Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.26-13 dated 2012-11-27 and 1.26-14 dated 2012-11-27
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/util.R | 4 +---
README.txt | 2 +-
inst/INSTALL_ME.txt | 48 ++++++++++++++++++++++++------------------------
inst/README.txt | 2 +-
inst/STATUS.txt | 2 +-
7 files changed, 37 insertions(+), 39 deletions(-)
More information about robustloggamma at CRAN
Permanent link
Title: Model-Based Boosting
Diff between mboost versions 2.1-3 dated 2012-09-27 and 2.2-0 dated 2012-11-27
Description: Functional gradient descent algorithm (boosting) for
optimizing general risk functions utilizing component-wise
(penalised) least squares estimates or regression trees as
base-learners for fitting generalized linear, additive and
interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre], Peter Buehlmann [aut], Thomas Kneib
[aut], Matthias Schmid [aut], Benjamin Hofner [aut]
Maintainer: Torsten Hothorn
mboost-2.1-3/mboost/data/datalist |only
mboost-2.1-3/mboost/vignettes/figures |only
mboost-2.1-3/mboost/vignettes/mboost_illustrations.R |only
mboost-2.2-0/mboost/DESCRIPTION | 14
mboost-2.2-0/mboost/MD5 | 124
mboost-2.2-0/mboost/NAMESPACE | 2
mboost-2.2-0/mboost/NEWS | 28
mboost-2.2-0/mboost/R/AAA.R | 10
mboost-2.2-0/mboost/R/bkronecker.R | 8
mboost-2.2-0/mboost/R/bl.R | 68
mboost-2.2-0/mboost/R/bmono.R | 140
mboost-2.2-0/mboost/R/buser.R | 2
mboost-2.2-0/mboost/R/crossvalidation.R | 3
mboost-2.2-0/mboost/R/family.R | 66
mboost-2.2-0/mboost/R/inference.R | 4
mboost-2.2-0/mboost/R/mboost.R | 2
mboost-2.2-0/mboost/R/plot.R | 20
mboost-2.2-0/mboost/data/Westbc.rda |binary
mboost-2.2-0/mboost/data/birds.rda |binary
mboost-2.2-0/mboost/data/bodyfat.rda |binary
mboost-2.2-0/mboost/data/wpbc.rda |binary
mboost-2.2-0/mboost/inst/AML_Bullinger.Rda |only
mboost-2.2-0/mboost/inst/CHANGES | 28
mboost-2.2-0/mboost/inst/doc/SurvivalEnsembles.Rnw | 46
mboost-2.2-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary
mboost-2.2-0/mboost/inst/doc/mboost.Rnw | 4
mboost-2.2-0/mboost/inst/doc/mboost.pdf |binary
mboost-2.2-0/mboost/inst/doc/mboost_illustrations.Rnw | 248 -
mboost-2.2-0/mboost/inst/doc/mboost_illustrations.pdf |binary
mboost-2.2-0/mboost/inst/doc/mboost_tutorial.Rnw | 10
mboost-2.2-0/mboost/inst/doc/mboost_tutorial.pdf |binary
mboost-2.2-0/mboost/inst/readAML_Bullinger.R |only
mboost-2.2-0/mboost/man/FP.Rd | 2
mboost-2.2-0/mboost/man/Family.Rd | 15
mboost-2.2-0/mboost/man/baselearners.Rd | 66
mboost-2.2-0/mboost/man/blackboost.Rd | 6
mboost-2.2-0/mboost/man/bodyfat.Rd | 10
mboost-2.2-0/mboost/man/cvrisk.Rd | 37
mboost-2.2-0/mboost/man/glmboost.Rd | 2
mboost-2.2-0/mboost/man/mboost.Rd | 2
mboost-2.2-0/mboost/man/mboost_package.Rd | 6
