Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 0.9
Title: Sample Selection Models
Diff between sampleSelection versions 0.7-2 dated 2012-08-14 and 1.0-2 dated 2014-06-24
More information about sampleSelection at CRAN
Description: Estimation of Sample Selection Models
Author: Arne Henningsen
Maintainer: Arne Henningsen
sampleSelection-0.7-2/sampleSelection/R/tobit2.R |only
sampleSelection-0.7-2/sampleSelection/man/fitted.probit.Rd |only
sampleSelection-0.7-2/sampleSelection/man/nObs.probit.Rd |only
sampleSelection-0.7-2/sampleSelection/man/sampleSelection-deprecated.Rd |only
sampleSelection-0.7-2/sampleSelection/sampleSelection.Rproj |only
sampleSelection-0.7-2/sampleSelection/tests/heckit.R |only
sampleSelection-0.7-2/sampleSelection/tests/heckit.Rout.save |only
sampleSelection-1.0-2/sampleSelection/DESCRIPTION | 19
sampleSelection-1.0-2/sampleSelection/MD5 | 111
sampleSelection-1.0-2/sampleSelection/NAMESPACE | 13
sampleSelection-1.0-2/sampleSelection/NEWS | 53
sampleSelection-1.0-2/sampleSelection/R/binaryChoice.R | 9
sampleSelection-1.0-2/sampleSelection/R/fitted.selection.R | 3
sampleSelection-1.0-2/sampleSelection/R/heckit2fit.R | 31
sampleSelection-1.0-2/sampleSelection/R/heckit5fit.R | 6
sampleSelection-1.0-2/sampleSelection/R/invMillsRatio.R | 6
sampleSelection-1.0-2/sampleSelection/R/linearPredictors.R | 4
sampleSelection-1.0-2/sampleSelection/R/logLik.probit.R |only
sampleSelection-1.0-2/sampleSelection/R/logLik.selection.R |only
sampleSelection-1.0-2/sampleSelection/R/model.frame.selection.R | 13
sampleSelection-1.0-2/sampleSelection/R/nObs.R | 12
sampleSelection-1.0-2/sampleSelection/R/predict.probit.R |only
sampleSelection-1.0-2/sampleSelection/R/predict.selection.R |only
sampleSelection-1.0-2/sampleSelection/R/print.summary.probit.R | 2
sampleSelection-1.0-2/sampleSelection/R/probit.R | 33
sampleSelection-1.0-2/sampleSelection/R/residuals.probit.R | 6
sampleSelection-1.0-2/sampleSelection/R/residuals.selection.R | 43
sampleSelection-1.0-2/sampleSelection/R/selection.R | 34
sampleSelection-1.0-2/sampleSelection/R/summary.probit.R | 2
sampleSelection-1.0-2/sampleSelection/R/tobit2Bfit.R | 48
sampleSelection-1.0-2/sampleSelection/R/tobit2fit.R | 78
sampleSelection-1.0-2/sampleSelection/build |only
sampleSelection-1.0-2/sampleSelection/inst/doc/selection.R |only
sampleSelection-1.0-2/sampleSelection/man/binaryChoice.Rd | 10
sampleSelection-1.0-2/sampleSelection/man/coef.selection.Rd | 10
sampleSelection-1.0-2/sampleSelection/man/fitted.selection.Rd | 25
sampleSelection-1.0-2/sampleSelection/man/heckit2fit.Rd | 11
sampleSelection-1.0-2/sampleSelection/man/invMillsRatio.Rd | 12
sampleSelection-1.0-2/sampleSelection/man/linearPredictors.Rd | 6
sampleSelection-1.0-2/sampleSelection/man/model.frame.binaryChoice.Rd | 4
sampleSelection-1.0-2/sampleSelection/man/model.frame.selection.Rd | 6
sampleSelection-1.0-2/sampleSelection/man/model.matrix.binaryChoice.Rd | 5
sampleSelection-1.0-2/sampleSelection/man/model.matrix.selection.Rd | 6
sampleSelection-1.0-2/sampleSelection/man/nlswork.Rd | 159
sampleSelection-1.0-2/sampleSelection/man/predict.probit.Rd |only
sampleSelection-1.0-2/sampleSelection/man/predict.selection.Rd |only
sampleSelection-1.0-2/sampleSelection/man/probit-methods.Rd |only
sampleSelection-1.0-2/sampleSelection/man/residuals.probit.Rd | 2
sampleSelection-1.0-2/sampleSelection/man/residuals.selection.Rd | 16
sampleSelection-1.0-2/sampleSelection/man/selection-methods.Rd |only
sampleSelection-1.0-2/sampleSelection/man/selection.Rd | 70
sampleSelection-1.0-2/sampleSelection/man/summary.probit.Rd | 2
sampleSelection-1.0-2/sampleSelection/man/summary.selection.Rd | 5
sampleSelection-1.0-2/sampleSelection/man/tobit2fit.Rd | 20
sampleSelection-1.0-2/sampleSelection/man/vcov.selection.Rd | 7
sampleSelection-1.0-2/sampleSelection/tests/Mroz87SelectionTest.R |only
sampleSelection-1.0-2/sampleSelection/tests/Mroz87SelectionTest.Rout.save |only
sampleSelection-1.0-2/sampleSelection/tests/binarySelectionOutcome.R | 139
sampleSelection-1.0-2/sampleSelection/tests/binarySelectionOutcome.Rout.save | 2699
sampleSelection-1.0-2/sampleSelection/tests/fail.R |only
sampleSelection-1.0-2/sampleSelection/tests/fail.Rout.save |only
sampleSelection-1.0-2/sampleSelection/tests/heckitIvTest.R |only
sampleSelection-1.0-2/sampleSelection/tests/heckitIvTest.Rout.save |only
sampleSelection-1.0-2/sampleSelection/tests/invMillsRatioTest.R |only
sampleSelection-1.0-2/sampleSelection/tests/invMillsRatioTest.Rout.save |only
sampleSelection-1.0-2/sampleSelection/tests/probit.R | 331
sampleSelection-1.0-2/sampleSelection/tests/probit.Rout.save | 8193
sampleSelection-1.0-2/sampleSelection/tests/selection.R | 808
sampleSelection-1.0-2/sampleSelection/tests/selection.Rout.save |99468 +++++-----
69 files changed, 64736 insertions(+), 47804 deletions(-)
Permanent link
Title: Rice Wavelet Toolbox wrapper
Diff between rwt versions 0.9.4 dated 2013-10-14 and 1.0.0 dated 2014-06-24
Description: Provides a set of functions for performing digital signal
processing.
