Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.49 dated 2015-12-29 and 1.51 dated 2016-03-14
Changelog | 34 ++++++++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- R/Functions.R | 48 +++++++++++++++++------------ R/blockwiseModulesC.R | 21 ++++++++++-- R/branchSplit.R | 4 +- R/consensusRepresentatives.R |only R/consensusTOM.R | 6 +++ R/corFunctions.R | 2 - R/heatmapWithLegend.R | 59 +++++++++++++++++++++--------------- R/matchLabels.R | 3 + man/TOMsimilarityFromExpr.Rd | 5 +++ man/WGCNA-package.Rd | 4 +- man/blockwiseConsensusModules.Rd | 9 +++++ man/blockwiseIndividualTOMs.Rd | 7 ++++ man/blockwiseModules.Rd | 9 +++++ man/consensusProjectiveKMeans.Rd | 2 - man/consensusRepresentatives.Rd |only man/consensusTOM.Rd | 14 ++++++++ man/selectFewestConsensusMissing.Rd |only src/corFunctions-unified.c | 30 ++++++++++++++---- src/networkFunctions.c | 33 ++++++++++++++------ 22 files changed, 248 insertions(+), 89 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8.7 dated 2016-02-23 and 0.8.9 dated 2016-03-14
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 +- R/internal.r | 2 +- R/monotypic.r | 7 +++++-- R/taxval.r | 15 +++++++++------ R/tv.coverperc.r | 2 +- R/tv.obs.r | 5 ++++- R/tv.site.r | 41 ++++++++++++++++++++++++----------------- R/vegetweb.r | 35 ++++++++--------------------------- inst/doc/vegdata.R | 2 +- inst/doc/vegdata.Rnw | 4 ++-- man/tv.site.Rd | 5 +++-- vignettes/vegdata.Rnw | 4 ++-- 14 files changed, 78 insertions(+), 80 deletions(-)
Title: Parameter Space Exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Also implements the PLUE method.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom <andrechalom@gmail.com>
Diff between pse versions 0.4.3 dated 2015-09-24 and 0.4.5 dated 2016-03-14
pse-0.4.3/pse/man/decoupling.Rd |only pse-0.4.3/pse/man/plotcv.Rd |only pse-0.4.3/pse/man/plotecdf.Rd |only pse-0.4.3/pse/man/plotscatter.Rd |only pse-0.4.3/pse/src/Makevars |only pse-0.4.5/pse/DESCRIPTION | 17 +- pse-0.4.5/pse/MD5 | 69 +++++----- pse-0.4.5/pse/NAMESPACE | 53 +++++--- pse-0.4.5/pse/NEWS | 6 pse-0.4.5/pse/R/LHS.R | 105 +++++++++++++++ pse-0.4.5/pse/R/LHScorcorr.R | 115 ++++++++++++----- pse-0.4.5/pse/R/PLUE.R | 102 +++++++++------ pse-0.4.5/pse/R/accessors.R | 43 ++++++ pse-0.4.5/pse/R/cluster.R | 22 +++ pse-0.4.5/pse/R/external.R | 7 + pse-0.4.5/pse/R/pic.R | 62 ++++++--- pse-0.4.5/pse/R/plotcv.R | 29 ++-- pse-0.4.5/pse/R/plotecdf.R | 45 ++++++ pse-0.4.5/pse/R/plotprcc.R | 2 pse-0.4.5/pse/R/plotscatter.R | 22 +-- pse-0.4.5/pse/R/sbma.R | 39 +++++ pse-0.4.5/pse/R/target.sbma.R | 15 ++ pse-0.4.5/pse/build/vignette.rds |binary pse-0.4.5/pse/inst/doc/multiple.R | 3 pse-0.4.5/pse/inst/doc/multiple.Rnw | 3 pse-0.4.5/pse/inst/doc/multiple.pdf |binary pse-0.4.5/pse/inst/doc/pse_tutorial.pdf |binary pse-0.4.5/pse/man/LHS.Rd | 211 ++++++++++++++++---------------- pse-0.4.5/pse/man/LHScorcorr.Rd | 84 ++++++------ pse-0.4.5/pse/man/PLUE.Rd | 119 ++++++++---------- pse-0.4.5/pse/man/accessors.Rd | 72 +++++----- pse-0.4.5/pse/man/cv.Rd | 20 +-- pse-0.4.5/pse/man/external.Rd |only pse-0.4.5/pse/man/machinefile.Rd | 46 ++---- pse-0.4.5/pse/man/pic.Rd | 60 +++++---- pse-0.4.5/pse/man/plots.Rd |only pse-0.4.5/pse/man/sbma.Rd | 60 ++++++--- pse-0.4.5/pse/man/target.sbma.Rd | 97 +++++++------- pse-0.4.5/pse/vignettes/multiple.Rnw | 3 39 files changed, 981 insertions(+), 550 deletions(-)
Title: NBD-Dirichlet Model of Consumer Buying Behavior for Marketing
Research
Description: The Dirichlet (aka NBD-Dirichlet) model describes the
purchase incidence and brand choice of consumer products. We
estimate the model and summarize various theoretical quantities
of interest to marketing researchers. Also provides functions
for making tables that compare observed and theoretical
statistics.
Author: Feiming Chen
Maintainer: Feiming Chen <feimingchen@yahoo.com>
Diff between NBDdirichlet versions 1.01 dated 2011-09-10 and 1.3 dated 2016-03-14
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- NAMESPACE | 3 +++ man/plot.dirichlet.Rd | 2 +- man/print.dirichlet.Rd | 5 +++-- man/summary.dirichlet.Rd | 2 +- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between eHOF versions 1.6 dated 2015-11-06 and 1.7 dated 2016-03-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Para.deriv.r | 6 +++--- R/Para.opt.r | 2 +- R/print.HOF.r | 2 +- man/HOF.Rd | 2 +- man/plot.HOF.Rd | 23 ++++++++--------------- 7 files changed, 24 insertions(+), 31 deletions(-)
Title: Ace Editor Bindings for Shiny
Description: Ace editor bindings to enable a rich text editing environment
within Shiny.
