7  About

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, please refer to Chapter 40.

7.1 Environment

This Quarto book is created under R version 4.5.2 (2025-10-31) with the aid of packages knitr (Xie 2025, v1.50; 2015; 2014), quarto (Allaire and Dervieux 2024, v1.5.1 with Quarto v1.8.26) and rmarkdown (Allaire et al. 2025, v2.30; Xie, Allaire, and Grolemund 2018; Xie, Dervieux, and Riederer 2020). Documentation and check are supported by packages roxygen2 (Wickham, Danenberg, et al. 2025, v7.3.3) and devtools (Wickham, Hester, et al. 2025, v2.4.6).

An Integrated Development Environment (IDE), e.g., RStudio (Posit Team 2025) or Positron, is not required, but highly recommended.

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

sw_vers
# ProductName:      macOS
# ProductVersion:       26.1
# BuildVersion:     25B78

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

Sys.info()[c('sysname', 'release', 'machine')]
#  sysname  release  machine 
# "Darwin" "25.1.0"  "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          5.2                         
# year           2025                        
# month          10                          
# day            31                          
# svn rev        88974                       
# language       R                           
# version.string R version 4.5.2 (2025-10-31)
# nickname       [Not] Part in a Rumble

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 (v0.3.2)

Package groupedHyperframe Enhances the spatstat.* family of packages (Baddeley, Rubak, and Turner 2015; Baddeley and Turner 2005).

Package groupedHyperframe Enhances package spatstat.explore (v3.6.0.1), with

• additional S3 methods to function-value-table ('fv', Table 15.1)
• new S3 generic function density_marks() (Table 27.3)
• new S3 generic functions Emark_(), Gcross_(), nncross_(), etc. (Table 27.17), the batch processes on eligible marks

Package groupedHyperframe Enhances package spatstat.geom (v3.6.1), with

• new S3 class 'groupedHyperframe' (Chapter 2, Section 3.1, Chapter 19) that inherits from the class 'hyperframe'
• additional S3 methods to point-pattern ('ppp', Table 27.1)
• additional S3 methods to tessellation ('tess', 🚧)
• additional S3 methods to the class 'anylist' (Table 13.1)
• additional S3 methods to the class 'solist' (🚧)
• additional S3 methods to the class 'ppplist' (Table 28.1)
• additional S3 methods to hyper data frame ('hyperframe', Table 20.1)
• new S3 class 'vectorlist' (Chapter 32) that inherits from the class 'anylist'
• new S3 class 'fvlist' (Chapter 16) that inherits from the class 'anylist'
• new S3 generic function as.groupedHyperframe() (Table 14.2)

7.2.2 groupedHyperframe.random (v0.2.0.20251031)

Package groupedHyperframe.random Enhances the package spatstat.random (v3.4.3).

7.2.3 hyper.gam (v0.2.1.20151031)

Package hyper.gam Enhances the package mgcv (Wood 2017, v1.9.4), with

• generalized additive models using a predictor of hypercolumn

7.3 Dependency

These packages all Imports packages

• cli (Csárdi 2025, v3.6.5), for attractive command line interfaces
• doParallel (v1.0.17) and foreach (v1.5.2) (Microsoft Corporation and Weston 2022a, 2022b) for parallel computing on Windows operating system; and parallel shipped with R version 4.5.2 (2025-10-31) on Unix-like operating systems

Some of these packages Imports or Suggests packages

• ggplot2 (Wickham 2016, v4.0.1), geomtextpath (Cameron and van den Brand 2025, v0.2.0), htmltools (Cheng et al. 2024, v0.5.8.1), htmlwidgets (Vaidyanathan et al. 2023, v1.6.4), patchwork (Pedersen 2025, v1.3.2), plotly (Sievert 2020, v4.11.0), scales (Wickham, Pedersen, and Seidel 2025, v1.4.0), for elegant visualizations
• knitr (Xie 2025, v1.50; 2015; 2014), for dynamic report generation
• methods shipped with R version 4.5.2 (2025-10-31), for advanced operations with groupGeneric functions

