Title: Analyze Multinomial Processing Tree Models
Diff between MPTinR versions 1.2.5 dated 2013-11-25 and 1.3.5 dated 2014-04-11
Description: MPTinR provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the contextree language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, MPTinR can fit a wide variety of other cognitive models such as SDT models (see fit.model). MPTinR supports multicore fitting and FIA calculation using the snowfall package. MPTinR can generate data from a model for e.g., simulation or parametric bootstrap and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann
ChangeLog | 24 ++++++++++++++++++++
DESCRIPTION | 31 +++++++++++++++++---------
MD5 | 41 +++++++++++++++++-----------------
NAMESPACE | 1
NEWS | 33 +++++++++++++++++++++++++++
R/bmpt.fia.R | 35 ++++++++++++++++++++++-------
R/fit.model.R | 51 ++++++++++++++++++++++++++++---------------
R/fit.mpt.R | 19 ++++++++++++----
R/get.mpt.fia.R | 6 ++---
R/lbmpt.to.bmpt.R |only
R/make.mpt.cf.R | 20 ++++++++++++++--
data/d.broeder.rda |binary
data/rb.fig1.data.rda |binary
data/rb.fig2.data.rda |binary
man/MPTinR-package.Rd | 11 +++++----
man/bmpt.fia.Rd | 13 ++++++++--
man/fit.model.Rd | 58 ++++++++++++++++++++++++++++++++++++++++++++++---
man/fit.mpt.Rd | 5 +++-
man/get.mpt.fia.Rd | 8 +++++-
man/make.mpt.cf.Rd | 38 +++++++++++++++++++++++++++-----
man/prediction.plot.Rd | 3 ++
src/determinant.cpp | 4 ++-
22 files changed, 317 insertions(+), 84 deletions(-)
Title: Import/Export routines for MALDIquant
Diff between MALDIquantForeign versions 0.6 dated 2014-01-28 and 0.7 dated 2014-04-11
More information about MALDIquantForeign at CRAN
Description: This package reads (tab, csv, Bruker fid, Ciphergen XML,
mzXML, mzML, imzML, Analyze 7.5, CDF) and writes (tab, csv, msd, mzML)
different file formats of mass spectrometry data into/from MALDIquant
objects.
Author: Sebastian Gibb [aut, cre],
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb
MALDIquantForeign-0.6/MALDIquantForeign/inst/tests |only
MALDIquantForeign-0.6/MALDIquantForeign/tests/test_all.R |only
MALDIquantForeign-0.7/MALDIquantForeign/DESCRIPTION | 11 -
MALDIquantForeign-0.7/MALDIquantForeign/MD5 | 104 +++++-----
MALDIquantForeign-0.7/MALDIquantForeign/NEWS | 16 +
MALDIquantForeign-0.7/MALDIquantForeign/R/import-functions.R | 24 --
MALDIquantForeign-0.7/MALDIquantForeign/R/package.R | 4
MALDIquantForeign-0.7/MALDIquantForeign/build |only
MALDIquantForeign-0.7/MALDIquantForeign/inst/doc |only
MALDIquantForeign-0.7/MALDIquantForeign/inst/exampledata |only
MALDIquantForeign-0.7/MALDIquantForeign/man/MALDIquantForeign-package.Rd | 2
MALDIquantForeign-0.7/MALDIquantForeign/man/import-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importBrukerFlex-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importCdf-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importCiphergenXml-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importImzMl-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importMzMl-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importMzXml-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/man/importTab-functions.Rd | 3
