Title: Regularized Structural Equation Modeling
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional structural
equation models.
Author: Ross Jacobucci[aut,cre],
Kevin J. Grimm [ctb],
Andreas M. Brandmaier [ctb],
Sarfaraz Serang [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 0.9.2 dated 2017-09-08 and 1.0.6 dated 2017-12-05
DESCRIPTION | 8 +- MD5 | 34 ++++---- R/coord_desc.R | 120 +++++++++++++++++++++++-------- R/cv_regsem.R | 169 ++++++++++++++++++++++++++++++++++++-------- R/fit_indices.R | 58 ++++++++------- R/multi_optim.R | 49 +++++++----- R/plot.R | 39 +++++++--- R/regsem.R | 56 ++++++++++---- R/soft.R | 7 + R/summary.cvregsem.R | 10 +- R/xmed_cat.R | 6 + man/cv_regsem.Rd | 51 ++++++++----- man/fit_indices.Rd | 12 +-- man/multi_optim.Rd | 40 +++++----- man/plot.cvregsem.Rd | 4 - man/regsem.Rd | 37 +++++---- man/xmed_cat.Rd | 8 +- src/regsem_rcpp_fit_fun.cpp | 8 +- 18 files changed, 489 insertions(+), 227 deletions(-)
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 0.9.7 dated 2016-02-26 and 0.9.9 dated 2017-12-05
DESCRIPTION | 13 ++--- MD5 | 99 ++++++++++++++++++++-------------------- NAMESPACE | 3 - NEWS | 14 +++++ R/TriMatch-package.R | 1 R/as.data.frame.list.R | 7 ++ R/merge.triangle.matches.R | 2 R/merge.triangle.psa.R | 2 R/plot.balance.R | 8 +-- R/plot.multibalance.R | 21 ++++++-- R/plot.triangle.matches.R | 2 R/plot.utils.R | 4 - R/summary.triangle.psa.R | 10 +--- R/triangle.match.R | 6 +- R/triangle.psa.R | 53 +++++++++++++++------ demo/tutoring.R | 5 -- man/OneToN.Rd | 1 man/TriMatch-package.Rd | 9 +-- man/as.data.frame.list.Rd | 7 +- man/balance.plot.Rd | 3 - man/boxdiff.plot.Rd | 1 man/covariateBalance.Rd | 1 man/data.frame.to.list.Rd |only man/distance.euclid.Rd | 3 - man/distances.plot.Rd | 1 man/loess3.plot.Rd | 1 man/maximumTreat.Rd | 1 man/merge.triangle.matches.Rd | 3 - man/merge.triangle.psa.Rd | 3 - man/multibalance.plot.Rd | 11 ++-- man/nmes.Rd | 9 +-- man/parallel.plot.Rd | 1 man/perpPt.Rd | 1 man/plot.balance.plots.Rd | 5 -- man/plot.triangle.matches.Rd | 3 - man/plot.triangle.psa.Rd | 1 man/print.balance.plots.Rd | 1 man/print.triangle.plot.Rd | 1 man/print.trimatch.summary.Rd | 1 man/segment1.Rd | 5 -- man/segment2.Rd | 5 -- man/star.Rd | 1 man/summary.balance.plots.Rd | 3 - man/summary.triangle.matches.Rd | 1 man/summary.triangle.psa.Rd | 1 man/summary.unmatched.Rd | 1 man/trimatch.Rd | 5 -- man/trimatch.apply2.Rd | 1 man/trips.Rd | 6 +- man/tutoring.Rd | 1 man/unmatched.Rd | 1 51 files changed, 185 insertions(+), 164 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-6 dated 2017-08-09 and 0.9-7 dated 2017-12-05
netmeta-0.9-6/netmeta/R/format.TE.R |only netmeta-0.9-6/netmeta/R/p.ci.R |only netmeta-0.9-7/netmeta/DESCRIPTION | 13 netmeta-0.9-7/netmeta/MD5 | 87 +++-- netmeta-0.9-7/netmeta/NAMESPACE | 21 - netmeta-0.9-7/netmeta/NEWS | 145 ++++++++ netmeta-0.9-7/netmeta/R/chkmultiarm.R | 24 - netmeta-0.9-7/netmeta/R/createC.R |only netmeta-0.9-7/netmeta/R/forest.netmeta.R | 24 - netmeta-0.9-7/netmeta/R/forest.netsplit.R |only netmeta-0.9-7/netmeta/R/netcomb.R |only netmeta-0.9-7/netmeta/R/netcomb.netmeta.R |only netmeta-0.9-7/netmeta/R/netgraph.R | 4 netmeta-0.9-7/netmeta/R/netheat.R | 25 + netmeta-0.9-7/netmeta/R/netleague.R | 140 ++++---- netmeta-0.9-7/netmeta/R/netmeasures.R | 12 netmeta-0.9-7/netmeta/R/netmeta-internal.R | 2 netmeta-0.9-7/netmeta/R/netmeta.R | 49 ++- netmeta-0.9-7/netmeta/R/netposet.R | 3 netmeta-0.9-7/netmeta/R/netsplit.R | 375 +++++++++++++++++++---- netmeta-0.9-7/netmeta/R/nma.additive.R |only netmeta-0.9-7/netmeta/R/prcombs.R |only netmeta-0.9-7/netmeta/R/prcomps.R |only netmeta-0.9-7/netmeta/R/print.decomp.design.R | 55 ++- netmeta-0.9-7/netmeta/R/print.netcomb.R |only netmeta-0.9-7/netmeta/R/print.netleague.R |only netmeta-0.9-7/netmeta/R/print.netmeta.R | 137 ++++++-- netmeta-0.9-7/netmeta/R/print.netsplit.R | 116 ++++--- netmeta-0.9-7/netmeta/R/print.summary.netcomb.R |only netmeta-0.9-7/netmeta/R/print.summary.netmeta.R | 267 ++++++++++++---- netmeta-0.9-7/netmeta/R/summary.netcomb.R |only netmeta-0.9-7/netmeta/R/summary.netmeta.R | 8 netmeta-0.9-7/netmeta/R/treats.R |only netmeta-0.9-7/netmeta/R/upgradenetmeta.R | 29 + netmeta-0.9-7/netmeta/R/uppertri.R |only netmeta-0.9-7/netmeta/data/Linde2016.csv.gz |only netmeta-0.9-7/netmeta/data/Senn2013.txt.gz |binary netmeta-0.9-7/netmeta/man/Linde2016.Rd |only netmeta-0.9-7/netmeta/man/Senn2013.Rd | 13 netmeta-0.9-7/netmeta/man/forest.netmeta.Rd | 9 netmeta-0.9-7/netmeta/man/forest.netsplit.Rd |only netmeta-0.9-7/netmeta/man/hasse.Rd | 13 netmeta-0.9-7/netmeta/man/netcomb.Rd |only netmeta-0.9-7/netmeta/man/netgraph.Rd | 2 netmeta-0.9-7/netmeta/man/netheat.Rd | 5 netmeta-0.9-7/netmeta/man/netleague.Rd | 47 ++ netmeta-0.9-7/netmeta/man/netmeasures.Rd | 2 netmeta-0.9-7/netmeta/man/netmeta.Rd | 47 ++ netmeta-0.9-7/netmeta/man/netposet.Rd | 15 netmeta-0.9-7/netmeta/man/netsplit.Rd | 102 ++++-- netmeta-0.9-7/netmeta/man/print.decomp.design.Rd | 19 - netmeta-0.9-7/netmeta/man/print.netcomb.Rd |only netmeta-0.9-7/netmeta/man/print.netmeta.Rd | 48 ++ netmeta-0.9-7/netmeta/man/smokingcessation.Rd | 12 netmeta-0.9-7/netmeta/man/treats.Rd |only 55 files changed, 1409 insertions(+), 461 deletions(-)
Title: Advanced Statistical Methods to Model and Adjust for Bias in
Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 "Small-Study Effects in Meta-Analysis":
- Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>;
- limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>;
- upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>.
