Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. Can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre],
Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>
Diff between nplr versions 0.1-5 dated 2016-09-04 and 0.1-6 dated 2016-11-20
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NAMESPACE | 3 +- NEWS | 9 ++++++ R/AllClasses.R | 15 +++++++++- R/AllGenerics.R | 27 ++++++++++++++++-- R/helpers.R | 73 ++++++++++++++++++--------------------------------- R/nplr.R | 20 ++----------- R/summary.nplr.R | 1 inst/doc/nplr.pdf |binary man/nplrAccessors.Rd | 4 ++ 11 files changed, 97 insertions(+), 83 deletions(-)
Title: Miscellaneous Tools and Utilities
Description: Miscellaneous small tools and utilities.
Many of them facilitate the work with matrices,
e.g. inserting rows or columns, creating symmetric matrices,
or checking for semidefiniteness.
Other tools facilitate the work with regression models,
e.g. extracting the standard errors,
obtaining the number of (estimated) parameters,
or calculating R-squared values.
Author: Arne Henningsen, Ott Toomet
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between miscTools versions 0.6-16 dated 2013-03-13 and 0.6-20 dated 2016-11-20
miscTools-0.6-16/miscTools/miscTools.Rproj |only miscTools-0.6-20/miscTools/DESCRIPTION | 17 ++ miscTools-0.6-20/miscTools/MD5 | 16 +- miscTools-0.6-20/miscTools/NAMESPACE | 11 + miscTools-0.6-20/miscTools/NEWS | 9 + miscTools-0.6-20/miscTools/R/semidef.R |only miscTools-0.6-20/miscTools/R/utils.R | 45 ------- miscTools-0.6-20/miscTools/man/semidefiniteness.Rd | 100 +++++++++++++---- miscTools-0.6-20/miscTools/tests/semidefTest.R |only miscTools-0.6-20/miscTools/tests/semidefTest.Rout.save |only miscTools-0.6-20/miscTools/tests/stdErTests.Rout.save | 19 +-- 11 files changed, 130 insertions(+), 87 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of
variables included in multiplicative interaction terms.
Author: Frederick Solt [aut],
Yue Hu [aut, cre],
Brenton Kenkel [ctb]
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.4 dated 2016-09-14 and 0.1.5 dated 2016-11-20
DESCRIPTION | 6 +++--- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 4 ++++ R/Interplot.R | 10 +++++----- R/Interplot_default.R | 15 ++++++++------- R/Interplot_mi.R | 37 ++++++++++++++++++++----------------- R/Interplot_mlm.R | 39 +++++++++++++++++++++------------------ R/Interplot_mlmmi.R | 39 +++++++++++++++++++++------------------ R/Interplot_plot.R | 3 ++- inst/CITATION | 4 ++-- inst/doc/interplot-vignette.R | 3 +++ inst/doc/interplot-vignette.Rmd | 9 +++++++++ inst/doc/interplot-vignette.html | 29 ++++++++++++++++------------- man/interplot.Rd | 9 ++++++--- man/interplot.default.Rd | 6 ++++-- man/interplot.lmerMod.Rd | 6 ++++-- man/interplot.lmmi.Rd | 6 ++++-- man/interplot.mlmmi.Rd | 6 ++++-- man/interplot.plot.Rd | 8 +++++--- vignettes/interplot-vignette.Rmd | 9 +++++++++ 20 files changed, 169 insertions(+), 117 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.12.0 dated 2016-09-12 and 2.12.0-1 dated 2016-11-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/include/src/stan/lang/ast_def.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides
the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the
customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Trustees of Columbia University [cph],
R Core Deveopment Team [cph] (R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.12.1 dated 2016-09-13 and 2.13.1 dated 2016-11-20
rstanarm-2.12.1/rstanarm/man/log_lik.Rd |only rstanarm-2.12.1/rstanarm/man/posterior_interval.Rd |only rstanarm-2.12.1/rstanarm/man/posterior_predict.Rd |only rstanarm-2.12.1/rstanarm/man/pp_check.Rd |only rstanarm-2.12.1/rstanarm/man/rstanarm-plots.Rd |only rstanarm-2.13.1/rstanarm/DESCRIPTION | 16 rstanarm-2.13.1/rstanarm/MD5 | 206 +- rstanarm-2.13.1/rstanarm/NAMESPACE | 54 rstanarm-2.13.1/rstanarm/R/data_block.R | 14 rstanarm-2.13.1/rstanarm/R/datasets.R | 9 rstanarm-2.13.1/rstanarm/R/gamm4_to_glmer.R |only rstanarm-2.13.1/rstanarm/R/log_lik.R |only rstanarm-2.13.1/rstanarm/R/loo.R | 95 - rstanarm-2.13.1/rstanarm/R/misc.R | 61 rstanarm-2.13.1/rstanarm/R/neg_binomial_2.R | 8 rstanarm-2.13.1/rstanarm/R/plots.R | 449 +++-- rstanarm-2.13.1/rstanarm/R/posterior_interval.R | 94 - rstanarm-2.13.1/rstanarm/R/posterior_linpred.R | 40 rstanarm-2.13.1/rstanarm/R/posterior_predict.R | 161 +- rstanarm-2.13.1/rstanarm/R/posterior_vs_prior.R | 225 +- rstanarm-2.13.1/rstanarm/R/pp_check.R | 796 ++++------ rstanarm-2.13.1/rstanarm/R/pp_data.R | 67 rstanarm-2.13.1/rstanarm/R/pp_validate.R | 136 - rstanarm-2.13.1/rstanarm/R/predictive_error.R |only rstanarm-2.13.1/rstanarm/R/predictive_interval.R |only rstanarm-2.13.1/rstanarm/R/print-and-summary.R | 63 rstanarm-2.13.1/rstanarm/R/prior_summary.R |only rstanarm-2.13.1/rstanarm/R/priors.R | 70 rstanarm-2.13.1/rstanarm/R/rstanarm-package.R | 65 rstanarm-2.13.1/rstanarm/R/stan_biglm.fit.R | 33 rstanarm-2.13.1/rstanarm/R/stan_gamm4.R | 164 +- rstanarm-2.13.1/rstanarm/R/stan_glm.R | 55 rstanarm-2.13.1/rstanarm/R/stan_glm.fit.R | 194 +- rstanarm-2.13.1/rstanarm/R/stan_glmer.R | 36 