Title: Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Description: A graphical user interface for interactive Markov chain Monte
Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
posterior sample. The interface is powered by RStudio's Shiny web
application framework and works with the output of MCMC programs written
in any programming language (and has extended functionality for Stan models
fit using the rstan and rstanarm packages).
Author: Jonah Gabry [aut, cre],
Stan Development Team [ctb],
Michael Andreae [ctb],
Michael Betancourt [ctb],
Bob Carpenter [ctb],
Yuanjun Gao [ctb],
Andrew Gelman [ctb],
Ben Goodrich [ctb],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between shinystan versions 2.1.0 dated 2016-01-06 and 2.2.0 dated 2016-05-24
shinystan-2.1.0/shinystan/R/array2shinystan.R |only shinystan-2.1.0/shinystan/R/as.shinystan.R |only shinystan-2.1.0/shinystan/R/chains2shinystan.R |only shinystan-2.1.0/shinystan/R/convenience.R |only shinystan-2.1.0/shinystan/R/eight_schools.R |only shinystan-2.1.0/shinystan/R/launch_shinystan_demo.R |only shinystan-2.1.0/shinystan/R/mcmc2shinystan.R |only shinystan-2.1.0/shinystan/R/model_code.R |only shinystan-2.1.0/shinystan/R/notes.R |only shinystan-2.1.0/shinystan/R/rename_model.R |only shinystan-2.1.0/shinystan/R/shinystan-class.R |only shinystan-2.1.0/shinystan/R/sso_info.R |only shinystan-2.1.0/shinystan/R/stan2shinystan.R |only shinystan-2.1.0/shinystan/R/stanreg2shinystan.R |only shinystan-2.1.0/shinystan/inst/ShinyStan/ggplot_fns_old.rda |only shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/utilities/ppcheck_names_descriptions.R |only shinystan-2.1.0/shinystan/man/eight_schools.Rd |only shinystan-2.1.0/shinystan/man/model_code.Rd |only shinystan-2.1.0/shinystan/man/notes.Rd |only shinystan-2.1.0/shinystan/man/sso_info.Rd |only shinystan-2.1.0/shinystan/tests/testthat/data_for_tests.R |only shinystan-2.1.0/shinystan/tests/testthat/test_manipulating_sso.R |only shinystan-2.1.0/shinystan/tests/testthat/test_options.R |only shinystan-2.2.0/shinystan/DESCRIPTION | 31 shinystan-2.2.0/shinystan/MD5 | 254 +++--- shinystan-2.2.0/shinystan/NAMESPACE | 7 shinystan-2.2.0/shinystan/NEWS.md |only shinystan-2.2.0/shinystan/R/deploy_shinystan.R | 164 +++- shinystan-2.2.0/shinystan/R/drop_parameters.R |only shinystan-2.2.0/shinystan/R/generate_quantity.R | 120 +-- shinystan-2.2.0/shinystan/R/launch_shinystan.R | 113 ++ shinystan-2.2.0/shinystan/R/misc.R | 174 ---- shinystan-2.2.0/shinystan/R/retrieve.R | 176 +++- shinystan-2.2.0/shinystan/R/shinystan-objects.R |only shinystan-2.2.0/shinystan/R/shinystan-package.R | 66 - shinystan-2.2.0/shinystan/R/sso-metadata.R |only shinystan-2.2.0/shinystan/R/update_sso.R | 84 +- shinystan-2.2.0/shinystan/R/zzz.R | 5 shinystan-2.2.0/shinystan/build/vignette.rds |binary shinystan-2.2.0/shinystan/data/eight_schools.rda |binary shinystan-2.2.0/shinystan/inst/ShinyStan/css/ShinyStan.css | 8 shinystan-2.2.0/shinystan/inst/ShinyStan/global.R | 17 shinystan-2.2.0/shinystan/inst/ShinyStan/global_utils.R | 260 +----- shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/gg_theme_elements.R | 97 +- shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/hmc_diagnostics_helpers.R | 88 +- shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/shinystan_helpers.R | 34 shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/summary_stats_helpers.R | 54 - shinystan-2.2.0/shinystan/inst/ShinyStan/html/accept_stat.html | 4 shinystan-2.2.0/shinystan/inst/ShinyStan/html/citation.html | 4 shinystan-2.2.0/shinystan/inst/ShinyStan/html/home_page_links.html | 31 shinystan-2.2.0/shinystan/inst/ShinyStan/html/mcse.html | 2 shinystan-2.2.0/shinystan/inst/ShinyStan/html/ndivergent.html | 56 - shinystan-2.2.0/shinystan/inst/ShinyStan/html/neff.html | 18 shinystan-2.2.0/shinystan/inst/ShinyStan/html/nleapfrog.html | 2 shinystan-2.2.0/shinystan/inst/ShinyStan/html/rhat.html | 6 shinystan-2.2.0/shinystan/inst/ShinyStan/html/stepsize.html | 6 shinystan-2.2.0/shinystan/inst/ShinyStan/html/treedepth.html | 15 shinystan-2.2.0/shinystan/inst/ShinyStan/server.R | 131 ++- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/debounce.R | 11 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ppcheck_helpers.R | 15 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_rep_vs_obs.R | 15 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_resids.R | 24 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_test_statistics.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/pp_utils.R | 73 + shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rep_vs_resid_rep.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rstanarm.R | 18 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/y_vs_avg_rep.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui/pp_get_y_and_yrep.R | 69 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/autocorr.R | 54 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/diagnostics.R | 392 +++++----- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/multitrace.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/rhat_neff_mcse.R | 96 +- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/summary_stats_sampler.R | 44 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ui/multitrace_customize.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/multiparameter_plot.R | 75 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/summary_stats.R | 18 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/summary_stats_latex.R | 50 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/ui/multiparam_selectize.R | 59 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/bivariate.R | 102 +- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/density.R | 144 ++- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/histogram.R | 62 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/multiview.R | 100 +- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/summary_stats_param.R | 35 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/trivariate.R | 76 - shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/ui/ui_trivariate_select_x.R | 10 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/extract_sso.R | 109 +- shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/make_param_list_with_groups_sort.R | 18 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/par_samps_reactive.R | 23 shinystan-2.2.0/shinystan/inst/ShinyStan/server_utils.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui.R | 274 +----- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_diagnose.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_estimate.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_explore.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_home.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_more_menu.R |only shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/about.R | 111 +- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/autocorr_customize.R | 75 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/bivariate_customize.R | 197 +++-- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/density_customize.R | 367 ++++++--- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_by_parameter.R | 28 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_customize.R | 55 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_help.R | 93 +- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_ndivergent.R | 16 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_sample.R | 40 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_stepsize.R | 15 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_treedepth.R | 34 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/dynamic_trace_helptext.R | 30 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/glossary.R | 92 +- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/help.R | 161 ++-- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/hist_customize.R | 81 +- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/model_code.R | 52 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/multiparam_customize.R | 152 ++- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/notepad.R | 50 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_about.R | 68 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_navlist.R | 216 +++-- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_navlist_rstanarm.R | 151 ++- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/rhat_neff_mcse_layout.R | 133 ++- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/sampler_stats_customize.R | 57 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_customize.R | 47 - shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_latex_main.R | 14 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_latex_sidebar.R | 71 + shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/trivariate_customize.R | 110 +- shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/trivariate_select.R | 31 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_utils.R |only shinystan-2.2.0/shinystan/inst/doc/deploy_shinystan.Rmd | 19 shinystan-2.2.0/shinystan/inst/doc/deploy_shinystan.html | 75 + shinystan-2.2.0/shinystan/inst/doc/shinystan-package.Rmd | 4 shinystan-2.2.0/shinystan/inst/doc/shinystan-package.html | 88 +- shinystan-2.2.0/shinystan/man/as.shinystan.Rd | 205 +++-- shinystan-2.2.0/shinystan/man/deploy_shinystan.Rd | 31 shinystan-2.2.0/shinystan/man/drop_parameters.Rd |only shinystan-2.2.0/shinystan/man/generate_quantity.Rd | 49 - shinystan-2.2.0/shinystan/man/launch_shinystan.Rd | 35 shinystan-2.2.0/shinystan/man/launch_shinystan_demo.Rd | 32 shinystan-2.2.0/shinystan/man/rename_model.Rd | 24 shinystan-2.2.0/shinystan/man/retrieve.Rd | 46 - shinystan-2.2.0/shinystan/man/shinystan-class.Rd | 50 - shinystan-2.2.0/shinystan/man/shinystan-metadata.Rd |only shinystan-2.2.0/shinystan/man/shinystan-package.Rd | 57 - shinystan-2.2.0/shinystan/man/update_sso.Rd | 27 shinystan-2.2.0/shinystan/tests/testthat/data_for_retrieve_tests.R |only shinystan-2.2.0/shinystan/tests/testthat/old_sso_for_tests.rda |only shinystan-2.2.0/shinystan/tests/testthat/stanfit2_for_tests.rda |only shinystan-2.2.0/shinystan/tests/testthat/test_creating_sso.R | 164 +++- shinystan-2.2.0/shinystan/tests/testthat/test_deploy_shinystan.R |only shinystan-2.2.0/shinystan/tests/testthat/test_misc.R |only shinystan-2.2.0/shinystan/tests/testthat/test_using_sso.R |only shinystan-2.2.0/shinystan/vignettes/deploy_shinystan.Rmd | 19 shinystan-2.2.0/shinystan/vignettes/shinystan-package.Rmd | 4 149 files changed, 4144 insertions(+), 3405 deletions(-)
Title: Graphing Nonlinear Relations Among Latent Variables from
Structural Equation Mixture Models
Description: Contains a graphical user interface to generate the diagnostic
plots proposed by Bauer (2005) and Pek & Chalmers (2015) to investigate
nonlinear bivariate relationships in latent regression models using structural
equation mixture models (SEMMs).