Author: Guido Schwarzer [aut, cre],
James R. Carpenter [aut],
Gerta Rücker [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between metasens versions 0.3-1 dated 2016-10-15 and 0.3-2 dated 2017-12-05
DESCRIPTION | 14 - MD5 | 54 +++--- NAMESPACE | 2 NEWS | 29 +++ R/copas.R | 314 ++++++++++++++++++++-------------------- R/copas.gradient.without.beta.R | 85 +++++----- R/copas.loglik.with.beta.R | 31 +-- R/copas.loglik.without.beta.R | 30 +-- R/forest.orbbound.R | 74 ++++----- R/funnel.limitmeta.R | 98 ++++++------ R/lambda.R | 2 R/limitmeta.R | 127 ++++++++-------- R/metasens-interal.R | 6 R/orbbound.R | 41 ++--- R/plot.copas.R | 173 +++++++++++----------- R/print.copas.R | 67 ++++---- R/print.limitmeta.R | 93 +++++------ R/print.orbbound.R | 136 ++++++++++------- R/print.summary.copas.R | 78 ++++++--- R/print.summary.limitmeta.R | 278 +++++++++++++++++++++++++---------- R/radialregression.R | 24 +-- R/summary.copas.R | 46 ++--- R/summary.limitmeta.R | 4 man/forest.orbbound.Rd | 2 man/orbbound.Rd | 2 man/print.copas.Rd | 27 ++- man/print.limitmeta.Rd | 59 ++++++- man/print.orbbound.Rd | 20 ++ 28 files changed, 1102 insertions(+), 814 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed);
- generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed);
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.8-4 dated 2017-08-11 and 4.9-0 dated 2017-12-05
meta-4.8-4/meta/R/format.tau.R |only meta-4.8-4/meta/src |only meta-4.9-0/meta/DESCRIPTION | 13 - meta-4.9-0/meta/MD5 | 118 +++++---- meta-4.9-0/meta/NAMESPACE | 16 - meta-4.9-0/meta/NEWS | 89 +++++++ meta-4.9-0/meta/R/backtransf.R | 2 meta-4.9-0/meta/R/bylabel.R | 11 meta-4.9-0/meta/R/catmeth.R | 47 ++- meta-4.9-0/meta/R/forest-internal.R | 89 +++---- meta-4.9-0/meta/R/forest.meta.R | 409 +++++++++++++++++++-------------- meta-4.9-0/meta/R/forest.metabind.R |only meta-4.9-0/meta/R/format.NA.R | 8 meta-4.9-0/meta/R/format.p.R | 64 +++-- meta-4.9-0/meta/R/formatCI.R |only meta-4.9-0/meta/R/formatN.R |only meta-4.9-0/meta/R/formatPT.R |only meta-4.9-0/meta/R/funnel.default.R | 1 meta-4.9-0/meta/R/is.log.effect.R |only meta-4.9-0/meta/R/is.mean.R |only meta-4.9-0/meta/R/kentau.R | 27 +- meta-4.9-0/meta/R/labbe.default.R | 5 meta-4.9-0/meta/R/labbe.metabin.R | 3 meta-4.9-0/meta/R/meta-internal.R | 26 +- meta-4.9-0/meta/R/metabin.R | 3 meta-4.9-0/meta/R/metabind.R |only meta-4.9-0/meta/R/metacont.R | 3 meta-4.9-0/meta/R/metacor.R | 1 meta-4.9-0/meta/R/metacr.R | 2 meta-4.9-0/meta/R/metacum.R | 19 + meta-4.9-0/meta/R/metagen.R | 1 meta-4.9-0/meta/R/metainc.R | 1 meta-4.9-0/meta/R/metainf.R | 19 + meta-4.9-0/meta/R/metamean.R |only meta-4.9-0/meta/R/metaprop.R | 48 +-- meta-4.9-0/meta/R/metarate.R | 1 meta-4.9-0/meta/R/p.ci.R | 4 meta-4.9-0/meta/R/print.meta.R | 212 ++++++++++------- meta-4.9-0/meta/R/print.summary.meta.R | 327 ++++++++++++++++---------- meta-4.9-0/meta/R/settings.meta.R | 129 ++++++---- meta-4.9-0/meta/R/subgroup.R | 62 ++++- meta-4.9-0/meta/R/summary.meta.R | 22 + meta-4.9-0/meta/R/trimfill.default.R | 3 meta-4.9-0/meta/R/trimfill.meta.R | 2 meta-4.9-0/meta/R/update.meta.R | 40 ++- meta-4.9-0/meta/R/xlab.R | 16 + meta-4.9-0/meta/inst/COPYRIGHTS | 7 meta-4.9-0/meta/man/bubble.Rd | 2 meta-4.9-0/meta/man/forest.Rd | 54 +++- meta-4.9-0/meta/man/labbe.Rd | 2 meta-4.9-0/meta/man/meta-package.Rd | 62 +++-- meta-4.9-0/meta/man/metabin.Rd | 15 - meta-4.9-0/meta/man/metabind.Rd |only meta-4.9-0/meta/man/metacont.Rd | 4 meta-4.9-0/meta/man/metacor.Rd | 4 meta-4.9-0/meta/man/metacum.Rd | 4 meta-4.9-0/meta/man/metagen.Rd | 7 meta-4.9-0/meta/man/metainc.Rd | 4 meta-4.9-0/meta/man/metainf.Rd | 4 meta-4.9-0/meta/man/metamean.Rd |only meta-4.9-0/meta/man/metaprop.Rd | 12 meta-4.9-0/meta/man/metarate.Rd | 4 meta-4.9-0/meta/man/metareg.Rd | 2 meta-4.9-0/meta/man/print.meta.Rd | 75 +++--- meta-4.9-0/meta/man/trimfill.Rd | 2 meta-4.9-0/meta/man/update.meta.Rd | 29 +- 66 files changed, 1357 insertions(+), 779 deletions(-)
Title: SemiParametric Transformation Model Methods
Description: Implements semiparametric transformation model two-phase estimation using calibration weights. The method in Fong and Gilbert (2015) Calibration weighted estimation of semiparametric transformation models for two-phase sampling. Statistics in Medicine <DOI:10.1002/sim.6439>.
Author: Youyi Fong [cre],
Krisztian Sebestyen [aut],
Martin Maechler [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between sptm versions 16.7-9 dated 2016-07-10 and 17.12-7 dated 2017-12-05
DESCRIPTION | 17 ++++++++++------- MD5 | 9 +++++---- NAMESPACE | 2 +- man/rstm.Rd | 10 ++++++++++ src/registerDynamicSymbol.c |only tests/doRUnit.R | 2 +- 6 files changed, 27 insertions(+), 13 deletions(-)
Title: Monte-Carlo Methods for Prediction Functions
Description: Marginalizes prediction functions using Monte-Carlo integration and computes permutation importance.
Author: Zachary Jones [aut, cre]
Maintainer: Zachary Jones <zmj@zmjones.com>
Diff between mmpf versions 0.0.3 dated 2017-03-05 and 0.0.4 dated 2017-12-05
DESCRIPTION | 6 LICENSE | 2 MD5 | 10 R/grid.R | 17 - build/vignette.rds |binary inst/doc/mmpf.html | 632 ++++++++++++++++++++++++++++++++++------------------- 6 files changed, 435 insertions(+), 232 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 0.4.4 dated 2017-05-22 and 1.0.0 dated 2017-12-05
foghorn-0.4.4/foghorn/man/show_cran_results.Rd |only foghorn-1.0.0/foghorn/DESCRIPTION | 17 foghorn-1.0.0/foghorn/MD5 | 46 - foghorn-1.0.0/foghorn/NAMESPACE | 28 foghorn-1.0.0/foghorn/NEWS.md | 35 foghorn-1.0.0/foghorn/R/api_cranchecks.R |only foghorn-1.0.0/foghorn/R/cran_check_table.R |only foghorn-1.0.0/foghorn/R/cran_details.R |only foghorn-1.0.0/foghorn/R/cran_files.R | 168 ++-- foghorn-1.0.0/foghorn/R/cran_results.R |only foghorn-1.0.0/foghorn/R/defaults.R |only foghorn-1.0.0/foghorn/R/deprecated.R |only foghorn-1.0.0/foghorn/R/foghorn-package.R | 4 foghorn-1.0.0/foghorn/R/foghorn.R | 415 +---------- foghorn-1.0.0/foghorn/R/utils.R |only foghorn-1.0.0/foghorn/R/visit_cran_check.R |only foghorn-1.0.0/foghorn/README.md | 103 +- foghorn-1.0.0/foghorn/build/vignette.rds |binary foghorn-1.0.0/foghorn/inst/doc/quick_start.R | 16 foghorn-1.0.0/foghorn/inst/doc/quick_start.Rmd | 44 - foghorn-1.0.0/foghorn/inst/doc/quick_start.html | 109 +- foghorn-1.0.0/foghorn/man/check_cran_results.Rd | 81 -- foghorn-1.0.0/foghorn/man/cran_details.Rd |only foghorn-1.0.0/foghorn/man/cran_results.Rd |only foghorn-1.0.0/foghorn/man/foghorn.Rd | 4 foghorn-1.0.0/foghorn/man/summary_cran_results.Rd | 25 foghorn-1.0.0/foghorn/man/visit_cran_check.Rd | 2 foghorn-1.0.0/foghorn/tests/testthat/test-foghorn.R | 207 +++-- foghorn-1.0.0/foghorn/tests/testthat/test-n_cran_platforms.R |only foghorn-1.0.0/foghorn/vignettes/quick_start.Rmd | 44 - 30 files changed, 568 insertions(+), 780 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models and non-informative right-censoring may be considered. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value distribution as an important special case.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.1.1 dated 2017-11-13 and 0.1.2 dated 2017-12-05
sglg-0.1.1/sglg/R/sglg.R |only sglg-0.1.2/sglg/DESCRIPTION | 6 sglg-0.1.2/sglg/MD5 | 46 +-- sglg-0.1.2/sglg/NAMESPACE | 1 sglg-0.1.2/sglg/R/Gu.R | 76 ++---- sglg-0.1.2/sglg/R/blockgs.R | 39 ++- sglg-0.1.2/sglg/R/code_example_sglg.R | 66 ++--- sglg-0.1.2/sglg/R/deBoor2.R | 95 +++---- sglg-0.1.2/sglg/R/envelope.sglg.R | 35 +- sglg-0.1.2/sglg/R/glg.R | 122 +++------ sglg-0.1.2/sglg/R/influence.sglg.R | 201 ++++++++-------- sglg-0.1.2/sglg/R/kmpar.R |only sglg-0.1.2/sglg/R/lss.R | 6 sglg-0.1.2/sglg/R/plot.npc.R | 21 - sglg-0.1.2/sglg/R/plot.sglg.R | 30 +- sglg-0.1.2/sglg/R/rglg.R | 3 sglg-0.1.2/sglg/R/sglg2.R |only sglg-0.1.2/sglg/R/shape.R | 4 sglg-0.1.2/sglg/R/ssurvglg.R | 326 +++++++++++--------------- sglg-0.1.2/sglg/R/summary.sglg.R | 114 +++------ sglg-0.1.2/sglg/R/survglg.R | 250 +++++++++---------- sglg-0.1.2/sglg/man/plotsurv.sglg.Rd |only sglg-0.1.2/sglg/man/sglg.Rd | 17 - sglg-0.1.2/sglg/man/ssurvglg.Rd | 6 sglg-0.1.2/sglg/man/survglg.Rd | 2 sglg-0.1.2/sglg/tests/testthat/test_survglg.R | 6 26 files changed, 689 insertions(+), 783 deletions(-)
Title: Calling Copy Number Alterations in Amplicon Sequencing Data
Description: Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls.
