Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-25 1.1.4
2018-09-11 1.1.3
2018-01-25 1.1.2
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.4.1 dated 2017-09-25 and 0.4.2 dated 2019-03-07
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/extmat.c | 10 ++++++---- 3 files changed, 11 insertions(+), 9 deletions(-)
Title: Large-Scale Bayesian Variable Selection Using Variational
Methods
Description: Fast algorithms for fitting Bayesian variable selection
models and computing Bayes factors, in which the outcome (or
response variable) is modeled using a linear regression or a
logistic regression. The algorithms are based on the variational
approximations described in "Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studies" (P. Carbonetto & M. Stephens, 2012,
<DOI:10.1214/12-BA703>). This software has been applied to large
data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto [aut, cre],
Matthew Stephens [aut],
David Gerard [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between varbvs versions 2.4-0 dated 2017-09-08 and 2.5-16 dated 2019-03-07
varbvs-2.4-0/varbvs/R/varbvscoefcred.R |only varbvs-2.4-0/varbvs/man/varbvscoefcred.Rd |only varbvs-2.4-0/varbvs/tests/testthat/data.singular.cov.RData |only varbvs-2.4-0/varbvs/tests/testthat/demo.cc.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.mix.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.mix.dense.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.qtl.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.test.mix.R |only varbvs-2.5-16/varbvs/DESCRIPTION | 19 varbvs-2.5-16/varbvs/MD5 | 131 +- varbvs-2.5-16/varbvs/NAMESPACE | 65 - varbvs-2.5-16/varbvs/R/RcppExports.R | 2 varbvs-2.5-16/varbvs/R/bayesfactor.R | 2 varbvs-2.5-16/varbvs/R/confint.varbvs.R |only varbvs-2.5-16/varbvs/R/misc.R | 44 varbvs-2.5-16/varbvs/R/plot.varbvs.R | 31 varbvs-2.5-16/varbvs/R/predict.varbvs.R | 62 varbvs-2.5-16/varbvs/R/subset.varbvs.R | 13 varbvs-2.5-16/varbvs/R/summary.varbvs.R | 61 varbvs-2.5-16/varbvs/R/varbvs.R | 307 +++- varbvs-2.5-16/varbvs/R/varbvs.properties.R |only varbvs-2.5-16/varbvs/R/varbvsbin.R | 25 varbvs-2.5-16/varbvs/R/varbvsbinupdate.R | 13 varbvs-2.5-16/varbvs/R/varbvsbinz.R | 26 varbvs-2.5-16/varbvs/R/varbvsbinzupdate.R | 13 varbvs-2.5-16/varbvs/R/varbvsindep.R | 14 varbvs-2.5-16/varbvs/R/varbvsmix.R | 12 varbvs-2.5-16/varbvs/R/varbvsmixupdate.R | 2 varbvs-2.5-16/varbvs/R/varbvsnorm.R | 22 varbvs-2.5-16/varbvs/R/varbvsnormupdate.R | 18 varbvs-2.5-16/varbvs/R/varbvsproxybf.R |only varbvs-2.5-16/varbvs/R/varbvspve.R | 6 varbvs-2.5-16/varbvs/README.md | 8 varbvs-2.5-16/varbvs/build/vignette.rds |binary varbvs-2.5-16/varbvs/demo |only varbvs-2.5-16/varbvs/inst/CITATION | 2 varbvs-2.5-16/varbvs/inst/code |only varbvs-2.5-16/varbvs/inst/datafiles |only varbvs-2.5-16/varbvs/inst/doc/cd.html | 336 +---- varbvs-2.5-16/varbvs/inst/doc/cfw.R | 3 varbvs-2.5-16/varbvs/inst/doc/cfw.Rmd | 13 varbvs-2.5-16/varbvs/inst/doc/cfw.html | 401 +----- varbvs-2.5-16/varbvs/inst/doc/cytokine.html | 346 +---- varbvs-2.5-16/varbvs/inst/doc/leukemia.R | 2 varbvs-2.5-16/varbvs/inst/doc/leukemia.Rmd | 2 varbvs-2.5-16/varbvs/inst/doc/leukemia.html | 772 ++++-------- varbvs-2.5-16/varbvs/man/plot.varbvs.Rd | 13 varbvs-2.5-16/varbvs/man/predict.varbvs.Rd | 55 varbvs-2.5-16/varbvs/man/subset.varbvs.Rd | 2 varbvs-2.5-16/varbvs/man/summary.varbvs.Rd | 48 varbvs-2.5-16/varbvs/man/varbvs-internal.Rd | 49 varbvs-2.5-16/varbvs/man/varbvs.Rd | 95 + varbvs-2.5-16/varbvs/man/varbvs.properties.Rd |only varbvs-2.5-16/varbvs/man/varbvsproxybf.Rd |only varbvs-2.5-16/varbvs/src/diagsq.c | 2 varbvs-2.5-16/varbvs/src/diagsq.h | 2 varbvs-2.5-16/varbvs/src/diagsqr.c | 2 varbvs-2.5-16/varbvs/src/init.c | 2 varbvs-2.5-16/varbvs/src/misc.c | 2 varbvs-2.5-16/varbvs/src/misc.h | 2 varbvs-2.5-16/varbvs/src/types.h | 2 varbvs-2.5-16/varbvs/src/varbvs.c | 2 varbvs-2.5-16/varbvs/src/varbvs.h | 2 varbvs-2.5-16/varbvs/src/varbvsnormupdate_rcpp.cpp | 2 varbvs-2.5-16/varbvs/src/varbvsr.c | 2 varbvs-2.5-16/varbvs/src/varbvsr.h | 2 varbvs-2.5-16/varbvs/tests/testthat.R | 2 varbvs-2.5-16/varbvs/tests/testthat/test_varbvs.R | 113 + varbvs-2.5-16/varbvs/tests/testthat/test_varbvsnormupdate.R | 20 varbvs-2.5-16/varbvs/vignettes/cfw.Rmd | 13 varbvs-2.5-16/varbvs/vignettes/leukemia.Rmd | 2 71 files changed, 1500 insertions(+), 1709 deletions(-)
Title: Single Transferable Vote Counting
Description: Implementations of the Single Transferable Vote counting
system. By default, it uses the Cambridge method for surplus allocation
and Droop method for quota calculation. Fractional surplus allocation
and the Hare quota are available as options.
Author: John Emerson [cre, aut],
Saksham Chandra [aut],
Lilla Orr [aut],
Efim Abrikosov [ctb],
Shadie Khubba [ctb],
William Meyerson [ctb],
Shylee Ezroni [ctb],
Junchao Ma [ctb]
Maintainer: John Emerson <john.emerson@yale.edu>
Diff between STV versions 1.0.0 dated 2018-03-23 and 1.0.1 dated 2019-03-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++-- tests/testthat/testExt.R | 5 +++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Description: Algorithms to create prognostic biomarkers using biological genesets or networks.
Author: Syed Haider [aut, cre],
Paul C. Boutros [aut],
Michal Grzadkowski [ctb]
Maintainer: Syed Haider <Syed.Haider@icr.ac.uk>
Diff between SIMMS versions 1.1.1 dated 2017-10-11 and 1.1.2 dated 2019-03-07
SIMMS-1.1.1/SIMMS/man/SIMMS.Rd |only SIMMS-1.1.2/SIMMS/DESCRIPTION | 26 +- SIMMS-1.1.2/SIMMS/MD5 | 110 +++++----- SIMMS-1.1.2/SIMMS/NAMESPACE | 87 ++++--- SIMMS-1.1.2/SIMMS/NEWS | 14 + SIMMS-1.1.2/SIMMS/R/SIMMS-package.R |only SIMMS-1.1.2/SIMMS/R/calculate.meta.survival.R | 37 +++ SIMMS-1.1.2/SIMMS/R/calculate.network.coefficients.R | 54 ++++ SIMMS-1.1.2/SIMMS/R/calculate.sensitivity.stats.R | 14 + SIMMS-1.1.2/SIMMS/R/create.KM.plot.R | 20 + SIMMS-1.1.2/SIMMS/R/create.classifier.multivariate.R | 51 ++++ SIMMS-1.1.2/SIMMS/R/create.classifier.univariate.R | 37 +++ SIMMS-1.1.2/SIMMS/R/create.sensitivity.plot.R | 26 ++ SIMMS-1.1.2/SIMMS/R/create.survivalplots.R | 43 +++ SIMMS-1.1.2/SIMMS/R/create.survobj.R | 109 ++++++--- SIMMS-1.1.2/SIMMS/R/derive.network.features.R | 61 +++++ SIMMS-1.1.2/SIMMS/R/dichotomize.dataset.R | 29 ++ SIMMS-1.1.2/SIMMS/R/dichotomize.meta.dataset.R | 39 +++ SIMMS-1.1.2/SIMMS/R/fit.coxmodel.R | 35 +++ SIMMS-1.1.2/SIMMS/R/fit.interaction.model.R | 46 +++- SIMMS-1.1.2/SIMMS/R/fit.survivalmodel.R | 32 ++ SIMMS-1.1.2/SIMMS/R/get.adjacency.matrix.R | 19 + SIMMS-1.1.2/SIMMS/R/get.chisq.stats.R | 28 ++ SIMMS-1.1.2/SIMMS/R/get.program.defaults.R | 18 + SIMMS-1.1.2/SIMMS/R/load.cancer.datasets.R | 35 +++ SIMMS-1.1.2/SIMMS/R/make.matrix.R | 15 + SIMMS-1.1.2/SIMMS/R/pred.survivalmodel.R | 38 +++ SIMMS-1.1.2/SIMMS/R/prepare.training.validation.datasets.R | 86 ++++++- SIMMS-1.1.2/SIMMS/build/vignette.rds |binary SIMMS-1.1.2/SIMMS/inst/doc/Using-SIMMS.R | 8 SIMMS-1.1.2/SIMMS/inst/doc/Using-SIMMS.Rmd | 18 - SIMMS-1.1.2/SIMMS/inst/doc/Using-SIMMS.html | 52 +++- SIMMS-1.1.2/SIMMS/inst/programdata/networkdb/test2 |only SIMMS-1.1.2/SIMMS/man/SIMMS-package.Rd |only SIMMS-1.1.2/SIMMS/man/calculate.meta.survival.Rd | 91 +++++--- SIMMS-1.1.2/SIMMS/man/calculate.network.coefficients.Rd | 62 ++++- SIMMS-1.1.2/SIMMS/man/calculate.sensitivity.stats.Rd | 20 + SIMMS-1.1.2/SIMMS/man/create.KM.plot.Rd | 42 ++- SIMMS-1.1.2/SIMMS/man/create.classifier.multivariate.Rd | 91 ++++++-- SIMMS-1.1.2/SIMMS/man/create.classifier.univariate.Rd | 64 ++++- SIMMS-1.1.2/SIMMS/man/create.sensitivity.plot.Rd | 59 +++-- SIMMS-1.1.2/SIMMS/man/create.survivalplots.Rd | 85 +++++-- SIMMS-1.1.2/SIMMS/man/create.survobj.Rd | 89 ++++---- SIMMS-1.1.2/SIMMS/man/derive.network.features.Rd | 73 ++++-- SIMMS-1.1.2/SIMMS/man/dichotomize.dataset.Rd | 48 ++-- SIMMS-1.1.2/SIMMS/man/dichotomize.meta.dataset.Rd | 94 +++++--- SIMMS-1.1.2/SIMMS/man/fit.coxmodel.Rd | 85 ++++--- SIMMS-1.1.2/SIMMS/man/fit.interaction.model.Rd | 48 +++- SIMMS-1.1.2/SIMMS/man/fit.survivalmodel.Rd | 60 +++-- SIMMS-1.1.2/SIMMS/man/get.adjacency.matrix.Rd | 26 +- SIMMS-1.1.2/SIMMS/man/get.chisq.stats.Rd | 27 +- SIMMS-1.1.2/SIMMS/man/get.program.defaults.Rd | 26 +- SIMMS-1.1.2/SIMMS/man/load.cancer.datasets.Rd | 92 +++++--- SIMMS-1.1.2/SIMMS/man/make.matrix.Rd | 23 +- SIMMS-1.1.2/SIMMS/man/pred.survivalmodel.Rd | 73 ++++-- SIMMS-1.1.2/SIMMS/man/prepare.training.validation.datasets.Rd | 82 +++++-- SIMMS-1.1.2/SIMMS/vignettes/Using-SIMMS.Rmd | 18 - 57 files changed, 1923 insertions(+), 642 deletions(-)
Title: Spatially Balanced Samples of Spatial Objects
Description: Routines for drawing samples from spatial objects, focused on spatially
balanced algorithms. Draws Halton Iterative Partition (HIP)
(Robertson et al., 2018; <doi:10.1007/s10651-018-0406-6>),
Balanced Acceptance Samples (BAS) (Robertson et al., 2013; <doi:10.1111/biom.12059>),
Generalized Random
Tessellation Stratified (GRTS) (Stevens and Olsen, 2004; <doi:10.1198/016214504000000250>),
Simple Systematic Samples (SSS) and
Simple Random Samples (SRS) from point, line, and polygon resources.
