Title: Update Chinese ID Card Number to Eighteen Digits
Description: The digits of the old version (before 2000 year) of 'Chinese ID Card Number' is 15, this package aims to update to the current version of 18 digits. Besides, this package can help check whether the given 'ID' is right or not.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between IDCard versions 0.2.0 dated 2017-11-08 and 0.3.0 dated 2017-11-22
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++++---- NAMESPACE | 2 ++ R/is.id.R |only data |only man/code.Rd |only man/id.15to18.Rd | 4 +++- man/id.15to18.single.Rd | 4 +++- man/is.id.Rd |only 9 files changed, 21 insertions(+), 10 deletions(-)
Title: A Clustering Method Based on Boosting on Single Attributes
Description: An overlap clustering algorithm for categorical ultra-dimension data.
Author: Peng Zhang [aut],
Kaixiu Jin [aut, cre]
Maintainer: Kaixiu Jin <jinkaixiu@zju.edu.cn>
Diff between boclust versions 0.1.0 dated 2017-11-15 and 0.1.1 dated 2017-11-22
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/Bossa_Clust.R | 21 +++++++++++++++++---- R/shiny_method.R | 8 ++++---- R/shiny_prepare.R | 3 +-- 6 files changed, 37 insertions(+), 21 deletions(-)
Title: Estimating Conditional Distributions
Description: Estimates conditional distributions and conditional quantiles. The versions of the methods in this package are primarily for use in multiple step procedures where the first step is to estimate a conditional distribution. In particular, there are functions for implementing distribution regression, quantile regression, and versions of local linear distribution regression; all in a unified framework. Distribution regression provides a way to flexibly model the distribution of some outcome Y conditional on covariates X without imposing parametric assumptions on the conditional distribution but providing more structure than fully nonparametric estimation (See Foresi and Peracchi (1995) <doi:10.2307/2291056> and Chernozhukov, Fernandez-Val, and Melly (2013) <doi:10.3982/ECTA10582>).
Author: Brantly Callaway [aut, cre],
Weige Huang [aut]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>
Diff between TempleMetrics versions 1.0.0 dated 2017-11-10 and 1.1.0 dated 2017-11-22
DESCRIPTION | 9 + MD5 | 37 +++++-- NAMESPACE | 16 +++ NEWS.md | 6 + R/TempleMetrics.R | 233 +++++++++++++++++++++++++++++++++++++++++++----- R/imports.R | 1 R/lldr.R |only R/zzz.R |only README.md | 21 +--- man/Fycondx.DR.Rd |only man/Fycondx.Rd | 20 +--- man/Fycondx.llDRlist.Rd |only man/Fycondx.rqs.Rd |only man/G.Rd |only man/dg.Rd |only man/distreg.Rd | 5 - man/drs.Rd | 5 - man/drs.inner.Rd | 5 - man/k.Rd |only man/llDR.Rd |only man/lldistreg.Rd |only man/lldr.inner.Rd |only man/lldr.inner.xvals.Rd |only man/lldr.inner.y.Rd |only man/lldrs.inner.Rd |only man/wgr.Rd |only man/wll.Rd |only man/wscore.Rd |only 28 files changed, 292 insertions(+), 66 deletions(-)
Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and model diagnostics, in the univariate
and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.5-0 dated 2017-02-10 and 1.5-1 dated 2017-11-22
DESCRIPTION | 14 +++--- MD5 | 44 +++++++++++---------- NEWS | 21 +++++++--- R/sn-funct.R | 39 ++++++++++++------- data/ais.rda |binary data/barolo.rda |binary data/frontier.rda |binary data/wines.rda |binary inst/CITATION | 8 +-- inst/doc/R.css |only inst/doc/how_to_sample.pdf |binary inst/doc/pkg-overview.html |only inst/doc/pkg_sn-intro.pdf |only inst/doc/selm-intervals.pdf |binary man/affineTransSECdistr.Rd | 20 +++++---- man/confint.selm.Rd | 11 +++-- man/dp2cp.Rd | 4 - man/makeSECdistr.Rd | 2 man/overview.Rd |only man/predict.selm.Rd | 4 + man/selm.Rd | 90 ++++++++++++++++++++++++++++++++++---------- man/selm.fit.Rd | 12 +++++ man/sn-package.Rd | 9 +++- man/summary.SECdistr.Rd | 84 +++++++++++++++++++++++++++++++++++------ man/symm-modulated-distr.Rd | 12 +++-- 25 files changed, 271 insertions(+), 103 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.12.0 dated 2017-10-16 and 0.13.0 dated 2017-11-22
DESCRIPTION | 13 MD5 | 60 ++- NAMESPACE | 17 - NEWS.md | 463 +++++++++++++++--------------- R/S3-methods.R | 65 +++- R/cv_error.R | 160 +++++----- R/find_beta.R | 378 ++++++++++++------------ R/gmd.R |only R/grpmean.R | 540 +++++++++++++++++------------------ R/icc.R | 118 +++++-- R/is_prime.R |only R/merMod_p.R | 20 - R/overdisp.R | 259 ++++++++-------- R/pca.R |only R/pred_vars.R | 49 ++- R/predictive_accuracy.R | 270 ++++++++--------- R/svy_scale_weights.R |only R/typical.R | 31 ++ README.md | 4 build/partial.rdb |binary inst/doc/anova-statistics.html | 4 inst/doc/mixedmodels-statistics.R | 4 inst/doc/mixedmodels-statistics.Rmd | 28 + inst/doc/mixedmodels-statistics.html | 42 ++ man/find_beta.Rd | 2 man/gmd.Rd |only man/icc.Rd | 9 man/is_prime.Rd |only man/overdisp.Rd | 17 - man/p_value.Rd | 3 man/pca.Rd |only man/pred_vars.Rd | 7 man/re_var.Rd | 13 man/scale_weights.Rd |only vignettes/mixedmodels-statistics.Rmd | 28 + 35 files changed, 1466 insertions(+), 1138 deletions(-)
Title: Estimating Time-Varying k-Order Mixed Graphical Models
Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.2-1 dated 2017-06-20 and 1.2-2 dated 2017-11-22
DESCRIPTION | 8 MD5 | 58 ++-- NAMESPACE | 10 NEWS | 14 + R/beepday2consec.R |only R/bwSelPredict.R | 11 R/bwSelect.R | 22 + R/glmnetRequirements.R | 11 R/lagData.R | 12 - R/mgm.R | 53 +++- R/mvar.R | 568 +++++++++++++++++++++++++++--------------------- R/mvarsampler.R | 7 R/nodeEst.R | 7 R/plotRes.R |only R/predict.mgm.R | 211 +++++++++++------ R/predictCore_stat.R | 162 +++++++------ R/print.mgm.R | 18 + R/print.resample.R |only R/resample.R |only R/showInteraction.R |only R/tvmvar.R | 34 +- R/tvmvarsampler.R | 25 +- data/symptom_data.RData |binary man/bwSelect.Rd | 7 man/datasets.Rd | 2 man/mgm.Rd | 6 man/mvar.Rd | 51 ++-- man/mvarsampler.Rd | 35 +- man/plotRes.Rd |only man/predict.mgm.Rd | 6 man/resample.Rd |only man/showInteraction.Rd |only man/tvmgm.Rd | 5 man/tvmvar.Rd | 1 34 files changed, 821 insertions(+), 523 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
The R Consortium [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.3 dated 2016-11-22 and 0.4.0 dated 2017-11-22
DESCRIPTION | 18 ++++---- MD5 | 40 +++++++++++++------ NAMESPACE | 8 +++ NEWS.md | 30 ++++++++++++++ R/args.R |only R/arith.R | 10 ++++ R/compat-purrr.R |only R/format.R | 11 +++-- R/hms.R | 84 ++++++++++++++++++++-------------------- R/parse.R |only R/pillar.R |only R/round.R |only R/zzz.R |only README.md | 8 ++- man/hms.Rd | 26 ++++++++---- man/parse_hms.Rd |only man/round_hms.Rd |only tests/testthat/helper-pillar.R |only tests/testthat/out |only tests/testthat/test-coercion.R | 11 +++-- tests/testthat/test-colformat.R |only tests/testthat/test-combine.R |only tests/testthat/test-construct.R | 21 ++++++++-- tests/testthat/test-output.R | 2 tests/testthat/test-parse.R |only tests/testthat/test-round.R |only 26 files changed, 186 insertions(+), 83 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon [aut, cre],
Bruno Herault [aut]
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between entropart versions 1.4-7 dated 2017-03-29 and 1.4-8 dated 2017-11-22
entropart-1.4-7/entropart/inst/doc/Introduction.Rnw |only entropart-1.4-7/entropart/inst/doc/Introduction.pdf |only entropart-1.4-7/entropart/vignettes/Introduction.Rnw |only entropart-1.4-8/entropart/DESCRIPTION | 21 ++- entropart-1.4-8/entropart/MD5 | 73 ++++++------ entropart-1.4-8/entropart/NEWS | 15 ++ entropart-1.4-8/entropart/R/AllenH.R | 6 entropart-1.4-8/entropart/R/ChaoPD.R | 4 entropart-1.4-8/entropart/R/HqzBeta.R | 14 -- entropart-1.4-8/entropart/R/PhyloApply.R | 6 entropart-1.4-8/entropart/R/Preprocess.Tree.R | 14 +- entropart-1.4-8/entropart/README.md |only entropart-1.4-8/entropart/build/vignette.rds |binary entropart-1.4-8/entropart/inst/doc/Introduction.R | 47 ++----- entropart-1.4-8/entropart/inst/doc/Introduction.Rmd |only entropart-1.4-8/entropart/inst/doc/Introduction.html |only entropart-1.4-8/entropart/inst/doc/Phylogenies.R |only entropart-1.4-8/entropart/inst/doc/Phylogenies.Rmd |only entropart-1.4-8/entropart/inst/doc/Phylogenies.html |only entropart-1.4-8/entropart/inst/doc/entropart.pdf |binary entropart-1.4-8/entropart/man/AlphaDiversity.Rd | 2 entropart-1.4-8/entropart/man/AlphaEntropy.Rd | 2 entropart-1.4-8/entropart/man/BetaDiversity.Rd | 2 entropart-1.4-8/entropart/man/BetaEntropy.Rd | 2 entropart-1.4-8/entropart/man/CommunityProfile.Rd | 2 entropart-1.4-8/entropart/man/DivEst.Rd | 2 entropart-1.4-8/entropart/man/DivPart.Rd | 2 entropart-1.4-8/entropart/man/DivProfile.Rd | 2 entropart-1.4-8/entropart/man/GammaDiversity.Rd | 2 entropart-1.4-8/entropart/man/GammaEntropy.Rd | 2 entropart-1.4-8/entropart/man/PDFD.Rd | 2 entropart-1.4-8/entropart/man/PPtree.Rd | 2 entropart-1.4-8/entropart/man/PhyloApply.Rd | 2 entropart-1.4-8/entropart/man/PhyloBetaEntropy.Rd | 2 entropart-1.4-8/entropart/man/PhyloDiversity.Rd | 2 entropart-1.4-8/entropart/man/PhyloEntropy.Rd | 2 entropart-1.4-8/entropart/man/Preprocess.Tree.Rd | 2 entropart-1.4-8/entropart/man/Rao.Rd | 2 entropart-1.4-8/entropart/man/SpeciesDistribution.Rd | 2 entropart-1.4-8/entropart/tests/testthat/testPhyloEntropy.R | 51 ++++++++ entropart-1.4-8/entropart/vignettes/Introduction.Rmd |only entropart-1.4-8/entropart/vignettes/Phylogenies.Rmd |only entropart-1.4-8/entropart/vignettes/entropart.bib | 12 - 43 files changed, 188 insertions(+), 113 deletions(-)
Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kent Russell [aut, cre] (R interface),
Gregor Aisch [aut, cph] (d3-jetpack creator,
https://github.com/gka/d3-jetpack),
Adam Pearce [aut] (core contributor to d3-jetpack),
Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 0.7.0 dated 2017-10-11 and 0.7.1 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/dependencies.R | 4 ++-- inst/www/d3/v4/API.md | 4 ++++ inst/www/d3/v4/dist/d3.min.js | 4 ++-- 6 files changed, 21 insertions(+), 13 deletions(-)
Title: Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Description: Implements novel nonparametric approaches to address
biases and confounding when comparing treatments or exposures in
observational studies of outcomes. While designed and appropriate for use
in studies involving medicine and the life sciences, the package can be
used in other situations involving outcomes with multiple confounders.