Author: Jan Budczies, Eva Romanovsky
Maintainer: Jan Budczies <jan.budczies@charite.de>
Diff between ioncopy versions 1.0 dated 2015-08-26 and 2.0 dated 2017-12-05
ioncopy-1.0/ioncopy/R/call.amplicons.R |only ioncopy-1.0/ioncopy/R/call.genes.R |only ioncopy-1.0/ioncopy/man/call.amplicons.Rd |only ioncopy-1.0/ioncopy/man/call.genes.Rd |only ioncopy-2.0/ioncopy/DESCRIPTION | 12 +-- ioncopy-2.0/ioncopy/MD5 | 34 +++++++--- ioncopy-2.0/ioncopy/NAMESPACE | 16 ++++ ioncopy-2.0/ioncopy/R/assess.CNA.R |only ioncopy-2.0/ioncopy/R/calculate.CN.R | 93 +++-------------------------- ioncopy-2.0/ioncopy/R/call.CNA.R |only ioncopy-2.0/ioncopy/R/heatmap.CNA.R |only ioncopy-2.0/ioncopy/R/read.coverages.R |only ioncopy-2.0/ioncopy/R/runIoncopy.R |only ioncopy-2.0/ioncopy/R/summarize.CNA.R |only ioncopy-2.0/ioncopy/inst |only ioncopy-2.0/ioncopy/man/assess.CNA.Rd |only ioncopy-2.0/ioncopy/man/calculate.CN.Rd | 29 +-------- ioncopy-2.0/ioncopy/man/call.CNA.Rd |only ioncopy-2.0/ioncopy/man/coverage.Rd | 2 ioncopy-2.0/ioncopy/man/heatmap.CNA.Rd |only ioncopy-2.0/ioncopy/man/ioncopy-package.Rd | 4 - ioncopy-2.0/ioncopy/man/read.coverages.Rd |only ioncopy-2.0/ioncopy/man/runIoncopy.Rd |only ioncopy-2.0/ioncopy/man/summarize.CNA.Rd |only 24 files changed, 62 insertions(+), 128 deletions(-)
Title: An Algorithm for Morphometric Characters Selection and
Statistical Validation in Morphological Taxonomy
Description: An algorithm (Guisande et al., 2016 <doi:10.11646/zootaxa.4162.3.10>) which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between VARSEDIG versions 1.4 dated 2017-09-01 and 1.5 dated 2017-12-05
DESCRIPTION | 6 +- MD5 | 10 ++-- NAMESPACE | 4 - R/VARSEDIG.R | 121 ++++++++++++-------------------------------------------- R/VARSEDIM.R |only man/VARSEDIG.Rd | 2 man/VARSEDIM.Rd |only 7 files changed, 39 insertions(+), 104 deletions(-)
Title: Studio Ghibli Palette Generator
Description: Colour palettes inspired by Studio Ghibli films, ported to R for your enjoyment.
Author: Ewen Henderson [aut, cre]
Maintainer: Ewen Henderson <ewenhenderson@gmail.com>
Diff between ghibli versions 0.1.0 dated 2017-08-14 and 0.1.1 dated 2017-12-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 +++++- R/colours.R | 8 +++++++- build/vignette.rds |binary inst/doc/ghibli-guide.html | 30 +++++++++++++++--------------- man/ghibli_palettes.Rd | 2 +- 7 files changed, 38 insertions(+), 28 deletions(-)
Title: Machine Learning Tools
Description: A collection of machine learning helper functions, particularly assisting in the Exploratory Data Analysis phase. Makes heavy use of the 'data.table' package for optimal speed and memory efficiency. Highlights include a versatile bin_data() function, sparsify() for converting a data.table to sparse matrix format with one-hot encoding, fast evaluation metrics, and empirical_cdf() for calculating empirical Multivariate Cumulative Distribution Functions.
Author: Ben Gorman
Maintainer: Ben Gorman <bgorman@GormAnalysis.com>
Diff between mltools versions 0.3.3 dated 2017-09-12 and 0.3.4 dated 2017-12-05
DESCRIPTION | 7 ++++--- MD5 | 29 +++++++++++++++++++---------- NAMESPACE | 3 +++ NEWS.md | 3 +++ R/explore_dataset.R | 2 +- R/mse.R |only R/msle.R |only R/replace_na.R | 2 +- R/rmse.R | 20 ++++++++++++-------- R/rmsle.R |only README.md | 1 + man/explore_dataset.Rd | 2 +- man/mse.Rd |only man/msle.Rd |only man/replace_na.Rd | 2 +- man/rmse.Rd | 14 ++++++++------ man/rmsle.Rd |only tests |only 18 files changed, 54 insertions(+), 31 deletions(-)
Title: Interface to 'X12-ARIMA'/'X13-ARIMA-SEATS' and Structure for
Batch Processing of Seasonal Adjustment
Description: The 'X13-ARIMA-SEATS' <https://www.census.gov/srd/www/x13as/> methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from 'R' with this package and 'X13-ARIMA-SEATS' binaries are provided by the 'R' package 'x13binary'.
Author: Alexander Kowarik <alexander.kowarik@statistik.gv.at>, Angelika Meraner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between x12 versions 1.8.0 dated 2017-04-26 and 1.9.0 dated 2017-12-05
x12-1.8.0/x12/README |only x12-1.9.0/x12/DESCRIPTION | 17 x12-1.9.0/x12/MD5 | 16 x12-1.9.0/x12/NEWS | 2 x12-1.9.0/x12/R/class.R | 847 +++++++++++++-------------- x12-1.9.0/x12/R/parameter-methods.R | 921 ++++++++++++++--------------- x12-1.9.0/x12/R/readx12Out.R | 28 x12-1.9.0/x12/R/x12work.R | 1124 ++++++++++++++++++------------------ x12-1.9.0/x12/README.md |only x12-1.9.0/x12/tests |only 10 files changed, 1480 insertions(+), 1475 deletions(-)
Title: Quantile Regression Neural Network
Description: Fit quantile regression neural network models with optional
left censoring, partial monotonicity constraints, generalized additive
model constraints, and the ability to fit multiple non-crossing quantile
functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005>
and Cannon (2017) <doi:10.17605/OSF.IO/WG7SN>.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between qrnn versions 1.1.3 dated 2015-07-23 and 2.0 dated 2017-12-05
qrnn-1.1.3/qrnn/R/tilted.huber.R |only qrnn-1.1.3/qrnn/R/tilted.huber.prime.R |only qrnn-1.1.3/qrnn/data/sinc.rda |only qrnn-1.1.3/qrnn/man/qrnn.eval.Rd |only qrnn-1.1.3/qrnn/man/qrnn.nlm.Rd |only qrnn-1.1.3/qrnn/man/qrnn.reshape.Rd |only qrnn-1.1.3/qrnn/man/sinc.Rd |only qrnn-1.1.3/qrnn/man/tilted.huber.Rd |only qrnn-1.1.3/qrnn/man/tilted.huber.prime.Rd |only qrnn-2.0/qrnn/DESCRIPTION | 15 - qrnn-2.0/qrnn/MD5 | 115 +++++---- qrnn-2.0/qrnn/NAMESPACE | 30 ++ qrnn-2.0/qrnn/R/censored.mean.R | 24 - qrnn-2.0/qrnn/R/composite.stack.R |only qrnn-2.0/qrnn/R/dquantile.R | 106 ++++---- qrnn-2.0/qrnn/R/dummy.code.R |only qrnn-2.0/qrnn/R/elu.R |only qrnn-2.0/qrnn/R/elu.prime.R |only qrnn-2.0/qrnn/R/gam.mask.R |only qrnn-2.0/qrnn/R/hramp.R | 26 +- qrnn-2.0/qrnn/R/hramp.prime.R | 32 +- qrnn-2.0/qrnn/R/huber.R | 16 - qrnn-2.0/qrnn/R/huber.prime.R | 20 - qrnn-2.0/qrnn/R/linear.R | 12 qrnn-2.0/qrnn/R/linear.prime.R | 12 qrnn-2.0/qrnn/R/pquantile.R | 92 +++---- qrnn-2.0/qrnn/R/qquantile.R | 128 +++++----- qrnn-2.0/qrnn/R/qrnn-rbf.R | 22 - qrnn-2.0/qrnn/R/qrnn.cost.R | 82 +++--- qrnn-2.0/qrnn/R/qrnn.eval.R | 30 +- qrnn-2.0/qrnn/R/qrnn.fit.R | 36 +- qrnn-2.0/qrnn/R/qrnn.initialize.R | 26 +- qrnn-2.0/qrnn/R/qrnn.nlm.R | 94 ++++--- qrnn-2.0/qrnn/R/qrnn.predict.R | 48 ++- qrnn-2.0/qrnn/R/qrnn.reshape.R | 32 +- qrnn-2.0/qrnn/R/rquantile.R | 40 +-- qrnn-2.0/qrnn/R/sigmoid.R | 12 qrnn-2.0/qrnn/R/sigmoid.prime.R | 12 qrnn-2.0/qrnn/R/softplus.R |only qrnn-2.0/qrnn/R/softplus.prime.R |only qrnn-2.0/qrnn/R/tilted.abs.R | 15 - qrnn-2.0/qrnn/R/tilted.approx.R |only qrnn-2.0/qrnn/R/tilted.approx.prime.R |only qrnn-2.0/qrnn/inst/CITATION | 32 +- qrnn-2.0/qrnn/man/YVRprecip.Rd | 126 +++++----- qrnn-2.0/qrnn/man/censored.mean.Rd | 60 ++-- qrnn-2.0/qrnn/man/composite.stack.Rd |only qrnn-2.0/qrnn/man/dummy.code.Rd |only qrnn-2.0/qrnn/man/elu.Rd |only qrnn-2.0/qrnn/man/elu.prime.Rd |only qrnn-2.0/qrnn/man/gam.style.Rd | 53 ++-- qrnn-2.0/qrnn/man/hramp.Rd | 58 ++-- qrnn-2.0/qrnn/man/hramp.prime.Rd | 58 ++-- qrnn-2.0/qrnn/man/huber.Rd | 52 ++-- qrnn-2.0/qrnn/man/huber.prime.Rd | 52 ++-- qrnn-2.0/qrnn/man/linear.Rd | 46 +-- qrnn-2.0/qrnn/man/linear.prime.Rd | 46 +-- qrnn-2.0/qrnn/man/mcqrnn.Rd |only qrnn-2.0/qrnn/man/qrnn-package.Rd | 150 +++++++----- qrnn-2.0/qrnn/man/qrnn-rbf.Rd | 101 ++++---- qrnn-2.0/qrnn/man/qrnn.cost.Rd | 126 ++++++---- qrnn-2.0/qrnn/man/qrnn.fit.Rd | 364 ++++++++++++++++++------------ qrnn-2.0/qrnn/man/qrnn.initialize.Rd | 56 ++-- qrnn-2.0/qrnn/man/qrnn.predict.Rd | 87 +++---- qrnn-2.0/qrnn/man/quantile.dtn.Rd | 246 ++++++++++---------- qrnn-2.0/qrnn/man/sigmoid.Rd | 46 +-- qrnn-2.0/qrnn/man/sigmoid.prime.Rd | 46 +-- qrnn-2.0/qrnn/man/softplus.Rd |only qrnn-2.0/qrnn/man/softplus.prime.Rd |only qrnn-2.0/qrnn/man/tilted.abs.Rd | 49 +--- qrnn-2.0/qrnn/man/tilted.approx.Rd |only qrnn-2.0/qrnn/man/tilted.approx.prime.Rd |only 72 files changed, 1586 insertions(+), 1345 deletions(-)
Title: Tools for Building OLS Regression Models
Description: Tools for building OLS regression models . Includes
comprehensive regression output, heteroskedasticity tests, collinearity diagnostics,
residual diagnostics, measures of influence, model fit assessment and variable selection procedures.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between olsrr versions 0.3.0 dated 2017-08-31 and 0.4.0 dated 2017-12-05
DESCRIPTION | 19 MD5 | 280 ++++++++++--- NAMESPACE | 16 NEWS.md | 16 R/RcppExports.R | 2 R/ols-added-variable-plot.R | 3 R/ols-all-possible-regression.R | 181 ++++---- R/ols-bartlett-test.R | 8 R/ols-best-subsets-regression.R | 9 R/ols-cooks-d-barplot.R | 4 R/ols-cooks-d-chart.R | 4 R/ols-data-auto.R |only R/ols-dfbetas-panel.R | 17 R/ols-dffits-plot.R | 4 R/ols-diagnostics-panel.R | 27 - R/ols-dsresid-vs-pred-plot.R | 4 R/ols-launch-app.R |only R/ols-regress_compute.R | 31 + R/ols-regression.R | 30 + R/ols-residual-fit-spread-plot.R | 3 R/ols-residual-plus-component-plot.R | 3 R/ols-response-profile.R | 3 R/ols-rstud-vs-lev-plot.R | 2 R/ols-stepaic-backward-regression.R | 4 R/ols-stepaic-both-regression.R | 6 R/ols-stepaic-forward-regression.R | 4 R/ols-stepwise-backward-regression.R | 8 R/ols-stepwise-forward-regression.R | 8 R/ols-stepwise-regression.R | 10 R/ols-studentized-residual-chart.R | 4 R/ols-studentized-residual-plot.R | 4 R/output.R | 622 ++++++++++++++--------------- R/utils.R | 86 +++- README.md | 231 ++++++++-- build/vignette.rds |binary data/auto.rda |only inst/application |only inst/doc/heteroskedasticity.html | 42 - inst/doc/influence_measures.html | 24 - inst/doc/intro.Rmd | 5 inst/doc/intro.html | 25 - inst/doc/reference-media.Rmd |only inst/doc/reference-media.html |only inst/doc/regression_diagnostics.html | 32 - inst/doc/residual_diagnostics.html | 14 inst/doc/variable_selection.html | 50 +- man/auto.Rd |only man/ols_all_subset.Rd | 4 man/ols_all_subset_betas.Rd |only man/ols_bartlett_test.Rd | 8 man/ols_best_subset.Rd | 4 man/ols_dfbetas_panel.Rd | 2 man/ols_diagnostic_panel.Rd | 3 man/ols_launch_app.Rd |only man/ols_regress.Rd | 12 man/ols_step_backward.Rd | 4 man/ols_step_forward.Rd | 4 man/ols_stepaic_backward.Rd | 4 man/ols_stepaic_both.Rd | 4 man/ols_stepaic_forward.Rd | 4 man/ols_stepwise.Rd | 4 src/RcppExports.cpp | 2 src/init.c | 4 tests/figs |only tests/testthat/test-all-possible.R | 48 ++ tests/testthat/test-avplots.R |only tests/testthat/test-bartlett-output.R |only tests/testthat/test-best-subsets-output.R |only tests/testthat/test-best-subsets.R | 15 tests/testthat/test-bp-output.R |only tests/testthat/test-collindiag.R | 34 + tests/testthat/test-correlations-output.R |only tests/testthat/test-correlations.R | 4 tests/testthat/test-ftest-output.R |only tests/testthat/test-info.R | 1 tests/testthat/test-loftest-output.R |only tests/testthat/test-norm-output.R |only tests/testthat/test-regress-output.R |only tests/testthat/test-regress.R | 9 tests/testthat/test-score-output.R |only tests/testthat/test-step-backward-output.R |only tests/testthat/test-step-forward-output.R |only tests/testthat/test-stepaic-b-output.R |only tests/testthat/test-stepaic-both-output.R |only tests/testthat/test-stepaic-f-output.R |only tests/testthat/test-stepwise-output.R |only tests/testthat/test-utility.R | 14 tests/testthat/test-visual.R |only vignettes/intro.Rmd | 5 vignettes/reference-media.Rmd |only 90 files changed, 1402 insertions(+), 636 deletions(-)
Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions
from ecological data. 'gambin' is short for 'gamma-binomial'. The main function
is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution
using maximum likelihood. Functions are also provided to generate the gambin distribution
and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre],
Michael Krabbe Borregaard [aut],
Karl Ugland [aut],
Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>
Diff between gambin versions 2.1.1 dated 2017-07-25 and 2.2.0 dated 2017-12-05
DESCRIPTION | 7 ++++--- MD5 | 10 ++++++---- NEWS.md | 4 ++++ R/data_docs.R | 17 +++++++++++++++++ data/fly.rda |only inst/doc/overview.html | 12 ++++++------ man/fly.Rd |only 7 files changed, 37 insertions(+), 13 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and compact letter displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph],
Jonathon Love [ctb],
Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 0.9.1 dated 2017-11-05 and 1.0 dated 2017-12-05
