References

ImportantDisclaimer

These packages (Note 1) are a one-person project undergoing rapid evolution. Backward compatibility (per Hadley Wickham) is provided as a courtesy rather than a guarantee.

Until further notice, these packages should

  • not be used as a basis for research grant applications,
  • not be cited as an actively maintained tool in a peer-reviewed manuscript,
  • not be used to support or fulfill requirements for pursuing an academic degree.

In addition, work primarily based on these packages (Note 1) should not be presented at academic conferences or similar scholarly venues.

Furthermore, a person’s ability to use these packages (Note 1) does not necessarily imply an understanding of their underlying mechanisms. Accordingly, demonstration of their use alone should not be considered sufficient evidence of expertise, nor should it be credited as a basis for academic promotion or advancement.

These statements do not apply to the contributors (Tip 1) to these packages (Note 1) with respect to their specific contributions.

These statements do not apply when the maintainer of these packages (Note 1), Tingting Zhan, is credited as the first author, the lead author, and/or the corresponding author in a peer-reviewed manuscript, or as the Principal Investigator or Co-Principal Investigator in a research grant application and/or a final research progress report.

These statements are advisory in nature and do not modify or restrict the rights granted under the GNU General Public License https://www.r-project.org/Licenses/.

Allaire, JJ, and Christophe Dervieux. 2024. quarto: R Interface to Quarto Markdown Publishing System. https://CRAN.R-project.org/package=quarto.
Allaire, JJ, Yihui Xie, Christophe Dervieux, et al. 2025. rmarkdown: Dynamic Documents for R. https://github.com/rstudio/rmarkdown.
Bache, Stefan Milton, and Hadley Wickham. 2025. magrittr: A Forward-Pipe Operator for R. https://CRAN.R-project.org/package=magrittr.
Baddeley, Adrian, Peter J. Diggle, Andrew Hardegen, Thomas Lawrence, Robin K. Milne, and Gopalan Nair. 2014. “On Tests of Spatial Pattern Based on Simulation Envelopes.” Ecological Monographs 84 (3): 477–89. https://doi.org/10.1890/13-2042.1.
Baddeley, Adrian, Ege Rubak, Suman Rakshit, and Gopalan Nair. 2025. ROC Curves for Spatial Point Patterns and Presence-Absence Data. https://doi.org/10.48550/arXiv.2506.03414.
Baddeley, Adrian, Ege Rubak, and Rolf Turner. 2015. Spatial Point Patterns: Methodology and Applications with R. Chapman; Hall/CRC Press. https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/p/book/9781482210200/.
Baddeley, Adrian, and Rolf Turner. 2005. spatstat: An R Package for Analyzing Spatial Point Patterns.” Journal of Statistical Software 12 (6): 1–42. https://doi.org/10.18637/jss.v012.i06.
Becker, Richard A., John M. Chambers, and Allan R. Wilks. 1988. The New S Language. 1st ed. Chapman; Hall/CRC. https://doi.org/10.1201/9781351074988.
Bengtsson, Henrik. 2025. matrixStats: Functions That Apply to Rows and Columns of Matrices (and to Vectors). https://CRAN.R-project.org/package=matrixStats.
Borchers, Hans W. 2025. pracma: Practical Numerical Math Functions. https://CRAN.R-project.org/package=pracma.
Cameron, Allan, and Teun van den Brand. 2025. geomtextpath: Curved Text in ggplot2. https://CRAN.R-project.org/package=geomtextpath.
Cheng, Joe, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie, and Jeff Allen. 2025. htmltools: Tools for HTML. https://CRAN.R-project.org/package=htmltools.
Csárdi, Gábor. 2025. cli: Helpers for Developing Command Line Interfaces. https://CRAN.R-project.org/package=cli.
Csárdi, Gábor, and Jim Hester. 2025. pak: Another Approach to Package Installation. https://CRAN.R-project.org/package=pak.
Csárdi, Gábor, Jim Hester, Hadley Wickham, Winston Chang, Martin Morgan, and Dan Tenenbaum. 2024. remotes: R Package Installation from Remote Repositories, Including ’GitHub’. https://CRAN.R-project.org/package=remotes.
