Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.3 dated 2016-11-04 and 1.0.4 dated 2016-11-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bayesian.R | 5 ++++- man/bayesian.Rd | 23 +++++++++++++++++++++++ 4 files changed, 34 insertions(+), 8 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data.
Author: Yves Croissant [aut, cre],
Giovanni Millo [aut],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Sch<c3><b6>nfelder [ctb],
Kevin Tappe [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between plm versions 1.5-12 dated 2015-12-14 and 1.6-4 dated 2016-11-29
plm-1.5-12/plm/man/index.plm.Rd |only plm-1.5-12/plm/tests/testpbgtest.R |only plm-1.6-4/plm/DESCRIPTION | 37 plm-1.6-4/plm/MD5 | 265 +- plm-1.6-4/plm/NAMESPACE | 149 - plm-1.6-4/plm/NEWS | 984 +++++--- plm-1.6-4/plm/R/attributes.R | 359 +- plm-1.6-4/plm/R/cipstest.R | 288 +- plm-1.6-4/plm/R/detect_lin_dep_alias.R |only plm-1.6-4/plm/R/divers.R | 548 ++-- plm-1.6-4/plm/R/ercomp.R | 541 ++-- plm-1.6-4/plm/R/fixef.R | 187 - plm-1.6-4/plm/R/index.R |only plm-1.6-4/plm/R/is.pconsecutive_pbalanced.R |only plm-1.6-4/plm/R/lagt.R |only plm-1.6-4/plm/R/make.pconsecutive_pbalanced.R |only plm-1.6-4/plm/R/options.R | 109 plm-1.6-4/plm/R/pFormula.R | 372 +-- plm-1.6-4/plm/R/panelmodel.R | 174 - plm-1.6-4/plm/R/pcce.R | 113 plm-1.6-4/plm/R/pcdtest.R | 321 +- plm-1.6-4/plm/R/pfunctions.R | 603 +++- plm-1.6-4/plm/R/pgmm.R | 1218 +++++----- plm-1.6-4/plm/R/pht.R | 424 +-- plm-1.6-4/plm/R/piest.R | 486 +-- plm-1.6-4/plm/R/plm.R | 36 plm-1.6-4/plm/R/plm.data.R | 270 +- plm-1.6-4/plm/R/plm.methods.R | 201 + plm-1.6-4/plm/R/pmg.R | 2 plm-1.6-4/plm/R/pserial.R | 162 - plm-1.6-4/plm/R/ptest.R | 495 ++-- plm-1.6-4/plm/R/vcovG.R | 250 +- plm-1.6-4/plm/R/within_intercept.R |only plm-1.6-4/plm/build/vignette.rds |binary plm-1.6-4/plm/data/Cigar.rda |binary plm-1.6-4/plm/data/Crime.rda |binary plm-1.6-4/plm/data/EmplUK.rda |binary plm-1.6-4/plm/data/Gasoline.rda |binary plm-1.6-4/plm/data/Grunfeld.rda |binary plm-1.6-4/plm/data/Hedonic.rda |binary plm-1.6-4/plm/data/LaborSupply.rda |binary plm-1.6-4/plm/data/Males.rda |binary plm-1.6-4/plm/data/Parity.rda |binary plm-1.6-4/plm/data/Produc.rda |binary plm-1.6-4/plm/data/RiceFarms.rda |binary plm-1.6-4/plm/data/Snmesp.rda |binary plm-1.6-4/plm/data/SumHes.rda |binary plm-1.6-4/plm/data/Wages.rda |binary plm-1.6-4/plm/inst/doc/plm.R | 27 plm-1.6-4/plm/inst/doc/plm.pdf |binary plm-1.6-4/plm/inst/doc/plm.rnw | 117 plm-1.6-4/plm/man/Cigar.Rd | 4 plm-1.6-4/plm/man/Crime.Rd | 10 plm-1.6-4/plm/man/EmplUK.Rd | 72 plm-1.6-4/plm/man/Gasoline.Rd | 2 plm-1.6-4/plm/man/Grunfeld.Rd | 2 plm-1.6-4/plm/man/Hedonic.Rd | 8 plm-1.6-4/plm/man/LaborSupply.Rd | 78 plm-1.6-4/plm/man/Males.Rd | 94 plm-1.6-4/plm/man/Parity.Rd | 2 plm-1.6-4/plm/man/Produc.Rd | 8 plm-1.6-4/plm/man/RiceFarms.Rd | 92 plm-1.6-4/plm/man/Snmesp.Rd | 2 plm-1.6-4/plm/man/SumHes.Rd | 2 plm-1.6-4/plm/man/Wages.Rd | 11 plm-1.6-4/plm/man/aneweytest.Rd | 4 plm-1.6-4/plm/man/cipstest.Rd | 23 plm-1.6-4/plm/man/detect_lin_dep_alias.Rd |only plm-1.6-4/plm/man/ercomp.Rd | 168 - plm-1.6-4/plm/man/fixef.plm.Rd | 77 plm-1.6-4/plm/man/index.Rd |only plm-1.6-4/plm/man/is.pbalanced.Rd |only plm-1.6-4/plm/man/is.pconsecutive.Rd |only plm-1.6-4/plm/man/lag_lead_diff.Rd |only plm-1.6-4/plm/man/make.pbalanced.Rd |only plm-1.6-4/plm/man/make.pconsecutive.Rd |only plm-1.6-4/plm/man/model.frame_model.matrix.Rd |only plm-1.6-4/plm/man/nobs.Rd | 16 plm-1.6-4/plm/man/pFormula.Rd | 121 plm-1.6-4/plm/man/pFtest.Rd | 17 plm-1.6-4/plm/man/pbgtest.Rd | 12 plm-1.6-4/plm/man/pbltest.Rd | 25 plm-1.6-4/plm/man/pbsytest.Rd | 10 plm-1.6-4/plm/man/pcce.Rd | 15 plm-1.6-4/plm/man/pcdtest.Rd | 82 plm-1.6-4/plm/man/pdata.frame.Rd | 93 plm-1.6-4/plm/man/pdim.Rd | 49 plm-1.6-4/plm/man/pdwtest.Rd | 6 plm-1.6-4/plm/man/pggls.Rd | 36 plm-1.6-4/plm/man/pgmm.Rd | 60 plm-1.6-4/plm/man/pht.Rd | 42 plm-1.6-4/plm/man/phtest.Rd | 42 plm-1.6-4/plm/man/piest.Rd | 12 plm-1.6-4/plm/man/plm-package.Rd |only plm-1.6-4/plm/man/plm.Rd | 100 plm-1.6-4/plm/man/plmtest.Rd | 70 plm-1.6-4/plm/man/pmg.Rd | 26 plm-1.6-4/plm/man/pmodel.response.Rd | 153 - plm-1.6-4/plm/man/pooltest.Rd | 8 plm-1.6-4/plm/man/pseries.Rd | 192 - plm-1.6-4/plm/man/punbalancedness.Rd |only plm-1.6-4/plm/man/purtest.Rd | 18 plm-1.6-4/plm/man/pvar.Rd | 43 plm-1.6-4/plm/man/pvcm.Rd | 8 plm-1.6-4/plm/man/pwaldtest.Rd |only plm-1.6-4/plm/man/pwartest.Rd | 12 plm-1.6-4/plm/man/pwfdtest.Rd | 49 plm-1.6-4/plm/man/pwtest.Rd | 26 plm-1.6-4/plm/man/r.squared.Rd | 20 plm-1.6-4/plm/man/sargan.Rd | 4 plm-1.6-4/plm/man/summary.plm.Rd |only plm-1.6-4/plm/man/vcovBK.Rd | 45 plm-1.6-4/plm/man/vcovDC.Rd | 39 plm-1.6-4/plm/man/vcovG.Rd | 28 plm-1.6-4/plm/man/vcovHC.Rd | 50 plm-1.6-4/plm/man/vcovNW.Rd | 45 plm-1.6-4/plm/man/vcovSCC.Rd | 49 plm-1.6-4/plm/man/within_intercept.Rd |only plm-1.6-4/plm/tests/testErrors.Rout.save | 86 plm-1.6-4/plm/tests/testEvaluation.R | 23 plm-1.6-4/plm/tests/testEvaluation.Rout.save | 121 plm-1.6-4/plm/tests/test_Estimators.R | 14 plm-1.6-4/plm/tests/test_R2_adj_R2.R |only plm-1.6-4/plm/tests/test_as.data.frame_as.matrix.R |only plm-1.6-4/plm/tests/test_as.list.pdata.frame.R |only plm-1.6-4/plm/tests/test_detect_lin_dep_alias.R |only plm-1.6-4/plm/tests/test_fitted.plm.R |only plm-1.6-4/plm/tests/test_fixef.R |only plm-1.6-4/plm/tests/test_fixef_comp_lm_plm.R |only plm-1.6-4/plm/tests/test_is.pconsecutive.R |only plm-1.6-4/plm/tests/test_lag_lead.R |only plm-1.6-4/plm/tests/test_lagt_leadt.R |only plm-1.6-4/plm/tests/test_make.pconsecutive_pbalanced.R |only plm-1.6-4/plm/tests/test_model.frame.R |only plm-1.6-4/plm/tests/test_model.matrix_effects.R |only plm-1.6-4/plm/tests/test_model.matrix_pmodel.response.R |only plm-1.6-4/plm/tests/test_model.matrix_pmodel.response_NA.R |only plm-1.6-4/plm/tests/test_pFtest.R |only plm-1.6-4/plm/tests/test_pFtest.Rout.save |only plm-1.6-4/plm/tests/test_pbgtest.R |only plm-1.6-4/plm/tests/test_pcdtest.R |only plm-1.6-4/plm/tests/test_pdata.frame_extract_class_est_mod.R |only plm-1.6-4/plm/tests/test_pdata.frame_id_index_more.R |only plm-1.6-4/plm/tests/test_pdata.frame_print_duplicated_rownames.R |only plm-1.6-4/plm/tests/test_pdata.frame_subsetting.R |only plm-1.6-4/plm/tests/test_pdata.frame_unused_levels.R |only plm-1.6-4/plm/tests/test_pdiff_fd.R |only plm-1.6-4/plm/tests/test_phtest_Hausman_regression.R | 80 plm-1.6-4/plm/tests/test_plm_na.action.R | 106 plm-1.6-4/plm/tests/test_plmtest_unbalanced.R |only plm-1.6-4/plm/tests/test_plmtest_unbalanced.Rout.save |only plm-1.6-4/plm/tests/test_pseries_subsetting.R |only plm-1.6-4/plm/tests/test_punbalancedness.R |only plm-1.6-4/plm/tests/test_pvar.R |only plm-1.6-4/plm/tests/test_pwaldtest.R |only plm-1.6-4/plm/tests/test_pwaldtest_vcovG_attr_cluster.R |only plm-1.6-4/plm/tests/test_pwtest.R |only plm-1.6-4/plm/tests/test_summary.plm_vcov.R |only plm-1.6-4/plm/tests/test_vcovG_lin_dep.R |only plm-1.6-4/plm/tests/test_within_intercept.R |only plm-1.6-4/plm/vignettes/bibliojss.bib | 1172 +++++---- plm-1.6-4/plm/vignettes/plm.rnw | 117 162 files changed, 7412 insertions(+), 5327 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Christen H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.3.3 dated 2016-09-06 and 0.3.4 dated 2016-11-29
ctmm-0.3.3/ctmm/man/akde.bandwidth.Rd |only ctmm-0.3.4/ctmm/DESCRIPTION | 16 - ctmm-0.3.4/ctmm/MD5 | 61 ++-- ctmm-0.3.4/ctmm/NAMESPACE | 12 ctmm-0.3.4/ctmm/NEWS | 32 ++ ctmm-0.3.4/ctmm/R/generic.R | 30 +- ctmm-0.3.4/ctmm/R/kde.R | 459 +++++++++++++++++++++----------- ctmm-0.3.4/ctmm/R/krige.R | 16 + ctmm-0.3.4/ctmm/R/likelihood.R | 34 +- ctmm-0.3.4/ctmm/R/optim.R |only ctmm-0.3.4/ctmm/R/overlap.R | 234 +++++++++++----- ctmm-0.3.4/ctmm/R/periodogram.R | 18 - ctmm-0.3.4/ctmm/R/select.R | 9 ctmm-0.3.4/ctmm/R/telemetry.R | 168 +++++++---- ctmm-0.3.4/ctmm/R/variogram.R | 260 ++++++++++-------- ctmm-0.3.4/ctmm/TODO | 51 ++- ctmm-0.3.4/ctmm/build/vignette.rds |binary ctmm-0.3.4/ctmm/inst/doc/akde.R | 27 - ctmm-0.3.4/ctmm/inst/doc/akde.Rmd | 40 +- ctmm-0.3.4/ctmm/inst/doc/akde.html | 56 +-- ctmm-0.3.4/ctmm/inst/doc/variogram.Rmd | 40 ++ ctmm-0.3.4/ctmm/inst/doc/variogram.html | 61 ++-- ctmm-0.3.4/ctmm/man/akde.Rd | 29 +- ctmm-0.3.4/ctmm/man/as.telemetry.Rd | 17 - ctmm-0.3.4/ctmm/man/bandwidth.Rd |only ctmm-0.3.4/ctmm/man/ctmm-package.Rd | 2 ctmm-0.3.4/ctmm/man/ctmm.fit.Rd | 5 ctmm-0.3.4/ctmm/man/export.Rd | 7 ctmm-0.3.4/ctmm/man/overlap.Rd | 39 +- ctmm-0.3.4/ctmm/man/simulate.ctmm.Rd | 15 - ctmm-0.3.4/ctmm/man/summary.ctmm.Rd | 5 ctmm-0.3.4/ctmm/vignettes/akde.Rmd | 40 +- ctmm-0.3.4/ctmm/vignettes/variogram.Rmd | 40 ++ 33 files changed, 1168 insertions(+), 655 deletions(-)
Title: Download Qualtrics Survey Data Directly into R
Description: Qualtrics <https://www.qualtrics.com/about/>
allows users to collect online data through surveys.
This package contains convenience functions to pull
survey results straight into R using the Qualtrics
API. See <https://api.qualtrics.com/> for more
information about the Qualtrics API.
Author: Jasper Ginn
Maintainer: Jasper Ginn <j.h.ginn@fgga.leidenuniv.nl>
Diff between qualtRics versions 0.1 dated 2016-10-18 and 0.3 dated 2016-11-29
DESCRIPTION | 8 +-- MD5 | 28 +++++++------ NAMESPACE | 5 +- R/constructHeader.R | 13 +++--- R/getSurvey.R | 98 ++++++++++++++++++++++++++++++++++-------------- R/getSurveys.R | 30 ++++++++++---- R/registerApiKey.R |only README.md | 45 +++++++++++++++++++--- build/vignette.rds |binary inst/doc/qualtRics.Rmd | 36 ++++++++++++++--- inst/doc/qualtRics.html | 32 +++++++++++---- man/constructHeader.Rd | 12 ++--- man/getSurvey.Rd | 21 +++++----- man/getSurveys.Rd | 17 +++----- man/registerApiKey.Rd |only vignettes/qualtRics.Rmd | 36 ++++++++++++++--- 16 files changed, 266 insertions(+), 115 deletions(-)
Title: Multivariate Synthetic Control Method Using Time Series
Description: Multivariate Synthetic Control Method Using Time Series.
