Title: Clustering by Fast Search and Find of Density Peaks
Description: An implementation of the clustering algorithm described by Alex
Rodriguez and Alessandro Laio (Science, 2014 vol. 344), along with tools to
inspect and visualize the results.
Author: Thomas Lin Pedersen [aut, cre],
Sean Hughes [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between densityClust versions 0.1-1 dated 2014-07-21 and 0.2.1 dated 2016-02-06
DESCRIPTION | 23 ++++++---- MD5 | 29 +++++++----- NAMESPACE | 9 +++ R/RcppExports.R |only R/densityClust.R | 101 +++++++++++++++++++++++++------------------- README.md | 1 man/clustered.Rd | 5 +- man/clusters.Rd | 17 +++---- man/densityClust-package.Rd | 22 +++++---- man/densityClust.Rd | 19 ++++---- man/estimateDc.Rd | 8 ++- man/findClusters.Rd | 8 ++- man/plotMDS.Rd | 4 + src |only tests |only 15 files changed, 149 insertions(+), 97 deletions(-)
Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, randomForest, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.2-1 dated 2016-01-05 and 2.2-2 dated 2016-02-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/setupF.R | 10 ++++++---- README.md | 3 +++ inst/tests/formulas.R | 2 +- inst/tests/nonstandard-packages.R | 7 ++++++- 7 files changed, 32 insertions(+), 16 deletions(-)
Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R that records plots
in a LaTeX-friendly format. The device transforms plotting
commands issued by R functions into LaTeX code blocks. When
included in a LaTeX document, these blocks are interpreted with
the help of 'TikZ'---a graphics package for TeX and friends
written by Till Tantau. Using the 'tikzDevice', the text of R
plots can contain LaTeX commands such as mathematical formula.
The device also allows arbitrary LaTeX code to be inserted into
the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb, cre],
Yihui Xie [ctb]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tikzDevice versions 0.9 dated 2015-11-17 and 0.10 dated 2016-02-06
DESCRIPTION | 37 +- MD5 | 49 ++- NEWS.md |only R/deviceUtils.R | 3 R/tikzDevice-package.R | 5 R/tikzInternal.R | 44 --- build/vignette.rds |binary inst/doc/tikzDevice.Rnw | 16 - inst/doc/tikzDevice.pdf |binary man/setTikzDefaults.Rd | 1 man/tikzDevice-package.Rd | 5 src/tikzDevice.c | 225 ++++++++-------- src/tikzDevice.h | 9 tests/testthat/Rplots.tex |only tests/testthat/Rplots_colors.tex |only tests/testthat/standard_graphs/base_raster.pdf |binary tests/testthat/standard_graphs/ggplot2_superscripts.pdf |binary tests/testthat/standard_graphs/ggplot2_test.pdf |binary tests/testthat/standard_graphs/grid_raster.pdf |binary tests/testthat/standard_graphs/raster_reflection.pdf |binary tests/testthat/test_graphics.R | 27 + vignettes/figs |only vignettes/refs.bib | 8 vignettes/tikzDevice-concordance.tex |only vignettes/tikzDevice.Rnw | 16 - 25 files changed, 219 insertions(+), 226 deletions(-)
Title: Identify and Visualize Significantly Responsive Branches in a
Phylogenetic Tree
Description: Takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values, and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance. Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches. Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.
Author: John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Diff between SigTree versions 1.10.2 dated 2015-07-18 and 1.10.3 dated 2016-02-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 9 ++++++++- inst/CITATION | 6 +++--- inst/doc/SigTree.Rnw | 8 ++++---- inst/doc/SigTree.pdf |binary vignettes/SigTree.Rnw | 8 ++++---- 7 files changed, 29 insertions(+), 22 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.4.0 dated 2016-02-02 and 0.4.1 dated 2016-02-06
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ R/ga.R | 2 +- R/mcf.R | 2 +- R/package.R | 5 ++--- R/report.R | 10 +++++----- data/ga.rda |binary inst/NEWS.Rd | 11 ++++++++++- man/get_profile.Rd | 2 +- man/get_webproperty.Rd | 2 +- man/list_accounts.Rd | 2 +- man/list_profiles.Rd | 2 +- man/list_webproperties.Rd | 2 +- 13 files changed, 41 insertions(+), 33 deletions(-)
Title: General Purpose 'Oai-PMH' Services Client
Description: A general purpose client to work with any 'OAI-PMH'
(Open Archives Initiative Protocol for 'Metadata' Harvesting) service.
