Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.47 dated 2015-06-15 and 1.48 dated 2015-10-29
Changelog | 65 +++++++++ DESCRIPTION | 12 - MD5 | 46 +++--- NAMESPACE | 20 ++ R/Functions.R | 272 +++++++++++++++++++++++---------------- R/blockwiseModulesC.R | 92 +++++++++++-- R/consensusTOM.R | 5 R/empiricalBayesLM.R | 18 ++ R/internalConstants.R | 2 R/labelPoints.R | 8 - R/useNThreads.R | 2 man/WGCNA-package.Rd | 4 man/bicovWeights.Rd | 13 + man/blockSize.Rd | 2 man/blockwiseConsensusModules.Rd | 2 man/consensusKME.Rd | 3 man/consensusProjectiveKMeans.Rd | 5 man/labelPoints.Rd | 8 - man/mergeCloseModules.Rd | 2 man/moduleEigengenes.Rd | 2 man/multiSetMEs.Rd | 6 man/projectiveKMeans.Rd | 5 src/corFunctions-unified.c | 8 - src/networkFunctions.c | 2 24 files changed, 429 insertions(+), 175 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-2 dated 2015-10-01 and 0.1-3 dated 2015-10-29
DESCRIPTION | 24 +++++---- MD5 | 112 ++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++ R/ants-data.R |only R/dispersion.R |only R/download.prism.R | 22 +++++--- R/gaussian.kernel.R |only R/insert.values.R |only R/land.metrics.R | 79 +++++++++++++++++++------------ R/pu-data.R |only R/sample.line.R | 16 ++++-- R/sample.poly.R |only R/shannons.R |only R/similarity.R |only R/tri.R |only data |only inst/NEWS | 15 +++++- man/ants.Rd |only man/bearing.distance.Rd | 12 +++- man/breeding.density.Rd | 30 +++++++----- man/concordance.Rd | 32 ++++++++---- man/conf.interval.Rd | 20 ++++---- man/correlogram.Rd | 23 +++++---- man/csi.Rd | 23 +++++---- man/dispersion.Rd |only man/download.daymet.Rd | 39 ++++++++++----- man/download.hansen.Rd | 20 +++++--- man/download.prism.Rd | 24 ++++++--- man/gaussian.kernel.Rd |only man/group.pdf.Rd | 15 ++++-- man/hexagons.Rd | 16 ++++-- man/idw.smoothing.Rd | 30 +++++++----- man/insert.values.Rd |only man/kl.divergence.Rd | 13 +++-- man/land.metrics.Rd | 67 ++++++++++++++++---------- man/local.min.max.Rd | 20 +++++--- man/loess.boot.Rd | 51 ++++++++++++-------- man/loess.ci.Rd | 26 ++++++---- man/logistic.regression.Rd | 61 ++++++++++++++---------- man/moments.Rd | 40 ++++++++-------- man/nni.Rd | 14 ++++- man/o.ring.Rd | 19 +++++-- man/optimal.k.Rd | 14 ++++- man/outliers.Rd | 24 ++++++--- man/parea.sample.Rd | 21 +++++--- man/plot.loess.boot.Rd | 16 ++++-- man/point.in.poly.Rd | 25 ++++++---- man/pp.subsample.Rd | 48 ++++++++++++------- man/print.loess.boot.Rd | 2 man/pseudo.absence.Rd | 52 ++++++++++++-------- man/pu.Rd |only man/raster.entropy.Rd | 16 ++++-- man/raster.vol.Rd | 21 +++++--- man/sample.line.Rd | 39 ++++++++------- man/sample.poly.Rd |only man/separability.Rd | 61 ++++++++++++++---------- man/shannons.Rd |only man/similarity.Rd |only man/sp.na.omit.Rd | 20 ++++---- man/stratified.random.Rd | 19 +++++-- man/summary.loess.boot.Rd | 2 man/tpi.Rd | 18 ++++--- man/trend.line.Rd | 6 ++ man/tri.Rd |only man/wt.centroid.Rd | 26 ++++++---- man/zonal.stats.Rd | 43 ++++++++++------- 66 files changed, 848 insertions(+), 497 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 2.9 dated 2014-09-10 and 3.0 dated 2015-10-29