Author: P. Roebuck, Rice University's DSP group
Maintainer: P. Roebuck
rwt-0.9.4/rwt/inst/LICENSE.mdacc |only
rwt-0.9.4/rwt/inst/LICENSE.note |only
rwt-0.9.4/rwt/inst/LICENSE.rice |only
rwt-1.0.0/rwt/DESCRIPTION | 15 +--
rwt-1.0.0/rwt/LICENSE | 2
rwt-1.0.0/rwt/MD5 | 122 +++++++++++++-------------
rwt-1.0.0/rwt/NAMESPACE | 9 +
rwt-1.0.0/rwt/NEWS | 27 +++++
rwt-1.0.0/rwt/R/daubcoeff.R | 2
rwt-1.0.0/rwt/R/daubcqf.R | 4
rwt-1.0.0/rwt/R/denoise.R | 2
rwt-1.0.0/rwt/R/hardTh.R | 2
rwt-1.0.0/rwt/R/makesig.R | 3
rwt-1.0.0/rwt/R/mdwt.R | 3
rwt-1.0.0/rwt/R/midwt.R | 3
rwt-1.0.0/rwt/R/mirdwt.R | 3
rwt-1.0.0/rwt/R/mrdwt.R | 3
rwt-1.0.0/rwt/R/plotSignalTransformation.R | 2
rwt-1.0.0/rwt/R/softTh.R | 2
rwt-1.0.0/rwt/R/zzz.R | 2
rwt-1.0.0/rwt/build |only
rwt-1.0.0/rwt/demo/denoise.R | 3
rwt-1.0.0/rwt/inst/COPYRIGHTS |only
rwt-1.0.0/rwt/man/daubcoeff-internal.Rd | 2
rwt-1.0.0/rwt/man/daubcqf.Rd | 13 +-
rwt-1.0.0/rwt/man/denoise.Rd | 2
rwt-1.0.0/rwt/man/makesig-internal.Rd | 2
rwt-1.0.0/rwt/man/makesig.Rd | 2
rwt-1.0.0/rwt/man/mdwt.Rd | 2
rwt-1.0.0/rwt/man/midwt.Rd | 2
rwt-1.0.0/rwt/man/mirdwt.Rd | 2
rwt-1.0.0/rwt/man/mrdwt.Rd | 2
rwt-1.0.0/rwt/man/plotSignalTransformation.Rd | 2
rwt-1.0.0/rwt/man/rwt-package.Rd |only
rwt-1.0.0/rwt/man/threshold.Rd | 2
rwt-1.0.0/rwt/src/Makevars | 2
rwt-1.0.0/rwt/src/Makevars-dbg |only
rwt-1.0.0/rwt/src/debug.h | 2
rwt-1.0.0/rwt/src/do_mdwt.c | 2
rwt-1.0.0/rwt/src/do_mdwt.h | 2
rwt-1.0.0/rwt/src/do_midwt.c | 2
rwt-1.0.0/rwt/src/do_midwt.h | 2
rwt-1.0.0/rwt/src/do_mirdwt.c | 2
rwt-1.0.0/rwt/src/do_mirdwt.h | 2
rwt-1.0.0/rwt/src/do_mrdwt.c | 2
rwt-1.0.0/rwt/src/do_mrdwt.h | 2
rwt-1.0.0/rwt/src/do_util.c | 2
rwt-1.0.0/rwt/src/do_util.h | 2
rwt-1.0.0/rwt/src/estimateL.c | 2
rwt-1.0.0/rwt/src/estimateL.h | 2
rwt-1.0.0/rwt/src/init.c |only
rwt-1.0.0/rwt/src/mdwt.c | 2
rwt-1.0.0/rwt/src/mdwt.h | 2
rwt-1.0.0/rwt/src/midwt.c | 2
rwt-1.0.0/rwt/src/midwt.h | 2
rwt-1.0.0/rwt/src/mirdwt.c | 2
rwt-1.0.0/rwt/src/mirdwt.h | 2
rwt-1.0.0/rwt/src/mrdwt.c | 2
rwt-1.0.0/rwt/src/mrdwt.h | 2
rwt-1.0.0/rwt/tests/daubcqf.R | 2
rwt-1.0.0/rwt/tests/hardTh.R | 2
rwt-1.0.0/rwt/tests/mdwt.R | 2
rwt-1.0.0/rwt/tests/midwt.R | 2
rwt-1.0.0/rwt/tests/mirdwt.R | 2
rwt-1.0.0/rwt/tests/mrdwt.R | 2
rwt-1.0.0/rwt/tests/softTh.R | 2
66 files changed, 183 insertions(+), 117 deletions(-)
Title: Utilities for Official Spanish Microdata
Diff between MicroDatosEs versions 0.6.1 dated 2014-05-12 and 0.6.2 dated 2014-06-24
Description: The MicroDatosEs package provides utilities for reading and processing microdata from Spanish official statistics with R
Author: Carlos J. Gil Bellosta [aut, cre],
Carlos Neira [ctb],
José Luis Cañadas Reche [ctb]
Maintainer: Carlos J. Gil Bellosta
DESCRIPTION | 11
MD5 | 10
R/censo2010.R | 6
inst/extdata/sampleCenso.txt | 2000 ++++++++++++++++-----------------
inst/metadata/censo_2010_mdat1.txt | 167 +-
inst/metadata/censo_2010_mdat2.txt | 2206 ++++++++++++++++++++++++++++++++++++-
6 files changed, 3284 insertions(+), 1116 deletions(-)
Title: MATLAB emulation package
Diff between matlab versions 1.0.1 dated 2014-02-08 and 1.0.2 dated 2014-06-24
Description: Emulate MATLAB code using R
Author: P. Roebuck
Maintainer: P. Roebuck
DESCRIPTION | 12 ++++++------
MD5 | 11 ++++++-----
NAMESPACE | 2 +-
NEWS | 8 ++++++++
build |only
inst/COPYRIGHTS | 13 ++++++++++++-
man/matlab-package.Rd | 12 ++++++------
7 files changed, 39 insertions(+), 19 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.05 dated 2014-05-10 and 2.10 dated 2014-06-24
Description: This package provides methods for obtaining least-squares means for various linear models. It can also compute contrasts or linear combinations of these least-squares means, comparisons of slopes, interaction plots, and compact letter displays.
