Title: Hidden Factor Graph Models
Description: Hidden Factor graph models generalise Hidden Markov Models to tree structured data. The distinctive feature of 'treeHFM' is that it learns a transition matrix for first order (sequential) and for second order (splitting) events. It can be applied to all discrete and continuous data that is structured as a binary tree. In the case of continuous observations, 'treeHFM' has Gaussian distributions as emissions.
Author: Henrik Failmezger, Achim Tresch
Maintainer: Henrik Failmezger <Henrik.Failmezger@googlemail.com>
Diff between treeHFM versions 1.0.2 dated 2016-09-06 and 1.0.3 dated 2016-09-18
DESCRIPTION | 8 - MD5 | 12 +- src/BaumWelch.cpp | 230 ++++++++++++++-------------------------------------- src/FactorGraph.cpp | 128 ++++++++++++---------------- src/FactorGraph.h | 20 +--- src/MaxSum.cpp | 170 +++++--------------------------------- src/SumProduct.cpp | 76 +++++++---------- 7 files changed, 196 insertions(+), 448 deletions(-)
Title: Perform Joins or Minus Queries on 'Excel' Files
Description: Performs Joins and Minus Queries on 'Excel' Files
fulljoinXL() Merges all rows of 2 'Excel' files based upon a common column in the files.
innerjoinXL() Merges all rows from base file and join file when the join condition is met.
leftjoinXL() Merges all rows from the base file, and all rows from the join file
if the join condition is met.
rightjoinXL() Merges all rows from the join file, and all rows from the base file if the join
condition is met.
minusXL() Performs 2 operations source-minus-target and target-minus-source
If the files are identical all output files will be empty.
Choose two 'Excel' files via a dialog box, and then follow prompts at the console to
choose a base or source file and columns to merge or minus on.
Author: Yvonne Glanville [aut, cre]
Maintainer: Yvonne Glanville <yvonneglanville@gmail.com>
Diff between joinXL versions 1.0.0 dated 2016-08-29 and 1.0.1 dated 2016-09-18
DESCRIPTION | 10 ++++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 11 +++++++++++ R/fulljoinXL.R | 11 +++++++++++ R/innerjoinXL.R | 13 +++++++++++++ R/leftjoinXL.R | 11 +++++++++++ R/minusXL.R | 12 ++++++++++++ R/rightjoinXL.R | 11 +++++++++++ inst/doc/Functionality.html | 4 ++-- man/fulljoinXL.Rd | 6 ++++++ man/innerjoinXL.Rd | 6 ++++++ man/leftjoinXL.Rd | 6 ++++++ man/minusXL.Rd | 7 +++++++ man/rightjoinXL.Rd | 6 ++++++ 14 files changed, 121 insertions(+), 19 deletions(-)
Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>
Diff between dggridR versions 0.1.10 dated 2016-08-16 and 0.1.11 dated 2016-09-18
DESCRIPTION | 8 ++-- MD5 | 17 +++++---- NAMESPACE | 1 NEWS | 13 ++++++- R/dggridR.R | 65 +++++++++++++++++++++++++++++++------ man/dg_env.Rd |only src/apps/dggrid/gridgen.cpp | 9 ++--- src/lib/dglib/lib/DgIDGG.cpp | 2 - src/lib/dglib/lib/DgOutKMLfile.cpp | 13 ++----- src/lib/dglib/lib/DgProjFuller.cpp | 6 +-- 10 files changed, 94 insertions(+), 40 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2-5 dated 2016-06-30 and 2.3-0 dated 2016-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 13 +++++++++++-- inst/doc/dbmss.pdf |binary src/Makevars | 1 + src/Makevars.win | 1 + 6 files changed, 22 insertions(+), 11 deletions(-)
Title: Create Waffle Chart Visualizations in R
Description: Square pie charts (a.k.a. waffle charts) can be used
to communicate parts of a whole for categorical quantities. To emulate the
percentage view of a pie chart, a 10x10 grid should be used with each square
representing 1% of the total. Modern uses of waffle charts do not
necessarily adhere to this rule and can be created with a grid of any
rectangular shape. Best practices suggest keeping the number of categories
small, just as should be done when creating pie charts. Tools are provided
to create waffle charts as well as stitch them together, and to use glyphs
for making isotype pictograms.