The 'OAI-PMH' protocol is described at
http://www.openarchives.org/OAI/openarchivesprotocol.html.
Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord',
'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and
'ListSets'.
Author: Scott Chamberlain [aut, cre],
Michal Bojanowski [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between oai versions 0.1.0 dated 2015-09-11 and 0.2.0 dated 2016-02-06
oai-0.1.0/oai/R/rbind_fill.R |only oai-0.1.0/oai/man/type_sum.Rd |only oai-0.2.0/oai/DESCRIPTION | 24 +- oai-0.2.0/oai/LICENSE | 2 oai-0.2.0/oai/MD5 | 89 +++++----- oai-0.2.0/oai/NAMESPACE | 29 ++- oai-0.2.0/oai/R/count_identifiers.R | 7 oai-0.2.0/oai/R/dumpers.R |only oai-0.2.0/oai/R/get_record.R | 16 + oai-0.2.0/oai/R/handle_errors.R |only oai-0.2.0/oai/R/id.R | 17 +- oai-0.2.0/oai/R/list_identifiers.R | 17 -- oai-0.2.0/oai/R/list_metadataformats.R | 7 oai-0.2.0/oai/R/list_records.R | 92 ----------- oai-0.2.0/oai/R/list_sets.R | 27 --- oai-0.2.0/oai/R/oai-package.R | 2 oai-0.2.0/oai/R/read_xml_safely.R |only oai-0.2.0/oai/R/tbldf.R | 68 ++++---- oai-0.2.0/oai/R/update_providers.R | 4 oai-0.2.0/oai/R/while_oai.R | 84 +++++++--- oai-0.2.0/oai/R/zzz.R | 125 +++++++++++++++ oai-0.2.0/oai/README.md | 102 +++++++++++- oai-0.2.0/oai/build/vignette.rds |binary oai-0.2.0/oai/inst/doc/oai_vignette.Rmd | 90 +++++++++- oai-0.2.0/oai/inst/doc/oai_vignette.html | 82 ++++++++- oai-0.2.0/oai/inst/vign/oai_vignette.Rmd | 34 +++- oai-0.2.0/oai/inst/vign/oai_vignette.md | 88 +++++++++- oai-0.2.0/oai/man/count_identifiers.Rd | 4 oai-0.2.0/oai/man/dumpers.Rd |only oai-0.2.0/oai/man/get_records.Rd | 8 oai-0.2.0/oai/man/id.Rd | 14 + oai-0.2.0/oai/man/list_identifiers.Rd | 4 oai-0.2.0/oai/man/list_metadataformats.Rd | 4 oai-0.2.0/oai/man/list_records.Rd | 5 oai-0.2.0/oai/man/list_sets.Rd | 2 oai-0.2.0/oai/man/load_providers.Rd | 2 oai-0.2.0/oai/man/oai-package.Rd | 2 oai-0.2.0/oai/man/providers.Rd | 2 oai-0.2.0/oai/man/tsum.Rd |only oai-0.2.0/oai/man/update_providers.Rd | 2 oai-0.2.0/oai/tests/testthat/test-count_identifiers.R | 7 oai-0.2.0/oai/tests/testthat/test-dumpers.R |only oai-0.2.0/oai/tests/testthat/test-get_records.R | 2 oai-0.2.0/oai/tests/testthat/test-handle_errors.R |only oai-0.2.0/oai/tests/testthat/test-id.R | 2 oai-0.2.0/oai/tests/testthat/test-list_identifiers.R | 17 -- oai-0.2.0/oai/tests/testthat/test-list_metadataformats.R | 2 oai-0.2.0/oai/tests/testthat/test-list_records.R | 2 oai-0.2.0/oai/tests/testthat/test-list_sets.R | 2 oai-0.2.0/oai/vignettes/oai_vignette.Rmd | 90 +++++++++- 50 files changed, 834 insertions(+), 345 deletions(-)
Title: Clustering via the Mean Shift Algorithm
Description: Clustering using the mean shift algorithm (multi-core processing is supported) or its blurring version.
Author: Mattia Ciollaro and Daren Wang
Maintainer: Mattia Ciollaro <mattiaciollaro@gmail.com>
Diff between MeanShift versions 1.0-1 dated 2016-02-02 and 1.0-2 dated 2016-02-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/blurredmeanshift.R | 30 ++++++++++++++++++++++++------ R/meanshift.R | 22 +++++++++++++++------- build/partial.rdb |binary man/MeanShift-package.Rd | 2 ++ man/bmsClustering.Rd | 12 ++++++------ man/msClustering.Rd | 16 ++++++++-------- 9 files changed, 68 insertions(+), 40 deletions(-)
Title: Dive Analysis and Calibration
Description: Utilities to represent, visualize, filter, analyse, and summarize
time-depth recorder (TDR) data. Miscellaneous functions for
handling location data are also provided.