MALDIquantForeign-0.7/MALDIquantForeign/tests/testthat |only
MALDIquantForeign-0.7/MALDIquantForeign/tests/testthat.R |only
MALDIquantForeign-0.7/MALDIquantForeign/vignettes |only
22 files changed, 96 insertions(+), 89 deletions(-)
Permanent link
Title: Kernel smoothing
Diff between ks versions 1.9.0 dated 2014-03-27 and 1.9.1 dated 2014-04-11
Description: Kernel smoothers for univariate and multivariate data
Author: Tarn Duong
Maintainer: Tarn Duong
ks-1.9.0/ks/man/pre.scale.Rd |only
ks-1.9.1/ks/CHANGELOG | 8 +++
ks-1.9.1/ks/DESCRIPTION | 10 +--
ks-1.9.1/ks/MD5 | 54 ++++++++++----------
ks-1.9.1/ks/NAMESPACE | 13 +++--
ks-1.9.1/ks/R/kcde.R | 16 ++++++
ks-1.9.1/ks/R/kcopula.R | 98 +++++++++++++++++++++++++++++++-------
ks-1.9.1/ks/R/kdde.R | 36 +++++++++++++
ks-1.9.1/ks/R/kde.R | 44 +----------------
ks-1.9.1/ks/build |only
ks-1.9.1/ks/inst/doc/kde.pdf |binary
ks-1.9.1/ks/man/Hbcv.Rd | 2
ks-1.9.1/ks/man/Hlscv.Rd | 4 -
ks-1.9.1/ks/man/Hpi.Rd | 15 +++--
ks-1.9.1/ks/man/Hscv.Rd | 10 ++-
ks-1.9.1/ks/man/contour.Rd | 6 +-
ks-1.9.1/ks/man/ise.mixt.Rd | 2
ks-1.9.1/ks/man/kcde.Rd | 29 ++++++-----
ks-1.9.1/ks/man/kcopula.Rd | 28 ++++++++--
ks-1.9.1/ks/man/kda.Rd | 26 ++++------
ks-1.9.1/ks/man/kdde.Rd | 22 +++++---
ks-1.9.1/ks/man/kde.Rd | 37 +++++++++-----
ks-1.9.1/ks/man/kde.local.test.Rd | 13 ++---
ks-1.9.1/ks/man/kde.test.Rd | 56 ++++++---------------
ks-1.9.1/ks/man/kfe.Rd |only
ks-1.9.1/ks/man/kroc.Rd | 41 +++++++--------
ks-1.9.1/ks/man/ks-internal.Rd | 2
ks-1.9.1/ks/man/ks-package.Rd | 19 +++----
ks-1.9.1/ks/man/plot.kde.Rd | 10 +--
ks-1.9.1/ks/man/pre.transform.Rd |only
30 files changed, 357 insertions(+), 244 deletions(-)
Title: Generic and biological sequences.
Diff between sequences versions 0.5.7 dated 2013-07-03 and 0.5.8 dated 2014-04-11
Description: Educational package used in R courses to illustrate OO programming
and package development. Using biological sequences (DNA and RNA)
as a working example.
Author: Laurent Gatto [aut, cre],
Robert Stojnic [aut]
Maintainer: Laurent Gatto
sequences-0.5.7/sequences/inst/tests |only
sequences-0.5.7/sequences/sandbox |only
sequences-0.5.7/sequences/tests/test-all.R |only
sequences-0.5.8/sequences/DESCRIPTION | 30 ++++++++++++-----------
sequences-0.5.8/sequences/MD5 | 14 +++++-----
sequences-0.5.8/sequences/NAMESPACE | 1
sequences-0.5.8/sequences/NEWS | 6 +++-
sequences-0.5.8/sequences/build |only
sequences-0.5.8/sequences/inst/doc/sequences.pdf |binary
sequences-0.5.8/sequences/tests/testthat |only
sequences-0.5.8/sequences/tests/testthat.R |only
11 files changed, 29 insertions(+), 22 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Diff between MALDIquant versions 1.9 dated 2014-01-14 and 1.10 dated 2014-04-11
Description: MALDIquant provides a complete analysis pipeline for MALDI-TOF
and other mass spectrometry data. Distinctive features include baseline
subtraction methods such as TopHat or SNIP, peak alignment using warping
functions, handling of replicated measurements as well as allowing spectra