DESCRIPTION | 8 - MD5 | 155 +++++++++++++------------- NAMESPACE | 3 R/0nly-internal.R | 23 +++ R/MCMC-support.R | 8 - R/aovlist-support.R | 2 R/betareg.support.R | 2 R/cld-emm.R | 8 - R/contrast.R | 14 +- R/countreg-support.R | 4 R/datasets.R | 8 - R/emm-contr.R | 6 - R/emm-list.R | 29 ++++ R/emmeans-package.R | 2 R/emmeans.R | 92 +++------------ R/emmip.R | 28 +--- R/emtrends.R | 2 R/gam-support.R | 42 ++++++- R/glht-support.R | 24 ++-- R/helpers.R | 18 +-- R/interfacing.R | 4 R/nested.R | 2 R/nonlin-support.R | 2 R/ordinal-support.R | 6 - R/plot.emm.R | 6 - R/ref-grid.R | 6 - R/rms-support.R | 4 R/summary.R | 200 ++++++++++++++++++++++++---------- R/wrappers.R | 4 R/xtable-method.R | 4 inst/NEWS | 39 ++++++ inst/doc/FAQs.html | 4 inst/doc/basics.html | 4 inst/doc/comparisons.R | 20 +-- inst/doc/comparisons.Rmd | 29 ++-- inst/doc/comparisons.html | 36 +++--- inst/doc/confidence-intervals.R | 24 ++-- inst/doc/confidence-intervals.Rmd | 34 +++-- inst/doc/confidence-intervals.html | 32 ++--- inst/doc/extending.R | 18 +-- inst/doc/extending.pdf |binary inst/doc/extending.rnw | 3 inst/doc/interactions.html | 4 inst/doc/messy-data.R | 12 +- inst/doc/messy-data.Rmd | 12 +- inst/doc/messy-data.html | 34 ++--- inst/doc/models.Rmd | 12 +- inst/doc/models.html | 92 ++++++++------- inst/doc/sophisticated.R | 16 +- inst/doc/sophisticated.Rmd | 16 +- inst/doc/sophisticated.html | 130 +++++++++++----------- inst/doc/transformations.R | 24 ++-- inst/doc/transformations.Rmd | 30 ++--- inst/doc/transformations.html | 82 ++++++------- inst/doc/transition-from-lsmeans.html | 4 inst/doc/utilities.R | 20 +-- inst/doc/utilities.Rmd | 41 ++++-- inst/doc/utilities.html | 49 ++++---- man/cld.emmGrid.Rd | 8 - man/contrast.Rd | 14 +- man/emm_list-object.Rd |only man/emmc-functions.Rd | 6 - man/emmeans-package.Rd | 2 man/emmeans.Rd | 6 - man/emmobj.Rd | 6 - man/glht-support.Rd | 22 +-- man/nutrition.Rd | 8 - man/plot.Rd | 6 - man/ref_grid.Rd | 3 man/summary.emmGrid.Rd | 188 ++++++++++++++++++++++++------- man/xtable.emmGrid.Rd | 4 vignettes/comparisons.Rmd | 29 ++-- vignettes/confidence-intervals.Rmd | 34 +++-- vignettes/extending.rnw | 3 vignettes/messy-data.Rmd | 12 +- vignettes/models.Rmd | 12 +- vignettes/sophisticated.Rmd | 16 +- vignettes/transformations.Rmd | 30 ++--- vignettes/utilities.Rmd | 41 ++++-- 79 files changed, 1146 insertions(+), 841 deletions(-)
Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs were recently proposed by Magrini et al. (2016) <ISBN:978-88-619-7061-8> as an extension of linear structural causal models (Pearl, 2000) <ISBN:978-0-521-89560-6>, where each factor of the joint probability distribution is a distributed-lag linear regression with constrained lag shapes. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.9 dated 2017-07-23 and 2.0 dated 2017-12-05
dlsem-1.9/dlsem/man/makePrediction.Rd |only dlsem-2.0/dlsem/DESCRIPTION | 14 - dlsem-2.0/dlsem/MD5 | 39 +-- dlsem-2.0/dlsem/NAMESPACE | 2 dlsem-2.0/dlsem/R/dlsem.r | 314 ++------------------------- dlsem-2.0/dlsem/build/vignette.rds |binary dlsem-2.0/dlsem/data/agres.rda |only dlsem-2.0/dlsem/inst/doc/dlsem_vignette.R | 34 +- dlsem-2.0/dlsem/inst/doc/dlsem_vignette.Rnw | 213 ++++++++---------- dlsem-2.0/dlsem/inst/doc/dlsem_vignette.pdf |binary dlsem-2.0/dlsem/man/agres.Rd |only dlsem-2.0/dlsem/man/auto.lagPlot.Rd | 1 dlsem-2.0/dlsem/man/causalEff.Rd | 10 dlsem-2.0/dlsem/man/dlsem-package.Rd | 33 +- dlsem-2.0/dlsem/man/dlsem.Rd | 28 +- dlsem-2.0/dlsem/man/edgeCoeff.Rd | 1 dlsem-2.0/dlsem/man/industry.Rd | 2 dlsem-2.0/dlsem/man/isIndep.Rd | 12 - dlsem-2.0/dlsem/man/lagPlot.Rd | 1 dlsem-2.0/dlsem/man/modelFit.Rd | 7 dlsem-2.0/dlsem/man/unirootTest.Rd | 11 dlsem-2.0/dlsem/vignettes/dlsem_vignette.Rnw | 213 ++++++++---------- 22 files changed, 328 insertions(+), 607 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-26 1.2-2
2009-02-06 1.1-6
2009-02-06 1.1-7
2006-04-19 1.1-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-15 1.8
2013-07-25 1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-22 1.1
2015-06-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-10 1.2.1
2013-08-29 1.01
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-22 1.0-3
2013-12-16 1.0-2
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 1.4-0 dated 2017-10-30 and 1.4-1 dated 2017-12-05
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 8 ++++++++ R/div.R | 36 +++++++++++++++++++++++++++--------- R/rnd.R | 35 +++++++++++++++++++++++++++++------ R/summary.taf.R | 39 ++++++++++++++++++++++----------------- R/taf.skeleton.R | 2 +- data/catage.long.rda |binary data/catage.taf.rda |binary data/catage.xtab.rda |binary data/summary.taf.rda |binary data/taf.colors.rda |binary man/div.Rd | 36 +++++++++++++++++++++++++++--------- man/rnd.Rd | 35 +++++++++++++++++++++++++++++------ man/summary.taf.Rd | 39 ++++++++++++++++++++++----------------- 15 files changed, 183 insertions(+), 83 deletions(-)
Title: Estimate Structured Additive Regression Models with 'BayesX'
Description: An R interface to estimate structured additive regression (STAR) models with 'BayesX'.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut] (0000-0003-0918-3766)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between R2BayesX versions 1.1-0 dated 2016-11-17 and 1.1-1 dated 2017-12-05
R2BayesX-1.1-0/R2BayesX/src/bayesx.c |only R2BayesX-1.1-1/R2BayesX/DESCRIPTION | 15 ++++++++------- R2BayesX-1.1-1/R2BayesX/MD5 | 11 ++++++----- R2BayesX-1.1-1/R2BayesX/NAMESPACE | 4 ++-- R2BayesX-1.1-1/R2BayesX/man/nbAndGraConversion.Rd | 11 +++++++++-- R2BayesX-1.1-1/R2BayesX/man/spAndBndConversion.Rd | 3 ++- R2BayesX-1.1-1/R2BayesX/src/R2BayesX_functions.c |only R2BayesX-1.1-1/R2BayesX/src/R2BayesX_init.c |only 8 files changed, 27 insertions(+), 17 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6.4 dated 2016-10-04 and 1.6.5 dated 2017-12-05
ChangeLog | 4360 +++++++++++++++++----------------- DESCRIPTION | 22 MD5 | 100 NAMESPACE | 3 R/boot.R | 4 R/draic.R | 526 ++-- R/hmm.R | 2 R/msm.R | 4004 +++++++++++++++---------------- R/mstate.R | 114 R/olddata.R | 140 - R/outputs.R | 3999 +++++++++++++++---------------- R/pearson.R | 7 R/phase.R | 4 R/simul.R | 736 ++--- R/utils.R | 23 build/vignette.rds |binary inst/NEWS | 21 inst/doc/msm-manual.R | 32 inst/doc/msm-manual.pdf |binary man/2phase.Rd | 276 +- man/cmodel.object.Rd | 40 man/ecmodel.object.Rd | 58 man/emodel.object.Rd | 72 man/hmm-dists.Rd | 2 man/model.frame.msm.Rd | 130 - man/msm.Rd | 9 man/msm.form.qoutput.Rd | 80 man/msm.object.Rd | 242 - man/plot.prevalence.msm.Rd | 2 man/plot.survfit.msm.Rd | 23 man/pmatrix.msm.Rd | 3 man/prevalence.msm.Rd | 4 man/qcmodel.object.Rd | 80 man/qgeneric.Rd | 6 man/qmatrix.msm.Rd | 5 man/qmodel.object.Rd | 102 man/simmulti.msm.Rd | 284 +- man/totlos.msm.Rd | 7 man/viterbi.msm.Rd | 6 src/expm.h |only src/lik.c | 9 src/msm-init.c |only src/pijt.c | 13 tests/test_base.R | 4 tests/testthat/helper.r | 54 tests/testthat/test_analyticp.r | 524 ++-- tests/testthat/test_datasumm.r | 80 tests/testthat/test_models.r | 1378 +++++----- tests/testthat/test_models_hmm.r | 2 tests/testthat/test_models_hmmmulti.r | 41 tests/testthat/test_utils.r | 13 vignettes/msm-manual.Rnw | 3 52 files changed, 8904 insertions(+), 8745 deletions(-)
Title: Learning Causal or Non-Causal Graphical Models Using Information
Theory
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Verny et al. Plos Comput Biol. (2017) <doi:10.1371/journal.pcbi.1005662>.