Author: Sebastian P. Luque <spluque@gmail.com>
Maintainer: Sebastian P. Luque <spluque@gmail.com>
Diff between diveMove versions 1.4.0 dated 2015-08-23 and 1.4.1 dated 2016-02-06
diveMove-1.4.0/diveMove/ChangeLog |only diveMove-1.4.1/diveMove/DESCRIPTION | 8 - diveMove-1.4.1/diveMove/MD5 | 107 ++++++++---------- diveMove-1.4.1/diveMove/NEWS | 5 diveMove-1.4.1/diveMove/R/AllClass.R | 1 diveMove-1.4.1/diveMove/R/AllGenerics.R | 1 diveMove-1.4.1/diveMove/R/AllMethod.R | 1 diveMove-1.4.1/diveMove/R/austFilter.R | 1 diveMove-1.4.1/diveMove/R/bouts.R | 1 diveMove-1.4.1/diveMove/R/calibrate.R | 1 diveMove-1.4.1/diveMove/R/detDive.R | 1 diveMove-1.4.1/diveMove/R/detPhase.R | 1 diveMove-1.4.1/diveMove/R/distSpeed.R | 1 diveMove-1.4.1/diveMove/R/diveStats.R | 1 diveMove-1.4.1/diveMove/R/oneDiveStats.R | 1 diveMove-1.4.1/diveMove/R/plotTDR.R | 1 diveMove-1.4.1/diveMove/R/readLocs.R | 1 diveMove-1.4.1/diveMove/R/readTDR.R | 1 diveMove-1.4.1/diveMove/R/speedStats.R | 1 diveMove-1.4.1/diveMove/R/stampDive.R | 1 diveMove-1.4.1/diveMove/R/zoc.R | 1 diveMove-1.4.1/diveMove/R/zzz.R | 1 diveMove-1.4.1/diveMove/README.md | 4 diveMove-1.4.1/diveMove/inst/CITATION | 2 diveMove-1.4.1/diveMove/inst/doc/diveMove.R | 12 +- diveMove-1.4.1/diveMove/inst/doc/diveMove.Rnw | 1 diveMove-1.4.1/diveMove/inst/doc/diveMove.pdf |binary diveMove-1.4.1/diveMove/man/TDR-accessors.Rd | 1 diveMove-1.4.1/diveMove/man/TDR-class.Rd | 1 diveMove-1.4.1/diveMove/man/TDRcalibrate-accessors.Rd | 1 diveMove-1.4.1/diveMove/man/TDRcalibrate-class.Rd | 1 diveMove-1.4.1/diveMove/man/austFilter.Rd | 1 diveMove-1.4.1/diveMove/man/bout-methods.Rd | 1 diveMove-1.4.1/diveMove/man/bout-misc.Rd | 1 diveMove-1.4.1/diveMove/man/bouts2MLE.Rd | 1 diveMove-1.4.1/diveMove/man/bouts2NLS.Rd | 1 diveMove-1.4.1/diveMove/man/calibrateDepth.Rd | 1 diveMove-1.4.1/diveMove/man/calibrateSpeed.Rd | 1 diveMove-1.4.1/diveMove/man/detDive-internal.Rd | 1 diveMove-1.4.1/diveMove/man/detPhase-internal.Rd | 1 diveMove-1.4.1/diveMove/man/distSpeed.Rd | 1 diveMove-1.4.1/diveMove/man/diveMove-internal.Rd | 1 diveMove-1.4.1/diveMove/man/diveMove-package.Rd | 1 diveMove-1.4.1/diveMove/man/diveStats.Rd | 1 diveMove-1.4.1/diveMove/man/dives.Rd | 1 diveMove-1.4.1/diveMove/man/extractDive-methods.Rd | 1 diveMove-1.4.1/diveMove/man/labDive-internal.Rd | 1 diveMove-1.4.1/diveMove/man/plotTDR-methods.Rd | 1 diveMove-1.4.1/diveMove/man/readLocs.Rd | 1 diveMove-1.4.1/diveMove/man/readTDR.Rd | 1 diveMove-1.4.1/diveMove/man/rqPlot.Rd | 1 diveMove-1.4.1/diveMove/man/sealLocs.Rd | 1 diveMove-1.4.1/diveMove/man/timeBudget-methods.Rd | 1 diveMove-1.4.1/diveMove/vignettes/Makefile | 1 diveMove-1.4.1/diveMove/vignettes/diveMove.Rnw | 1 55 files changed, 68 insertions(+), 117 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.9 dated 2016-01-17 and 2.0 dated 2016-02-06
DESCRIPTION | 6 ++--- MD5 | 17 +++++++------- NEWS | 20 ++++++++++++++++- R/DJL-internal.R |only R/roc.dea.R | 4 ++- R/roc.sf.R | 2 + R/target.arrival.dea.R | 6 +++-- R/target.arrival.sf.R | 2 + R/target.spec.dea.R | 56 +++++++++++++++++++++++++++++++++---------------- man/target.spec.dea.Rd | 21 ++++++++++++++---- 10 files changed, 96 insertions(+), 38 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results.