Author: Bethany Kok [aut],
Jolynn Pek [aut],
Sonya Sterba [ctb],
Dan Bauer [ctb],
Phil Chalmers [cre, aut]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between plotSEMM versions 2.1 dated 2015-10-04 and 2.2 dated 2016-05-24
DESCRIPTION | 29 +++++++++++++++-------------- MD5 | 14 +++++++------- NAMESPACE | 2 +- man/plotSEMM.Rd | 2 +- man/plotSEMM_GUI.Rd | 4 ++-- man/plotSEMM_contour.Rd | 18 +++++++++--------- man/plotSEMM_probability.Rd | 2 +- man/plotSEMM_setup.Rd | 2 +- 8 files changed, 37 insertions(+), 36 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Future versions will include functionality for the Ar-Ar, Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, including isochrons, age spectra, ternary diagrams, kernel density estimates, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 0.2 dated 2016-05-05 and 0.3 dated 2016-05-24
IsoplotR-0.2/IsoplotR/man/I.A.Rd |only IsoplotR-0.2/IsoplotR/man/get.covmat.Rd |only IsoplotR-0.2/IsoplotR/man/get.ellipse.Rd |only IsoplotR-0.2/IsoplotR/man/get.ratios.Rd |only IsoplotR-0.3/IsoplotR/DESCRIPTION | 8 - IsoplotR-0.3/IsoplotR/MD5 | 37 ++++-- IsoplotR-0.3/IsoplotR/NAMESPACE | 19 ++- IsoplotR-0.3/IsoplotR/R/UPb.R | 130 ++++++++++++----------- IsoplotR-0.3/IsoplotR/R/concordia.R | 142 +++++++++++++++++-------- IsoplotR-0.3/IsoplotR/R/constants.R | 153 ++++++++++++++-------------- IsoplotR-0.3/IsoplotR/R/discordia.R |only IsoplotR-0.3/IsoplotR/R/errorellipse.R | 4 IsoplotR-0.3/IsoplotR/R/io.R | 15 ++ IsoplotR-0.3/IsoplotR/R/json.R |only IsoplotR-0.3/IsoplotR/R/regression.R |only IsoplotR-0.3/IsoplotR/R/toolbox.R | 49 +------- IsoplotR-0.3/IsoplotR/R/zzz.R |only IsoplotR-0.3/IsoplotR/data/UPb.rda |binary IsoplotR-0.3/IsoplotR/inst/constants.json |only IsoplotR-0.3/IsoplotR/man/I.R.Rd |only IsoplotR-0.3/IsoplotR/man/concordia.age.Rd |only IsoplotR-0.3/IsoplotR/man/concordia.plot.Rd | 10 + IsoplotR-0.3/IsoplotR/man/discordia.age.Rd |only IsoplotR-0.3/IsoplotR/man/ellipse.Rd |only IsoplotR-0.3/IsoplotR/man/lambda.Rd | 20 ++- IsoplotR-0.3/IsoplotR/man/settings.Rd |only IsoplotR-0.3/IsoplotR/man/yorkfit.Rd |only 27 files changed, 327 insertions(+), 260 deletions(-)
Title: Google Analytics API into R
Description: R library for interacting with the Google Analytics
Reporting API v3 and v4.
Author: Mark Edmondson [aut, cre],
Artem Klevtsov [ctb],
Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAnalyticsR versions 0.1.0 dated 2016-05-12 and 0.1.1 dated 2016-05-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/ga_v4_get.R | 4 ++-- README.md | 10 +++++----- inst/doc/googleAnalyticsR.html | 4 ++-- 6 files changed, 22 insertions(+), 18 deletions(-)
More information about googleAnalyticsR at CRAN
Permanent link
Title: Programmatic Interface to the API Serving UC Berkeley's Natural
History Data
Description: The ecoengine provides access to more than 5 million georeferenced
specimen records from the University of California, Berkeley's Natural History
Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>
Diff between ecoengine versions 1.9.1 dated 2015-03-30 and 1.10.0 dated 2016-05-24
ecoengine-1.10.0/ecoengine/DESCRIPTION | 21 +-- ecoengine-1.10.0/ecoengine/LICENSE |only ecoengine-1.10.0/ecoengine/MD5 | 59 ++++----- ecoengine-1.10.0/ecoengine/NAMESPACE | 6 ecoengine-1.10.0/ecoengine/NEWS | 6 ecoengine-1.10.0/ecoengine/R/ecoengine_package.R | 1 ecoengine-1.10.0/ecoengine/R/ee_browse_photos.R | 9 - ecoengine-1.10.0/ecoengine/R/ee_checklists.R | 104 ++++++++++------ ecoengine-1.10.0/ecoengine/R/ee_observations.R | 23 +-- ecoengine-1.10.0/ecoengine/R/ee_photos.R | 115 ++++++++++-------- ecoengine-1.10.0/ecoengine/R/ee_search.R | 7 - ecoengine-1.10.0/ecoengine/R/ee_sources.R | 1 ecoengine-1.10.0/ecoengine/R/ee_utils.R | 14 +- ecoengine-1.10.0/ecoengine/man/california_counties.Rd | 2 ecoengine-1.10.0/ecoengine/man/checklist_details.Rd | 2 ecoengine-1.10.0/ecoengine/man/ecoengine.Rd | 4 ecoengine-1.10.0/ecoengine/man/ee_about.Rd | 3 ecoengine-1.10.0/ecoengine/man/ee_cbind.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_checklists.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_footprints.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_observations.Rd | 4 ecoengine-1.10.0/ecoengine/man/ee_pages.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_paginator.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_photos.Rd | 4 ecoengine-1.10.0/ecoengine/man/ee_search.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_search_obs.Rd | 2 ecoengine-1.10.0/ecoengine/man/ee_sources.Rd | 2 ecoengine-1.10.0/ecoengine/man/full_sensor_list.Rd | 2 ecoengine-1.10.0/ecoengine/man/print.ecoengine.Rd | 2 ecoengine-1.10.0/ecoengine/man/view_photos.Rd | 2 ecoengine-1.9.1/ecoengine/R/ee_map.R |only ecoengine-1.9.1/ecoengine/man/ee_map.Rd |only 32 files changed, 230 insertions(+), 177 deletions(-)
Title: Hierarchical Spatial Autoregressive Model (HSAR)
Description: A library of the Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm.