Author: Bob Rudis <bob@rud.is>, Dave Gandy (FontAwesome)
Maintainer: Bob Rudis <bob@rud.is>
Diff between waffle versions 0.5.0 dated 2015-12-15 and 0.6.0 dated 2016-09-18
DESCRIPTION | 14 +++++++------- MD5 | 5 +++-- R/waffle.R | 39 ++++++++++++++++++++------------------- README.md |only 4 files changed, 30 insertions(+), 28 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.2.0.7 dated 2015-01-21 and 1.4.1 dated 2016-09-18
RgoogleMaps-1.2.0.7/RgoogleMaps/R/GetMap.OSM.R |only RgoogleMaps-1.2.0.7/RgoogleMaps/man/GetMap.OSM.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/DESCRIPTION | 16 - RgoogleMaps-1.4.1/RgoogleMaps/MD5 | 63 ++++-- RgoogleMaps-1.4.1/RgoogleMaps/NAMESPACE | 5 RgoogleMaps-1.4.1/RgoogleMaps/NEWS | 12 + RgoogleMaps-1.4.1/RgoogleMaps/R/GetBingMap.R |only RgoogleMaps-1.4.1/RgoogleMaps/R/GetMap.R | 138 +++++++++------ RgoogleMaps-1.4.1/RgoogleMaps/R/GetMapTiles.R |only RgoogleMaps-1.4.1/RgoogleMaps/R/GetOsmMap.R |only RgoogleMaps-1.4.1/RgoogleMaps/R/LatLon2XY.R | 1 RgoogleMaps-1.4.1/RgoogleMaps/R/LatLon2XY.centered.R | 15 + RgoogleMaps-1.4.1/RgoogleMaps/R/MapBackground.R | 1 RgoogleMaps-1.4.1/RgoogleMaps/R/PlotOnMapTiles.R |only RgoogleMaps-1.4.1/RgoogleMaps/R/PlotOnStaticMap.R | 9 RgoogleMaps-1.4.1/RgoogleMaps/R/ReadMapTile.R | 1 RgoogleMaps-1.4.1/RgoogleMaps/R/SpatialToPBS.R | 48 +++-- RgoogleMaps-1.4.1/RgoogleMaps/R/XY2LatLon.R | 29 +-- RgoogleMaps-1.4.1/RgoogleMaps/R/degreeAxis.R | 8 RgoogleMaps-1.4.1/RgoogleMaps/R/getGeoCode.R | 52 ++++- RgoogleMaps-1.4.1/RgoogleMaps/R/plotmap.R |only RgoogleMaps-1.4.1/RgoogleMaps/README |only RgoogleMaps-1.4.1/RgoogleMaps/data/incidents.rda |only RgoogleMaps-1.4.1/RgoogleMaps/inst/CITATION | 4 RgoogleMaps-1.4.1/RgoogleMaps/man/GetBingMap.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/man/GetMap.Rd | 21 +- RgoogleMaps-1.4.1/RgoogleMaps/man/GetMapTiles.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/man/GetOsmMap.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/man/LatLon2XY.Rd | 3 RgoogleMaps-1.4.1/RgoogleMaps/man/PlotOnMapTiles.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/man/PlotOnStaticMap.Rd | 8 RgoogleMaps-1.4.1/RgoogleMaps/man/RgoogleMaps-package.Rd | 84 ++++++--- RgoogleMaps-1.4.1/RgoogleMaps/man/SpatialToPBS.Rd | 3 RgoogleMaps-1.4.1/RgoogleMaps/man/XY2LatLon.Rd | 4 RgoogleMaps-1.4.1/RgoogleMaps/man/columbus.Rd | 132 +++++++------- RgoogleMaps-1.4.1/RgoogleMaps/man/degreeAxis.Rd | 2 RgoogleMaps-1.4.1/RgoogleMaps/man/getGeoCode.Rd | 4 RgoogleMaps-1.4.1/RgoogleMaps/man/incidents.Rd |only RgoogleMaps-1.4.1/RgoogleMaps/man/pennLC.Rd | 72 +++---- RgoogleMaps-1.4.1/RgoogleMaps/man/plotmap.Rd |only 40 files changed, 443 insertions(+), 292 deletions(-)
Title: Relationship Inference for DNA Mixtures
Description: Makes relationship inference involving DNA mixtures with unknown profiles.
