Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between StereoMorph versions 1.6.1 dated 2017-03-14 and 1.6.2 dated 2018-10-09
DESCRIPTION | 10 +- MD5 | 35 +++++----- NAMESPACE | 1 R/alignLandmarksToMidline.R | 55 ++++++++++++---- R/avectors.R | 7 +- R/btShapes.R |only R/calibrateCameras.R | 15 ++-- R/distancePointToPlane.R |only R/estimateDLTCoefficients.R | 3 R/extractFrames.R | 2 R/pointsAtEvenSpacing.R | 6 - R/polyArea.R |only R/reconstructStereoSets.R | 11 +-- R/reflectMissingLandmarks.R | 52 +++++++++++++-- inst/CITATION | 4 - inst/extdata/apps/digitizeImages/session_parameters.txt | 2 inst/extdata/apps/digitizeImages/www/digitize_image.js | 2 man/StereoMorph-package.Rd | 7 +- man/alignLandmarksToMidline.Rd | 3 man/extractFrames.Rd | 2 20 files changed, 155 insertions(+), 62 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets
typically used with the 'Gene Set Enrichment Analysis' (GSEA) software
(Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015
<doi:10.1016/j.cels.2015.12.004>) in a standard R data frame with key-value
pairs. Included are the original human gene symbols and Entrez IDs as well
as the equivalents for various frequently studied model organisms such as
mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 6.1.1 dated 2018-04-12 and 6.2.1 dated 2018-10-09
DESCRIPTION | 20 ++++--- MD5 | 24 ++++---- NEWS.md | 4 + R/functions.R | 4 - R/sysdata.rda |binary README.md | 91 ++++----------------------------- build/vignette.rds |binary inst/doc/msigdbr-intro.R | 11 ++++ inst/doc/msigdbr-intro.Rmd | 53 +++++++++++++------ inst/doc/msigdbr-intro.html | 121 ++++++++++++++++++++++++++------------------ man/msigdbr.Rd | 7 +- man/msigdbr_show_species.Rd | 4 - vignettes/msigdbr-intro.Rmd | 53 +++++++++++++------ 13 files changed, 203 insertions(+), 189 deletions(-)
Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare
the execution time of R expressions.
Author: Olaf Mersmann [aut],
Claudia Beleites [ctb],
Rainer Hurling [ctb],
Ari Friedman [ctb],
Joshua M. Ulrich [cre]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between microbenchmark versions 1.4-4 dated 2018-01-24 and 1.4-5 dated 2018-10-09
DESCRIPTION | 12 +++++--- MD5 | 23 ++++++++------- NAMESPACE | 4 ++ R/autoplot.R | 2 - R/internal.R | 2 - R/microbenchmark.R | 28 +++++++++++++++---- R/zzz.R |only configure.ac | 28 ------------------- inst/tests/test_regression.R | 59 ++++++++++++++++++++++++++++++++++++++--- man/autoplot.microbenchmark.Rd | 4 +- man/microbenchmark.Rd | 16 +++++++++-- src/init.c | 4 +- src/nanotimer.c | 5 ++- 13 files changed, 125 insertions(+), 62 deletions(-)
More information about microbenchmark at CRAN
Permanent link
Title: Bayesian Modeling via Frequentist Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>
Diff between BayesGOF versions 5.1 dated 2018-10-05 and 5.2 dated 2018-10-09
DESCRIPTION | 8 MD5 | 30 - R/DS.Finite.Bayes.R | 29 + R/DS.micro.inf.bbu.R | 2 R/DS.micro.inf.nnu.R | 2 R/DS.micro.inf.pge.R | 2 R/DS.micro.inf.pgu.R | 2 R/plot.DS_FB_obj.R | 29 + R/print.DS_FB_obj.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette_BayesGOF.Rmd | 28 - inst/doc/vignette_BayesGOF.html | 864 +++++++++++++++++++--------------------- man/DS.Finite.Bayes.Rd | 2 man/DS.micro.inf.Rd | 10 vignettes/vignette_BayesGOF.Rmd | 28 - 16 files changed, 538 insertions(+), 500 deletions(-)
Title: Build and Grade Multiple Choice Exams with Randomized Content
Description: Using as input a 'LaTeX' file with a multiple choice exam, this package will produce several versions with randomized contents of the same exam. Functions for grading are also available.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between RndTexExams versions 1.4.1 dated 2018-01-13 and 1.5 dated 2018-10-09
