Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.1.6 dated 2015-05-08 and 0.1.19 dated 2015-07-16
SpecHelpers-0.1.19/SpecHelpers/DESCRIPTION | 10 ++++----- SpecHelpers-0.1.19/SpecHelpers/MD5 | 23 ++++++++++----------- SpecHelpers-0.1.19/SpecHelpers/NAMESPACE | 16 ++++++++++++++ SpecHelpers-0.1.19/SpecHelpers/NEWS | 3 ++ SpecHelpers-0.1.19/SpecHelpers/R/avgLambda.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/gatherCsv.R | 2 - SpecHelpers-0.1.19/SpecHelpers/R/gatherSpecFiles.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/makeSpec.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/plot2DNMRspec.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/plotNMRspec.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/qMS.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/txt2csv.R | 1 SpecHelpers-0.1.6/SpecHelpers/README.md |only 13 files changed, 46 insertions(+), 18 deletions(-)
Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. Ongoing developments of the package
focus on offering easy to use tools for creating other spatio-dynamic
models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.0 dated 2014-06-27 and 1.1 dated 2015-07-16
DESCRIPTION | 13 +++++---- MD5 | 61 ++++++++++++++++++++++++++------------------ NAMESPACE | 7 ++++- NEWS | 6 ++-- R/animate_bs.R | 2 - R/animate_model.R | 2 - R/animate_rb.R | 2 - R/animate_sm.R | 2 - R/animate_ss.R | 2 - R/mc_dynmodv2_7_functions.R | 7 ++--- R/mrgf.R |only R/plot_maps.R | 10 +++---- R/rnd_init_maps.R | 8 ++--- R/run_model.R | 3 +- R/spdynmod.R | 2 + build/vignette.rds |binary inst/doc/isem2013_jml.pdf |binary inst/extdata/y1984_rs.asc |only inst/extdata/y1992_mod.asc |only inst/extdata/y1992_rs.asc |only inst/extdata/y1995_mod.asc |only inst/extdata/y1995_rs.asc |only inst/extdata/y1997_mod.asc |only inst/extdata/y1997_rs.asc |only inst/extdata/y2001_mod.asc |only inst/extdata/y2001_rs.asc |only inst/extdata/y2008_mod.asc |only inst/extdata/y2008_rs.asc |only man/animate_bs.Rd | 3 +- man/animate_model.Rd | 3 +- man/animate_rb.Rd | 3 +- man/animate_sm.Rd | 3 +- man/animate_ss.Rd | 3 +- man/mrgf.Rd |only man/neigh_cell.Rd | 3 +- man/plot_maps.Rd | 3 +- man/run_model.Rd | 3 +- man/spdynmod.Rd | 3 +- 38 files changed, 94 insertions(+), 60 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-2 dated 2015-06-05 and 1.2-3 dated 2015-07-16
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 11 +++++++++++ NEWS | 14 ++++++++++---- R/sn-funct.R | 23 ++++++++++++----------- R/zzz.R | 7 ++++--- man/dmsn.Rd | 33 +++++++++++++++++---------------- man/dmst.Rd | 28 +++++++++++++++------------- man/selm.Rd | 7 ++++--- 9 files changed, 86 insertions(+), 63 deletions(-)
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://eml.berkeley.edu//~train/trainsonnier.pdf.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.1.0 dated 2015-06-08 and 1.1.1 dated 2015-07-16
DESCRIPTION | 9 +++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 4 ++++ NEWS | 3 +++ R/doHB.R | 2 +- R/writeModel.R | 4 +--- build/vignette.rds |binary inst/doc/RSGHB_HowTo.pdf |binary man/doHB.Rd | 3 ++- man/writeModel.Rd | 2 +- tools |only 11 files changed, 27 insertions(+), 19 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.3.2 dated 2015-05-03 and 1.3.3 dated 2015-07-16
DESCRIPTION | 8 MD5 | 30 +-- NAMESPACE | 4 R/RcppExports.R | 66 +++--- R/gibbs.R | 509 +++++++++++++++++++++++++++------------------------- R/manhattan.R | 2 R/report.R |only R/snpQC.R | 10 - man/Internals.Rd | 1 man/NAM-package.Rd | 66 +++--- man/cleanREP.Rd |only man/gibbs.Rd | 165 ++++++++-------- man/report.Rd |only man/snpH2.Rd | 2 man/snpQC.Rd | 5 src/RcppExports.cpp | 23 ++ src/SAMP.cpp | 2 src/SAMP2.cpp |only 18 files changed, 478 insertions(+), 415 deletions(-)
Title: Markov Chain Monte Carlo
Description: Simulates continuous distributions of random vectors using
Markov chain Monte Carlo (MCMC). Users specify the distribution by an
R function that evaluates the log unnormalized density. Algorithms
are random walk Metropolis algorithm (function metrop), simulated
tempering (function temper), and morphometric random walk Metropolis
(Johnson and Geyer, Annals of Statistics, 2012, function morph.metrop),
which achieves geometric ergodicity by change of variable.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif T. Johnson
<ltjohnson@google.com>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between mcmc versions 0.9-3 dated 2014-04-02 and 0.9-4 dated 2015-07-16
