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 57.

7.1 Environment

This Quarto book is created under R version 4.5.2 (2025-10-31) with the aid of packages knitr (Xie 2025a, v1.51; 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). Package(s) sloop (Wickham 2019, v1.0.1) and xfun (Xie 2025b, v0.55) are also used in the creation of this book.

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:       26.2
# BuildVersion:     25C56
Listing 7.2: macOS version on author’s computer, in R 
Sys.info()[c('sysname', 'release', 'machine')]
#  sysname  release  machine 
# "Darwin" "25.2.0"  "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

Package groupedHyperframe (v0.3.2.20251225) Enhances the spatstat.* family of packages (Baddeley, Rubak, and Turner 2015; Baddeley and Turner 2005).

Package groupedHyperframe Enhances package spatstat.explore (v3.6.0.5) with

  • additional S3 methods to function-value-table ('fv', Table 20.1)
  • new S3 generic function density_marks() (Table 36.4)
  • new S3 generic functions Emark_(), Gcross_(), nncross_(), etc. (Table 36.19)

Package groupedHyperframe Enhances package spatstat.geom (v3.6.1.16) with

  • new S3 class 'groupedHyperframe' (Chapter 2, Section 3.1, Chapter 25) that inherits from the class 'hyperframe'
  • additional S3 methods to point-pattern ('ppp', Table 36.1)
  • additional S3 methods to tessellation ('tess', Table 40.1)
  • additional S3 methods to the class 'anylist' (Table 15.1)
  • additional S3 methods to the class 'solist' (🚧)
  • additional S3 methods to the class 'ppplist' (Table 37.1)
  • additional S3 methods to hyper data frame ('hyperframe', Table 26.1)
  • new S3 class 'vectorlist' (Chapter 41) that inherits from the class 'anylist'
  • new S3 class 'fvlist' (Chapter 21) that inherits from the class 'anylist'
  • new S3 generic function as.groupedHyperframe() (Table 18.2)

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

7.2.2 groupedHyperframe.random

Package groupedHyperframe.random (v0.2.0.20251221) Enhances the package spatstat.random (v3.4.3.2).

7.2.3 hyper.gam

Package hyper.gam (v0.2.1.20151215) 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

Some of these packages Imports or Suggests packages

7.3.1 groupedHyperframe

Package groupedHyperframe (v0.3.2.20251225) Imports packages

Package groupedHyperframe Suggests packages

7.3.2 groupedHyperframe.random

Package groupedHyperframe.random (v0.2.0.20251221) Depends on package

  • groupedHyperframe (v0.3.2.20251225)

Package groupedHyperframe.random Imports packages

7.3.3 hyper.gam

Package hyper.gam (v0.2.1.20151215) Depends on package

  • groupedHyperframe (v0.3.2.20251225)

Package hyper.gam Imports packages

Package hyper.gam Suggests packages

7.3.4 maxEff

Package maxEff (v0.2.1) Depends on package

  • groupedHyperframe (v0.3.2.20251225)

Package maxEff Imports packages

Package maxEff Suggests packages

7.4 Function Name Conflict

A function name conflict exists between

when loading both packages

  • groupedHyperframe (v0.3.2.20251225), which Imports package spatstat.explore (v3.6.0.5)
  • hyper.gam (v0.2.1.20151215), 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.