Title: Fantastic Heatmap
Description: R function to plot high quality, elegant heatmap using 'ggplot2' graphics .
Some of the important features of this package are, coloring of row/column side tree with
respect to the number of user defined cuts in the cluster, add annotations to both columns
and rows, option to input annotation palette for tree and column annotations and multiple
parameters to modify aesthetics (style, color, font) of texts in the plot.
Author: Vaishali Tumulu and Sivasish Sindiri
Maintainer: Sivasish Sindiri<sentisci@gmail.com>
Diff between fheatmap versions 1.0.0 dated 2015-05-03 and 1.0.1 dated 2015-12-09
fheatmap-1.0.0/fheatmap/man/figures |only fheatmap-1.0.1/fheatmap/DESCRIPTION | 14 fheatmap-1.0.1/fheatmap/MD5 | 20 fheatmap-1.0.1/fheatmap/NAMESPACE | 21 fheatmap-1.0.1/fheatmap/NEWS |only fheatmap-1.0.1/fheatmap/R/fheatmap.R | 1805 ++++++++++---------- fheatmap-1.0.1/fheatmap/man/annotation_col.Rd | 38 fheatmap-1.0.1/fheatmap/man/annotation_col_color.Rd | 36 fheatmap-1.0.1/fheatmap/man/annotation_row.Rd | 39 fheatmap-1.0.1/fheatmap/man/annotation_row_color.Rd | 38 fheatmap-1.0.1/fheatmap/man/fheatmap-package.Rd | 321 ++- fheatmap-1.0.1/fheatmap/man/fheatmap_data.Rd | 68 12 files changed, 1261 insertions(+), 1139 deletions(-)
Title: Regularized Cox Model
Description: Cox model regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty, and their adaptive forms, such as adaptive lasso and net adjusting for signs of linked coefficients. Moreover, it treats the number of non-zero coefficients as another tuning parameter and simultaneously selects with the regularization parameter \code{lambda}. In addition, it fits a varying coefficient Cox model by kernel smoothing, incorporated with the aforementioned penalties. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
Author: Xiang Li, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li <xl2473@columbia.edu>
Diff between Coxnet versions 0.1-1 dated 2015-03-22 and 0.2 dated 2015-12-09
DESCRIPTION | 10 MD5 | 31 - NAMESPACE | 4 R/Coxnet.R | 65 ++- R/RcppExports.R | 40 ++ R/coxini.R | 131 +++----- R/coxprep.R | 102 +++--- R/coxsplit.R | 27 + R/loCoxnet.R |only R/print.Coxnet.R | 39 +- inst/include/Coxnet_RcppExports.h | 190 +++++++++++ man/Coxnet-package.Rd | 18 - man/Coxnet.Rd | 103 ++++-- man/coxsplit.Rd | 21 - man/print.Coxnet.Rd | 4 src/Coxnet.cpp | 619 +++++++++++++++++++++++++++++++++++++- src/RcppExports.cpp | 447 +++++++++++++++++++++++++++ 17 files changed, 1578 insertions(+), 273 deletions(-)
Title: Advanced Gene Set Enrichment Analysis
Description: Implements an algorithm to conduct advanced
gene set enrichment analysis on the results of genomics experiments.