Author: Trestle Technology, LLC [aut],
Jeff Allen [cre],
Institut de Radioprotection et de Surete Nucleaire [cph],
Ajax.org B.V. [ctb, cph] (Ace)
Maintainer: Jeff Allen <cran@trestletechnology.net>
Diff between shinyAce versions 0.1.0 dated 2013-11-05 and 0.2.1 dated 2016-03-14
shinyAce-0.1.0/shinyAce/inst/www/ace/ext-options.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/mode-html_completions.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/mode-mushcode_high_rules.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/mode-tmsnippet.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/snippets/html_completions.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/snippets/mushcode_high_rules.js |only shinyAce-0.1.0/shinyAce/inst/www/ace/theme-kr.js |only shinyAce-0.2.1/shinyAce/DESCRIPTION | 27 shinyAce-0.2.1/shinyAce/LICENSE | 4 shinyAce-0.2.1/shinyAce/MD5 | 608 +++++----- shinyAce-0.2.1/shinyAce/NAMESPACE | 5 shinyAce-0.2.1/shinyAce/NEWS |only shinyAce-0.2.1/shinyAce/R/ace-autocomplete.R |only shinyAce-0.2.1/shinyAce/R/ace-editor.R | 156 ++ shinyAce-0.2.1/shinyAce/R/update-ace-editor.R | 27 shinyAce-0.2.1/shinyAce/README.md | 52 shinyAce-0.2.1/shinyAce/inst/examples/01-basic/server.R | 4 shinyAce-0.2.1/shinyAce/inst/examples/02-eval/ui.R | 4 shinyAce-0.2.1/shinyAce/inst/examples/03-knitr/ui.R | 6 shinyAce-0.2.1/shinyAce/inst/examples/04-shinyui/ui.R | 4 shinyAce-0.2.1/shinyAce/inst/examples/05-hotkeys |only shinyAce-0.2.1/shinyAce/inst/examples/06-autocomplete |only shinyAce-0.2.1/shinyAce/inst/tests/test-js-quote.R | 8 shinyAce-0.2.1/shinyAce/inst/www/ace/ace.js | 10 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-beautify.js |only shinyAce-0.2.1/shinyAce/inst/www/ace/ext-chromevox.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-elastic_tabstops_lite.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-emmet.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-error_marker.js |only shinyAce-0.2.1/shinyAce/inst/www/ace/ext-keybinding_menu.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-language_tools.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-linking.js |only shinyAce-0.2.1/shinyAce/inst/www/ace/ext-modelist.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-old_ie.js | 6 shinyAce-0.2.1/shinyAce/inst/www/ace/ext-searchbox.js | 6 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Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel
hydraulics. Provides functions for computing normal and critical depths,
steady-state water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.1 dated 2015-10-16 and 1.2 dated 2016-03-14
DESCRIPTION | 17 ++++---- MD5 | 38 ++++++++++++------- NAMESPACE | 3 + NEWS |only R/graduallyvariedflow_v2.r | 11 +++-- R/shinydemos.r |only build/vignette.rds |binary inst/CITATION |only inst/doc/publication-reproduction.R |only inst/doc/publication-reproduction.Rmd |only inst/doc/publication-reproduction.html |only inst/doc/quickstart.html | 4 +- inst/shiny-examples |only man/channel_geom.Rd | 6 +-- man/compute_profile.Rd | 30 +++++++-------- man/conveyance.Rd | 6 +-- man/critical_depth.Rd | 10 ++--- man/demo_shiny.Rd |only man/froude.Rd | 12 +++--- man/normal_depth.Rd | 10 ++--- man/rivr-package.Rd | 13 +++--- man/route_wave.Rd | 64 ++++++++++++++++----------------- man/waterolympics.Rd | 14 +++---- vignettes/publication-reproduction.Rmd |only 24 files changed, 126 insertions(+), 112 deletions(-)
Title: Regression Discontinuity Estimation
Description: Provides the tools to undertake estimation in
Regression Discontinuity Designs. Both sharp and fuzzy designs are
supported. Estimation is accomplished using local linear regression.
A provided function will utilize Imbens-Kalyanaraman optimal
bandwidth calculation. A function is also included to test the
assumption of no-sorting effects.
Author: Drew Dimmery
Maintainer: Drew Dimmery <drewd@nyu.edu>
Diff between rdd versions 0.56 dated 2013-10-11 and 0.57 dated 2016-03-14
DESCRIPTION | 13 - MD5 | 38 +-- NAMESPACE | 19 + NEWS | 3 R/DCdensity.R | 473 +++++++++++++++++++++++---------------------- R/IKbandwidth.R | 205 +++++++++---------- R/RDestimate.R | 547 ++++++++++++++++++++++++++--------------------------- R/kernelwts.R | 100 ++++----- R/plot.RD.R | 5 R/print.RD.R | 40 +-- R/rdd-package.R | 30 +- R/summary.RD.R | 191 +++++++++--------- man/DCdensity.Rd | 133 +++++------- man/IKbandwidth.Rd | 80 +++---- man/RDestimate.Rd | 259 +++++++++++-------------- man/kernelwts.Rd | 85 +++----- man/plot.RD.Rd | 60 ++--- man/print.RD.Rd | 45 ++-- man/rdd-package.Rd | 50 ++-- man/summary.RD.Rd | 58 ++--- 20 files changed, 1206 insertions(+), 1228 deletions(-)
Title: Maximal Information-Based Nonparametric Exploration R Package
for Variable Analysis
Description: R wrapper for 'cmine' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation 'cmine'
can be found at 'http://mpba.fbk.eu/cmine'.
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide
Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman
[ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi <filosi@fbk.eu>
Diff between minerva versions 1.4.1 dated 2014-08-26 and 1.4.5 dated 2016-03-14
DESCRIPTION | 21 +++--- MD5 | 22 +++--- NAMESPACE | 3 NEWS | 7 ++ R/mine.R | 136 ++++++++++++++++++++++++++++++------------ inst |only man/mine.Rd | 7 +- man/minerva-package.Rd | 4 - src/mine.c | 155 ++++++++++++++++++++++++++++++++++++++++++------- src/mine.h | 16 ++++- src/mine_interface.c | 35 ++++++++--- tests/test_minepy.R |only tests/testspellman0.R | 2 13 files changed, 315 insertions(+), 93 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>
Diff between ggmcmc versions 0.7.3 dated 2016-01-04 and 0.8 dated 2016-03-14
