Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Diff between Rchoice versions 0.2 dated 2014-12-17 and 0.3 dated 2015-04-29
Description: An implementation of simulated maximum likelihood method for the estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters for cross-sectional and longitudinal data.
Author: Mauricio Sarrias
Maintainer: Mauricio Sarrias
Rchoice-0.2/Rchoice/build |only
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Rchoice-0.3/Rchoice/R/Rchoice.logLiks.R | 3
Rchoice-0.3/Rchoice/R/Rchoice.methods.R | 79 ++++++++++++++++++--------
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Title: Plot a Model's Response and Residuals
Diff between plotmo versions 2.2.1 dated 2015-01-07 and 3.0.0 dated 2015-04-29
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
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Title: Easy Handling Discrete Time Markov Chains
Diff between markovchain versions 0.1.1 dated 2015-02-21 and 0.2 dated 2015-04-29
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato
ChangeLog | 15 ++++
DESCRIPTION | 19 +++---
MD5 | 35 ++++++-----
NAMESPACE | 3
NEWS | 8 +-
R/1_functions4Fitting.R | 58 +------------------
R/2_probabilistic.R | 30 ++++++---
R/RcppExports.R |only
R/zzz.R |only
README.md |only
build/vignette.rds |binary
inst/CITATION | 8 +-
inst/doc/an_introduction_to_markovchain_package.Rnw | 20 ++----
inst/doc/an_introduction_to_markovchain_package.pdf |binary
man/absorbingStates.Rd | 10 +++
man/blanden.Rd | 2
man/markovchain-package.Rd | 6 -
man/markovchainFit.Rd | 6 +
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vignettes/an_introduction_to_markovchain_package.Rnw | 20 ++----
20 files changed, 120 insertions(+), 120 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Diff between dfmta versions 1.3-1 dated 2015-04-26 and 1.3-2 dated 2015-04-29
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
configure | 18 +++++++++---------
src/dfmta.cpp | 2 +-
4 files changed, 17 insertions(+), 17 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Diff between dfcomb versions 2.1-1 dated 2015-04-26 and 2.1-3 dated 2015-04-29
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/dfcomb.R | 13 +++++++------
configure | 18 +++++++++---------
man/CombIncrease_next.Rd | 16 +++++++++++-----
src/logistic.cpp | 4 +++-
6 files changed, 39 insertions(+), 30 deletions(-)
Title: Selection of Samples and Parameter Estimation in Finite
Population
Diff between TeachingSampling versions 3.2.1 dated 2014-03-27 and 3.2.2 dated 2015-04-29
More information about TeachingSampling at CRAN
Description: Allows the user to draw probabilistic samples and make inferences from a finite population based on several sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas
DESCRIPTION | 19 +++++++++----------
MD5 | 6 +++---
R/PikHol.r | 30 ++++++++++++++++--------------
man/PikHol.rd | 41 ++++++++++++++++++++++++++++++++++++++++-
4 files changed, 68 insertions(+), 28 deletions(-)
Permanent link
Title: Sample Size Calculations for Complex Surveys
Diff between samplesize4surveys versions 2.1.0 dated 2014-09-21 and 2.2.0 dated 2015-04-29
More information about samplesize4surveys at CRAN
Description: Computes the required sample size for estimation of totals, means
and proportions under complex sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas
DESCRIPTION | 10 +-
MD5 | 39 ++++++----
NAMESPACE | 3
R/ss4ddp.R |only
R/ss4dp.R | 190 ++++++++++++++++++++++++++---------------------------
data |only
man/BigLucyT0T1.rd |only
man/DEFF.Rd | 3
man/ICC.Rd | 3
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man/ss4m.Rd | 3
man/ss4mH.Rd | 3
man/ss4p.Rd | 3
man/ss4pH.Rd | 3
man/ss4stm.Rd | 3
22 files changed, 152 insertions(+), 132 deletions(-)
Permanent link
Title: Extraction of Business Financial Information from 'XBRL'
Documents
Diff between XBRL versions 0.99.15 dated 2015-02-13 and 0.99.16 dated 2015-04-29
Description:
Functions to extract business financial information from
an Extensible Business Reporting Language ('XBRL') instance file and the
associated collection of files that defines its 'Discoverable' Taxonomy
Set ('DTS').