Author: Russell V. Lenth
Maintainer: Russ Lenth
DESCRIPTION | 8 ++--
MD5 | 40 +++++++++++---------
NAMESPACE | 6 +++
R/aovlist-support.R |only
R/helpers.R | 5 +-
R/lsm.list.R |only
R/lsmeans.R | 12 +-----
R/ref.grid.R | 32 ++++++++++++++--
inst/NEWS | 12 +++++-
inst/doc/extending.pdf |binary
inst/doc/lsmeans-changes.pdf |binary
inst/doc/using-lsmeans.pdf |binary
inst/doc/using-lsmeans.rnw | 4 +-
man/cld.Rd | 3 +
man/contrast.Rd | 12 +++---
man/lsmeans.Rd | 7 ++-
man/ref.grid.Rd | 3 +
man/summary.Rd | 5 ++
man/update.Rd | 42 ++++++++++++----------
tests/tests1.R | 24 +++++++++++-
tests/tests1.Rout.save | 82 ++++++++++++++++++++++++++++++++++++-------
vignettes/using-lsmeans.rnw | 4 +-
22 files changed, 213 insertions(+), 88 deletions(-)
Title: Inventorymodel
Diff between InventorymodelPackage versions 1.0.1 dated 2014-06-14 and 1.0.2 dated 2014-06-24
More information about InventorymodelPackage at CRAN
Description: This package describes the associated cost games to inventory situations.
Author: Alejandro Saavedra Nieves
Maintainer: Alejandro Saavedra Nieves
DESCRIPTION | 6 +++---
MD5 | 4 ++--
man/Inventorymodel-package.Rd | 20 ++++++++++----------
3 files changed, 15 insertions(+), 15 deletions(-)
Permanent link
Title: A package for statistical analysis in epidemiology.
Diff between Epi versions 1.1.49 dated 2013-05-15 and 1.1.65 dated 2014-06-24
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation and manupulation of multistate data - the
Lexis suite of functions.
Also contains a function for interval censored data and some useful
functions for tabulation and plotting.
Contains some epidemiological datasets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen
Epi-1.1.49/Epi/Examples |only
Epi-1.1.49/Epi/man/apc.lines.Rd |only
Epi-1.1.49/Epi/man/apc.plot.Rd |only
Epi-1.1.65/Epi/CHANGES | 123 ++
Epi-1.1.65/Epi/DESCRIPTION | 36
Epi-1.1.65/Epi/MD5 | 100 +-
Epi-1.1.65/Epi/NAMESPACE | 9
Epi-1.1.65/Epi/R/NArray.R |only
Epi-1.1.65/Epi/R/Ns.r |only
Epi-1.1.65/Epi/R/ROC.R | 2
Epi-1.1.65/Epi/R/Relevel.R | 30
Epi-1.1.65/Epi/R/apc.fit.R | 606 ++++++-------
Epi-1.1.65/Epi/R/apc.frame.R | 6
Epi-1.1.65/Epi/R/apc.plot.R | 20
Epi-1.1.65/Epi/R/boxes.MS.R | 106 +-
Epi-1.1.65/Epi/R/ci.lin.R | 4
Epi-1.1.65/Epi/R/cutLexis.R | 4
Epi-1.1.65/Epi/R/detrend.R | 1
Epi-1.1.65/Epi/R/foreign.R | 22
Epi-1.1.65/Epi/R/gen.exp.R | 24
Epi-1.1.65/Epi/R/lexis.R | 43
Epi-1.1.65/Epi/R/plotEst.R | 6
Epi-1.1.65/Epi/R/projection.ip.r | 1
Epi-1.1.65/Epi/R/simLexis.R | 276 ++++--
Epi-1.1.65/Epi/R/splitLexis.R | 4
Epi-1.1.65/Epi/R/stack.Lexis.R | 2
Epi-1.1.65/Epi/build |only
Epi-1.1.65/Epi/data/M.dk.rda |binary
Epi-1.1.65/Epi/data/N.dk.rda |binary
Epi-1.1.65/Epi/data/Y.dk.rda |binary
Epi-1.1.65/Epi/data/testisDK.rda |only
Epi-1.1.65/Epi/inst/doc/Follow-up.R | 71 -
Epi-1.1.65/Epi/inst/doc/Follow-up.pdf | 1486 +++++++++++++++-------------------
Epi-1.1.65/Epi/inst/doc/Follow-up.rnw | 79 -
Epi-1.1.65/Epi/inst/doc/index.html | 3
Epi-1.1.65/Epi/inst/doc/sim-Lexis.R |only
Epi-1.1.65/Epi/inst/doc/sim-Lexis.pdf |binary
Epi-1.1.65/Epi/inst/doc/sim-Lexis.rnw |only
Epi-1.1.65/Epi/man/DMlate.Rd | 6
Epi-1.1.65/Epi/man/Lexis.Rd | 39
Epi-1.1.65/Epi/man/NArray.Rd |only
Epi-1.1.65/Epi/man/Ns.Rd |only
Epi-1.1.65/Epi/man/apc.fit.Rd | 35
Epi-1.1.65/Epi/man/apc.frame.Rd | 2
Epi-1.1.65/Epi/man/boxes.MS.Rd | 24
Epi-1.1.65/Epi/man/ci.lin.Rd | 31
Epi-1.1.65/Epi/man/clogistic.Rd | 13
Epi-1.1.65/Epi/man/foreign.Lexis.Rd | 8
Epi-1.1.65/Epi/man/gen.exp.Rd | 19
Epi-1.1.65/Epi/man/lines.apc.Rd |only
Epi-1.1.65/Epi/man/occup.Rd | 4
Epi-1.1.65/Epi/man/pc.lines.Rd |only
Epi-1.1.65/Epi/man/plot.apc.Rd |only