mcmc-0.9-3/mcmc/inst/doc/bfst.tex |only mcmc-0.9-3/mcmc/inst/doc/debug.tex |only mcmc-0.9-3/mcmc/inst/doc/demo.tex |only mcmc-0.9-3/mcmc/inst/doc/morph.tex |only mcmc-0.9-4/mcmc/ChangeLog | 3 + mcmc-0.9-4/mcmc/DESCRIPTION | 20 +++++--- mcmc-0.9-4/mcmc/MD5 | 62 ++++++++++++++++--------- mcmc-0.9-4/mcmc/NAMESPACE | 1 mcmc-0.9-4/mcmc/build/vignette.rds |binary mcmc-0.9-4/mcmc/inst/doc/bfst.pdf |binary mcmc-0.9-4/mcmc/inst/doc/debug.Rnw | 6 +- mcmc-0.9-4/mcmc/inst/doc/debug.pdf |binary mcmc-0.9-4/mcmc/inst/doc/demo.pdf |binary mcmc-0.9-4/mcmc/inst/doc/metrop.pdf |binary mcmc-0.9-4/mcmc/inst/doc/morph.pdf |binary mcmc-0.9-4/mcmc/inst/doc/temper.pdf |binary mcmc-0.9-4/mcmc/man/metrop.Rd | 2 mcmc-0.9-4/mcmc/man/morph.metrop.Rd | 4 - mcmc-0.9-4/mcmc/man/temper.Rd | 6 +- mcmc-0.9-4/mcmc/tests/circle.Rout.save |only mcmc-0.9-4/mcmc/tests/initseq.Rout.save |only mcmc-0.9-4/mcmc/tests/isotropic.Rout.save |only mcmc-0.9-4/mcmc/tests/logit.R | 2 mcmc-0.9-4/mcmc/tests/logit.Rout.save |only mcmc-0.9-4/mcmc/tests/logitbat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitfun.Rout.save |only mcmc-0.9-4/mcmc/tests/logitfunarg.Rout.save |only mcmc-0.9-4/mcmc/tests/logitidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitlogidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitmat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitnegidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitsub.Rout.save |only mcmc-0.9-4/mcmc/tests/logitsubbat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitvec.Rout.save |only mcmc-0.9-4/mcmc/tests/morph.Rout.save |only mcmc-0.9-4/mcmc/tests/morph.metrop.R | 6 +- mcmc-0.9-4/mcmc/tests/morph.metrop.Rout.save |only mcmc-0.9-4/mcmc/tests/morphtoo.Rout.save |only mcmc-0.9-4/mcmc/tests/saveseed.Rout.save |only mcmc-0.9-4/mcmc/tests/saveseedmorph.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-par.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-ser-witch.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-ser.R | 15 +++++- mcmc-0.9-4/mcmc/tests/temp-ser.Rout.save |only mcmc-0.9-4/mcmc/vignettes/debug.Rnw | 6 +- 45 files changed, 90 insertions(+), 43 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: We efficiently approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of our calculations, we also
obtain approximate standard errors for estimated predictive errors, and for
the comparison of predictive errors between two models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.0 dated 2015-06-26 and 0.1.2 dated 2015-07-16
loo-0.1.0/loo/R/loo_and_waic.R |only loo-0.1.0/loo/R/loo_and_waic_diff.R |only loo-0.1.0/loo/R/vgisloo.R |only loo-0.1.0/loo/R/vgislw.R |only loo-0.1.0/loo/man/loo_and_waic_diff.Rd |only loo-0.1.0/loo/man/vgisloo.Rd |only loo-0.1.0/loo/man/vgislw.Rd |only loo-0.1.2/loo/DESCRIPTION | 29 +-- loo-0.1.2/loo/MD5 | 58 +++--- loo-0.1.2/loo/NAMESPACE | 15 + loo-0.1.2/loo/R/compare.R |only loo-0.1.2/loo/R/deprecated.R |only loo-0.1.2/loo/R/extract_log_lik.R | 13 - loo-0.1.2/loo/R/gpdfit.R | 25 +- loo-0.1.2/loo/R/helpers.R | 150 ++++++++++++---- loo-0.1.2/loo/R/loo.R |only loo-0.1.2/loo/R/loo_package.R | 210 +++++++++++------------ loo-0.1.2/loo/R/misc.R |only loo-0.1.2/loo/R/print.R | 36 ++- loo-0.1.2/loo/R/psisloo.R |only loo-0.1.2/loo/R/psislw.R |only loo-0.1.2/loo/R/waic.R |only loo-0.1.2/loo/inst/doc/Example.R | 17 - loo-0.1.2/loo/inst/doc/Example.Rmd | 23 +- loo-0.1.2/loo/inst/doc/Example.html | 21 +- loo-0.1.2/loo/man/compare.Rd |only loo-0.1.2/loo/man/extract_log_lik.Rd | 10 - loo-0.1.2/loo/man/gpdfit.Rd | 6 loo-0.1.2/loo/man/loo-package.Rd | 210 +++++++++++------------ loo-0.1.2/loo/man/loo.Rd |only loo-0.1.2/loo/man/loo_and_waic.Rd | 24 -- loo-0.1.2/loo/man/nlist.Rd |only loo-0.1.2/loo/man/print.loo.Rd | 24 +- loo-0.1.2/loo/man/psisloo.Rd |only loo-0.1.2/loo/man/psislw.Rd |only loo-0.1.2/loo/man/waic.Rd |only loo-0.1.2/loo/tests/testthat/test_gpdfit.R | 6 loo-0.1.2/loo/tests/testthat/test_helpers.R | 28 +-- loo-0.1.2/loo/tests/testthat/test_loo_and_waic.R | 61 +++--- loo-0.1.2/loo/vignettes/Example.Rmd | 23 +- 40 files changed, 572 insertions(+), 417 deletions(-)
Title: GAMLSS Data
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 4.2-7 dated 2014-01-11 and 4.3-0 dated 2015-07-16
DESCRIPTION | 10 +++---- MD5 | 67 ++++++++++++++++++++++++++---------------------- data/CD4.rda |binary data/LGAclaims.rda |binary data/Mums.rda |binary data/VictimsOfCrime.rda |binary data/acidity.rda |binary data/aep.rda |binary data/aids.rda |binary data/alveolar.rda |binary data/computer.rda |binary data/datalist | 4 ++ data/db.rda |binary data/dbbmi.rda |binary data/fabric.rda |binary data/film30.rda |binary data/film90.rda |binary data/glass.rda |binary data/hodges.rda |binary data/hodges1.rda |binary data/lice.rda |binary data/margolin.rda |binary data/mvi.rda |only data/mviBig.rda |only data/parzen.rda |binary data/polio.rda |binary data/rent.rda |binary data/rent99.polys.rda |only data/rent99.rda |only data/species.rda |binary data/stylo.rda |binary data/tensile.rda |binary data/tse.rda |binary data/usair.rda |binary data/vas5.rda |binary man/mvi.Rd |only man/rent99.Rd |only man/rent99.polys.Rd |only 38 files changed, 46 insertions(+), 35 deletions(-)
Title: Demos for GAMLSS
