Title: Least-squares means
Diff between lsmeans versions 0.99-80 dated 2012-09-20 and 1.00-00 dated 2012-10-19
Description: This package provides the function 'lsmeans' for
outputting so-called least-squares means for factor
combinations in an 'lm', 'lme', or 'lmer' object. It can also
compute contrasts or linear combinations of these least-squares
means, and several standard contrast families are provided.
Author: Russell V. Lenth
Maintainer: Russ Lenth
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans-8-R-fig.pdf |only
lsmeans-1.00-00/lsmeans/DESCRIPTION | 11
lsmeans-1.00-00/lsmeans/MD5 | 35 -
lsmeans-1.00-00/lsmeans/R/KRstuff.R | 4
lsmeans-1.00-00/lsmeans/R/lsmeans.R | 93 ++-
lsmeans-1.00-00/lsmeans/data |only
lsmeans-1.00-00/lsmeans/inst/NEWS | 14
lsmeans-1.00-00/lsmeans/inst/doc/using-lsmeans.Rnw | 268 ++++++----
lsmeans-1.00-00/lsmeans/inst/doc/using-lsmeans.pdf |binary
lsmeans-1.00-00/lsmeans/lsmeans-Ex.R | 94 ++-
lsmeans-1.00-00/lsmeans/man/fiber.Rd |only
lsmeans-1.00-00/lsmeans/man/lsmeans.Rd | 84 +--
lsmeans-1.00-00/lsmeans/man/nutrition.Rd |only
lsmeans-1.00-00/lsmeans/man/pairwise.lsmc.Rd | 19
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-nutr-intplot-fig.pdf |only
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-nutr-scatter-fig.pdf |only
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-oats-intplot-fig.pdf |binary
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-oats-intplot2-fig.pdf |only
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-typing-glht-plot-fig.pdf |only
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-typing-scatter-fig.pdf |binary
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans-warp-intplot-fig.pdf |binary
lsmeans-1.00-00/lsmeans/vignettes/using-lsmeans.Rnw | 268 ++++++----
22 files changed, 591 insertions(+), 299 deletions(-)
Title: General Frailty models using a semi_parametrical penalized
likelihood estimation or a parametrical estimation
Diff between frailtypack versions 2.2-25 dated 2012-09-06 and 2.2-26 dated 2012-10-19
Description: Frailtypack now fits several classes of frailty models
using a penalized likelihood estimation on the hazard function
but also a parametrical 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 of recurrent events with terminal event. Prediction
values are available. Left truncated, 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
DESCRIPTION | 10
MD5 | 84 +--
NEWS | 21
R/SurvIC.R | 70 +-
R/additivePenal.R | 22
R/factor.names.R | 48 -
R/frailtyPenal.R | 83 ++-
R/plot.nestedPenal.additivePenal.R | 8
R/slope.R | 2
R/summary.jointPenal.R | 36 -
R/survival.R | 214 ++++----
R/terminal.R | 2
demo/frailtypack_nestedPenal.R | 2
man/NestedfrailtyPenal.Rd | 461 +++++++++---------
man/SurvIC.Rd | 102 ++--
man/additivePenal.Rd | 446 ++++++++---------
man/dataNested.Rd | 86 +--
man/diabetes.Rd | 54 +-
man/frailtyPenal.Rd | 486 +++++++++----------
man/frailtypack-package.Rd | 7
man/plotAdditive.Rd | 108 ++--
man/plotFrailtyPenal.Rd | 142 ++---
man/plotJointPenal.Rd | 166 +++---
man/plotNestedPenal.Rd | 102 ++--
man/printAdditive.Rd | 128 ++---
man/printFrailtyPenal.Rd | 130 ++---
man/printJointPenal.Rd | 146 ++---
man/printNestedPenal.Rd | 128 ++---
man/readmission.Rd | 72 +-
man/subcluster.Rd | 102 ++--
man/summaryAdditive.Rd | 114 ++--
man/summaryFrailtyPenal.Rd | 128 ++---
man/summaryJointPenal.Rd | 134 ++---
man/summaryNestedPenal.Rd | 106 ++--
man/survival.Rd | 84 +--
man/terminal.Rd | 114 ++--
src/aamarq98o.f90 | 926 ++++++++++++++++++-------------------
src/funcpansplines.f90 | 25
src/funcpascpm_intcens.f90 | 652 +++++++++++++-------------
src/funcpasweib_intcens.f90 | 550 ++++++++++-----------
src/nested.f90 | 61 ++
src/risque.f90 | 140 ++---
src/survival.f90 | 492 +++++++++----------
43 files changed, 3555 insertions(+), 3439 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Diff between C50 versions 0.0.9 dated 2012-08-30 and 0.1.0-013 dated 2012-10-19
Description: C5.0 decision trees and rule-based models for pattern
recognition
Author: Max Kuhn, Steve Weston, Nathan Coulter. C code for C5.0 by R.