Epi-1.1.65/Epi/man/plotEst.Rd | 16
Epi-1.1.65/Epi/man/simLexis.Rd | 162 ++-
Epi-1.1.65/Epi/man/splitLexis.Rd | 4
Epi-1.1.65/Epi/man/testisDK.Rd |only
Epi-1.1.65/Epi/vignettes |only
58 files changed, 1860 insertions(+), 1567 deletions(-)
Title: Binary Graph Analysis Tools
Diff between bingat versions 1.0 dated 2014-03-07 and 1.1 dated 2014-06-24
Description: This package provides tools to analyze binary graph objects.
Author: Terrence Brooks, Berkley Shands, Skye Buckner-Petty, Patricio S. La Rosa, Elena Deych, William D. Shannon
Maintainer: Berkley Shands
bingat-1.0/bingat/man/glmReg.Rd |only
bingat-1.0/bingat/man/glrtReg.Rd |only
bingat-1.1/bingat/DESCRIPTION | 10 ++++----
bingat-1.1/bingat/MD5 | 31 +++++++++++++--------------
bingat-1.1/bingat/NAMESPACE | 2 -
bingat-1.1/bingat/NEWS |only
bingat-1.1/bingat/R/estLogLik.R | 14 +++++++-----
bingat-1.1/bingat/R/estTau.R | 11 +++++++--
bingat-1.1/bingat/R/getGibbsMixture.R | 27 +++++++++++++----------
bingat-1.1/bingat/R/getLoglikeMixture.R | 15 +++----------
bingat-1.1/bingat/R/glmReg.R | 35 +++++++++++--------------------
bingat-1.1/bingat/R/glrtPvalue.R | 18 +++++++--------
bingat-1.1/bingat/R/glrtReg.R | 5 ----
bingat-1.1/bingat/R/graphNetworkPlot.R | 6 ++---
bingat-1.1/bingat/R/rGibbs.R | 2 -
bingat-1.1/bingat/man/BinGAT-internal.Rd | 2 +
bingat-1.1/bingat/man/getGibbsMixture.Rd | 1
bingat-1.1/bingat/man/glrtPvalue.Rd | 3 --
18 files changed, 86 insertions(+), 96 deletions(-)
Title: Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Diff between bujar versions 0.1-3 dated 2014-05-01 and 0.1-4 dated 2014-06-24
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Including L_2 boosting with componentwise linear least squares, componentwise smoothing splines, P-splines, regression trees and boosted MARS. Other high-dimensional tools include elastic net and MARS.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang
DESCRIPTION | 14 ++++++++------
MD5 | 4 ++--
man/bujar.Rd | 2 +-
3 files changed, 11 insertions(+), 9 deletions(-)
Title: Get Weather Data from the Web
Diff between weatherData versions 0.4 dated 2014-04-30 and 0.4.1 dated 2014-06-24
Description: Functions that help in fetching weather data from
websites. Given a location and a date range, these functions help fetch
weather data (temperature, pressure etc.) for any weather related analysis.
Author: Ram Narasimhan
Maintainer: Ram Narasimhan
weatherData-0.4.1/weatherData/DESCRIPTION | 8 ++---
weatherData-0.4.1/weatherData/MD5 | 18 +++----------
weatherData-0.4.1/weatherData/R/wrapper_functions.R | 5 ++-
weatherData-0.4.1/weatherData/README.md | 7 +++++
weatherData-0.4.1/weatherData/man/getCurrentTemperature.Rd | 2 +
weatherData-0.4.1/weatherData/man/weatherData-package.Rd | 9 +-----
weatherData-0.4/weatherData/inst |only
weatherData-0.4/weatherData/tests |only
8 files changed, 24 insertions(+), 25 deletions(-)
Title: Gene-level statistics for Pedigree Data
Diff between pedgene versions 1.4 dated 2014-03-20 and 2.1 dated 2014-06-24
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Dan Schaid and Jason Sinnwell
Maintainer: Jason Sinnwell
DESCRIPTION | 14 -
MD5 | 22 +-
NAMESPACE | 1
R/pedgene.R | 84 +++++--
R/pedgene.stats.R | 122 +++++------
inst/doc/pedgene.Rnw | 10
inst/doc/pedgene.pdf |binary
man/pedgene.Rd | 103 ++++++---
tests/test.pedgene.Rout.save | 52 ++--
tests/test.pedgene.expanded.R | 60 ++++-
tests/test.pedgene.expanded.Rout.save | 358 ++++++++++++++++++++--------------
vignettes/pedgene.Rnw | 10
12 files changed, 508 insertions(+), 328 deletions(-)
Title: Reading, manipulation and writing BAM (Binary alignment) files.