rstanarm-2.13.1/rstanarm/R/stan_lm.R | 4 rstanarm-2.13.1/rstanarm/R/stan_polr.R | 139 - rstanarm-2.13.1/rstanarm/R/stan_polr.fit.R | 31 rstanarm-2.13.1/rstanarm/R/stanreg-methods.R | 140 - rstanarm-2.13.1/rstanarm/R/stanreg.R | 4 rstanarm-2.13.1/rstanarm/build/vignette.rds |binary rstanarm-2.13.1/rstanarm/demo/ARM_Ch05.R | 4 rstanarm-2.13.1/rstanarm/demo/ARM_Ch08.R | 10 rstanarm-2.13.1/rstanarm/exec/continuous.stan | 37 rstanarm-2.13.1/rstanarm/inst/NEWS | 14 rstanarm-2.13.1/rstanarm/inst/doc/aov.R | 2 rstanarm-2.13.1/rstanarm/inst/doc/aov.html | 20 rstanarm-2.13.1/rstanarm/inst/doc/binomial.R | 2 rstanarm-2.13.1/rstanarm/inst/doc/binomial.html | 12 rstanarm-2.13.1/rstanarm/inst/doc/children/SETTINGS-rstan.txt | 2 rstanarm-2.13.1/rstanarm/inst/doc/continuous.R | 11 rstanarm-2.13.1/rstanarm/inst/doc/continuous.Rmd | 18 rstanarm-2.13.1/rstanarm/inst/doc/continuous.html | 59 rstanarm-2.13.1/rstanarm/inst/doc/count.R | 6 rstanarm-2.13.1/rstanarm/inst/doc/count.Rmd | 4 rstanarm-2.13.1/rstanarm/inst/doc/count.html | 12 rstanarm-2.13.1/rstanarm/inst/doc/glmer.R | 14 rstanarm-2.13.1/rstanarm/inst/doc/glmer.Rmd | 38 rstanarm-2.13.1/rstanarm/inst/doc/glmer.html | 57 rstanarm-2.13.1/rstanarm/inst/doc/lm.R | 2 rstanarm-2.13.1/rstanarm/inst/doc/lm.html | 18 rstanarm-2.13.1/rstanarm/inst/doc/polr.R | 2 rstanarm-2.13.1/rstanarm/inst/doc/polr.html | 4 rstanarm-2.13.1/rstanarm/inst/doc/pooling.R | 42 rstanarm-2.13.1/rstanarm/inst/doc/pooling.Rmd | 56 rstanarm-2.13.1/rstanarm/inst/doc/pooling.html | 77 rstanarm-2.13.1/rstanarm/inst/doc/rstanarm.R | 2 rstanarm-2.13.1/rstanarm/inst/doc/rstanarm.Rmd | 348 ++-- rstanarm-2.13.1/rstanarm/inst/doc/rstanarm.html | 12 rstanarm-2.13.1/rstanarm/man/adapt_delta.Rd | 2 rstanarm-2.13.1/rstanarm/man/as.matrix.stanreg.Rd | 2 rstanarm-2.13.1/rstanarm/man/figures |only rstanarm-2.13.1/rstanarm/man/get_y.Rd | 2 rstanarm-2.13.1/rstanarm/man/log_lik.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/loo.stanreg.Rd | 52 rstanarm-2.13.1/rstanarm/man/plot.stanreg.Rd | 161 +- rstanarm-2.13.1/rstanarm/man/posterior_interval.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/posterior_linpred.Rd | 21 rstanarm-2.13.1/rstanarm/man/posterior_predict.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/posterior_vs_prior.Rd | 24 rstanarm-2.13.1/rstanarm/man/pp_check.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/pp_validate.Rd | 46 rstanarm-2.13.1/rstanarm/man/predict.stanreg.Rd | 2 rstanarm-2.13.1/rstanarm/man/predictive_error.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/predictive_interval.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/print.stanreg.Rd | 2 rstanarm-2.13.1/rstanarm/man/prior_summary.stanreg.Rd |only rstanarm-2.13.1/rstanarm/man/priors.Rd | 69 rstanarm-2.13.1/rstanarm/man/rstanarm-datasets.Rd | 9 rstanarm-2.13.1/rstanarm/man/rstanarm-package.Rd | 66 rstanarm-2.13.1/rstanarm/man/stan_biglm.Rd | 2 rstanarm-2.13.1/rstanarm/man/stan_gamm4.Rd | 81 - rstanarm-2.13.1/rstanarm/man/stan_glm.Rd | 65 rstanarm-2.13.1/rstanarm/man/stan_glmer.Rd | 17 rstanarm-2.13.1/rstanarm/man/stan_lm.Rd | 6 rstanarm-2.13.1/rstanarm/man/stan_polr.Rd | 36 rstanarm-2.13.1/rstanarm/man/stanreg-methods.Rd | 79 rstanarm-2.13.1/rstanarm/man/summary.stanreg.Rd | 5 rstanarm-2.13.1/rstanarm/src/include/models.hpp | 26 rstanarm-2.13.1/rstanarm/tests/testthat/test_loo.R | 149 + rstanarm-2.13.1/rstanarm/tests/testthat/test_methods.R | 446 +++-- rstanarm-2.13.1/rstanarm/tests/testthat/test_misc.R | 3 rstanarm-2.13.1/rstanarm/tests/testthat/test_plots.R | 103 - rstanarm-2.13.1/rstanarm/tests/testthat/test_posterior_predict.R | 17 rstanarm-2.13.1/rstanarm/tests/testthat/test_pp_check.R | 135 + rstanarm-2.13.1/rstanarm/tests/testthat/test_pp_validate.R | 3 rstanarm-2.13.1/rstanarm/tests/testthat/test_stan_functions.R | 13 rstanarm-2.13.1/rstanarm/tests/testthat/test_stan_glmer.R | 32 rstanarm-2.13.1/rstanarm/vignettes/children/SETTINGS-rstan.txt | 2 rstanarm-2.13.1/rstanarm/vignettes/continuous.Rmd | 18 rstanarm-2.13.1/rstanarm/vignettes/count.Rmd | 4 rstanarm-2.13.1/rstanarm/vignettes/glmer.Rmd | 38 rstanarm-2.13.1/rstanarm/vignettes/pooling.Rmd | 56 rstanarm-2.13.1/rstanarm/vignettes/rstanarm.Rmd | 348 ++-- 113 files changed, 3770 insertions(+), 2686 deletions(-)
Title: Tools for Working with Aerobiological Data
Description: A set of functions for working with aerobiological data (e.g. calculation of pollen season limits, replacement of outliers).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between pollen versions 0.40 dated 2016-10-02 and 0.50.0 dated 2016-11-20
DESCRIPTION | 13 +++--- MD5 | 19 ++++++-- NAMESPACE | 4 + R/outliers_replacer.R |only R/pollen_season.R | 34 +++++++++++---- README.md | 90 ++++++++---------------------------------- build |only inst |only man/outliers_replacer.Rd |only man/pollen_season.Rd | 10 +++- tests/testthat/test-seasons.R | 27 ++++++++---- vignettes |only 12 files changed, 93 insertions(+), 104 deletions(-)
Title: Extended Rasch Modeling
Description: Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Löf-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices.
