Title: Functions for updating and installing a new version of R and
other software - from R
Diff between installr versions 0.9 dated 2013-03-29 and 0.9.2 dated 2013-05-16
Description: The 'installr' package aims at making the process of
updating R on Windows as easy as possible. Also, the package
contains a (growing) set of functions for allowing users to
install new software (on Windows OS) using R. By simply running
the installr() function, the user can easily select (via a GUI
interface) a software to install. There are also dedicated
functions for installing each software, such as: updateR(),
install.Rtools(), install.pandoc(), and many more. While for
Linux users, the installation process of new software may be
just running a short line of code, for the regular Windows user
it often includes browsing online, finding the latest version,
downloading it, running the installer, and deleting the
installation file. All of these steps are automatically done
using functions in this package.
Author: Tal Galili
Maintainer: Tal Galili
DESCRIPTION | 13 +
MD5 | 54 ++++----
NAMESPACE | 4
NEWS | 69 ++++++++--
R/install.r | 220 +++++++++++++++++++++++++++++----
R/os.manage.r | 24 ++-
R/updateR.r | 149 ++++++++++++++++++++--
R/zzz.r | 20 +--
README.md | 8 -
man/ask.user.for.a.row.Rd | 7 -
man/ask.user.yn.question.Rd | 12 +
man/browse.latest.R.NEWS.Rd |only
man/checkMD5sums2.Rd |only
man/copy.packages.between.libraries.Rd | 11 +
man/cranometer.Rd |only
man/file.name.from.url.Rd | 3
man/get.installed.R.folders.Rd | 12 +
man/install.GraphicsMagick.Rd | 7 -
man/install.ImageMagick.Rd | 5
man/install.Rtools.Rd | 8 -
man/install.URL.Rd | 4
man/install.npptor.Rd | 7 -
man/install.pandoc.Rd | 8 -
man/os.hibernate.Rd | 4
man/os.lock.Rd | 4
man/os.manage.Rd | 7 -
man/os.shutdown.Rd | 5
man/os.sleep.Rd | 4
man/require2.Rd |only
man/updateR.Rd | 17 ++
30 files changed, 553 insertions(+), 133 deletions(-)
Title: Functions for optimal matching
Diff between optmatch versions 0.8-1 dated 2013-01-03 and 0.8-3 dated 2013-05-16
Description: Functions for optimal matching, including full matching
Author: Ben B. Hansen
Maintainer: Mark M. Fredrickson
optmatch-0.8-1/optmatch/R/pscore.dist.R |only
optmatch-0.8-1/optmatch/checkoutput.txt |only
optmatch-0.8-1/optmatch/tmp.txt |only
optmatch-0.8-1/optmatch/vignettes |only
optmatch-0.8-3/optmatch/DESCRIPTION | 35 -
optmatch-0.8-3/optmatch/MD5 | 77 +--
optmatch-0.8-3/optmatch/NAMESPACE | 7
optmatch-0.8-3/optmatch/NEWS | 24 +
optmatch-0.8-3/optmatch/R/InfinitySparseMatrix.R | 43 +-
optmatch-0.8-3/optmatch/R/boxplot-methods.R |only
optmatch-0.8-3/optmatch/R/caliper.R | 5
optmatch-0.8-3/optmatch/R/deprecated.R |only
optmatch-0.8-3/optmatch/R/fill.NAs.R | 4
optmatch-0.8-3/optmatch/R/fullmatch.R | 4
optmatch-0.8-3/optmatch/R/makedist.R | 14
optmatch-0.8-3/optmatch/R/match_on.R | 193 ++++++----
optmatch-0.8-3/optmatch/R/matched.R | 4
optmatch-0.8-3/optmatch/R/mdist.R | 45 ++
optmatch-0.8-3/optmatch/R/pairmatch.R | 5
optmatch-0.8-3/optmatch/R/summary.optmatch.R | 2
optmatch-0.8-3/optmatch/bigdatatest.R |only
optmatch-0.8-3/optmatch/data/plantdist.rda |binary
optmatch-0.8-3/optmatch/debug_bad_case.rda |only
optmatch-0.8-3/optmatch/debug_no_within.rda |only
optmatch-0.8-3/optmatch/inst/examples/caliper.R | 18
optmatch-0.8-3/optmatch/inst/examples/makeInfinitySparseMatrix.R | 7
optmatch-0.8-3/optmatch/inst/examples/match_on.R | 7
optmatch-0.8-3/optmatch/inst/tests/test.InfinitySparseMatrix.R | 8
