Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.3 dated 2017-06-08 and 1.4.4 dated 2017-09-01
DESCRIPTION | 6 ++-- MD5 | 40 +++++++++++++++--------------- NEWS.md | 10 +++++++ README.md | 11 ++------ build/vignette.rds |binary inst/doc/unitizer.Rmd | 5 ++- inst/doc/unitizer.html | 3 +- inst/doc/unitizer_index.Rmd | 7 +++-- inst/doc/unitizer_index.html | 4 +-- inst/doc/unitizer_interactive_env.Rmd | 2 - inst/doc/unitizer_miscellaneous.Rmd | 30 +++++++++++++++++++++- inst/doc/unitizer_miscellaneous.html | 17 ++++++++++++ inst/doc/unitizer_reproducible_tests.Rmd | 2 - inst/doc/unitizer_tests.Rmd | 2 - tests/testthat/testthat.exec.R | 12 ++++++++- vignettes/unitizer.Rmd | 5 ++- vignettes/unitizer_index.Rmd | 7 +++-- vignettes/unitizer_interactive_env.Rmd | 2 - vignettes/unitizer_miscellaneous.Rmd | 30 +++++++++++++++++++++- vignettes/unitizer_reproducible_tests.Rmd | 2 - vignettes/unitizer_tests.Rmd | 2 - 21 files changed, 143 insertions(+), 56 deletions(-)
Title: Data Frames in R for Make
Description: A solution for reproducible code and
high-performance computing.
Author: William Michael Landau [aut, cre],
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@lilly.com>
Diff between drake versions 4.0.0 dated 2017-08-04 and 4.1.0 dated 2017-09-01
DESCRIPTION | 41 ++-- MD5 | 165 ++++++++-------- NAMESPACE | 9 R/Makefile.R | 6 R/build.R | 144 ++++++++------ R/cache.R | 158 +++++++++------ R/check.R | 85 ++++---- R/clean.R | 108 +++++++--- R/config.R | 104 +++++----- R/console.R | 40 ++-- R/current.R | 34 ++- R/dataframes_graph.R | 205 ++++++++------------ R/dataframes_graph_utils.R |only R/debug.R | 63 +++--- R/dependencies.R | 149 +++++++++----- R/deprecate.R | 60 ++++-- R/envir.R | 53 +++-- R/examples.R | 165 ++++++++-------- R/find.R | 4 R/hash.R | 100 ++++++---- R/lapply.R | 8 R/make.R | 1 R/mclapply.R | 8 R/package.R | 19 + R/parLapply.R | 57 +++-- R/parallel.R | 35 +-- R/parallel_ui.R | 178 +++++++++-------- R/plotgraph.R | 206 ++++++++++++-------- R/test.R | 145 ++++++++++---- R/timestamp.R | 10 - R/timing.R |only R/tips.R | 38 ++- R/zzz.R | 7 inst/doc/caution.R | 22 +- inst/doc/caution.Rmd | 40 +++- inst/doc/caution.html | 61 +++--- inst/doc/drake.R | 5 inst/doc/drake.Rmd | 20 +- inst/doc/drake.html | 39 +-- inst/doc/quickstart.R | 28 -- inst/doc/quickstart.Rmd | 81 +++++--- inst/doc/quickstart.html | 318 +++++++++++--------------------- inst/examples/basic/basic.R | 4 man/build_times.Rd |only man/cached.Rd | 20 +- man/check.Rd | 8 man/clean.Rd | 14 - man/config.Rd | 10 - man/dataframes_graph.Rd | 52 +++-- man/default_graph_title.Rd |only man/default_parallelism.Rd | 2 man/drake-package.Rd | 8 man/example_drake.Rd | 12 - man/examples_drake.Rd | 4 man/get_cache.Rd |only man/imported.Rd | 4 man/load_basic_example.Rd | 14 - man/max_useful_jobs.Rd | 68 +++--- man/parallelism_choices.Rd | 40 ++-- man/plot_graph.Rd | 71 ++++--- man/possible_targets.Rd | 2 man/prune.Rd | 2 man/render_graph.Rd | 38 ++- man/shell_file.Rd | 2 man/status.Rd | 13 - tests/extra |only tests/testthat/test-Makefile.R | 20 +- tests/testthat/test-basic.R | 96 +++++---- tests/testthat/test-cache.R | 206 +++++++++++--------- tests/testthat/test-checking.R |only tests/testthat/test-command-changes.R | 2 tests/testthat/test-console.R |only tests/testthat/test-edge-cases.R | 179 +++++++++++++----- tests/testthat/test-envir.R | 2 tests/testthat/test-examples.R | 9 tests/testthat/test-full-build.R | 14 - tests/testthat/test-generate.R | 4 tests/testthat/test-import-file.R | 24 +- tests/testthat/test-import-object.R | 2 tests/testthat/test-intermediate-file.R | 6 tests/testthat/test-namespaced.R | 6 tests/testthat/test-other-features.R | 163 ++++------------ tests/testthat/test-parallel-ui.R |only tests/testthat/test-plan.R | 107 ++++++---- tests/testthat/test-testing.R |only vignettes/caution.Rmd | 40 +++- vignettes/drake.Rmd | 20 +- vignettes/quickstart.Rmd | 81 +++++--- 88 files changed, 2492 insertions(+), 1896 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.0-8 dated 2017-03-24 and 0.0-9 dated 2017-09-01
DESCRIPTION | 16 +- MD5 | 32 +++-- NAMESPACE | 7 + R/LCBD.comp.R | 75 +++++++------ R/beta.div.R | 95 ++++++++++------ R/beta.div.comp.R | 281 +++++++++++++------------------------------------ R/dist.ldc.R | 54 ++++++--- R/msr.4thcorner.R |only R/msr.R | 2 R/msr.varipart.R |only build/vignette.rds |binary inst/doc/tutorial.html | 4 man/LCBD.comp.Rd | 44 ++++++- man/beta.div.Rd | 76 ++++++++----- man/beta.div.comp.Rd | 54 +++++---- man/dist.ldc.Rd | 42 ++++--- man/msr.4thcorner.Rd |only man/msr.Rd | 2 man/msr.varipart.Rd |only 19 files changed, 402 insertions(+), 382 deletions(-)
Title: A Consistent and Intuitive Platform to Explore the Dependencies
of Packages on the Comprehensive R Archive Network Like
Repositories
Description: Interactively explore various dependencies of a package(s) (on the Comprehensive R Archive Network Like repositories) and perform analysis using tidy philosophy. Most of the functions return a 'tibble' object (enhancement of 'dataframe') which can be used for further analysis. The package offers functions to produce 'network' and 'igraph' dependency graphs. The 'plot' method produces a static plot based on 'ggnetwork' and 'plotd3' function produces an interactive D3 plot based on 'networkD3'.
Author: KS Srikanth [aut, cre],
Singh Nikhil [aut]
Maintainer: KS Srikanth <sri.teach@gmail.com>
Diff between pkggraph versions 0.2.0 dated 2017-06-02 and 0.2.2 dated 2017-09-01
pkggraph-0.2.0/pkggraph/man/plot.Rd |only pkggraph-0.2.2/pkggraph/DESCRIPTION | 11 - pkggraph-0.2.2/pkggraph/MD5 | 96 +++++------ pkggraph-0.2.2/pkggraph/NAMESPACE | 3 pkggraph-0.2.2/pkggraph/NEWS.md | 7 pkggraph-0.2.2/pkggraph/R/direct.R | 14 - pkggraph-0.2.2/pkggraph/R/get_dependencies.R | 2 pkggraph-0.2.2/pkggraph/R/get_neighborhood.R | 6 pkggraph-0.2.2/pkggraph/R/indirect.R | 14 - pkggraph-0.2.2/pkggraph/R/infix.R | 12 - pkggraph-0.2.2/pkggraph/R/init.R | 59 ++---- pkggraph-0.2.2/pkggraph/R/pkggraph_package.R | 2 pkggraph-0.2.2/pkggraph/R/plot.R | 15 + pkggraph-0.2.2/pkggraph/R/plotd3.R | 2 pkggraph-0.2.2/pkggraph/R/rely.R | 8 pkggraph-0.2.2/pkggraph/README.md | 13 + pkggraph-0.2.2/pkggraph/build/vignette.rds |binary pkggraph-0.2.2/pkggraph/data/sysdata.rda |binary pkggraph-0.2.2/pkggraph/inst/doc/vignette_pkggraph.R | 4 pkggraph-0.2.2/pkggraph/inst/doc/vignette_pkggraph.Rmd | 6 pkggraph-0.2.2/pkggraph/inst/doc/vignette_pkggraph.html | 102 ++++++------ pkggraph-0.2.2/pkggraph/man/deptable.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_all_dependencies.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_all_reverse_dependencies.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_depends.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_enhances.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_imports.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_linkingto.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_neighborhood.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_reverse_depends.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_reverse_enhances.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_reverse_imports.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_reverse_linkingto.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_reverse_suggests.Rd | 2 pkggraph-0.2.2/pkggraph/man/get_suggests.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-depends-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-enhances-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-imports-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-linkingto-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-relies-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/grapes-suggests-grapes.Rd | 2 pkggraph-0.2.2/pkggraph/man/init.Rd | 8 pkggraph-0.2.2/pkggraph/man/make_neighborhood_graph.Rd | 2 pkggraph-0.2.2/pkggraph/man/neighborhood_graph.Rd | 2 pkggraph-0.2.2/pkggraph/man/packmeta.Rd | 2 pkggraph-0.2.2/pkggraph/man/plot.pkggraph.Rd |only pkggraph-0.2.2/pkggraph/man/plotd3.Rd | 2 pkggraph-0.2.2/pkggraph/man/relies.Rd | 2 pkggraph-0.2.2/pkggraph/man/reverse_relies.Rd | 2 pkggraph-0.2.2/pkggraph/vignettes/vignette_pkggraph.Rmd | 6 50 files changed, 227 insertions(+), 215 deletions(-)
Title: Three-Way Data Analysis Through Densities
Description: The three-way data consists of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides tools to manage such data and functional methods (principal component analysis, multidimensional scaling, cluster analysis, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza[aut, cre], Pierre Santagostini [aut], Smail Yousfi [aut], Gilles Hunault [ctb], Julie Bourbeillon [ctb], Besnik Pumo [ctb], Sabine Demotes-Mainard [aut]
Maintainer: Rachid Boumaza <rachid.boumaza@agrocampus-ouest.fr>
Diff between dad versions 3.0.0 dated 2017-07-27 and 3.0.1 dated 2017-09-01
DESCRIPTION | 8 +- MD5 | 22 ++--- NAMESPACE | 34 ++++++-- R/appendtofolderh.R | 18 ++-- R/as.data.frame.folder.R | 2 R/as.folder.data.frame.R | 4 - R/as.folderh.foldermtg.R | 26 +++--- R/fdiscd.misclass.R | 12 +-- R/fdiscd.predict.R | 12 +-- R/folder.R | 10 +- R/folderh.R | 182 ++++++++++++++++++++++++----------------------- man/dad-package.Rd | 4 - 12 files changed, 176 insertions(+), 158 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.6-13 dated 2017-04-25 and 0.6-15 dated 2017-09-01
ChangeLog | 50 ++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++-------------- R/localG.R | 21 +++++++++++++---- R/localmoran.R | 16 ++++++++----- R/moran.exact.R | 2 - R/mtmoran.R | 2 - R/spBreg.R | 34 +++++++++++++++++----------- build/vignette.rds |binary inst/ChangeLog | 50 ++++++++++++++++++++++++++++++++++++++++++ inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/sids.pdf |binary man/localG.Rd | 5 ++-- man/localmoran.Rd | 5 ++-- man/localmoran.exact.Rd | 7 ++--- man/predict.sarlm.Rd | 6 ++--- 18 files changed, 182 insertions(+), 58 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling based on 'Boost', 'Eigen' and 'NLopt'. The 'rvinecopulib'
package implements the core features of the popular 'VineCopula' package, in
particular inference algorithms for both vine copula and bivariate copula
models. Advantages over 'VineCopula' are a sleeker and more modern API,
improved performances, especially in high dimensions, nonparametric and
multi-parameter families. The 'rvinecopulib' package includes headers and
sources from the 'vinecopulib' C++ library (currently version 0.1.0). Thus
users do not need to install 'vinecopulib' itself in order to use
'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under
the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.1.0.1.0 dated 2017-08-30 and 0.1.0.1.1 dated 2017-09-01
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/bicop_methods.R | 2 +- R/rvinecopulib.R | 17 +++++++++++------ man/bicop_methods.Rd | 2 +- man/rvinecopulib.Rd | 17 +++++++++++------ src/bicop/class.cpp | 2 +- src/vinecop/tools_select.cpp | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test_bicop.R | 1 + tests/testthat/test_bicop_dist.R | 1 + tests/testthat/test_vinecop_dist.R | 1 + 13 files changed, 61 insertions(+), 38 deletions(-)
Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler'
Permissions Checker
Description: Provides functions to download and parse 'robots.txt' files.
