Title: Soft Classification Performance Measures
Description: An extension of sensitivity, specificity, positive and negative
predictive value to continuous predicted and reference memberships in
[0, 1].
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>
Diff between softclassval versions 1.0-20150416 dated 2015-04-16 and 1.0-20160527 dated 2016-05-27
softclassval-1.0-20150416/softclassval/tests/tests.Rout |only softclassval-1.0-20160527/softclassval/DESCRIPTION | 13 +- softclassval-1.0-20160527/softclassval/MD5 | 32 ++--- softclassval-1.0-20160527/softclassval/NAMESPACE | 4 softclassval-1.0-20160527/softclassval/R/hardclasses.R | 29 ++--- softclassval-1.0-20160527/softclassval/R/operators.R | 57 +++++----- softclassval-1.0-20160527/softclassval/man/checkrp.Rd | 2 softclassval-1.0-20160527/softclassval/man/dev.Rd | 4 softclassval-1.0-20160527/softclassval/man/factor2matrix.Rd | 2 softclassval-1.0-20160527/softclassval/man/hard.Rd | 4 softclassval-1.0-20160527/softclassval/man/hardclasses.Rd | 2 softclassval-1.0-20160527/softclassval/man/nsamples.Rd | 2 softclassval-1.0-20160527/softclassval/man/operators.Rd | 4 softclassval-1.0-20160527/softclassval/man/performance.Rd | 7 + softclassval-1.0-20160527/softclassval/man/postproc.Rd | 4 softclassval-1.0-20160527/softclassval/man/softclassval-package.Rd | 2 softclassval-1.0-20160527/softclassval/man/softclassval.unittest.Rd | 2 softclassval-1.0-20160527/softclassval/tests/tests.Rout.save |only 18 files changed, 94 insertions(+), 76 deletions(-)
Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>
Diff between arrayhelpers versions 0.76-20120816 dated 2012-08-17 and 1.0-20160527 dated 2016-05-27
arrayhelpers-0.76-20120816/arrayhelpers/R/validate.R |only arrayhelpers-0.76-20120816/arrayhelpers/tests/tests.Rout |only arrayhelpers-1.0-20160527/arrayhelpers/DESCRIPTION | 31 +-- arrayhelpers-1.0-20160527/arrayhelpers/MD5 | 53 ++--- arrayhelpers-1.0-20160527/arrayhelpers/NAMESPACE | 17 + arrayhelpers-1.0-20160527/arrayhelpers/R/arrayhelpers.R | 34 +-- arrayhelpers-1.0-20160527/arrayhelpers/R/colSums.R | 8 arrayhelpers-1.0-20160527/arrayhelpers/R/countrows.R | 3 arrayhelpers-1.0-20160527/arrayhelpers/R/rowsum.R | 2 arrayhelpers-1.0-20160527/arrayhelpers/R/slice.R | 40 ++++ arrayhelpers-1.0-20160527/arrayhelpers/R/unittestdata.R |only arrayhelpers-1.0-20160527/arrayhelpers/R/unittests.R |only arrayhelpers-1.0-20160527/arrayhelpers/man/array2df.Rd | 57 ++--- arrayhelpers-1.0-20160527/arrayhelpers/man/array2vec.Rd | 33 +-- arrayhelpers-1.0-20160527/arrayhelpers/man/arrayhelpers-package.Rd | 12 + arrayhelpers-1.0-20160527/arrayhelpers/man/arrayhelpers.unittest.Rd | 16 - arrayhelpers-1.0-20160527/arrayhelpers/man/colSums.Rd | 97 ++++------ arrayhelpers-1.0-20160527/arrayhelpers/man/countrows.Rd | 15 - arrayhelpers-1.0-20160527/arrayhelpers/man/delold.Rd | 15 + arrayhelpers-1.0-20160527/arrayhelpers/man/dropdimnames.Rd | 19 + arrayhelpers-1.0-20160527/arrayhelpers/man/ensuredim.Rd | 24 +- arrayhelpers-1.0-20160527/arrayhelpers/man/groupsum.Rd | 35 +-- arrayhelpers-1.0-20160527/arrayhelpers/man/makeNd.Rd | 81 ++++---- arrayhelpers-1.0-20160527/arrayhelpers/man/ndim.Rd | 18 - arrayhelpers-1.0-20160527/arrayhelpers/man/numericindex.Rd | 16 - arrayhelpers-1.0-20160527/arrayhelpers/man/rowsum.Rd | 30 +-- arrayhelpers-1.0-20160527/arrayhelpers/man/slice.Rd | 32 +-- arrayhelpers-1.0-20160527/arrayhelpers/man/stack.Rd | 29 +- arrayhelpers-1.0-20160527/arrayhelpers/man/ta.Rd | 19 + arrayhelpers-1.0-20160527/arrayhelpers/tests/tests.Rout.save |only 30 files changed, 386 insertions(+), 350 deletions(-)
Title: Simultaneous Generation of Multivariate Binary and Normal
Variates
Description: Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012).
Author: Anup Amatya, Hakan Demirtas
Maintainer: Anup Amatya <aamatya@nmsu.edu>
Diff between BinNor versions 2.0 dated 2012-05-24 and 2.1 dated 2016-05-27
DESCRIPTION | 18 ++++++++---------- MD5 | 6 +++--- NAMESPACE | 15 +++------------ man/BinNor-package.Rd | 9 +++++---- 4 files changed, 19 insertions(+), 29 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.0-1 dated 2016-03-15 and 1.0-2 dated 2016-05-27
VGAM-1.0-1/VGAM/R/add1.vglm.q |only VGAM-1.0-1/VGAM/R/plot.vglm.q |only VGAM-1.0-1/VGAM/R/step.vglm.q |only VGAM-1.0-1/VGAM/man/ozibetaUC.Rd |only VGAM-1.0-1/VGAM/man/rlplot.egev.Rd |only VGAM-1.0-2/VGAM/BUGS | 16 VGAM-1.0-2/VGAM/DESCRIPTION | 13 VGAM-1.0-2/VGAM/MD5 | 424 - VGAM-1.0-2/VGAM/NAMESPACE | 52 VGAM-1.0-2/VGAM/NEWS | 58 VGAM-1.0-2/VGAM/R/Links.R | 4 VGAM-1.0-2/VGAM/R/aamethods.q | 9 VGAM-1.0-2/VGAM/R/attrassign.R | 36 VGAM-1.0-2/VGAM/R/bAIC.q | 2 VGAM-1.0-2/VGAM/R/build.terms.vlm.q | 8 VGAM-1.0-2/VGAM/R/calibrate.q | 4 VGAM-1.0-2/VGAM/R/cao.R | 12 VGAM-1.0-2/VGAM/R/cao.fit.q | 124 VGAM-1.0-2/VGAM/R/coef.vlm.q | 4 VGAM-1.0-2/VGAM/R/confint.vlm.R | 20 VGAM-1.0-2/VGAM/R/cqo.R | 8 VGAM-1.0-2/VGAM/R/cqo.fit.q | 39 VGAM-1.0-2/VGAM/R/deviance.vlm.q | 4 VGAM-1.0-2/VGAM/R/effects.vglm.q | 2 VGAM-1.0-2/VGAM/R/family.actuary.R | 1219 ++-- VGAM-1.0-2/VGAM/R/family.aunivariate.R | 1064 ++++ VGAM-1.0-2/VGAM/R/family.basics.R | 182 VGAM-1.0-2/VGAM/R/family.binomial.R | 145 VGAM-1.0-2/VGAM/R/family.bivariate.R | 182 VGAM-1.0-2/VGAM/R/family.categorical.R | 196 VGAM-1.0-2/VGAM/R/family.censored.R | 54 VGAM-1.0-2/VGAM/R/family.circular.R | 31 VGAM-1.0-2/VGAM/R/family.exp.R | 10 VGAM-1.0-2/VGAM/R/family.extremes.R | 1448 +++-- VGAM-1.0-2/VGAM/R/family.functions.R | 3 VGAM-1.0-2/VGAM/R/family.genetic.R | 45 VGAM-1.0-2/VGAM/R/family.glmgam.R | 67 VGAM-1.0-2/VGAM/R/family.loglin.R | 4 VGAM-1.0-2/VGAM/R/family.math.R | 10 VGAM-1.0-2/VGAM/R/family.mixture.R | 26 VGAM-1.0-2/VGAM/R/family.nonlinear.R | 12 VGAM-1.0-2/VGAM/R/family.normal.R | 317 - VGAM-1.0-2/VGAM/R/family.others.R | 463 + VGAM-1.0-2/VGAM/R/family.positive.R | 383 - VGAM-1.0-2/VGAM/R/family.qreg.R | 376 - VGAM-1.0-2/VGAM/R/family.rcim.R | 26 VGAM-1.0-2/VGAM/R/family.rcqo.R | 16 VGAM-1.0-2/VGAM/R/family.robust.R | 18 VGAM-1.0-2/VGAM/R/family.rrr.R | 172 VGAM-1.0-2/VGAM/R/family.sur.R | 8 VGAM-1.0-2/VGAM/R/family.survival.R | 24 VGAM-1.0-2/VGAM/R/family.ts.R | 1051 ++-- VGAM-1.0-2/VGAM/R/family.univariate.R | 1581 ++---- VGAM-1.0-2/VGAM/R/family.vglm.R | 4 VGAM-1.0-2/VGAM/R/family.zeroinf.R | 5779 +++++++++++++---------- VGAM-1.0-2/VGAM/R/fittedvlm.R | 2 VGAM-1.0-2/VGAM/R/formula.vlm.q | 2 VGAM-1.0-2/VGAM/R/generic.q | 2 VGAM-1.0-2/VGAM/R/links.q | 24 VGAM-1.0-2/VGAM/R/logLik.vlm.q | 2 VGAM-1.0-2/VGAM/R/lrwaldtest.R | 8 VGAM-1.0-2/VGAM/R/model.matrix.vglm.q | 182 VGAM-1.0-2/VGAM/R/mux.q | 14 VGAM-1.0-2/VGAM/R/nobs.R | 2 VGAM-1.0-2/VGAM/R/penvps.R |only VGAM-1.0-2/VGAM/R/plot.vgam.R |only VGAM-1.0-2/VGAM/R/plot.vglm.R |only VGAM-1.0-2/VGAM/R/predict.vgam.q | 7 VGAM-1.0-2/VGAM/R/predict.vglm.q | 8 VGAM-1.0-2/VGAM/R/predict.vlm.q | 20 VGAM-1.0-2/VGAM/R/print.vglm.q | 8 VGAM-1.0-2/VGAM/R/print.vlm.q | 2 VGAM-1.0-2/VGAM/R/psfun.R |only VGAM-1.0-2/VGAM/R/psv2magic.R |only VGAM-1.0-2/VGAM/R/qrrvglm.control.q | 13 VGAM-1.0-2/VGAM/R/qtplot.q | 27 VGAM-1.0-2/VGAM/R/residuals.vlm.q | 8 VGAM-1.0-2/VGAM/R/rrvglm.R | 13 VGAM-1.0-2/VGAM/R/rrvglm.control.q | 2 VGAM-1.0-2/VGAM/R/rrvglm.fit.q | 17 VGAM-1.0-2/VGAM/R/s.q | 2 VGAM-1.0-2/VGAM/R/s.vam.q | 14 VGAM-1.0-2/VGAM/R/simulate.vglm.R | 17 VGAM-1.0-2/VGAM/R/smart.R | 8 VGAM-1.0-2/VGAM/R/summary.vgam.q | 4 VGAM-1.0-2/VGAM/R/summary.vglm.q | 2 VGAM-1.0-2/VGAM/R/summary.vlm.q | 4 VGAM-1.0-2/VGAM/R/vgam.R | 133 VGAM-1.0-2/VGAM/R/vgam.control.q | 10 VGAM-1.0-2/VGAM/R/vgam.fit.q | 131 VGAM-1.0-2/VGAM/R/vgam.match.q | 8 VGAM-1.0-2/VGAM/R/vglm.R | 17 VGAM-1.0-2/VGAM/R/vglm.control.q | 2 VGAM-1.0-2/VGAM/R/vglm.fit.q | 273 - VGAM-1.0-2/VGAM/R/vlm.R | 4 VGAM-1.0-2/VGAM/R/vlm.wfit.q | 138 VGAM-1.0-2/VGAM/R/vsmooth.spline.q | 40 VGAM-1.0-2/VGAM/build/vignette.rds |binary VGAM-1.0-2/VGAM/data/Huggins89.t1.rda |binary VGAM-1.0-2/VGAM/data/Huggins89table1.rda |binary VGAM-1.0-2/VGAM/data/alclevels.rda |binary VGAM-1.0-2/VGAM/data/alcoff.rda |binary VGAM-1.0-2/VGAM/data/auuc.rda |binary VGAM-1.0-2/VGAM/data/backPain.rda |binary VGAM-1.0-2/VGAM/data/beggs.rda |binary VGAM-1.0-2/VGAM/data/car.all.rda |binary VGAM-1.0-2/VGAM/data/cfibrosis.rda |binary VGAM-1.0-2/VGAM/data/corbet.rda |binary VGAM-1.0-2/VGAM/data/crashbc.rda |binary VGAM-1.0-2/VGAM/data/crashf.rda |binary VGAM-1.0-2/VGAM/data/crashi.rda |binary VGAM-1.0-2/VGAM/data/crashmc.rda |binary VGAM-1.0-2/VGAM/data/crashp.rda |binary VGAM-1.0-2/VGAM/data/crashtr.rda |binary VGAM-1.0-2/VGAM/data/deermice.rda |binary VGAM-1.0-2/VGAM/data/ducklings.rda |binary VGAM-1.0-2/VGAM/data/finney44.rda |binary VGAM-1.0-2/VGAM/data/flourbeetle.rda |binary VGAM-1.0-2/VGAM/data/hspider.rda |binary VGAM-1.0-2/VGAM/data/lakeO.rda |binary VGAM-1.0-2/VGAM/data/leukemia.rda |binary VGAM-1.0-2/VGAM/data/marital.nz.rda |binary VGAM-1.0-2/VGAM/data/melbmaxtemp.rda |binary VGAM-1.0-2/VGAM/data/pneumo.rda |binary VGAM-1.0-2/VGAM/data/prinia.rda |binary VGAM-1.0-2/VGAM/data/ruge.rda |binary VGAM-1.0-2/VGAM/data/toxop.rda |binary VGAM-1.0-2/VGAM/data/venice.rda |binary VGAM-1.0-2/VGAM/data/venice90.rda |binary VGAM-1.0-2/VGAM/data/wine.rda |binary VGAM-1.0-2/VGAM/inst/doc/categoricalVGAM.pdf |binary VGAM-1.0-2/VGAM/inst/doc/crVGAM.pdf |binary VGAM-1.0-2/VGAM/man/AR1.Rd | 257 - VGAM-1.0-2/VGAM/man/AR1EIM.Rd |only VGAM-1.0-2/VGAM/man/AR1UC.Rd | 14 VGAM-1.0-2/VGAM/man/CommonVGAMffArguments.Rd | 22 VGAM-1.0-2/VGAM/man/Select.Rd | 3 VGAM-1.0-2/VGAM/man/VGAM-package.Rd | 19 VGAM-1.0-2/VGAM/man/betaII.Rd | 3 VGAM-1.0-2/VGAM/man/betaR.Rd | 1 VGAM-1.0-2/VGAM/man/betabinomUC.Rd | 45 VGAM-1.0-2/VGAM/man/betaff.Rd | 3 VGAM-1.0-2/VGAM/man/binom2.orUC.Rd | 18 VGAM-1.0-2/VGAM/man/binormal.Rd | 2 VGAM-1.0-2/VGAM/man/binormalUC.Rd | 2 VGAM-1.0-2/VGAM/man/calibrate.qrrvglm.control.Rd | 2 VGAM-1.0-2/VGAM/man/cens.gumbel.Rd | 2 VGAM-1.0-2/VGAM/man/clo.Rd | 2 VGAM-1.0-2/VGAM/man/cumulative.Rd | 3 VGAM-1.0-2/VGAM/man/dagum.Rd | 4 VGAM-1.0-2/VGAM/man/depvar.Rd | 2 VGAM-1.0-2/VGAM/man/dirichlet.Rd | 9 VGAM-1.0-2/VGAM/man/double.expbinomial.Rd | 2 VGAM-1.0-2/VGAM/man/ducklings.Rd | 2 VGAM-1.0-2/VGAM/man/fisk.Rd | 3 VGAM-1.0-2/VGAM/man/gaussianff.Rd | 2 VGAM-1.0-2/VGAM/man/gev.Rd | 119 VGAM-1.0-2/VGAM/man/gevUC.Rd | 62 