Two generalizations of the synthetic control method (which has already an
implementation in package 'Synth') are implemented: first, 'MSCMT' allows
for using multiple outcome variables, second, time series can be supplied as
economic predictors.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
Author: Martin Becker [aut, cre],
Stefan Kloessner [aut],
Karline Soetaert [com],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.0.0 dated 2016-07-25 and 1.1.0 dated 2016-11-29
DESCRIPTION | 15 - MD5 | 60 ++--- NAMESPACE | 8 NEWS | 43 +++ R/DiD.r | 2 R/Helpers.r | 49 ++++ R/ModularOptimization.r | 489 ++++++++++++++++++++++++++++++----------- R/compare.r |only R/determine_v.r | 31 +- R/ggplot.r | 301 +++++++++++++++++-------- R/improveSynth.r | 6 R/mscmt.r | 55 ++-- R/prepare.r | 14 - R/print.r | 57 ++++ R/zzz.r |only inst/doc/CheckingSynth.Rmd | 10 inst/doc/CheckingSynth.html | 33 +- inst/doc/UsingTimeSeries.R | 6 inst/doc/UsingTimeSeries.Rmd | 6 inst/doc/UsingTimeSeries.html | 92 +++---- inst/doc/WorkingWithMSCMT.R | 6 inst/doc/WorkingWithMSCMT.Rmd | 14 - inst/doc/WorkingWithMSCMT.html | 141 +++-------- man/MSCMTfunction.Rd | 28 -- man/compare.Rd |only man/did.Rd | 2 man/ggplot.mscmt.Rd | 21 + src/DE.c |only src/MSCMT.c | 13 - src/MSCMT.h | 15 + vignettes/CheckingSynth.Rmd | 10 vignettes/UsingTimeSeries.Rmd | 6 vignettes/WorkingWithMSCMT.Rmd | 14 - 33 files changed, 998 insertions(+), 549 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 0.1-1 dated 2016-11-17 and 0.1-2 dated 2016-11-29
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- inst/NEWS.Rd | 7 ++++++- inst/doc/mlt.pdf |binary tests/timedep_covar.R |only tests/timedep_covar.Rout.save |only 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 0.1-0 dated 2016-11-10 and 0.1-1 dated 2016-11-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/R.R | 8 ++++---- inst/NEWS.Rd | 9 ++++++++- 4 files changed, 19 insertions(+), 12 deletions(-)
Title: Extract-Transform-Load Framework for Medium Data
Description: A framework for loading medium-sized data from
the Internet to a local or remote relational database management system.
This package itself doesn't do much more than provide a toy example and set up
the method structure. Packages that depend on this package will facilitate the
construction and maintenance of their respective databases.
Author: Ben Baumer [aut, cre],
Carson Sievert [ctb]
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Diff between etl versions 0.3.4 dated 2016-11-15 and 0.3.5 dated 2016-11-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 +++++++- R/etl_create.R | 5 +++-- R/utils.R | 19 ++++++++++++++----- man/etl_create.Rd | 5 +++-- 6 files changed, 36 insertions(+), 19 deletions(-)
Title: B Cell Receptor Somatic Hyper Mutation Analysis
Description: Includes a set of functions to analyze for instance nucleotide frequencies as well as transition and transversion. Can reconstruct germline sequences based on the international ImMunoGeneTics information system (IMGT/HighV-QUEST) outputs, calculate and plot the difference (%) of nucleotides at 6 positions around a mutation to identify and characterize hotspot motifs as well as calculate and plot average mutation frequencies of nucleotide mutations resulting in amino acid substitution.
