Title: Pull Data from 'trakt.tv'
Diff between tRakt versions 0.7.4 dated 2015-02-23 and 0.9.0 dated 2015-02-24
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk
DESCRIPTION | 13 -
MD5 | 98 ++++----
NAMESPACE | 4
R/api.R | 25 +-
R/trakt.getEpisodeData.R | 63 ++---
R/trakt.getFullShowData.R | 32 +-
R/trakt.getSeasons.R | 11
R/trakt.search.R | 21 -
R/trakt.search.byid.R | 15 -
R/trakt.show.people.R | 20 +
R/trakt.show.related.R | 18 +
R/trakt.show.season.R | 41 ++-
R/trakt.show.stats.R | 13 -
R/trakt.show.summary.R | 19 -
R/trakt.shows.popular.R | 21 +
R/trakt.shows.trending.R | 25 +-
R/trakt.user.collection.R | 5
R/trakt.user.followers.R |only
R/trakt.user.following.R |only
R/trakt.user.friends.R |only
R/trakt.user.ratings.R |only
R/trakt.user.stats.R | 10
R/trakt.user.watched.R | 18 -
R/trakt.user.watchlist.R | 4
README.md | 39 ---
inst/doc/tRakt-Usage.R | 10
inst/doc/tRakt-Usage.Rmd | 10
inst/doc/tRakt-Usage.html | 180 +++++++--------
man/get_trakt_credentials.Rd | 7
man/trakt.api.call.Rd | 5
man/trakt.getEpisodeData.Rd | 19 +
man/trakt.getFullShowData.Rd | 11
man/trakt.getSeasons.Rd | 11
man/trakt.search.Rd | 9
man/trakt.search.byid.Rd | 7
man/trakt.show.people.Rd | 15 +
man/trakt.show.related.Rd | 15 +
man/trakt.show.season.Rd | 14 +
man/trakt.show.stats.Rd | 11
man/trakt.show.summary.Rd | 11
man/trakt.shows.popular.Rd | 16 +
man/trakt.shows.trending.Rd | 16 +
man/trakt.user.collection.Rd | 9
man/trakt.user.followers.Rd |only
man/trakt.user.following.Rd |only
man/trakt.user.friends.Rd |only
man/trakt.user.ratings.Rd |only
man/trakt.user.stats.Rd | 16 +
man/trakt.user.watched.Rd | 9
man/trakt.user.watchlist.Rd | 9
vignettes/tRakt-Usage.Rmd | 10
vignettes/tRakt-Usage_files/figure-html/Graphing_1-1.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-2.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-3.png |binary
54 files changed, 575 insertions(+), 360 deletions(-)
Title: A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]
Diff between aroma.apd versions 0.5.0 dated 2014-02-27 and 0.6.0 dated 2015-02-24
Description: DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 27 +++++++++++++++------------
MD5 | 30 ++++++++++++++++++------------
NEWS | 7 +++++++
R/cdfToApdMap.R | 8 ++++----
R/celToApd.R | 10 +++++-----
R/gtypeCelToPQ.R | 17 +++++++++--------
R/readApdRectangle.R | 6 +++---
R/readApdUnits.R | 24 ++++++++++--------------
R/updateApdUnits.R | 18 ++++++++++--------
R/zzz.R | 14 ++++++++------
man/aroma.apd-package.Rd | 2 +-
man/gtypeCelToPQ.Rd | 4 ++--
man/readApdUnits.Rd | 6 ------
tests |only
14 files changed, 92 insertions(+), 81 deletions(-)
Title: Tools for Nuclear Magnetic Resonance Spectrum Alignment and
Quantitative Analysis
Diff between speaq versions 1.2.0 dated 2015-01-14 and 1.2.1 dated 2015-02-24
Description: We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Related publication is available at http://www.biomedcentral.com/1471-2105/12/405/.
Author: Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Maintainer: Trung Nghia Vu
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
NEWS | 6 ++++++
man/speaq-package.Rd | 6 +++---
4 files changed, 19 insertions(+), 13 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Diff between rfUtilities versions 1.0 dated 2014-11-21 and 1.0-1 dated 2015-02-24
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans
rfUtilities-1.0-1/rfUtilities/DESCRIPTION | 26 +++++-----
rfUtilities-1.0-1/rfUtilities/MD5 | 34 ++++++++------
rfUtilities-1.0-1/rfUtilities/NAMESPACE | 3 -
rfUtilities-1.0-1/rfUtilities/R/multi.collinear.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.class.sensitivity.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.classBalance.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.crossValidation.R | 6 +-
rfUtilities-1.0-1/rfUtilities/R/rf.modelSel.R | 8 +--
rfUtilities-1.0-1/rfUtilities/R/rf.partial.ci.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.partial.prob.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.significance.R | 12 ++--
rfUtilities-1.0-1/rfUtilities/inst |only
rfUtilities-1.0-1/rfUtilities/man/multi.collinear.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.class.sensitivity.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.classBalance.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.crossValidation.Rd | 7 +-
rfUtilities-1.0-1/rfUtilities/man/rf.modelSel.Rd | 9 ++-
rfUtilities-1.0-1/rfUtilities/man/rf.partial.ci.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.partial.prob.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.significance.Rd | 13 ++---
rfUtilities-1.0/rfUtilities/R/MultiColinear.R |only
rfUtilities-1.0/rfUtilities/R/probPartialPlot.R |only
rfUtilities-1.0/rfUtilities/R/rf.ClassBalance.R |only
rfUtilities-1.0/rfUtilities/man/MultiColinear.Rd |only
rfUtilities-1.0/rfUtilities/man/probPartialPlot.Rd |only
rfUtilities-1.0/rfUtilities/man/rf.ClassBalance.Rd |only
26 files changed, 64 insertions(+), 54 deletions(-)
Title: R interface to Global Biotic Interactions