VGAM-1.0-2/VGAM/man/gpd.Rd | 5 VGAM-1.0-2/VGAM/man/gpdUC.Rd | 34 VGAM-1.0-2/VGAM/man/gumbel.Rd | 25 VGAM-1.0-2/VGAM/man/gumbelUC.Rd | 2 VGAM-1.0-2/VGAM/man/guplot.Rd | 2 VGAM-1.0-2/VGAM/man/huber.Rd | 2 VGAM-1.0-2/VGAM/man/huberUC.Rd | 2 VGAM-1.0-2/VGAM/man/identitylink.Rd | 2 VGAM-1.0-2/VGAM/man/inv.paralogistic.Rd | 2 VGAM-1.0-2/VGAM/man/linkfun.Rd | 2 VGAM-1.0-2/VGAM/man/logc.Rd | 4 VGAM-1.0-2/VGAM/man/loge.Rd | 2 VGAM-1.0-2/VGAM/man/logoff.Rd | 2 VGAM-1.0-2/VGAM/man/lomax.Rd | 3 VGAM-1.0-2/VGAM/man/marital.nz.Rd | 2 VGAM-1.0-2/VGAM/man/melbmaxtemp.Rd | 2 VGAM-1.0-2/VGAM/man/multilogit.Rd | 2 VGAM-1.0-2/VGAM/man/multinomial.Rd | 21 VGAM-1.0-2/VGAM/man/nbcanlink.Rd | 2 VGAM-1.0-2/VGAM/man/negbinomial.Rd | 110 VGAM-1.0-2/VGAM/man/negbinomial.size.Rd | 4 VGAM-1.0-2/VGAM/man/normal.vcm.Rd | 17 VGAM-1.0-2/VGAM/man/notdocumentedyet.Rd | 35 VGAM-1.0-2/VGAM/man/oiposbinomUC.Rd |only VGAM-1.0-2/VGAM/man/oipospoisUC.Rd |only VGAM-1.0-2/VGAM/man/oipospoisson.Rd |only VGAM-1.0-2/VGAM/man/oxtemp.Rd | 2 VGAM-1.0-2/VGAM/man/paralogistic.Rd | 3 VGAM-1.0-2/VGAM/man/plotrcim0.Rd | 9 VGAM-1.0-2/VGAM/man/plotvgam.Rd | 2 VGAM-1.0-2/VGAM/man/plotvglm.Rd | 99 VGAM-1.0-2/VGAM/man/poissonff.Rd | 2 VGAM-1.0-2/VGAM/man/posbinomUC.Rd | 6 VGAM-1.0-2/VGAM/man/posgeomUC.Rd | 2 VGAM-1.0-2/VGAM/man/posnegbinUC.Rd | 9 VGAM-1.0-2/VGAM/man/posnegbinomial.Rd | 17 VGAM-1.0-2/VGAM/man/pospoisUC.Rd | 7 VGAM-1.0-2/VGAM/man/pospoisson.Rd | 4 VGAM-1.0-2/VGAM/man/ps.Rd |only VGAM-1.0-2/VGAM/man/qrrvglm.control.Rd | 6 VGAM-1.0-2/VGAM/man/qtplot.gumbel.Rd | 7 VGAM-1.0-2/VGAM/man/reciprocal.Rd | 2 VGAM-1.0-2/VGAM/man/rlplot.gevff.Rd |only VGAM-1.0-2/VGAM/man/rrvglm.control.Rd | 2 VGAM-1.0-2/VGAM/man/rrvglm.optim.control.Rd | 2 VGAM-1.0-2/VGAM/man/s.Rd | 17 VGAM-1.0-2/VGAM/man/sinmad.Rd | 4 VGAM-1.0-2/VGAM/man/trplot.qrrvglm.Rd | 6 VGAM-1.0-2/VGAM/man/undocumented-methods.Rd | 2 VGAM-1.0-2/VGAM/man/vgam.Rd | 18 VGAM-1.0-2/VGAM/man/vgam.control.Rd | 10 VGAM-1.0-2/VGAM/man/vglm.Rd | 1 VGAM-1.0-2/VGAM/man/vglm.control.Rd | 4 VGAM-1.0-2/VGAM/man/zanegbinomial.Rd | 47 VGAM-1.0-2/VGAM/man/zapoisson.Rd | 4 VGAM-1.0-2/VGAM/man/zetaff.Rd | 9 VGAM-1.0-2/VGAM/man/zibinomUC.Rd | 17 VGAM-1.0-2/VGAM/man/zibinomial.Rd | 4 VGAM-1.0-2/VGAM/man/zinegbinomial.Rd | 35 VGAM-1.0-2/VGAM/man/zipebcom.Rd | 9 VGAM-1.0-2/VGAM/man/zipoisUC.Rd | 5 VGAM-1.0-2/VGAM/man/zipoisson.Rd | 40 VGAM-1.0-2/VGAM/man/zoabetaR.Rd |only VGAM-1.0-2/VGAM/man/zoabetaUC.Rd |only 222 files changed, 10636 insertions(+), 7589 deletions(-)
Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for
Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>
Diff between TipDatingBeast versions 0.1-6 dated 2015-07-29 and 1.0-2 dated 2016-05-27
TipDatingBeast-0.1-6/TipDatingBeast/R/RandomCluster2.R |only TipDatingBeast-0.1-6/TipDatingBeast/R/RandomDates2.R |only TipDatingBeast-0.1-6/TipDatingBeast/inst/example/Flu.xml |only TipDatingBeast-0.1-6/TipDatingBeast/inst/example/Flu2.xml |only TipDatingBeast-0.1-6/TipDatingBeast/inst/example/clusters.Flu2.csv |only TipDatingBeast-0.1-6/TipDatingBeast/man/Flu.Rd |only TipDatingBeast-0.1-6/TipDatingBeast/man/Flu2.Rd |only TipDatingBeast-0.1-6/TipDatingBeast/man/RandomCluster2.Rd |only TipDatingBeast-0.1-6/TipDatingBeast/man/RandomDates2.Rd |only TipDatingBeast-0.1-6/TipDatingBeast/man/clusters.Flu2.Rd |only TipDatingBeast-1.0-2/TipDatingBeast/DESCRIPTION | 13 TipDatingBeast-1.0-2/TipDatingBeast/MD5 | 47 - TipDatingBeast-1.0-2/TipDatingBeast/NAMESPACE | 7 TipDatingBeast-1.0-2/TipDatingBeast/R/ListTaxa.R | 97 ++- TipDatingBeast-1.0-2/TipDatingBeast/R/Plot_DRT.R |only TipDatingBeast-1.0-2/TipDatingBeast/R/Plot_LOOCV.R |only TipDatingBeast-1.0-2/TipDatingBeast/R/RandomCluster.R | 258 ++++++--- TipDatingBeast-1.0-2/TipDatingBeast/R/RandomDates.R | 197 +++++- TipDatingBeast-1.0-2/TipDatingBeast/R/TaxaOut.R | 279 ++++++--- TipDatingBeast-1.0-2/TipDatingBeast/R/TaxonOut.R | 285 +++++++--- TipDatingBeast-1.0-2/TipDatingBeast/inst/example/Flu_BEAST_18.xml |only TipDatingBeast-1.0-2/TipDatingBeast/inst/example/Flu_BEAST_232.xml |only TipDatingBeast-1.0-2/TipDatingBeast/inst/example/Tutorial_TipDatingBEAST.pdf |only TipDatingBeast-1.0-2/TipDatingBeast/man/Flu_BEAST_18.Rd |only TipDatingBeast-1.0-2/TipDatingBeast/man/Flu_BEAST_232.Rd |only TipDatingBeast-1.0-2/TipDatingBeast/man/ListTaxa.Rd | 4 TipDatingBeast-1.0-2/TipDatingBeast/man/PlotDRT.Rd |only TipDatingBeast-1.0-2/TipDatingBeast/man/PlotLOOCV.Rd |only TipDatingBeast-1.0-2/TipDatingBeast/man/RandomCluster.Rd | 43 - TipDatingBeast-1.0-2/TipDatingBeast/man/RandomDates.Rd | 19 TipDatingBeast-1.0-2/TipDatingBeast/man/TaxaOut.Rd | 23 TipDatingBeast-1.0-2/TipDatingBeast/man/TaxonOut.Rd | 16 TipDatingBeast-1.0-2/TipDatingBeast/man/TipDatingBeast-package.Rd | 12 TipDatingBeast-1.0-2/TipDatingBeast/man/clusters.Flu.Rd | 4 34 files changed, 933 insertions(+), 371 deletions(-)
More information about TipDatingBeast at CRAN
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Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Among available
features there are: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 1.0-1 dated 2015-10-22 and 1.1.1 dated 2016-05-27