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Thomas Rusch [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between eRm versions 0.15-6 dated 2015-11-12 and 0.15-7 dated 2016-11-20
DESCRIPTION | 10 MD5 | 54 ++-- R/LRtest.Rm.R | 435 ++++++++++++++++++++-------------------- build/partial.rdb |binary build/vignette.rds |binary data/llraDat1.rda |binary data/llraDat2.rda |binary data/llradat3.rda |binary data/lltmdat1.rda |binary data/lltmdat2.rda |binary data/lpcmdat.rda |binary data/lrsmdat.rda |binary data/pcmdat.rda |binary data/pcmdat2.rda |binary data/raschdat1.rda |binary data/raschdat1_RM_fitted.RData |binary data/raschdat1_RM_lrres2.RData |binary data/raschdat1_RM_plotDIF.RData |binary data/raschdat2.rda |binary data/raschdat3.rda |binary data/raschdat4.rda |binary data/rsmdat.rda |binary data/xmpl.RData |binary data/xmplbig.RData |binary inst/NEWS.Rd | 5 inst/doc/eRm.R | 214 +++++++++---------- inst/doc/eRm.pdf |binary man/Waldtest.Rd | 116 +++++----- 28 files changed, 418 insertions(+), 416 deletions(-)
Title: CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks
Description: Implementation of the CCDr (Concave penalized Coordinate Descent with reparametrization) structure learning algorithm as described in Aragam and Zhou (2015) <http://www.jmlr.org/papers/v16/aragam15a.html>. This is a fast, score-based method for learning Bayesian networks that uses sparse regularization and block-cyclic coordinate descent.
Author: Bryon Aragam [aut, cre],
Dacheng Zhang [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between ccdrAlgorithm versions 0.0.1 dated 2016-08-10 and 0.0.2 dated 2016-11-20
DESCRIPTION | 18 +- MD5 | 36 +++-- NAMESPACE | 3 NEWS.md |only R/RcppExports.R | 10 - R/ccdrAlgorithm-functions.R |only R/ccdrAlgorithm-main.R | 64 ++++++++- R/s3-SparseBlockMatrixR.R | 60 +++------ R/s3-generics.R | 1 R/zzz.R | 2 README.md | 4 src/RcppExports.cpp | 34 ++--- src/algorithm.h | 246 +++++++++++++++++++++---------------- src/penalties.h | 23 ++- src/rcpp_wrap.cpp | 16 +- tests/testthat/test-ccdr_call.R |only tests/testthat/test-ccdr_gridR.R | 43 +++--- tests/testthat/test-ccdr_ivn.R |only tests/testthat/test-ccdr_singleR.R | 61 +++++++++ tests/testthat/test-default_run.R | 54 ++++++++ tests/testthat/test-s3_as.R | 12 - 21 files changed, 462 insertions(+), 225 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currently it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.49 dated 2015-12-27 and 0.50 dated 2016-11-20
meteoForecast-0.49/meteoForecast/ChangeLog |only meteoForecast-0.50/meteoForecast/DESCRIPTION | 12 ++++---- meteoForecast-0.50/meteoForecast/MD5 | 19 ++++++------ meteoForecast-0.50/meteoForecast/NAMESPACE | 1 meteoForecast-0.50/meteoForecast/R/envir.R | 4 ++ meteoForecast-0.50/meteoForecast/R/rasterMeteoGalicia.R | 2 - meteoForecast-0.50/meteoForecast/R/zzz.R | 4 ++ meteoForecast-0.50/meteoForecast/inst/CITATION | 17 ++++++----- meteoForecast-0.50/meteoForecast/man/getRaster.Rd | 3 +- meteoForecast-0.50/meteoForecast/man/options.Rd | 2 - meteoForecast-0.50/meteoForecast/man/vars.Rd | 24 ++++++++++++---- 11 files changed, 54 insertions(+), 34 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from
'SPSS' or 'Stata' with 'haven' or 'foreign'.