The package implements a family of methods for nonparametric bias
correction when comparing treatments in cross-sectional, case-control,
and survival analysis settings, including competing risks with censoring.
The approach extends to bias-corrected personalized predictions of
treatment outcome differences, and analysis of heterogeneity of treatment
effect-sizes across patient subgroups.
Author: Nicolas R. Lauve [aut],
Stuart J. Nelson [aut],
S. Stanley Young [aut],
Robert L. Obenchain [aut],
Melania Pintilie [ctb],
Martin Kutz [ctb],
Christophe G. Lambert [aut, cre]
Maintainer: Christophe G. Lambert <cglambert@unm.edu>
Diff between LocalControl versions 1.0.1 dated 2017-06-03 and 1.1.0 dated 2017-11-22
LocalControl-1.0.1/LocalControl/man/localControlClassic.Rd |only LocalControl-1.0.1/LocalControl/man/localControlCompetingRisks.Rd |only LocalControl-1.0.1/LocalControl/man/localControlCompetingRisksConfidence.Rd |only LocalControl-1.0.1/LocalControl/man/localControlNearestNeighbors.Rd |only LocalControl-1.0.1/LocalControl/man/localControlNearestNeighborsConfidence.Rd |only LocalControl-1.0.1/LocalControl/man/plotLocalControlCIF.Rd |only LocalControl-1.0.1/LocalControl/man/plotLocalControlLTD.Rd |only LocalControl-1.1.0/LocalControl/DESCRIPTION | 26 LocalControl-1.1.0/LocalControl/MD5 | 51 LocalControl-1.1.0/LocalControl/NAMESPACE | 13 LocalControl-1.1.0/LocalControl/NEWS.md | 28 LocalControl-1.1.0/LocalControl/R/RcppExports.R | 6 LocalControl-1.1.0/LocalControl/R/clusteringLC.R | 183 - LocalControl-1.1.0/LocalControl/R/dataDesc.R | 6 LocalControl-1.1.0/LocalControl/R/deprecatedLC.R |only LocalControl-1.1.0/LocalControl/R/localControl.R | 960 ++++------ LocalControl-1.1.0/LocalControl/README.md | 2 LocalControl-1.1.0/LocalControl/data/framingham.rda |binary LocalControl-1.1.0/LocalControl/man/LocalControl-deprecated.Rd |only LocalControl-1.1.0/LocalControl/man/LocalControl.Rd |only LocalControl-1.1.0/LocalControl/man/LocalControlClassic.Rd |only LocalControl-1.1.0/LocalControl/man/LocalControlCompetingRisksConfidence.Rd |only LocalControl-1.1.0/LocalControl/man/LocalControlNearestNeighborsConfidence.Rd |only LocalControl-1.1.0/LocalControl/man/UPSLTDdist.Rd | 8 LocalControl-1.1.0/LocalControl/man/UPSaltdd.Rd | 6 LocalControl-1.1.0/LocalControl/man/UPSboxplot.Rd | 14 LocalControl-1.1.0/LocalControl/man/UPShclus.Rd | 2 LocalControl-1.1.0/LocalControl/man/UPSivadj.Rd | 2 LocalControl-1.1.0/LocalControl/man/framingham.Rd | 2 LocalControl-1.1.0/LocalControl/man/plot.LocalControlCR.Rd |only LocalControl-1.1.0/LocalControl/man/plot.LocalControlCS.Rd |only LocalControl-1.1.0/LocalControl/src/LocalControl.cpp | 2 LocalControl-1.1.0/LocalControl/src/RcppExports.cpp | 6 LocalControl-1.1.0/LocalControl/src/init.c | 14 34 files changed, 687 insertions(+), 644 deletions(-)
Title: Explanation of Predictions for Classification and Regression
Models
Description: Generates explanations for classification and regression models and visualizes them.
Explanations are generated for individual predictions as well as for models as a whole. Two explanation methods
are included, EXPLAIN and IME. The EXPLAIN method is fast but might miss explanations expressed redundantly
in the model. The IME method is slower as it samples from all feature subsets.
For the EXPLAIN method see Robnik-Sikonja and Kononenko (2008) <doi:10.1109/TKDE.2007.190734>,
and the IME method is described in Strumbelj and Kononenko (2010, JMLR, vol. 11:1-18).
All models in package 'CORElearn' are natively supported, for other prediction models a wrapper function is provided
and illustrated for models from packages 'randomForest', 'nnet', and 'e1071'.
Author: Marko Robnik-Sikonja
Maintainer: Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>
Diff between ExplainPrediction versions 1.1.8 dated 2017-04-03 and 1.2.3 dated 2017-11-22
ChangeLog | 5 DESCRIPTION | 10 MD5 | 10 R/explain.R | 1654 +++++++++++++++++++++++------------------------- man/explanation.Rd | 164 ++-- man/wrap4Explanation.Rd | 2 6 files changed, 901 insertions(+), 944 deletions(-)
More information about ExplainPrediction at CRAN
Permanent link
Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you
run 'Domino' commands (e.g., "run", "upload", "download") directly from your
R environment. Under the hood, it uses R's system function to run the 'Domino'
executable, which must be installed as a prerequisite. 'Domino' is a service
that makes it easy to run your code on scalable hardware, with integrated
version control and collaboration features designed for analytical workflows
(see <http://www.dominodatalab.com> for more information).
Author: Jacek Glodek <jacek@theiterators.com>
Maintainer: Nick Elprin <nick@dominodatalab.com>
Diff between domino versions 0.3.0 dated 2016-07-10 and 0.3.1 dated 2017-11-22
domino-0.3.0/domino/tests/testthat/domino.log |only domino-0.3.1/domino/DESCRIPTION | 8 ++--- domino-0.3.1/domino/MD5 | 9 ++--- domino-0.3.1/domino/R/domino-package.R | 40 +++++++++++++------------- domino-0.3.1/domino/R/domino.R | 32 ++++++-------------- domino-0.3.1/domino/tests/testthat.R | 4 +- 6 files changed, 41 insertions(+), 52 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.2 dated 2017-11-09 and 0.9.3 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/filters.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Gene-Based Association Analysis for Complex Traits
Description: Gene based association test between a group of SNPs and traits
including familial (both continuous and binary) traits, multivariate
continuous (both independent and familial) traits, longitudinal continuous
traits and survival traits. Part of methods were previously published in
Maity et al (2012) <doi:10.1002/gepi.21663>, Chen et al (2013)
<doi:10.1002/gepi.21703>, Chen et al (2014) <doi:10.1002/gepi.21791>, Yan
et al (2015) <doi:10.1159/000375409>, Yan et al (2015)
<doi:10.1534/genetics.115.178590> and Yan et al (2015)
<doi:10.1159/000445057>.