Frames are 'SpatialPoints', 'SpatialLines', or 'SpatialPolygons'
objects from package 'sp'.
Author: Trent McDonald [cre, aut],
Aidan McDonald [aut] (HIP sampling methods),
Michael Kleinsausser [ctb]
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between SDraw versions 2.1.3 dated 2016-06-13 and 2.1.8 dated 2019-03-07
SDraw-2.1.3/SDraw/R/hal.line.r |only SDraw-2.1.3/SDraw/R/hal.point.r |only SDraw-2.1.3/SDraw/R/hal.polygon.r |only SDraw-2.1.3/SDraw/man/hal.line.Rd |only SDraw-2.1.3/SDraw/man/hal.point.Rd |only SDraw-2.1.3/SDraw/man/hal.polygon.Rd |only SDraw-2.1.8/SDraw/DESCRIPTION | 46 +++---- SDraw-2.1.8/SDraw/MD5 | 156 +++++++++++++----------- SDraw-2.1.8/SDraw/NAMESPACE | 11 + SDraw-2.1.8/SDraw/NEWS.md |only SDraw-2.1.8/SDraw/R/SDraw-package.r | 2 SDraw-2.1.8/SDraw/R/WY.r | 3 SDraw-2.1.8/SDraw/R/bas.line.r | 33 ++--- SDraw-2.1.8/SDraw/R/bas.point.r | 5 SDraw-2.1.8/SDraw/R/bas.polygon.r | 5 SDraw-2.1.8/SDraw/R/extended.gcd.r | 4 SDraw-2.1.8/SDraw/R/getJ.R |only SDraw-2.1.8/SDraw/R/grts.line.r | 2 SDraw-2.1.8/SDraw/R/grts.point.r | 4 SDraw-2.1.8/SDraw/R/grts.polygon.r | 2 SDraw-2.1.8/SDraw/R/halton.coefficients.R |only SDraw-2.1.8/SDraw/R/halton.indicies.r | 16 +- SDraw-2.1.8/SDraw/R/halton.indicies.vector.r | 3 SDraw-2.1.8/SDraw/R/halton.lattice.polygon.r | 10 - SDraw-2.1.8/SDraw/R/halton.lattice.r | 6 SDraw-2.1.8/SDraw/R/hip.lattice.polygon.r |only SDraw-2.1.8/SDraw/R/hip.plot.lattice.r |only SDraw-2.1.8/SDraw/R/hip.point.r |only SDraw-2.1.8/SDraw/R/hip.polygon.r |only SDraw-2.1.8/SDraw/R/plot.sdrawSample.R | 4 SDraw-2.1.8/SDraw/R/plotLattice.R |only SDraw-2.1.8/SDraw/R/sdraw.SpatialLines.r | 1 SDraw-2.1.8/SDraw/R/sdraw.SpatialPoints.r | 2 SDraw-2.1.8/SDraw/R/sdraw.SpatialPolygons.r | 12 - SDraw-2.1.8/SDraw/R/sdraw.r | 29 ++-- SDraw-2.1.8/SDraw/R/srs.point.r | 2 SDraw-2.1.8/SDraw/R/srs.polygon.r | 2 SDraw-2.1.8/SDraw/R/sss.point.r | 4 SDraw-2.1.8/SDraw/R/sss.polygon.r | 6 SDraw-2.1.8/SDraw/R/voronoi.polygons.r | 2 SDraw-2.1.8/SDraw/build |only SDraw-2.1.8/SDraw/data/HI.coast.rda |binary SDraw-2.1.8/SDraw/data/WA.cities.rda |binary SDraw-2.1.8/SDraw/data/WA.rda |binary SDraw-2.1.8/SDraw/data/WY.rda |binary SDraw-2.1.8/SDraw/inst |only SDraw-2.1.8/SDraw/man/HI.coast.Rd | 1 SDraw-2.1.8/SDraw/man/SDraw-package.Rd | 19 +- SDraw-2.1.8/SDraw/man/WA.Rd | 1 SDraw-2.1.8/SDraw/man/WA.cities.Rd | 1 SDraw-2.1.8/SDraw/man/WY.Rd | 4 SDraw-2.1.8/SDraw/man/bas.line.Rd | 40 +++--- SDraw-2.1.8/SDraw/man/bas.point.Rd | 12 - SDraw-2.1.8/SDraw/man/bas.polygon.Rd | 12 - SDraw-2.1.8/SDraw/man/extended.gcd.Rd | 11 - SDraw-2.1.8/SDraw/man/getJ.Rd |only SDraw-2.1.8/SDraw/man/grts.line.Rd | 9 - SDraw-2.1.8/SDraw/man/grts.point.Rd | 11 - SDraw-2.1.8/SDraw/man/grts.polygon.Rd | 9 - SDraw-2.1.8/SDraw/man/halton.Rd | 7 - SDraw-2.1.8/SDraw/man/halton.coefficients.Rd |only SDraw-2.1.8/SDraw/man/halton.frame.Rd | 7 - SDraw-2.1.8/SDraw/man/halton.indices.CRT.Rd | 11 - SDraw-2.1.8/SDraw/man/halton.indices.Rd | 21 +-- SDraw-2.1.8/SDraw/man/halton.indices.vector.Rd | 14 +- SDraw-2.1.8/SDraw/man/halton.lattice.Rd | 11 - SDraw-2.1.8/SDraw/man/halton.lattice.polygon.Rd | 15 +- SDraw-2.1.8/SDraw/man/hip.lattice.polygon.Rd |only SDraw-2.1.8/SDraw/man/hip.plot.lattice.Rd |only SDraw-2.1.8/SDraw/man/hip.point.Rd |only SDraw-2.1.8/SDraw/man/hip.polygon.Rd |only SDraw-2.1.8/SDraw/man/lineLength.Rd | 7 - SDraw-2.1.8/SDraw/man/maxU.Rd | 7 - SDraw-2.1.8/SDraw/man/plotLattice.Rd |only SDraw-2.1.8/SDraw/man/plotSample.Rd | 11 - SDraw-2.1.8/SDraw/man/polygonArea.Rd | 7 - SDraw-2.1.8/SDraw/man/primes.Rd | 1 SDraw-2.1.8/SDraw/man/sdraw.Rd | 52 ++++---- SDraw-2.1.8/SDraw/man/srs.line.Rd | 7 - SDraw-2.1.8/SDraw/man/srs.point.Rd | 9 - SDraw-2.1.8/SDraw/man/srs.polygon.Rd | 9 - SDraw-2.1.8/SDraw/man/sss.line.Rd | 7 - SDraw-2.1.8/SDraw/man/sss.point.Rd | 11 - SDraw-2.1.8/SDraw/man/sss.polygon.Rd | 16 +- SDraw-2.1.8/SDraw/man/voronoi.polygons.Rd | 3 SDraw-2.1.8/SDraw/vignettes |only 86 files changed, 375 insertions(+), 360 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-10 dated 2018-01-31 and 0.2-11 dated 2019-03-07
ChangeLog | 14 +++ DESCRIPTION | 8 +- MD5 | 116 ++++++++++++++--------------- R/00_control.r | 8 +- R/01_simple.r | 2 R/fcn_emcluster.r | 2 R/fcn_init_EM.r | 10 +- R/fcn_init_other_shortem.r | 2 R/fcn_summary.r | 6 + data/EMC.rda |binary inst/doc/EMCluster-guide.pdf |binary man/00_EMCluster-package.Rd | 2 man/11_d.EMControl.Rd | 12 +-- man/12_d.dataset.Rd | 2 man/21_init.EM.Rd | 4 - man/22_emcluster.Rd | 2 man/23_emgroup.Rd | 2 man/30_assign.class.Rd | 2 man/31_em.ic.Rd | 2 man/32_em.step.Rd | 2 man/40_lmt.Rd | 2 man/91_mvn.Rd | 2 man/92_convert.Rd | 2 man/99_plotem.Rd | 2 man/99_plotmd.Rd | 2 man/a0_project.on.2d.Rd | 2 man/a1_plotppcontour.Rd | 2 man/xx_Jaccard.Rd | 2 man/xx_RRand.Rd | 2 man/xx_recolor.Rd | 2 man/yy_print.summary.Rd | 2 man/zx_all.post_I_information.Rd | 2 man/zy_all.lmt.Rd | 2 man/zz_all.internal.Rd | 2 src/M_emcluster.c | 8 +- src/M_emgroup.c | 6 + src/M_init_other.c | 8 +- src/R_M_emgroup.c | 35 ++++++-- src/R_emcluster.c | 33 +++++--- src/R_init_other_shortem.c | 33 +++++--- src/emgroup.c | 9 +- src/init_other.c | 21 +++-- src/it_R_emptr.c | 35 +++++--- src/it_R_init_EM.c | 22 +++-- src/it_init_EM.c | 23 +++-- src/it_tool.h | 8 +- src/mb_em_EM.c | 14 ++- src/mb_rand_EM.c | 14 ++- src/mb_tool.h | 36 +++++---- src/rand_EM.c | 19 +++- src/ss_M_emcluster.c | 8 +- src/ss_M_rand_EM.c | 10 +- src/ss_R_emcluster.c | 32 +++++--- src/ss_init_other.c | 19 +++- src/ss_mb_em_EM.c | 11 +- src/ss_mb_rand_EM.c | 11 +- src/ss_mb_tool.h | 30 ++++--- src/ss_rand_EM.c | 16 ++-- vignettes/EMCluster-include/02-em_init.tex | 2 59 files changed, 415 insertions(+), 274 deletions(-)
Title: Predicting Categorical and Continuous Outcomes Using One in Ten
Rule
Description: Predicts categorical or continuous outcomes while concentrating on four key points. These are Cross-validation, Accuracy, Regression and Rule of Ten or "one in ten rule" (CARRoT). It performs the cross-validation specified number of times by partitioning the input into training and test set and fitting linear/multinomial/binary regression models to the training set. All regression models satisfying a rule of ten events per variable are fitted and the ones with the best predictive power are given as an output. Best predictive power is understood as highest accuracy in case of binary/multinomial outcomes, smallest absolute and relative errors in case of continuous outcomes. For binary case there is also an option of finding a regression model which gives the highest AUROC (Area Under Receiver Operating Curve) value. The option of parallel toolbox is also available. Methods are described in Peduzzi et al. (1996) <doi:10.1016/S0895-4356(96)00236-3> and Rhemtulla et al. (2012) <doi:10.1037/a0029315>.
