Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly maximizing the log likelihood function. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 1.0.0 dated 2017-01-14 and 1.0.1 dated 2017-01-15
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/RcppExports.R | 4 ---- R/hmmsim.R | 2 +- R/hsmmviterbi.R | 6 +++--- R/package.R | 4 ++-- man/hmmsim.Rd | 6 ++++-- man/hsmmviterbi.Rd | 6 +++--- man/package-ziphsmm.Rd | 4 ++-- src/RcppExports.cpp | 25 ------------------------- src/rcpparma_hello_world.cpp | 14 ++++++-------- 11 files changed, 35 insertions(+), 64 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.5 dated 2016-11-21 and 1.7.6 dated 2017-01-15
TMB-1.7.5/TMB/R/mcmc.R |only TMB-1.7.5/TMB/inst/examples/mcmc_examples.R |only TMB-1.7.5/TMB/man/run_mcmc.Rd |only TMB-1.7.5/TMB/man/run_mcmc.hmc.Rd |only TMB-1.7.5/TMB/man/run_mcmc.nuts.Rd |only TMB-1.7.5/TMB/man/run_mcmc.rwm.Rd |only TMB-1.7.6/TMB/DESCRIPTION | 10 TMB-1.7.6/TMB/MD5 | 29 -- TMB-1.7.6/TMB/NAMESPACE | 3 TMB-1.7.6/TMB/NEWS | 15 + TMB-1.7.6/TMB/R/sdreport.R | 14 - TMB-1.7.6/TMB/inst/include/convenience.hpp | 102 ++++--- TMB-1.7.6/TMB/inst/include/distributions_R.hpp | 207 +++++++++++++++- TMB-1.7.6/TMB/inst/include/lgamma.hpp | 20 + TMB-1.7.6/TMB/inst/include/tiny_ad/atomic.hpp | 12 TMB-1.7.6/TMB/inst/include/tiny_ad/compois |only TMB-1.7.6/TMB/inst/include/tiny_ad/tiny_ad/tiny_ad.hpp | 70 +++-- TMB-1.7.6/TMB/inst/include/tiny_ad/tiny_ad/tiny_vec.hpp | 9 TMB-1.7.6/TMB/man/sdreport.Rd | 14 - 19 files changed, 364 insertions(+), 141 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (see 'citation("recmap")' for details). This algorithm
draws maps according to a given statistical value (e.g. election results,
population or epidemiological data). The basic idea of the RecMap algorithm is
that each map region (e.g. different countries) is represented by a
rectangle. The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about RecMap is
provided by a vignette included in this package.
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 0.5.4 dated 2016-07-24 and 0.5.16 dated 2017-01-15
DESCRIPTION | 12 - MD5 | 44 +++--- NAMESPACE | 14 +- R/RcppExports.R | 6 R/recmap.R | 210 ++++++++++++++++++++++++++------ README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 23 +++ inst/doc/recmap.R | 58 +------- inst/doc/recmap.Rmd | 89 +------------ inst/doc/recmap.html | 102 +++++++-------- inst/extdata/us_state_election_2004.csv | 2 man/plot.recmap.Rd | 14 +- man/recmap.Rd | 10 - man/recmap2sp.Rd | 26 +-- man/recmapGA.Rd | 13 + man/sp2recmap.Rd |only man/summary.recmap.Rd | 4 src/RcppExports.cpp | 32 ++-- src/Rrecmap.cpp | 4 src/recmap.h | 10 - tests/testthat/test-sp.R |only vignettes/recmap.Rmd | 89 +------------ 24 files changed, 384 insertions(+), 383 deletions(-)
Title: Monitor the Total and Peak RAM Used by an Expression or Function
Description: When working with big data sets, RAM conservation is critically
important. However, it is not always enough to just monitor the
size of the objects created. So-called "copy-on-modify" behavior,
characteristic of R, means that some expressions or functions may
require an unexpectedly large amount of RAM overhead. For example,
replacing a single value in a matrix duplicates that matrix in the
back-end, making this task require twice as much RAM as that used
by the matrix itself. This package makes it easy to monitor the total
and peak RAM used so that developers can quickly identify and
eliminate RAM hungry code.
