuettel and James Joseph Balamuta (2017). Extending R with C++: A Brief Introduction to Rcpp. PeerJ Preprints 5:e3188v1. URL https://doi.org/10.7287/peerj.preprints.3188v1.
RcppArmadillo	Dirk Eddelbuettel, Conrad Sanderson (2014). RcppArmadillo: Accelerating R with high-performance C++ linear algebra. Computational Statistics and Data Analysis, Volume 71, March 2014, pages 1054-1063. URL http://dx.doi.org/10.1016/j.csda.2013.02.005
RcppEigen	Douglas Bates, Dirk Eddelbuettel (2013). Fast and Elegant Numerical Linear Algebra Using the RcppEigen Package. Journal of Statistical Software, 52(5), 1-24. URL https://www.jstatsoft.org/v52/i05/.
RCurl	Duncan Temple Lang (2022). RCurl: General Network (HTTP/FTP/…) Client Interface for R. R package version 1.98-1.6. https://CRAN.R-project.org/package=Rcurl
readr	Hadley Wickham, Jim Hester and Romain Francois (2018). readr: Read Rectangular Text Data. R package version 1.3.1. https://CRAN.R-project.org/package=readr
readxl	Hadley Wickham and Jennifer Bryan (2022). readxl: Read Excel Files. R package version 1.4.0. https://CRAN.R-project.org/package=readxl
rebird	Rafael Maia, Scott Chamberlain, Andy Teucher and Sebastian Pardo (2021). rebird: R Client for the eBird Database of Bird Observations. R package version 1.3.0. https://CRAN.R-project.org/package=rebird
recipes	Max Kuhn and Hadley Wickham (2022). recipes: Preprocessing and Feature Engineering Steps for Modeling. R package version 0.2.0. https://CRAN.R-project.org/package=recipes
rematch	Gabor Csardi (2016). rematch: Match Regular Expressions with a Nicer ‘API’. R package version 1.0.1. https://CRAN.R-project.org/package=rematch
rematch2	Gábor Csárdi (2020). rematch2: Tidy Output from Regular Expression Matching. R package version 2.1.2. https://CRAN.R-project.org/package=rematch2
remotes	Gábor Csárdi, Jim Hester, Hadley Wickham, Winston Chang, Martin Morgan and Dan Tenenbaum (2021). remotes: R Package Installation from Remote Repositories, Including ‘GitHub’. R package version 2.4.2. https://CRAN.R-project.org/package=remotes
repr	Philipp Angerer, Thomas Kluyver and Jan Schulz (2022). repr: Serializable Representations. R package version 1.1.4. https://CRAN.R-project.org/package=repr
reprex	Jennifer Bryan, Jim Hester, David Robinson and Hadley Wickham (2021). reprex: Prepare Reproducible Example Code via the Clipboard. R package version 2.0.1. https://CRAN.R-project.org/package=reprex
reshape	H. Wickham. Reshaping data with the reshape package. Journal of Statistical Software, 21(12), 2007.
reshape2	Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/.
rex	Kevin Ushey, Jim Hester and Robert Krzyzanowski (2021). rex: Friendly Regular Expressions. R package version 1.2.1. https://CRAN.R-project.org/package=rex
rgbif	Chamberlain S, Barve V, Mcglinn D, Oldoni D, Desmet P, Geffert L, Ram K (2022). _rgbif: Interface to the Global Biodiversity Information Facility API_. R package version 3.7.2, <URL: https://CRAN.R-project.org/package=rgbif>. Chamberlain S, Boettiger C (2017). “R Python, and Ruby clients for GBIF species occurrence data.” _PeerJ PrePrints_. <URL: https://doi.org/10.7287/peerj.preprints.3304v1>.
rgdal	Roger Bivand, Tim Keitt and Barry Rowlingson (2019). rgdal: Bindings for the ‘Geospatial’ Data Abstraction Library. R package version 1.4-8. https://CRAN.R-project.org/package=rgdal
rgeos	Roger Bivand and Colin Rundel (2020). rgeos: Interface to Geometry Engine – Open Source (‘GEOS’). R package version 0.5-3. https://CRAN.R-project.org/package=rgeos
RgoogleMaps	Markus Loecher and Karl Ropkins (2015). RgoogleMaps and loa: Unleashing R Graphics Power on Map Tiles. Journal of Statistical Software 63(4), 1-18. URL http://www.jstatsoft.org/v63/i04/.
