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Generalized Nonlinear Models
Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Relative Contribution of Effects in a Regression Model
Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
'vcd' Extensions and Additions
Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Plackett-Luce Models for Rankings
Functions to prepare rankings data and fit the Plackett-Luce model
jointly attributed to Plackett (1975)
Biochemically Intuitive Generalized Loewe Model
Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
Data from Surveys Conducted by Forwards
Anonymized data from surveys conducted by Forwards < https://forwards.github.io/>, the R Foundation task force on women and other under-represented groups. Currently, a single data set of responses to a survey of attendees at useR! 2016 < https://www.r-project.org/useR-2016/>, the R user conference held at Stanford University, Stanford, California, USA, June 27 - June 30 2016.
'Roxygen' to 'Markdown'
Converts elements of 'roxygen' documentation to 'markdown'.
Log-Multiplicative Models, Including Association Models
Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart. Functions allow computing the intrinsic association coefficient (and therefore the Altham index), including via the Bayes shrinkage estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.