Description: Demos for smoothing and gamlss.family distributions.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby <r.rigby@londonmet.ac.uk>, Paul Eilers <p.eilers@erasmusmc.nl>, Brian Marx \email{bmarx@LSU.EDU}, Konstantinos Pateras <kostas.pateras@gmail.com> with contributions from Larisa Kosidou.
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.demo versions 4.3-1 dated 2015-02-04 and 4.3-3 dated 2015-07-16
DESCRIPTION | 11 ++++--- MD5 | 4 +- NAMESPACE | 87 +++++++++++++++++++++++++++++++----------------------------- 3 files changed, 53 insertions(+), 49 deletions(-)
Title: Interactive Exploration of Contour Data
Description: Interactive tools to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. The functions in this package create
interactive web pages showing the contoured data, possibly with
slices from the original matrix parallel to each dimension. The interactive
behavior is created using the D3.js 'JavaScript' library by Mike Bostock.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between exCon versions 0.1.9 dated 2015-06-23 and 0.1.12 dated 2015-07-16
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 ++ NEWS | 4 ++++ R/exCon-package.R | 2 +- R/exCon.R | 2 ++ man/exCon-package.Rd | 2 +- 7 files changed, 22 insertions(+), 14 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, shared objects, vignettes, or function documentation. It is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The rstan package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.6.0-10 dated 2015-02-10 and 2.7.0 dated 2015-07-16
StanHeaders-2.6.0-10/StanHeaders/README.md |only StanHeaders-2.6.0-10/StanHeaders/inst/CITATION |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/agrad |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/agrad.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/command |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/common |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/common.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/error_handling |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/error_handling.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/gm |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/gm.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/io |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/io.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/functions |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/functions.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/matrix |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/matrix.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/meta |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/meta.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/ode |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/ode.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/seq_view.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/mcmc |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/mcmc.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/memory |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/memory.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/meta |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/meta.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/model |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/model.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/optimization |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/prob |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/prob.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/version.hpp |only StanHeaders-2.7.0/StanHeaders/DESCRIPTION | 61 StanHeaders-2.7.0/StanHeaders/LICENSE | 2 StanHeaders-2.7.0/StanHeaders/MD5 | 1890 +++++----- StanHeaders-2.7.0/StanHeaders/NAMESPACE | 6 StanHeaders-2.7.0/StanHeaders/inst/include/src |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math.hpp | 673 +++ StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/fwd |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/memory |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/mix |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/prim |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/rev |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/version.hpp |only StanHeaders-2.7.0/StanHeaders/man |only 47 files changed, 1788 insertions(+), 844 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.3 dated 2015-07-12 and 1.5.5 dated 2015-07-16
refGenome-1.5.3/refGenome/src/range_partition.h |only refGenome-1.5.5/refGenome/DESCRIPTION | 8 ++++---- refGenome-1.5.5/refGenome/MD5 | 5 ++--- refGenome-1.5.5/refGenome/src/refGenome.h | 3 --- 4 files changed, 6 insertions(+), 10 deletions(-)
Title: NCA Calculation and Population PK Model Diagnosis
Description: A flexible tool is presented here that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) simulation-based posterior predictive checks for a population
pharmacokinetic (PK) model using NCA metrics.