rhub	Gábor Csárdi and Maëlle Salmon (2019). rhub: Connect to ‘R-hub’. R package version 1.1.1. https://CRAN.R-project.org/package=rhub
ridigbio	Francois Michonneau and Matthew Collins (2017). ridigbio: Interface to the iDigBio Data API. R package version 0.3.5. https://CRAN.R-project.org/package=ridigbio
rio	Chung-hong Chan, Geoffrey CH Chan, Thomas J. Leeper, and Jason Becker (2021). rio: A Swiss-army knife for data file I/O. R package version 0.5.29.
rJava	Simon Urbanek (2021). rJava: Low-Level R to Java Interface. R package version 1.0-6. https://CRAN.R-project.org/package=rJava
rjson	Alex Couture-Beil (2022). rjson: JSON for R. R package version 0.2.21. https://CRAN.R-project.org/package=rjson
rlang	Lionel Henry and Hadley Wickham (2022). rlang: Functions for Base Types and Core R and ‘Tidyverse’ Features. R package version 1.0.2. https://CRAN.R-project.org/package=rlang
rmarkdown	Yihui Xie and J.J. Allaire and Garrett Grolemund (2018). R Markdown: The Definitive Guide. Chapman and Hall/CRC. ISBN 9781138359338. URL https://bookdown.org/yihui/rmarkdown. Yihui Xie and Christophe Dervieux and Emily Riederer (2020). R Markdown Cookbook. Chapman and Hall/CRC. ISBN 9780367563837. URL https://bookdown.org/yihui/rmarkdown-cookbook.
rms	Frank E Harrell Jr (2021). rms: Regression Modeling Strategies. R package version 6.2-0. https://CRAN.R-project.org/package=rms
RMySQL	Jeroen Ooms, David James, Saikat DebRoy, Hadley Wickham and Jeffrey Horner (2021). RMySQL: Database Interface and ‘MySQL’ Driver for R. R package version 0.10.23. https://CRAN.R-project.org/package=RMySQL
RODBC	Brian Ripley and Michael Lapsley (2021). RODBC: ODBC Database Access. R package version 1.3-19. https://CRAN.R-project.org/package=RODBC
roxygen2	Hadley Wickham, Peter Danenberg, Gábor Csárdi and Manuel Eugster (2021). roxygen2: In-Line Documentation for R. R package version 7.1.2. https://CRAN.R-project.org/package=roxygen2
rpart	Terry Therneau and Beth Atkinson (2022). rpart: Recursive Partitioning and Regression Trees. R package version 4.1.16. https://CRAN.R-project.org/package=rpart
RPostgreSQL	Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga and Neil Tiffin (2021). RPostgreSQL: R Interface to the ‘PostgreSQL’ Database System. R package version 0.7-3. https://CRAN.R-project.org/package=RPostgreSQL
rprojroot	Kirill Müller (2022). rprojroot: Finding Files in Project Subdirectories. R package version 2.0.3. https://CRAN.R-project.org/package=rprojroot
rsample	Julia Silge, Fanny Chow, Max Kuhn and Hadley Wickham (2021). rsample: General Resampling Infrastructure. R package version 0.1.1. https://CRAN.R-project.org/package=rsample
RSQLite	Kirill Müller, Hadley Wickham, David A. James and Seth Falcon (2022). RSQLite: SQLite Interface for R. R package version 2.2.14. https://CRAN.R-project.org/package=RSQLite
rstudioapi	Kevin Ushey, JJ Allaire, Hadley Wickham and Gary Ritchie (2020). rstudioapi: Safely Access the RStudio API. R package version 0.13. https://CRAN.R-project.org/package=rstudioapi
RUnit	Matthias Burger, Klaus Juenemann and Thomas Koenig (2018). RUnit: R Unit Test Framework. R package version 0.4.32. https://CRAN.R-project.org/package=Runit
rversions	Gábor Csárdi (2021). rversions: Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’. R package version 2.1.1. https://CRAN.R-project.org/package=rversions
rvertnet	Scott Chamberlain (2021). rvertnet: Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records. R package version 0.8.2. https://CRAN.R-project.org/package=rvertnet
rvest	Hadley Wickham (2021). rvest: Easily Harvest (Scrape) Web Pages. R package version 1.0.2. https://CRAN.R-project.org/package=rvest
s2	Dewey Dunnington, Edzer Pebesma and Ege Rubak (2021). s2: Spherical Geometry Operators Using the S2 Geometry Library. R package version 1.0.7. https://CRAN.R-project.org/package=s2
