Title: Minimax and Minimax Projection Designs
Description: Provides two main functions: mMcPSO() and
miniMaxPro(), which generates minimax designs and minimax projection designs using
a hybrid clustering - particle swarm optimization (PSO) algorithm. These designs can be used
in a variety of settings, e.g., as space-filling designs for computer experiments or
sensor allocation designs. A detailed description of the two designs and the employed
algorithms can be found in Mak and Joseph (2016) <https://arxiv.org/abs/1602.03938>.
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Diff between minimaxdesign versions 0.1.0.1 dated 2016-07-08 and 0.1.1 dated 2016-11-22
minimaxdesign-0.1.0.1/minimaxdesign/R/header.R |only minimaxdesign-0.1.0.1/minimaxdesign/man/CtoB2.Rd |only minimaxdesign-0.1.0.1/minimaxdesign/man/mMcrit.Rd |only minimaxdesign-0.1.0.1/minimaxdesign/man/mMcrit_pr.Rd |only minimaxdesign-0.1.0.1/minimaxdesign/man/refine.Rd |only minimaxdesign-0.1.1/minimaxdesign/DESCRIPTION | 14 - minimaxdesign-0.1.1/minimaxdesign/MD5 | 31 +- minimaxdesign-0.1.1/minimaxdesign/NAMESPACE | 2 minimaxdesign-0.1.1/minimaxdesign/R/RcppExports.R | 14 - minimaxdesign-0.1.1/minimaxdesign/R/designcrit.R |only minimaxdesign-0.1.1/minimaxdesign/R/minimax.R |only minimaxdesign-0.1.1/minimaxdesign/man/CtoA.Rd | 14 - minimaxdesign-0.1.1/minimaxdesign/man/CtoB.Rd | 6 minimaxdesign-0.1.1/minimaxdesign/man/mMcPSO.Rd | 37 +- minimaxdesign-0.1.1/minimaxdesign/man/miniMaxPro.Rd | 21 + minimaxdesign-0.1.1/minimaxdesign/man/minimaxdesign-package.Rd | 4 minimaxdesign-0.1.1/minimaxdesign/src/CtoB.cpp | 3 minimaxdesign-0.1.1/minimaxdesign/src/RcppExports.cpp | 99 ++++--- minimaxdesign-0.1.1/minimaxdesign/src/mMcrit.cpp | 126 +++++++++- minimaxdesign-0.1.1/minimaxdesign/src/subfunc.cpp | 2 20 files changed, 257 insertions(+), 116 deletions(-)
Title: Algorithm for Searching the Space of Gaussian Directed Acyclic
Graph Models Through Moment Fractional Bayes Factors
Description: We propose an objective Bayesian algorithm for searching the space of Gaussian directed acyclic graph (DAG) models. The algorithm proposed makes use of moment fractional Bayes factors (MFBF) and thus it is suitable for learning sparse graph. The algorithm is implemented by using Armadillo: an open-source C++ linear algebra library.
Author: Davide Altomare, Guido Consonni and Luca La Rocca
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between FBFsearch versions 1.0 dated 2013-04-13 and 1.1 dated 2016-11-22
DESCRIPTION | 21 ++---- MD5 | 30 ++++---- NAMESPACE | 5 - data/datalist | 14 ++-- man/FBF_GS.Rd | 176 ++++++++++++++++++++++++++-------------------------- man/FBF_LS.Rd | 133 ++++++++++++++++++++------------------- man/FBF_RS.Rd | 170 +++++++++++++++++++++++++------------------------- man/dataHuman.Rd | 68 ++++++++++---------- man/dataPub.Rd | 58 ++++++++--------- man/dataSim100.Rd | 54 +++++++-------- man/dataSim200.Rd | 58 ++++++++--------- man/dataSim50.Rd | 60 ++++++++--------- man/dataSim6.Rd | 46 ++++++------- man/dataSimHuman.Rd | 66 +++++++++---------- src/FBFsearch.cpp | 124 ++++++++++++++++++++++-------------- src/Makevars | 2 16 files changed, 561 insertions(+), 524 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <http://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.12.2 dated 2016-08-10 and 1.14.2 dated 2016-11-22
crunch-1.12.2/crunch/R/categorical-array.R |only crunch-1.12.2/crunch/R/find.R |only crunch-1.12.2/crunch/R/log.R |only crunch-1.12.2/crunch/R/merge-datasets.R |only crunch-1.12.2/crunch/R/multiple-response.R |only crunch-1.12.2/crunch/inst/doc/array-card.png |only crunch-1.12.2/crunch/man/extendDataset.Rd |only crunch-1.12.2/crunch/man/prepareBindInputs.Rd |only crunch-1.12.2/crunch/man/selectFrom.Rd |only crunch-1.12.2/crunch/tests/testthat/api/datasets-relative-urls.json |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset1 |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset1.json |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset2 |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset2.json |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset3 |only crunch-1.12.2/crunch/tests/testthat/api/datasets/dataset3.json |only crunch-1.12.2/crunch/tests/testthat/test-expression.R |only crunch-1.12.2/crunch/vignettes/array-card.png |only crunch-1.14.2/crunch/DESCRIPTION | 10 crunch-1.14.2/crunch/MD5 | 428 +++-- crunch-1.14.2/crunch/NAMESPACE | 19 crunch-1.14.2/crunch/R/AllClasses.R | 4 crunch-1.14.2/crunch/R/AllGenerics.R | 2 crunch-1.14.2/crunch/R/add-subvariable.R | 65 crunch-1.14.2/crunch/R/add-variable.R | 27 crunch-1.14.2/crunch/R/api.R | 4 crunch-1.14.2/crunch/R/append-dataset.R | 28 crunch-1.14.2/crunch/R/as-data-frame.R | 4 crunch-1.14.2/crunch/R/auth.R | 29 crunch-1.14.2/crunch/R/categories.R | 13 crunch-1.14.2/crunch/R/compare-datasets.R | 22 crunch-1.14.2/crunch/R/copy.R | 12 crunch-1.14.2/crunch/R/crunch.R | 6 crunch-1.14.2/crunch/R/crunchbox.R |only crunch-1.14.2/crunch/R/cube-query.R | 30 crunch-1.14.2/crunch/R/dataset-extract.R | 81 + crunch-1.14.2/crunch/R/dataset.R | 77 - crunch-1.14.2/crunch/R/drop-rows.R | 10 crunch-1.14.2/crunch/R/export-dataset.R | 8 crunch-1.14.2/crunch/R/expressions.R | 141 + crunch-1.14.2/crunch/R/filters.R | 5 crunch-1.14.2/crunch/R/fork-and-merge.R | 9 crunch-1.14.2/crunch/R/get-datasets.R | 16 crunch-1.14.2/crunch/R/github.R | 17 crunch-1.14.2/crunch/R/hide-variables.R | 62 crunch-1.14.2/crunch/R/join-dataset.R | 126 + crunch-1.14.2/crunch/R/make-array.R |only crunch-1.14.2/crunch/R/misc.R | 31 crunch-1.14.2/crunch/R/new-dataset.R | 45 crunch-1.14.2/crunch/R/session.R |only crunch-1.14.2/crunch/R/shoji-catalog.R | 8 crunch-1.14.2/crunch/R/shoji-entity.R |only crunch-1.14.2/crunch/R/shoji-order-slots.R | 13 crunch-1.14.2/crunch/R/shoji-order.R | 188 ++ crunch-1.14.2/crunch/R/show.R | 38 crunch-1.14.2/crunch/R/subvariables.R | 58 crunch-1.14.2/crunch/R/univariate.R | 33 crunch-1.14.2/crunch/R/variable-catalog.R | 15 crunch-1.14.2/crunch/R/variable-delete.R |only crunch-1.14.2/crunch/R/variable-metadata.R | 89 - crunch-1.14.2/crunch/R/variable-summary.R | 11 crunch-1.14.2/crunch/R/variable-to-R.R | 86 - crunch-1.14.2/crunch/R/variable-type.R | 5 crunch-1.14.2/crunch/R/variable-update.R | 14 crunch-1.14.2/crunch/R/variable.R | 45 crunch-1.14.2/crunch/R/versions.R | 4 crunch-1.14.2/crunch/R/weight.R |only crunch-1.14.2/crunch/R/zcl.R | 13 crunch-1.14.2/crunch/build/vignette.rds |binary crunch-1.14.2/crunch/inst/doc/analyze.html | 404 ++--- crunch-1.14.2/crunch/inst/doc/array-variables.Rmd | 6 crunch-1.14.2/crunch/inst/doc/array-variables.html | 68 crunch-1.14.2/crunch/inst/doc/datasets.html | 28 crunch-1.14.2/crunch/inst/doc/derive.html | 18 crunch-1.14.2/crunch/inst/doc/export.R |only crunch-1.14.2/crunch/inst/doc/export.Rmd |only crunch-1.14.2/crunch/inst/doc/export.html |only crunch-1.14.2/crunch/inst/doc/filters.Rmd | 4 crunch-1.14.2/crunch/inst/doc/filters.html | 4 crunch-1.14.2/crunch/inst/doc/getting-started.R | 4 crunch-1.14.2/crunch/inst/doc/getting-started.Rmd | 8 crunch-1.14.2/crunch/inst/doc/getting-started.html | 16 crunch-1.14.2/crunch/inst/doc/variable-order.html | 286 ---- crunch-1.14.2/crunch/inst/doc/variables.html | 104 - crunch-1.14.2/crunch/man/ShojiOrder-length.Rd | 3 crunch-1.14.2/crunch/man/addSubvariable.Rd | 17 crunch-1.14.2/crunch/man/appendDataset.Rd | 10 crunch-1.14.2/crunch/man/createWithMetadataAndFile.Rd | 5 crunch-1.14.2/crunch/man/crunch.Rd | 4 crunch-1.14.2/crunch/man/crunchBox.Rd |only crunch-1.14.2/crunch/man/dataset-extract.Rd | 9 crunch-1.14.2/crunch/man/dedupeOrder.Rd |only crunch-1.14.2/crunch/man/delete.Rd | 8 crunch-1.14.2/crunch/man/deleteSubvariables.Rd | 15 crunch-1.14.2/crunch/man/deleteVariables.Rd | 21 crunch-1.14.2/crunch/man/describe-catalog.Rd | 3 crunch-1.14.2/crunch/man/duplicated.Rd |only crunch-1.14.2/crunch/man/embedCrunchBox.Rd |only crunch-1.14.2/crunch/man/flattenOrder.Rd |only crunch-1.14.2/crunch/man/flipArrays.Rd |only crunch-1.14.2/crunch/man/hiddenVariables.Rd | 5 crunch-1.14.2/crunch/man/hideVariables.Rd | 16 crunch-1.14.2/crunch/man/joinDatasets.Rd |only crunch-1.14.2/crunch/man/locateEntity.Rd |only crunch-1.14.2/crunch/man/makeArray.Rd | 34 crunch-1.14.2/crunch/man/mergeFork.Rd | 8 crunch-1.14.2/crunch/man/moveToGroup.Rd |only crunch-1.14.2/crunch/man/preCrunchBoxCheck.Rd |only crunch-1.14.2/crunch/man/removeEmptyGroups.Rd |only crunch-1.14.2/crunch/man/session-extract.Rd |only crunch-1.14.2/crunch/man/session.Rd | 9 crunch-1.14.2/crunch/man/settings.Rd |only crunch-1.14.2/crunch/man/show-crunch.Rd | 6 crunch-1.14.2/crunch/man/tokenAuth.Rd |only crunch-1.14.2/crunch/man/tuple-methods.Rd | 14 crunch-1.14.2/crunch/man/urls.Rd | 12 crunch-1.14.2/crunch/man/variable-extract.Rd | 10 crunch-1.14.2/crunch/man/variableMetadata.Rd | 5 crunch-1.14.2/crunch/man/weight.Rd | 2 crunch-1.14.2/crunch/man/which.Rd |only crunch-1.14.2/crunch/tests/testthat/api/accounts/account1.json | 2 crunch-1.14.2/crunch/tests/testthat/api/accounts/account1/users.json | 2 crunch-1.14.2/crunch/tests/testthat/api/datasets-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets.json | 8 crunch-1.14.2/crunch/tests/testthat/api/datasets/1 |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/2 |only crunch-1.14.2/crunch/tests/testthat/api/datasets/2.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/3 |only crunch-1.14.2/crunch/tests/testthat/api/datasets/3.json |only crunch-1.14.2/crunch/tests/testthat/api/projects/project1/datasets.json | 2 crunch-1.14.2/crunch/tests/testthat/api/projects/project1/datasets/order.json | 2 crunch-1.14.2/crunch/tests/testthat/api/teams.json | 2 crunch-1.14.2/crunch/tests/testthat/api/teams/team1.json | 2 crunch-1.14.2/crunch/tests/testthat/api/teams/team1/members.json | 2 crunch-1.14.2/crunch/tests/testthat/api/users/user1.json | 2 crunch-1.14.2/crunch/tests/testthat/helper-contexts.R | 33 crunch-1.14.2/crunch/tests/testthat/helper-expectations.R | 4 crunch-1.14.2/crunch/tests/testthat/helper.R | 2 crunch-1.14.2/crunch/tests/testthat/test-active-filter.R | 183 +- crunch-1.14.2/crunch/tests/testthat/test-add-array.R | 46 crunch-1.14.2/crunch/tests/testthat/test-add-subvariable.R | 37 crunch-1.14.2/crunch/tests/testthat/test-add-variable-definition.R | 7 crunch-1.14.2/crunch/tests/testthat/test-append-arrays.R | 46 crunch-1.14.2/crunch/tests/testthat/test-append-conflicts.R | 29 crunch-1.14.2/crunch/tests/testthat/test-append-debug.R | 72 - 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crunch-1.14.2/crunch/tests/testthat/test-progress.R | 6 crunch-1.14.2/crunch/tests/testthat/test-projects.R | 23 crunch-1.14.2/crunch/tests/testthat/test-session.R | 16 crunch-1.14.2/crunch/tests/testthat/test-share.R | 6 crunch-1.14.2/crunch/tests/testthat/test-shoji.R | 4 crunch-1.14.2/crunch/tests/testthat/test-update-with-missing.R | 265 ++- crunch-1.14.2/crunch/tests/testthat/test-update.R | 2 crunch-1.14.2/crunch/tests/testthat/test-variable-catalog.R | 66 crunch-1.14.2/crunch/tests/testthat/test-variable-delete.R | 189 +- crunch-1.14.2/crunch/tests/testthat/test-variable-metadata.R | 25 crunch-1.14.2/crunch/tests/testthat/test-variable-order.R | 715 ++++++---- crunch-1.14.2/crunch/tests/testthat/test-variable-summary.R | 42 crunch-1.14.2/crunch/tests/testthat/test-variable-type.R | 4 crunch-1.14.2/crunch/tests/testthat/test-variables.R | 8 crunch-1.14.2/crunch/tests/testthat/test-versioning.R | 8 crunch-1.14.2/crunch/tests/testthat/test-weighting.R | 199 +- crunch-1.14.2/crunch/vignettes/array-variables.Rmd | 6 crunch-1.14.2/crunch/vignettes/export.Rmd |only crunch-1.14.2/crunch/vignettes/filters.Rmd | 4 crunch-1.14.2/crunch/vignettes/getting-started.Rmd | 8 202 files changed, 4851 insertions(+), 3851 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.9 dated 2016-10-02 and 1.10 dated 2016-11-22
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++------------- R/mif2_methods.R | 14 +++++----- R/pmcmc_methods.R | 14 ++++++---- R/pomp.R | 68 ++++++++++++--------------------------------------- R/trajectory_pomp.R | 2 - build/partial.rdb |binary data/LondonYorke.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 21 +++++++++++++++ inst/NEWS.Rd | 14 ++++++++++ man/pmcmc.Rd | 2 + man/simulate_pomp.Rd | 2 - src/SSA_simulator.c | 2 - src/euler.c | 4 +-- src/pomp_fun.c | 4 +-- src/probe_marginal.c | 6 +++- 18 files changed, 101 insertions(+), 94 deletions(-)
Title: Fitting the Centered Autologistic and Sparse Spatial Generalized
Linear Mixed Models for Areal Data
Description: Provides tools for analyzing spatial data, especially non-Gaussian areal data. The current version supports the sparse
spatial generalized linear mixed model of Hughes and Haran (2013) <DOI:10.1111/j.1467-9868.2012.01041.x> and the centered
autologistic model of Caragea and Kaiser (2009) <DOI:10.1198/jabes.2009.07032>.
