Sun, 26 Jun 2016

Package survival updated to version 2.39-5 with previous version 2.39-4 dated 2016-05-11

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

Diff between survival versions 2.39-4 dated 2016-05-11 and 2.39-5 dated 2016-06-26

 survival-2.39-4/survival/noweb/code.pdf            |only
 survival-2.39-4/survival/vignettes/.install_extras |only
 survival-2.39-4/survival/vignettes/mstate.rda      |only
 survival-2.39-5/survival/DESCRIPTION               |    6 
 survival-2.39-5/survival/MD5                       |   72 ++++++----
 survival-2.39-5/survival/R/plot.survfit.R          |    6 
 survival-2.39-5/survival/R/survfit.matrix.R        |   67 ++-------
 survival-2.39-5/survival/R/survfitms.R             |   15 +-
 survival-2.39-5/survival/R/tmerge.R                |   27 ++-
 survival-2.39-5/survival/inst/NEWS.Rd              |   23 +++
 survival-2.39-5/survival/inst/doc/adjcurve.pdf     |binary
 survival-2.39-5/survival/inst/doc/compete.Rnw      |   17 ++
 survival-2.39-5/survival/inst/doc/compete.pdf      |binary
 survival-2.39-5/survival/inst/doc/splines.R        |   61 +++++---
 survival-2.39-5/survival/inst/doc/splines.Rnw      |  151 +++++++++++----------
 survival-2.39-5/survival/inst/doc/splines.pdf      |binary
 survival-2.39-5/survival/inst/doc/tests.pdf        |binary
 survival-2.39-5/survival/inst/doc/timedep.R        |   13 -
 survival-2.39-5/survival/inst/doc/timedep.Rnw      |   45 +++++-
 survival-2.39-5/survival/inst/doc/timedep.pdf      |binary
 survival-2.39-5/survival/inst/doc/validate.pdf     |binary
 survival-2.39-5/survival/man/survfit.coxph.Rd      |    9 +
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 survival-2.39-5/survival/vignettes/splines.Rnw     |  151 +++++++++++----------
 survival-2.39-5/survival/vignettes/timedep.Rnw     |   45 +++++-
 33 files changed, 536 insertions(+), 294 deletions(-)

More information about survival at CRAN
Permanent link

Package npROCRegression updated to version 1.0-2 with previous version 1.0-1 dated 2016-06-22

Title: Kernel-Based Nonparametric ROC Regression Modelling
Description: Implements several nonparametric regression approaches for the inclusion of covariate information on the receiver operating characteristic (ROC) framework.
Author: Maria Xose Rodriguez-Alvarez [aut, cre], Javier Roca-Pardinas [aut]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@uvigo.es>

Diff between npROCRegression versions 1.0-1 dated 2016-06-22 and 1.0-2 dated 2016-06-26

 DESCRIPTION                    |   14 ++++++------
 MD5                            |    9 ++++----
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 inst/doc/npROCRegression.html  |   14 ++++++------
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 6 files changed, 43 insertions(+), 43 deletions(-)

More information about npROCRegression at CRAN
Permanent link

Package magicaxis updated to version 2.0.0 with previous version 1.9.4 dated 2015-06-10

Title: Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>

Diff between magicaxis versions 1.9.4 dated 2015-06-10 and 2.0.0 dated 2016-06-26

 DESCRIPTION              |   12 +--
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 NAMESPACE                |    8 ++
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More information about magicaxis at CRAN
Permanent link

Package googlesheets updated to version 0.2.1 with previous version 0.2.0 dated 2016-03-18

Title: Manage Google Spreadsheets from R
Description: Interact with Google Sheets from R.
Author: Jennifer Bryan [aut, cre], Joanna Zhao [aut]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>

Diff between googlesheets versions 0.2.0 dated 2016-03-18 and 0.2.1 dated 2016-06-26