Diff between rbamtools versions 2.9.2 dated 2014-06-12 and 2.9.11 dated 2014-06-24
Description: This package provides an interface to functions of the
'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers
DESCRIPTION | 8
MD5 | 104 +-
R/rbamtools.r | 1738 ++++++++++++++++++++++++-------------------
inst/doc/rbamtools.pdf |binary
man/alignDepth-class.Rd | 1
man/bamAlign-class.Rd | 1
man/bamCount.Rd | 1
man/bamCountAll.Rd | 1
man/bamGapList-class.Rd | 1
man/bamRange-class.Rd | 69 +
man/bamRange.Rd | 38
man/bamReader-class.Rd | 1
man/bamWriter-class.Rd | 29
man/bamWriter.Rd | 26
man/countNucs.Rd | 8
man/create.idx.batch.Rd | 4
man/gapList-class.Rd | 9
man/gapSiteList-class.Rd | 15
man/getHeaderText-methods.Rd | 9
man/getNextAlign-methods.Rd | 23
man/getQualDf.Rd | 16
man/getVal.Rd | 1
man/rbamtools-package.Rd | 7
man/setVal.Rd | 1
src/Makevars | 2
src/align_list.h | 350 ++++----
src/bitmask.h | 25
src/gapSiteList.h | 27
src/gapSiteListList.h | 3
src/gap_list.h | 21
src/rbamtools.c | 974 ++++++++++--------------
src/rbamtools.h | 125 +--
src/samtools/bam.c | 34
src/samtools/bam.h | 80 -
src/samtools/bam_aux.c | 3
src/samtools/bam_endian.h | 4
src/samtools/bam_import.c | 148 +--
src/samtools/bam_index.c | 88 --
src/samtools/bam_sort.c | 123 ---
src/samtools/bgzf.c | 87 --
src/samtools/bgzf.h | 18
src/samtools/faidx.c | 114 --
src/samtools/khash.h | 7
src/samtools/kseq.h | 4
src/samtools/ksort.h | 2
src/samtools/kstring.c | 45 -
src/samtools/kstring.h | 2
src/samtools/razf.c | 62 -
src/samtools/razf.h | 6
src/samtools/rdef.h | 60 -
src/samtools/sam.c | 27
src/samtools/sam_header.c | 58 -
src/samtools/sam_header.h | 1
53 files changed, 2149 insertions(+), 2462 deletions(-)
Title: A Data Analysis Tool for Pharmacokinetics
Diff between PKfit versions 1.2.1 dated 2014-04-20 and 1.2.2 dated 2014-06-24
Description: PKfit is a nonlinear regression (including a genetic
algorithm) program which was designed to perform model/curve
fitting and model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
PKfit-1.2.1/PKfit/R/sbolus.mm.out.R |only
PKfit-1.2.1/PKfit/R/sbolus1.out.R |only
PKfit-1.2.1/PKfit/R/sbolus2.out.R |only
PKfit-1.2.1/PKfit/R/sfirst.mm.out.R |only
PKfit-1.2.1/PKfit/R/sfirst1.out.R |only
PKfit-1.2.1/PKfit/R/sfirst2.out.R |only
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PKfit-1.2.1/PKfit/R/sone.noniv.route.R |only
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PKfit-1.2.1/PKfit/R/szero.mm.out.R |only
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PKfit-1.2.1/PKfit/man/szero.mm.out.Rd |only
PKfit-1.2.1/PKfit/man/szero.out.Rd |only
PKfit-1.2.2/PKfit/DESCRIPTION | 12
PKfit-1.2.2/PKfit/MD5 | 136 ++---
PKfit-1.2.2/PKfit/NEWS | 58 ++
PKfit-1.2.2/PKfit/R/OutputFilez.R |only
PKfit-1.2.2/PKfit/R/PK.fit.R | 11
PKfit-1.2.2/PKfit/R/PK.sim.MD.R |only
PKfit-1.2.2/PKfit/R/PK.sim.R | 18
PKfit-1.2.2/PKfit/R/PK.sim.SD.R |only
PKfit-1.2.2/PKfit/R/aicllsbc.R | 29 -
PKfit-1.2.2/PKfit/R/data.manipulate.R | 6
PKfit-1.2.2/PKfit/R/description_version.r |only
PKfit-1.2.2/PKfit/R/fbolus1.R | 256 ++++-----
PKfit-1.2.2/PKfit/R/fbolus2.R | 146 ++---
PKfit-1.2.2/PKfit/R/fbolus3.R | 138 ++---
PKfit-1.2.2/PKfit/R/fbolus3.mm.R |only
PKfit-1.2.2/PKfit/R/ffirst.lag.R | 232 +++-----
PKfit-1.2.2/PKfit/R/ffirst.nolag.R | 226 +++-----
PKfit-1.2.2/PKfit/R/ffirst2.R | 142 ++---
PKfit-1.2.2/PKfit/R/finfu1.R | 220 +++-----
PKfit-1.2.2/PKfit/R/finfu2.R | 133 ++---
PKfit-1.2.2/PKfit/R/fmacro.one.R | 149 ++---
PKfit-1.2.2/PKfit/R/fmacro.three.R | 153 ++---
PKfit-1.2.2/PKfit/R/fmacro.two.R | 141 ++---
PKfit-1.2.2/PKfit/R/fzero.nolag.R | 227 +++-----
PKfit-1.2.2/PKfit/R/iv.bolus.demo.R | 14
PKfit-1.2.2/PKfit/R/legacy.functions.R | 48 -
PKfit-1.2.2/PKfit/R/mmpk.demo.R | 15
PKfit-1.2.2/PKfit/R/montecarlo.R | 14
PKfit-1.2.2/PKfit/R/plotting.lin.R | 70 ++
PKfit-1.2.2/PKfit/R/plotting.non.R | 67 ++
PKfit-1.2.2/PKfit/R/plotting.sim.R | 33 -
PKfit-1.2.2/PKfit/R/run.R | 1
PKfit-1.2.2/PKfit/R/savefile.R | 3
PKfit-1.2.2/PKfit/R/sbolus1.R | 502 ++++++++++++++++--
PKfit-1.2.2/PKfit/R/sbolus2.R | 326 ++++++++++--
PKfit-1.2.2/PKfit/R/sfirst.nolag.R | 715 ++++++++++++++++++++++++---
PKfit-1.2.2/PKfit/R/sfirst2.R | 309 ++++++++++-
PKfit-1.2.2/PKfit/R/sinfu1.R | 530 +++++++++++++++++---
PKfit-1.2.2/PKfit/R/sinfu2.R | 319 ++++++++++--
PKfit-1.2.2/PKfit/R/smacro.R | 6
PKfit-1.2.2/PKfit/R/smacro.one.R | 127 ++++