RndTexExams-1.4.1/RndTexExams/R/rte_test_cheating.R |only RndTexExams-1.4.1/RndTexExams/inst/doc/rte-vignette_testing_cheating.R |only RndTexExams-1.4.1/RndTexExams/inst/doc/rte-vignette_testing_cheating.Rmd |only RndTexExams-1.4.1/RndTexExams/inst/doc/rte-vignette_testing_cheating.html |only RndTexExams-1.4.1/RndTexExams/man/rte.test.cheating.Rd |only RndTexExams-1.4.1/RndTexExams/vignettes/rte-vignette_testing_cheating.Rmd |only RndTexExams-1.5/RndTexExams/DESCRIPTION | 12 +++--- RndTexExams-1.5/RndTexExams/MD5 | 16 ++------ RndTexExams-1.5/RndTexExams/NAMESPACE | 2 - RndTexExams-1.5/RndTexExams/NEWS.md | 4 ++ RndTexExams-1.5/RndTexExams/build/vignette.rds |binary RndTexExams-1.5/RndTexExams/inst/doc/rte-vignette_creating_exams.html | 19 +++------- 12 files changed, 22 insertions(+), 31 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.11 dated 2018-07-17 and 0.12 dated 2018-10-09
DESCRIPTION | 17 ++++++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 1 - NEWS | 5 +++++ R/eval.r | 2 +- R/parse.r | 8 ++++++-- R/replay.r | 10 +++++----- R/traceback.r | 6 +++--- R/watcher.r | 4 ++-- man/is.message.Rd | 5 ----- 10 files changed, 41 insertions(+), 35 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph],
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph],
MDPI [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.5 dated 2018-07-06 and 0.6 dated 2018-10-09
/tmp/cranberry7b2c281232eb/rticles-0.5/rticles/inst/rmarkdown/templates/sim_article/resources/WileyNJD-v2.cls |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/DESCRIPTION | 20 + /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/MD5 | 85 +++++-- /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/NAMESPACE | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/NEWS | 13 + /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/R/biometrics_article.R |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/R/copernicus_article.R |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/R/rjournal_article.R | 2 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/R/rsos_article.R | 2 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/R/sage_article.R |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/README.md | 19 + /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/acm_article/resources/template.tex | 8 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/acm_article/skeleton/skeleton.Rmd | 2 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/biometrics_article |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/copernicus_article |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/elsevier_article/resources/template.tex | 2 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/ieee_article/resources/template.tex | 114 ++++++++-- /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/ieee_article/skeleton/skeleton.Rmd | 51 +++- /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/jss_article/skeleton/jss.cls | 6 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/mdpi_article/skeleton/mdpi.cls | 6 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/mnras_article/skeleton/mnras.cls | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/rsos_article/resources/template.tex | 16 - /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/rsos_article/skeleton/rsos.cls | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/rsos_article/skeleton/skeleton.Rmd | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/rss_article/resources/template.tex | 2 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/rss_article/skeleton/skeleton.Rmd | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/inst/rmarkdown/templates/sage_article |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/acs_article.Rd | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/aea_article.Rd | 3 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/ams_article.Rd | 3 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/biometrics_article.Rd |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/copernicus_article.Rd |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/ieee_article.Rd | 6 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/plos_article.Rd | 3 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/rsos_article.Rd | 4 /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/man/sage_article.Rd |only /tmp/cranberry7b2c281232eb/rticles-0.6/rticles/tests/testit/test-formats.R | 3 rticles/inst/rmarkdown/templates/sim_article/skeleton/WileyNJD-v2.cls | 4 38 files changed, 289 insertions(+), 109 deletions(-)
Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimates are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 0.5.1 dated 2018-06-25 and 0.5.2 dated 2018-10-09
DESCRIPTION | 8 ++++---- MD5 | 50 +++++++++++++++++++++++++------------------------- R/FixNA.R | 15 +++++++++++---- R/LADLEinternal.R | 4 ++-- R/PVC.R | 15 +++++++++++---- R/SOBIladle.R | 2 +- R/gFOBI.R | 15 +++++++++++---- R/gJADE.R | 15 +++++++++++---- R/gSOBI.R | 22 +++++++++++++++------- R/vSOBI.R | 15 +++++++++++---- inst/ChangeLog | 7 +++++++ man/AMUSEasymp.Rd | 7 ++++--- man/AMUSEboot.Rd | 18 +++++++++--------- man/AMUSEladle.Rd | 6 +++--- man/FixNA.Rd | 9 ++++++--- man/PVC.Rd | 11 +++++++---- man/SOBIasymp.Rd | 7 ++++--- man/SOBIboot.Rd | 30 ++++++++++++++---------------- man/SOBIladle.Rd | 14 +++++++------- man/gFOBI.Rd | 15 +++++++++------ man/gJADE.Rd | 15 +++++++++------ man/gSOBI.Rd | 11 +++++++---- man/lbtest.Rd | 2 +- man/tsBSS-package.Rd | 15 ++++++++------- man/tssdr.Rd | 4 ++-- man/vSOBI.Rd | 11 +++++++---- 26 files changed, 206 insertions(+), 137 deletions(-)
Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis
are included in this package. In particular, it computes standard errors for
parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>
Diff between EFAutilities versions 1.2.2 dated 2018-05-21 and 1.2.3 dated 2018-10-09
EFAutilities-1.2.2/EFAutilities/R/CIs20170808_c.R |only EFAutilities-1.2.2/EFAutilities/R/efa20171208_c.R |only EFAutilities-1.2.3/EFAutilities/DESCRIPTION | 8 EFAutilities-1.2.3/EFAutilities/MD5 | 14 EFAutilities-1.2.3/EFAutilities/NEWS.md | 3 EFAutilities-1.2.3/EFAutilities/R/CIs20171005_c.R |only EFAutilities-1.2.3/EFAutilities/R/ModelTest20170816_c.R | 374 ++++++------- EFAutilities-1.2.3/EFAutilities/R/PolycorGamma20161107_c.R | 3 EFAutilities-1.2.3/EFAutilities/R/efa20181005_c.R |only EFAutilities-1.2.3/EFAutilities/R/efaMR20170811.R | 62 ++ 10 files changed, 265 insertions(+), 199 deletions(-)
Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from
international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Author: Daniel Caro <dcarov@gmail.com>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <dcarov@gmail.com>
Diff between intsvy versions 2.2 dated 2018-09-20 and 2.3 dated 2018-10-09
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 ++ R/intsvy.select.merge.R | 4 ++-- R/intsvy.var.label.R | 4 ++-- R/pirls.table.R | 11 +++++++++++ man/intsvy-package.Rd | 4 ++-- man/pirls.table.Rd | 1 + 8 files changed, 32 insertions(+), 18 deletions(-)
More information about RGoogleAnalytics at CRAN
Permanent link
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Diff between bayou versions 2.1 dated 2018-06-07 and 2.1.1 dated 2018-10-09
bayou-2.1.1/bayou/DESCRIPTION | 8 bayou-2.1.1/bayou/MD5 | 27 +- bayou-2.1.1/bayou/NAMESPACE | 2 bayou-2.1.1/bayou/R/bayou-deprecated.R |only bayou-2.1.1/bayou/R/bayou-likelihood.R | 2 bayou-2.1.1/bayou/R/bayou-mcmc-utilities.R | 2 bayou-2.1.1/bayou/R/bayou-mcmc.R | 19 + bayou-2.1.1/bayou/man/bayou-deprecated.Rd |only bayou-2.1.1/bayou/man/bayou.lik.Rd | 2 bayou-2.1.1/bayou/man/load.bayou.Rd | 2 bayou-2.1.1/bayou/man/make.prior.Rd | 30 +- bayou-2.1.1/bayou/man/plotRegimes.Rd | 1 bayou-2.1.1/bayou/man/pull.pars.Rd | 14 - bayou-2.1.1/bayou/src/RcppExports.cpp | 4 bayou-2.1.1/bayou/src/branches.cpp | 310 ++++++++++++++--------------- bayou-2.1/bayou/man/bayou.mcmc.Rd |only 16 files changed, 217 insertions(+), 206 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using
state space models. The first implemented model is described in Fahrmeir
(1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the
Extended Kalman filter is replaced by an unscented Kalman filter and other
options including particle filters. The implemented particle filters support