sandwich	Zeileis A, Köll S, Graham N (2020). “Various Versatile Variances: An Object-Oriented Implementation of Clustered Covariances in R.” _Journal of Statistical Software_, 95(1), 1-36. doi: 10.18637/jss.v095.i01 (URL: https://doi.org/10.18637/jss.v095.i01). If sandwich is applied to lm() models, please also cite: Zeileis A (2004). “Econometric Computing with HC and HAC Covariance Matrix Estimators.” _Journal of Statistical Software_, 11(10), 1-17. doi: 10.18637/jss.v011.i10 (URL: https://doi.org/10.18637/jss.v011.i10). If sandwich is applied to models other than lm(), please also cite: Zeileis A (2006). “Object-Oriented Computation of Sandwich Estimators.” _Journal of Statistical Software_, 16(9), 1-16. doi: 10.18637/jss.v016.i09 (URL: https://doi.org/10.18637/jss.v016.i09).
sass	Joe Cheng, Timothy Mastny, Richard Iannone, Barret Schloerke and Carson Sievert (2022). sass: Syntactically Awesome Style Sheets (‘Sass’). R package version 0.4.1. https://CRAN.R-project.org/package=sass
scales	Hadley Wickham and Dana Seidel (2022). scales: Scale Functions for Visualization. R package version 1.2.0. https://CRAN.R-project.org/package=scales
SDMTools	VanDerWal J, Falconi A, Januchowski S, Shoo L and Storlie C (2014). SDMTools. http://www.rforge.net/SDMTools/
selectr	Potter S (2012). “Introducing the selectr Package.” The University of Auckland, Auckland, New Zealand. <URL: http://stattech.wordpress.fos.auckland.ac.nz/2012-10-introducing-the-selectr-package/>.
sessioninfo	Hadley Wickham, Winston Chang, Robert Flight, Kirill Müller and Jim Hester (2021). sessioninfo: R Session Information. R package version 1.2.2. https://CRAN.R-project.org/package=sessioninfo
sf	Pebesma, E., 2018. Simple Features for R: Standardized Support for Spatial Vector Data. The R Journal 10 (1), 439-446, https://doi.org/10.32614/RJ-2018-009
sfheaders	David Cooley (2020). sfheaders: Converts Between R Objects and Simple Feature Objects. R package version 0.4.0. https://CRAN.R-project.org/package=sfheaders
sgeostat	S original by James J. Majure Iowa State University and R port + extensions by Albrecht Gebhardt (2016). sgeostat: An Object-Oriented Framework for Geostatistical Modeling in S+. R package version 1.0-27. https://CRAN.R-project.org/package=sgeostat
shape	Karline Soetaert (2021). shape: Functions for Plotting Graphical Shapes, Colors. R package version 1.4.6. https://CRAN.R-project.org/package=shape
shiny	Winston Chang, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke, Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert and Barbara Borges (2021). shiny: Web Application Framework for R. R package version 1.7.1. https://CRAN.R-project.org/package=shiny
slider	Davis Vaughan (2021). slider: Sliding Window Functions. R package version 0.2.2. https://CRAN.R-project.org/package=slider
snow	Luke Tierney, A. J. Rossini, Na Li and H. Sevcikova (2021). snow: Simple Network of Workstations. R package version 0.4-4. https://CRAN.R-project.org/package=snow
snowfall	Jochen Knaus (2015). snowfall: Easier cluster computing (based on snow).. R package version 1.84-6.1. https://CRAN.R-project.org/package=snowfall
sourcetools	Kevin Ushey (2018). sourcetools: Tools for Reading, Tokenizing and Parsing R Code. R package version 0.1.7. https://CRAN.R-project.org/package=sourcetools
sp	Pebesma, E.J., R.S. Bivand, 2005. Classes and methods for spatial data in R. R News 5 (2), https://cran.r-project.org/doc/Rnews/. Roger S. Bivand, Edzer Pebesma, Virgilio Gomez-Rubio, 2013. Applied spatial data analysis with R, Second edition. Springer, NY. https://asdar-book.org/
spacetime	Edzer Pebesma (2012). spacetime: Spatio-Temporal Data in R. Journal of Statistical Software, 51(7), 1-30. URL https://www.jstatsoft.org/v51/i07/. Roger S. Bivand, Edzer Pebesma, Virgilio Gomez-Rubio, 2013. Applied spatial data analysis with R, Second edition. Springer, NY. https://asdar-book.org/