with different resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb
MALDIquant-1.10/MALDIquant/DESCRIPTION | 11
MALDIquant-1.10/MALDIquant/MD5 | 163 +++--
MALDIquant-1.10/MALDIquant/NAMESPACE | 10
MALDIquant-1.10/MALDIquant/NEWS | 78 ++
MALDIquant-1.10/MALDIquant/R/Deprecated.R | 284 ----------
MALDIquant-1.10/MALDIquant/R/detectPeaks-methods.R | 38 -
MALDIquant-1.10/MALDIquant/R/determineWarpingFunctions-functions.R | 56 -
MALDIquant-1.10/MALDIquant/R/estimateBaseline-functions.R | 77 --
MALDIquant-1.10/MALDIquant/R/estimateNoise-functions.R | 34 +
MALDIquant-1.10/MALDIquant/R/estimateNoise-methods.R | 17
MALDIquant-1.10/MALDIquant/R/localMaxima-functions.R | 16
MALDIquant-1.10/MALDIquant/R/merge-functions.R | 12
MALDIquant-1.10/MALDIquant/R/removeBaseline-methods.R | 23
MALDIquant-1.10/MALDIquant/R/replaceNegativeIntensityValues-functions.R |only
MALDIquant-1.10/MALDIquant/R/transformIntensity-methods.R | 24
MALDIquant-1.10/MALDIquant/R/trim-methods.R | 9
MALDIquant-1.10/MALDIquant/R/valid-methods.R | 10
MALDIquant-1.10/MALDIquant/R/which.closest-functions.R | 6
MALDIquant-1.10/MALDIquant/build |only
MALDIquant-1.10/MALDIquant/demo/baseline.R | 1
MALDIquant-1.10/MALDIquant/demo/peaks.R | 1
MALDIquant-1.10/MALDIquant/demo/warping.R | 1
MALDIquant-1.10/MALDIquant/demo/workflow.R | 6
MALDIquant-1.10/MALDIquant/inst/doc |only
MALDIquant-1.10/MALDIquant/man/MALDIquant-defunct.Rd |only
MALDIquant-1.10/MALDIquant/man/MALDIquant-deprecated.Rd | 51 -
MALDIquant-1.10/MALDIquant/man/MALDIquant-package.Rd | 6
MALDIquant-1.10/MALDIquant/man/detectPeaks-methods.Rd | 2
MALDIquant-1.10/MALDIquant/man/determineWarpingFunctions-functions.Rd | 5
MALDIquant-1.10/MALDIquant/man/estimateBaselineConvexHull-functions.Rd | 5
MALDIquant-1.10/MALDIquant/man/mergeMassPeaks-functions.Rd | 5
MALDIquant-1.10/MALDIquant/man/removeBaseline-methods.Rd | 2
MALDIquant-1.10/MALDIquant/man/transformIntensity-methods.Rd | 5
MALDIquant-1.10/MALDIquant/tests/testthat |only
MALDIquant-1.10/MALDIquant/tests/testthat.R |only
MALDIquant-1.10/MALDIquant/vignettes |only
MALDIquant-1.9/MALDIquant/inst/tests |only
MALDIquant-1.9/MALDIquant/tests/test_all.R |only
38 files changed, 306 insertions(+), 652 deletions(-)
Title: Estimation of extended mixed models using latent classes and
latent processes
Diff between lcmm versions 1.6.3 dated 2013-03-14 and 1.6.4 dated 2014-04-11
Description: This package provides functions for the estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
DESCRIPTION | 20
MD5 | 170 +--
NAMESPACE | 22
NEWS | 140 +-
R/Contlcmm.R | 126 +-
R/Jointlcmm.R | 2234 ++++++++++++++++++++++------------------
R/Ordlcmm.R | 135 ++
R/VarCov.Jointlcmm.R |only
R/VarCov.hlme.R |only
R/VarCov.lcmm..R |only
R/VarCov.multlcmm.R |only
R/VarCovRE.Jointlcmm.R |only
R/VarCovRE.hlme.R |only
R/VarCovRE.lcmm.R |only
R/VarCovRE.multlcmm.R |only
R/VarExpl.Jointlcmm.R |only
R/VarExpl.hlme.R |only
R/VarExpl.lcmm.R |only
R/VarExpl.multlcmm.R |only
R/WaldMult.R |only
R/dynpred.R |only
R/epoce.R | 947 ++++++++--------
R/estimates.Jointlcmm.R |only
R/estimates.hlme.R |only