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>
Diff between KMgene versions 1.1 dated 2017-11-09 and 1.2 dated 2017-11-22
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 35 ++++++++++++++++++++++++++++------- NAMESPACE | 20 ++++++++++++++++++++ R/CoxKM.R |only R/Data_CoxKM_data.R |only R/MFKM.R | 16 ++++++---------- R/MFKMO.R | 5 ----- R/c.KMgene.R |only R/coxlr.fit.R |only R/ginv_s.R |only R/pchisqsum2.R |only R/prepCoxKM.R |only R/saddle.R |only data/CoxKM_data.RData |only data/LKM_numID_int.RData |binary man/CoxKM.Rd |only man/CoxKM_data.Rd |only man/MFKM.Rd | 16 ++++++---------- man/MFKMO.Rd | 5 ----- man/prepCoxKM.Rd |only src |only 21 files changed, 75 insertions(+), 49 deletions(-)
Title: Interim Analysis of Operational Futility in Randomized Trials
with Time-to-Event Endpoints and Fixed Follow-Up
Description: Randomized clinical trials commonly follow participants for a time-to-event efficacy endpoint for a fixed period of time. Consequently, at the time when the last enrolled participant completes their follow-up, the number of observed endpoints is a random variable. Assuming data collected through an interim timepoint, simulation-based estimation and inferential procedures in the standard right-censored failure time analysis framework are conducted for the distribution of the number of endpoints--in total as well as by treatment arm--at the end of the follow-up period. The future (i.e., yet unobserved) enrollment, endpoint, and dropout times are generated according to mechanisms specified in the simTrial() function in the 'seqDesign' package. A Bayesian model for the endpoint rate, offering the option to specify a robust mixture prior distribution, is used for generating future data (see the vignette for details).
Author: Yingying Zhuang and Michal Juraska, with contributions from Doug Grove, Peter B. Gilbert, Alexander R. Luedtke, Sanne Roels, and An Vandebosch
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between futility versions 0.1 dated 2017-07-28 and 0.2 dated 2017-11-22
DESCRIPTION | 12 MD5 | 15 - R/futility.R | 380 +++++++++++++++++++++++-------- inst/doc/bayesianIncidenceRateModel.Rnw | 50 +++- inst/doc/bayesianIncidenceRateModel.pdf |binary man/completeTrial.byArm.Rd | 12 man/completeTrial.pooledArms.Rd | 23 + vignettes/bayesianIncidenceRateModel.Rnw | 50 +++- vignettes/references.bib |only 9 files changed, 407 insertions(+), 135 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre],
Hironobu Takahashi [cph],
Hajime Baba [cph],
Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.6.3-1 dated 2016-04-13 and 0.6.4 dated 2017-11-22
ChangeLog | 9 +++++++++ DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++----------- NAMESPACE | 12 ++++++------ R/JapanPrefecturesMap.R | 5 +++-- R/jyear.R | 19 ++++++++++++++++++- R/zen2han.R | 26 +++++++++++++++----------- man/JapanPrefecturesMap.Rd | 3 ++- man/Nippon-package.Rd | 4 ++-- man/sanitizeZenkaku.Rd |only man/wareki2AD.Rd |only src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/init.c |only src/rkakasi.c | 2 ++ src/rkakasi.c.orig |only 16 files changed, 79 insertions(+), 41 deletions(-)
Title: Summarise a Distribution Through Coloured Intervals
Description: Implements the functionality of the 'fanplot' package as 'geoms'
for 'ggplot2'. Designed for summarising MCMC samples from a posterior
distribution, where a visualisation is desired for several values of a
continuous covariate. Increasing posterior intervals of the sampled quantity
are mapped to a continuous colour scale.
Author: Jason Hilton [aut, cre]
Maintainer: Jason Hilton <jason_hilton@yahoo.com>
Diff between ggfan versions 0.1.0 dated 2017-11-14 and 0.1.1 dated 2017-11-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/geom_fan.html | 44 ++++++++++++++++++++++---------------------- inst/doc/ggfan_stan.html | 12 ++++++------ 5 files changed, 41 insertions(+), 37 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from <https://www.bls.gov/>. The U.S. Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 3.0.1 dated 2017-10-05 and 3.1.1 dated 2017-11-22
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Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using
state space models. The first implemented model is described in Fahrmeir
(1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the
Extended Kalman filter is replaced by an unscented Kalman filter and other
options including particle filters.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.4.0 dated 2017-09-16 and 0.5.0 dated 2017-11-22
dynamichazard-0.4.0/dynamichazard/inst/doc/Sim_study_with_logit.pdf |only dynamichazard-0.4.0/dynamichazard/inst/doc/Sim_study_with_logit.pdf.asis |only dynamichazard-0.4.0/dynamichazard/man/hatvalues.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/man/logLik.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/man/model.frame.ddformula.Rd |only dynamichazard-0.4.0/dynamichazard/man/plot.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/man/plot.fahrmeier_94_SpaceErrors.Rd |only dynamichazard-0.4.0/dynamichazard/man/predict.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/man/print.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/man/residuals.fahrmeier_94.Rd |only dynamichazard-0.4.0/dynamichazard/src/exp_model_funcs.h |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/UKF3.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/UKF5.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/UKF6.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/boot_print.RDS.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/boot_print_two.RDS.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/ddhazard_changed_by.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/previous_results/ddhazard_exp_bin.RDS |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testUKF.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testbigglm_wrapper.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testboot_est.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testddhazard.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testdesign_mat_and_risk_obj.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testloglike.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testoptions.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testplot.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testpredict.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testprint.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testresiduals.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/teststatic_glm.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testtest_utils.R |only dynamichazard-0.4.0/dynamichazard/tests/testthat/testweights.R |only dynamichazard-0.4.0/dynamichazard/vignettes/Sim_study_with_logit.pdf.asis |only dynamichazard-0.4.0/dynamichazard/vignettes/pbc_data.bib |only dynamichazard-0.5.0/dynamichazard/DESCRIPTION | 6 dynamichazard-0.5.0/dynamichazard/MD5 | 287 ++--- dynamichazard-0.5.0/dynamichazard/NAMESPACE | 25 dynamichazard-0.5.0/dynamichazard/NEWS.md | 57 - dynamichazard-0.5.0/dynamichazard/R/HDs.R |only dynamichazard-0.5.0/dynamichazard/R/PF.R | 72 - dynamichazard-0.5.0/dynamichazard/R/RcppExports.R | 34 dynamichazard-0.5.0/dynamichazard/R/boot_est.R | 162 +- dynamichazard-0.5.0/dynamichazard/R/ddhazard.R | 550 +++++----- dynamichazard-0.5.0/dynamichazard/R/get_design_matrix.R | 260 +--- dynamichazard-0.5.0/dynamichazard/R/hatvalues.R | 86 - dynamichazard-0.5.0/dynamichazard/R/loglike.R | 47 dynamichazard-0.5.0/dynamichazard/R/options.R | 7 dynamichazard-0.5.0/dynamichazard/R/plot.R | 77 - dynamichazard-0.5.0/dynamichazard/R/predict.R | 219 ++- dynamichazard-0.5.0/dynamichazard/R/print.R | 129 +- dynamichazard-0.5.0/dynamichazard/R/residuals.R | 79 - dynamichazard-0.5.0/dynamichazard/R/risk_obj.R | 77 - dynamichazard-0.5.0/dynamichazard/R/roxygen_tags.R | 2 dynamichazard-0.5.0/dynamichazard/R/shiny_app.R | 8 dynamichazard-0.5.0/dynamichazard/R/static_glm.R | 118 +- dynamichazard-0.5.0/dynamichazard/R/summary.R |only dynamichazard-0.5.0/dynamichazard/R/test_utils.R | 69 - dynamichazard-0.5.0/dynamichazard/build/vignette.rds |binary dynamichazard-0.5.0/dynamichazard/data |only dynamichazard-0.5.0/dynamichazard/inst/doc/Bootstrap_illustration.pdf |binary dynamichazard-0.5.