Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting.
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph]
Maintainer: Julien Vollering <julien.vollering@hvl.no>
Diff between MIAmaxent versions 0.4.0 dated 2017-02-14 and 1.0.0 dated 2018-11-13
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MIAmaxent-1.0.0/MIAmaxent/man/figures/workflow-flowchart.pdf |binary MIAmaxent-1.0.0/MIAmaxent/man/figures/workflow-flowchart.png |binary MIAmaxent-1.0.0/MIAmaxent/man/modelFromLambdas.Rd |only MIAmaxent-1.0.0/MIAmaxent/man/plotFOP.Rd | 177 MIAmaxent-1.0.0/MIAmaxent/man/plotResp.Rd | 139 MIAmaxent-1.0.0/MIAmaxent/man/predict.iwlr.Rd |only MIAmaxent-1.0.0/MIAmaxent/man/projectModel.Rd | 207 MIAmaxent-1.0.0/MIAmaxent/man/readData.Rd | 210 MIAmaxent-1.0.0/MIAmaxent/man/release_questions.Rd | 25 MIAmaxent-1.0.0/MIAmaxent/man/selectDVforEV.Rd | 185 MIAmaxent-1.0.0/MIAmaxent/man/selectEV.Rd | 209 MIAmaxent-1.0.0/MIAmaxent/man/testAUC.Rd | 115 MIAmaxent-1.0.0/MIAmaxent/man/toydata_dvs.Rd | 56 MIAmaxent-1.0.0/MIAmaxent/man/toydata_seldvs.Rd | 58 MIAmaxent-1.0.0/MIAmaxent/man/toydata_selevs.Rd | 62 MIAmaxent-1.0.0/MIAmaxent/man/toydata_sp1po.Rd | 55 MIAmaxent-1.0.0/MIAmaxent/vignettes/a-modeling-example.Rmd |only MIAmaxent-1.0.0/MIAmaxent/vignettes/a-modeling-example.html.asis |only 89 files changed, 6532 insertions(+), 6634 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <http://data.neonscience.org>
or through the NEON Data API (see <http://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Christine Laney <claney@battelleecology.org>, Claire Lunch <clunch@battelleecology.org>
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.0.0 dated 2018-11-03 and 1.0.1 dated 2018-11-13
neonUtilities-1.0.0/neonUtilities/inst/extdata/NEON_gp |only neonUtilities-1.0.1/neonUtilities/DESCRIPTION | 6 ++-- neonUtilities-1.0.1/neonUtilities/MD5 | 15 +++------- neonUtilities-1.0.1/neonUtilities/R/getVariables.R | 2 - neonUtilities-1.0.1/neonUtilities/R/stackByTable.R | 2 - neonUtilities-1.0.1/neonUtilities/README.md | 11 ++++++- neonUtilities-1.0.1/neonUtilities/tests/testthat/test_stackByTable.R | 5 ++- 7 files changed, 22 insertions(+), 19 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial
clustering of applications with noise) and OPTICS (ordering points to identify
the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier
factor) algorithm. The implementations use the kd-tree data structure (from
library ANN) for faster k-nearest neighbor search. An R interface to fast kNN
and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-2 dated 2018-05-18 and 1.1-3 dated 2018-11-13
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 8 build/vignette.rds |binary inst/doc/dbscan.Rnw | 18 - inst/doc/dbscan.pdf |binary inst/doc/hdbscan.html | 507 ++++++++++++++++++-------------------------------- man/dbscan.Rd | 2 man/pointdensity.Rd | 2 src/R_density.cpp | 2 vignettes/dbscan.Rnw | 18 - 11 files changed, 230 insertions(+), 355 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.56.1 dated 2018-09-21 and 0.57.0 dated 2018-11-13
skpr-0.56.1/skpr/src/covarianceMatrix.cpp |only skpr-0.57.0/skpr/DESCRIPTION | 8 skpr-0.57.0/skpr/MD5 | 55 ++-- skpr-0.57.0/skpr/NEWS | 25 +- skpr-0.57.0/skpr/R/RcppExports.R | 4 skpr-0.57.0/skpr/R/calc_conservative_anticoef.R |only skpr-0.57.0/skpr/R/convert_blockcolumn_rownames.R |only skpr-0.57.0/skpr/R/convert_model_dots.R |only skpr-0.57.0/skpr/R/eval_design.R | 220 +++++-------------- skpr-0.57.0/skpr/R/eval_design_custom_mc.R | 45 +-- skpr-0.57.0/skpr/R/eval_design_mc.R | 146 +++--------- skpr-0.57.0/skpr/R/eval_design_survival_mc.R | 52 +--- skpr-0.57.0/skpr/R/gen_design.R | 66 +---- skpr-0.57.0/skpr/R/generate_noise_block.R |only skpr-0.57.0/skpr/R/normalize_numeric_runmatrix.R |only skpr-0.57.0/skpr/R/rearrange_formula_by_order.R |only skpr-0.57.0/skpr/R/remove_skpr_blockcols.R |only skpr-0.57.0/skpr/R/skprGUI.R | 16 - skpr-0.57.0/skpr/R/skprGUIbrowser.R | 1 skpr-0.57.0/skpr/R/skprGUIserver.R | 12 - skpr-0.57.0/skpr/inst/shiny/skprGUI/server.R | 16 - skpr-0.57.0/skpr/man/calc_conservative_anticoef.Rd |only skpr-0.57.0/skpr/man/convert_blockcolumn_rownames.Rd |only skpr-0.57.0/skpr/man/convert_model_dots.Rd |only skpr-0.57.0/skpr/man/eval_design.Rd | 16 - skpr-0.57.0/skpr/man/eval_design_custom_mc.Rd | 14 - skpr-0.57.0/skpr/man/eval_design_mc.Rd | 22 + skpr-0.57.0/skpr/man/eval_design_survival_mc.Rd | 8 skpr-0.57.0/skpr/man/generate_noise_block.Rd |only skpr-0.57.0/skpr/man/normalize_numeric_runmatrix.Rd |only skpr-0.57.0/skpr/man/rearrange_formula_by_order.Rd |only skpr-0.57.0/skpr/man/remove_skpr_blockcols.Rd |only skpr-0.57.0/skpr/src/RcppExports.cpp | 12 - skpr-0.57.0/skpr/src/genOptimalDesign.cpp | 84 +++++-- skpr-0.57.0/skpr/tests/testthat/Rplots.pdf |binary skpr-0.57.0/skpr/tests/testthat/testExampleCode.R | 38 +-- 36 files changed, 362 insertions(+), 498 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.3 dated 2018-06-22 and 0.3.4 dated 2018-11-13
ChangeLog | 8 +++++ DESCRIPTION | 8 ++--- MD5 | 43 ++++++++++++++-------------- NEWS.md | 4 ++ R/help.R | 2 - R/parse.R | 22 +++++++++++++- R/read.R | 5 +-- R/utils.R | 4 +- README.md | 9 +++++ build/vignette.rds |binary inst/doc/configr.R | 6 +++ inst/doc/configr.Rmd | 7 ++++ inst/doc/configr.html | 61 +++++++++++++++++++++++++++------------- inst/doc/filetypes.html | 4 +- inst/extdata/config.global.toml |only man/eval.config.Rd | 5 +-- man/eval.config.sections.Rd | 4 +- man/fetch.config.Rd | 4 +- man/get.config.type.Rd | 3 + man/parse.extra.Rd | 6 ++- man/read.config.Rd | 4 +- tests/testthat/test_k_parse.R | 10 ++++++ vignettes/configr.Rmd | 7 ++++ 23 files changed, 163 insertions(+), 63 deletions(-)
Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction
techniques from R packages and a common
interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between dimRed versions 0.2.1 dated 2018-11-09 and 0.2.2 dated 2018-11-13
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 3 R/nnmf.R | 3 R/quality.R | 2 inst/doc/dimensionality-reduction.pdf | 4413 +++++++++++++++++----------------- tests/testthat/test_NNMF.R | 10 7 files changed, 2266 insertions(+), 2187 deletions(-)
Title: Deming, Theil-Sen, Passing-Bablock and Total Least Squares
Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>
Diff between deming versions 1.3 dated 2018-10-08 and 1.4 dated 2018-11-13
/tmp/cranberry1d084bca7b78/deming-1.3/deming/R/thielsen.R |only /tmp/cranberry1d084bca7b78/deming-1.3/deming/R/thielsen.fit.R |only /tmp/cranberry1d084bca7b78/deming-1.3/deming/cleanup |only /tmp/cranberry1d084bca7b78/deming-1.3/deming/man/thielsen.Rd |only /tmp/cranberry1d084bca7b78/deming-1.3/deming/tests/thiel.R |only /tmp/cranberry1d084bca7b78/deming-1.3/deming/tests/thiel.Rout.save |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/DESCRIPTION | 9 /tmp/cranberry1d084bca7b78/deming-1.4/deming/MD5 | 35 +-- /tmp/cranberry1d084bca7b78/deming-1.4/deming/NAMESPACE | 4 /tmp/cranberry1d084bca7b78/deming-1.4/deming/R/theilsen.R |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/R/theilsen.fit.R |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/build/vignette.rds |binary /tmp/cranberry1d084bca7b78/deming-1.4/deming/inst/NEWS.Rd | 16 + /tmp/cranberry1d084bca7b78/deming-1.4/deming/inst/doc/deming.R | 45 +++- /tmp/cranberry1d084bca7b78/deming-1.4/deming/inst/doc/deming.Rnw | 95 +++++++--- /tmp/cranberry1d084bca7b78/deming-1.4/deming/inst/doc/deming.pdf |binary /tmp/cranberry1d084bca7b78/deming-1.4/deming/man/theilsen.Rd |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/noweb/deming.R |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/tests/double.R | 4 /tmp/cranberry1d084bca7b78/deming-1.4/deming/tests/double.Rout.save | 4 /tmp/cranberry1d084bca7b78/deming-1.4/deming/tests/theil.R |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/tests/theil.Rout.save |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/vignettes/deming-001.pdf |only /tmp/cranberry1d084bca7b78/deming-1.4/deming/vignettes/deming.Rnw | 95 +++++++--- deming/R/deming.R | 18 + 25 files changed, 237 insertions(+), 88 deletions(-)
Title: Drug Interaction Modeling Based on Loewe Additivity Following
Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based
on the Loewe additivity model, following Harbron's approach (Statistics in
Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling
of the drug interaction index and supports "2-stage" estimation in addition
to "1-stage" estimation, including bootstrap-based confidence intervals.
The method requires data on the monotherapy responses and the package
accommodates both checkerboard and ray designs. Functions are available for
graphical exploration of model goodness-of-fit and diagnostics, as well as
for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between drugCombo versions 1.0.2 dated 2018-06-15 and 1.0.3 dated 2018-11-13
drugCombo |only 1 file changed
Title: Convert a Matrix of Raw Values into Nice and Tidy Data
Description: Functions to help dealing with raw data from measurements, like
reading and transforming raw values organized in matrices, calculating and
converting concentrations and calculating precision of duplicates /
triplicates / ... . It is compatible with and building on top of some
'tidyverse'-packages.
Author: Eike Christian Kühn [aut, cre]
Maintainer: Eike Christian Kühn <eike.kuehn@pixelwoelkchen.de>
Diff between bioset versions 0.2.2 dated 2018-04-17 and 0.2.3 dated 2018-11-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/calc.R | 4 ++-- R/set.R | 11 ++++++++++- build/vignette.rds |binary inst/doc/introduction.html | 10 ++++++++-- 7 files changed, 34 insertions(+), 14 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.1.1 dated 2018-08-07 and 0.1.2 dated 2018-11-13
DESCRIPTION | 8 - MD5 | 22 ++-- R/RaceID.R | 241 ++++++++++++++++++++++++++++++------------------- R/RaceID_utils.R | 3 inst/doc/RaceID.R | 3 inst/doc/RaceID.Rmd | 13 +- inst/doc/RaceID.html | 36 +++---- man/plotexpmap.Rd | 8 + man/plotmap.Rd | 4 man/plotmarkergenes.Rd | 13 ++ man/plotsymbolsmap.Rd | 11 ++ vignettes/RaceID.Rmd | 13 +- 12 files changed, 236 insertions(+), 139 deletions(-)
Title: Bayesian Additive Regression Trees Using Particle Gibbs Sampler
and Gibbs/Metropolis-Hastings Sampler
Description: The Particle Gibbs sampler and Gibbs/Metropolis-Hastings sampler were implemented
to fit Bayesian additive regression tree model. Construction of the model (training) and prediction
for a new data set (testing) can be separated. Our reference papers are:
Lakshminarayanan B, Roy D, Teh Y W. Particle Gibbs for Bayesian additive regression trees[C],
Artificial Intelligence and Statistics. 2015: 553-561,
<http://proceedings.mlr.press/v38/lakshminarayanan15.pdf>
and Chipman, H., George, E., and McCulloch R. (2010) Bayesian Additive Regression Trees. The Annals of Applied Statistics, 4,1, 266-298, <doi:10.1214/09-aoas285>.