Cui, Erjia, Ciprian M. Crainiceanu, and Andrew Leroux. 2021. “Additive Functional Cox Model.” Journal of Computational and Graphical Statistics 30 (3): 780–93. https://doi.org/10.1080/10618600.2020.1853550.
Diggle, Peter. 1985. “A Kernel Method for Smoothing Point Process Data.” Journal of the Royal Statistical Society: Series C 34 (2): 138–47. https://doi.org/10.2307/2347366.
Gellar, Jonathan E., Elizabeth Colantuoni, Dale M. Needham, and Ciprian M. Crainiceanu. 2015. “Cox Regression Models with Functional Covariates for Survival Data.” Statistical Modelling 15 (3): 256–78. https://doi.org/10.1177/1471082X14565526.
Grolemund, Garrett. 2014. Hands-on Programming with R. O’Reilly Media, Inc. https://www.oreilly.com/library/view/hands-on-programming-with/9781449359089/.
Hartigan, John A., and M. A. Wong. 1979. “A K-Means Clustering Algorithm.” Journal of the Royal Statistical Society: Series C (Applied Statistics) 28 (1): 100–108. https://doi.org/10.2307/2346830.
Henry, Lionel, and Hadley Wickham. 2026. rlang: Functions for Base Types and Core R and Tidyverse Features. https://CRAN.R-project.org/package=rlang.
Hothorn, Torsten, Kurt Hornik, and Achim Zeileis. 2006. “Unbiased Recursive Partitioning: A Conditional Inference Framework.” Journal of Computational and Graphical Statistics 15 (3): 651–74. https://doi.org/10.1198/106186006X133933.
Hubert, Lawrence J., and Reginald G. Golledge. 1982. “Measuring Association Between Spatially Defined Variables: Tjøstheim’s Index and Some Extensions.” Geographical Analysis 14 (3): 273–78. https://doi.org/10.1111/j.1538-4632.1982.tb00077.x.
James, Gareth M. 2002. “Generalized Linear Models with Functional Predictors.” Journal of the Royal Statistical Society Series B: Statistical Methodology 64 (3): 411–32. https://doi.org/10.1111/1467-9868.00342.
Kuhn, Max. 2008. “Building Predictive Models in R Using the caret Package.” Journal of Statistical Software 28 (5): 1–26. https://doi.org/10.18637/jss.v028.i05.
Maechler, Martin, Peter Rousseeuw, Anja Struyf, Mia Hubert, and Kurt Hornik. 2025. cluster: Cluster Analysis Basics and Extensions. https://CRAN.R-project.org/package=cluster.
Matérn, Bertil. 1986. Spatial Variation. Springer. https://doi.org/10.1007/978-1-4615-7892-5.
McLean, Mathew W., Giles Hooker, Ana-Maria Staicu, Fabian Scheipl, and David Ruppert. 2014. “Functional Generalized Additive Models.” Journal of Computational and Graphical Statistics 23 (1): 249–69. https://doi.org/10.1080/10618600.2012.729985.
Mersmann, Olaf. 2024. microbenchmark: Accurate Timing Functions. https://CRAN.R-project.org/package=microbenchmark.
Microsoft Corporation, and Steve Weston. 2022a. doParallel: Foreach Parallel Adaptor for the parallel Package. https://CRAN.R-project.org/package=doParallel.
Microsoft Corporation, and Steve Weston. 2022b. foreach: Provides Foreach Looping Construct. https://CRAN.R-project.org/package=foreach.
Myllymäki, Mari, and Tomáš Mrkvička. 2024. GET: Global Envelopes in R.” Journal of Statistical Software 111 (3): 1–40. https://doi.org/10.18637/jss.v111.i03.
Myllymäki, Mari, Tomáš Mrkvička, Pavel Grabarnik, Henri Seijo, and Ute Hahn. 2016. “Global Envelope Tests for Spatial Processes.” Journal of the Royal Statistical Society Series B: Statistical Methodology 79 (2): 381–404. https://doi.org/10.1111/rssb.12172.
Pedersen, Thomas Lin. 2025. patchwork: The Composer of Plots. https://CRAN.R-project.org/package=patchwork.
Penttinen, Antti, Dietrich Stoyan, and Helena M. Henttonen. 1992. “Marked Point Processes in Forest Statistics.” Forest Science 38 (4): 806–24. https://doi.org/10.1093/forestscience/38.4.806.
Pinheiro, José, Douglas Bates, and R Core Team. 2025. nlme: Linear and Nonlinear Mixed Effects Models. https://CRAN.R-project.org/package=nlme.
Posit Team. 2026. RStudio: Integrated Development Environment for R. Posit Software, PBC. https://posit.co/.
R Core Team. 2026. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https://www.R-project.org/.