DESCRIPTION | 17 INSTALL | 10 LICENSE | 6 MD5 | 541 +++++++++++++++---------------- NAMESPACE | 10 NEWS | 34 + R/ICU_settings.R | 2 R/compare.R | 2 R/draft_encdetect.R | 2 R/draft_files.R | 2 R/encoding.R | 4 R/encoding_conversion.R | 2 R/encoding_detection.R | 2 R/encoding_management.R | 2 R/escape.R | 2 R/install.R | 2 R/internal_prepare_arg.R | 19 - R/internal_test.R | 2 R/join.R | 76 +++- R/length.R | 2 R/locale.R | 34 - R/locale_management.R | 2 R/opts.R | 2 R/pad.R | 2 R/random.R | 2 R/reverse.R | 2 R/search.R | 9 R/search_count_4.R | 2 R/search_count_bound.R | 2 R/search_detect_4.R | 26 - R/search_extract_4.R | 2 R/search_extract_bound.R | 2 R/search_locate_4.R | 2 R/search_locate_bound.R | 2 R/search_match_4.R | 2 R/search_replace_4.R | 4 R/search_replace_na.R | 2 R/search_split_4.R | 2 R/search_split_bound.R | 6 R/search_startsendswith_4.R | 14 R/search_subset_4.R | 114 +++++- R/sort.R | 2 R/stats.R | 2 R/stringi-package.R | 25 - R/sub.R | 41 +- R/time_calendar.R | 2 R/time_format.R | 2 R/time_symbols.R | 2 R/time_zone.R | 2 R/todo_charclass.R | 2 R/todo_justify.R | 2 R/todo_rbnf.R | 2 R/todo_search_in.R | 2 R/todo_split.R | 2 R/trans_casemap.R | 2 R/trans_normalization.R | 2 R/trans_other.R | 2 R/trans_transliterate.R | 2 R/trim.R | 2 R/utils.R | 2 R/wrap.R | 2 configure | 18 - inst/AUTHORS | 3 inst/CITATION | 11 man/oper_comparison.Rd | 41 -- man/oper_plus.Rd | 3 man/stri_compare.Rd | 43 -- man/stri_count.Rd | 8 man/stri_count_boundaries.Rd | 73 ---- man/stri_datetime_add.Rd | 18 - man/stri_datetime_create.Rd | 17 man/stri_datetime_fields.Rd | 17 man/stri_datetime_format.Rd | 17 man/stri_datetime_fstr.Rd | 17 man/stri_datetime_now.Rd | 16 man/stri_datetime_symbols.Rd | 17 man/stri_detect.Rd | 33 - man/stri_dup.Rd | 6 man/stri_duplicated.Rd | 91 +---- man/stri_enc_detect.Rd | 12 man/stri_enc_detect2.Rd | 54 --- man/stri_enc_fromutf32.Rd | 12 man/stri_enc_info.Rd | 7 man/stri_enc_isascii.Rd | 12 man/stri_enc_isutf16.Rd | 10 man/stri_enc_isutf8.Rd | 12 man/stri_enc_list.Rd | 7 man/stri_enc_mark.Rd | 7 man/stri_enc_set.Rd | 6 man/stri_enc_toascii.Rd | 12 man/stri_enc_tonative.Rd | 12 man/stri_enc_toutf32.Rd | 12 man/stri_enc_toutf8.Rd | 14 man/stri_encode.Rd | 12 man/stri_escape_unicode.Rd | 3 man/stri_extract.Rd | 19 - man/stri_extract_boundaries.Rd | 85 ---- man/stri_flatten.Rd | 7 man/stri_info.Rd | 2 man/stri_install.Rd | 3 man/stri_isempty.Rd | 7 man/stri_join.Rd | 22 - man/stri_join_list.Rd |only man/stri_length.Rd | 7 man/stri_list2matrix.Rd | 3 man/stri_locale_info.Rd | 8 man/stri_locale_list.Rd | 7 man/stri_locale_set.Rd | 6 man/stri_locate.Rd | 20 - man/stri_locate_boundaries.Rd | 99 +---- man/stri_match.Rd | 25 - man/stri_numbytes.Rd | 7 man/stri_opts_brkiter.Rd | 23 - man/stri_opts_collator.Rd | 47 -- man/stri_opts_fixed.Rd | 4 man/stri_opts_regex.Rd | 4 man/stri_order.Rd | 45 -- man/stri_pad.Rd | 2 man/stri_rand_lipsum.Rd | 5 man/stri_rand_shuffle.Rd | 5 man/stri_rand_strings.Rd | 5 man/stri_read_lines.Rd | 4 man/stri_read_raw.Rd | 4 man/stri_replace.Rd | 14 man/stri_replace_na.Rd | 23 - man/stri_reverse.Rd | 3 man/stri_split.Rd | 11 man/stri_split_boundaries.Rd | 80 +--- man/stri_split_lines.Rd | 32 - man/stri_startsendswith.Rd | 23 - man/stri_stats_general.Rd | 3 man/stri_stats_latex.Rd | 3 man/stri_sub.Rd | 44 -- man/stri_subset.Rd | 72 ++-- man/stri_timezone_info.Rd | 18 - man/stri_timezone_list.Rd | 18 - man/stri_timezone_set.Rd | 20 - man/stri_trans_casemap.Rd | 83 +--- man/stri_trans_char.Rd | 19 - man/stri_trans_general.Rd | 19 - man/stri_trans_list.Rd | 19 - man/stri_trans_nf.Rd | 13 man/stri_trim.Rd | 24 - man/stri_unescape_unicode.Rd | 3 man/stri_unique.Rd | 46 -- man/stri_width.Rd | 6 man/stri_wrap.Rd | 69 --- man/stri_write_lines.Rd | 4 man/stringi-arguments.Rd | 37 +- man/stringi-encoding.Rd | 53 +-- man/stringi-locale.Rd | 104 ++--- man/stringi-package.Rd | 41 +- man/stringi-search-boundaries.Rd | 84 +--- man/stringi-search-charclass.Rd | 25 - man/stringi-search-coll.Rd | 65 +-- man/stringi-search-fixed.Rd | 22 - man/stringi-search-regex.Rd | 29 - man/stringi-search.Rd | 166 +-------- src/stri_ICU_settings.cpp | 2 src/stri_TODO_justify.cpp | 2 src/stri_TODO_splitpos.cpp | 2 src/stri_TODO_uchar.cpp | 2 src/stri_brkiter.cpp | 2 src/stri_brkiter.h | 2 src/stri_bytesearch_matcher.h | 2 src/stri_collator.cpp | 2 src/stri_common.cpp | 2 src/stri_compare.cpp | 2 src/stri_container_base.cpp | 2 src/stri_container_base.h | 2 src/stri_container_bytesearch.cpp | 2 src/stri_container_bytesearch.h | 2 src/stri_container_charclass.h | 2 src/stri_container_double.h | 2 src/stri_container_integer.h | 2 src/stri_container_listint.cpp | 2 src/stri_container_listint.h | 2 src/stri_container_listraw.cpp | 2 src/stri_container_listraw.h | 2 src/stri_container_listutf8.cpp | 2 src/stri_container_listutf8.h | 2 src/stri_container_logical.h | 2 src/stri_container_regex.cpp | 2 src/stri_container_regex.h | 2 src/stri_container_usearch.cpp | 2 src/stri_container_usearch.h | 2 src/stri_container_utf16.cpp | 2 