Ultimately the package makes it easy to check if bots
(spiders, crawler, scrapers, ...) are allowed to access specific
resources on a domain.
Author: Peter Meissner [aut, cre],
Oliver Keys [ctb],
Rich Fitz John [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between robotstxt versions 0.4.0 dated 2017-07-16 and 0.4.1 dated 2017-09-01
robotstxt-0.4.0/robotstxt/R/permissions.R |only robotstxt-0.4.1/robotstxt/DESCRIPTION | 14 robotstxt-0.4.1/robotstxt/MD5 | 91 + robotstxt-0.4.1/robotstxt/NAMESPACE | 20 robotstxt-0.4.1/robotstxt/NEWS.md | 137 +- robotstxt-0.4.1/robotstxt/R/get_robotstxt.R |only robotstxt-0.4.1/robotstxt/R/get_robotstxt_http_get.R |only robotstxt-0.4.1/robotstxt/R/guess_domain.R |only robotstxt-0.4.1/robotstxt/R/parse_robotstxt.R | 308 ------ robotstxt-0.4.1/robotstxt/R/path_allowed.R |only robotstxt-0.4.1/robotstxt/R/paths_allowed.R |only robotstxt-0.4.1/robotstxt/R/pipe.R |only robotstxt-0.4.1/robotstxt/R/print_robotstxt.R |only robotstxt-0.4.1/robotstxt/R/print_robotstxt_text.R |only robotstxt-0.4.1/robotstxt/R/remove_domain.R |only robotstxt-0.4.1/robotstxt/R/robotstxt.R | 244 ++-- robotstxt-0.4.1/robotstxt/R/rt_cache.R |only robotstxt-0.4.1/robotstxt/R/rt_get_comments.R |only robotstxt-0.4.1/robotstxt/R/rt_get_fields.R |only robotstxt-0.4.1/robotstxt/R/rt_get_fields_worker.R |only robotstxt-0.4.1/robotstxt/R/rt_get_useragent.R |only robotstxt-0.4.1/robotstxt/R/sanitize_path.R |only robotstxt-0.4.1/robotstxt/R/sanitize_permission_values.R |only robotstxt-0.4.1/robotstxt/R/sanitize_permissions.R |only robotstxt-0.4.1/robotstxt/R/tools.R | 2 robotstxt-0.4.1/robotstxt/R/valid_robotstxt.R | 4 robotstxt-0.4.1/robotstxt/README.md | 256 ++--- robotstxt-0.4.1/robotstxt/build/vignette.rds |binary robotstxt-0.4.1/robotstxt/inst/doc/using_robotstxt.R | 96 - robotstxt-0.4.1/robotstxt/inst/doc/using_robotstxt.html | 588 ++++++------ robotstxt-0.4.1/robotstxt/inst/robotstxts/robots_cdc.txt |only robotstxt-0.4.1/robotstxt/inst/robotstxts/robots_cdc2.txt |only robotstxt-0.4.1/robotstxt/man/get_robotstxt.Rd | 46 robotstxt-0.4.1/robotstxt/man/get_robotstxt_http_get.Rd | 34 robotstxt-0.4.1/robotstxt/man/guess_domain.Rd | 28 robotstxt-0.4.1/robotstxt/man/is_valid_robotstxt.Rd | 28 robotstxt-0.4.1/robotstxt/man/named_list.Rd | 30 robotstxt-0.4.1/robotstxt/man/parse_robotstxt.Rd | 34 robotstxt-0.4.1/robotstxt/man/path_allowed.Rd | 58 - robotstxt-0.4.1/robotstxt/man/paths_allowed.Rd | 56 - robotstxt-0.4.1/robotstxt/man/pipe.Rd |only robotstxt-0.4.1/robotstxt/man/print.robotstxt.Rd | 32 robotstxt-0.4.1/robotstxt/man/print.robotstxt_text.Rd | 32 robotstxt-0.4.1/robotstxt/man/remove_domain.Rd | 28 robotstxt-0.4.1/robotstxt/man/robotstxt.Rd | 128 +- robotstxt-0.4.1/robotstxt/man/rt_cache.Rd | 28 robotstxt-0.4.1/robotstxt/man/rt_get_comments.Rd | 30 robotstxt-0.4.1/robotstxt/man/rt_get_fields.Rd | 38 robotstxt-0.4.1/robotstxt/man/rt_get_fields_worker.Rd | 44 robotstxt-0.4.1/robotstxt/man/rt_get_rtxt.Rd | 32 robotstxt-0.4.1/robotstxt/man/rt_get_useragent.Rd | 30 robotstxt-0.4.1/robotstxt/man/rt_list_rtxt.Rd | 26 robotstxt-0.4.1/robotstxt/man/sanitize_path.Rd | 36 robotstxt-0.4.1/robotstxt/man/sanitize_permission_values.Rd | 30 robotstxt-0.4.1/robotstxt/man/sanitize_permissions.Rd | 30 robotstxt-0.4.1/robotstxt/tests/testthat/test_parser.R | 20 robotstxt-0.4.1/robotstxt/tests/testthat/test_permissions.R | 374 +++---- 57 files changed, 1389 insertions(+), 1623 deletions(-)
Title: NUtrient Cycling and COMpetition Model Undisturbed Open Bog
Ecosystems in a Temperate to Sub-Boreal Climate
Description: Modelling the vegetation, carbon, nitrogen and water dynamics of undisturbed open bog ecosystems in a temperate to sub-boreal climate. The executable of the model can downloaded from <https://github.com/jeroenpullens/NUCOMBog>.
Author: J.W.M. Pullens [aut, cre],
R. Silveyra Gonzalez [aut],
M. Bagnara [aut],
F. Hartig [aut]
Maintainer: J.W.M. Pullens <jeroenpullens@gmail.com>
Diff between NUCOMBog versions 1.0.4 dated 2017-05-02 and 1.0.4.1 dated 2017-09-01
NUCOMBog-1.0.4.1/NUCOMBog/DESCRIPTION | 8 NUCOMBog-1.0.4.1/NUCOMBog/MD5 | 64 NUCOMBog-1.0.4.1/NUCOMBog/NAMESPACE | 18 NUCOMBog-1.0.4.1/NUCOMBog/NEWS | 37 NUCOMBog-1.0.4.1/NUCOMBog/R/NUCOMBog.R | 32 NUCOMBog-1.0.4.1/NUCOMBog/R/combine_setup_parameters.R | 50 NUCOMBog-1.0.4.1/NUCOMBog/R/copytestdata.R | 80 NUCOMBog-1.0.4.1/NUCOMBog/R/getData.R | 148 NUCOMBog-1.0.4.1/NUCOMBog/R/make_filenames.r | 36 NUCOMBog-1.0.4.1/NUCOMBog/R/make_param_file.R | 76 NUCOMBog-1.0.4.1/NUCOMBog/R/runNUCOM.r | 106 NUCOMBog-1.0.4.1/NUCOMBog/R/runNUCOM_wrapper.R | 40 NUCOMBog-1.0.4.1/NUCOMBog/R/runparallelNUCOM.r | 182 NUCOMBog-1.0.4.1/NUCOMBog/R/setupNUCOM.r | 160 NUCOMBog-1.0.4.1/NUCOMBog/build/vignette.rds |binary NUCOMBog-1.0.4.1/NUCOMBog/inst/doc/NUCOMBog.ltx | 394 NUCOMBog-1.0.4.1/NUCOMBog/inst/doc/NUCOMBog.pdf |binary NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/input/ClimLVMfut.txt | 2426 - NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/input/ClimLVMhis.txt | 5618 +-- NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/input/ClimWLMfut.txt | 2426 - NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/input/ClimWLMhis.txt | 5618 +-- NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/input/param.txt | 408 NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/output/outmo.txt | 5626 +-- NUCOMBog-1.0.4.1/NUCOMBog/inst/extdata/output/outyr.txt | 478 NUCOMBog-1.0.4.1/NUCOMBog/man/NUCOMBog.Rd | 50 NUCOMBog-1.0.4.1/NUCOMBog/man/copytestdata.Rd | 72 NUCOMBog-1.0.4.1/NUCOMBog/man/getData.Rd | 70 NUCOMBog-1.0.4.1/NUCOMBog/man/runNUCOM.Rd | 80 NUCOMBog-1.0.4.1/NUCOMBog/man/runparallelNUCOM.Rd | 82 NUCOMBog-1.0.4.1/NUCOMBog/man/setupNUCOM.Rd | 180 NUCOMBog-1.0.4.1/NUCOMBog/vignettes/NUCOMBog.ltx | 394 NUCOMBog-1.0.4.1/NUCOMBog/vignettes/library.bib |19064 ++++++------ NUCOMBog-1.0.4/NUCOMBog/R/MPISapply.R |only NUCOMBog-1.0.4/NUCOMBog/vignettes/framed.sty |only 34 files changed, 22012 insertions(+), 22011 deletions(-)
Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.4.0 dated 2017-08-20 and 0.4.2 dated 2017-09-01
DESCRIPTION | 6 +- MD5 | 34 ++++++++------ NEWS.md | 11 ++++ R/geojsonio-package.r | 92 +++++++++++++++++++++------------------ R/onLoad.R | 2 README.md | 90 ++++++++++++++++++++++++++------------ inst/doc/geojsonio_vignette.Rmd | 6 +- inst/doc/geojsonio_vignette.html | 6 +- inst/img/unnamed-chunk-19-1.png |only inst/img/unnamed-chunk-21-1.png |only inst/js/README.md |only inst/js/topojson-server.js |only inst/vign/geojsonio_vignette.Rmd | 2 inst/vign/geojsonio_vignette.md | 6 +- man/canada_cities.Rd | 13 ++--- man/geojsonio-deprecated.Rd | 8 +-- man/geojsonio.Rd | 54 ++++++++++++---------- man/states.Rd | 4 - man/us_cities.Rd | 13 ++--- vignettes/geojsonio_vignette.Rmd | 6 +- 20 files changed, 210 insertions(+), 143 deletions(-)
Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions.