DESCRIPTION | 9 +++-- MD5 | 67 +++++++++++++++++++++++++------------------- NEWS | 35 ++++++++++++++++++++++ R/functions.R | 2 - R/ggs.R | 35 ++++++++++++++++++---- R/ggs_Rhat.R | 9 +++-- R/ggs_autocorrelation.R | 19 +++++++++--- R/ggs_caterpillar.R | 12 +++++-- R/ggs_compare_partial.R | 11 +++++-- R/ggs_crosscorrelation.R | 7 +++- R/ggs_density.R | 9 ++++- R/ggs_geweke.R | 6 +++ R/ggs_histogram.R | 13 ++++++-- R/ggs_pairs.R | 15 +++++++-- R/ggs_running.R | 11 +++++-- R/ggs_separation.R | 55 +++++++++++++++++++----------------- R/ggs_traceplot.R | 9 ++++- build |only inst/doc |only man/custom.sort.Rd |only man/ggs_Rhat.Rd | 4 +- man/ggs_autocorrelation.Rd | 4 +- man/ggs_caterpillar.Rd | 4 +- man/ggs_compare_partial.Rd | 5 ++- man/ggs_crosscorrelation.Rd | 4 +- man/ggs_density.Rd | 4 +- man/ggs_geweke.Rd | 4 +- man/ggs_histogram.Rd | 4 +- man/ggs_pairs.Rd | 4 +- man/ggs_running.Rd | 5 ++- man/ggs_separation.Rd | 9 +++-- man/ggs_traceplot.Rd | 4 +- vignettes |only 33 files changed, 269 insertions(+), 110 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: Provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm or numerical integration. PACE is useful for the analysis of data that have been generated by a sample of underlying (but usually not fully observed) random trajectories. It does not rely on pre-smoothing of trajectories, which is problematic if functional data are sparsely sampled. PACE provides options for functional regression and correlation, for Longitudinal Data Analysis, the analysis of stochastic processes from samples of realized trajectories, and for the analysis of underlying dynamics. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Xiongtao Dai,
Pantelis Z. Hadjipantelis,
Hao Ji,
Hans-Georg Mueller,
Jane-Ling Wang
Maintainer: Pantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
Diff between fdapace versions 0.1.0 dated 2016-03-13 and 0.1.1 dated 2016-03-14
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/GetCrCovYX.R | 2 +- inst/doc/fdapaceVignette.pdf |binary man/GetCrCovYX.Rd | 2 +- src/CPPlwls1d.cpp | 2 +- src/Rmullwlsk.cpp | 5 +++-- src/RmullwlskCC.cpp | 3 ++- 8 files changed, 20 insertions(+), 18 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-9 dated 2015-12-01 and 5.0-10 dated 2016-03-14
DESCRIPTION | 20 +- MD5 | 200 +++++++++++++---------- NAMESPACE | 12 - R/create-json.R | 29 +++ R/model-ar.R |only R/model-arima.R |only R/model-bayes.R | 8 R/model-binchoice-gee.R | 5 R/model-binchoice-survey.R |only R/model-exp.R | 10 - R/model-factor-bayes.R | 8 R/model-gamma-survey.R |only R/model-gamma.R | 16 + R/model-gee.R | 20 +- R/model-glm.R | 11 - R/model-logit-bayes.R | 1 R/model-logit-survey.R |only R/model-lognorm.R | 26 +-- R/model-ls.R | 12 + R/model-ma.R |only R/model-negbinom.R | 16 + R/model-normal-survey.R |only R/model-normal.R | 18 +- R/model-poisson-gee.R | 4 R/model-poisson-survey.R |only R/model-probit-gee.R | 1 R/model-probit-survey.R |only R/model-quantile.R | 14 + R/model-relogit.R | 10 - R/model-survey.R |only R/model-timeseries.R |only R/model-tobit.R | 23 +- R/model-weibull.R | 26 +-- R/model-zelig.R | 205 ++++++++++++++++++++++- R/plots.R | 308 ++++++++++++++++++++++++++---------- R/utils.R | 3 R/wrappers.R | 8 data/friendship.RData |binary data/sna.ex.RData |binary inst/JSON/zelig5models.json | 78 +++++++++ man/Median.Rd | 2 man/Mode.Rd | 2 man/Zelig-ar-class.Rd |only man/Zelig-arima-class.Rd |only man/Zelig-bayes-class.Rd | 5 man/Zelig-binchoice-class.Rd | 2 man/Zelig-binchoice-gee-class.Rd | 6 man/Zelig-binchoice-survey-class.Rd |only man/Zelig-class.Rd | 9 - man/Zelig-exp-class.Rd | 5 man/Zelig-factor-bayes-class.Rd | 5 man/Zelig-gamma-class.Rd | 2 man/Zelig-gamma-gee-class.Rd | 2 man/Zelig-gamma-survey-class.Rd |only man/Zelig-gee-class.Rd | 5 man/Zelig-glm-class.Rd | 5 man/Zelig-logit-bayes-class.Rd | 2 man/Zelig-logit-class.Rd | 2 man/Zelig-logit-gee-class.Rd | 2 man/Zelig-logit-survey-class.Rd |only man/Zelig-lognorm-class.Rd | 5 man/Zelig-ls-class.Rd | 5 man/Zelig-ma-class.Rd |only man/Zelig-mlogit-bayes-class.Rd | 2 man/Zelig-negbin-class.Rd | 5 man/Zelig-normal-bayes-class.Rd | 2 man/Zelig-normal-class.Rd | 2 man/Zelig-normal-gee-class.Rd | 2 man/Zelig-normal-survey-class.Rd |only man/Zelig-oprobit-bayes-class.Rd | 2 man/Zelig-poisson-bayes-class.Rd | 2 man/Zelig-poisson-class.Rd | 2 man/Zelig-poisson-gee-class.Rd | 2 man/Zelig-poisson-survey-class.Rd |only man/Zelig-probit-bayes-class.Rd | 2 man/Zelig-probit-class.Rd | 2 man/Zelig-probit-gee-class.Rd | 2 man/Zelig-probit-survey-class.Rd |only man/Zelig-quantile-class.Rd | 5 man/Zelig-relogit-class.Rd | 5 man/Zelig-survey-class.Rd |only man/Zelig-timeseries-class.Rd |only man/Zelig-tobit-bayes-class.Rd | 2 man/Zelig-tobit-class.Rd | 5 man/Zelig-weibull-class.Rd | 5 man/avg.Rd | 2 man/ci.plot.Rd | 11 - man/cluster.formula.Rd | 2 man/coef-Zelig-method.Rd | 2 man/fitted-Zelig-method.Rd | 2 man/plot-Zelig-ANY-method.Rd | 2 man/predict-Zelig-method.Rd | 2 man/qi.plot.Rd | 4 man/reduce.Rd | 2 man/relogit.Rd | 2 man/rocplot.Rd | 4 man/setfactor.Rd | 2 man/setval.Rd | 2 man/setx.Rd | 8 man/sim.Rd | 10 - man/simacf.Rd |only man/simulations.plot.Rd | 2 man/stat.Rd | 2 man/statlevel.Rd | 6 man/statmat.Rd | 6 man/summary-Zelig-method.Rd | 2 man/table.levels.Rd | 2 man/vcov-Zelig-method.Rd | 2 man/zelig.Rd | 4 man/zeligACFplot.Rd |only man/zeligARMAbreakforecaster.Rd |only man/zeligARMAlongrun.Rd |only man/zeligARMAnextstep.Rd |only man/zeligArimaWrapper.Rd |only man/zeligPlyrMutate.Rd | 2 115 files changed, 900 insertions(+), 392 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 1.0.15 dated 2016-03-11 and 1.0.16 dated 2016-03-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/gershunov.R | 3 +++ inst/Changelog | 4 ++++ 4 files changed, 13 insertions(+), 6 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.5 dated 2016-02-11 and 1.6 dated 2016-03-14