spam	Furrer, R., Flury R. and Gerber, F. (2022). spam: SPArse Matrix. R package version 2.8-0. URL https://CRAN.R-project.org/package=spam Reinhard Furrer, Stephan R. Sain (2010). spam: A Sparse Matrix R Package with Emphasis on MCMC Methods for Gaussian Markov Random Fields. Journal of Statistical Software, 36(10), 1-25. https://doi.org/10.18637/jss.v036.i10. Florian Gerber, Reinhard Furrer (2015). Pitfalls in the Implementation of Bayesian Hierarchical Modeling of Areal Count Data: An Illustration Using BYM and Leroux Models. Journal of Statistical Software, Code Snippets, 63(1), 1-32. https://doi.org/10.18637/jss.v063.c01. F. Gerber, K. Moesinger, R. Furrer (2017), Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data. Computer & Geoscience 104, 109-119, https://doi.org/10.1016/j.cageo.2016.11.015.
SparseM	Roger Koenker (2021). SparseM: Sparse Linear Algebra. R package version 1.81. https://CRAN.R-project.org/package=SparseM
spatial	Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
spatialwidget	David Cooley (2020). spatialwidget: Formats Spatial Data for Use in Htmlwidgets. R package version 0.2.3. https://CRAN.R-project.org/package=spatialwidget
spatstat	Adrian Baddeley, Ege Rubak, Rolf Turner (2015). Spatial Point Patterns: Methodology and Applications with R. London: Chapman and Hall/CRC Press, 2015. URL https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/9781482210200/ If you use hybrid models, please also cite: Adrian Baddeley, Rolf Turner, Jorge Mateu, Andrew Bevan (2013). Hybrids of Gibbs Point Process Models and Their Implementation. Journal of Statistical Software, 55(11), 1-43. DOI: 10.18637/jss.v055.i11 In survey articles, please cite the original paper on spatstat: Adrian Baddeley, Rolf Turner (2005). spatstat: An R Package for Analyzing Spatial Point Patterns. Journal of Statistical Software 12(6), 1-42. DOI: 10.18637/jss.v012.i06
spatstat.core	Adrian Baddeley, Ege Rubak, Rolf Turner (2015). Spatial Point Patterns: Methodology and Applications with R. London: Chapman and Hall/CRC Press, 2015. URL https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/9781482210200/
spatstat.data	Adrian Baddeley, Rolf Turner and Ege Rubak (2022). spatstat.data: Datasets for ‘spatstat’ Family. R package version 2.2-0. https://CRAN.R-project.org/package=spatstat.data
spatstat.geom	Adrian Baddeley, Ege Rubak, Rolf Turner (2015). Spatial Point Patterns: Methodology and Applications with R. London: Chapman and Hall/CRC Press, 2015. URL https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/9781482210200/
spatstat.linnet	Adrian Baddeley, Ege Rubak, Rolf Turner (2015). Spatial Point Patterns: Methodology and Applications with R. London: Chapman and Hall/CRC Press, 2015. URL https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/9781482210200/
spatstat.sparse	Adrian Baddeley, Rolf Turner and Ege Rubak (2022). spatstat.sparse: Sparse Three-Dimensional Arrays and Linear Algebra Utilities. R package version 2.1-1. https://CRAN.R-project.org/package=spatstat.sparse
spatstat.utils	Adrian Baddeley, Rolf Turner and Ege Rubak (2022). spatstat.utils: Utility Functions for ‘spatstat’. R package version 2.3-1. https://CRAN.R-project.org/package=spatstat.utils
spelling	Jeroen Ooms and Jim Hester (2020). spelling: Tools for Spell Checking in R. R package version 2.2. https://CRAN.R-project.org/package=spelling
splancs	Barry Rowlingson and Peter Diggle (2022). splancs: Spatial and Space-Time Point Pattern Analysis. R package version 2.01-43. https://CRAN.R-project.org/package=splancs
splines	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
spocc	Scott Chamberlain (2021). spocc: Interface to Species Occurrence Data Sources. R package version 1.2.0. https://CRAN.R-project.org/package=spocc
spThin	Aiello-Lammens, M. E., Boria, R. A., Radosavljevic, A. , Vilela, B. and Anderson, R. P. (2015). spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography, 38: 541-545. URL https://onlinelibrary.wiley.com/doi/10.1111/ecog.01132.