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.R | 36 dynamichazard-0.5.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.Rmd | 73 - dynamichazard-0.5.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.pdf |binary dynamichazard-0.5.0/dynamichazard/inst/doc/Diagnostics.R | 108 - dynamichazard-0.5.0/dynamichazard/inst/doc/Diagnostics.Rmd | 163 -- dynamichazard-0.5.0/dynamichazard/inst/doc/Diagnostics.pdf |binary dynamichazard-0.5.0/dynamichazard/inst/doc/Particle_filtering.pdf |binary dynamichazard-0.5.0/dynamichazard/inst/doc/ddhazard.R | 47 dynamichazard-0.5.0/dynamichazard/inst/doc/ddhazard.Rmd | 478 ++------ dynamichazard-0.5.0/dynamichazard/inst/doc/ddhazard.pdf |binary dynamichazard-0.5.0/dynamichazard/inst/shiny/app.R | 16 dynamichazard-0.5.0/dynamichazard/man/PF_EM.Rd | 46 dynamichazard-0.5.0/dynamichazard/man/ddFixed.Rd | 29 dynamichazard-0.5.0/dynamichazard/man/ddhazard.Rd | 140 +- dynamichazard-0.5.0/dynamichazard/man/ddhazard_app.Rd | 8 dynamichazard-0.5.0/dynamichazard/man/ddhazard_boot.Rd | 35 dynamichazard-0.5.0/dynamichazard/man/get_risk_obj.Rd | 43 dynamichazard-0.5.0/dynamichazard/man/get_survival_case_weights_and_data.Rd | 49 dynamichazard-0.5.0/dynamichazard/man/hatvalues.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/man/hds.Rd |only dynamichazard-0.5.0/dynamichazard/man/logLik.PF_clouds.Rd | 6 dynamichazard-0.5.0/dynamichazard/man/logLik.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/man/plot.PF_clouds.Rd | 2 dynamichazard-0.5.0/dynamichazard/man/plot.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/man/plot.ddhazard_space_errors.Rd |only dynamichazard-0.5.0/dynamichazard/man/predict.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/man/print.ddhazard_boot.Rd | 10 dynamichazard-0.5.0/dynamichazard/man/residuals.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/man/static_glm.Rd | 37 dynamichazard-0.5.0/dynamichazard/man/summary.ddhazard.Rd |only dynamichazard-0.5.0/dynamichazard/src/BLAS_LAPACK/R_BLAS_LAPACK.cpp | 10 dynamichazard-0.5.0/dynamichazard/src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp | 2 dynamichazard-0.5.0/dynamichazard/src/Makevars | 2 dynamichazard-0.5.0/dynamichazard/src/Makevars.win | 2 dynamichazard-0.5.0/dynamichazard/src/PF.cpp | 14 dynamichazard-0.5.0/dynamichazard/src/PF/PF_data.h | 8 dynamichazard-0.5.0/dynamichazard/src/PF/PF_utils.h | 19 dynamichazard-0.5.0/dynamichazard/src/PF/densities.h | 85 - dynamichazard-0.5.0/dynamichazard/src/PF/resamplers.h | 7 dynamichazard-0.5.0/dynamichazard/src/RcppExports.cpp | 99 - dynamichazard-0.5.0/dynamichazard/src/bigglm_wrapper.cpp | 82 + dynamichazard-0.5.0/dynamichazard/src/bigglm_wrapper.h | 83 - dynamichazard-0.5.0/dynamichazard/src/ddhazard.h | 209 --- dynamichazard-0.5.0/dynamichazard/src/ddhazard/EKF_solver.cpp | 445 +++----- dynamichazard-0.5.0/dynamichazard/src/ddhazard/GMA_solver.cpp | 124 -- dynamichazard-0.5.0/dynamichazard/src/ddhazard/SMA_solver.cpp | 178 +-- dynamichazard-0.5.0/dynamichazard/src/ddhazard/UKF_solver.cpp | 198 +-- dynamichazard-0.5.0/dynamichazard/src/ddhazard_fit.cpp | 425 +++---- dynamichazard-0.5.0/dynamichazard/src/estimate_fixed_effects_M_step.h | 51 dynamichazard-0.5.0/dynamichazard/src/family.cpp |only dynamichazard-0.5.0/dynamichazard/src/family.h |only dynamichazard-0.5.0/dynamichazard/src/for_tests.cpp | 46 dynamichazard-0.5.0/dynamichazard/src/loglike.cpp | 108 - dynamichazard-0.5.0/dynamichazard/src/problem_data.cpp |only dynamichazard-0.5.0/dynamichazard/src/problem_data.h | 444 ++++---- dynamichazard-0.5.0/dynamichazard/src/risk_obj.cpp | 12 dynamichazard-0.5.0/dynamichazard/src/sample_funcs.cpp | 4 dynamichazard-0.5.0/dynamichazard/src/utils.cpp | 51 dynamichazard-0.5.0/dynamichazard/src/utils.h | 35 dynamichazard-0.5.0/dynamichazard/tests/testthat/helper.R | 121 -- dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/E_step_fixed_exp_head_neck.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/E_step_sim_exp_UKF.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/E_step_sim_exp_UKF_order_two.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/PF_EM_print |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/PF_clouds_print |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/Rossi_pearson.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/Rossi_state.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/UKF4.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/boot_print |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/boot_print_w_o_fixed |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_boot_help_page.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_loglike.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_order_one.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_order_two.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_predict_response.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_predict_term.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/ddhazard_help_page_residuals.RDS |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/fixed_terms1.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/fixed_terms_UKF_exp.RDS |binary 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dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/summary_ddhazard_print |only dynamichazard-0.5.0/dynamichazard/tests/testthat/previous_results/whas_state.RDS |binary dynamichazard-0.5.0/dynamichazard/tests/testthat/test_PF.R | 55 - dynamichazard-0.5.0/dynamichazard/tests/testthat/test_SMA.R | 42 dynamichazard-0.5.0/dynamichazard/tests/testthat/test_UKF.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_bigglm_wrapper.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_boot_est.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_cpp_utils.R | 40 dynamichazard-0.5.0/dynamichazard/tests/testthat/test_ddhazard_n_EKF.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_design_mat_and_risk_obj.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_fixed_effects_in_E_step.R | 51 dynamichazard-0.5.0/dynamichazard/tests/testthat/test_fixed_effects_in_M_step.R | 154 +- dynamichazard-0.5.0/dynamichazard/tests/testthat/test_loglike.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_options.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_plot.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_predict.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_print.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_residuals.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_shiny_app.R | 21 dynamichazard-0.5.0/dynamichazard/tests/testthat/test_static_glm.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_summary.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_test_utils.R |only dynamichazard-0.5.0/dynamichazard/tests/testthat/test_weights.R |only dynamichazard-0.5.0/dynamichazard/vignettes/Comparing_methods_for_logistic_models.Rmd | 73 - dynamichazard-0.5.0/dynamichazard/vignettes/Diagnostics.Rmd | 163 -- dynamichazard-0.5.0/dynamichazard/vignettes/bibliography.bib |only dynamichazard-0.5.0/dynamichazard/vignettes/ddhazard.Rmd | 478 ++------ 194 files changed, 3364 insertions(+), 4274 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo and parallel importance sampling type weighted
Markov chain Monte Carlo. Gaussian, Poisson, binomial, or negative binomial
observation densities, stochastic volatility models with Gaussian state
dynamics, as well as general non-linear Gaussian models and discretised diffusion models
are supported.
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.1-1 dated 2017-07-12 and 0.1.2 dated 2017-11-22
