7  About

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/.

NoteR Terminology

R terminology may differ from that commonly used in mathematics and statistics. For explanations and references to the terms and abbreviations used in this Quarto book (Note 2), please refer to Chapter 60.

7.1 Environment

This Quarto book (Note 2) is created under R version 4.5.3 (2026-03-11) with the aid of packages knitr (Xie 2025, v1.51, GPL; Xie 2015, 2014), quarto (Allaire and Dervieux 2024, v1.5.1, MIT + file LICENSE with Quarto v1.9.35) and rmarkdown (Allaire et al. 2025, v2.30, GPL–3; Xie et al. 2018, 2020). Documentation and check are supported by packages roxygen2 (Wickham, Danenberg, et al. 2025, v7.3.3, MIT + file LICENSE) and devtools (Wickham et al. 2026, v2.5.0, MIT + file LICENSE). Package(s) kableExtra (Zhu 2024, v1.4.0, MIT + file LICENSE), sloop (Wickham 2019, v1.0.1, GPL–3) and xfun (Xie 2026, v0.57, MIT + file LICENSE) are also used in the creation of this book.

An Integrated Development Environment (IDE), e.g., RStudio (Posit Team 2026) or Positron, is not required, but highly recommended.

Listing 7.1: macOS version on author’s computer, in Terminal

sw_vers
# ProductName:      macOS
# ProductVersion:       26.4
# BuildVersion:     25E246

Listing 7.2: macOS version on author’s computer, in R

Sys.info()[c('sysname', 'release', 'machine')]
#  sysname  release  machine 
# "Darwin" "25.4.0"  "arm64"

Listing 7.3: R version on author’s computer

R.version
#                _                           
# platform       aarch64-apple-darwin20      
# arch           aarch64                     
# os             darwin20                    
# system         aarch64, darwin20           
# status                                     
# major          4                           
# minor          5.3                         
# year           2026                        
# month          03                          
# day            11                          
# svn rev        89597                       
# language       R                           
# version.string R version 4.5.3 (2026-03-11)
# nickname       Reassured Reassurer

Readers are strongly advised to download and install the latest R version 4.5.3 (2026-03-11) for macOS (Listing 7.4) or for Windows (Listing 7.5).

Listing 7.4: Download latest version of R for macOS

'https://cran.r-project.org/bin/macosx/' |>
  knitr::include_url(height = '220px')

Listing 7.5: Download latest version of R for Windows

'https://cran.r-project.org/bin/windows/base/' |>
  knitr::include_url(height = '120px')

7.2 Enhancement

The author sincerely thanks Prof. Adrian Baddeley for recognizing their submitted suggestions and/or bug reports in

• package spatstat.explore version 3.4-0.
• package spatstat.geom version 3.3-5.

7.2.1 groupedHyperframe

Package groupedHyperframe (v0.4.0, GPL-2) Enhances the spatstat.* family of packages (Baddeley et al. 2015; Baddeley and Turner 2005) with

• additional S3 generic functions and/or methods to
  • function-value-table (fv.object, Table 20.1)
  • point-pattern (ppp.object, Table 36.1)
  • to tessellation (Table 42.1)
  • to hyper data frame (hyperframe, Table 26.1)
• new S3 class 'groupedHyperframe' (Table 25.1) that inherits from the class 'hyperframe' and new S3 generic function as.groupedHyperframe() (Table 26.3) and aggregate2hyper() (Table 18.1)
• new S3 class 'vectorlist' (Table 43.1) that inherits from the class 'anylist'
• new S3 class 'fvlist' (Table 21.1) that inherits from the class 'anylist'

Package groupedHyperframe Enhances package GET (Myllymäki and Mrkvička 2024, v1.0.7, GPL–3) with

• new S3 generic function rlabelRes() (Table 36.20)

Package groupedHyperframe Enhances package survival (Therneau 2026, v3.8.6, LGPL (>= 2)) with

• additional S3 methods to survival object ('Surv', Chapter 41)

7.2.2 groupedHyperframe.random

Package groupedHyperframe.random (v0.2.4, GPL-2) Enhances the package spatstat.random (v3.4.5, GPL (>= 2)).

7.2.3 hyper.gam

Package hyper.gam (v0.2.4, GPL-2) Enhances the package mgcv (Wood 2017, v1.9.4, GPL (>= 2)), with

• generalized additive models using a predictor of hypercolumn

7.3 Dependency

These packages (Note 1) all Imports packages

• cli (Csárdi 2025, v3.6.5, MIT + file LICENSE), for attractive command line interfaces

Some of these packages (Note 1) Imports or Suggests packages

• ggplot2 (Wickham 2016, v4.0.2, MIT + file LICENSE), geomtextpath (Cameron and van den Brand 2025, v0.2.0, MIT + file LICENSE), htmltools (Cheng et al. 2025, v0.5.9, GPL (>= 2)), htmlwidgets (Vaidyanathan et al. 2023, v1.6.4, MIT + file LICENSE), patchwork (Pedersen 2025, v1.3.2, MIT + file LICENSE), plotly (Sievert 2020, v4.12.0, MIT + file LICENSE), scales (Wickham, Pedersen, et al. 2025, v1.4.0, MIT + file LICENSE), for elegant visualizations
• knitr (Xie 2025, v1.51, GPL; Xie 2015, 2014), for dynamic report generation
• methods, splines (R version 4.5.3 (2026-03-11))