Author: Samuel R. Borstein <sam@borstein.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between AnnotationBustR versions 1.0 dated 2017-03-02 and 1.1 dated 2017-09-01
AnnotationBustR-1.0/AnnotationBustR/README.md |only AnnotationBustR-1.1/AnnotationBustR/DESCRIPTION | 16 AnnotationBustR-1.1/AnnotationBustR/MD5 | 36 - AnnotationBustR-1.1/AnnotationBustR/NEWS.md |only AnnotationBustR-1.1/AnnotationBustR/R/AnnotationBust.R | 185 +++++++-- AnnotationBustR-1.1/AnnotationBustR/R/DataDoc.R | 24 - AnnotationBustR-1.1/AnnotationBustR/R/MergeSearchTerms.R | 22 + AnnotationBustR-1.1/AnnotationBustR/R/pkgname.R | 4 AnnotationBustR-1.1/AnnotationBustR/build/vignette.rds |binary AnnotationBustR-1.1/AnnotationBustR/data/cpDNAterms.RData |binary AnnotationBustR-1.1/AnnotationBustR/data/mtDNAterms.RData |binary AnnotationBustR-1.1/AnnotationBustR/data/mtDNAtermsPlants.RData |only AnnotationBustR-1.1/AnnotationBustR/inst/doc/AnnotationBustR-vignette.Rmd | 126 ++++-- AnnotationBustR-1.1/AnnotationBustR/inst/doc/AnnotationBustR-vignette.html | 203 ++++++++-- AnnotationBustR-1.1/AnnotationBustR/man/AnnotationBust.Rd | 58 ++ AnnotationBustR-1.1/AnnotationBustR/man/AnnotationBustR.Rd | 4 AnnotationBustR-1.1/AnnotationBustR/man/MergeSearchTerms.Rd | 12 AnnotationBustR-1.1/AnnotationBustR/man/cpDNAterms.Rd | 2 AnnotationBustR-1.1/AnnotationBustR/man/mtDNAterms.Rd | 6 AnnotationBustR-1.1/AnnotationBustR/man/mtDNAtermsPlants.Rd |only AnnotationBustR-1.1/AnnotationBustR/vignettes/AnnotationBustR-vignette.Rmd | 126 ++++-- 21 files changed, 647 insertions(+), 177 deletions(-)
More information about AnnotationBustR at CRAN
Permanent link
Title: Statistical Procedures for Agricultural Research
Description: Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <fmendiburu@lamolina.edu.pe>
Diff between agricolae versions 1.2-6 dated 2017-08-05 and 1.2-7 dated 2017-09-01
agricolae-1.2-6/agricolae/R/order.group.R |only agricolae-1.2-6/agricolae/R/order.stat.R |only agricolae-1.2-6/agricolae/man/order.group.Rd |only agricolae-1.2-6/agricolae/man/order.stat.Rd |only agricolae-1.2-7/agricolae/DESCRIPTION | 9 agricolae-1.2-7/agricolae/MD5 | 230 ++++----- agricolae-1.2-7/agricolae/NAMESPACE | 5 agricolae-1.2-7/agricolae/NEWS | 18 agricolae-1.2-7/agricolae/R/BIB.test.R | 394 ++++++++------- agricolae-1.2-7/agricolae/R/DAU.test.R | 279 +++++------ agricolae-1.2-7/agricolae/R/HSD.test.R | 240 +++++---- agricolae-1.2-7/agricolae/R/LSD.test.R | 71 +- agricolae-1.2-7/agricolae/R/Median.test.R | 169 ++++-- agricolae-1.2-7/agricolae/R/PBIB.test.R | 61 +- agricolae-1.2-7/agricolae/R/REGW.test.R | 269 +++++----- agricolae-1.2-7/agricolae/R/SNK.test.R | 248 +++++---- agricolae-1.2-7/agricolae/R/bar.err.R | 19 agricolae-1.2-7/agricolae/R/bar.group.R | 16 agricolae-1.2-7/agricolae/R/carolina.R | 2 agricolae-1.2-7/agricolae/R/duncan.test.R | 275 +++++----- agricolae-1.2-7/agricolae/R/durbin.test.R | 260 +++++----- agricolae-1.2-7/agricolae/R/friedman.R | 280 +++++------ agricolae-1.2-7/agricolae/R/group.R |only agricolae-1.2-7/agricolae/R/kruskal.R | 59 +- agricolae-1.2-7/agricolae/R/nonadditivity.R | 6 agricolae-1.2-7/agricolae/R/orderPvalue.R | 13 agricolae-1.2-7/agricolae/R/plot.graph.freq.R | 1 agricolae-1.2-7/agricolae/R/resampling.cv.R | 10 agricolae-1.2-7/agricolae/R/scheffe.test.R | 64 +- agricolae-1.2-7/agricolae/R/sp.plot.R | 2 agricolae-1.2-7/agricolae/R/ssp.plot.R | 2 agricolae-1.2-7/agricolae/R/stability.par.R | 9 agricolae-1.2-7/agricolae/R/strip.plot.R | 2 agricolae-1.2-7/agricolae/R/waerden.test.R | 238 ++++----- agricolae-1.2-7/agricolae/R/waller.test.R | 251 +++++---- agricolae-1.2-7/agricolae/inst/doc/tutorial.R | 483 +++++++++---------- agricolae-1.2-7/agricolae/inst/doc/tutorial.Rnw | 503 +++++++++++--------- agricolae-1.2-7/agricolae/inst/doc/tutorial.pdf |binary agricolae-1.2-7/agricolae/inst/external/dataStb.csv |only agricolae-1.2-7/agricolae/inst/external/ssp.csv |only agricolae-1.2-7/agricolae/man/AMMI.contour.Rd | 7 agricolae-1.2-7/agricolae/man/BIB.test.Rd | 19 agricolae-1.2-7/agricolae/man/DAU.test.Rd | 31 - agricolae-1.2-7/agricolae/man/HSD.test.Rd | 30 - agricolae-1.2-7/agricolae/man/LSD.test.Rd | 44 - agricolae-1.2-7/agricolae/man/PBIB.test.Rd | 32 - agricolae-1.2-7/agricolae/man/REGW.test.Rd | 30 - agricolae-1.2-7/agricolae/man/SNK.test.Rd | 36 - agricolae-1.2-7/agricolae/man/VanderWarden.Rd | 33 - agricolae-1.2-7/agricolae/man/agricolae-package.Rd | 4 agricolae-1.2-7/agricolae/man/audpc.Rd | 5 agricolae-1.2-7/agricolae/man/audps.Rd | 4 agricolae-1.2-7/agricolae/man/bar.err.Rd | 18 agricolae-1.2-7/agricolae/man/bar.group.Rd | 8 agricolae-1.2-7/agricolae/man/carolina.Rd | 7 agricolae-1.2-7/agricolae/man/consensus.Rd | 8 agricolae-1.2-7/agricolae/man/correl.Rd | 4 agricolae-1.2-7/agricolae/man/correlation.Rd | 2 agricolae-1.2-7/agricolae/man/cv.model.Rd | 5 agricolae-1.2-7/agricolae/man/cv.similarity.Rd | 2 agricolae-1.2-7/agricolae/man/design.ab.Rd | 4 agricolae-1.2-7/agricolae/man/design.alpha.Rd | 16 agricolae-1.2-7/agricolae/man/design.bib.Rd | 8 agricolae-1.2-7/agricolae/man/design.crd.Rd | 4 agricolae-1.2-7/agricolae/man/design.cyclic.Rd | 6 agricolae-1.2-7/agricolae/man/design.dau.Rd | 12 agricolae-1.2-7/agricolae/man/design.graeco.Rd | 4 agricolae-1.2-7/agricolae/man/design.lattice.Rd | 8 agricolae-1.2-7/agricolae/man/design.lsd.Rd | 4 agricolae-1.2-7/agricolae/man/design.rcbd.Rd | 5 agricolae-1.2-7/agricolae/man/design.split.Rd | 4 agricolae-1.2-7/agricolae/man/design.strip.Rd | 4 agricolae-1.2-7/agricolae/man/design.youden.rd | 5 agricolae-1.2-7/agricolae/man/duncan.test.Rd | 33 - agricolae-1.2-7/agricolae/man/durbin.test.Rd | 22 agricolae-1.2-7/agricolae/man/friedman.Rd | 33 - agricolae-1.2-7/agricolae/man/graph.freq.Rd | 4 agricolae-1.2-7/agricolae/man/hcut.Rd | 2 agricolae-1.2-7/agricolae/man/hgroups.Rd | 2 agricolae-1.2-7/agricolae/man/index.bio.Rd | 5 agricolae-1.2-7/agricolae/man/index.smith.Rd | 4 agricolae-1.2-7/agricolae/man/intervals.freq.Rd | 2 agricolae-1.2-7/agricolae/man/join.freq.Rd | 2 agricolae-1.2-7/agricolae/man/kendall.Rd | 3 agricolae-1.2-7/agricolae/man/kruskal.Rd | 31 - agricolae-1.2-7/agricolae/man/lastC.Rd | 8 agricolae-1.2-7/agricolae/man/lateblight.Rd | 12 agricolae-1.2-7/agricolae/man/lineXtester.Rd | 36 - agricolae-1.2-7/agricolae/man/median.rd | 43 + agricolae-1.2-7/agricolae/man/montecarlo.Rd | 13 agricolae-1.2-7/agricolae/man/nonadditivity.Rd | 7 agricolae-1.2-7/agricolae/man/normal.freq.Rd | 6 agricolae-1.2-7/agricolae/man/ogive.freq.Rd | 4 agricolae-1.2-7/agricolae/man/orderPvalue.Rd | 12 agricolae-1.2-7/agricolae/man/path.analysis.Rd | 4 agricolae-1.2-7/agricolae/man/plot.graph.freq.Rd | 4 agricolae-1.2-7/agricolae/man/plot.group.Rd |only agricolae-1.2-7/agricolae/man/plotAMMI.Rd | 11 agricolae-1.2-7/agricolae/man/polygon.freq.Rd | 4 agricolae-1.2-7/agricolae/man/reg.homog.Rd | 13 agricolae-1.2-7/agricolae/man/resampling.cv.Rd | 5 agricolae-1.2-7/agricolae/man/resampling.model.Rd | 5 agricolae-1.2-7/agricolae/man/scheffe.test.Rd | 28 - agricolae-1.2-7/agricolae/man/similarity.Rd | 2 agricolae-1.2-7/agricolae/man/skewness.Rd | 3 agricolae-1.2-7/agricolae/man/sp.plot.Rd | 5 agricolae-1.2-7/agricolae/man/ssp.plot.Rd | 42 - agricolae-1.2-7/agricolae/man/stability.nonpar.Rd | 4 agricolae-1.2-7/agricolae/man/stability.par.Rd | 27 - agricolae-1.2-7/agricolae/man/stat.freq.Rd | 2 agricolae-1.2-7/agricolae/man/strip.plot.Rd | 53 -- agricolae-1.2-7/agricolae/man/sturges.freq.Rd | 3 agricolae-1.2-7/agricolae/man/summary.graph.freq.Rd | 1 agricolae-1.2-7/agricolae/man/table.freq.Rd | 1 agricolae-1.2-7/agricolae/man/tapply.stat.Rd | 4 agricolae-1.2-7/agricolae/man/vark.Rd | 6 agricolae-1.2-7/agricolae/man/waller.Rd | 6 agricolae-1.2-7/agricolae/man/waller.test.Rd | 27 - agricolae-1.2-7/agricolae/man/zigzag.Rd | 2 agricolae-1.2-7/agricolae/vignettes/tutorial.Rnw | 503 +++++++++++--------- 120 files changed, 3117 insertions(+), 2833 deletions(-)
Title: Ecological Indicators
Description: Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.
Author: Cstor Guisande Gonzlez
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>
Diff between EcoIndR versions 1.1 dated 2017-07-03 and 1.2 dated 2017-09-01
DESCRIPTION | 6 +++--- MD5 | 3 ++- inst |only 3 files changed, 5 insertions(+), 4 deletions(-)
Title: An Algorithm for Morphometric Characters Selection and
Statistical Validation in Morphological Taxonomy
Description: An algorithm (Guisande et al., 2016 <doi:10.11646/zootaxa.4162.3.10>) which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Author: Cstor Guisande Gonzlez
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>
Diff between VARSEDIG versions 1.3 dated 2016-11-05 and 1.4 dated 2017-09-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/characiformes.RData |binary inst/CITATION | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut],
Yixuan Qiu [ctb],
R Core Team [cph] (Cairo code from X11 device),
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.1.5 dated 2017-08-08 and 0.1.6 dated 2017-09-01
gdtools-0.1.5/gdtools/src/registerDynamicSymbol.c |only gdtools-0.1.6/gdtools/DESCRIPTION | 8 gdtools-0.1.6/gdtools/MD5 | 28 +- gdtools-0.1.6/gdtools/NAMESPACE | 2 gdtools-0.1.6/gdtools/NEWS | 9 gdtools-0.1.6/gdtools/R/RcppExports.R | 61 ++++- gdtools-0.1.6/gdtools/R/m_str_extents.R |only gdtools-0.1.6/gdtools/inst/include/gdtools_RcppExports.h | 36 +-- gdtools-0.1.6/gdtools/inst/include/gdtools_types.h | 2 gdtools-0.1.6/gdtools/man/glyphs_match.Rd |only gdtools-0.1.6/gdtools/man/m_str_extents.Rd |only gdtools-0.1.6/gdtools/man/str_extents.Rd | 2 gdtools-0.1.6/gdtools/man/str_metrics.Rd | 2 gdtools-0.1.6/gdtools/src/CairoContext.cpp | 36 +++ gdtools-0.1.6/gdtools/src/Makevars.in | 1 gdtools-0.1.6/gdtools/src/RcppExports.cpp | 154 ++++++++++----- gdtools-0.1.6/gdtools/src/font_metrics.cpp | 67 ++++++ 17 files changed, 302 insertions(+), 106 deletions(-)
Title: Frequency Domain Based Analysis: Dynamic PCA
Description: Implementation of dynamic principal component
analysis (DPCA), simulation of VAR and VMA processes and frequency domain tools.