Author: Alina Bazarova [aut, cre],
Marko Raseta [aut]
Maintainer: Alina Bazarova <a.bazarova@bham.ac.uk>
Diff between CARRoT versions 1.5.0 dated 2018-11-27 and 2.0.0 dated 2019-03-07
DESCRIPTION | 6 MD5 | 21 NAMESPACE | 1 R/carrot_functions.R | 1540 +++++++++++++++++++++++++++------------------- build/partial.rdb |binary man/compute_max_length.Rd | 6 man/cross_val.Rd | 12 man/find_int.Rd |only man/get_indices.Rd | 4 man/get_predictions.Rd | 8 man/regr_ind.Rd | 10 man/regr_whole.Rd | 10 12 files changed, 953 insertions(+), 665 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Tao Yang [aut],
Zonglin He [aut],
Adam Elder [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2018.10-17 dated 2018-10-30 and 2019.3-6 dated 2019-03-07
ChangeLog | 5 +- DESCRIPTION | 12 +++-- MD5 | 36 ++++++++-------- NAMESPACE | 4 - R/chngpt.test.R | 3 - R/chngptm.R | 72 +++++++++++++++++++++----------- inst/doc/chngpt-vignette.pdf |binary inst/unitTests/runit.chngpt.test.R | 1 inst/unitTests/runit.chngptm.linear.R | 1 inst/unitTests/runit.chngptm.logistic.R | 50 +++++++++++++--------- inst/unitTests/runit.hinge.test.R | 1 man/chngptm.Rd | 30 +++++++------ man/performance.unit.test.Rd | 3 - src/fastgrid.cc | 2 src/fastgrid2.cc | 5 +- src/fastgrid_binomial.cpp |only src/fastgrid_binomial_wrapper.cpp |only src/grid.cc | 2 src/registerDynamicSymbol.c | 2 src/twoD.cc | 2 20 files changed, 140 insertions(+), 91 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-1 dated 2017-07-19 and 0.4-2 dated 2019-03-07
DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 6 R/spDiag.R | 118 +++ R/spPredict.R | 1604 +++++++++++++++++++++++++--------------------- R/spRecover.R | 716 ++++++++++++-------- R/spSVC.R |only data/PM10.dat.tab.gz |only data/PM10.poly.RData |only data/SVCMvData.dat.tab.gz |only man/PM10.dat.Rd |only man/PM10.poly.Rd |only man/SVCMvData.dat.Rd |only man/spDiag.Rd | 15 man/spGLM.Rd | 2 man/spLM.Rd | 2 man/spMvGLM.Rd | 2 man/spMvLM.Rd | 2 man/spPredict.Rd | 158 +++- man/spRecover.Rd | 63 + man/spSVC.Rd |only src/Makevars | 4 src/spMisalignGLM.cpp | 4 src/spSVC.cpp |only src/spSVCPredictJoint.cpp |only src/spSVCPredictMarg.cpp |only src/spSVCRecover.cpp |only src/util.cpp | 92 ++ src/util.h | 6 29 files changed, 1738 insertions(+), 1112 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results) and a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inra.fr>
Diff between SOMbrero versions 1.2-3 dated 2018-02-05 and 1.2-4 dated 2019-03-07
SOMbrero-1.2-3/SOMbrero/inst/doc/doc-SOMbrero-package.R |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-SOMbrero-package.Rmd |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-SOMbrero-package.html |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-grids.R |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-grids.Rmd |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-grids.html |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-korrespSOM.R |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-korrespSOM.Rmd |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-korrespSOM.html |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-numericSOM.R |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-numericSOM.Rmd |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-numericSOM.html |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-relationalSOM.R |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-relationalSOM.Rmd |only SOMbrero-1.2-3/SOMbrero/inst/doc/doc-relationalSOM.html |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-SOMbrero-package.Rmd |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-grids.Rmd |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-korrespSOM.Rmd |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-korrespSOM_cache |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-numericSOM.Rmd |only SOMbrero-1.2-3/SOMbrero/vignettes/doc-relationalSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/DESCRIPTION | 15 - SOMbrero-1.2-4/SOMbrero/MD5 | 97 ++++++----- SOMbrero-1.2-4/SOMbrero/build/vignette.rds |binary SOMbrero-1.2-4/SOMbrero/inst/CITATION | 10 - SOMbrero-1.2-4/SOMbrero/inst/doc/a-doc-SOMbrero-package.R |only SOMbrero-1.2-4/SOMbrero/inst/doc/a-doc-SOMbrero-package.Rmd |only SOMbrero-1.2-4/SOMbrero/inst/doc/a-doc-SOMbrero-package.html |only SOMbrero-1.2-4/SOMbrero/inst/doc/b-doc-grids.R |only SOMbrero-1.2-4/SOMbrero/inst/doc/b-doc-grids.Rmd |only SOMbrero-1.2-4/SOMbrero/inst/doc/b-doc-grids.html |only SOMbrero-1.2-4/SOMbrero/inst/doc/c-doc-numericSOM.R |only SOMbrero-1.2-4/SOMbrero/inst/doc/c-doc-numericSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/inst/doc/c-doc-numericSOM.html |only SOMbrero-1.2-4/SOMbrero/inst/doc/d-doc-korrespSOM.R |only SOMbrero-1.2-4/SOMbrero/inst/doc/d-doc-korrespSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/inst/doc/d-doc-korrespSOM.html |only SOMbrero-1.2-4/SOMbrero/inst/doc/e-doc-relationalSOM.R |only SOMbrero-1.2-4/SOMbrero/inst/doc/e-doc-relationalSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/inst/doc/e-doc-relationalSOM.html |only SOMbrero-1.2-4/SOMbrero/inst/shiny/ui.R | 19 +- SOMbrero-1.2-4/SOMbrero/man/SOMbrero-package.Rd | 4 SOMbrero-1.2-4/SOMbrero/man/initGrid.Rd | 8 SOMbrero-1.2-4/SOMbrero/man/initSOM.Rd | 8 SOMbrero-1.2-4/SOMbrero/man/plot.myGrid.Rd | 2 SOMbrero-1.2-4/SOMbrero/man/plot.somRes.Rd | 4 SOMbrero-1.2-4/SOMbrero/man/predict.somRes.Rd | 2 SOMbrero-1.2-4/SOMbrero/man/presidentielles2002.Rd | 3 SOMbrero-1.2-4/SOMbrero/man/projectIGraph.somRes.Rd | 6 SOMbrero-1.2-4/SOMbrero/man/protoDist.somRes.Rd | 6 SOMbrero-1.2-4/SOMbrero/man/quality.Rd | 6 SOMbrero-1.2-4/SOMbrero/man/somRes.plotting.Rd | 2 SOMbrero-1.2-4/SOMbrero/man/sombreroGUI.Rd | 2 SOMbrero-1.2-4/SOMbrero/man/superClass.Rd | 12 - SOMbrero-1.2-4/SOMbrero/man/trainSOM.Rd | 8 SOMbrero-1.2-4/SOMbrero/tests/testthat/test-prediction.R | 16 - SOMbrero-1.2-4/SOMbrero/vignettes/a-doc-SOMbrero-package.Rmd |only SOMbrero-1.2-4/SOMbrero/vignettes/b-doc-grids.Rmd |only SOMbrero-1.2-4/SOMbrero/vignettes/c-doc-numericSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/vignettes/c-doc-numericSOM_cache |only SOMbrero-1.2-4/SOMbrero/vignettes/d-doc-korrespSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/vignettes/d-doc-korrespSOM_cache |only SOMbrero-1.2-4/SOMbrero/vignettes/e-doc-relationalSOM.Rmd |only SOMbrero-1.2-4/SOMbrero/vignettes/e-doc-relationalSOM_cache |only 64 files changed, 121 insertions(+), 109 deletions(-)
Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations.
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between probably versions 0.0.1 dated 2018-12-18 and 0.0.2 dated 2019-03-07
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 1 NEWS.md | 10 + R/threshold_perf.R | 6 - R/vctrs-compat.R | 10 + inst/doc/equivocal-zones.html | 48 ++++++-- inst/doc/where-to-use.R | 10 - inst/doc/where-to-use.Rmd | 10 - inst/doc/where-to-use.html | 228 +++++++++++++++++++++------------------ tests/testthat/test-class-pred.R | 7 - vignettes/where-to-use.Rmd | 10 - 12 files changed, 217 insertions(+), 155 deletions(-)
Title: Generate Random Given and Surnames
Description: Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner [aut, cre]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between randomNames versions 1.0-0.0 dated 2017-06-06 and 1.4-0.0 dated 2019-03-07
DESCRIPTION | 16 - MD5 | 31 +- NAMESPACE | 2 R/randomNames.R | 4 R/zzz.R | 2 build/vignette.rds |binary inst/CITATION | 8 inst/NEWS | 34 +- inst/doc/randomNames.R | 27 +- inst/doc/randomNames.Rmd | 26 + inst/doc/randomNames.html | 386 ++++++++++++++++++++++------- man/randomNames-package.Rd | 6 man/randomNamesData.Rd | 8 vignettes/randomNames.Rmd | 26 + vignettes/releases/randomNames-0.0-1.Rmd | 13 vignettes/releases/randomNames-1.0-0.0.Rmd | 15 - vignettes/releases/randomNames-1.4-0.0.Rmd |only 17 files changed, 439 insertions(+), 165 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.0.2 dated 2018-10-17 and 1.1.0 dated 2019-03-07
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 2 +- NEWS | 9 ++++++++- R/01-labelMatcher.R | 16 ++++++++++++++++ inst/doc/Thresher.pdf |binary man/matchLabels.Rd | 13 ++++++++++++- tests/01-remap.R |only tests/01-remap.Rout.save |only 9 files changed, 49 insertions(+), 13 deletions(-)
Title: Maximum Likelihood Inference on Multi-State Trees
Description: Inference of a multi-states birth-death model from a phylogeny, comprising a number of states N, birth and death rates for each state and on which edges each state appears. Inference is done using a hybrid approach: states are progressively added in a greedy approach. For a fixed number of states N the best model is selected via maximum likelihood. Reference: J. Barido-Sottani and T. Stadler (2017) <doi:10.1101/215491>.