Author: Joseph Larmarange [aut, cre],
Daniel Ludecke [ctb],
Hadley Wickham [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 0.2.3 dated 2016-06-21 and 1.0.0 dated 2016-11-20
DESCRIPTION | 11 + MD5 | 49 ++++---- NAMESPACE | 32 +++++ NEWS.md | 15 +- R/copy_labels.R | 2 R/labelled.R | 96 +++++----------- R/na_values.R |only R/remove_labels.R | 99 ++++++++++++++--- R/to_character.R | 1 R/to_factor.R | 1 R/val_labels.R | 16 ++ R/var_label.R | 4 build/vignette.rds |binary inst/doc/intro_labelled.R | 40 ++++++ inst/doc/intro_labelled.Rmd | 66 +++++++++++ inst/doc/intro_labelled.html | 236 +++++++++++++++++++++++++++++++++++++---- man/copy_labels.Rd | 6 - man/labelled.Rd | 15 +- man/labelled_spss.Rd |only man/na_values.Rd |only man/remove_labels.Rd | 48 ++++---- man/to_character.Rd | 3 man/to_factor.Rd | 3 man/val_labels.Rd | 3 man/var_label.Rd | 12 -- tests/testthat/test-labelled.r | 37 ++++++ vignettes/intro_labelled.Rmd | 66 +++++++++++ 27 files changed, 662 insertions(+), 199 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.15.0 dated 2016-05-11 and 0.16.0 dated 2016-11-20
git2r-0.15.0/git2r/src/libgit2/src/delta-apply.c |only git2r-0.15.0/git2r/src/libgit2/src/delta-apply.h |only git2r-0.15.0/git2r/src/libgit2/src/diff_patch.c |only git2r-0.15.0/git2r/src/libgit2/src/diff_patch.h |only git2r-0.15.0/git2r/src/libgit2/src/transports/auth_negotiate.c |only git2r-0.15.0/git2r/src/libgit2/src/win32/pthread.h |only git2r-0.16.0/git2r/DESCRIPTION | 7 git2r-0.16.0/git2r/MD5 | 374 - git2r-0.16.0/git2r/NAMESPACE | 3 git2r-0.16.0/git2r/NEWS | 33 git2r-0.16.0/git2r/R/credential.r | 40 git2r-0.16.0/git2r/R/index.r | 62 git2r-0.16.0/git2r/R/libgit2.r | 2 git2r-0.16.0/git2r/R/reflog.r | 42 git2r-0.16.0/git2r/R/repository.r | 27 git2r-0.16.0/git2r/R/reset.r | 74 git2r-0.16.0/git2r/R/status.r | 34 git2r-0.16.0/git2r/R/tag.r | 79 git2r-0.16.0/git2r/configure | 147 git2r-0.16.0/git2r/configure.ac | 72 git2r-0.16.0/git2r/man/cred_ssh_key.Rd | 5 git2r-0.16.0/git2r/man/index_remove_bypath-methods.Rd |only git2r-0.16.0/git2r/man/reflog-methods.Rd | 13 git2r-0.16.0/git2r/man/reset-methods.Rd | 48 git2r-0.16.0/git2r/man/ssh_key_needs_passphrase.Rd |only git2r-0.16.0/git2r/man/status-methods.Rd | 18 git2r-0.16.0/git2r/man/tag_delete-methods.Rd |only git2r-0.16.0/git2r/src/Makevars.in | 52 git2r-0.16.0/git2r/src/Makevars.win | 7 git2r-0.16.0/git2r/src/git2r.c | 4 git2r-0.16.0/git2r/src/git2r_arg.c | 40 git2r-0.16.0/git2r/src/git2r_arg.h | 4 git2r-0.16.0/git2r/src/git2r_index.c | 26 git2r-0.16.0/git2r/src/git2r_push.c | 19 git2r-0.16.0/git2r/src/git2r_remote.c | 2 git2r-0.16.0/git2r/src/git2r_reset.c | 57 git2r-0.16.0/git2r/src/git2r_reset.h | 3 git2r-0.16.0/git2r/src/git2r_status.c | 14 git2r-0.16.0/git2r/src/git2r_status.h | 3 git2r-0.16.0/git2r/src/git2r_tag.c | 30 git2r-0.16.0/git2r/src/git2r_tag.h | 1 git2r-0.16.0/git2r/src/libgit2/include/git2.h | 1 git2r-0.16.0/git2r/src/libgit2/include/git2/blob.h | 67 git2r-0.16.0/git2r/src/libgit2/include/git2/checkout.h | 7 git2r-0.16.0/git2r/src/libgit2/include/git2/commit.h | 76 git2r-0.16.0/git2r/src/libgit2/include/git2/common.h | 4 git2r-0.16.0/git2r/src/libgit2/include/git2/diff.h | 69 git2r-0.16.0/git2r/src/libgit2/include/git2/errors.h | 3 git2r-0.16.0/git2r/src/libgit2/include/git2/index.h | 25 git2r-0.16.0/git2r/src/libgit2/include/git2/merge.h | 11 git2r-0.16.0/git2r/src/libgit2/include/git2/odb.h | 48 git2r-0.16.0/git2r/src/libgit2/include/git2/pack.h | 8 git2r-0.16.0/git2r/src/libgit2/include/git2/patch.h | 2 git2r-0.16.0/git2r/src/libgit2/include/git2/proxy.h |only git2r-0.16.0/git2r/src/libgit2/include/git2/refs.h | 11 git2r-0.16.0/git2r/src/libgit2/include/git2/remote.h | 21 git2r-0.16.0/git2r/src/libgit2/include/git2/repository.h | 21 git2r-0.16.0/git2r/src/libgit2/include/git2/revwalk.h | 10 git2r-0.16.0/git2r/src/libgit2/include/git2/signature.h | 13 git2r-0.16.0/git2r/src/libgit2/include/git2/submodule.h | 14 git2r-0.16.0/git2r/src/libgit2/include/git2/sys/merge.h |only git2r-0.16.0/git2r/src/libgit2/include/git2/sys/odb_backend.h | 11 git2r-0.16.0/git2r/src/libgit2/include/git2/sys/remote.h |only git2r-0.16.0/git2r/src/libgit2/include/git2/sys/stream.h | 3 git2r-0.16.0/git2r/src/libgit2/include/git2/sys/time.h |only git2r-0.16.0/git2r/src/libgit2/include/git2/sys/transport.h | 4 git2r-0.16.0/git2r/src/libgit2/include/git2/tag.h | 9 git2r-0.16.0/git2r/src/libgit2/include/git2/tree.h | 55 git2r-0.16.0/git2r/src/libgit2/include/git2/version.h | 6 git2r-0.16.0/git2r/src/libgit2/src/annotated_commit.c | 179 git2r-0.16.0/git2r/src/libgit2/src/annotated_commit.h | 7 git2r-0.16.0/git2r/src/libgit2/src/apply.c |only git2r-0.16.0/git2r/src/libgit2/src/apply.h |only git2r-0.16.0/git2r/src/libgit2/src/array.h | 3 git2r-0.16.0/git2r/src/libgit2/src/attrcache.c | 19 git2r-0.16.0/git2r/src/libgit2/src/blame_git.c | 26 git2r-0.16.0/git2r/src/libgit2/src/blob.c | 110 git2r-0.16.0/git2r/src/libgit2/src/branch.c | 12 git2r-0.16.0/git2r/src/libgit2/src/buffer.c | 272 git2r-0.16.0/git2r/src/libgit2/src/buffer.h | 8 git2r-0.16.0/git2r/src/libgit2/src/cache.c | 9 git2r-0.16.0/git2r/src/libgit2/src/checkout.c | 138 git2r-0.16.0/git2r/src/libgit2/src/clone.c | 8 git2r-0.16.0/git2r/src/libgit2/src/commit.c | 249 git2r-0.16.0/git2r/src/libgit2/src/commit_list.c | 11 git2r-0.16.0/git2r/src/libgit2/src/commit_list.h | 1 git2r-0.16.0/git2r/src/libgit2/src/common.h | 5 git2r-0.16.0/git2r/src/libgit2/src/config.c | 6 git2r-0.16.0/git2r/src/libgit2/src/config_file.c | 30 git2r-0.16.0/git2r/src/libgit2/src/crlf.c | 1 git2r-0.16.0/git2r/src/libgit2/src/curl_stream.c | 112 git2r-0.16.0/git2r/src/libgit2/src/delta.c | 300 git2r-0.16.0/git2r/src/libgit2/src/delta.h | 139 git2r-0.16.0/git2r/src/libgit2/src/describe.c | 2 git2r-0.16.0/git2r/src/libgit2/src/diff.c | 1601 ----- git2r-0.16.0/git2r/src/libgit2/src/diff.h | 136 git2r-0.16.0/git2r/src/libgit2/src/diff_driver.c | 10 git2r-0.16.0/git2r/src/libgit2/src/diff_file.c | 3 git2r-0.16.0/git2r/src/libgit2/src/diff_generate.c |only git2r-0.16.0/git2r/src/libgit2/src/diff_generate.h |only git2r-0.16.0/git2r/src/libgit2/src/diff_parse.c |only git2r-0.16.0/git2r/src/libgit2/src/diff_parse.h |only git2r-0.16.0/git2r/src/libgit2/src/diff_print.c | 420 - git2r-0.16.0/git2r/src/libgit2/src/diff_stats.c | 49 git2r-0.16.0/git2r/src/libgit2/src/diff_tform.c | 1 git2r-0.16.0/git2r/src/libgit2/src/diff_tform.h |only git2r-0.16.0/git2r/src/libgit2/src/diff_xdiff.c | 18 git2r-0.16.0/git2r/src/libgit2/src/diff_xdiff.h | 10 git2r-0.16.0/git2r/src/libgit2/src/fetchhead.c | 25 git2r-0.16.0/git2r/src/libgit2/src/filebuf.c | 9 git2r-0.16.0/git2r/src/libgit2/src/filebuf.h | 1 git2r-0.16.0/git2r/src/libgit2/src/fileops.c | 23 git2r-0.16.0/git2r/src/libgit2/src/fileops.h | 10 git2r-0.16.0/git2r/src/libgit2/src/fnmatch.c | 23 git2r-0.16.0/git2r/src/libgit2/src/global.c | 52 git2r-0.16.0/git2r/src/libgit2/src/ignore.c | 61 git2r-0.16.0/git2r/src/libgit2/src/index.c | 255 git2r-0.16.0/git2r/src/libgit2/src/index.h | 2 git2r-0.16.0/git2r/src/libgit2/src/iterator.c | 3054 +++++----- git2r-0.16.0/git2r/src/libgit2/src/iterator.h | 121 git2r-0.16.0/git2r/src/libgit2/src/merge.c | 236 git2r-0.16.0/git2r/src/libgit2/src/merge.h | 63 git2r-0.16.0/git2r/src/libgit2/src/merge_driver.c |only git2r-0.16.0/git2r/src/libgit2/src/merge_driver.h |only git2r-0.16.0/git2r/src/libgit2/src/merge_file.c | 60 git2r-0.16.0/git2r/src/libgit2/src/mwindow.c | 27 git2r-0.16.0/git2r/src/libgit2/src/mwindow.h | 3 git2r-0.16.0/git2r/src/libgit2/src/netops.c | 22 git2r-0.16.0/git2r/src/libgit2/src/object_api.c | 20 git2r-0.16.0/git2r/src/libgit2/src/odb.c | 320 - git2r-0.16.0/git2r/src/libgit2/src/odb_loose.c | 22 git2r-0.16.0/git2r/src/libgit2/src/odb_pack.c | 31 git2r-0.16.0/git2r/src/libgit2/src/openssl_stream.c | 77 git2r-0.16.0/git2r/src/libgit2/src/openssl_stream.h | 106 git2r-0.16.0/git2r/src/libgit2/src/pack-objects.c | 183 git2r-0.16.0/git2r/src/libgit2/src/pack-objects.h | 25 git2r-0.16.0/git2r/src/libgit2/src/pack.c | 26 git2r-0.16.0/git2r/src/libgit2/src/pack.h | 2 git2r-0.16.0/git2r/src/libgit2/src/patch.c |only git2r-0.16.0/git2r/src/libgit2/src/patch.h |only git2r-0.16.0/git2r/src/libgit2/src/patch_generate.c |only git2r-0.16.0/git2r/src/libgit2/src/patch_generate.h |only git2r-0.16.0/git2r/src/libgit2/src/patch_parse.c |only git2r-0.16.0/git2r/src/libgit2/src/patch_parse.h |only git2r-0.16.0/git2r/src/libgit2/src/path.c | 39 git2r-0.16.0/git2r/src/libgit2/src/path.h | 18 git2r-0.16.0/git2r/src/libgit2/src/pathspec.c | 2 git2r-0.16.0/git2r/src/libgit2/src/pool.h | 5 git2r-0.16.0/git2r/src/libgit2/src/pqueue.c | 17 git2r-0.16.0/git2r/src/libgit2/src/pqueue.h | 1 git2r-0.16.0/git2r/src/libgit2/src/proxy.c |only git2r-0.16.0/git2r/src/libgit2/src/proxy.h |only git2r-0.16.0/git2r/src/libgit2/src/push.c | 2 git2r-0.16.0/git2r/src/libgit2/src/rebase.c | 126 git2r-0.16.0/git2r/src/libgit2/src/refdb.c | 6 git2r-0.16.0/git2r/src/libgit2/src/refdb_fs.c | 132 git2r-0.16.0/git2r/src/libgit2/src/reflog.c | 9 git2r-0.16.0/git2r/src/libgit2/src/refs.c | 14 git2r-0.16.0/git2r/src/libgit2/src/refspec.c | 6 git2r-0.16.0/git2r/src/libgit2/src/remote.c | 121 git2r-0.16.0/git2r/src/libgit2/src/repository.c | 291 git2r-0.16.0/git2r/src/libgit2/src/reset.c | 2 git2r-0.16.0/git2r/src/libgit2/src/revparse.c | 11 git2r-0.16.0/git2r/src/libgit2/src/revwalk.c | 446 - git2r-0.16.0/git2r/src/libgit2/src/settings.c | 16 git2r-0.16.0/git2r/src/libgit2/src/signature.c | 27 git2r-0.16.0/git2r/src/libgit2/src/sortedcache.c | 19 git2r-0.16.0/git2r/src/libgit2/src/stash.c | 28 git2r-0.16.0/git2r/src/libgit2/src/status.c | 1 git2r-0.16.0/git2r/src/libgit2/src/stream.h | 4 git2r-0.16.0/git2r/src/libgit2/src/submodule.c | 20 git2r-0.16.0/git2r/src/libgit2/src/sysdir.c | 88 git2r-0.16.0/git2r/src/libgit2/src/sysdir.h | 5 git2r-0.16.0/git2r/src/libgit2/src/tag.c | 10 git2r-0.16.0/git2r/src/libgit2/src/thread-utils.h | 56 git2r-0.16.0/git2r/src/libgit2/src/transport.c | 8 git2r-0.16.0/git2r/src/libgit2/src/transports/http.c | 49 git2r-0.16.0/git2r/src/libgit2/src/transports/local.c | 5 git2r-0.16.0/git2r/src/libgit2/src/transports/smart.c | 6 git2r-0.16.0/git2r/src/libgit2/src/transports/smart.h | 1 git2r-0.16.0/git2r/src/libgit2/src/transports/smart_pkt.c | 10 git2r-0.16.0/git2r/src/libgit2/src/transports/smart_protocol.c | 28 git2r-0.16.0/git2r/src/libgit2/src/transports/winhttp.c | 155 git2r-0.16.0/git2r/src/libgit2/src/tree-cache.c | 9 git2r-0.16.0/git2r/src/libgit2/src/tree.c | 278 git2r-0.16.0/git2r/src/libgit2/src/tsort.c | 9 git2r-0.16.0/git2r/src/libgit2/src/unix/posix.h | 10 git2r-0.16.0/git2r/src/libgit2/src/unix/pthread.h |only git2r-0.16.0/git2r/src/libgit2/src/util.c | 33 git2r-0.16.0/git2r/src/libgit2/src/util.h | 10 git2r-0.16.0/git2r/src/libgit2/src/varint.c |only git2r-0.16.0/git2r/src/libgit2/src/varint.h |only git2r-0.16.0/git2r/src/libgit2/src/vector.c | 58 git2r-0.16.0/git2r/src/libgit2/src/vector.h | 8 git2r-0.16.0/git2r/src/libgit2/src/win32/posix.h | 3 git2r-0.16.0/git2r/src/libgit2/src/win32/precompiled.h | 2 git2r-0.16.0/git2r/src/libgit2/src/win32/reparse.h | 5 git2r-0.16.0/git2r/src/libgit2/src/win32/thread.h |only git2r-0.16.0/git2r/src/libgit2/src/zstream.c | 45 git2r-0.16.0/git2r/src/libgit2/src/zstream.h | 9 git2r-0.16.0/git2r/tests/index.R | 28 git2r-0.16.0/git2r/tests/push.R | 5 git2r-0.16.0/git2r/tests/reflog.R | 4 git2r-0.16.0/git2r/tests/repository.R | 14 git2r-0.16.0/git2r/tests/tag.R | 9 205 files changed, 7605 insertions(+), 5313 deletions(-)
Title: Biodiversity Data Visualizations
Description: Provides a set of functions to create basic visualizations to quickly
preview different aspects of biodiversity information such as inventory
completeness, extent of coverage (taxonomic, temporal and geographic), gaps
and biases.
Author: Vijay Barve <vijay.barve@gmail.com>, Javier Otegui
<javier.otegui@gmail.com>
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between bdvis versions 0.2.6 dated 2016-05-19 and 0.2.9 dated 2016-11-20
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- NEWS | 4 ++- R/bdcomplete.R | 54 +++++++++++++++++++++++++++----------------------- R/chronohorogram.R | 49 +++++++++++++++++++++++++++------------------ R/mapgrid.R | 12 +++++------ README.md | 2 - man/bdcomplete.Rd | 11 +++++++--- man/chronohorogram.Rd | 4 ++- man/mapgrid.Rd | 12 +++++------ 10 files changed, 100 insertions(+), 74 deletions(-)
Title: Mixed-Pair Mutual Information Estimators
Description: Uses a kernel smoothing approach to calculate Mutual Information
for comparisons between all types of variables including continuous vs
continuous, continuous vs discrete and discrete vs discrete. Uses a
nonparametric bias correction giving Bias Corrected Mutual Information
(BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited to
large genomic datasets.
Author: Chris Pardy
Maintainer: Chris Pardy <cooliomcdude@gmail.com>
Diff between mpmi versions 0.41 dated 2014-09-22 and 0.42 dated 2016-11-20
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS | 3 +++ build/vignette.rds |binary 5 files changed, 13 insertions(+), 9 deletions(-)
Title: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Description: The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker
Maintainer: Katharine M. Mullen <mullenkate@gmail.com>
Diff between minpack.lm versions 1.2-0 dated 2015-11-24 and 1.2-1 dated 2016-11-20
minpack.lm-1.2-0/minpack.lm/LICENSE |only minpack.lm-1.2-1/minpack.lm/DESCRIPTION | 8 ++++---- minpack.lm-1.2-1/minpack.lm/LICENSE.note |only minpack.lm-1.2-1/minpack.lm/MD5 | 10 +++++----- minpack.lm-1.2-1/minpack.lm/NEWS | 5 +++++ minpack.lm-1.2-1/minpack.lm/R/nlsLM.R | 7 +++++-- minpack.lm-1.2-1/minpack.lm/THANKS | 14 ++++++++------ 7 files changed, 27 insertions(+), 17 deletions(-)
More information about infraFDTD.assist at CRAN
Permanent link
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-7 dated 2016-06-17 and 0.2-0 dated 2016-11-20
gimme-0.1-7/gimme/R/deconvolve_funcs.R |only gimme-0.1-7/gimme/R/spm_funcs.R |only gimme-0.1-7/gimme/data/ts1.rda |only gimme-0.1-7/gimme/data/ts2.rda |only gimme-0.1-7/gimme/data/ts3.rda |only gimme-0.1-7/gimme/data/ts4.rda |only gimme-0.1-7/gimme/data/ts5.rda |only gimme-0.1-7/gimme/man/ts1.Rd |only gimme-0.1-7/gimme/man/ts2.Rd |only gimme-0.1-7/gimme/man/ts3.Rd |only gimme-0.1-7/gimme/man/ts4.Rd |only gimme-0.1-7/gimme/man/ts5.Rd |only gimme-0.2-0/gimme/DESCRIPTION | 11 gimme-0.2-0/gimme/MD5 | 39 gimme-0.2-0/gimme/NAMESPACE | 18 gimme-0.2-0/gimme/R/aggSEM.R | 111 + gimme-0.2-0/gimme/R/gimme-data.R | 55 gimme-0.2-0/gimme/R/gimme-pkg.R | 7 gimme-0.2-0/gimme/R/gimme.R | 1938 ++++++++++++++++++--------------- gimme-0.2-0/gimme/R/indSEM.R | 62 - gimme-0.2-0/gimme/R/print.aggSEMp.R |only gimme-0.2-0/gimme/R/print.gimmep.R |only gimme-0.2-0/gimme/R/print.indSEMp.R |only gimme-0.2-0/gimme/data/simData.rda |only gimme-0.2-0/gimme/data/ts.rda |only gimme-0.2-0/gimme/man/aggSEM.Rd | 44 gimme-0.2-0/gimme/man/gimmeSEM.Rd | 143 +- gimme-0.2-0/gimme/man/indSEM.Rd | 38 gimme-0.2-0/gimme/man/simData.Rd |only gimme-0.2-0/gimme/man/ts.Rd |only 30 files changed, 1330 insertions(+), 1136 deletions(-)
Title: Utilities for Learning Sparse Bayesian Networks
Description: A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data.