PKfit-1.2.2/PKfit/R/smacro.one.out.R | 6
PKfit-1.2.2/PKfit/R/smacro.three.R | 135 ++++-
PKfit-1.2.2/PKfit/R/smacro.three.out.R | 6
PKfit-1.2.2/PKfit/R/smacro.two.R | 149 ++++-
PKfit-1.2.2/PKfit/R/smacro.two.out.R | 6
PKfit-1.2.2/PKfit/R/sone.iv.route.MD.R |only
PKfit-1.2.2/PKfit/R/sone.iv.route.SD.R |only
PKfit-1.2.2/PKfit/R/sone.noniv.route.MD.R |only
PKfit-1.2.2/PKfit/R/sone.noniv.route.SD.R |only
PKfit-1.2.2/PKfit/R/stwo.MD.all.R |only
PKfit-1.2.2/PKfit/R/stwo.SD.all.R |only
PKfit-1.2.2/PKfit/R/szero.nolag.R | 497 ++++++++++++++++--
PKfit-1.2.2/PKfit/R/zzz.R | 13
PKfit-1.2.2/PKfit/man/OutputFilez.rd |only
PKfit-1.2.2/PKfit/man/PK.sim.MD.Rd |only
PKfit-1.2.2/PKfit/man/PK.sim.SD.Rd |only
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PKfit-1.2.2/PKfit/man/fbolus3.mm.Rd |only
PKfit-1.2.2/PKfit/man/plot.sim.Rd | 4
PKfit-1.2.2/PKfit/man/sone.iv.route.MD.Rd |only
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PKfit-1.2.2/PKfit/man/sone.noniv.route.MD.Rd |only
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PKfit-1.2.2/PKfit/man/stwo.SD.all.Rd |only
94 files changed, 4473 insertions(+), 1875 deletions(-)
Title: Network meta-analysis with R
Diff between netmeta versions 0.4-4 dated 2014-05-27 and 0.5-0 dated 2014-06-24
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 13 ++--
MD5 | 28 ++++----
NAMESPACE | 2
NEWS | 28 ++++++++
R/decomp.design.R | 150 ++++++++++--------------------------------------
R/decomp.tau.R |only
R/netheat.R | 45 +++++++++-----
R/netmeasures.R | 12 +++
R/netmeta.R | 9 +-
R/nma.krahn.R | 121 +++++++++++++++++++-------------------
R/print.decomp.design.R | 30 +++++++--
R/tau.within.R |only
man/decomp.design.Rd | 102 +++++++++++++++++++++++---------
man/netheat.Rd | 32 +++++++++-
man/netmeasures.Rd | 70 ++++++++++++++--------
man/netmeta.Rd | 7 +-
16 files changed, 365 insertions(+), 284 deletions(-)
Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Diff between HSAUR2 versions 1.1-9 dated 2014-02-01 and 1.1-10 dated 2014-06-24
Description: Functions, data sets, analyses and examples from the
second edition of the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2008). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
the package contains Sweave code for producing slides for selected
chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 -
MD5 | 106 +++++++++++++-------------
build/vignette.rds |binary
data/BCG.rda |binary
data/CYGOB1.rda |binary
data/Lanza.rda |binary
data/birthdeathrates.rda |binary
data/bladdercancer.rda |binary
data/epilepsy.rda |binary
data/foster.rda |binary
data/heptathlon.rda |binary
data/meteo.rda |binary
data/orallesions.rda |binary
data/phosphate.rda |binary
data/pistonrings.rda |binary
data/planets.rda |binary
data/plasma.rda |binary
data/polyps.rda |binary
data/rearrests.rda |binary
data/roomwidth.rda |binary
data/schizophrenia.rda |binary
data/schizophrenia2.rda |binary
data/smoking.rda |binary
data/students.rda |binary
data/suicides.rda |binary
data/toothpaste.rda |binary
data/voting.rda |binary
data/water.rda |binary
data/watervoles.rda |binary
data/waves.rda |binary
data/weightgain.rda |binary
inst/NEWS | 5 +
inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
inst/doc/Ch_analysis_of_variance.pdf |binary
inst/doc/Ch_cluster_analysis.pdf |binary
inst/doc/Ch_conditional_inference.pdf |binary
inst/doc/Ch_density_estimation.pdf |binary
inst/doc/Ch_errata.pdf |binary
inst/doc/Ch_gam.pdf |binary
inst/doc/Ch_graphical_display.pdf |binary
inst/doc/Ch_introduction_to_R.pdf |binary
inst/doc/Ch_logistic_regression_glm.pdf |binary
inst/doc/Ch_meta_analysis.pdf |binary
inst/doc/Ch_multidimensional_scaling.pdf |binary
inst/doc/Ch_multiple_linear_regression.pdf |binary
inst/doc/Ch_principal_components_analysis.pdf |binary
inst/doc/Ch_recursive_partitioning.R | 2
inst/doc/Ch_recursive_partitioning.Rnw | 4
inst/doc/Ch_recursive_partitioning.pdf |binary
inst/doc/Ch_simple_inference.pdf |binary
inst/doc/Ch_simultaneous_inference.pdf |binary
inst/doc/Ch_survival_analysis.pdf |binary
vignettes/Ch_recursive_partitioning.Rnw | 4
54 files changed, 67 insertions(+), 62 deletions(-)
Title: Functional Data Analysis: K-Mean Alignment
Diff between fdakma versions 1.1 dated 2014-05-23 and 1.1.1 dated 2014-06-24
Description: The package fdakma jointly performs clustering and alignment of a multidimensional or unidimensional functional dataset.