These frequency domain methods for dimensionality reduction of multivariate time series
were introduced by David Brillinger in his book Time Series (1974). We follow implementation
guidelines as described in Hormann, Kidzinski and Hallin (2016),
Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.
Author: Hormann S., Kidzinski L.
Maintainer: Kidzinski L. <lukasz.kidzinski@stanford.edu>
Diff between freqdom versions 1.0.4 dated 2015-09-06 and 2.0.1 dated 2017-09-01
freqdom-1.0.4/freqdom/R/dpca.inverse.R |only freqdom-1.0.4/freqdom/R/dprcomp.R |only freqdom-1.0.4/freqdom/R/invfourier.R |only freqdom-1.0.4/freqdom/R/lagreg.est.R |only freqdom-1.0.4/freqdom/R/rbb.R |only freqdom-1.0.4/freqdom/R/rbm.R |only freqdom-1.0.4/freqdom/R/reg.dim.est.R |only freqdom-1.0.4/freqdom/R/reg.est.R |only freqdom-1.0.4/freqdom/R/reglag.boot.R |only freqdom-1.0.4/freqdom/R/reglag.significance.R |only freqdom-1.0.4/freqdom/R/speclagreg.K.R |only freqdom-1.0.4/freqdom/R/speclagreg.K.crossval.R |only freqdom-1.0.4/freqdom/R/speclagreg.K.experimental.R |only freqdom-1.0.4/freqdom/R/speclagreg.K.threshold.R |only freqdom-1.0.4/freqdom/R/speclagreg.R |only freqdom-1.0.4/freqdom/data |only freqdom-1.0.4/freqdom/demo/dpca.nino.R |only freqdom-1.0.4/freqdom/demo/dpca.pm10.R |only freqdom-1.0.4/freqdom/demo/reg.est.R |only freqdom-1.0.4/freqdom/demo/reglag.est.simulation.R |only freqdom-1.0.4/freqdom/demo/reglag.gsl.R |only freqdom-1.0.4/freqdom/demo/reglag.ice.river.R |only freqdom-1.0.4/freqdom/demo/reglag.pm10.R |only freqdom-1.0.4/freqdom/demo/reglag.test.bm.R |only freqdom-1.0.4/freqdom/demo/reglag.test.simulation.R |only freqdom-1.0.4/freqdom/inst |only freqdom-1.0.4/freqdom/man/MSE.Rd |only freqdom-1.0.4/freqdom/man/dpca.inverse.Rd |only freqdom-1.0.4/freqdom/man/dprcomp.Rd |only freqdom-1.0.4/freqdom/man/freqdom.inverse.Rd |only freqdom-1.0.4/freqdom/man/freqdom.kronecker.Rd |only freqdom-1.0.4/freqdom/man/freqdom.ratio.Rd |only freqdom-1.0.4/freqdom/man/grapes-c-grapes.Rd |only freqdom-1.0.4/freqdom/man/grapes-x-grapes.Rd |only freqdom-1.0.4/freqdom/man/invfourier.Rd |only freqdom-1.0.4/freqdom/man/lagged.cov.Rd |only freqdom-1.0.4/freqdom/man/lagreg.est.Rd |only freqdom-1.0.4/freqdom/man/linproc.Rd |only freqdom-1.0.4/freqdom/man/norm.spec.Rd |only freqdom-1.0.4/freqdom/man/plot.freqdom.Rd |only freqdom-1.0.4/freqdom/man/pseudoinverse.Rd |only freqdom-1.0.4/freqdom/man/rbb.Rd |only freqdom-1.0.4/freqdom/man/rbm.Rd |only freqdom-1.0.4/freqdom/man/reg.dim.est.Rd |only freqdom-1.0.4/freqdom/man/reg.est.Rd |only freqdom-1.0.4/freqdom/man/reglag.significance.Rd |only freqdom-1.0.4/freqdom/man/speclagreg.K.Rd |only freqdom-1.0.4/freqdom/man/speclagreg.Rd |only freqdom-2.0.1/freqdom/DESCRIPTION | 28 +-- freqdom-2.0.1/freqdom/MD5 | 185 ++++++++------------ freqdom-2.0.1/freqdom/NAMESPACE | 43 +--- freqdom-2.0.1/freqdom/R/MSE.R | 51 ++--- freqdom-2.0.1/freqdom/R/cov.structure.R | 64 ++++-- freqdom-2.0.1/freqdom/R/dpca.KLexpansion.R |only freqdom-2.0.1/freqdom/R/dpca.R |only freqdom-2.0.1/freqdom/R/dpca.filters.R |only freqdom-2.0.1/freqdom/R/dpca.scores.R | 42 +++- freqdom-2.0.1/freqdom/R/dpca.var.R |only freqdom-2.0.1/freqdom/R/filter.process.R | 84 +++++---- freqdom-2.0.1/freqdom/R/fourier.inverse.R |only freqdom-2.0.1/freqdom/R/fourier.transform.R | 64 +++--- freqdom-2.0.1/freqdom/R/freqdom-package.R |only freqdom-2.0.1/freqdom/R/freqdom.R | 67 ++++++- freqdom-2.0.1/freqdom/R/freqdom.eigen.R | 176 ++++++++++--------- freqdom-2.0.1/freqdom/R/freqdom.eigen.helpers.R | 46 ++-- freqdom-2.0.1/freqdom/R/freqdom.inverse.R | 108 +++++++---- freqdom-2.0.1/freqdom/R/freqdom.kronecker.R | 84 +++++---- freqdom-2.0.1/freqdom/R/freqdom.lags.R | 2 freqdom-2.0.1/freqdom/R/freqdom.product.R | 84 +++++---- freqdom-2.0.1/freqdom/R/freqdom.ratio.R | 36 ++- freqdom-2.0.1/freqdom/R/freqdom.trace.R |only freqdom-2.0.1/freqdom/R/freqdom.transpose.R | 42 +++- freqdom-2.0.1/freqdom/R/is.freqdom.R | 16 - freqdom-2.0.1/freqdom/R/is.timedom.R | 12 - freqdom-2.0.1/freqdom/R/lagged.cov.R | 64 ++++-- freqdom-2.0.1/freqdom/R/linproc.R | 12 - freqdom-2.0.1/freqdom/R/norm.spec.R | 3 freqdom-2.0.1/freqdom/R/operators.R | 41 +++- freqdom-2.0.1/freqdom/R/plot.freqdom.R | 15 - freqdom-2.0.1/freqdom/R/pseudoinverse.R | 6 freqdom-2.0.1/freqdom/R/rar.R | 111 +++++------- freqdom-2.0.1/freqdom/R/rev.R | 26 ++ freqdom-2.0.1/freqdom/R/rma.R | 88 ++++++--- freqdom-2.0.1/freqdom/R/spectral.density.R | 118 ++++++------ freqdom-2.0.1/freqdom/R/summary.timedom.R | 32 ++- freqdom-2.0.1/freqdom/R/timedom.R | 80 ++++++-- freqdom-2.0.1/freqdom/R/timedom.norms.R | 48 +++-- freqdom-2.0.1/freqdom/R/timedom.trunc.R | 32 +-- freqdom-2.0.1/freqdom/demo/00Index | 10 - freqdom-2.0.1/freqdom/demo/dpca.population.R | 7 freqdom-2.0.1/freqdom/demo/dpca.simulation.R | 10 - freqdom-2.0.1/freqdom/man/cov.structure.Rd | 43 ++-- freqdom-2.0.1/freqdom/man/dpca.KLexpansion.Rd |only freqdom-2.0.1/freqdom/man/dpca.Rd |only freqdom-2.0.1/freqdom/man/dpca.filters.Rd |only freqdom-2.0.1/freqdom/man/dpca.scores.Rd | 43 +++- freqdom-2.0.1/freqdom/man/dpca.var.Rd |only freqdom-2.0.1/freqdom/man/filter.process.Rd | 37 ++-- freqdom-2.0.1/freqdom/man/fourier.inverse.Rd |only freqdom-2.0.1/freqdom/man/fourier.transform.Rd | 35 ++- freqdom-2.0.1/freqdom/man/freqdom-package.Rd |only freqdom-2.0.1/freqdom/man/freqdom.Rd | 42 +++- freqdom-2.0.1/freqdom/man/freqdom.eigen.Rd | 27 +- freqdom-2.0.1/freqdom/man/freqdom.product.Rd | 35 ++- freqdom-2.0.1/freqdom/man/freqdom.transpose.Rd | 21 +- freqdom-2.0.1/freqdom/man/grapes-times-grapes.Rd | 21 -- freqdom-2.0.1/freqdom/man/is.freqdom.Rd | 15 - freqdom-2.0.1/freqdom/man/is.timedom.Rd | 15 - freqdom-2.0.1/freqdom/man/plus-.freqdom.Rd |only freqdom-2.0.1/freqdom/man/plus-.timedom.Rd |only freqdom-2.0.1/freqdom/man/plus.freqdom.Rd |only freqdom-2.0.1/freqdom/man/print.freqdom.Rd |only freqdom-2.0.1/freqdom/man/print.timedom.Rd |only freqdom-2.0.1/freqdom/man/rar.Rd | 53 +++-- freqdom-2.0.1/freqdom/man/rev.Rd |only freqdom-2.0.1/freqdom/man/rev.timedom.Rd |only freqdom-2.0.1/freqdom/man/rma.Rd | 44 +++- freqdom-2.0.1/freqdom/man/spectral.density.Rd | 61 +++--- freqdom-2.0.1/freqdom/man/summary.freqdom.Rd |only freqdom-2.0.1/freqdom/man/summary.timedom.Rd |only freqdom-2.0.1/freqdom/man/timedom.Rd | 40 +++- freqdom-2.0.1/freqdom/man/timedom.norms.Rd | 32 ++- freqdom-2.0.1/freqdom/man/timedom.trunc.Rd | 21 -- freqdom-2.0.1/freqdom/tests/convolution.R | 29 +-- freqdom-2.0.1/freqdom/tests/cov.structure.R |only freqdom-2.0.1/freqdom/tests/dpca.R |only freqdom-2.0.1/freqdom/tests/filtering.R | 25 +- freqdom-2.0.1/freqdom/tests/fourier.R | 10 - freqdom-2.0.1/freqdom/tests/integration.R |only 129 files changed, 1541 insertions(+), 1045 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 2.12.3 dated 2017-08-01 and 2.12.4 dated 2017-09-01
DESCRIPTION | 10 MD5 | 8 R/prediction.R | 5047 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary man/prediction.Rd | 25 5 files changed, 2544 insertions(+), 2546 deletions(-)
More information about CytobankAPIstats at CRAN
Permanent link
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial(Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses Stan and JAGS as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 0.9 dated 2017-07-08 and 0.9.1 dated 2017-09-01