Diff between rglobi versions 0.2.4 dated 2015-01-28 and 0.2.5 dated 2015-02-24
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
source all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen
rglobi-0.2.4/rglobi/rglobi_0.2.4.tar.gz |only
rglobi-0.2.5/rglobi/DESCRIPTION | 8 ++--
rglobi-0.2.5/rglobi/MD5 | 7 +---
rglobi-0.2.5/rglobi/README.md | 41 +++++++++++++++---------
rglobi-0.2.5/rglobi/tests/testthat/test-globi.R | 2 -
5 files changed, 35 insertions(+), 23 deletions(-)
Title: Visualization Methods for Raster Data
Diff between rasterVis versions 0.32 dated 2014-10-25 and 0.35 dated 2015-02-24
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro
ChangeLog | 18 ++---
DESCRIPTION | 16 ++--
MD5 | 18 ++---
NAMESPACE | 2
R/grid.R | 26 +++++++
R/streamplot.R | 53 +++++++---------
R/vectorplot.R | 153 ++++++++++++++++++++++++++++++++---------------
README.md | 2
man/hovmoller-methods.Rd | 51 ++++++++++-----
man/vectorplot.Rd | 49 ++++++++++-----
10 files changed, 249 insertions(+), 139 deletions(-)
Title: Nonparametric Stability Analysis
Diff between phenability versions 1.0 dated 2014-04-23 and 2.0 dated 2015-02-24
Description: An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
Author: Leonardo Castelo Branco
Maintainer: Leonardo C. Branco
DESCRIPTION | 10 +-
MD5 | 21 ++--
R/fox.R | 62 ++++++++-----
R/kang.R | 54 ++++++++---
R/nahu.R | 212 +++++++++++++++++++++++---------------------
R/phenability-internal.R |only
R/thsu.R | 213 ++++++++++++++++++++++++---------------------
man/fox.Rd | 11 +-
man/kang.Rd | 9 +
man/nahu.Rd | 9 +
man/phenability-package.Rd | 15 ++-
man/thsu.Rd | 9 +
12 files changed, 357 insertions(+), 268 deletions(-)
Title: Methods for Maximum Likelihood Estimation
Diff between likelihood versions 1.6 dated 2014-06-27 and 1.7 dated 2015-02-24
Description: Tools for maximum likelihood estimation of parameters
of scientific models.
Author: Lora Murphy
Maintainer: Lora Murphy
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/anneal.R | 7 +++++--
man/anneal.Rd | 4 ++--
man/simulated_annealing_algorithm.Rd | 4 ++--
5 files changed, 18 insertions(+), 15 deletions(-)
Title: Freedom from Disease
Diff between FFD versions 1.0-2 dated 2013-04-22 and 1.0-6 dated 2015-02-24
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka
DESCRIPTION | 25 +++++------------
MD5 | 24 ++++++++--------
NAMESPACE | 1
R/FFD_GUI-internal.R | 6 ++--
R/FFD_GUI.R | 3 +-
R/computeAlphaLimitedSampling.R | 2 -
R/computeAposterioriError.R | 14 ++++-----
build |only
inst/doc/FFD-intro.R |only
inst/doc/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
inst/doc/FFD-intro.pdf |binary
man/lls.Rd | 6 ++--
vignettes/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
vignettes/FFD.bib | 9 ++++++
14 files changed, 106 insertions(+), 100 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Diff between clinfun versions 1.0.6 dated 2014-07-22 and 1.0.9 dated 2015-02-24
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan
CHANGES | 13 +++++++++
DESCRIPTION | 6 ++--
INDEX | 3 ++
MD5 | 18 ++++++-------
NAMESPACE | 2 -
R/calogrank.R | 3 +-
R/coxphQuantile.R | 32 +++++++++++------------
R/fedesign.R | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
R/permlogrank.R | 9 +++---
man/fedesign.Rd | 16 +++++++++--
10 files changed, 139 insertions(+), 37 deletions(-)
Title: Applied Econometrics with R
Diff between AER versions 1.2-2 dated 2014-01-28 and 1.2-3 dated 2015-02-24
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 13 -
MD5 | 282 +++++++++++++++++------------------
NAMESPACE | 4
NEWS | 9 +
R/dispersiontest.R | 9 -
R/tobit.R | 6
build/vignette.rds |binary
data/Affairs.rda |binary
data/ArgentinaCPI.rda |binary
data/BankWages.rda |binary
data/BenderlyZwick.rda |binary
data/BondYield.rda |binary
data/CASchools.rda |binary
data/CPS1985.rda |binary
data/CPS1988.rda |binary
data/CPSSW04.rda |binary
data/CPSSW3.rda |binary
data/CPSSW8.rda |binary
data/CPSSW9204.rda |binary
data/CPSSW9298.rda |binary
data/CPSSWEducation.rda |binary
data/CartelStability.rda |binary
data/ChinaIncome.rda |binary
data/CigarettesB.rda |binary
data/CigarettesSW.rda |binary
data/CollegeDistance.rda |binary
data/ConsumerGood.rda |binary
data/CreditCard.rda |binary
data/DJFranses.rda |binary
data/DoctorVisits.rda |binary
data/DutchAdvert.rda |binary
data/DutchSales.rda |binary
data/Electricity1955.rda |binary
data/Electricity1970.rda |binary
data/EquationCitations.rda |binary
data/Equipment.rda |binary
data/EuroEnergy.rda |binary
data/Fatalities.rda |binary
data/Fertility.rda |binary
data/Fertility2.rda |binary
data/FrozenJuice.rda |binary
data/GSOEP9402.rda |binary
data/GSS7402.rda |binary
data/GermanUnemployment.rda |binary
data/GrowthDJ.rda |binary
data/GrowthSW.rda |binary
data/Grunfeld.rda |binary
data/Guns.rda |binary
data/HMDA.rda |binary
data/HealthInsurance.rda |binary
data/HousePrices.rda |binary
data/Journals.rda |binary
data/KleinI.rda |binary
data/Longley.rda |binary
data/MASchools.rda |binary
data/ManufactCosts.rda |binary
data/MarkDollar.rda |binary