Author: Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi, Simone Vantini, Valeria Vitelli
Maintainer: Alice Parodi
fdakma-1.1.1/fdakma/DESCRIPTION | 12
fdakma-1.1.1/fdakma/MD5 | 23
fdakma-1.1.1/fdakma/R/kma.R | 4038 +++++++++++-----------------
fdakma-1.1.1/fdakma/R/kma.compare.R | 486 +--
fdakma-1.1.1/fdakma/R/kma.show.results.R | 705 +---
fdakma-1.1.1/fdakma/R/kma.similarity.R | 468 +--
fdakma-1.1.1/fdakma/data/kma.data.rda |binary
fdakma-1.1.1/fdakma/man/fdakma-package.Rd | 6
fdakma-1.1.1/fdakma/man/kma.Rd | 23
fdakma-1.1.1/fdakma/man/kma.compare.Rd | 19
fdakma-1.1.1/fdakma/man/kma.show.results.Rd | 10
fdakma-1.1.1/fdakma/man/kma.similarity.Rd | 12
fdakma-1.1/fdakma/R/fdakma-internal.R |only
13 files changed, 2475 insertions(+), 3327 deletions(-)
Title: Isotope pattern, profile and centroid calculation for mass
spectrometry.
Diff between enviPat versions 1.7 dated 2014-06-19 and 1.8 dated 2014-06-24
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NEWS | 5 +++++
R/check_several.R | 2 +-
R/envelope.R | 26 ++++++++++++++------------
R/enviPat.R | 3 +--
R/isopattern.R | 36 ++++++++++++++++++++----------------
R/vdetect.R | 30 +++++++++++++++++-------------
man/envelope.Rd | 5 +++--
man/isopattern.Rd | 4 +++-
man/vdetect.Rd | 4 +++-
src/main.c | 5 -----
12 files changed, 82 insertions(+), 68 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-21 0.8-0
2013-06-04 0.7-0
2012-03-20 0.6-5
2009-11-26 0.6-3
2009-04-15 0.6-2
2008-11-03 0.6-1
2008-05-14 0.5-1
Title: Robust periodogram methods for irregularly sampled time series
and robust periodicity detection methods
Diff between RobPer versions 1.0 dated 2013-10-01 and 1.1 dated 2014-06-24
Description: Package to calculate periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit. Artificial light curves can be generated using the function tsgen. For more details see Thieler, Fried and Rathjens (2013).
Author: Anita M. Thieler, Jonathan Rathjens and Roland Fried, with contributions from Brenton R. Clarke, Uwe Ligges, Matias Salibian-Barrera, Gert Willems and Victor Yohai
Maintainer: Jonathan Rathjens
RobPer-1.0/RobPer/R/CvMbeta.R |only
RobPer-1.0/RobPer/R/Mscale.R |only
RobPer-1.0/RobPer/R/WtellerOpt.R |only
RobPer-1.0/RobPer/R/f.w.R |only
RobPer-1.0/RobPer/R/fwOpt.R |only
RobPer-1.0/RobPer/R/is.wholenumber.R |only
RobPer-1.0/RobPer/R/loss.S.R |only
RobPer-1.0/RobPer/R/our.solve.R |only
RobPer-1.0/RobPer/R/psiOpt.R |only
RobPer-1.0/RobPer/R/psixOpt.R |only
RobPer-1.0/RobPer/R/rho.R |only
RobPer-1.0/RobPer/R/rhoOpt.R |only
RobPer-1.0/RobPer/R/scale1.R |only
RobPer-1.0/RobPer/R/stepsampler.R |only
RobPer-1.0/RobPer/man/RobPer-package.Rd |only
RobPer-1.1/RobPer/DESCRIPTION | 17 -
RobPer-1.1/RobPer/MD5 | 109 ++++---
RobPer-1.1/RobPer/NAMESPACE | 3
RobPer-1.1/RobPer/R/FastS.R | 253 +++++++++--------
RobPer-1.1/RobPer/R/FastTau.R | 404 ++++++++++++++-------------
RobPer-1.1/RobPer/R/IRWLS.R | 44 +--
RobPer-1.1/RobPer/R/IWLSiteration.R | 109 ++++---
RobPer-1.1/RobPer/R/RobPer.R | 467 ++++++++++++++++----------------
RobPer-1.1/RobPer/R/TK95.R | 36 +-
RobPer-1.1/RobPer/R/TK95_uneq.R | 33 +-
RobPer-1.1/RobPer/R/Xgen.R | 100 +++---
RobPer-1.1/RobPer/R/betaCvMfit.R | 59 ++--
RobPer-1.1/RobPer/R/checkbest.R | 75 ++---
RobPer-1.1/RobPer/R/disturber.R | 25 -
RobPer-1.1/RobPer/R/lc_noise.R | 50 +--
RobPer-1.1/RobPer/R/re.s.R | 119 ++++----
RobPer-1.1/RobPer/R/sampler.R | 58 ++-
RobPer-1.1/RobPer/R/signalgen.R | 37 +-
RobPer-1.1/RobPer/R/singlePerM.R | 112 ++++---
RobPer-1.1/RobPer/R/singlePernotM.R | 199 +++++++------
RobPer-1.1/RobPer/R/tsgen.R | 60 +---
RobPer-1.1/RobPer/build |only