Author: Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
Maintainer: Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
Diff between BCellMA versions 0.1 dated 2016-11-03 and 0.3.2 dated 2016-11-29
BCellMA-0.1/BCellMA/R/aa_plotgg_skal.R |only BCellMA-0.1/BCellMA/R/addLetter.R |only BCellMA-0.1/BCellMA/R/letterA.R |only BCellMA-0.1/BCellMA/R/letterC.R |only BCellMA-0.1/BCellMA/R/letterG.R |only BCellMA-0.1/BCellMA/R/letterT.R |only BCellMA-0.1/BCellMA/R/sysdata.rda |only BCellMA-0.3.2/BCellMA/DESCRIPTION | 18 +- BCellMA-0.3.2/BCellMA/MD5 | 64 ++++----- BCellMA-0.3.2/BCellMA/NAMESPACE | 2 BCellMA-0.3.2/BCellMA/R/aa_cdr3_dist.R | 12 - BCellMA-0.3.2/BCellMA/R/aa_dist.R | 21 +-- BCellMA-0.3.2/BCellMA/R/aa_plot.R | 18 +- BCellMA-0.3.2/BCellMA/R/aa_zaehlen2.R | 16 +- BCellMA-0.3.2/BCellMA/R/data.R | 12 - BCellMA-0.3.2/BCellMA/R/germlineReconstr.R | 3 BCellMA-0.3.2/BCellMA/R/intern.R |only BCellMA-0.3.2/BCellMA/R/na_funktion.R | 12 + BCellMA-0.3.2/BCellMA/R/nucleotide_matation.R | 3 BCellMA-0.3.2/BCellMA/R/targetingMatrix.R | 7 - BCellMA-0.3.2/BCellMA/R/targeting_motiv.R | 144 +++++++++++---------- BCellMA-0.3.2/BCellMA/R/targeting_motive_plot.R | 8 - BCellMA-0.3.2/BCellMA/build |only BCellMA-0.3.2/BCellMA/inst |only BCellMA-0.3.2/BCellMA/man/IMGTtab2.Rd | 3 BCellMA-0.3.2/BCellMA/man/IMGTtab7.Rd | 3 BCellMA-0.3.2/BCellMA/man/IMGTtab8.Rd | 3 BCellMA-0.3.2/BCellMA/man/Klassen.Rd | 3 BCellMA-0.3.2/BCellMA/man/aa_cdr3_dist.Rd | 12 - BCellMA-0.3.2/BCellMA/man/aa_dist.Rd | 14 +- BCellMA-0.3.2/BCellMA/man/aa_plot.Rd | 16 +- BCellMA-0.3.2/BCellMA/man/germlineReconstr.Rd | 3 BCellMA-0.3.2/BCellMA/man/na_funktion.Rd |only BCellMA-0.3.2/BCellMA/man/nucleotide_mutation.Rd | 2 BCellMA-0.3.2/BCellMA/man/targetingMatrix.Rd | 9 - BCellMA-0.3.2/BCellMA/man/targeting_motiv.Rd | 9 - BCellMA-0.3.2/BCellMA/man/targeting_motive_plot.Rd | 9 - BCellMA-0.3.2/BCellMA/vignettes |only 38 files changed, 228 insertions(+), 198 deletions(-)
Title: Optimization Toolbox for Solving Linear Systems
Description: Solves linear systems of form Ax=b via Gauss elimination,
LU decomposition, Gauss-Seidel, Conjugate Gradient Method (CGM) and Cholesky methods.
Author: Prakash (PKS Prakash) <prakash2@uwalumni.com>
Maintainer: Prakash <prakash2@uwalumni.com>
Diff between optR versions 1.1.1 dated 2014-06-23 and 1.2.5 dated 2016-11-29
DESCRIPTION | 19 - MD5 | 77 +++--- NAMESPACE | 31 +- R/LU.R | 174 +++++++------- R/cgm.R | 96 +++---- R/choleskiDecomposition.R | 167 ++++++------- R/forwardsubsitution_Cholesky.R | 29 +- R/gauss.R | 242 ++++++++++---------- R/gaussSeidel.R | 24 + R/newtonRapshon.R |only R/optR.R | 481 +++++++++++++++++++++------------------- R/optRFun.R |only R/optR_fit.R | 134 +++++------ R/predict_optR.R | 2 R/solveMethods.R | 70 ++--- R/updateWeightsobs.R |only man/LU.decompose.Rd | 47 +-- man/LU.optR.Rd | 61 ++--- man/LUsplit.Rd | 49 ++-- man/cgm.Rd | 73 +++--- man/choleskiDecomposition.Rd | 46 +-- man/choleskilm.Rd | 61 ++--- man/forwardsubsitution.optR.Rd | 39 +-- man/gaussSeidel.Rd | 74 +++--- man/hatMatrix.Rd | 57 ++-- man/inv.optR.Rd | 49 ++-- man/jacobian.Rd |only man/machinePrecision.Rd | 35 +- man/newtonRapson.Rd |only man/nonDiagMultipication.Rd | 43 +-- man/opt.matrix.reorder.Rd | 53 ++-- man/optR.Rd | 93 +++---- man/optR.backsubsitution.Rd | 39 +-- man/optR.default.Rd | 112 ++++----- man/optR.fit.Rd | 93 +++---- man/optR.formula.Rd | 114 +++++---- man/optR.gauss.Rd | 65 ++--- man/optR.multiplyfactor.Rd | 43 +-- man/optRFun.Rd |only man/optRFun.newtonRapson.Rd |only man/predict.optR.Rd | 51 ++-- man/print.optR.Rd | 47 +-- man/summary.optR.Rd | 47 +-- 43 files changed, 1518 insertions(+), 1419 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.0 dated 2016-10-04 and 2.1 dated 2016-11-29
DESCRIPTION | 8 MD5 | 50 - NAMESPACE | 3 R/gjamGibbs.r | 2 R/gjamHfunctions.R | 1510 +++++++++++++++++++++++++-------------- R/gjamSpec2Trait.r | 7 R/gjamTrimY.r | 26 inst/CITATION | 4 inst/doc/gjamDimRedVignette.R | 5 inst/doc/gjamDimRedVignette.Rmd | 15 inst/doc/gjamDimRedVignette.html | 19 inst/doc/gjamTraitsVignette.R | 71 - inst/doc/gjamTraitsVignette.Rmd | 42 - inst/doc/gjamTraitsVignette.html | 121 --- inst/doc/gjamVignette.R | 76 + inst/doc/gjamVignette.Rmd | 126 ++- inst/doc/gjamVignette.html | 169 ++-- man/gjam-package.Rd | 2 man/gjamGibbs.Rd | 28 man/gjamIIE.Rd | 2 man/gjamPredict.Rd | 8 man/gjamSpec2Trait.Rd | 6 man/gjamTrimY.Rd | 6 vignettes/gjamDimRedVignette.Rmd | 15 vignettes/gjamTraitsVignette.Rmd | 42 - vignettes/gjamVignette.Rmd | 126 ++- 26 files changed, 1525 insertions(+), 964 deletions(-)
Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.4.8 dated 2016-11-04 and 1.4.9 dated 2016-11-29
DESCRIPTION | 12 +++----- MD5 | 59 ++++++++++++++++++++++++++++------------- NAMESPACE | 2 - NEWS | 3 ++ R/bm_as_bm.r | 4 +- R/bm_bind.r | 12 ++++---- R/bm_grm.r | 9 +++++- R/bm_hwe.r |only R/bm_ld_thinner.r | 8 ++++- R/bm_stats.r | 58 ++++++++++++++++++++-------------------- R/gwas.r | 67 ++++++++++++++++++++++++++++++++--------------- R/lmm_simu.r | 2 - inst/doc/gaston.R | 20 +++++++------- inst/doc/gaston.Rnw | 7 ++-- inst/doc/gaston.pdf |binary man/GRM.Rd | 5 ++- man/LD.thin.Rd | 9 +++--- man/association.test.Rd | 48 +++++++++++++++++++++------------ man/set.hwe.Rd | 3 ++ src/gwas_lm_quanti.cpp |only src/m4_stats.cpp | 30 +++++++++++---------- vignettes/gaston-015.pdf |only vignettes/gaston-016.pdf |only vignettes/gaston-026.pdf |only vignettes/gaston-028.pdf |only vignettes/gaston-029.pdf |only vignettes/gaston-030.pdf |only vignettes/gaston-033.pdf |only vignettes/gaston-037.pdf |only vignettes/gaston-039.pdf |only vignettes/gaston-040.pdf |only vignettes/gaston-041.pdf |only vignettes/gaston-042.pdf |only vignettes/gaston-044.pdf |only vignettes/gaston-048.pdf |only vignettes/gaston-052.pdf |only vignettes/gaston-053.pdf |only vignettes/gaston-054.pdf |only vignettes/gaston-055.pdf |only vignettes/gaston-056.pdf |only vignettes/gaston.Rnw | 7 ++-- 41 files changed, 224 insertions(+), 141 deletions(-)
Title: Coclustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The blockcluster package provides a bridge between the C++
core library and the R statistical computing environment. This package
allows to co-cluster binary, contingency, continuous and categorical
data-sets. It also provides utility functions to visualize the results.
This package may be useful for various applications in fields of Data
mining, Information retrieval, Biology, computer vision and many more. More
information about the project and comprehensive tutorial can be found on
the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Josselin Demont [ctb],
Gerard Goavert [ctb],
Vincent Brault [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 4.0.2 dated 2015-11-27 and 4.2.0 dated 2016-11-29
blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/FuzzyCEMInit.h |only blockcluster-4.2.0/blockcluster/DESCRIPTION | 14 blockcluster-4.2.0/blockcluster/MD5 | 139 + blockcluster-4.2.0/blockcluster/R/RCocluster.R | 75 + blockcluster-4.2.0/blockcluster/R/cocluster.R | 224 --- blockcluster-4.2.0/blockcluster/R/coclusterBinary.R | 36 blockcluster-4.2.0/blockcluster/R/coclusterCategorical.R | 28 blockcluster-4.2.0/blockcluster/R/coclusterContingency.R | 11 blockcluster-4.2.0/blockcluster/R/coclusterContinuous.R | 15 blockcluster-4.2.0/blockcluster/R/coclusterStrategy.R | 23 blockcluster-4.2.0/blockcluster/R/optionclasses.R | 55 blockcluster-4.2.0/blockcluster/build/vignette.rds |binary blockcluster-4.2.0/blockcluster/data/binarydata.rda |binary blockcluster-4.2.0/blockcluster/data/categoricaldata.rda |binary blockcluster-4.2.0/blockcluster/data/contingencydatalist.rda |binary blockcluster-4.2.0/blockcluster/data/contingencydataunknown.rda |binary blockcluster-4.2.0/blockcluster/data/gaussiandata.rda |binary blockcluster-4.2.0/blockcluster/inst/doc/blockcluster_tutorial.R | 7 blockcluster-4.2.0/blockcluster/inst/doc/blockcluster_tutorial.Rnw | 88 - blockcluster-4.2.0/blockcluster/inst/doc/blockcluster_tutorial.pdf |binary blockcluster-4.2.0/blockcluster/man/binarydata.Rd | 8 blockcluster-4.2.0/blockcluster/man/categoricaldata.Rd | 8 blockcluster-4.2.0/blockcluster/man/cocluster.Rd | 2 blockcluster-4.2.0/blockcluster/man/coclusterBinary.Rd | 2 blockcluster-4.2.0/blockcluster/man/coclusterCategorical.Rd | 2 blockcluster-4.2.0/blockcluster/man/coclusterContingency.Rd | 2 blockcluster-4.2.0/blockcluster/man/coclusterContinuous.Rd | 2 blockcluster-4.2.0/blockcluster/man/coclusterStrategy.Rd | 12 blockcluster-4.2.0/blockcluster/man/contingencydatalist.Rd | 18 blockcluster-4.2.0/blockcluster/man/contingencydataunknown.Rd | 8 