Title: API for UK Gas Market Information
Description: Allows users to access live UK gas market information via National Grid's API.
Author: Timothy Wong [aut, cre]
Maintainer: Timothy Wong <timothy.wong@hotmail.co.uk>
Diff between ukgasapi versions 0.10 dated 2015-10-18 and 0.13 dated 2015-10-25
DESCRIPTION | 12 +++++------ MD5 | 6 ++--- R/dataItemExplorer.R | 52 +++++++++++++++++++++++------------------------- man/dataItemExplorer.Rd | 19 ++++++----------- 4 files changed, 41 insertions(+), 48 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.7.1 dated 2015-08-12 and 0.7.2 dated 2015-10-25
DESCRIPTION | 8 - MD5 | 14 +- NEWS | 9 + R/modules-smd.R | 8 + R/tableone-package.R | 2 build/vignette.rds |binary inst/doc/smd.html | 254 ++++++++++++++++++++++++------------------------ man/tableone-package.Rd | 2 8 files changed, 155 insertions(+), 142 deletions(-)
Title: Optimization of Sample Configurations using Spatial Simulated
Annealing
Description: Methods to optimize sample configurations using spatial simulated
annealing. Multiple objective functions are implemented for various
purposes, such as variogram estimation, trend estimation, and spatial
interpolation. A general purpose spatial simulated annealing function
enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre],
Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths],
Gerard B M Heuvelink [ths],
Edzer Pebesma [ctb],
Jon Skoien [ctb],
Joshua French [ctb],
Pierre Roudier [ctb],
Dick Brus [ctb],
Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between spsann versions 1.0.1 dated 2015-07-31 and 1.0-2 dated 2015-10-25
DESCRIPTION | 8 ++++---- MD5 | 45 ++++++++++++++++++++++++--------------------- NAMESPACE | 2 ++ R/AAA.R | 8 +++++--- R/SPSANNtools.R | 28 +++++++++++++++++++--------- R/check-spsann-arguments.R | 1 + R/optimACDC.R | 22 +++++++++++++++++----- R/optimCLHS.R |only R/optimCORR.R | 16 ++++++++++++++-- R/optimDIST.R | 4 ++-- R/optimPPL.R | 21 +++++++++++---------- R/optimSPAN.R | 25 +++++++++++++++++++++---- R/plotting-options.R | 8 +++++++- R/prepare-clhs-covars.R |only R/spsann.R | 4 ++-- man/optimACDC.Rd | 28 ++++++++++++++-------------- man/optimCLHS.Rd |only man/optimCORR.Rd | 22 +++++++++++----------- man/optimDIST.Rd | 22 +++++++++++----------- man/optimMKV.Rd | 18 +++++++++--------- man/optimMSSD.Rd | 18 +++++++++--------- man/optimPPL.Rd | 18 +++++++++--------- man/optimSPAN.Rd | 24 ++++++++++++------------ man/optimUSER.Rd | 18 +++++++++--------- man/spsann-package.Rd | 4 ++-- 25 files changed, 215 insertions(+), 149 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert <cpsievert1@gmail.com>
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between pitchRx versions 1.8 dated 2015-10-13 and 1.8.1 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 22 ++++++++++++++-------- R/animateFX.R | 1 - R/scrape.R | 1 - 5 files changed, 23 insertions(+), 19 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3 and K4 to characterize
distributions with left and right, symmetric or asymmetric fat tails in market
finance, neuroscience and other disciplines. Two algorithms to estimate with
