Title: Efficient Constrained Based Modelling in R
Description: This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybil versions 1.3.0 dated 2015-06-17 and 1.3.2 dated 2015-11-17
DESCRIPTION | 14 +- MD5 | 37 +++--- NAMESPACE | 4 R/deadEndMetabolite.R | 2 R/fluxDistributionClass.R | 2 R/generateWT.R | 92 +++++++++------ R/optObj_cplexAPIClass.R | 8 - R/optObj_glpkAPIClass.R | 24 +-- R/optObj_lpSolveAPIClass.R | 4 R/rmReact.R | 2 R/sysBiolAlg_fbaEasyConstraintClass.R |only R/sysBiolAlg_mtfEasyConstraintClass.R |only README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 24 +++ inst/doc/sybil.R | 181 ++++++++++++++++++++---------- inst/doc/sybil.Rnw | 75 ++++++++++++ inst/doc/sybil.pdf |binary man/readTSVmod.Rd | 2 man/sysBiolAlg_fbaEasyConstraint-class.Rd |only vignettes/sybil.Rnw | 75 ++++++++++++ 21 files changed, 407 insertions(+), 141 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.6.0 dated 2015-07-24 and 1.6.1 dated 2015-11-17
ChangeLog | 3 DESCRIPTION | 18 - MD5 | 41 +-- R/AllGenerics.R | 4 R/emomLM.R | 13 - R/margskewnorm.R |only R/modelSelection.R | 92 ++++++-- R/pmomLM.R | 12 - R/pmomPM.R | 2 R/rmom.R | 11 - R/zellnerLM.R | 12 - build/vignette.rds |binary data/hald.rda |binary inst/doc/mombf.pdf |binary man/msfit-class.Rd | 3 man/postProb.Rd | 6 man/rnlp.Rd | 4 src/cstat.cpp | 130 ++++++------ src/cstat.h | 4 src/do_mombf.h | 3 src/modelSel.cpp | 559 +++++++++++++++++++++++++++++++++++++---------------- src/modelSel.h | 26 +- 22 files changed, 636 insertions(+), 307 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, cph],
Dirk Metzler [ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.2.0 dated 2015-11-11 and 0.2.1 dated 2015-11-17
coala-0.2.0/coala/man/coala.Rd |only coala-0.2.1/coala/DESCRIPTION | 20 +-- coala-0.2.1/coala/MD5 | 62 +++++---- coala-0.2.1/coala/NAMESPACE | 8 + coala-0.2.1/coala/NEWS.md | 11 + coala-0.2.1/coala/R/RcppExports.R | 74 ++++++++--- coala-0.2.1/coala/R/coala.R | 11 - coala-0.2.1/coala/R/feature_mutation.R | 2 coala-0.2.1/coala/R/feature_recombination.R | 3 coala-0.2.1/coala/R/feature_sample.R | 2 coala-0.2.1/coala/R/segsites.R | 13 + coala-0.2.1/coala/R/simulator_ms.R | 4 coala-0.2.1/coala/R/simulator_msms.R | 4 coala-0.2.1/coala/R/simulator_scrm.R | 4 coala-0.2.1/coala/R/simulator_seqgen.R | 8 - coala-0.2.1/coala/R/sumstat.R | 98 +++++++++++++-- coala-0.2.1/coala/README.md |only coala-0.2.1/coala/inst/doc/coala-abc.html | 2 coala-0.2.1/coala/inst/doc/coala-extend.html | 2 coala-0.2.1/coala/inst/doc/coala-install.Rmd | 2 coala-0.2.1/coala/inst/doc/coala-install.html | 4 coala-0.2.1/coala/inst/doc/coala-intro.html | 18 +- coala-0.2.1/coala/inst/include/coala.h | 4 coala-0.2.1/coala/man/activate_seqgen.Rd | 2 coala-0.2.1/coala/man/calc_sumstats_from_data.Rd |only coala-0.2.1/coala/man/coala-package.Rd |only coala-0.2.1/coala/man/create_locus_trio.Rd |only coala-0.2.1/coala/man/create_segsites.Rd |only coala-0.2.1/coala/src/RcppExports.cpp | 40 +++--- coala-0.2.1/coala/src/parse_seqgen_output.cpp | 2 coala-0.2.1/coala/src/seg_sites.cpp | 63 +++++++-- coala-0.2.1/coala/tests/testthat/test-simulator-seqgen.R | 6 coala-0.2.1/coala/tests/testthat/test-sumstat-class.R | 72 ++++++++--- coala-0.2.1/coala/tests/testthat/test-travis-setup.R | 5 coala-0.2.1/coala/vignettes/coala-install.Rmd | 2 35 files changed, 384 insertions(+), 164 deletions(-)
