Title: Tint is not Tufte
Description: A 'tufte'-alike style for 'rmarkdown'.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.0.2 dated 2016-10-07 and 0.0.3 dated 2016-10-15
ChangeLog | 41 +++++++ DESCRIPTION | 8 - MD5 | 20 ++- README.md | 36 +++++- inst/NEWS.Rd |only inst/examples |only inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 30 ++--- inst/rmarkdown/templates/html/template.yaml | 2 inst/rmarkdown/templates/pdf/resources/tintPdf-template.tex | 63 ++++++++++++ inst/rmarkdown/templates/pdf/skeleton/skeleton.Rmd | 31 +++-- inst/rmarkdown/templates/pdf/template.yaml | 2 tests |only 12 files changed, 182 insertions(+), 51 deletions(-)
Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 0.6.2 dated 2016-09-19 and 0.6.3 dated 2016-10-15
sunburstR-0.6.2/sunburstR/inst/htmlwidgets/lib/d3 |only sunburstR-0.6.3/sunburstR/DESCRIPTION | 19 ++++---- sunburstR-0.6.3/sunburstR/MD5 | 11 +---- sunburstR-0.6.3/sunburstR/NEWS.md | 6 ++ sunburstR-0.6.3/sunburstR/R/sunburst.R | 33 ++++++++------- sunburstR-0.6.3/sunburstR/inst/htmlwidgets/sunburst.yaml | 4 - 6 files changed, 38 insertions(+), 35 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.7 dated 2016-03-17 and 1.1.8 dated 2016-10-15
SSN-1.1.7/SSN/R/Torgegram.r |only SSN-1.1.7/SSN/inst/doc/SSN.R |only SSN-1.1.7/SSN/src/additiveFunctionValues.cpp |only SSN-1.1.8/SSN/DESCRIPTION | 11 +++++---- SSN-1.1.8/SSN/MD5 | 32 ++++++++++++++++----------- SSN-1.1.8/SSN/NAMESPACE | 9 ++++--- SSN-1.1.8/SSN/R/FCSD.R |only SSN-1.1.8/SSN/R/FCSD01.R |only SSN-1.1.8/SSN/R/FUDJ.R |only SSN-1.1.8/SSN/R/FUSD.R |only SSN-1.1.8/SSN/R/Torgegram.R |only SSN-1.1.8/SSN/R/reachNeiSSN.R |only SSN-1.1.8/SSN/build/vignette.rds |binary SSN-1.1.8/SSN/data/mf04.rda |binary SSN-1.1.8/SSN/data/mf04p.rda |binary SSN-1.1.8/SSN/data/modelFits.rda |binary SSN-1.1.8/SSN/inst/doc/SSN.pdf |binary SSN-1.1.8/SSN/inst/doc/STARS.pdf |binary SSN-1.1.8/SSN/man/FCSD.Rd |only SSN-1.1.8/SSN/man/FCSD01.Rd |only SSN-1.1.8/SSN/man/FUDJ.Rd |only SSN-1.1.8/SSN/man/FUSD.Rd |only SSN-1.1.8/SSN/man/reachNeiSSN.Rd |only SSN-1.1.8/SSN/src/init.c | 4 +-- 24 files changed, 33 insertions(+), 23 deletions(-)
Title: Similarity Regression
Description: Functions for performing Bayesian similarity regression,
and evaluating the probability of association between sets of ontological terms
and binary response vector. A random model is compared with one in which
the log odds of a true response is linked to the semantic similarity
between terms and a latent characteristic ontological profile.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 2.1 dated 2016-08-16 and 3.0 dated 2016-10-15
SimReg-2.1/SimReg/R/functions.R |only SimReg-2.1/SimReg/R/generics.R |only SimReg-2.1/SimReg/R/multiSimReg.R |only SimReg-2.1/SimReg/R/plots.R |only SimReg-2.1/SimReg/R/simReg.R |only SimReg-2.1/SimReg/man/P-open-paren-gamma-equals-1-close-paren.Rd |only SimReg-2.1/SimReg/man/P_y_given_x.Rd |only SimReg-2.1/SimReg/man/acceptance_traces.Rd |only SimReg-2.1/SimReg/man/as.data.frame.sim_reg_summary.Rd |only SimReg-2.1/SimReg/man/as_row_leaves.Rd |only SimReg-2.1/SimReg/man/final_sample.Rd |only SimReg-2.1/SimReg/man/full_names.Rd |only SimReg-2.1/SimReg/man/log_odds_trace.Rd |only SimReg-2.1/SimReg/man/multi_sim_reg.Rd |only SimReg-2.1/SimReg/man/phi_plot.Rd |only SimReg-2.1/SimReg/man/plot.