Author: Joelle Barido-Sottani [aut, cre]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between ML.MSBD versions 1.1.0 dated 2018-07-09 and 1.1.1 dated 2019-03-07
DESCRIPTION | 10 MD5 | 28 +- NEWS.md | 4 R/ML_MSBD.R | 18 + R/likelihood_MSBD.R | 8 R/likelihood_MSBD_unresolved.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Using_ML.MSBD.R | 7 inst/doc/Using_ML.MSBD.Rmd | 7 inst/doc/Using_ML.MSBD.html | 397 ++++++++++++++++++-------------------- man/ML_MSBD.Rd | 16 - man/likelihood_MSBD.Rd | 8 man/likelihood_MSBD_unresolved.Rd | 12 - vignettes/Using_ML.MSBD.Rmd | 7 15 files changed, 265 insertions(+), 265 deletions(-)
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.1-5 dated 2018-11-14 and 0.2 dated 2019-03-07
GJRM-0.1-5/GJRM/R/AT2.r |only GJRM-0.1-5/GJRM/R/penAprL.R |only GJRM-0.1-5/GJRM/R/print.AT2.r |only GJRM-0.1-5/GJRM/man/AT2.Rd |only GJRM-0.1-5/GJRM/man/print.AT2.Rd |only GJRM-0.2/GJRM/ChangeLog | 4 GJRM-0.2/GJRM/DESCRIPTION | 8 GJRM-0.2/GJRM/MD5 | 135 +++++++------ GJRM-0.2/GJRM/NAMESPACE | 12 - GJRM-0.2/GJRM/R/AT.r | 8 GJRM-0.2/GJRM/R/CopulaCLM.r | 78 ++++---- GJRM-0.2/GJRM/R/Dpens.R |only GJRM-0.2/GJRM/R/Dpens2.R |only GJRM-0.2/GJRM/R/PE.r |only GJRM-0.2/GJRM/R/SemiParBIV.r | 4 GJRM-0.2/GJRM/R/ass.dp.r | 2 GJRM-0.2/GJRM/R/ass.ms.r | 2 GJRM-0.2/GJRM/R/bCopulaCLMgHsCont.R | 25 ++ GJRM-0.2/GJRM/R/bcont23twoParC.R | 2 GJRM-0.2/GJRM/R/bcont3.R | 2 GJRM-0.2/GJRM/R/bcont32twoParC.R | 1 GJRM-0.2/GJRM/R/bcont3twoParC.R | 2 GJRM-0.2/GJRM/R/bconttwoParC.R | 2 GJRM-0.2/GJRM/R/bcorrec.R | 8 GJRM-0.2/GJRM/R/bcorrec2.R | 6 GJRM-0.2/GJRM/R/bcorrecDiscr.R | 2 GJRM-0.2/GJRM/R/bprobgHsContUniv.r | 13 - GJRM-0.2/GJRM/R/copulaSampleSel.r | 4 GJRM-0.2/GJRM/R/distrHs.r | 351 ++++++++++++++++++++++++++++++------ GJRM-0.2/GJRM/R/distrHsAT.r | 21 ++ GJRM-0.2/GJRM/R/distrHsAT1.r | 75 ++++++- GJRM-0.2/GJRM/R/distrHsATDiscr.r | 42 ++++ GJRM-0.2/GJRM/R/distrHsATDiscr2.r | 21 ++ GJRM-0.2/GJRM/R/distrHsDiscr.r | 237 ++++++++++++++++++++---- GJRM-0.2/GJRM/R/esp.tr.R | 3 GJRM-0.2/GJRM/R/eta.tr.R | 7 GJRM-0.2/GJRM/R/form.eq12.r | 25 +- GJRM-0.2/GJRM/R/gamls.upsv.r | 4 GJRM-0.2/GJRM/R/gamlss.r | 8 GJRM-0.2/GJRM/R/ggm.Deriv.R | 153 ++++++++++++--- GJRM-0.2/GJRM/R/ggm.DerivOPT1.R |only GJRM-0.2/GJRM/R/ggm.DerivOPT2.R |only GJRM-0.2/GJRM/R/ggmtrust.R | 105 +++++++++- GJRM-0.2/GJRM/R/ggmtrust.path.R | 12 - GJRM-0.2/GJRM/R/gjrm.r | 8 GJRM-0.2/GJRM/R/hazsurv.plot.r | 40 ++++ GJRM-0.2/GJRM/R/imputeCounter.r | 18 - GJRM-0.2/GJRM/R/imputeSS.r | 29 ++ GJRM-0.2/GJRM/R/int.postcheck.R | 50 +---- GJRM-0.2/GJRM/R/jc.probs.r | 23 +- GJRM-0.2/GJRM/R/jc.probs7.r |only GJRM-0.2/GJRM/R/overall.sv.r | 6 GJRM-0.2/GJRM/R/post.check.R | 59 +++++- GJRM-0.2/GJRM/R/pp.r | 7 GJRM-0.2/GJRM/R/pream.wm.r | 99 +++------- GJRM-0.2/GJRM/R/pred.mvt.r | 30 +++ GJRM-0.2/GJRM/R/predict2.CLM.r |only GJRM-0.2/GJRM/R/prediction.CLM.r |only GJRM-0.2/GJRM/R/print.PE.r |only GJRM-0.2/GJRM/R/print.gamlss.r | 12 + GJRM-0.2/GJRM/R/pscr.r | 9 GJRM-0.2/GJRM/R/pscr0.r | 11 + GJRM-0.2/GJRM/R/rIC.R | 6 GJRM-0.2/GJRM/R/resp.check.R | 24 +- GJRM-0.2/GJRM/R/rob.const.R | 32 --- GJRM-0.2/GJRM/R/rob.int.R | 8 GJRM-0.2/GJRM/R/sim.resp.R | 47 ++++ GJRM-0.2/GJRM/R/startsn.r | 13 - GJRM-0.2/GJRM/man/Dpens.Rd |only GJRM-0.2/GJRM/man/GJRM-package.Rd | 31 +-- GJRM-0.2/GJRM/man/PE.Rd |only GJRM-0.2/GJRM/man/eta.tr.Rd | 7 GJRM-0.2/GJRM/man/ggmtrust.Rd | 18 + GJRM-0.2/GJRM/man/gjrm.Rd | 21 +- GJRM-0.2/GJRM/man/hazsurv.plot.Rd | 2 GJRM-0.2/GJRM/man/jc.probs.Rd | 1 GJRM-0.2/GJRM/man/print.PE.Rd |only 77 files changed, 1491 insertions(+), 504 deletions(-)
Title: Efficient Constrained Based Modelling
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between sybil versions 2.1.2 dated 2018-08-15 and 2.1.5 dated 2019-03-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/addExchReact.R | 5 +++-- R/optObj_cplexAPIClass.R | 8 ++++---- build/vignette.rds |binary inst/NEWS.Rd | 30 +++++++++++++++++++++++++++--- inst/doc/sybil.pdf |binary man/Ec_core.Rd | 2 -- man/modelorg2ExPA.Rd | 2 -- 9 files changed, 46 insertions(+), 25 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high
dimensional data. Ensembles of classification, regression, survival and
probability prediction trees are supported. Data from genome-wide association
studies can be analyzed efficiently. In addition to data frames, datasets of
class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix')
can be directly analyzed.
Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between ranger versions 0.11.1 dated 2019-01-24 and 0.11.2 dated 2019-03-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ tests/testthat/test_jackknife.R | 31 ------------------------------- 4 files changed, 10 insertions(+), 38 deletions(-)
Title: Exact Variable-Subset Selection in Linear Regression
Description: Exact and approximation algorithms for variable-subset
selection in ordinary linear regression models. Either compute all
submodels with the lowest residual sum of squares, or determine the
single-best submodel according to a pre-determined statistical
criterion. Hofmann, Gatu, Kontoghiorghes, Colubi, Zeileis (2018,
submitted).
Author: Marc Hofmann [aut, cre],
Cristian Gatu [aut],
Erricos J. Kontoghiorghes [aut],
Ana Colubi [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Martin Moene [cph] (for the GSL Lite library),
Microsoft Corporation [cph] (for the GSL Lite library),
Free Software Foundation, Inc. [cph] (for snippets from the GNU ISO C++
Library)
Maintainer: Marc Hofmann <marc.hofmann@gmail.com>
Diff between lmSubsets versions 0.3 dated 2018-05-01 and 0.4 dated 2019-03-07
DESCRIPTION | 10 +- MD5 | 125 +++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |only inst/CITATION | 4 inst/doc |only man/lmSelect.Rd | 4 man/lmSubsets.Rd | 4 src/include/mcs/core/detail/givens.hh | 2 src/include/mcs/core/detail/lapack.hh | 2 src/include/mcs/core/detail/lapack.inc | 2 src/include/mcs/core/detail/matrix.hh | 2 src/include/mcs/core/detail/matrix.inc | 2 src/include/mcs/core/detail/matrix_impl.hh | 2 src/include/mcs/core/detail/subscript.hh | 2 src/include/mcs/core/detail/vector.hh | 2 src/include/mcs/core/detail/vector.inc | 2 src/include/mcs/core/detail/vector_impl.hh | 2 src/include/mcs/core/givens.hh | 2 src/include/mcs/core/lapack.hh | 2 src/include/mcs/core/matrix.hh | 2 src/include/mcs/core/vector.hh | 2 src/include/mcs/detail/fortran.hh | 2 src/include/mcs/detail/interrupt.hh | 2 src/include/mcs/subset/abba.hh | 2 src/include/mcs/subset/aic.hh | 2 src/include/mcs/subset/bba.hh | 2 src/include/mcs/subset/dca.hh | 2 src/include/mcs/subset/detail/abba.hh | 2 src/include/mcs/subset/detail/aic.hh | 2 src/include/mcs/subset/detail/aux_heap.hh | 2 src/include/mcs/subset/detail/bba.hh | 2 src/include/mcs/subset/detail/dca.hh | 2 src/include/mcs/subset/detail/dca_node.hh | 2 src/include/mcs/subset/detail/dca_partial.hh | 2 src/include/mcs/subset/detail/dca_preo.hh | 2 src/include/mcs/subset/detail/dca_qrz.hh | 2 src/include/mcs/subset/detail/dca_result.hh | 2 src/include/mcs/subset/detail/dca_state.hh | 2 src/include/mcs/subset/detail/dca_subset.hh | 2 src/include/mcs/subset/detail/hbba.hh | 2 src/include/mcs/subset/detail/log_lik.hh | 2 src/include/mcs/subset/detail/subset.hh | 2 src/include/mcs/subset/hbba.hh | 2 src/include/mcs/subset/subset.hh | 2 src/include/mcs/subset/table.hh | 2 src/include/mcs/util/algo.hh | 2 src/include/mcs/util/detail/algo.hh | 2 src/include/mcs/util/detail/function_traits.hh | 2 src/include/mcs/util/detail/misc.hh | 2 src/include/mcs/util/function_traits.hh | 2 src/include/mcs/util/misc.hh | 2 src/lmSubsets.cc | 2 vignettes |only 54 files changed, 133 insertions(+), 104 deletions(-)
Title: Gower's Distance
Description: Compute Gower's distance (or similarity) coefficient between records. Compute
the top-n matches between records. Core algorithms are executed in parallel on systems
supporting OpenMP.
Author: Mark van der Loo [aut, cre],
David Turner [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between gower versions 0.1.2 dated 2017-02-23 and 0.2.0 dated 2019-03-07
gower-0.1.2/gower/inst/doc/intro.Rmd |only gower-0.1.2/gower/inst/doc/intro.html |only gower-0.1.2/gower/vignettes/intro.Rmd |only gower-0.2.0/gower/DESCRIPTION | 19 ++-- gower-0.2.0/gower/MD5 | 26 +++--- gower-0.2.0/gower/NEWS | 8 ++ gower-0.2.0/gower/R/gower.R | 101 ++++++++++++++++++++------ gower-0.2.0/gower/build/vignette.rds |binary gower-0.2.0/gower/inst/doc/intro.R | 41 +++++++++- gower-0.2.0/gower/inst/doc/intro.Rnw |only gower-0.2.0/gower/inst/doc/intro.pdf |only gower-0.2.0/gower/man/gower_dist.Rd | 11 ++ gower-0.2.0/gower/man/gower_topn.Rd | 12 ++- gower-0.2.0/gower/src/R_register_native.c | 8 +- gower-0.2.0/gower/src/gower.c | 64 +++++++++------- gower-0.2.0/gower/tests/testthat/test_gower.R | 47 +++++++++++- gower-0.2.0/gower/vignettes/intro.Rnw |only 17 files changed, 255 insertions(+), 82 deletions(-)
Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This
focus has led to a lack of facilities for composing specialised plots.