Quinlan
Maintainer: Max Kuhn
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/predict.C5.0.R | 4 ++--
man/C5.0.Rd | 2 +-
man/predict.C5.0.Rd | 5 ++++-
5 files changed, 15 insertions(+), 12 deletions(-)
Title: Goodness-of-fit functions for comparison of simulated and
observed hydrological time series
Diff between hydroGOF versions 0.3-4 dated 2012-07-03 and 0.3-5 dated 2012-10-19
Description: S3 functions implementing both statistical and graphical
goodness-of-fit measures between observed and simulated values,
mainly oriented to be used during the calibration, validation,
and application of hydrological models. Missing values in
observed and/or simulated values can be removed before
computations. Comments / questions / collaboration of any kind
are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre]
Maintainer: Mauricio Zambrano Bigiarini
DESCRIPTION | 12 +-
MD5 | 20 +--
NAMESPACE | 2
NEWS | 12 ++
R/KGE.R | 211 +++++++++++++++++++++++++++++------------
R/ggof.R | 132 +++++++++++++------------
inst/doc/hydroGOF_Vignette.pdf |binary
man/KGE.Rd | 93 ++++++++++++++----
man/ggof.Rd | 6 -
man/hydroGOF-package.Rd | 31 +++---
man/pbias.Rd | 4
11 files changed, 350 insertions(+), 173 deletions(-)
More information about DiscreteInverseWeibull at CRAN
Permanent link
Title: Bayesian treed Gaussian process models
Diff between tgp versions 2.4-7 dated 2012-04-20 and 2.4-8 dated 2012-10-19
Description: Bayesian nonstationary, semiparametric nonlinear
regression and design by treed Gaussian processes (GPs) with
jumps to the limiting linear model (LLM). Special cases also
implemented include Bayesian linear models, CART, treed linear
models, stationary separable and isotropic GPs, and GP
single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing,
designed for visualization of tgp-class output. Sensitivity
analysis and multi-resolution models are supported. Sequential
experimental design and adaptive sampling functions are also
provided, including ALM, ALC, and expected improvement. The
latter supports derivative-free optimization of noisy black-box
functions.
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
tgp-2.4-7/tgp/src/bessel_k.c |only
tgp-2.4-7/tgp/src/bessel_k.h |only
tgp-2.4-8/tgp/ChangeLog | 10 ++
tgp-2.4-8/tgp/DESCRIPTION | 7 -
tgp-2.4-8/tgp/MD5 | 40 ++++-----
tgp-2.4-8/tgp/R/tgp.R | 2
tgp-2.4-8/tgp/data/exp2d.rda |binary
tgp-2.4-8/tgp/demo/optim.R | 41 +++------
tgp-2.4-8/tgp/inst/doc/tgp.pdf |binary
tgp-2.4-8/tgp/inst/doc/tgp2.pdf |binary
tgp-2.4-8/tgp/man/default.itemps.Rd | 2
tgp-2.4-8/tgp/src/all_draws.c | 5 -
tgp-2.4-8/tgp/src/all_draws.h | 2
tgp-2.4-8/tgp/src/gen_covar.c | 13 --
tgp-2.4-8/tgp/src/gen_covar.h | 6 -
tgp-2.4-8/tgp/src/linalg.c | 158 ++++++++++++++++++++----------------
tgp-2.4-8/tgp/src/linalg.h | 36 +++++---
tgp-2.4-8/tgp/src/matern.cc | 10 +-
tgp-2.4-8/tgp/src/matrix.c | 73 +++++++++++++++-
tgp-2.4-8/tgp/src/matrix.h | 5 +
tgp-2.4-8/tgp/src/rhelp.c | 3
tgp-2.4-8/tgp/src/rhelp.h | 9 +-
22 files changed, 259 insertions(+), 163 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
(fda.usc)
Diff between fda.usc versions 0.9.8.1 dated 2012-07-03 and 1.0.0 dated 2012-10-19
Description: The R package fda.usc carries out exploratory and
descriptive analysis of functional data such as depth
measurements or functional atypical curves detection, functions
to compute functional regression models with a scalar response,
supervised and unsupervised classification methods and
functional analysis of variance.