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
ChangeLog | 6 ++++++
DESCRIPTION | 36 +++++++++---------------------------
MD5 | 8 ++++----
configure.in | 2 +-
src/xbrlProcessFacts.cpp | 16 ++++++++++++++++
5 files changed, 36 insertions(+), 32 deletions(-)
Title: Time Series Database Interface
Diff between TSdbi versions 2013.9-1 dated 2013-09-29 and 2015.1-1 dated 2015-04-29
Description: Provides a common interface to time series databases. The
objective is to define a standard interface so users can retrieve time
series data from various sources with a simple, common, set of
commands, and so programs can be written to be portable with respect
to the data source. The SQL implementations also provide a database
table design, so users needing to set up a time series database
have a reasonably complete way to do this easily. The interface
provides for a variety of options with respect to the representation
of time series in R. The interface, and the SQL implementations, also
handle vintages of time series data (sometime called editions or
realtime data). There is also a (not yet well tested) mechanism to
handle multilingual data documentation.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
MD5 | 14 +++++++-------
NAMESPACE | 1 +
NEWS | 17 +++++++++++++++--
R/TSdbi.R | 41 ++++++++++++++++++++++++++---------------
build/vignette.rds |binary
man/TSconnect.Rd | 18 ++++++++++--------
man/TSget.Rd | 27 ++++++++++++++-------------
8 files changed, 80 insertions(+), 52 deletions(-)
More information about replicatedpp2w at CRAN
Permanent link
Title: Phenotypic Integration Index
Diff between PHENIX versions 1.1 dated 2015-01-27 and 1.2 dated 2015-04-29
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++++--------------
NAMESPACE | 2 +-
NEWS | 8 ++++++++
R/pint.jack.R |only
R/pintsc.boot.R | 7 +++++--
R/pintsc.jack.R |only
man/PHENIX-package.Rd | 2 +-
man/cor.par.Rd | 2 +-
man/paeonia.Rd | 2 +-
man/pint.Rd | 8 ++++----
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man/pintsc.Rd | 4 ++--
man/pintsc.boot.Rd | 6 +++---
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man/pintsc.p.Rd | 4 ++--
man/tussilago.Rd | 4 ++--
19 files changed, 57 insertions(+), 42 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Diff between KFAS versions 1.1.0 dated 2015-04-18 and 1.1.1 dated 2015-04-29
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-1.1.0/KFAS/README.md |only
KFAS-1.1.0/KFAS/tests/testthat/testSSMarima.R |only
KFAS-1.1.1/KFAS/ChangeLog | 6
KFAS-1.1.1/KFAS/DESCRIPTION | 8
KFAS-1.1.1/KFAS/MD5 | 51 -
KFAS-1.1.1/KFAS/R/KFAS-package.R | 37 +
KFAS-1.1.1/KFAS/R/KFS.R | 4
KFAS-1.1.1/KFAS/R/SSMarima.R | 5
KFAS-1.1.1/KFAS/R/SSMcycle.R | 6
KFAS-1.1.1/KFAS/R/SSMseasonal.R | 184 ++----
KFAS-1.1.1/KFAS/R/SSMtrend.R | 9
KFAS-1.1.1/KFAS/R/artransform.R | 4
KFAS-1.1.1/KFAS/R/ldl.R | 11
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KFAS-1.1.1/KFAS/src/artransform.f95 | 44 -
KFAS-1.1.1/KFAS/src/declarations.h | 2
KFAS-1.1.1/KFAS/src/filter1step.f95 | 8
KFAS-1.1.1/KFAS/src/filter1stepnovar.f95 | 158 ++---
KFAS-1.1.1/KFAS/src/init.c | 2
KFAS-1.1.1/KFAS/src/kfilter.f95 | 5
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KFAS-1.1.1/KFAS/tests/testthat/testArima.R |only
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KFAS-1.1.1/KFAS/tests/testthat/testNumerical.R | 116 +--
29 files changed, 740 insertions(+), 669 deletions(-)
Title: Forecastable Component Analysis
Diff between ForeCA versions 0.2.0 dated 2015-02-20 and 0.2.2 dated 2015-04-29
Description: Implementation of Forecastable Component Analysis ('ForeCA'),
including main algorithms and auxiliary function (summary, plotting, etc.)
to apply 'ForeCA' to multivariate time series data.