blockcluster-4.2.0/blockcluster/man/gaussiandata.Rd | 8 blockcluster-4.2.0/blockcluster/src/BinaryDataExchange.cpp | 4 blockcluster-4.2.0/blockcluster/src/CategoricalDataExchange.cpp | 4 blockcluster-4.2.0/blockcluster/src/ContingencyDataExchange.cpp | 1 blockcluster-4.2.0/blockcluster/src/ContinuousDataExchange.cpp | 1 blockcluster-4.2.0/blockcluster/src/IDataExchange.cpp | 19 blockcluster-4.2.0/blockcluster/src/IDataExchange.h | 2 blockcluster-4.2.0/blockcluster/src/Makevars.win |only blockcluster-4.2.0/blockcluster/src/Rcoclustmain.cpp | 35 blockcluster-4.2.0/blockcluster/src/coclust/get_symbolic_link.sh | 32 blockcluster-4.2.0/blockcluster/src/coclust/get_symbolic_link_without_trunk.sh |only blockcluster-4.2.0/blockcluster/src/coclust/src/Algorithms/GibbsAlgo.cpp |only blockcluster-4.2.0/blockcluster/src/coclust/src/Algorithms/GibbsAlgo.h |only blockcluster-4.2.0/blockcluster/src/coclust/src/Algorithms/IAlgo.h | 4 blockcluster-4.2.0/blockcluster/src/coclust/src/CoClustFacade/CoCluster.cpp | 34 blockcluster-4.2.0/blockcluster/src/coclust/src/CoClustFacade/CoCluster.h | 52 blockcluster-4.2.0/blockcluster/src/coclust/src/Initialization/EMInit.h |only blockcluster-4.2.0/blockcluster/src/coclust/src/Initialization/IInit.h | 4 blockcluster-4.2.0/blockcluster/src/coclust/src/InputParameters/InputParameters.cpp | 37 blockcluster-4.2.0/blockcluster/src/coclust/src/InputParameters/InputParameters.h | 23 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/BinaryLBModel.cpp | 264 +++ blockcluster-4.2.0/blockcluster/src/coclust/src/Models/BinaryLBModel.h | 15 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.cpp | 214 ++- blockcluster-4.2.0/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.h | 9 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/CategoricalLBModel.cpp | 660 +++++++++ blockcluster-4.2.0/blockcluster/src/coclust/src/Models/CategoricalLBModel.h | 24 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContingencyLBModel.cpp | 696 +++++++--- blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContingencyLBModel.h | 9 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.cpp | 494 +++++++ blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.h | 15 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContinuousLBModel.cpp | 122 + blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContinuousLBModel.h | 12 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.cpp | 120 + blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.h | 7 blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ICoClustModel.cpp | 70 - blockcluster-4.2.0/blockcluster/src/coclust/src/Models/ICoClustModel.h | 34 blockcluster-4.2.0/blockcluster/src/coclust/src/Strategy/IStrategy.h | 12 blockcluster-4.2.0/blockcluster/src/coclust/src/Strategy/XStrategyAlgo.cpp | 8 blockcluster-4.2.0/blockcluster/src/coclust/src/enumerations/enumerations.h | 5 blockcluster-4.2.0/blockcluster/src/test/test.cpp | 2 blockcluster-4.2.0/blockcluster/tests |only blockcluster-4.2.0/blockcluster/vignettes/blockcluster_tutorial.Rnw | 88 - 72 files changed, 3071 insertions(+), 848 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-26 0.9.2
2015-03-11 0.8.6
2015-02-20 0.8.5
2014-11-18 0.8.4
2014-10-23 0.8.3
2014-10-21 0.8.2
Title: Econometric Models for Spatial Panel Data
Description: ML and GM estimation and diagnostic testing of econometric models for spatial panel data.
Author: Giovanni Millo [aut, cre],
Gianfranco Piras [aut]
Maintainer: Giovanni Millo <giovanni.millo@generali.com>
Diff between splm versions 1.3-7 dated 2014-12-20 and 1.4-6 dated 2016-11-29
ChangeLog | 50 + DESCRIPTION | 21 MD5 | 47 + NAMESPACE | 18 R/bsjktest.formula.R | 4 R/bsktest.R | 1241 ++++++++++++++++++++----------------------------- R/fixed_effects.R | 50 + R/likelihoodsFE.R | 176 +++--- R/pbsjkREtest.R |only R/print.summary.splm.R | 109 ++-- R/rwtest.R |only R/slmtest.R |only R/spfeml.R | 46 + R/sphtest.R | 186 ++++--- R/spml.R | 46 + R/spreml.R | 75 ++ data/Insurance.rda |binary data/RiceFarms.rda |binary data/itaww.rda |binary data/riceww.rda |binary data/usaww.rda |binary man/bsjktest.Rd | 2 man/bsktest.Rd | 7 man/rwtest.Rd |only man/slmtest.Rd |only man/spgm.Rd | 2 man/spml.Rd | 1 27 files changed, 1029 insertions(+), 1052 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling.