Author: John Hughes <jphughesjr@gmail.com> and Xiaohui Cui
Maintainer: John Hughes <jphughesjr@gmail.com>
Diff between ngspatial versions 1.1-1 dated 2016-08-15 and 1.1-2 dated 2016-11-22
DESCRIPTION | 15 +++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/autologistic.R | 2 +- R/zzz.R | 5 ++--- inst/CITATION | 4 ++-- src/moller.cpp | 8 ++++---- src/perfsampler.cpp | 4 ++-- src/perfsampler.h | 2 +- 9 files changed, 29 insertions(+), 30 deletions(-)
Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut, cre],
Rich FitzJohn [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between incidence versions 1.0.0 dated 2016-11-03 and 1.0.1 dated 2016-11-22
incidence-1.0.0/incidence/inst/doc/customize-plot.R |only incidence-1.0.0/incidence/inst/doc/customize-plot.Rmd |only incidence-1.0.0/incidence/inst/doc/customize-plot.html |only incidence-1.0.0/incidence/inst/doc/incidence-class.R |only incidence-1.0.0/incidence/inst/doc/incidence-class.Rmd |only incidence-1.0.0/incidence/inst/doc/incidence-class.html |only incidence-1.0.1/incidence/DESCRIPTION | 8 incidence-1.0.1/incidence/MD5 | 38 - incidence-1.0.1/incidence/NEWS.md | 24 - incidence-1.0.1/incidence/README.md | 355 ++++------------ incidence-1.0.1/incidence/build/vignette.rds |binary incidence-1.0.1/incidence/inst/doc/customize_plot.R | 6 incidence-1.0.1/incidence/inst/doc/customize_plot.Rmd | 8 incidence-1.0.1/incidence/inst/doc/customize_plot.html | 36 - incidence-1.0.1/incidence/inst/doc/incidence_class.R | 4 incidence-1.0.1/incidence/inst/doc/incidence_class.Rmd | 6 incidence-1.0.1/incidence/inst/doc/incidence_class.html | 8 incidence-1.0.1/incidence/inst/doc/overview.R | 7 incidence-1.0.1/incidence/inst/doc/overview.Rmd | 13 incidence-1.0.1/incidence/inst/doc/overview.html | 44 + incidence-1.0.1/incidence/vignettes/customize_plot.Rmd | 8 incidence-1.0.1/incidence/vignettes/incidence_class.Rmd | 6 incidence-1.0.1/incidence/vignettes/overview.Rmd | 13 23 files changed, 231 insertions(+), 353 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso', a method to include different types of variables in paired
comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and
can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used
to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1-2 dated 2015-09-28 and 0.1-3 dated 2016-11-22
BTLLasso-0.1-2/BTLLasso/data/GLES.rda |only BTLLasso-0.1-2/BTLLasso/data/GLESsmall.rda |only BTLLasso-0.1-2/BTLLasso/man/BTLLasso.ctrl.Rd |only BTLLasso-0.1-3/BTLLasso/DESCRIPTION | 14 BTLLasso-0.1-3/BTLLasso/MD5 | 76 +-- BTLLasso-0.1-3/BTLLasso/NAMESPACE | 7 BTLLasso-0.1-3/BTLLasso/R/BTLLasso-package.R |only BTLLasso-0.1-3/BTLLasso/R/BTLLasso.R | 486 +++++++++++++-------- BTLLasso-0.1-3/BTLLasso/R/RcppExports.R | 4 BTLLasso-0.1-3/BTLLasso/R/bin.fit.Cpp.R | 16 BTLLasso-0.1-3/BTLLasso/R/bootstrap.R | 177 ++++++- BTLLasso-0.1-3/BTLLasso/R/ci.BTLLasso.R | 263 +++++++++-- BTLLasso-0.1-3/BTLLasso/R/create.design.R |only BTLLasso-0.1-3/BTLLasso/R/cum.fit.Cpp.R | 29 - BTLLasso-0.1-3/BTLLasso/R/cv.BTLLasso.R | 265 +++++++---- BTLLasso-0.1-3/BTLLasso/R/design.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/fit.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/fit.cv.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/functions.R | 256 +++++++---- BTLLasso-0.1-3/BTLLasso/R/paths.R | 247 +++++++++- BTLLasso-0.1-3/BTLLasso/R/penalties.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/print.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/print.boot.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/print.cv.BTLLasso.R | 161 ++++++ BTLLasso-0.1-3/BTLLasso/R/response.BTLLasso.R |only BTLLasso-0.1-3/BTLLasso/R/singlepaths.R | 269 ++++++++++- BTLLasso-0.1-3/BTLLasso/data/Buli1516.RData |only BTLLasso-0.1-3/BTLLasso/data/GLES.RData |only BTLLasso-0.1-3/BTLLasso/data/GLESsmall.RData |only BTLLasso-0.1-3/BTLLasso/data/SimData.RData |only BTLLasso-0.1-3/BTLLasso/man/BTLLasso-package.Rd | 122 ++--- BTLLasso-0.1-3/BTLLasso/man/BTLLasso.Rd | 200 +++++--- BTLLasso-0.1-3/BTLLasso/man/Buli1516.Rd |only BTLLasso-0.1-3/BTLLasso/man/GLES.Rd | 99 ++-- BTLLasso-0.1-3/BTLLasso/man/GLESsmall.Rd | 129 ++--- BTLLasso-0.1-3/BTLLasso/man/SimData.Rd |only BTLLasso-0.1-3/BTLLasso/man/boot.BTLLasso.Rd | 188 ++++---- BTLLasso-0.1-3/BTLLasso/man/ci.BTLLasso.Rd | 150 ++++-- BTLLasso-0.1-3/BTLLasso/man/ctrl.BTLLasso.Rd |only BTLLasso-0.1-3/BTLLasso/man/cv.BTLLasso.Rd | 240 ++++++---- BTLLasso-0.1-3/BTLLasso/man/paths.Rd | 130 +++-- BTLLasso-0.1-3/BTLLasso/man/print.BTLLasso.Rd |only BTLLasso-0.1-3/BTLLasso/man/print.boot.BTLLasso.Rd |only BTLLasso-0.1-3/BTLLasso/man/print.cv.BTLLasso.Rd | 49 -- BTLLasso-0.1-3/BTLLasso/man/response.BTLLasso.Rd |only BTLLasso-0.1-3/BTLLasso/man/singlepaths.Rd | 168 ++++--- BTLLasso-0.1-3/BTLLasso/src/Makevars | 3 BTLLasso-0.1-3/BTLLasso/src/Makevars.win | 4 BTLLasso-0.1-3/BTLLasso/src/RcppExports.cpp | 101 ++-- BTLLasso-0.1-3/BTLLasso/src/cppfunctions.cpp | 125 +++-- 50 files changed, 2713 insertions(+), 1265 deletions(-)
Title: Generalized Pareto Distribution and Peaks Over Threshold
Description: Some functions useful to perform a Peak Over Threshold
analysis in univariate and bivariate cases. A user's guide is
available.
Author: Mathieu Ribatet [aut], Christophe Dutang [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between POT versions 1.1-5 dated 2016-11-08 and 1.1-6 dated 2016-11-22
POT-1.1-5/POT/man/dens.uvpot.Rd |only POT-1.1-5/POT/man/pp.uvpot.Rd |only POT-1.1-5/POT/man/qq.uvpot.Rd |only POT-1.1-5/POT/man/retlev.mcpot.Rd |only POT-1.1-5/POT/man/retlev.uvpot.Rd |only POT-1.1-6/POT/DESCRIPTION | 6 +- POT-1.1-6/POT/MD5 | 63 ++++++++++----------- POT-1.1-6/POT/NAMESPACE | 43 +++++++------- POT-1.1-6/POT/R/bvpot-fitBvGPD.R | 36 +++++------- POT-1.1-6/POT/R/mcpot-fitMcGPD.R | 36 +++++------- POT-1.1-6/POT/R/pot-gen-coef.R |only POT-1.1-6/POT/R/util-GPD-mle.R | 79 +++++++++++++-------------- POT-1.1-6/POT/R/util-GPD-mple.R | 82 +++++++++++++++------------- POT-1.1-6/POT/R/uvpot-fitPP.R | 91 +++++++++---------------------- POT-1.1-6/POT/R/uvpot-gen-retlev.R | 27 +++------ POT-1.1-6/POT/build/vignette.rds |binary POT-1.1-6/POT/inst/ChangeLog | 89 +++++++++++++++++------------- POT-1.1-6/POT/man/chimeas.Rd | 2 POT-1.1-6/POT/man/clust.Rd | 2 POT-1.1-6/POT/man/coef.pot.Rd |only POT-1.1-6/POT/man/convassess.Rd | 13 +++- POT-1.1-6/POT/man/dens.Rd | 49 ++++++++++++++-- POT-1.1-6/POT/man/dexi.Rd | 4 - POT-1.1-6/POT/man/exiplot.Rd | 6 +- POT-1.1-6/POT/man/fitBvGPD.Rd | 6 +- POT-1.1-6/POT/man/fitexi.Rd | 10 +-- POT-1.1-6/POT/man/logLik.pot.Rd | 4 - POT-1.1-6/POT/man/pp.Rd | 49 +++++++++++++++- POT-1.1-6/POT/man/print.bvpot.Rd | 2 POT-1.1-6/POT/man/print.mcpot.Rd | 2 POT-1.1-6/POT/man/print.uvpot.Rd | 2 POT-1.1-6/POT/man/qq.Rd | 55 ++++++++++++++++--- POT-1.1-6/POT/man/retlev.Rd | 107 +++++++++++++++++++++++++++++++++++-- POT-1.1-6/POT/man/simmcpot.Rd | 4 - POT-1.1-6/POT/man/specdens.Rd | 4 - POT-1.1-6/POT/man/summary.pot.Rd | 4 - 36 files changed, 536 insertions(+), 341 deletions(-)
Title: Forgetting Factor Methods for Change Detection in Streaming Data
Description: An implementation of the adaptive forgetting factor scheme described in Bodenham and Adams (2016) <doi:10.1007/s11222-016-9684-8> which adaptively estimates the mean and variance of a stream in order to detect multiple changepoints in streaming data. The implementation is in C++ and uses Rcpp. Additionally, implementations of the fixed forgetting factor scheme from the same paper, as well as the classic CUSUM and EWMA methods, are included.
Author: Dean Bodenham
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>
Diff between ffstream versions 0.1.2 dated 2016-11-13 and 0.1.5 dated 2016-11-22
ffstream-0.1.2/ffstream/inst/doc/ffstream_html_full.html |only ffstream-0.1.2/ffstream/inst/doc/ffstream_pdf.pdf |only ffstream-0.1.5/ffstream/DESCRIPTION | 10 +- ffstream-0.1.5/ffstream/MD5 | 56 +++++++-------- ffstream-0.1.5/ffstream/R/zzz.R | 2 ffstream-0.1.5/ffstream/build/vignette.rds |binary ffstream-0.1.5/ffstream/inst/doc/ffstream_html.Rmd | 4 - ffstream-0.1.5/ffstream/inst/doc/ffstream_html.html | 4 - ffstream-0.1.5/ffstream/src/aff.cpp | 10 +- ffstream-0.1.5/ffstream/src/aff.h | 6 - ffstream-0.1.5/ffstream/src/affcd.cpp | 4 - ffstream-0.1.5/ffstream/src/cusumcd.cpp | 8 +- ffstream-0.1.5/ffstream/src/cusumcd.h | 11 +- ffstream-0.1.5/ffstream/src/detectVectors.cpp | 2 ffstream-0.1.5/ffstream/src/detectVectors.h | 2 ffstream-0.1.5/ffstream/src/detector.cpp | 2 ffstream-0.1.5/ffstream/src/detector.h | 4 - ffstream-0.1.5/ffstream/src/ewmacd.cpp | 8 +- ffstream-0.1.5/ffstream/src/ewmacd.h | 12 +-- ffstream-0.1.5/ffstream/src/fff.cpp | 6 - ffstream-0.1.5/ffstream/src/fff.h | 19 ++--- ffstream-0.1.5/ffstream/src/fffcd.cpp | 6 - ffstream-0.1.5/ffstream/src/fffcd.h | 6 - ffstream-0.1.5/ffstream/src/processVectors.cpp | 2 ffstream-0.1.5/ffstream/src/processVectors.h | 4 - ffstream-0.1.5/ffstream/src/utils.cpp | 2 ffstream-0.1.5/ffstream/src/utils.h | 27 ++++++- ffstream-0.1.5/ffstream/tests/testthat/test7_initewma.R | 1 ffstream-0.1.5/ffstream/tests/testthat/testx10_ewmacd.R | 9 ++ ffstream-0.1.5/ffstream/vignettes/ffstream_html.Rmd | 4 - 30 files changed, 133 insertions(+), 98 deletions(-)
Title: Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF)
Description: Provides a collection of standard methods to detect differential item functioning among dichotomously scored items. Methods for uniform and non-uniform DIF, based on test-score or IRT methods, for comparing two or more than two groups of respondents, are available (Magis, Beland, Tuerlinckx and De Boeck,A General Framework and an R Package for the Detection of Dichotomous Differential Item Functioning, Behavior Research Methods, 42, 2010, 847-862 <doi:10.3758/BRM.42.3.847>).