SQUAREM	Du Y, Varadhan R (2020). “SQUAREM: An R Package for Off-the-Shelf Acceleration of EM, MM and Other EM-Like Monotone Algorithms.” _Journal of Statistical Software_, 92(7), 1-41. doi: 10.18637/jss.v092.i07 (URL: https://doi.org/10.18637/jss.v092.i07).
stars	Edzer Pebesma (2021). stars: Spatiotemporal Arrays, Raster and Vector Data Cubes. R package version 0.5-5. https://CRAN.R-project.org/package=stars
statmod	Giner, G, and Smyth, GK (2016). statmod: probability calculations for the inverse Gaussian distribution. R Journal 8(1), 339-351. (pinvgauss, qinvgauss, dinvguass and rinvgauss functions) Phipson B, and Smyth GK (2010). Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology, Volume 9, Issue 1, Article 39. (permp function) Hu, Y, and Smyth, GK (2009). ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. Journal of Immunological Methods 347, 70-78. (elda and limdil functions) Smyth, G. K. (1998). Optimization and nonlinear equations. In: Encyclopedia of Biostatistics, P. Armitage and T. Colton (eds.), Wiley, London, pp. 3174-3180. (glmgam.fit, glmnb.fit and fitNBP functions) Smyth, G. K. (1998). Numerical integration. In: Encyclopedia of Biostatistics, P. Armitage and T. Colton (eds.), Wiley, London, pp. 3088-3095. (gauss.quad and gauss.quad.prob functions) Smyth, G. K. (2002). An efficient algorithm for REML in heteroscedastic regression. Journal of Computational and Graphical Statistics 11, 836-847. (remlscore, randomizedBlock, and mixedModel2 functions) Dunn, P. K., and Smyth, G. K. (1996). Randomized quantile residuals. J. Comput. Graph. Statist., 5, 236-244. (qresid functions)
stats	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
stats4	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
stringdist	van der Loo M (2014). “The stringdist package for approximate string matching.” _The R Journal_, 6, 111-122. <URL: https://CRAN.R-project.org/package=stringdist>.
stringi	Gagolewski M (2021). “stringi: Fast and portable character string processing in R.” _Journal of Statistical Software_. to appear. Gagolewski M (2021). _stringi: Fast and portable character string processing in R_. R package version 1.7.6, <URL: https://stringi.gagolewski.com/>.
stringr	Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0. https://CRAN.R-project.org/package=stringr
survival	Therneau T (2022). _A Package for Survival Analysis in R_. R package version 3.3-1, <URL: https://CRAN.R-project.org/package=survival>. Terry M. Therneau, Patricia M. Grambsch (2000). _Modeling Survival Data: Extending the Cox Model_. Springer, New York. ISBN 0-387-98784-3.
svglite	Hadley Wickham, Lionel Henry, Thomas Lin Pedersen, T Jake Luciani, Matthieu Decorde and Vaudor Lise (2022). svglite: An ‘SVG’ Graphics Device. R package version 2.1.0. https://CRAN.R-project.org/package=svglite
svMisc	Grosjean, Ph. (2022). SciViews-R. UMONS, Mons, Belgium. URL https://www.sciviews.org/SciViews-R/.