'ForeCA' is a novel dimension reduction (DR) technique for temporally
dependent signals. Contrary to other popular DR methods, such as 'PCA' or 'ICA',
'ForeCA' takes time dependency explicitly into account and searches for the
most ''forecastable'' signal. The measure of forecastability is based on
the Shannon entropy of the spectral density of the transformed signal.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
DESCRIPTION | 24 +--
MD5 | 88 +++++++------
NAMESPACE | 5
NEWS | 35 +++++
R/Omega.R | 5
R/SDF2mvspectrum.R | 13 --
R/complete_controls.R | 12 -
R/discrete_entropy.R | 1
R/foreca-utils.R | 25 ++-
R/foreca.EM-aux.R | 51 ++++++--
R/foreca.EM.one_weightvector.R | 41 ++----
R/foreca.R | 52 ++++----
R/initialize_weightvector.R | 36 +++++
R/mvspec2mvspectrum.R | 1
R/mvspectrum-utils.R |only
R/mvspectrum.R | 164 +++++++++++++-------------
R/quadratic_form.R | 46 ++++++-
R/spectral_entropy.R | 19 ++-
R/univariate_spectrum-functions.R | 7 -
R/whiten.R | 10 +
man/ForeCA-package.Rd | 2
man/Omega.Rd | 2
man/common-arguments.Rd | 2
man/complete-controls.Rd | 10 -
man/continuous_entropy.Rd | 2
man/discrete_entropy.Rd | 2
man/foreca-utils.Rd | 2
man/foreca.EM-aux.Rd | 18 ++
man/foreca.EM.one_weightvector.Rd | 2
man/foreca.Rd | 12 -
man/foreca.one_weightvector-utils.Rd | 2
man/initialize_weightvector.Rd | 10 +
man/mvspectrum-utils.Rd |only
man/mvspectrum.Rd | 22 ++-
man/mvspectrum2wcov.Rd | 2
man/quadratic_form.Rd | 27 +++-
man/sfa.Rd | 2
man/spectral_entropy.Rd | 4
man/whiten.Rd | 2
tests/testthat/helper_mvspectrum_methods.R | 3
tests/testthat/test_foreca.EM-aux.R | 19 ++-
tests/testthat/test_initialize_weightvector.R | 1
tests/testthat/test_mvspectrum.R | 99 +++++++++++----
tests/testthat/test_mvspectrum2wcov.R | 4
tests/testthat/test_quadratic_form.R | 52 ++++++++
tests/testthat/test_whiten.R | 10 +
46 files changed, 627 insertions(+), 321 deletions(-)
Title: Fitting Step-Functions
Diff between stepR versions 1.0-1 dated 2015-03-04 and 1.0-2 dated 2015-04-29
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Thomas Hotz [aut, cre],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Thomas Hotz
ChangeLog | 20 ++++++++++++++++++++
DESCRIPTION | 14 ++++++++------
MD5 | 18 +++++++++---------
R/jumpint.R | 4 ++--
R/smuceR.R | 10 +++++++---
R/stepbound.R | 2 +-
R/steppath.R | 2 +-
man/family.Rd | 4 ++--
man/sdrobnorm.Rd | 2 ++
tests/tests.R | 3 +++
10 files changed, 55 insertions(+), 24 deletions(-)
Title: Measures of Risk for the Compound Poisson Risk Process with
Diffusion
Diff between sdprisk versions 1.0-3 dated 2013-12-30 and 1.1-0 dated 2015-04-29
Description: The main purpose of this package is to provide saddlepoint
approximations to some measures of risk, based on the compound Poisson risk
process that is perturbed by a Brownian motion. Various approximation
methods for the probability of ruin are also included. Furthermore, exact
values of both the risk measures as well as the probability of ruin are
available if the individual claims follow a hypo-exponential distribution
(i. e., if it can be represented as a sum of independent exponentially
distributed random variables with different rate parameters).
Author: Benjamin Baumgartner [aut, cre],
Riccardo Gatto [ctb, ths],
Sebastian Szugat [ctb]
Maintainer: Benjamin Baumgartner
DESCRIPTION | 33 +++++++++++++++++++++++++++------
MD5 | 11 ++++++-----
R/boundsRuinprob.R | 3 +--
R/qhypoexp.R |only
R/rhypoexp.R | 23 +++++++++++++++++------
inst/CITATION | 11 ++++++-----
man/hypoexp.Rd | 12 ++++++++++--
7 files changed, 67 insertions(+), 26 deletions(-)
Title: Type-Specific Failure Rate and Hazard Rate on Competing Risks
Data
Diff between NPMLEcmprsk versions 2.0 dated 2014-12-09 and 2.1 dated 2015-04-29
Description: Given a failure type, the function computes covariate-specific probability of failure over time and covariate-specific conditional hazard rate based on possibly right-censored competing risk data. Specifically, it computes the non-parametric maximum-likelihood estimates of these quantities and their asymptotic variances in a semi-parametric mixture model for competing-risks data, as described in Chang et al. (2007a).