Author: Pingyu Wang [aut, cre],
Dai Feng [aut],
Yang Bai [aut],
Qiuyue Shi [aut],
Zhicheng Zhao [aut],
Fei Su [aut],
Hugh Chipman [aut],
Robert McCulloch [aut]
Maintainer: Pingyu Wang <applewangpingyu@gmail.com>
Diff between pgbart versions 0.6.12 dated 2018-07-06 and 0.6.15 dated 2018-11-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/pgbart_train.R | 4 ++-- src/Serialize.h | 13 ++++++------- src/mbart.cpp | 4 ++-- 6 files changed, 20 insertions(+), 21 deletions(-)
Title: Quantification of Fate Bias in Multipotent Progenitors
Description: Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between FateID versions 0.1.4 dated 2018-08-07 and 0.1.5 dated 2018-11-13
DESCRIPTION | 10 ++-- MD5 | 8 +-- R/FateID_functions.R | 117 ++++++++++++++++++++++++++++++++------------------ inst/doc/FateID.html | 28 +++++------ man/plotexpression.Rd | 11 ++++ 5 files changed, 110 insertions(+), 64 deletions(-)
Title: Mode Testing and Exploring
Description: Different examples and methods for testing (including different proposals described in Ameijeiras-Alonso et al., 2018 <DOI:10.1007/s11749-018-0611-5>) and exploring (including the mode tree, mode forest and SiZer) the number of modes using nonparametric techniques.
Author: Jose Ameijeiras-Alonso [aut,cre],
Rosa M. Crujeiras [aut],
Alberto Rodríguez-Casal [aut],
The R Core Team 1996-2012 [ctb,cph] (C function 'BinDist2' obtained from package 'stats'),
The R Foundation 2005 [ctb,cph] (C function 'BinDist2' obtained from package 'stats')
Maintainer: Jose Ameijeiras-Alonso <jose.ameijeirasalonso@kuleuven.be>
Diff between multimode versions 1.3 dated 2018-06-13 and 1.4 dated 2018-11-13
DESCRIPTION | 12 - MD5 | 24 +-- NAMESPACE | 1 R/graphical_tools_lin.R | 294 +++++++++++++++++++++++++++++++++++++++++++++-- R/mode_testing_lin.R | 4 man/locmodes.Rd | 2 man/modeforest.Rd | 5 man/modetest.Rd | 6 man/modetree.Rd | 5 man/multimode-package.Rd | 10 - man/plot.gtmod.Rd | 15 +- man/sizer.Rd | 7 - man/stamps.Rd | 4 13 files changed, 336 insertions(+), 53 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Andreas Alfons, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Kamil Barton, Ben Bolker, Hans W. Borchers, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Romain Francois, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Soeren Hojsgaard, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Christopher Jackson, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Duncan Temple Lang, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Henric Nilsson, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Nathan Russell, Nick Sabbe, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Karline Soetaert, Werner A. Stahel, Alec Stephenson, Mark Stevenson, Matthias Templ, Terry Therneau, Yves Tille, Adrian Trapletti, Joshua Ulrich, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Hadley Wickham, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.25 dated 2018-08-14 and 0.99.26 dated 2018-11-13
DescTools-0.99.25/DescTools/man/PartitionBy.Rd |only DescTools-0.99.26/DescTools/DESCRIPTION | 10 DescTools-0.99.26/DescTools/MD5 | 57 + DescTools-0.99.26/DescTools/NAMESPACE | 24 DescTools-0.99.26/DescTools/NEWS | 52 + DescTools-0.99.26/DescTools/R/Desc.R | 8 DescTools-0.99.26/DescTools/R/DescTools.r | 604 +++++++++++++++---- DescTools-0.99.26/DescTools/R/DoBy.r |only DescTools-0.99.26/DescTools/R/LinMod.R | 76 ++ DescTools-0.99.26/DescTools/R/SpecialPlots.r | 1 DescTools-0.99.26/DescTools/R/StatsAndCIs.r | 381 +++++++++-- DescTools-0.99.26/DescTools/data/d.whisky.rda |binary DescTools-0.99.26/DescTools/data/xlConst.rda |only DescTools-0.99.26/DescTools/man/Abstract.Rd | 2 DescTools-0.99.26/DescTools/man/BinomCI.Rd | 12 DescTools-0.99.26/DescTools/man/BinomDiffCI.Rd | 72 +- DescTools-0.99.26/DescTools/man/Cross.Rd |only DescTools-0.99.26/DescTools/man/CrossN.Rd |only DescTools-0.99.26/DescTools/man/DescTools-package.Rd | 12 DescTools-0.99.26/DescTools/man/DoBy.Rd |only DescTools-0.99.26/DescTools/man/Dot.Rd |only DescTools-0.99.26/DescTools/man/Format.Rd | 3 DescTools-0.99.26/DescTools/man/Lc.Rd | 1 DescTools-0.99.26/DescTools/man/OddsRatio.Rd | 9 DescTools-0.99.26/DescTools/man/Outlier.Rd | 23 DescTools-0.99.26/DescTools/man/PlotDot.Rd | 3 DescTools-0.99.26/DescTools/man/PlotQQ.Rd | 12 DescTools-0.99.26/DescTools/man/Sample.Rd |only DescTools-0.99.26/DescTools/man/TMod.Rd | 18 DescTools-0.99.26/DescTools/man/TOne.Rd | 20 DescTools-0.99.26/DescTools/man/XLView.Rd | 76 ++ DescTools-0.99.26/DescTools/man/d.whisky.Rd | 16 DescTools-0.99.26/DescTools/man/dir.choose.Rd |only DescTools-0.99.26/DescTools/man/wdConst.Rd | 6 34 files changed, 1211 insertions(+), 287 deletions(-)
Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption, timeout,
background tasks, and streaming STDIN / STDOUT / STDERR over binary or text
connections. Arguments on Windows automatically get encoded and quoted to work on different
locales. On Unix platforms the package also provides functions for evaluating
expressions inside a temporary fork. Such evaluations have no side effects on the
main R process, and support reliable interrupts and timeouts. This provides the
basis for a sandboxing mechanism.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between sys versions 2.0 dated 2018-11-06 and 2.1 dated 2018-11-13
DESCRIPTION | 6 +-- MD5 | 15 ++++--- NEWS | 5 ++ R/exec.R | 22 ++++++----- man/exec.Rd | 7 ++- src/exec.c | 83 ++++++++++++++++++++++++++++++++---------- src/init.c | 4 +- src/win32/exec.c | 32 +++++++++++++--- tests/testthat/test-timeout.R |only 9 files changed, 127 insertions(+), 47 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.6-8 dated 2018-11-10 and 0.6-9 dated 2018-11-13
DESCRIPTION | 8 +++--- MD5 | 6 ++-- configure | 77 ++--------------------------------------------------------- configure.ac | 5 ++- 4 files changed, 13 insertions(+), 83 deletions(-)
Title: Visualize Alpha-Helical Peptide Sequences
Description: Create publication-quality, 2-dimensional visualizations of alpha-helical peptide
sequences. Specifically, allows the user to programmatically generate
helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of
alpha-helical oligopeptides. See Wadhwa RR, et al. (2018)
<doi:10.21105/joss.01008> for more information.
Author: Raoul Wadhwa [cre, aut],
Regina Stevens-Truss [aut],
Vigneshwar Subramanian [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Diff between helixvis versions 0.9.1 dated 2018-06-25 and 1.0.1 dated 2018-11-13
DESCRIPTION | 26 +++---- MD5 | 26 +++++-- NAMESPACE | 1 R/data.R |only R/draw_wenxiang.R | 173 +++++++++++++++++++++++++++++---------------------- R/draw_wheel.R | 136 +++++++++++++++++++++------------------- build |only data |only inst |only man/draw_wenxiang.Rd | 14 +++- man/draw_wheel.Rd | 14 +++- man/sequence.Rd |only tests |only vignettes |only 14 files changed, 232 insertions(+), 158 deletions(-)
Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models.
Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and
Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>.