a high accuracy distribution parameters, quantiles, value-at-risk and expected
shortfall. Also, power hyperbolas and power hyperbolic functions. This is a
major update that breaks compatibility with previous versions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.2-3 dated 2015-07-08 and 1.4-1 dated 2015-10-25
FatTailsR-1.2-3/FatTailsR/R/b_trigohp.R |only FatTailsR-1.2-3/FatTailsR/R/c_logishp.R |only FatTailsR-1.2-3/FatTailsR/R/d_conversion.R |only FatTailsR-1.2-3/FatTailsR/R/e_kiener1.R |only FatTailsR-1.2-3/FatTailsR/R/f_kiener2.R |only FatTailsR-1.2-3/FatTailsR/R/g_kiener3.R |only FatTailsR-1.2-3/FatTailsR/R/h_kiener4.R |only FatTailsR-1.2-3/FatTailsR/R/i_moments.R |only FatTailsR-1.2-3/FatTailsR/R/j_tailskiener.R |only FatTailsR-1.2-3/FatTailsR/R/k_estimation.R |only FatTailsR-1.2-3/FatTailsR/R/l_regression.R |only FatTailsR-1.2-3/FatTailsR/R/m_regression2.R |only FatTailsR-1.2-3/FatTailsR/R/n_regression3.R |only FatTailsR-1.2-3/FatTailsR/R/z_data.R |only FatTailsR-1.2-3/FatTailsR/man/ckiener.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkappa6.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkienerX.Rd |only FatTailsR-1.2-3/FatTailsR/man/fitkienerLX.Rd |only FatTailsR-1.4-1/FatTailsR/DESCRIPTION | 29 +-- FatTailsR-1.4-1/FatTailsR/MD5 | 103 ++++++------ FatTailsR-1.4-1/FatTailsR/NAMESPACE | 87 +++++++++- FatTailsR-1.4-1/FatTailsR/NEWS | 69 ++++++-- FatTailsR-1.4-1/FatTailsR/R/a_FatTailsR-package.R | 150 ++++++++++------- FatTailsR-1.4-1/FatTailsR/R/b_data.R |only FatTailsR-1.4-1/FatTailsR/R/c_trigohp.R |only FatTailsR-1.4-1/FatTailsR/R/d_logishp.R |only FatTailsR-1.4-1/FatTailsR/R/e_conversion.R |only FatTailsR-1.4-1/FatTailsR/R/f_kiener1.R |only FatTailsR-1.4-1/FatTailsR/R/g_kiener2.R |only FatTailsR-1.4-1/FatTailsR/R/h_kiener3.R |only FatTailsR-1.4-1/FatTailsR/R/i_kiener4.R |only FatTailsR-1.4-1/FatTailsR/R/j_moments.R |only FatTailsR-1.4-1/FatTailsR/R/k_tailskiener.R |only FatTailsR-1.4-1/FatTailsR/R/l_estimation.R |only FatTailsR-1.4-1/FatTailsR/R/m_laplaceroll.R |only FatTailsR-1.4-1/FatTailsR/R/n_estimation2.R |only FatTailsR-1.4-1/FatTailsR/R/o_regression.R |only FatTailsR-1.4-1/FatTailsR/data/datalist |only FatTailsR-1.4-1/FatTailsR/data/dfData.rda |binary FatTailsR-1.4-1/FatTailsR/data/tData.rda |binary FatTailsR-1.4-1/FatTailsR/data/xData.rda |binary FatTailsR-1.4-1/FatTailsR/data/zData.rda |binary FatTailsR-1.4-1/FatTailsR/man/FatTailsR.Rd | 145 +++++++++-------- FatTailsR-1.4-1/FatTailsR/man/aw2k.Rd | 119 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/checkquantiles.Rd | 46 ++++- FatTailsR-1.4-1/FatTailsR/man/ckiener1234.Rd |only FatTailsR-1.4-1/FatTailsR/man/dfData.Rd | 56 ------ FatTailsR-1.4-1/FatTailsR/man/dimdim.Rd |only FatTailsR-1.4-1/FatTailsR/man/elevenprobs.Rd | 51 ++---- FatTailsR-1.4-1/FatTailsR/man/estimkiener11.Rd | 118 ++++++------- FatTailsR-1.4-1/FatTailsR/man/exfit0.Rd |only FatTailsR-1.4-1/FatTailsR/man/exphp.Rd | 13 - FatTailsR-1.4-1/FatTailsR/man/extractData.Rd |only FatTailsR-1.4-1/FatTailsR/man/fitkienerX.Rd |only FatTailsR-1.4-1/FatTailsR/man/getDSdata.Rd | 44 ++--- FatTailsR-1.4-1/FatTailsR/man/getnamesk.Rd |only FatTailsR-1.4-1/FatTailsR/man/kashp.Rd | 8 FatTailsR-1.4-1/FatTailsR/man/kiener1.Rd | 96 +++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener2.Rd | 103 ++++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener3.Rd | 120 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kiener4.Rd | 113 ++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kmoments.Rd | 186 +++++++++++----------- FatTailsR-1.4-1/FatTailsR/man/laplacegaussnorm.Rd | 17 +- FatTailsR-1.4-1/FatTailsR/man/loghp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logishp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logit.Rd | 44 +++-- FatTailsR-1.4-1/FatTailsR/man/pk2pk.Rd | 80 ++++----- FatTailsR-1.4-1/FatTailsR/man/pprobs0.Rd |only FatTailsR-1.4-1/FatTailsR/man/regkienerLX.Rd | 139 +++++++++------- FatTailsR-1.4-1/FatTailsR/man/roundcoefk.Rd |only FatTailsR-1.4-1/FatTailsR/man/tData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/xData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/zData.Rd | 6 73 files changed, 1251 insertions(+), 711 deletions(-)
Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sValues versions 0.1.1 dated 2015-09-13 and 0.1.2 dated 2015-10-25
sValues-0.1.1/sValues/README.md |only sValues-0.1.2/sValues/DESCRIPTION | 9 +-- sValues-0.1.2/sValues/MD5 | 21 ++++--- sValues-0.1.2/sValues/NAMESPACE | 2 sValues-0.1.2/sValues/R/internal_functions.R | 12 +--- sValues-0.1.2/sValues/R/sValues.R | 74 +++++++++++++++------------ sValues-0.1.2/sValues/inst/doc/sValues.R | 3 - sValues-0.1.2/sValues/inst/doc/sValues.Rnw | 3 - sValues-0.1.2/sValues/inst/doc/sValues.pdf |binary sValues-0.1.2/sValues/man/sValues.Rd | 36 ++++++++----- sValues-0.1.2/sValues/tests |only sValues-0.1.2/sValues/vignettes/sValues.Rnw | 3 - 12 files changed, 86 insertions(+), 77 deletions(-)
Title: Mixed Tempered Stable Distribution
Description: We provide detailed functions for univariate Mixed Tempered Stable distribution.
Author: Lorenzo Mercuri, Edit Rroji
Maintainer: Lorenzo Mercuri <lorenzo.mercuri@unimi.it>
Diff between MixedTS versions 1.0.3 dated 2015-07-17 and 1.0.4 dated 2015-10-25
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/MixedTS.R | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.14 dated 2015-10-11 and 0.99.15 dated 2015-10-25
DescTools-0.99.14/DescTools/R/test.DescTools.r |only DescTools-0.99.15/DescTools/DESCRIPTION | 8 DescTools-0.99.15/DescTools/MD5 | 47 +- DescTools-0.99.15/DescTools/NAMESPACE | 4 DescTools-0.99.15/DescTools/NEWS | 17 + DescTools-0.99.15/DescTools/R/DescTools.r | 282 ++++++++++------- DescTools-0.99.15/DescTools/inst/doc/Combinatorics.pdf |binary DescTools-0.99.15/DescTools/inst/doc/TablesInR.pdf |binary DescTools-0.99.15/DescTools/man/Abind.Rd | 11 DescTools-0.99.15/DescTools/man/BarnardTest.Rd |only DescTools-0.99.15/DescTools/man/BubbleLegend.Rd | 36 +- DescTools-0.99.15/DescTools/man/DateFunctions.Rd | 15 DescTools-0.99.15/DescTools/man/DescTools-package.Rd | 2 DescTools-0.99.15/DescTools/man/FindColor.Rd | 23 - DescTools-0.99.15/DescTools/man/Keywords.Rd | 6 DescTools-0.99.15/DescTools/man/PlotFun.Rd | 36 +- DescTools-0.99.15/DescTools/man/PlotMosaic.Rd | 14 DescTools-0.99.15/DescTools/man/Stamp.Rd | 4 DescTools-0.99.15/DescTools/man/StrPos.Rd | 9 DescTools-0.99.15/DescTools/man/SysInfo.Rd | 14 DescTools-0.99.15/DescTools/man/VarCI.Rd | 15 DescTools-0.99.15/DescTools/src/Barnard.c |only DescTools-0.99.15/DescTools/src/aux_fct.cpp | 25 - DescTools-0.99.15/DescTools/src/between.c | 91 +++-- DescTools-0.99.15/DescTools/src/between.h | 16 DescTools-0.99.15/DescTools/tests/misc.R | 26 - 26 files changed, 410 insertions(+), 291 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.3.0 dated 2015-06-16 and 3.3.1 dated 2015-10-25
BUGS | 2 DESCRIPTION | 12 - MD5 | 43 +++--- NAMESPACE | 7 - R/InitMHP.DynMLE.blockdiag.R | 203 +++++++++++++++++--------------- R/combine.networks.R | 108 +++++++++++++++-- R/ergm.godfather.R | 2 R/stergm.EGMME.SA.R | 4 R/stergm.getMCMCsample.R | 4 R/zzz.R | 10 + inst/NEWS.Rd | 74 ++++++++--- inst/doc/STERGM.pdf |binary man/ergm-terms.Rd | 4 man/stergm.Rd | 8 - man/tergm-package.Rd | 5 src/MHproposals_DynMLE.c | 2 src/MHproposals_DynMLE_block.c | 132 ++++++++++++++++++++ src/MHproposals_DynMoME.c | 2 tests/combine.networks.R | 34 +++++ tests/dynamic_MLE.R | 36 +++-- tests/dynamic_MLE_2.R | 38 ++++- tests/dynamic_MLE_blockdiag.R | 27 ++-- tests/dynamic_MLE_blockdiag.bipartite.R |only 23 files changed, 556 insertions(+), 201 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 4 functions, one for extracting relevant URLs, one for extracting features out of given URLs, one that does both together and one that constructs graphs based on the structure of a thread.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 1.1.1 dated 2015-07-04 and 2.0.0 dated 2015-10-25
DESCRIPTION | 12 +-- MD5 | 13 ++- NAMESPACE | 1 R/RedditExtractoR.R | 170 +++++++++++++++++++++++++++++++++++++++++-------- man/construct_graph.Rd |only man/get_reddit.Rd | 5 - man/reddit_content.Rd | 3 man/reddit_urls.Rd | 6 - 8 files changed, 167 insertions(+), 43 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The "M" in the name "geeM" is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel <lmcda4@lsuhsc.edu>
Diff between geeM versions 0.7.4 dated 2015-05-25 and 0.8.0 dated 2015-10-25
DESCRIPTION | 9 MD5 | 14 - NAMESPACE | 5 R/geem.R | 717 ++++++++++++++++++++++++++++++-------------------------- R/print.R | 142 ++++++----- R/updatealpha.R | 301 ++++++++++++----------- R/utility.R | 54 +++- man/geem.Rd | 332 +++++++++++++------------ 8 files changed, 861 insertions(+), 713 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010). Please see an eprint at http://arxiv.org/pdf/1507.06055.pdf for more details.
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.1 dated 2015-07-27 and 1.1.2 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.4 dated 2015-03-10 and 1.5 dated 2015-10-25