Author: Chayan Acharya [aut, cre],
Andrew C. Hooker [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut]
Maintainer: Chayan Acharya <chayan.acharya@farmbio.uu.se>
Diff between ncappc versions 0.1 dated 2015-03-04 and 0.2 dated 2015-07-16
ncappc-0.1/ncappc/inst/misc/figTab.Rmd |only ncappc-0.1/ncappc/inst/misc/figTab.Rnw |only ncappc-0.1/ncappc/inst/misc/figTabNoSim.Rmd |only ncappc-0.1/ncappc/inst/misc/figTabNoSim.Rnw |only ncappc-0.1/ncappc/inst/misc/ncappcReport.Rmd |only ncappc-0.1/ncappc/inst/misc/ncappcReport.Rnw |only ncappc-0.1/ncappc/tests/testthat.R |only ncappc-0.1/ncappc/vignettes/conc.png |only ncappc-0.2/ncappc/DESCRIPTION | 16 ncappc-0.2/ncappc/MD5 | 68 ncappc-0.2/ncappc/NAMESPACE | 18 ncappc-0.2/ncappc/R/calc.stat.R | 104 ncappc-0.2/ncappc/R/dv.plot.R | 4 ncappc-0.2/ncappc/R/est.nca.R | 233 + ncappc-0.2/ncappc/R/histobs.plot.R | 70 ncappc-0.2/ncappc/R/histpop.plot.R | 60 ncappc-0.2/ncappc/R/nca.deviation.plot.R | 14 ncappc-0.2/ncappc/R/nca.npde.R | 5 ncappc-0.2/ncappc/R/nca.npde.plot.R | 9 ncappc-0.2/ncappc/R/nca.pde.deviation.outlier.R | 157 - ncappc-0.2/ncappc/R/ncappc.R | 1987 +++++++-------- ncappc-0.2/ncappc/README.md | 13 ncappc-0.2/ncappc/build/vignette.rds |binary ncappc-0.2/ncappc/inst/doc/ncappc-vignette.Rmd | 3 ncappc-0.2/ncappc/inst/doc/ncappc-vignette.html | 329 +- ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA-PPC.Rmd |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA-PPC.Rnw |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA.Rmd |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA.Rnw |only ncappc-0.2/ncappc/man/calc.stat.Rd | 2 ncappc-0.2/ncappc/man/est.nca.Rd | 27 ncappc-0.2/ncappc/man/histobs.plot.Rd | 24 ncappc-0.2/ncappc/man/histpop.plot.Rd | 9 ncappc-0.2/ncappc/man/nca.deviation.plot.Rd | 7 ncappc-0.2/ncappc/man/nca.pde.deviation.outlier.Rd | 33 ncappc-0.2/ncappc/man/ncappc.Rd | 51 ncappc-0.2/ncappc/tests/testthat/testthat.R |only ncappc-0.2/ncappc/vignettes/Sub-CommandLineArguments.Rmd | 161 - ncappc-0.2/ncappc/vignettes/Sub-Output.Rmd | 15 ncappc-0.2/ncappc/vignettes/conc.jpeg |only ncappc-0.2/ncappc/vignettes/ncappc-vignette.Rmd | 3 ncappc-0.2/ncappc/vignettes/ncappc-vignette.md | 179 - 42 files changed, 1925 insertions(+), 1676 deletions(-)
Title: Sparse Time Series Chain Graphical Models
Description: Computes sparse vector autoregressive coefficients and precision
matrices for time series chain graphical models.
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz <f.abegaz.yazew@rug.nl>
Diff between SparseTSCGM versions 2.1.1 dated 2014-08-21 and 2.2 dated 2015-07-16
SparseTSCGM-2.1.1/SparseTSCGM/R/sim.data.R |only SparseTSCGM-2.2/SparseTSCGM/DESCRIPTION | 16 ++++++------- SparseTSCGM-2.2/SparseTSCGM/MD5 | 20 ++++++++--------- SparseTSCGM-2.2/SparseTSCGM/NAMESPACE | 2 - SparseTSCGM-2.2/SparseTSCGM/R/compute.sparse.tscgm.R | 4 +-- SparseTSCGM-2.2/SparseTSCGM/R/sim.data.r |only SparseTSCGM-2.2/SparseTSCGM/R/sparse.tscgm.R | 10 ++++---- SparseTSCGM-2.2/SparseTSCGM/man/SparseTSCGM-package.Rd | 10 ++++---- SparseTSCGM-2.2/SparseTSCGM/man/plot.tscgm.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/plot.tscgm.ar2.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/sim.data.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/sparse.tscgm.Rd | 4 +-- 12 files changed, 39 insertions(+), 39 deletions(-)
Title: Read and Write TIFF Files
Description: Reads and writes TIFF format images and
returns them as a pixmap object. Because the resulting object
can be very large for even modestly sized TIFF images, images
can be reduced as they are read for improved performance. This
package is a wrapper around libtiff (www.libtiff.org), on which
it depends (i.e. the libtiff shared library must be on your
PATH for the binary to work, and tiffio.h must be on your
system to build the package from source). By using libtiff's
highlevel TIFFReadRGBAImage function, this package inherently
supports a wide range of image formats and compression schemes.
This package also provides an implementation of the Ridler
Autothresholding algorithm for easy generation of binary masks.