Author: Navreet Kaur, Thore Egeland, Guro Dorum
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Diff between relMix versions 1.1 dated 2016-07-15 and 1.2 dated 2016-09-18
DESCRIPTION | 10 - MD5 | 52 +++++- NAMESPACE | 10 - R/createDatamatrix.R | 184 ++++++++++----------- R/relMix.R | 157 +++++++++--------- R/relMixGUI.R | 442 +++++++++++++++++++++++++++++++++++---------------- build |only inst |only man/relMix.Rd | 13 - man/relMixGUI.Rd | 4 vignettes |only 11 files changed, 547 insertions(+), 325 deletions(-)
Title: Interactive Viewing of Spatial Objects in R
Description: Methods to view spatial objects interactively.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Environmental Informatics Marburg [ctb]
Maintainer: Tim Appelhans <admin@environmentalinformatics-marburg.de>
Diff between mapview versions 1.1.0 dated 2016-06-13 and 1.2.0 dated 2016-09-18
DESCRIPTION | 12 - MD5 | 72 ++++-- NAMESPACE | 6 NEWS | 18 + R/RcppExports.R | 10 R/addHomeButton.R |only R/addLogo.R |only R/brewControls.R | 5 R/createLegend.R | 76 ++++++- R/garnishMap.R |only R/leafletControls.R | 44 +++- R/leafletView.R | 242 +++++++++++++++++------ R/mapView.R | 115 +++++++--- R/mapshot.R | 10 R/mapviewColors.R | 18 + R/mapviewOptions.R | 4 R/plainView.R | 72 ++---- R/raster2PNG.R | 6 R/simpleControls.R |only R/sortableLayersControl.R |only README.md | 62 +++++ data/atlStorms2005.rda |binary data/breweries91.rda |binary data/gadmCHE.rda |binary data/poppendorf.rda |binary inst/htmlwidgets/lib/HomeButton |only inst/htmlwidgets/lib/cubeView_style/cubeView.css | 4 inst/htmlwidgets/lib/slideView_style/style.css | 51 ++++ inst/htmlwidgets/lib/sortable_layers_control |only inst/htmlwidgets/plainView.js | 38 ++- inst/htmlwidgets/slideView.js | 24 +- man/addHomeButton.Rd |only man/addLogo.Rd |only man/garnishMap.Rd |only man/mapView.Rd | 34 ++- man/plainView.Rd | 57 +---- man/polygonData.sf.Rd |only src/RcppExports.cpp | 104 +++++---- src/mapviewCppFun.cpp | 18 + 39 files changed, 758 insertions(+), 344 deletions(-)
Title: Computational Methods for Numerical Analysis
Description: Provides the source and examples for James P. Howard, II,
"Computational Methods for Numerical Analysis with R,"
<https://jameshoward.us/cmna>, a forthcoming book on
numerical methods in R.
Author: James P. Howard, II [aut, cre]
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between cmna versions 0.2.2 dated 2016-09-17 and 0.3.0 dated 2016-09-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/findiff.R | 17 +++-------------- R/mcintegrate.R | 24 ++++++++++-------------- README.md | 2 +- man/findiff.Rd | 8 ++------ man/mcint.Rd | 8 ++------ 7 files changed, 28 insertions(+), 51 deletions(-)
Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial
inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioinactivation versions 1.1.2 dated 2016-03-21 and 1.1.3 dated 2016-09-18
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- R/make_predictions.R | 10 +++++-- inst/doc/inactivation.Rmd | 51 +++++++++++++++++++++------------------- inst/doc/inactivation.html | 56 ++++++++++++++++++++++---------------------- man/predict_inactivation.Rd | 8 +++--- vignettes/inactivation.Rmd | 51 +++++++++++++++++++++------------------- 7 files changed, 105 insertions(+), 91 deletions(-)
More information about bioinactivation at CRAN
Permanent link
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 2.5-0 dated 2016-07-15 and 3.0-0 dated 2016-09-18