sys	Jeroen Ooms (2020). sys: Powerful and Reliable Tools for Running System Commands in R. R package version 3.4. https://CRAN.R-project.org/package=sys
systemfonts	Thomas Lin Pedersen, Jeroen Ooms and Devon Govett (2022). systemfonts: System Native Font Finding. R package version 1.0.4. https://CRAN.R-project.org/package=systemfonts
tcltk	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
TeachingDemos	Greg Snow (2020). TeachingDemos: Demonstrations for Teaching and Learning. R package version 2.12. https://CRAN.R-project.org/package=TeachingDemos
tensor	Jonathan Rougier (2012). tensor: Tensor product of arrays. R package version 1.5. https://CRAN.R-project.org/package=tensor
terra	Robert J. Hijmans (2022). terra: Spatial Data Analysis. R package version 1.5-21. https://CRAN.R-project.org/package=terra
testthat	Hadley Wickham. testthat: Get Started with Testing. The R Journal, vol. 3, no. 1, pp. 5–10, 2011
TH.data	Torsten Hothorn (2022). TH.data: TH’s Data Archive. R package version 1.1-1. https://CRAN.R-project.org/package=TH.data
tibble	Kirill Müller and Hadley Wickham (2022). tibble: Simple Data Frames. R package version 3.1.7. https://CRAN.R-project.org/package=tibble
tidymodels	Kuhn et al., (2020). Tidymodels: a collection of packages for modeling and machine learning using tidyverse principles. https://www.tidymodels.org
tidyr	Hadley Wickham and Maximilian Girlich (2022). tidyr: Tidy Messy Data. R package version 1.2.0. https://CRAN.R-project.org/package=tidyr
tidyselect	Lionel Henry and Hadley Wickham (2022). tidyselect: Select from a Set of Strings. R package version 1.1.2. https://CRAN.R-project.org/package=tidyselect
tidyverse	Wickham et al., (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686, https://doi.org/10.21105/joss.01686
timeDate	Diethelm Wuertz, Tobias Setz, Yohan Chalabi, Martin Maechler and Joe W. Byers (2018). timeDate: Rmetrics – Chronological and Calendar Objects. R package version 3043.102. https://CRAN.R-project.org/package=timeDate
tinytex	Yihui Xie (2022). tinytex: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents. R package version 0.38. Yihui Xie (2019) TinyTeX: A lightweight, cross-platform, and easy-to-maintain LaTeX distribution based on TeX Live. TUGboat 40 (1): 30–32. https://tug.org/TUGboat/Contents/contents40-1.html
tmap	Tennekes M (2018). “tmap: Thematic Maps in R.” _Journal of Statistical Software_, 84(6), 1-39. doi: 10.18637/jss.v084.i06 (URL: https://doi.org/10.18637/jss.v084.i06).
tmaptools	Martijn Tennekes (2021). tmaptools: Thematic Map Tools. R package version 3.1-1. https://CRAN.R-project.org/package=tmaptools
tools	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
triebeard	Oliver Keyes, Drew Schmidt and Yuuki Takano (2016). triebeard: ‘Radix’ Trees in ‘Rcpp’. R package version 0.3.0. https://CRAN.R-project.org/package=triebeard
tripack	Fortran code by R. J. Renka. R functions by Albrecht Gebhardt. With contributions from Stephen Eglen <stephen@anc.ed.ac.uk>, Sergei Zuyev and Denis White (2020). tripack: Triangulation of Irregularly Spaced Data. R package version 1.3-9.1. https://CRAN.R-project.org/package=tripack
tseries	Adrian Trapletti and Kurt Hornik (2022). tseries: Time Series Analysis and Computational Finance. R package version 0.10-51.
TTR	Joshua Ulrich (2021). TTR: Technical Trading Rules. R package version 0.24.3. https://CRAN.R-project.org/package=TTR
tune	Max Kuhn (2022). tune: Tidy Tuning Tools. R package version 0.2.0. https://CRAN.R-project.org/package=tune
tzdb	Davis Vaughan (2022). tzdb: Time Zone Database Information. R package version 0.3.0. https://CRAN.R-project.org/package=tzdb
ucminf	Hans Bruun Nielsen and Stig Bousgaard Mortensen (2016). ucminf: General-Purpose Unconstrained Non-Linear Optimization. R package version 1.1-4. https://CRAN.R-project.org/package=ucminf
units	Pebesma E, Mailund T, Hiebert J (2016). “Measurement Units in R.” _R Journal_, 8(2), 486-494. doi: 10.32614/RJ-2016-061 (URL: https://doi.org/10.32614/RJ-2016-061).