Author: Manuel Febrero-Bande, Manuel Oviedo de la Fuente
Maintainer: Manuel Oviedo de la Fuente
fda.usc-0.9.8.1/fda.usc/R/classif.knn.R |only
fda.usc-1.0.0/fda.usc/DESCRIPTION | 21 +-
fda.usc-1.0.0/fda.usc/MD5 | 235 +++++++++++------------
fda.usc-1.0.0/fda.usc/NAMESPACE | 15 -
fda.usc-1.0.0/fda.usc/NEWS | 17 +
fda.usc-1.0.0/fda.usc/R/CV.S.R | 25 ++
fda.usc-1.0.0/fda.usc/R/Descriptive.R | 7
fda.usc-1.0.0/fda.usc/R/GCV.S.R | 39 +++
fda.usc-1.0.0/fda.usc/R/anova.RPm.R | 3
fda.usc-1.0.0/fda.usc/R/anova.RPm.boot.R | 2
fda.usc-1.0.0/fda.usc/R/classif.glm.R | 5
fda.usc-1.0.0/fda.usc/R/classif.gsam.R | 8
fda.usc-1.0.0/fda.usc/R/classif.np.r | 11 -
fda.usc-1.0.0/fda.usc/R/create.fdata.basis.R | 22 ++
fda.usc-1.0.0/fda.usc/R/depth.FM.r | 42 ++--
fda.usc-1.0.0/fda.usc/R/depth.RP.r | 25 +-
fda.usc-1.0.0/fda.usc/R/depth.RPD.r | 65 +++---
fda.usc-1.0.0/fda.usc/R/depth.RT.r |only
fda.usc-1.0.0/fda.usc/R/depth.mode.r | 91 +++++---
fda.usc-1.0.0/fda.usc/R/dfv.test.R | 3
fda.usc-1.0.0/fda.usc/R/fda.usc.internal.R | 11 -
fda.usc-1.0.0/fda.usc/R/fdata.R | 128 ++++++++++++
fda.usc-1.0.0/fda.usc/R/fdata2pc.r | 13 -
fda.usc-1.0.0/fda.usc/R/flm.test.R | 10
fda.usc-1.0.0/fda.usc/R/fregre.gkam.r | 11 -
fda.usc-1.0.0/fda.usc/R/fregre.glm.R | 27 +-
fda.usc-1.0.0/fda.usc/R/fregre.gsam.R | 79 ++-----
fda.usc-1.0.0/fda.usc/R/fregre.lm.R | 2
fda.usc-1.0.0/fda.usc/R/metric.dist.R |only
fda.usc-1.0.0/fda.usc/R/omit.fdata.R | 55 +++++
fda.usc-1.0.0/fda.usc/R/outliers.depth.pond.r | 24 ++
fda.usc-1.0.0/fda.usc/R/outliers.depth.trim.r | 35 ++-
fda.usc-1.0.0/fda.usc/R/plot.fdata.R | 62 +++++-
fda.usc-1.0.0/fda.usc/R/predict.classif.R | 59 +++--
fda.usc-1.0.0/fda.usc/R/predict.fregre.glm.R | 1
fda.usc-1.0.0/fda.usc/R/print.classif.r | 4
fda.usc-1.0.0/fda.usc/R/summary.classif.R | 8
fda.usc-1.0.0/fda.usc/R/summary.fdata.comp.r | 2
fda.usc-1.0.0/fda.usc/R/summary.fregre.fd.r | 13 -
fda.usc-1.0.0/fda.usc/inst |only
fda.usc-1.0.0/fda.usc/man/CV.S.Rd | 2
fda.usc-1.0.0/fda.usc/man/Depth.Rd | 12 -
fda.usc-1.0.0/fda.usc/man/Descriptive.Rd | 27 +-
fda.usc-1.0.0/fda.usc/man/GCV.S.Rd | 7
fda.usc-1.0.0/fda.usc/man/Kernel.Rd | 2
fda.usc-1.0.0/fda.usc/man/Kernel.asymmetric.Rd | 4
fda.usc-1.0.0/fda.usc/man/Kernel.integrate.Rd | 7
fda.usc-1.0.0/fda.usc/man/Outliers.fdata.Rd | 14 -
fda.usc-1.0.0/fda.usc/man/S.basis.Rd | 4
fda.usc-1.0.0/fda.usc/man/S.np.Rd | 4
fda.usc-1.0.0/fda.usc/man/Var.y.Rd | 4
fda.usc-1.0.0/fda.usc/man/aemet.Rd | 7
fda.usc-1.0.0/fda.usc/man/anova.RPm.Rd | 2
fda.usc-1.0.0/fda.usc/man/anova.hetero.Rd | 3
fda.usc-1.0.0/fda.usc/man/classif.gkam.Rd | 26 +-