BANOVA-0.9.1/BANOVA/DESCRIPTION | 8 BANOVA-0.9.1/BANOVA/MD5 | 253 - BANOVA-0.9.1/BANOVA/NAMESPACE | 92 BANOVA-0.9.1/BANOVA/NEWS | 71 BANOVA-0.9.1/BANOVA/R/BANOVA.Bern.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.BernNormal.R | 268 - BANOVA-0.9.1/BANOVA/R/BANOVA.Bin.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.BinNormal.R | 267 - BANOVA-0.9.1/BANOVA/R/BANOVA.MultiNormal.R | 205 - BANOVA-0.9.1/BANOVA/R/BANOVA.Multinomial.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.Normal.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.NormalNormal.R | 305 - BANOVA-0.9.1/BANOVA/R/BANOVA.PNormal.R | 286 - BANOVA-0.9.1/BANOVA/R/BANOVA.Poisson.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.T.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.TNormal.R | 260 - BANOVA-0.9.1/BANOVA/R/BANOVA.build.R | 38 BANOVA-0.9.1/BANOVA/R/BANOVA.floodlight.R | 44 BANOVA-0.9.1/BANOVA/R/BANOVA.mediation.R | 394 +- BANOVA-0.9.1/BANOVA/R/BANOVA.model.R | 62 BANOVA-0.9.1/BANOVA/R/BANOVA.ordMultiNormal.R | 28 BANOVA-0.9.1/BANOVA/R/BANOVA.ordMultinomial.R | 16 BANOVA-0.9.1/BANOVA/R/BANOVA.run.R | 994 ++--- BANOVA-0.9.1/BANOVA/R/BAnova.R | 22 BANOVA-0.9.1/BANOVA/R/JAGSgen.PNormal.R | 274 - BANOVA-0.9.1/BANOVA/R/JAGSgen.TNormal.R | 276 - BANOVA-0.9.1/BANOVA/R/JAGSgen.bernNormal.R | 258 - BANOVA-0.9.1/BANOVA/R/JAGSgen.binNormal.R | 260 - BANOVA-0.9.1/BANOVA/R/JAGSgen.multiNormal.R | 276 - BANOVA-0.9.1/BANOVA/R/JAGSgen.normalNormal.R | 287 - BANOVA-0.9.1/BANOVA/R/JAGSgen.ordmultiNormal.R | 344 - BANOVA-0.9.1/BANOVA/R/cal.mediation.effects.R | 381 +- BANOVA-0.9.1/BANOVA/R/conv.diag.R | 38 BANOVA-0.9.1/BANOVA/R/conv.geweke.heidel.R | 82 BANOVA-0.9.1/BANOVA/R/design.matrix.R | 248 - BANOVA-0.9.1/BANOVA/R/effect.matrix.factor.R | 74 BANOVA-0.9.1/BANOVA/R/effect.matrix.interaction.R | 136 BANOVA-0.9.1/BANOVA/R/effect.matrix.mediator.R | 156 BANOVA-0.9.1/BANOVA/R/est.R | 196 - BANOVA-0.9.1/BANOVA/R/est.multi.R | 112 BANOVA-0.9.1/BANOVA/R/floodlight.analysis.R | 434 +- BANOVA-0.9.1/BANOVA/R/get.interactions.R | 60 BANOVA-0.9.1/BANOVA/R/get.values.R | 52 BANOVA-0.9.1/BANOVA/R/multi.design.matrix.R | 588 +-- BANOVA-0.9.1/BANOVA/R/multi.effect.matrix.factor.R | 92 BANOVA-0.9.1/BANOVA/R/multi.effect.matrix.interaction.R | 156 BANOVA-0.9.1/BANOVA/R/multi.predict.means.R | 244 - BANOVA-0.9.1/BANOVA/R/multi.print.table.means.R | 1788 +++++----- BANOVA-0.9.1/BANOVA/R/pValues.R | 26 BANOVA-0.9.1/BANOVA/R/pairs.R | 32 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.Bern.R | 12 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.Bin.R | 12 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.Multinomial.R | 2 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.Normal.R | 11 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.Poisson.R | 17 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.R | 74 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.T.R | 11 BANOVA-0.9.1/BANOVA/R/predict.BANOVA.ordMultinomial.R | 11 BANOVA-0.9.1/BANOVA/R/predict.means.R | 324 - BANOVA-0.9.1/BANOVA/R/print.BANOVA.Bern.R | 16 BANOVA-0.9.1/BANOVA/R/print.BANOVA.Bin.R | 16 BANOVA-0.9.1/BANOVA/R/print.BANOVA.R | 10 BANOVA-0.9.1/BANOVA/R/print.BANOVA.floodlight.R | 36 BANOVA-0.9.1/BANOVA/R/print.BANOVA.mediation.R | 16 BANOVA-0.9.1/BANOVA/R/print.BANOVA.ordMultinomial.R | 20 BANOVA-0.9.1/BANOVA/R/print.ancova.effect.R | 14 BANOVA-0.9.1/BANOVA/R/print.conv.diag.R | 28 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.Bern.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.Bin.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.Multinomial.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.Normal.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.Poisson.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.R | 50 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.T.R | 40 BANOVA-0.9.1/BANOVA/R/print.summary.BANOVA.ordMultinomial.R | 40 BANOVA-0.9.1/BANOVA/R/print.table.means.R | 1699 ++++----- BANOVA-0.9.1/BANOVA/R/printCoefmat.R | 12 BANOVA-0.9.1/BANOVA/R/ssquares.R | 70 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.Bern.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.Bin.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.Multinomial.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.Normal.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.Poisson.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.R | 28 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.T.R | 16 BANOVA-0.9.1/BANOVA/R/summary.BANOVA.ordMultinomial.R | 16 BANOVA-0.9.1/BANOVA/R/table.ANCOVA.R | 596 +-- BANOVA-0.9.1/BANOVA/R/table.coefficients.R | 128 BANOVA-0.9.1/BANOVA/R/table.predictions.R | 278 - BANOVA-0.9.1/BANOVA/R/table.pvalue.R | 46 BANOVA-0.9.1/BANOVA/R/trace.plot.R | 34 BANOVA-0.9.1/BANOVA/R/traceplot.R | 40 BANOVA-0.9.1/BANOVA/inst/stan/Bernoulli_Normal.stan | 70 BANOVA-0.9.1/BANOVA/inst/stan/Binomial_Normal.stan | 76 BANOVA-0.9.1/BANOVA/inst/stan/Multinomial_Normal.stan | 84 BANOVA-0.9.1/BANOVA/inst/stan/Multinomial_Normal_slow.stan | 96 BANOVA-0.9.1/BANOVA/inst/stan/Normal_Normal.stan | 80 BANOVA-0.9.1/BANOVA/inst/stan/Poisson_Normal.stan | 72 BANOVA-0.9.1/BANOVA/inst/stan/T_Normal.stan | 86 BANOVA-0.9.1/BANOVA/inst/stan/ordMultinomial_Normal.stan | 88 BANOVA-0.9.1/BANOVA/inst/stan/ordMultinomial_Normal_dirichlet.stan | 102 BANOVA-0.9.1/BANOVA/inst/stan/single_Bernoulli.stan | 38 BANOVA-0.9.1/BANOVA/inst/stan/single_Binomial.stan | 44 BANOVA-0.9.1/BANOVA/inst/stan/single_Multinomial.stan | 56 BANOVA-0.9.1/BANOVA/inst/stan/single_Normal.stan | 52 BANOVA-0.9.1/BANOVA/inst/stan/single_Poisson.stan | 40 BANOVA-0.9.1/BANOVA/inst/stan/single_T.stan | 54 BANOVA-0.9.1/BANOVA/inst/stan/single_ordMultinomial.stan | 56 BANOVA-0.9.1/BANOVA/man/BANOVA-package.Rd | 130 BANOVA-0.9.1/BANOVA/man/BANOVA.Bernoulli.Rd | 12 BANOVA-0.9.1/BANOVA/man/BANOVA.Binomial.Rd | 14 BANOVA-0.9.1/BANOVA/man/BANOVA.Multinomial.Rd | 14 BANOVA-0.9.1/BANOVA/man/BANOVA.Normal.Rd | 16 BANOVA-0.9.1/BANOVA/man/BANOVA.Poisson.Rd | 18 BANOVA-0.9.1/BANOVA/man/BANOVA.T.Rd | 16 BANOVA-0.9.1/BANOVA/man/BANOVA.model.Rd | 66 BANOVA-0.9.1/BANOVA/man/BANOVA.ordMultinomial.Rd | 19 BANOVA-0.9.1/BANOVA/man/BANOVA.run.Rd | 10 BANOVA-0.9.1/BANOVA/man/BAnova.Rd | 2 BANOVA-0.9.1/BANOVA/man/choicedata.Rd | 134 BANOVA-0.9.1/BANOVA/man/colorad.Rd | 88 BANOVA-0.9.1/BANOVA/man/goalstudy.Rd | 2 BANOVA-0.9.1/BANOVA/man/ipadstudy.Rd | 98 BANOVA-0.9.1/BANOVA/man/pairs.BANOVA.Rd | 66 BANOVA-0.9.1/BANOVA/man/table.pvalues.Rd | 2 BANOVA-0.9.1/BANOVA/man/trace.plot.Rd | 2 BANOVA-0.9.1/BANOVA/src/install.libs.R | 182 - BANOVA-0.9/BANOVA/README.md |only 128 files changed, 8336 insertions(+), 8231 deletions(-)
Title: Create Muller Plots of Evolutionary Dynamics
Description: Create plots that combine a phylogeny and frequency dynamics.
Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo".
Inspired by similar plots in publications of the labs of RE Lenski and JE
Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose
code this package exploits).
Author: Robert Noble [aut, cre]
Maintainer: Robert Noble <robjohnnoble@gmail.com>
Diff between ggmuller versions 0.2.0 dated 2017-09-01 and 0.2.1 dated 2017-09-01
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/MullerPlot.R | 30 +++++++++++------------------- inst/doc/ggmuller.R | 2 +- inst/doc/ggmuller.Rmd | 6 +++--- inst/doc/ggmuller.html | 10 +++++----- vignettes/ggmuller.Rmd | 6 +++--- 7 files changed, 32 insertions(+), 40 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Description: Some functions of 'ade4' and 'stats' are combined in order to obtain a partition of the rows of a data table, with columns representing variables of scales: quantitative, qualitative or frequency.
First, a principal axes method is performed and then, a combination of Ward agglomerative hierarchical classification and K-means is performed, using some of the first coordinates obtained from the previous principal axes method.
The function 'kmeansW', a modification of 'kmeans', programmed in C++, is included, in order to permit to have different weights of the elements to be clustered. Some complementary functions and datasets are included.
See, for example:
Lebart, L. and Piron, M. and Morineau, A. (2006).
Statitique exploratoire multidimensionnelle, Dunod, Paris.
Author: Campo Elias Pardo <cepardot@unal.edu.co>,
Pedro Cesar del Campo <pcdelcampon@unal.edu.co> and
Camilo Jose Torres <cjtorresj@unal.edu.co>,
with the contributions from.
Ivan Diaz <ildiazm@unal.edu.co>,
Mauricio Sadinle <msadinleg@unal.edu.co>.
Maintainer: Campo Elias Pardo <cepardot@unal.edu.co>
Diff between FactoClass versions 1.1.4 dated 2017-08-09 and 1.1.6 dated 2017-09-01
DESCRIPTION | 28 ++++++++++++++++------------ MD5 | 6 +++--- R/stableclus.R | 6 +++--- man/stableclus.Rd | 8 ++++---- 4 files changed, 26 insertions(+), 22 deletions(-)
Title: Implementation of Augmented Network Log Anomaly Detection
Procedures
Description: Implements procedures to aid in detecting network log anomalies. By
combining various multivariate analytic approaches relevant to network anomaly
detection, it provides cyber analysts efficient means to detect suspected
anomalies requiring further evaluation.