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/print.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/prune_sim_mat.Rd |only SimReg-2.1/SimReg/man/s.Rd |only SimReg-2.1/SimReg/man/s_phi.Rd |only SimReg-2.1/SimReg/man/s_x.Rd |only SimReg-2.1/SimReg/man/sim_reg_mc.Rd |only SimReg-2.1/SimReg/man/sim_reg_summary.Rd |only SimReg-2.1/SimReg/man/subset_sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/summary.sim_reg_samples.Rd |only SimReg-2.1/SimReg/man/term_marginals_from_phi_vec.Rd |only SimReg-2.1/SimReg/man/term_pair_marginals.Rd |only SimReg-2.1/SimReg/src/Chain.cpp |only SimReg-2.1/SimReg/src/Chain.h |only SimReg-2.1/SimReg/src/DeltaLikelihood.cpp |only SimReg-2.1/SimReg/src/DeltaLikelihood.h |only SimReg-2.1/SimReg/src/HPO.cpp |only SimReg-2.1/SimReg/src/HPO.h |only SimReg-2.1/SimReg/src/Interface.cpp |only SimReg-2.1/SimReg/src/Interface.h |only SimReg-2.1/SimReg/src/Likelihood.cpp |only SimReg-2.1/SimReg/src/Likelihood.h |only SimReg-2.1/SimReg/src/Similarity.cpp |only SimReg-2.1/SimReg/src/Similarity.h |only SimReg-2.1/SimReg/src/State.cpp |only SimReg-2.1/SimReg/src/State.h |only SimReg-2.1/SimReg/src/TermList.cpp |only SimReg-2.1/SimReg/src/TermList.h |only SimReg-2.1/SimReg/src/Update.cpp |only SimReg-2.1/SimReg/src/Update.h |only SimReg-2.1/SimReg/src/Utils.cpp |only SimReg-2.1/SimReg/src/Utils.h |only SimReg-3.0/SimReg/DESCRIPTION | 22 - SimReg-3.0/SimReg/MD5 | 97 ++--- SimReg-3.0/SimReg/NAMESPACE | 55 +-- SimReg-3.0/SimReg/R/RcppExports.R |only SimReg-3.0/SimReg/R/generic.R |only SimReg-3.0/SimReg/R/inference.R |only SimReg-3.0/SimReg/R/ml.R |only SimReg-3.0/SimReg/R/phi-priors.R |only SimReg-3.0/SimReg/R/pick.R |only SimReg-3.0/SimReg/R/plot.R |only SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.R | 9 SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.Rmd | 24 - SimReg-3.0/SimReg/inst/doc/SimReg-Introduction.html | 66 +-- SimReg-3.0/SimReg/inst/doc/SimReg-Priors.R | 19 - SimReg-3.0/SimReg/inst/doc/SimReg-Priors.Rmd | 42 +- SimReg-3.0/SimReg/inst/doc/SimReg-Priors.html | 97 ++--- SimReg-3.0/SimReg/man/SimReg-package.Rd | 26 - SimReg-3.0/SimReg/man/get_term_marginals.Rd |only SimReg-3.0/SimReg/man/get_terms.Rd |only SimReg-3.0/SimReg/man/log_BF.Rd |only SimReg-3.0/SimReg/man/plot.sim_reg_summary.Rd | 20 - SimReg-3.0/SimReg/man/plot_term_marginals.Rd |only SimReg-3.0/SimReg/man/print.sim_reg_output.Rd |only SimReg-3.0/SimReg/man/print.sim_reg_summary.Rd | 9 SimReg-3.0/SimReg/man/prob_association.Rd |only SimReg-3.0/SimReg/man/sim_reg.Rd | 168 +--------- SimReg-3.0/SimReg/man/sum_log_probs.Rd |only SimReg-3.0/SimReg/man/summary.sim_reg_output.Rd |only SimReg-3.0/SimReg/man/term_marginals.Rd | 12 SimReg-3.0/SimReg/src/RcppExports.cpp |only SimReg-3.0/SimReg/src/bgml.cpp |only SimReg-3.0/SimReg/src/fml.cpp |only SimReg-3.0/SimReg/src/ml.cpp |only SimReg-3.0/SimReg/src/utils.h |only SimReg-3.0/SimReg/vignettes/SimReg-Introduction.Rmd | 24 - SimReg-3.0/SimReg/vignettes/SimReg-Priors.Rmd | 42 +- 83 files changed, 255 insertions(+), 477 deletions(-)
Title: 'IUCN' Red List Client
Description: 'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client.