DESCRIPTION | 10 MD5 | 106 +++++----- NAMESPACE | 20 + NEWS | 23 ++ NEWS.md | 22 +- R/S3-methods.R | 96 +++++++-- R/as_labelled.R | 46 ++++ R/cronb.R | 14 - R/cv.R | 27 ++ R/drop_labels.R |only R/fill_labels.R | 2 R/frq.R | 65 +++++- R/get_label.R | 9 R/get_labels.R | 502 ++++++++++++++++++++++++-------------------------- R/group_var.R | 434 +++++++++++++++++++++---------------------- R/icc.R | 107 +++++++--- R/mean_n.R | 164 ++++++++-------- R/mic.R | 6 R/overdisp.R | 163 ++++++++++------ R/pseudo_r2.R | 117 +++++++++++ R/rec.R | 12 + R/rec_pattern.R |only R/ref_lvl.R | 7 R/set_label.R | 353 +++++++++++++++++------------------ R/set_labels.R | 12 - R/str_contains.R |only R/to_factor.R | 9 R/to_long.R | 260 +++++++++++++------------ R/unlabel.R | 17 - R/weight.R | 193 ++++++++++--------- R/zap_labels.R | 6 README.md | 85 ++++---- build |only man/cronb.Rd | 6 man/cv.Rd | 5 man/drop_labels.Rd |only man/fill_labels.Rd | 3 man/frq.Rd | 5 man/get_frq.Rd |only man/get_label.Rd | 3 man/get_labels.Rd | 4 man/group_var.Rd | 14 - man/icc.Rd | 116 ++++++----- man/lbl_df.Rd |only man/mic.Rd | 6 man/overdisp.Rd | 51 ++++- man/r2.Rd |only man/rec_pattern.Rd |only man/set_label.Rd | 3 man/set_labels.Rd | 3 man/sjmisc-package.Rd | 4 man/str_contains.Rd |only man/to_factor.Rd | 3 man/to_long.Rd | 10 man/unlabel.Rd | 15 - man/weight.Rd | 7 man/weight2.Rd | 1 man/zap_labels.Rd | 3 man/zap_unlabelled.Rd | 3 59 files changed, 1803 insertions(+), 1349 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>
Diff between piecewiseSEM versions 1.0.3 dated 2016-02-01 and 1.1 dated 2016-03-14
DESCRIPTION | 10 +-- MD5 | 78 +++++++++++++------------ NAMESPACE | 8 +- NEWS.md | 19 ++++++ R/filter.exogenous.R | 50 ++++++---------- R/get.basis.set.R | 13 +--- R/get.dag.R | 62 +++++++++++++++----- R/get.model.control.R | 4 - R/get.random.formula.R | 14 ++-- R/get.scaled.data.R | 55 ++++++++++++------ R/get.scaled.model.R |only R/get.sort.dag.R |only R/partial.resid.R | 112 ++++++++++++++++++++++-------------- R/sem.aic.R | 12 +-- R/sem.basis.set.R | 117 ++++++++++++++++++++++++++++++-------- R/sem.coefs.R | 60 ++++++++++++++----- R/sem.fisher.c.R | 10 +-- R/sem.fit.R | 22 ++----- R/sem.lavaan.R | 6 + R/sem.missing.paths.R | 134 +++++++++++++++++++++++++++++++------------- R/sem.model.fits.R | 55 ++++++++++++------ R/sem.plot.R |only R/sem.predict.R | 13 ++-- README.md | 63 ++++++++++---------- build/vignette.rds |binary inst/doc/piecewiseSEM.R | 7 +- inst/doc/piecewiseSEM.Rmd | 12 ++- inst/doc/piecewiseSEM.html | 129 +++++++++++++++++++++++++----------------- man/filter.exogenous.Rd | 2 man/get.scaled.model.Rd |only man/get.sort.dag.Rd |only man/piecewiseSEM-package.Rd | 10 +-- man/sem.aic.Rd | 8 -- man/sem.basis.set.Rd | 2 man/sem.coefs.Rd | 4 - man/sem.fisher.c.Rd | 8 -- man/sem.fit.Rd | 79 +++++++++++++------------ man/sem.lavaan.Rd | 42 ++++++------- man/sem.missing.paths.Rd | 22 ++++--- man/sem.model.fits.Rd | 2 man/sem.plot.Rd |only man/sem.predict.Rd | 2 vignettes/piecewiseSEM.Rmd | 12 ++- 43 files changed, 778 insertions(+), 480 deletions(-)
Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph
proposed by Rosenbaum is useful
for checking some properties of various
sorts of latent scale, this program generates commands
to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between latdiag versions 0.2-1 dated 2015-01-16 and 0.2-2 dated 2016-03-14
latdiag-0.2-1/latdiag/inst/doc |only latdiag-0.2-2/latdiag/DESCRIPTION | 20 +++++++++++--------- latdiag-0.2-2/latdiag/MD5 | 7 +++---- latdiag-0.2-2/latdiag/NEWS | 6 +++++- latdiag-0.2-2/latdiag/man/latdiag-package.Rd | 2 +- 5 files changed, 20 insertions(+), 15 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos <martin.loos@alumni.ethz.ch>
Diff between enviPat versions 2.0 dated 2015-06-05 and 2.1 dated 2016-03-14
DESCRIPTION | 8 MD5 | 24 NAMESPACE | 3 NEWS | 6 R/check_chemform.R | 9 R/enviPat.R | 2 R/getR.R | 12 data/isotopes.rda |binary man/check_chemform.Rd | 3 man/check_ded.Rd | 2 man/isowrap.Rd | 1 src/data.h | 2728 -------------------------------------------------- src/main.c | 2 13 files changed, 46 insertions(+), 2754 deletions(-)
Title: R Interface for PreSens Fiber Optic Data
Description: Makes output files from select PreSens Fiber Optic Oxygen
Transmitters easier to work with in R. See http://www.presens.de for more
information about PreSens (Precision Sensing GmbH).
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between presens versions 1.0.0 dated 2015-02-10 and 2.0.0 dated 2016-03-14
DESCRIPTION | 15 ++++--- MD5 | 16 +++---- NAMESPACE | 3 - NEWS | 6 ++ R/import_o2.R | 106 ++++++++++++++++++++++++++++------------------------ R/o2_unit_conv.R | 77 ++++++++++++++++++++++++++----------- man/import_o2.Rd | 33 +++++++++------- man/o2_unit_conv.Rd | 36 +++++++++++++---- man/presens.Rd | 2 9 files changed, 185 insertions(+), 109 deletions(-)
Title: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos <Martin.Loos@eawag.ch>
Diff between nontarget versions 1.7 dated 2015-01-17 and 1.8 dated 2016-03-14
DESCRIPTION | 14 MD5 | 54 +- NAMESPACE | 8 NEWS | 9 R/adduct.search.R | 14 R/combine.R | 8 R/homol.search.R | 972 +++++++++++++++++++++++++++++++++++++---------- R/make.isos.R | 6 R/nontarget.R | 2 R/pattern.search.R | 572 ++++++++++++++------------- R/pattern.search2.R | 137 +++--- R/plotcomp.R | 6 R/plothomol.R | 37 + R/rm.sat.R | 8 man/adduct.search.Rd | 4 man/combine.Rd | 32 - man/homol.search.Rd | 125 +++--- man/make.isos.Rd | 2 man/nontarget-package.Rd | 38 - man/pattern.search.Rd | 6 man/pattern.search2.Rd | 16 man/plotcomp.Rd | 4 man/plothomol.Rd | 40 + man/rm.sat.Rd | 7 src/homologues.cpp | 511 +++++++++++------------- src/massCpp.cpp | 18 src/quantization.cpp | 20 src/searchTree.cpp | 778 +++++++++++++++++++++++++++++++++++-- 28 files changed, 2409 insertions(+), 1039 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-125 dated 2016-02-27 and 3.1-126 dated 2016-03-14
ChangeLog | 6 ++++ DESCRIPTION | 8 ++--- MD5 | 14 +++++----- R/lmList.R | 27 ++++++++------------ R/nlme.R | 40 ++++++++++++----------------- R/nlsList.R | 47 +++++++++++++++------------------- tests/augPred_lab.R | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++++ tests/nlme2.R | 37 +++++++++++++++++++++++++++ 8 files changed, 173 insertions(+), 76 deletions(-)
Title: Peak Picking for High Resolution Mass Spectrometry Data
Description: Sequential partitioning, clustering and peak detection of
centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw
data plot.