Author: Guanpeng Dong, Richard Harris, Angelos Mimis
Maintainer: Angelos Mimis <mimis@panteion.gr>
Diff between HSAR versions 0.3.6 dated 2015-12-22 and 0.4.0 dated 2016-05-24
HSAR-0.3.6/HSAR/data/land_prices.RData |only HSAR-0.3.6/HSAR/man/land_prices.Rd |only HSAR-0.4.0/HSAR/DESCRIPTION | 10 - HSAR-0.4.0/HSAR/MD5 | 54 ++++--- HSAR-0.4.0/HSAR/NAMESPACE | 9 + HSAR-0.4.0/HSAR/R/RcppExports.R | 16 +- HSAR-0.4.0/HSAR/R/data_checks.R |only HSAR-0.4.0/HSAR/R/hsar.R | 58 ++++++- HSAR-0.4.0/HSAR/R/print.hsar.R |only HSAR-0.4.0/HSAR/R/sar.R | 42 +++++ HSAR-0.4.0/HSAR/R/summary.hsar.R | 103 +++++++------ HSAR-0.4.0/HSAR/R/utils.R |only HSAR-0.4.0/HSAR/build |only HSAR-0.4.0/HSAR/data/Beijingdistricts.RData |only HSAR-0.4.0/HSAR/data/datalist | 4 HSAR-0.4.0/HSAR/data/landSPDF.RData |only HSAR-0.4.0/HSAR/data/landprice.RData |only HSAR-0.4.0/HSAR/inst |only HSAR-0.4.0/HSAR/man/Beijingdistricts.Rd |only HSAR-0.4.0/HSAR/man/HSAR-package.Rd | 19 +- HSAR-0.4.0/HSAR/man/hsar.Rd | 164 +++++++++++++++++----- HSAR-0.4.0/HSAR/man/landSPDF.Rd |only HSAR-0.4.0/HSAR/man/landprice.Rd |only HSAR-0.4.0/HSAR/man/sar.Rd | 90 +++++++----- HSAR-0.4.0/HSAR/man/summary.mcmc_hsar.Rd | 23 +-- HSAR-0.4.0/HSAR/man/summary.mcmc_hsar_lambda_0.Rd |only HSAR-0.4.0/HSAR/man/summary.mcmc_hsar_rho_0.Rd |only HSAR-0.4.0/HSAR/man/summary.mcmc_sar.Rd | 16 -- HSAR-0.4.0/HSAR/src/RcppExports.cpp | 48 ++++-- HSAR-0.4.0/HSAR/src/hsar.cpp | 129 +++++++++-------- HSAR-0.4.0/HSAR/src/hsar_lambda_0.cpp | 115 ++++++++------- HSAR-0.4.0/HSAR/src/hsar_rho_0.cpp | 106 ++++++++------ HSAR-0.4.0/HSAR/src/sar.cpp | 80 ++++++---- HSAR-0.4.0/HSAR/vignettes |only 34 files changed, 699 insertions(+), 387 deletions(-)
Title: Computing the Gini-Based Coefficients for Weighted and Negative
Attributes
Description: Gini-based coefficients and plot of the ordinary and generalized curve of maximum inequality in the presence of weighted and negative attributes.
Author: Emanuela Raffinetti, Fabio Aimar
Maintainer: Emanuela Raffinetti <emanuela.raffinetti@unimi.it>
Diff between GiniWegNeg versions 1.0 dated 2016-01-13 and 1.0.1 dated 2016-05-24
GiniWegNeg-1.0.1/GiniWegNeg/DESCRIPTION | 14 ++-- GiniWegNeg-1.0.1/GiniWegNeg/MD5 | 28 ++++----- GiniWegNeg-1.0.1/GiniWegNeg/R/GRSVc.R | 12 ++-- GiniWegNeg-1.0.1/GiniWegNeg/R/Gini_CTR_BS.R | 44 +++++++-------- GiniWegNeg-1.0.1/GiniWegNeg/R/Gini_RSV.R | 22 +++---- GiniWegNeg-1.0.1/GiniWegNeg/R/PGini_RSV.R |only GiniWegNeg-1.0.1/GiniWegNeg/R/RSVc.R | 12 ++-- GiniWegNeg-1.0.1/GiniWegNeg/data/BI2012.rda |binary GiniWegNeg-1.0.1/GiniWegNeg/man/BI2012.Rd | 26 ++++----- GiniWegNeg-1.0.1/GiniWegNeg/man/GRSVc.Rd | 48 ++++++++-------- GiniWegNeg-1.0.1/GiniWegNeg/man/GiniWegNeg-package.Rd | 37 ++++++------- GiniWegNeg-1.0.1/GiniWegNeg/man/Gini_CTR_BS.Rd | 41 ++++++++------ GiniWegNeg-1.0.1/GiniWegNeg/man/Gini_RSV.Rd | 43 +++++++++------ GiniWegNeg-1.0.1/GiniWegNeg/man/PGini_RSV.Rd |only GiniWegNeg-1.0.1/GiniWegNeg/man/RSVc.Rd | 51 +++++++++--------- GiniWegNeg-1.0/GiniWegNeg/R/Gini.R |only GiniWegNeg-1.0/GiniWegNeg/man/Gini.Rd |only 17 files changed, 200 insertions(+), 178 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-7 dated 2016-05-13 and 1.2-8 dated 2016-05-24
DESCRIPTION | 8 MD5 | 22 R/g.analyse.R | 1878 ++++++++++++++++++++++++++-------------------------- R/g.getbout.R | 9 R/g.getmeta.R | 25 R/g.inspectfile.R | 412 +++++------ R/g.part2.R | 308 ++++---- R/g.shell.GGIR.R | 6 R/g.wavread.R | 4 inst/NEWS.Rd | 9 man/GGIR-package.Rd | 4 man/g.analyse.Rd | 15 12 files changed, 1372 insertions(+), 1328 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.2.2 dated 2016-05-22 and 1.2.3 dated 2016-05-24
DESCRIPTION | 8 ++-- MD5 | 12 +++--- NEWS.md | 3 + R/gtdd_download_TD_data.R | 43 +++++++++++++++++++--- inst/doc/gtdd-vignette.html | 10 +++-- man/download.TD.data.Rd | 86 ++++++++++++++++++++++---------------------- man/read.TD.files.Rd | 86 ++++++++++++++++++++++---------------------- 7 files changed, 144 insertions(+), 104 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides
the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the
customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Trustees of Columbia University [cph],
R Core Deveopment Team [cph] (R/pp_data.R, R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.9.0-3 dated 2016-02-13 and 2.9.0-4 dated 2016-05-24
rstanarm-2.9.0-3/rstanarm/data/example_model.rda |only rstanarm-2.9.0-3/rstanarm/man/plots.Rd |only rstanarm-2.9.0-4/rstanarm/DESCRIPTION | 12 rstanarm-2.9.0-4/rstanarm/MD5 | 196 - rstanarm-2.9.0-4/rstanarm/NAMESPACE | 7 rstanarm-2.9.0-4/rstanarm/R/adapt_delta.R | 31 rstanarm-2.9.0-4/rstanarm/R/as.matrix.stanreg.R | 4 rstanarm-2.9.0-4/rstanarm/R/example_model.R | 4 rstanarm-2.9.0-4/rstanarm/R/loo.R | 70 rstanarm-2.9.0-4/rstanarm/R/misc.R | 80 rstanarm-2.9.0-4/rstanarm/R/plots.R | 39 rstanarm-2.9.0-4/rstanarm/R/posterior_interval.R | 5 rstanarm-2.9.0-4/rstanarm/R/posterior_predict.R | 66 rstanarm-2.9.0-4/rstanarm/R/posterior_vs_prior.R |only rstanarm-2.9.0-4/rstanarm/R/pp_check.R | 86 rstanarm-2.9.0-4/rstanarm/R/pp_data.R | 12 rstanarm-2.9.0-4/rstanarm/R/pp_validate.R |only rstanarm-2.9.0-4/rstanarm/R/print-and-summary.R | 19 rstanarm-2.9.0-4/rstanarm/R/priors.R | 50 rstanarm-2.9.0-4/rstanarm/R/rstanarm-package.R | 2 rstanarm-2.9.0-4/rstanarm/R/shinystan.R | 72 rstanarm-2.9.0-4/rstanarm/R/stan_gamm4.R | 11 rstanarm-2.9.0-4/rstanarm/R/stan_glm.R | 3 rstanarm-2.9.0-4/rstanarm/R/stan_glm.fit.R | 41 rstanarm-2.9.0-4/rstanarm/R/stan_glmer.R | 29 rstanarm-2.9.0-4/rstanarm/R/stan_lm.R | 8 rstanarm-2.9.0-4/rstanarm/R/stan_lm.fit.R | 4 rstanarm-2.9.0-4/rstanarm/R/stan_polr.R | 128 rstanarm-2.9.0-4/rstanarm/R/stan_polr.fit.R | 2 rstanarm-2.9.0-4/rstanarm/R/stanmodels.R | 4 rstanarm-2.9.0-4/rstanarm/R/stanreg-methods.R | 29 rstanarm-2.9.0-4/rstanarm/R/stanreg.R | 20 rstanarm-2.9.0-4/rstanarm/R/zzz.R | 4 rstanarm-2.9.0-4/rstanarm/cleanup | 1 rstanarm-2.9.0-4/rstanarm/cleanup.win | 1 rstanarm-2.9.0-4/rstanarm/exec/lm.stan | 10 rstanarm-2.9.0-4/rstanarm/inst/NEWS | 17 rstanarm-2.9.0-4/rstanarm/inst/chunks/priors_glm.stan | 10 rstanarm-2.9.0-4/rstanarm/inst/chunks/tdata_glm.stan | 15 rstanarm-2.9.0-4/rstanarm/inst/chunks/tparameters_glm.stan | 23 rstanarm-2.9.0-4/rstanarm/inst/doc/aov.Rmd | 12 rstanarm-2.9.0-4/rstanarm/inst/doc/aov.html | 46 rstanarm-2.9.0-4/rstanarm/inst/doc/binomial.Rmd | 14 rstanarm-2.9.0-4/rstanarm/inst/doc/binomial.html | 42 rstanarm-2.9.0-4/rstanarm/inst/doc/continuous.Rmd | 8 rstanarm-2.9.0-4/rstanarm/inst/doc/continuous.html | 82 rstanarm-2.9.0-4/rstanarm/inst/doc/count.Rmd | 8 rstanarm-2.9.0-4/rstanarm/inst/doc/count.html | 32 rstanarm-2.9.0-4/rstanarm/inst/doc/glmer.Rmd | 6 rstanarm-2.9.0-4/rstanarm/inst/doc/glmer.html | 18 rstanarm-2.9.0-4/rstanarm/inst/doc/lm.Rmd | 17 rstanarm-2.9.0-4/rstanarm/inst/doc/lm.html | 47 rstanarm-2.9.0-4/rstanarm/inst/doc/polr.Rmd | 17 rstanarm-2.9.0-4/rstanarm/inst/doc/polr.html | 32 rstanarm-2.9.0-4/rstanarm/inst/doc/pooling.Rmd | 2 rstanarm-2.9.0-4/rstanarm/inst/doc/pooling.html | 116 rstanarm-2.9.0-4/rstanarm/inst/doc/rstanarm.Rmd | 5 rstanarm-2.9.0-4/rstanarm/inst/doc/rstanarm.html | 32 rstanarm-2.9.0-4/rstanarm/man/adapt_delta.Rd | 31 rstanarm-2.9.0-4/rstanarm/man/as.matrix.stanreg.Rd | 3 rstanarm-2.9.0-4/rstanarm/man/example_model.Rd | 4 rstanarm-2.9.0-4/rstanarm/man/loo.stanreg.Rd | 12 rstanarm-2.9.0-4/rstanarm/man/pairs.stanreg.Rd | 1 rstanarm-2.9.0-4/rstanarm/man/plot.stanreg.Rd | 19 rstanarm-2.9.0-4/rstanarm/man/posterior_interval.Rd | 1 rstanarm-2.9.0-4/rstanarm/man/posterior_predict.Rd | 3 rstanarm-2.9.0-4/rstanarm/man/posterior_vs_prior.Rd |only rstanarm-2.9.0-4/rstanarm/man/pp_check.Rd | 5 rstanarm-2.9.0-4/rstanarm/man/pp_validate.Rd |only rstanarm-2.9.0-4/rstanarm/man/priors.Rd | 48 rstanarm-2.9.0-4/rstanarm/man/rstanarm-package.Rd | 2 rstanarm-2.9.0-4/rstanarm/man/rstanarm-plots.Rd |only rstanarm-2.9.0-4/rstanarm/man/shinystan.Rd | 69 rstanarm-2.9.0-4/rstanarm/man/stan_gamm4.Rd | 28 rstanarm-2.9.0-4/rstanarm/man/stan_glm.Rd | 28 rstanarm-2.9.0-4/rstanarm/man/stan_glmer.Rd | 29 rstanarm-2.9.0-4/rstanarm/man/stan_lm.Rd | 5 rstanarm-2.9.0-4/rstanarm/man/stanreg-methods.Rd | 5 rstanarm-2.9.0-4/rstanarm/man/summary.stanreg.Rd | 9 rstanarm-2.9.0-4/rstanarm/src/include/models.hpp | 1622 ++-------- rstanarm-2.9.0-4/rstanarm/tests/testthat.R | 1 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_loo.R | 74 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_methods.R | 43 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_misc.R | 31 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_plots.R | 44 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_posterior_predict.R | 113 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_pp_check.R | 2 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_pp_validate.R |only rstanarm-2.9.0-4/rstanarm/tests/testthat/test_predict.R | 2 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_functions.R | 10 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_glm.R | 6 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_glmer.R | 9 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_lm.R | 16 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_polr.R | 21 rstanarm-2.9.0-4/rstanarm/vignettes/aov.Rmd | 12 rstanarm-2.9.0-4/rstanarm/vignettes/binomial.Rmd | 14 rstanarm-2.9.0-4/rstanarm/vignettes/continuous.Rmd | 8 rstanarm-2.9.0-4/rstanarm/vignettes/count.Rmd | 8 rstanarm-2.9.0-4/rstanarm/vignettes/glmer.Rmd | 6 rstanarm-2.9.0-4/rstanarm/vignettes/lm.Rmd | 17 rstanarm-2.9.0-4/rstanarm/vignettes/polr.Rmd | 17 rstanarm-2.9.0-4/rstanarm/vignettes/pooling.Rmd | 2 rstanarm-2.9.0-4/rstanarm/vignettes/rstanarm.Rmd | 5 103 files changed, 1919 insertions(+), 2117 deletions(-)
Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including
constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer
functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: Steve Juggins <Stephen.Juggins@ncl.ac.uk>
Diff between rioja versions 0.9-6 dated 2016-04-04 and 0.9-7 dated 2016-05-24
DESCRIPTION | 8 +-- MD5 | 32 ++++++------ R/MAT.r | 100 ++++++++++++++++++++++++++++++++------- R/PTF.r | 7 +- R/WAPLS.r | 11 ++-- R/inkspot.r | 11 +++- R/strat.plot.r | 129 +++++++++++++++++++++++++++++++++++---------------- inst/ChangeLog | 8 +++ man/IKFA.Rd | 2 man/MAT.Rd | 2 man/MLRC.Rd | 2 man/MR.Rd | 2 man/WA.Rd | 2 man/WAPLS.Rd | 2 man/inkspot.Rd | 3 + man/rioja.package.Rd | 6 +- man/strat.plot.Rd | 8 +-- 17 files changed, 237 insertions(+), 98 deletions(-)
Title: Free Sorting Data Analysis
Description: Provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).