Author: Cedric Simillion
Maintainer: Cedric Simillion <cedric.simillion@dkf.unibe.ch>
Diff between SetRank versions 1.0.0 dated 2015-12-08 and 1.0.1 dated 2015-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/analysis.R | 3 ++- R/buildSets.R | 4 +++- inst/doc/vignette.pdf |binary man/buildSetCollection.Rd | 1 + 6 files changed, 14 insertions(+), 10 deletions(-)
More information about sensitivity2x2xk at CRAN
Permanent link
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Hadley Wickham [aut],
JJ Allaire [aut, cre],
Kevin Ushey [ctb],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rstudioapi versions 0.3.1 dated 2015-04-06 and 0.4.0 dated 2015-12-09
DESCRIPTION | 14 +++++++++----- MD5 | 30 +++++++++++++++++++----------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 5 +++++ R/document-api.R |only R/document-methods.R |only R/misc.R |only R/stubs.R | 7 ++++++- man/callFun.Rd | 2 +- man/document-mutation.Rd |only man/document_position.Rd |only man/document_range.Rd |only man/getActiveDocumentContext.Rd |only man/getVersion.Rd | 2 +- man/hasFun.Rd | 2 +- man/isAvailable.Rd | 2 +- man/navigateToFile.Rd |only man/sourceMarkers.Rd | 1 - man/versionInfo.Rd | 1 - man/viewer.Rd | 2 +- 20 files changed, 67 insertions(+), 25 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between rmdformats versions 0.1 dated 2015-12-08 and 0.1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/create.doc.R | 2 -- R/html_clean.R | 13 ------------- R/html_docco.R | 13 ------------- R/pilltabs.R | 6 ++++++ inst/doc/introduction.html | 4 ++-- man/create.doc.Rd | 2 -- man/html_clean.Rd | 14 -------------- man/html_docco.Rd | 14 -------------- man/pilltabs.Rd | 7 +++++++ 11 files changed, 29 insertions(+), 74 deletions(-)
Title: Risk Management
Description: Computes risk measures from data, as well as performs risk management procedures.
Author: Marcelo Brutti Righi
Maintainer: Marcelo Brutti Righi <marcelobrutti@hotmail.com>
Diff between riskR versions 1.0 dated 2015-10-19 and 1.1 dated 2015-12-09
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++++--------------- R/risk.R | 20 ++++++++------------ R/risk.decision.R | 12 ++++++------ R/risk.hedge.R | 10 +++++----- R/risk.port.R | 10 +++++----- R/risk.port2.R |only R/risk.req.R | 6 +++--- R/risk.roll.R | 8 ++++---- build/partial.rdb |binary data |only man/returns.Rd |only man/risk.Rd | 26 +++++++++++++------------- man/risk.decision.Rd | 18 +++++++++++------- man/risk.hedge.Rd | 20 ++++++++++++-------- man/risk.port.Rd | 20 ++++++++++++-------- man/risk.port2.Rd |only man/risk.req.Rd | 18 +++++++++++------- man/risk.roll.Rd | 20 ++++++++++++-------- man/riskR-package.Rd | 2 ++ 20 files changed, 128 insertions(+), 106 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-level, high-performance MongoDB client based on libmongoc and
jsonlite. Includes support for aggregation, indexing, map-reduce, streaming,
SSL encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.6 dated 2015-10-31 and 0.7 dated 2015-12-09
DESCRIPTION | 20 MD5 | 152 ++--- NAMESPACE | 2 NEWS | 7 R/object.R | 23 R/stream.R | 26 configure | 2 inst/doc/intro.Rmd | 9 inst/doc/intro.html | 15 man/mongo.Rd | 23 src/Makevars.in | 6 src/Makevars.win | 4 src/bson/bcon.h | 18 src/bson/bson-atomic.h | 2 src/bson/bson-compat.h | 3 src/bson/bson-config.h | 37 + src/bson/bson-json.c | 54 - src/bson/bson-string.c | 4 src/bson/bson-version.h | 15 src/bson/bson.c | 6 src/mongoc/mongoc-async-cmd.c | 3 src/mongoc/mongoc-bulk-operation-private.h | 1 src/mongoc/mongoc-bulk-operation.c | 12 src/mongoc/mongoc-bulk-operation.h | 2 src/mongoc/mongoc-client-pool.c | 8 src/mongoc/mongoc-client-private.h | 29 - src/mongoc/mongoc-client.c | 186 +++++- src/mongoc/mongoc-client.h | 4 src/mongoc/mongoc-cluster-private.h | 21 src/mongoc/mongoc-cluster.c | 175 +++--- src/mongoc/mongoc-collection-private.h | 2 src/mongoc/mongoc-collection.c | 450 +++++++++++---- src/mongoc/mongoc-collection.h | 12 src/mongoc/mongoc-cursor-array-private.h | 1 src/mongoc/mongoc-cursor-array.c | 29 - src/mongoc/mongoc-cursor-cursorid-private.h | 13 src/mongoc/mongoc-cursor-cursorid.c | 233 ++++++-- src/mongoc/mongoc-cursor-private.h | 57 + src/mongoc/mongoc-cursor.c | 657 ++++++++++++++++++----- src/mongoc/mongoc-cursor.h | 35 - src/mongoc/mongoc-database-private.h | 5 src/mongoc/mongoc-database.c | 135 +++- src/mongoc/mongoc-database.h | 5 src/mongoc/mongoc-error.h | 4 src/mongoc/mongoc-find-and-modify-private.h |only src/mongoc/mongoc-find-and-modify.c |only src/mongoc/mongoc-find-and-modify.h |only src/mongoc/mongoc-gridfs-file-private.h | 3 src/mongoc/mongoc-gridfs-file.c | 69 +- src/mongoc/mongoc-gridfs.c | 4 src/mongoc/mongoc-host-list-private.h | 4 src/mongoc/mongoc-host-list.c | 13 src/mongoc/mongoc-host-list.h | 5 src/mongoc/mongoc-log.c | 7 src/mongoc/mongoc-matcher.h | 6 src/mongoc/mongoc-read-concern-private.h |only src/mongoc/mongoc-read-concern.c |only src/mongoc/mongoc-read-concern.h |only src/mongoc/mongoc-read-prefs-private.h | 3 src/mongoc/mongoc-read-prefs.c | 2 src/mongoc/mongoc-rpc-private.h | 5 src/mongoc/mongoc-rpc.c | 39 + src/mongoc/mongoc-server-description-private.h | 8 src/mongoc/mongoc-server-description.c | 78 ++ src/mongoc/mongoc-server-stream-private.h | 6 src/mongoc/mongoc-server-stream.c | 12 src/mongoc/mongoc-thread-private.h | 2 src/mongoc/mongoc-topology-description-private.h | 1 src/mongoc/mongoc-topology-description.c | 104 +++ src/mongoc/mongoc-topology-scanner.c | 3 src/mongoc/mongoc-uri.c | 26 src/mongoc/mongoc-uri.h | 2 src/mongoc/mongoc-util-private.h | 5 src/mongoc/mongoc-util.c | 45 + src/mongoc/mongoc-version.h | 16 src/mongoc/mongoc-write-command-private.h | 2 src/mongoc/mongoc-write-command.c | 133 +++- src/mongoc/mongoc-write-concern.c | 12 tools/winlibs.R | 4 vignettes/intro.Rmd | 9 80 files changed, 2320 insertions(+), 815 deletions(-)
Title: Robust Linear Quantile Regression
Description: It fits a robust linear quantile regression model using a new family of zero-quantile distributions for the error term.
This family of distribution includes skewed versions of the Normal, Student's t, Laplace, Slash and Contaminated Normal distribution.
It provides estimates and full inference. It also provides envelopes plots for assessing the fit and confidences bands when several quantiles are provided simultaneously.
Author: Christian E. Galarza, Luis Benites, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between lqr versions 1.0 dated 2015-11-06 and 1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/EMonly.R | 2 +- R/FUNCTION.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Tools for Harnessing 'MLBAM' 'Gameday' Data and Visualizing
'pitchfx'
Description: With 'pitchRx', one can easily obtain Major League Baseball Advanced
Media's 'Gameday' data (as well as store it in a remote database). The
'Gameday' website hosts a wealth of data in XML format, but perhaps most
interesting is 'pitchfx'. Among other things, 'pitchfx' data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D 'scatterplots'
of the baseball's flight path. 'pitchfx' data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. 'pitchRx' provides an easy
and robust way to generate strike-zone plots using the 'ggplot2' package.
Author: Carson Sievert <cpsievert1@gmail.com>
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between pitchRx versions 1.8.1 dated 2015-10-25 and 1.8.2 dated 2015-12-09
DESCRIPTION | 25 +++++++++++++------------ MD5 | 6 +++--- NEWS | 6 ++++++ R/scrape.R | 1 + 4 files changed, 23 insertions(+), 15 deletions(-)
Title: Combine Data from Positive and Negative Ionization Mode Finding
Common Entities
Description: Find common entities detected in both positive and negative
ionization mode, delete this entity in the less sensible mode and combine both
matrices.