bssm-0.1.1-1/bssm/inst/doc/bssm.html |only bssm-0.1.1-1/bssm/inst/doc/growth_model.html |only bssm-0.1.1-1/bssm/src/function_pointers.h |only bssm-0.1.1-1/bssm/src/mgn_ssm.h |only bssm-0.1.1-1/bssm/src/weighted_obm.cpp |only bssm-0.1.2/bssm/DESCRIPTION | 19 bssm-0.1.2/bssm/MD5 | 189 - bssm-0.1.2/bssm/NAMESPACE | 12 bssm-0.1.2/bssm/NEWS | 16 bssm-0.1.2/bssm/R/RcppExports.R | 194 + bssm-0.1.2/bssm/R/bootstrap_filter.R | 48 bssm-0.1.2/bssm/R/initial_signal.R | 10 bssm-0.1.2/bssm/R/kfilter.R | 17 bssm-0.1.2/bssm/R/loglik.R | 11 bssm-0.1.2/bssm/R/models.R | 493 +++- bssm-0.1.2/bssm/R/particle_smoother.R | 34 bssm-0.1.2/bssm/R/predict.R | 256 +- bssm-0.1.2/bssm/R/print_mcmc.R | 90 bssm-0.1.2/bssm/R/run_mcmc.R | 632 ++++- bssm-0.1.2/bssm/R/sim_smoother.R | 15 bssm-0.1.2/bssm/R/smoother.R | 15 bssm-0.1.2/bssm/build/vignette.rds |binary bssm-0.1.2/bssm/inst/CITATION | 6 bssm-0.1.2/bssm/inst/doc/bssm.R | 14 bssm-0.1.2/bssm/inst/doc/bssm.Rmd | 33 bssm-0.1.2/bssm/inst/doc/bssm.pdf |only bssm-0.1.2/bssm/inst/doc/growth_model.R | 20 bssm-0.1.2/bssm/inst/doc/growth_model.Rmd | 50 bssm-0.1.2/bssm/inst/doc/growth_model.pdf |only bssm-0.1.2/bssm/man/bootstrap_filter.Rd | 6 bssm-0.1.2/bssm/man/bsm.Rd | 16 bssm-0.1.2/bssm/man/gssm.Rd | 2 bssm-0.1.2/bssm/man/lgg_ssm.Rd |only bssm-0.1.2/bssm/man/mv_gssm.Rd | 6 bssm-0.1.2/bssm/man/ng_ar1.Rd |only bssm-0.1.2/bssm/man/ng_bsm.Rd | 16 bssm-0.1.2/bssm/man/ngssm.Rd | 8 bssm-0.1.2/bssm/man/nlg_ssm.Rd | 16 bssm-0.1.2/bssm/man/particle_smoother.Rd | 6 bssm-0.1.2/bssm/man/predict.Rd | 17 bssm-0.1.2/bssm/man/run_mcmc.Rd | 4 bssm-0.1.2/bssm/man/run_mcmc_g.Rd | 17 bssm-0.1.2/bssm/man/run_mcmc_ng.Rd | 89 bssm-0.1.2/bssm/man/sde_ssm.Rd |only bssm-0.1.2/bssm/man/summary.mcmc_output.Rd | 8 bssm-0.1.2/bssm/man/svm.Rd | 14 bssm-0.1.2/bssm/src/R_approx.cpp | 21 bssm-0.1.2/bssm/src/R_auxiliary_filter.cpp | 52 bssm-0.1.2/bssm/src/R_bootstrap_filter.cpp | 40 bssm-0.1.2/bssm/src/R_ekf.cpp | 62 bssm-0.1.2/bssm/src/R_ekpf.cpp | 40 bssm-0.1.2/bssm/src/R_kfilter.cpp | 49 bssm-0.1.2/bssm/src/R_loglik.cpp | 66 bssm-0.1.2/bssm/src/R_mcmc.cpp | 468 +++- bssm-0.1.2/bssm/src/R_milstein.cpp |only bssm-0.1.2/bssm/src/R_predict.cpp | 86 bssm-0.1.2/bssm/src/R_psi.cpp | 68 bssm-0.1.2/bssm/src/R_sde.cpp |only bssm-0.1.2/bssm/src/R_sde_state_sampler.cpp |only bssm-0.1.2/bssm/src/R_smoother.cpp | 72 bssm-0.1.2/bssm/src/R_ukf.cpp | 20 bssm-0.1.2/bssm/src/RcppExports.cpp | 1049 ++++++--- bssm-0.1.2/bssm/src/bssm.h | 4 bssm-0.1.2/bssm/src/conditional_dist.cpp | 8 bssm-0.1.2/bssm/src/dmvnorm.cpp | 6 bssm-0.1.2/bssm/src/lgg_ssm.cpp |only bssm-0.1.2/bssm/src/lgg_ssm.h |only bssm-0.1.2/bssm/src/mcmc.cpp | 1062 ++++++---- bssm-0.1.2/bssm/src/mcmc.h | 24 bssm-0.1.2/bssm/src/mgg_ssm.cpp | 461 ++-- bssm-0.1.2/bssm/src/mgg_ssm.h | 6 bssm-0.1.2/bssm/src/milstein.cpp |only bssm-0.1.2/bssm/src/milstein_functions.h |only bssm-0.1.2/bssm/src/ng_loglik.cpp | 2 bssm-0.1.2/bssm/src/ng_loglik.h | 2 bssm-0.1.2/bssm/src/nlg_amcmc.cpp | 639 +++--- bssm-0.1.2/bssm/src/nlg_amcmc.h | 32 bssm-0.1.2/bssm/src/nlg_ssm.cpp | 872 ++++---- bssm-0.1.2/bssm/src/nlg_ssm.h | 70 bssm-0.1.2/bssm/src/psd_chol.cpp | 4 bssm-0.1.2/bssm/src/rep_mat.cpp | 26 bssm-0.1.2/bssm/src/rep_mat.h | 3 bssm-0.1.2/bssm/src/sde_amcmc.cpp |only bssm-0.1.2/bssm/src/sde_amcmc.h |only bssm-0.1.2/bssm/src/sde_ssm.cpp |only bssm-0.1.2/bssm/src/sde_ssm.h |only bssm-0.1.2/bssm/src/ugg_ssm.cpp | 208 - bssm-0.1.2/bssm/src/ugg_ssm.h | 5 bssm-0.1.2/bssm/src/ung_amcmc.cpp | 726 +++--- bssm-0.1.2/bssm/src/ung_amcmc.h | 42 bssm-0.1.2/bssm/src/ung_ar1.cpp |only bssm-0.1.2/bssm/src/ung_ar1.h |only bssm-0.1.2/bssm/src/ung_ssm.cpp | 310 +- bssm-0.1.2/bssm/src/ung_ssm.h | 4 bssm-0.1.2/bssm/tests/testthat/bsf_reference/bsf_binomial_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/bsf_reference/bsf_gssm_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/bsf_reference/bsf_nbinomial_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/bsf_reference/bsf_poisson_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/bsf_reference/bsf_svm_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/mcmc_reference/mcmc_bsm_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/mcmc_reference/mcmc_poisson_ref.rda |binary bssm-0.1.2/bssm/tests/testthat/mcmc_reference/mcmc_smv_ref.rda |only bssm-0.1.2/bssm/tests/testthat/test_mcmc.R | 14 bssm-0.1.2/bssm/vignettes/bssm.Rmd | 33 bssm-0.1.2/bssm/vignettes/bssm.bib | 18 bssm-0.1.2/bssm/vignettes/growth_model.Rmd | 50 bssm-0.1.2/bssm/vignettes/growth_model_functions.cpp | 19 bssm-0.1.2/bssm/vignettes/sde_functions.cpp |only 108 files changed, 5653 insertions(+), 3489 deletions(-)
Title: Multivariate Information Inductive Causation
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Verny et al. Plos Comput Biol. (2017) <doi:10.1371/journal.pcbi.1005662>.
Author: Nadir Sella [aut, cre],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Nadir Sella <nadir.sella@curie.fr>
Diff between miic versions 0.1 dated 2017-10-09 and 1.0 dated 2017-11-22
miic-0.1/miic/src/skeleton.h |only miic-1.0/miic/DESCRIPTION | 10 - miic-1.0/miic/MD5 | 43 +++--- miic-1.0/miic/R/evaluate_efn.R | 25 ++- miic-1.0/miic/R/miic.R | 48 +++++-- miic-1.0/miic/R/miic.orient.R | 25 --- miic-1.0/miic/R/miic.skeleton.R | 64 ++++++--- miic-1.0/miic/R/miic.utils.R | 4 miic-1.0/miic/man/miic.Rd | 10 - miic-1.0/miic/src/computeEnsInformation.cpp | 50 +++---- miic-1.0/miic/src/computeInfo.cpp | 34 ++--- miic-1.0/miic/src/computeInfo_interface.cpp | 147 +++++++++------------- miic-1.0/miic/src/confidenceCut.cpp | 22 +-- miic-1.0/miic/src/crosscorrelation.cpp | 13 + miic-1.0/miic/src/miic_init.c | 8 - miic-1.0/miic/src/orientationProbability.cpp | 42 +----- miic-1.0/miic/src/probaOrientation.cpp | 15 +- miic-1.0/miic/src/skeleton.cpp | 99 ++++++++++----- miic-1.0/miic/src/skeletonInitialization.cpp | 15 -- miic-1.0/miic/src/skeletonIteration.cpp | 9 - miic-1.0/miic/src/structure.h | 9 + miic-1.0/miic/src/utilities.cpp | 177 ++++++++++++++++++--------- miic-1.0/miic/src/utilities.h | 2 23 files changed, 481 insertions(+), 390 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.6 dated 2016-07-29 and 0.3.7 dated 2017-11-22
DESCRIPTION | 8 +-- MD5 | 73 +++++++++++++++------------- R/convertDVH.R | 104 +++++++++++++++++++---------------------- R/getEUD.R | 19 +++++-- R/getMetric.R | 38 ++++++++++++--- R/parseConstraint.R | 2 R/parseEclipse.R | 51 +++++++++++++++----- R/parseMetric.R | 6 +- R/parsePRIMO.R |only R/parsePRIMO_v015.R |only R/parsePinnacleDVH.R | 4 + R/parseProSoma.R |only R/readDVH.R | 18 +++---- R/showConstraint.R | 39 +++++++++++---- R/showDVH.R | 116 ++++++++++++++++++++++++++++++++-------------- R/unitConversion.R | 38 +++++++++++---- R/unix/parseDVH.R | 22 ++++++-- R/windows/parseDVH.R | 20 ++++++- build/vignette.rds |binary data/dataConstr.rda |binary data/dataMZ.rda |binary inst/ChangeLog | 18 ++++++- inst/DVHshiny/ABOUT.md | 9 +-- inst/DVHshiny/server.R | 83 ++++++++++++++++++++++++++------ inst/DVHshiny/ui.R | 2 inst/doc/DVHmetrics.Rnw | 2 inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 6 +- inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 6 +- man/dataConstr.Rd | 4 - man/getEQD2.Rd | 4 - man/getMetric.Rd | 2 man/readDVH.Rd | 19 +++++-- man/showConstraint.Rd | 19 +++++-- man/showDVH.Rd | 22 +++++--- vignettes/DVHmetrics.Rnw | 2 vignettes/DVHshiny.Rnw | 6 +- vignettes/lit.bib | 39 +++++++-------- 39 files changed, 532 insertions(+), 269 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-11 0.8.0
2017-08-28 0.7.0
Title: A Structural Equation Embedded Likelihood Framework for Causal
Discovery
Description: Provides the SELF criteria to learn causal structure. Please cite "Ruichu Cai, Jie Qiao, Zhenjie Zhang, Zhifeng Hao. SELF: Structural Equational Embedded Likelihood Framework for Causal Discovery. AAAI. 2018."
Author: Ruichu Cai [ths, aut],
Jie Qiao [aut, cre],
Zhenjie Zhang [ths, aut],
Zhifeng Hao [ths, aut]
Maintainer: Jie Qiao <qiaojie2004@vip.qq.com>
Diff between SELF versions 0.1.0 dated 2017-11-13 and 0.1.1 dated 2017-11-22
DESCRIPTION | 20 ++++++++++---------- MD5 | 21 +++++++++++---------- NEWS.md | 6 ++++++ R/fast_hill_climb.R | 4 ++-- R/utility_functions.R | 21 ++++++++++++--------- inst |only man/SELF-package.Rd | 4 ++-- man/fhc.Rd | 4 ++-- man/indicators.Rd | 4 ++-- man/randomGraph.Rd | 8 +++++--- man/synthetic_data_linear.Rd | 2 +- man/synthetic_data_nonlinear.Rd | 2 +- 12 files changed, 54 insertions(+), 42 deletions(-)
Title: An R Interface to the 'ROPTLIB' Library for Riemannian Manifold
Optimization
Description: An R interface to version 0.3 of the 'ROPTLIB' optimization library
(see <http://www.math.fsu.edu/~whuang2> for more information). Optimize real-
valued functions over manifolds such as Stiefel, Grassmann, and Symmetric
Positive Definite matrices.