DESCRIPTION | 14 +++--- LICENCE | 2 MD5 | 62 +++++++++++++------------- NAMESPACE | 17 ++++++- NEWS | 3 + R/STS.R | 8 +-- R/zzz.r | 2 build/vignette.rds |binary demo/Sim.DiffProc.R | 38 ++++++++++++++++ inst/doc/FitSDE.Rnw | 2 inst/doc/FitSDE.pdf |binary inst/doc/Introduction.R | 6 +- inst/doc/Introduction.Rnw | 20 ++++---- inst/doc/Introduction.pdf |binary inst/doc/SDEs.R | 81 +++++++++++++++++++++++++--------- inst/doc/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |only man/Sim.DiffProc-package.Rd | 21 +++------ man/bridgesde1d.Rd | 1 man/bridgesde2d.Rd | 1 man/bridgesde3d.Rd | 1 man/fitsde.Rd | 2 man/plot2d.Rd | 2 man/snssde1d.Rd | 2 man/snssde2d.Rd | 2 man/snssde3d.Rd | 2 src/Sim.DiffProc.c | 24 ++-------- vignettes/Core_FitSDE.tex | 22 ++++----- vignettes/FitSDE.Rnw | 2 vignettes/Introduction.Rnw | 20 ++++---- vignettes/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- vignettes/Thumbs.db |only 33 files changed, 365 insertions(+), 196 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as Ghostscript is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-3 dated 2015-09-20 and 0.4-4 dated 2015-10-29
DESCRIPTION | 21 +++++++++++---------- MD5 | 14 +++++++------- inst/NEWS.Rd | 8 +++++++- man/showtext.auto.Rd | 2 +- man/showtext.begin.Rd | 10 +++++----- man/showtext.end.Rd | 2 +- man/showtext.opts.Rd | 10 +++++----- src/devfuns.c | 35 +++++++++++++++++++---------------- 8 files changed, 56 insertions(+), 46 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.16 dated 2015-04-08 and 1.17 dated 2015-10-29
DESCRIPTION | 8 +- MD5 | 28 ++++--- NAMESPACE | 9 +- R/ancRECON.R | 196 ++++++++++++++++++++++++++++++-------------------- R/corDISC.R | 77 +++++++++++-------- R/corHMM.R | 43 ++++++---- R/corPAINT.R | 67 +++++++++-------- R/lewisMkv.R |only R/rayDISC.R | 82 +++++++++++--------- R/readNexusMorph.R |only man/ancRECON.Rd | 7 - man/corDISC.Rd | 8 +- man/corHMM.Rd | 12 ++- man/corPAINT.Rd | 2 man/lewisMkv.Rd |only man/rayDISC.Rd | 4 - man/readNexusMorph.Rd |only 17 files changed, 319 insertions(+), 224 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.1 dated 2015-06-13 and 1.1.1 dated 2015-10-29
DESCRIPTION | 8 MD5 | 22 - NAMESPACE | 5 R/A_ExonPtnAlign_functions.R | 2 R/BIGDAWG.R | 934 +++++++++++++++++++++---------------------- R/update_wrapper.R | 7 build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 6 inst/doc/BIGDAWG.html | 14 man/BIGDAWG.Rd | 6 man/UpdateRelease.Rd | 4 vignettes/BIGDAWG.Rmd | 6 12 files changed, 510 insertions(+), 504 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-20 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-29 2.1.1
2015-07-28 2.1
2015-05-14 2.0
2015-03-21 1.3
2015-01-10 1.1
2014-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-13 1.1.1
2014-05-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-22 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-02 1.1
2013-11-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-07 1.1.3
2013-09-12 1.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-12 1.1.3
2014-01-24 1.1.2
2013-04-06 1.1.1
2013-03-05 1.1
2013-02-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-20 1.01
2012-10-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-01 1.0.12
2015-06-19 1.0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-28 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-12 1.7-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-17 0.1.3
2014-12-04 0.1.1
2014-11-20 0.1.0
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-2 dated 2015-06-24 and 2.7-5 dated 2015-10-29