Author: Martin Loos
Maintainer: Martin Loos <Martin.Loos@eawag.ch>
Diff between enviPick versions 1.3 dated 2014-11-29 and 1.4 dated 2016-03-14
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 4 ++++ NEWS | 4 ++++ R/enviPick.R | 2 +- R/mzagglom.r | 2 +- R/mzclust.R | 34 +++++++++++++++++----------------- R/mzpick.R | 3 ++- R/readMSdata.R | 6 +++++- 9 files changed, 47 insertions(+), 34 deletions(-)
Title: A Tool for Calculation and Optimization of the Expected Gain
from Multi-Stage Selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, Jose Marulanda, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi <mi_xue_fei@hotmail.com>
Diff between selectiongain versions 2.0.40 dated 2014-12-29 and 2.0.50.1 dated 2016-03-14
DESCRIPTION | 16 +-- MD5 | 18 +-- NAMESPACE | 5 - R/multistagecor.R | 161 ++++++++++++++++++++++++++++++-- R/multistagegain.R | 73 ++++++++++++-- R/multistageoptimum.grid.R | 196 ++++++++++++++++++++++++++++++---------- R/multistageoptimum.search.R | 192 +++++++++++++++++++++++++++++++++------ man/multistagegain.Rd | 4 man/multistageoptimum.grid.Rd | 20 +++- man/multistageoptimum.search.Rd | 23 +++- 10 files changed, 579 insertions(+), 129 deletions(-)
Title: Boosting Functional Regression Models
Description: Regression models for functional data, i.e., scalar-on-function,
function-on-scalar and function-on-function regression models, are fitted
by a component-wise gradient boosting algorithm.
Author: Sarah Brockhaus [aut, cre],
David Ruegamer [ctb],
Torsten Hothorn [ctb],
with contributions by many others (see inst/CONTRIBUTIONS) [ctb]
Maintainer: Sarah Brockhaus <Sarah.Brockhaus@stat.uni-muenchen.de>
Diff between FDboost versions 0.0-8 dated 2015-02-16 and 0.1-0 dated 2016-03-14
FDboost-0.0-8/FDboost/R/internalsMboost.R |only FDboost-0.1-0/FDboost/DESCRIPTION | 36 FDboost-0.1-0/FDboost/MD5 | 117 + FDboost-0.1-0/FDboost/NAMESPACE | 65 + FDboost-0.1-0/FDboost/R/FDboost.R | 923 ++++++++++---- FDboost-0.1-0/FDboost/R/FDboostLSS.R |only FDboost-0.1-0/FDboost/R/baselearners.R | 944 ++++++++++---- FDboost-0.1-0/FDboost/R/baselearnersX.R |only FDboost-0.1-0/FDboost/R/constrainedX.R |only FDboost-0.1-0/FDboost/R/crossvalidation.R | 612 +++++---- FDboost-0.1-0/FDboost/R/hmatrix.R |only FDboost-0.1-0/FDboost/R/methods.R | 1338 +++++++++++++-------- FDboost-0.1-0/FDboost/R/utilityFunctions.R | 232 +++ FDboost-0.1-0/FDboost/build/vignette.rds |binary FDboost-0.1-0/FDboost/inst/CITATION | 16 FDboost-0.1-0/FDboost/inst/CONTRIBUTIONS |only FDboost-0.1-0/FDboost/inst/NEWS.Rd |only FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.R | 4 FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.Rnw | 11 FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.pdf |binary FDboost-0.1-0/FDboost/inst/doc/FLAM_fuel.Rnw | 10 FDboost-0.1-0/FDboost/inst/doc/FLAM_fuel.pdf |binary FDboost-0.1-0/FDboost/inst/doc/FLAM_viscosity.Rnw | 9 FDboost-0.1-0/FDboost/inst/doc/FLAM_viscosity.pdf |binary FDboost-0.1-0/FDboost/inst/sim/readme.txt |only FDboost-0.1-0/FDboost/inst/sim/run_FDboost.R | 1 FDboost-0.1-0/FDboost/inst/sim/run_pffr.R | 1 FDboost-0.1-0/FDboost/inst/sim/simfuns.R | 4 FDboost-0.1-0/FDboost/inst/simHist |only FDboost-0.1-0/FDboost/man/FDboost.Rd | 391 ++++-- FDboost-0.1-0/FDboost/man/FDboostLSS.Rd |only FDboost-0.1-0/FDboost/man/anisotropic_Kronecker.Rd |only FDboost-0.1-0/FDboost/man/bbsc.Rd | 27 FDboost-0.1-0/FDboost/man/bhistx.Rd |only FDboost-0.1-0/FDboost/man/bsignal.Rd | 162 +- FDboost-0.1-0/FDboost/man/coef.FDboost.Rd | 28 FDboost-0.1-0/FDboost/man/cvrisk.FDboostLSS.Rd |only FDboost-0.1-0/FDboost/man/extract.blg.Rd | 16 FDboost-0.1-0/FDboost/man/fitted.FDboost.Rd | 8 FDboost-0.1-0/FDboost/man/fuelSubset.Rd | 120 + FDboost-0.1-0/FDboost/man/funMRD.Rd | 2 FDboost-0.1-0/FDboost/man/funMSE.Rd | 2 FDboost-0.1-0/FDboost/man/funRsquared.Rd | 2 FDboost-0.1-0/FDboost/man/funplot.Rd | 5 FDboost-0.1-0/FDboost/man/getTime.Rd |only FDboost-0.1-0/FDboost/man/getTime.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/grapes-Xc-grapes.Rd |only FDboost-0.1-0/FDboost/man/hmatrix.Rd |only FDboost-0.1-0/FDboost/man/integrationWeights.Rd | 16 FDboost-0.1-0/FDboost/man/is.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/o_control.Rd | 2 FDboost-0.1-0/FDboost/man/plot.FDboost.Rd | 33 FDboost-0.1-0/FDboost/man/plot.validateFDboost.Rd | 36 FDboost-0.1-0/FDboost/man/predict.FDboost.Rd | 11 FDboost-0.1-0/FDboost/man/print.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/residuals.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/sub-.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/summary.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/truncateTime.Rd | 2 FDboost-0.1-0/FDboost/man/validateFDboost.Rd | 201 ++- FDboost-0.1-0/FDboost/man/viscosity.Rd | 124 - FDboost-0.1-0/FDboost/man/wide2long.Rd |only FDboost-0.1-0/FDboost/vignettes/FLAM_canada.Rnw | 11 FDboost-0.1-0/FDboost/vignettes/FLAM_fuel.Rnw | 10 FDboost-0.1-0/FDboost/vignettes/FLAM_viscosity.Rnw | 9 65 files changed, 3766 insertions(+), 1781 deletions(-)
Title: Dandelion Plot for R-Mode Exploratory Factor Analysis
Description: Contains the function used to create the Dandelion Plot. Dandelion Plot is a visualization method for R-mode Exploratory Factor Analysis.