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between peakRAM versions 1.0.1 dated 2016-12-04 and 1.0.2 dated 2017-01-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 9 +++++++-- R/peakRAM.R | 14 +++++++------- inst/doc/peakRAM.html | 16 ++++++++-------- 5 files changed, 31 insertions(+), 26 deletions(-)
Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with additional support for multi-step adaptive MCP-net
(MSAMNet) and multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 2.0 dated 2017-01-05 and 2.1 dated 2017-01-15
DESCRIPTION | 15 +- MD5 | 51 +++++---- NAMESPACE | 8 + NEWS.md | 15 ++ R/aenet.R | 1 R/amnet.R | 13 +- R/asnet.R | 13 +- R/msaenet-eval.R | 39 +++---- R/msaenet-inspect.R | 40 ++++++- R/msaenet-package.R | 2 R/msaenet-sim.R | 243 +++++++++++++++++++++++++++++++++++++++++--- R/msaenet-tune-ncvreg.R | 39 ++----- R/msamnet.R | 12 +- R/msasnet.R | 12 +- README.md | 4 inst/doc/msaenet.html | 4 man/aenet.Rd | 1 man/amnet.Rd | 9 + man/asnet.Rd | 9 + man/msaenet-package.Rd | 2 man/msaenet.fn.Rd |only man/msaenet.mse.Rd |only man/msaenet.sim.binomial.Rd |only man/msaenet.sim.cox.Rd |only man/msaenet.sim.gaussian.Rd | 4 man/msaenet.sim.poisson.Rd |only man/msaenet.tune.ncvreg.Rd | 2 man/msamnet.Rd | 9 + man/msasnet.Rd | 9 + 29 files changed, 444 insertions(+), 112 deletions(-)
Title: Drawing Hasse Diagram
Description: Drawing Hasse diagram - visualization of transitive reduction of a finite partially ordered set.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek <k.ciomek@gmail.com>
Diff between hasseDiagram versions 0.1.1 dated 2014-07-29 and 0.1.2 dated 2017-01-15
DESCRIPTION | 14 +++--- LICENSE | 2 MD5 | 14 +++--- NAMESPACE | 38 +++++++++++++++++- R/hasse.R | 89 +++++++++++++++++++++++++++++++++----------- man/generateRandomData.Rd | 3 - man/hasse.Rd | 3 - man/hasseDiagram-package.Rd | 6 +- 8 files changed, 127 insertions(+), 42 deletions(-)
Title: Construct, Evaluate and Plot Value and Utility Functions
Description: Construct and plot objective hierarchies and associated value and utility functions.
Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables.
Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies.
Get numerical results of the evaluations in standard R data types for further processing.
Author: Peter Reichert <peter.reichert@eawag.ch>
with contributions by Nele Schuwirth <nele.schuwirth@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Diff between utility versions 1.3 dated 2014-10-14 and 1.4 dated 2017-01-15
DESCRIPTION | 8 MD5 | 100 +++++-- NAMESPACE | 16 + R/utility.aggregate.r | 111 +++++++ R/utility.aggregation.r | 377 +-------------------------- R/utility.aux.r | 5 R/utility.conversion.intpol.r | 4 R/utility.conversion.parfun.r | 4 R/utility.endnode.classcounts.r |only R/utility.plot.r | 49 ++- man/evaluate.utility.endnode.classcounts.Rd |only man/figures |only man/plot.utility.aggregation.Rd | 4 man/plot.utility.conversion.intpol.Rd | 4 man/plot.utility.conversion.parfun.Rd | 4 man/plot.utility.endnode.classcounts.Rd |only man/print.utility.endnode.classcounts.Rd |only man/summary.utility.endnode.classcounts.Rd |only man/updatepar.utility.endnode.classcounts.Rd |only man/utility-package.Rd | 21 + man/utility.aggregate.add.Rd | 43 ++- man/utility.aggregate.addmin.Rd | 44 ++- man/utility.aggregate.addpower.Rd |only man/utility.aggregate.addsplitpower.Rd |only man/utility.aggregate.bonusmalus.Rd |only man/utility.aggregate.cobbdouglas.Rd | 43 ++- man/utility.aggregate.geo.Rd | 43 ++- man/utility.aggregate.geooff.Rd | 44 ++- man/utility.aggregate.harmo.Rd | 43 ++- man/utility.aggregate.harmooff.Rd | 44 ++- man/utility.aggregate.max.Rd | 43 ++- man/utility.aggregate.min.Rd | 43 ++- man/utility.aggregate.mix.Rd | 44 ++- man/utility.aggregate.mult.Rd | 47 ++- man/utility.aggregate.revaddpower.Rd |only man/utility.aggregate.revaddsplitpower.Rd |only man/utility.aggregate.revgeo.Rd | 43 ++- man/utility.aggregate.revgeooff.Rd | 44 ++- man/utility.aggregate.revharmo.Rd | 43 ++- man/utility.aggregate.revharmooff.Rd | 45 ++- man/utility.aggregation.create.Rd | 25 + man/utility.endnode.classcounts.create.Rd |only man/utility.endnode.intpol1d.create.Rd | 1 43 files changed, 743 insertions(+), 646 deletions(-)
Title: Inference for Hidden Markov and Semi-Markov Models
Description: Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.