Author: Monica Calderon-Santiago
Maintainer: Monica Calderon-Santiago <b42casam@uco.es>
Diff between MScombine versions 1.0 dated 2015-11-20 and 1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/FilterbyRT.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Linear Regression Based on Linear Structure Between Covariates
Description: Linear regression based on a recursive structural equation model
(explicit multiples correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics (Boxplot with confidence intervals, etc) and regression trees.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>
Diff between CorReg versions 1.0.5 dated 2015-06-09 and 1.1.1 dated 2015-12-09
DESCRIPTION | 27 +++++++++++----------- MD5 | 56 ++++++++++++++++++++++++---------------------- NAMESPACE | 44 ++++++++++++++++++++++++++++++++++-- NEWS | 11 ++++++--- R/A_clere.R | 2 - R/BoxPlot.R |only R/CorReg-package.R | 7 ++++- R/Estep.R | 2 - R/MSE_loc.R | 3 -- R/Terminator.R | 3 +- R/alphabet.R |only R/anthem.R |only R/correg.R | 33 ++++++++++++++++++--------- R/density_estimation.R | 4 ++- R/mixture_generator.R | 4 ++- R/structureFinder.R | 6 +++- man/BicZ.Rd | 4 +-- man/BoxPlot.Rd |only man/Conan.Rd | 4 +-- man/CorReg-package.Rd | 31 +++++++++++++------------ man/MSE_loc.Rd | 14 ++++------- man/Terminator.Rd | 6 +++- man/compare_struct.Rd | 2 - man/correg.Rd | 16 ++++++------- man/density_estimation.Rd | 6 +++- man/matplot_zone.Rd | 4 +-- man/mixture_generator.Rd | 3 +- man/readZ.Rd | 2 - man/recursive_tree.Rd | 8 +++--- man/showdata.Rd | 8 ++++-- man/structureFinder.Rd | 24 +++++++++++-------- 31 files changed, 208 insertions(+), 126 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web APIs for chemical information.
Author: Eduard Szöcs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szöcs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.3.1 dated 2015-09-27 and 0.0.4.0 dated 2015-12-09
webchem-0.0.3.1/webchem/man/cir_query.Rd |only webchem-0.0.3.1/webchem/man/csid_compinfo.Rd |only webchem-0.0.3.1/webchem/man/csid_extcompinfo.Rd |only webchem-0.0.3.1/webchem/man/ppdb_query.Rd |only webchem-0.0.4.0/webchem/DESCRIPTION | 21 webchem-0.0.4.0/webchem/MD5 | 101 +- webchem-0.0.4.0/webchem/NAMESPACE | 24 webchem-0.0.4.0/webchem/NEWS | 54 + webchem-0.0.4.0/webchem/R/alanwood.R | 24 webchem-0.0.4.0/webchem/R/chemid.R |only webchem-0.0.4.0/webchem/R/chemspider.R | 533 ++++++++++++++- webchem-0.0.4.0/webchem/R/cir.R | 24 webchem-0.0.4.0/webchem/R/cts.R | 12 webchem-0.0.4.0/webchem/R/etox.R | 16 webchem-0.0.4.0/webchem/R/physprop.R | 23 webchem-0.0.4.0/webchem/R/ppdb.R | 22 webchem-0.0.4.0/webchem/R/pubchem.R | 91 +- webchem-0.0.4.0/webchem/R/utils.R |only webchem-0.0.4.0/webchem/R/webchem-defunct.R |only webchem-0.0.4.0/webchem/R/webchem-deprecated.R | 44 + webchem-0.0.4.0/webchem/inst |only webchem-0.0.4.0/webchem/man/alanwood.Rd | 6 webchem-0.0.4.0/webchem/man/chemid.Rd |only webchem-0.0.4.0/webchem/man/cid_compinfo.Rd | 2 webchem-0.0.4.0/webchem/man/cir.Rd |only webchem-0.0.4.0/webchem/man/cs_compinfo.Rd |only webchem-0.0.4.0/webchem/man/cs_convert.Rd |only webchem-0.0.4.0/webchem/man/cs_csid_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_extcompinfo.