fda.usc-1.0.0/fda.usc/man/classif.glm.Rd | 13 -
fda.usc-1.0.0/fda.usc/man/classif.gsam.Rd | 9
fda.usc-1.0.0/fda.usc/man/classif.np.Rd | 5
fda.usc-1.0.0/fda.usc/man/cond.F.Rd | 12 -
fda.usc-1.0.0/fda.usc/man/cond.mode.Rd | 12 -
fda.usc-1.0.0/fda.usc/man/cond.quantile.Rd | 2
fda.usc-1.0.0/fda.usc/man/create.fdata.basis.Rd | 4
fda.usc-1.0.0/fda.usc/man/depth.FM.Rd | 14 -
fda.usc-1.0.0/fda.usc/man/depth.RP.Rd | 15 -
fda.usc-1.0.0/fda.usc/man/depth.RPD.Rd | 14 -
fda.usc-1.0.0/fda.usc/man/depth.RT.rd |only
fda.usc-1.0.0/fda.usc/man/depth.mode.Rd | 21 +-
fda.usc-1.0.0/fda.usc/man/dev.S.Rd | 7
fda.usc-1.0.0/fda.usc/man/dfv.test.Rd | 2
fda.usc-1.0.0/fda.usc/man/fda.usc-package.Rd | 30 ++
fda.usc-1.0.0/fda.usc/man/fda.usc.internal.Rd | 6
fda.usc-1.0.0/fda.usc/man/fdata.Rd | 25 +-
fda.usc-1.0.0/fda.usc/man/fdata.bootstrap.Rd | 7
fda.usc-1.0.0/fda.usc/man/fdata.cen.Rd | 2
fda.usc-1.0.0/fda.usc/man/fdata.deriv.Rd | 13 -
fda.usc-1.0.0/fda.usc/man/fdata2fd.Rd | 6
fda.usc-1.0.0/fda.usc/man/fdata2pc.Rd | 7
fda.usc-1.0.0/fda.usc/man/fdata2pls.Rd | 5
fda.usc-1.0.0/fda.usc/man/flm.test.Rd | 6
fda.usc-1.0.0/fda.usc/man/fregre.basis.Rd | 7
fda.usc-1.0.0/fda.usc/man/fregre.basis.cv.Rd | 7
fda.usc-1.0.0/fda.usc/man/fregre.bootstrap.Rd | 10
fda.usc-1.0.0/fda.usc/man/fregre.gkam.Rd | 40 +--
fda.usc-1.0.0/fda.usc/man/fregre.glm.Rd | 14 -
fda.usc-1.0.0/fda.usc/man/fregre.gsam.Rd | 15 -
fda.usc-1.0.0/fda.usc/man/fregre.lm.Rd | 7
fda.usc-1.0.0/fda.usc/man/fregre.np.Rd | 5
fda.usc-1.0.0/fda.usc/man/fregre.np.cv.Rd | 8
fda.usc-1.0.0/fda.usc/man/fregre.pc.Rd | 10
fda.usc-1.0.0/fda.usc/man/fregre.pc.cv.Rd | 9
fda.usc-1.0.0/fda.usc/man/fregre.plm.Rd | 11 -
fda.usc-1.0.0/fda.usc/man/fregre.pls.Rd | 8
fda.usc-1.0.0/fda.usc/man/fregre.pls.cv.Rd | 8
fda.usc-1.0.0/fda.usc/man/h.default.Rd | 17 -
fda.usc-1.0.0/fda.usc/man/influence.fdata.Rd | 5
fda.usc-1.0.0/fda.usc/man/influence.quan.Rd | 2
fda.usc-1.0.0/fda.usc/man/inprod.fdata.Rd | 2
fda.usc-1.0.0/fda.usc/man/int.simpson.Rd | 2
fda.usc-1.0.0/fda.usc/man/kmeans.fd.Rd | 2
fda.usc-1.0.0/fda.usc/man/metric.dist.Rd |only
fda.usc-1.0.0/fda.usc/man/metric.lp.Rd | 6
fda.usc-1.0.0/fda.usc/man/min.basis.Rd | 12 -
fda.usc-1.0.0/fda.usc/man/min.np.Rd | 10
fda.usc-1.0.0/fda.usc/man/norm.fdata.Rd | 2
fda.usc-1.0.0/fda.usc/man/phoneme.Rd | 2
fda.usc-1.0.0/fda.usc/man/plot.fdata.Rd | 20 +
fda.usc-1.0.0/fda.usc/man/poblenou.Rd | 2
fda.usc-1.0.0/fda.usc/man/predict.classif.Rd | 17 -
fda.usc-1.0.0/fda.usc/man/predict.fregre.fd.Rd | 82 ++++----
fda.usc-1.0.0/fda.usc/man/predict.fregre.gkam.Rd | 26 +-