Author: Philippe Courcoux
Maintainer: Philippe Courcoux <philippe.courcoux@oniris-nantes.fr>
Diff between FreeSortR versions 1.1 dated 2014-08-29 and 1.2 dated 2016-05-24
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +++ R/MdsDiss.R | 4 ++-- R/MdsSort.R | 2 +- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models, stochastic
agent-based, and stochastic network models. Network models use
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features
an easy API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 1.2.5 dated 2016-03-09 and 1.2.6 dated 2016-05-24
DESCRIPTION | 33 ++++++------- MD5 | 20 ++++---- NEWS | 17 ++++++ R/EpiModel-package.r | 6 +- R/dcm.mods.R | 11 +--- R/dendo.R | 86 ++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/Intro.html | 13 ++--- man/EpiModel-package.Rd | 6 +- man/as.phylo.transmat.Rd | 4 + tests/testthat/test-transmat-dendo.R | 24 +++++++++ 11 files changed, 139 insertions(+), 81 deletions(-)
Title: Ridge Estimation of the Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.1.9 dated 2016-05-10 and 0.2.0 dated 2016-05-24
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- inst/NEWS.Rd |only man/evaluateVAR1fit.Rd | 2 +- man/ragt2ridges-package.Rd | 2 +- 5 files changed, 10 insertions(+), 9 deletions(-)
Title: Tests of Fit for some Probability Distributions
Description: Goodness-of-fit tests for gamma, inverse Gaussian, lognormal, Weibull, Frechet, Gumbel, univariate normal, multivariate normal, Cauchy, Laplace or double exponential, exponential and generalized Pareto distributions. Parameter estimators for gamma, inverse Gaussian and generalized Pareto distributions.
Author: Elizabeth Gonzalez-Estrada, Jose A. Villasenor-Alva
Maintainer: Elizabeth Gonzalez-Estrada <egonzalez@colpos.mx>
Diff between goft versions 1.2 dated 2015-09-22 and 1.3.1 dated 2016-05-24
goft-1.2/goft/R/gpd.fit.R |only goft-1.2/goft/R/gpd.test-internal.R |only goft-1.2/goft/R/gpd.test.R |only goft-1.2/goft/R/ig.test-internal.R |only goft-1.2/goft/man/gpd.fit.Rd |only goft-1.2/goft/man/gpd.test.Rd |only goft-1.3.1/goft/DESCRIPTION | 13 ++--- goft-1.3.1/goft/MD5 | 60 +++++++++++++++--------- goft-1.3.1/goft/NAMESPACE | 11 ++-- goft-1.3.1/goft/R/cauchy.test.R |only goft-1.3.1/goft/R/de.test.R |only goft-1.3.1/goft/R/ev.test.R |only goft-1.3.1/goft/R/exp.test.R |only goft-1.3.1/goft/R/gamma.fit.R | 26 ++++++---- goft-1.3.1/goft/R/gamma.test.R | 33 +++++++------ goft-1.3.1/goft/R/gp.fit.R |only goft-1.3.1/goft/R/gp.test.R |only goft-1.3.1/goft/R/ig.fit.R | 17 +++---- goft-1.3.1/goft/R/ig.test.R | 82 +++++++++++++++++++++++++++------- goft-1.3.1/goft/R/lnorm.test.R |only goft-1.3.1/goft/R/mvShapiro.Test.R | 43 +++++++++-------- goft-1.3.1/goft/R/normal.R | 43 ++++++++--------- goft-1.3.1/goft/R/weibull.test.R |only goft-1.3.1/goft/data/o3.RData |only goft-1.3.1/goft/data/o3max.RData |only goft-1.3.1/goft/data/strength.RData |only goft-1.3.1/goft/inst/history.txt | 25 +++++++--- goft-1.3.1/goft/man/cauchy.test.Rd |only goft-1.3.1/goft/man/de.test.Rd |only goft-1.3.1/goft/man/ev.test.Rd |only goft-1.3.1/goft/man/exp.test.Rd |only goft-1.3.1/goft/man/gamma.fit.Rd | 19 ++++--- goft-1.3.1/goft/man/gamma.test.Rd | 24 ++++++--- goft-1.3.1/goft/man/goats.Rd | 6 +- goft-1.3.1/goft/man/gp.fit.Rd |only goft-1.3.1/goft/man/gp.test.Rd |only goft-1.3.1/goft/man/ig.fit.Rd | 10 ++-- goft-1.3.1/goft/man/ig.test.Rd | 42 ++++++++++++----- goft-1.3.1/goft/man/lnorm.test.Rd |only goft-1.3.1/goft/man/mvShapiro.Test.Rd | 23 ++++----- goft-1.3.1/goft/man/normal.Rd | 17 +++---- goft-1.3.1/goft/man/o3max.Rd |only goft-1.3.1/goft/man/ozone.Rd |only goft-1.3.1/goft/man/strength.Rd |only goft-1.3.1/goft/man/weibull.test.Rd |only 45 files changed, 306 insertions(+), 188 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.3.0 dated 2016-04-15 and 1.4.0 dated 2016-05-24
biogas-1.3.0/biogas/R/densBg.R |only biogas-1.4.0/biogas/ChangeLog | 91 +++ biogas-1.4.0/biogas/DESCRIPTION | 10 biogas-1.4.0/biogas/MD5 | 57 +- biogas-1.4.0/biogas/NEWS | 21 biogas-1.4.0/biogas/R/checkArgClassValue.R | 6 biogas-1.4.0/biogas/R/cumBg.R | 268 ++++++++--- biogas-1.4.0/biogas/R/interp.R | 4 biogas-1.4.0/biogas/R/stdVol.R | 11 biogas-1.4.0/biogas/R/summBg.R | 8 biogas-1.4.0/biogas/build/vignette.rds |binary biogas-1.4.0/biogas/data/comp.rda |binary biogas-1.4.0/biogas/data/comp2.rda |binary biogas-1.4.0/biogas/data/mass.rda |binary biogas-1.4.0/biogas/data/massw.rda |binary biogas-1.4.0/biogas/data/setup.rda |binary biogas-1.4.0/biogas/data/setup2.rda |binary biogas-1.4.0/biogas/data/strawComp.rda |only biogas-1.4.0/biogas/data/strawMass.rda |only biogas-1.4.0/biogas/data/strawPressure.rda |only biogas-1.4.0/biogas/data/strawSetup.rda |only biogas-1.4.0/biogas/data/vol.rda |binary biogas-1.4.0/biogas/data/vol2.rda |binary biogas-1.4.0/biogas/inst/doc/biogas_quick_start.Rnw | 2 biogas-1.4.0/biogas/inst/doc/biogas_quick_start.pdf |binary biogas-1.4.0/biogas/inst/doc/predBg_function.pdf |binary biogas-1.4.0/biogas/man/cumBg.Rd | 179 +++++-- biogas-1.4.0/biogas/man/stdVol.Rd | 9 biogas-1.4.0/biogas/man/strawComp.Rd |only biogas-1.4.0/biogas/man/strawMass.Rd |only biogas-1.4.0/biogas/man/strawPressure.Rd |only biogas-1.4.0/biogas/man/strawSetup.Rd |only biogas-1.4.0/biogas/tests/testthat/test_HighLevelFunctions.R | 20 biogas-1.4.0/biogas/vignettes/biogas_quick_start.Rnw | 2 34 files changed, 524 insertions(+), 164 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.1 dated 2016-03-03 and 2.1.3 dated 2016-05-24