Author: Andrew McCarthy [aut, cre],
Brandon Greenwell [aut],
Bradley Boehmke [aut],
Robert Gutierrez [aut],
Kenneth Bauer [ctb],
Trevor Bihl [ctb],
Cade Saie [ctb]
Maintainer: Andrew McCarthy <andrew.mccarthy@theperducogroup.com>
Diff between anomalyDetection versions 0.1.2 dated 2017-07-08 and 0.2.2 dated 2017-09-01
anomalyDetection-0.1.2/anomalyDetection/R/tabulated_state_vector.R |only anomalyDetection-0.1.2/anomalyDetection/tools/anomalyDetection_logo.png |only anomalyDetection-0.2.2/anomalyDetection/DESCRIPTION | 59 anomalyDetection-0.2.2/anomalyDetection/MD5 | 108 - anomalyDetection-0.2.2/anomalyDetection/NAMESPACE | 37 anomalyDetection-0.2.2/anomalyDetection/NEWS.md |only anomalyDetection-0.2.2/anomalyDetection/R/RcppExports.R |only anomalyDetection-0.2.2/anomalyDetection/R/anomalyDetection.R |only anomalyDetection-0.2.2/anomalyDetection/R/bd_row.R | 152 - anomalyDetection-0.2.2/anomalyDetection/R/block_inspect.R | 120 - anomalyDetection-0.2.2/anomalyDetection/R/data.R | 36 anomalyDetection-0.2.2/anomalyDetection/R/factor_analysis.R | 316 +-- anomalyDetection-0.2.2/anomalyDetection/R/get_all_factors.R | 96 - anomalyDetection-0.2.2/anomalyDetection/R/hmat.R |only anomalyDetection-0.2.2/anomalyDetection/R/horns_curve.R | 142 - anomalyDetection-0.2.2/anomalyDetection/R/kaisers_index.R | 128 - anomalyDetection-0.2.2/anomalyDetection/R/mahalanobis_distance.R | 189 -- anomalyDetection-0.2.2/anomalyDetection/R/mc_adjust.R | 310 +-- anomalyDetection-0.2.2/anomalyDetection/R/pca.R | 250 +- anomalyDetection-0.2.2/anomalyDetection/R/pipe.R | 52 anomalyDetection-0.2.2/anomalyDetection/R/tabulate_state_vector.R |only anomalyDetection-0.2.2/anomalyDetection/README.md | 72 anomalyDetection-0.2.2/anomalyDetection/build/vignette.rds |binary anomalyDetection-0.2.2/anomalyDetection/inst/doc/Introduction.R | 204 +- anomalyDetection-0.2.2/anomalyDetection/inst/doc/Introduction.Rmd | 529 +++-- anomalyDetection-0.2.2/anomalyDetection/inst/doc/Introduction.html | 900 +++++----- anomalyDetection-0.2.2/anomalyDetection/man/anomalyDetection.Rd |only anomalyDetection-0.2.2/anomalyDetection/man/bd_row.Rd | 92 - anomalyDetection-0.2.2/anomalyDetection/man/factor_analysis.Rd | 90 - anomalyDetection-0.2.2/anomalyDetection/man/factor_analysis_results.Rd | 100 - anomalyDetection-0.2.2/anomalyDetection/man/get_all_factors.Rd | 56 anomalyDetection-0.2.2/anomalyDetection/man/hmat.Rd |only anomalyDetection-0.2.2/anomalyDetection/man/horns_curve.Rd | 84 anomalyDetection-0.2.2/anomalyDetection/man/inspect_block.Rd | 62 anomalyDetection-0.2.2/anomalyDetection/man/kaisers_index.Rd | 98 - anomalyDetection-0.2.2/anomalyDetection/man/mahalanobis_distance.Rd | 117 - anomalyDetection-0.2.2/anomalyDetection/man/mc_adjust.Rd | 94 - anomalyDetection-0.2.2/anomalyDetection/man/pipe.Rd | 56 anomalyDetection-0.2.2/anomalyDetection/man/principal_components.Rd | 122 - anomalyDetection-0.2.2/anomalyDetection/man/principal_components_result.Rd | 94 - anomalyDetection-0.2.2/anomalyDetection/man/security_logs.Rd | 52 anomalyDetection-0.2.2/anomalyDetection/man/tabulate_state_vector.Rd | 82 anomalyDetection-0.2.2/anomalyDetection/src |only anomalyDetection-0.2.2/anomalyDetection/tests/testthat.R | 8 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_bd_row.R | 60 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_factor_analysis.R | 66 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_factor_analysis_results.R | 84 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_get_all_factors.R | 36 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_hmat.R |only anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_horns_curve.R | 46 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_inspect_block.R | 26 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_kaisers_index.R | 56 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_mahalanobis_distance.R | 44 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_mc_adjust.R | 26 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_principal_components.R | 50 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_principal_components_result.R | 80 anomalyDetection-0.2.2/anomalyDetection/tests/testthat/test_tabulate_state_vector.R | 45 anomalyDetection-0.2.2/anomalyDetection/tools/anomalyDetection-logo.png |binary anomalyDetection-0.2.2/anomalyDetection/vignettes/Introduction.Rmd | 529 +++-- 59 files changed, 3065 insertions(+), 2990 deletions(-)
More information about anomalyDetection at CRAN
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Title: Easily Tidy Data with 'spread()' and 'gather()' Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.7.0 dated 2017-08-16 and 0.7.1 dated 2017-09-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 20 ++++++++++++++++++++ man/tidyr-package.Rd | 4 ++-- tests/testthat/test-drop_na.R | 4 ++-- 5 files changed, 31 insertions(+), 11 deletions(-)
Title: Nonparametric Robust Estimation and Inference Methods using
Local Polynomial Regression and Kernel Density Estimation
Description: Tools for data-driven statistical analysis using local polynomial regression and kernel density methods.
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between nprobust versions 0.0.1 dated 2016-11-07 and 0.1.0 dated 2017-09-01
nprobust-0.0.1/nprobust/R/kdfunctions.R |only nprobust-0.0.1/nprobust/R/lpfunctions.R |only nprobust-0.0.1/nprobust/man/nprobust-internal.Rd |only nprobust-0.0.1/nprobust/src/hrbc.cpp |only nprobust-0.1.0/nprobust/DESCRIPTION | 16 nprobust-0.1.0/nprobust/MD5 | 38 - nprobust-0.1.0/nprobust/NAMESPACE | 13 nprobust-0.1.0/nprobust/R/RcppExports.R | 4 nprobust-0.1.0/nprobust/R/kdbwselect.R | 335 +++++++++++---- nprobust-0.1.0/nprobust/R/kdrobust.R | 291 ++++++------- nprobust-0.1.0/nprobust/R/lpbwselect.R | 465 +++++++++------------ nprobust-0.1.0/nprobust/R/lprobust.R | 501 ++++++++++------------- nprobust-0.1.0/nprobust/R/npfunctions.R |only nprobust-0.1.0/nprobust/R/nprobust.plot.R |only nprobust-0.1.0/nprobust/man/kdbwselect.Rd | 87 +-- nprobust-0.1.0/nprobust/man/kdrobust.Rd | 99 ++-- nprobust-0.1.0/nprobust/man/lpbwselect.Rd | 140 +++--- nprobust-0.1.0/nprobust/man/lprobust.Rd | 162 +++---- nprobust-0.1.0/nprobust/man/nprobust-package.Rd | 17 nprobust-0.1.0/nprobust/man/nprobust.plot.Rd |only nprobust-0.1.0/nprobust/src/Makevars | 7 nprobust-0.1.0/nprobust/src/Makevars.win | 6 nprobust-0.1.0/nprobust/src/RcppExports.cpp | 18 nprobust-0.1.0/nprobust/src/lpbwce.cpp |only 24 files changed, 1140 insertions(+), 1059 deletions(-)
More information about DelayedEffect.Design at CRAN
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Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Ian Johnson [ctb, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.5-2 dated 2017-03-12 and 1.5-3 dated 2017-09-01
DESCRIPTION | 8 ++-- MD5 | 62 ++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md | 16 +++++++++ R/AllGenerics.R | 3 + R/apriori.R | 6 +++ R/eclat.R | 14 +++++--- R/interestMeasures.R | 22 ++++++++----- R/itemMatrix.R | 10 ++++++ README.md | 40 ++++++++++++++++++++++-- build/vignette.rds |binary data/Adult.rda |binary data/AdultUCI.rda |binary data/Epub.rda |binary data/Groceries.rda |binary data/Income.rda |binary data/IncomeESL.rda |binary data/Mushroom.rda |binary data/SunBai.rda |binary inst/doc/arules.pdf |binary man/Income.Rd | 2 - man/dissimilarity.Rd | 7 +++- man/interestMeasure.Rd | 18 +++++++++-- man/itemMatrix-class.Rd | 7 ++++ man/rules-class.Rd | 3 + src/issubset.c | 5 ++- src/matrix.c | 58 ++++++++++++++++++++++------------- src/ptree.c | 14 ++++---- src/rapriori.c | 67 +++++++++++++++++++++-------------------- src/similarity.c | 29 +++++++++-------- src/warm.c | 17 ++++++---- tests/testthat/test-measures.R | 7 ++++ 32 files changed, 276 insertions(+), 140 deletions(-)
Title: Neyman-Pearson (NP) Classification Algorithms and NP Receiver
Operating Characteristic (NP-ROC) Curves
Description: In many binary classification applications, such as disease diagnosis and spam detection, practitioners commonly face the need to limit type I error (i.e., the conditional probability of misclassifying a class 0 observation as class 1) so that it remains below a desired threshold. To address this need, the Neyman-Pearson (NP) classification paradigm is a natural choice; it minimizes type II error (i.e., the conditional probability of misclassifying a class 1 observation as class 0) while enforcing an upper bound, alpha, on the type I error. Although the NP paradigm has a century-long history in hypothesis testing, it has not been well recognized and implemented in classification schemes. Common practices that directly limit the empirical type I error to no more than alpha do not satisfy the type I error control objective because the resulting classifiers are still likely to have type I errors much larger than alpha. As a result, the NP paradigm has not been properly implemented for many classification scenarios in practice. In this work, we develop the first umbrella algorithm that implements the NP paradigm for all scoring-type classification methods, including popular methods such as logistic regression, support vector machines and random forests. Powered by this umbrella algorithm, we propose a novel graphical tool for NP classification methods: NP receiver operating characteristic (NP-ROC) bands, motivated by the popular receiver operating characteristic (ROC) curves. NP-ROC bands will help choose in a data adaptive way and compare different NP classifiers. The paper is available at <arXiv:1608.03109>.
Author: Yang Feng, Jingyi Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between nproc versions 2.0.6 dated 2017-03-04 and 2.0.8 dated 2017-09-01
ChangeLog | 7 ++- DESCRIPTION | 17 ++++---- MD5 | 44 +++++++++++----------- R/compare.R | 19 ++++----- R/lines.nproc.R | 15 +++++-- R/npc.R | 57 ++++++---------------------- R/npfuns.R | 3 + R/nproc.R | 63 +++++++++---------------------- R/plot.nproc.R | 7 +-- R/rocCV.R | 2 - build/vignette.rds |binary inst/doc/nproc-demo.R | 23 ++++------- inst/doc/nproc-demo.Rmd | 92 ++++++++++++++++++++++------------------------ inst/doc/nproc-demo.pdf |binary man/compare.Rd | 10 ++--- man/lines.nproc.Rd | 11 +++++ man/npc.Rd | 34 +++++++---------- man/nproc.Rd | 43 +++++---------------- man/plot.nproc.Rd | 5 +- man/predict.npc.Rd | 1 man/rocCV.Rd | 3 - vignettes/nproc-demo.Rmd | 92 ++++++++++++++++++++++------------------------ vignettes/nproc-demo.html |only vignettes/nproc-demo.md |only 24 files changed, 232 insertions(+), 316 deletions(-)
Title: Tests for Genetic Association/Gene-Environment Interaction in
Longitudinal Studies
Description: Functions for genome-wide association studies (GWAS)/gene-environment-wide interaction studies (GEWIS) with longitudinal outcomes and exposures. He et al. (2017) "Set-Based Tests for Gene-Environment Interaction in Longitudinal Studies" and He et al. (2017) "Rare-variant association tests in longitudinal studies, with an application to the Multi-Ethnic Study of Atherosclerosis (MESA)".