Author: Chung-Hsing Chen, I-Shou Chang and Chao A. Hsiung
Maintainer: Chung-Hsing Chen
DESCRIPTION | 10 +++++-----
MD5 | 6 ++++--
R/improved_CompetingRisk_Code_v10.2.r |only
R/improved_CompetingRisk_Code_v10.3.r |only
man/NPMLEcmprsk.Rd | 4 ++--
5 files changed, 11 insertions(+), 9 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Diff between evmix versions 2.4 dated 2015-01-23 and 2.5 dated 2015-04-29
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the evd package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott
DESCRIPTION | 8 -
MD5 | 225 +++++++++++++++++++--------------------
NAMESPACE | 2
R/checking.r | 7 +
R/evmix-package.r | 4
R/evmixdiag.r | 126 ++++++++++++---------
R/fbckdengpd.r | 4
R/fbckdengpdcon.r | 4
R/fbetagpd.r | 4
R/fbetagpdcon.r | 4
R/fgammagpd.r | 4
R/fgammagpdcon.r | 4
R/fgkg.r | 6 -
R/fgkgcon.r | 3
R/fgng.r | 5
R/fgngcon.r | 6 -
R/fhpdcon.r | 2
R/fitmgng.r | 2
R/fitmnormgpd.r | 2
R/fitmweibullgpd.r | 2
R/fkdengpd.r | 4
R/fkdengpdcon.r | 5
R/flognormgpd.r | 4
R/flognormgpdcon.r | 4
R/fmgamma.r | 7 +
R/fmgammagpd.r | 18 ++-
R/fmgammagpdcon.r | 18 ++-
R/fnormgpd.r | 16 +-
R/fnormgpdcon.r | 4
R/fpsden.r | 14 ++
R/fpsdengpd.r | 4
R/fweibullgpd.r | 26 ++--
R/fweibullgpdcon.r | 4
R/hillplot.r | 40 +++++-
R/mrlplot.r | 3
R/pickandsplot.r | 25 +++-
R/tcplot.r | 9 +
inst/CITATION | 4
inst/doc/Rd2.pdf |binary
inst/doc/evmix_supplementary.pdf |only
man/bckden.Rd | 2
man/bckdengpd.Rd | 2
man/bckdengpdcon.Rd | 2
man/betagpd.Rd | 2
man/betagpdcon.Rd | 2
man/checking.Rd | 2
man/dwm.Rd | 2
man/evmix-package.Rd | 6 -
man/evmix.diag.Rd | 2
man/fbckden.Rd | 2
man/fbckdengpd.Rd | 4
man/fbckdengpdcon.Rd | 4
man/fbetagpd.Rd | 4
man/fbetagpdcon.Rd | 4
man/fdwm.Rd | 2
man/fgammagpd.Rd | 4
man/fgammagpdcon.Rd | 4
man/fgkg.Rd | 4
man/fgkgcon.Rd | 4
man/fgng.Rd | 4
man/fgngcon.Rd | 4
man/fgpd.Rd | 2
man/fhpd.Rd | 2
man/fhpdcon.Rd | 4
man/fitmgng.Rd | 4
man/fitmnormgpd.Rd | 4
man/fitmweibullgpd.Rd | 4
man/fkden.Rd | 2
man/fkdengpd.Rd | 4
man/fkdengpdcon.Rd | 4
man/flognormgpd.Rd | 4
man/flognormgpdcon.Rd | 4
man/fmgamma.Rd | 2
man/fmgammagpd.Rd | 4
man/fmgammagpdcon.Rd | 4
man/fnormgpd.Rd | 6 -
man/fnormgpdcon.Rd | 4
man/fpsden.Rd | 2
man/fpsdengpd.Rd | 4
man/fweibullgpd.Rd | 6 -
man/fweibullgpdcon.Rd | 4
man/gammagpd.Rd | 2
man/gammagpdcon.Rd | 2
man/gkg.Rd | 2
man/gkgcon.Rd | 2
man/gng.Rd | 2
man/gngcon.Rd | 2
man/gpd.Rd | 2
man/hillplot.Rd | 5
man/hpd.Rd | 2
man/hpdcon.Rd | 2
man/internal.Rd | 2
man/itmgng.Rd | 2
man/itmnormgpd.Rd | 2
man/itmweibullgpd.Rd | 2
man/kden.Rd | 2
man/kdengpd.Rd | 2
man/kdengpdcon.Rd | 2
man/kernels.Rd | 2
man/kfun.Rd | 2
man/lognormgpd.Rd | 2
man/lognormgpdcon.Rd | 2
man/mgamma.Rd | 2
man/mgammagpd.Rd | 2
man/mgammagpdcon.Rd | 2
man/mrlplot.Rd | 2
man/normgpd.Rd | 2
man/normgpdcon.Rd | 2
man/pickandsplot.Rd | 5
man/psden.Rd | 2
man/psdengpd.Rd | 2
man/tcplot.Rd | 2
man/weibullgpd.Rd | 2
man/weibullgpdcon.Rd | 2
114 files changed, 480 insertions(+), 365 deletions(-)
Title: Data for the Synbreed Package
Diff between synbreedData versions 1.4 dated 2013-12-12 and 1.5 dated 2015-04-29
Description: Data sets for the 'synbreed' package with three data sets from cattle, maize and mice to illustrate the functions in the 'synbreed' R package. All data sets are stored in the gpData format introduced in the 'synbreed'
package. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Theresa Albrecht, Hans-Juergen Auinger, Chris-Carolin Schoen with contributions by Malena Erbe, Ulrike Ober and Christian Reimer
Maintainer: Valentin Wimmer
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
data/cattle.RData |binary
data/maize.RData |binary
data/mice.RData |binary
man/mice.Rd | 2 +-
6 files changed, 13 insertions(+), 12 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Diff between sn versions 1.2-0 dated 2015-03-25 and 1.2-1 dated 2015-04-29
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini
DESCRIPTION | 10 +--
MD5 | 20 +++---
NEWS | 14 +++-
R/sn-funct.R | 151 ++++++++++++++++++++++++++++++++-----------------
R/sn_S4.R | 9 +-
man/dp2cp.Rd | 8 +-
man/extractSECdistr.Rd | 2
man/selm-class.Rd | 5 +
man/selm.Rd | 23 ++++++-
man/selm.fit.Rd | 20 +++---
man/sn-st.info.Rd | 6 -
11 files changed, 176 insertions(+), 92 deletions(-)
Title: Chinese Text Segmentation
Diff between jiebaR versions 0.4 dated 2015-01-04 and 0.5 dated 2015-04-29
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng
DESCRIPTION | 8
MD5 | 57 ++--
NAMESPACE | 2
NEWS | 12 +
R/RcppExports.R | 4
R/filter.R |only
R/jiebar.R | 22 +
R/keywords.R | 21 +
R/overload.R | 30 +-
R/print.R | 15 -
R/quick.R | 63 +++--
R/segment.R | 103 ++++++--
R/simhash.R | 4
R/tagger.R | 108 ++++++---
R/tools.R | 6
README.md | 408 +---------------------------------
build/vignette.rds |binary
inst/include/lib/HMMSegment.hpp | 12 -
inst/include/lib/KeywordExtractor.hpp | 42 +++
inst/include/segtype.hpp | 16 +
inst/model |only
man/edit_dict.Rd | 2
man/filter_segment.Rd |only
man/keywords.Rd | 3
man/tagging.Rd | 2
man/worker.Rd | 4
src/Makevars.win | 6
src/RcppExports.cpp | 318 ++++++++++----------------
src/segtype.cpp | 5
tests/testthat/bylines.utf8 |only
tests/testthat/test-cut.R | 1
31 files changed, 545 insertions(+), 729 deletions(-)
Title: Geographically Weighted Logistic Elastic Net Regression
Diff between GWLelast versions 1.0 dated 2015-04-20 and 1.1 dated 2015-04-29
Description: Fit a geographically weighted logistic elastic net regression.