'ggforce' aims to be a collection of mainly new stats and geoms that fills
this gap. All additional functionality is aimed to come through the official
extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggforce versions 0.1.3 dated 2018-07-07 and 0.2.0 dated 2019-03-07
ggforce-0.1.3/ggforce/build/partial.rdb |only ggforce-0.2.0/ggforce/DESCRIPTION | 52 ggforce-0.2.0/ggforce/LICENSE |only ggforce-0.2.0/ggforce/MD5 | 141 +- ggforce-0.2.0/ggforce/NAMESPACE | 140 +- ggforce-0.2.0/ggforce/NEWS.md | 48 ggforce-0.2.0/ggforce/R/RcppExports.R | 20 ggforce-0.2.0/ggforce/R/aaa.R | 23 ggforce-0.2.0/ggforce/R/arc.R | 300 ++--- ggforce-0.2.0/ggforce/R/arc_bar.R | 403 +++---- ggforce-0.2.0/ggforce/R/bezier.R | 399 +++---- ggforce-0.2.0/ggforce/R/bspline.R | 361 +++--- ggforce-0.2.0/ggforce/R/bspline_closed.R |only ggforce-0.2.0/ggforce/R/circle.R | 142 -- ggforce-0.2.0/ggforce/R/diagonal.R |only ggforce-0.2.0/ggforce/R/diagonal_wide.R |only ggforce-0.2.0/ggforce/R/ellipse.R |only ggforce-0.2.0/ggforce/R/facet_grid_paginate.R | 115 +- ggforce-0.2.0/ggforce/R/facet_stereo.R |only ggforce-0.2.0/ggforce/R/facet_wrap_paginate.R | 186 ++- ggforce-0.2.0/ggforce/R/facet_zoom.R | 649 +++++++----- ggforce-0.2.0/ggforce/R/ggforce_package.R | 73 - ggforce-0.2.0/ggforce/R/interpolate.R | 148 +- ggforce-0.2.0/ggforce/R/link.R | 271 ++--- ggforce-0.2.0/ggforce/R/mark_circle.R |only ggforce-0.2.0/ggforce/R/mark_ellipse.R |only ggforce-0.2.0/ggforce/R/mark_hull.R |only ggforce-0.2.0/ggforce/R/mark_label.R |only ggforce-0.2.0/ggforce/R/mark_rect.R |only ggforce-0.2.0/ggforce/R/parallel_sets.R |only ggforce-0.2.0/ggforce/R/position-jitternormal.R |only ggforce-0.2.0/ggforce/R/regon.R |only ggforce-0.2.0/ggforce/R/scale-depth.R |only ggforce-0.2.0/ggforce/R/scale-unit.R | 194 ++- ggforce-0.2.0/ggforce/R/shape.R |only ggforce-0.2.0/ggforce/R/sina.R | 532 +++++----- ggforce-0.2.0/ggforce/R/spiro.R |only ggforce-0.2.0/ggforce/R/themes.R | 19 ggforce-0.2.0/ggforce/R/trans.R | 156 +- ggforce-0.2.0/ggforce/R/trans_linear.R |only ggforce-0.2.0/ggforce/R/utilities.R |only ggforce-0.2.0/ggforce/R/voronoi.R |only ggforce-0.2.0/ggforce/README.md | 125 -- ggforce-0.2.0/ggforce/build/vignette.rds |binary ggforce-0.2.0/ggforce/inst/doc/Visual_Guide.R | 121 ++ ggforce-0.2.0/ggforce/inst/doc/Visual_Guide.Rmd | 236 ++++ ggforce-0.2.0/ggforce/inst/doc/Visual_Guide.html | 1115 ++++++++++++++------- ggforce-0.2.0/ggforce/man/facet_grid_paginate.Rd | 11 ggforce-0.2.0/ggforce/man/facet_stereo.Rd |only ggforce-0.2.0/ggforce/man/facet_wrap_paginate.Rd | 37 ggforce-0.2.0/ggforce/man/facet_zoom.Rd | 36 ggforce-0.2.0/ggforce/man/figures |only ggforce-0.2.0/ggforce/man/gather_set_data.Rd |only ggforce-0.2.0/ggforce/man/geom_arc.Rd | 144 +- ggforce-0.2.0/ggforce/man/geom_arc_bar.Rd | 153 +- ggforce-0.2.0/ggforce/man/geom_bezier.Rd | 170 +-- ggforce-0.2.0/ggforce/man/geom_bspline.Rd | 184 +-- ggforce-0.2.0/ggforce/man/geom_bspline_closed.Rd |only ggforce-0.2.0/ggforce/man/geom_circle.Rd | 123 +- ggforce-0.2.0/ggforce/man/geom_delvor.Rd |only ggforce-0.2.0/ggforce/man/geom_diagonal.Rd |only ggforce-0.2.0/ggforce/man/geom_diagonal_wide.Rd |only ggforce-0.2.0/ggforce/man/geom_ellipse.Rd |only ggforce-0.2.0/ggforce/man/geom_link.Rd | 162 +-- ggforce-0.2.0/ggforce/man/geom_mark_circle.Rd |only ggforce-0.2.0/ggforce/man/geom_mark_ellipse.Rd |only ggforce-0.2.0/ggforce/man/geom_mark_hull.Rd |only ggforce-0.2.0/ggforce/man/geom_mark_rect.Rd |only ggforce-0.2.0/ggforce/man/geom_parallel_sets.Rd |only ggforce-0.2.0/ggforce/man/geom_regon.Rd |only ggforce-0.2.0/ggforce/man/geom_shape.Rd |only ggforce-0.2.0/ggforce/man/geom_sina.Rd | 220 ++-- ggforce-0.2.0/ggforce/man/geom_spiro.Rd |only ggforce-0.2.0/ggforce/man/ggforce-extensions.Rd | 38 ggforce-0.2.0/ggforce/man/ggforce-package.Rd | 76 - ggforce-0.2.0/ggforce/man/linear_trans.Rd |only ggforce-0.2.0/ggforce/man/n_pages.Rd | 9 ggforce-0.2.0/ggforce/man/position_jitternormal.Rd |only ggforce-0.2.0/ggforce/man/power_trans.Rd | 9 ggforce-0.2.0/ggforce/man/radial_trans.Rd | 11 ggforce-0.2.0/ggforce/man/scale_depth.Rd |only ggforce-0.2.0/ggforce/man/scale_unit.Rd | 26 ggforce-0.2.0/ggforce/man/theme_no_axes.Rd | 2 ggforce-0.2.0/ggforce/man/trans_reverser.Rd | 10 ggforce-0.2.0/ggforce/src/RcppExports.cpp | 74 + ggforce-0.2.0/ggforce/src/bSpline.cpp | 173 +-- ggforce-0.2.0/ggforce/src/bezier.cpp | 132 +- ggforce-0.2.0/ggforce/src/deBoor.cpp | 74 - ggforce-0.2.0/ggforce/src/deBoor.h | 20 ggforce-0.2.0/ggforce/src/ellipseEnclose.cpp |only ggforce-0.2.0/ggforce/src/enclose.cpp |only ggforce-0.2.0/ggforce/src/pointPath.cpp |only ggforce-0.2.0/ggforce/vignettes/Visual_Guide.Rmd | 236 ++++ 93 files changed, 4852 insertions(+), 3247 deletions(-)
Title: Implements Measures for the Comparison of Two Partitions
Description: Provides several measures ((dis)similarity, distance/metric,
correlation, entropy) for comparing two partitions of the same set of
objects. The different measures can be assigned to three different
classes: Pair comparison (containing the famous Jaccard and Rand
indices), set based, and information theory based.
Many of the implemented measures can be found in
Albatineh AN, Niewiadomska-Bugaj M and Mihalko D (2006)
<doi:10.1007/s00357-006-0017-z> and
Meila M (2007) <doi:10.1016/j.jmva.2006.11.013>.
Partitions are represented by vectors of class labels which allow a
straightforward integration with existing clustering algorithms
(e.g. kmeans()). The package is mostly based on the S4 object system.
Author: Fabian Ball [aut, cre, cph, ctb],
Andreas Geyer-Schulz [cph]
Maintainer: Fabian Ball <mail@fabian-ball.de>
Diff between partitionComparison versions 0.2.4 dated 2018-10-04 and 0.2.5 dated 2019-03-07
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- build/partial.rdb |binary man/partitionComparison-package.Rd | 10 +++++++++- 4 files changed, 20 insertions(+), 12 deletions(-)
More information about partitionComparison at CRAN
Permanent link
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.7.10 dated 2019-02-24 and 0.8.1 dated 2019-03-07
DESCRIPTION | 14 +- MD5 | 30 +++-- NAMESPACE | 18 +++ NEWS.md | 13 ++ R/CreateTableOneJS.R | 161 ++++++++++++++++++++++++-------- R/forestcox.R |only R/label.R | 2 R/svyCreateTableOneJS.R | 141 +++++++++++++++++++++------- README.md | 144 +++++++++++++++++++++------- inst/doc/jstable.R | 15 ++ inst/doc/jstable.Rmd | 21 +++- inst/doc/jstable.html | 48 ++++++--- man/TableSubgroupCox.Rd |only man/TableSubgroupMultiCox.Rd |only tests/testthat/test-CreateTableOneJS.R | 12 ++ tests/testthat/test-forestcox.R |only tests/testthat/test-svyCreateTableOne.R | 22 +++- vignettes/jstable.Rmd | 21 +++- 18 files changed, 515 insertions(+), 147 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.10 dated 2018-04-06 and 1.11 dated 2019-03-07
DESCRIPTION | 10 +++--- MD5 | 60 +++++++++++++++++++-------------------- NEWS | 11 ++++++- R/projShapes.R | 11 +++++-- build/vignette.rds |binary inst/doc/Anthropometry.R | 5 +++ inst/doc/Anthropometry.Rnw | 5 +++ inst/doc/Anthropometry.pdf |binary man/Anthropometry-package.Rd | 8 ++--- man/HartiganShapes.Rd | 1 man/TDDclust.Rd | 1 man/archetypesBoundary.Rd | 1 man/archetypoids.Rd | 1 man/cdfDissWomenPrototypes.Rd | 3 + man/computSizesHipamAnthropom.Rd | 1 man/computSizesTrimowa.Rd | 1 man/descrDissTrunks.Rd | 1 man/hipamAnthropom.Rd | 3 + man/percentilsArchetypoid.Rd | 1 man/plotPrototypes.Rd | 1 man/plotTreeHipamAnthropom.Rd | 1 man/plotTrimmOutl.Rd | 1 man/screeArchetypal.Rd | 1 man/stepArchetypesRawData.Rd | 1 man/stepArchetypoids.Rd | 1 man/trimmOutl.Rd | 1 man/trimmedLloydShapes.Rd | 1 man/trimowa.Rd | 3 + man/xyplotPCArchetypes.Rd | 1 src/cast.c | 8 ++--- vignettes/Anthropometry.Rnw | 5 +++ 31 files changed, 101 insertions(+), 48 deletions(-)
Title: Load Data from 'MyTarget API v2'
Description: Allows work with 'MyTarget API v2'
<https://target.my.com/doc/apiv2/ru/detailed.html> and
load data by ads, campaigns, agency clients and statistic from
your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rmytarget versions 2.1.3 dated 2019-02-14 and 2.1.4 dated 2019-03-07
DESCRIPTION | 8 ++--- MD5 | 8 ++--- NEWS.md | 4 ++ R/myTarGetStats.R | 74 +++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary 5 files changed, 49 insertions(+), 45 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.0.1 dated 2019-01-29 and 2.0.2 dated 2019-03-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/modelparamssummary.R | 18 +++++++++++------- R/modelparamstransform.R | 21 ++++++++++++++++++--- 4 files changed, 36 insertions(+), 17 deletions(-)
Title: Modified Rand and Wallace Indices
Description: It provides functions to compute the values of different modifications of the Rand and Wallace indices. The indices are used to measure the stability or similarity of two partitions obtained on two different sets of units with a non-empty intercept. Splitting and merging of clusters can (depends on the selected index) have a different effect on the value of the indices. The indices are proposed in Cugmas and Ferligoj (2018) <http://ibmi.mf.uni-lj.si/mz/2018/no-1/Cugmas2018.pdf>.