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles Raiche (UQAM)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between difR versions 4.6 dated 2015-04-29 and 4.7 dated 2016-11-22
difR-4.6/difR/LICENSE |only difR-4.7/difR/DESCRIPTION | 14 difR-4.7/difR/MD5 | 71 +-- difR-4.7/difR/NAMESPACE | 9 difR-4.7/difR/NEWS | 76 +++ difR-4.7/difR/R/Logistik.R | 63 +-- difR-4.7/difR/R/dichoDif.r | 241 +++++++----- difR-4.7/difR/R/difBD.r | 275 ++++++++----- difR-4.7/difR/R/difGMH.r | 287 ++++++++------ difR-4.7/difR/R/difGenLogistic.R | 204 ++++++---- difR-4.7/difR/R/difGenLord.r | 663 +++++++++++++++++++-------------- difR-4.7/difR/R/difLRT.r | 302 ++++++++------- difR-4.7/difR/R/difLogReg.R | 35 + difR-4.7/difR/R/difLogistic.r | 232 +++++++---- difR-4.7/difR/R/difLord.r | 706 ++++++++++++++++++++--------------- difR-4.7/difR/R/difMH.r | 209 ++++++---- difR-4.7/difR/R/difRaju.r | 723 ++++++++++++++++++++---------------- difR-4.7/difR/R/genDichoDif.R | 147 ++++--- difR-4.7/difR/R/selectDif.r | 50 +- difR-4.7/difR/R/selectGenDif.R | 26 - difR-4.7/difR/inst/CITATION | 23 - difR-4.7/difR/man/Logistik.rd | 20 difR-4.7/difR/man/dichoDif.rd | 8 difR-4.7/difR/man/difBD.rd | 14 difR-4.7/difR/man/difGMH.rd | 13 difR-4.7/difR/man/difGenLogistic.rd | 12 difR-4.7/difR/man/difGenLord.rd | 17 difR-4.7/difR/man/difLRT.rd | 18 difR-4.7/difR/man/difLogReg.rd | 5 difR-4.7/difR/man/difLogistic.rd | 22 - difR-4.7/difR/man/difLord.rd | 19 difR-4.7/difR/man/difMH.rd | 17 difR-4.7/difR/man/difR-package.Rd | 1 difR-4.7/difR/man/difRaju.rd | 16 difR-4.7/difR/man/genDichoDif.rd | 8 difR-4.7/difR/man/selectDif.rd | 5 difR-4.7/difR/man/selectGenDif.rd | 5 37 files changed, 2789 insertions(+), 1767 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.7.0 dated 2016-04-05 and 3.8.0 dated 2016-11-22
DESCRIPTION | 8 +-- MD5 | 16 +++--- NEWS | 15 +++++ R/Deriv.R | 111 ++++++++++++++++++++++++++++++-------------- R/Simplify.R | 43 +++++++++-------- inst/CITATION | 4 - man/Deriv-package.Rd | 5 - man/Deriv.Rd | 41 ++++++++++++++-- tests/testthat/test_Deriv.R | 26 ++++++++-- 9 files changed, 190 insertions(+), 79 deletions(-)
Title: Companion to Applied Linear Statistical Models
Description: Functions and Data set presented in Applied Linear Statistical Models Fifth Edition (Chapters 1-9 and 16-18), Michael H. Kutner; Christopher J. Nachtsheim; John Neter; William Li, 2005. (ISBN-10: 0071122214, ISBN-13: 978-0071122214) that do not exist in R, are gathered in this package. The whole book will be covered in the next versions.
Author: Ali Ghanbari <a.ghanbari541@gmail.com>
Maintainer: Ali Ghanbari <a.ghanbari541@gmail.com>
Diff between ALSM versions 0.1.1 dated 2016-10-30 and 0.1.2 dated 2016-11-22
DESCRIPTION | 12 ++++-------- MD5 | 14 ++++++++------ NAMESPACE | 2 ++ R/16_17_18_oneway.R | 27 ++++++++++++++++----------- R/17_ss.towway.R |only R/3_boxcox.sse.R | 4 ++-- R/6_ci.reg.R | 2 +- man/17_ssea.oneway.Rd |only man/oneway.Rd | 4 +++- 9 files changed, 36 insertions(+), 29 deletions(-)
Title: Selective Editing via Mixture Models
Description: Detection of outliers and influential errors using a latent variable model.
Author: Ugo Guarnera, Teresa Buglielli
Maintainer: Teresa Buglielli <bugliell@istat.it>
Diff between SeleMix versions 0.9.1 dated 2013-12-12 and 1.0.1 dated 2016-11-22
DESCRIPTION | 16 +-- MD5 | 30 +++-- NAMESPACE | 8 + NEWS | 4 R/check.vars.r | 84 ++++++++++----- R/ml.est.R | 218 +++++++++++++++++++++++++---------------- R/pred.y.r | 2 R/sel.pairs.r | 14 +- R/sel.plot.R |only build/vignette.rds |binary inst/doc/SeleMix-vignette.Rnw | 2 man/ml.est.Rd | 4 man/sel.edit.Rd | 6 - man/sel.pairs.Rd | 5 man/sel.plot.Rd |only vignettes/SeleMix-vignette.Rnw | 2 vignettes/selemix.bib | 17 ++- 17 files changed, 260 insertions(+), 152 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Jonas Haslbeck, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.4.0 dated 2016-10-29 and 1.4.1 dated 2016-11-22
DESCRIPTION | 8 MD5 | 19 +- NAMESPACE | 7 NEWS | 8 R/PLOT.R | 6 R/ggmFit.R |only R/glasso_methods.R | 11 + R/palettes.R |only R/qgraph.R | 436 +++++++++++++++++++++++++++++++++++------------------ man/EBICglasso.Rd | 5 man/ggmFit.Rd |only man/qgraph.Rd | 8 12 files changed, 348 insertions(+), 160 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-1 dated 2016-10-14 and 0.9-2 dated 2016-11-22
DESCRIPTION | 12 +++++----- MD5 | 30 ++++++++++++------------- NAMESPACE | 2 - NEWS | 18 +++++++++++++++ R/as.data.frame.netmeta.R | 7 +++-- R/decomp.design.R | 3 -- R/forest.netmeta.R | 7 +++-- R/netgraph.R | 54 ++++++++++++++++++++++++++++------------------ R/netheat.R | 3 -- R/netmeasures.R | 4 +-- R/nma.krahn.R | 21 ++++++++--------- R/print.decomp.design.R | 9 ++++--- R/print.netmeta.R | 4 +-- R/print.summary.netmeta.R | 3 -- R/tau.within.R | 3 -- man/netgraph.Rd | 11 ++++++--- 16 files changed, 112 insertions(+), 79 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
The R Consortium [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.2 dated 2016-06-17 and 0.3 dated 2016-11-22
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/hms.R | 11 ++++++----- README.md | 6 +++--- man/hms.Rd | 17 +++++++++-------- tests/testthat/test-lubridate.R | 8 +++----- tests/testthat/test-output.R | 5 +++++ 8 files changed, 44 insertions(+), 33 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models
using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 1.1.0 dated 2016-10-11 and 1.2.0 dated 2016-11-22