fda.usc-1.0.0/fda.usc/man/predict.fregre.glm.Rd | 4
fda.usc-1.0.0/fda.usc/man/predict.fregre.gsam.Rd | 19 +
fda.usc-1.0.0/fda.usc/man/predict.fregre.lm.Rd | 8
fda.usc-1.0.0/fda.usc/man/predict.fregre.plm.Rd | 11 -
fda.usc-1.0.0/fda.usc/man/rproc2fdata.Rd | 2
fda.usc-1.0.0/fda.usc/man/semimetric.NPFDA.Rd | 5
fda.usc-1.0.0/fda.usc/man/summary.classif.Rd | 9
fda.usc-1.0.0/fda.usc/man/summary.fdata.comp.Rd | 28 +-
fda.usc-1.0.0/fda.usc/man/summary.fregre.fd.Rd | 2
fda.usc-1.0.0/fda.usc/man/summary.fregre.gkam.Rd | 4
fda.usc-1.0.0/fda.usc/man/tecator.Rd | 14 -
fda.usc-1.0.0/fda.usc/script/jss757.R |only
122 files changed, 1302 insertions(+), 714 deletions(-)
Title: Interface to the Corpus Query Protocol
Diff between rcqp versions 0.1 dated 2012-06-26 and 0.3 dated 2012-10-19
Description: implements Corpus Query Protocol functions based on the
CWB software. Rely on CWB (GPL v2), PCRE (BSD licence), glib2
(LGPL).
Author: Bernard Desgraupes
Maintainer: Sylvain Loiseau, University of Paris 13
rcqp-0.1/rcqp/src/Makevars |only
rcqp-0.1/rcqp/src/Makevars.win |only
rcqp-0.1/rcqp/src/cwb/cl/endian.c |only
rcqp-0.1/rcqp/src/cwb/cl/endian.h |only
rcqp-0.1/rcqp/src/cwb/cl/lex.creg.c |only
rcqp-0.1/rcqp/svn-commit.2.tmp |only
rcqp-0.1/rcqp/svn-commit.tmp |only
rcqp-0.3/rcqp/DESCRIPTION | 11
rcqp-0.3/rcqp/MD5 | 259 ++++++-------
rcqp-0.3/rcqp/NEWS |only
rcqp-0.3/rcqp/R/s3.R | 5
rcqp-0.3/rcqp/configure | 194 +++++----
rcqp-0.3/rcqp/configure.win | 2
rcqp-0.3/rcqp/inst/doc/rcqp.Rnw.svg | 33 +
rcqp-0.3/rcqp/inst/doc/rcqp.pdf |binary
rcqp-0.3/rcqp/src/Makevars.in | 18
rcqp-0.3/rcqp/src/cwb/AUTHORS | 2
rcqp-0.3/rcqp/src/cwb/COPYING | 2
rcqp-0.3/rcqp/src/cwb/CQi/auth.c | 12
rcqp-0.3/rcqp/src/cwb/CQi/cqpserver.c | 182 ++++-----
rcqp-0.3/rcqp/src/cwb/CQi/server.c | 98 ++--
rcqp-0.3/rcqp/src/cwb/cl/attributes.c | 109 ++---
rcqp-0.3/rcqp/src/cwb/cl/bitfields.c | 8
rcqp-0.3/rcqp/src/cwb/cl/bitio.c | 6
rcqp-0.3/rcqp/src/cwb/cl/cdaccess.c | 42 +-
rcqp-0.3/rcqp/src/cwb/cl/cl_endian.c |only
rcqp-0.3/rcqp/src/cwb/cl/cl_endian.h |only
rcqp-0.3/rcqp/src/cwb/cl/class-mapping.c | 16
rcqp-0.3/rcqp/src/cwb/cl/corpus.c | 41 --
rcqp-0.3/rcqp/src/cwb/cl/depend.mk | 12
rcqp-0.3/rcqp/src/cwb/cl/globals.c | 2
rcqp-0.3/rcqp/src/cwb/cl/globals.h | 2
rcqp-0.3/rcqp/src/cwb/cl/lexhash.c | 6
rcqp-0.3/rcqp/src/cwb/cl/macros.c | 70 +--
rcqp-0.3/rcqp/src/cwb/cl/makecomps.c | 34 -
rcqp-0.3/rcqp/src/cwb/cl/registry.output |only
rcqp-0.3/rcqp/src/cwb/cl/registry.tab.c | 2
rcqp-0.3/rcqp/src/cwb/cl/registry.y | 2
rcqp-0.3/rcqp/src/cwb/cl/registry.yy.c | 8
rcqp-0.3/rcqp/src/cwb/cl/regopt.c | 40 +-