Author: Marjan Cugmas [aut, cre]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>
Diff between mri versions 1.0.0 dated 2019-02-13 and 1.0.1 dated 2019-03-07
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- man/MRI.Rd | 8 ++++---- man/MW1.Rd | 8 ++++---- man/MW2.Rd | 8 ++++---- man/fromTableToVectors.Rd | 2 +- 6 files changed, 23 insertions(+), 22 deletions(-)
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <olena.yavorska@ludwig.ox.ac.uk>
James Staley <james.staley@bristol.ac.uk>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.3.0 dated 2018-03-03 and 0.4.0 dated 2019-03-07
DESCRIPTION | 15 MD5 | 123 ++--- NAMESPACE | 6 NEWS | 6 R/1Data.R | 5 R/AllClasses.R | 93 ++++ R/AllGenerics.R | 111 ++++ R/extract.pheno.csv-function.R | 6 R/getter-methods.R | 12 R/mr_conmix-methods.R |only R/mr_egger-methods.R | 5 R/mr_mvegger-methods.R |only R/pheno_input-function.R |only R/show-methods.R | 86 +++ build/vignette.rds |binary man/Egger-class.Rd | 122 ++--- man/IVW-class.Rd | 86 +-- man/MRAll-class.Rd | 38 - man/MRConMix-class.Rd |only man/MRHetPen-class.Rd | 74 +-- man/MRInput-class.Rd | 84 +-- man/MRMBE-class.Rd | 74 +-- man/MRMVInput-class.Rd | 76 +-- man/MVEgger-class.Rd |only man/MVIVW-class.Rd | 78 +-- man/MaxLik-class.Rd | 82 +-- man/WeightedMedian-class.Rd | 66 +- man/calcium.Rd | 68 +- man/ci_normal.Rd | 62 +- man/ci_t.Rd | 66 +- man/coursedata.Rd | 28 - man/decimals.Rd | 54 +- man/egger.bounds.Rd | 78 +-- man/extract.pheno.csv.Rd | 156 +++--- man/getter.Rd | 98 ++-- man/het.weight.Rd | 62 +- man/ldlc.Rd | 102 ++-- man/loglikelihood.Rd | 58 +- man/loglikelihoodcorrel.Rd | 58 +- man/loglikelihoodrhocorrel.Rd | 54 +- man/mbe_boot.Rd | 64 +- man/mbe_est.Rd | 58 +- man/model.prior.Rd | 58 +- man/mr_allmethods.Rd | 86 +-- man/mr_conmix.Rd |only man/mr_egger.Rd | 176 +++---- man/mr_hetpen.Rd | 126 ++--- man/mr_input.Rd | 118 ++--- man/mr_ivw.Rd | 190 ++++---- man/mr_maxlik.Rd | 143 +++--- man/mr_mbe.Rd | 140 +++--- man/mr_median.Rd | 176 +++---- man/mr_mvegger.Rd |only man/mr_mvinput.Rd | 112 ++-- man/mr_mvivw.Rd | 132 ++--- man/mr_plot.Rd | 106 ++-- man/penalised.weights.Rd | 66 +- man/penalised.weights.delta.Rd | 70 +-- man/pheno_input.Rd |only man/phenoscanner.Rd |only man/r.weights.Rd | 58 +- man/r.weights.delta.Rd | 76 +-- man/simpleCap.Rd | 50 +- man/values.Rd | 46 +- man/weighted.median.Rd | 54 +- man/weighted.median.boot.se.Rd | 76 +-- vignettes/Vignette_MR.html | 930 ++++++++++++++--------------------------- 67 files changed, 2687 insertions(+), 2616 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Title: 'cpt-city' Colour Gradients
Description: Incorporates colour gradients from the 'cpt-city' web archive available at <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between cptcity versions 1.0.3 dated 2018-04-18 and 1.0.4 dated 2019-03-07
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/cpt.R | 7 +++++-- R/lucky.R | 21 +++++++++++++-------- man/cpt.Rd | 6 +++++- man/lucky.Rd | 6 +++++- tests/testthat/test-cpt.R | 6 ++++++ tests/testthat/test-lucky.R | 5 +++++ 8 files changed, 51 insertions(+), 24 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: ORPHANED
Diff between sivipm versions 1.1-4.1 dated 2019-01-14 and 1.1-4.2 dated 2019-03-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- tests/excornell0.Rout.save | 22 +++++++++++----------- tests/excornell1.Rout.save | 24 ++++++++++++------------ 4 files changed, 29 insertions(+), 29 deletions(-)
Title: Selection of Linear Estimators
Description: Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Author: Yannick Baraud, Christophe Giraud, Sylvie Huet
Maintainer: ORPHANED
Diff between LINselect versions 1.1 dated 2017-04-20 and 1.1.1 dated 2019-03-07
DESCRIPTION | 13 ++++++++----- MD5 | 4 ++-- tests/TesttuneLasso.Rout.save | 10 +++++----- 3 files changed, 15 insertions(+), 12 deletions(-)
Title: Visualize Probability Distributions
Description: Visualize and compute percentiles/probabilities of normal, t, f, chi square
and binomial distributions.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between vistributions versions 0.1.0 dated 2018-11-30 and 0.1.1 dated 2019-03-07
DESCRIPTION | 8 ++-- MD5 | 34 ++++++++++---------- NAMESPACE | 4 +- NEWS.md | 4 ++ R/vdist-app.R | 18 ++++++---- R/vdist-binomial.R | 47 +++++++--------------------- R/vdist-chisquare.R | 27 +++++++--------- R/vdist-f.R | 27 +++++++--------- R/vdist-normal.R | 24 +++++--------- R/vdist-t.R | 29 +++++++---------- R/vdist-utils.R |only R/zzz.R |only README.md | 32 ++++++++++++++----- build/vignette.rds |binary inst/application/logic/logic_chisq.R | 2 - inst/application/ui.R | 1 inst/application/ui/ui_dist_home.R | 4 +- inst/doc/introduction-to-vistributions.html | 24 +++++++++++++- man/vdist_launch_app.Rd | 6 +-- 19 files changed, 154 insertions(+), 137 deletions(-)
Title: Split, Combine and Compress PDF Files
Description: Content-preserving transformations transformations of PDF files such
as split, combine, and compress. This package interfaces directly to the 'qpdf'
C++ API and does not require any command line utilities. Note that 'qpdf' does
not read actual content from PDF files: to extract text and data you need the
'pdftools' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jay Berkenbilt [cph] (Author of libqpdf)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between qpdf versions 1.0 dated 2019-02-28 and 1.1 dated 2019-03-07
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NEWS |only configure |only src/Makevars | 1 - 5 files changed, 7 insertions(+), 6 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from this libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 2.0.1 dated 2018-12-14 and 3.0.0 dated 2019-03-07
multinet-2.0.1/multinet/src/eclat/include |only multinet-3.0.0/multinet/DESCRIPTION | 10 multinet-3.0.0/multinet/MD5 | 157 +--- multinet-3.0.0/multinet/NAMESPACE | 9 multinet-3.0.0/multinet/NEWS |only multinet-3.0.0/multinet/R/datasets.R | 24 multinet-3.0.0/multinet/R/deprecated.R | 363 +++++++++- multinet-3.0.0/multinet/R/functions.R | 91 +- multinet-3.0.0/multinet/man/ActorMeasures.Rd | 56 - multinet-3.0.0/multinet/man/Attributes.Rd | 71 - multinet-3.0.0/multinet/man/Classes.Rd | 4 multinet-3.0.0/multinet/man/Communities.Rd | 46 - multinet-3.0.0/multinet/man/Conversion.Rd | 2 multinet-3.0.0/multinet/man/Deprecated.Rd |only multinet-3.0.0/multinet/man/Directionality.Rd | 24 multinet-3.0.0/multinet/man/DistanceMeasures.Rd | 8 multinet-3.0.0/multinet/man/Generation.Rd | 28 multinet-3.0.0/multinet/man/IO.Rd | 20 multinet-3.0.0/multinet/man/LayerMeasures.Rd | 86 +- multinet-3.0.0/multinet/man/Layout.Rd | 14 multinet-3.0.0/multinet/man/Manipulation.Rd | 88 +- multinet-3.0.0/multinet/man/Navigation.Rd | 18 multinet-3.0.0/multinet/man/Plot.Rd | 15 multinet-3.0.0/multinet/man/Predefined.Rd | 62 - multinet-3.0.0/multinet/man/Properties.Rd | 86 +- multinet-3.0.0/multinet/man/Transformation.Rd | 10 multinet-3.0.0/multinet/src/include/core/attributes/AttributeStore.h | 2 multinet-3.0.0/multinet/src/include/core/attributes/MainMemoryAttributeStore.h | 2 multinet-3.0.0/multinet/src/include/core/attributes/Text.h | 1 multinet-3.0.0/multinet/src/include/core/attributes/Value.h | 1 multinet-3.0.0/multinet/src/include/core/datastructures/containers/Attributed.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/DefaultEQ.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/DefaultLT.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/LabeledSharedPtrSortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/LabeledUniquePtrSortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/PtrSortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/SharedPtrEQ.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/SharedPtrLT.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/SharedPtrSortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/SortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/SortedRandomSetEntry.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/UniquePtrEQ.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/UniquePtrLT.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/containers/UniquePtrSortedRandomSet.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/objects/NamedObject.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/objects/Object.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/observers/GenericObserver.h | 5 multinet-3.0.0/multinet/src/include/core/datastructures/observers/Observer.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/observers/ObserverStore.h | 2 multinet-3.0.0/multinet/src/include/core/datastructures/observers/Subject.h | 2 multinet-3.0.0/multinet/src/include/mnet/community/glouvain.h | 2 multinet-3.0.0/multinet/src/include/mnet/community/infomap.h | 13 multinet-3.0.0/multinet/src/include/mnet/community/modularity.h | 95 -- multinet-3.0.0/multinet/src/include/mnet/datastructures/graphs/MultilayerNetwork.h | 3 multinet-3.0.0/multinet/src/include/mnet/datastructures/layers/SimpleGraphLayer.h | 6 multinet-3.0.0/multinet/src/include/net/community/Community.h | 5 multinet-3.0.0/multinet/src/include/net/datastructures/graphs/Graph.h | 3 multinet-3.0.0/multinet/src/include/net/datastructures/objects/GenericEdge.h | 2 multinet-3.0.0/multinet/src/include/net/datastructures/stores/AttributeStoreWrapper.h | 1 multinet-3.0.0/multinet/src/include/net/datastructures/stores/EdgeStore.h | 2 multinet-3.0.0/multinet/src/include/net/datastructures/stores/GenericEdgeStore.h | 2 multinet-3.0.0/multinet/src/include/net/datastructures/stores/GenericSimpleEdgeStore.h | 2 multinet-3.0.0/multinet/src/include/net/datastructures/stores/MultiEdgeStore.h | 1 multinet-3.0.0/multinet/src/include/net/datastructures/stores/SimpleEdgeStore.h | 2 multinet-3.0.0/multinet/src/include/net/datastructures/stores/VertexStore.h | 4 multinet-3.0.0/multinet/src/infomap/infomap/InfomapBase.cpp | 19 multinet-3.0.0/multinet/src/infomap/infomap/InfomapGreedyTypeSpecialized.h | 2 multinet-3.0.0/multinet/src/lib/infomap/infomap/InfomapBase.cpp | 19 multinet-3.0.0/multinet/src/lib/infomap/infomap/InfomapGreedyTypeSpecialized.h | 2 multinet-3.0.0/multinet/src/multinet/core/attributes/conversion.cpp | 1 multinet-3.0.0/multinet/src/multinet/mnet/datastructures/graphs/AttributedTwoModeNetwork.cpp | 6 multinet-3.0.0/multinet/src/rcpp_module_definition.cpp | 113 +-- 72 files changed, 923 insertions(+), 723 deletions(-)
Title: Supports Developing, Building and Deploying R Solution
Description: Supports safe and reproducible solutions development in R.
It will help you with environment separation per project,
dependency management, local packages creation and preparing
deployment packs for your solutions.
Author: Walerian Sokolowski [aut, cre],
Wit Jakuczun [aut],
Yulia Yakimechko [aut],
Mateusz Kalinowski [aut],
Ryszard Szymanski [aut],
WLOG Solutions [cph],
R Consortium [ctb] (Definitions of system requirements are taken from
sysreqsdb project.)
Maintainer: Walerian Sokolowski <rsuite@wlogsolutions.com>
Diff between RSuite versions 0.35-250 dated 2019-01-07 and 0.36-252 dated 2019-03-07
DESCRIPTION | 6 - MD5 | 36 +++--- NEWS.md | 9 + R/00_init.R | 4 R/02_api_prj.R | 48 ++++++-- R/04_api_repo.R | 2 R/14_setup_structure.R | 4 R/15_zip_project.R | 67 ++++++++--- R/19_pack_helpers.R | 40 ++++-- R/22_repo_adapter_s3.R | 222 ++++++++++++++++++------------------- R/29_repo_manager_s3.R | 13 +- R/32_rc_adapter_git.R | 56 ++++++++- R/50_pkg_deployment.R | 6 - R/52_dependencies.R | 2 R/98_shell.R | 21 +++ inst/doc/RSuite-vignette.html | 127 ++++++++++----------- inst/extdata/builtin_templates.zip |binary man/prj_build.Rd | 6 - man/prj_pack.Rd | 6 - 19 files changed, 409 insertions(+), 266 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Alexander Robitzsch [ctb],
Gerko Vink [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Rianne Schouten [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.3.0 dated 2018-07-27 and 3.4.0 dated 2019-03-07
mice-3.3.0/mice/tests/testthat/Rplots.pdf |only mice-3.3.0/mice/tests/testthat/test-fix.coef.R |only mice-3.4.0/mice/DESCRIPTION | 15 +-- mice-3.4.0/mice/MD5 | 105 +++++++++++------------- mice-3.4.0/mice/NEWS.md | 36 ++++++++ mice-3.4.0/mice/R/check.deprecated.R |only mice-3.4.0/mice/R/md.pattern.R | 13 ++ mice-3.4.0/mice/R/method.R | 8 - mice-3.4.0/mice/R/mice-package.R | 2 mice-3.4.0/mice/R/mice.R | 1 mice-3.4.0/mice/R/mids2spss.R | 2 mice-3.4.0/mice/R/nelsonaalen.R | 2 mice-3.4.0/mice/R/predictorMatrix.R | 4 mice-3.4.0/mice/R/sampler.R | 18 ++-- mice-3.4.0/mice/man/ampute.Rd | 6 - mice-3.4.0/mice/man/appendbreak.Rd | 3 mice-3.4.0/mice/man/bwplot.mids.Rd | 4 mice-3.4.0/mice/man/fluxplot.Rd | 3 mice-3.4.0/mice/man/md.pattern.Rd | 5 - mice-3.4.0/mice/man/mdc.Rd | 8 - mice-3.4.0/mice/man/mice.Rd | 7 - mice-3.4.0/mice/man/mice.impute.2l.bin.Rd | 1 mice-3.4.0/mice/man/mice.impute.2l.lmer.Rd | 1 mice-3.4.0/mice/man/mice.impute.2l.norm.Rd | 1 mice-3.4.0/mice/man/mice.impute.2l.pan.Rd | 1 mice-3.4.0/mice/man/mice.impute.2lonly.mean.Rd | 1 mice-3.4.0/mice/man/mice.impute.2lonly.norm.Rd | 1 mice-3.4.0/mice/man/mice.impute.2lonly.pmm.Rd | 1 mice-3.4.0/mice/man/mice.impute.cart.Rd | 1 mice-3.4.0/mice/man/mice.impute.jomoImpute.Rd | 1 mice-3.4.0/mice/man/mice.impute.lda.Rd | 1 mice-3.4.0/mice/man/mice.impute.logreg.Rd | 1 mice-3.4.0/mice/man/mice.impute.logreg.boot.Rd | 1 mice-3.4.0/mice/man/mice.impute.mean.Rd | 1 mice-3.4.0/mice/man/mice.impute.midastouch.Rd | 4 mice-3.4.0/mice/man/mice.impute.norm.Rd | 1 mice-3.4.0/mice/man/mice.impute.norm.boot.Rd | 1 mice-3.4.0/mice/man/mice.impute.norm.nob.Rd | 1 mice-3.4.0/mice/man/mice.impute.norm.predict.Rd | 1 mice-3.4.0/mice/man/mice.impute.panImpute.Rd | 1 mice-3.4.0/mice/man/mice.impute.pmm.Rd | 1 mice-3.4.0/mice/man/mice.impute.polr.Rd | 1 mice-3.4.0/mice/man/mice.impute.polyreg.Rd | 1 mice-3.4.0/mice/man/mice.impute.quadratic.Rd | 1 mice-3.4.0/mice/man/mice.impute.rf.Rd | 1 mice-3.4.0/mice/man/mice.impute.ri.Rd | 1 mice-3.4.0/mice/man/mipo.Rd | 5 - mice-3.4.0/mice/man/norm.draw.Rd | 1 mice-3.4.0/mice/man/plot.mids.Rd | 4 mice-3.4.0/mice/man/quickpred.Rd | 4 mice-3.4.0/mice/man/squeeze.Rd | 3 mice-3.4.0/mice/man/summary.Rd | 3 mice-3.4.0/mice/man/xyplot.mids.Rd | 4 mice-3.4.0/mice/tests/testthat/test-parlmice.R | 1 mice-3.4.0/mice/tests/testthat/test-pool.R | 8 + 55 files changed, 192 insertions(+), 111 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided.