more general state space models.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.5.3 dated 2018-07-01 and 0.6.0 dated 2018-10-09
DESCRIPTION | 9 MD5 | 263 +- NAMESPACE | 6 NEWS.md | 11 R/PF.R | 1014 ++++++++-- R/RcppExports.R | 24 R/boot_est.R | 5 R/ddhazard.R | 540 +++-- R/get_design_matrix.R | 119 + R/hatvalues.R | 3 R/loglike.R | 3 R/plot.R | 26 R/predict.R | 3 R/residuals.R | 2 R/static_glm.R | 59 inst/doc/Bootstrap_illustration.pdf |binary inst/doc/Comparing_methods_for_logistic_models.R | 50 inst/doc/Comparing_methods_for_logistic_models.Rmd | 63 inst/doc/Comparing_methods_for_logistic_models.pdf |binary inst/doc/Diagnostics.R | 20 inst/doc/Diagnostics.Rmd | 20 inst/doc/Diagnostics.pdf |binary inst/doc/Particle_filtering.pdf |binary inst/doc/ddhazard.pdf |binary inst/shiny/app.R | 11 man/PF_EM.Rd | 278 ++ man/PF_control.Rd | 9 man/PF_forward_filter.Rd |only man/ddFixed.Rd | 7 man/ddhazard.Rd | 41 man/ddhazard_boot.Rd | 2 man/ddhazard_control.Rd |only man/get_Q_0.Rd |only man/get_survival_case_weights_and_data.Rd | 6 man/hatvalues.ddhazard.Rd | 2 man/logLik.ddhazard.Rd | 2 man/plot.PF_clouds.Rd | 5 man/plot.ddhazard.Rd | 2 man/predict.ddhazard.Rd | 2 man/residuals.ddhazard.Rd | 2 man/static_glm.Rd | 2 src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp | 2 src/Makevars | 4 src/Makevars.win | 6 src/PF.cpp | 229 +- src/PF/PF_data.h | 221 +- src/PF/PF_utils.cpp |only src/PF/PF_utils.h | 406 ---- src/PF/PFs.h | 211 -- src/PF/densities.h | 166 - src/PF/est_params.h |only src/PF/est_params_RW.cpp | 73 src/PF/est_params_dens.cpp |only src/PF/get_work_blocks.h |only src/PF/importance_samplers.h | 257 +- src/PF/resamplers.h | 94 src/PF/smoother_output.cpp | 2 src/PF/taylor_normal_approx.cpp |only src/PF_fixed_effects.cpp | 188 + src/RcppExports.cpp | 97 src/arma_BLAS_LAPACK.h | 4 src/bigglm_wrapper.cpp | 70 src/bigglm_wrapper.h | 14 src/ddhazard.h | 48 src/ddhazard/EKF_solver.cpp | 61 src/ddhazard/GMA_solver.cpp | 15 src/ddhazard/SMA_solver.cpp | 32 src/ddhazard/UKF_solver.cpp | 42 src/ddhazard_fit.cpp | 88 src/estimate_fixed_effects_M_step.cpp |only src/estimate_fixed_effects_M_step.h | 114 - src/family.cpp | 20 src/family.h | 171 + src/for_tests.cpp | 54 src/lin_maps.cpp | 78 src/lin_maps.h | 33 src/loglike.cpp | 45 src/parallel_glm.cpp | 2 src/parallel_qr.cpp | 3 src/parallel_qr.h | 1 src/problem_data.h | 35 src/utils.cpp | 8 tests/testthat.R | 2 tests/testthat/VAR_data.RDS |only tests/testthat/VAR_restrict_vs_non_data.RDS |only tests/testthat/helper.R | 3 tests/testthat/previous_results/AUX_normal_approx_w_cloud_mean_cloud_means.RDS |binary tests/testthat/previous_results/AUX_normal_approx_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/Brier_AUX_normal_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/PF_EM_print | 8 tests/testthat/previous_results/PF_VARS.RDS |only tests/testthat/previous_results/PF_VARS_non_zero_mean_inter.RDS |only tests/testthat/previous_results/PF_VARS_non_zero_mean_slope.RDS |only tests/testthat/previous_results/PF_head_neck_cloud_means.RDS |binary tests/testthat/previous_results/PF_head_neck_w_Brier_method_cloud_means.RDS |binary tests/testthat/previous_results/PF_normal_approx_w_cloud_mean_cloud_means.RDS |binary tests/testthat/previous_results/PF_normal_approx_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/bootstrap_filter_cloud_means.RDS |binary tests/testthat/previous_results/print_ddhazard | 2 tests/testthat/previous_results/print_ddhazard_UKF | 2 tests/testthat/previous_results/print_ddhazard_exp | 2 tests/testthat/previous_results/summary_ddhazard_UKF_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_UKF_print | 2 tests/testthat/previous_results/summary_ddhazard_all_coef_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_all_coef_print | 2 tests/testthat/previous_results/summary_ddhazard_exp_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_exp_print | 2 tests/testthat/previous_results/summary_ddhazard_fixed_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_fixed_print | 2 