7.3.1 groupedHyperframe (v0.3.2)

Package groupedHyperframe Imports packages

• GET (Myllymäki and Mrkvička 2024, v1.0.7), for global envelope test (Section 27.13)
• matrixStats (Bengtsson 2025, v1.5.0), for matrix arithmetic
• pracma (Borchers 2025, v2.4.6), for (cumulative) trapezoidal integration (Chapter 11)
• SpatialPack (Vallejos, Osorio, and Bevilacqua 2020, v0.4.1), for Tjøstheim (1978)’s coefficient of spatial association (Section 27.12)
• spatstat.explore (v3.6.0.1), spatstat.geom (v3.6.1), spatstat.random (v3.4.3), for spatial statistics

Package groupedHyperframe Suggests packages

• rpart (T. Therneau and Atkinson 2025, v4.1.24), required by function spatstat.explore::rocEngine() (v3.6.0.1)
• spatstat.data (v3.1.9), for spatial data set examples
• survival (T. M. Therneau 2024, v3.8.3) (Chapter 9)

7.3.2 groupedHyperframe.random (v0.2.0.20251031)

Package groupedHyperframe.random Depends on package

• groupedHyperframe (v0.3.2)

Package groupedHyperframe.random Imports packages

• MASS (Venables and Ripley 2002, v7.3.65), for function MASS::mvrnorm()
• spatstat.geom (v3.6.1) and spatstat.random (v3.4.3), for operation and simulation of ppp.object and marks

7.3.3 hyper.gam (v0.2.1.20151031)

Package hyper.gam Depends on package

• groupedHyperframe (v0.3.2)

Package hyper.gam Imports packages

• caret (Kuhn 2008, v7.0.1), for \(k\)-fold prediction
• mgcv (Wood 2017, v1.9.4), for fitting generalized additive models
• nlme (Pinheiro, Bates, and R Core Team 2025, v3.1.168), to import the S3 generic function nlme::getData()

Package hyper.gam Suggests packages

• spatstat.geom (Baddeley, Rubak, and Turner 2015, v3.6.1), for hyperframe data structure

7.3.4 maxEff (v0.2.1)

Package maxEff Depends on package

• groupedHyperframe (v0.3.2)

Package maxEff Imports packages

• caret (Kuhn 2008, v7.0.1), for data partition
• rpart (T. Therneau and Atkinson 2025, v4.1.24), for recursive partitioning
• spatstat.geom (Baddeley, Rubak, and Turner 2015, v3.6.1), for hyperframe data structure

Package maxEff Suggests packages

• survival (T. M. Therneau 2024, v3.8.3)

7.3.5 Function Name Conflicts

A function name conflict exists between

• spatstat.explore::plot.roc() (Baddeley, Rubak, and Turner 2015, v3.6.0.1)
• pROC::plot.roc() (Robin et al. 2011, v1.19.0.1)

when loading both packages

• groupedHyperframe (v0.3.2), which Imports package spatstat.explore (v3.6.0.1)
• hyper.gam (v0.2.1.20151031), which Imports package caret (v7.0.1) which Imports package pROC (v1.19.0.1)

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, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, 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. London: 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. 2024. 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.

Microsoft Corporation, and Steve Weston. 2022a. doParallel: Foreach Parallel Adaptor for the parallel Package. https://CRAN.R-project.org/package=doParallel.

———. 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.

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. 2025. RStudio: Integrated Development Environment for R. Boston, MA: Posit Software, PBC. https://posit.co/.

Robin, Xavier, 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: 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. 2024. 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. New York: Springer. http://srb2gv.mat.utfsm.cl/.

Venables, William N., and Brian D. Ripley. 2002. Modern Applied Statistics with S. Fourth. New York: 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, 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. 2025. 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.

———. 2015. Dynamic Documents with R and knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.

———. 2025. knitr: A General-Purpose Package for Dynamic Report Generation in R. https://yihui.org/knitr/.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.