Author: Nadir Sella [aut, cre],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Nadir Sella <nadir.sella@curie.fr>
Diff between miic versions 1.0 dated 2017-11-22 and 1.0.1 dated 2017-12-05
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/miic.R | 2 +- man/miic.Rd | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Subtracting Summary Statistics of One or more Cohorts from
Meta-GWAS Results
Description: If results from a meta-GWAS are used for validation in one of the cohorts that was included in the meta-analysis, this will yield biased (i.e. too optimistic) results. The validation cohort needs to be independent from the meta-GWAS results. MetaSubtract will subtract the results of the respective cohort from the meta-GWAS results analytically without having to redo the meta-GWAS analysis using the leave-one-out methodology. It can handle different meta-analyses methods and takes into account if single or double genomic control correction was applied to the original meta-analysis. It can be used for whole GWAS, but also for a limited set of SNPs or other genetic markers.
Author: Ilja M. Nolte
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between MetaSubtract versions 1.2 dated 2017-10-13 and 1.3 dated 2017-12-05
DESCRIPTION | 8 - MD5 | 10 +- R/MetaSubtract.r | 149 ++++++++++++++++++++--------------- inst/extdata/alternative_headers.txt | 5 - inst/extdata/cohort1_results.txt | 2 man/MetaSubtract-package.Rd | 2 6 files changed, 102 insertions(+), 74 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.4-0 dated 2017-06-05 and 1.4-1 dated 2017-12-05
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/MCMCmixfactanal.R | 3 +++ R/hidden.R | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (0000-0002-6485-8781)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.0.7 dated 2017-11-01 and 0.1.0 dated 2017-12-05
DESCRIPTION | 6 +- MD5 | 23 +++++----- NAMESPACE | 2 NEWS | 5 ++ R/geom_image.R | 52 +++++++++++++++++++----- R/geom_subview.R | 107 +++++++++++++++++++++++++++++++------------------- inst/doc/ggimage.R | 48 ++++++++++++++++++++++ inst/doc/ggimage.Rmd | 66 ++++++++++++++++++++++++++++++ inst/doc/ggimage.html | 84 +++++++++++++++++++++++++++++++++++---- inst/extdata |only man/geom_image.Rd | 4 + man/geom_subview.Rd | 15 ++++--- vignettes/ggimage.Rmd | 66 ++++++++++++++++++++++++++++++ 13 files changed, 398 insertions(+), 80 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Gert Janssenswillen [aut, cre],
Marijke Swennen [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between edeaR versions 0.7.1 dated 2017-09-07 and 0.7.2 dated 2017-12-05
edeaR-0.7.1/edeaR/R/activity_frequence_case.R |only edeaR-0.7.1/edeaR/R/filter_attributes.R |only edeaR-0.7.1/edeaR/R/selfloops.R |only edeaR-0.7.1/edeaR/man/filter_attributes.Rd |only edeaR-0.7.2/edeaR/DESCRIPTION | 24 edeaR-0.7.2/edeaR/MD5 | 295 +-- edeaR-0.7.2/edeaR/NAMESPACE | 71 edeaR-0.7.2/edeaR/R/activity_frequency.R | 104 - edeaR-0.7.2/edeaR/R/activity_frequency_activity.R | 9 edeaR-0.7.2/edeaR/R/activity_frequency_case.R |only edeaR-0.7.2/edeaR/R/activity_frequency_log.R | 3 edeaR-0.7.2/edeaR/R/activity_frequency_trace.R | 15 edeaR-0.7.2/edeaR/R/activity_presence.R | 76 edeaR-0.7.2/edeaR/R/edeaR.R | 20 edeaR-0.7.2/edeaR/R/end_activities.R | 87 - edeaR-0.7.2/edeaR/R/end_activities_activity.R | 12 edeaR-0.7.2/edeaR/R/end_activities_case.R | 7 edeaR-0.7.2/edeaR/R/end_activities_log.R | 18 edeaR-0.7.2/edeaR/R/end_activities_resource.R | 8 edeaR-0.7.2/edeaR/R/end_activities_resource_activity.R | 13 edeaR-0.7.2/edeaR/R/filter_activity.R | 65 edeaR-0.7.2/edeaR/R/filter_activity_frequency.R | 147 + edeaR-0.7.2/edeaR/R/filter_activity_presence.R | 78 - edeaR-0.7.2/edeaR/R/filter_case.R | 45 edeaR-0.7.2/edeaR/R/filter_endpoints.R | 84 - edeaR-0.7.2/edeaR/R/filter_endpoints_percentile.R | 55 edeaR-0.7.2/edeaR/R/filter_endpoints_sets.R | 41 edeaR-0.7.2/edeaR/R/filter_precedence.R | 137 - edeaR-0.7.2/edeaR/R/filter_processing_time.R | 103 - edeaR-0.7.2/edeaR/R/filter_processing_time_percentile.R | 31 edeaR-0.7.2/edeaR/R/filter_processing_time_threshold.R | 35 edeaR-0.7.2/edeaR/R/filter_resource.R | 44 edeaR-0.7.2/edeaR/R/filter_resource_frequency.R | 108 + edeaR-0.7.2/edeaR/R/filter_throughput_time.R | 109 - edeaR-0.7.2/edeaR/R/filter_throughput_time_percentile.R | 31 edeaR-0.7.2/edeaR/R/filter_throughput_time_threshold.R | 46 edeaR-0.7.2/edeaR/R/filter_time_period.R | 178 +- edeaR-0.7.2/edeaR/R/filter_trace_frequency.R | 101 - edeaR-0.7.2/edeaR/R/filter_trace_frequency_percentile.R | 44 edeaR-0.7.2/edeaR/R/filter_trace_frequency_threshold.R | 43 edeaR-0.7.2/edeaR/R/filter_trace_length.R | 108 - edeaR-0.7.2/edeaR/R/filter_trace_length_percentile.R | 31 edeaR-0.7.2/edeaR/R/filter_trace_length_threshold.R | 35 edeaR-0.7.2/edeaR/R/filter_trim.R | 100 - edeaR-0.7.2/edeaR/R/generate_pattern_dummies.R | 5 edeaR-0.7.2/edeaR/R/idle_time.R | 110 - edeaR-0.7.2/edeaR/R/idle_time_case.R | 27 edeaR-0.7.2/edeaR/R/idle_time_log.R | 4 edeaR-0.7.2/edeaR/R/idle_time_resource.R | 26 edeaR-0.7.2/edeaR/R/idle_time_trace.R | 16 edeaR-0.7.2/edeaR/R/number_of_repetitions.R | 180 +- edeaR-0.7.2/edeaR/R/number_of_selfloops.R | 168 +- edeaR-0.7.2/edeaR/R/number_of_traces.R | 52 edeaR-0.7.2/edeaR/R/plot.activity_frequency.R | 2 edeaR-0.7.2/edeaR/R/plot.activity_presence.R | 1 edeaR-0.7.2/edeaR/R/plot.end_activity.R | 1 edeaR-0.7.2/edeaR/R/plot.number_of_repetitions.R | 2 edeaR-0.7.2/edeaR/R/plot.number_of_selfloops.R | 1 edeaR-0.7.2/edeaR/R/plot.r | 4 edeaR-0.7.2/edeaR/R/plot.referral_matrix.R | 4 edeaR-0.7.2/edeaR/R/plot.resource_frequency.R | 4 edeaR-0.7.2/edeaR/R/plot.resource_involvement.R | 2 edeaR-0.7.2/edeaR/R/plot.resource_specialisation.R | 3 edeaR-0.7.2/edeaR/R/plot.start_activities.R | 1 edeaR-0.7.2/edeaR/R/plot.trace_coverage.R | 4 edeaR-0.7.2/edeaR/R/plot.trace_length.R | 3 edeaR-0.7.2/edeaR/R/processing_time.R | 123 - edeaR-0.7.2/edeaR/R/processing_time_activity.R | 39 edeaR-0.7.2/edeaR/R/processing_time_activity_instance.R |only edeaR-0.7.2/edeaR/R/processing_time_case.R | 34 edeaR-0.7.2/edeaR/R/processing_time_log.R | 13 edeaR-0.7.2/edeaR/R/processing_time_resource.R | 56 