brms-1.1.0/brms/inst/doc/brms_families.pdf |only brms-1.1.0/brms/man/logLik.brmsfit.Rd |only brms-1.1.0/brms/man/pp_check.Rd |only brms-1.2.0/brms/DESCRIPTION | 14 brms-1.2.0/brms/MD5 | 155 +-- brms-1.2.0/brms/NAMESPACE | 27 brms-1.2.0/brms/R/brm.R | 26 brms-1.2.0/brms/R/brmsfit-helpers.R | 221 +++- brms-1.2.0/brms/R/brmsfit-methods.R | 800 ++++++++++------- brms-1.2.0/brms/R/brmsformula.R | 15 brms-1.2.0/brms/R/data-helpers.R | 139 +- brms-1.2.0/brms/R/distributions.R | 7 brms-1.2.0/brms/R/extract_draws.R | 143 +-- brms-1.2.0/brms/R/families.R | 54 - brms-1.2.0/brms/R/fitted.R | 10 brms-1.2.0/brms/R/generics.R | 146 ++- brms-1.2.0/brms/R/linear_predictor.R | 5 brms-1.2.0/brms/R/loglik.R | 9 brms-1.2.0/brms/R/make_stancode.R | 5 brms-1.2.0/brms/R/make_standata.R | 20 brms-1.2.0/brms/R/misc-methods.R | 7 brms-1.2.0/brms/R/misc.R | 8 brms-1.2.0/brms/R/plots.R | 36 brms-1.2.0/brms/R/predict.R | 11 brms-1.2.0/brms/R/priors.R | 492 +++++----- brms-1.2.0/brms/R/stan-helpers.R | 80 + brms-1.2.0/brms/R/stan-predictor.R | 185 +-- brms-1.2.0/brms/R/sysdata.rda |binary brms-1.2.0/brms/R/validate.R | 203 ++-- brms-1.2.0/brms/README.md | 16 brms-1.2.0/brms/build/vignette.rds |binary brms-1.2.0/brms/inst/NEWS.Rd | 71 + brms-1.2.0/brms/inst/chunks/fun_hurdle_lognormal.stan |only brms-1.2.0/brms/inst/doc/brms.ltx | 2 brms-1.2.0/brms/inst/doc/brms.pdf |binary brms-1.2.0/brms/inst/doc/brms_distreg.R |only brms-1.2.0/brms/inst/doc/brms_distreg.Rmd |only brms-1.2.0/brms/inst/doc/brms_distreg.html |only brms-1.2.0/brms/inst/doc/brms_families.Rmd | 21 brms-1.2.0/brms/inst/doc/brms_families.html |only brms-1.2.0/brms/inst/doc/brms_monotonic.R |only brms-1.2.0/brms/inst/doc/brms_monotonic.Rmd |only brms-1.2.0/brms/inst/doc/brms_monotonic.html |only brms-1.2.0/brms/inst/doc/brms_nonlinear.R |only brms-1.2.0/brms/inst/doc/brms_nonlinear.Rmd |only brms-1.2.0/brms/inst/doc/brms_nonlinear.html |only brms-1.2.0/brms/inst/doc/brms_phylogenetics.R |only brms-1.2.0/brms/inst/doc/brms_phylogenetics.Rmd |only brms-1.2.0/brms/inst/doc/brms_phylogenetics.html |only brms-1.2.0/brms/man/LOO.Rd | 19 brms-1.2.0/brms/man/VarCorr.brmsfit.Rd | 6 brms-1.2.0/brms/man/WAIC.Rd | 15 brms-1.2.0/brms/man/brm.Rd | 21 brms-1.2.0/brms/man/brmsfamily.Rd | 27 brms-1.2.0/brms/man/brmsfit-class.Rd | 8 brms-1.2.0/brms/man/coef.brmsfit.Rd | 7 brms-1.2.0/brms/man/expose_functions.Rd | 2 brms-1.2.0/brms/man/fitted.brmsfit.Rd | 16 brms-1.2.0/brms/man/fixef.brmsfit.Rd | 2 brms-1.2.0/brms/man/hypothesis.Rd | 35 brms-1.2.0/brms/man/log_lik.brmsfit.Rd |only brms-1.2.0/brms/man/make_stancode.Rd | 2 brms-1.2.0/brms/man/make_standata.Rd | 2 brms-1.2.0/brms/man/marginal_effects.Rd | 22 brms-1.2.0/brms/man/marginal_smooths.Rd |only brms-1.2.0/brms/man/plot.brmsfit.Rd | 27 brms-1.2.0/brms/man/posterior_samples.Rd | 6 brms-1.2.0/brms/man/pp_check.brmsfit.Rd | 51 - brms-1.2.0/brms/man/predict.brmsfit.Rd | 26 brms-1.2.0/brms/man/print.brmsprior.Rd |only brms-1.2.0/brms/man/prior_samples.Rd | 4 brms-1.2.0/brms/man/prior_summary.brmsfit.Rd |only brms-1.2.0/brms/man/ranef.brmsfit.Rd | 6 brms-1.2.0/brms/man/residuals.brmsfit.Rd | 16 brms-1.2.0/brms/man/set_prior.Rd | 97 +- brms-1.2.0/brms/man/summary.brmsfit.Rd | 15 brms-1.2.0/brms/tests/testthat/tests.brmsfit-methods.R | 61 - brms-1.2.0/brms/tests/testthat/tests.data-helpers.R | 2 brms-1.2.0/brms/tests/testthat/tests.make_stancode.R | 39 brms-1.2.0/brms/tests/testthat/tests.make_standata.R | 12 brms-1.2.0/brms/tests/testthat/tests.misc.R | 3 brms-1.2.0/brms/tests/testthat/tests.priors.R | 68 - brms-1.2.0/brms/tests/testthat/tests.stan-helpers.R | 30 brms-1.2.0/brms/tests/testthat/tests.stan_functions.R | 11 brms-1.2.0/brms/tests/testthat/tests.validate.R | 29 brms-1.2.0/brms/vignettes/brms.ltx | 2 brms-1.2.0/brms/vignettes/brms_distreg.Rmd |only brms-1.2.0/brms/vignettes/brms_families.Rmd | 21 brms-1.2.0/brms/vignettes/brms_monotonic.Rmd |only brms-1.2.0/brms/vignettes/brms_nonlinear.Rmd |only brms-1.2.0/brms/vignettes/brms_phylogenetics.Rmd |only 91 files changed, 2184 insertions(+), 1454 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.1 dated 2016-11-18 and 3.1.1 dated 2016-11-22
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/buffesm.R | 24 ++++++++++++++++-------- man/x2pCO2.Rd | 2 +- 5 files changed, 30 insertions(+), 17 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.15 dated 2016-11-09 and 1.15.1 dated 2016-11-22
DESCRIPTION | 12 +++++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 1 + R/block.R | 2 +- R/citation.R | 1 + R/engine.R | 8 ++++---- R/hooks-extra.R | 33 +++++++++++++++++++++++++++++---- R/params.R | 22 +++------------------- README.md | 14 +++++++------- build/knitr.pdf |binary inst/doc/knit_expand.html | 4 ++-- inst/doc/knit_print.html | 13 +++++++------ inst/doc/knitr-intro.html | 10 +++++----- inst/doc/knitr-markdown.html | 2 +- inst/doc/knitr-refcard.pdf |binary man/chunk_hook.Rd | 8 ++++++++ 16 files changed, 91 insertions(+), 69 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.2-2 dated 2016-10-31 and 0.2-4 dated 2016-11-22
sf-0.2-2/sf/configure.win |only sf-0.2-2/sf/inst/doc/sfr.R |only sf-0.2-2/sf/inst/doc/sfr.Rmd |only sf-0.2-2/sf/inst/doc/sfr.html |only sf-0.2-2/sf/man/crs.Rd |only sf-0.2-2/sf/vignettes/nc.gpkg |only sf-0.2-2/sf/vignettes/sfr.Rmd |only sf-0.2-4/sf/DESCRIPTION | 12 sf-0.2-4/sf/MD5 | 187 +- sf-0.2-4/sf/NAMESPACE | 27 sf-0.2-4/sf/R/RcppExports.R | 24 sf-0.2-4/sf/R/arith.R | 41 sf-0.2-4/sf/R/crs.R | 182 +- sf-0.2-4/sf/R/db.R |only sf-0.2-4/sf/R/geom.R | 79 - sf-0.2-4/sf/R/grid.R | 20 sf-0.2-4/sf/R/plot.R | 6 sf-0.2-4/sf/R/read.R | 281 +-- sf-0.2-4/sf/R/sf.R | 64 sf-0.2-4/sf/R/sfc.R | 86 - sf-0.2-4/sf/R/sp.R | 13 sf-0.2-4/sf/R/tidy.R |only sf-0.2-4/sf/R/transform.R | 17 sf-0.2-4/sf/R/wkb.R | 51 sf-0.2-4/sf/R/wkt.R | 2 sf-0.2-4/sf/build/vignette.rds |binary sf-0.2-4/sf/cleanup | 1 sf-0.2-4/sf/configure | 1831 ++++++++++++++++++++++++- sf-0.2-4/sf/configure.in | 228 ++- sf-0.2-4/sf/demo/00Index | 1 sf-0.2-4/sf/demo/affine.R |only sf-0.2-4/sf/demo/nc.R | 13 sf-0.2-4/sf/inst/doc/sf1.R |only sf-0.2-4/sf/inst/doc/sf1.Rmd |only sf-0.2-4/sf/inst/doc/sf1.html |only sf-0.2-4/sf/inst/doc/sf2.R |only sf-0.2-4/sf/inst/doc/sf2.Rmd |only sf-0.2-4/sf/inst/doc/sf2.html |only sf-0.2-4/sf/inst/doc/sf3.R |only sf-0.2-4/sf/inst/doc/sf3.Rmd |only sf-0.2-4/sf/inst/doc/sf3.html |only sf-0.2-4/sf/inst/shape/storms_xyz.dbf |only sf-0.2-4/sf/inst/shape/storms_xyz.shp |only sf-0.2-4/sf/inst/shape/storms_xyz.shx |only sf-0.2-4/sf/inst/shape/storms_xyz_feature.dbf |only sf-0.2-4/sf/inst/shape/storms_xyz_feature.shp |only sf-0.2-4/sf/inst/shape/storms_xyz_feature.shx |only sf-0.2-4/sf/inst/shape/storms_xyzm.dbf |only sf-0.2-4/sf/inst/shape/storms_xyzm.shp |only sf-0.2-4/sf/inst/shape/storms_xyzm.shx |only sf-0.2-4/sf/inst/shape/storms_xyzm_feature.dbf |only sf-0.2-4/sf/inst/shape/storms_xyzm_feature.shp |only sf-0.2-4/sf/inst/shape/storms_xyzm_feature.shx |only sf-0.2-4/sf/man/bind.Rd |only sf-0.2-4/sf/man/dplyr.Rd |only sf-0.2-4/sf/man/geos.Rd | 41 sf-0.2-4/sf/man/plot.Rd | 6 sf-0.2-4/sf/man/rawToHex.Rd |only sf-0.2-4/sf/man/sf.Rd | 8 sf-0.2-4/sf/man/sfc.Rd | 10 sf-0.2-4/sf/man/st_as_binary.Rd | 10 sf-0.2-4/sf/man/st_as_grob.Rd | 4 sf-0.2-4/sf/man/st_as_sf.Rd | 4 sf-0.2-4/sf/man/st_as_sfc.Rd | 7 sf-0.2-4/sf/man/st_crs.Rd |only sf-0.2-4/sf/man/st_drivers.Rd | 4 sf-0.2-4/sf/man/st_drop_zm.Rd | 4 sf-0.2-4/sf/man/st_geometry.Rd | 4 sf-0.2-4/sf/man/st_geometry_type.Rd | 4 sf-0.2-4/sf/man/st_is_longlat.Rd | 4 sf-0.2-4/sf/man/st_list.Rd |only sf-0.2-4/sf/man/st_read.Rd | 39 sf-0.2-4/sf/man/st_transform.Rd | 5 sf-0.2-4/sf/man/st_viewport.Rd | 4 sf-0.2-4/sf/man/st_write.Rd | 19 sf-0.2-4/sf/man/st_write_db.Rd | 19 sf-0.2-4/sf/man/summary.sfc.Rd | 4 sf-0.2-4/sf/man/tibble.Rd | 8 sf-0.2-4/sf/src/RcppExports.cpp | 65 sf-0.2-4/sf/src/bbox.cpp | 2 sf-0.2-4/sf/src/gdal.cpp | 119 + sf-0.2-4/sf/src/gdal.h | 2 sf-0.2-4/sf/src/gdal_geom.cpp | 47 sf-0.2-4/sf/src/gdal_read.cpp | 124 + sf-0.2-4/sf/src/gdal_write.cpp | 31 sf-0.2-4/sf/src/geos.cpp | 250 +-- sf-0.2-4/sf/src/wkb.cpp | 105 - sf-0.2-4/sf/tests/Rplots.pdf |only sf-0.2-4/sf/tests/crs.R |only sf-0.2-4/sf/tests/crs.Rout.save |only sf-0.2-4/sf/tests/dplyr.R |only sf-0.2-4/sf/tests/dplyr.Rout.save |only sf-0.2-4/sf/tests/gdal_geom.R | 32 sf-0.2-4/sf/tests/gdal_geom.Rout.save | 97 - sf-0.2-4/sf/tests/geos.R | 2 sf-0.2-4/sf/tests/geos.Rout.save | 17 sf-0.2-4/sf/tests/grid.Rout.save | 26 sf-0.2-4/sf/tests/pg.R | 11 sf-0.2-4/sf/tests/pg.Rout.save | 15 sf-0.2-4/sf/tests/read.R |only sf-0.2-4/sf/tests/read.Rout.save |only sf-0.2-4/sf/tests/roundtrip.R | 1 sf-0.2-4/sf/tests/roundtrip.Rout.save | 30 sf-0.2-4/sf/tests/sfc.R | 11 sf-0.2-4/sf/tests/sfc.Rout.save | 61 sf-0.2-4/sf/tests/testthat/test_gdal.R | 6 sf-0.2-4/sf/tests/testthat/test_read.R | 29 sf-0.2-4/sf/tests/testthat/test_sf.R | 8 sf-0.2-4/sf/tests/testthat/test_sfc.R | 14 sf-0.2-4/sf/tests/testthat/test_tm.R | 11 sf-0.2-4/sf/tests/wkb.R | 4 sf-0.2-4/sf/tests/wkb.Rout.save | 13 sf-0.2-4/sf/tests/write.R | 2 sf-0.2-4/sf/tests/write.Rout.save |only sf-0.2-4/sf/vignettes/rw.html |only sf-0.2-4/sf/vignettes/sf1.Rmd |only sf-0.2-4/sf/vignettes/sf2.Rmd |only sf-0.2-4/sf/vignettes/sf3.Rmd |only sf-0.2-4/sf/vignettes/sfr.html |only 119 files changed, 3518 insertions(+), 991 deletions(-)
Title: SA Counterparty Credit Risk under Basel III
Description: Computes the Exposure-At-Default based on standardized approach
of the Basel III Regulatory framework (SA-CCR). Currently, trade types of all
the five major asset classes have been created and, given the inheritance-
based structure of the application, the addition of further trade types
is straightforward. The application returns a list of trees (one per CSA) after
automatically separating the trades based on the CSAs, the hedging sets, the
netting sets and the risk factors. The basis and volatility transactions are
also identified and treated in specific hedging sets whereby the corresponding
penalty factors are applied. All the examples appearing on the
regulatory paper (including the margined and the un-margined workflow) have been
implemented.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between SACCR versions 1.5 dated 2016-03-04 and 2.0 dated 2016-11-22
SACCR-1.5/SACCR/R/CSA.R |only SACCR-1.5/SACCR/R/Commodity.R |only SACCR-1.5/SACCR/R/Credit.R |only SACCR-1.5/SACCR/R/FX.R |only SACCR-1.5/SACCR/R/IRD.R |only SACCR-1.5/SACCR/R/Swap.R |only SACCR-1.5/SACCR/R/Trade.R |only SACCR-1.5/SACCR/R/Vol.R |only SACCR-1.5/SACCR/man/CSA-class.Rd |only SACCR-1.5/SACCR/man/CommSwap-class.Rd |only SACCR-1.5/SACCR/man/Commodity-class.Rd |only SACCR-1.5/SACCR/man/CreditIndex-class.Rd |only SACCR-1.5/SACCR/man/CreditSingle-class.Rd |only SACCR-1.5/SACCR/man/FXSwap-class.Rd |only SACCR-1.5/SACCR/man/IRDSwap-class.Rd |only SACCR-1.5/SACCR/man/IRDSwapVol-class.Rd |only SACCR-1.5/SACCR/man/IRDSwaption-class.Rd |only SACCR-2.0/SACCR/DESCRIPTION | 38 +-- SACCR-2.0/SACCR/MD5 | 87 +++---- SACCR-2.0/SACCR/NAMESPACE | 26 +- SACCR-2.0/SACCR/R/CalcAddon.R | 298 ++++++++++++------------ SACCR-2.0/SACCR/R/CalcRC.R | 42 ++- SACCR-2.0/SACCR/R/CalculateFactorMult.R |only SACCR-2.0/SACCR/R/CreateTradeGraph.R |only SACCR-2.0/SACCR/R/ExampleBasisVol.R | 16 - SACCR-2.0/SACCR/R/ExampleComm.R | 14 - SACCR-2.0/SACCR/R/ExampleCredit.R | 15 - SACCR-2.0/SACCR/R/ExampleFX.R | 14 - SACCR-2.0/SACCR/R/ExampleIRD.R | 14 - SACCR-2.0/SACCR/R/ExampleIRDCommMargined.R | 49 ++- SACCR-2.0/SACCR/R/ExampleIRDCredit.R | 21 - SACCR-2.0/SACCR/R/GroupCommTrades.R |only SACCR-2.0/SACCR/R/GroupCreditTrades.R |only SACCR-2.0/SACCR/R/GroupEquityTrades.R |only SACCR-2.0/SACCR/R/GroupFXTrades.R |only SACCR-2.0/SACCR/R/GroupIRDTrades.R |only SACCR-2.0/SACCR/R/GroupTrades.R |only SACCR-2.0/SACCR/R/HandleBasisVol.R | 70 +++-- SACCR-2.0/SACCR/R/SACCRCalculator.R |only SACCR-2.0/SACCR/R/SingleTradeAddon.R |only SACCR-2.0/SACCR/R/runExampleCalcs.R | 70 ++++- SACCR-2.0/SACCR/inst/extdata/CSA.csv |only SACCR-2.0/SACCR/inst/extdata/CSA_basel.csv |only SACCR-2.0/SACCR/inst/extdata/coll.csv |only SACCR-2.0/SACCR/inst/extdata/coll_basel.csv |only SACCR-2.0/SACCR/inst/extdata/example_trades.csv |only SACCR-2.0/SACCR/man/CalcAddon.Rd | 11 SACCR-2.0/SACCR/man/CalcEAD.Rd | 2 SACCR-2.0/SACCR/man/CalcPFE.Rd | 2 SACCR-2.0/SACCR/man/CalcRC.Rd | 8 SACCR-2.0/SACCR/man/CreateTradeGraph.Rd |only SACCR-2.0/SACCR/man/ExampleBasisVol.Rd | 2 SACCR-2.0/SACCR/man/ExampleComm.Rd | 2 SACCR-2.0/SACCR/man/ExampleCredit.Rd | 2 SACCR-2.0/SACCR/man/ExampleFX.Rd | 2 SACCR-2.0/SACCR/man/ExampleIRD.Rd | 2 SACCR-2.0/SACCR/man/ExampleIRDCommMargined.Rd | 2 SACCR-2.0/SACCR/man/ExampleIRDCredit.Rd | 2 SACCR-2.0/SACCR/man/HandleBasisVol.Rd | 9 SACCR-2.0/SACCR/man/LoadSupervisoryData.Rd | 2 SACCR-2.0/SACCR/man/SACCRCalculator.Rd |only SACCR-2.0/SACCR/man/SingleTradeAddon.Rd |only 62 files changed, 475 insertions(+), 347 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions in the 2.11.x series are supported.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.13 dated 2016-07-08 and 1.0.14 dated 2016-11-22