urca	Pfaff, B. (2008) Analysis of Integrated and Cointegrated Time Series with R. Second Edition. Springer, New York. ISBN 0-387-27960-1
urltools	Os Keyes, Jay Jacobs, Drew Schmidt, Mark Greenaway, Bob Rudis, Alex Pinto, Maryam Khezrzadeh, Peter Meilstrup, Adam M. Costello, Jeff Bezanson, Peter Meilstrup and Xueyuan Jiang (2019). urltools: Vectorised Tools for URL Handling and Parsing. R package version 1.7.3. https://CRAN.R-project.org/package=urltools
usdm	Naimi B, Hamm Na, Groen TA, Skidmore AK, Toxopeus AG (2014). “Where is positional uncertainty a problem for species distribution modelling.” _Ecography_, 37, 191-203. doi: 10.1111/j.1600-0587.2013.00205.x (URL: https://doi.org/10.1111/j.1600-0587.2013.00205.x).
usethis	Hadley Wickham, Jennifer Bryan and Malcolm Barrett (2021). usethis: Automate Package and Project Setup. R package version 2.1.5. https://CRAN.R-project.org/package=usethis
utf8	Patrick O. Perry (2021). utf8: Unicode Text Processing. R package version 1.2.2. https://CRAN.R-project.org/package=utf8
utils	R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
uuid	Simon Urbanek and Theodore Ts’o (2022). uuid: Tools for Generating and Handling of UUIDs. R package version 1.1-0. https://CRAN.R-project.org/package=uuid
vctrs	Hadley Wickham, Lionel Henry and Davis Vaughan (2022). vctrs: Vector Helpers. R package version 0.4.1. https://CRAN.R-project.org/package=vctrs
vdiffr	Lionel Henry, Thomas Lin Pedersen, T Jake Luciani, Matthieu Decorde and Vaudor Lise (2022). vdiffr: Visual Regression Testing and Graphical Diffing. R package version 1.0.4. https://CRAN.R-project.org/package=vdiffr
vegan	Jari Oksanen, Gavin L. Simpson, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R.B. O’Hara, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner, Matt Barbour, Michael Bedward, Ben Bolker, Daniel Borcard, Gustavo Carvalho, Michael Chirico, Miquel De Caceres, Sebastien Durand, Heloisa Beatriz Antoniazi Evangelista, Rich FitzJohn, Michael Friendly, Brendan Furneaux, Geoffrey Hannigan, Mark O. Hill, Leo Lahti, Dan McGlinn, Marie-Helene Ouellette, Eduardo Ribeiro Cunha, Tyler Smith, Adrian Stier, Cajo J.F. Ter Braak and James Weedon (2022). vegan: Community Ecology Package. R package version 2.6-2. https://CRAN.R-project.org/package=vegan
viridis	Simon Garnier, Noam Ross, Robert Rudis, Antônio P. Camargo, Marco Sciaini, and Cédric Scherer (2021). Rvision – Colorblind-Friendly Color Maps for R. R package version 0.6.2.
viridisLite	Simon Garnier, Noam Ross, Robert Rudis, Antônio P. Camargo, Marco Sciaini, and Cédric Scherer (2021). Rvision – Colorblind-Friendly Color Maps for R. R package version 0.4.0.
visreg	Breheny P and Burchett W (2017). Visualization of Regression Models Using visreg. The R Journal, 9: 56-71.