edeaR-0.7.2/edeaR/R/processing_time_resource_activity.R | 67 edeaR-0.7.2/edeaR/R/processing_time_trace.R | 48 edeaR-0.7.2/edeaR/R/redo_repetitions_referral_matrix.R | 22 edeaR-0.7.2/edeaR/R/redo_selfloops_referral_matrix.R | 23 edeaR-0.7.2/edeaR/R/resource_frequency.R | 121 - edeaR-0.7.2/edeaR/R/resource_frequency_activity.R | 24 edeaR-0.7.2/edeaR/R/resource_frequency_case.R | 28 edeaR-0.7.2/edeaR/R/resource_frequency_log.R | 15 edeaR-0.7.2/edeaR/R/resource_frequency_resource.R | 9 edeaR-0.7.2/edeaR/R/resource_frequency_resource_activity.R | 46 edeaR-0.7.2/edeaR/R/resource_involvement.R | 87 - edeaR-0.7.2/edeaR/R/resource_involvement_case.R | 9 edeaR-0.7.2/edeaR/R/resource_involvement_resource.R | 16 edeaR-0.7.2/edeaR/R/resource_involvement_resource_activity.R | 15 edeaR-0.7.2/edeaR/R/resource_specialisation.R | 120 - edeaR-0.7.2/edeaR/R/resource_specialisation_activity.R | 9 edeaR-0.7.2/edeaR/R/resource_specialisation_case.R | 26 edeaR-0.7.2/edeaR/R/resource_specialisation_log.R | 19 edeaR-0.7.2/edeaR/R/resource_specialisation_resource.R | 12 edeaR-0.7.2/edeaR/R/rework_functions.R | 849 ++++------- edeaR-0.7.2/edeaR/R/size_of_repetitions.R | 140 + edeaR-0.7.2/edeaR/R/size_of_selfloops.R | 107 - edeaR-0.7.2/edeaR/R/start_activities.R | 89 - edeaR-0.7.2/edeaR/R/start_activities_activity.R | 10 edeaR-0.7.2/edeaR/R/start_activities_case.R | 8 edeaR-0.7.2/edeaR/R/start_activities_log.R | 14 edeaR-0.7.2/edeaR/R/start_activities_resource.R | 9 edeaR-0.7.2/edeaR/R/start_activities_resource_activity.R | 13 edeaR-0.7.2/edeaR/R/throughput_time.R | 118 - edeaR-0.7.2/edeaR/R/throughput_time_case.R | 5 edeaR-0.7.2/edeaR/R/throughput_time_log.R | 14 edeaR-0.7.2/edeaR/R/throughput_time_trace.R | 25 edeaR-0.7.2/edeaR/R/trace_coverage.R | 76 edeaR-0.7.2/edeaR/R/trace_coverage_case.R | 6 edeaR-0.7.2/edeaR/R/trace_coverage_log.R | 38 edeaR-0.7.2/edeaR/R/trace_coverage_trace.R | 9 edeaR-0.7.2/edeaR/R/trace_length.R | 106 - edeaR-0.7.2/edeaR/R/trace_length_case.R | 7 edeaR-0.7.2/edeaR/R/trace_length_log.R | 11 edeaR-0.7.2/edeaR/R/trace_length_trace.R | 66 edeaR-0.7.2/edeaR/R/utils.R | 195 ++ edeaR-0.7.2/edeaR/build |only edeaR-0.7.2/edeaR/inst |only edeaR-0.7.2/edeaR/man/activity_frequency.Rd | 41 edeaR-0.7.2/edeaR/man/activity_presence.Rd | 27 edeaR-0.7.2/edeaR/man/end_activities.Rd | 48 edeaR-0.7.2/edeaR/man/filter_activity.Rd | 37 edeaR-0.7.2/edeaR/man/filter_activity_frequency.Rd | 52 edeaR-0.7.2/edeaR/man/filter_activity_presence.Rd | 48 edeaR-0.7.2/edeaR/man/filter_case.Rd | 37 edeaR-0.7.2/edeaR/man/filter_endpoints.Rd | 50 edeaR-0.7.2/edeaR/man/filter_precedence.Rd | 47 edeaR-0.7.2/edeaR/man/filter_processing_time.Rd | 53 edeaR-0.7.2/edeaR/man/filter_resource.Rd | 37 edeaR-0.7.2/edeaR/man/filter_resource_frequency.Rd | 54 edeaR-0.7.2/edeaR/man/filter_throughput_time.Rd | 53 edeaR-0.7.2/edeaR/man/filter_time_period.Rd | 54 edeaR-0.7.2/edeaR/man/filter_trace_frequency.Rd | 52 edeaR-0.7.2/edeaR/man/filter_trace_length.Rd | 47 edeaR-0.7.2/edeaR/man/filter_trim.Rd | 47 edeaR-0.7.2/edeaR/man/idle_time.Rd | 52 edeaR-0.7.2/edeaR/man/number_of_repetitions.Rd | 78 - edeaR-0.7.2/edeaR/man/number_of_selfloops.Rd | 93 + edeaR-0.7.2/edeaR/man/number_of_traces.Rd | 25 edeaR-0.7.2/edeaR/man/plot.Rd | 5 edeaR-0.7.2/edeaR/man/processing_time.Rd | 63 edeaR-0.7.2/edeaR/man/redo_repetitions_referral_matrix.Rd | 18 edeaR-0.7.2/edeaR/man/redo_selfloops_referral_matrix.Rd | 18 edeaR-0.7.2/edeaR/man/resource_frequency.Rd | 61 edeaR-0.7.2/edeaR/man/resource_involvement.Rd | 54 edeaR-0.7.2/edeaR/man/resource_specialisation.Rd | 60 edeaR-0.7.2/edeaR/man/size_of_repetitions.Rd | 41 edeaR-0.7.2/edeaR/man/size_of_selfloops.Rd | 41 edeaR-0.7.2/edeaR/man/start_activities.Rd | 49 edeaR-0.7.2/edeaR/man/throughput_time.Rd | 47 edeaR-0.7.2/edeaR/man/trace_coverage.Rd | 39 edeaR-0.7.2/edeaR/man/trace_length.Rd | 49 edeaR-0.7.2/edeaR/vignettes |only 150 files changed, 4597 insertions(+), 3057 deletions(-)
Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful software
developed by RTE to simulate and study electric power systems
(more information about Antares here: <https://antares.rte-france.com>).
This package provides functions that create interactive charts to help
Antares users visually explore the results of their simulations.
Author: Jalal-Edine ZAWAM [aut, cre],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between antaresViz versions 0.11 dated 2017-07-17 and 0.11.2 dated 2017-12-05
DESCRIPTION | 20 MD5 | 72 NEWS | 4 R/catColorPal.R | 66 R/get_data_for_comp.R | 92 R/leafletDragPoints.R | 104 R/map.R | 604 ++-- R/map_deps.R | 60 R/map_helpers.R | 648 ++-- R/map_layout.R | 698 ++--- R/map_legends.R | 322 +- R/map_options.R | 216 - R/map_plugins.R | 182 - R/plot.R | 676 ++-- R/plot_barplot.R | 118 R/plot_heatmap.R | 266 - R/plot_stats.R | 298 +- R/plot_ts.R | 188 - R/prettyNumbers.R | 68 R/savePlotAsPng.R | 68 R/setInteractivity.R | 54 R/stack.R | 238 - R/stack_aliases.R | 150 - R/stack_exchanges.R | 334 +- R/stack_prod.R | 674 ++-- inst/htmlwidgets/leafletDragPoints.js | 140 - inst/htmlwidgets/leafletDragPoints.yaml | 30 inst/htmlwidgets/lib/font-awesome-4.6.3/css/font-awesome.min.css | 6 inst/htmlwidgets/lib/font-awesome-4.6.3/fonts/fontawesome-webfont.svg | 1368 +++++----- inst/htmlwidgets/lib/leaflet-0.7.7/leaflet.css | 958 +++---- inst/htmlwidgets/lib/leaflet-0.7.7/leaflet.js | 16 inst/htmlwidgets/lib/markers/leaflet-vector-markers.css | 108 tests/testthat.R | 8 tests/testthat/helper-init.R | 46 tests/testthat/test-catColorPal.R | 86 tests/testthat/test-continuousColorPal.R | 138 - tests/testthat/test-get_data_for_comp.R | 72 37 files changed, 4601 insertions(+), 4595 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-05 0.2.2
Title: Summarizing Distributions of Latent Structures
Description: Summaries of distributions on clusterings and feature allocations are provided. Specifically, point estimates are obtained by the sequentially-allocated latent structure optimization (SALSO) algorithm to minimize squared error loss, absolute error loss, Binder loss, or the lower bound of the variation of information loss. Clustering uncertainty can be assessed with the confidence calculations and the associated plot.