Author: Daisuke Yoneoka, Eiko Saito
Maintainer: Daisuke Yoneoka
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 1 -
R/GWLelastic.R | 2 +-
4 files changed, 8 insertions(+), 9 deletions(-)
Title: Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF)
Diff between difR versions 4.5 dated 2013-04-07 and 4.6 dated 2015-04-29
Description: Collection of traditional methods to detect differential item functioning among dichotomously scored items.
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles Raiche (UQAM)
Maintainer: David Magis
difR-4.5/difR/R/Logistik.r |only
difR-4.6/difR/DESCRIPTION | 21 -
difR-4.6/difR/LICENSE | 4
difR-4.6/difR/MD5 | 116 +++++----
difR-4.6/difR/NAMESPACE | 26 ++
difR-4.6/difR/NEWS | 60 +++++
difR-4.6/difR/R/Logistik.R |only
difR-4.6/difR/R/dichoDif.r | 61 +++--
difR-4.6/difR/R/difBD.r | 92 +++++--
difR-4.6/difR/R/difGMH.r | 90 +++++--
difR-4.6/difR/R/difGenLogistic.R | 387 +++++++++++++++++++--------------
difR-4.6/difR/R/difGenLord.r | 134 +++++++----
difR-4.6/difR/R/difLRT.r | 24 +-
difR-4.6/difR/R/difLogReg.R |only
difR-4.6/difR/R/difLogistic.r | 184 +++++++++------
difR-4.6/difR/R/difLord.r | 142 ++++++++----
difR-4.6/difR/R/difMH.r | 119 ++++++----
difR-4.6/difR/R/difRaju.r | 132 +++++++----
difR-4.6/difR/R/difStd.r | 105 ++++++--
difR-4.6/difR/R/difTID.r | 102 +++++---
difR-4.6/difR/R/genDichoDif.R | 55 +++-
difR-4.6/difR/R/genLogistik.R | 109 ++++-----
difR-4.6/difR/R/selectDif.r | 18 -
difR-4.6/difR/R/selectGenDif.R | 8
difR-4.6/difR/inst/CITATION | 12 -
difR-4.6/difR/man/LRT.Rd | 8
difR-4.6/difR/man/Logistik.rd | 66 +++--
difR-4.6/difR/man/LordChi2.rd | 30 +-
difR-4.6/difR/man/RajuZ.rd | 36 +--
difR-4.6/difR/man/breslowDay.rd | 6
difR-4.6/difR/man/contrastMatrix.rd | 6
difR-4.6/difR/man/dichoDif.rd | 131 ++++-------
difR-4.6/difR/man/difBD.rd | 36 +--
difR-4.6/difR/man/difGMH.rd | 43 ++-
difR-4.6/difR/man/difGenLogistic.rd | 75 +++---
difR-4.6/difR/man/difGenLord.rd | 81 +++---
difR-4.6/difR/man/difLRT.rd | 30 +-
difR-4.6/difR/man/difLogReg.rd |only
difR-4.6/difR/man/difLogistic.rd | 90 ++++---
difR-4.6/difR/man/difLord.rd | 76 +++---
difR-4.6/difR/man/difMH.rd | 40 ++-
difR-4.6/difR/man/difR-package.Rd | 10
difR-4.6/difR/man/difRaju.rd | 88 ++++---
difR-4.6/difR/man/difStd.rd | 41 ++-
difR-4.6/difR/man/difTID.Rd | 37 +--
difR-4.6/difR/man/genDichoDif.rd | 94 +++-----
difR-4.6/difR/man/genLogistik.rd | 43 ++-
difR-4.6/difR/man/genLordChi2.rd | 34 +-
difR-4.6/difR/man/genMantelHaenszel.rd | 14 -
difR-4.6/difR/man/itemPar1PL.rd | 10
difR-4.6/difR/man/itemPar2PL.rd | 2
difR-4.6/difR/man/itemPar3PL.rd | 4
difR-4.6/difR/man/itemPar3PLconst.rd | 6
difR-4.6/difR/man/itemParEst.rd | 16 -
difR-4.6/difR/man/itemRescale.rd | 25 +-
difR-4.6/difR/man/mantelHaenszel.rd | 12 -
difR-4.6/difR/man/selectDif.rd | 98 +++-----
difR-4.6/difR/man/selectGenDif.rd | 90 +++----
difR-4.6/difR/man/stdPDIF.rd | 10
difR-4.6/difR/man/subtestLogistic.rd | 38 +--
difR-4.6/difR/man/trItemDiff.Rd | 4
61 files changed, 2033 insertions(+), 1398 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Diff between dae versions 2.4-0 dated 2014-12-10 and 2.7-0 dated 2015-04-29