Author: Bryon Aragam [aut, cre],
Jiaying Gu [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebnUtils versions 0.0.2 dated 2016-08-05 and 0.0.3 dated 2016-11-20
sparsebnUtils-0.0.2/sparsebnUtils/man/random.psd.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-get_coef_matrix.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-get_solution.R |only sparsebnUtils-0.0.3/sparsebnUtils/DESCRIPTION | 8 sparsebnUtils-0.0.3/sparsebnUtils/MD5 | 71 +++-- sparsebnUtils-0.0.3/sparsebnUtils/NAMESPACE | 16 - sparsebnUtils-0.0.3/sparsebnUtils/NEWS.md |only sparsebnUtils-0.0.3/sparsebnUtils/R/bnlearn-compatibility.R | 7 sparsebnUtils-0.0.3/sparsebnUtils/R/s3-edgeList.R | 47 +++ sparsebnUtils-0.0.3/sparsebnUtils/R/s3-generics.R | 60 +--- sparsebnUtils-0.0.3/sparsebnUtils/R/s3-sparse.R | 75 ++++- sparsebnUtils-0.0.3/sparsebnUtils/R/s3-sparsebnFit.R | 72 +++++ sparsebnUtils-0.0.3/sparsebnUtils/R/s3-sparsebnPath.R | 81 ++---- sparsebnUtils-0.0.3/sparsebnUtils/R/sparsebnUtils-functions.R | 128 ++++++++-- sparsebnUtils-0.0.3/sparsebnUtils/R/sparsebnUtils-generate.R | 45 ++- sparsebnUtils-0.0.3/sparsebnUtils/R/sparsebnUtils-inference.R | 79 +----- sparsebnUtils-0.0.3/sparsebnUtils/R/sparsebnUtils-options.R | 2 sparsebnUtils-0.0.3/sparsebnUtils/R/sparsebnUtils-selection.R | 84 ++++++ sparsebnUtils-0.0.3/sparsebnUtils/README.md | 19 + sparsebnUtils-0.0.3/sparsebnUtils/man/as.edgeList.Rd |only sparsebnUtils-0.0.3/sparsebnUtils/man/as.sparse.Rd |only sparsebnUtils-0.0.3/sparsebnUtils/man/edgeList.Rd | 3 sparsebnUtils-0.0.3/sparsebnUtils/man/fit_multinom_dag.Rd | 21 - sparsebnUtils-0.0.3/sparsebnUtils/man/get.nodes.Rd |only sparsebnUtils-0.0.3/sparsebnUtils/man/get.solution.Rd | 9 sparsebnUtils-0.0.3/sparsebnUtils/man/random.dag.Rd | 14 - sparsebnUtils-0.0.3/sparsebnUtils/man/random.spd.Rd |only sparsebnUtils-0.0.3/sparsebnUtils/man/select.Rd |only sparsebnUtils-0.0.3/sparsebnUtils/man/select.parameter.Rd | 2 sparsebnUtils-0.0.3/sparsebnUtils/man/setGraphPackage.Rd | 2 sparsebnUtils-0.0.3/sparsebnUtils/man/sparse.Rd | 5 sparsebnUtils-0.0.3/sparsebnUtils/man/sparsebn-functions.Rd | 18 + sparsebnUtils-0.0.3/sparsebnUtils/man/sparsebnData.Rd | 3 sparsebnUtils-0.0.3/sparsebnUtils/man/sparsebnFit.Rd | 70 ++++- sparsebnUtils-0.0.3/sparsebnUtils/man/sparsebnPath.Rd | 22 + sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/helper-sparsebnUtils-generate_objects.R | 22 + sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-as.R |only sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-col_classes.R | 7 sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-cor_vector.R | 50 +++ sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-fit_multinom_dag.R | 34 -- sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-random_dag.R |only sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-random_spd.R |only sparsebnUtils-0.0.3/sparsebnUtils/tests/testthat/test-select.R |only 43 files changed, 729 insertions(+), 347 deletions(-)
Title: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
Description: A programmatic interface to various 'SNP' 'datasets'
on the web: 'OpenSNP' (<https://opensnp.org>), 'NBCIs' 'dbSNP' database
(<https://www.ncbi.nlm.nih.gov/projects/SNP>), and Broad Institute 'SNP'
Annotation and Proxy Search
(<http://archive.broadinstitute.org/mpg/snap/ldsearch.php>). Functions
are included for searching for 'SNPs' for the Broad Institute and 'NCBI'.
For 'OpenSNP', functions are included for getting 'SNPs', and data for
'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.