Author: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Diff between Matching versions 4.9-3 dated 2018-05-06 and 4.9-5 dated 2019-03-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GenMatching.R | 4 ++-- R/Matching.R | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.2.0 dated 2018-11-12 and 0.2.1 dated 2019-03-07
DESCRIPTION | 8 MD5 | 35 NAMESPACE | 1 NEWS.md | 8 R/deprivation_decile.R | 21 R/fingertips_data.R | 2 R/indicator_metadata.R | 36 R/indicators.R | 6 R/retrieve_data.R | 34 R/utils.R | 9 build/vignette.rds |binary inst/doc/lifeExpectancy.Rmd | 2 inst/doc/lifeExpectancy.html | 3129 +---------------------------------- inst/doc/selectIndicatorsRedRed.html | 342 --- man/add_timestamp.Rd |only tests/testthat/test-deprivation.R | 14 tests/testthat/test-extract.R | 6 tests/testthat/test-metadata.R | 2 vignettes/lifeExpectancy.Rmd | 2 19 files changed, 365 insertions(+), 3292 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides
C implementations of the association mining algorithms Apriori and Eclat.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Ian Johnson [ctb, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.6-2 dated 2018-12-03 and 1.6-3 dated 2019-03-07
DESCRIPTION | 12 ++--- MD5 | 30 +++++++------- NEWS.md | 9 ++++ R/apriori.R | 5 -- R/eclat.R | 5 -- R/read_write.R | 24 +++++++---- R/warm.R | 4 - inst/CITATION | 81 +++++++++++++++------------------------ inst/doc/arules.pdf |binary man/read.transactions.Rd | 24 +++++++++-- man/transactions-class.Rd | 10 +++- src/ptree.c | 8 +-- src/rapriori.c | 6 ++ src/similarity.c | 6 +- src/warm.c | 24 ++++++----- tests/testthat/test-read_write.R | 25 +++++++++++- 16 files changed, 161 insertions(+), 112 deletions(-)
Title: Parallel Utilities for Lambda Selection along a Regularization
Path
Description: Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.
Author: Zachary Kurtz [aut, cre],
Christian Müller [aut, ctb]
Maintainer: Zachary Kurtz <zdkurtz@gmail.com>
Diff between pulsar versions 0.3.4 dated 2018-09-02 and 0.3.5 dated 2019-03-07
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS | 7 + inst/doc/other-criteria.R | 7 + inst/doc/other-criteria.Rmd | 7 + inst/doc/other-criteria.html | 151 ++++++++++++++++++++----------------------- tests/testthat/pulsarfuns.R | 7 + tests/testthat/test_pulsar.R | 2 vignettes/other-criteria.Rmd | 7 + 9 files changed, 110 insertions(+), 102 deletions(-)
Title: Estimation for Multivariate Normal and Student-t Data with
Monotone Missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is monotone.
Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions fail,
the package can handle a nearly arbitrary amount of missing data.
The current version supports maximum likelihood inference and
a full Bayesian approach employing scale-mixtures for Gibbs sampling.
Monotone data augmentation extends this Bayesian approach to arbitrary
missingness patterns. A fully functional standalone interface to the
Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown),
Horseshoe (from Carvalho, Polson, & Scott), and ridge regression
with model selection via Reversible Jump, and student-t errors
(from Geweke) is also provided.
Author: Robert B. Gramacy <rbg@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between monomvn versions 1.9-8 dated 2018-09-14 and 1.9-9 dated 2019-03-07
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/bmonomvn.R | 2 +- R/regress.lars.R | 3 ++- man/bmonomvn.Rd | 18 +++++++----------- src/matrix.c | 4 ++-- 7 files changed, 30 insertions(+), 25 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.2.6 dated 2019-02-24 and 0.2.7 dated 2019-03-07
DESCRIPTION | 10 MD5 | 140 ++++++++-- NAMESPACE | 1 R/capabilities.R | 16 + R/completion.R | 50 ++- R/diagnostics.R | 26 + R/document.R | 150 +++++++--- R/formatting.R | 36 ++ R/handlers-general.R | 52 +++ R/handlers-langfeatures.R | 273 ++++++++++++++++++-- R/handlers-textsync.R | 55 +++- R/handlers-workspace.R | 58 +++- R/hover.R | 31 +- R/interfaces.R |only R/languageserver.R | 10 R/protocol.R | 19 + R/signature.R | 18 + R/utils.R | 88 ++++++ R/workspace.R | 84 ++++-- README.md | 10 man/LanguageServer.Rd |only man/Logger.Rd |only man/Message.Rd |only man/Namespace.Rd |only man/Notification.Rd |only man/Request.Rd |only man/Response.Rd |only man/ResponseErrorMessage.Rd |only man/ServerCapabilities.Rd |only man/Workspace.Rd |only man/arg_completion.Rd |only man/cancel_request.Rd |only man/check_scope.Rd |only man/code_action_params.Rd |only man/code_lens_params.Rd |only man/code_lens_resolve.Rd |only man/completion_item_resolve.Rd |only man/completion_params.Rd |only man/completion_reply.Rd |only man/detect_closure.Rd |only man/detect_function.Rd |only man/detect_hover.Rd |only man/detect_token.Rd |only man/diagnose_file.Rd |only man/diagnostics.Rd |only man/did_change_configuration_params.Rd |only man/did_change_text_document_params.Rd |only man/did_close_text_document_params.Rd |only man/did_open_text_document_params.Rd |only man/did_save_text_document_params.Rd |only man/document_backward_search.Rd |only man/document_formatting_params.Rd |only man/document_line.Rd |only man/document_link_params.Rd |only man/document_link_resolve.Rd |only man/document_on_type_formatting_params.Rd |only man/document_range_formatting_params.Rd |only man/document_symbol_params.Rd |only man/find_config.Rd |only man/find_package.Rd |only man/formatting_reply.Rd |only man/getppid.Rd |only man/hover_reply.Rd |only man/is_directory.Rd |only man/is_package.Rd |only man/is_rmarkdown.Rd |only man/location.Rd |only man/log_write.Rd |only man/merge_list.Rd |only man/on_exit.Rd |only man/on_initialize.Rd |only man/on_initialized.Rd |only man/on_shutdown.Rd |only man/package_completion.Rd |only man/parse_document.Rd |only man/path_from_uri.Rd |only man/position.Rd |only man/range.Rd |only man/range_formatting_reply.Rd |only man/reference_params.Rd |only man/rename_params.Rd |only man/sanitize_names.Rd |only man/signature_reply.Rd |only man/stdin_read_char.Rd |only man/stdin_read_line.Rd |only man/stylize.Rd |only man/text_document_code_action.Rd |only man/text_document_code_lens.Rd |only man/text_document_color_presentation.Rd |only man/text_document_completion.Rd |only man/text_document_definition.Rd |only man/text_document_did_change.Rd |only man/text_document_did_close.Rd |only man/text_document_did_open.Rd |only man/text_document_did_save.Rd |only man/text_document_document_color.Rd |only man/text_document_document_highlight.Rd |only man/text_document_document_link.Rd |only man/text_document_document_symbol.Rd |only man/text_document_folding_range.Rd |only man/text_document_formatting.Rd |only man/text_document_hover.Rd |only man/text_document_implementation.Rd |only man/text_document_on_type_formatting.Rd |only man/text_document_position_params.Rd |only man/text_document_prepare_rename.Rd |only man/text_document_range_formatting.Rd |only man/text_document_references.Rd |only man/text_document_rename.Rd |only man/text_document_signature_help.Rd |only man/text_document_type_definition.Rd |only man/text_document_will_save.Rd |only man/text_document_will_save_wait_until.Rd |only man/text_edit.Rd |only man/throttle.Rd |only man/to_string.Rd |only man/will_save_text_document_params.Rd |only man/workspace_completion.Rd |only man/workspace_did_change_configuration.Rd |only man/workspace_did_change_watched_files.Rd |only man/workspace_did_change_workspace_folder_params.Rd |only man/workspace_execute_command.Rd |only man/workspace_symbol.Rd |only 123 files changed, 935 insertions(+), 192 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: High Performance Container Data Types
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.1.4 dated 2019-02-27 and 0.1.5 dated 2019-03-07
DESCRIPTION | 10 ++++---- MD5 | 44 +++++++++++++++++++------------------- R/deque.R | 20 +++++++++++++++++ R/dict.R | 17 +++++++++----- R/ordereddict.R | 33 ++++++++++++++++------------ R/queue.R | 10 ++++++++ R/stack.R | 10 ++++++++ man/Deque.Rd | 2 + man/DequeL.Rd | 2 + man/Dict.Rd | 5 ++-- man/OrderedDict.Rd | 5 ++-- man/OrderedDictL.Rd | 5 ++-- man/Queue.Rd | 1 man/QueueL.Rd | 1 man/Stack.Rd | 1 man/StackL.Rd | 1 src/collections.c | 3 +- src/dict.c | 12 ++++++++-- src/dict.h | 4 ++- tests/testthat/test_deque.R | 28 +++++++++++++++++++----- tests/testthat/test_ordereddict.R | 2 + tests/testthat/test_queue.R | 12 ++++++++-- tests/testthat/test_stack.R | 10 ++++++-- 23 files changed, 171 insertions(+), 67 deletions(-)
Title: Create and (Interactively) Modify Nested Hierarchies
Description: Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats.