src/stri_container_utf16.h | 2 src/stri_container_utf8.cpp | 2 src/stri_container_utf8.h | 2 src/stri_container_utf8_indexable.cpp | 2 src/stri_container_utf8_indexable.h | 2 src/stri_encoding_conversion.cpp | 2 src/stri_encoding_detection.cpp | 2 src/stri_encoding_management.cpp | 2 src/stri_escape.cpp | 2 src/stri_exception.cpp | 2 src/stri_exception.h | 2 src/stri_exports.h | 30 - src/stri_external.h | 2 src/stri_interval.h | 2 src/stri_intvec.h | 2 src/stri_join.cpp | 50 ++ src/stri_length.cpp | 2 src/stri_macros.h | 12 src/stri_messages.h | 7 src/stri_pad.cpp | 2 src/stri_prepare_arg.cpp | 2 src/stri_random.cpp | 2 src/stri_reverse.cpp | 2 src/stri_search_boundaries_count.cpp | 2 src/stri_search_boundaries_extract.cpp | 2 src/stri_search_boundaries_locate.cpp | 2 src/stri_search_boundaries_split.cpp | 2 src/stri_search_class_count.cpp | 2 src/stri_search_class_detect.cpp | 9 src/stri_search_class_extract.cpp | 2 src/stri_search_class_locate.cpp | 2 src/stri_search_class_replace.cpp | 32 + src/stri_search_class_split.cpp | 2 src/stri_search_class_startsendswith.cpp | 2 src/stri_search_class_subset.cpp | 84 ++++ src/stri_search_class_trim.cpp | 2 src/stri_search_coll_count.cpp | 2 src/stri_search_coll_detect.cpp | 11 src/stri_search_coll_extract.cpp | 2 src/stri_search_coll_locate.cpp | 2 src/stri_search_coll_replace.cpp | 30 + src/stri_search_coll_split.cpp | 2 src/stri_search_coll_startsendswith.cpp | 2 src/stri_search_coll_subset.cpp | 80 ++++ src/stri_search_common.cpp | 2 src/stri_search_fixed_count.cpp | 2 src/stri_search_fixed_detect.cpp | 11 src/stri_search_fixed_extract.cpp | 2 src/stri_search_fixed_locate.cpp | 2 src/stri_search_fixed_replace.cpp | 27 + src/stri_search_fixed_split.cpp | 2 src/stri_search_fixed_startsendswith.cpp | 2 src/stri_search_fixed_subset.cpp | 73 ++++ src/stri_search_in.cpp | 2 src/stri_search_other_replace.cpp | 2 src/stri_search_other_split.cpp | 2 src/stri_search_regex_count.cpp | 9 src/stri_search_regex_detect.cpp | 16 src/stri_search_regex_extract.cpp | 17 src/stri_search_regex_locate.cpp | 15 src/stri_search_regex_match.cpp | 19 - src/stri_search_regex_replace.cpp | 34 + src/stri_search_regex_split.cpp | 2 src/stri_search_regex_subset.cpp | 93 +++++ src/stri_sort.cpp | 2 src/stri_stats.cpp | 2 src/stri_string8.h | 8 src/stri_string8buf.h | 2 src/stri_stringi.cpp | 363 ++++++++++---------- src/stri_stringi.h | 2 src/stri_sub.cpp | 33 + src/stri_test.cpp | 2 src/stri_time_calendar.cpp | 2 src/stri_time_format.cpp | 2 src/stri_time_symbols.cpp | 2 src/stri_time_zone.cpp | 2 src/stri_trans_casemap.cpp | 2 src/stri_trans_normalization.cpp | 2 src/stri_trans_other.cpp | 2 src/stri_trans_transliterate.cpp | 2 src/stri_ucnv.cpp | 2 src/stri_ucnv.h | 2 src/stri_uloc.cpp | 2 src/stri_utils.cpp | 2 src/stri_wrap.cpp | 2 272 files changed, 2268 insertions(+), 2476 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.700.6.0 dated 2016-05-05 and 0.7.100.3.0 dated 2016-05-27
ChangeLog | 25 DESCRIPTION | 8 MD5 | 392 configure | 3934 +++++++++- configure.ac |only inst/NEWS.Rd | 20 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloLapack.h.in | 6 inst/include/armadillo | 46 inst/include/armadillo_bits/Cube_bones.hpp | 6 inst/include/armadillo_bits/Cube_meat.hpp | 68 inst/include/armadillo_bits/GenCube_bones.hpp | 4 inst/include/armadillo_bits/Gen_bones.hpp | 4 inst/include/armadillo_bits/Mat_meat.hpp | 8 inst/include/armadillo_bits/Proxy.hpp | 242 inst/include/armadillo_bits/ProxyCube.hpp | 38 inst/include/armadillo_bits/SpMat_bones.hpp | 2 inst/include/armadillo_bits/SpMat_meat.hpp | 12 inst/include/armadillo_bits/SpProxy.hpp | 28 inst/include/armadillo_bits/arma_cmath.hpp | 12 inst/include/armadillo_bits/arma_config.hpp | 9 inst/include/armadillo_bits/arma_rng.hpp | 1 inst/include/armadillo_bits/arma_version.hpp | 8 inst/include/armadillo_bits/auxlib_meat.hpp | 98 inst/include/armadillo_bits/compiler_setup.hpp | 104 inst/include/armadillo_bits/config.hpp | 14 inst/include/armadillo_bits/config.hpp.cmake | 14 inst/include/armadillo_bits/debug.hpp | 123 inst/include/armadillo_bits/def_lapack.hpp | 72 inst/include/armadillo_bits/def_superlu.hpp | 8 inst/include/armadillo_bits/diagmat_proxy.hpp | 6 inst/include/armadillo_bits/diagview_meat.hpp | 12 inst/include/armadillo_bits/diskio_meat.hpp | 8 inst/include/armadillo_bits/eGlueCube_bones.hpp | 6 inst/include/armadillo_bits/eGlue_bones.hpp | 8 inst/include/armadillo_bits/eOpCube_bones.hpp | 6 inst/include/armadillo_bits/eOp_bones.hpp | 8 inst/include/armadillo_bits/eglue_core_meat.hpp | 42 inst/include/armadillo_bits/eop_aux.hpp | 40 inst/include/armadillo_bits/eop_core_bones.hpp | 3 inst/include/armadillo_bits/eop_core_meat.hpp | 31 inst/include/armadillo_bits/fn_accu.hpp | 22 inst/include/armadillo_bits/fn_all.hpp | 9 inst/include/armadillo_bits/fn_any.hpp | 9 inst/include/armadillo_bits/fn_approx_equal.hpp | 4 inst/include/armadillo_bits/fn_as_scalar.hpp | 27 inst/include/armadillo_bits/fn_chol.hpp | 3 inst/include/armadillo_bits/fn_clamp.hpp | 2 inst/include/armadillo_bits/fn_conv.hpp | 2 