Title: Extraction of Business Financial Information from 'XBRL'
Documents
Description:
Functions to extract business financial information from
an Extensible Business Reporting Language ('XBRL') instance file and the
associated collection of files that defines its 'Discoverable' Taxonomy
Set ('DTS').
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso <rbertolusso@rice.edu>
Diff between XBRL versions 0.99.16 dated 2015-04-29 and 0.99.17 dated 2016-07-01
ChangeLog | 12 +++++++++++ DESCRIPTION | 10 ++++----- MD5 | 24 +++++++++++------------ NAMESPACE | 1 R/XBRL.R | 53 +++++++++++++++++++++++++++++++++++++++++++++------- R/xbrlDoAll.R | 8 ++++++- R/xbrlParse.R | 3 ++ configure.in | 2 - man/XBRL-package.Rd | 9 +++++--- man/XBRL.Rd | 4 +-- man/low-level.Rd | 10 +++++---- man/xbrlDoAll.Rd | 9 +++++--- man/xbrlSECdev01.Rd | 4 +-- 13 files changed, 109 insertions(+), 40 deletions(-)
Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen <mehmet.suzen@physics.org>
Diff between isingLenzMC versions 0.2.3 dated 2015-03-01 and 0.2.5 dated 2016-07-01
DESCRIPTION | 15 +++++++++------ MD5 | 14 +++++++++----- NAMESPACE | 3 +++ NEWS | 8 ++++++++ README.md |only build/vignette.rds |binary inst/CITATION | 6 ++++++ inst/examples/powerLawErgodicity |only 8 files changed, 35 insertions(+), 11 deletions(-)
Title: Variable Selection in Finite Mixture of AFT Regression and FMR
Description: Provides parameter estimation as well as variable selection in
Finite Mixture of Accelerated Failure Time Regression and Finite
Mixture of Regression Models.
Furthermore, this package provides Ridge Regression and Elastic Net.
Author: Farhad Shokoohi <shokoohi@icloud.com>
Abbas Khalili
Masoud Asgharian
Shili Lin
Maintainer: Farhad Shokoohi <shokoohi@icloud.com>
Diff between fmrs versions 1.0-7 dated 2016-04-29 and 1.0-9 dated 2016-07-01
DESCRIPTION | 10 MD5 | 60 +- NEWS | 28 - R/AllClasses.R | 26 R/AllGenerics.R | 184 +++++- R/AllMethods.R | 331 +++++++++++- build/vignette.rds |binary inst/doc/usingfmrs.R | 35 - inst/doc/usingfmrs.Rmd | 35 - inst/doc/usingfmrs.html | 153 ++--- man/BIC-methods.Rd | 2 man/coefficients-methods.Rd | 2 man/dispersion-methods.Rd | 4 man/fitted-methods.Rd | 2 man/fmrs.gendata-methods.Rd | 16 man/fmrs.mle-methods.Rd | 22 man/fmrs.tunsel-methods.Rd | 19 man/fmrs.varsel-methods.Rd | 21 man/fmrsfit-class.Rd | 6 man/fmrstunpar-class.Rd | 6 man/logLik-methods.Rd | 2 man/mixProp-methods.Rd | 2 man/ncomp-methods.Rd | 2 man/ncov-methods.Rd | 2 man/nobs-methods.Rd | 4 man/residuals-methods.Rd | 2 man/show-methods.Rd | 26 man/summary-methods.Rd | 24 man/weights-methods.Rd | 2 src/fmrs.c | 1159 ++++++++++++++++++++++++++------------------ vignettes/usingfmrs.Rmd | 35 - 31 files changed, 1452 insertions(+), 770 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see: (i) "Life tables
with covariates: Dynamic model for nonlinear analysis of longitudinal data"
by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80),
<DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of
longitudinal data on aging and mortality" by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(iii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.3.1 dated 2016-05-24 and 1.3.2 dated 2016-07-01
DESCRIPTION | 8 +- MD5 | 16 ++-- NAMESPACE | 2 R/prepare_data.R | 1 R/simdata_gamma_frailty.R |only R/spm.R | 2 R/spm_time-dependent.R | 6 - README.md | 139 ++++++++++++++++++++++++++++++++++++------- man/simdata_gamma_frailty.Rd |only man/spm_time_dep.Rd | 6 - 10 files changed, 141 insertions(+), 39 deletions(-)
Title: Wrapper for the 'Hypothes.is' Web Annotation Service
Description: Interact with the application programming interface for the web
annotation service 'Hypothes.is' (See <http://hypothes.is> for more
information.) Allows users to download data about public annotations, and
create, retrieve, update, and delete their own annotations.
Author: Matthew Lincoln [aut, cre]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between hypothesisr versions 0.1.0 dated 2016-06-13 and 0.1.1 dated 2016-07-01
DESCRIPTION | 16 ++++++++-------- MD5 | 8 +++++--- NEWS.md |only README.md | 1 + tests/testthat/test_search.R | 8 +++++++- tests/testthat/token.rds |only 6 files changed, 21 insertions(+), 12 deletions(-)
Title: Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator
Description: This is a port of Jonathan Shewchuk's Triangle library to
R. From his description: "Triangle generates exact Delaunay
triangulations, constrained Delaunay triangulations, conforming
Delaunay triangulations, Voronoi diagrams, and high-quality
triangular meshes. The latter can be generated with no small or
large angles, and are thus suitable for finite element analysis."