dae-2.7-2/dae/R/proj.canon.v3.r |only dae-2.7-2/dae/R/projs.canon.v3.r |only dae-2.7-5/dae/DESCRIPTION | 11 +++-- dae-2.7-5/dae/MD5 | 38 ++++++++++--------- dae-2.7-5/dae/NAMESPACE | 9 ++++ dae-2.7-5/dae/R/Interaction.ABC.Plot.r | 12 ++++-- dae-2.7-5/dae/R/NoReps.r | 59 +++++++++++++++++++++++++++--- dae-2.7-5/dae/R/mat.functions.r | 2 - dae-2.7-5/dae/R/proj.canon.v4.r |only dae-2.7-5/dae/R/projs.canon.v4.r |only dae-2.7-5/dae/build |only dae-2.7-5/dae/inst/NEWS.Rd | 22 +++++++++++ dae-2.7-5/dae/inst/doc/dae-manual.pdf |binary dae-2.7-5/dae/man/dae-package.Rd | 23 ++++------- dae-2.7-5/dae/man/detect.diff.Rd |only dae-2.7-5/dae/man/efficiency.criteria.Rd | 17 +++++--- dae-2.7-5/dae/man/interaction.ABC.plot.Rd | 23 ++++++++--- dae-2.7-5/dae/man/no.reps.Rd | 10 ++--- dae-2.7-5/dae/man/power.exp.Rd | 2 - dae-2.7-5/dae/man/projs.canon.Rd | 27 +++++++++---- dae-2.7-5/dae/man/projs.structure.Rd | 47 ++++++++++++++++------- dae-2.7-5/dae/man/summary.p2canon.Rd | 26 +++++++------ dae-2.7-5/dae/man/summary.pcanon.Rd | 20 +++++----- 23 files changed, 239 insertions(+), 109 deletions(-)
Title: Learning Bayesian Network Classifiers from Data
Description: Implementation of different algorithms for learning discrete Bayesian network classifiers from data, including wrapper algorithms and those based on Chow-Liu's algorithm.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut]
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
Diff between bnclassify versions 0.3.0 dated 2015-07-30 and 0.3.1 dated 2015-10-29
DESCRIPTION | 9 +++--- MD5 | 42 ++++++++++++++++++----------- NAMESPACE | 1 R/0bnclassify-doc.R | 45 ++++++++++++++++++++++++------- R/bnc-dag-operate.R | 10 +++++- R/learn-params-awnb.R | 2 - R/learn-params.R | 2 - README.md | 2 - build/vignette.rds |binary man/bnc.Rd | 4 +- man/cv.Rd | 4 +- man/learn_params.Rd | 53 +++++++++++++++++++++++++------------ man/plot.bnc_dag.Rd | 4 ++ man/wrapper.Rd | 4 +- tests/testthat/test-learn-params.R | 11 +++++++ tests/testthat/test-wrap-grain.R | 6 ++-- vignettes/bnclassify.Rmd | 27 +++++++++++------- vignettes/bnclassify_cache |only 18 files changed, 154 insertions(+), 72 deletions(-)
Title: Augments the Use of 'Asreml' in Fitting Mixed Models
Description: Assists in automating the testing of terms in mixed models when 'asreml' is used
to fit the models. The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the
fitting of a sequence of models is kept in a data frame. Procedures are available for choosing
models that conform to the hierarchy or marginality principle and for displaying predictions
for significant terms in tables and graphs. The package 'asreml' provides a computationally
efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It can be
purchased from 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R', who will supply a zip file for
local installation/updating.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between asremlPlus versions 2.0-0 dated 2015-06-24 and 2.0-2 dated 2015-10-29
DESCRIPTION | 10 ++--- MD5 | 26 +++++++------- NAMESPACE | 8 +++- R/reml.v19.r | 76 +++++++++++++++++++++++++++++++++++++---- R/variogram.faces.v2.r | 6 ++- build |only inst/NEWS.Rd | 14 +++++++ inst/doc/asremlPlus-manual.pdf |binary man/addrm.terms.asrtests.Rd | 10 ++++- man/asremlPlus-package.Rd | 22 +++++------ man/newrcov.asrtests.Rd |only man/pred.present.asreml.Rd | 9 ++-- man/predictionplot.asreml.Rd | 11 +++-- man/testrcov.asrtests.Rd | 13 +++---- man/variofaces.Rd | 11 ++++- 15 files changed, 160 insertions(+), 56 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 0.65-1 dated 2015-05-27 and 1.0-0 dated 2015-10-29