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 googlesheets-0.2.1/googlesheets/R/gs_download.R                                      |   15 
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 googlesheets-0.2.1/googlesheets/R/gs_read_csv.R                                      |    6 
 googlesheets-0.2.1/googlesheets/R/gs_read_listfeed.R                                 |    6 
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 googlesheets-0.2.1/googlesheets/R/httr-helpers.R                                     |   21 
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 googlesheets-0.2.1/googlesheets/inst/doc/basic-usage.html                            |  953 +++++-----
 googlesheets-0.2.1/googlesheets/inst/doc/formulas-and-formatted-numbers.R            |   22 
 googlesheets-0.2.1/googlesheets/inst/doc/formulas-and-formatted-numbers.Rmd          |   46 
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 googlesheets-0.2.1/googlesheets/inst/shiny-examples/01_read-public-sheet/ui.R        |    2 
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 googlesheets-0.2.1/googlesheets/inst/shiny-examples/04_embedded-google-form/server.R |    4 
 googlesheets-0.2.1/googlesheets/inst/shiny-examples/20_gs-explorer/README.Rmd        |   21 
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 googlesheets-0.2.1/googlesheets/man/gs_browse.Rd                                     |    5 
 googlesheets-0.2.1/googlesheets/man/gs_delete.Rd                                     |    2 
 googlesheets-0.2.1/googlesheets/man/gs_download.Rd                                   |    7 
 googlesheets-0.2.1/googlesheets/man/gs_grepdel.Rd                                    |    6 
 googlesheets-0.2.1/googlesheets/man/gs_read.Rd                                       |    2 
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 googlesheets-0.2.1/googlesheets/man/gs_read_csv.Rd                                   |    2 
 googlesheets-0.2.1/googlesheets/man/gs_read_listfeed.Rd                              |    2 
 googlesheets-0.2.1/googlesheets/man/gs_reshape_cellfeed.Rd                           |    2 
 googlesheets-0.2.1/googlesheets/man/gs_simplify_cellfeed.Rd                          |    2 
 googlesheets-0.2.1/googlesheets/man/gs_ws_modify.Rd                                  |    2 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-auth.R                           |   28 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-cell-specification.R             |    4 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-gs-ls.R                          |    2 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-gs-permissions.R                 |    2 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-gs-register.R                    |    2 
 googlesheets-0.2.1/googlesheets/tests/testthat/test-interactive.R                    |   10 
 googlesheets-0.2.1/googlesheets/vignettes/basic-usage.Rmd                            |  349 ++-
 googlesheets-0.2.1/googlesheets/vignettes/formulas-and-formatted-numbers.Rmd         |   46 
 googlesheets-0.2.1/googlesheets/vignettes/managing-auth-tokens.Rmd                   |  210 ++
 69 files changed, 2287 insertions(+), 1365 deletions(-)

More information about googlesheets at CRAN
Permanent link

New package future.BatchJobs with initial version 0.12.0
Package: future.BatchJobs
Version: 0.12.0
Depends: R (>= 3.2.0), future (>= 1.0.0)
Imports: BatchJobs (>= 1.6), R.utils
Suggests: listenv, markdown, R.rsp
VignetteBuilder: R.rsp
Title: A Future for BatchJobs
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Simple parallel and distributed processing using futures that utilizes the 'BatchJobs' framework, e.g. 'fit %<-% { glm.fit(x, y) }'. This package implements the Future API of the 'future' package.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/future.BatchJobs
BugReports: https://github.com/HenrikBengtsson/future.BatchJobs/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-26 00:20:15 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-06-26 12:39:35

More information about future.BatchJobs at CRAN
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New package tableHTML with initial version 0.2.10
Package: tableHTML
Type: Package
Title: A Tool to Create HTML Tables
Version: 0.2.10
Authors@R: person("Theo", "Boutaris", email = "teoboot2007@hotmail.com", role = c("aut", "cre", "cph"))
URL: https://lyzander.github.io/tableHTML
BugReports: https://github.com/LyzandeR/tableHTML/issues
Depends: R (>= 3.2.0)
Imports: htmltools, magrittr
Description: A tool to easily create and style HTML tables, which are compatible with shiny.
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-25 18:22:36 UTC; teoboot
Author: Theo Boutaris [aut, cre, cph]
Maintainer: Theo Boutaris <teoboot2007@hotmail.com>
Repository: CRAN
Date/Publication: 2016-06-26 09:30:36