Author: Artur Manukyan, Ahmet Sedef, Erhan Cene, Ibrahim Demir
Maintainer: Artur Manukyan <artur-man@hotmail.com>
Diff between DandEFA versions 1.5 dated 2014-04-25 and 1.6 dated 2016-03-14
DESCRIPTION | 16 +- MD5 | 12 - NAMESPACE | 4 R/dandelion.R | 370 +++++++++++++++++++++++++++---------------------------- man/dandelion.Rd | 18 +- man/factload.Rd | 5 man/timss2011.Rd | 4 7 files changed, 218 insertions(+), 211 deletions(-)
Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series
and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis <peter.ellis2013nz@gmail.com>
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>
Diff between ggseas versions 0.2.1 dated 2016-02-29 and 0.3.0 dated 2016-03-14
DESCRIPTION | 10 ++++----- MD5 | 25 ++++++++++++++--------- NAMESPACE | 3 ++ R/decompose-seasonal.R | 32 ++++++++++++++++++++++++------ R/ggsdc.R | 48 ++++++++++++++++++++++++++++++++------------- R/helper_funcs.R |only R/stat_index.R |only R/stat_rollapplyr.R |only R/stl-seasonal.R | 34 ++++++++++++++++++++++++-------- R/x13-seasonal.R | 32 ++++++++++++++++++++++++------ man/ggsdc.Rd | 15 +++++++++++++- man/stat_decomp.Rd | 52 +++++++++++++++++++++++++++++++++++++------------ man/stat_index.Rd |only man/stat_rollapplyr.Rd |only man/stat_seas.Rd | 51 ++++++++++++++++++++++++++++++++++++------------ man/stat_stl.Rd | 48 +++++++++++++++++++++++++++++++++------------ 16 files changed, 264 insertions(+), 86 deletions(-)
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier Census programs called
X-11 and X-12 as well as the SEATS program by the Bank of Spain. Census
offers both source and binary versions -- which this package integrates
for use by other R packages.
Author: Dirk Eddelbuettel and Christoph Sax
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 0.1.1 dated 2016-02-10 and 0.1.2 dated 2016-03-14
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 2 +- configure | 4 ++-- configure.win | 28 ++++++++++++++-------------- 6 files changed, 40 insertions(+), 26 deletions(-)
Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of trading
strategies, based on the Sharpe ratio and overfit of the same.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between SharpeR versions 1.0.0 dated 2015-06-18 and 1.1.0 dated 2016-03-14
SharpeR-1.0.0/SharpeR/inst/tests |only SharpeR-1.0.0/SharpeR/tests/run-all.R |only SharpeR-1.1.0/SharpeR/.Rinstignore | 1 SharpeR-1.1.0/SharpeR/DESCRIPTION | 15 - SharpeR-1.1.0/SharpeR/MD5 | 107 ++++----- SharpeR-1.1.0/SharpeR/NAMESPACE | 32 ++ SharpeR-1.1.0/SharpeR/R/SharpeR.r | 16 + SharpeR-1.1.0/SharpeR/R/distributions.r | 19 - SharpeR-1.1.0/SharpeR/R/estimation.r | 108 ++++++--- SharpeR-1.1.0/SharpeR/R/sr.r | 139 +++++++++--- SharpeR-1.1.0/SharpeR/R/tests.r | 15 - SharpeR-1.1.0/SharpeR/R/utils.r | 12 - SharpeR-1.1.0/SharpeR/README.md | 42 +++ SharpeR-1.1.0/SharpeR/build/vignette.rds |binary SharpeR-1.1.0/SharpeR/inst/doc/SharpeR.pdf |binary SharpeR-1.1.0/SharpeR/inst/doc/SharpeRatio.pdf |binary SharpeR-1.1.0/SharpeR/inst/extdata/autocorr_study.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/haircut_study.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/hotelling_power_rule.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/ret_data.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/skew_study.rda |binary SharpeR-1.1.0/SharpeR/man/NEWS.Rd | 19 + SharpeR-1.1.0/SharpeR/man/SharpeR.Rd | 47 +--- SharpeR-1.1.0/SharpeR/man/as.del_sropt.Rd | 24 +- SharpeR-1.1.0/SharpeR/man/as.sr.Rd | 40 +-- SharpeR-1.1.0/SharpeR/man/as.sropt.Rd | 36 +-- SharpeR-1.1.0/SharpeR/man/confint.Rd | 53 +--- SharpeR-1.1.0/SharpeR/man/del_sropt.Rd | 43 +-- SharpeR-1.1.0/SharpeR/man/dsr.Rd | 50 +--- SharpeR-1.1.0/SharpeR/man/dsropt.Rd | 48 +--- SharpeR-1.1.0/SharpeR/man/inference.Rd | 35 +-- SharpeR-1.1.0/SharpeR/man/is.del_sropt.Rd | 5 SharpeR-1.1.0/SharpeR/man/is.sr.Rd | 28 -- SharpeR-1.1.0/SharpeR/man/is.sropt.Rd | 17 - SharpeR-1.1.0/SharpeR/man/ism_vcov.Rd | 21 - SharpeR-1.1.0/SharpeR/man/pco_sropt.Rd | 36 +-- SharpeR-1.1.0/SharpeR/man/plambdap.Rd | 30 -- SharpeR-1.1.0/SharpeR/man/power.sr_test.Rd | 63 ++--- SharpeR-1.1.0/SharpeR/man/power.sropt_test.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/predint.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/print.Rd | 29 -- SharpeR-1.1.0/SharpeR/man/reannualize.Rd | 44 +-- SharpeR-1.1.0/SharpeR/man/se.Rd | 31 -- SharpeR-1.1.0/SharpeR/man/sm_vcov.Rd | 15 - SharpeR-1.1.0/SharpeR/man/sr.Rd | 51 +--- SharpeR-1.1.0/SharpeR/man/sr_equality_test.Rd | 55 +--- SharpeR-1.1.0/SharpeR/man/sr_test.Rd | 41 +-- SharpeR-1.1.0/SharpeR/man/sr_unpaired_test.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/sr_vcov.Rd | 52 ++-- SharpeR-1.1.0/SharpeR/man/sric.Rd |only SharpeR-1.1.0/SharpeR/man/sropt.Rd | 40 +-- SharpeR-1.1.0/SharpeR/man/sropt_test.Rd | 30 +- SharpeR-1.1.0/SharpeR/man/summary.Rd |only SharpeR-1.1.0/SharpeR/tests/testthat |only SharpeR-1.1.0/SharpeR/tests/testthat.R |only 55 files changed, 835 insertions(+), 780 deletions(-)
Title: Provides Access to Databases Through the ODBC Interface
Description: An implementation of R's DBI interface using ODBC package as a
back-end. This allows R to connect to any DBMS that has a ODBC driver.