vegan3d-0.65-1/vegan3d/README.md |only vegan3d-1.0-0/vegan3d/DESCRIPTION | 10 - vegan3d-1.0-0/vegan3d/MD5 | 38 ++-- vegan3d-1.0-0/vegan3d/NAMESPACE | 15 + vegan3d-1.0-0/vegan3d/R/ordiplot3d.R | 11 + vegan3d-1.0-0/vegan3d/R/ordirgl.R | 33 +++- vegan3d-1.0-0/vegan3d/R/orditree3d.R |only vegan3d-1.0-0/vegan3d/R/orglellipse.R |only vegan3d-1.0-0/vegan3d/R/orglpoints.R | 18 +- vegan3d-1.0-0/vegan3d/R/orglsegments.R | 20 ++ vegan3d-1.0-0/vegan3d/R/orglspantree.R |only vegan3d-1.0-0/vegan3d/R/orglspider.R | 16 +- vegan3d-1.0-0/vegan3d/R/orgltext.R | 12 + vegan3d-1.0-0/vegan3d/R/rgl.isomap.R | 16 +- vegan3d-1.0-0/vegan3d/R/rgl.renyiaccum.R | 5 vegan3d-1.0-0/vegan3d/R/scores.ordiplot3d.R |only vegan3d-1.0-0/vegan3d/build |only vegan3d-1.0-0/vegan3d/inst |only vegan3d-1.0-0/vegan3d/man/ordiplot3d.Rd | 123 ++++++++------- vegan3d-1.0-0/vegan3d/man/ordirgl.Rd | 208 +++++++++++++++++---------- vegan3d-1.0-0/vegan3d/man/orditree3d.Rd |only vegan3d-1.0-0/vegan3d/man/rgl.isomap.Rd | 32 ++-- vegan3d-1.0-0/vegan3d/man/rgl.renyiaccum.Rd | 6 vegan3d-1.0-0/vegan3d/man/vegan3d-package.Rd |only 24 files changed, 360 insertions(+), 203 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete non-equally spaced observations on a finite time interval based on expansions of the convolution kernel, the unknown function and the observed signal over Laguerre functions basis. It implements the methodology proposed in the paper "Laplace deconvolution on the basis of time domain data and its application to Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y. Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.1 dated 2015-10-29 and 1.0.2 dated 2015-10-29
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/LagLaplaceDeconvolution.R | 62 +++++++++++++++++--------------------------- man/LagLaplDeconv.Rd | 36 ++++++++++++------------- 4 files changed, 48 insertions(+), 64 deletions(-)
Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine)
and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate
as well as vine copula selection are provided. Models can be estimated
either sequentially or by joint maximum likelihood estimation.
Sampling algorithms and plotting methods are also included.
Data is assumed to lie in the unit hypercube (so-called copula
data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt
<tobias.erhardt@tum.de>
Diff between CDVine versions 1.3 dated 2015-07-30 and 1.4 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/zzz.R | 5 +++++ man/CDVine-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015).
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology).
Author: Thomas Yee [aut, cre, cph],
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 0.9-7 dated 2015-03-17 and 1.0-0 dated 2015-10-29
DESCRIPTION | 20 +++++++++------ MD5 | 68 ++++++++++++++++++++++++++------------------------- NAMESPACE | 6 ++++ NEWS | 18 +++++++++++++ R/family.fishing.R | 51 ++++---------------------------------- data/bb.de.rda |binary data/bd.us.rda |only data/belcap.rda |binary data/crashf.au.rda |binary data/crime.us.rda |binary data/datalist | 1 data/exam1.rda |binary data/fibre15.rda |binary data/fibre1dot5.rda |binary data/gala.rda |binary data/hued.rda |binary data/huie.rda |binary data/huse.rda |binary data/oly12.rda |binary data/prison.us.rda |binary data/profs.nz.rda |binary data/rainfall.rda |binary data/rugby.rda |binary data/rugby.ties.rda |binary data/students.tw.rda |binary data/trapO.rda |binary data/tube10.rda |binary data/ugss.rda |binary data/vtinpat.rda |binary data/wffc.indiv.rda |binary data/wffc.nc.rda |binary data/wffc.rda |binary data/wffc.teams.rda |binary data/xs.nz.rda |binary inst/CITATION | 39 +++++++++++++++++++++++++++++ man/bd.us.Rd |only 36 files changed, 118 insertions(+), 85 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 0.9-8 dated 2015-05-11 and 1.0-0 dated 2015-10-29