rscala-1.0.13/rscala/R/scalaInterpreter.R |only rscala-1.0.13/rscala/inst/java/rscala_2.11-1.0.13.jar |only rscala-1.0.13/rscala/java/rscala_2.11-1.0.13-sources.jar |only rscala-1.0.14/rscala/DESCRIPTION | 8 rscala-1.0.14/rscala/MD5 | 34 ++-- rscala-1.0.14/rscala/NAMESPACE | 37 +--- rscala-1.0.14/rscala/NEWS | 23 ++ rscala-1.0.14/rscala/R/common.R | 40 ---- rscala-1.0.14/rscala/R/protocol.R | 5 rscala-1.0.14/rscala/R/rServer.R | 6 rscala-1.0.14/rscala/R/scala.R |only rscala-1.0.14/rscala/inst/java/rscala_2.10-1.0.14.jar |only rscala-1.0.14/rscala/inst/java/rscala_2.11-1.0.14.jar |only rscala-1.0.14/rscala/inst/java/rscala_2.12-1.0.14.jar |only rscala-1.0.14/rscala/java/rscala_2.10-1.0.14-sources.jar |only rscala-1.0.14/rscala/java/rscala_2.11-1.0.14-sources.jar |only rscala-1.0.14/rscala/java/rscala_2.12-1.0.14-sources.jar |only rscala-1.0.14/rscala/man/close.Rd | 2 rscala-1.0.14/rscala/man/constructor.Rd | 101 ++++++------ rscala-1.0.14/rscala/man/eval.Rd | 125 +++++++-------- rscala-1.0.14/rscala/man/print.Rd | 2 rscala-1.0.14/rscala/man/rscala-package.Rd | 14 - rscala-1.0.14/rscala/man/settings.Rd | 23 +- 23 files changed, 195 insertions(+), 225 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics)
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.5.2 dated 2016-10-11 and 0.6.1 dated 2016-11-22
DESCRIPTION | 11 + MD5 | 93 ++++++++------- NEWS.md |only R/RcppExports.R | 12 +- R/etc_create_samples.R | 29 +++- R/etc_utils_autoplot.R | 69 ++++------- R/etc_utils_dataframe.R | 69 +++++++++-- R/etc_utils_fortify.R | 84 +++++++++----- R/etc_utils_plot.R | 24 +--- R/etc_utils_validate_args.R | 1 R/g_auc.R | 25 +++- R/g_part.R | 54 ++++++++- R/g_pauc.R | 14 +- R/main_evalmod.R | 33 +++-- R/mm1_create_mmdat.R | 16 ++ R/mm2_join_data.R | 65 +++++++++- R/pl2_pipeline_main_basic.R | 13 -- R/pl6_calc_average.R | 9 - R/precrec.R | 62 +++++++--- README.md | 40 +++--- build/vignette.rds |binary inst/doc/introduction.Rmd | 27 ++-- inst/doc/introduction.html | 166 ++++++++++++++-------------- man/as.data.frame.Rd | 31 ++++- man/auc.Rd | 30 +++-- man/autoplot.Rd | 24 +--- man/create_sim_samples.Rd | 29 +++- man/evalmod.Rd | 33 +++-- man/fortify.Rd | 84 +++++++++----- man/join_labels.Rd | 34 ++++- man/join_scores.Rd | 31 ++++- man/mmdata.Rd | 16 ++ man/part.Rd | 54 ++++++++- man/pauc.Rd | 15 +- man/plot.Rd | 21 --- man/precrec.Rd | 72 ++++++++---- src/RcppExports.cpp | 39 +++++- src/calc_avg_curve.cpp | 6 - src/calc_avg_point.cpp | 9 - src/conv_vec.cpp |only src/conv_vec.h |only src/convert_curve_avg_df.cpp |only src/convert_curve_df.cpp |only tests/testthat/test_g_datamatrix1_curves.R | 21 +++ tests/testthat/test_g_datamatrix2_points.R | 21 +++ tests/testthat/test_pl2_1_pl_main_basic.R | 2 tests/testthat/test_pl2_1_pl_main_rocprc.R | 6 - tests/testthat/test_pl6_1_calc_avg_points.R | 44 +++---- tests/testthat/test_pl6_2_calc_avg_curves.R | 12 +- vignettes/introduction.Rmd | 27 ++-- 50 files changed, 1021 insertions(+), 556 deletions(-)
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating precision-recall curves under various conditions.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 0.5.2 dated 2016-10-11 and 0.6.2 dated 2016-11-22
DESCRIPTION | 11 +++++----- MD5 | 47 ++++++++++++++++++++++----------------------- NEWS.md |only R/data_interface.R | 6 +++++ R/data_zzz.R | 3 ++ R/g_autoplot.R | 2 + R/main_benchmark.R | 3 ++ R/main_evalcurves.R | 1 R/prcbench.R | 3 -- R/tool_interface.R | 4 +++ README.md | 30 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/introduction.Rmd | 2 - inst/doc/introduction.html | 22 ++++++++++----------- man/TestDataB.Rd | 1 man/TestDataC.Rd | 2 + man/autoplot.Rd | 2 + man/create_testset.Rd | 4 +++ man/create_toolset.Rd | 2 + man/create_usrdata.Rd | 2 + man/create_usrtool.Rd | 2 + man/prcbench.Rd | 3 -- man/run_benchmark.Rd | 3 ++ man/run_evalcurve.Rd | 1 vignettes/introduction.Rmd | 2 - 25 files changed, 98 insertions(+), 60 deletions(-)
Title: Parallel Tree
Description:
Provides two functions: Group_function() and Parallel_Tree(). Group_function() applies a given function (e.g.,mean()) to input variable(s) by group across levels. Has additional data management options.
Parallel_Tree() uses 'ggplot2' to create a parallel coordinate plots (technically a facsimile of parallel coordinate plots in a Cartesian coordinate system).
Used in combination these functions can create parallel tree plots, a variant of parallel coordinate plots, which are useful for visualizing multilevel data.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>
Diff between ParallelTree versions 0.1.1 dated 2016-05-30 and 0.1.2 dated 2016-11-22
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/Grouping_function.R | 9 +++-- R/Parallel_Tree.R | 76 ++++++++++++++++++++++++++++++++++---------------- man/Group_function.Rd | 4 +- man/Parallel_Tree.Rd | 31 +++++++++++++------- 6 files changed, 89 insertions(+), 47 deletions(-)
Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region. Accommodates , without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>
Diff between MBHdesign versions 1.0.60 dated 2016-11-20 and 1.0.61 dated 2016-11-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/sysdata.rda |binary inst/doc/MBHdesign.Rnw | 2 +- inst/doc/MBHdesign.pdf |binary vignettes/MBHdesign.Rnw | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Transcriptomic Dynamics Models in Field Conditions
Description: Provides functionality for constructing
statistical models of transcriptomic dynamics in field conditions.
It further offers the function to predict expression of a gene given
the attributes of samples and meteorological data.