Author: Jonathan Richard Shewchuk [ctb, cph],
David C. Sterratt [cph, aut, cre],
Elias Pipping [ctb]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between RTriangle versions 1.6-0.7 dated 2016-05-11 and 1.6-0.8 dated 2016-07-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 9 +++++++++ R/triangle.R | 6 +++++- tests/testthat/test-triangulate.R | 33 ++++++++++++++++++++++++++++++++- 5 files changed, 54 insertions(+), 10 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling.
Markov models (homogeneous and non-homogeneous)
for health economic evaluation. Model comparison,
sensitivity and probabilistic analysis.
Author: Kevin Zarca [aut], Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.3.2 dated 2016-06-13 and 0.3.3 dated 2016-07-01
COPYING | 30 - DESCRIPTION | 6 MD5 | 241 ++++----- NAMESPACE | 188 +++---- R/density.R | 150 +++--- R/efficiency_frontier.R | 42 - R/gho_mortality.R | 196 +++---- R/imports.R | 122 ++-- R/matrix_define.R | 258 +++++----- R/matrix_eval.R | 166 +++--- R/matrix_plot.R | 112 ++-- R/model_define.R | 180 +++---- R/model_eval.R | 360 +++++++------- R/model_print.R | 148 ++--- R/newdata.R | 220 ++++---- R/param_define.R | 234 ++++----- R/param_eval.R | 56 +- R/param_print.R | 22 R/resamp_define.R | 364 +++++++------- R/resamp_eval.R | 222 ++++---- R/resamp_print.R | 158 +++--- R/run_model_define.R | 406 ++++++++-------- R/run_model_summary.R | 230 ++++----- R/sensitivity_define.R | 94 +-- R/sensitivity_eval.R | 72 +- R/sensitivity_print.R | 292 +++++------ R/states_define.R | 444 ++++++++--------- R/states_eval.R | 56 +- R/states_print.R | 82 +-- R/utils.R | 203 ++++---- README.md | 109 ++-- build/vignette.rds |binary inst/doc/homogeneous.R | 297 +++++------ inst/doc/homogeneous.Rmd | 484 +++++++++---------- inst/doc/homogeneous.html | 629 ++++++++++++------------- inst/doc/introduction.R | 113 ++-- inst/doc/introduction.Rmd | 294 +++++------ inst/doc/introduction.html | 534 ++++++++++----------- inst/doc/non-homogeneous.R | 282 ++++++----- inst/doc/non-homogeneous.Rmd | 501 ++++++++++---------- inst/doc/non-homogeneous.html | 719 +++++++++++++++-------------- inst/doc/probabilistic.R | 340 ++++++------- inst/doc/probabilistic.Rmd | 490 +++++++++---------- inst/doc/probabilistic.html | 592 +++++++++++------------ inst/doc/reproduction.R |only inst/doc/reproduction.Rmd |only inst/doc/reproduction.html |only inst/doc/sensitivity.R | 300 ++++++------ inst/doc/sensitivity.Rmd | 398 ++++++++-------- inst/doc/sensitivity.html | 278 +++++------ inst/examples/example_define_matrix.R | 92 +-- inst/examples/example_define_model.R | 40 - inst/examples/example_define_parameters.R | 110 ++-- inst/examples/example_define_resample.R | 32 - inst/examples/example_define_state.R | 10 inst/examples/example_eval_model.R | 44 - inst/examples/example_eval_model_newdata.R | 54 +- inst/examples/example_eval_parameters.R | 12 inst/examples/example_run_models.R | 106 ++-- inst/examples/example_run_newdata.R | 104 ++-- inst/examples/example_run_probabilistic.R | 128 ++--- inst/examples/example_run_sensitivity.R | 112 ++-- man/check_matrix.Rd | 52 +- man/check_names.Rd | 42 - man/check_states.Rd | 42 - man/compute_counts.Rd | 64 +- man/compute_icer.Rd | 42 - man/compute_values.Rd | 44 - man/define_correlation.Rd | 64 +- man/define_distrib.Rd | 100 ++-- man/define_matrix.Rd | 238 ++++----- man/define_model.Rd | 118 ++-- man/define_multinom.Rd | 40 - man/define_parameters.Rd | 230 ++++----- man/define_sensitivity.Rd | 64 +- man/define_state.Rd | 96 +-- man/define_state_list.Rd | 126 ++--- man/discount.Rd | 61 +- man/eval_matrix.Rd | 48 - man/eval_model.Rd | 130 ++--- man/eval_model_newdata.Rd | 144 ++--- man/eval_parameters.Rd | 62 +- man/eval_resample.Rd | 42 - man/eval_state_list.Rd | 48 - man/get_frontier.Rd | 36 - man/get_matrix.Rd | 46 - man/get_matrix_order.Rd | 44 - man/get_model.Rd | 40 - man/get_parameter_names.Rd | 40 - man/get_parameters.Rd | 40 - man/get_state_names.Rd | 40 - man/get_state_number.Rd | 42 - man/get_state_value_names.Rd | 40 - man/get_who_mr_.Rd | 72 +- man/is.wholenumber.Rd | 42 - man/list_all_same.Rd | 36 - man/modify.Rd | 50 +- man/normal.Rd | 96 +-- man/normalize_ce.Rd | 42 - man/plot.eval_model_list.Rd | 58 +- man/plot.eval_sensitivity.Rd | 62 +- man/plot.probabilistic.Rd | 60 +- man/plur.Rd | 36 - man/run_models.Rd | 252 +++++----- man/run_newdata.Rd | 160 +++--- man/run_probabilistic.Rd | 178 +++---- man/run_sensitivity.Rd | 160 +++--- man/summary.eval_model_list.Rd | 42 - tests/testthat.R | 8 tests/testthat/Rplots.pdf |only tests/testthat/test_gho.R | 62 +- tests/testthat/test_matrix.R | 416 ++++++++-------- tests/testthat/test_model.R | 596 ++++++++++++------------ tests/testthat/test_newdata.R | 438 ++++++++--------- tests/testthat/test_parameters.R | 236 ++++----- tests/testthat/test_run_model.R | 599 ++++++++++++------------ tests/testthat/test_sensitivity.R | 222 ++++---- tests/testthat/test_states.R | 432 ++++++++--------- vignettes/homogeneous.Rmd | 484 +++++++++---------- vignettes/introduction.Rmd | 294 +++++------ vignettes/non-homogeneous.Rmd | 501 ++++++++++---------- vignettes/probabilistic.Rmd | 490 +++++++++---------- vignettes/reproduction.Rmd |only vignettes/sensitivity.Rmd | 398 ++++++++-------- 124 files changed, 10728 insertions(+), 10617 deletions(-)
Title: Make 'ggplot2' Graphics Interactive Using 'htmlwidgets'
Description: Create interactive 'ggplot2' graphics that are usable in the 'RStudio'
viewer pane, in 'R Markdown' documents and in 'Shiny' apps.