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
Maintainer: Chris Brien
DESCRIPTION | 22 ++++---
MD5 | 90 +++++++++++++++++++-----------
NAMESPACE | 31 +++++++++-
R/Interaction.ABC.Plot.r | 45 ++++++++-------
R/dae.utilties.r |only
R/fac.functions.r | 13 ++--
R/fac.layout.r | 16 ++++-
R/fac.match.r | 54 +++++++++++++-----
R/harmonic.mean.r |only
R/mat.functions.r | 52 ++++++++++++++++-
R/proj.canon.v3.r |only
R/proj.r | 107 +++++++++++++-----------------------
R/projs.canon.v3.r |only
data/Sensory3Phase.dat.rda |only
inst/doc/dae-manual.pdf |binary
inst/doc/daeDesignRandomization.pdf |binary
man/Sensory3Phase.dat.Rd |only
man/as.numfac.Rd | 3 -
man/correct.degfree.Rd | 4 -
man/dae-package.Rd |only
man/decomp.relate.Rd | 33 +++++------
man/degfree.Rd | 4 -
man/efficiencies.p2canon.Rd |only
man/efficiencies.pcanon.Rd |only
man/efficiency.criteria.Rd |only
man/fac.layout.Rd | 34 ++++++-----
man/fac.match.Rd | 37 +++++++++---
man/fac.vcmat.Rd | 2
man/fitted.aovlist.Rd | 2
man/fitted.errors.rd | 2
man/get.daeTolerance.Rd | 9 ++-
man/harmonic.mean.Rd |only
man/interaction.ABC.plot.Rd | 13 +---
man/is.allzero.Rd | 4 -
man/is.projector.Rd | 3 -
man/mat.ar1.Rd | 2
man/mat.banded.Rd |only
man/mat.dirprod.Rd | 2
man/mat.dirsum.Rd |only
man/mat.exp.Rd |only
man/print.summary.p2canon.Rd |only
man/print.summary.pcanon.Rd |only
man/proj2.combine.Rd |only
man/proj2.decomp.Rd | 58 +------------------
man/proj2.efficiency.Rd | 32 ++++------
man/proj2.eigen.Rd |only
man/proj2.ops.Rd | 72 +-----------------------
man/projector.Rd | 17 +++--
man/projs.2canon.Rd |only
man/projs.canon.Rd |only
man/projs.combine.p2canon.Rd |only
man/projs.structure.Rd |only
man/resid.errors.Rd | 2
man/residuals.aovlist.Rd | 2
man/set.daeTolerance.Rd | 26 ++++++--
man/summary.p2canon.Rd |only
man/summary.pcanon.Rd |only
man/tukey.1df.Rd | 2
58 files changed, 408 insertions(+), 387 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Diff between phytools versions 0.4-45 dated 2015-02-05 and 0.4-56 dated 2015-04-29
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 53 ++++++++++++++++++--
MD5 | 84 ++++++++++++++++-----------------
NAMESPACE | 4 -
R/bmPlot.R | 5 +
R/branching.diffusion.R | 34 +++++++++----
R/collapseTree.R |only
R/contMap.R | 20 +++++--
R/densityMap.R | 46 ++++++++++++------
R/fancyTree.R | 20 +++++++
R/fastAnc.R | 4 -
R/map.to.singleton.R | 7 +-
R/phenogram.R | 18 +++++--
R/phyl.pca.R | 56 ++++++++++++++++++++--
R/plotBranchbyTrait.R | 3 -
R/plotSimmap.R | 31 +++++++-----
R/plotTree.wBars.R | 49 ++++++++++++++-----
R/utilities.R | 114 ++++++++++++++++++++++++---------------------
man/add.color.bar.Rd | 2
man/add.random.Rd | 2
man/bind.tip.Rd | 2
man/bmPlot.Rd | 2
man/branching.diffusion.Rd | 6 +-
man/collapseTree.Rd |only
man/contMap.Rd | 2
man/densityMap.Rd | 2
man/fancyTree.Rd | 2
man/fastBM.Rd | 2
man/lambda.transform.Rd | 4 -
man/ltt.Rd | 2
man/nodeHeights.Rd | 2
man/orderMappedEdge.Rd | 2
man/pbtree.Rd | 2
man/phenogram.Rd | 4 -
man/phyl.RMA.Rd | 2
man/phyl.pairedttest.Rd | 4 -
man/phyl.pca.Rd | 4 -
man/phyl.vcv.Rd | 4 -
man/phyloDesign.Rd | 2
man/plot.backbonePhylo.Rd | 24 +++++++++