Author: Zihuai He, Seunggeun Lee, Bhramar Mukherjee, Min Zhang
Maintainer: Zihuai He <zihuai@umich.edu>
Diff between LGEWIS versions 0.2 dated 2015-10-14 and 1.1 dated 2017-09-01
DESCRIPTION | 14 +- MD5 | 30 ++--- NAMESPACE | 4 R/GA.R | 221 ++++++++++++++++++++++------------------- R/GEI.R | 16 -- R/Main_SSD.R | 18 +-- data/LGEWIS.example.rda |binary man/GA.SSD.All.Rd | 76 +------------- man/GA.SSD.OneSet_SetIndex.Rd | 75 +------------ man/GA.prelim.Rd | 7 - man/GA.test.Rd | 34 ++---- man/GEI.SSD.All.Rd | 71 ------------- man/GEI.SSD.OneSet_SetIndex.Rd | 74 ------------- man/GEI.prelim.Rd | 8 - man/GEI.test.Rd | 10 + man/LGEWIS_example.Rd | 13 ++ 16 files changed, 217 insertions(+), 454 deletions(-)
Title: Chemometrics with R - Multivariate Data Analysis in the Natural
Sciences and Life Sciences
Description: Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011). Data used in the package are available from github.
Author: Ron Wehrens
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ChemometricsWithR versions 0.1.10 dated 2017-08-21 and 0.1.11 dated 2017-09-01
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- build/partial.rdb |binary man/MCR.Rd | 2 ++ 4 files changed, 10 insertions(+), 9 deletions(-)
More information about ChemometricsWithR at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-12 0.1.3
2012-01-04 0.1.2
2011-02-17 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-14 1.2.11
More information about StakeholderAnalysis at CRAN
Permanent link
Title: Provides Tools for Dimension Reduction Methods
Description: Reduction methods through slice inverse regression approaches. It mainly designed for illustrating the articles "A graphical tool for selecting the number of slices and the dimension of the model in SIR and SAVE approaches" (Liquet, B., Saracco, J. (2012) <doi:10.1007/s00180-011-0241-9>) and "Comparison of sliced inverse regression approaches for underdetermined cases”.
Author: Raphaël Coudret, Benoît Liquet and Jérôme Saracco
Maintainer: Benoit Liquet <benoit.liquet@univ-pau.fr>
Diff between edrGraphicalTools versions 2.1 dated 2013-11-09 and 2.2 dated 2017-09-01
DESCRIPTION | 17 +++++++---------- MD5 | 20 ++++++++++---------- NAMESPACE | 7 ++++++- R/edrGraphicalTools-internal.R | 2 +- man/criterionRkh.Rd | 2 +- man/edr.Rd | 2 +- man/edrGraphicalTools-package.Rd | 2 +- man/edrSelec.Rd | 9 +++++---- man/edrUnderdet.Rd | 8 ++++---- man/plot.edr.Rd | 2 +- src/dggev.c | 15 ++++++++++++++- 11 files changed, 51 insertions(+), 35 deletions(-)
More information about edrGraphicalTools at CRAN
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Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme-value and other copula families, as well as their rotations,
mixtures and asymmetrizations. Nested Archimedean copulas, related
tools and special functions. Methods for density, distribution, random
number generation, bivariate dependence measures, Rosenblatt transform,
Kendall distribution function, perspective and contour plots. Fitting of
copula models with potentially partly fixed parameters, including
standard errors. Serial independence tests, copula specification tests
(independence, exchangeability, radial symmetry, extreme-value
dependence, goodness-of-fit) and model selection based on
cross-validation. Empirical copula, smoothed versions, and
non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert <marius.hofert@uwaterloo.ca>,
Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>, and
Jun Yan <jun.yan@uconn.edu>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 0.999-17 dated 2017-06-18 and 0.999-18 dated 2017-09-01
DESCRIPTION | 18 MD5 | 88 +-- NAMESPACE | 1 R/Auxiliaries.R | 2 R/Classes.R | 2 R/Copula.R | 2 R/K.R | 52 +- R/amhCopula.R | 4 R/cCopula.R | 34 - R/cop_objects.R | 50 + R/dC-dc.R | 14 R/fgmCopula.R | 4 R/fitCopula.R | 2 R/frankCopula.R | 4 R/galambosCopula.R | 2 R/ggraph-tools.R | 3 R/graphics.R | 19 R/margCopula.R |only R/normalCopula.R | 2 R/tCopula.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 18 inst/doc/AC_Liouville.html | 343 ++++--------- inst/doc/AR_Clayton.html | 392 ++++----------- inst/doc/Frank-Rmpfr.pdf |binary inst/doc/GIG.html | 692 ++++++++++----------------- inst/doc/NALC.html | 634 +++++++++--------------- inst/doc/copula_GARCH.Rmd | 3 inst/doc/copula_GARCH.html | 442 +++++------------ inst/doc/dNAC.html | 594 ++++++++--------------- inst/doc/logL_visualization.html | 991 ++++++++++++++------------------------- inst/doc/nacopula-pkg.pdf |binary inst/doc/qrng.html | 892 ++++++++++++----------------------- inst/doc/rhoAMH-dilog.pdf |binary inst/doc/tail_compatibility.html | 728 +++++++++++----------------- inst/doc/wild_animals.html | 781 ++++++++++++------------------ man/Copula.Rd | 14 man/K.Rd | 28 - man/archmCopula.Rd | 23 man/contourplot2-methods.Rd | 25 man/margCopula.Rd |only man/wireframe2-methods.Rd | 2 man/xvCopula.Rd | 20 tests/rstable-ex.R | 29 - vignettes/copula_GARCH.Rmd | 3 46 files changed, 2628 insertions(+), 4331 deletions(-)
Title: Wrap R Functions for Debugging and Parametric Programming
Description: Powerful tools for writing and debugging R code. Provides: 'let()' which converts non-standard evaluation interfaces to
parametric standard evaluation interface, 'DebugFnW()' to capture function context on error for
debugging, and ':=' named map builder, and lambda-abstraction.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 0.4.1 dated 2017-08-24 and 0.4.2 dated 2017-09-01
wrapr-0.4.1/wrapr/R/zzz.R |only wrapr-0.4.2/wrapr/DESCRIPTION | 10 +- wrapr-0.4.2/wrapr/MD5 | 44 ++++---- wrapr-0.4.2/wrapr/NAMESPACE | 2 wrapr-0.4.2/wrapr/NEWS.md | 5 + wrapr-0.4.2/wrapr/R/bpipe.R | 31 +++--- wrapr-0.4.2/wrapr/R/lambda.R | 33 ++++-- wrapr-0.4.2/wrapr/R/let.R | 8 - wrapr-0.4.2/wrapr/R/namedMapBuilder.R | 53 ++++++---- wrapr-0.4.2/wrapr/README.md | 109 +++++++++++++++------- wrapr-0.4.2/wrapr/build/vignette.rds |binary wrapr-0.4.2/wrapr/inst/doc/CornerCases.html | 4 wrapr-0.4.2/wrapr/inst/doc/DebugFnW.html | 6 - wrapr-0.4.2/wrapr/inst/doc/SubstitutionModes.html | 4 wrapr-0.4.2/wrapr/inst/doc/dot_pipe.R | 15 ++- wrapr-0.4.2/wrapr/inst/doc/dot_pipe.Rmd | 39 ++++++- wrapr-0.4.2/wrapr/inst/doc/dot_pipe.html | 31 ++++-- wrapr-0.4.2/wrapr/inst/doc/lambda.R |only wrapr-0.4.2/wrapr/inst/doc/lambda.Rmd |only wrapr-0.4.2/wrapr/inst/doc/lambda.html |only wrapr-0.4.2/wrapr/inst/doc/let.html | 6 - wrapr-0.4.2/wrapr/inst/doc/named_map_builder.html | 4 wrapr-0.4.2/wrapr/man/defineLambda.Rd |only wrapr-0.4.2/wrapr/man/named_map_builder.Rd | 10 +- wrapr-0.4.2/wrapr/vignettes/dot_pipe.Rmd | 39 ++++++- wrapr-0.4.2/wrapr/vignettes/lambda.Rmd |only 26 files changed, 302 insertions(+), 151 deletions(-)
Title: The Moving Epidemic Method Web Application
Description: Web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between memapp versions 2.3 dated 2017-07-08 and 2.4 dated 2017-09-01
DESCRIPTION | 10 MD5 | 8 inst/shinyapp/helpers.R | 30 inst/shinyapp/server.R | 7130 +++++++++++++++++++++++------------------------- inst/shinyapp/ui.R | 25 5 files changed, 3605 insertions(+), 3598 deletions(-)
Title: Low-Level Interface to the '.NET' Virtual Machine Along the
Lines of the R C/Call API
Description: Low-level interface to '.NET' virtual machine along the lines of the R C .call interface. Can create '.NET' object, call methods, get or set properties, call static functions, etc.
Author: Jonathan Shore <jonathan.shore@gmail.com>
Maintainer: Jonathan Shore <jonathan.shore@gmail.com>
Diff between rDotNet versions 0.9.0 dated 2017-08-30 and 0.9.1 dated 2017-09-01
DESCRIPTION | 8 MD5 | 97 ++++--- NAMESPACE | 1 NEWS.md | 6 R/Driver.R | 6 R/Initialize.R | 27 +- README.md | 11 inst/server/Library.cs | 466 +++++++++++++++++++------------------- inst/server/Main.cs | 2 src/CLRApi.cpp | 2 src/CLRApi.hpp | 2 src/CLRFactory.cpp | 2 src/CLRFactory.hpp | 2 src/CLRObjectRef.cpp | 2 src/CLRObjectRef.hpp | 2 src/Common.hpp | 2 src/Driver.cpp | 2 src/RValue.hpp | 2 src/TcpClient.cpp | 8 src/TcpClient.hpp | 2 src/io/BufferedSocketReader.hpp | 2 src/io/BufferedSocketWriter.hpp | 2 src/io/FileUtils.hpp | 2 src/msgs/CLRMessage.hpp | 2 src/msgs/CLRValue.hpp | 2 src/msgs/ctrl/CLRCallMethod.hpp | 4 src/msgs/ctrl/CLRCallStatic.hpp | 4 src/msgs/ctrl/CLRCreateObject.hpp | 4 src/msgs/ctrl/CLRGetIndexed.hpp | 4 src/msgs/ctrl/CLRGetProperty.hpp | 4 src/msgs/ctrl/CLRRelease.hpp | 4 src/msgs/ctrl/CLRSetProperty.hpp | 4 src/msgs/data/CLRBool.hpp | 4 src/msgs/data/CLRBoolArray.hpp | 4 src/msgs/data/CLRByte.hpp | 4 src/msgs/data/CLRException.hpp | 4 src/msgs/data/CLRFloat64.hpp | 4 src/msgs/data/CLRFloat64Array.hpp | 4 src/msgs/data/CLRInt32.hpp | 4 src/msgs/data/CLRInt32Array.hpp | 4 src/msgs/data/CLRInt64.hpp | 3 src/msgs/data/CLRMatrix.hpp | 4 src/msgs/data/CLRNull.hpp | 3 src/msgs/data/CLRObjectArray.hpp | 3 src/msgs/data/CLRString.hpp | 3 src/msgs/data/CLRStringArray.hpp | 2 src/msgs/data/CLRVector.hpp | 2 tests/Tests.R | 5 tests/testthat |only 49 files changed, 379 insertions(+), 368 deletions(-)
Title: Fast and Simple Object Serialization to Protocol Buffers
Description: Optimized C++ implementations for reading and writing protocol-buffers.