RobPer-1.1/RobPer/inst/doc |only
RobPer-1.1/RobPer/man/FastS.Rd | 6
RobPer-1.1/RobPer/man/FastTau.Rd | 24 -
RobPer-1.1/RobPer/man/RobPer-package.rd |only
RobPer-1.1/RobPer/man/RobPer.Rd | 32 +-
RobPer-1.1/RobPer/man/TK95.Rd | 7
RobPer-1.1/RobPer/man/TK95_uneq.Rd | 8
RobPer-1.1/RobPer/man/Xgen.Rd | 7
RobPer-1.1/RobPer/man/betaCvMfit.Rd | 5
RobPer-1.1/RobPer/man/lc_noise.Rd | 6
RobPer-1.1/RobPer/man/sampler.Rd | 2
RobPer-1.1/RobPer/man/signalgen.Rd | 2
RobPer-1.1/RobPer/man/tsgen.Rd | 61 +---
RobPer-1.1/RobPer/tests |only
RobPer-1.1/RobPer/vignettes |only
52 files changed, 1363 insertions(+), 1166 deletions(-)
Title: Gaussian Processes Modeling
Diff between GPfit versions 0.1-0 dated 2012-08-09 and 0.2-0 dated 2014-06-24
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld, Hugh Chipman, Pritam Ranjan
Maintainer: Hugh Chipman
DESCRIPTION | 16 +++----
MD5 | 34 +++++++-------
NAMESPACE | 2
R/GP_deviance.R | 16 ++-----
R/GP_fit.R | 86 ++++++++++++++++++++++++++++++-------
R/corr_matrix.R | 44 ++++++++++++++-----
R/dev_wrapper.R | 4 -
R/plot.GP.R | 22 +++++----
R/predict.GP.R | 116 ++++++++++++++++++++++++++++++++++++++++++---------
R/print.GP.R | 6 ++
man/GP_deviance.Rd | 19 +++++---
man/GP_fit.Rd | 43 +++++++++++++-----
man/GPfit-package.Rd | 25 +++++-----
man/corr_matrix.Rd | 87 +++++++++++++++++++++++++++++---------
man/plot.GP.Rd | 31 ++++++++-----
man/predict.GP.Rd | 32 ++++++++++----
man/print.GP.Rd | 7 ++-
man/summary.GP.Rd | 9 ++-
18 files changed, 428 insertions(+), 171 deletions(-)
Title: Multivariate partitioning
Diff between mvpart versions 1.6-1 dated 2013-04-19 and 1.6-2 dated 2014-06-24
Description: Multivariate regression trees
Author: rpart by Terry M Therneau and Beth Atkinson
Maintainer: Glenn De'ath
mvpart-1.6-1/mvpart/Readme |only
mvpart-1.6-2/mvpart/Changelog | 29 +++++++++++++++++++++
mvpart-1.6-2/mvpart/DESCRIPTION | 19 ++++++-------
mvpart-1.6-2/mvpart/MD5 | 19 ++++++-------
mvpart-1.6-2/mvpart/R/rpart.exp.R | 44 ++++++++++++++++----------------
mvpart-1.6-2/mvpart/man/cmds.diss.Rd | 3 +-
mvpart-1.6-2/mvpart/man/labels.rpart.Rd | 37 ++++++++++++++------------
mvpart-1.6-2/mvpart/man/mvpart.Rd | 3 +-
mvpart-1.6-2/mvpart/man/plotcp.Rd | 31 +++++++++++-----------
mvpart-1.6-2/mvpart/man/spider.Rd | 31 ++++++++--------------
mvpart-1.6-2/mvpart/src/xval.c | 4 +-
11 files changed, 122 insertions(+), 98 deletions(-)
Title: A Multiscale Test of Spatial Stationarity for LS2W processes
Diff between LS2Wstat versions 2.0-2 dated 2014-06-18 and 2.0-3 dated 2014-06-24
Description: Wavelet-based methods for testing stationarity and quadtree segmenting of images
Author: Sarah Taylor [aut], Matt Nunes [aut, cre], Idris Eckley [ctb, ths]
Maintainer: Matt Nunes
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
R/zzz.R | 1 +
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Classical Goodness-of-Fit Tests for Univariate Distributions
Diff between goftest versions 1.0-1 dated 2014-06-09 and 1.0-2 dated 2014-06-24
Description: Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit
for continuous univariate distributions, using
efficient algorithms.
Author: Julian Faraway [aut],
George Marsaglia [aut],
John Marsaglia [aut],
Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley
DESCRIPTION | 10 ++--
MD5 | 15 ++++--
NAMESPACE | 1
R/RCS/andarl.R,v | 117 ++++++++++++++++++++++++++++++++++++++++++++--------
R/RCS/cvmtest.R,v | 85 ++++++++++++++++++++++++++++++++-----
R/RCS/recog.R,v |only
R/andarl.R | 26 ++++++++---
R/cvmtest.R | 26 ++++++++---
R/recog.R |only
man/recogniseCdf.Rd |only
10 files changed, 230 insertions(+), 50 deletions(-)