Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at (http://www.phidot.org/software/mark/downloads/)
but is not open source.
Author: Jeff Laake <jeff.laake@noaa.gov> with code contributions from Eldar
Rakhimberdiev, Ben Augustine and Daniel Turek, and example data and
analysis from Bret Collier, Jay Rotella, David Pavlacky, and Andrew Paul.
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between RMark versions 2.1.12 dated 2015-03-15 and 2.1.13 dated 2015-06-04
DESCRIPTION | 8 +-- MD5 | 49 +++++++++++---------- NAMESPACE | 3 + NEWS | 22 +++++++++ R/RMark-package.R | 32 +++++++------ R/convert.link.to.real.r | 2 R/covariate.predictions.r | 100 +++++++++++++++++++++++++------------------ R/extract.mark.output.R | 11 ++-- R/make.mark.model.R | 42 +++++++++++++----- R/mark.R | 6 +- R/model.table.R | 4 + R/process.ch.R |only R/process.data.R | 2 R/read.mark.binary.R | 32 +++++++------ R/read.mark.binary.linux.R | 32 +++++++------ R/store.r | 2 R/utility.r | 92 +++++++++++++++++++++++++++++++++++++++ inst/MarkModels.pdf |binary man/MStruncate.Rd |only man/covariate.predictions.Rd | 12 ++++- man/deer.Rd | 2 man/larksparrow.Rd | 24 +++++----- man/make.mark.model.Rd | 5 +- man/mallard.Rd | 1 man/mark.Rd | 5 +- man/process.ch.Rd |only man/wwdo.popan.Rd | 2 27 files changed, 338 insertions(+), 152 deletions(-)
Title: Terminal Progress Bars
Description: Terminal progress bars. They are
configurable, may include percentage, elapsed time, and/or
the estimated completion time. They work in the command line,
in Emacs, R Studio, Windows Rgui and Mac OSX R.app. The package
also provides a C++ API, that works with or without Rcpp.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between progress versions 1.0.1 dated 2015-05-30 and 1.0.2 dated 2015-06-04
DESCRIPTION | 6 ++--- MD5 | 11 ++++++--- inst/NEWS.md |only inst/README.md |only inst/include/RProgress.h | 50 ++++++++++++++++++++++---------------------- inst/progresstest/NAMESPACE | 1 inst/progresstest/R/test.R | 6 ++++- tests/testthat/test-cpp.R |only 8 files changed, 41 insertions(+), 33 deletions(-)
Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.13.4 dated 2015-02-25 and 1.14.0 dated 2015-06-04
MuMIn-1.13.4/MuMIn/R/beta.weights.R |only MuMIn-1.13.4/MuMIn/tests/_gam.R |only MuMIn-1.14.0/MuMIn/DESCRIPTION | 19 - MuMIn-1.14.0/MuMIn/MD5 | 81 ++++---- MuMIn-1.14.0/MuMIn/NAMESPACE | 30 +-- MuMIn-1.14.0/MuMIn/NEWS | 39 +++- MuMIn-1.14.0/MuMIn/R/DIC.R | 8 MuMIn-1.14.0/MuMIn/R/coefTable.R | 18 - MuMIn-1.14.0/MuMIn/R/coeffs.R | 18 - MuMIn-1.14.0/MuMIn/R/dredge.R | 62 ++++-- MuMIn-1.14.0/MuMIn/R/ext.R | 272 ++++++++-------------------- MuMIn-1.14.0/MuMIn/R/getAllTerms.R | 51 ++++- MuMIn-1.14.0/MuMIn/R/glm-link-new.R |only MuMIn-1.14.0/MuMIn/R/is.R | 9 MuMIn-1.14.0/MuMIn/R/methods-nobs.R | 13 - MuMIn-1.14.0/MuMIn/R/methods-predict.R |only MuMIn-1.14.0/MuMIn/R/model.avg.R | 51 +++-- MuMIn-1.14.0/MuMIn/R/model.sel.R | 31 ++- MuMIn-1.14.0/MuMIn/R/pdredge.R | 37 ++- MuMIn-1.14.0/MuMIn/R/predict-new.R |only MuMIn-1.14.0/MuMIn/R/predict.R | 8 MuMIn-1.14.0/MuMIn/R/quasiLik.R | 34 ++- MuMIn-1.14.0/MuMIn/R/r.squaredGLMM.R | 11 - MuMIn-1.14.0/MuMIn/R/r.squaredLR.R | 32 ++- MuMIn-1.14.0/MuMIn/R/std.coef.R |only MuMIn-1.14.0/MuMIn/R/stdize.R | 27 ++ MuMIn-1.14.0/MuMIn/R/updateable.R | 10 - MuMIn-1.14.0/MuMIn/R/utils-models.R | 11 - MuMIn-1.14.0/MuMIn/data/Beetle.rda |binary MuMIn-1.14.0/MuMIn/data/Cement.rda |binary MuMIn-1.14.0/MuMIn/data/GPA.rda |only MuMIn-1.14.0/MuMIn/man/ICs.Rd | 2 MuMIn-1.14.0/MuMIn/man/QIC.Rd | 8 MuMIn-1.14.0/MuMIn/man/avgpred.Rd |only MuMIn-1.14.0/MuMIn/man/dredge.Rd | 14 + MuMIn-1.14.0/MuMIn/man/glm.link.Rd |only MuMIn-1.14.0/MuMIn/man/gpa.Rd |only MuMIn-1.14.0/MuMIn/man/importance.Rd | 4 MuMIn-1.14.0/MuMIn/man/mod.sel.Rd | 9 MuMIn-1.14.0/MuMIn/man/model-utils.Rd | 34 +-- MuMIn-1.14.0/MuMIn/man/model.avg.Rd | 11 - MuMIn-1.14.0/MuMIn/man/pdredge.Rd | 3 MuMIn-1.14.0/MuMIn/man/std.coef.Rd |only MuMIn-1.14.0/MuMIn/man/stdize.Rd | 43 ++-- MuMIn-1.14.0/MuMIn/man/supported-classes.Rd | 5 MuMIn-1.14.0/MuMIn/tests/coxme.R | 14 - MuMIn-1.14.0/MuMIn/tests/misc-tests.R | 4 47 files changed, 575 insertions(+), 448 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.2.4 dated 2014-11-21 and 1.2.5 dated 2015-06-04
bpcp-1.2.4/bpcp/demo/Figure3.R |only bpcp-1.2.4/bpcp/demo/Figure4.R |only bpcp-1.2.4/bpcp/demo/Simulation.R |only bpcp-1.2.4/bpcp/demo/SimulationBootOnly.R |only bpcp-1.2.5/bpcp/DESCRIPTION | 8 ++--- bpcp-1.2.5/bpcp/MD5 | 36 +++++++++++++---------- bpcp-1.2.5/bpcp/NAMESPACE | 2 - bpcp-1.2.5/bpcp/NEWS | 8 +++++ bpcp-1.2.5/bpcp/R/bpcp2sample.R | 5 +-- bpcp-1.2.5/bpcp/R/kmciFunctions.R | 40 ++++++++++++++++++++------ bpcp-1.2.5/bpcp/demo/00Index | 14 +++------ bpcp-1.2.5/bpcp/demo/FigureSclerosis.R |only bpcp-1.2.5/bpcp/demo/FigureWilms.R |only bpcp-1.2.5/bpcp/demo/NotesMMandMC.R |only bpcp-1.2.5/bpcp/demo/Simulation2013.R |only bpcp-1.2.5/bpcp/demo/Simulation2015.R |only bpcp-1.2.5/bpcp/demo/SimulationBootOnly2013.R |only bpcp-1.2.5/bpcp/inst/CITATION | 27 +++++++++++++---- bpcp-1.2.5/bpcp/inst/doc |only bpcp-1.2.5/bpcp/man/bpcp-internal.Rd | 5 +-- bpcp-1.2.5/bpcp/man/bpcp-package.Rd | 14 +++++---- bpcp-1.2.5/bpcp/man/bpcp2samp.Rd | 4 +- bpcp-1.2.5/bpcp/man/bpcpControl.Rd |only bpcp-1.2.5/bpcp/man/fixtdiff.Rd | 4 +- bpcp-1.2.5/bpcp/man/kmciALL.Rd | 15 +++++---- 25 files changed, 118 insertions(+), 64 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.2 dated 2015-01-08 and 1.5.3 dated 2015-06-04
ssym-1.5.2/ssym/R/itpM.R |only ssym-1.5.2/ssym/R/itpM2.R |only ssym-1.5.2/ssym/R/itpM3.R |only ssym-1.5.2/ssym/R/lambda.hat.R |only ssym-1.5.2/ssym/R/print.ssym.R |only ssym-1.5.2/ssym/man/itpM.Rd |only ssym-1.5.2/ssym/man/itpM2.Rd |only ssym-1.5.2/ssym/man/itpM3.Rd |only ssym-1.5.2/ssym/man/lambda.hat.Rd |only ssym-1.5.3/ssym/DESCRIPTION | 16 ssym-1.5.3/ssym/MD5 | 115 +-- ssym-1.5.3/ssym/NAMESPACE | 16 ssym-1.5.3/ssym/R/AIC.ssym.R | 9 ssym-1.5.3/ssym/R/BIC.ssym.R | 9 ssym-1.5.3/ssym/R/coef.ssym.R | 2 ssym-1.5.3/ssym/R/envelope.R |only ssym-1.5.3/ssym/R/estfun.ssym.R | 2 ssym-1.5.3/ssym/R/extra.parameter.R |only ssym-1.5.3/ssym/R/influence.ssym.R | 35 ssym-1.5.3/ssym/R/itpE.R | 55 + ssym-1.5.3/ssym/R/itpE2.R | 68 + ssym-1.5.3/ssym/R/itpE3.R | 42 + ssym-1.5.3/ssym/R/itpEC.R |only ssym-1.5.3/ssym/R/itpEC2.R |only ssym-1.5.3/ssym/R/logLik.ssym.R | 7 ssym-1.5.3/ssym/R/ncs.R | 82 +- ssym-1.5.3/ssym/R/np.graph.R | 153 ++-- ssym-1.5.3/ssym/R/plot.ssym.R | 26 ssym-1.5.3/ssym/R/psp.R | 56 + ssym-1.5.3/ssym/R/residuals.ssym.R | 5 ssym-1.5.3/ssym/R/ssym.l.R | 1240 +++++++++------------------------ ssym-1.5.3/ssym/R/ssym.l2.R |only ssym-1.5.3/ssym/R/ssym.nl.R | 818 ++++++++------------- ssym-1.5.3/ssym/R/summary.ssym.R | 131 +-- ssym-1.5.3/ssym/R/vcov.ssym.R | 3 ssym-1.5.3/ssym/data/Baboons.rda |only ssym-1.5.3/ssym/data/Steel.rda |only ssym-1.5.3/ssym/man/AIC.ssym.Rd | 2 ssym-1.5.3/ssym/man/BIC.ssym.Rd | 2 ssym-1.5.3/ssym/man/Baboons.Rd |only ssym-1.5.3/ssym/man/Biaxial.Rd | 2 ssym-1.5.3/ssym/man/Claims.Rd | 4 ssym-1.5.3/ssym/man/Erabbits.Rd | 15 ssym-1.5.3/ssym/man/Ovocytes.Rd | 6 ssym-1.5.3/ssym/man/Steel.Rd |only ssym-1.5.3/ssym/man/coef.ssym.Rd | 2 ssym-1.5.3/ssym/man/envelope.Rd |only ssym-1.5.3/ssym/man/estfun.ssym.Rd | 2 ssym-1.5.3/ssym/man/extra.parameter.Rd |only ssym-1.5.3/ssym/man/fitted.ssym.Rd | 2 ssym-1.5.3/ssym/man/influence.ssym.Rd | 2 ssym-1.5.3/ssym/man/itpE.Rd | 2 ssym-1.5.3/ssym/man/itpE2.Rd | 2 ssym-1.5.3/ssym/man/itpE3.Rd | 2 ssym-1.5.3/ssym/man/itpEC.Rd |only ssym-1.5.3/ssym/man/itpEC2.Rd |only ssym-1.5.3/ssym/man/logLik.ssym.Rd | 2 ssym-1.5.3/ssym/man/ncs.Rd | 23 ssym-1.5.3/ssym/man/np.graph.Rd | 39 - ssym-1.5.3/ssym/man/plot.ssym.Rd | 6 ssym-1.5.3/ssym/man/print.ssym.Rd | 4 ssym-1.5.3/ssym/man/psp.Rd | 17 ssym-1.5.3/ssym/man/residuals.ssym.Rd | 2 ssym-1.5.3/ssym/man/rvgs.Rd | 8 ssym-1.5.3/ssym/man/ssym-package.Rd | 14 ssym-1.5.3/ssym/man/ssym.l.Rd | 262 ++++-- ssym-1.5.3/ssym/man/ssym.l2.Rd |only ssym-1.5.3/ssym/man/ssym.nl.Rd | 222 +++-- ssym-1.5.3/ssym/man/summary.ssym.Rd | 4 ssym-1.5.3/ssym/man/vcov.ssym.Rd | 2 70 files changed, 1604 insertions(+), 1936 deletions(-)
Title: Predicting Species Accumulation Curves
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>
Diff between preseqR versions 1.1.1 dated 2015-04-01 and 1.2.1 dated 2015-06-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/continued_fraction.R | 16 ++++++++++------ README.md | 4 ++-- man/preseqR.rfa.curve.Rd | 6 +++++- man/preseqR.rfa.species.accum.curve.Rd | 6 +++++- 6 files changed, 31 insertions(+), 19 deletions(-)
Title: Genetic Analysis Package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
Diff between gap versions 1.1-13 dated 2015-06-03 and 1.1-14 dated 2015-06-04
ChangeLog | 4 +++ DESCRIPTION | 15 ++++++------- MD5 | 46 ++++++++++++++++++++-------------------- inst/doc/gap.Rnw | 2 - inst/doc/gap.pdf |binary inst/doc/h2.R | 35 +----------------------------- inst/doc/h2.Rnw | 15 ++++++------- inst/doc/h2.pdf |binary inst/doc/jss.pdf |binary inst/doc/pedtodot.pdf |binary inst/doc/rnews.pdf |binary vignettes/figures/4w.pdf |binary vignettes/figures/ESplot.pdf |binary vignettes/figures/MCMCglmm1.pdf |binary vignettes/figures/asplot.pdf |binary vignettes/figures/bugs.pdf |binary vignettes/figures/h2.pdf |binary vignettes/figures/h2l.pdf |binary vignettes/figures/jags.pdf |binary vignettes/figures/l51.pdf |binary vignettes/figures/lukas.pdf |binary vignettes/figures/qqunif.pdf |binary vignettes/gap.Rnw | 2 - vignettes/h2.Rnw | 15 ++++++------- 24 files changed, 52 insertions(+), 82 deletions(-)