BAMMtools-2.1.1/BAMMtools/R/BAMMlikelihood.R |only BAMMtools-2.1.1/BAMMtools/R/print.credibleshiftset.R |only BAMMtools-2.1.1/BAMMtools/R/richColors.R |only BAMMtools-2.1.1/BAMMtools/man/BAMMtools-internal.Rd |only BAMMtools-2.1.1/BAMMtools/man/BAMMtools-package.Rd |only BAMMtools-2.1.3/BAMMtools/DESCRIPTION | 24 BAMMtools-2.1.3/BAMMtools/MD5 | 198 ++-- BAMMtools-2.1.3/BAMMtools/NAMESPACE | 128 +- BAMMtools-2.1.3/BAMMtools/R/BAMMtools-data.R |only BAMMtools-2.1.3/BAMMtools/R/BAMMtools-package.R |only BAMMtools-2.1.3/BAMMtools/R/addBAMMlegend.R | 76 + BAMMtools-2.1.3/BAMMtools/R/addBAMMshifts.R | 66 + BAMMtools-2.1.3/BAMMtools/R/as.bammdata.R | 5 BAMMtools-2.1.3/BAMMtools/R/as.phylo.bammdata.R | 1 BAMMtools-2.1.3/BAMMtools/R/assignColorBreaks.R | 59 + BAMMtools-2.1.3/BAMMtools/R/bammLikelihood.R |only BAMMtools-2.1.3/BAMMtools/R/bammcolors.R | 20 BAMMtools-2.1.3/BAMMtools/R/barLegend.R | 38 BAMMtools-2.1.3/BAMMtools/R/cohorts.R | 59 + BAMMtools-2.1.3/BAMMtools/R/colorMap.R | 10 BAMMtools-2.1.3/BAMMtools/R/computeBayesFactors.R | 54 + BAMMtools-2.1.3/BAMMtools/R/credibleShiftSet.R | 224 ++++- BAMMtools-2.1.3/BAMMtools/R/cumulativeShiftProbsTree.R | 2 BAMMtools-2.1.3/BAMMtools/R/distinctShiftConfigurations.R | 75 + BAMMtools-2.1.3/BAMMtools/R/dtRates.R | 57 + BAMMtools-2.1.3/BAMMtools/R/generateControlFile.R | 44 - BAMMtools-2.1.3/BAMMtools/R/getBestShiftConfiguration.R | 75 + BAMMtools-2.1.3/BAMMtools/R/getBranchShiftPriors.R | 49 + BAMMtools-2.1.3/BAMMtools/R/getCladeRates.R | 74 + BAMMtools-2.1.3/BAMMtools/R/getCohortMatrix.R | 52 + BAMMtools-2.1.3/BAMMtools/R/getEventData.R | 157 +++ BAMMtools-2.1.3/BAMMtools/R/getJenksBreaks.R | 53 + BAMMtools-2.1.3/BAMMtools/R/getMarginalBranchRateMatrix.R | 39 BAMMtools-2.1.3/BAMMtools/R/getMeanBranchLengthTree.R | 39 BAMMtools-2.1.3/BAMMtools/R/getRateThroughTimeMatrix.R | 111 ++ BAMMtools-2.1.3/BAMMtools/R/getShiftNodesFromIndex.R | 37 BAMMtools-2.1.3/BAMMtools/R/getTipRates.R | 76 + BAMMtools-2.1.3/BAMMtools/R/getmrca.R | 26 BAMMtools-2.1.3/BAMMtools/R/marginalOddsRatioBranches.R | 46 + BAMMtools-2.1.3/BAMMtools/R/marginalShiftProbsTree.R | 68 + BAMMtools-2.1.3/BAMMtools/R/maximumShiftCredibility.R | 64 + BAMMtools-2.1.3/BAMMtools/R/plot.bammdata.R | 245 +++++ BAMMtools-2.1.3/BAMMtools/R/plot.bammshifts.R | 78 + BAMMtools-2.1.3/BAMMtools/R/plot.credibleshiftset.R | 63 + BAMMtools-2.1.3/BAMMtools/R/plotPrior.R | 24 BAMMtools-2.1.3/BAMMtools/R/plotRateThroughTime.R | 132 +++ BAMMtools-2.1.3/BAMMtools/R/print.bammdata.R | 1 BAMMtools-2.1.3/BAMMtools/R/rateLegend.R | 4 BAMMtools-2.1.3/BAMMtools/R/ratesHistogram.R | 44 + BAMMtools-2.1.3/BAMMtools/R/samplingProbs.R | 68 + BAMMtools-2.1.3/BAMMtools/R/setBAMMpriors.R | 73 + BAMMtools-2.1.3/BAMMtools/R/speciesByRatesMatrix.R | 52 + BAMMtools-2.1.3/BAMMtools/R/subsetEventData.R | 29 BAMMtools-2.1.3/BAMMtools/R/subtreeBAMM.R | 38 BAMMtools-2.1.3/BAMMtools/R/summary.bammdata.R | 30 BAMMtools-2.1.3/BAMMtools/R/summary.credibleshiftset.R | 50 + BAMMtools-2.1.3/BAMMtools/R/testTimeVariableBranches.R | 114 ++ BAMMtools-2.1.3/BAMMtools/R/traitDependentBAMM.R | 130 ++ BAMMtools-2.1.3/BAMMtools/R/transparentColor.R | 20 BAMMtools-2.1.3/BAMMtools/R/writeEventData.R | 20 BAMMtools-2.1.3/BAMMtools/man/BAMMlikelihood.Rd | 128 +- BAMMtools-2.1.3/BAMMtools/man/BAMMtools-data.Rd | 151 ++- BAMMtools-2.1.3/BAMMtools/man/BAMMtools.Rd |only BAMMtools-2.1.3/BAMMtools/man/ShiftProbsTree.Rd | 93 +- BAMMtools-2.1.3/BAMMtools/man/addBAMMlegend.Rd | 151 +-- BAMMtools-2.1.3/BAMMtools/man/addBAMMshifts.Rd | 118 +- BAMMtools-2.1.3/BAMMtools/man/assignColorBreaks.Rd | 126 +- BAMMtools-2.1.3/BAMMtools/man/cohorts.Rd | 124 +- BAMMtools-2.1.3/BAMMtools/man/computeBayesFactors.Rd | 73 - BAMMtools-2.1.3/BAMMtools/man/credibleShiftSet.Rd | 345 ++++--- BAMMtools-2.1.3/BAMMtools/man/distinctShiftConfigurations.Rd | 123 +- BAMMtools-2.1.3/BAMMtools/man/dtRates.Rd | 98 +- BAMMtools-2.1.3/BAMMtools/man/generateControlFile.Rd | 73 - BAMMtools-2.1.3/BAMMtools/man/getBestShiftConfiguration.Rd | 95 +- BAMMtools-2.1.3/BAMMtools/man/getBranchShiftPriors.Rd | 77 - BAMMtools-2.1.3/BAMMtools/man/getCladeRates.Rd | 100 +- BAMMtools-2.1.3/BAMMtools/man/getCohortMatrix.Rd | 71 - BAMMtools-2.1.3/BAMMtools/man/getEventData.Rd | 276 +++--- BAMMtools-2.1.3/BAMMtools/man/getJenksBreaks.Rd | 88 -- BAMMtools-2.1.3/BAMMtools/man/getMarginalBranchRateMatrix.Rd | 63 - BAMMtools-2.1.3/BAMMtools/man/getMeanBranchLengthTree.Rd | 65 - BAMMtools-2.1.3/BAMMtools/man/getRateThroughTimeMatrix.Rd | 187 ++-- BAMMtools-2.1.3/BAMMtools/man/getShiftNodesFromIndex.Rd | 55 - BAMMtools-2.1.3/BAMMtools/man/getTipRates.Rd | 132 +-- BAMMtools-2.1.3/BAMMtools/man/getmrca.Rd | 48 - BAMMtools-2.1.3/BAMMtools/man/marginalOddsRatioBranches.Rd | 78 - BAMMtools-2.1.3/BAMMtools/man/maximumShiftCredibility.Rd | 98 +- BAMMtools-2.1.3/BAMMtools/man/plot.bammdata.Rd | 483 +++++------ BAMMtools-2.1.3/BAMMtools/man/plot.bammshifts.Rd | 159 +-- BAMMtools-2.1.3/BAMMtools/man/plot.credibleshiftset.Rd | 151 +-- BAMMtools-2.1.3/BAMMtools/man/plotPrior.Rd | 63 - BAMMtools-2.1.3/BAMMtools/man/plotRateThroughTime.Rd | 339 +++---- BAMMtools-2.1.3/BAMMtools/man/ratesHistogram.Rd | 106 +- BAMMtools-2.1.3/BAMMtools/man/richColors.Rd |only BAMMtools-2.1.3/BAMMtools/man/samplingProbs.Rd | 110 +- BAMMtools-2.1.3/BAMMtools/man/setBAMMpriors.Rd | 134 +-- BAMMtools-2.1.3/BAMMtools/man/speciesByRatesMatrix.Rd | 87 + BAMMtools-2.1.3/BAMMtools/man/subsetEventData.Rd | 52 - BAMMtools-2.1.3/BAMMtools/man/subtreeBAMM.Rd | 62 - BAMMtools-2.1.3/BAMMtools/man/summary.bammdata.Rd | 65 - BAMMtools-2.1.3/BAMMtools/man/summary.credibleshiftset.Rd | 86 - BAMMtools-2.1.3/BAMMtools/man/testTimeVariableBranches.Rd | 125 +- BAMMtools-2.1.3/BAMMtools/man/traitDependentBAMM.Rd | 222 +++-- BAMMtools-2.1.3/BAMMtools/man/transparentColor.Rd | 35 BAMMtools-2.1.3/BAMMtools/man/writeEventData.Rd | 38 105 files changed, 5911 insertions(+), 2763 deletions(-)
Title: Comparison of Alternative Multiple Sequence Alignments
Description: Methods for comparing two alternative multiple
sequence alignments (MSAs) to determine whether they align homologous residues in
the same columns as one another. It then classifies similarities and differences
into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative
to the other. Summarising these categories for each MSA column yields information
on which sequence regions are agreed upon my both MSAs, and which differ. Several
plotting functions enable easily visualisation of the comparison data for analysis.