ChangeLog |only DESCRIPTION | 20 - LICENCE.note |only MD5 | 263 +++++++------- NAMESPACE | 68 +++ NEWS | 63 +++ R/Links.R | 14 R/build.terms.vlm.q | 36 + R/calibrate.q | 15 R/coef.vlm.q | 9 R/confint.vlm.R |only R/family.aunivariate.R | 20 - R/family.basics.R | 30 + R/family.binomial.R | 147 +++++-- R/family.bivariate.R | 66 ++- R/family.categorical.R | 37 + R/family.censored.R | 268 ++++++++++++++ R/family.circular.R | 4 R/family.exp.R | 2 R/family.extremes.R | 14 R/family.genetic.R | 20 - R/family.glmgam.R | 70 ++- R/family.loglin.R | 4 R/family.mixture.R | 8 R/family.nonlinear.R | 4 R/family.normal.R | 758 ++++++++++++++++++++++++++-------------- R/family.others.R | 12 R/family.positive.R | 31 - R/family.qreg.R | 144 ++++--- R/family.rcim.R | 25 + R/family.robust.R | 2 R/family.rrr.R | 317 ++++++++--------- R/family.survival.R | 4 R/family.ts.R | 130 ++++--- R/family.univariate.R | 199 ++++++---- R/family.zeroinf.R | 31 + R/formula.vlm.q | 99 +++++ R/links.q | 797 +++++++++++++++++++++++-------------------- R/model.matrix.vglm.q | 38 +- R/qtplot.q | 20 - R/summary.vglm.q | 39 +- R/vglm.R | 6 R/vglm.fit.q | 2 R/vlm.wfit.q | 2 build/vignette.rds |binary data/Huggins89.t1.rda |binary data/Huggins89table1.rda |binary data/alclevels.rda |binary data/alcoff.rda |binary data/auuc.rda |binary data/backPain.rda |binary data/beggs.rda |binary data/car.all.rda |binary data/cfibrosis.rda |binary data/corbet.rda |binary data/crashbc.rda |binary data/crashf.rda |binary data/crashi.rda |binary data/crashmc.rda |binary data/crashp.rda |binary data/crashtr.rda |binary data/deermice.rda |binary data/ducklings.rda |binary data/finney44.rda |binary data/flourbeetle.rda |binary data/hspider.rda |binary data/lakeO.rda |binary data/leukemia.rda |binary data/marital.nz.rda |binary data/melbmaxtemp.rda |binary data/pneumo.rda |binary data/prinia.rda |binary data/ruge.rda |binary data/toxop.rda |binary data/venice.rda |binary data/venice90.rda |binary data/wine.rda |binary inst/CITATION | 61 ++- inst/doc/categoricalVGAM.pdf |binary inst/doc/crVGAM.R | 4 inst/doc/crVGAM.Rnw | 46 +- inst/doc/crVGAM.pdf |binary man/AA.Aa.aa.Rd | 1 man/AR1.Rd | 11 man/CommonVGAMffArguments.Rd | 29 + man/Links.Rd | 127 +++++- man/SURff.Rd | 2 man/VGAM-package.Rd | 9 man/acat.Rd | 4 man/alaplace3.Rd | 7 man/betabinomUC.Rd | 20 + man/binomialff.Rd | 10 man/binormal.Rd | 10 man/brat.Rd | 4 man/bratUC.Rd | 4 man/cauchit.Rd | 2 man/cens.poisson.Rd | 32 + man/cloglog.Rd | 5 man/confintvglm.Rd |only man/cratio.Rd | 4 man/cumulative.Rd | 6 man/explink.Rd | 2 man/fisherz.Rd | 2 man/foldsqrt.Rd | 2 man/formulavlm.Rd |only man/gengamma.Rd | 10 man/golf.Rd | 22 - man/has.intercept.Rd |only man/identitylink.Rd | 2 man/logc.Rd | 2 man/loge.Rd | 2 man/logit.Rd | 18 man/lognormal.Rd | 6 man/multilogit.Rd | 2 man/multinomial.Rd | 4 man/nbcanlink.Rd | 19 - man/nbolf.Rd | 16 man/negbinomial.Rd | 16 man/notdocumentedyet.Rd | 34 + man/polf.Rd | 17 man/posnormal.Rd | 69 ++- man/probit.Rd | 2 man/propodds.Rd | 2 man/rayleigh.Rd | 3 man/rhobit.Rd | 7 man/sratio.Rd | 6 man/summaryvglm.Rd |only man/tobit.Rd | 100 ++--- man/triangle.Rd | 9 man/undocumented-methods.Rd | 12 man/vcovvlm.Rd |only man/vglm.Rd | 17 man/weibull.mean.Rd |only man/weibullR.Rd | 1 man/wine.Rd | 6 vignettes/crVGAM.Rnw | 46 +- vignettes/crVGAM.bib | 20 + 137 files changed, 3133 insertions(+), 1579 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with SparseM/Matrix are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 1.2-1 dated 2015-09-30 and 1.3-0 dated 2015-10-29