Author: Eric Kort <eric.kort@vai.org>
Maintainer: Eric Kort <eric.kort@vai.org>
Diff between rtiff versions 1.4.4 dated 2014-02-14 and 1.4.5 dated 2015-07-16
rtiff-1.4.4/rtiff/LICENSE |only rtiff-1.4.5/rtiff/DESCRIPTION | 25 +++++++++++-------------- rtiff-1.4.5/rtiff/MD5 | 10 +++++----- rtiff-1.4.5/rtiff/R/readTiff.R | 10 +++++++--- rtiff-1.4.5/rtiff/cleanup |only rtiff-1.4.5/rtiff/man/readTiff.Rd | 10 +++++++--- rtiff-1.4.5/rtiff/src/rtiff.c | 1 - 7 files changed, 30 insertions(+), 26 deletions(-)
Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format (described at
<https://github.com/toml-lang/toml>) suitable for both human editing as well
as the common uses of a machine-readable format. This package uses 'Rcpp' to
connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.0.3 dated 2015-04-27 and 0.0.4 dated 2015-07-16
ChangeLog | 21 ++++++++++++++++++++- DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- R/parseToml.R | 2 +- README.md | 28 +++++++++++++++++++++++++--- inst/include/cpptoml.h | 18 ++++++++++++++++-- src/Makevars | 2 +- src/parse.cpp | 1 + 8 files changed, 81 insertions(+), 25 deletions(-)
Title: An R Package for Reading and Writing BAM (Binary Alignment)
Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.12.1 dated 2015-07-15 and 2.12.2 dated 2015-07-16
DESCRIPTION | 6 - MD5 | 10 +-- inst/doc/rbamtools.pdf |binary src/extptr.h | 2 src/range_partition.h | 92 ++++++++++++++-------------- src/rbamtools.cpp | 157 +++++++++++++++++++++++++++---------------------- 6 files changed, 143 insertions(+), 124 deletions(-)
Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras <virmantas.kvedaras@mif.vu.lt>, Vaidotas Zemlys
<vaidotas.zemlys@mif.vu.lt>
Maintainer: Vaidotas Zemlys <zemlys@gmail.com>
Diff between midasr versions 0.4 dated 2015-03-10 and 0.5 dated 2015-07-16
midasr-0.4/midasr/inst/tests |only midasr-0.5/midasr/DESCRIPTION | 9 midasr-0.5/midasr/MD5 | 158 +++---- midasr-0.5/midasr/NAMESPACE | 45 ++ midasr-0.5/midasr/NEWS | 204 +++++---- midasr-0.5/midasr/R/lagspec.R | 48 ++ midasr-0.5/midasr/R/midas_r_methods.R | 53 +- midasr-0.5/midasr/R/midasreg.R | 370 +++++++++------- midasr-0.5/midasr/R/modsel.R | 3 midasr-0.5/midasr/R/nonparametric.R | 1 midasr-0.5/midasr/R/simulate.R | 491 +++++++++++----------- midasr-0.5/midasr/R/tests.R | 548 ++++++++++++------------- midasr-0.5/midasr/README.md | 5 midasr-0.5/midasr/inst/CITATION | 24 - midasr-0.5/midasr/man/USpayems.Rd | 2 midasr-0.5/midasr/man/USqgdp.Rd | 2 midasr-0.5/midasr/man/USrealgdp.Rd | 2 midasr-0.5/midasr/man/USunempr.Rd | 2 midasr-0.5/midasr/man/agk.test.Rd | 2 midasr-0.5/midasr/man/almonp.Rd | 2 midasr-0.5/midasr/man/almonp_gradient.Rd | 2 midasr-0.5/midasr/man/amidas_table.Rd | 2 midasr-0.5/midasr/man/amweights.Rd | 2 midasr-0.5/midasr/man/average_forecast.Rd | 2 midasr-0.5/midasr/man/check_mixfreq.Rd | 2 midasr-0.5/midasr/man/coef.midas_r.Rd | 2 midasr-0.5/midasr/man/deriv_tests.Rd | 2 midasr-0.5/midasr/man/deviance.midas_r.Rd | 2 midasr-0.5/midasr/man/dmls.Rd | 2 midasr-0.5/midasr/man/expand_amidas.Rd | 2 midasr-0.5/midasr/man/expand_weights_lags.Rd | 2 midasr-0.5/midasr/man/fmls.Rd | 2 midasr-0.5/midasr/man/forecast.midas_r.Rd | 4 midasr-0.5/midasr/man/genexp.Rd |only midasr-0.5/midasr/man/genexp_gradient.Rd |only midasr-0.5/midasr/man/get_estimation_sample.Rd | 2 midasr-0.5/midasr/man/gompertzp.Rd | 2 midasr-0.5/midasr/man/gompertzp_gradient.Rd | 2 midasr-0.5/midasr/man/hAh_test.Rd | 2 midasr-0.5/midasr/man/hAhr_test.Rd | 2 midasr-0.5/midasr/man/harstep.Rd | 2 midasr-0.5/midasr/man/harstep_gradient.Rd | 2 midasr-0.5/midasr/man/hf_lags_table.Rd | 2 midasr-0.5/midasr/man/imidas_r.Rd | 2 midasr-0.5/midasr/man/lcauchyp.Rd | 2 midasr-0.5/midasr/man/lcauchyp_gradient.Rd | 2 midasr-0.5/midasr/man/lf_lags_table.Rd | 2 midasr-0.5/midasr/man/lws_table-add.Rd | 2 midasr-0.5/midasr/man/midas_auto_sim.Rd | 2 midasr-0.5/midasr/man/midas_r.Rd | 5 midasr-0.5/midasr/man/midas_r.fit.Rd | 2 midasr-0.5/midasr/man/midas_r_ic_table.Rd | 2 midasr-0.5/midasr/man/midas_r_np.Rd | 2 midasr-0.5/midasr/man/midas_r_simple.Rd | 2 midasr-0.5/midasr/man/midas_sim.Rd | 2 midasr-0.5/midasr/man/midas_u.Rd | 2 midasr-0.5/midasr/man/midasr-package.Rd | 2 midasr-0.5/midasr/man/mls.Rd | 2 midasr-0.5/midasr/man/modsel.Rd | 2 midasr-0.5/midasr/man/nakagamip.Rd | 2 midasr-0.5/midasr/man/nakagamip_gradient.Rd | 2 midasr-0.5/midasr/man/nbeta.Rd | 2 midasr-0.5/midasr/man/nbetaMT.Rd | 2 midasr-0.5/midasr/man/nbetaMT_gradient.Rd | 2 midasr-0.5/midasr/man/nbeta_gradient.Rd | 2 midasr-0.5/midasr/man/nealmon.Rd | 2 midasr-0.5/midasr/man/nealmon_gradient.Rd | 2 midasr-0.5/midasr/man/oos_prec.Rd | 2 midasr-0.5/midasr/man/plot_midas_coef.Rd | 2 midasr-0.5/midasr/man/polystep.Rd | 2 midasr-0.5/midasr/man/polystep_gradient.Rd | 2 midasr-0.5/midasr/man/predict.midas_r.Rd | 2 midasr-0.5/midasr/man/prep_hAh.Rd | 2 midasr-0.5/midasr/man/rvsp500.Rd | 2 midasr-0.5/midasr/man/select_and_forecast.Rd | 2 midasr-0.5/midasr/man/simulate.midas_r.Rd | 2 midasr-0.5/midasr/man/split_data.Rd | 2 midasr-0.5/midasr/man/update_weights.Rd | 2 midasr-0.5/midasr/man/weights_table.Rd | 2 midasr-0.5/midasr/tests |only 80 files changed, 1117 insertions(+), 973 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-42 dated 2015-07-02 and 7.3-43 dated 2015-07-16
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown <patrick.brown@utoronto.ca> [aut, cre]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.3.1 dated 2015-07-07 and 1.3.2 dated 2015-07-16
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- R/colourScale.R | 9 +++++++-- R/getTiles.R | 6 +++++- R/insetMap.R | 8 ++++---- R/map.new.R | 34 ++++++++++++++-------------------- inst/doc/mapLayers.pdf |binary inst/doc/mapmisc.pdf |binary man/map.new.Rd |only man/scaleBar.Rd | 12 +----------- 10 files changed, 46 insertions(+), 52 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-3 dated 2015-07-08 and 1.0-4 dated 2015-07-16
DESCRIPTION | 12 ++-- MD5 | 105 +++++++++++++++++++------------------- NAMESPACE | 2 R/cache.R | 16 +++-- R/codes.R | 66 +++++++++++++++++++---- R/corpus.R | 2 R/dataset.R | 13 +++- R/db_api.R | 22 ++++++- R/manifesto.R | 3 - R/manifestoR-package.r | 1 R/scaling_general.R | 8 +- build/vignette.rds |binary inst/doc/manifestoRworkflow.pdf |binary man/ManifestoAvailability.Rd | 2 man/ManifestoCorpus.Rd | 2 man/ManifestoDocument.Rd | 2 man/ManifestoDocumentMeta.Rd | 2 man/ManifestoSource.Rd | 2 man/cmp_codes.Rd | 2 man/codes.Rd | 2 man/corpusupdate.Rd | 9 ++- man/count_codes.Rd | 9 ++- man/formatids.Rd | 2 man/formatmpds.Rd | 2 man/get_mpdb.Rd | 7 +- man/get_viacache.Rd | 2 man/manifestoR.Rd | 2 man/median_voter.Rd | 2 man/mp_availability.Rd | 2 man/mp_bootstrap.Rd | 2 man/mp_cite.Rd | 2 man/mp_coreversions.Rd | 2 man/mp_corpus.Rd | 2 man/mp_corpusversions.Rd | 2 man/mp_emptycache.Rd | 2 man/mp_interpolate.Rd | 2 man/mp_load_cache.Rd | 2 man/mp_maindataset.Rd | 2 man/mp_metadata.Rd | 2 man/mp_save_cache.Rd | 2 man/mp_scale.Rd | 2 man/mp_setapikey.Rd | 2 man/mp_use_corpus_version.Rd | 2 man/mp_view_originals.Rd | 2 man/mpdb_api_request.Rd | 2 man/null_to_na.Rd | 2 man/readManifesto.Rd | 2 man/rep.data.frame.Rd | 2 man/rescale.Rd | 2 man/rile.Rd | 2 man/scale.Rd | 2 man/vanilla.Rd | 2 vignettes/manifestoRworkflow.Rmd | 9 +-- vignettes/manifestoRworkflow.html |only 54 files changed, 216 insertions(+), 140 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova <alku@dtu.dk>
Diff between lmerTest versions 2.0-28 dated 2015-07-14 and 2.0-29 dated 2015-07-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 3 +-- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: Functions to Explore L-Systems (Lindenmayer Systems)
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can
be used to simulate biological forms and certain kinds of fractals.