Author: David Gohel [aut, cre],
Mike Bostock [cph] (d3.js)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.3.0 dated 2016-05-04 and 0.3.1 dated 2016-07-01
ggiraph-0.3.0/ggiraph/inst/doc/custom_rendering.R |only ggiraph-0.3.0/ggiraph/inst/doc/custom_rendering.Rmd |only ggiraph-0.3.0/ggiraph/inst/doc/custom_rendering.html |only ggiraph-0.3.0/ggiraph/inst/shiny/server.R |only ggiraph-0.3.0/ggiraph/inst/shiny/ui.R |only ggiraph-0.3.0/ggiraph/vignettes/custom_rendering.Rmd |only ggiraph-0.3.1/ggiraph/DESCRIPTION | 9 ggiraph-0.3.1/ggiraph/MD5 | 73 ++++--- ggiraph-0.3.1/ggiraph/NAMESPACE | 4 ggiraph-0.3.1/ggiraph/NEWS | 13 + ggiraph-0.3.1/ggiraph/R/geom_bar_interactive.r |only ggiraph-0.3.1/ggiraph/R/geom_boxplot_interactive.R |only ggiraph-0.3.1/ggiraph/R/geom_path_interactive.R | 36 +++ ggiraph-0.3.1/ggiraph/R/geom_point_interactive.R | 4 ggiraph-0.3.1/ggiraph/R/geom_polygon_interactive.R | 10 ggiraph-0.3.1/ggiraph/R/geom_rect_interactive.R | 7 ggiraph-0.3.1/ggiraph/R/geom_segment_interactive.R | 6 ggiraph-0.3.1/ggiraph/R/geom_text_interactive.R | 6 ggiraph-0.3.1/ggiraph/R/ggiraph.R | 34 ++- ggiraph-0.3.1/ggiraph/build/vignette.rds |binary ggiraph-0.3.1/ggiraph/inst/doc/custom_effects.R |only ggiraph-0.3.1/ggiraph/inst/doc/custom_effects.Rmd |only ggiraph-0.3.1/ggiraph/inst/doc/custom_effects.html |only ggiraph-0.3.1/ggiraph/inst/doc/ggiraph.R | 66 ++---- ggiraph-0.3.1/ggiraph/inst/doc/ggiraph.Rmd | 95 ++++----- ggiraph-0.3.1/ggiraph/inst/doc/ggiraph.html | 124 ++++++------ ggiraph-0.3.1/ggiraph/inst/doc/shiny.R |only ggiraph-0.3.1/ggiraph/inst/doc/shiny.Rmd |only ggiraph-0.3.1/ggiraph/inst/doc/shiny.html |only ggiraph-0.3.1/ggiraph/inst/htmlwidgets/ggiraph.js | 70 ++---- ggiraph-0.3.1/ggiraph/inst/htmlwidgets/ggiraph.yaml | 5 ggiraph-0.3.1/ggiraph/inst/htmlwidgets/lib/html_ggiraph.css |only ggiraph-0.3.1/ggiraph/inst/shiny/cars |only ggiraph-0.3.1/ggiraph/inst/shiny/crimes |only ggiraph-0.3.1/ggiraph/man/geom_bar_interactive.Rd |only ggiraph-0.3.1/ggiraph/man/geom_boxplot_interactive.Rd |only ggiraph-0.3.1/ggiraph/man/geom_map_interactive.Rd | 6 ggiraph-0.3.1/ggiraph/man/geom_path_interactive.Rd | 17 + ggiraph-0.3.1/ggiraph/man/geom_point_interactive.Rd | 4 ggiraph-0.3.1/ggiraph/man/geom_polygon_interactive.Rd | 6 ggiraph-0.3.1/ggiraph/man/geom_rect_interactive.Rd | 6 ggiraph-0.3.1/ggiraph/man/geom_segment_interactive.Rd | 6 ggiraph-0.3.1/ggiraph/man/geom_text_interactive.Rd | 6 ggiraph-0.3.1/ggiraph/man/ggiraph.Rd | 10 ggiraph-0.3.1/ggiraph/vignettes/custom_effects.Rmd |only ggiraph-0.3.1/ggiraph/vignettes/ggiraph.Rmd | 95 ++++----- ggiraph-0.3.1/ggiraph/vignettes/shiny.Rmd |only 47 files changed, 397 insertions(+), 321 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for
differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
This method may be useful for high-throughput biological data (microarray, sequencing, ...).