data/MarkPound.rda |binary
data/Medicaid1986.rda |binary
data/Mortgage.rda |binary
data/MotorCycles.rda |binary
data/Municipalities.rda |binary
data/MurderRates.rda |binary
data/NMES1988.rda |binary
data/NYSESW.rda |binary
data/NaturalGas.rda |binary
data/OECDGas.rda |binary
data/OECDGrowth.rda |binary
data/OlympicTV.rda |binary
data/OrangeCounty.rda |binary
data/PSID1976.rda |binary
data/PSID1982.rda |binary
data/PSID7682.rda |binary
data/Parade2005.rda |binary
data/PepperPrice.rda |binary
data/PhDPublications.rda |binary
data/ProgramEffectiveness.rda |binary
data/RecreationDemand.rda |binary
data/ResumeNames.rda |binary
data/SIC33.rda |binary
data/STAR.rda |binary
data/ShipAccidents.rda |binary
data/SmokeBan.rda |binary
data/SportsCards.rda |binary
data/StrikeDuration.rda |binary
data/SwissLabor.rda |binary
data/TeachingRatings.rda |binary
data/TechChange.rda |binary
data/TradeCredit.rda |binary
data/TravelMode.rda |binary
data/UKInflation.rda |binary
data/UKNonDurables.rda |binary
data/USAirlines.rda |binary
data/USConsump1950.rda |binary
data/USConsump1979.rda |binary
data/USConsump1993.rda |binary
data/USCrudes.rda |binary
data/USGasB.rda |binary
data/USGasG.rda |binary
data/USInvest.rda |binary
data/USMacroB.rda |binary
data/USMacroG.rda |binary
data/USMacroSW.rda |binary
data/USMacroSWM.rda |binary
data/USMacroSWQ.rda |binary
data/USMoney.rda |binary
data/USProdIndex.rda |binary
data/USSeatBelts.rda |binary
data/USStocksSW.rda |binary
data/WeakInstrument.rda |binary
inst/doc/AER.pdf |binary
inst/doc/Sweave-journals.pdf |binary
man/Baltagi2002.Rd | 1
man/BenderlyZwick.Rd | 4
man/CigarettesB.Rd | 4
man/DoctorVisits.Rd | 2
man/Equipment.Rd | 2
man/EuroEnergy.Rd | 4
man/GSOEP9402.Rd | 2
man/GSS7402.Rd | 2
man/GrowthDJ.Rd | 2
man/HousePrices.Rd | 2
man/MarkDollar.Rd | 2
man/MarkPound.Rd | 2
man/Mortgage.Rd | 4
man/Municipalities.Rd | 2
man/NMES1988.Rd | 2
man/NaturalGas.Rd | 4
man/OECDGas.Rd | 4
man/OrangeCounty.Rd | 4
man/PSID1982.Rd | 4
man/RecreationDemand.Rd | 2
man/TradeCredit.Rd | 4
man/USConsump1993.Rd | 4
man/USCrudes.Rd | 4
man/USGasB.Rd | 4
man/USMacroB.Rd | 4
man/tobit.Rd | 2
tests/Ch-Intro.Rout.save | 20 +-
tests/Ch-LinearRegression.R | 1
tests/Ch-LinearRegression.Rout.save | 11 -
tests/Ch-Microeconometrics.Rout.save | 12 -
142 files changed, 214 insertions(+), 230 deletions(-)
Title: Nomograms for Right-Censored Outcomes from Survey Designs
Diff between SvyNom versions 1.0 dated 2012-12-07 and 1.1 dated 2015-02-24
Description: Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
Author: Mithat Gonen, Marinela Capanu
Maintainer: Mithat Gonen
DESCRIPTION | 15 +++++++--------
MD5 | 17 ++++++++++-------
NAMESPACE | 7 +++++++
R/SvyNom.R |only
data/noNA.txt |only
inst |only
man/SvyNom-package.Rd | 17 +++++++++--------
man/noNA.Rd | 2 +-
man/svycox.calibrate.Rd | 10 +++++++---
man/svycox.nomogram.Rd | 17 ++++++++++-------
man/svycox.validate.Rd | 24 ++++++++++++++----------
11 files changed, 65 insertions(+), 44 deletions(-)
Title: Histogram-Valued Data Analysis
Diff between HistDAWass versions 0.1 dated 2015-02-18 and 0.1.1 dated 2015-02-24
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
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/HistDAWass-package.R | 2 +-
R/unsuperv_classification.R | 2 +-
man/HistDAWass-package.Rd | 2 +-
man/WH_hclust.Rd | 2 +-
6 files changed, 13 insertions(+), 13 deletions(-)
Title: Construction Methods of some Series of PBIB Designs
Diff between CombinS versions 1.0 dated 2013-12-12 and 1.1 dated 2015-02-24
Description: The Combinatory Method (s) to Construct a series of PBIB designs and we give their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib
CombinS-1.0/CombinS/R/PBIB4.R |only
CombinS-1.0/CombinS/R/PBIB5.R |only
CombinS-1.0/CombinS/R/PBIB7.R |only
CombinS-1.0/CombinS/man/PBIB4.Rd |only
CombinS-1.0/CombinS/man/PBIB5.Rd |only
CombinS-1.0/CombinS/man/PBIB7.Rd |only
CombinS-1.1/CombinS/DESCRIPTION | 17 ++----
CombinS-1.1/CombinS/MD5 | 26 +++++----
CombinS-1.1/CombinS/R/CombS.R | 79 +++++++++++++++++++----------
CombinS-1.1/CombinS/R/GPBIB4A.R |only
CombinS-1.1/CombinS/R/GPBIB4B.R |only
CombinS-1.1/CombinS/R/GPBIB5.R |only
CombinS-1.1/CombinS/R/GPBIB7A.R |only
CombinS-1.1/CombinS/R/GPBIB7B.R |only
CombinS-1.1/CombinS/R/UType.R |only
CombinS-1.1/CombinS/man/CombS.Rd | 51 ++++++++++--------
CombinS-1.1/CombinS/man/CombinS-package.Rd | 52 +++++++++++++------
CombinS-1.1/CombinS/man/GPBIB4A.Rd |only
CombinS-1.1/CombinS/man/GPBIB4B.Rd |only
CombinS-1.1/CombinS/man/GPBIB5.Rd |only
CombinS-1.1/CombinS/man/GPBIB7A.Rd |only
CombinS-1.1/CombinS/man/GPBIB7B.Rd |only
CombinS-1.1/CombinS/man/UType.Rd |only
23 files changed, 143 insertions(+), 82 deletions(-)
Title: Partial Least Squares Regression with Backward Selection of
Predictors
Diff between autopls versions 1.2-7 dated 2013-08-13 and 1.3 dated 2015-02-24
Description: Some convenience functions for pls regression, including backward
variable selection and validation procedures, image based predictions
and plotting.