Briefly, in an L-system a series of symbols in a string are replaced
iteratively according to rules to give a more complex string. Eventually,
the symbols are translated into turtle graphics for plotting. Wikipedia has
a very good introduction: en.wikipedia.org/wiki/L-system This package
provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between LindenmayeR versions 0.1.4 dated 2015-04-16 and 0.1.6 dated 2015-07-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 3 +++ man/LindenmayeR-package.Rd | 2 +- man/Lsys.Rd | 2 +- man/drawLsys.Rd | 2 +- 7 files changed, 17 insertions(+), 14 deletions(-)
Title: Belief Function Implementation
Description: Some basic functions to implement belief functions including:
transformation between belief functions using the method introduced by
Philippe Smets (arXiv:1304.1122 [cs.AI]), evidence combination, evidence
discounting, decision-making, and constructing masses. Currently, thirteen
combination rules and five decision rules are supported. It can also be
used to generate different types of random masses when working on belief
combination and conflict management.
Author: Kuang Zhou <kzhoumath@163.com>; Arnaud Martin
<arnaud.martin@univ-rennes1.fr>
Maintainer: Kuang Zhou <kzhoumath@163.com>
Diff between ibelief versions 1.1 dated 2015-05-15 and 1.2 dated 2015-07-16
ibelief-1.1/ibelief/R/LCRule.R |only ibelief-1.1/ibelief/man/LCRule.Rd |only ibelief-1.2/ibelief/DESCRIPTION | 17 + ibelief-1.2/ibelief/MD5 | 30 +- ibelief-1.2/ibelief/NAMESPACE | 3 ibelief-1.2/ibelief/NEWS | 18 + ibelief-1.2/ibelief/R/BayesianMass.R | 2 ibelief-1.2/ibelief/R/DST.R | 334 ++++++++++++++++++++++++------ ibelief-1.2/ibelief/R/DST_fmt_functions.R | 3 ibelief-1.2/ibelief/R/LCPrinciple.R |only ibelief-1.2/ibelief/R/RandomMass.R | 224 +++++++++++++++----- ibelief-1.2/ibelief/R/decisionDST.R | 2 ibelief-1.2/ibelief/R/discounting.R | 4 ibelief-1.2/ibelief/README.md | 22 + ibelief-1.2/ibelief/man/DST.Rd | 134 +++++++----- ibelief-1.2/ibelief/man/LCPrincple.Rd |only ibelief-1.2/ibelief/man/RandomMass.Rd | 121 ++++++---- ibelief-1.2/ibelief/man/decisionDST.Rd | 94 ++++---- 18 files changed, 704 insertions(+), 304 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach
to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e.,
data described by univariate histograms. The methods and the basic statistics for
histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification techniques,
least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unina2.it>
Diff between HistDAWass versions 0.1.2 dated 2015-03-17 and 0.1.3 dated 2015-07-16
DESCRIPTION | 11 - MD5 | 194 ++++++++++++++-------------- NAMESPACE | 24 +++ R/Fuzzy_cmeans.R | 2 R/Kohonen_maps.R | 1 R/Met_HTS.R | 6 R/Met_MatH.R | 4 R/Met_distributionH.R | 1 R/Utility.R | 1 R/principal_components.R | 4 R/regression.R | 1 R/unsuperv_classification.R | 2 data/HData.RData |binary man/Age_Pyramids_2014.Rd | 2 man/Agronomique.Rd | 2 man/BLOOD.Rd | 2 man/BloodBRITO.Rd | 2 man/Center.cell.MatH-methods.Rd | 2 man/China_Month.Rd | 2 man/China_Seas.Rd | 2 man/DouglasPeucker.Rd | 2 man/HTS-class.Rd | 2 man/HTS.exponential.smoothing.Rd | 2 man/HTS.moving.averages.Rd | 2 man/HTS.predict.knn.Rd | 2 man/HistDAWass-package.Rd | 2 man/MatH-class.Rd | 2 man/OzoneFull.Rd | 2 man/OzoneH.Rd | 2 man/RetHTS.Rd | 2 man/ShortestDistance.Rd | 2 man/TMatH-class.Rd | 2 man/TdistributionH-class.Rd | 2 man/WH.1d.PCA.Rd | 2 man/WH.MultiplePCA.Rd | 2 man/WH.SSQ-methods.Rd | 2 man/WH.SSQ2-methods.Rd | 2 man/WH.bind-methods.Rd | 2 man/WH.bind.col-methods.Rd | 2 man/WH.bind.row-methods.Rd | 2 man/WH.correlation-methods.Rd | 2 man/WH.correlation2-methods.Rd | 2 man/WH.mat.prod-methods.Rd | 2 man/WH.mat.sum-methods.Rd | 2 man/WH.regression.GOF.Rd | 2 man/WH.regression.two.components.Rd | 2 man/WH.regression.two.components.predict.Rd | 2 man/WH.var.covar-methods.Rd | 2 man/WH.var.covar2-methods.Rd | 2 man/WH.vec.mean-methods.Rd | 2 man/WH.vec.sum-methods.Rd | 2 man/WH_2d_Adaptive_Kohonen_maps.Rd | 2 man/WH_2d_Kohonen_maps.Rd | 2 man/WH_adaptive.kmeans.Rd | 2 man/WH_adaptive_fcmeans.Rd | 2 man/WH_fcmeans.Rd | 4 man/WH_hclust.Rd | 2 man/WH_kmeans.Rd | 2 man/WassSqDistH-methods.Rd | 2 man/checkEmptyBins-methods.Rd | 2 