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>
Diff between AlignStat versions 1.1.3 dated 2016-03-18 and 1.2.1 dated 2016-05-24
DESCRIPTION | 12 +- MD5 | 38 +++--- NAMESPACE | 1 R/AlignStat.R | 1 R/Plots.R | 51 ++++++++ R/compare_alignments.R | 181 ++++++++++++++++++++++++++----- README.md | 46 ++++++- data/comparison_alignment.rda |binary data/reference_alignment.rda |binary man/AlignStat.Rd | 1 man/compare_alignments.Rd | 13 +- man/plot_SP_summary.Rd |only tests/testthat/AlignmentA.fasta |only tests/testthat/AlignmentB.clustal |only tests/testthat/AlignmentB.fasta |only tests/testthat/GrammicidinsClustal.fasta |only tests/testthat/GrammicidinsMuscle.fasta |only tests/testthat/categories.rda |binary tests/testthat/means.rda |binary tests/testthat/prepared_com.rda |binary tests/testthat/prepared_ref.rda |binary tests/testthat/results.rda |binary tests/testthat/test-align.R | 47 ++++++-- 23 files changed, 324 insertions(+), 67 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 1.4 dated 2016-04-14 and 1.6 dated 2016-05-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/expsize.R | 3 ++- man/surveyplanning-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 10 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between scatterplot3d versions 0.3-36 dated 2015-07-29 and 0.3-37 dated 2016-05-24
CHANGES | 1 + DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/scatterplot3d.R | 22 +++++++++++++++++----- build/vignette.rds |binary inst/doc/s3d.pdf |binary man/scatterplot3d.Rd | 8 ++++++-- 8 files changed, 36 insertions(+), 19 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.6-1 dated 2016-04-07 and 1.6-2 dated 2016-05-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/java/SDMX.jar |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.3.1 dated 2016-04-26 and 2.3.2 dated 2016-05-24
DESCRIPTION | 8 MD5 | 12 - R/autoevenn.R | 4 R/evenn.R | 478 ++++++++++++++++++++++++++++++--------------------- man/autoevenn.Rd | 5 man/eVenn-package.Rd | 4 man/evenn.Rd | 5 7 files changed, 305 insertions(+), 211 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
Dirk Eddelbuettel [ctb] (ziggurat rnorm sources),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 1.8.0 dated 2016-04-08 and 1.9.0 dated 2016-05-24
spaMM-1.8.0/spaMM/src/Makevars |only spaMM-1.9.0/spaMM/DESCRIPTION | 14 spaMM-1.9.0/spaMM/MD5 | 143 ++--- spaMM-1.9.0/spaMM/NAMESPACE | 12 spaMM-1.9.0/spaMM/R/COMPoisson.R | 5 spaMM-1.9.0/spaMM/R/CanonizeRanPars.R |only spaMM-1.9.0/spaMM/R/GLM.fit.R | 27 spaMM-1.9.0/spaMM/R/HLCor.R | 141 +---- spaMM-1.9.0/spaMM/R/HLFactorList.R | 58 +- spaMM-1.9.0/spaMM/R/HLfit.R | 559 +++++++------------- spaMM-1.9.0/spaMM/R/HLfit_Internals.R | 476 ++++++++++++----- spaMM-1.9.0/spaMM/R/LR.R | 11 spaMM-1.9.0/spaMM/R/LevenbergMstep.R | 4 spaMM-1.9.0/spaMM/R/MakeCovEst.R | 12 spaMM-1.9.0/spaMM/R/RcppExports.R | 32 - spaMM-1.9.0/spaMM/R/SEMbetalambda.R | 290 ++++------ spaMM-1.9.0/spaMM/R/auglinmodfit.R | 75 +- spaMM-1.9.0/spaMM/R/bloc_lambda.R |only spaMM-1.9.0/spaMM/R/confint.R | 33 - spaMM-1.9.0/spaMM/R/corrHLfit-internals.R | 124 ++-- spaMM-1.9.0/spaMM/R/corrHLfit.R | 122 +--- spaMM-1.9.0/spaMM/R/corrMM.LRT.R | 114 ++-- spaMM-1.9.0/spaMM/R/correlationFns.R | 26 spaMM-1.9.0/spaMM/R/dispGammaGLM.R | 2 spaMM-1.9.0/spaMM/R/extractors.R | 68 ++ spaMM-1.9.0/spaMM/R/fitme.R | 301 ++++++---- spaMM-1.9.0/spaMM/R/iterateSmooth.R | 19 spaMM-1.9.0/spaMM/R/locoptimthroughsmooth.R | 23 spaMM-1.9.0/spaMM/R/logL_from_SEMsample.R |only spaMM-1.9.0/spaMM/R/mapMM.R | 11 spaMM-1.9.0/spaMM/R/migraineLike.R | 3 spaMM-1.9.0/spaMM/R/negbin.R | 59 +- spaMM-1.9.0/spaMM/R/plot.HLfit.R | 2 spaMM-1.9.0/spaMM/R/predict.R | 32 - spaMM-1.9.0/spaMM/R/preprocess.R | 64 +- spaMM-1.9.0/spaMM/R/simulate.HL.R | 6 spaMM-1.9.0/spaMM/R/summary.HL.R | 182 +++--- spaMM-1.9.0/spaMM/R/update.HL.R | 17 spaMM-1.9.0/spaMM/data/Loaloa.RData |binary spaMM-1.9.0/spaMM/data/arabidopsis.RData |binary spaMM-1.9.0/spaMM/data/blackcap.RData |binary spaMM-1.9.0/spaMM/data/freight.RData |binary spaMM-1.9.0/spaMM/data/landMask.RData |binary spaMM-1.9.0/spaMM/data/oceanmask.RData |binary spaMM-1.9.0/spaMM/data/salamander.RData |binary spaMM-1.9.0/spaMM/data/scotlip.RData |binary spaMM-1.9.0/spaMM/data/seaMask.RData |binary spaMM-1.9.0/spaMM/data/seeds.RData |binary spaMM-1.9.0/spaMM/data/wafers.RData |binary spaMM-1.9.0/spaMM/data/welding.RData |binary spaMM-1.9.0/spaMM/data/worldcountries.RData |binary spaMM-1.9.0/spaMM/inst/NEWS.Rd | 27 spaMM-1.9.0/spaMM/man/COMPoisson.Rd | 22 spaMM-1.9.0/spaMM/man/GLM.fit.Rd | 12 spaMM-1.9.0/spaMM/man/HLCor.Rd | 20 spaMM-1.9.0/spaMM/man/HLfit.Rd | 33 - spaMM-1.9.0/spaMM/man/corrHLfit.Rd | 4 spaMM-1.9.0/spaMM/man/corrMatrix.Rd |only spaMM-1.9.0/spaMM/man/designL.from.Corr.Rd | 5 spaMM-1.9.0/spaMM/man/extractors.Rd | 18 spaMM-1.9.0/spaMM/man/fitme.Rd |only spaMM-1.9.0/spaMM/man/fixed.LRT.Rd | 16 spaMM-1.9.0/spaMM/man/mapMM.Rd | 46 - spaMM-1.9.0/spaMM/man/negbin.Rd |only spaMM-1.9.0/spaMM/man/options.Rd | 2 spaMM-1.9.0/spaMM/man/predict.Rd | 2 spaMM-1.9.0/spaMM/man/spaMM-internal-Rcpp.Rd | 8 spaMM-1.9.0/spaMM/man/spaMM-internal.Rd | 17 spaMM-1.9.0/spaMM/man/spaMM.Rd | 2 spaMM-1.9.0/spaMM/src/Makevars.win | 8 spaMM-1.9.0/spaMM/src/RcppExports.cpp | 133 +++- spaMM-1.9.0/spaMM/src/Rcpp_gibbs.cpp |only spaMM-1.9.0/spaMM/src/Zigg.h |only spaMM-1.9.0/spaMM/src/Ziggurat.h |only spaMM-1.9.0/spaMM/src/pMVN.cpp | 1 spaMM-1.9.0/spaMM/src/spaMM_linear.cpp | 242 ++++---- spaMM-1.9.0/spaMM/src/zrnorm.cpp |only spaMM-1.9.0/spaMM/tests/testthat/test-multinomial.R | 2 78 files changed, 2061 insertions(+), 1626 deletions(-)
Title: Printing Results of Statistical Computing in a Publishable Way
Description: Takes the output of statistical tests and transforms it in a
publish-friendly pattern. Currently only APA (American Psychological
Association) style is supported with output to HTML, LaTeX, Markdown and
plain text. It is easily customizable, extendable and can be used well
with 'knitr'. Additionally 'pubprint' offers a memory system that allows
to save and retrieve results of computations.