Author: Scott Chamberlain [aut, cre],
Kevin Ushey [aut],
Hao Zhu [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rsnps versions 0.1.6 dated 2015-03-03 and 0.2.0 dated 2016-11-20
rsnps-0.1.6/rsnps/NEWS |only rsnps-0.2.0/rsnps/DESCRIPTION | 41 + rsnps-0.2.0/rsnps/LICENSE | 2 rsnps-0.2.0/rsnps/MD5 | 99 ++-- rsnps-0.2.0/rsnps/NAMESPACE | 25 - rsnps-0.2.0/rsnps/NEWS.md |only rsnps-0.2.0/rsnps/R/LDSearch.R | 209 ++++----- rsnps-0.2.0/rsnps/R/NCBI_snp_query.R | 200 +++++---- rsnps-0.2.0/rsnps/R/NCBI_snp_query2.R |only rsnps-0.2.0/rsnps/R/allgensnp.R | 29 - rsnps-0.2.0/rsnps/R/allphenotypes.R | 53 +- rsnps-0.2.0/rsnps/R/annotations.R | 71 +-- rsnps-0.2.0/rsnps/R/download_users.R | 68 +-- rsnps-0.2.0/rsnps/R/fetch_genotypes.R | 65 +-- rsnps-0.2.0/rsnps/R/genotypes.R | 32 - rsnps-0.2.0/rsnps/R/phenotypes.R | 65 +-- rsnps-0.2.0/rsnps/R/phenotypes_byid.R | 41 - rsnps-0.2.0/rsnps/R/rsnps-package.R |only rsnps-0.2.0/rsnps/R/users.R | 28 - rsnps-0.2.0/rsnps/R/utils.R | 14 rsnps-0.2.0/rsnps/README.md | 122 ++--- rsnps-0.2.0/rsnps/build/vignette.rds |binary rsnps-0.2.0/rsnps/inst/doc/rsnps_vignette.Rmd | 344 +++++++--------- rsnps-0.2.0/rsnps/inst/doc/rsnps_vignette.html | 342 +++++++-------- rsnps-0.2.0/rsnps/inst/ignore |only rsnps-0.2.0/rsnps/inst/vign/rsnps_vignette.Rmd | 11 rsnps-0.2.0/rsnps/inst/vign/rsnps_vignette.md | 344 +++++++--------- rsnps-0.2.0/rsnps/man/LDSearch.Rd | 29 - rsnps-0.2.0/rsnps/man/NCBI_snp_query.Rd | 56 +- rsnps-0.2.0/rsnps/man/NCBI_snp_query2.Rd |only rsnps-0.2.0/rsnps/man/allgensnp.Rd | 6 rsnps-0.2.0/rsnps/man/allphenotypes.Rd | 8 rsnps-0.2.0/rsnps/man/annotations.Rd | 20 rsnps-0.2.0/rsnps/man/download_users.Rd | 6 rsnps-0.2.0/rsnps/man/fetch_genotypes.Rd | 49 +- rsnps-0.2.0/rsnps/man/flip.Rd | 2 rsnps-0.2.0/rsnps/man/genotypes.Rd | 5 rsnps-0.2.0/rsnps/man/phenotypes.Rd | 4 rsnps-0.2.0/rsnps/man/phenotypes_byid.Rd | 15 rsnps-0.2.0/rsnps/man/read_users.Rd | 22 - rsnps-0.2.0/rsnps/man/rsnps-package.Rd |only rsnps-0.2.0/rsnps/man/rsnpsCache.Rd | 5 rsnps-0.2.0/rsnps/man/split_to_df.Rd | 8 rsnps-0.2.0/rsnps/man/swap.Rd | 2 rsnps-0.2.0/rsnps/man/tryget.Rd | 2 rsnps-0.2.0/rsnps/man/users.Rd | 6 rsnps-0.2.0/rsnps/tests/test-all.R |only rsnps-0.2.0/rsnps/tests/testthat/test-LDSearch.R |only rsnps-0.2.0/rsnps/tests/testthat/test-NCBI_snp_query.R |only rsnps-0.2.0/rsnps/tests/testthat/test-NCBI_snp_query2.R |only rsnps-0.2.0/rsnps/tests/testthat/test-allphenotypes.R | 8 rsnps-0.2.0/rsnps/tests/testthat/test-annotations.R | 17 rsnps-0.2.0/rsnps/tests/testthat/test-genotypes.R | 14 rsnps-0.2.0/rsnps/tests/testthat/test-phenotypes.R | 17 rsnps-0.2.0/rsnps/tests/testthat/test-phenotypes_byid.R | 17 rsnps-0.2.0/rsnps/vignettes/rsnps_vignette.Rmd | 344 +++++++--------- 56 files changed, 1408 insertions(+), 1459 deletions(-)
Title: Group Sorted L1 Penalized Estimation
Description: Group SLOPE is a penalized linear regression method that is used
for adaptive selection of groups of significant predictors in a
high-dimensional linear model.
The Group SLOPE method can control the (group) false discovery rate at a
user-specified level (i.e., control the expected proportion of irrelevant
among all selected groups of predictors).
Author: Alexej Gossmann [aut, cre],
Damian Brzyski [aut],
Weijie Su [aut],
Malgorzata Bogdan [aut],
Ewout van den Berg [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3),
Emmanuel Candes [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3)
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>
Diff between grpSLOPE versions 0.2.0 dated 2016-10-20 and 0.2.1 dated 2016-11-20
grpSLOPE-0.2.0/grpSLOPE/man/sigma.grpSLOPE.Rd |only grpSLOPE-0.2.1/grpSLOPE/DESCRIPTION | 6 +- grpSLOPE-0.2.1/grpSLOPE/MD5 | 24 ++++---- grpSLOPE-0.2.1/grpSLOPE/NAMESPACE | 3 - grpSLOPE-0.2.1/grpSLOPE/R/generics.R | 11 +++ grpSLOPE-0.2.1/grpSLOPE/R/grpslope.R | 26 ++++++-- grpSLOPE-0.2.1/grpSLOPE/README.md | 2 grpSLOPE-0.2.1/grpSLOPE/build/vignette.rds |binary grpSLOPE-0.2.1/grpSLOPE/inst/doc/basic-usage.Rmd | 2 grpSLOPE-0.2.1/grpSLOPE/inst/doc/basic-usage.html | 6 +- grpSLOPE-0.2.1/grpSLOPE/man/sigma.Rd |only grpSLOPE-0.2.1/grpSLOPE/tests/testthat/test_grpSLOPE.R | 50 +++++++++++++++++ grpSLOPE-0.2.1/grpSLOPE/tests/testthat/test_lambda.R | 5 + grpSLOPE-0.2.1/grpSLOPE/vignettes/basic-usage.Rmd | 2 14 files changed, 108 insertions(+), 29 deletions(-)