More information about odds.converter at CRAN
Permanent link
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml versions 2.3 dated 2015-05-20 and 2.3.1 dated 2015-06-04
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/kml.R | 8 ++++++++ 3 files changed, 15 insertions(+), 7 deletions(-)
Title: Model Based Clustering for Mixed Data
Description: Model-based clustering of mixed data (i.e. data which consist of continuous, binary, ordinal or nominal variables) using a parsimonious mixture of latent Gaussian variable models.
Author: Damien McParland
Maintainer: Damien McParland <damien.mcparland@ucd.ie>
Diff between clustMD versions 1.0 dated 2014-06-12 and 1.1 dated 2015-06-04
DESCRIPTION | 10 - MD5 | 22 +- R/E.step.R | 82 +++++----- R/M.step.R | 397 ++++++++++++++++++++++++++------------------------- R/ObsLogLikelihood.R | 88 +++++------ R/clustMD-internal.R | 260 ++++++++++++++++----------------- R/clustMD.R | 331 ++++++++++++++++++++++-------------------- R/npars_clustMD.R | 74 ++++----- R/perc.cutoffs.R | 10 - R/z.moments.R | 84 +++++----- R/z.nom.diag.R | 34 ++-- man/clustMD.Rd | 16 +- 12 files changed, 718 insertions(+), 690 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.2-06 dated 2015-01-23 and 1.2-07 dated 2015-06-04
PowerTOST-1.2-06/PowerTOST/R/power2.R |only PowerTOST-1.2-07/PowerTOST/DESCRIPTION | 14 ++-- PowerTOST-1.2-07/PowerTOST/MD5 | 31 ++++----- PowerTOST-1.2-07/PowerTOST/NAMESPACE | 2 PowerTOST-1.2-07/PowerTOST/NEWS | 10 ++ PowerTOST-1.2-07/PowerTOST/R/Fieller.R | 14 ++-- PowerTOST-1.2-07/PowerTOST/R/expSampleSize.R | 1 PowerTOST-1.2-07/PowerTOST/R/pa.scABE.R | 78 ++++++++++++----------- PowerTOST-1.2-07/PowerTOST/R/power_scABEL.R | 23 ++---- PowerTOST-1.2-07/PowerTOST/R/pwrA_S3methods.R | 3 PowerTOST-1.2-07/PowerTOST/R/samplesize_scABEL.R | 33 +++++---- PowerTOST-1.2-07/PowerTOST/R/scABEL.R |only PowerTOST-1.2-07/PowerTOST/man/pa.ABE.Rd | 11 +-- PowerTOST-1.2-07/PowerTOST/man/pa.scABE.Rd | 6 + PowerTOST-1.2-07/PowerTOST/man/power.TOST.Rd | 16 +--- PowerTOST-1.2-07/PowerTOST/man/power.scABEL.Rd | 10 ++ PowerTOST-1.2-07/PowerTOST/man/sampleN.scABEL.Rd | 12 ++- PowerTOST-1.2-07/PowerTOST/man/scABEL.Rd |only 18 files changed, 144 insertions(+), 120 deletions(-)
Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>
Diff between clusterCrit versions 1.2.4 dated 2014-12-11 and 1.2.5 dated 2015-06-04
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ build/clusterCrit.pdf |binary build/partial.rdb |binary build/vignette.rds |binary inst/benchmark/Makefile | 17 +++-------------- inst/unitTests/Makefile | 14 +------------- src/logFile.f95 |only src/timer.f95 |only 9 files changed, 17 insertions(+), 38 deletions(-)
Title: Coarsened Exact Matching
Description: Implementation of the Coarsened Exact Matching algorithm.