mboost-2.2-0/mboost/man/stabsel.Rd | 18
mboost-2.2-0/mboost/man/wpbc.Rd | 12
mboost-2.2-0/mboost/tests/Examples/mboost-Ex.Rout.save | 2000 ++++++-----
mboost-2.2-0/mboost/tests/birds_Biometrics.Rout.save | 145
mboost-2.2-0/mboost/tests/bugfixes.Rout.save | 45
mboost-2.2-0/mboost/tests/regtest-baselearner.R | 16
mboost-2.2-0/mboost/tests/regtest-baselearner.Rout.save | 114
mboost-2.2-0/mboost/tests/regtest-blackboost.Rout.save | 11
mboost-2.2-0/mboost/tests/regtest-family.R | 39
mboost-2.2-0/mboost/tests/regtest-family.Rout.save | 86
mboost-2.2-0/mboost/tests/regtest-gamboost.Rout.save | 67
mboost-2.2-0/mboost/tests/regtest-glmboost.Rout.save | 11
mboost-2.2-0/mboost/tests/regtest-hatmatrix.Rout.save | 11
mboost-2.2-0/mboost/vignettes/SurvivalEnsembles.Rnw | 46
mboost-2.2-0/mboost/vignettes/SurvivalEnsembles.Rout.save | 73
mboost-2.2-0/mboost/vignettes/mboost.Rnw | 4
mboost-2.2-0/mboost/vignettes/mboost.Rout.save | 45
mboost-2.2-0/mboost/vignettes/mboost_illustrations.Rnw | 248 -
mboost-2.2-0/mboost/vignettes/mboost_illustrations.Rout.save | 142
mboost-2.2-0/mboost/vignettes/mboost_tutorial.Rnw | 10
mboost-2.2-0/mboost/vignettes/mboost_tutorial.Rout.save | 440 +-
mboost-2.2-0/mboost/vignettes/setup.R | 2
63 files changed, 2612 insertions(+), 1946 deletions(-)
Title: minerva: Maximal Information-Based Nonparametric Exploration R
package for Variable Analysis
Diff between minerva versions 1.1 dated 2012-10-15 and 1.2 dated 2012-11-27
Description: R wrapper for cmine implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family)
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide
Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman
[ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi
DESCRIPTION | 10 +-
MD5 | 24 ++++-
NAMESPACE | 1
NEWS | 3
R/mine.R | 77 ++++++++++---------
man/mine.Rd | 39 ++++++---
man/minerva-package.Rd | 6 -
missfont.log |only
src/mine_interface.c | 54 ++++++++++---
tests/MINE.jar |only
tests/MINEJAVA.sh |only
tests/Spellman.csv |only
tests/Spellman.csv,0-vs-1,cv=0.0,B=n^0.6,Results.csv |only
tests/Spellman.csv,0-vs-1,cv=0.0,B=n^0.6,Status.txt |only
tests/Spellman.csv,mv=0,cv=0.0,B=n^0.6,Results.csv |only
tests/Spellman.csv,mv=0,cv=0.0,B=n^0.6,Status.txt |only
tests/hs_err_pid16149.log |only
tests/valgrind.out |only
18 files changed, 141 insertions(+), 73 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-17 0.9.6
2012-09-23 0.9.5
2012-08-22 0.9.4
2012-08-13 0.9.3
2012-08-06 0.9.2
2012-07-29 0.9.1
Title: R and Hive
Diff between RHive versions 0.0-6 dated 2012-06-05 and 0.0-7 dated 2012-11-27
Description: RHive is an R extension facilitating distributed computing
via HIVE query. It provides an easy to use HQL like SQL and R
objects and functions in HQL.