vroom	Jim Hester, Hadley Wickham and Jennifer Bryan (2021). vroom: Read and Write Rectangular Text Data Quickly. R package version 1.5.7. https://CRAN.R-project.org/package=vroom
waldo	Hadley Wickham (2022). waldo: Find Differences Between R Objects. R package version 0.4.0. https://CRAN.R-project.org/package=waldo
warp	Davis Vaughan (2020). warp: Group Dates. R package version 0.2.0. https://CRAN.R-project.org/package=warp
wellknown	Scott Chamberlain and Os Keyes (2021). wellknown: Convert Between ‘WKT’ and ‘GeoJSON’. R package version 0.7.4. https://CRAN.R-project.org/package=wellknown
whisker	Edwin de Jonge (2019). whisker: {{mustache}} for R, Logicless Templating. R package version 0.4. https://CRAN.R-project.org/package=whisker
whoami	Gábor Csárdi (2019). whoami: Username, Full Name, Email Address, ‘GitHub’ Username of the Current User. R package version 1.3.0. https://CRAN.R-project.org/package=whoami
widgetframe	Bhaskar Karambelkar (2017). widgetframe: ‘Htmlwidgets’ in Responsive ‘iframes’. R package version 0.3.1. https://CRAN.R-project.org/package=widgetframe
withr	Jim Hester, Lionel Henry, Kirill Müller, Kevin Ushey, Hadley Wickham and Winston Chang (2022). withr: Run Code ‘With’ Temporarily Modified Global State. R package version 2.5.0. https://CRAN.R-project.org/package=withr
wk	Dewey Dunnington and Edzer Pebesma (2022). wk: Lightweight Well-Known Geometry Parsing. R package version 0.6.0. https://CRAN.R-project.org/package=wk
workflows	Davis Vaughan (2022). workflows: Modeling Workflows. R package version 0.2.6. https://CRAN.R-project.org/package=workflows
workflowsets	Max Kuhn (2022). workflowsets: Create a Collection of ‘tidymodels’ Workflows. R package version 0.2.1. https://CRAN.R-project.org/package=workflowsets
writexl	Jeroen Ooms (2021). writexl: Export Data Frames to Excel ‘xlsx’ Format. R package version 1.4.0. https://CRAN.R-project.org/package=writexl
xfun	Yihui Xie (2022). xfun: Supporting Functions for Packages Maintained by ‘Yihui Xie’. R package version 0.31. https://CRAN.R-project.org/package=xfun
XML	Duncan Temple Lang (2022). XML: Tools for Parsing and Generating XML Within R and S-Plus. R package version 3.99-0.9. https://CRAN.R-project.org/package=XML
xml2	Hadley Wickham, Jim Hester and Jeroen Ooms (2021). xml2: Parse XML. R package version 1.3.3. https://CRAN.R-project.org/package=xml2
xmlparsedata	Gábor Csárdi (2021). xmlparsedata: Parse Data of ‘R’ Code as an ‘XML’ Tree. R package version 1.0.5. https://CRAN.R-project.org/package=xmlparsedata
xopen	Gábor Csárdi, Fathi Boudra, Rex Dieter, Kevin Krammer and Jeremy White (2018). xopen: Open System Files, ‘URLs’, Anything. R package version 1.0.0. https://CRAN.R-project.org/package=xopen
xtable	David B. Dahl, David Scott, Charles Roosen, Arni Magnusson and Jonathan Swinton (2019). xtable: Export Tables to LaTeX or HTML. R package version 1.8-4. https://CRAN.R-project.org/package=xtable
xts	Jeffrey A. Ryan and Joshua M. Ulrich (2020). xts: eXtensible Time Series. R package version 0.12.1. https://CRAN.R-project.org/package=xts
yaml	Shawn P Garbett, Jeremy Stephens, Kirill Simonov, Yihui Xie, Zhuoer Dong, Hadley Wickham, Jeffrey Horner, reikoch, Will Beasley, Brendan O’Connor, Gregory R. Warnes, Michael Quinn and Zhian N. Kamvar (2022). yaml: Methods to Convert R Data to YAML and Back. R package version 2.3.5. https://CRAN.R-project.org/package=yaml
yardstick	Max Kuhn and Davis Vaughan (2021). yardstick: Tidy Characterizations of Model Performance. R package version 0.0.9. https://CRAN.R-project.org/package=yardstick
zeallot	Nathan Teetor (2018). zeallot: Multiple, Unpacking, and Destructuring Assignment. R package version 0.1.0. https://CRAN.R-project.org/package=zeallot
zip	Gábor Csárdi, Kuba Podgórski and Rich Geldreich (2021). zip: Cross-Platform ‘zip’ Compression. R package version 2.2.0. https://CRAN.R-project.org/package=zip
zoo	Achim Zeileis and Gabor Grothendieck (2005). zoo: S3 Infrastructure for Regular and Irregular Time Series. Journal of Statistical Software, 14(6), 1-27. doi:10.18637/jss.v014.i06. https://www.jstatsoft.org/article/view/v014i06

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