Probabilities are associated with genes/probes in the dataset and there is no problem of
multiple tests when using this method. For aCGH data, segmentation results are obtained by
merging the significant probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.4.1 dated 2015-11-08 and 1.5 dated 2016-07-01
fcros-1.4.1/fcros/R/fcrosChrMerge.R |only fcros-1.4.1/fcros/R/fcrosChrPlot.R |only fcros-1.4.1/fcros/R/fcrosChrPlot2.R |only fcros-1.4.1/fcros/R/fcrosChrSegment.R |only fcros-1.4.1/fcros/R/fcrosChrSegmentC.R |only fcros-1.4.1/fcros/R/fcrosChrSummary.R |only fcros-1.4.1/fcros/R/fcrosHistoPlot.R |only fcros-1.4.1/fcros/R/fcrosVolcanoPlot.R |only fcros-1.4.1/fcros/R/rmat.R |only fcros-1.4.1/fcros/man/fcrosChrMerge.Rd |only fcros-1.4.1/fcros/man/fcrosChrPlot.Rd |only fcros-1.4.1/fcros/man/fcrosChrPlot2.Rd |only fcros-1.4.1/fcros/man/fcrosChrSegment.Rd |only fcros-1.4.1/fcros/man/fcrosChrSegmentC.Rd |only fcros-1.4.1/fcros/man/fcrosChrSummary.Rd |only fcros-1.4.1/fcros/man/fcrosHistoPlot.Rd |only fcros-1.4.1/fcros/man/fcrosVolcanoPlot.Rd |only fcros-1.4.1/fcros/man/rmatCalc.Rd |only fcros-1.5/fcros/DESCRIPTION | 10 +- fcros-1.5/fcros/MD5 | 97 ++++++++++++++++----------- fcros-1.5/fcros/NAMESPACE | 4 - fcros-1.5/fcros/R/chrMerge.R |only fcros-1.5/fcros/R/chrPlot.R |only fcros-1.5/fcros/R/chrPlot2.R |only fcros-1.5/fcros/R/chrSegment.R |only fcros-1.5/fcros/R/dataSummary.R |only fcros-1.5/fcros/R/fc2Calc.R |only fcros-1.5/fcros/R/fcros.R | 106 ++++++++++++++++++++---------- fcros-1.5/fcros/R/fcrosC.R | 24 +++--- fcros-1.5/fcros/R/fcrosMod.R | 61 +++++++++++++++-- fcros-1.5/fcros/R/fcrosTopN.R | 7 + fcros-1.5/fcros/R/fcrosWrite.R | 50 +++++++++----- fcros-1.5/fcros/R/fvalTopN.R |only fcros-1.5/fcros/R/fvalVolcanoPlot.R |only fcros-1.5/fcros/R/histoPlot.R |only fcros-1.5/fcros/R/moyStdCalc.R |only fcros-1.5/fcros/R/pfco.R |only fcros-1.5/fcros/R/pfcoMod.R |only fcros-1.5/fcros/R/pvalTopN.R |only fcros-1.5/fcros/R/pvalVolcanoPlot.R |only fcros-1.5/fcros/R/rmatCalc.R | 2 fcros-1.5/fcros/R/rmatTrim.R |only fcros-1.5/fcros/R/tprobaCalc.R |only fcros-1.5/fcros/R/voomReads.R |only fcros-1.5/fcros/man/cghData.Rd | 34 +++++---- fcros-1.5/fcros/man/cghInfo.Rd | 26 ++++--- fcros-1.5/fcros/man/chrMerge.rd |only fcros-1.5/fcros/man/chrPlot.rd |only fcros-1.5/fcros/man/chrPlot2.rd |only fcros-1.5/fcros/man/chrSegment.rd |only fcros-1.5/fcros/man/dataSummary.rd |only fcros-1.5/fcros/man/fc2Calc.rd |only fcros-1.5/fcros/man/fcros-package.Rd | 49 +++++++++---- fcros-1.5/fcros/man/fcros.Rd | 8 +- fcros-1.5/fcros/man/fcros2.Rd | 4 - fcros-1.5/fcros/man/fcrosC.Rd | 6 - fcros-1.5/fcros/man/fcrosFCmat.Rd | 22 +++--- fcros-1.5/fcros/man/fcrosMod.Rd | 14 +-- fcros-1.5/fcros/man/fcrosRead.Rd | 5 - fcros-1.5/fcros/man/fcrosTopN.Rd | 23 +++--- fcros-1.5/fcros/man/fcrosTtest.Rd | 10 +- fcros-1.5/fcros/man/fcrosWrite.Rd | 29 +++++--- fcros-1.5/fcros/man/fdata.Rd | 49 +++++++------ fcros-1.5/fcros/man/fvalTopN.rd |only fcros-1.5/fcros/man/fvalVolcanoPlot.rd |only fcros-1.5/fcros/man/histoPlot.rd |only fcros-1.5/fcros/man/moyStdCalc.rd |only fcros-1.5/fcros/man/pfco.rd |only fcros-1.5/fcros/man/pfcoMod.rd |only fcros-1.5/fcros/man/pvalTopN.rd |only fcros-1.5/fcros/man/pvalVolcanoPlot.rd |only fcros-1.5/fcros/man/rmatCalc.rd |only fcros-1.5/fcros/man/rmatTrim.rd |only fcros-1.5/fcros/man/tprobaCalc.rd |only fcros-1.5/fcros/man/voomReads.rd |only fcros-1.5/fcros/src/fcros.cpp | 106 +++++++++++++++++++++++++++++- 76 files changed, 501 insertions(+), 245 deletions(-)
Title: Evidential Distance-Based Classification
Description: Different evidential distance-based classifiers, which provide
outputs in the form of Dempster-Shafer mass functions. The methods are: the
