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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "stops" in publications use:'
type: software
license:
- GPL-2.0-only
- GPL-3.0-only
title: 'stops: Structure Optimized Proximity Scaling'
version: 1.8-2
identifiers:
- type: doi
  value: 10.32614/CRAN.package.stops
abstract: Methods that use flexible variants of multidimensional scaling (MDS) which
  incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit
  fit with structure considerations to find optimal hyperparameters, also known as
  structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<https://doi.org/10.1007/s11222-022-10197-w>).
  The package contains various functions, wrappers, methods and classes for fitting,
  plotting and displaying different 1-way MDS models with ratio, interval, ordinal
  optimal scaling in a STOPS framework. These cover essentially the functionality
  of the package smacofx, including Torgerson (classical) scaling with power transformations
  of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with
  powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical
  SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities,
  r-stress MDS, MDS with powers of dissimilarities and configuration distances, elastic
  scaling powers of dissimilarities and configuration distances, Sammon mapping powers
  of dissimilarities and configuration distances, power stress MDS (POST-MDS), approximate
  power stress, Box-Cox MDS, local MDS, Isomap, curvilinear component analysis (CLCA),
  curvilinear distance analysis (CLDA) and sparsified (power) multidimensional scaling
  and (power) multidimensional distance analysis (experimental models from smacofx
  influenced by CLCA). All of these models can also be fit by optimizing over hyperparameters
  based on goodness-of-fit fit only (i.e., no structure considerations). The package
  further contains functions for optimization, specifically the adaptive Luus-Jaakola
  algorithm and a wrapper for Bayesian optimization with treed Gaussian process with
  jumps to linear models, and functions for various c-structuredness indices.
authors:
- family-names: Rusch
  given-names: Thomas
  email: thomas.rusch@wu.ac.at
  orcid: https://orcid.org/0000-0002-7773-2096
- family-names: Mair
  given-names: Patrick
  orcid: https://orcid.org/0000-0003-0100-6511
preferred-citation:
  type: manual
  title: 'stops: Structure Optimized Proximity Scaling'
  authors:
  - family-names: Rusch
    given-names: Thomas
    email: thomas.rusch@wu.ac.at
    orcid: https://orcid.org/0000-0002-7773-2096
  - family-names: Mair
    given-names: Patrick
    orcid: https://orcid.org/0000-0003-0100-6511
  year: '2024'
  notes: R package version 1.8-2
  url: https://CRAN.R-project.org/package=stops
repository: https://CRAN.R-project.org/package=stops
repository-code: https://r-forge.r-project.org/projects/stops/
url: https://r-forge.r-project.org/projects/stops/
date-released: '2024-09-22'
contact:
- family-names: Rusch
  given-names: Thomas
  email: thomas.rusch@wu.ac.at
  orcid: https://orcid.org/0000-0002-7773-2096
references:
- type: article
  title: Structure-based hyperparameter selection with Bayesian optimization in multidimensional
    scaling
  authors:
  - family-names: Rusch
    given-names: Thomas
    email: thomas.rusch@wu.ac.at
    orcid: https://orcid.org/0000-0002-7773-2096
  - family-names: Mair
    given-names: Patrick
    email: mair@fas.harvard.edu
    orcid: https://orcid.org/0000-0003-0100-6511
  - family-names: Hornik
    given-names: Kurt
    email: Kurt.Hornik@R-project.org
    orcid: https://orcid.org/0000-0003-4198-9911
  journal: Statistics and Computing
  year: '2023'
  volume: '33'
  issue: '28'
  doi: 10.1007/s11222-022-10197-w
  start: 1-18
- type: report
  title: Minimizing rstress using nested majorization
  authors:
  - family-names: Leeuw
    given-names: Jan
    name-particle: de
  - family-names: Groenen
    given-names: Patrick
  - family-names: Mair
    given-names: Patrick
    email: mair@fas.harvard.edu
    orcid: https://orcid.org/0000-0003-0100-6511
  year: '2016'
  url: https://rpubs.com/deleeuw/142619
  institution:
    name: UCLA
- type: article
  title: Stress functions for nonlinear dimension reduction, proximity analysis, and
    graph drawing.
  authors:
  - family-names: Chen
    given-names: Lisha
  - family-names: Buja
    given-names: Andreas
  journal: Journal of Machine Learning Research
  year: '2013'
  volume: '14'
  start: 1145-1173
- type: article
  title: Local multidimensional scaling for nonlinear dimension reduction, graph drawing,
    and proximity analysis.
  authors:
  - family-names: Chen
    given-names: Lisha
  - family-names: Buja
    given-names: Andreas
  journal: Journal of the American Statistical Association
  year: '2009'
  volume: '104'
  start: 209-219