Author: NexR
Maintainer: tim.yang
RHive-0.0-6/RHive/inst/javasrc/build |only
RHive-0.0-7/RHive/DESCRIPTION | 8 +--
RHive-0.0-7/RHive/MD5 | 65 ++---------------------------
RHive-0.0-7/RHive/R/rhive.R | 66 ++++++++++++++++++++----------
RHive-0.0-7/RHive/inst/java/rhive_udf.jar |binary
RHive-0.0-7/RHive/inst/javasrc/build.num | 4 -
RHive-0.0-7/RHive/man/rhive-connect.Rd | 5 +-
7 files changed, 60 insertions(+), 88 deletions(-)
Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.25-15 dated 2012-08-14 and 1.26-13 dated 2012-11-27
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 8 +-
MD5 | 56 ++++++++--------
R/add_threshold.R | 10 +-
R/effectplot.R | 10 +-
R/est.rf.R | 8 +-
R/fitqtl.R | 5 +
R/mqmaugment.R | 10 ++
R/mqmscan.R | 24 +++----
R/phyloqtl_scan.R | 73 +++++++++++++++------
R/scanone.R | 13 ++-
R/scantwo.R | 11 ++-
R/summary.scanone.R | 4 -
R/util.R | 135 ++++++++++++++++++++++++----------------
inst/INSTALL_ME.txt | 16 ++--
inst/STATUS.txt | 57 ++++++++++++++++
inst/TODO.txt | 17 -----
inst/docs/Sources/rqtltour2.tex | 20 +++++
inst/docs/rqtltour2.R | 5 +
inst/docs/rqtltour2.pdf |binary
man/c.scantwoperm.Rd | 8 +-
man/locateXO.Rd | 3
man/multitrait.Rd | 4 -
man/qtl-internal.Rd | 3
man/read.cross.Rd | 18 +++--
man/subset.cross.Rd | 39 +++++------
man/summary.scantwoperm.Rd | 5 -
man/xaxisloc.scanone.Rd | 2
src/util.c | 25 +++++--
src/util.h | 10 +-
29 files changed, 382 insertions(+), 217 deletions(-)
Title: Time series costationarity determination
Diff between costat versions 2.0 dated 2012-11-27 and 2.1 dated 2012-11-27
Description: Contains functions that can determine whether a time
series is second-order stationary or not (and hence evidence
for locally stationarity). Given two non-stationary series
(i.e. locally stationary series) this package can then
discover time-varying linear combinations that are second-order
stationary.
Author: Guy Nason, Alessandro Cardinali
Maintainer: Guy Nason
DESCRIPTION | 11 ++++++-----
MD5 | 14 +++++++-------
R/BootTOS.R | 2 +-
R/findstysols.R | 2 +-
R/getpvals.R | 2 +-
man/BootTOS.Rd | 4 ++--
man/findstysols.Rd | 2 +-
man/getpvals.Rd | 2 +-
8 files changed, 20 insertions(+), 19 deletions(-)
Title: A GTK GUI for fitting and comparing GLM and GLMM in R
Diff between R2STATS versions 0.68-30 dated 2012-11-22 and 0.68-31 dated 2012-11-27
Description: R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing
GLM or GLMM (based on Douglas Bates' lme4 package) in R. It is
designed to make comparisons between numerous models easy, both
numerically and graphically, which may be useful for teaching.
Relevant plots are automatically produced for each model
family. R2STATS is *not* a generic graphical interface for R,
but a GUI for statistical modelling in a model comparison
approach.
Author: Yvonnick Noel, University of Brittany, France
Maintainer: Yvonnick Noel
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 5 +++++
R/r2sInterface.R | 5 ++++-
4 files changed, 16 insertions(+), 8 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between metrumrg versions 5.26 dated 2012-11-24 and 5.27 dated 2012-11-27
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of
detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma
metrumrg-5.26/metrumrg/inst/example/project/nonmem/ctl/template.pmn |only
metrumrg-5.27/metrumrg/DESCRIPTION | 8 ++++----
metrumrg-5.27/metrumrg/MD5 | 10 +++++-----
metrumrg-5.27/metrumrg/R/runNonmem.R | 8 ++++----
metrumrg-5.27/metrumrg/inst/example/project/nonmem/ctl/template.pnm |only
metrumrg-5.27/metrumrg/man/NONR.Rd | 4 ++--
metrumrg-5.27/metrumrg/man/metrumrg-package.Rd | 4 ++--
7 files changed, 17 insertions(+), 17 deletions(-)
Title: General Frailty models using a semi_parametric penalized
likelihood estimation or a parametric estimation
Diff between frailtypack versions 2.2-26 dated 2012-10-19 and 2.2-27 dated 2012-11-27
Description: Frailtypack now fits several classes of frailty models
using a penalized likelihood estimation on the hazard function
but also a parametric estimation. 1) A shared gamma frailty
model and Cox proportional hazard model. Clustered and
recurrent survival times can be studied (the
Andersen-Gill(1982) approach has been implemented for recurrent
events). An automatic choice of the smoothing parameter is
possible using an approximated cross-validation procedure. 2)
Additive frailty models for proportional hazard models with two
correlated random effects (intercept random effect with random
slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma
random effects. 4) Joint frailty models in the context of joint
modelling for recurrent events with terminal event for
clustered data or not. Prediction values are available. Left
truncated (not for Joint model), right-censored data,
interval-censored data (only for Cox proportional hazard and
shared frailty model) and strata (max=2) are allowed. The
package includes concordance measures for Cox proportional
hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
frailtypack-2.2-26/frailtypack/data/dataJoint.rda |only
frailtypack-2.2-26/frailtypack/data/dataJointClus.rda |only
frailtypack-2.2-26/frailtypack/man/dataJoint.Rd |only
frailtypack-2.2-26/frailtypack/man/dataJointClus.Rd |only
frailtypack-2.2-27/frailtypack/DESCRIPTION | 19
frailtypack-2.2-27/frailtypack/MD5 | 73 -
frailtypack-2.2-27/frailtypack/NAMESPACE | 1
frailtypack-2.2-27/frailtypack/NEWS | 13
frailtypack-2.2-27/frailtypack/R/additivePenal.R | 7
frailtypack-2.2-27/frailtypack/R/frailtyPenal.R | 235 ++-
frailtypack-2.2-27/frailtypack/R/num.id.R |only
frailtypack-2.2-27/frailtypack/R/print.additivePenal.R | 8
frailtypack-2.2-27/frailtypack/R/print.frailtyPenal.R | 5
frailtypack-2.2-27/frailtypack/R/print.jointPenal.R | 25
frailtypack-2.2-27/frailtypack/R/print.nestedPenal.R | 5
frailtypack-2.2-27/frailtypack/demo/frailtypack_nestedPenal.R | 2
frailtypack-2.2-27/frailtypack/man/JointfrailtyPenal.Rd | 94 -
frailtypack-2.2-27/frailtypack/man/NestedfrailtyPenal.Rd | 24
frailtypack-2.2-27/frailtypack/man/additivePenal.Rd | 22
frailtypack-2.2-27/frailtypack/man/frailtyPenal.Rd | 30
frailtypack-2.2-27/frailtypack/man/frailtypack-package.Rd | 18
frailtypack-2.2-27/frailtypack/man/hazard.Rd | 6
frailtypack-2.2-27/frailtypack/man/num.id.Rd |only
frailtypack-2.2-27/frailtypack/man/subcluster.Rd | 5
frailtypack-2.2-27/frailtypack/man/survival.Rd | 6
frailtypack-2.2-27/frailtypack/src/Adonnees.f90 |only
frailtypack-2.2-27/frailtypack/src/Aparameters.f90 | 23
frailtypack-2.2-27/frailtypack/src/aaOptim.f90 | 13