optmatch-0.8-3/optmatch/inst/tests/test.caliper.R | 8
optmatch-0.8-3/optmatch/inst/tests/test.fullmatch.R | 15
optmatch-0.8-3/optmatch/inst/tests/test.match_on.R | 56 ++
optmatch-0.8-3/optmatch/man/caliper-methods.Rd | 20 -
optmatch-0.8-3/optmatch/man/exactMatch.Rd | 3
optmatch-0.8-3/optmatch/man/fill.NAs.rd | 26 +
optmatch-0.8-3/optmatch/man/fullmatch.Rd | 4
optmatch-0.8-3/optmatch/man/makeInfinitySparseMatrix.Rd | 7
optmatch-0.8-3/optmatch/man/match_on-methods.Rd | 142 +++++--
optmatch-0.8-3/optmatch/man/optmatch-defunct.Rd |only
optmatch-0.8-3/optmatch/man/pairmatch.Rd | 4
optmatch-0.8-3/optmatch/src/mahalanobisHelper.c |only
optmatch-0.8-3/optmatch/src/subsetInfSparseMatrix.c |only
optmatch-0.8-3/optmatch/tests/mdist.R | 17
optmatch-0.8-3/optmatch/tests/mdist.Rout.save | 23 -
43 files changed, 594 insertions(+), 233 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.6.6 dated 2013-04-05 and 1.6.8 dated 2013-05-16
Description: The package dlnm contains functions to specify and run
distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 10 +++++-----
MD5 | 29 +++++++++++++++--------------
R/crossreduce.R | 2 +-
R/summary.crossreduce.R | 1 +
inst/CITATION | 35 ++---------------------------------
inst/ChangeLog | 12 ++++++++++++
inst/doc/dlnmOverview.R |only
inst/doc/dlnmOverview.Rnw | 2 +-
inst/doc/dlnmOverview.pdf |binary
man/chicagoNMMAPS.Rd | 4 ++--
man/crossbasis.Rd | 3 +--
man/crosspred.Rd | 2 +-
man/crossreduce.Rd | 3 +--
man/dlnm-package.Rd | 2 +-
man/onebasis.Rd | 3 +--
man/plot.crossreduce.Rd | 2 +-
16 files changed, 45 insertions(+), 65 deletions(-)
Title: genome-wide SNP association analysis
Diff between GenABEL versions 1.7-4 dated 2013-02-23 and 1.7-6 dated 2013-05-16
Description: a package for genome-wide association analysis between
quantitative or binary traits and single-nucleotide
polymorphisms (SNPs).
Author: GenABEL project developers
Maintainer: Yurii Aulchenko
CHANGES.LOG | 576 +++++++++++++++++++++--------------------
DESCRIPTION | 10
MD5 | 88 +++---
R/ccfast.R | 2
R/ccfast.new.R | 2
R/cocohet.R | 389 ++++++++++++++-------------
R/egscore.R | 68 ++++
R/export.plink.R | 144 ++++++----
R/hom.R | 79 +++++
R/ibs.R | 19 -
R/load.gwaa.data.R | 2
R/polygenic.R | 9
R/qtscore.R | 2
R/snp.names.R | 2
R/zzz.R | 4
inst/doc/GenABEL-tutorial.pdf |binary
inst/unitTests/runit.exports.R | 18 +
man/GenABEL.Rd | 2
man/catable.Rd | 3
man/ccfast.Rd | 3
man/check.marker-class.Rd | 6
man/check.marker.Rd | 13
man/cocohet.Rd | 118 +++++---
man/convert.snp.affymetrix.Rd | 3
man/convert.snp.mach.Rd | 3
man/egscore.Rd | 156 ++++++-----
man/egscore.old.Rd | 3
man/emp.qtscore.Rd | 4
man/export.merlin.Rd | 7
man/export.plink.Rd | 2
man/hom.Rd | 161 ++++++-----
man/hom.old.Rd | 3
man/ibs.Rd | 19 -
man/ibs.old.Rd | 3
man/merge.snp.data.Rd | 3
man/mmscore.Rd | 3
man/npsubtreated.Rd | 9
man/plot.check.marker.Rd | 3
man/qtscore.Rd | 2
man/scan.haplo.2D.Rd | 3
man/scan.haplo.Rd | 3
man/snp.subset.Rd | 3
man/srdta.Rd | 3
src/export_plink.cpp | 14
src/frutil.cpp | 1
45 files changed, 1166 insertions(+), 804 deletions(-)
Title: Flexible writing of snpStats objects to flat files
Diff between snpStatsWriter versions 1.0.2 dated 2013-01-28 and 1.5-1 dated 2013-05-16
More information about snpStatsWriter at CRAN
Description: Write snpStats objects to disk in formats suitable for
reading by snphap, phase, mach, IMPUTE, beagle, and (almost)
anything else that expects a rectangular format.