tests/testthat/previous_results/summary_ddhazard_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_one_coef_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_one_coef_print | 2 tests/testthat/previous_results/summary_ddhazard_one_digit_object.RDS |binary tests/testthat/previous_results/summary_ddhazard_one_digit_print | 2 tests/testthat/previous_results/summary_ddhazard_print | 2 tests/testthat/previous_results/survival_lung_example_cloud_means.RDS |binary tests/testthat/test_GMA.R | 91 tests/testthat/test_PF.R | 536 ++++- tests/testthat/test_SMA.R | 98 tests/testthat/test_UKF.R | 89 tests/testthat/test_bigglm_wrapper.R | 12 tests/testthat/test_boot_est.R | 21 tests/testthat/test_ddhazard_n_EKF.R | 158 + tests/testthat/test_design_mat_and_risk_obj.R | 51 tests/testthat/test_fixed_effects_in_E_step.R | 54 tests/testthat/test_fixed_effects_in_M_step.R | 61 tests/testthat/test_get_start_values.R |only tests/testthat/test_hatvalues.R | 6 tests/testthat/test_help_page_examples.R | 255 ++ tests/testthat/test_loglike.R | 58 tests/testthat/test_plot.R | 22 tests/testthat/test_predict.R | 13 tests/testthat/test_print.R | 20 tests/testthat/test_residuals.R | 49 tests/testthat/test_static_glm.R | 2 tests/testthat/test_summary.R | 8 tests/testthat/test_test_utils.R | 4 tests/testthat/test_weights.R | 13 vignettes/Comparing_methods_for_logistic_models.Rmd | 63 vignettes/Diagnostics.Rmd | 20 140 files changed, 4370 insertions(+), 2872 deletions(-)
Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate the
outputs of the two main components of the Canadian Forest Fire Danger Rating
System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and
the Fire Behaviour Prediction (FBP) System. Some functions have two versions,
table and raster based.
Author: Xianli Wang, Alan Cantin, Marc-André Parisien, Mike Wotton, Kerry
Anderson, Brett Moore, Tom Schiks, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>
Diff between cffdrs versions 1.7.6 dated 2017-04-06 and 1.8.1 dated 2018-10-09
DESCRIPTION | 22 ++++++++------- MD5 | 27 ++++++++++++------ NAMESPACE | 2 + R/direction.r |only R/fireSeason.r | 73 ++++++++++++++++++++++++++++++++++++++++++++++++-- R/lros.r |only R/pros.r |only data/test_lros.txt.gz |only data/test_pros.txt.gz |only man/cffdrs-package.Rd | 14 +++++---- man/fbp.Rd | 2 - man/fbpRaster.Rd | 2 - man/fireSeason.Rd | 11 ++++--- man/fwi.Rd | 2 - man/fwiRaster.Rd | 2 - man/lros.Rd |only man/pros.Rd |only man/test_lros.Rd |only man/test_pros.Rd |only 19 files changed, 122 insertions(+), 35 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between rjags versions 4-6 dated 2016-02-19 and 4-7 dated 2018-10-09
DESCRIPTION | 12 +++---- MD5 | 15 +++++---- NAMESPACE | 5 +-- R/jags.R | 81 +++++++++++++++++++++++++++++++++++++++++----------- R/mcarray.R | 42 +++++++++++++++++++------- R/utilities.R |only man/jags.samples.Rd | 18 +++++++++-- man/jags.version.Rd |only src/init.c |only src/jags.cc | 16 ++++------ 10 files changed, 135 insertions(+), 54 deletions(-)
Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>),
Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Cochrane Library (<http://www.cochranelibrary.com/>)
and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 2.0.0 dated 2018-09-10 and 2.0.1 dated 2018-10-09
DESCRIPTION | 15 MD5 | 34 - NAMESPACE | 11 NEWS | 17 R/biblioAnalysis.R | 6 R/citations.R | 2 R/convert2df.R | 8 R/networkPlot.R | 17 R/plotThematicEvolution.R |only R/rpys.R |only R/sourceGrowth.R |only R/summary.bibliometrix.R | 64 +- R/thematicEvolution.R | 151 +++--- build/partial.rdb |binary inst/biblioshiny/server.R | 817 ++++++++++++++++++++++++++---------- inst/biblioshiny/ui.R | 334 ++++++++++++-- inst/doc/bibliometrix-vignette.html | 63 +- man/plotThematicEvolution.Rd |only man/rpys.Rd |only man/sourceGrowth.Rd |only man/thematicEvolution.Rd | 39 - 21 files changed, 1150 insertions(+), 428 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-01 0.1.3
2016-10-04 0.1.2
2016-09-21 0.1.1
Title: Partition-Assisted Clustering and Multiple Alignments of
Networks
Description: Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.