hergm-2.5-0/hergm/data/sampson.RData |only hergm-2.5-0/hergm/man/bali.Rd |only hergm-2.5-0/hergm/man/example.Rd |only hergm-2.5-0/hergm/man/hergm.gof.Rd |only hergm-2.5-0/hergm/man/hergm.mcmc.diagnostics.Rd |only hergm-2.5-0/hergm/man/sampson.Rd |only hergm-3.0-0/hergm/DESCRIPTION | 11 - hergm-3.0-0/hergm/MD5 | 78 ++++---- hergm-3.0-0/hergm/NAMESPACE | 7 hergm-3.0-0/hergm/R/hergm.R | 35 ++- hergm-3.0-0/hergm/R/hergm.gof.R | 115 +++++------- hergm-3.0-0/hergm/R/hergm.initialize.R | 2 hergm-3.0-0/hergm/R/hergm.mcmc.R | 45 ++-- hergm-3.0-0/hergm/R/hergm.mcmc.diagnostics.R | 98 +++++++++- hergm-3.0-0/hergm/R/hergm.misc.R | 88 ++++++--- hergm-3.0-0/hergm/R/hergm.multiple.R | 14 - hergm-3.0-0/hergm/R/hergm.permutation.wrapper.R | 2 hergm-3.0-0/hergm/R/hergm.plot.R | 77 ++++++-- hergm-3.0-0/hergm/R/hergm.postprocess.R | 168 +++++++++--------- hergm-3.0-0/hergm/R/hergm.preprocess.R | 63 ++++-- hergm-3.0-0/hergm/R/hergm.print.R |only hergm-3.0-0/hergm/R/hergm.relabel.R | 30 +-- hergm-3.0-0/hergm/R/hergm.set.mcmc.R | 27 +- hergm-3.0-0/hergm/R/hergm.simulate.R | 83 ++++---- hergm-3.0-0/hergm/R/hergm.summary.R | 42 ---- hergm-3.0-0/hergm/R/hergm.terms.R | 59 +++++- hergm-3.0-0/hergm/R/hergm.wrapper.R | 3 hergm-3.0-0/hergm/R/zzz.R | 4 hergm-3.0-0/hergm/data/bunt.RData |only hergm-3.0-0/hergm/data/kapferer.RData |only hergm-3.0-0/hergm/man/bali.rd |only hergm-3.0-0/hergm/man/bunt.rd |only hergm-3.0-0/hergm/man/example.rd |only hergm-3.0-0/hergm/man/hergm-internal.Rd | 6 hergm-3.0-0/hergm/man/hergm.Rd | 224 +++++++++++++++--------- hergm-3.0-0/hergm/man/hergm.gof.rd |only hergm-3.0-0/hergm/man/hergm.mcmc.diagnostics.rd |only hergm-3.0-0/hergm/man/hergm.plot.Rd | 39 +--- hergm-3.0-0/hergm/man/hergm.postprocess.Rd | 54 ++--- hergm-3.0-0/hergm/man/hergm.print.Rd |only hergm-3.0-0/hergm/man/hergm.simulate.Rd | 42 ++-- hergm-3.0-0/hergm/man/hergm.summary.Rd | 28 +-- hergm-3.0-0/hergm/man/hergm.terms.Rd | 51 +---- hergm-3.0-0/hergm/man/kapferer.rd |only hergm-3.0-0/hergm/src/changestats.c | 95 ++++++++++ hergm-3.0-0/hergm/src/changestats.h | 2 hergm-3.0-0/hergm/src/h_ergm.c | 9 hergm-3.0-0/hergm/src/netstats.c | 3 48 files changed, 966 insertions(+), 638 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution.
It provides the density function, distribution function, and Quantile-Quantile plots.
It implements a variety of estimation methods for the distribution, including diagnostic plots.
Estimation methods include the starship (all 4 parameterisations), method of L-Moments for the GLD GPD type and a number of methods for only the FKML parameterisation.
These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>,
Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.3.3 dated 2016-04-20 and 2.4 dated 2016-09-18
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++++---- NAMESPACE | 5 ++++- R/fit.gpd.R |only R/lmoment.R |only R/methods.R | 24 ++++++++++++++++++++++++ TODO | 4 ++-- man/fit.gpd.Rd |only man/gld.lmoments.Rd |only 9 files changed, 46 insertions(+), 15 deletions(-)
Title: Co-Occurrence Network
Description: Read and preprocess fasta format data, and construct the co-occurrence network for downstream analyses. This R package is to construct the co-occurrence network with the algorithm developed by Du (2008) <DOI:10.1101/gr.6969007>. It could be used to transform the data with high-dimension, such as DNA or protein sequence, into co-occurrence networks. Co-occurrence network could not only capture the co-variation pattern between variables, such as the positions in DNA or protein sequences, but also reflect the relationship between samples. Although it is originally used in DNA and protein sequences, it could be also used to other kinds of data, such as SNP.
Author: Yuanqiang Zou <jerrytsou2001@gmail.com>, Yousong Peng <pys2013@hnu.edu.cn> and Taijiao Jiang <taijiao@moon.ibp.ac.cn>
Maintainer: Yuanqiang Zou <jerrytsou2001@gmail.com>
Diff between cooccurNet versions 0.1.1 dated 2016-09-05 and 0.1.2 dated 2016-09-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/readfasta.R | 24 +++++++++++++++++++----- man/cooccurNet.Rd | 4 ++-- 4 files changed, 28 insertions(+), 14 deletions(-)