Author: Chris Wallace
Maintainer: Chris Wallace
ChangeLog | 16 ++++++++++++++++
DESCRIPTION | 11 +++++++----
MD5 | 15 ++++++++++-----
NAMESPACE | 1 +
R/write.R | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
README.md |only
inst |only
man/write.snphap.Rd |only
src/writers.c | 12 ++++++------
9 files changed, 88 insertions(+), 15 deletions(-)
Permanent link
Title: Visualizing the performance of scoring classifiers.
Diff between ROCR versions 1.0-4 dated 2009-12-14 and 1.0-5 dated 2013-05-16
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different
cross-validation or bootstrapping runs can be averaged by
different methods, and standard deviations, standard errors or
box plots can be used to visualize the variability across the
runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot
can be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.
Author: Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
Maintainer: Tobias Sing
ROCR-1.0-4/ROCR/CITATION |only
ROCR-1.0-4/ROCR/LICENCE |only
ROCR-1.0-5/ROCR/DESCRIPTION | 15 ++++++++-------
ROCR-1.0-5/ROCR/MD5 |only
ROCR-1.0-5/ROCR/NAMESPACE |only
ROCR-1.0-5/ROCR/NEWS | 5 +++++
ROCR-1.0-5/ROCR/R/zzz.R | 18 +++++++++---------
ROCR-1.0-5/ROCR/README | 10 ++++++++++
ROCR-1.0-5/ROCR/data/ROCR.hiv.rda |binary
ROCR-1.0-5/ROCR/data/ROCR.simple.rda |binary
ROCR-1.0-5/ROCR/data/ROCR.xval.rda |binary
ROCR-1.0-5/ROCR/inst |only
12 files changed, 32 insertions(+), 16 deletions(-)
Title: Bayesian Estimation of Tumor Purity and Clonality
Diff between PurBayes versions 1.2 dated 2013-04-12 and 1.3 dated 2013-05-16
Description: PurBayes is an MCMC-based algorithm that uses
next-generation sequencing data to estimate tumor purity and
clonality for paired tumor-normal data.
Author: Nicholas B. Larson
Maintainer: Nicholas B. Larson
PurBayes-1.2/PurBayes/R/PurBayes.R |only
PurBayes-1.2/PurBayes/man/PB.plot.Rd |only
PurBayes-1.2/PurBayes/man/write.PB.Rd |only
PurBayes-1.3/PurBayes/DESCRIPTION | 8 ++++----
PurBayes-1.3/PurBayes/MD5 | 15 ++++++++-------
PurBayes-1.3/PurBayes/NAMESPACE | 12 ++++++------
PurBayes-1.3/PurBayes/R/PurBayes.r |only
PurBayes-1.3/PurBayes/man/PurBayes-package.Rd | 7 ++++---
PurBayes-1.3/PurBayes/man/PurBayes.Rd | 14 +++++++++-----
PurBayes-1.3/PurBayes/man/plot.PurBayes.Rd |only
PurBayes-1.3/PurBayes/man/print.summary.PurBayes.Rd |only
PurBayes-1.3/PurBayes/man/summary.PurBayes.Rd |only
12 files changed, 31 insertions(+), 25 deletions(-)
Title: Diagnostic and prognostic meta analysis (metamisc)
Diff between metamisc versions 0.0.4 dated 2013-01-21 and 0.1.0 dated 2013-05-16
Description: This package provides functions for diagnostic and
prognostic meta-analyses. It estimates univariate, bivariate
and multivariate models, and allows the aggregation of
previously published prediction models with new data.