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.3.0 dated 2015-12-21 and 0.4.0 dated 2016-02-06
coala-0.3.0/coala/R/par_zero_inflation.R |only coala-0.3.0/coala/man/activate_ms.Rd |only coala-0.3.0/coala/man/activate_msms.Rd |only coala-0.3.0/coala/man/activate_seqgen.Rd |only coala-0.3.0/coala/man/create_locus_trio.Rd |only coala-0.3.0/coala/man/create_segsites.Rd |only coala-0.3.0/coala/man/locus_single.Rd |only coala-0.3.0/coala/man/par_expr.Rd |only coala-0.3.0/coala/man/plus-.coalmodel.Rd |only coala-0.4.0/coala/DESCRIPTION | 17 coala-0.4.0/coala/MD5 | 274 ++++++------- coala-0.4.0/coala/NAMESPACE | 9 coala-0.4.0/coala/NEWS.md | 18 coala-0.4.0/coala/R/RcppExports.R | 45 -- coala-0.4.0/coala/R/cache.R | 5 coala-0.4.0/coala/R/coala.R | 2 coala-0.4.0/coala/R/feature.R | 3 coala-0.4.0/coala/R/feature_growth.R | 43 +- coala-0.4.0/coala/R/feature_ignore_singletons.R | 10 coala-0.4.0/coala/R/feature_migration.R | 73 +-- coala-0.4.0/coala/R/feature_mutation.R | 108 ++--- coala-0.4.0/coala/R/feature_outgroup.R | 10 coala-0.4.0/coala/R/feature_pop_merge.R | 25 - coala-0.4.0/coala/R/feature_recombination.R | 31 - coala-0.4.0/coala/R/feature_sample.R | 2 coala-0.4.0/coala/R/feature_selection.R | 49 +- coala-0.4.0/coala/R/feature_size_change.R | 36 + coala-0.4.0/coala/R/feature_unphased.R | 24 - coala-0.4.0/coala/R/import_popgenome.R | 2 coala-0.4.0/coala/R/interface_abc.R |only coala-0.4.0/coala/R/locus.R | 81 ++- coala-0.4.0/coala/R/model.R | 51 +- coala-0.4.0/coala/R/model_build.R | 35 + coala-0.4.0/coala/R/model_check.R | 9 coala-0.4.0/coala/R/model_getters.R | 3 coala-0.4.0/coala/R/model_simulate.R | 16 coala-0.4.0/coala/R/onLoad.R | 12 coala-0.4.0/coala/R/parameter.R | 72 ++- coala-0.4.0/coala/R/parameter_prior.R | 2 coala-0.4.0/coala/R/parameter_variation.R | 14 coala-0.4.0/coala/R/parameter_zero_inflation.R |only coala-0.4.0/coala/R/search_executable.R | 1 coala-0.4.0/coala/R/segsites.R | 50 ++ coala-0.4.0/coala/R/simulator_class.R | 17 coala-0.4.0/coala/R/simulator_ms.R | 18 coala-0.4.0/coala/R/simulator_msms.R | 38 + coala-0.4.0/coala/R/simulator_scrm.R | 35 + coala-0.4.0/coala/R/simulator_seqgen.R | 45 +- coala-0.4.0/coala/R/sumstat.R | 21 coala-0.4.0/coala/R/sumstat_dna.R | 18 coala-0.4.0/coala/R/sumstat_file.R | 22 - 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Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.0.1 dated 2016-01-24 and 1.0.2 dated 2016-02-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/qrPlot.R | 4 ++-- inst/doc/IPCCExample.html | 9 +++++++-- man/cdfquantreg-package.Rd | 4 ++-- 6 files changed, 28 insertions(+), 15 deletions(-)