inst/include/armadillo_bits/fn_conv_to.hpp | 32 inst/include/armadillo_bits/fn_cor.hpp | 4 inst/include/armadillo_bits/fn_cov.hpp | 4 inst/include/armadillo_bits/fn_cross.hpp | 3 inst/include/armadillo_bits/fn_cumprod.hpp | 6 inst/include/armadillo_bits/fn_cumsum.hpp | 6 inst/include/armadillo_bits/fn_det.hpp | 16 inst/include/armadillo_bits/fn_diagmat.hpp | 6 inst/include/armadillo_bits/fn_diagvec.hpp | 3 inst/include/armadillo_bits/fn_diff.hpp | 4 inst/include/armadillo_bits/fn_dot.hpp | 20 inst/include/armadillo_bits/fn_eig_gen.hpp | 3 inst/include/armadillo_bits/fn_eig_pair.hpp | 3 inst/include/armadillo_bits/fn_eig_sym.hpp | 5 inst/include/armadillo_bits/fn_eigs_gen.hpp | 5 inst/include/armadillo_bits/fn_eigs_sym.hpp | 5 inst/include/armadillo_bits/fn_elem.hpp | 143 inst/include/armadillo_bits/fn_eps.hpp | 21 inst/include/armadillo_bits/fn_expmat.hpp | 3 inst/include/armadillo_bits/fn_eye.hpp | 8 inst/include/armadillo_bits/fn_fft.hpp | 8 inst/include/armadillo_bits/fn_fft2.hpp | 6 inst/include/armadillo_bits/fn_find.hpp | 12 inst/include/armadillo_bits/fn_find_unique.hpp | 4 inst/include/armadillo_bits/fn_flip.hpp | 4 inst/include/armadillo_bits/fn_hist.hpp | 5 inst/include/armadillo_bits/fn_histc.hpp | 4 inst/include/armadillo_bits/fn_inv.hpp | 9 inst/include/armadillo_bits/fn_join.hpp | 14 inst/include/armadillo_bits/fn_kmeans.hpp | 10 inst/include/armadillo_bits/fn_kron.hpp | 13 inst/include/armadillo_bits/fn_logmat.hpp | 2 inst/include/armadillo_bits/fn_max.hpp | 30 inst/include/armadillo_bits/fn_mean.hpp | 21 inst/include/armadillo_bits/fn_median.hpp | 8 inst/include/armadillo_bits/fn_min.hpp | 29 inst/include/armadillo_bits/fn_misc.hpp | 26 inst/include/armadillo_bits/fn_nonzeros.hpp | 4 inst/include/armadillo_bits/fn_norm.hpp | 12 inst/include/armadillo_bits/fn_normalise.hpp | 4 inst/include/armadillo_bits/fn_numel.hpp | 7 inst/include/armadillo_bits/fn_ones.hpp | 12 inst/include/armadillo_bits/fn_pinv.hpp | 3 inst/include/armadillo_bits/fn_princomp.hpp | 3 inst/include/armadillo_bits/fn_prod.hpp | 15 inst/include/armadillo_bits/fn_randg.hpp | 16 inst/include/armadillo_bits/fn_randi.hpp | 12 inst/include/armadillo_bits/fn_randn.hpp | 12 inst/include/armadillo_bits/fn_randu.hpp | 14 inst/include/armadillo_bits/fn_rank.hpp | 6 inst/include/armadillo_bits/fn_regspace.hpp | 3 inst/include/armadillo_bits/fn_repmat.hpp | 4 inst/include/armadillo_bits/fn_schur.hpp | 5 inst/include/armadillo_bits/fn_shift.hpp | 2 inst/include/armadillo_bits/fn_shuffle.hpp | 4 inst/include/armadillo_bits/fn_size.hpp | 14 inst/include/armadillo_bits/fn_solve.hpp | 8 inst/include/armadillo_bits/fn_sort.hpp | 6 inst/include/armadillo_bits/fn_sort_index.hpp | 6 inst/include/armadillo_bits/fn_speye.hpp | 6 inst/include/armadillo_bits/fn_spones.hpp | 3 inst/include/armadillo_bits/fn_sprandn.hpp | 7 inst/include/armadillo_bits/fn_sprandu.hpp | 7 inst/include/armadillo_bits/fn_spsolve.hpp | 3 inst/include/armadillo_bits/fn_sqrtmat.hpp | 2 inst/include/armadillo_bits/fn_stddev.hpp | 8 inst/include/armadillo_bits/fn_strans.hpp | 6 inst/include/armadillo_bits/fn_sum.hpp | 29 inst/include/armadillo_bits/fn_svd.hpp | 5 inst/include/armadillo_bits/fn_svds.hpp | 14 inst/include/armadillo_bits/fn_syl_lyap.hpp | 5 inst/include/armadillo_bits/fn_symmat.hpp | 6 inst/include/armadillo_bits/fn_toeplitz.hpp | 11 inst/include/armadillo_bits/fn_trace.hpp | 10 inst/include/armadillo_bits/fn_trans.hpp | 9 inst/include/armadillo_bits/fn_trapz.hpp | 2 inst/include/armadillo_bits/fn_trig.hpp | 26 inst/include/armadillo_bits/fn_trimat.hpp | 4 inst/include/armadillo_bits/fn_trunc_exp.hpp | 6 inst/include/armadillo_bits/fn_trunc_log.hpp | 5 inst/include/armadillo_bits/fn_unique.hpp | 3 inst/include/armadillo_bits/fn_var.hpp | 11 inst/include/armadillo_bits/fn_vectorise.hpp | 5 inst/include/armadillo_bits/fn_zeros.hpp | 14 inst/include/armadillo_bits/glue_cross_meat.hpp | 4 inst/include/armadillo_bits/glue_max_meat.hpp | 10 inst/include/armadillo_bits/glue_min_meat.hpp | 8 inst/include/armadillo_bits/glue_mixed_meat.hpp | 34 inst/include/armadillo_bits/glue_relational_meat.hpp | 10 inst/include/armadillo_bits/glue_solve_meat.hpp | 4 inst/include/armadillo_bits/glue_times_meat.hpp | 6 inst/include/armadillo_bits/include_superlu.hpp | 99 inst/include/armadillo_bits/newarp_DenseGenMatProd_bones.hpp |only inst/include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp |only inst/include/armadillo_bits/newarp_DoubleShiftQR_bones.hpp |only inst/include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp |only inst/include/armadillo_bits/newarp_EigsSelect.hpp |only inst/include/armadillo_bits/newarp_GenEigsSolver_bones.hpp |only inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp |only inst/include/armadillo_bits/newarp_SortEigenvalue.hpp |only inst/include/armadillo_bits/newarp_SparseGenMatProd_bones.hpp |only inst/include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp |only inst/include/armadillo_bits/newarp_SymEigsSolver_bones.hpp |only inst/include/armadillo_bits/newarp_SymEigsSolver_meat.hpp |only