These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Diff between sdcHierarchies versions 0.16 dated 2019-02-28 and 0.17 dated 2019-03-07
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 10 ++++++++++ R/hier_convert.R | 7 +++---- R/hier_helpers.R | 8 +++++--- R/hier_import.R | 33 +++++++++++++++++---------------- R/hier_match.R |only R/hier_to_tree.R |only README.md | 13 ++++++++++++- inst/doc/usage.html | 22 +++++++++++----------- man/hier_import.Rd | 32 ++++++++++++++++++-------------- man/hier_match.Rd |only man/hier_to_tree.Rd |only tests/testthat/test_hier_match.R |only tests/testthat/test_hier_to_tree.R |only tests/testthat/test_issue7.R |only tests/testthat/test_issue8.R |only 18 files changed, 101 insertions(+), 64 deletions(-)
More information about sdcHierarchies at CRAN
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Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight and simpler than both), tools
for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.6 dated 2019-02-01 and 0.2.7 dated 2019-03-07
reproducible-0.2.6/reproducible/man/fixErrors.SpatialPolygons.Rd |only reproducible-0.2.7/reproducible/DESCRIPTION | 12 reproducible-0.2.7/reproducible/MD5 | 69 reproducible-0.2.7/reproducible/NAMESPACE | 17 reproducible-0.2.7/reproducible/NEWS.md | 16 reproducible-0.2.7/reproducible/R/cache-helpers.R | 19 reproducible-0.2.7/reproducible/R/cache.R | 65 reproducible-0.2.7/reproducible/R/checksums.R | 2 reproducible-0.2.7/reproducible/R/cloud.R | 285 + reproducible-0.2.7/reproducible/R/download.R | 8 reproducible-0.2.7/reproducible/R/gis.R | 30 reproducible-0.2.7/reproducible/R/options.R | 4 reproducible-0.2.7/reproducible/R/postProcess.R | 527 ++ reproducible-0.2.7/reproducible/R/preProcess.R | 95 reproducible-0.2.7/reproducible/R/prepInputs.R | 51 reproducible-0.2.7/reproducible/R/reproducible-package.R | 4 reproducible-0.2.7/reproducible/inst/WORDLIST | 81 reproducible-0.2.7/reproducible/inst/doc/Intro-to-Cache.html | 1884 +++++----- reproducible-0.2.7/reproducible/man/CacheDigest.Rd | 6 reproducible-0.2.7/reproducible/man/cache.Rd | 4 reproducible-0.2.7/reproducible/man/cloudSyncCache.Rd | 81 reproducible-0.2.7/reproducible/man/cropInputs.Rd | 4 reproducible-0.2.7/reproducible/man/fixErrors.Rd | 20 reproducible-0.2.7/reproducible/man/makeMemoisable.Rd | 2 reproducible-0.2.7/reproducible/man/maskInputs.Rd | 3 reproducible-0.2.7/reproducible/man/postProcess.Rd | 40 reproducible-0.2.7/reproducible/man/postProcessHelpers.Rd | 2 reproducible-0.2.7/reproducible/man/projectInputs.Rd | 4 reproducible-0.2.7/reproducible/man/reproducible-package.Rd | 4 reproducible-0.2.7/reproducible/man/reproducibleOptions.Rd | 2 reproducible-0.2.7/reproducible/tests/testthat/helper-allEqual.R | 12 reproducible-0.2.7/reproducible/tests/testthat/test-cache.R | 58 reproducible-0.2.7/reproducible/tests/testthat/test-cacheHelpers.R | 3 reproducible-0.2.7/reproducible/tests/testthat/test-download.R | 12 reproducible-0.2.7/reproducible/tests/testthat/test-gis.R | 30 reproducible-0.2.7/reproducible/tests/testthat/test-prepInputs.R | 476 +- 36 files changed, 2399 insertions(+), 1533 deletions(-)
Title: Main Effects and Interactions in Mixed and Incomplete Data
Description: Generalized low-rank models for mixed and incomplete data frames. The main function may be used for dimensionality reduction of imputation of numeric, binary and count data (simultaneously). Main effects such as column means, group effects, or effects of row-column side information (e.g. user/item attributes in recommendation system) may also be modelled in addition to the low-rank model. Geneviève Robin, Olga Klopp, Julie Josse, Éric Moulines, Robert Tibshirani (2018) <arXiv:1806.09734>.
Author: Geneviève Robin
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between mimi versions 0.1.0 dated 2019-01-11 and 0.2.0 dated 2019-03-07
mimi-0.1.0/mimi/R/mimi-internal.R |only mimi-0.1.0/mimi/R/mimi-tools.R |only mimi-0.1.0/mimi/man/armijo.alpha.Rd |only mimi-0.1.0/mimi/man/armijo.lr.Rd |only mimi-0.1.0/mimi/man/covmatC.Rd |only mimi-0.1.0/mimi/man/covmatR.Rd |only mimi-0.1.0/mimi/man/irwls.cov.Rd |only mimi-0.1.0/mimi/man/irwls.lr.Rd |only mimi-0.1.0/mimi/man/log_factorial.Rd |only mimi-0.1.0/mimi/man/mimi.cov.Rd |only mimi-0.1.0/mimi/man/mimi.lr.Rd |only mimi-0.1.0/mimi/man/quad_approx.Rd |only mimi-0.1.0/mimi/man/wght.Rd |only mimi-0.1.0/mimi/man/wlra.Rd |only mimi-0.2.0/mimi/DESCRIPTION | 12 - mimi-0.2.0/mimi/MD5 | 45 ++-- mimi-0.2.0/mimi/NAMESPACE | 7 mimi-0.2.0/mimi/R/armijo.alpha.R |only mimi-0.2.0/mimi/R/armijo.alpha.ml.R |only mimi-0.2.0/mimi/R/armijo.lr.R |only mimi-0.2.0/mimi/R/covmat.R |only mimi-0.2.0/mimi/R/cv.mimi.R |only mimi-0.2.0/mimi/R/grad_alpha.R |only mimi-0.2.0/mimi/R/irwls.cov.R |only mimi-0.2.0/mimi/R/irwls.lr.R |only mimi-0.2.0/mimi/R/irwls.ml.R |only mimi-0.2.0/mimi/R/log_factorial.R |only mimi-0.2.0/mimi/R/mcgd.cov.R |only mimi-0.2.0/mimi/R/mcgd.lr.R |only mimi-0.2.0/mimi/R/mcgd.ml.R |only mimi-0.2.0/mimi/R/mimi.R | 356 ++--------------------------------- mimi-0.2.0/mimi/R/mimi.cov.R |only mimi-0.2.0/mimi/R/mimi.lr.R |only mimi-0.2.0/mimi/R/mimi.ml.R |only mimi-0.2.0/mimi/R/quad_approx.R |only mimi-0.2.0/mimi/R/wght.R |only mimi-0.2.0/mimi/R/wlra.R |only mimi-0.2.0/mimi/man/covmat.Rd | 24 +- mimi-0.2.0/mimi/man/cv.mimi.Rd | 19 + mimi-0.2.0/mimi/man/mimi.Rd | 27 +- 40 files changed, 101 insertions(+), 389 deletions(-)
Title: Low-Rank Interactions in Count Data with Covariates
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 2.1.1 dated 2019-02-26 and 2.1.2 dated 2019-03-07
lori-2.1.1/lori/data |only lori-2.1.1/lori/man/aravo.Rd |only lori-2.1.1/lori/man/plot.Rd |only lori-2.1.2/lori/DESCRIPTION | 8 +- lori-2.1.2/lori/MD5 | 35 +++++------ lori-2.1.2/lori/NAMESPACE | 2 lori-2.1.2/lori/R/altmin.R | 53 +++++++---------- lori-2.1.2/lori/R/cv.lori.R | 96 ++++++++++++++++++++----------- lori-2.1.2/lori/R/grad.R | 4 - lori-2.1.2/lori/R/lori.R | 53 ++++++++++++----- lori-2.1.2/lori/R/mcgd.R |only lori-2.1.2/lori/R/mi.lori.R | 108 +++++++++++++++++++++++++---------- lori-2.1.2/lori/R/plot.interaction.R | 45 +++++--------- lori-2.1.2/lori/R/pool.lori.R | 2 lori-2.1.2/lori/R/qut.R | 2 lori-2.1.2/lori/man/cv.lori.Rd | 34 ++++++----- lori-2.1.2/lori/man/lori.Rd | 16 +++-- lori-2.1.2/lori/man/mi.lori.Rd | 12 ++- lori-2.1.2/lori/man/plot.lori.Rd |only lori-2.1.2/lori/man/pool.lori.Rd | 4 - lori-2.1.2/lori/man/qut.Rd | 4 - 21 files changed, 287 insertions(+), 191 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.2.1 dated 2018-10-15 and 0.2.2 dated 2019-03-07
DESCRIPTION | 8 MD5 | 20 NEWS.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 32 - inst/REFERENCES.bib | 8 inst/doc/hdme-package.html | 724 ++++++++++++++++++++++------------ man/fit_corrected_lasso.Rd | 3 man/gmu_lasso_binomial.Rd | 3 tests/testthat/test_corrected_lasso.R | 1 11 files changed, 528 insertions(+), 277 deletions(-)
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph],
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.1.0 dated 2019-01-17 and 1.2.0 dated 2019-03-07
DESCRIPTION | 10 ++++----- MD5 | 25 +++++++++++++----------- NAMESPACE | 3 ++ NEWS | 14 +++++++++++++ R/future_by.R |only R/globals.R | 32 +++++++++++++------------------ R/rng.R | 15 ++++++-------- inst/doc/future.apply-1-overview.html | 3 +- inst/doc/future.apply-1-overview.md.rsp | 3 +- man/future_by.Rd |only tests/future_by.R |only tests/future_lapply,globals.R | 17 ++++++++++++++++ tests/stdout.R | 6 ----- tests/utils.R | 2 - vignettes/future.apply-1-overview.md.rsp | 3 +- 15 files changed, 82 insertions(+), 51 deletions(-)
Title: Bayesian Calibration of Complex Computer Codes
Description: Performs Bayesian calibration of computer models as per
Kennedy and O'Hagan 2001. The package includes routines to find the
hyperparameters and parameters; see the help page for stage1() for a
worked example using the toy dataset. A tutorial is provided in the
calex.Rnw vignette; and a suite of especially simple one dimensional
examples appears in inst/doc/one.dim/.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between calibrator versions 1.2-6 dated 2013-12-09 and 1.2-8 dated 2019-03-07
DESCRIPTION | 18 ++++---- MD5 | 92 ++++++++++++++++++++--------------------- NAMESPACE | 7 ++- R/calibrator.R | 88 ++++++++++++++++++++++++++------------- build/partial.rdb |only build/vignette.rds |binary data/toys.rda |binary inst/doc/calex.R | 2 inst/doc/calex.Rnw | 9 ++-- inst/doc/calex.pdf |binary man/C1.Rd | 3 - man/D1.fun.Rd | 3 - man/D2.fun.Rd | 3 - man/E.theta.toy.Rd | 3 - man/EK.eqn10.supp.Rd | 19 ++------ man/Ez.eqn7.supp.Rd | 3 - man/Ez.eqn9.supp.Rd | 3 - man/H.fun.Rd | 5 +- man/H1.toy.Rd | 3 - man/V.fun.Rd | 3 - man/V1.Rd | 3 - man/V2.Rd | 3 - man/Vd.Rd | 3 - man/W.Rd | 4 + man/W1.Rd | 4 + man/W2.Rd | 3 - man/beta1hat.fun.Rd | 3 - man/beta2hat.fun.Rd | 3 - man/betahat.fun.koh.Rd | 3 - man/calibrator-package.Rd |only man/cov.p5.supp.Rd | 3 - man/create.new.toy.datasets.Rd | 3 - man/dists.2frames.Rd | 3 - man/etahat.Rd | 4 + man/extractor.toy.Rd | 3 - man/h1.Rd | 3 - man/hbar.fun.toy.Rd | 3 - man/p.eqn4.supp.Rd | 3 - man/p.eqn8.supp.Rd | 3 - man/p.page4.Rd | 3 - man/phi.fun.toy.Rd | 4 + man/prob.psi1.Rd | 3 - man/reality.Rd | 3 - man/stage1.Rd | 3 - man/tee.Rd | 3 - man/toys.Rd | 3 - man/tt.fun.Rd | 3 - vignettes/calex.Rnw | 9 ++-- 48 files changed, 214 insertions(+), 141 deletions(-)
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test
that is needed for a given power and two sided type I error rate. The method works for metric data with and without
ties, count data, ordered categorical data, and even dichotomous data.
But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect.
For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Arne C. Bathke [aut],
Edgar Brunner [aut],
Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Frank Konietschke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between WMWssp versions 0.3.4 dated 2018-07-08 and 0.3.6 dated 2019-03-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/samplesize.R | 6 +++--- README.md | 5 +++-- inst/CITATION | 14 +++++++------- man/WMWssp.Rd | 6 +++--- man/WMWssp_maximize.Rd | 2 +- man/WMWssp_minimize.Rd | 2 +- tests/testthat/test_MinMax.R | 10 ++++++---- tests/testthat/test_WMWssp.R | 10 ++++++---- 10 files changed, 44 insertions(+), 39 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.0.0 dated 2019-02-26 and 1.0.1 dated 2019-03-07
DESCRIPTION | 6 MD5 | 14 NEWS.md | 4 R/zzz.R | 2 README.md | 52 +- inst/doc/USCSXenaTools.Rmd | 6 inst/doc/USCSXenaTools.html | 836 ++++++++++++++++++++++---------------------- vignettes/USCSXenaTools.Rmd | 6 8 files changed, 475 insertions(+), 451 deletions(-)