Functions and datasets to support Venables and
Ripley, `Modern Applied Statistics with S' (4th edition).

R (>= 1.9.0), graphics, stats, lattice, nlme, survival

GPL (version 2 or later)  See file LICENCE.

R (>= 2.4.0), grDevices, graphics, stats, utils

R (>= 2.5.0), R (<= 2.9.2), grDevices, graphics, stats, utils

R (>= 2.0.0), graphics, stats, lattice, nlme, survival

This is a package to visualize risk prediction models.  For each
predictor, a color bar represents the contribution to the linear predictor
or latent variable.  A conversion from the linear predictor to the
estimated risk or survival is also given.  (Cumulative) contribution charts
enable to visualize how the estimated risk for one particular observation
is obtained by the model. Several options allow to choose different color
maps, and to select the zero level of the contributions.  The package is
able to deal with 'glm', 'coxph', 'mfp', 'multinom' and 'ksvm' objects.  For 'ksvm'
objects, the visualization is not always exact.  Functions providing tools
to indicate the accuracy of the approximation are provided in addition to
the visualization.
Hmisc, survival, fields, R2HTML, viridis, kernlab, ROCR,
ggplot2, shiny, methods, stats, grDevices, graphics, utils

This is a package to visualize risk prediction models. For each
predictor, a color bar represents the contribution to the linear predictor or
latent variable. A conversion from the linear predictor to the estimated risk
or survival is also given. (Cumulative) contribution charts enable to visualize
how the estimated risk for one particular observation is obtained by the model.
Several options allow to choose different color maps, and to select the zero
level of the contributions. The package is able to deal with 'glm', 'coxph',
'mfp', 'multinom' and 'ksvm' objects. For 'ksvm' objects, the visualization
is not always exact. Functions providing tools to indicate the accuracy of the
approximation are provided in addition to the visualization.

Calculates the enrichment of associated variant set (AVS) for an array of genomic regions. The AVS is the collection of disjoint LD blocks computed from a list of disease associated SNPs and their linked (LD) SNPs. VSE generates a null distribution of matched random variant sets (MRVSs) from 1000 Genome Project Phase III data that are identical to AVS, LD block by block. It then computes the enrichment of AVS intersecting with user provided genomic features (e.g., histone marks or transcription factor binding sites) compared with the null distribution.