evidential K-nearest neighbor rule and the evidential neural network.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evclass versions 1.0.2 dated 2016-06-22 and 1.1.0 dated 2016-07-01
DESCRIPTION | 10 ++-- MD5 | 32 ++++++------- NAMESPACE | 1 R/EkNNfit.R | 2 R/EkNNinit.R | 1 R/EkNNval.R | 4 + R/decision.R |only R/evclass.R | 7 ++ R/proDSfit.R | 5 +- R/proDSinit.R | 1 R/proDSval.R | 5 +- inst/doc/Introduction.R | 51 ++++++++++++++++++++ inst/doc/Introduction.Rmd | 77 ++++++++++++++++++++++++++++++- inst/doc/Introduction.html | 110 ++++++++++++++++++++++++++++++++++++++------- man/decision.Rd |only man/evclass.Rd | 7 ++ man/proDSval.Rd | 2 vignettes/Introduction.Rmd | 77 ++++++++++++++++++++++++++++++- 18 files changed, 338 insertions(+), 54 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures for random effects. ML/REML estimates are obtained using the Average Information, Expectation-Maximization, Newton-Raphson, or Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models can be fitted for mixed models with a single random effect.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.8 dated 2016-06-06 and 1.9 dated 2016-07-01
sommer-1.8/sommer/R/bag.R |only sommer-1.8/sommer/man/bag.Rd |only sommer-1.9/sommer/CHANGELOG | 33 sommer-1.9/sommer/DESCRIPTION | 12 sommer-1.9/sommer/MD5 | 76 + sommer-1.9/sommer/NAMESPACE | 39 sommer-1.9/sommer/R/AI.R | 1182 ++++++++++++++++-------------- sommer-1.9/sommer/R/AI2.R | 841 +++++++++++++++------ sommer-1.9/sommer/R/AI3.R | 456 ++++++----- sommer-1.9/sommer/R/EM.R | 706 ++++++++--------- sommer-1.9/sommer/R/EM2.R | 366 ++++----- sommer-1.9/sommer/R/EMMA.R | 592 ++++++++++----- sommer-1.9/sommer/R/EMMAM.R |only sommer-1.9/sommer/R/MMERM.R |only sommer-1.9/sommer/R/NR.R | 26 sommer-1.9/sommer/R/NR22.R | 5 sommer-1.9/sommer/R/TP.prep.R | 10 sommer-1.9/sommer/R/atcg1234.R | 7 sommer-1.9/sommer/R/eigenGWAS.R |only sommer-1.9/sommer/R/hits.R |only sommer-1.9/sommer/R/manhattan.R |only sommer-1.9/sommer/R/mmer.R | 380 ++++++--- sommer-1.9/sommer/R/mmer2.R | 12 sommer-1.9/sommer/R/mmerSNOW.R | 984 +++++++++++------------- sommer-1.9/sommer/R/score.calc.R | 3 sommer-1.9/sommer/inst/CITATION | 4 sommer-1.9/sommer/man/AI2.Rd | 89 +- sommer-1.9/sommer/man/CPdata.Rd | 92 ++ sommer-1.9/sommer/man/E.mat.Rd | 5 sommer-1.9/sommer/man/EMMA.Rd | 16 sommer-1.9/sommer/man/EMMAM.Rd |only sommer-1.9/sommer/man/MMERM.Rd |only sommer-1.9/sommer/man/TP.prep.Rd | 31 sommer-1.9/sommer/man/anova.MMERM1.Rd |only sommer-1.9/sommer/man/coef.MMERM1.Rd |only sommer-1.9/sommer/man/eigenGWAS.Rd |only sommer-1.9/sommer/man/fitted.MMERM1.Rd |only sommer-1.9/sommer/man/hits.Rd |only sommer-1.9/sommer/man/manhattan.Rd |only sommer-1.9/sommer/man/mmer.Rd | 145 ++- sommer-1.9/sommer/man/mmer2.Rd | 88 +- sommer-1.9/sommer/man/mmerSNOW.Rd | 6 sommer-1.9/sommer/man/plot.MMERM1.Rd |only sommer-1.9/sommer/man/residuals.MMERM1.Rd |only sommer-1.9/sommer/man/sommer-package.Rd | 129 ++- sommer-1.9/sommer/man/summary.MMERM1.Rd |only sommer-1.9/sommer/vignettes/sommer.Rmd | 79 +- sommer-1.9/sommer/vignettes/sommer.html | 182 +++- 48 files changed, 3996 insertions(+), 2600 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-11 dated 2016-06-13 and 1.0-12 dated 2016-07-01
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/ModisDownload.R | 32 ++++++++++++++++++++------------ 3 files changed, 28 insertions(+), 20 deletions(-)
Title: Data Integration Feature for Force.com and Salesforce.com
Description: Insert, update,
retrieve, delete and bulk operate datasets with a SaaS based CRM
Salesforce.com and a PaaS based application platform Force.com from R.