Author: Sebastian Schmidtlein, with contributions from C. Oldenburg and H. Feilhauer
and with a code snipped borrowed from Bjorn-Helge Mevik
Maintainer: Sebastian Schmidtlein
DESCRIPTION | 20 ++++++++++++--------
MD5 | 22 +++++++++++-----------
NAMESPACE | 1 +
R/autopls.R | 21 +++++----------------
R/autoplsVAL.R | 2 +-
R/postprocessing.R | 2 +-
R/predict.autopls.R | 14 +++++++-------
R/predict.slim.R | 14 +++++++-------
R/prepro.R | 2 +-
man/autopls.Rd | 36 ++++++++++++++++++++----------------
man/autoplsVAL.Rd | 12 +++++++++---
man/murnau.X.Rd | 2 +-
12 files changed, 76 insertions(+), 72 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Diff between daff versions 0.1.1 dated 2015-02-23 and 0.1.2 dated 2015-02-24
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches.
Changes to data can be made visible by using render_diff. Daff uses the V8 package to
wrap the 'daff.js' javascript library which is included in the package.
Daff exposes a subset of 'daff.js' functionality, tailored for usage within R.
Author: Paul Fitzpatrick [aut] (javascript original,
http://paulfitz.github.io/daff/),
Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge
DESCRIPTION | 9 ++++-----
MD5 | 11 ++++++-----
NEWS |only
R/TableView.R | 6 ++++--
README.md | 13 ++++++++++---
inst/js/util.js | 7 +++++--
tests/testthat/testdiff-data.R | 6 ++++++
7 files changed, 35 insertions(+), 17 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Diff between cds versions 1.0 dated 2015-02-16 and 1.0.1 dated 2015-02-24
Description: This is an implementation of constrained dual scaling for detecting response
styles in categorical data, including utility functions. The procedure involves adding
additional columns to the data matrix representing the boundaries between the rating categories.
The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are
sought which provide optimal scores for the rating categories. These optimal scores are
constrained to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can be diagnosed
from the optimal scores for said cluster, and this can be used to construct an
imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees
DESCRIPTION | 8 ++---
MD5 | 10 +++----
R/cds.sim.R | 4 +-
R/sensory.R | 79 +++------------------------------------------------------
man/cds.sim.Rd | 4 +-
man/sensory.Rd | 79 +++------------------------------------------------------
6 files changed, 23 insertions(+), 161 deletions(-)
Title: Test Analysis Modules
Diff between TAM versions 1.4-1 dated 2015-01-16 and 1.5-2 dated 2015-02-24
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 18 -
MD5 | 153 ++++++-----
NAMESPACE | 44 +++
R/IRT.WrightMap.R | 37 ++
R/IRT.data.tam.R |only
R/IRT.expectedCounts.tam.R |only
R/IRT.irfprob.tam.R | 6
R/IRT.likelihood.TAM.R | 6
R/IRT.linearCFA.R |only
R/IRT.modelfit.tam.R |only
R/IRT.threshold.R |only
R/calc_exp_TK.R | 2
R/calc_prob.v5.R | 9
R/doparse.R | 6
R/extend.label.group.R | 5
R/lavaanify.IRT.R | 5
R/msq.itemfit.R |only
R/mstep.regression.R | 4
R/plot.ctt.R | 50 +++
R/plot.tam.R | 2
R/plotDevianceTAM.R | 8
R/predict.tam.R |only
R/summary.msq.itemfit.R |only
R/tam.mml.2pl.R | 38 ++
R/tam.mml.3pl.R | 21 +
R/tam.mml.R | 18 +
R/tam.mml.mfr.R | 10
R/tam.modelfit.R | 321 ++++++++++++-------------
R/tam.modelfit.func.R |only
R/tam.parameterfix.defaults.R |only
R/tam.pv.R | 10
R/tamaan.3pl.trait.R | 1
R/tamaan.R | 6
R/tamaanify.R | 7
R/tamaanify.define.method.R | 12
R/tamaanify.modelconstraint.loadings.R | 28 ++
R/tamaanify.proc.lavaanmodel.R | 2
R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R | 4
data/data.cqc01.rda |binary
data/data.cqc02.rda |binary
data/data.cqc03.rda |binary
data/data.cqc04.rda |binary
data/data.cqc05.rda |binary
data/data.ctest1.rda |binary
data/data.ctest2.rda |binary
data/data.ex08.rda |binary
data/data.ex10.rda |binary
data/data.ex11.rda |binary
data/data.ex12.rda |binary
data/data.ex14.rda |binary
data/data.ex15.rda |binary
data/data.exJ03.rda |binary
data/data.fims.Aus.Jpn.raw.rda |binary
data/data.fims.Aus.Jpn.scored.rda |binary
data/data.geiser.rda |binary
data/data.gpcm.rda |binary
data/data.janssen.rda |binary
data/data.janssen2.rda |binary
data/data.mc.rda |binary
data/data.numeracy.rda |binary
data/data.timssAusTwn.rda |binary