The 'IUCN' Red List is a global list of threatened and endangered species.
Functions cover all of the Red List 'API' routes. An 'API' key is required.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rredlist versions 0.1.0 dated 2016-01-26 and 0.2.0 dated 2016-10-15
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 + NEWS.md | 24 +++++++++++++++++++++- R/rl_common_names.R | 4 +-- R/rl_habitats.R | 6 ++--- R/rl_history.R |only R/rl_measures.R | 6 ++--- R/rl_narrative.R | 6 ++--- R/rl_search.R | 6 ++--- R/rl_sp_citation.R | 6 ++--- R/rl_sp_count.R | 2 - R/rl_synonyms.R | 4 +-- R/rl_threats.R | 6 ++--- R/rredlist-package.R | 30 ++++++++++++++------------- R/zzz.R | 6 +++-- README.md | 25 +++++++++-------------- man/rl_common_names.Rd | 4 +-- man/rl_habitats.Rd | 9 +++++--- man/rl_history.Rd |only man/rl_measures.Rd | 4 +-- man/rl_narrative.Rd | 4 +-- man/rl_search.Rd | 4 +-- man/rl_sp_citation.Rd | 4 +-- man/rl_sp_count.Rd | 4 +-- man/rl_synonyms.Rd | 4 +-- man/rl_threats.Rd | 4 +-- man/rredlist-package.Rd | 30 ++++++++++++++------------- 28 files changed, 148 insertions(+), 118 deletions(-)
Title: Nonparametric Boundary Regression
Description: A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.
Author: Abdelaati Daouia <Abdelaati.Daouia@tse-fr.eu>, Thibault Laurent <thibault.laurent@univ-tlse1.fr>, Hohsuk Noh <word5810@gmail.com>
Maintainer: Thibault Laurent <thibault.laurent@univ-tlse1.fr>
Diff between npbr versions 1.3 dated 2016-06-20 and 1.4 dated 2016-10-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/kern_smooth.R | 2 +- inst/doc/ex-npbr.pdf |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Estimation of Multivariate Long-Memory Models Parameters
Description: Computation of an estimation of the long-memory parameters and
the long-run covariance matrix using a multivariate model
(Lobato (1999) <10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are
implemented: a Fourier based approach (Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>) and a wavelet based
approach (Achard and Gannaz (2016) <10.1111/jtsa.12170>).
Author: Sophie Achard [aut, cre],
Irene Gannaz [aut]
Maintainer: Sophie Achard <sophie.achard@gipsa-lab.fr>
Diff between multiwave versions 1.0 dated 2015-10-28 and 1.1 dated 2016-10-15
multiwave-1.0/multiwave/R/varfima.R |only multiwave-1.0/multiwave/man/varfima.Rd |only multiwave-1.1/multiwave/DESCRIPTION | 14 +++--- multiwave-1.1/multiwave/MD5 | 52 +++++++++++------------ multiwave-1.1/multiwave/NAMESPACE | 2 multiwave-1.1/multiwave/R/fivarma.R |only multiwave-1.1/multiwave/R/mfw.R | 18 +++---- multiwave-1.1/multiwave/R/mww.R | 21 ++++----- multiwave-1.1/multiwave/R/mww_wav.R | 20 ++++---- multiwave-1.1/multiwave/man/DWTexact.Rd | 4 - multiwave-1.1/multiwave/man/K_eval.Rd | 5 +- multiwave-1.1/multiwave/man/compute_nj.Rd | 5 +- multiwave-1.1/multiwave/man/fivarma.Rd |only multiwave-1.1/multiwave/man/mfw.Rd | 7 +-- multiwave-1.1/multiwave/man/mfw_cov_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mfw_eval.Rd | 7 +-- multiwave-1.1/multiwave/man/multiwave-package.Rd | 7 +-- multiwave-1.1/multiwave/man/mww.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_cov_eval.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mww_wav.Rd | 7 +-- multiwave-1.1/multiwave/man/mww_wav_cov_eval.Rd | 6 +- multiwave-1.1/multiwave/man/mww_wav_eval.Rd | 6 +- multiwave-1.1/multiwave/man/psi_hat_exact.Rd | 5 +- multiwave-1.1/multiwave/man/scaling_filter.Rd | 5 +- multiwave-1.1/multiwave/man/scaling_function.Rd | 5 +- multiwave-1.1/multiwave/man/toeplitz_nonsym.Rd | 5 +- multiwave-1.1/multiwave/man/varma.Rd | 6 +- multiwave-1.1/multiwave/man/vfracdiff.Rd | 6 +- 29 files changed, 126 insertions(+), 113 deletions(-)
Title: Advanced Statistical Methods to Model and Adjust for Bias in
Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 "Small-Study Effects in Meta-Analysis":
- Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>;
- limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>;
- upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>.