Author: Kofi P. Adragni [aut, cph],
Sean R. Martin [aut, cre, cph],
Andrew M. Raim [aut, cph],
Wen Huang [aut, cph]
Maintainer: Sean R. Martin <smarti1@umbc.edu>
Diff between ManifoldOptim versions 0.1.3 dated 2017-03-31 and 0.1.4 dated 2017-11-22
ManifoldOptim-0.1.3/ManifoldOptim/inst/examples/product_rproblem.R |only ManifoldOptim-0.1.3/ManifoldOptim/inst/include/MatrixManifoldOptimProblem.h |only ManifoldOptim-0.1.3/ManifoldOptim/inst/include/VectorManifoldOptimProblem.h |only ManifoldOptim-0.1.4/ManifoldOptim/DESCRIPTION | 24 - ManifoldOptim-0.1.4/ManifoldOptim/MD5 | 64 +-- ManifoldOptim-0.1.4/ManifoldOptim/NAMESPACE | 3 ManifoldOptim-0.1.4/ManifoldOptim/R/ManifoldOptim-package.R | 107 +++++ ManifoldOptim-0.1.4/ManifoldOptim/R/manifold_optim.R | 17 ManifoldOptim-0.1.4/ManifoldOptim/R/params.R | 19 + ManifoldOptim-0.1.4/ManifoldOptim/R/util.R | 8 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/cpp_pkg/driver.R | 6 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/cpp_sourceCpp/driver.R | 35 + ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/cpp_standalone/brockett_problem.cpp | 32 + ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/cpp_standalone/driver.R | 6 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/rproblem/driver-minimal.Rin | 1 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/rproblem/driver-withhessian.R | 6 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/brockett/rproblem/driver.R | 12 ManifoldOptim-0.1.4/ManifoldOptim/inst/examples/normal_mle_sphere |only ManifoldOptim-0.1.4/ManifoldOptim/inst/include/ManifoldOptim.h | 2 ManifoldOptim-0.1.4/ManifoldOptim/inst/include/ManifoldOptimProblem.h | 107 +++++ ManifoldOptim-0.1.4/ManifoldOptim/man/Design-of-C-plus-plus-code.Rd |only ManifoldOptim-0.1.4/ManifoldOptim/man/Problem-definition.Rd | 10 ManifoldOptim-0.1.4/ManifoldOptim/man/get.deriv.params.Rd |only ManifoldOptim-0.1.4/ManifoldOptim/man/manifold.optim.Rd | 15 ManifoldOptim-0.1.4/ManifoldOptim/src/Makevars | 3 ManifoldOptim-0.1.4/ManifoldOptim/src/Makevars.win | 3 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/BrockettProblem.cpp | 36 + ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptim.cpp | 34 - ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptim.h | 13 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ManifoldOptimModule.cpp | 7 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ProblemAdapter.cpp | 188 ---------- ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/ProblemAdapter.h | 16 ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/RProblem.cpp | 39 +- ManifoldOptim-0.1.4/ManifoldOptim/src/ManifoldOptim/RProblem.h | 8 ManifoldOptim-0.1.4/ManifoldOptim/src/MyRcppExports.cpp | 12 ManifoldOptim-0.1.4/ManifoldOptim/src/Others/RegisterDynamicSymbol.cpp |only 36 files changed, 475 insertions(+), 358 deletions(-)
Title: Linear Combination Fitting
Description: Baseline correction, normalization and linear combination fitting (LCF)
of X-ray absorption near edge structure (XANES) spectra.
The package includes data loading of .xmu files exported from 'ATHENA' (Ravel and Newville, 2005) <doi:10.1107/S0909049505012719>.
Loaded spectra can be background corrected and all standards can be fitted at once.
Two linear combination fitting functions can be used:
(1) fit_athena(): Simply fitting combinations of standards as in ATHENA,
(2) fit_float(): Fitting all standards with changing baseline correction and edge-step normalization parameters.
Author: Florian Werner [aut, cre]
Maintainer: Florian Werner <florian.werner@wzw.tum.de>
Diff between LCF versions 1.6-6 dated 2017-02-17 and 1.7.0 dated 2017-11-22
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/LC_fit.R | 2 +- R/initial_load.R | 7 ++++--- R/read_raw_spec.R | 24 +++++++++++++++++++++--- man/LCF_solve_QP.Rd | 1 - man/LC_fit.Rd | 3 +-- man/bkg_corr.Rd | 1 - man/fit_athena.Rd | 1 - man/fit_float.Rd | 1 - man/initial_load.Rd | 7 ++++--- man/plot_LCF.Rd | 1 - man/read_raw_spec.Rd | 7 ++++--- man/specdat.Rd | 1 - man/std_df.Rd | 1 - 15 files changed, 54 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-04 0.1.1
2016-01-04 0.1.2
Title: React Helpers
Description: Make it easy to use 'React' in R with helper
dependency functions, embedded 'Babel' transpiler,
and examples.
Author: Facebook Inc [aut, cph] (React library in lib,
https://facebook.github.io/react; see AUTHORS for full list of
contributors),
Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between reactR versions 0.1.3 dated 2017-10-12 and 0.1.4 dated 2017-11-22
reactR-0.1.3/reactR/inst/www/react/LICENSE |only reactR-0.1.4/reactR/DESCRIPTION | 16 reactR-0.1.4/reactR/LICENSE | 2 reactR-0.1.4/reactR/MD5 | 25 - reactR-0.1.4/reactR/NEWS.md | 4 reactR-0.1.4/reactR/R/meta.R | 2 reactR-0.1.4/reactR/inst/doc/intro_reactR.Rmd | 4 reactR-0.1.4/reactR/inst/doc/intro_reactR.html | 12 reactR-0.1.4/reactR/inst/examples/antd.R | 2 reactR-0.1.4/reactR/inst/examples/office-fabric.R | 64 ++- reactR-0.1.4/reactR/inst/examples/semiotic.R |only reactR-0.1.4/reactR/inst/www/react/LICENSE.txt |only reactR-0.1.4/reactR/inst/www/react/react-dom.min.js | 393 +++++++++----------- reactR-0.1.4/reactR/inst/www/react/react.min.js | 43 +- reactR-0.1.4/reactR/vignettes/intro_reactR.Rmd | 4 15 files changed, 304 insertions(+), 267 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.7 dated 2017-05-18 and 1.8 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/gui.R | 5 ++--- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks (Nowick et al. (2009) <doi:10.1073/pnas.0911376106>) given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between wTO versions 1.4.0 dated 2017-11-12 and 1.4.1 dated 2017-11-22
DESCRIPTION | 6 MD5 | 36 ++-- NAMESPACE | 1 R/Correlation.Overlap.R | 2 R/Cut.off2.R | 1 R/NetVis.R | 326 +++++++++++++++++++++++---------------------- R/sample_ind.R | 1 R/wTO.Complete2.R | 1 R/wTO.Consensus.R | 11 - R/wTO.R | 59 ++++---- R/wTO.in.line.R | 81 +++++------ man/Correlation.Overlap.Rd | 3 man/Cut.off.Rd | 3 man/NetVis.Rd | 3 man/sample_ind.Rd | 3 man/wTO.Complete.Rd | 3 man/wTO.Consensus.Rd | 4 man/wTO.Rd | 3 man/wTO.in.line.Rd | 3 19 files changed, 297 insertions(+), 253 deletions(-)
Title: Dyadic Network Analysis
Description: Contains functions for dyadic network analysis.
Author: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Maintainer: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Diff between dyads versions 1.0 dated 2017-10-10 and 1.1 dated 2017-11-22
DESCRIPTION | 10 - MD5 | 14 + NAMESPACE | 27 ++- R/internalFunctionsDyads.R | 337 ++++++++++++++++++++++++++++++++------------- R/j2.R |only build/partial.rdb |binary man/dyads-package.Rd | 10 - man/j2.Rd |only man/p2.Rd | 7 9 files changed, 286 insertions(+), 119 deletions(-)
Title: Distributions and Gradients
Description: Provides density, distribution function, quantile function and random generation for the split-t distribution, and computes the mean, variance, skewness and kurtosis for the split-t distribution (Li, F, Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
Author: Feng Li, Jiayue Zeng
Maintainer: Jiayue Zeng <zengjiayue@126.com>
Diff between dng versions 0.1.0 dated 2017-09-20 and 0.1.1 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/rcpp_dsplitt.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 2.9 dated 2017-10-16 and 3.0 dated 2017-11-22
DESCRIPTION | 10 +- MD5 | 66 ++++++++-------- NAMESPACE | 2 R/bic.mixvmf.R | 7 - R/circ.cor2.R | 1 R/conc.test.R | 8 - R/cosap.R |only R/dirknn.R | 23 +---- R/embed.circaov.R | 4 R/fishkent.R | 5 - R/ggvm.R | 1 R/hcf.circaov.R | 18 ++-- R/het.aov.R | 10 -- R/het.circaov.R | 6 - R/kent.mle.R | 2 R/knn.reg.R | 3 R/knnreg.tune.R | 182 +++++++-------------------------------------- R/lr.aov.R | 32 +++---- R/lr.circaov.R | 14 +-- R/mix.vmf.R | 68 ++++++---------- R/pvm.R | 5 - R/spherconc.test.R | 1 R/tang.conc.R | 8 - R/vm.kde.R | 6 - R/vmf.kde.R | 3 R/vmfkde.tune.R | 30 +++---- R/vmkde.tune.R | 15 +-- man/Directional-package.Rd | 8 - man/ESAGsim.Rd | 3 man/bic.mixvmf.Rd | 8 - man/circ.cor1.Rd | 8 - man/circlin.cor.Rd | 12 +- man/cosap.Rd |only man/knnreg.tune.Rd | 13 +-- man/matrixfisher.mle.Rd | 7 - 35 files changed, 210 insertions(+), 379 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I', 'APLE', 'Gearys C', 'Hubert/Mantel' general cross