man/plotBranchbyTrait.Rd | 2
man/plotSimmap.Rd | 6 +-
man/plotTree.wBars.Rd | 3 -
man/reroot.Rd | 2
man/setMap.Rd | 2
44 files changed, 435 insertions(+), 206 deletions(-)
Title: Pretty Descriptive Stats
Diff between prettyR versions 2.1 dated 2015-01-20 and 2.1-1 dated 2015-04-29
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NEWS | 4 ++++
R/R2html.R | 2 +-
R/brkdn.R | 2 +-
R/decimal.align.R | 4 ++--
R/delim.table.R | 4 ++--
R/describe.R | 6 +++---
R/htmlize.R | 4 ++--
R/print.freq.R | 2 +-
R/print.xtab.R | 6 +++---
R/truncString.R | 3 +--
12 files changed, 35 insertions(+), 32 deletions(-)
Title: Topographic and Geologic Mapping
Diff between GEOmap versions 2.2-2 dated 2014-01-05 and 2.3-5 dated 2015-04-29
Description: Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
GEOmap-2.2-2/GEOmap/inst/doc/GEOmap.R |only
GEOmap-2.2-2/GEOmap/inst/doc/GEOmap.Rnw |only
GEOmap-2.2-2/GEOmap/vignettes |only
GEOmap-2.3-5/GEOmap/DESCRIPTION | 14 ++---
GEOmap-2.3-5/GEOmap/MD5 | 73 +++++++++++++--------------
GEOmap-2.3-5/GEOmap/NAMESPACE | 2
GEOmap-2.3-5/GEOmap/NEWS | 2
GEOmap-2.3-5/GEOmap/R/DATUMinfo.R |only
GEOmap-2.3-5/GEOmap/R/Ellipsoidal.Distance.R | 2
GEOmap-2.3-5/GEOmap/R/GLOBE.ORTH.R | 3 -
GEOmap-2.3-5/GEOmap/R/MAPconstants.R | 2
GEOmap-2.3-5/GEOmap/R/UTM.ll.R |only
GEOmap-2.3-5/GEOmap/R/UTM.xy.R |only
GEOmap-2.3-5/GEOmap/R/UTMzone.R |only
GEOmap-2.3-5/GEOmap/R/geoLEGEND.R | 32 +++++++++--
GEOmap-2.3-5/GEOmap/R/maps2GEOmap.R | 40 +++++++-------
GEOmap-2.3-5/GEOmap/R/plotGEOmap.R | 2
GEOmap-2.3-5/GEOmap/R/setPROJ.R | 45 ++++++++++++++--
GEOmap-2.3-5/GEOmap/R/subsetTOPO.R | 3 -
GEOmap-2.3-5/GEOmap/build/vignette.rds |binary
GEOmap-2.3-5/GEOmap/demo/weathermap.R | 2
GEOmap-2.3-5/GEOmap/inst/doc/GEOmap.pdf |binary
GEOmap-2.3-5/GEOmap/man/BASICTOPOMAP.Rd | 6 +-
GEOmap-2.3-5/GEOmap/man/DATUMinfo.Rd |only
GEOmap-2.3-5/GEOmap/man/GETXprofile.Rd | 4 +
GEOmap-2.3-5/GEOmap/man/NSWath.Rd | 4 +
GEOmap-2.3-5/GEOmap/man/UTM.ll.Rd |only
GEOmap-2.3-5/GEOmap/man/UTM.xy.Rd |only
GEOmap-2.3-5/GEOmap/man/UTMzone.Rd |only
GEOmap-2.3-5/GEOmap/man/XSECEQ.Rd | 6 +-
GEOmap-2.3-5/GEOmap/man/XSECwin.Rd | 10 ++-
GEOmap-2.3-5/GEOmap/man/addLLXY.Rd | 8 +-
GEOmap-2.3-5/GEOmap/man/geoLEGEND.Rd | 64 ++++++++++++++++++++---
GEOmap-2.3-5/GEOmap/man/insideGEOmapXY.Rd | 7 +-
GEOmap-2.3-5/GEOmap/man/plotGEOmapXY.Rd | 12 +---
GEOmap-2.3-5/GEOmap/man/plotUTM.Rd | 7 ++
GEOmap-2.3-5/GEOmap/man/plothypos.Rd | 10 ++-
GEOmap-2.3-5/GEOmap/man/setPROJ.Rd | 11 +++-
GEOmap-2.3-5/GEOmap/man/utm.sphr.ll.Rd | 1
GEOmap-2.3-5/GEOmap/man/utm.sphr.xy.Rd | 2
40 files changed, 253 insertions(+), 121 deletions(-)
Title: A Package for Image Analysis of DCE-MRI (S4 Implementation)
Diff between dcemriS4 versions 0.51 dated 2013-12-30 and 0.55 dated 2015-04-29
Description: A collection of routines and documentation that allows one to
perform voxel-wise quantitative analysis of dynamic contrast-enhanced MRI
(DEC-MRI) and diffusion-weighted imaging (DWI) data, with emphasis on
oncology applications.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [ctb]
Maintainer: Brandon Whitcher
dcemriS4-0.51/dcemriS4/man/aif.Rd |only
dcemriS4-0.51/dcemriS4/man/conv_fft.Rd |only