More information about tableHTML at CRAN
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New package InspectChangepoint with initial version 1.0
Package: InspectChangepoint
Type: Package
Title: High-Dimensional Changepoint Estimation via Sparse Projection
Version: 1.0
Date: 2016-06-24
Author: Tengyao Wang
Maintainer: Tengyao Wang <t.wang@statslab.cam.ac.uk>
Imports: stats, graphics, MASS
Description: Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.
License: GPL-3
NeedsCompilation: no
Packaged: 2016-06-25 17:53:30 UTC; tengyao
Repository: CRAN
Date/Publication: 2016-06-26 09:17:50

More information about InspectChangepoint at CRAN
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Package couchDB updated to version 1.4.1 with previous version 1.3.0 dated 2014-09-09

Title: Connect to and Work with CouchDB Databases
Description: Interface to the couchDB document database <http://couchdb.apache.org>.
Author: Aleksander Dietrichson [aut, cre], Frans van Dunn<c3><a9> [ctb]
Maintainer: Aleksander Dietrichson <sasha@xrrch.com>

Diff between couchDB versions 1.3.0 dated 2014-09-09 and 1.4.1 dated 2016-06-26

 DESCRIPTION                         |   28 +-
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 NAMESPACE                           |    2 
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More information about couchDB at CRAN
Permanent link

Package XGR updated to version 1.0.2 with previous version 1.0.1 dated 2016-04-22

Title: Exploring Genomic Relations for Precision Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.0.1 dated 2016-04-22 and 1.0.2 dated 2016-06-26

 DESCRIPTION                     |   34 +++--
 MD5                             |  157 ++++++++++++++++++--------
 NAMESPACE                       |   41 ++++++
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 108 files changed, 1228 insertions(+), 710 deletions(-)

More information about XGR at CRAN
Permanent link

Package WARN updated to version 1.2-1 with previous version 1.2-0 dated 2016-02-23

Title: Weaning Age Reconstruction with Nitrogen Isotope Analysis
Description: This estimates precise weaning ages for a given skeletal population by analyzing the stable nitrogen isotope ratios of them. Bone collagen turnover rates estimated anew and the approximate Bayesian computation (ABC) were adopted in this package.
Author: Takumi Tsutaya
Maintainer: Takumi Tsutaya <tsutayatakumi@gmail.com>

Diff between WARN versions 1.2-0 dated 2016-02-23 and 1.2-1 dated 2016-06-26

 ChangeLog           |   10 +++++++---
 DESCRIPTION         |    8 ++++----
 MD5                 |   10 +++++-----
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 man/WARN-package.Rd |    4 ++--
 6 files changed, 35 insertions(+), 20 deletions(-)

More information about WARN at CRAN
Permanent link

Package tutorial updated to version 0.4.0 with previous version 0.3.1 dated 2016-05-13

Title: Convert R Markdown Files to DataCamp Light HTML Files
Description: DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light-weight implementation of the DataCamp UI, that allows you to embed interactive exercises inside HTML documents. The tutorial package makes it easy to create these HTML files from R Markdown files. An extension to knitr, tutorial detects appropriately formatted code chunks and replaces them with DataCamp Light readable chunks in the resulting HTML file.
Author: Filip Schouwenaars
Maintainer: Filip Schouwenaars <filip@datacamp.com>

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Package preprocomb updated to version 0.3.0 with previous version 0.2.0 dated 2016-01-01

Title: Tools for Preprocessing Combinations
Description: Preprocessing is often the most time-consuming phase in data analysis and preprocessing transformations interdependent in unexpected ways. This package helps to make preprocessing faster and more effective. It provides an S4 framework for creating and evaluating preprocessing combinations for classification, clustering and outlier detection. The framework supports adding of user-defined preprocessors and preprocessing phases. Default preprocessors can be used for low variance removal, missing value imputation, scaling, outlier removal, noise smoothing, feature selection and class imbalance correction.
Author: Markus Vattulainen
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>

Diff between preprocomb versions 0.2.0 dated 2016-01-01 and 0.3.0 dated 2016-06-26

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Package simLife updated to version 0.2.3 with previous version 0.2.1 dated 2016-06-25

Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

Diff between simLife versions 0.2.1 dated 2016-06-25 and 0.2.3 dated 2016-06-26

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