Author: Jared O'Connell <jaredoconnell@gmail.com>, Søren Højsgaard
<sorenh@math.aau.dk>
Maintainer: Jared O'Connell <jaredoconnell@gmail.com>
Diff between mhsmm versions 0.4.14 dated 2014-12-22 and 0.4.16 dated 2017-01-15
ChangeLog | 19 DESCRIPTION | 11 MD5 | 22 NAMESPACE | 31 + R/hmm_functions.R | 30 - R/hsmm_functions.R | 1012 ++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/DHMM1.R | 18 inst/doc/DHMM1.pdf |binary inst/doc/DHMM2.pdf |binary vignettes/fig/dhmm-clsfig1.pdf |binary vignettes/fig/dhmm-clsfig2.pdf |binary 12 files changed, 598 insertions(+), 545 deletions(-)
Title: Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions
Description: Fully Bayesian inference for estimating the number of clusters and related parameters to heterogeneous binary data.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between BayesBinMix versions 1.3 dated 2016-09-09 and 1.4 dated 2017-01-15
DESCRIPTION | 10 +- MD5 | 15 ++- NAMESPACE | 7 + R/coupledMetropolis.R | 159 +++++++++++++++++++++++++++++++++-------- man/allocationSamplerBinMix.Rd | 6 + man/collapsedGibbsBinMix.Rd | 3 man/coupledMetropolis.Rd | 135 ++++++++++++++++++++-------------- man/gibbsBinMix.Rd | 3 man/print.bbm.object.Rd |only 9 files changed, 238 insertions(+), 100 deletions(-)
Title: Unicode Data and Utilities
Description: Data from Unicode 9.0.0 and related utilities.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between Unicode versions 8.0.0-1 dated 2016-03-15 and 9.0.0-1 dated 2017-01-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/basics.R | 8 ++++---- R/charfuns.R | 2 +- R/sysdata.rda |binary 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Harvest Metadata Using OAI-PMH v2.0
Description:
Harvest metadata using the Open Archives Initiative Protocol for Metadata
Harvesting (OAI-PMH) version 2.0.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between OAIHarvester versions 0.2-1 dated 2016-08-21 and 0.2-2 dated 2017-01-15
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- R/apply.R | 2 +- R/pmh.R | 4 +++- inst/doc/oaih.pdf |binary 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Fits a Non-Parametric Bayesian Source Attribution Model
Description: Implements a non-parametric source attribution model
to attribute cases of disease to sources in Bayesian framework with source and
type effects. Type effects are clustered using a Dirichlet Process. Multiple
times and locations are supported.
Author: Poppy Miller [aut, cre, cph],
Chris Jewell [aut],
Jonathan Marshall [ctb],
Nigel French [ctb]
Maintainer: Poppy Miller <p.miller@lancaster.ac.uk>
Diff between sourceR versions 0.2.0 dated 2016-06-21 and 1.0.0 dated 2017-01-15
sourceR-0.2.0/sourceR/R/MCMC_loop.R |only sourceR-0.2.0/sourceR/R/RcppExports.R |only sourceR-0.2.0/sourceR/R/calc_niter.R |only sourceR-0.2.0/sourceR/R/check_input.R |only sourceR-0.2.0/sourceR/R/flatten.R |only sourceR-0.2.0/sourceR/R/heatmap_types.R |only sourceR-0.2.0/sourceR/R/subset_posterior.R |only sourceR-0.2.0/sourceR/R/summary.R |only sourceR-0.2.0/sourceR/R/wrapper.R |only sourceR-0.2.0/sourceR/README.md |only sourceR-0.2.0/sourceR/build |only sourceR-0.2.0/sourceR/data/sim_SA.rda |only sourceR-0.2.0/sourceR/inst |only sourceR-0.2.0/sourceR/man/flatten.Rd |only sourceR-0.2.0/sourceR/man/heatmap_types.Rd |only sourceR-0.2.0/sourceR/man/saBayes.Rd |only sourceR-0.2.0/sourceR/man/sim_SA.Rd |only sourceR-0.2.0/sourceR/man/sourceR-package.Rd |only sourceR-0.2.0/sourceR/man/subset_posterior.Rd |only sourceR-0.2.0/sourceR/man/summary.Rd |only sourceR-0.2.0/sourceR/src |only sourceR-0.2.0/sourceR/tests |only sourceR-0.2.0/sourceR/vignettes |only sourceR-1.0.0/sourceR/DESCRIPTION | 35 +++---- sourceR-1.0.0/sourceR/MD5 | 110 ++++++++-------------- sourceR-1.0.0/sourceR/NAMESPACE | 37 +++---- sourceR-1.0.0/sourceR/R/HaldDP_inits.R |only sourceR-1.0.0/sourceR/R/HaldDP_priors.R |only sourceR-1.0.0/sourceR/R/R6_tests.R |only sourceR-1.0.0/sourceR/R/acceptance.R |only sourceR-1.0.0/sourceR/R/campy.R |only sourceR-1.0.0/sourceR/R/credibleIntervals.R |only sourceR-1.0.0/sourceR/R/heatmap.R |only sourceR-1.0.0/sourceR/R/interface.R |only sourceR-1.0.0/sourceR/R/mcmc.R |only sourceR-1.0.0/sourceR/R/model.R |only sourceR-1.0.0/sourceR/R/node.R |only sourceR-1.0.0/sourceR/R/onlineCov.R |only sourceR-1.0.0/sourceR/R/posterior.R |only sourceR-1.0.0/sourceR/R/sim_SA_data.R |only sourceR-1.0.0/sourceR/R/sim_SA_prev.R |only sourceR-1.0.0/sourceR/R/sim_SA_true.R |only sourceR-1.0.0/sourceR/R/utils.R |only sourceR-1.0.0/sourceR/data/sim_SA_data.rda |only sourceR-1.0.0/sourceR/data/sim_SA_prev.rda |only sourceR-1.0.0/sourceR/data/sim_SA_true.rda |binary sourceR-1.0.0/sourceR/man/AdaptiveDirMRW.Rd |only sourceR-1.0.0/sourceR/man/AdaptiveLogDirMRW.Rd |only sourceR-1.0.0/sourceR/man/AdaptiveMultiMRW.Rd |only sourceR-1.0.0/sourceR/man/DPModel_impl.Rd |only sourceR-1.0.0/sourceR/man/DataNode.Rd |only sourceR-1.0.0/sourceR/man/DirichletNode.Rd |only sourceR-1.0.0/sourceR/man/DirichletProcessNode.Rd |only sourceR-1.0.0/sourceR/man/FormulaNode.Rd |only sourceR-1.0.0/sourceR/man/GammaNode.Rd |only sourceR-1.0.0/sourceR/man/HaldDP.Rd |only sourceR-1.0.0/sourceR/man/Node.Rd |only sourceR-1.0.0/sourceR/man/PoisGammaDPUpdate.Rd |only sourceR-1.0.0/sourceR/man/PoissonNode.Rd |only sourceR-1.0.0/sourceR/man/StochasticNode.Rd |only sourceR-1.0.0/sourceR/man/campy.Rd | 50 ++++------ sourceR-1.0.0/sourceR/man/sim_SA_data.Rd |only sourceR-1.0.0/sourceR/man/sim_SA_prev.Rd |only sourceR-1.0.0/sourceR/man/sim_SA_true.Rd | 44 ++++---- 64 files changed, 119 insertions(+), 157 deletions(-)
Title: High Performance Implementation of the Naive Bayes Algorithm
Description: High performance implementation of the Naive Bayes algorithm.
Author: Michal Majka
Maintainer: Michal Majka <michalmajka@hotmail.com>
Diff between naivebayes versions 0.9.0 dated 2017-01-05 and 0.9.1 dated 2017-01-15
DESCRIPTION | 6 +++--- MD5 | 5 +++-- R/naive_bayes.R | 8 +++----- inst |only 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich;
Yulia R. Gel;
Calvin Chu;
Xingyu Wang
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>
Diff between funtimes versions 2.2 dated 2016-04-27 and 3.0 dated 2017-01-15
DESCRIPTION | 14 - MD5 | 36 ++-- NAMESPACE | 3 R/ARest.R |only R/BICC.R |only R/CSlideCluster.R | 2 R/purity.R |only R/sync.test.R | 322 ++++++++++++++++++++----------------------- R/wavk.test.R | 323 ++++++++++++++++++-------------------------- man/ARest.Rd |only man/BICC.Rd |only man/CExpandSlideCluster.Rd | 14 - man/CExpandWindowCluster.Rd | 12 - man/CHomogeneity.Rd | 14 - man/CNeighbor.Rd | 16 +- man/CSlideCluster.Rd | 12 - man/CWindowCluster.Rd | 32 ++-- man/HVK.Rd | 10 - man/WAVK.Rd | 23 +-- man/purity.Rd |only man/sync.test.Rd | 150 ++++++++++---------- man/wavk.test.Rd | 123 +++++++++------- 22 files changed, 526 insertions(+), 580 deletions(-)
Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between clue versions 0.3-52 dated 2016-12-02 and 0.3-53 dated 2017-01-15
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/addtree.R | 2 +- R/classes.R | 2 +- R/consensus.R | 6 +++--- R/dissimilarity.R | 12 ++++++------ R/fuzziness.R | 3 +-- R/hierarchy.R | 4 ++-- R/lattice.R | 4 ++-- R/objects.R | 2 +- R/pava.R | 4 ++-- R/pclust.R | 2 +- R/ultrametric.R | 11 +++++------ R/utilities.R | 4 ++-- build/partial.rdb |binary inst/doc/clue.pdf |binary 16 files changed, 46 insertions(+), 48 deletions(-)