Markov models (decision trees, homogeneous and non-homogeneous)
for health economic evaluation. Model comparison,
sensitivity and probabilistic analysis.
Author: Antoine Filipovic-Pierucci [aut, cre],
Kevin Zarca [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.7.0 dated 2016-11-21 and 0.7.1 dated 2016-11-29
DESCRIPTION | 6 - MD5 | 31 ++++--- NEWS.md | 6 + R/covariance.R | 8 +- R/strategy_print.R | 3 inst/doc/a-introduction.html | 4 - inst/doc/b-time-dependency.html | 4 - inst/doc/c-homogeneous.html | 4 - inst/doc/d-non-homogeneous.html | 4 - inst/doc/e-probabilistic.html | 24 +++--- inst/doc/f-sensitivity.html | 4 - inst/doc/g-heterogeneity.html | 160 ++++++++++++++++++++-------------------- inst/doc/h-tabular.html | 6 - inst/doc/i-reproduction.html | 4 - inst/examples/example_update.R | 6 - inst/tmp/j-multiple.Rmd |only man/update-model.Rd | 6 - 17 files changed, 144 insertions(+), 136 deletions(-)
Title: Continuous Optimization using Memetic Algorithms with Local
Search Chains (MA-LS-Chains) in R
Description: An implementation of an algorithm family for continuous
optimization called memetic algorithms with local search chains
(MA-LS-Chains). Memetic algorithms are hybridizations of genetic
algorithms with local search methods. They are especially suited
for continuous optimization.
Author: Christoph Bergmeir, Daniel Molina, José M. Benítez
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between Rmalschains versions 0.2-2 dated 2014-06-06 and 0.2-3 dated 2016-11-29
ChangeLog | 12 ++ DESCRIPTION | 11 +- MD5 | 24 ++-- NAMESPACE | 7 - R/Rmalschains-package.R | 4 R/malschains.R | 1 inst/CITATION | 34 ++++-- man/Rmalschains-package.Rd | 240 +++++++++++++++++++-------------------------- man/malschains.Rd | 88 ++++++---------- man/malschains.control.Rd | 116 +++++++-------------- man/print.malschains.Rd | 21 +-- src/Makevars.win | 22 ++-- src/newmat6.cpp | 2 13 files changed, 265 insertions(+), 317 deletions(-)
Title: R Actuarial Workshops
Description: In order to facilitate R instruction for actuaries, we have organized several
sets of publicly available data of interest to non-life actuaries. In addition, we suggest
a set of packages, which most practicing actuaries will use routinely. Finally, there is
an R markdown skeleton for basic reserve analysis.
Author: Brian A. Fannin [aut, cre]
Maintainer: Brian A. Fannin <FanninQED@yahoo.com>
Diff between raw versions 0.1.3 dated 2016-11-10 and 0.1.4 dated 2016-11-29
DESCRIPTION | 9 ++-- MD5 | 12 +++--- NAMESPACE | 2 + NEWS |only R/InstallSuggestions.R | 82 +++++++++++++++++++++++++++++++++++---------- inst/doc/raw.html | 4 +- man/InstallSuggestions.Rd | 8 +++- man/PackageDependencies.Rd |only 8 files changed, 87 insertions(+), 30 deletions(-)
Title: Generalized Multistate Simulation Model
Description: Simulate and analyze multistate models with general hazard
functions. gems provides functionality for the preparation of hazard functions
and parameters, simulation from a general multistate model and predicting future
events. The multistate model is not required to be a Markov model and may take
the history of previous events into account. In the basic version, it allows
to simulate from transition-specific hazard function, whose parameters are
multivariable normally distributed.
Author: Luisa Salazar Vizcaya, Nello Blaser, Thomas Gsponer
Maintainer: Luisa Salazar Vizcaya <luisa.salazar@ispm.unibe.ch>
Diff between gems versions 1.0.0 dated 2015-03-11 and 1.1.0 dated 2016-11-29
ChangeLog | 3 DESCRIPTION | 17 +++-- MD5 | 34 +++++----- NAMESPACE | 4 - R/gems.r | 101 ++++++++++++++++++------------- build/vignette.rds |binary inst/doc/gems.pdf |binary man/ArtCohort.Rd | 16 ++-- man/PosteriorProbabilities.Rd | 10 +-- man/cumulativeIncidence.Rd | 8 +- man/gems.Rd | 22 +++--- man/generateHazardMatrix.Rd | 8 +- man/generateParameterCovarianceMatrix.Rd | 8 +- man/generateParameterMatrix.Rd | 8 +- man/simulateCohort.Rd | 24 +++---- man/tavi.Rd | 20 +++--- man/transition.structure.Rd | 14 ++-- man/transitionProbabilities.Rd | 8 +- 18 files changed, 174 insertions(+), 131 deletions(-)