cit-1.4/cit/R/C_CIT_V5.R |only cit-1.4/cit/man/cit.Rd |only cit-1.4/cit/man/plotcit.Rd |only cit-1.4/cit/src/cit_v7.cpp |only cit-1.5/cit/DESCRIPTION | 12 ++++++------ cit-1.5/cit/MD5 | 24 +++++++++++++++++------- cit-1.5/cit/NAMESPACE | 4 +++- cit-1.5/cit/R/C_CIT_V12.R |only cit-1.5/cit/man/cit-package.Rd | 10 +++++----- cit-1.5/cit/man/cit.bp.Rd |only cit-1.5/cit/man/cit.cp.Rd |only cit-1.5/cit/man/fdr.cit.Rd |only cit-1.5/cit/man/fdr.od.Rd |only cit-1.5/cit/man/iuq.Rd |only cit-1.5/cit/man/linreg.Rd |only cit-1.5/cit/src/citconlog2_perm_v5.cpp |only cit-1.5/cit/src/citconlog2_v3.cpp |only cit-1.5/cit/src/citconlog2cvr_v3.cpp |only cit-1.5/cit/src/citconlog3_perm_v5.cpp |only cit-1.5/cit/src/citconlog3cvr_perm_v6.cpp |only cit-1.5/cit/src/logisticfunc.cpp |only cit-1.5/cit/src/logisticfunc.h |only 22 files changed, 31 insertions(+), 19 deletions(-)
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Diff between bayou versions 1.0.1 dated 2014-07-31 and 1.1.0 dated 2015-10-25
DESCRIPTION | 15 - MD5 | 112 +++++----- NAMESPACE | 6 R/bayou-likelihood.R | 19 - R/bayou-mcmc-utilities.R | 60 ++++- R/bayou-mcmc.R | 14 - R/bayou-package.R | 5 R/bayou-plotting.R | 364 +++++++++++++++------------------- R/bayou-prior.R | 47 ++-- R/bayou-simulation.r | 5 R/bayou-steppingstone.R | 60 +++-- R/conversion-utilities.R | 7 R/probability.R | 12 - man/Lposterior.Rd | 34 +-- man/OU.lik.Rd | 41 +-- man/OU.repar.Rd | 14 - man/OUphenogram.Rd | 40 +-- man/OUwie2bayou.Rd | 14 - man/QG.alpha.Rd | 13 - man/QG.sig2.Rd | 13 - man/bayou-package.Rd | 11 - man/bayou.lik.Rd | 29 +- man/bayou.mcmc.Rd | 102 +++------ man/bayou2OUwie.Rd | 22 -- man/cdpois.Rd | 25 +- man/combine.chains.Rd | 15 - man/dataSim.Rd | 33 +-- man/dhalfcauchy.Rd | 28 +- man/dloc.Rd | 32 +- man/dsb.Rd | 63 ++--- man/gelman.R.Rd | 27 +- man/identifyBranches.Rd | 37 +-- man/load.bayou.Rd | 32 +- man/make.powerposteriorFn.Rd | 29 +- man/make.prior.Rd | 128 +++++------ man/make.refFn.Rd | 46 +--- man/makeTransparent.Rd | 13 - man/overparameterize.startingPoint.Rd |only man/parmap.W.Rd | 28 +- man/pars2simmap.Rd | 28 +- man/phenogram.density.Rd | 47 +--- man/plot.bayouMCMC.Rd | 13 - man/plot.ssMCMC.Rd | 19 - man/plotBayoupars.Rd | 12 - man/plotRegimes.Rd |only man/plotSimmap.mcmc.Rd | 113 ++-------- man/print.bayouFit.Rd | 11 - man/print.priorFn.Rd | 11 - man/print.refFn.Rd | 11 - man/print.ssMCMC.Rd | 10 man/priorSim.Rd | 22 -- man/pull.pars.Rd | 28 +- man/regime.plot.Rd | 27 +- man/set.burnin.Rd | 14 - man/simmap.W.Rd | 34 +-- man/steppingstone.Rd | 98 ++------- man/summary.bayouMCMC.Rd | 17 - src/RcppExports.cpp | 50 +--- 58 files changed, 978 insertions(+), 1182 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.13.2 dated 2015-05-27 and 2.14.0 dated 2015-10-25
DESCRIPTION | 14 MD5 | 40 +- NAMESPACE | 29 + NEWS | 18 - R/999.AromaAffymetrix.R | 6 R/999.DEPRECATED.R | 50 -- R/AffyGenePDInfo.writeCdf.R | 2 R/AffymetrixCdfFile.COUNTS.R | 1 R/AffymetrixCelSet.R | 34 - R/AvgPlm.R | 2 R/DChipGenomeInformation.R | 3 R/DChipSnpInformation.R | 3 R/SnpChipEffectSet.extractAlleleSet.R | 9 R/UnitModel.fitCnProbes.R | 8 inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R | 178 +++++----- inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R | 1 man/ArrayExplorer.Rd | 2 man/DChipGenomeInformation.Rd | 3 man/DChipSnpInformation.Rd | 3 man/Non-documented_objects.Rd | 7 man/nbrOfGroupsPerUnit.AffymetrixCdfFile.Rd | 4 21 files changed, 188 insertions(+), 229 deletions(-)
More information about aroma.affymetrix at CRAN
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