Author: Thomas Debray
Maintainer: Thomas Debray
metamisc-0.0.4/metamisc/man/predict.uvmeta.Rd |only
metamisc-0.1.0/metamisc/DESCRIPTION | 17
metamisc-0.1.0/metamisc/MD5 | 36 -
metamisc-0.1.0/metamisc/NAMESPACE | 5
metamisc-0.1.0/metamisc/R/riley.r | 47 +-
metamisc-0.1.0/metamisc/R/uvmeta.r | 451 +++++++++++++-------
metamisc-0.1.0/metamisc/data/Collins.rda |only
metamisc-0.1.0/metamisc/data/Daniels.rda |binary
metamisc-0.1.0/metamisc/data/Kertai.rda |binary
metamisc-0.1.0/metamisc/data/Roberts.rda |binary
metamisc-0.1.0/metamisc/data/Scheidler.rda |binary
metamisc-0.1.0/metamisc/inst/model/uvmeta_fixef.bug | 3
metamisc-0.1.0/metamisc/inst/model/uvmeta_ranef.bug | 4
metamisc-0.1.0/metamisc/man/Collins.Rd |only
metamisc-0.1.0/metamisc/man/Daniels.Rd | 10
metamisc-0.1.0/metamisc/man/metamisc-package.Rd | 4
metamisc-0.1.0/metamisc/man/plot.riley.Rd | 6
metamisc-0.1.0/metamisc/man/rileyDA.Rd | 3
metamisc-0.1.0/metamisc/man/rileyES.Rd | 5
metamisc-0.1.0/metamisc/man/uvmeta-class.Rd |only
metamisc-0.1.0/metamisc/man/uvmeta.Rd | 45 +
21 files changed, 410 insertions(+), 226 deletions(-)
Title: Complex survey structural equation modeling (SEM)
Diff between lavaan.survey versions 0.7 dated 2013-02-07 and 0.8 dated 2013-05-16
Description: Fit structural equation models (SEM) including factor
analysis, multivariate regression models with latent variables
and many other latent variable models while correcting
estimates, standard errors, and chi-square-derived fit measures
for a complex sampling design. Incorporate clustering,
stratification, sampling weights, and finite population
corrections into a SEM analysis. Wrapper around packages
lavaan and survey.
Author: Daniel Oberski
Maintainer: Daniel Oberski
DESCRIPTION | 11 ++++++-----
MD5 | 7 ++++---
NAMESPACE | 1 +
R/lavaan.survey.R | 41 ++++++++++++++++++++++++++++++++++++++---
man/pval.pFsum.Rd |only
5 files changed, 49 insertions(+), 11 deletions(-)
Title: Model selection and multimodel inference based on (Q)AIC(c)
Diff between AICcmodavg versions 1.29 dated 2013-04-22 and 1.30 dated 2013-05-16
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also features functions to
conduct classic model averaging (multimodel inference) for a
given parameter of interest and predicted values, as well as a
shrinkage version of model averaging parameter estimates.