Author: Guido Schwarzer [aut, cre],
James Carpenter [aut],
Gerta Rücker [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between metasens versions 0.3-0 dated 2016-02-17 and 0.3-1 dated 2016-10-15
DESCRIPTION | 18 ++++++++++-------- MD5 | 15 ++++++++------- NEWS | 9 +++++++++ R/plot.copas.R | 8 ++++---- man/copas.Rd | 8 ++++---- man/limitmeta.Rd | 4 ++-- man/metasens-package.Rd |only man/orbbound.Rd | 2 +- man/plot.copas.Rd | 4 ++-- 9 files changed, 40 insertions(+), 28 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models, and
overlaying multi-polygon objects. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason Fisher [aut, cre]
Maintainer: Jason Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.1.2 dated 2016-09-16 and 0.2.1 dated 2016-10-15
DESCRIPTION | 6 +-- MD5 | 46 ++++++++++++------------- NEWS | 11 ++++++ R/AddInsetMap.R | 14 +++---- R/BumpDisconnectCells.R | 14 +++---- R/ExportRasterStack.R | 2 - R/PlotCrossSection.R | 80 ++++++++++++++++++++------------------------- R/PlotGraph.R | 12 ++---- R/PlotMap.R | 75 +++++++++++++++++++++++++++++++----------- R/ReplaceInTemplate.R | 4 +- R/RmSmallCellChunks.R | 14 +++---- R/SetPolygons.R | 16 ++++----- R/SummariseBudget.R | 3 - README.md | 9 +++-- man/AddInsetMap.Rd | 14 +++---- man/BumpDisconnectCells.Rd | 14 +++---- man/ExportRasterStack.Rd | 2 - man/PlotCrossSection.Rd | 66 ++++++++++++++++++++++--------------- man/PlotGraph.Rd | 11 ++---- man/PlotMap.Rd | 56 +++++++++++++++++++++++-------- man/ReplaceInTemplate.Rd | 4 +- man/RmSmallCellChunks.Rd | 14 +++---- man/SetPolygons.Rd | 16 ++++----- man/SummariseBudget.Rd | 3 - 24 files changed, 287 insertions(+), 219 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>
Diff between Grace versions 0.4.2 dated 2016-10-04 and 0.4.3 dated 2016-10-15
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/grace.test.R | 9 ++++++--- man/grace.test.Rd | 8 ++++---- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: Dynamic Models for Survival Data
Description: Functions to fit time-varying coefficient models for interval
censored and right censored survival data. Three major approaches are
implemented: 1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data; 2)
Spline based time-varying coefficient Cox model for right censored data; 3)
Transformation model with time-varying coefficients for right censored data
using estimating equations.
Author: Wenjie Wang [cre, aut],
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between dynsurv versions 0.3-2 dated 2016-08-30 and 0.3-3 dated 2016-10-15
ChangeLog | 11 DESCRIPTION | 21 - MD5 | 26 - R/data.R | 6 inst/CITATION | 12 man/bcos.Rd | 2 man/tooth.Rd | 4 src/CoxModel.h | 330 +++++++++-------- src/DynamicCoxModel.h | 17 src/DynamicGORHModel.h | 19 - src/DynamicModel.h | 905 ++++++++++++++++++++++++------------------------- src/IntRegModel.h | 2 src/TimeIndepModel.h | 4 src/TimeVaryingModel.h | 12 14 files changed, 700 insertions(+), 671 deletions(-)
Title: Collocation Inference for Dynamic Systems
Description: These functions implement collocation-inference
for continuous-time and discrete-time stochastic processes.