R/estimates.lcmm.R |only
R/estimates.multlcmm.R |only
R/hlme.R | 207 ++-
R/lcmm.R | 25
R/link.confint.lcmm.R |only
R/link.confint.multlcmm.R |only
R/multlcmm.R | 1488 ++++++++++++++------------
R/plot.Diffepoce.R | 126 +-
R/plot.Jointlcmm.R | 60 -
R/plot.baselinerisk.Jointlcmm.R | 144 ++
R/plot.dynpred.R |only
R/plot.epoce.R | 85 +
R/plot.hlme.R | 61 -
R/plot.lcmm.R | 72 -
R/plot.linkfunction.lcmm.R | 106 +
R/plot.linkfunction.multlcmm.R | 243 +++-
R/plot.multlcmm.R | 41
R/plot.postprob.Jointlcmm.R | 92 +
R/plot.postprob.hlme.R | 81 +
R/plot.postprob.lcmm.R | 81 +
R/plot.postprob.multlcmm.R | 50
R/plot.predict.Jointlcmm.R | 953 ++++++++++-------
R/plot.predict.hlme.R | 787 ++++++++------
R/plot.predict.lcmm.R | 833 +++++++++-----
R/plot.predict.multlcmm.R |only
R/plot.survival.Jointlcmm.R | 145 ++
R/postprob.Jointlcmm.R | 164 +-
R/postprob.hlme.R | 93 +
R/postprob.lcmm.R | 88 +
R/postprob.multlcmm.R | 100 +
R/predictL.multlcmm.R | 269 ++--
R/predictY.Jointlcmm.R | 50
R/predictY.hlme.R | 43
R/predictY.lcmm.R | 134 --
R/predictY.multlcmm.R | 14
R/print.multlcmm.R | 2
R/summary.Jointlcmm.R | 11
R/summary.hlme.R | 9
R/summary.lcmm.R | 10
R/summary.multlcmm.R | 645 +++++------
data/paquid.rda |only
man/Diffepoce.Rd | 24
man/Jointlcmm.Rd | 50
man/VarCov.Rd |only
man/VarCovRE.Rd |only
man/VarExpl.Rd |only
man/WaldMult.Rd |only
man/dynpred.Rd |only
man/epoce.Rd | 24
man/estimates.Rd |only
man/hlme.Rd | 62 -
man/lcmm-package.Rd | 25
man/lcmm.Rd | 62 -
man/link.confint.Rd |only
man/multlcmm.rd | 24
man/paquid.Rd |only
man/plot.baselinerisk.Rd | 15
man/plot.dynpred.Rd |only
man/plot.lcmm.Rd | 7
man/plot.linkfunction.Rd | 14
man/plot.postprob.Rd | 7
man/plot.pred.accuracy.Rd | 18
man/plot.predict.Rd | 45
man/plot.survival.Rd | 13
man/postprob.Rd | 27
man/predictL.Rd | 7
man/predictY.Rd | 12
man/print.lcmm.Rd | 82 -
man/summary.lcmm.Rd | 89 -
src/AOptim.f90 | 1799 ++++++++++++++++----------------
src/Jointhet.f90 | 73 -
src/calculusTransfo.f90 |only
src/cvpl.f90 | 4
src/hetmixCont.f90 | 33
src/hetmixContMult.f90 | 257 ++--
src/hetmixOrd.f90 | 10
src/hetmixlin.f90 | 3
src/predictCont.f90 | 6
src/predictDyn.f90 |only
103 files changed, 8159 insertions(+), 5739 deletions(-)
Title: Grain-size Statistics and Description of Sediment
Diff between G2Sd versions 2.1 dated 2014-03-11 and 2.1-1 dated 2014-04-11
Description: gives full descriptive statistics and a
physical description of sediment obtained with metric or phi
sieves according to the grain size distribution.
Author: Regis K. Gallon (MNHN), Jerome Fournier (CNRS|MNHN)
Maintainer: Regis K. Gallon
DESCRIPTION | 12 ++++++------
MD5 | 9 +++++----
R/granplot.R | 13 +++++++------
inst/extdata/shinyapps |only
inst/extdata/ui.R | 3 ++-
man/granplot.Rd | 11 +++++++++--
6 files changed, 29 insertions(+), 19 deletions(-)
Title: Radiocarbon dating, age-depth modelling, relative sea level rate
estimation, and non-parametric phase modelling
Diff between Bchron versions 4.0 dated 2014-04-01 and 4.1 dated 2014-04-11
Description: This package enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM).