dcemriS4-0.51/dcemriS4/man/cpmg.Rd |only
dcemriS4-0.51/dcemriS4/man/dam.Rd |only
dcemriS4-0.51/dcemriS4/man/dce_bayes.Rd |only
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dcemriS4-0.51/dcemriS4/man/dce_spline.Rd |only
dcemriS4-0.51/dcemriS4/man/dcemri.Rd |only
dcemriS4-0.51/dcemriS4/man/dwi.Rd |only
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dcemriS4-0.51/dcemriS4/man/find_center.Rd |only
dcemriS4-0.51/dcemriS4/man/flipangle.Rd |only
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dcemriS4-0.51/dcemriS4/man/rcbv.Rd |only
dcemriS4-0.55/dcemriS4/DESCRIPTION | 39
dcemriS4-0.55/dcemriS4/LICENSE | 2
dcemriS4-0.55/dcemriS4/MD5 | 95 +-
dcemriS4-0.55/dcemriS4/NAMESPACE | 61 -
dcemriS4-0.55/dcemriS4/R/aif.R | 116 ++
dcemriS4-0.55/dcemriS4/R/cpmg.R | 102 +-
dcemriS4-0.55/dcemriS4/R/dcemriS4-package.R |only
dcemriS4-0.55/dcemriS4/R/dcemri_bayes.R | 202 +++-
dcemriS4-0.55/dcemriS4/R/dcemri_lm.R | 220 ++++-
dcemriS4-0.55/dcemriS4/R/dcemri_map.R | 174 +++-
dcemriS4-0.55/dcemriS4/R/dcemri_spline.R | 173 +++
dcemriS4-0.55/dcemriS4/R/dwi.R | 132 ++-
dcemriS4-0.55/dcemriS4/R/flipangle.R | 249 ++++-
dcemriS4-0.55/dcemriS4/R/kineticmodel.R | 78 +
dcemriS4-0.55/dcemriS4/R/model.R | 73 +
dcemriS4-0.55/dcemriS4/R/rcbv.R | 76 +
dcemriS4-0.55/dcemriS4/R/template_matching.R | 162 +++
dcemriS4-0.55/dcemriS4/R/wrappers.R | 7
dcemriS4-0.55/dcemriS4/R/zzz.R | 7
dcemriS4-0.55/dcemriS4/build/vignette.rds |binary
dcemriS4-0.55/dcemriS4/data/buckley.rda |binary
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.R | 6
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.Rnw | 25
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.pdf |binary
dcemriS4-0.55/dcemriS4/man/ADC-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/CPMG-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/aif-models.Rd |only
dcemriS4-0.55/dcemriS4/man/aifParameters.Rd | 55 -
dcemriS4-0.55/dcemriS4/man/buckley.Rd | 72 -
dcemriS4-0.55/dcemriS4/man/compartmentalModel.Rd | 81 -
dcemriS4-0.55/dcemriS4/man/convFFT.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.bayes-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.lm-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.map-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.spline-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemriS4-package.Rd | 133 ---
dcemriS4-0.55/dcemriS4/man/doubleAngleMethod.Rd |only
dcemriS4-0.55/dcemriS4/man/expConv.Rd | 34
dcemriS4-0.55/dcemriS4/man/extractAIF.Rd |only
dcemriS4-0.55/dcemriS4/man/fastTemplateMatching.Rd |only
dcemriS4-0.55/dcemriS4/man/findCenter.Rd |only
dcemriS4-0.55/dcemriS4/man/kineticModel.Rd |only
dcemriS4-0.55/dcemriS4/man/rcbv-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/relaxation-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/shift3D.Rd | 56 -
dcemriS4-0.55/dcemriS4/src/Makevars | 2
dcemriS4-0.55/dcemriS4/tests/Examples/dcemriS4-Ex.Rout.save | 522 +++++-------
dcemriS4-0.55/dcemriS4/tests/testthat |only
dcemriS4-0.55/dcemriS4/tests/testthat.R |only
dcemriS4-0.55/dcemriS4/vignettes/dcemriS4.Rnw | 25
65 files changed, 2052 insertions(+), 927 deletions(-)