S3 Object & Method

Disclaimer

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 the basis for research grant applications or referenced in final research progress reports,
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/.

Caution 1: Prerequisite

Caution 1.1, Caution 2.1

The S3 generic functions and methods from

the spatstat.* family of packages (Baddeley et al. 2015; Baddeley and Turner 2005), especially spatstat.geom (v3.7.3, GPL (>= 2)), spatstat.explore (v3.8.0, GPL (>= 2)), spatstat.random (v3.4.5, GPL (>= 2)).
other contributed packages, e.g., mgcv (Wood 2017, v1.9.4, GPL (>= 2)), rpart (Therneau and Atkinson 2025, v4.1.27, GPL–2 | GPL-3), etc.

This part is organized by the S3 object class, in alphabetical order, then the S3 methods for each class. The names of S3 classes defined in these packages (Note 1) are rendered in italic font, e.g.,

groupedHyperframe in 15 groupedHyperframe
hyper_gam in 17 hyper_gam from gam
node1 in 21 node1 from function
vectorlist in 30 vectorlist from anylist

41 Statistical Topics, on the other hand, organizes the content of this part according to the statistical functionalities, i.e., the S3 generic functions. 41 Statistical Topics is an ideal starting point for readers who are not experts in R.

The R code-chunks in this part are categorized by purpose, including,

Advanced, to discuss advanced topics and experimental features for expert R users.
Benchmark, to compare computing cost using package microbenchmark (Mersmann 2024, v1.5.0, BSD_2_clause + file LICENSE).
Data, to create and/or inspect R objects for subsequent operations.
Example, to show how to use functions from these packages (Note 1).
Exception, to demonstrate the exception-handling mechanisms of functions from these packages (Note 1).
Figure, to generate elegant visualizations.
Future, to list upcoming tasks for these packages (Note 1).
Previously, to copy R code from earlier chapters.
Review, to demonstrate usage of functions from R version 4.5.3 (2026-03-11), or from contributed packages other than these packages (Note 1).
Table, to create HTML tables using the function knitr::kable() (Xie 2025, v1.51, GPL).
Workaround, to present alternative solutions to specific problems.

Readers aiming to extend the these packages (Note 1) or integrate them into their own workflows are strongly encouraged to study this part thoroughly.