man/compP-methods.Rd | 2 man/compQ-methods.Rd | 2 man/crwtransform-methods.Rd | 2 man/data2hist.Rd | 2 man/distributionH-class.Rd | 2 man/dotpW-methods.Rd | 2 man/extract-methods.Rd | 2 man/get.MatH.main.info-methods.Rd | 2 man/get.MatH.ncols-methods.Rd | 2 man/get.MatH.nrows-methods.Rd | 2 man/get.MatH.rownames-methods.Rd | 2 man/get.MatH.stats-methods.Rd | 2 man/get.MatH.varnames-methods.Rd | 2 man/get.distr-methods.Rd | 2 man/get.histo-methods.Rd | 2 man/get.m-methods.Rd | 2 man/get.s-methods.Rd | 2 man/is.registeredMH-methods.Rd | 2 man/kurtH-methods.Rd | 2 man/meanH-methods.Rd | 2 man/minus.Rd | 2 man/plot-HTS.Rd | 8 - man/plot-MatH.Rd | 4 man/plot-TdistributionH.Rd | 2 man/plot-distributionH.Rd | 2 man/plotPredVsObs.Rd | 2 man/plot_errors.Rd | 2 man/plus-methods.Rd | 2 man/rQQ-methods.Rd | 2 man/register-methods.Rd | 2 man/registerMH-methods.Rd | 2 man/show-MatH-methods.Rd | 2 man/show-distributionH-methods.Rd | 2 man/skewH-methods.Rd | 2 man/stations_coordinates.Rd | 2 man/stdH-methods.Rd | 2 man/subsetHTS-methods.Rd | 2 man/times-methods.Rd | 2 98 files changed, 234 insertions(+), 197 deletions(-)
Title: Visualization of Functional Analysis Data
Description: Implementation of multilayered visualizations for enhanced graphical
representation of functional analysis data. It combines and integrates omics
data derived from expression and functional annotation enrichment analyses.
Its plotting functions have been developed with an hierarchical structure in
mind: starting from a general overview to identify the most enriched
categories (modified bar plot, bubble plot) to a more detailed one displaying
different types of relevant information for the molecules in a given set of
categories (circle plot, chord plot, cluster plot, Venn diagram).
Author: Wencke Walter, Fatima Sanchez-Cabo
Maintainer: Wencke Walter <wencke.walter@arcor.de>
Diff between GOplot versions 1.0 dated 2015-01-30 and 1.0.1 dated 2015-07-16
DESCRIPTION | 17 MD5 | 54 +- NAMESPACE | 6 R/GOCluster.R | 274 ++++++++++++--- R/GOCore.R | 757 ++++++++++++++++-------------------------- R/GOVenn.R | 24 - README.md |only build/vignette.rds |binary inst/doc/GOplot_vignette.Rmd | 4 inst/doc/GOplot_vignette.html | 543 +++++++++--------------------- man/EC.Rd | 2 man/GOBar.Rd | 2 man/GOBubble.Rd | 10 man/GOChord.Rd | 4 man/GOCircle.Rd | 2 man/GOCluster.Rd | 18 man/GOVenn.Rd | 2 man/bezier.Rd | 2 man/chord_dat.Rd | 40 +- man/circleFun.Rd | 2 man/circle_dat.Rd | 2 man/draw_table.Rd | 6 man/get_overlap.Rd | 2 man/get_overlap2.Rd | 2 man/theme_blank.Rd | 2 vignettes/GOBar.png |only vignettes/GOBubble1.png |binary vignettes/GOBubble2.png |binary vignettes/GOCirc.png |binary 29 files changed, 794 insertions(+), 983 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized singular value decomposition of a matrix pair, utilizing Lapack routines.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.5 dated 2015-02-12 and 1.6 dated 2015-07-16
DESCRIPTION | 20 ++++++++++---------- MD5 | 33 +++++++++++++++++++++++++++------ NAMESPACE | 12 +++++++++--- NEWS | 5 +++++ R/gsvd.R |only R/lapackerror.R | 5 +++++ man/geigen-package.Rd | 5 ++++- man/gqz.Rd | 10 +++++----- man/gsvd.Rd |only man/gsvdaux.Rd |only src/xdggsvd.f |only tests/testgsvd.R |only tests/tgsvd1.R |only tests/tgsvd1.Rout.save |only tests/tgsvd2.R |only tests/tgsvd2.Rout.save |only tests/tgsvd3.R |only tests/tgsvd3.Rout.save |only tests/tgsvd4.R |only tests/tgsvd4.Rout.save |only tests/tgsvd5.R |only tests/tgsvd5.Rout.save |only tests/tgsvd6.R |only tests/tgsvd6.Rout.save |only tests/tgsvd7.R |only tests/tgsvd7.Rout.save |only tests/tgsvd8.R |only tests/tgsvd8.Rout.save |only 28 files changed, 65 insertions(+), 25 deletions(-)
Title: Fitting an Interval Response Variable Using gamlss.family
Distributions
Description: This is an add-on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>, Nicoleta Mortan
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.cens versions 4.3.1 dated 2015-02-03 and 4.3-2 dated 2015-07-16
DESCRIPTION | 14 ++-- MD5 | 10 +-- NAMESPACE | 44 +++++++------- data/lip.rda |binary man/cens.d.Rd | 2 man/gamlss.cens-package.Rd | 140 ++++++++++++++++++++++----------------------- 6 files changed, 106 insertions(+), 104 deletions(-)