Parametric models from the special exponential family (SEF) are based on
Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and
Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
Author: Takeshi Emura, Ya-Hsuan Hu
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between double.truncation versions 1.1 dated 2018-08-01 and 1.2 dated 2018-11-13
DESCRIPTION | 12 +++++++----- MD5 | 6 ++++-- R/NPMLE.R |only man/NPMLE.Rd |only man/double.truncation-package.Rd | 10 ++++++++++ 5 files changed, 21 insertions(+), 7 deletions(-)
More information about double.truncation at CRAN
Permanent link
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.3 dated 2018-10-10 and 1.30.4 dated 2018-11-13
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ R/version.R | 21 +++++++++++------- R/zzz.R | 6 ----- build/vignette.rds |binary inst/doc/BiocManager.html | 41 ++++++++++++++++++------------------- tests/testthat/test_repositories.R | 10 +++++---- tests/testthat/test_version.R | 29 ++++++++++++++++++++++++++ 8 files changed, 80 insertions(+), 47 deletions(-)
Title: Quadrangle Mesh
Description: Create a standard quadrangle mesh from 'raster' data for flexible
plotting and conversion to other mesh forms. The standard output 'quadmesh' is an 'mesh3d' object
used by the 'rgl' package. This is used for plotting raster data in 3D with or without textures, and
allows the application of a map projection without data loss.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between quadmesh versions 0.1.0 dated 2016-06-13 and 0.2.0 dated 2018-11-13
quadmesh-0.1.0/quadmesh/R/quadmesh.r |only quadmesh-0.2.0/quadmesh/DESCRIPTION | 23 +++++-- quadmesh-0.2.0/quadmesh/MD5 | 40 ++++++++++-- quadmesh-0.2.0/quadmesh/NAMESPACE | 37 +++++------ quadmesh-0.2.0/quadmesh/NEWS.md | 31 +++++++-- quadmesh-0.2.0/quadmesh/R/mesh-plot.R |only quadmesh-0.2.0/quadmesh/R/netcdf.R |only quadmesh-0.2.0/quadmesh/R/primitives.R |only quadmesh-0.2.0/quadmesh/R/quadmesh-package.R |only quadmesh-0.2.0/quadmesh/R/quadmesh.R |only quadmesh-0.2.0/quadmesh/R/textures.R |only quadmesh-0.2.0/quadmesh/R/utils.R |only quadmesh-0.2.0/quadmesh/README.md | 73 ++++++++++++++++------- quadmesh-0.2.0/quadmesh/build |only quadmesh-0.2.0/quadmesh/data |only quadmesh-0.2.0/quadmesh/inst |only quadmesh-0.2.0/quadmesh/man/etopo.Rd |only quadmesh-0.2.0/quadmesh/man/figures |only quadmesh-0.2.0/quadmesh/man/llh2xyz.Rd |only quadmesh-0.2.0/quadmesh/man/mesh_plot.Rd |only quadmesh-0.2.0/quadmesh/man/quadmesh-package.Rd |only quadmesh-0.2.0/quadmesh/man/quadmesh.Rd | 69 ++++++++++++--------- quadmesh-0.2.0/quadmesh/man/triangulate_quads.Rd |only quadmesh-0.2.0/quadmesh/man/worldll.Rd |only quadmesh-0.2.0/quadmesh/man/xymap.Rd |only quadmesh-0.2.0/quadmesh/tests |only quadmesh-0.2.0/quadmesh/vignettes |only 27 files changed, 185 insertions(+), 88 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-29 0.2.0
2018-03-06 0.1.1
Title: Tools to Manipulate and Query Semantic Data
Description: The Resource Description Framework, or 'RDF' is a widely used
data representation model that forms the cornerstone of the
Semantic Web. 'RDF' represents data as a graph rather than
the familiar data table or rectangle of relational databases.
The 'rdflib' package provides a friendly and concise user interface
for performing common tasks on 'RDF' data, such as reading, writing
and converting between the various serializations of 'RDF' data,
including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld';
creating new 'RDF' graphs, and performing graph queries using 'SPARQL'.