frailtypack-2.2-27/frailtypack/src/aaOptimres.f90 | 19
frailtypack-2.2-27/frailtypack/src/aaUseFunctionG.f90 |only
frailtypack-2.2-27/frailtypack/src/afuncpasres.f90 | 67 -
frailtypack-2.2-27/frailtypack/src/aresidusMartingale.f90 | 96 -
frailtypack-2.2-27/frailtypack/src/funcpaGcpm.f90 |only
frailtypack-2.2-27/frailtypack/src/funcpaGsplines.f90 |only
frailtypack-2.2-27/frailtypack/src/funcpaGweib.f90 |only
frailtypack-2.2-27/frailtypack/src/funcpajcpm.f90 | 6
frailtypack-2.2-27/frailtypack/src/funcpajsplines.f90 | 7
frailtypack-2.2-27/frailtypack/src/funcpajweib.f90 | 23
frailtypack-2.2-27/frailtypack/src/funcpancpm.f90 | 1
frailtypack-2.2-27/frailtypack/src/funcpansplines.f90 | 1
frailtypack-2.2-27/frailtypack/src/funcpanweib.f90 | 1
frailtypack-2.2-27/frailtypack/src/joint.f90 | 668 ++++++----
frailtypack-2.2-27/frailtypack/src/nested.f90 | 20
43 files changed, 1030 insertions(+), 513 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 3.25 dated 2012-09-11 and 4.00 dated 2012-11-27
Description: Methods and tools for displaying and analysing univariate
time series forecasts including exponential smoothing via state
space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 12 ++++++++
DESCRIPTION | 14 +++++----
MD5 | 69 ++++++++++++++++++++++++-----------------------
NAMESPACE | 10 +++++-
R/HoltWintersNew.R |only
R/arfima.R | 2 +
R/arima.R | 48 +++++++++++++++++---------------
R/bats.R | 5 +++
R/errors.R | 12 +++++++-
R/ets.R | 11 ++++---
R/etsforecast.R | 64 +++++++++++++++++++++----------------------
R/forecast.R | 27 +++++++++++++++++-
R/forecast2.R | 9 ++++--
R/forecastBATS.R | 13 ++++++--
R/forecastTBATS.R | 12 +++++---
R/lm.R | 9 ++++--
R/newarima2.R | 58 +++++++++++++++++++++++++++------------
R/nnetar.R |only
man/accuracy.Rd | 2 -
man/auto.arima.Rd | 2 -
man/bats.Rd | 3 +-
man/forecast.StructTS.Rd | 3 +-
man/forecast.lm.Rd | 7 ++--
man/forecast.stl.Rd | 10 ++++--
man/forecastplot.Rd | 5 +--
man/gold.Rd | 2 -
man/msts.Rd | 5 ++-
man/nnetar.Rd |only
man/seasonplot.Rd | 6 ++--
man/ses.Rd | 28 ++++++++++---------
man/simulate.Rd | 4 ++
man/spline.f.Rd | 6 ++--
man/tbats.Rd | 3 +-
man/ts.display.Rd | 4 +-
man/wineind.Rd | 2 -
man/woolyrnq.Rd | 2 -
src/calcBATS.h | 35 ++++++++++++++++++++++-
37 files changed, 329 insertions(+), 175 deletions(-)
Title: Time series costationarity determination
Diff between costat versions 1.1-1 dated 2010-08-31 and 2.0 dated 2012-11-27
Description: Contains functions that can determine whether a time
series is second-order stationary or not (and hence evidence
for locally stationarity). Given two non-stationary series
(i.e. locally stationary series) this package can then
discover time-varying linear combinations that are second-order
stationary.
Author: Guy Nason, Alessandro Cardinali
Maintainer: Guy Nason
costat-1.1-1/costat/R/COEFscale.R |only
costat-1.1-1/costat/R/CrossWP.R |only
costat-1.1-1/costat/R/crosslacv.R |only
costat-1.1-1/costat/R/ewcrossspec.R |only
costat-1.1-1/costat/R/myTOS.R |only
costat-1.1-1/costat/R/plottstosscan.R |only
costat-1.1-1/costat/R/tstosscan.R |only
costat-1.1-1/costat/data/x2.rda |only
costat-1.1-1/costat/data/y2.rda |only
costat-1.1-1/costat/man/COEFscale.Rd |only
costat-1.1-1/costat/man/CrossWP.Rd |only