Other handy functions enable the computation of relative
variable importance, evidence ratios, and confidence sets for
the best model. The present version works with Cox regression
('coxph' class), linear models ('lm' class), generalized linear
models ('glm' class), linear models fit by generalized least
squares ('gls' class), linear mixed models ('lme' class),
generalized linear mixed models ('mer' class), multinomial and
ordinal logistic regressions ('multinom', 'polr', 'clm', and
'clmm' classes), robust regression models ('rlm' class),
nonlinear models ('nls' class), and nonlinear mixed models
('nlme' class). The package also supports various models
incorporating detection probabilities such as single-season
occupancy models ('unmarkedFitOccu' and 'unmarkedFitOccuFP
classes), multiple-season occupancy models ('unmarkedFitColExt'
class), single-season heterogeneity models ('unmarkedFitOccuRN'
class), single-season and multiple-season N-mixture models for
repeated counts ('unmarkedFitPCount' and 'unmarkedFitPCO'
classes, respectively), and distance sampling models
('unmarkedFitDS' and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
inst/NEWS | 6 ++++++
man/AICcmodavg-package.Rd | 4 ++--
man/extract.LL.Rd | 23 ++++++++++++++++-------
man/mb.gof.test.Rd | 3 ++-
man/modavg.effect.Rd | 3 ++-
man/modavg.shrink.Rd | 2 ++
man/predictSE.zip.Rd | 3 +++
9 files changed, 45 insertions(+), 23 deletions(-)
Title: ADI (average dominance index) and social network graphs with
dual directions
Diff between Dominance versions 0.9.9 dated 2013-05-07 and 0.9.11 dated 2013-05-16
Description: The package can calculate ADI (Average Dominance Index)
and can build social network graphs with dual directions, can
build a Music Notation Graph
Author: Knut Krueger, with contributions from Konstanze Krueger
Maintainer: Knut Krueger
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/ADI.R | 13 +++++++------
man/ADI.Rd | 3 ++-
man/musicnotation.Rd | 8 +++++---
man/sociogram.Rd | 3 ++-
6 files changed, 26 insertions(+), 21 deletions(-)
Title: DDalpha-Classifier
Diff between ddalpha versions 1.0.3 dated 2013-02-28 and 1.0.4 dated 2013-05-16
Description: Contains DDalpha-classifier and associated functions
Author: Oleksii Pokotylo, Pavlo Mozharovskyi
Maintainer: Oleksii Pokotylo
DESCRIPTION | 8 ++---
MD5 | 42 ++++++++++++++---------------
R/ddalpha-internal.r | 23 +++++++++++++---
R/ddalpha.classify.r | 63 +++++++++++++++++++++++++++++++-------------
R/ddalpha.train.r | 15 ++++++++++
R/depth.randomTukey.r | 9 ++++++
R/depth.space.randomTukey.r | 9 ++++++
R/depth.space.zonoid.r | 13 +++++++--
R/depth.zonoid.r | 10 ++++++
R/is.in.convex.r | 9 ++++++
man/depth.randomTukey.Rd | 2 -
src/AlphaProcedure.cpp | 13 +++++++++
src/AlphaProcedure.h | 13 +++++++++
src/DataStructures.h | 9 ++++++
src/Knn.cpp | 9 ++++++
src/Knn.h | 9 ++++++
src/TukeyDepth.cpp | 13 +++++++++
src/TukeyDepth.h | 13 +++++++++
src/ZonoidDepth.cpp | 55 +++++++++++++++++++++++++++++++++++++-
src/ZonoidDepth.h | 8 ++++-
src/ddalpha.cpp | 20 +++++++++++--
src/stdafx.h | 9 ++++++
22 files changed, 316 insertions(+), 58 deletions(-)
Title: Spatial analysis of animal track data
Diff between trip versions 1.1-12 dated 2012-11-06 and 1.1-14 dated 2013-05-16
Description: Functions for accessing and manipulating spatial data for
animal tracking. Filter for speed and create time spent plots
from animal track data.