They provide model-based smoothing, gradient-matching,
generalized profiling and forwards prediction error methods.
Author: Giles Hooker <gjh27@cornell.edu>,
Luo Xiao <lx42@cornell.edu>,
James Ramsay <ramsay@psych.mcgill.ca>
Maintainer: Giles Hooker <gjh27@cornell.edu>
Diff between CollocInfer versions 1.0.2 dated 2015-08-20 and 1.0.3 dated 2016-10-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/CollocInferPlots.R | 11 ++++++----- man/CollocInferPlots.rd | 4 +++- 4 files changed, 16 insertions(+), 13 deletions(-)
Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-4 dated 2016-03-08 and 1.5-5 dated 2016-10-15
mnormt-1.5-4/mnormt/INDEX |only mnormt-1.5-5/mnormt/DESCRIPTION | 8 ++++---- mnormt-1.5-5/mnormt/MD5 | 13 ++++++------- mnormt-1.5-5/mnormt/NEWS | 7 ++++--- mnormt-1.5-5/mnormt/R/mnormt.R | 4 +--- mnormt-1.5-5/mnormt/inst/CITATION | 2 +- mnormt-1.5-5/mnormt/man/dmnorm.Rd | 35 +++++++++++++++++++++-------------- mnormt-1.5-5/mnormt/man/dmt.Rd | 35 +++++++++++++++-------------------- 8 files changed, 52 insertions(+), 52 deletions(-)
More information about fontLiberation at CRAN
Permanent link
Title: Biometric Exploratory Analysis Creation House
Description: A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.
Author: Danni Yu [aut, cre],
Michael Man [aut],
ChenChen Yu [com]
Maintainer: Danni Yu <danni.yu@gmail.com>
Diff between BEACH versions 1.1.1 dated 2016-10-05 and 1.1.2 dated 2016-10-15
DESCRIPTION | 18 +- MD5 | 15 +- NAMESPACE | 2 build/partial.rdb |binary inst/app/README.md | 2 inst/app/data |only inst/app/functions/BridgingAnalysis_configuration.csv | 1 inst/app/server.r | 127 ++++++++++++------ inst/app/ui.r | 7 9 files changed, 111 insertions(+), 61 deletions(-)
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast
Clustering Using Adaptive Density Peak Detection). The work is built and
improved upon the idea of Rodriguez and Laio (2014)<DOI:10.1126/science.1242072>.
ADPclust clusters data by finding density peaks in a density-distance plot
generated from local multivariate Gaussian density estimation. It includes
an automatic centroids selection and parameter optimization algorithm, which
finds the number of clusters and cluster centroids by comparing average
silhouettes on a grid of testing clustering results; It also includes a user
interactive algorithm that allows the user to manually selects cluster
centroids from a two dimensional "density-distance plot". Here is the
research article associated with this package: "Wang, Xiao-Feng, and
Yifan Xu (2015)<DOI:10.1177/0962280215609948> Fast clustering using adaptive
density peak detection." Statistical methods in medical research". url:
http://smm.sagepub.com/content/early/2015/10/15/0962280215609948.abstract.