Reiss, Philip T., Jeff Goldsmith, Han Lin Shang, and R. Todd Ogden. 2017. “Methods for Scalar-on-Function Regression.” International Statistical Review 85 (2): 228–49. https://doi.org/10.1111/insr.12163.
Robin, Xavier, Natacha Turck, Alexandre Hainard, et al. 2011. pROC: An Open-Source Package for R and S+ to Analyze and Compare ROC Curves.” BMC Bioinformatics 12: 77. https://doi.org/10.1186/1471-2105-12-77.
Schlather, Martin, Jr Ribeiro Paulo J., and Peter J. Diggle. 2003. “Detecting Dependence Between Marks and Locations of Marked Point Processes.” Journal of the Royal Statistical Society Series B: Statistical Methodology 66 (1): 79–93. https://doi.org/10.1046/j.1369-7412.2003.05343.x.
Sievert, Carson. 2020. Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman; Hall/CRC. https://plotly-r.com.
Stoyan, Helga, and Dietrich Stoyan. 1994. Fractals, Random Shapes and Point Fields: Methods of Geometrical Statistics. John Wiley; Sons. https://www.wiley.com/Fractals%2C+Random+Shapes+and+Point+Fields%3A+Methods+of+Geometrical+Statistics-p-9780471937579.
Therneau, Terry M. 2026. A Package for Survival Analysis in R. https://CRAN.R-project.org/package=survival.
Therneau, Terry, and Beth Atkinson. 2025. rpart: Recursive Partitioning and Regression Trees. https://CRAN.R-project.org/package=rpart.
Tjøstheim, Dag. 1978. “A Measure of Association for Spatial Variables.” Biometrika 65 (1): 109–14. https://doi.org/10.1093/biomet/65.1.109.
Vaidyanathan, Ramnath, Yihui Xie, JJ Allaire, Joe Cheng, Carson Sievert, and Kenton Russell. 2023. htmlwidgets: HTML Widgets for R. https://CRAN.R-project.org/package=htmlwidgets.
Vallejos, R., F. Osorio, and M. Bevilacqua. 2020. Spatial Relationships Between Two Georeferenced Variables: With Applications in R. Springer. http://srb2gv.mat.utfsm.cl/.
Van Lieshout, M. N. M., and A. J. Baddeley. 1999. “Indices of Dependence Between Types in Multivariate Point Patterns.” Scandinavian Journal of Statistics 26 (4): 511–32. https://doi.org/10.1111/1467-9469.00165.
Venables, William N., and Brian D. Ripley. 2002. Modern Applied Statistics with S. Fourth. Springer. https://www.stats.ox.ac.uk/pub/MASS4/.
Wälder, Olga, and Dietrich Stoyan. 1996. “On Variograms in Point Process Statistics.” Biometrical Journal 38 (8): 895–905. https://doi.org/10.1002/bimj.4710380802.
Wickham, Hadley. 2016. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
Wickham, Hadley. 2019a. Advanced R. 2nd ed. Chapman & Hall/CRC. https://adv-r.hadley.nz/.
Wickham, Hadley. 2019b. sloop: Helpers for ’OOP’ in R. https://CRAN.R-project.org/package=sloop.
Wickham, Hadley, Peter Danenberg, Gábor Csárdi, and Manuel Eugster. 2025. roxygen2: In-Line Documentation for R. https://CRAN.R-project.org/package=roxygen2.
Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan. 2026. devtools: Tools to Make Developing R Packages Easier. https://CRAN.R-project.org/package=devtools.
Wickham, Hadley, Thomas Lin Pedersen, and Dana Seidel. 2025. scales: Scale Functions for Visualization. https://CRAN.R-project.org/package=scales.
Wood, Simon N. 2003. “Thin-Plate Regression Splines.” Journal of the Royal Statistical Society B: Statistical Methodology 65 (1): 95–114. https://doi.org/10.1111/1467-9868.00374.
Wood, Simon N. 2006. “Low-Rank Scale-Invariant Tensor Product Smooths for Generalized Additive Mixed Models.” Biometrics 62 (4): 1025–36. https://doi.org/10.1111/j.1541-0420.2006.00574.x.
Wood, Simon N. 2017. Generalized Additive Models: An Introduction with R. 2nd ed. Chapman; Hall/CRC.
Xie, Yihui. 2014. knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
Xie, Yihui. 2015. Dynamic Documents with R and knitr. 2nd ed. Chapman; Hall/CRC. https://yihui.org/knitr/.
Xie, Yihui. 2025. knitr: A General-Purpose Package for Dynamic Report Generation in R. https://yihui.org/knitr/.
Xie, Yihui. 2026. xfun: Supporting Functions for Packages Maintained by Yihui Xie. https://CRAN.R-project.org/package=xfun.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.
Zhu, Hao. 2024. kableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax. https://CRAN.R-project.org/package=kableExtra.