Author: Michael Sumner[aut, cre], Sebastian Luque [ctb]
Maintainer: Michael D. Sumner
trip-1.1-12/trip/R/TimeOrderedRecords.R |only
trip-1.1-12/trip/R/oc.colors.R |only
trip-1.1-12/trip/R/tripFunctions.R |only
trip-1.1-12/trip/man/TimeOrderedRecords.Rd |only
trip-1.1-12/trip/man/as.SpatialLinesDataFrame.Rd |only
trip-1.1-12/trip/man/as.ltraj.Rd |only
trip-1.1-12/trip/man/as.ppp.Rd |only
trip-1.1-12/trip/man/readDiag.Rd |only
trip-1.1-12/trip/man/trip.Rd |only
trip-1.1-12/trip/man/trip.split.exact.Rd |only
trip-1.1-12/trip/man/tripTransform.Rd |only
trip-1.1-12/trip/man/virtuals.Rd |only
trip-1.1-14/trip/ChangeLog |only
trip-1.1-14/trip/DESCRIPTION | 24
trip-1.1-14/trip/MD5 | 78 +-
trip-1.1-14/trip/NAMESPACE | 147 ----
trip-1.1-14/trip/NEWS | 16
trip-1.1-14/trip/R/AllClass.R |only
trip-1.1-14/trip/R/AllGenerics.R |only
trip-1.1-14/trip/R/AllMethod.R |only
trip-1.1-14/trip/R/filter.penSS.R | 93 +-
trip-1.1-14/trip/R/oc.theme.R | 66 +
trip-1.1-14/trip/R/readDiag.R | 43 -
trip-1.1-14/trip/R/speedfilter.R | 167 +---
trip-1.1-14/trip/R/trackDistance.R | 91 +-
trip-1.1-14/trip/R/trip.R | 785 ++++++++++-------------
trip-1.1-14/trip/R/trip.split.R | 130 ++-
trip-1.1-14/trip/R/trip2other.R | 127 ---
trip-1.1-14/trip/R/tripGrid.R | 195 +----
trip-1.1-14/trip/TODO | 60 +
trip-1.1-14/trip/man/TimeOrderedRecords-class.Rd | 107 ++-
trip-1.1-14/trip/man/adjust.duplicateTimes.Rd | 72 +-
trip-1.1-14/trip/man/argos.sigma.Rd | 54 +
trip-1.1-14/trip/man/as.Other.Rd |only
trip-1.1-14/trip/man/as.trip.Rd |only
trip-1.1-14/trip/man/cut.trip.Rd |only
trip-1.1-14/trip/man/filter.penSS.Rd | 131 ++-
trip-1.1-14/trip/man/forceCompliance.Rd | 45 -
trip-1.1-14/trip/man/makeGridTopology.Rd | 43 -
trip-1.1-14/trip/man/oc.theme.Rd | 49 +
trip-1.1-14/trip/man/readArgos.Rd | 155 +++-
trip-1.1-14/trip/man/sepIdGaps.Rd | 75 +-
trip-1.1-14/trip/man/speedfilter.Rd | 112 ++-
trip-1.1-14/trip/man/trackDistance.Rd | 40 -
trip-1.1-14/trip/man/trip-accessors.Rd |only
trip-1.1-14/trip/man/trip-class.Rd | 269 +++++--
trip-1.1-14/trip/man/trip-deprecated.Rd |only
trip-1.1-14/trip/man/trip-internal.Rd | 42 -
trip-1.1-14/trip/man/trip-methods.Rd |only
trip-1.1-14/trip/man/tripGrid.Rd | 58 +
trip-1.1-14/trip/man/tripGrid.interp.Rd | 110 ++-
51 files changed, 1846 insertions(+), 1538 deletions(-)
Title: Visualization of spatial and spatio-temporal objects in Google
Earth
Diff between plotKML versions 0.3-4 dated 2013-04-18 and 0.3-5 dated 2013-05-16
Description: Writes sp-class, spacetime-class, raster-class and similar
spatial and spatio-temporal objects to KML following some basic
cartographic rules. Suitable for visualization of complete
analysis outputs.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan
Beaudette [ctb], Edzer Pebesma [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/layer.RasterBrick.R | 7 ++++++-
R/plotKML.sp.R | 16 ++++++++--------
man/gpxbtour.Rd | 9 ++++-----
man/layer.RasterBrick.Rd | 5 ++++-
man/layer.STTDF.Rd | 12 +++++++-----
man/layer.SoilProfileCollection.Rd | 20 +++++++++++---------
man/plotKML.Rd | 13 ++++++++-----
man/reproject.Rd | 19 +++++++++++--------
man/spMetadata.Rd | 22 ++++++++++++----------
man/vect2rast.Rd | 15 +++++++++------
12 files changed, 95 insertions(+), 73 deletions(-)
Title: Firth's bias reduced logistic regression
Diff between logistf versions 1.10 dated 2010-04-25 and 1.20 dated 2013-05-16
Description: Firth's bias reduced logistic regression approach with
penalized profile likelihood based confidence intervals for
parameter estimates.