Author: Andrew Parnell
Maintainer: Andrew Parnell
Bchron-4.0/Bchron/R/zzz.R |only
Bchron-4.0/Bchron/man/TestRSLdata.Rd |only
Bchron-4.1/Bchron/DESCRIPTION | 10
Bchron-4.1/Bchron/MD5 | 38 +-
Bchron-4.1/Bchron/NAMESPACE | 4
Bchron-4.1/Bchron/R/BchronCalibrate.R | 5
Bchron-4.1/Bchron/R/BchronDensity.R | 3
Bchron-4.1/Bchron/R/BchronDensityFast.R | 3
Bchron-4.1/Bchron/R/BchronRSL.R | 5
Bchron-4.1/Bchron/R/Bchronology.R | 256 --------------------
Bchron-4.1/Bchron/R/plot.BchronCalibratedDates.R | 10
Bchron-4.1/Bchron/R/plot.BchronDensityRun.R | 5
Bchron-4.1/Bchron/R/plot.BchronDensityRunFast.R | 5
Bchron-4.1/Bchron/R/plot.BchronRSLRun.R | 4
Bchron-4.1/Bchron/R/plot.BchronologyRun.R | 7
Bchron-4.1/Bchron/R/predict.BchronologyRun.R |only
Bchron-4.1/Bchron/R/summary.BchronCalibratedDates.R | 6
Bchron-4.1/Bchron/R/summary.BchronologyRun.R | 55 ++--
Bchron-4.1/Bchron/man/Bchronology.Rd | 10
Bchron-4.1/Bchron/man/TestRSLData.Rd |only
Bchron-4.1/Bchron/man/predict.BchronologyRun.Rd |only
Bchron-4.1/Bchron/man/summary.BchronologyRun.Rd | 7
Bchron-4.1/Bchron/src |only
23 files changed, 111 insertions(+), 322 deletions(-)
Title: Power and Sample size distribution of 2-stage BE studies via
simulations
Diff between Power2Stage versions 0.0-7 dated 2014-02-13 and 0.0-8 dated 2014-04-11
Description: Contains functions to calculate power and sample size distribution
of 2-stage BE studies with a 2x2 crossover design according to
Potvin et.al. / Montague et. al. modified to include a futility Nmax
and modified to do the sample size estimation step with PE and mse
of stage 1 as well as the power calculation steps according to
Karalis & Macheras.
The third function calculates power and sample size distribution
of 2-stage BE studies with a futility criterion for the point
estimator of T/R from stage 1.
The fourth function calculates power of non-adaptive group
sequential (2-stage) BE studies.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 6 ++++++
R/power_2stage_KM.R | 24 +++++++++++++-----------
man/power.2stage.KM.Rd | 5 +++--
5 files changed, 30 insertions(+), 21 deletions(-)
Title: Iterator construct for R
Diff between iterators versions 1.0.6 dated 2012-04-16 and 1.0.7 dated 2014-04-11
Description: Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection
of data.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 18 ++++++++++--------
MD5 | 13 ++++++++-----
build |only
inst/doc/iterators.R |only
inst/doc/iterators.pdf |binary
inst/doc/writing.R |only
inst/doc/writing.pdf |binary
inst/unitTests/icountnTest.R | 36 ++++++++++++++++++------------------
inst/unitTests/recycleTest.R | 20 ++++++++++----------
9 files changed, 46 insertions(+), 41 deletions(-)
Title: Foreach looping construct for R
Diff between foreach versions 1.4.1 dated 2013-06-06 and 1.4.2 dated 2014-04-11
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation
of a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Revolution Analytics, Steve Weston
Maintainer: Revolution Analytics
DESCRIPTION | 14 +++++++-------
MD5 | 9 +++++----
build |only
inst/doc/foreach.pdf |binary
inst/doc/nested.pdf |binary
tests/doRUnit.R | 11 ++++++-----
6 files changed, 18 insertions(+), 16 deletions(-)