data/data.timssAusTwn.scored.rda |binary
data/sim.facets.rda |binary
data/sim.mfr.rda |binary
data/sim.rasch.missing.rda |binary
data/sim.rasch.pweights.rda |binary
data/sim.rasch.rda |binary
inst/NEWS | 56 +++-
man/IRT.WrightMap.Rd | 5
man/IRT.data.tam.Rd |only
man/IRT.expectedCounts.tam.Rd |only
man/IRT.likelihood.tam.Rd | 8
man/IRT.linearCFA.Rd |only
man/IRT.threshold.Rd |only
man/TAM-package.Rd | 4
man/data.cqc.Rd | 2
man/msq.itemfit.Rd |only
man/plot.tam.Rd | 18 -
man/predict.Rd |only
man/tam.ctt.Rd | 13 -
man/tam.fit.Rd | 2
man/tam.jml.Rd | 2
man/tam.latreg.Rd | 8
man/tam.mml.Rd | 60 ++++
man/tam.modelfit.Rd | 72 ++++-
src/msq_itemfit.cpp |only
86 files changed, 724 insertions(+), 359 deletions(-)
Title: Survival Analysis
Diff between survival versions 2.37-7 dated 2014-01-22 and 2.38-1 dated 2015-02-24
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau
survival-2.37-7/survival/R/basehaz.S |only
survival-2.37-7/survival/inst/doc/sourcecode.pdf |only
survival-2.37-7/survival/src/msurv.c |only
survival-2.37-7/survival/vignettes/raheart.rda |only
survival-2.38-1/survival/.Rinstignore |only
survival-2.38-1/survival/DESCRIPTION | 21
survival-2.38-1/survival/MD5 | 306 ++++---
survival-2.38-1/survival/NAMESPACE | 20
survival-2.38-1/survival/R/agreg.fit.R | 37
survival-2.38-1/survival/R/agsurv.R | 1
survival-2.38-1/survival/R/anova.coxph.S | 52 -
survival-2.38-1/survival/R/anova.coxphlist.S | 5
survival-2.38-1/survival/R/basehaz.R |only
survival-2.38-1/survival/R/cch.R | 4
survival-2.38-1/survival/R/clogit.R | 21
survival-2.38-1/survival/R/coxexact.fit.R | 3
survival-2.38-1/survival/R/coxpenal.fit.R | 82 +
survival-2.38-1/survival/R/coxph.R | 58 -
survival-2.38-1/survival/R/coxph.detail.S | 1
survival-2.38-1/survival/R/frailty.controlaic.S | 2
survival-2.38-1/survival/R/frailty.controlgauss.S | 1
survival-2.38-1/survival/R/frailty.gamma.S | 11
survival-2.38-1/survival/R/frailty.gammacon.S | 1
survival-2.38-1/survival/R/frailty.gaussian.S | 11
survival-2.38-1/survival/R/frailty.t.S | 4
survival-2.38-1/survival/R/logLik.coxph.R | 13
survival-2.38-1/survival/R/model.matrix.coxph.R | 4
survival-2.38-1/survival/R/neardate.R |only
survival-2.38-1/survival/R/plot.survfit.R | 64 -
survival-2.38-1/survival/R/predict.coxph.penal.S | 9
survival-2.38-1/survival/R/predict.survreg.S | 5
survival-2.38-1/survival/R/print.coxph.S | 3
survival-2.38-1/survival/R/print.coxph.penal.S | 3
survival-2.38-1/survival/R/print.summary.coxph.S | 4
survival-2.38-1/survival/R/print.summary.coxph.penal.S | 4
survival-2.38-1/survival/R/print.summary.survexp.R | 13
survival-2.38-1/survival/R/print.summary.survfit.S | 11
survival-2.38-1/survival/R/print.summary.survfitms.S | 11
survival-2.38-1/survival/R/print.summary.survreg.S | 1
survival-2.38-1/survival/R/print.survexp.S | 12
survival-2.38-1/survival/R/print.survreg.penal.S | 3
survival-2.38-1/survival/R/pspline.S | 7
survival-2.38-1/survival/R/pyears.R | 20
survival-2.38-1/survival/R/strata.S | 24
survival-2.38-1/survival/R/summary.survreg.S | 2
survival-2.38-1/survival/R/survSplit.R | 4
survival-2.38-1/survival/R/survexp.R | 2
survival-2.38-1/survival/R/survfit.R | 2
survival-2.38-1/survival/R/survfitCI.R | 1
survival-2.38-1/survival/R/survfitTurnbull.S | 6
survival-2.38-1/survival/R/survfitms.R | 16
survival-2.38-1/survival/R/survreg.S | 5
survival-2.38-1/survival/R/survreg.distributions.S | 26
survival-2.38-1/survival/R/survreg.fit.S | 3
survival-2.38-1/survival/R/tmerge.R |only
survival-2.38-1/survival/R/xtras.R | 35
survival-2.38-1/survival/build/vignette.rds |binary
survival-2.38-1/survival/cleanup |only
survival-2.38-1/survival/cleanup.win |only
survival-2.38-1/survival/data/cgd.rda |binary
survival-2.38-1/survival/data/datalist | 6
survival-2.38-1/survival/data/kidney.rda |binary
survival-2.38-1/survival/data/mgus.rda |binary
survival-2.38-1/survival/data/mgus2.rda |only
survival-2.38-1/survival/data/ovarian.rda |binary
survival-2.38-1/survival/data/rats.rda |binary
survival-2.38-1/survival/data/transplant.rda |only
survival-2.38-1/survival/inst/CITATION | 12
survival-2.38-1/survival/inst/NEWS.Rd | 81 +
survival-2.38-1/survival/inst/NEWS.Rd.orig |only
survival-2.38-1/survival/inst/doc/adjcurve.R | 170 ++-