Author: Nagi Teramo [aut, cre],
Shinichi Takayanagi [aut]
Maintainer: Nagi Teramo <teramonagi@gmail.com>
Diff between RODBCDBI versions 0.1 dated 2015-12-02 and 0.1.1 dated 2016-03-14
DESCRIPTION | 15 +++- LICENSE | 2 MD5 | 50 ++++++++------- NAMESPACE | 4 - R/ODBCConnection.R | 27 +++++++- R/ODBCDriver.R | 60 ++++++++++++++----- R/ODBCResult.R | 38 +++++++----- R/RODBCDBI.R | 16 ++--- README.md | 38 ++++++++++-- man/ODBC.Rd | 15 +++- man/ODBCConnection-class.Rd | 11 --- man/ODBCDriver-class.Rd | 11 ++- man/ODBCResult-class.Rd | 6 - man/RODBCDBI.Rd | 4 - man/dbConnect-ODBCDriver-method.Rd |only man/dbDisconnect.Rd | 2 man/dbExistsTable-ODBCConnection-character-method.Rd | 5 + man/dbGetInfo-ODBCConnection-method.Rd |only man/dbListFields-ODBCConnection-character-method.Rd | 2 man/dbListTables-ODBCConnection-method.Rd | 2 man/dbReadTable-ODBCConnection-character-method.Rd | 6 - man/dbRemoveTable-ODBCConnection-character-method.Rd | 2 man/dbWriteTable.Rd | 10 +-- man/odbc-meta.Rd | 5 + man/odbc-query.Rd | 8 -- tests/testthat/test-ODBCConnection.R | 16 +++-- tests/testthat/test-ODBCDriver.R |only tests/testthat/test-ODBCResult.R |only 28 files changed, 237 insertions(+), 118 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut, cph],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 2.0.16 dated 2015-12-20 and 3.4.1 dated 2016-03-14
plotly-2.0.16/plotly/R/build_function.R |only plotly-2.0.16/plotly/R/colour_conversion.R |only plotly-2.0.16/plotly/R/corresp_one_one.R |only plotly-2.0.16/plotly/R/marker_conversion.R |only plotly-2.0.16/plotly/R/trace_generation.R |only plotly-2.0.16/plotly/man/ggplot_build2.Rd |only plotly-2.0.16/plotly/man/group2NA.Rd |only plotly-2.0.16/plotly/man/layer2traces.Rd |only plotly-2.0.16/plotly/man/paramORdefault.Rd |only plotly-2.0.16/plotly/man/toFill.Rd |only plotly-2.0.16/plotly/man/toWidget.Rd |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-build2.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-categorical.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-environment.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-legend-name.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-stack.R |only plotly-2.0.16/plotly/tests/testthat/test-unimplemented.R |only plotly-3.4.1/plotly/DESCRIPTION | 20 plotly-3.4.1/plotly/MD5 | 181 - plotly-3.4.1/plotly/NAMESPACE | 57 plotly-3.4.1/plotly/NEWS | 175 + plotly-3.4.1/plotly/R/figure.R | 2 plotly-3.4.1/plotly/R/ggplotly.R | 1729 ++++------ plotly-3.4.1/plotly/R/imports.R |only plotly-3.4.1/plotly/R/layers2traces.R |only plotly-3.4.1/plotly/R/plotly.R | 157 plotly-3.4.1/plotly/R/plotly_IMAGE.R | 8 plotly-3.4.1/plotly/R/plotly_POST.R | 69 plotly-3.4.1/plotly/R/print.R | 74 plotly-3.4.1/plotly/R/process.R | 5 plotly-3.4.1/plotly/R/shiny.R | 28 plotly-3.4.1/plotly/R/signup.R | 2 plotly-3.4.1/plotly/R/subplots.R | 10 plotly-3.4.1/plotly/R/toRGB.R |only plotly-3.4.1/plotly/R/utils.R | 110 plotly-3.4.1/plotly/README.md | 48 plotly-3.4.1/plotly/build/vignette.rds |binary plotly-3.4.1/plotly/inst/doc/intro.R | 3 plotly-3.4.1/plotly/inst/doc/intro.Rmd | 6 plotly-3.4.1/plotly/inst/doc/intro.html | 98 plotly-3.4.1/plotly/inst/examples/Movies/server.R | 2 plotly-3.4.1/plotly/inst/examples/lmGadget |only plotly-3.4.1/plotly/inst/examples/map_click |only plotly-3.4.1/plotly/inst/examples/onRenderHover |only plotly-3.4.1/plotly/inst/examples/plotly3DEvents |only plotly-3.4.1/plotly/inst/examples/plotlyEvents |only plotly-3.4.1/plotly/inst/examples/plotlyLinkedBrush |only plotly-3.4.1/plotly/inst/examples/plotlyLinkedClick |only plotly-3.4.1/plotly/inst/htmlwidgets/lib/plotlyjs/LICENSE | 2 plotly-3.4.1/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 75 plotly-3.4.1/plotly/inst/htmlwidgets/plotly.js | 76 plotly-3.4.1/plotly/inst/htmlwidgets/plotly.yaml | 2 plotly-3.4.1/plotly/inst/plotlyjs.R | 22 plotly-3.4.1/plotly/man/as.widget.Rd |only plotly-3.4.1/plotly/man/bbox.Rd |only plotly-3.4.1/plotly/man/config.Rd | 40 plotly-3.4.1/plotly/man/embed_notebook.Rd | 12 plotly-3.4.1/plotly/man/event_data.Rd |only plotly-3.4.1/plotly/man/geom2trace.Rd |only plotly-3.4.1/plotly/man/gg2list.Rd | 14 plotly-3.4.1/plotly/man/ggplotly.Rd | 35 plotly-3.4.1/plotly/man/knit_print.plotly.Rd | 2 plotly-3.4.1/plotly/man/plot_ly.Rd | 6 plotly-3.4.1/plotly/man/plotly_IMAGE.Rd | 2 plotly-3.4.1/plotly/man/plotly_POST.Rd | 32 plotly-3.4.1/plotly/man/print.plotly.Rd | 2 plotly-3.4.1/plotly/man/toRGB.Rd | 6 plotly-3.4.1/plotly/man/to_basic.Rd |only plotly-3.4.1/plotly/tests/testthat.R | 2 plotly-3.4.1/plotly/tests/testthat/test-cookbook-axes.R | 165 plotly-3.4.1/plotly/tests/testthat/test-cookbook-lines.R | 107 plotly-3.4.1/plotly/tests/testthat/test-cookbook-scatterplots.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-abline.R | 5 plotly-3.4.1/plotly/tests/testthat/test-ggplot-area.R | 59 plotly-3.4.1/plotly/tests/testthat/test-ggplot-bar.R | 79 plotly-3.4.1/plotly/tests/testthat/test-ggplot-boxplot.R | 23 plotly-3.4.1/plotly/tests/testthat/test-ggplot-contour.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-date.R | 40 plotly-3.4.1/plotly/tests/testthat/test-ggplot-density.R | 30 plotly-3.4.1/plotly/tests/testthat/test-ggplot-density2d.R | 64 plotly-3.4.1/plotly/tests/testthat/test-ggplot-errorbar-horizontal.R | 10 plotly-3.4.1/plotly/tests/testthat/test-ggplot-errorbar.R | 36 plotly-3.4.1/plotly/tests/testthat/test-ggplot-facets.R | 95 plotly-3.4.1/plotly/tests/testthat/test-ggplot-heatmap.R | 43 plotly-3.4.1/plotly/tests/testthat/test-ggplot-hex.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-histogram.R | 77 plotly-3.4.1/plotly/tests/testthat/test-ggplot-hline.R | 5 plotly-3.4.1/plotly/tests/testthat/test-ggplot-labels.R | 25 plotly-3.4.1/plotly/tests/testthat/test-ggplot-legend.R | 132 plotly-3.4.1/plotly/tests/testthat/test-ggplot-map.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-path.R | 66 plotly-3.4.1/plotly/tests/testthat/test-ggplot-point.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-polygons.R | 132 plotly-3.4.1/plotly/tests/testthat/test-ggplot-rect.R | 47 plotly-3.4.1/plotly/tests/testthat/test-ggplot-segment.R | 61 plotly-3.4.1/plotly/tests/testthat/test-ggplot-smooth.R | 25 plotly-3.4.1/plotly/tests/testthat/test-ggplot-step.R | 2 plotly-3.4.1/plotly/tests/testthat/test-ggplot-text.R | 37 plotly-3.4.1/plotly/tests/testthat/test-ggplot-theme.R | 53 plotly-3.4.1/plotly/tests/testthat/test-ggplot-ticks.R | 298 - plotly-3.4.1/plotly/tests/testthat/test-ggplot-tooltip.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-violin.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-vline.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-ylim.R | 17 plotly-3.4.1/plotly/tests/testthat/test-mean-error-bars.R | 192 - plotly-3.4.1/plotly/tests/testthat/test-plotly-getfigure.R | 16 plotly-3.4.1/plotly/tests/testthat/test-plotly-subplot.R | 3 plotly-3.4.1/plotly/tests/testthat/test-plotly.R | 32 plotly-3.4.1/plotly/vignettes/intro.Rmd | 6 109 files changed, 2521 insertions(+), 2602 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package evaluates the mass balance and extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to check the compound names associated to Chemical Entities of Biological Interest (ChEBI) database <https://www.ebi.ac.uk/chebi>.