costat-1.1-1/costat/man/crosslacv.Rd |only
costat-1.1-1/costat/man/ewcrossspec.Rd |only
costat-1.1-1/costat/man/myTOS.Rd |only
costat-1.1-1/costat/man/plottstosscan.Rd |only
costat-1.1-1/costat/man/tstosscan.Rd |only
costat-1.1-1/costat/man/x2.Rd |only
costat-1.1-1/costat/man/y2.Rd |only
costat-2.0/costat/DESCRIPTION | 22 +--
costat-2.0/costat/MD5 |only
costat-2.0/costat/NAMESPACE | 15 +-
costat-2.0/costat/NEWS |only
costat-2.0/costat/R/AntiAR.R |only
costat-2.0/costat/R/BootTOS.R |only
costat-2.0/costat/R/COEFbothscale.R | 85 +++++++++---
costat-2.0/costat/R/EWSsmoothRM.R |only
costat-2.0/costat/R/LCTS.R | 73 ++++++----
costat-2.0/costat/R/LCTSres.R | 174 +++++++++++++++-----------
costat-2.0/costat/R/TOSts.R | 21 ++-
costat-2.0/costat/R/coeftofn.R | 44 ++++--
costat-2.0/costat/R/extractCS.R |only
costat-2.0/costat/R/findstysols.R | 91 ++++++++++---
costat-2.0/costat/R/getpvals.R |only
costat-2.0/costat/R/lacv.R | 89 ++++++++++++-
costat-2.0/costat/R/localvar.R | 23 +--
costat-2.0/costat/R/mergexy.R | 127 +++++++++++++++---
costat-2.0/costat/R/plot.BootTOS.R |only
costat-2.0/costat/R/plot.csBiFunction.R |only
costat-2.0/costat/R/plot.csFSS.R |only
costat-2.0/costat/R/plot.csFSSgr.R |only
costat-2.0/costat/R/plot.lacv.R |only
costat-2.0/costat/R/plotBS.R | 38 ++---
costat-2.0/costat/R/print.csBiFunction.R |only
costat-2.0/costat/R/print.csFSS.R |only
costat-2.0/costat/R/print.csFSSgr.R |only
costat-2.0/costat/R/print.lacv.R |only
costat-2.0/costat/R/prodcomb.R | 46 ++++--
costat-2.0/costat/R/summary.csBiFunction.R |only
costat-2.0/costat/R/summary.csFSS.R |only
costat-2.0/costat/R/summary.csFSSgr.R |only
costat-2.0/costat/R/summary.lacv.R |only
costat-2.0/costat/data/fret.rda |only
costat-2.0/costat/data/sret.rda |only
costat-2.0/costat/man/AntiAR.Rd |only
costat-2.0/costat/man/BootTOS.Rd |only
costat-2.0/costat/man/COEFbothscale.Rd | 78 +++++++----
costat-2.0/costat/man/EWSsmoothRM.Rd |only
costat-2.0/costat/man/LCTS.Rd | 22 ++-
costat-2.0/costat/man/LCTSres.Rd | 68 +++++-----
costat-2.0/costat/man/SP500FTSElr.Rd | 8 -
costat-2.0/costat/man/TOSts.Rd | 18 +-
costat-2.0/costat/man/coeftofn.Rd | 29 +++-
costat-2.0/costat/man/costat-package.Rd | 131 ++++---------------
costat-2.0/costat/man/extractCS.Rd |only
costat-2.0/costat/man/findstysols.Rd | 160 +++++++++++++++--------
costat-2.0/costat/man/fret.Rd |only
costat-2.0/costat/man/getpvals.Rd |only
costat-2.0/costat/man/lacv.Rd | 85 +++++-------
costat-2.0/costat/man/localvar.Rd | 20 +-
costat-2.0/costat/man/mergexy.Rd | 38 ++---
costat-2.0/costat/man/plot.BootTOS.Rd |only
costat-2.0/costat/man/plot.csBiFunction.Rd |only
costat-2.0/costat/man/plot.csFSS.Rd |only
costat-2.0/costat/man/plot.csFSSgr.Rd |only
costat-2.0/costat/man/plot.lacv.Rd |only
costat-2.0/costat/man/plotBS.Rd | 15 +-
costat-2.0/costat/man/print.csBiFunction.Rd |only
costat-2.0/costat/man/print.csFSS.Rd |only
costat-2.0/costat/man/print.csFSSgr.Rd |only
costat-2.0/costat/man/print.lacv.Rd |only
costat-2.0/costat/man/prodcomb.Rd | 18 +-
costat-2.0/costat/man/sret.Rd |only
costat-2.0/costat/man/summary.csBiFunction.Rd |only
costat-2.0/costat/man/summary.csFSS.Rd |only
costat-2.0/costat/man/summary.csFSSgr.Rd |only
costat-2.0/costat/man/summary.lacv.Rd |only