Currently supports 'rexp.proto' for serializing R objects and 'geobuf.proto' for
geojson data. This lightweight package is complementary to the much larger
'RProtoBuf' package which provides a full featured toolkit for working with
protocol-buffers in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between protolite versions 1.6 dated 2017-03-16 and 1.7 dated 2017-09-01
protolite-1.6/protolite/src/register.c |only protolite-1.7/protolite/DESCRIPTION | 8 +++---- protolite-1.7/protolite/MD5 | 20 +++++++++--------- protolite-1.7/protolite/NEWS | 4 +++ protolite-1.7/protolite/R/RcppExports.R | 12 +++++++--- protolite-1.7/protolite/R/startup.R |only protolite-1.7/protolite/README.md | 2 - protolite-1.7/protolite/cleanup | 1 protolite-1.7/protolite/configure | 19 ++--------------- protolite-1.7/protolite/src/Makevars.in | 1 protolite-1.7/protolite/src/RcppExports.cpp | 31 ++++++++++++++++++++++++---- protolite-1.7/protolite/src/init.cpp | 5 +++- 12 files changed, 63 insertions(+), 40 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and
metadata from a PDF file. Also supports high quality rendering of PDF documents info
PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between pdftools versions 1.3 dated 2017-06-12 and 1.4 dated 2017-09-01
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/RcppExports.R | 18 +++++++++--------- R/render.R | 6 ++++-- src/Makevars.in | 1 + src/Makevars.win | 14 +++++++------- src/RcppExports.cpp | 36 ++++++++++++++++++------------------ src/bindings.cpp | 2 +- tools/winlibs.R | 8 +++++--- 10 files changed, 62 insertions(+), 53 deletions(-)
Title: The Moving Epidemic Method R Package
Description: Tools to model influenza epidemics and to monitor influenza surveillance.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.9 dated 2017-07-08 and 2.10 dated 2017-09-01
DESCRIPTION | 8 +-- MD5 | 24 +++++------ R/calcular.indicadores.2.timings.R | 7 +-- R/calcular.indicadores.R | 12 ++--- R/memgoodness.R | 4 + R/optimum.by.inspection.R | 76 +++++++++++++++++++++---------------- R/roc.analysis.R | 71 ++++++++++++++++++---------------- R/transformdata.R | 3 - R/transformseries.odd.R | 7 ++- R/transformseries.twowaves.R | 2 man/optimum.by.inspection.Rd | 6 +- man/transformseries.odd.Rd | 4 - man/transformseries.twowaves.Rd | 4 - 13 files changed, 126 insertions(+), 102 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.16.2 dated 2017-04-04 and 1.16.4 dated 2017-09-01
DESCRIPTION | 8 +++--- MD5 | 32 ++++++++++++++------------- NEWS | 24 ++++++++++++++++++++ R/as.matrix-functions.R | 2 - R/binPeaks-functions.R | 4 +-- R/calculateLabelPositions-functions.R | 2 - R/constructor-functions.R | 8 ++++-- R/coordinates-methods.R | 10 +++++--- R/determineWarpingFunctions-functions.R | 2 - R/grouper-functions.R | 6 +---- R/reorder-functions.R |only R/replaceNegativeIntensityValues-functions.R | 4 +-- R/valid-methods.R | 3 ++ inst/doc/MALDIquant-intro.pdf |binary tests/testthat/test_constructor-functions.R | 2 + tests/testthat/test_coordinates-methods.R | 2 + tests/testthat/test_reorder.R |only tests/testthat/test_valid-functions.R | 5 ++++ 18 files changed, 77 insertions(+), 37 deletions(-)
Title: Fast Probabilistic Record Linkage with Missing Data
Description: Implements a Fellegi-Sunter probabilistic record linkage model that allows for missing data
and the inclusion of auxiliary information. This includes functionalities to conduct a merge of two datasets under the Fellegi-Sunter model
using the Expectation-Maximization algorithm. In addition, tools for preparing, adjusting, and summarizing
data merges are included. The package implements methods described in Enamorado, Fifield,
and Imai (2017) ''Using a Probabilistic Model to Assist Merging of Large-scale Administrative
Records'', available at <http://imai.princeton.edu/research/linkage.html>.
Author: Ted Enamorado [aut, cre],
Ben Fifield [aut],
Kosuke Imai [aut]
Maintainer: Ted Enamorado <fastlinkr@gmail.com>
Diff between fastLink versions 0.1.1 dated 2017-07-11 and 0.2.0 dated 2017-09-01
fastLink-0.1.1/fastLink/R/cleanAddressUSPS.R |only fastLink-0.1.1/fastLink/man/cleanAddressUSPS.Rd |only fastLink-0.2.0/fastLink/DESCRIPTION | 14 +++---- fastLink-0.2.0/fastLink/MD5 | 36 +++++++++++------- fastLink-0.2.0/fastLink/NAMESPACE | 15 +++++++ fastLink-0.2.0/fastLink/R/emlinkMARmov.R | 35 ++++++++++++++--- fastLink-0.2.0/fastLink/R/fastLink-package.R | 4 +- fastLink-0.2.0/fastLink/R/fastLink.R | 47 +++++++++++++++++++----- fastLink-0.2.0/fastLink/R/gammaCK2par.R | 22 ++++++++--- fastLink-0.2.0/fastLink/R/getPosterior.R |only fastLink-0.2.0/fastLink/R/inspectEM.R |only fastLink-0.2.0/fastLink/R/matchesLink.R | 1 fastLink-0.2.0/fastLink/R/plot.R |only fastLink-0.2.0/fastLink/R/preprocText.R |only fastLink-0.2.0/fastLink/R/print.R |only fastLink-0.2.0/fastLink/R/tableCounts.R | 3 - fastLink-0.2.0/fastLink/man/emlinkMARmov.Rd | 7 ++- fastLink-0.2.0/fastLink/man/fastLink-package.Rd | 4 +- fastLink-0.2.0/fastLink/man/fastLink.Rd | 9 +++- fastLink-0.2.0/fastLink/man/getPosterior.Rd |only fastLink-0.2.0/fastLink/man/inspectEM.Rd |only fastLink-0.2.0/fastLink/man/plot.fastLink.Rd |only fastLink-0.2.0/fastLink/man/preprocText.Rd |only fastLink-0.2.0/fastLink/man/print.inspectEM.Rd |only fastLink-0.2.0/fastLink/src/m_func_cpp.cpp | 4 +- 25 files changed, 143 insertions(+), 58 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the 'cmark' reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format. The latest version of
this package also adds support for Github extensions including tables, autolinks
and strikethrough text.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between commonmark versions 1.2 dated 2017-03-01 and 1.4 dated 2017-09-01
DESCRIPTION | 12 MD5 | 89 NAMESPACE | 1 NEWS | 5 R/extensions.R | 2 R/markdown.R | 13 man/commonmark.Rd | 7 man/extensions.Rd | 2 src/Makevars | 20 src/cmark/arena.c | 31 src/cmark/blocks.c | 21 src/cmark/buffer.c | 6 src/cmark/cmark.c | 8 src/cmark/cmark.h | 40 src/cmark/cmark_export.h | 2 src/cmark/cmark_extension_api.h | 28 src/cmark/cmark_version.h | 5 src/cmark/commonmark.c | 14 src/cmark/html.c | 18 src/cmark/inlines.c | 325 src/cmark/inlines.h | 4 src/cmark/iterator.c | 1 src/cmark/latex.c | 32 src/cmark/main.c | 25 src/cmark/node.c | 2 src/cmark/node.h | 1 src/cmark/plaintext.c |only src/cmark/references.c | 108 src/cmark/references.h | 8 src/cmark/render.c | 15 src/cmark/scanners.c |18222 +++++++++++++++++++------------- src/cmark/scanners.h | 2 src/cmark/syntax_extension.c | 14 src/cmark/syntax_extension.h | 2 src/cmark/utf8.h | 11 src/extensions.c | 10 src/extensions/autolink.c | 25 src/extensions/cmarkextensions_export.h | 2 src/extensions/core-extensions.c | 12 src/extensions/core-extensions.h | 8 src/extensions/ext_scanners.c | 565 src/extensions/ext_scanners.h | 6 src/extensions/strikethrough.c | 5 src/extensions/table.c | 390 src/extensions/tagfilter.c | 3 src/wrapper.c | 7 46 files changed, 12460 insertions(+), 7669 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-14 1.2
2010-04-15 1.1
2009-11-01 1.0
Title: Who are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation,
and other attributes, such as gender and age. The method utilizes the Bayes'
Rule to compute the posterior probability of each racial category for any given
individual. The package implements methods described in Imai and Khanna (2015)
"Improving Ecological Inference by Predicting Individual Ethnicity from Voter
Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut, cre], Hubert Jin [ctb]
Maintainer: Kabir Khanna <kkhanna@princeton.edu>
Diff between wru versions 0.1-6 dated 2017-08-17 and 0.1-7 dated 2017-09-01
ChangeLog | 1 + DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- tests |only 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Computation of v Values for U and Copula C(U, v)
Description: Computation the value of one of two uniformly
distributed marginals if the copula probability value is known
and the value of the second marginal is also known.
Computation and plotting corresponding cumulative
distribution function or survival function.
The numerical definition of a common area limited by lines
of the cumulative distribution function and survival function.
Approximate quantification of the probability of this area.
Author: Josef Brejcha
Maintainer: Josef Brejcha <brchjo@gmail.com>
Diff between vfcp versions 1.1.0 dated 2017-05-30 and 1.2.0 dated 2017-09-01
DESCRIPTION | 14 +++++++++----- MD5 | 42 ++++++++++++++++++++++++++---------------- NAMESPACE | 28 ++++++++++++++++++++++++++++ NEWS | 20 ++++++++++++++++++++ R/CSmeze.R |only R/fxa.R |only R/prunikus.R |only R/vfcfg.R | 3 +++ R/vfeduo.R |only R/vfex.R | 4 +++- R/vfmargi.R | 2 +- R/vfmrg.R | 12 +++++++++++- R/vfpint.R |only R/vfploto.R | 32 ++++++++++++++++++++++++++------ R/vfpripo.R | 19 ++++++++++--------- man/CSmeze.Rd |only man/fxa.Rd |only man/prunikus.Rd |only man/vfcp-package.Rd | 10 +++++++--- man/vfeduo.Rd |only man/vfex.Rd | 2 +- man/vfmargi.Rd | 2 +- man/vfmrg.Rd | 24 +++++++++++++++++------- man/vfpint.Rd |only man/vfplot.Rd | 2 +- man/vfploto.Rd | 25 ++++++++++++++++--------- man/vfpripo.Rd | 10 +++++++--- 27 files changed, 187 insertions(+), 64 deletions(-)
Title: Constrained Spatiotemporal Mixed Models for Exposure Estimation
Description: The approach of constrained spatiotemporal mixed models is to make reliable estimation of air pollutant concentrations at high spatiotemporal
resolution (Li, L., Lurmann, F., Habre, R., Urman, R., Rappaport, E., Ritz, B., Chen, J., Gilliland, F., Wu, J., (2017) <doi:10.1021/acs.est.7b01864>).
This package is an extensive tool for this modeling approach with support of block Kriging (Goovaerts, P. (1997) <http://www.gbv.de/dms/goettingen/229148123.pdf>)
and uses the PM2.5 modeling as examples. It provides the following functionality:
(1) Extraction of covariates from the satellite images such as GeoTiff and NC4 raster;
(2) Generation of temporal basis functions to simulate the seasonal trends in the study regions;
(3) Generation of the regional monthly or yearly means of air pollutant concentration;
(4) Generation of Thiessen polygons and spatial effect modeling;
(5) Ensemble modeling for spatiotemporal mixed models, supporting multi-core parallel computing;
(6) Integrated predictions with or without weights of the model's performance, supporting multi-core parallel computing;
(7) Constrained optimization to interpolate the missing values;
(8) Generation of the grid surfaces of air pollutant concentration estimates at high resolution;
(9) Block Kriging for regional mean estimation at multiple scales.
Author: Lianfa Li,
Maintainer: Lianfa Li <lspatial@gmail.com>
Diff between sptemExp versions 0.1.0 dated 2017-08-29 and 0.1.1 dated 2017-09-01
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/genTBasisFun.R | 1 - R/parATimePredict.R | 2 -- R/weiA2Ens.R | 4 +++- man/noweiAvg.Rd | 1 - src/noweiAvg.cpp | 6 ++++-- 7 files changed, 16 insertions(+), 16 deletions(-)