Author: Iacus, Stefano M., King, Gary, Porro, Giuseppe
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between cem versions 1.1.10 dated 2014-03-25 and 1.1.16 dated 2015-06-04
.Rinstignore | 7 +- DESCRIPTION | 17 +++---- MD5 | 85 +++++++++++++++++++++++++---------- NAMESPACE | 12 +++- R/att.R | 8 ++- R/cem.R | 2 R/cem.main.R | 16 ++---- R/imbspace.plot.R | 2 R/k2k.R | 92 ++++++++++++++++++++++++++++++++++++-- R/relax.cem.R | 35 +++++++++++--- R/relax.plot.R | 9 ++- R/search.match.R | 4 - R/spacegraph.R | 4 - build/vignette.rds |binary inst/doc/Columbus_egg.jpg |only inst/doc/DW.tex |only inst/doc/JSS-paper.tex |only inst/doc/JSSstyle |only inst/doc/JSSstyle.zip |only inst/doc/att.tex |only inst/doc/balance-scale-redone.jpg |only inst/doc/cem.R | 90 ++++++++++++++++++------------------- inst/doc/cem.Rnw | 67 +++++++++++++-------------- inst/doc/cem.bib |only inst/doc/cem.pdf |binary inst/doc/coarsen1.pdf |only inst/doc/coarsen2.pdf |only inst/doc/d.tex |only inst/doc/imbalance.tex |only inst/doc/index.shtml |only inst/doc/outdata1.csv |only inst/doc/outdata2.csv |only inst/doc/outdata3.csv |only inst/doc/outdata4.csv |only inst/doc/outdata5.csv |only inst/doc/pair.tex |only inst/doc/resprev.tex |only inst/doc/teff.pdf |only inst/doc/upquote.sty |only man/L1.profile.Rd | 16 +++--- man/att.Rd | 2 man/cem.Rd | 1 man/combine.spacegraphs.Rd | 3 - man/imbspace.plot.Rd | 8 ++- man/k2k.Rd | 5 +- man/relax.cem.Rd | 6 +- man/spacegraph.Rd | 9 ++- vignettes/cem.Rnw | 4 + 48 files changed, 333 insertions(+), 171 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2 dated 2015-05-04 and 1.2.1 dated 2015-06-04
ChangeLog | 3 +++ DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/mask2Te.R | 2 +- man/sglasso-package.Rd | 4 ++-- src/sglasso_ccd_path.f90 | 4 ++-- src/sglasso_ccd_single.f90 | 4 ++-- src/sglasso_ccm_path.f90 | 4 ++-- src/sglasso_ccm_single.f90 | 4 ++-- 9 files changed, 28 insertions(+), 25 deletions(-)
Title: A Stacked Autoencoder Implementation with Interface to
'neuralnet'
Description: An implementation of a stacked sparse autoencoder for dimension reduction of features and pre-training of feed-forward neural networks
with the 'neuralnet' package is contained within this package. The package also includes a predict function for the stacked autoencoder object to generate the compressed
representation of new data if required. For the purposes of this package, 'stacked' is defined in line with http://ufldl.stanford.edu/wiki/index.php/Stacked_Autoencoders .
The underlying sparse autoencoder is defined in the documentation of 'autoencoder'.
Author: Stephen Hogg [aut, cre],
Eugene Dubossarsky [aut]
Maintainer: Stephen Hogg <saenet.r@gmail.com>
Diff between SAENET versions 1.0 dated 2015-02-03 and 1.1 dated 2015-06-04
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/SAENET.R | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and proportional odds models and fully parametric Cox-PH and proportional odds models. Also includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.3 dated 2015-06-03 and 1.2.4 dated 2015-06-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/icenReg_files/ic_par.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.3.0 dated 2015-06-03 and 0.3.1 dated 2015-06-04
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NEWS | 4 ++++ README.md | 6 +++++- build/vignette.rds |binary vignettes/introduction.Rmd | 2 +- 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.33 dated 2015-05-27 and 1.35 dated 2015-06-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/aSPUpath.r | 8 ++++---- README.md | 17 +++++++---------- 4 files changed, 18 insertions(+), 21 deletions(-)