Author: Yifan (Ethan) Xu [aut, cre],
Xiao-Feng Wang [aut]
Maintainer: Yifan (Ethan) Xu <ethan.yifanxu@gmail.com>
Diff between ADPclust versions 0.6.5 dated 2015-12-03 and 0.7 dated 2016-10-15
ADPclust-0.6.5/ADPclust/R/ADPclust-package.r |only ADPclust-0.6.5/ADPclust/R/belongsTo.R |only ADPclust-0.6.5/ADPclust/R/checkh.R |only ADPclust-0.6.5/ADPclust/R/findCluster.R |only ADPclust-0.6.5/ADPclust/R/findClusterAuto.R |only ADPclust-0.6.5/ADPclust/R/findFd.R |only ADPclust-0.6.5/ADPclust/R/pickCenter.R |only ADPclust-0.6.5/ADPclust/R/pickOutlier.R |only ADPclust-0.6.5/ADPclust/R/plotClust.R |only ADPclust-0.6.5/ADPclust/man/ADPclust.Rd |only ADPclust-0.6.5/ADPclust/man/findCluster.Rd |only ADPclust-0.6.5/ADPclust/man/findClusterAuto.Rd |only ADPclust-0.6.5/ADPclust/man/findFd.Rd |only ADPclust-0.7/ADPclust/DESCRIPTION | 34 +- ADPclust-0.7/ADPclust/MD5 | 106 +++--- ADPclust-0.7/ADPclust/NAMESPACE | 22 - ADPclust-0.7/ADPclust/R/ADPclust.R | 304 ++++++++++-------- ADPclust-0.7/ADPclust/R/AMISE.R | 12 ADPclust-0.7/ADPclust/R/FindCentersAutoD.R |only ADPclust-0.7/ADPclust/R/FindCentersAutoV.R |only ADPclust-0.7/ADPclust/R/FindClustersAuto.R |only ADPclust-0.7/ADPclust/R/FindClustersGivenCenters.R |only ADPclust-0.7/ADPclust/R/FindClustersManual.R |only ADPclust-0.7/ADPclust/R/FindDistm.R |only ADPclust-0.7/ADPclust/R/FindFD.R |only ADPclust-0.7/ADPclust/R/FindH.R |only ADPclust-0.7/ADPclust/R/FindSilhouette.R |only ADPclust-0.7/ADPclust/R/IsDup.R |only ADPclust-0.7/ADPclust/R/PickCenters.R |only ADPclust-0.7/ADPclust/R/ROT.R | 8 ADPclust-0.7/ADPclust/R/clust10.R | 4 ADPclust-0.7/ADPclust/R/clust3.R | 4 ADPclust-0.7/ADPclust/R/clust5.1.R | 4 ADPclust-0.7/ADPclust/R/clust5.R | 2 ADPclust-0.7/ADPclust/R/dat_gene.R | 4 ADPclust-0.7/ADPclust/R/defCol.R | 4 ADPclust-0.7/ADPclust/R/plot.adpclust.R | 123 +++---- ADPclust-0.7/ADPclust/R/summary.adpclust.R | 25 - ADPclust-0.7/ADPclust/build/vignette.rds |binary ADPclust-0.7/ADPclust/inst/doc/ADPclust.R | 23 - ADPclust-0.7/ADPclust/inst/doc/ADPclust.Rmd | 40 +- ADPclust-0.7/ADPclust/inst/doc/ADPclust.html | 172 +++++----- ADPclust-0.7/ADPclust/man/AMISE.Rd | 10 ADPclust-0.7/ADPclust/man/FindCentersAutoD.Rd |only ADPclust-0.7/ADPclust/man/FindCentersAutoV.Rd |only ADPclust-0.7/ADPclust/man/FindClustersAuto.Rd |only ADPclust-0.7/ADPclust/man/FindClustersGivenCenters.Rd |only ADPclust-0.7/ADPclust/man/FindClustersManual.Rd |only ADPclust-0.7/ADPclust/man/FindDistm.Rd |only ADPclust-0.7/ADPclust/man/FindFD.Rd |only ADPclust-0.7/ADPclust/man/FindH.Rd |only ADPclust-0.7/ADPclust/man/ROT.Rd | 8 ADPclust-0.7/ADPclust/man/adpclust.Rd |only ADPclust-0.7/ADPclust/man/clust10.Rd | 4 ADPclust-0.7/ADPclust/man/clust3.Rd | 4 ADPclust-0.7/ADPclust/man/clust5.1.Rd | 4 ADPclust-0.7/ADPclust/man/clust5.Rd | 2 ADPclust-0.7/ADPclust/man/dat_gene.Rd | 4 ADPclust-0.7/ADPclust/man/defCol.Rd |only ADPclust-0.7/ADPclust/man/plot.adpclust.Rd | 10 ADPclust-0.7/ADPclust/man/summary.adpclust.Rd | 9 ADPclust-0.7/ADPclust/tests |only ADPclust-0.7/ADPclust/vignettes/ADPclust.Rmd | 40 +- 63 files changed, 547 insertions(+), 439 deletions(-)