rcqp-0.3/rcqp/src/cwb/cl/special-chars.c | 10
rcqp-0.3/rcqp/src/cwb/cl/storage.c | 48 +-
rcqp-0.3/rcqp/src/cwb/cl/windows-mmap.c | 10
rcqp-0.3/rcqp/src/cwb/config/site/linux-release | 2
rcqp-0.3/rcqp/src/cwb/config/site/osx-release | 2
rcqp-0.3/rcqp/src/cwb/config/site/standard | 2
rcqp-0.3/rcqp/src/cwb/config/site/windows-release | 2
rcqp-0.3/rcqp/src/cwb/cqp/ascii-print.c | 8
rcqp-0.3/rcqp/src/cwb/cqp/builtins.c | 4
rcqp-0.3/rcqp/src/cwb/cqp/concordance.c | 14
rcqp-0.3/rcqp/src/cwb/cqp/context_descriptor.c | 10
rcqp-0.3/rcqp/src/cwb/cqp/corpmanag.c | 44 +-
rcqp-0.3/rcqp/src/cwb/cqp/cqp.c | 51 +-
rcqp-0.3/rcqp/src/cwb/cqp/cqpcl.c | 12
rcqp-0.3/rcqp/src/cwb/cqp/eval.c | 84 ++--
rcqp-0.3/rcqp/src/cwb/cqp/groups.c | 8
rcqp-0.3/rcqp/src/cwb/cqp/hash.c | 51 +-
rcqp-0.3/rcqp/src/cwb/cqp/lex.yy.c | 6
rcqp-0.3/rcqp/src/cwb/cqp/llquery.c | 40 +-
rcqp-0.3/rcqp/src/cwb/cqp/macro.c | 68 +--
rcqp-0.3/rcqp/src/cwb/cqp/macro.h | 4
rcqp-0.3/rcqp/src/cwb/cqp/matchlist.c | 24 -
rcqp-0.3/rcqp/src/cwb/cqp/options.c | 156 +++----
rcqp-0.3/rcqp/src/cwb/cqp/output.c | 29 -
rcqp-0.3/rcqp/src/cwb/cqp/output.h | 2
rcqp-0.3/rcqp/src/cwb/cqp/parse_actions.c | 34 -
rcqp-0.3/rcqp/src/cwb/cqp/parser.tab.c | 16
rcqp-0.3/rcqp/src/cwb/cqp/parser.y | 16
rcqp-0.3/rcqp/src/cwb/cqp/parser.yy.c | 8
rcqp-0.3/rcqp/src/cwb/cqp/print-modes.c | 2
rcqp-0.3/rcqp/src/cwb/cqp/print-modes.h | 2
rcqp-0.3/rcqp/src/cwb/cqp/ranges.c | 18
rcqp-0.3/rcqp/src/cwb/cqp/regex2dfa.c | 74 +--
rcqp-0.3/rcqp/src/cwb/cqp/symtab.c | 26 -
rcqp-0.3/rcqp/src/cwb/cqp/targets.c | 12
rcqp-0.3/rcqp/src/cwb/cqp/tree.c | 174 ++++----
rcqp-0.3/rcqp/src/cwb/cqp/variables.c | 12
rcqp-0.3/rcqp/src/cwb/doc/code_overview.html | 4
rcqp-0.3/rcqp/src/cwb/doc/code_overview.textile | 2
rcqp-0.3/rcqp/src/cwb/doc/coding-standards.html | 2
rcqp-0.3/rcqp/src/cwb/doc/html/bc_s.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/closed.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/cwb-encode_8c.html | 2
rcqp-0.3/rcqp/src/cwb/doc/html/cwb-huffcode_8c.html | 8
rcqp-0.3/rcqp/src/cwb/doc/html/doxygen.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/globals_8h.html | 2
rcqp-0.3/rcqp/src/cwb/doc/html/macro_8c.html | 8
rcqp-0.3/rcqp/src/cwb/doc/html/macro_8h.html | 8
rcqp-0.3/rcqp/src/cwb/doc/html/matchlist_8c.html | 8
rcqp-0.3/rcqp/src/cwb/doc/html/matchlist_8h.html | 8
rcqp-0.3/rcqp/src/cwb/doc/html/nav_f.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/nav_h.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/open.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/regex2dfa_8c.html | 12