Author: Ye Henry Li, Dangna Li
Maintainer: Ye Henry Li <hlowl2@gmail.com>
Diff between PAC versions 1.0.10 dated 2018-03-06 and 1.1.0 dated 2018-10-09
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between mindr versions 1.1.0 dated 2017-07-19 and 1.1.5 dated 2018-10-09
DESCRIPTION | 12 - LICENSE |only MD5 | 22 +- NAMESPACE | 3 R/foo.R | 299 +++++++++++++++++++++++++++++++------- inst/examples/md/bookdownplus1.md | 2 inst/examples/mm/bookdownplus.mm | 2 man/dir2.Rd |only man/markmap.Rd | 11 + man/md2mm.Rd | 8 - man/mdtxt2mmtxt.Rd |only man/outline.Rd | 8 - man/theme.Rd | 2 man/tree2mm.Rd |only 14 files changed, 294 insertions(+), 75 deletions(-)
Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between dglars versions 2.0.1 dated 2018-04-24 and 2.1.0 dated 2018-10-09
ChangeLog | 4 ++ DESCRIPTION | 16 ++------ MD5 | 56 ++++++++++++++-------------- NAMESPACE | 7 +-- R/AIC.dglars.R | 10 ++--- R/BIC.dglars.R | 2 - R/coef.dglars.R | 11 ++--- R/cvdglars.R | 2 - R/cvdglars.fit.R | 2 - R/dglars.fit.R | 26 ++++++------- R/gdf.R | 1 R/grcv.R |only R/logLik.dglars.R | 41 +++++++++++--------- R/make_summary_table.R | 6 +-- R/phihat.R | 26 ++++++++----- R/predict.dglars.R | 10 ++--- R/print.dglars.R | 2 - R/summary.dglars.R | 2 - man/AIC.dglars.Rd | 97 ++++++++++++++++++++++++++----------------------- man/coef.cvdglars.Rd | 15 +++++-- man/coef.dglars.Rd | 28 ++++++++------ man/cvdglars.Rd | 4 ++ man/dglars-package.Rd | 30 +++++++-------- man/grcv.Rd |only man/logLik.dglars.Rd | 55 +++++++++++++++++++++++---- man/phihat.Rd | 55 +++++++++++++++++---------- man/plot.cvdglars.Rd | 2 + man/plot.dglars.Rd | 4 ++ man/predict.dglars.Rd | 55 +++++++++++---------------- man/summary.dglars.Rd | 64 ++++++++++---------------------- 30 files changed, 341 insertions(+), 292 deletions(-)
Title: Nucleome Imaging Toolbox
Description: Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between nucim versions 1.0.0 dated 2016-12-05 and 1.0.6 dated 2018-10-09
DESCRIPTION | 19 +- MD5 | 98 ++++++----- NEWS | 8 R/classes.R | 2 R/colorsinclasses.R | 3 R/compute_distance2border.R | 2 R/dapimask_file.R | 2 R/find_spots.R | 2 R/splitchannels.R | 4 R/spots_combined.R | 6 README.md | 28 ++- build/vignette.rds |binary inst/CITATION |only inst/doc/DAPIclassification.Rmd | 158 ++++++++--------- inst/doc/DAPIclassification.html | 276 ++++++------------------------- inst/doc/publications.R |only inst/doc/publications.Rmd |only inst/doc/publications.html |only inst/doc/workflow.html |only inst/doc/workflow.html.asis |only inst/doc/workflow_many.Rmd |only inst/doc/workflow_many.html |only man/barplot_with_interval.Rd | 5 man/barplot_with_interval_23.Rd | 1 man/class.neighbours.Rd | 1 man/class.neighbours.folder.Rd | 1 man/classify.Rd | 1 man/classify.folder.Rd | 4 man/classify.single.Rd | 1 man/classify.table.Rd | 5 man/colors.in.classes.Rd | 7 man/colors.in.classes.folder.Rd | 1 man/compute.distance2border.Rd | 3 man/dapimask.Rd | 1 man/dapimask.file.Rd | 3 man/dapimask.folder.Rd | 1 man/find.spots.file.Rd | 5 man/find.spots.folder.Rd | 5 man/heatmap.color.Rd | 1 man/heatmap7.Rd | 1 man/nearestClassDistances.folder.Rd | 5 man/plot_classify.folder.Rd | 5 man/plot_colors.in.classes.folder.Rd | 1 man/plot_nearestClassDistances.folder.Rd | 1 man/splitchannel.Rd | 1 man/splitchannels.Rd | 3 man/splitchannels.file.Rd | 1 man/splitchannels.folder.Rd | 3 man/spots.combined.Rd | 3 man/spots.combined.file.Rd | 11 - man/spots.combined.folder.Rd | 3 man/t_colors.in.classes.folder.Rd | 1 vignettes/DAPIclassification.Rmd | 158 ++++++++--------- vignettes/workflow.html.asis |only vignettes/workflow_many.Rmd |only 55 files changed, 344 insertions(+), 507 deletions(-)
Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with
utility functions.