ChangeLog | 36 ++++++++++ DESCRIPTION | 8 +- MD5 | 80 +++++++++++------------ R/definitions.R | 2 R/math.R | 103 +++++++++++++++--------------- inst/NEWS | 21 +++++- man/allequal.Rd | 7 -- man/nearestdist.Rd | 10 +- man/operations.Rd | 4 + man/rdist.Rd | 13 +++ tests/constructors.Rout.save | 4 - tests/covmat.Rout.save | 4 - tests/crossprod.Rout.save | 4 - tests/demo_article-jss-example1.Rout.save | 4 - tests/demo_article-jss-example2.Rout.save | 4 - tests/demo_article-jss.Rout.save | 4 - tests/demo_cholesky.Rout.save | 4 - tests/demo_jss15-BYM.Rout.save | 4 - tests/demo_jss15-Leroux.Rout.save | 4 - tests/demo_spam.Rout.save | 4 - tests/demo_timing.Rout.save | 4 - tests/diff.Rout.save | 4 - tests/dim.Rout.save | 4 - tests/displays.Rout.save | 4 - tests/dist.Rout.save | 4 - tests/foreign.Rout.save | 2 tests/helper.Rout.save | 4 - tests/jss_areal_counts.Rout.save | 4 - tests/kronecker.Rout.save | 4 - tests/math.R | 18 ++++- tests/math.Rout.save | 22 +++++- tests/mle.Rout.save | 4 - tests/norm.Rout.save | 4 - tests/ops.Rout.save | 5 - tests/overall.Rout.save | 4 - tests/permutation.Rout.save | 4 - tests/rowcolstats.Rout.save | 4 - tests/solve.Rout.save | 4 - tests/spamlist.Rout.save | 4 - tests/subsetting.Rout.save | 4 - tests/xybind.Rout.save | 4 - 41 files changed, 266 insertions(+), 173 deletions(-)
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Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between onlinePCA versions 1.2 dated 2015-08-12 and 1.3 dated 2015-10-29
DESCRIPTION | 12 ++++---- MD5 | 52 +++++++++++++++++++----------------- NAMESPACE | 12 ++++---- NEWS | 16 ++++++++++- R/batchpca.R | 23 +++++++++++----- R/bsoipca.R |only R/incRpca.R | 2 - R/incRpca.block.R |only R/incRpca.rc.R | 2 - R/perturbationRpca.R | 2 - R/secularRpca.R | 35 +++++++++++++++++------- man/batchpca.Rd | 63 +++++++++++++++++++------------------------- man/bsoipca.Rd |only man/ccipca.Rd | 33 +++++++++++------------ man/coef2fd.Rd | 24 ++++------------ man/create.basis.Rd | 41 +++++++++------------------- man/fd2coef.Rd | 26 ++++-------------- man/ghapca.Rd | 19 ++++--------- man/impute.Rd | 2 - man/incRpca.Rd | 47 ++++++++++++++------------------ man/incRpca.block.Rd |only man/incRpca.rc.Rd | 67 +++++++++++++++++++++-------------------------- man/onlinePCA-package.Rd | 10 ++----- man/perturbationRpca.Rd | 50 ++++++++++++++--------------------- man/secularRpca.Rd | 31 +++++++-------------- man/sgapca.Rd | 19 ++++--------- man/snlpca.Rd | 36 ++++++++----------------- man/updateCovariance.Rd | 10 +++---- man/updateMean.Rd | 13 ++++----- 29 files changed, 293 insertions(+), 354 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.3-0 dated 2015-10-24 and 1.3-2 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/25-addControlList.R | 19 +++++++++++++------ R/maxBFGS.R | 2 +- R/maxBFGSR.R | 2 +- R/maxCG.R | 2 +- R/maxNM.R | 2 +- R/maxNR.R | 2 +- R/maxOptim.R | 2 +- R/maxSANN.R | 2 +- man/maxNR.Rd | 2 +- 12 files changed, 41 insertions(+), 29 deletions(-)