inst/include/armadillo_bits/newarp_TridiagEigen_bones.hpp |only inst/include/armadillo_bits/newarp_TridiagEigen_meat.hpp |only inst/include/armadillo_bits/newarp_UpperHessenbergEigen_bones.hpp |only inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp |only inst/include/armadillo_bits/newarp_UpperHessenbergQR_bones.hpp |only inst/include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp |only inst/include/armadillo_bits/newarp_cx_attrib.hpp |only inst/include/armadillo_bits/op_all_meat.hpp | 10 inst/include/armadillo_bits/op_any_meat.hpp | 10 inst/include/armadillo_bits/op_chol_meat.hpp | 2 inst/include/armadillo_bits/op_clamp_meat.hpp | 4 inst/include/armadillo_bits/op_cx_scalar_meat.hpp | 26 inst/include/armadillo_bits/op_diagmat_meat.hpp | 8 inst/include/armadillo_bits/op_dot_meat.hpp | 10 inst/include/armadillo_bits/op_fft_meat.hpp | 6 inst/include/armadillo_bits/op_find_meat.hpp | 12 inst/include/armadillo_bits/op_find_unique_meat.hpp | 4 inst/include/armadillo_bits/op_htrans_meat.hpp | 6 inst/include/armadillo_bits/op_inv_meat.hpp | 8 inst/include/armadillo_bits/op_logmat_meat.hpp | 4 inst/include/armadillo_bits/op_max_meat.hpp | 12 inst/include/armadillo_bits/op_median_meat.hpp | 10 inst/include/armadillo_bits/op_min_meat.hpp | 18 inst/include/armadillo_bits/op_misc_meat.hpp | 18 inst/include/armadillo_bits/op_nonzeros_meat.hpp | 4 inst/include/armadillo_bits/op_norm_meat.hpp | 18 inst/include/armadillo_bits/op_pinv_meat.hpp | 2 inst/include/armadillo_bits/op_princomp_meat.hpp | 2 inst/include/armadillo_bits/op_prod_meat.hpp | 4 inst/include/armadillo_bits/op_relational_meat.hpp | 10 inst/include/armadillo_bits/op_reshape_meat.hpp | 6 inst/include/armadillo_bits/op_sort_index_meat.hpp | 6 inst/include/armadillo_bits/op_strans_meat.hpp | 6 inst/include/armadillo_bits/op_unique_meat.hpp | 6 inst/include/armadillo_bits/op_vectorise_meat.hpp | 6 inst/include/armadillo_bits/podarray_meat.hpp | 4 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 17 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 352 inst/include/armadillo_bits/spdiagview_meat.hpp | 22 inst/include/armadillo_bits/spop_max_meat.hpp | 19 inst/include/armadillo_bits/spop_mean_meat.hpp | 10 inst/include/armadillo_bits/spop_min_meat.hpp | 19 inst/include/armadillo_bits/spop_sum_meat.hpp | 4 inst/include/armadillo_bits/spop_var_meat.hpp | 4 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 2 inst/include/armadillo_bits/subview_cube_meat.hpp | 18 inst/include/armadillo_bits/subview_each_meat.hpp | 4 inst/include/armadillo_bits/subview_elem1_meat.hpp | 6 inst/include/armadillo_bits/subview_meat.hpp | 18 inst/include/armadillo_bits/wall_clock_bones.hpp | 4 inst/include/armadillo_bits/wall_clock_meat.hpp | 6 inst/include/armadillo_bits/wrapper_lapack.hpp | 158 inst/include/armadillo_bits/wrapper_superlu.hpp | 10 207 files changed, 6333 insertions(+), 1195 deletions(-)
Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and Poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between penalized versions 0.9-46 dated 2016-04-18 and 0.9-47 dated 2016-05-27
ChangeLog | 8 ++++++-- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/penfit.R | 14 +++++++++----- inst/doc/penalized.pdf |binary 6 files changed, 25 insertions(+), 17 deletions(-)
Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects. Wrapper functions to estimate the standard limited dependent variable models are also included.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>
Diff between oglmx versions 1.0.3 dated 2015-07-31 and 2.0.0.0 dated 2016-05-27
DESCRIPTION | 10 MD5 | 18 R/oglmx-functions.R | 1386 +++++++++++++++++++++++++------------------- R/oglmx.margins-functions.R | 29 build/partial.rdb |binary man/logit.reg.Rd | 4 man/oglmx.Rd | 21 man/ologit.reg.Rd | 16 man/oprobit.reg.Rd | 15 man/probit.reg.Rd | 4 10 files changed, 871 insertions(+), 632 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.4.3 dated 2016-04-28 and 1.4.4 dated 2016-05-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/glmmLasso_RE.R | 38 ++++++++++++++++++++++++++++++++++---- man/glmmLasso.rd | 4 ++-- 4 files changed, 43 insertions(+), 13 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 1.2.6 dated 2015-08-31 and 1.2.7 dated 2016-05-27
DESCRIPTION | 8 ++-- MD5 | 34 +++++++++---------- R/main.R | 46 +++++++++++++++++++++++-- build/clusterCrit.pdf |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/clusterCrit.R | 26 +++++++------- inst/doc/clusterCrit.Rnw | 50 ++++++++++++++++------------ inst/doc/clusterCrit.pdf |binary inst/unitTests/intCriteria/runit_g_plus.R | 4 +- inst/unitTests/intCriteria/runit_gamma.R | 4 +- inst/unitTests/intCriteria/runit_tau.R | 4 +- inst/unitTests/others/runit_bestCriterion.R | 4 +- src/critCalc.f95 | 9 ++++- src/critUtils.f95 | 24 +++++++------ src/criteria.c | 48 +++++++++++++++----------- src/criteria.h | 2 - vignettes/clusterCrit.Rnw | 50 ++++++++++++++++------------ 18 files changed, 193 insertions(+), 120 deletions(-)
Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Compositional versions 1.2 dated 2016-04-01 and 1.3 dated 2016-05-27