rcqp-0.3/rcqp/src/cwb/doc/html/regex2dfa_8h.html | 4
rcqp-0.3/rcqp/src/cwb/doc/html/storage_8c.html | 4
rcqp-0.3/rcqp/src/cwb/doc/html/storage_8h.html | 4
rcqp-0.3/rcqp/src/cwb/doc/html/struct_redir.html | 4
rcqp-0.3/rcqp/src/cwb/doc/html/tab_a.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/tab_b.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/tab_h.png |binary
rcqp-0.3/rcqp/src/cwb/doc/html/tab_s.png |binary
rcqp-0.3/rcqp/src/cwb/doc/unicode_roadmap.html | 2
rcqp-0.3/rcqp/src/cwb/doc/version-numbering-rules.html | 2
rcqp-0.3/rcqp/src/cwb/editline/examples/completion_test.c | 14
rcqp-0.3/rcqp/src/cwb/editline/src/editline.c | 6
rcqp-0.3/rcqp/src/cwb/editline/test.c | 4
rcqp-0.3/rcqp/src/cwb/editline/test_sh.c | 4
rcqp-0.3/rcqp/src/cwb/install-scripts/cwb-install-mac-osx | 2
rcqp-0.3/rcqp/src/cwb/instutils/cwb-config.in | 2
rcqp-0.3/rcqp/src/cwb/utils/cwb-align-encode.c | 130 +++---
rcqp-0.3/rcqp/src/cwb/utils/cwb-align-show.c | 106 ++---
rcqp-0.3/rcqp/src/cwb/utils/cwb-align.c | 186 ++++-----
rcqp-0.3/rcqp/src/cwb/utils/cwb-atoi.c | 28 -
rcqp-0.3/rcqp/src/cwb/utils/cwb-check-input.c | 114 ++---
rcqp-0.3/rcqp/src/cwb/utils/cwb-compress-rdx.c | 80 ++--
rcqp-0.3/rcqp/src/cwb/utils/cwb-decode-nqrfile.c | 22 -
rcqp-0.3/rcqp/src/cwb/utils/cwb-decode.c | 276 +++++++-------
rcqp-0.3/rcqp/src/cwb/utils/cwb-describe-corpus.c | 94 ++--
rcqp-0.3/rcqp/src/cwb/utils/cwb-encode.c | 262 ++++++-------
rcqp-0.3/rcqp/src/cwb/utils/cwb-huffcode.c | 152 +++----
rcqp-0.3/rcqp/src/cwb/utils/cwb-itoa.c | 28 -
rcqp-0.3/rcqp/src/cwb/utils/cwb-lexdecode.c | 92 ++--
rcqp-0.3/rcqp/src/cwb/utils/cwb-makeall.c | 144 +++----
rcqp-0.3/rcqp/src/cwb/utils/cwb-s-decode.c | 36 -
rcqp-0.3/rcqp/src/cwb/utils/cwb-s-encode.c | 142 +++----
rcqp-0.3/rcqp/src/cwb/utils/cwb-scan-corpus.c | 178 ++++-----
rcqp-0.3/rcqp/src/cwb/utils/feature_maps.c | 126 +++---
rcqp-0.3/rcqp/src/cwb/utils/feature_maps.h | 2
rcqp-0.3/rcqp/src/makeRCompatible.c | 2
rcqp-0.3/rcqp/src/makeRCompatible.h | 30 -
rcqp-0.3/rcqp/src/rcqp.h | 21 -
rcqp-0.3/rcqp/src/rcqpCommands.c | 71 +--
rcqp-0.3/rcqp/src/rcqpCommands.h | 24 -
rcqp-0.3/rcqp/src/rcqpUtils.c | 23 -
rcqp-0.3/rcqp/src/rcqpUtils.h | 26 -
136 files changed, 2422 insertions(+), 2392 deletions(-)
Title: Dynamic Extensions for Network Objects
Diff between networkDynamic versions 0.2-2 dated 2012-03-09 and 0.3.1 dated 2012-10-19
More information about networkDynamic at CRAN
Description: Simple interface routines to facilitate the handling of
network objects with complex intertemporal data.