product statistic, Empirical Bayes estimates and 'Assunção/Reis' Index,
'Getis/Ord' G and multicoloured join count statistics, local 'Moran's I'
and 'Getis/Ord' G, 'saddlepoint' approximations and exact tests for global
and local 'Moran's I'; and functions for estimating spatial simultaneous
'autoregressive' ('SAR') lag and error models, impact measures for lag
models, weighted and 'unweighted' 'SAR' and 'CAR' spatial regression models,
semi-parametric and Moran 'eigenvector' spatial filtering, 'GM SAR' error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut] (0000-0003-2392-6140),
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.6-15 dated 2017-09-01 and 0.7-4 dated 2017-11-22
spdep-0.6-15/spdep/data/NY_data.rda |only spdep-0.6-15/spdep/data/afcon.rda |only spdep-0.6-15/spdep/data/auckland.rda |only spdep-0.6-15/spdep/data/baltimore.rda |only spdep-0.6-15/spdep/data/boston.rda |only spdep-0.6-15/spdep/data/datalist |only spdep-0.6-15/spdep/data/elect80.rda |only spdep-0.6-15/spdep/data/getisord.rda |only spdep-0.6-15/spdep/data/hopkins.rda |only spdep-0.6-15/spdep/data/house.RData |only spdep-0.6-15/spdep/data/huddersfield.rda |only spdep-0.6-15/spdep/data/nc.sids.rda |only spdep-0.6-15/spdep/data/used.cars.rda |only spdep-0.6-15/spdep/data/wheat.rda |only spdep-0.6-15/spdep/inst/README |only spdep-0.6-15/spdep/inst/etc/shapes/NY8_utm18.dbf |only spdep-0.6-15/spdep/inst/etc/shapes/NY8_utm18.prj |only spdep-0.6-15/spdep/inst/etc/shapes/NY8_utm18.shp |only spdep-0.6-15/spdep/inst/etc/shapes/NY8_utm18.shx |only spdep-0.6-15/spdep/inst/etc/shapes/auckland.dbf |only spdep-0.6-15/spdep/inst/etc/shapes/auckland.shp |only spdep-0.6-15/spdep/inst/etc/shapes/auckland.shx |only spdep-0.6-15/spdep/inst/etc/shapes/boston_tracts.dbf |only spdep-0.6-15/spdep/inst/etc/shapes/boston_tracts.prj |only spdep-0.6-15/spdep/inst/etc/shapes/boston_tracts.shp |only spdep-0.6-15/spdep/inst/etc/shapes/boston_tracts.shx |only spdep-0.6-15/spdep/inst/etc/shapes/sids.dbf |only spdep-0.6-15/spdep/inst/etc/shapes/sids.shp |only spdep-0.6-15/spdep/inst/etc/shapes/sids.shx |only spdep-0.6-15/spdep/inst/etc/shapes/wheat.dbf |only spdep-0.6-15/spdep/inst/etc/shapes/wheat.shp |only spdep-0.6-15/spdep/inst/etc/shapes/wheat.shx |only spdep-0.6-15/spdep/inst/etc/weights/NY_nb.gal |only spdep-0.6-15/spdep/inst/etc/weights/baltk4.GWT |only spdep-0.6-15/spdep/inst/etc/weights/ncCC89.gal |only spdep-0.6-15/spdep/inst/etc/weights/ncCR85.gal |only spdep-0.6-15/spdep/man/NY_data.Rd |only spdep-0.6-15/spdep/man/afcon.Rd |only spdep-0.6-15/spdep/man/auckland.Rd |only spdep-0.6-15/spdep/man/baltimore.Rd |only spdep-0.6-15/spdep/man/boston.Rd |only spdep-0.6-15/spdep/man/elect80.Rd |only spdep-0.6-15/spdep/man/getisord.Rd |only spdep-0.6-15/spdep/man/hopkins.Rd |only spdep-0.6-15/spdep/man/house.Rd |only spdep-0.6-15/spdep/man/huddersfield.Rd |only spdep-0.6-15/spdep/man/nc.sids.Rd |only spdep-0.6-15/spdep/man/used.cars.Rd |only spdep-0.6-15/spdep/man/wheat.Rd |only spdep-0.7-4/spdep/ChangeLog | 116 ++++++++ spdep-0.7-4/spdep/DESCRIPTION | 43 +-- spdep-0.7-4/spdep/MD5 | 267 +++++++------------ spdep-0.7-4/spdep/NAMESPACE | 1 spdep-0.7-4/spdep/R/globalG.R | 39 +- spdep-0.7-4/spdep/R/localG.R | 19 - spdep-0.7-4/spdep/R/localmoran.R | 36 +- spdep-0.7-4/spdep/R/nb2lines.R | 4 spdep-0.7-4/spdep/R/sp.mantel.R | 2 spdep-0.7-4/spdep/build/vignette.rds |binary spdep-0.7-4/spdep/inst/CITATION | 2 spdep-0.7-4/spdep/inst/ChangeLog | 116 ++++++++ spdep-0.7-4/spdep/inst/doc/CO69.R | 97 +++--- spdep-0.7-4/spdep/inst/doc/CO69.Rnw | 13 spdep-0.7-4/spdep/inst/doc/CO69.pdf |binary spdep-0.7-4/spdep/inst/doc/SpatialFiltering.R | 14 spdep-0.7-4/spdep/inst/doc/SpatialFiltering.Rnw | 14 spdep-0.7-4/spdep/inst/doc/SpatialFiltering.pdf |binary spdep-0.7-4/spdep/inst/doc/nb.R | 14 spdep-0.7-4/spdep/inst/doc/nb.Rnw | 14 spdep-0.7-4/spdep/inst/doc/nb.pdf |binary spdep-0.7-4/spdep/inst/doc/nb_igraph.R | 70 ++-- spdep-0.7-4/spdep/inst/doc/nb_igraph.Rmd | 69 ++-- spdep-0.7-4/spdep/inst/doc/nb_igraph.html | 41 ++ spdep-0.7-4/spdep/inst/doc/nb_sf.R |only spdep-0.7-4/spdep/inst/doc/nb_sf.Rmd |only spdep-0.7-4/spdep/inst/doc/nb_sf.html |only spdep-0.7-4/spdep/inst/doc/sids.R | 98 +++--- spdep-0.7-4/spdep/inst/doc/sids.Rnw | 18 - spdep-0.7-4/spdep/inst/doc/sids.pdf |binary spdep-0.7-4/spdep/man/EBImoran.mc.Rd | 4 spdep-0.7-4/spdep/man/EBest.Rd | 17 - spdep-0.7-4/spdep/man/EBlocal.Rd | 16 - spdep-0.7-4/spdep/man/GMerrorsar.Rd | 6 spdep-0.7-4/spdep/man/LR.sarlm.Rd | 4 spdep-0.7-4/spdep/man/MCMCsamp.Rd | 4 spdep-0.7-4/spdep/man/ME.Rd | 8 spdep-0.7-4/spdep/man/SpatialFiltering.Rd | 6 spdep-0.7-4/spdep/man/aggregate.nb.Rd | 2 spdep-0.7-4/spdep/man/anova.sarlm.Rd | 4 spdep-0.7-4/spdep/man/aple.Rd | 4 spdep-0.7-4/spdep/man/aple.mc.Rd | 2 spdep-0.7-4/spdep/man/aple.plot.Rd | 2 spdep-0.7-4/spdep/man/autocov_dist.Rd | 5 spdep-0.7-4/spdep/man/bhicv.Rd | 5 spdep-0.7-4/spdep/man/bptest.sarlm.Rd | 2 spdep-0.7-4/spdep/man/card.Rd | 6 spdep-0.7-4/spdep/man/choynowski.Rd | 4 spdep-0.7-4/spdep/man/columbus.Rd | 60 ---- spdep-0.7-4/spdep/man/compon.Rd | 4 spdep-0.7-4/spdep/man/diffnb.Rd | 4 spdep-0.7-4/spdep/man/dnearneigh.Rd | 4 spdep-0.7-4/spdep/man/do_ldet.Rd | 2 spdep-0.7-4/spdep/man/edit.nb.Rd | 5 spdep-0.7-4/spdep/man/eire.Rd | 89 ------ spdep-0.7-4/spdep/man/errorsarlm.Rd | 2 spdep-0.7-4/spdep/man/globalG.test.Rd | 8 spdep-0.7-4/spdep/man/graphneigh.Rd | 4 spdep-0.7-4/spdep/man/gstsls.Rd | 2 spdep-0.7-4/spdep/man/impacts.sarlm.Rd | 12 spdep-0.7-4/spdep/man/include.self.Rd | 4 spdep-0.7-4/spdep/man/joincount.multi.Rd | 2 spdep-0.7-4/spdep/man/knearneigh.Rd | 4 spdep-0.7-4/spdep/man/knn2nb.Rd | 4 spdep-0.7-4/spdep/man/lagmess.Rd | 6 spdep-0.7-4/spdep/man/lagsarlm.Rd | 6 spdep-0.7-4/spdep/man/lee.Rd | 2 spdep-0.7-4/spdep/man/lee.mc.Rd | 2 spdep-0.7-4/spdep/man/lee.test.Rd | 2 spdep-0.7-4/spdep/man/lextrB.Rd | 4 spdep-0.7-4/spdep/man/listw2sn.Rd | 2 spdep-0.7-4/spdep/man/lm.morantest.exact.Rd | 9 spdep-0.7-4/spdep/man/lm.morantest.sad.Rd | 9 spdep-0.7-4/spdep/man/localG.Rd | 5 spdep-0.7-4/spdep/man/localmoran.Rd | 7 spdep-0.7-4/spdep/man/localmoran.exact.Rd | 9 spdep-0.7-4/spdep/man/localmoran.sad.Rd | 9 spdep-0.7-4/spdep/man/mat2listw.Rd | 4 spdep-0.7-4/spdep/man/moran.plot.Rd | 2 spdep-0.7-4/spdep/man/nb2INLA.Rd | 4 spdep-0.7-4/spdep/man/nb2WB.Rd | 4 spdep-0.7-4/spdep/man/nb2blocknb.Rd | 2 spdep-0.7-4/spdep/man/nb2lines.Rd | 11 spdep-0.7-4/spdep/man/nb2listw.Rd | 6 spdep-0.7-4/spdep/man/nb2mat.Rd | 5 spdep-0.7-4/spdep/man/nbdists.Rd | 5 spdep-0.7-4/spdep/man/nblag.Rd | 5 spdep-0.7-4/spdep/man/nboperations.Rd | 4 spdep-0.7-4/spdep/man/p.adjustSP.Rd | 2 spdep-0.7-4/spdep/man/plot.nb.Rd | 5 spdep-0.7-4/spdep/man/poly2nb.Rd | 6 spdep-0.7-4/spdep/man/probmap.Rd | 37 +- spdep-0.7-4/spdep/man/read.gwt2nb.Rd | 4 spdep-0.7-4/spdep/man/sacsarlm.Rd | 2 spdep-0.7-4/spdep/man/set.spChkOption.Rd | 2 spdep-0.7-4/spdep/man/skater.Rd | 2 spdep-0.7-4/spdep/man/sp.correlogram.Rd | 4 spdep-0.7-4/spdep/man/spautolm.Rd | 14 spdep-0.7-4/spdep/man/stsls.Rd | 4 spdep-0.7-4/spdep/man/subset.listw.Rd | 5 spdep-0.7-4/spdep/man/subset.nb.Rd | 5 spdep-0.7-4/spdep/man/summary.nb.Rd | 5 spdep-0.7-4/spdep/man/testnb.Rd | 5 spdep-0.7-4/spdep/man/trW.Rd | 6 spdep-0.7-4/spdep/man/tri2nb.Rd | 5 spdep-0.7-4/spdep/man/write.nb.gal.Rd | 5 spdep-0.7-4/spdep/vignettes/CO69.Rnw | 13 spdep-0.7-4/spdep/vignettes/SpatialFiltering.Rnw | 14 spdep-0.7-4/spdep/vignettes/nb.Rnw | 14 spdep-0.7-4/spdep/vignettes/nb_igraph.Rmd | 69 ++-- spdep-0.7-4/spdep/vignettes/nb_sf.Rmd |only spdep-0.7-4/spdep/vignettes/sids.Rnw | 18 - 161 files changed, 1035 insertions(+), 753 deletions(-)
Title: Solving Ordinary Differential Equations to Understand
Luminescence
Description: A collection of functions to simulate luminescence signals in quartz and Al2O3 based on published models.