Author: Takekatsu Hiramura [aut, cre],
Steven Mortimer [ctb],
Alexis Iglauer [ctb]
Maintainer: Takekatsu Hiramura <thira@plavox.info>
Diff between RForcecom versions 0.9 dated 2016-05-30 and 1.0 dated 2016-07-01
DESCRIPTION | 12 +++++----- MD5 | 44 ++++++++++++++++++------------------- NAMESPACE | 9 ++++--- R/RForcecom.R | 11 ++++----- R/rforcecom.abortBulkJob.R | 11 ++++----- R/rforcecom.checkBatchStatus.R | 11 ++++----- R/rforcecom.closeBulkJob.R | 11 ++++----- R/rforcecom.create.R | 13 +++++----- R/rforcecom.createBulkJob.R | 11 ++++----- R/rforcecom.delete.R | 13 +++++----- R/rforcecom.getBatchDetails.R | 15 +++++------- R/rforcecom.getBulkQueryResult.R | 15 +++++------- R/rforcecom.getObjectDescription.R | 13 +++++----- R/rforcecom.getObjectList.R | 13 +++++----- R/rforcecom.getServerTimestamp.R | 13 +++++----- R/rforcecom.login.R | 13 +++++----- R/rforcecom.logout.R | 11 ++++----- R/rforcecom.query.R | 13 +++++----- R/rforcecom.queryMore.R | 11 ++++----- R/rforcecom.search.R | 15 +++++------- R/rforcecom.update.R | 13 +++++----- R/rforcecom.upsert.R | 15 +++++------- man/RForcecom.Rd | 6 ++--- 23 files changed, 147 insertions(+), 165 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (see 'citation("recmap")' for details). This algorithm
draws maps according to a given statistical value (e. g. election results,
population or epidemiological data). The basic idea of the RecMap algorithm is
that each map region (e. g. different countries) is represented by a
rectangle. The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about 'RecMap' is
provided by a vignette included in this package and a 'RecMap gallery' site at
<http://cartodraw.science/recmap/gallery>.
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 0.4.0 dated 2016-06-13 and 0.5.0 dated 2016-07-01
DESCRIPTION | 24 +++++++++++------------- MD5 | 21 +++++++++++---------- R/recmap.R | 9 --------- R/zzz.R |only README.md | 27 ++++++++++++++++++++++++++- inst/NEWS.Rd | 11 ++++++++++- inst/doc/recmap.R | 3 ++- inst/doc/recmap.Rmd | 5 +++-- inst/doc/recmap.html | 27 +++++++++++++-------------- man/plot_recmap.Rd | 9 +++++---- man/recmap.Rd | 48 ++++++++++++++++++++++++++++-------------------- vignettes/recmap.Rmd | 5 +++-- 12 files changed, 112 insertions(+), 77 deletions(-)
Title: Simultaneous Generation of Multivariate Data with Poisson and
Normal Marginals
Description: Generates multivariate data with count and continuous variables with a pre-specified correlation matrix. The count and continuous variables are assumed to have Poisson and normal marginals, respectively. The data generation mechanism is a combination of the normal to anything principle and a connection between Poisson and normal correlations in the mixture.
Author: Anup Amatya and Hakan Demirtas
Maintainer: Anup Amatya <aamatya@nmsu.edu>
Diff between PoisNor versions 1.0 dated 2014-03-19 and 1.1 dated 2016-07-01
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- NAMESPACE | 1 + man/PoisNor-package.Rd | 6 +++--- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Calculation of Low Flow Statistics for Daily Stream Flow Data
Description: The "Manual on Low-flow Estimation and Prediction", published by
the World Meteorological Organisation (WMO), gives a comprehensive summary on
how to analyse stream flow data focusing on low-flows. This packages provides
functions to compute the described statistics and produces plots similar to the
ones in the manual.
Author: Daniel Koffler, Tobias Gauster and Gregor Laaha
Maintainer: Tobias Gauster <t.gauster@boku.ac.at>
Diff between lfstat versions 0.8.0 dated 2015-09-29 and 0.9.0 dated 2016-07-01
DESCRIPTION | 18 MD5 | 122 NAMESPACE | 186 NEWS.md | 62 R/1NAs.R | 52 R/2processes.R | 308 R/3lfindices.R | 1318 R/5extreme.R | 1237 R/6streamdef.R | 444 R/7multistation.R | 104 R/hyear.R | 255 R/import.R |only R/lfobj.R | 244 R/methods.R | 72 R/misc.R | 567 R/options.R | 40 R/pooling.R | 753 R/readsheets.R | 145 README.md | 46 inst/samplesheets/16610709.dat |64412 +++++++++--------- inst/samplesheets/9104020.day |75468 +++++++++++----------- inst/samplesheets/QTag200071.dat |32190 ++++----- man/BFI.Rd | 110 man/apply.seasonal.Rd |only man/as.xts.lfobj.Rd | 72 man/baseflow.Rd | 82 man/cdf_ev.Rd | 84 man/check_distribution.Rd | 60 man/createlfobj.Rd | 172 man/evfit.Rd | 101 man/evquantile.Rd | 56 man/fill_na.Rd |only man/find_droughts.Rd | 118 man/flowunit.Rd |only man/gringorten.Rd | 52 man/hyear_start.Rd | 88 man/ma.Rd | 66 man/ngaruroro.Rd | 46 man/plot.deficit.Rd | 58 man/pool_ic.Rd | 116 man/rfa.Rd | 108 man/rpline.Rd | 51 man/streamdef.Rd | 186 man/summary.deficit.Rd | 77 man/trace_value.Rd | 67 man/tyears.Rd | 220 man/tyearsS.Rd | 164 man/vary_threshold.Rd | 66 man/water_year.Rd | 134 tests/testthat.R | 6 tests/testthat/Q-Tagesmittel-207373.csv |12472 +-- tests/testthat/QMittelTag207373.txt |12468 +-- tests/testthat/tallaksen-ngaruroro-baseflow.csv | 7308 +- tests/testthat/tallaksen-ray-baseflow.csv | 2194 tests/testthat/tallaksen-sequent-peak-storage.csv | 7302 +- tests/testthat/tallaksen-sequent-peak-summary.csv | 76 tests/testthat/test-baseflow.R | 78 tests/testthat/test-grouping.R |only tests/testthat/test-import.R |only tests/testthat/test-mam.R |only tests/testthat/test-pooling.R |only tests/testthat/test-sequent-peak.R | 100 tests/testthat/test-streamdef.R | 356 tests/testthat/test-summary_deficit.R |only tests/testthat/test-tyear.R | 558 tests/testthat/test-unit.R |only tests/testthat/test-utils.R | 147 67 files changed, 111989 insertions(+), 111473 deletions(-)
Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of 'RJSONIO', but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with a web API. The implementation is
based on the mapping described in the vignette (Ooms, 2014). In addition to
converting JSON data from/to R objects, 'jsonlite' contains functions to
stream, validate, and prettify JSON data. The unit tests included with the
package verify that all edge cases are encoded and decoded consistently for
use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between jsonlite versions 0.9.22 dated 2016-06-15 and 1.0 dated 2016-07-01
DESCRIPTION | 6 ++--- MD5 | 31 ++++++++++++++------------- NAMESPACE | 2 + NEWS | 7 ++++++ R/asJSON.raw.R | 4 +-- R/base64.R | 23 +++++++++++++++----- R/fromJSON.R | 2 - R/pack.R | 12 +++++----- build/vignette.rds |binary inst/doc/json-mapping.pdf |binary man/base64.Rd |only man/fromJSON.Rd | 2 - src/Makevars | 10 ++++---- src/num_to_char.c | 40 ++++++++++++++++------------------- src/r-base64.c | 6 ++--- src/yajl/yajl_gen.c | 2 - tests/testthat/test-toJSON-numeric.R | 1 17 files changed, 85 insertions(+), 63 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.2 dated 2016-01-27 and 0.3 dated 2016-07-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/cvGrace.R | 29 +++++++++++++++++++++-------- R/grace.R | 10 +++++++++- R/grace.test.R | 10 ++++++++-- 5 files changed, 46 insertions(+), 19 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package '\href{http://docs.ggplot2.org/current/}{ggplot2}'
is a plotting system based on the grammar of graphics. '\href{https://
ggobi.github.io/ggally}{GGally}' extends 'ggplot2' by adding several functions
to reduce the complexity of combining geometric objects with transformed data.
Some of these functions include a pairwise plot matrix, a two group pairwise plot
matrix, a parallel coordinates plot, a survival plot, and several functions to
plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs, ggduo, and ggally_*.
contributor for all functions.),
Jason Crowley [aut] (ggparcoord),
Di Cook [aut, ths] (ggscatmat, gglyph),
Heike Hofmann [ths],
Hadley Wickham [ths],
Francois Briatte [aut] (ggcorr, ggnet, ggnet2),
Moritz Marbach [aut] (ggnet, ggnet2),
Edwin Thoen [aut] (ggsurv),
Amos Elberg [aut] (ggnetworkmap),
Joseph Larmarange [aut] (ggcoef)
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 1.1.0 dated 2016-06-02 and 1.2.0 dated 2016-07-01
GGally-1.1.0/GGally/inst/doc/ggcoef.R |only GGally-1.1.0/GGally/inst/doc/gglyph.R |only GGally-1.1.0/GGally/inst/doc/ggmatrix.R |only GGally-1.1.0/GGally/inst/doc/ggnetworkmap.R |only GGally-1.1.0/GGally/inst/doc/ggpairs.R |only GGally-1.1.0/GGally/inst/doc/ggscatmat.R |only GGally-1.1.0/GGally/inst/doc/ggsurv.R |only GGally-1.1.0/GGally/man/eval_ggpair.Rd |only GGally-1.1.0/GGally/man/mapping_color_fill.Rd |only GGally-1.2.0/GGally/DESCRIPTION | 37 GGally-1.2.0/GGally/MD5 | 139 +- GGally-1.2.0/GGally/NAMESPACE | 4 GGally-1.2.0/GGally/NEWS | 38 GGally-1.2.0/GGally/R/data-australia-pisa-2012.R |only GGally-1.2.0/GGally/R/find-combo.R | 116 + GGally-1.2.0/GGally/R/gg-plots.R | 29 