Author: Georg Heinze
Maintainer: Georg Heinze
logistf-1.10/logistf/INDEX |only
logistf-1.10/logistf/R/logistf.fit.r |only
logistf-1.10/logistf/data/sex2.txt |only
logistf-1.10/logistf/data/sexagg.txt |only
logistf-1.10/logistf/man/logistfplot.Rd |only
logistf-1.10/logistf/man/logistpl.control.Rd |only
logistf-1.10/logistf/man/sexagg.Rd |only
logistf-1.20/logistf/DESCRIPTION | 21 -
logistf-1.20/logistf/MD5 |only
logistf-1.20/logistf/NAMESPACE | 24 +
logistf-1.20/logistf/R/CLIP.confint.r |only
logistf-1.20/logistf/R/CLIP.profile.r |only
logistf-1.20/logistf/R/PVR.confint.r |only
logistf-1.20/logistf/R/anova.logistf.r |only
logistf-1.20/logistf/R/cholLinpack.R |only
logistf-1.20/logistf/R/extractAIC.logistf.r |only
logistf-1.20/logistf/R/inverseLinpack.R |only
logistf-1.20/logistf/R/logistf.R | 350 ++------------------
logistf-1.20/logistf/R/logistf.control.R |only
logistf-1.20/logistf/R/logistf.fit.R |only
logistf-1.20/logistf/R/logistf.fit.old.R |only
logistf-1.20/logistf/R/logistf.pdf.R |only
logistf-1.20/logistf/R/logistftest.R |only
logistf-1.20/logistf/R/logistpl.R |only
logistf-1.20/logistf/R/logistpl.control.r |only
logistf-1.20/logistf/R/logistpl.old.R |only
logistf-1.20/logistf/R/plot.logistf.profile.r |only
logistf-1.20/logistf/R/pool.RR.r |only
logistf-1.20/logistf/R/print.logistf.R |only
logistf-1.20/logistf/R/print.logistftest.R |only
logistf-1.20/logistf/R/profile.logistf.r |only
logistf-1.20/logistf/R/summary.logistf.R |only
logistf-1.20/logistf/data/sex2.txt.gz |only
logistf-1.20/logistf/data/sexagg.txt.gz |only
logistf-1.20/logistf/man/CLIP.confint.Rd |only
logistf-1.20/logistf/man/CLIP.profile.Rd |only
logistf-1.20/logistf/man/PVR.confint.Rd |only
logistf-1.20/logistf/man/add1.logistf.Rd |only
logistf-1.20/logistf/man/anova.logistf.Rd |only
logistf-1.20/logistf/man/backward.Rd |only
logistf-1.20/logistf/man/is.logistf.Rd |only
logistf-1.20/logistf/man/logistf-package.Rd |only
logistf-1.20/logistf/man/logistf.Rd | 385 ++++++++++-------------
logistf-1.20/logistf/man/logistf.control.Rd | 19 -
logistf-1.20/logistf/man/logistftest.Rd | 49 +-
logistf-1.20/logistf/man/logistpl.control.rd |only
logistf-1.20/logistf/man/plot.logistf.profile.Rd |only
logistf-1.20/logistf/man/pool.RR.rd |only
logistf-1.20/logistf/man/print.logistf.Rd |only
logistf-1.20/logistf/man/print.logistftest.Rd |only
logistf-1.20/logistf/man/profile.logistf.Rd |only
logistf-1.20/logistf/man/sex2.Rd | 48 +-
logistf-1.20/logistf/man/summary.logistf.Rd |only
logistf-1.20/logistf/man/vcov.logistf.Rd |only
logistf-1.20/logistf/src |only
55 files changed, 319 insertions(+), 577 deletions(-)
Title: General Smoothing Splines
Diff between gss versions 2.0-13 dated 2013-03-09 and 2.0-14 dated 2013-05-16
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu
Maintainer: Chong Gu
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 33 +++++++++++++++++----------------
R/cdssden.R | 8 ++++----
R/mkran1.R |only
R/project.sscden.R | 19 ++++++++++++-------
R/project.sscden1.R | 46 ++++++++++++++++++++++++++++++----------------
R/project.ssden1.R | 3 ++-
R/project.sshzd1.R | 3 ++-
R/sscden.R | 28 ++++++++++++++++------------
R/sscden1.R | 26 ++++++++++++++------------
R/ssden.R | 16 ++++++++++------
R/ssden1.R | 16 ++++++++++------
man/drkpk.Rd | 6 ++++--
src/dnewton.f | 26 ++++++++++++++------------
src/ratfor/dnewton.r | 2 +-
src/ratfor/reg.r | 2 +-
src/reg.f | 26 ++++++++++++++------------
18 files changed, 161 insertions(+), 113 deletions(-)
Title: Spatial point patterns analysis
Diff between ads versions 1.2-11 dated 2012-07-19 and 1.2-13 dated 2013-05-16
Description: Perform first- and second-order multi-scale analyses
derived from Ripley's K-function, for univariate, multivariate
and marked mapped data in rectangular, circular or irregular
shaped sampling windows, with test of statistical significance
based on Monte Carlo simulations.