survival-2.38-1/survival/inst/doc/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/inst/doc/adjcurve.pdf |binary
survival-2.38-1/survival/inst/doc/compete.R |only
survival-2.38-1/survival/inst/doc/compete.Rnw |only
survival-2.38-1/survival/inst/doc/compete.pdf |only
survival-2.38-1/survival/inst/doc/splines.R |only
survival-2.38-1/survival/inst/doc/splines.Rnw |only
survival-2.38-1/survival/inst/doc/splines.pdf |only
survival-2.38-1/survival/inst/doc/tests.R | 25
survival-2.38-1/survival/inst/doc/tests.Rnw | 213 ++--
survival-2.38-1/survival/inst/doc/tests.pdf |binary
survival-2.38-1/survival/inst/doc/timedep.R | 130 ++-
survival-2.38-1/survival/inst/doc/timedep.Rnw | 735 ++++++++++++-----
survival-2.38-1/survival/inst/doc/timedep.pdf |binary
survival-2.38-1/survival/man/basehaz.Rd | 45 -
survival-2.38-1/survival/man/bladder.Rd | 8
survival-2.38-1/survival/man/cgd.Rd | 52 -
survival-2.38-1/survival/man/cgd0.Rd |only
survival-2.38-1/survival/man/cluster.Rd | 6
survival-2.38-1/survival/man/dsurvreg.Rd | 4
survival-2.38-1/survival/man/frailty.Rd | 6
survival-2.38-1/survival/man/mgus.Rd | 48 -
survival-2.38-1/survival/man/mgus2.Rd |only
survival-2.38-1/survival/man/neardate.Rd |only
survival-2.38-1/survival/man/ovarian.Rd | 3
survival-2.38-1/survival/man/pbcseq.Rd | 11
survival-2.38-1/survival/man/plot.survfit.Rd | 21
survival-2.38-1/survival/man/predict.coxph.Rd | 26
survival-2.38-1/survival/man/print.survfit.Rd | 4
survival-2.38-1/survival/man/rats.Rd | 7
survival-2.38-1/survival/man/strata.Rd | 11
survival-2.38-1/survival/man/summary.survfit.Rd | 3
survival-2.38-1/survival/man/survexp.Rd | 9
survival-2.38-1/survival/man/survfit.Rd | 3
survival-2.38-1/survival/man/survfit.coxph.Rd | 15
survival-2.38-1/survival/man/survfit.formula.Rd | 13
survival-2.38-1/survival/man/survreg.Rd | 2
survival-2.38-1/survival/man/survreg.object.Rd | 105 +-
survival-2.38-1/survival/man/tmerge.Rd |only
survival-2.38-1/survival/man/transplant.Rd |only
survival-2.38-1/survival/noweb |only
survival-2.38-1/survival/src/agexact.c | 1
survival-2.38-1/survival/src/agfit4.c | 4
survival-2.38-1/survival/src/agfit5.c | 151 ---
survival-2.38-1/survival/src/agmart.c | 6
survival-2.38-1/survival/src/agmart2.c | 2
survival-2.38-1/survival/src/agmart3.c |only
survival-2.38-1/survival/src/coxfit6.c | 37
survival-2.38-1/survival/src/init.c | 7
survival-2.38-1/survival/src/pyears2.c | 1
survival-2.38-1/survival/src/pyears3b.c | 1
survival-2.38-1/survival/src/survfitci.c | 2
survival-2.38-1/survival/src/survproto.h | 10
survival-2.38-1/survival/src/tmerge.c |only
survival-2.38-1/survival/tests/book1.R | 2
survival-2.38-1/survival/tests/book1.Rout.save | 12
survival-2.38-1/survival/tests/book2.R | 9
survival-2.38-1/survival/tests/book2.Rout.save | 20
survival-2.38-1/survival/tests/book3.R | 2
survival-2.38-1/survival/tests/book3.Rout.save | 13
survival-2.38-1/survival/tests/fr_rat1.R | 6
survival-2.38-1/survival/tests/fr_rat1.Rout.save | 24
survival-2.38-1/survival/tests/fr_resid.R | 10
survival-2.38-1/survival/tests/fr_resid.Rout.save | 23
survival-2.38-1/survival/tests/fr_simple.R | 2
survival-2.38-1/survival/tests/fr_simple.Rout.save | 11
survival-2.38-1/survival/tests/gray1.rda |binary
survival-2.38-1/survival/tests/model.matrix.R | 4
survival-2.38-1/survival/tests/model.matrix.Rout.save | 11
survival-2.38-1/survival/tests/plot.R |only
survival-2.38-1/survival/tests/plot1.pdf.save |only
survival-2.38-1/survival/tests/pspline.R | 21
survival-2.38-1/survival/tests/pspline.Rout.save | 36
survival-2.38-1/survival/tests/quantile.R | 6
survival-2.38-1/survival/tests/quantile.Rout.save | 14
survival-2.38-1/survival/tests/survreg2.R | 4
survival-2.38-1/survival/tests/survreg2.Rout.save | 13
survival-2.38-1/survival/tests/testci.R | 43
survival-2.38-1/survival/tests/testci.Rout.save | 51 -
survival-2.38-1/survival/tests/tt.R | 10
survival-2.38-1/survival/tests/tt.Rout.save | 18
survival-2.38-1/survival/vignettes/.install_extras |only
survival-2.38-1/survival/vignettes/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/vignettes/compete.Rnw |only
survival-2.38-1/survival/vignettes/figures |only
survival-2.38-1/survival/vignettes/splines.Rnw |only
survival-2.38-1/survival/vignettes/tests.Rnw | 213 ++--