Author: Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco
[aut]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.1 dated 2016-02-16 and 0.2 dated 2016-03-14
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++--------------------- NEWS | 4 +++ R/chebi.formula.R | 2 - R/chebi.id.R | 4 +-- R/compartments.R | 10 +++---- R/is.chebi.R | 10 ++----- R/is.validsyntax.R | 4 +-- R/metabolites.R | 30 +++++++++++----------- R/minval-internal.R | 21 +++++++++++----- R/orphan.products.R | 13 +++++---- R/orphan.reactants.R | 10 +++---- R/products.R | 21 +++++++++------- R/reactants.R | 21 +++++++++------- R/toChEBI.R | 34 +++++++++++++------------ R/unbalanced.R | 63 ++++++++++++++++-------------------------------- data/chebi.RData |binary man/chebi.candidates.Rd | 18 ------------- man/chebi.formula.Rd | 6 ---- man/compartments.Rd | 2 + man/glugln.Rd | 2 - man/metabolites.Rd | 24 +++++++++--------- man/minval-package.Rd | 4 +-- man/orphan.products.Rd | 2 - man/orphan.reactants.Rd | 14 +++++----- man/products.Rd | 4 +-- man/reactants.Rd | 4 +-- man/unbalanced.Rd | 6 ++-- 28 files changed, 186 insertions(+), 209 deletions(-)
Title: Binary Dimensionality Reduction
Description: Dimensionality reduction techniques for binary data including
logistic PCA.
Author: Andrew J. Landgraf
Maintainer: Andrew J. Landgraf <andland@gmail.com>
Diff between logisticPCA versions 0.1 dated 2015-10-05 and 0.2 dated 2016-03-14
DESCRIPTION | 15 LICENSE | 4 MD5 | 75 +- NAMESPACE | 58 - NEWS.md |only R/convexLogisticPCA.R | 917 +++++++++++++------------- R/data.R | 58 - R/logisticPCA-package.R | 24 R/logisticPCA.R | 1068 ++++++++++++++++--------------- R/logisticSVD.R | 970 ++++++++++++++-------------- README.md | 97 +- build/vignette.rds |binary inst/CITATION | 36 - inst/doc/logisticPCA.R | 115 +-- inst/doc/logisticPCA.Rmd | 343 +++++---- inst/doc/logisticPCA.html | 475 ++++++------- man/convexLogisticPCA.Rd | 160 ++-- man/cv.clpca.Rd | 92 +- man/cv.lpca.Rd | 92 +- man/cv.lsvd.Rd | 84 +- man/fitted.lpca.Rd | 72 +- man/fitted.lsvd.Rd | 72 +- man/house_votes84.Rd | 76 +- man/inv.logit.mat.Rd | 50 - man/log_like_Bernoulli.Rd | 42 - man/logisticPCA-package.Rd | 28 man/logisticPCA.Rd | 161 ++-- man/logisticSVD.Rd | 164 ++-- man/plot.clpca.Rd | 76 +- man/plot.cv.lpca.Rd | 64 - man/plot.lpca.Rd | 76 +- man/plot.lsvd.Rd | 76 +- man/predict.clpca.Rd | 86 +- man/predict.lpca.Rd | 86 +- man/predict.lsvd.Rd | 122 +-- man/project.Fantope.Rd | 42 - tests/testthat/test-dimensions.R | 375 +++++----- tests/testthat/test-dimensions_missing.R | 365 ++++------ vignettes/logisticPCA.Rmd | 343 +++++---- 39 files changed, 3575 insertions(+), 3484 deletions(-)
Title: Learning Data Cleaning, Visual Analysis and Model Performance
Description: Learn data cleaning, visual data analysis and model performance assessment (KS, AUC and ROC), package core is in the vignette documentation explaining last topics as a tutorial.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>
Diff between funModeling versions 1.0 dated 2016-02-07 and 1.1 dated 2016-03-14
funModeling-1.0/funModeling/man/cross_iterator.Rd |only funModeling-1.1/funModeling/DESCRIPTION | 8 funModeling-1.1/funModeling/MD5 | 18 - funModeling-1.1/funModeling/NEWS |only funModeling-1.1/funModeling/R/cross_plot.R | 267 ++++++++---------- funModeling-1.1/funModeling/inst/doc/funModeling.R | 11 funModeling-1.1/funModeling/inst/doc/funModeling.Rmd | 25 - funModeling-1.1/funModeling/inst/doc/funModeling.html | 18 - funModeling-1.1/funModeling/man/cross_plot.Rd | 13 funModeling-1.1/funModeling/man/massive_cross_plot.Rd | 11 funModeling-1.1/funModeling/vignettes/funModeling.Rmd | 25 - 11 files changed, 180 insertions(+), 216 deletions(-)
Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of
flow cytometry samples using the curvHDR method.
Author: Matt Wand [aut, cre],
George Luta [aut],
Ulrike Naumann [aut],
Mathew W. McLean [ctb],
Dai Feng [ctb],
Luke Tierney [ctb],
Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>
Diff between curvHDR versions 1.0-3 dated 2011-12-23 and 1.1-0 dated 2016-03-14
curvHDR-1.0-3/curvHDR/doc |only curvHDR-1.1-0/curvHDR/DESCRIPTION | 30 +++++++++++---- curvHDR-1.1-0/curvHDR/MD5 | 20 ++++++---- curvHDR-1.1-0/curvHDR/NAMESPACE | 34 +++++++++++++++++- curvHDR-1.1-0/curvHDR/R/curvHDRfilter.r | 49 ++++++++++++++------------ curvHDR-1.1-0/curvHDR/R/inpolygon.r |only curvHDR-1.1-0/curvHDR/R/plot.curvHDRfilter.r | 2 - curvHDR-1.1-0/curvHDR/R/plot3D.r | 4 +- curvHDR-1.1-0/curvHDR/R/separateTriPolyh.r | 8 +--- curvHDR-1.1-0/curvHDR/R/t2ve.r |only curvHDR-1.1-0/curvHDR/R/vertexTriangles.r |only curvHDR-1.1-0/curvHDR/man/curvHDR-internal.Rd | 2 - curvHDR-1.1-0/curvHDR/src |only curvHDR-1.1-0/curvHDR/vignettes |only 14 files changed, 101 insertions(+), 48 deletions(-)