Author: Koji Iwayama [cre],
Yuri Aisaka [aut]
Maintainer: Koji Iwayama <fieldtranscriptome@gmail.com>
Diff between FIT versions 0.0.1 dated 2016-07-26 and 0.0.2 dated 2016-11-22
DESCRIPTION | 6 MD5 | 36 NAMESPACE | 32 R/FIT.R | 2 R/Model.R | 4 R/RcppExports.R | 46 R/Train.R | 29 build/vignette.rds |binary inst/doc/FIT.R | 300 inst/doc/FIT.Rmd | 18 inst/doc/FIT.html |55596 +++++++++++++++++++++++++++++++++++++++- inst/extdata/prediction.weather |binary inst/extdata/train.weather |binary src/RcppExports.cpp | 42 src/init.h | 8 src/optim.h | 2 src/prep.h | 11 src/train.cpp | 9 vignettes/FIT.Rmd | 5 19 files changed, 55467 insertions(+), 679 deletions(-)
Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.0.5 dated 2016-08-16 and 1.1.0 dated 2016-11-22
cdfquantreg-1.0.5/cdfquantreg/R/qrDistributions.R |only cdfquantreg-1.1.0/cdfquantreg/DESCRIPTION | 8 cdfquantreg-1.1.0/cdfquantreg/MD5 | 38 cdfquantreg-1.1.0/cdfquantreg/NEWS | 8 cdfquantreg-1.1.0/cdfquantreg/R/bugsLikelihood.R | 243 ++- cdfquantreg-1.1.0/cdfquantreg/R/cdfquantreg.R | 11 cdfquantreg-1.1.0/cdfquantreg/R/qrCdf.R |only cdfquantreg-1.1.0/cdfquantreg/R/qrFamily.R | 132 + cdfquantreg-1.1.0/cdfquantreg/R/qrGrad.R | 745 +++++++--- cdfquantreg-1.1.0/cdfquantreg/R/qrLogLik.R | 363 +++- cdfquantreg-1.1.0/cdfquantreg/R/qrLogLikFun.R | 621 ++++++-- cdfquantreg-1.1.0/cdfquantreg/R/qrPdf.R |only cdfquantreg-1.1.0/cdfquantreg/R/qrStart.R | 2 cdfquantreg-1.1.0/cdfquantreg/R/qrqq.R |only cdfquantreg-1.1.0/cdfquantreg/inst/doc/CDFQuantregIntroduction.Rmd | 10 cdfquantreg-1.1.0/cdfquantreg/inst/doc/CDFQuantregIntroduction.html | 64 cdfquantreg-1.1.0/cdfquantreg/inst/doc/IPCCExample.html | 82 - cdfquantreg-1.1.0/cdfquantreg/inst/doc/Smithson_Verkuilen2006Example.html | 128 - cdfquantreg-1.1.0/cdfquantreg/man/cdfqrFamily.Rd | 83 - cdfquantreg-1.1.0/cdfquantreg/man/cdfquantreg-package.Rd | 10 cdfquantreg-1.1.0/cdfquantreg/man/dq.Rd | 14 cdfquantreg-1.1.0/cdfquantreg/vignettes/CDFQuantregIntroduction.Rmd | 10 22 files changed, 1958 insertions(+), 614 deletions(-)
Title: Genomic Data Retrieval with R
Description: Perform meta-genomic data retrieval and functional annotation retrieval with
R.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between biomartr versions 0.1.0 dated 2016-08-07 and 0.2.0 dated 2016-11-22
biomartr-0.1.0/biomartr/R/sequence_io.R |only biomartr-0.1.0/biomartr/man/download_database.Rd |only biomartr-0.2.0/biomartr/DESCRIPTION | 20 biomartr-0.2.0/biomartr/MD5 | 145 - biomartr-0.2.0/biomartr/NAMESPACE | 17 biomartr-0.2.0/biomartr/NEWS.md | 119 biomartr-0.2.0/biomartr/R/connected.to.internet.R |only biomartr-0.2.0/biomartr/R/download_database.R | 67 biomartr-0.2.0/biomartr/R/download_database_all.R |only biomartr-0.2.0/biomartr/R/get.ensembl.info.R |only biomartr-0.2.0/biomartr/R/get.ensemblgenome.info.R |only biomartr-0.2.0/biomartr/R/getCDS.R | 394 ++ biomartr-0.2.0/biomartr/R/getENSEMBL.Annotation.R |only biomartr-0.2.0/biomartr/R/getENSEMBL.Seq.R |only biomartr-0.2.0/biomartr/R/getENSEMBLGENOMES.Annotation.R |only biomartr-0.2.0/biomartr/R/getENSEMBLGENOMES.Seq.R |only biomartr-0.2.0/biomartr/R/getGENOMEREPORT.R |only biomartr-0.2.0/biomartr/R/getGFF.R |only biomartr-0.2.0/biomartr/R/getGenome.R | 380 ++ biomartr-0.2.0/biomartr/R/getGroups.R |only biomartr-0.2.0/biomartr/R/getKingdomAssemblySummary.R |only biomartr-0.2.0/biomartr/R/getKingdoms.R | 86 biomartr-0.2.0/biomartr/R/getMetaGenomeAnnotations.R |only biomartr-0.2.0/biomartr/R/getMetaGenomeSummary.R |only biomartr-0.2.0/biomartr/R/getMetaGenomes.R |only biomartr-0.2.0/biomartr/R/getProteome.R | 380 ++ biomartr-0.2.0/biomartr/R/getSubgroups.R |only biomartr-0.2.0/biomartr/R/getSummaryFile.R |only biomartr-0.2.0/biomartr/R/is.ensembl.alive.R |only biomartr-0.2.0/biomartr/R/is.ensemblgenomes.alive.R |only biomartr-0.2.0/biomartr/R/is.genome.available.R |only biomartr-0.2.0/biomartr/R/listDatabases.R | 151 - biomartr-0.2.0/biomartr/R/listGenomes.R | 414 ++- biomartr-0.2.0/biomartr/R/listGroups.R |only biomartr-0.2.0/biomartr/R/listKingdoms.R |only biomartr-0.2.0/biomartr/R/listMetaGenomes.R |only biomartr-0.2.0/biomartr/R/listSubgroups.R |only biomartr-0.2.0/biomartr/R/meta.retrieval.R | 218 - biomartr-0.2.0/biomartr/R/meta.retrieval.all.R |only biomartr-0.2.0/biomartr/R/read_cds.R |only biomartr-0.2.0/biomartr/R/read_genome.R |only biomartr-0.2.0/biomartr/R/read_gff.R |only biomartr-0.2.0/biomartr/R/read_proteome.R |only biomartr-0.2.0/biomartr/R/refseqOrganisms.R | 13 biomartr-0.2.0/biomartr/R/utils.R | 114 biomartr-0.2.0/biomartr/README.md | 112 biomartr-0.2.0/biomartr/build/vignette.rds |binary biomartr-0.2.0/biomartr/inst/doc/Database_Retrieval.Rmd | 125 biomartr-0.2.0/biomartr/inst/doc/Database_Retrieval.html | 105 biomartr-0.2.0/biomartr/inst/doc/Evolutionary_Transcriptomics.html | 4 biomartr-0.2.0/biomartr/inst/doc/Functional_Annotation.R | 36 biomartr-0.2.0/biomartr/inst/doc/Functional_Annotation.Rmd | 100 biomartr-0.2.0/biomartr/inst/doc/Functional_Annotation.html | 92 biomartr-0.2.0/biomartr/inst/doc/Introduction.Rmd | 26 biomartr-0.2.0/biomartr/inst/doc/Introduction.html | 28 biomartr-0.2.0/biomartr/inst/doc/MetaGenome_Retrieval.R |only biomartr-0.2.0/biomartr/inst/doc/MetaGenome_Retrieval.Rmd |only biomartr-0.2.0/biomartr/inst/doc/MetaGenome_Retrieval.html |only biomartr-0.2.0/biomartr/inst/doc/Sequence_Retrieval.R | 375 ++ biomartr-0.2.0/biomartr/inst/doc/Sequence_Retrieval.Rmd | 1321 +++++++--- biomartr-0.2.0/biomartr/inst/doc/Sequence_Retrieval.html | 1024 +++++-- biomartr-0.2.0/biomartr/man/download.database.Rd |only biomartr-0.2.0/biomartr/man/download.database.all.Rd |only biomartr-0.2.0/biomartr/man/getCDS.Rd | 51 biomartr-0.2.0/biomartr/man/getGFF.Rd |only biomartr-0.2.0/biomartr/man/getGenome.Rd | 46 biomartr-0.2.0/biomartr/man/getGroups.Rd |only biomartr-0.2.0/biomartr/man/getKingdomAssemblySummary.Rd |only biomartr-0.2.0/biomartr/man/getKingdoms.Rd | 21 biomartr-0.2.0/biomartr/man/getMetaGenomeAnnotations.Rd |only biomartr-0.2.0/biomartr/man/getMetaGenomeSummary.Rd |only biomartr-0.2.0/biomartr/man/getMetaGenomes.Rd |only biomartr-0.2.0/biomartr/man/getProteome.Rd | 42 biomartr-0.2.0/biomartr/man/getSubgroups.Rd |only biomartr-0.2.0/biomartr/man/getSummaryFile.Rd |only biomartr-0.2.0/biomartr/man/is.genome.available.Rd | 24 biomartr-0.2.0/biomartr/man/listDatabases.Rd | 23 biomartr-0.2.0/biomartr/man/listGenomes.Rd | 69 biomartr-0.2.0/biomartr/man/listGroups.Rd |only biomartr-0.2.0/biomartr/man/listKingdoms.Rd |only biomartr-0.2.0/biomartr/man/listMetaGenomes.Rd |only biomartr-0.2.0/biomartr/man/listSubgroups.Rd |only biomartr-0.2.0/biomartr/man/meta.retrieval.Rd | 22 biomartr-0.2.0/biomartr/man/meta.retrieval.all.Rd |only biomartr-0.2.0/biomartr/man/read_cds.Rd | 15 biomartr-0.2.0/biomartr/man/read_genome.Rd | 26 biomartr-0.2.0/biomartr/man/read_gff.Rd |only biomartr-0.2.0/biomartr/man/read_proteome.Rd | 30 biomartr-0.2.0/biomartr/man/refseqOrganisms.Rd | 3 biomartr-0.2.0/biomartr/tests/testthat/test-download.database.R |only biomartr-0.2.0/biomartr/tests/testthat/test-getCDS.R | 32 biomartr-0.2.0/biomartr/tests/testthat/test-getGFF.R |only biomartr-0.2.0/biomartr/tests/testthat/test-getGenome.R | 48 biomartr-0.2.0/biomartr/tests/testthat/test-getProteome.R | 32 biomartr-0.2.0/biomartr/tests/testthat/test-is.genome.available.R | 53 biomartr-0.2.0/biomartr/vignettes/Database_Retrieval.Rmd | 125 biomartr-0.2.0/biomartr/vignettes/Functional_Annotation.Rmd | 100 biomartr-0.2.0/biomartr/vignettes/Introduction.Rmd | 26 biomartr-0.2.0/biomartr/vignettes/MetaGenome_Retrieval.Rmd |only biomartr-0.2.0/biomartr/vignettes/Sequence_Retrieval.Rmd | 1321 +++++++--- 100 files changed, 5405 insertions(+), 2570 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 6.0-1 dated 2016-01-29 and 6.0-2 dated 2016-11-22
ChangeLog | 10 ++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 18 +++++++++--------- R/adjustments.R | 4 +++- R/get_outputs.R | 2 ++ R/plot_functions.R | 2 +- R/predict.pop.R | 23 +++++++++++++---------- man/age.specific.migration.Rd | 11 +++++++---- man/bayesPop-package.Rd | 6 +++--- tests/run_tests.R | 16 +++++++++------- 10 files changed, 64 insertions(+), 41 deletions(-)
Title: Graphical User Interface for bayesTFR, bayesLife and bayesPop
Description: Provides graphical user interface for the packages 'bayesTFR', 'bayesLife' and 'bayesPop'.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesDem versions 2.5-0 dated 2016-03-20 and 2.5-1 dated 2016-11-22
ChangeLog | 4 ++++ DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/tfr-mcmc.R | 2 +- R/tfr-predict.R | 4 ++-- man/bayesDem-package.Rd | 6 +++--- 6 files changed, 22 insertions(+), 18 deletions(-)