GGally-1.2.0/GGally/R/ggcoef.R | 82 - GGally-1.2.0/GGally/R/ggcorr.R | 2 GGally-1.2.0/GGally/R/ggmatrix.R | 1 GGally-1.2.0/GGally/R/ggmatrix_make_plot.R |only GGally-1.2.0/GGally/R/ggmatrix_print.R | 22 GGally-1.2.0/GGally/R/ggnet.R | 2 GGally-1.2.0/GGally/R/ggnet2.R | 2 GGally-1.2.0/GGally/R/ggnetworkmap.R | 16 GGally-1.2.0/GGally/R/ggpairs.R | 887 +++++++++----- GGally-1.2.0/GGally/R/ggpairs_getput.R | 137 -- GGally-1.2.0/GGally/R/ggpairs_internal_plots.R | 45 GGally-1.2.0/GGally/R/ggparcoord.R | 55 GGally-1.2.0/GGally/R/ggsurv.R | 47 GGally-1.2.0/GGally/R/utils.R | 6 GGally-1.2.0/GGally/README.md | 7 GGally-1.2.0/GGally/build/vignette.rds |binary GGally-1.2.0/GGally/data/australia_PISA2012.rda |only GGally-1.2.0/GGally/inst/doc/ggcoef.Rmd | 83 - GGally-1.2.0/GGally/inst/doc/ggcoef.html | 180 -- GGally-1.2.0/GGally/inst/doc/gglyph.Rmd | 42 GGally-1.2.0/GGally/inst/doc/gglyph.html | 139 -- GGally-1.2.0/GGally/inst/doc/ggmatrix.Rmd | 195 --- GGally-1.2.0/GGally/inst/doc/ggmatrix.html | 291 ---- GGally-1.2.0/GGally/inst/doc/ggnetworkmap.Rmd | 128 -- GGally-1.2.0/GGally/inst/doc/ggnetworkmap.html | 210 --- GGally-1.2.0/GGally/inst/doc/ggpairs.Rmd | 175 -- GGally-1.2.0/GGally/inst/doc/ggpairs.html | 258 ---- GGally-1.2.0/GGally/inst/doc/ggscatmat.Rmd | 31 GGally-1.2.0/GGally/inst/doc/ggscatmat.html | 123 - GGally-1.2.0/GGally/inst/doc/ggsurv.Rmd | 88 - GGally-1.2.0/GGally/inst/doc/ggsurv.html | 188 -- GGally-1.2.0/GGally/man/australia_PISA2012.Rd |only GGally-1.2.0/GGally/man/find_plot_type.Rd | 15 GGally-1.2.0/GGally/man/getPlot.Rd | 6 GGally-1.2.0/GGally/man/ggally_barDiag.Rd | 2 GGally-1.2.0/GGally/man/ggally_ratio.Rd | 2 GGally-1.2.0/GGally/man/ggally_smooth.Rd | 6 GGally-1.2.0/GGally/man/ggcoef.Rd | 8 GGally-1.2.0/GGally/man/ggcorr.Rd | 2 GGally-1.2.0/GGally/man/ggduo.Rd |only GGally-1.2.0/GGally/man/ggnet.Rd | 2 GGally-1.2.0/GGally/man/ggnet2.Rd | 2 GGally-1.2.0/GGally/man/ggpairs.Rd | 42 GGally-1.2.0/GGally/man/ggparcoord.Rd | 55 GGally-1.2.0/GGally/man/ggsurv.Rd | 6 GGally-1.2.0/GGally/man/mapping_color_to_fill.Rd |only GGally-1.2.0/GGally/man/plot_types.Rd | 2 GGally-1.2.0/GGally/man/putPlot.Rd | 12 GGally-1.2.0/GGally/tests/testthat/test-gg-plots.R | 48 GGally-1.2.0/GGally/tests/testthat/test-gglegend.R | 26 GGally-1.2.0/GGally/tests/testthat/test-ggmatrix.R | 21 GGally-1.2.0/GGally/tests/testthat/test-ggmatrix_getput.R | 31 GGally-1.2.0/GGally/tests/testthat/test-ggscatmat.R | 11 GGally-1.2.0/GGally/tests/testthat/test-ggsurv.R | 49 GGally-1.2.0/GGally/tests/testthat/test-zzz_ggpairs.R | 633 ++++++--- GGally-1.2.0/GGally/vignettes/ggcoef.Rmd | 83 - GGally-1.2.0/GGally/vignettes/gglyph.Rmd | 42 GGally-1.2.0/GGally/vignettes/ggmatrix.Rmd | 195 --- GGally-1.2.0/GGally/vignettes/ggnetworkmap.Rmd | 128 -- GGally-1.2.0/GGally/vignettes/ggpairs.Rmd | 175 -- GGally-1.2.0/GGally/vignettes/ggscatmat.Rmd | 31 GGally-1.2.0/GGally/vignettes/ggsurv.Rmd | 88 - 78 files changed, 1849 insertions(+), 3679 deletions(-)
Title: Network Visualization in the 'ggplot2' Framework
Description: Network visualization in the 'ggplot2' framework. Network
functionality is provided in a single 'ggplot2' layer by calling the geom 'net'.
Layouts are calculated using the 'sna' package, example networks are included.
Author: Samantha Tyner, Heike Hofmann
Maintainer: Samantha Tyner <sctyner@iastate.edu>
Diff between geomnet versions 0.1.0 dated 2016-05-30 and 0.1.2.1 dated 2016-07-01
DESCRIPTION | 13 ++++--- MD5 | 14 +++++--- R/geom-net.r | 26 +++++++-------- build |only inst |only man/geom_net.Rd | 26 +++++---------- vignettes/comparing-graph-drawing-speed.Rmd | 47 ++++++++++++---------------- 7 files changed, 60 insertions(+), 66 deletions(-)
Title: Simulation from Endpoint-Conditioned Continuous Time Markov
Chains
Description: Draw sample paths for endpoint-conditioned continuous time Markov chains via modified rejection sampling or uniformization.
Author: Jon Fintzi [aut, cre]
Maintainer: Jon Fintzi <fintzij@uw.edu>
Diff between ECctmc versions 0.1.0 dated 2016-02-12 and 0.2.1 dated 2016-07-01
DESCRIPTION | 6 +- MD5 | 14 +++--- R/RcppExports.R | 4 + build/vignette.rds |binary inst/doc/ECctmc_vignette.html | 22 ++++----- inst/include |only src/RcppExports.cpp | 98 ++++++++++++++++++++++++++++++++++++++---- src/simulation_functions.cpp | 1 8 files changed, 115 insertions(+), 30 deletions(-)