Title: Benford Analysis for Data Validation and Forensic Analytics
Description: The Benford Analysis package provides tools that make it easier to
validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between benford.analysis versions 0.1.2.1 dated 2015-10-07 and 0.1.3 dated 2015-11-17
DESCRIPTION | 7 ++-- MD5 | 66 +++++++++++++++++++------------------- NAMESPACE | 2 - R/functions-new.R | 14 ++------ R/get.functions.R | 2 - R/internal.functions-new-code-2.R | 16 ++++----- README.md | 2 - man/MAD.Rd | 2 - man/benford.Rd | 17 +++++---- man/benford.analysis.Rd | 13 ++++--- man/census.2000_2010.Rd | 2 - man/census.2009.Rd | 4 +- man/chisq.Rd | 2 - man/corporate.payment.Rd | 2 - man/dfactor.Rd | 4 +- man/duplicatesTable.Rd | 2 - man/extract.digits.Rd | 12 +++--- man/getBfd.Rd | 4 +- man/getData.Rd | 4 +- man/getDigits.Rd | 6 +-- man/getDuplicates.Rd | 2 - man/getSuspects.Rd | 2 - man/lakes.perimeter.Rd | 2 - man/mantissa.Rd | 4 +- man/marc.Rd | 4 +- man/p.these.digits.Rd | 2 - man/p.this.digit.at.n.Rd | 2 - man/plot.Benford.Rd | 2 - man/print.Benford.Rd | 2 - man/sino.forest.Rd | 2 - man/suspectsTable.Rd | 6 +-- man/taxable.incomes.1978.Rd | 2 - tests/testthat/test-benford.R | 25 +++++++++++++- tests/testthat/test-extract.R | 5 ++ 34 files changed, 135 insertions(+), 110 deletions(-)
More information about benford.analysis at CRAN
Permanent link
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 0.8.1 dated 2015-01-07 and 0.9 dated 2015-11-17
tikzDevice-0.8.1/tikzDevice/inst/NEWS.Rd |only tikzDevice-0.8.1/tikzDevice/tests/testthat/Rplots.tex |only tikzDevice-0.8.1/tikzDevice/tests/testthat/Rplots_colors.tex |only tikzDevice-0.8.1/tikzDevice/vignettes/figs |only tikzDevice-0.9/tikzDevice/DESCRIPTION | 24 +-- tikzDevice-0.9/tikzDevice/MD5 | 72 +++------- tikzDevice-0.9/tikzDevice/NAMESPACE | 14 + tikzDevice-0.9/tikzDevice/R/cacheMetrics.R | 11 + tikzDevice-0.9/tikzDevice/R/latexStrWidth.R | 43 +++-- tikzDevice-0.9/tikzDevice/R/tikz.R | 8 - tikzDevice-0.9/tikzDevice/R/tikzDevice-package.R | 6 tikzDevice-0.9/tikzDevice/R/tikzInternal.R | 26 --- tikzDevice-0.9/tikzDevice/R/zzz.R | 2 tikzDevice-0.9/tikzDevice/build/vignette.rds |binary tikzDevice-0.9/tikzDevice/inst/doc/tikzDevice.R | 2 tikzDevice-0.9/tikzDevice/inst/doc/tikzDevice.pdf |binary tikzDevice-0.9/tikzDevice/man/anyMultibyteUTF8Characters.Rd | 4 tikzDevice-0.9/tikzDevice/man/getLatexStrWidth.Rd | 26 ++- tikzDevice-0.9/tikzDevice/man/gridToDevice.Rd | 4 tikzDevice-0.9/tikzDevice/man/sanitizeTexString.Rd | 4 tikzDevice-0.9/tikzDevice/man/setTikzDefaults.Rd | 6 tikzDevice-0.9/tikzDevice/man/tikz.Rd | 13 + tikzDevice-0.9/tikzDevice/man/tikzAnnotate.Rd | 17 +- tikzDevice-0.9/tikzDevice/man/tikzCompilerInfo.Rd | 4 tikzDevice-0.9/tikzDevice/man/tikzDevice-package.Rd | 2 tikzDevice-0.9/tikzDevice/src/tikzDevice.c | 18 +- tikzDevice-0.9/tikzDevice/src/tikzDevice.h | 3 tikzDevice-0.9/tikzDevice/tests/testthat/helper_reporters.R | 29 +--- tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/base_raster.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/grid_raster.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/raster_reflection.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/test_graphics.R | 1 tikzDevice-0.9/tikzDevice/tests/testthat/test_metrics_dict.R | 51 ++++--- 33 files changed, 223 insertions(+), 167 deletions(-)