Author: R. Pelissier and F. Goreaud
Maintainer: Raphael Pelissier
DESCRIPTION | 11 ++---
MD5 | 24 +++++------
R/fads.R | 25 +++++++----
R/spp.R | 10 ++++
data/BPoirier.rda |binary
data/Couepia.rda |binary
man/plot.spp.Rd | 9 ++--
man/spp.Rd | 6 --
man/swin.Rd | 7 ---
man/triangulate.Rd | 4 -
src/Zlibs.c | 114 ++++++++++++++++++++++++++++-------------------------
src/triangulate.c | 32 +++++++-------
src/triangulate.h | 2
13 files changed, 132 insertions(+), 112 deletions(-)
Title: spsmooth: An Extension Package for 'mgcv'.
Diff between spsmooth versions 1.0-1 dated 2013-03-22 and 1.1-0 dated 2013-05-16
Description: Produces Slepian smoother basis objects for use in
Generalized Additive Models, as estimated by package:mgcv.
Author: Wesley Burr, with contributions from Karim Rahim
Maintainer: Wesley Burr
spsmooth-1.0-1/spsmooth/LICENSE |only
spsmooth-1.1-0/spsmooth/DESCRIPTION | 13 ++---
spsmooth-1.1-0/spsmooth/MD5 | 10 ++--
spsmooth-1.1-0/spsmooth/R/spmgcv.R | 57 ++++++++++++++++--------
spsmooth-1.1-0/spsmooth/gnugpl2.txt |only
spsmooth-1.1-0/spsmooth/man/chicago.Rd | 11 ++--
spsmooth-1.1-0/spsmooth/man/spsmooth-package.Rd | 4 -
7 files changed, 59 insertions(+), 36 deletions(-)
Title: Accelerated Failure Time Model with Generalized Estimating
Equations
Diff between aftgee versions 0.3-14 dated 2013-01-10 and 0.3-20 dated 2013-05-16
Description: This package features both rank-based estimates and least
square estimates to the Accelerated Failure Time (AFT) model.
For rank-based estimation, it provides approaches that include
the computationally efficient Gehan's weight and the general's
weight such as the logrank weight. For the least square
estimation, the estimating equation is solved with Generalized
Estimating Equations (GEE). Moreover, in multivariate cases,
the dependence working correlation structure can be specified
in GEE's setting.
Author: Sy Han (Steven) Chiou, Sangwook Kang, Jun Yan
Maintainer: Sy Han (Steven) Chiou
ChangeLog | 12 +
DESCRIPTION | 15 +
MD5 | 20 +-
NAMESPACE | 4
R/aftgee.R | 17 +-
R/smoothRR.R | 382 ++++++++++++++++++++++++++++++++++++++------------
man/aftgee-package.Rd | 16 +-
man/aftgee.Rd | 4
man/aftgee.control.Rd | 6
man/smoothrr.Rd | 35 ++--
src/aftgee.c | 130 ++++++++++++++++-
11 files changed, 492 insertions(+), 149 deletions(-)