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>
Diff between funData versions 1.3-1 dated 2018-10-02 and 1.3-2 dated 2018-10-09
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 6 ++++++ 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time data.
Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>,
Lin et al. (2000) <doi:10.1111/1467-9868.00259>,
Wang et al. (2001) <doi:10.1198/016214501753209031>,
Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>,
Huang and Wang (2004) <doi:10.1198/016214504000001033>, and more.
Author: Sy Han (Steven) Chiou [aut, cre],
Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.1.4 dated 2018-05-30 and 1.1.5 dated 2018-10-09
reReg-1.1.4/reReg/R/readmission.R |only reReg-1.1.4/reReg/data |only reReg-1.1.4/reReg/man/readmission.Rd |only reReg-1.1.4/reReg/src/registerDynamicSymbol.c |only reReg-1.1.5/reReg/ChangeLog | 5 reReg-1.1.5/reReg/DESCRIPTION | 32 reReg-1.1.5/reReg/MD5 | 46 reReg-1.1.5/reReg/NAMESPACE | 30 reReg-1.1.5/reReg/R/plot.R | 695 +++++++---- reReg-1.1.5/reReg/R/reReg.R | 1621 ++++++++++++++------------ reReg-1.1.5/reReg/R/reReg_data.R |only reReg-1.1.5/reReg/R/reReg_pkg.R | 33 reReg-1.1.5/reReg/R/reSurv.R | 108 + reReg-1.1.5/reReg/R/simu.R |only reReg-1.1.5/reReg/R/summary.R | 27 reReg-1.1.5/reReg/inst |only reReg-1.1.5/reReg/man/plot.reReg.Rd | 43 reReg-1.1.5/reReg/man/plot.reSurv.Rd | 54 reReg-1.1.5/reReg/man/plotCSM.Rd |only reReg-1.1.5/reReg/man/plotEvents.Rd | 45 reReg-1.1.5/reReg/man/plotHaz.Rd | 32 reReg-1.1.5/reReg/man/plotRate.Rd | 32 reReg-1.1.5/reReg/man/reReg-package.Rd | 37 reReg-1.1.5/reReg/man/reReg.Rd | 166 +- reReg-1.1.5/reReg/man/reSurv.Rd | 29 reReg-1.1.5/reReg/man/simDat.Rd |only reReg-1.1.5/reReg/src/Ghosh.c | 232 +++ reReg-1.1.5/reReg/src/init.c |only reReg-1.1.5/reReg/src/reReg.c | 398 ++---- 29 files changed, 2211 insertions(+), 1454 deletions(-)
Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rmgarch versions 1.3-0 dated 2015-12-28 and 1.3-5 dated 2018-10-09
rmgarch-1.3-0/rmgarch/vignettes/The_rmgarch_models.tex |only rmgarch-1.3-5/rmgarch/ChangeLog | 109 rmgarch-1.3-5/rmgarch/DESCRIPTION | 10 rmgarch-1.3-5/rmgarch/MD5 | 87 rmgarch-1.3-5/rmgarch/NAMESPACE | 5 rmgarch-1.3-5/rmgarch/R/copula-fn.R | 434 - rmgarch-1.3-5/rmgarch/R/copula-methods.R | 1068 +-- rmgarch-1.3-5/rmgarch/R/gogarch-distributions.R | 20 rmgarch-1.3-5/rmgarch/R/gogarch-main.R | 1507 ++-- rmgarch-1.3-5/rmgarch/R/gogarch-methods.R | 5165 +++++++-------- rmgarch-1.3-5/rmgarch/R/rdcc-main.R | 182 rmgarch-1.3-5/rmgarch/R/rdcc-methods.R | 2684 +++---- rmgarch-1.3-5/rmgarch/R/rdcc-plots.R | 3211 ++++----- rmgarch-1.3-5/rmgarch/R/rmgarch-functions.R | 56 rmgarch-1.3-5/rmgarch/R/rmgarch-ica.R | 3260 ++++----- rmgarch-1.3-5/rmgarch/R/rmgarch-mmean.R | 1065 +-- rmgarch-1.3-5/rmgarch/R/rmgarch-scenario.R | 19 rmgarch-1.3-5/rmgarch/README.md | 10 rmgarch-1.3-5/rmgarch/build/vignette.rds |binary rmgarch-1.3-5/rmgarch/inst/doc/The_rmgarch_models.pdf |binary rmgarch-1.3-5/rmgarch/inst/rmgarch.tests/rmgarch.test1.R | 2206 +++--- rmgarch-1.3-5/rmgarch/inst/rmgarch.tests/rmgarch.test3.R | 3018 ++++---- rmgarch-1.3-5/rmgarch/inst/rmgarch.tests/rmgarch.test6.R |only rmgarch-1.3-5/rmgarch/man/DCCfilter-class.Rd | 170 rmgarch-1.3-5/rmgarch/man/DCCfit-class.Rd | 182 rmgarch-1.3-5/rmgarch/man/DCCforecast-class.Rd | 128 rmgarch-1.3-5/rmgarch/man/DCCroll-class.Rd | 139 rmgarch-1.3-5/rmgarch/man/DCCsim-class.Rd | 112 rmgarch-1.3-5/rmgarch/man/cGARCHfit-class.Rd | 136 rmgarch-1.3-5/rmgarch/man/cGARCHsim-class.Rd | 112 rmgarch-1.3-5/rmgarch/man/dccroll-methods.Rd | 5 rmgarch-1.3-5/rmgarch/man/goGARCHfilter-class.Rd | 328 rmgarch-1.3-5/rmgarch/man/goGARCHfit-class.Rd | 388 - rmgarch-1.3-5/rmgarch/man/goGARCHforecast-class.Rd | 364 - rmgarch-1.3-5/rmgarch/man/goGARCHroll-class.Rd | 210 rmgarch-1.3-5/rmgarch/man/goGARCHsim-class.Rd | 208 rmgarch-1.3-5/rmgarch/man/gogarchsim-methods.Rd | 99 rmgarch-1.3-5/rmgarch/man/rmgarch-package.Rd | 162 rmgarch-1.3-5/rmgarch/src/Makevars | 3 rmgarch-1.3-5/rmgarch/src/Makevars.win | 3 rmgarch-1.3-5/rmgarch/src/copulas.cpp | 4 rmgarch-1.3-5/rmgarch/src/ica.cpp | 2 rmgarch-1.3-5/rmgarch/src/ica.h | 1 rmgarch-1.3-5/rmgarch/src/init.c |only rmgarch-1.3-5/rmgarch/src/rdcc.cpp | 12 rmgarch-1.3-5/rmgarch/src/rmdist.h | 1 46 files changed, 13688 insertions(+), 13197 deletions(-)
Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to Bayesian Statistics, Bolstad, W.M. (2017), John Wiley & Sons ISBN 978-1-118-09156-2.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Bolstad versions 0.2-39 dated 2018-08-29 and 0.2-40 dated 2018-10-09
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/normgcp.r | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.2.0 dated 2018-08-14 and 1.3.0 dated 2018-10-09
DESCRIPTION | 7 +- MD5 | 32 +++++------ R/RcppExports.R | 8 -- R/align.R | 148 ++++++++++++++++++++++++++++++---------------------- R/aphid.R | 6 -- R/derivePHMM.R | 89 ++++++++++++++++++++----------- R/train.R | 79 ++++++++++++++++----------- R/utils.R | 83 +++++++++++++++++++++++------ R/weight.R | 88 +++++++++++++++++++++--------- README.md | 1 man/align.Rd | 16 +---- man/aphid.Rd | 6 -- man/derivePHMM.Rd | 18 ++---- man/train.Rd | 29 ++++------ man/weight.Rd | 54 +++++++++++------- src/RcppExports.cpp | 28 --------- src/utils.cpp | 119 ++--------------------------------------- 17 files changed, 406 insertions(+), 405 deletions(-)