Compositional-1.2/Compositional/R/alfadist.R.R |only Compositional-1.2/Compositional/R/esov.compreg.R |only Compositional-1.2/Compositional/man/esov.compreg.Rd |only Compositional-1.3/Compositional/DESCRIPTION | 12 - Compositional-1.3/Compositional/MD5 | 109 ++++++---- Compositional-1.3/Compositional/NAMESPACE | 13 - Compositional-1.3/Compositional/R/alfa.R | 9 Compositional-1.3/Compositional/R/alfa.knn.R |only Compositional-1.3/Compositional/R/alfa.reg.R | 36 +-- Compositional-1.3/Compositional/R/alfadist.R |only Compositional-1.3/Compositional/R/alfaknn.tune.R |only Compositional-1.3/Compositional/R/alfapcr.tune.R | 4 Compositional-1.3/Compositional/R/alfarda.tune.R | 1 Compositional-1.3/Compositional/R/alfaridge.tune.R | 3 Compositional-1.3/Compositional/R/bivt.contour.R | 22 +- Compositional-1.3/Compositional/R/comp.kerncontour.R | 54 ++--- Compositional-1.3/Compositional/R/comp.knn.R | 93 +++++--- Compositional-1.3/Compositional/R/comp.test.R |only Compositional-1.3/Compositional/R/compknn.tune.R | 28 +- Compositional-1.3/Compositional/R/diri.contour.R | 39 ++- Compositional-1.3/Compositional/R/diri.nr.R | 118 +++++++---- Compositional-1.3/Compositional/R/diri.reg.R | 13 - Compositional-1.3/Compositional/R/eel.test1.R |only Compositional-1.3/Compositional/R/eel.test2.R |only Compositional-1.3/Compositional/R/el.test1.R |only Compositional-1.3/Compositional/R/el.test2.R |only Compositional-1.3/Compositional/R/hotel1T2.R |only Compositional-1.3/Compositional/R/hotel2T2.R |only Compositional-1.3/Compositional/R/james.R |only Compositional-1.3/Compositional/R/js.compreg.R |only Compositional-1.3/Compositional/R/kl.compreg.R | 10 Compositional-1.3/Compositional/R/maov.R |only Compositional-1.3/Compositional/R/maovjames.R |only Compositional-1.3/Compositional/R/mixnorm.contour.R | 42 ++- Compositional-1.3/Compositional/R/norm.contour.R | 44 ++-- Compositional-1.3/Compositional/R/rda.R | 3 Compositional-1.3/Compositional/R/skewnorm.contour.R | 109 +++++----- Compositional-1.3/Compositional/R/spat.med.R | 17 + Compositional-1.3/Compositional/R/spatmed.reg.R | 114 ++++++---- Compositional-1.3/Compositional/R/ternary.R | 7 Compositional-1.3/Compositional/man/Compositional-package.Rd | 4 Compositional-1.3/Compositional/man/alfa.rda.Rd | 1 Compositional-1.3/Compositional/man/alfa.reg.Rd | 4 Compositional-1.3/Compositional/man/alfa.ridge.Rd | 10 Compositional-1.3/Compositional/man/alfaridge.tune.Rd | 4 Compositional-1.3/Compositional/man/comp.knn.Rd | 9 Compositional-1.3/Compositional/man/comp.reg.Rd | 2 Compositional-1.3/Compositional/man/comp.test.Rd |only Compositional-1.3/Compositional/man/compknn.tune.Rd | 54 ++--- Compositional-1.3/Compositional/man/diri.nr.Rd | 19 + Compositional-1.3/Compositional/man/diri.reg.Rd | 4 Compositional-1.3/Compositional/man/eel.test1.Rd |only Compositional-1.3/Compositional/man/eel.test2.Rd |only Compositional-1.3/Compositional/man/el.test1.Rd |only Compositional-1.3/Compositional/man/el.test2.Rd |only Compositional-1.3/Compositional/man/glm.pcr.Rd | 4 Compositional-1.3/Compositional/man/glmpcr.tune.Rd | 3 Compositional-1.3/Compositional/man/hotel1T2.Rd |only Compositional-1.3/Compositional/man/hotel2T2.Rd |only Compositional-1.3/Compositional/man/james.Rd |only Compositional-1.3/Compositional/man/kl.compreg.Rd | 14 - Compositional-1.3/Compositional/man/maov.Rd |only Compositional-1.3/Compositional/man/maovjames.Rd |only Compositional-1.3/Compositional/man/multivreg.Rd | 4 Compositional-1.3/Compositional/man/ols.compreg.Rd | 4 Compositional-1.3/Compositional/man/rdiri.Rd | 10 Compositional-1.3/Compositional/man/skewnorm.contour.Rd | 2 Compositional-1.3/Compositional/man/spatmed.reg.Rd | 36 +-- Compositional-1.3/Compositional/man/sym.test.Rd | 4 69 files changed, 649 insertions(+), 443 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.1.1.0 dated 2016-02-11 and 1.1.1.1 dated 2016-05-27
SpatPCA-1.1.1.0/SpatPCA/src/Makevars.win |only SpatPCA-1.1.1.1/SpatPCA/DESCRIPTION | 8 ++-- SpatPCA-1.1.1.1/SpatPCA/MD5 | 9 ++-- SpatPCA-1.1.1.1/SpatPCA/R/SpatPCA.R | 47 ++++++++++++++----------- SpatPCA-1.1.1.1/SpatPCA/man/SpatPCA-package.Rd | 6 +-- SpatPCA-1.1.1.1/SpatPCA/man/spatpca.Rd | 38 +++++++++++--------- 6 files changed, 60 insertions(+), 48 deletions(-)
Title: Generation of Up to Four Different Types of Variables
Description: Generation of a chosen number of count, binary, ordinal, and continuous (via Fleishman polynomials) random variables, with specified correlations and marginal properties.
Author: Hakan Demirtas, Rachel Nordgren, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between PoisBinOrdNonNor versions 1.0 dated 2015-05-17 and 1.1 dated 2016-05-27
DESCRIPTION | 16 +-- MD5 | 10 - NAMESPACE | 9 + man/PoisBinOrdNonNor-package.Rd | 111 ++++++++++----------- man/find.cor.mat.star.Rd | 209 +++++++++++++++++++--------------------- man/genPBONN.Rd | 189 +++++++++++++++++------------------- 6 files changed, 272 insertions(+), 272 deletions(-)
More information about PoisBinOrdNonNor at CRAN
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