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_csid.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_inchikey.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_smiles.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_csid.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_inchi.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_smiles_inchi.Rd |only webchem-0.0.4.0/webchem/man/cts_compinfo.Rd | 7 webchem-0.0.4.0/webchem/man/cts_convert.Rd | 2 webchem-0.0.4.0/webchem/man/etox_basic.Rd | 2 webchem-0.0.4.0/webchem/man/etox_targets.Rd | 2 webchem-0.0.4.0/webchem/man/etox_tests.Rd | 2 webchem-0.0.4.0/webchem/man/extr_num.Rd |only webchem-0.0.4.0/webchem/man/get_cid.Rd | 2 webchem-0.0.4.0/webchem/man/get_csid.Rd | 2 webchem-0.0.4.0/webchem/man/get_etoxid.Rd | 2 webchem-0.0.4.0/webchem/man/is.cas.Rd |only webchem-0.0.4.0/webchem/man/is.inchikey.Rd |only webchem-0.0.4.0/webchem/man/is.inchikey_cs.Rd |only webchem-0.0.4.0/webchem/man/pan.Rd | 2 webchem-0.0.4.0/webchem/man/parse_mol.Rd |only webchem-0.0.4.0/webchem/man/physprop.Rd | 2 webchem-0.0.4.0/webchem/man/ppdb.Rd |only webchem-0.0.4.0/webchem/man/ppdb_buildidx.Rd | 2 webchem-0.0.4.0/webchem/man/ppdb_idx.Rd | 5 webchem-0.0.4.0/webchem/man/webchem-defunct.Rd |only webchem-0.0.4.0/webchem/man/webchem-deprecated.Rd | 26 webchem-0.0.4.0/webchem/tests/testthat/test-alanwood.R | 7 webchem-0.0.4.0/webchem/tests/testthat/test-chemid.R |only webchem-0.0.4.0/webchem/tests/testthat/test-chemspider.R | 259 ++++++- webchem-0.0.4.0/webchem/tests/testthat/test-cir.R | 16 webchem-0.0.4.0/webchem/tests/testthat/test-cts.R | 18 webchem-0.0.4.0/webchem/tests/testthat/test-etox.R | 4 webchem-0.0.4.0/webchem/tests/testthat/test-physprop.R | 3 webchem-0.0.4.0/webchem/tests/testthat/test-ppdb.R | 8 webchem-0.0.4.0/webchem/tests/testthat/test-pubchem.R | 11 webchem-0.0.4.0/webchem/tests/testthat/test-utils.R |only 67 files changed, 1163 insertions(+), 218 deletions(-)
Title: Common Infrastructure for Extensions of Exponential Random Graph
Models
Description: Datasets and definitions of generic functions used in dependencies of the xergm package.
Author: Philip Leifeld [aut, cre]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between xergm.common versions 1.5.4 dated 2015-09-20 and 1.6 dated 2015-12-09
DESCRIPTION | 14 ++++----- MD5 | 10 +++--- R/preprocess.R | 79 +++++++++++++++++++++++++++++++++++++------------------ data/chemnet.rda |binary data/knecht.rda |binary man/chemnet.Rd | 2 - 6 files changed, 67 insertions(+), 38 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-0 dated 2015-10-27 and 1.2-1 dated 2015-12-09
DESCRIPTION | 10 MD5 | 36 +- R/g.analyse.R | 10 R/g.calibrate.R | 20 - R/g.create.sp.mat.R | 17 - R/g.getbout.R | 9 R/g.getmeta.R | 54 ++-- R/g.part1.R | 531 ++++++++++++++++++++------------------- R/g.part2.R | 4 R/g.part3.R | 167 ++++++------ R/g.part4.R | 78 ++--- R/g.report.part2.R | 2 R/g.report.part4.R | 698 ++++++++++++++++++++++++++-------------------------- R/g.shell.GGIR.R | 109 ++++++-- R/g.sib.det.R | 4 inst/NEWS.Rd | 11 man/GGIR-package.Rd | 9 man/g.part3.Rd | 169 ++++++------ man/g.shell.GGIR.Rd | 325 ++++++++++++------------ 19 files changed, 1184 insertions(+), 1079 deletions(-)