This package wraps the low level 'redland' R package which
provides direct bindings to the 'redland' C library. Additionally,
the package supports the newer and more developer friendly
'JSON-LD' format through the 'jsonld' package. The package
interface takes inspiration from the Python 'rdflib' library.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Bryce Mecum [rev] (<https://orcid.org/0000-0002-0381-3766>),
Anna Krystalli [rev] (<https://orcid.org/0000-0002-2378-4915>),
Viktor Senderov [ctb] (<https://orcid.org/0000-0003-3340-5963>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rdflib versions 0.1.0 dated 2018-03-09 and 0.2.0 dated 2018-11-13
rdflib-0.1.0/rdflib/inst/doc/data-lake.R |only rdflib-0.1.0/rdflib/inst/doc/data-lake.Rmd |only rdflib-0.1.0/rdflib/inst/doc/data-lake.html |only rdflib-0.1.0/rdflib/inst/examples/as_rdf.R |only rdflib-0.1.0/rdflib/inst/examples/getResults.R |only rdflib-0.1.0/rdflib/inst/examples/rdf_table.R |only rdflib-0.1.0/rdflib/vignettes/data-lake.Rmd |only rdflib-0.2.0/rdflib/DESCRIPTION | 36 rdflib-0.2.0/rdflib/MD5 | 82 rdflib-0.2.0/rdflib/NAMESPACE | 13 rdflib-0.2.0/rdflib/NEWS.md | 11 rdflib-0.2.0/rdflib/R/as_rdf.R |only rdflib-0.2.0/rdflib/R/rdf.R | 178 rdflib-0.2.0/rdflib/R/rdf_has_bdb.R | 43 rdflib-0.2.0/rdflib/R/rdf_methods.R | 48 rdflib-0.2.0/rdflib/R/rdf_parse.R | 4 rdflib-0.2.0/rdflib/R/rdf_serialize.R | 40 rdflib-0.2.0/rdflib/R/utilities.R | 14 rdflib-0.2.0/rdflib/R/write_nquads.R |only rdflib-0.2.0/rdflib/README.md | 71 rdflib-0.2.0/rdflib/build/vignette.rds |binary rdflib-0.2.0/rdflib/inst/CITATION | 2 rdflib-0.2.0/rdflib/inst/WORDLIST |only rdflib-0.2.0/rdflib/inst/doc/rdf_intro.R | 10 rdflib-0.2.0/rdflib/inst/doc/rdf_intro.Rmd | 18 rdflib-0.2.0/rdflib/inst/doc/rdf_intro.html | 2807 +------------- rdflib-0.2.0/rdflib/inst/docker |only rdflib-0.2.0/rdflib/inst/examples/rdf-wo-redland.R |only rdflib-0.2.0/rdflib/inst/examples/storage_types.R | 26 rdflib-0.2.0/rdflib/inst/extdata/ex.xml | 2 rdflib-0.2.0/rdflib/inst/extdata/github.json |only rdflib-0.2.0/rdflib/inst/extdata/vita.json | 4 rdflib-0.2.0/rdflib/inst/notebook |only rdflib-0.2.0/rdflib/man/as_rdf.Rd |only rdflib-0.2.0/rdflib/man/c.rdf.Rd | 3 rdflib-0.2.0/rdflib/man/rdf.Rd | 47 rdflib-0.2.0/rdflib/man/rdf_parse.Rd | 4 rdflib-0.2.0/rdflib/man/rdf_serialize.Rd | 26 rdflib-0.2.0/rdflib/man/rdflib-package.Rd | 16 rdflib-0.2.0/rdflib/man/read_nquads.Rd |only rdflib-0.2.0/rdflib/man/write_nquads.Rd |only rdflib-0.2.0/rdflib/tests/spelling.R |only rdflib-0.2.0/rdflib/tests/testthat/test-parse-serialize.R | 21 rdflib-0.2.0/rdflib/tests/testthat/test-rdf.R | 34 rdflib-0.2.0/rdflib/tests/testthat/test-rdf_add.R | 1 rdflib-0.2.0/rdflib/tests/testthat/test-rdf_storage.R |only rdflib-0.2.0/rdflib/tests/testthat/test-utilities.R |only rdflib-0.2.0/rdflib/vignettes/articles |only rdflib-0.2.0/rdflib/vignettes/rdf_intro.Rmd | 18 49 files changed, 694 insertions(+), 2885 deletions(-)
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.4.1 dated 2018-09-10 and 1.4.2 dated 2018-11-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/recplot2.R | 4 ++-- README.md | 1 + 4 files changed, 9 insertions(+), 8 deletions(-)