Title: Sparse Learning Algorithms Using a LASSO-Type Penalty for
Coefficient Estimation and Model Prediction
Description: Coefficient estimation and model prediction based on the LASSO sparse
learning algorithm and its improved versions such as Bolasso, bootstrap ranking
LASSO, two-stage hybrid LASSO and others. These LASSO estimation procedures are
applied in the fields of variable selection, graphical modeling and ensemble
learning. The bagging LASSO model uses a Monte Carlo cross-entropy algorithm to
determine the best base-level models and improve predictive performance.
Author: Pi Guo, Yuantao Hao
Maintainer: Pi Guo <guopi.01@163.com>
Diff between SparseLearner versions 1.0.1 dated 2015-10-13 and 1.0-2 dated 2015-11-17
DESCRIPTION | 20 +++++++++++--------- MD5 | 12 ++++++++++-- NAMESPACE | 10 +++++++++- R/Bagging.lasso.R |only R/Plot.importance.R |only R/Predict.bagging.R |only R/Print.bagging.R |only man/Bagging.lasso.Rd |only man/Plot.importance.Rd |only man/Predict.bagging.Rd |only man/Print.bagging.Rd |only 11 files changed, 30 insertions(+), 12 deletions(-)
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Author: Bart Smeets [aut],
Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.0.0 dated 2015-11-15 and 3.0.1 dated 2015-11-17
DESCRIPTION | 11 +++---- MD5 | 45 ++++++++++++++--------------- R/simulator.R | 60 +++++++++++++++++++++------------------ R/wrap.R | 12 ++++++- inst/doc/introduction.html | 42 +++++++++++++-------------- man/add_generator.Rd | 2 - man/add_resource.Rd | 2 - man/get_capacity.Rd | 2 - man/get_mon_arrivals.Rd | 2 - man/get_mon_resources.Rd | 2 - man/get_queue_count.Rd | 2 - man/get_queue_size.Rd | 2 - man/get_server_count.Rd | 2 - man/now.Rd | 2 - man/peek.Rd | 2 - man/reset.Rd | 2 - man/run.Rd | 2 - man/simmer.Rd | 2 - src/simmer_rcpp.cpp | 2 - src/simulator.h | 2 - tests/testthat/test-activity.R | 3 + tests/testthat/test-simmer.R | 10 ++++++ tests/testthat/test-trajectory.R | 18 +++++++++++ tests/testthat/test-wrap.R |only 24 files changed, 137 insertions(+), 94 deletions(-)
Title: Binning and Plotting of Linearly Referenced Data
Description: Short for 'linear binning', the linbin package provides functions
for manipulating, binning, and plotting linearly referenced data. Although
developed for data collected on river networks, it can be used with any interval
or point data referenced to a 1-dimensional coordinate system. Flexible bin
generation and batch processing makes it easy to compute and visualize variables
at multiple scales, useful for identifying patterns within and between variables
and investigating the influence of scale of observation on data interpretation.
