References
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.
Bache, Stefan Milton, and Hadley Wickham. 2025. magrittr: A Forward-Pipe Operator for
R. https://CRAN.R-project.org/package=magrittr.
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. 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.
Becker, Richard A., John M. Chambers, and Allan R. Wilks. 1988. The
New S Language. 1st ed. Boca Raton, FL: 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. 2023. 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.
Chervoneva, Inna, Amy R Peck, Misung Yi, Boris Freydin, and Hallgeir
Rui. 2021. “Quantification of Spatial Tumor Heterogeneity in
Immunohistochemistry Staining Images.” Bioinformatics 37
(10): 1452–60. https://doi.org/10.1093/bioinformatics/btaa965.
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.
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.
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. New York, NY:
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.
———. 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.
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. 2025. RStudio: Integrated Development Environment for
R. Boston, MA: Posit Software, PBC. https://posit.co/.
R Core Team. 2025. R: A Language and Environment for
Statistical Computing. Vienna, Austria: 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, 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.
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. 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/.
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. New York: 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, 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. 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.
———. 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.
———. 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.
Yi, Misung, Tingting Zhan, Amy R. Peck, Jeffrey A. Hooke, Albert J.
Kovatich, Craig D. Shriver, Hai Hu, Yunguang Sun, Hallgeir Rui, and Inna
Chervoneva. 2023a. “Quantile Index Biomarkers Based on Single-Cell
Expression Data.” Laboratory Investigation 103 (8):
100158. https://doi.org/10.1016/j.labinv.2023.100158.
———. 2023b. “Selection of Optimal Quantile Protein Biomarkers
Based on Cell-Level Immunohistochemistry Data.” BMC
Bioinformatics 24 (1): 298. https://doi.org/10.1186/s12859-023-05408-8.
Yi, Misung, Tingting Zhan, Hallgeir Rui, and Inna Chervoneva. 2025.
“Functional Protein Biomarkers Based on Distributions of
Expression Levels in Single-Cell Imaging Data.”
Bioinformatics 41 (5): btaf182. https://doi.org/10.1093/bioinformatics/btaf182.
Zhan, Tingting, Misung Yi, and Inna Chervoneva. 2025. “Quantile
Index Predictors Using r Package ‘Hyper.gam‘.”
Bioinformatics 41 (8): btaf430. https://doi.org/10.1093/bioinformatics/btaf430.