86 files changed, 962 insertions(+), 576 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 5.15-044 dated 2012-10-03 and 5.15-045 dated 2012-11-27
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/predictionFunction.R | 1 -
R/probFunction.R | 1 -
R/resamples.R | 6 +++---
R/train.default.R | 4 ++--
R/workflows.R | 5 ++++-
inst/NEWS.Rd | 14 ++++++++++++++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.Rnw | 4 +---
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
vignettes/caretSelection.Rnw | 4 +---
14 files changed, 42 insertions(+), 31 deletions(-)
Title: Bootstrapped Response and Correlation Functions
Diff between bootRes versions 1.2.2 dated 2012-05-03 and 1.2.3 dated 2012-11-27
Description: Calculation of Bootstrapped Response and Correlation
Functions for Use in Dendroclimatology
Author: Christian Zang
Maintainer: Christian Zang
bootRes-1.2.2/bootRes/Changelog |only
bootRes-1.2.3/bootRes/DESCRIPTION | 6 +--
bootRes-1.2.3/bootRes/MD5 | 15 ++++---
bootRes-1.2.3/bootRes/R/climdispatch.R | 6 +--
bootRes-1.2.3/bootRes/R/mdcc.R | 17 ++++++++
bootRes-1.2.3/bootRes/inst |only
bootRes-1.2.3/bootRes/man/bootRes-package.Rd | 52 ++++++++++++++++++---------
bootRes-1.2.3/bootRes/man/dcc.Rd | 5 +-
bootRes-1.2.3/bootRes/man/dcplot.Rd | 4 +-
9 files changed, 71 insertions(+), 34 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.10.0 dated 2012-11-14 and 0.10.1 dated 2012-11-27
Description: The Rcpp package provides R functions as well as a C++
library which facilitate the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Rcpp attributes provide a high-level syntax for declaring C++ functions
as callable from R and automatically generating the code
required to invoke them. Attributes are intended to facilitate
both interactive use of C++ within R sessions as well as to
support R package development. Attributes are built on top of
Rcpp modules and their implementation is based on previous work
in the inline package.
Many examples are included, and over 870 unit tests in over 390 unit
test functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic, and it is still available for code relying on the
older interface. New development should always use this Rcpp
package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel
ChangeLog | 187 +++
DESCRIPTION | 18
MD5 | 208 ++--
R/00_classes.R | 3
R/Attributes.R | 39
R/Rcpp.package.skeleton.R | 50 -
TODO | 56 -
inst/NEWS.Rd | 55 +
inst/announce/ANNOUNCE-0.10.0.txt | 2
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-attributes.pdf |binary
inst/doc/Rcpp-attributes/Rcpp-attributes.Rnw | 559 ++++++++---
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-modules/Rcpp-modules.Rnw | 8
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 8
inst/doc/unitTests-results/Rcpp-unitTests.html | 10
inst/doc/unitTests-results/Rcpp-unitTests.txt | 61 -
inst/examples/Misc/piBySimulation.r |only
inst/examples/Misc/piSugar.cpp |only
inst/include/Rcpp.h | 4
inst/include/Rcpp/DataFrame.h | 2
inst/include/Rcpp/Fast.h | 4
inst/include/Rcpp/Module.h | 79 -
inst/include/Rcpp/Vector.h | 1
inst/include/Rcpp/as.h | 2
inst/include/Rcpp/config.h | 2
inst/include/Rcpp/exceptions.h | 1
inst/include/Rcpp/internal/SEXP_Iterator.h |only
inst/include/Rcpp/internal/export.h | 10
inst/include/Rcpp/internal/r_coerce.h | 11