Author: Rudolf Siegel [aut, cre]
Maintainer: Rudolf Siegel <rs.os@t-online.de>
Diff between pubprint versions 0.2 dated 2016-05-12 and 0.2.1 dated 2016-05-24
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- NEWS.md | 6 ++++ R/out_html.R | 64 ++++++++++++++++++++++++++----------------------- README.md | 4 +-- inst/doc/pubprint.Rnw | 2 - inst/doc/pubprint.pdf |binary vignettes/pubprint.Rnw | 2 - 8 files changed, 56 insertions(+), 44 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Multiple Aggregation Prediction Algorithm
Description: Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>
Diff between MAPA versions 1.9 dated 2014-11-21 and 1.9.1 dated 2016-05-24
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 3 +++ R/MAPA.R | 2 ++ 5 files changed, 18 insertions(+), 9 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see: (i) "Life tables
with covariates: Dynamic model for nonlinear analysis of longitudinal data"
by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80),
<DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of
longitudinal data on aging and mortality" by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(iii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.2.1 dated 2016-04-12 and 1.3.1 dated 2016-05-24
stpm-1.2.1/stpm/R/simdata_gen.R |only stpm-1.2.1/stpm/man/fill_last.Rd |only stpm-1.2.1/stpm/man/optimize.Rd |only stpm-1.2.1/stpm/man/setlb.Rd |only stpm-1.2.1/stpm/man/setub.Rd |only stpm-1.2.1/stpm/man/simdata_cont2.Rd |only stpm-1.3.1/stpm/DESCRIPTION | 8 stpm-1.3.1/stpm/MD5 | 65 - stpm-1.3.1/stpm/NAMESPACE | 3 stpm-1.3.1/stpm/R/prepare_data.R | 131 ++- stpm-1.3.1/stpm/R/simdata_cont.R | 228 ----- stpm-1.3.1/stpm/R/simdata_discr.R | 28 stpm-1.3.1/stpm/R/simdata_gen_cont.R |only stpm-1.3.1/stpm/R/simdata_time-dep.R | 51 - stpm-1.3.1/stpm/R/spm.R | 28 stpm-1.3.1/stpm/R/spm_continuous.R | 166 ++-- stpm-1.3.1/stpm/R/spm_discrete.R | 9 stpm-1.3.1/stpm/R/spm_gen.R | 433 +++++++--- stpm-1.3.1/stpm/R/spm_projection.R | 40 - stpm-1.3.1/stpm/R/spm_time-dependent.R | 735 +++++++++--------- stpm-1.3.1/stpm/R/stpm-package.R | 4 stpm-1.3.1/stpm/man/prepare_data.Rd | 29 stpm-1.3.1/stpm/man/prepare_data_discr.Rd | 3 stpm-1.3.1/stpm/man/simdata_cont.Rd | 38 stpm-1.3.1/stpm/man/simdata_discr.Rd | 13 stpm-1.3.1/stpm/man/simdata_gen.Rd | 69 + stpm-1.3.1/stpm/man/simdata_time_dep.Rd | 14 stpm-1.3.1/stpm/man/spm.Rd | 23 stpm-1.3.1/stpm/man/spm_continuous.Rd | 9 stpm-1.3.1/stpm/man/spm_discrete.Rd | 4 stpm-1.3.1/stpm/man/spm_gen.Rd | 73 + stpm-1.3.1/stpm/man/spm_projection.Rd | 24 stpm-1.3.1/stpm/man/spm_time_dep.Rd | 10 stpm-1.3.1/stpm/src/simdataND.cpp | 141 --- stpm-1.3.1/stpm/src/spm_integral_MD.cpp | 1064 +++++++++++++++++++++------ stpm-1.3.1/stpm/vignettes/stpm-vignette.Rmd | 216 +++-- stpm-1.3.1/stpm/vignettes/stpm-vignette.html | 513 ++++++++----- 37 files changed, 2559 insertions(+), 1613 deletions(-)
Title: Distributed-Lag Structural Equation Modelling
Description: Fit distributed-lag structural equation models and perform path analysis at different time lags.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.0 dated 2016-05-19 and 1.0.1 dated 2016-05-24
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/dlsem.r | 13 +++++++++---- data/agres.rda |binary man/agres.Rd | 2 +- man/dlaglm.Rd | 8 ++++---- man/dlsem-package.Rd | 12 ++++++------ man/dlsem.Rd | 46 +++++++++++++++++++++++++++------------------- man/isIndep.Rd | 10 +++++----- man/lagPlot.Rd | 14 +++++++------- man/pathAnal.Rd | 10 +++++----- man/pathCoeff.Rd | 10 +++++----- 12 files changed, 84 insertions(+), 71 deletions(-)
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Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 3.4 dated 2015-11-29 and 3.5 dated 2016-05-24
DESCRIPTION | 8 MD5 | 77 ++++----- NAMESPACE | 8 R/DNA.R | 346 +++++++++++++++++++++++++++++++++++++++-- R/clustal.R | 27 ++- R/dist.topo.R | 91 ++++------ R/plot.phylo.R | 20 +- R/plot.phyloExtra.R |only R/read.nexus.R | 2 R/root.R | 29 +-- build/vignette.rds |binary data/hivtree.newick.rda |binary data/landplants.newick.rda |binary data/opsin.newick.rda |binary inst/doc/MoranI.Rnw | 2 inst/doc/MoranI.pdf |binary man/AAbin.Rd |only man/DNAbin.Rd | 2 man/DNAbin2indel.Rd | 3 man/LTT.Rd | 3 man/additive.Rd | 1 man/all.equal.phylo.Rd | 2 man/alview.Rd | 12 - man/ape-internal.Rd | 1 man/boot.phylo.Rd | 48 ++++- man/checkAlignment.Rd |only man/clustal.Rd | 2 man/def.Rd | 2 man/del.gaps.Rd | 29 ++- man/dist.dna.Rd | 6 man/diversity.contrast.test.Rd | 2 man/image.DNAbin.Rd | 3 man/makeNodeLabel.Rd | 2 man/mcmc.popsize.Rd | 8 man/plot.phyloExtra.Rd |only man/read.GenBank.Rd | 2 man/root.Rd | 2 man/trans.Rd |only man/write.nexus.data.Rd | 4 src/ape.c | 6 src/dist_dna.c | 218 +++++++++++++++++++++++++ vignettes/MoranI.Rnw | 2 42 files changed, 794 insertions(+), 176 deletions(-)