survival-2.38-1/survival/vignettes/timedep.Rnw | 735 ++++++++++++-----
159 files changed, 3225 insertions(+), 2032 deletions(-)
Title: Causal Inference in Spatiotemporal Event Data
Diff between mwa versions 0.4 dated 2014-12-17 and 0.4.1 dated 2015-02-24
Description: Matched Wake Analysis (mwa) grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte
DESCRIPTION | 12 ++---
MD5 | 20 ++++----
R/mwa.R | 107 +++++++++++++++++++++++++++++++++++++--------
man/matchedwake.Rd | 8 +--
man/mwa-package.Rd | 6 +-
man/mwa_data.Rd | 6 +-
man/plot.matchedwake.Rd | 2
man/print.matchedwake.Rd | 2
man/slideWakeMatch.Rd | 2
man/slidingWake.Rd | 2
man/summary.matchedwake.Rd | 4 -
11 files changed, 122 insertions(+), 49 deletions(-)
Title: Digital PCR Analysis
Diff between dpcR versions 0.1.3.2 dated 2014-12-24 and 0.1.3.3 dated 2015-02-24
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut]
Maintainer: Michal Burdukiewicz
CHANGELOG | 3 +
DESCRIPTION | 8 ++--
MD5 | 80 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
R/count_test-class.R | 1
R/qpcrpp.R | 2 -
man/adpcr-class.Rd | 3 +
man/adpcr2ppp.Rd | 3 +
man/binarize.Rd | 3 +
man/bind_dpcr-methods.Rd | 3 +
man/bioamp.Rd | 3 +
man/compare_dens.Rd | 3 +
man/count_test-class.Rd | 7 ++--
man/create_dpcr.Rd | 3 +
man/ddpcr-class.Rd | 3 +
man/dpcR-package.Rd | 3 +
man/dpcr_density.Rd | 3 +
man/dpcr_density_gui.Rd | 3 +
man/extract_dpcr.Rd | 3 +
man/limit_cq.Rd | 3 +
man/many_peaks.Rd | 3 +
man/moments-methods.Rd | 3 +
man/num2int.Rd | 3 +
man/pds.Rd | 3 +
man/pds_raw.Rd | 3 +
man/plot.qpcrpp.Rd | 4 +-
man/plot_panel.Rd | 3 +
man/plot_vic_fam.Rd | 3 +
man/qpcr2pp.Rd | 3 +
man/qpcr_analyser.Rd | 3 +
man/qpcrpp-class.Rd | 3 +
man/rtadpcr-class.Rd | 3 +
man/show-methods.Rd | 3 +
man/sim_adpcr.Rd | 3 +
man/sim_ddpcr.Rd | 3 +
man/summary-methods.Rd | 3 +
man/test_counts.Rd | 3 +
man/test_counts_gui.Rd | 3 +
man/test_panel.Rd | 3 +
man/test_peaks.Rd | 3 +
man/test_ratio.Rd | 3 +
41 files changed, 124 insertions(+), 82 deletions(-)
Title: Spatial Analysis and Modeling
Diff between spatialEco versions 0.1-0 dated 2015-02-02 and 0.1-1 dated 2015-02-24
Description: Utilities to support spatial data manipulation, query, sampling and modeling.
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 subsampling, 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
DESCRIPTION | 8 +-
MD5 | 81 +++++++++++++----------
NAMESPACE | 3
R/breeding.density.R | 6 -
R/correlogram.R | 4 -
R/csi.R |only
R/download.daymet.R | 6 -
R/download.prism.R | 4 -
R/idw.smoothing.R | 6 -
R/land.metrics.R | 2
R/local.min.max.R |only
R/logistic.regression.R | 58 ++++++++++-------
R/moments.R | 6 -
R/nni.R | 14 ++--
R/o.ring.R | 6 -
R/optimal.k.R | 2
R/outliers.R |only
R/parea.sample.R | 2
R/point.in.poly.R | 13 +--
R/pp.subsample.R | 2
R/pseudo.absence.R | 6 -
R/separability.R | 8 +-
R/stratified.random.R | 4 -
R/trend.line.R | 2
inst/NEWS |only
man/breeding.density.Rd | 130 +++++++++++++++++++-------------------
man/correlogram.Rd | 4 -
man/csi.Rd |only
man/download.daymet.Rd | 6 -
man/download.prism.Rd | 4 -
man/idw.smoothing.Rd | 90 +++++++++++++-------------
man/land.metrics.Rd | 118 +++++++++++++++++-----------------
man/local.min.max.Rd |only
man/logistic.regression.Rd | 36 ++++++----
man/moments.Rd | 6 -
man/nni.Rd | 88 +++++++++++++-------------
man/o.ring.Rd | 78 +++++++++++------------
man/optimal.k.Rd | 100 ++++++++++++++---------------
man/outliers.Rd |only
man/parea.sample.Rd | 108 +++++++++++++++----------------
man/pp.subsample.Rd | 2
man/pseudo.absence.Rd | 6 -
man/separability.Rd | 152 ++++++++++++++++++++++-----------------------
man/stratified.random.Rd | 150 ++++++++++++++++++++++----------------------
man/trend.line.Rd | 86 ++++++++++++-------------
45 files changed, 717 insertions(+), 690 deletions(-)
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.10.1 dated 2015-01-15 and 0.10.2 dated 2015-02-24
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
configure | 10 ++++++++++
src/Makevars.win | 4 ++--
tools/winlibs.R | 4 ++--
5 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools for Working with JavaScript in R
Diff between js versions 0.1 dated 2015-02-15 and 0.2 dated 2015-02-24
Description: A set of utility functions for working with JavaScript in R.