"networkDynamic" is a part of the "statnet" suite of packages
for network analysis.
Author: Carter T. Butts [aut], Ayn Leslie-Cook [aut], Pavel N.
Krivitsky [aut], Skye Bender-deMoll [aut, cre], Zack Almquist
[ctb], David R. Hunter [ctb], Li Wang [ctb], Kirk Li [ctb],
Steven M. Goodreau [ctb], Martina Morris [ctb]
Maintainer: Skye Bender-deMoll
ChangeLog | 11
DESCRIPTION | 36
MD5 | 62
NAMESPACE | 18
R/access.R | 1815 ++++++++-------
R/access.attributes.R |only
R/duration.matrix.R | 76
R/extract.R | 155 -
R/utilities.R | 822 ++++--
R/zzz.R | 53
data/windsurfers.rda |binary
inst/doc/networkDynamic.Rnw | 66
inst/doc/networkDynamic.pdf |binary
man/Newcomb.Rd | 145 -
man/activate.Rd | 274 +-
man/activity.attribute.Rd | 152 -
man/add.active.Rd |only
man/as.data.frame.networkDynamic.Rd | 23
man/as.networkDynamic.Rd | 112
man/delete.activity.Rd |only
man/duration.matrix.Rd |only
man/get.timing.info.Rd |only
man/is.active.Rd | 174 -
man/network.dynamic.check.Rd | 46
man/network.extensions.Rd | 38
man/network.extract.Rd | 50
man/networkDynamic-package.Rd | 3
man/networkDynamic.Rd |only
man/print.networkDynamic.Rd | 115
man/windsurfers.Rd | 164 -
tests/activate_tests.R | 4252 ++++++++++++++++++------------------
tests/converter_tests.R | 470 +++
tests/get_tests.R | 62
tests/network_tests.R | 34
vignettes/networkDynamic.Rnw | 66
35 files changed, 5239 insertions(+), 4055 deletions(-)
Permanent link
Title: Calls CNV from exome sequence data
Diff between ExomeDepth versions 0.8.4 dated 2012-08-24 and 0.9.1 dated 2012-10-19
Description: Calls copy number variants (CNVs) from targeted sequence
data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
DESCRIPTION | 6 -
MD5 | 28 ++++---
R/class_definition.R | 45 ++++++++++-
R/countBamInGranges.R | 34 ++++++--
R/optimize_reference_set.R | 4 -
R/plot_CNVs_method.R | 2
data/Conrad.hg19.RData |only
data/datalist | 2
data/exons.hg19.X.RData |only
inst/doc/ExomeDepth-vignette.Rnw | 138 +++++++++++++++++++++++++++++++++++-
inst/doc/ExomeDepth-vignette.pdf |binary
man/AnnotateExtra-methods.Rd |only
man/AnnotateExtra.Rd |only
man/Conrad.hg19.common.CNVs.Rd |only
man/countBamInGRanges.exomeDepth.Rd | 4 -
man/exons.hg19.Rd | 2
man/exons.hg19.X.Rd |only
man/getBamCounts.Rd | 6 +
18 files changed, 236 insertions(+), 35 deletions(-)