Author: Ethan Z. Welty [aut, cre],
Christian E. Torgersen [ctb] (author support and guidance),
Samuel J. Brenkman [ctb] (elwha and quinault datasets),
Jeffrey J. Duda [ctb] (elwha dataset),
Jonathan B. Armstrong [ctb] (fishmotion dataset)
Maintainer: Ethan Z. Welty <ethan.welty+linbin@gmail.com>
Diff between linbin versions 0.1.0 dated 2015-02-17 and 0.1.1 dated 2015-11-17
DESCRIPTION | 25 +++++---- MD5 | 90 ++++++++++++++++---------------- NAMESPACE | 3 - R/datasets.R | 40 +++++++------- R/event_creation.R | 4 - R/event_metrics.R | 2 R/plot_events.R | 6 +- R/sample_events.R | 2 README.md | 4 + build/vignette.rds |binary inst/CITATION | 16 ++++- inst/doc/examples.R | 14 ++--- inst/doc/examples.Rmd | 8 +- inst/doc/examples.html | 86 ++++++++++++++++++------------- inst/doc/introduction.R | 28 +++++----- inst/doc/introduction.html | 110 +++++++++++++++++++++++----------------- man/as_events.Rd | 4 - man/build_function_call.Rd | 2 man/crop_events.Rd | 2 man/cut_events.Rd | 2 man/elwha.Rd | 16 ++--- man/event_coverage.Rd | 2 man/event_gaps.Rd | 4 - man/event_overlaps.Rd | 2 man/event_range.Rd | 2 man/events.Rd | 4 - man/fill_event_gaps.Rd | 2 man/find_intersecting_events.Rd | 4 - man/fishmotion.Rd | 4 - man/if_else.Rd | 2 man/is_events.Rd | 2 man/is_not_integer.Rd | 2 man/netmap.Rd | 2 man/overlapping_events.Rd | 4 - man/plot_events.Rd | 10 +-- man/plot_events_single.Rd | 14 ++--- man/quinault.Rd | 26 ++++----- man/read_events.Rd | 4 - man/rgrep_exact.Rd | 2 man/sample_events.Rd | 4 - man/sampling_functions.Rd | 2 man/seq_events.Rd | 2 man/simple.Rd | 2 man/sorted_events.Rd | 2 man/transform_events.Rd | 2 vignettes/examples.Rmd | 8 +- 46 files changed, 314 insertions(+), 264 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.4.1 dated 2015-11-16 and 0.4.2 dated 2015-11-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gergm.R | 8 ++++++-- man/GERGM.Rd | 7 ++++++- src/Makevars | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include 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 1.6 dated 2015-11-07 and 1.7 dated 2015-11-17
DESCRIPTION | 9 - MD5 | 34 ++--- NEWS | 22 +++ R/DJL-internal.R | 250 ++++++++++++++++++++--------------------- data/dataset.airplane.2017.rda |binary data/dataset.engine.2015.rda |binary data/dataset.hev.2013.rda |binary man/dataset.airplane.2017.Rd | 4 man/dataset.hev.2013.Rd | 2 man/map.soa.ddf.Rd | 6 man/map.soa.dea.Rd | 6 man/map.soa.sbm.Rd | 6 man/map.soa.sf.Rd | 20 +-- man/roc.dea.Rd | 12 - man/roc.sf.Rd | 18 +- man/target.arrival.dea.Rd | 4 man/target.arrival.sf.Rd | 6 man/target.spec.dea.Rd | 10 - 18 files changed, 209 insertions(+), 200 deletions(-)