inst/include/Rcpp/internal/r_vector.h | 18
inst/include/Rcpp/internal/wrap.h | 35
inst/include/Rcpp/internal/wrap_end.h |only
inst/include/Rcpp/iostream/Rostream.h | 11
inst/include/Rcpp/macros/unroll.h | 24
inst/include/Rcpp/module/class.h | 3
inst/include/Rcpp/module/class_Base.h |only
inst/include/Rcpp/stats/random/random.h | 2
inst/include/Rcpp/stats/random/rbeta.h | 19
inst/include/Rcpp/stats/random/rbinom.h | 21
inst/include/Rcpp/stats/random/rcauchy.h | 15
inst/include/Rcpp/stats/random/rchisq.h | 7
inst/include/Rcpp/stats/random/rexp.h | 20
inst/include/Rcpp/stats/random/rf.h | 20
inst/include/Rcpp/stats/random/rgamma.h | 31
inst/include/Rcpp/stats/random/rgeom.h | 7
inst/include/Rcpp/stats/random/rhyper.h | 17
inst/include/Rcpp/stats/random/rlnorm.h | 17
inst/include/Rcpp/stats/random/rlogis.h | 19
inst/include/Rcpp/stats/random/rnbinom.h | 7
inst/include/Rcpp/stats/random/rnbinom_mu.h | 5
inst/include/Rcpp/stats/random/rnchisq.h | 11
inst/include/Rcpp/stats/random/rnorm.h | 38
inst/include/Rcpp/stats/random/rpois.h | 17
inst/include/Rcpp/stats/random/rsignrank.h | 17
inst/include/Rcpp/stats/random/rt.h | 7
inst/include/Rcpp/stats/random/runif.h | 21
inst/include/Rcpp/stats/random/rweibull.h | 29
inst/include/Rcpp/stats/random/rwilcox.h | 16
inst/include/Rcpp/sugar/functions/clamp.h |only
inst/include/Rcpp/sugar/functions/duplicated.h |only
inst/include/Rcpp/sugar/functions/functions.h | 7
inst/include/Rcpp/sugar/functions/mapply/mapply_2.h | 93 +
inst/include/Rcpp/sugar/functions/mapply/mapply_3.h | 39
inst/include/Rcpp/sugar/functions/match.h |only
inst/include/Rcpp/sugar/functions/minmax.h |only
inst/include/Rcpp/sugar/functions/pmax.h | 104 --
inst/include/Rcpp/sugar/functions/pmin.h | 106 --
inst/include/Rcpp/sugar/functions/pow.h | 73 -
inst/include/Rcpp/sugar/functions/self_match.h |only
inst/include/Rcpp/sugar/functions/setdiff.h |only
inst/include/Rcpp/sugar/functions/table.h |only
inst/include/Rcpp/sugar/functions/unique.h | 66 -
inst/include/Rcpp/sugar/logical/SingleLogicalResult.h | 16
inst/include/Rcpp/sugar/sets.h | 27
inst/include/Rcpp/sugar/sugar.h | 1
inst/include/Rcpp/sugar/tools |only
inst/include/Rcpp/traits/comparator_type.h |only
inst/include/Rcpp/vector/00_forward_proxy.h | 6
inst/include/Rcpp/vector/Matrix.h | 6
inst/include/Rcpp/vector/MatrixBase.h | 6
inst/include/Rcpp/vector/MatrixColumn.h | 56 -
inst/include/Rcpp/vector/MatrixRow.h | 2
inst/include/Rcpp/vector/RangeIndexer.h | 28
inst/include/Rcpp/vector/Vector.h | 144 +-
inst/include/Rcpp/vector/converter.h | 3
inst/include/Rcpp/vector/proxy.h | 28
inst/include/Rcpp/vector/traits.h | 16
inst/include/RcppCommon.h | 8
inst/skeleton/rcpp_hello_world_attributes.cpp |only
inst/unitTests/cpp |only
inst/unitTests/runit.reg_0_10_1.R |only
inst/unitTests/runit.sugar.R | 895 +-----------------
man/CppClass-class.Rd | 1
man/Rcpp.package.skeleton.Rd | 16
man/compileAttributes.Rd | 2
man/evalCpp.Rd | 9
man/exportAttribute.Rd | 17
man/interfacesAttribute.Rd | 7
man/sourceCpp.Rd | 18
src/Attributes.cpp | 192 ++-
src/AttributesParser.cpp | 114 +-
src/AttributesParser.h | 17
src/Module.cpp | 5
src/RcppCommon.cpp | 12
src/coerce.cpp | 60 +
src/exceptions.cpp | 1
113 files changed, 2252 insertions(+), 1783 deletions(-)