Author: David B. Dahl [aut, cre],
Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between sdols versions 1.3 dated 2017-12-01 and 1.4 dated 2017-12-05
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 12 ++++++++++++ R/dlso.R | 9 ++++++--- R/salso.R | 18 +++++++++++++----- inst/java/scala-2.11/sdols.jar |binary inst/java/scala-2.12/sdols.jar |binary java/sdols-sources.jar |binary man/dlso.Rd | 5 ++++- man/salso.Rd | 9 ++++++++- 10 files changed, 56 insertions(+), 23 deletions(-)
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.4.1 dated 2017-06-19 and 0.4.2 dated 2017-12-05
DESCRIPTION | 32 +++++++++++--------------------- MD5 | 8 ++++---- NEWS | 6 +++++- R/sticker.R | 4 ++-- README.md | 10 +++------- 5 files changed, 25 insertions(+), 35 deletions(-)
Title: Event Data Repository
Description: Event dataset repository including both real-life and artificial event logs. They can be used in combination with functionalities provided by the 'bupaR' packages 'edeaR', 'processmapR', etc.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between eventdataR versions 0.1.1 dated 2017-09-03 and 0.1.2 dated 2017-12-05
eventdataR-0.1.1/eventdataR/data/BPIC15_1_imported.rda |only eventdataR-0.1.1/eventdataR/data/csv_example.rda |only eventdataR-0.1.1/eventdataR/data/datalist |only eventdataR-0.1.1/eventdataR/data/example_log.rda |only eventdataR-0.1.1/eventdataR/man/BPIC15_1_imported.Rd |only eventdataR-0.1.1/eventdataR/man/csv_example.Rd |only eventdataR-0.1.2/eventdataR/DESCRIPTION | 14 ++--- eventdataR-0.1.2/eventdataR/MD5 | 26 +++------ eventdataR-0.1.2/eventdataR/R/datasets_documentation.R | 27 ---------- eventdataR-0.1.2/eventdataR/data/BPIC14_incident_case_attributes.rda |binary eventdataR-0.1.2/eventdataR/data/BPIC14_incident_log.rda |binary eventdataR-0.1.2/eventdataR/data/BPIC15_1.rda |binary eventdataR-0.1.2/eventdataR/data/patients.rda |binary eventdataR-0.1.2/eventdataR/data/sepsis.rda |binary eventdataR-0.1.2/eventdataR/inst/doc/eventdataR.html | 4 - eventdataR-0.1.2/eventdataR/man/example_log.Rd | 9 --- eventdataR-0.1.2/eventdataR/man/sepsis.Rd | 1 17 files changed, 23 insertions(+), 58 deletions(-)
Title: Bayesian Nonparametric Modeling in R
Description: Functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Linear Dependent Tailfree Processes, Mixtures of
Triangular distributions, Random Bernstein polynomials priors
and Dependent Bernstein Polynomials. The package also includes
models considering Penalized B-Splines.
Includes semiparametric models for marginal and conditional
density estimation, ROC curve analysis, interval censored data,
binary regression models, generalized linear mixed models, IRT
type models, and generalized additive models. Also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the 'coda' package.
Author: Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando
Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Maintainer: ORPHANED
Diff between DPpackage versions 1.1-7 dated 2017-09-14 and 1.1-7.1 dated 2017-12-05
DESCRIPTION | 8 MD5 | 188 ++++++++--------- src/BDPdensity.f | 40 +-- src/CSDPbinaryl.f | 104 ++++----- src/DPMdencens.f | 78 +++---- src/DPMglmmgam.f | 110 +++++----- src/DPMglmmlogit.f | 94 ++++---- src/DPMglmmpois.f | 92 ++++---- src/DPMglmmprob.f | 70 +++--- src/DPMlm.f | 62 ++--- src/DPMlmm.f | 72 +++--- src/DPMmeta.f | 58 ++--- src/DPMolmmp.f | 72 +++--- src/DPMrasch.f | 70 +++--- src/DPMraschpoisson.f | 86 ++++---- src/DPMraschpoissonh.f | 76 +++---- src/DPbetabinom.f | 52 ++-- src/DPbinaryc.f | 60 ++--- src/DPbinaryl.f | 60 ++--- src/DPbinaryp.f | 60 ++--- src/DPbivdensityg.f | 54 ++--- src/DPbivdensityn.f | 54 ++--- src/DPdensityg.f | 56 ++--- src/DPdensityn.f | 48 ++-- src/DPdensityreg.f | 124 +++++------ src/DPglmmgam.f | 100 ++++----- src/DPglmmlogit.f | 78 +++---- src/DPglmmlogita.f | 78 +++---- src/DPglmmpois.f | 76 +++---- src/DPglmmprob.f | 66 +++--- src/DPlmm.f | 66 +++--- src/DPmeta.f | 50 ++-- src/DPmultmeta.f | 45 ++-- src/DPolmmp.f | 69 +++--- src/DPrasch.f | 72 +++--- src/DPraschpoisson.f | 74 +++--- src/DPsurvint.f | 47 ++-- src/FPTbinaryl.f | 69 +++--- src/HDPMcdensity.f | 94 ++++---- src/HDPMdensity.f | 68 +++--- src/LDBDPdensity.f | 154 +++++++------- src/LDDPdensity.f | 175 ++++++++-------- src/LDDPrasch.f | 118 +++++------ src/LDDPraschpoisson.f | 118 +++++------ src/LDDPsurvival.f | 167 +++++++-------- src/LDDPtwopl.f | 162 +++++++-------- src/LDPDdoublyintsba.f | 286 +++++++++++++------------- src/LDTFPdensity.f | 154 +++++++------- src/LDTFPglmmpois.f | 166 +++++++-------- src/LDTFPsurvival.f | 156 +++++++------- src/PSgamgam.f | 104 ++++----- src/PSgamgauss.f | 80 +++---- src/PSgamlogit.f | 86 ++++---- src/PSgampois.f | 86 ++++---- src/PSgamprob.f | 78 +++---- src/PTglmmgam.f | 118 +++++------ src/PTglmmlogit.f | 112 +++++----- src/PTglmmpois.f | 112 +++++----- src/PTglmmprob.f | 104 ++++----- src/PTlm.f | 89 ++++---- src/PTlmm.f | 104 ++++----- src/PTlmp.f | 89 ++++---- src/PTmdensity.f | 79 +++---- src/PTmdensityf.f | 136 ++++++------ src/PTmdensityp.f | 79 +++---- src/PTmeta.f | 92 ++++---- src/PTolmmp.f | 101 ++++----- src/PTrasch.f | 120 +++++------ src/PTraschpoisson.f | 136 ++++++------ src/PTsurv.f | 135 ++++++------ src/PTudensity.f | 46 ++-- src/PTudensityp.f | 52 ++-- src/Pbinary.f | 36 +-- src/Plm.f | 34 +-- src/TDPdensity.f | 38 +-- src/TDPdensitypl.f | 44 ++-- src/ToolsBDP.f | 34 +-- src/ToolsDDP.f | 106 ++++----- src/ToolsDP.f | 4 src/ToolsDPM.f | 45 ++-- src/ToolsDistributions.f | 92 ++++---- src/ToolsHMM.f | 48 ++-- src/ToolsIntegrate.f | 6 src/ToolsLDTFP.f | 390 ++++++++++++++++++------------------ src/ToolsMatrix.f | 48 ++-- src/ToolsPT.f | 502 +++++++++++++++++++++++------------------------ src/ToolsPTsampler.f | 48 ++-- src/ToolsPolynomials.f | 14 - src/ToolsRSBA.f | 146 ++++++------- src/ToolsRnumbers.f | 151 +++++++------- src/ToolsSB.f | 34 +-- src/ToolsSlice.f | 66 +++--- src/ToolsStat.f | 6 src/ToolsSweep.f | 8 src/ToolsTDP.f | 22 +- 95 files changed, 4327 insertions(+), 4289 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty.
Supported model families include cumulative probability, stopping ratio,
continuation ratio, and adjacent category. These families are a subset of
vector glm's which belong to a model class we call the elementwise link
multinomial-ordinal (ELMO) class. Each family in this class links a vector
of covariates to a vector of class probabilities. Each of these families
has a parallel form, which is appropriate for ordinal response data, as
well as a nonparallel form that is appropriate for an unordered categorical
response, or as a more flexible model for ordinal data. The parallel model
has a single set of coefficients, whereas the nonparallel model has a set of
coefficients for each response category except the baseline category. It is
also possible to fit a model with both parallel and nonparallel terms, which
we call the semi-parallel model. The semi-parallel model has the flexibility
of the nonparallel model, but the elastic net penalty shrinks it toward the
parallel model. For details, refer to Wurm, Hanlon, and Rathouz (2017)
<arXiv:1706.05003>.
Author: Michael Wurm [aut, cre],
Paul Rathouz [aut],
Bret Hanlon [aut]
Maintainer: Michael Wurm <wurm@uwalumni.com>
Diff between ordinalNet versions 2.3 dated 2017-10-03 and 2.4 dated 2017-12-05
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Non-Homogeneous Markov Switching Autoregressive Models
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations. Penalization methods are implemented for Markov Switching Vector Autoregressive Models of order 1 only. Most functions of the package handle missing values.
Author: Valerie Monbet
Maintainer: Valerie Monbet <valerie.monbet@gmail.com>
Diff between NHMSAR versions 1.6 dated 2017-08-31 and 1.7 dated 2017-12-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Mstep.nh.MSAR.VM.R | 12 ++++++------ R/cross.cor.MSAR.R | 4 ++-- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.1.5 dated 2017-11-15 and 1.1.6 dated 2017-12-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/network_permutation.R | 30 ++++++++++++++++++++++++++---- R/network_swap.R | 34 +++++++++++++++++++++++++++++----- man/asnipe-package.Rd | 4 ++-- man/network_swap.Rd | 9 ++++++--- 6 files changed, 72 insertions(+), 23 deletions(-)