7.3.1 groupedHyperframe

Package groupedHyperframe (v0.4.0, GPL-2) Imports packages

• GET (Myllymäki and Mrkvička 2024, v1.0.7, GPL–3)
• matrixStats (Bengtsson 2025, v1.5.0, Artistic–2.0), for matrix arithmetic
• pracma (Borchers 2025, v2.4.6, GPL (>= 3)), for (cumulative) trapezoidal integration (Chapter 11)
• SpatialPack (Vallejos et al. 2020, v0.4.1, GPL–3), for Tjøstheim (1978)’s coefficient of spatial association (Section 36.11)
• spatstat.explore (v3.8.0, GPL (>= 2)), spatstat.geom (v3.7.3, GPL (>= 2)), spatstat.random (v3.4.5, GPL (>= 2)), for spatial statistics
• survival (Therneau 2026, v3.8.6, LGPL (>= 2)), for the un-exported S3 method
  • as.data.frame.Surv(), so that the function hyperframe() recognizes a survival, or time-to-event, Surv-column in a hyper data frame, instead of treating it as a matrix-hypercolumn.

Package groupedHyperframe Suggests packages

• rpart (Therneau and Atkinson 2025, v4.1.24, GPL–2 | GPL-3), required by the function rocEngine() (v3.8.0, GPL (>= 2))
• spatstat.data (v3.1.9, GPL (>= 2)), for spatial data set examples

7.3.2 groupedHyperframe.random

Package groupedHyperframe.random (v0.2.4, GPL-2) Depends on package

• groupedHyperframe (v0.4.0, GPL-2)

Package groupedHyperframe.random Imports packages

• MASS (Venables and Ripley 2002, v7.3.65, GPL–2 | GPL-3), for the function mvrnorm() (Chapter 48)
• spatstat.geom (v3.7.3, GPL (>= 2)) and spatstat.random (v3.4.5, GPL (>= 2)), for operation and simulation of \(x\)- and \(y\)-coordinates and marks of point-patterns

7.3.3 hyper.gam

Package hyper.gam (v0.2.4, GPL-2) Depends on package

• groupedHyperframe (v0.4.0, GPL-2)

Package hyper.gam Imports packages

• caret (Kuhn 2008, v7.0.1, GPL (>= 2)), for \(k\)-fold prediction
• mgcv (Wood 2017, v1.9.4, GPL (>= 2)), for fitting generalized additive models
• nlme (Pinheiro et al. 2025, v3.1.168, GPL (>= 2)), for the S3 generic function nlme::getData()

Package hyper.gam Suggests packages

• spatstat.geom (Baddeley et al. 2015, v3.7.3, GPL (>= 2)), for hyperframe data structure

7.3.4 maxEff

Package maxEff (v0.2.4, GPL-2) Depends on package

• groupedHyperframe (v0.4.0, GPL-2)

Package maxEff Imports packages

• caret (Kuhn 2008, v7.0.1, GPL (>= 2)), for data partition
• rpart (Therneau and Atkinson 2025, v4.1.24, GPL–2 | GPL-3), for recursive partitioning
• spatstat.geom (Baddeley et al. 2015, v3.7.3, GPL (>= 2)), for hyperframe data structure

Package maxEff Suggests packages

• survival (Therneau 2026, v3.8.6, LGPL (>= 2))

7.4 Function Name Conflict

A function name conflict exists between

• spatstat.explore::plot.roc() (Baddeley et al. 2015, v3.8.0, GPL (>= 2))
• pROC::plot.roc() (Robin et al. 2011, v1.19.0.1, GPL (>= 3))

when loading both packages

• groupedHyperframe (v0.4.0, GPL-2), which Imports package spatstat.explore (v3.8.0, GPL (>= 2))
• hyper.gam (v0.2.4, GPL-2), which Imports package caret (v7.0.1, GPL (>= 2)) which Imports package pROC (v1.19.0.1, GPL (>= 3))

This function name clash is potentially hazardous as the S3 classes, both named 'roc', created by functions spatstat.explore::roc() and pROC::roc() are totally different.

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.

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.

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.

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.

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.

Pedersen, Thomas Lin. 2025. patchwork: The Composer of Plots. https://CRAN.R-project.org/package=patchwork.

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/.

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.

Sievert, Carson. 2020. Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman; Hall/CRC. https://plotly-r.com.

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/.

Venables, William N., and Brian D. Ripley. 2002. Modern Applied Statistics with S. Fourth. Springer. https://www.stats.ox.ac.uk/pub/MASS4/.

Wickham, Hadley. 2016. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.

Wickham, Hadley. 2019. 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. 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.