Currently includes functions to compile, validate, reformat, optimize
and analyze JavaScript code.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 12 ++--
MD5 | 17 ++++--
NAMESPACE | 1
NEWS |only
R/coffee.R |only
inst/doc/intro.R | 13 +++++
inst/doc/intro.Rmd | 35 +++++++++++--
inst/doc/intro.html | 126 ++++++++++++++++++++++++++++++++++++++++++++++----
inst/example |only
inst/js/coffee.min.js |only
man/coffee_compile.Rd |only
vignettes/intro.Rmd | 35 +++++++++++--
12 files changed, 208 insertions(+), 31 deletions(-)
Title: Integrative Bayesian Analysis of Transcriptomic and CGH Data
Diff between iBATCGH versions 1.1 dated 2014-09-13 and 1.2 dated 2015-02-24
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression.
Author: Alberto Cassese
Maintainer: Alberto Cassese
DESCRIPTION | 18 +++++++++---------
MD5 | 8 ++++----
src/Makevars | 2 +-
src/Makevars.win | 3 +--
src/ProbitMain.cpp | 8 +++++---
5 files changed, 20 insertions(+), 19 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 2.0.0 dated 2015-02-16 and 2.0.1 dated 2015-02-24
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
FunChisq-2.0.0/FunChisq/src/Makevars |only
FunChisq-2.0.0/FunChisq/src/Makevars.win |only
FunChisq-2.0.0/FunChisq/src/TransitionTableIO.cpp |only
FunChisq-2.0.0/FunChisq/tests/testthat/test_EFT.R |only
FunChisq-2.0.1/FunChisq/DESCRIPTION | 10 -
FunChisq-2.0.1/FunChisq/MD5 | 39 +++----
FunChisq-2.0.1/FunChisq/NAMESPACE | 3
FunChisq-2.0.1/FunChisq/NEWS | 58 +++++------
FunChisq-2.0.1/FunChisq/man/FunChisq-package.Rd | 10 -
FunChisq-2.0.1/FunChisq/man/cp.fun.chisq.test.Rd | 16 +--
FunChisq-2.0.1/FunChisq/man/fun.chisq.test.Rd | 48 ++++-----
FunChisq-2.0.1/FunChisq/src/AdjustPvalue.cpp | 88 ++++++++---------
FunChisq-2.0.1/FunChisq/src/ChisqDirTest.cpp | 2
FunChisq-2.0.1/FunChisq/src/ChisqTests.cpp | 66 ++++++------
FunChisq-2.0.1/FunChisq/src/ChisqTests.h | 2
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.cpp | 29 +----
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.h | 4
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.cpp | 20 +--
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.h | 10 +
FunChisq-2.0.1/FunChisq/src/StatDistributions.cpp | 4
FunChisq-2.0.1/FunChisq/src/TransitionTable.cpp | 26 ++---
FunChisq-2.0.1/FunChisq/src/TransitionTable.h | 6 -
FunChisq-2.0.1/FunChisq/tests/testthat/test_FunChisq.R |only
23 files changed, 214 insertions(+), 227 deletions(-)
Title: Cairo-based Graphics Device Driver
Diff between cairoDevice versions 2.21 dated 2015-01-20 and 2.22 dated 2015-02-24
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
src/cairoDevice.c | 3 ---
3 files changed, 8 insertions(+), 11 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Diff between aroma.cn versions 1.5.0 dated 2013-10-17 and 1.6.0 dated 2015-02-24
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson
aroma.cn-1.5.0/aroma.cn/R/PSCBS.flips.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.calibrateC1C2.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.deShearC1C2.R |only
aroma.cn-1.5.0/aroma.cn/inst/NEWS |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/ortho |only
aroma.cn-1.5.0/aroma.cn/man/calibrateC1C2.PairedPSCBS.Rd |only
aroma.cn-1.5.0/aroma.cn/man/deShearC1C2_20120922.PairedPSCBS.Rd |only
aroma.cn-1.6.0/aroma.cn/DESCRIPTION | 27
aroma.cn-1.6.0/aroma.cn/MD5 | 90
aroma.cn-1.6.0/aroma.cn/NAMESPACE | 47
aroma.cn-1.6.0/aroma.cn/NEWS |only
aroma.cn-1.6.0/aroma.cn/R/009.setup.R | 6
aroma.cn-1.6.0/aroma.cn/R/021.dynamic_imports.R |only
aroma.cn-1.6.0/aroma.cn/R/AbstractCurveNormalization.R | 11
aroma.cn-1.6.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R |only
aroma.cn-1.6.0/aroma.cn/R/C1C2.R | 72
aroma.cn-1.6.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R | 14
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.CALL2.R | 2
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.NORM.R | 4
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.PLOT3.R | 5
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.backgroundCorrect.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPscbsModel.R | 10
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurve.XTRAS.R | 2
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurveNormalization.R | 6
aroma.cn-1.6.0/aroma.cn/R/TotalFracBSnpData.R | 2
aroma.cn-1.6.0/aroma.cn/R/TumorBoostNormalization.R | 3
aroma.cn-1.6.0/aroma.cn/R/XYCurveNormalization.R | 4
aroma.cn-1.6.0/aroma.cn/R/callXXorXY.numeric.R | 6
aroma.cn-1.6.0/aroma.cn/R/normalizeMirroredBAFsByRegions.R | 7
aroma.cn-1.6.0/aroma.cn/R/normalizePrincipalCurve.matrix.R | 5
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex | 1020 +++++-----
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex | 414 ++--
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R | 54
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R | 34
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R | 204 +-
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R | 62
aroma.cn-1.6.0/aroma.cn/man/AbstractCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/Non-documented_objects.Rd | 36
aroma.cn-1.6.0/aroma.cn/man/PairedPscbsModel.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/PrincipalCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnKernelSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TumorBoostNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/XYCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd | 75
aroma.cn-1.6.0/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd | 61
aroma.cn-1.6.0/aroma.cn/tests |only
52 files changed, 1100 insertions(+), 1201 deletions(-)