Author: Johannes Friedrich [aut, trl, cre],
Sebastian Kreutzer [aut, ths],
Christoph Schmidt [aut, ths]
Maintainer: Johannes Friedrich <johannes.friedrich@uni-bayreuth.de>
Diff between RLumModel versions 0.2.2 dated 2017-10-13 and 0.2.3 dated 2017-11-22
DESCRIPTION | 8 +- MD5 | 41 ++++++----- NEWS.md | 15 ++++ R/RLumModel-package.R | 2 R/create_DRT.sequence.R | 4 - R/create_SAR.sequence.R | 24 +++--- R/model_LuminescenceSignals.R | 45 ++++++------- R/set_pars.R | 35 +++++++++- R/simulate_RF.R | 13 ++- R/simulate_RF_and_heating.R | 8 ++ R/simulate_irradiation.R | 10 ++ inst/doc/RLumModel_-_Getting_started_with_RLumModel.html | 8 +- inst/doc/RLumModel_-_Simulating_luminescence_in_Al2O3.html | 4 - inst/doc/RLumModel_-_Using_own_parameter_sets.html | 4 - man/RLumModel-package.Rd | 2 man/model_LuminescenceSignals.Rd | 4 - man/read_SEQ2R.Rd | 2 tests/testthat/test-model_LuminescenceSignals.R | 25 ++++++- tests/testthat/test-own-parameter-sets.R |only tests/testthat/test-simulate_RF.R | 26 +++++++ tests/testthat/test-simulate_RF_and_heating.R | 27 +++++++ tests/testthat/test-simulate_irradiation.R | 9 ++ 22 files changed, 232 insertions(+), 84 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joeseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <mail@richard-schuster.com>
Diff between prioritizr versions 3.0.1 dated 2017-11-08 and 3.0.3 dated 2017-11-22
DESCRIPTION | 6 MD5 | 86 +-- R/ArrayParameter-proto.R | 2 R/add_default_solver.R | 16 R/add_gurobi_solver.R | 11 R/add_lpsymphony_solver.R | 25 R/add_rsymphony_solver.R | 20 R/internal.R | 37 + R/solvers.R | 4 README.md | 8 inst/doc/gurobi_installation.Rmd | 2 inst/doc/gurobi_installation.html | 424 ++++++++++----- inst/doc/prioritizr_basics.Rmd | 2 inst/doc/prioritizr_basics.html | 390 +++++++++----- inst/doc/publication_record.Rmd | 2 inst/doc/publication_record.html | 276 ++++++---- inst/doc/quick_start.Rmd | 2 inst/doc/quick_start.html | 612 +++++++++++++---------- man/add_gurobi_solver.Rd | 7 man/add_lsymphony_solver.Rd | 14 man/add_rsymphony_solver.Rd | 14 man/solvers.Rd | 4 tests/testthat/test_add_boundary_penalties.R | 2 tests/testthat/test_add_connected_constraints.R | 3 tests/testthat/test_add_connectivity_penalties.R | 2 tests/testthat/test_add_corridor_constraints.R | 3 tests/testthat/test_add_cuts_portfolio.R | 3 tests/testthat/test_add_locked_in_constraints.R | 4 tests/testthat/test_add_locked_out_constraints.R | 8 tests/testthat/test_add_max_cover_objective.R | 11 tests/testthat/test_add_max_features_objective.R | 8 tests/testthat/test_add_max_phylo_objective.R | 10 tests/testthat/test_add_max_utility_objective.R | 8 tests/testthat/test_add_min_set_objective.R | 8 tests/testthat/test_add_neighbor_constraints.R | 3 tests/testthat/test_add_shuffle_portfolio.R | 5 tests/testthat/test_decisions.R | 3 tests/testthat/test_marxan_problem.R | 5 tests/testthat/test_solve.R | 12 tests/testthat/test_solvers.R | 2 vignettes/gurobi_installation.Rmd | 2 vignettes/prioritizr_basics.Rmd | 2 vignettes/publication_record.Rmd | 2 vignettes/quick_start.Rmd | 2 44 files changed, 1317 insertions(+), 755 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, particle filtering, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <http://r-nimble.org>.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-Bergman, Nick Michaud, Fritz Obermeyer, Duncan Temple Lang, and see AUTHORS file for additional contributors.
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6-7 dated 2017-11-15 and 0.6-8 dated 2017-11-22
nimble-0.6-7/nimble/inst/make/Makevars |only nimble-0.6-7/nimble/inst/make/Makevars_lib |only nimble-0.6-8/nimble/DESCRIPTION | 8 ++++---- nimble-0.6-8/nimble/INSTALL | 6 +++--- nimble-0.6-8/nimble/MD5 | 22 ++++++++++------------ nimble-0.6-8/nimble/NEWS | 4 +++- nimble-0.6-8/nimble/R/MCMC_samplers.R | 2 +- nimble-0.6-8/nimble/R/options.R | 2 ++ nimble-0.6-8/nimble/man/nimbleMCMC.Rd | 9 +++++---- nimble-0.6-8/nimble/man/runCrossValidate.Rd | 14 +++++++------- nimble-0.6-8/nimble/man/runMCMC.Rd | 8 ++++---- nimble-0.6-8/nimble/man/withNimbleOptions.Rd | 2 ++ nimble-0.6-8/nimble/src/Makevars.in | 2 +- 13 files changed, 42 insertions(+), 37 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.3 dated 2017-05-21 and 5.4 dated 2017-11-22
mclust-5.3/mclust/inst/doc/index.html |only mclust-5.3/mclust/inst/doc/mclust-weights.pdf |only mclust-5.3/mclust/inst/doc/mclust4.pdf |only mclust-5.4/mclust/DESCRIPTION | 8 mclust-5.4/mclust/MD5 | 213 +-- mclust-5.4/mclust/R/bootstrap.R | 154 -- mclust-5.4/mclust/R/densityMclust.R | 22 mclust-5.4/mclust/R/gmmhd.R | 40 mclust-5.4/mclust/R/init.R | 2 mclust-5.4/mclust/R/mclust.R | 841 ++++---------- mclust-5.4/mclust/R/options.R | 9 mclust-5.4/mclust/R/toremove.R |only mclust-5.4/mclust/R/util.R | 40 mclust-5.4/mclust/R/zzz.R | 31 mclust-5.4/mclust/build/vignette.rds |binary mclust-5.4/mclust/data/Baudry_etal_2010_JCGS_examples.rda |binary mclust-5.4/mclust/data/GvHD.rda |binary mclust-5.4/mclust/data/acidity.rda |binary mclust-5.4/mclust/data/chevron.rda |binary mclust-5.4/mclust/data/cross.rda |binary mclust-5.4/mclust/data/diabetes.rda |binary mclust-5.4/mclust/data/thyroid.rda |binary mclust-5.4/mclust/data/wreath.rda |binary mclust-5.4/mclust/inst/CITATION | 57 mclust-5.4/mclust/inst/NEWS | 21 mclust-5.4/mclust/inst/doc/mclust.R | 75 - mclust-5.4/mclust/inst/doc/mclust.Rmd | 128 +- mclust-5.4/mclust/inst/doc/mclust.html | 434 ++++--- mclust-5.4/mclust/man/Mclust.Rd | 28 mclust-5.4/mclust/man/MclustDA.Rd | 20 mclust-5.4/mclust/man/MclustDR.Rd | 11 mclust-5.4/mclust/man/MclustDRsubsel.Rd | 6 mclust-5.4/mclust/man/adjustedRandIndex.Rd | 5 mclust-5.4/mclust/man/bic.Rd | 13 mclust-5.4/mclust/man/cdens.Rd | 10 mclust-5.4/mclust/man/cdensE.Rd | 10 mclust-5.4/mclust/man/cdfMclust.Rd | 7 mclust-5.4/mclust/man/clPairs.Rd | 19 mclust-5.4/mclust/man/classError.Rd | 7 mclust-5.4/mclust/man/combMat.Rd | 3 mclust-5.4/mclust/man/coordProj.Rd | 19 mclust-5.4/mclust/man/covw.Rd | 1 mclust-5.4/mclust/man/cvMclustDA.Rd | 13 mclust-5.4/mclust/man/decomp2sigma.Rd | 9 mclust-5.4/mclust/man/defaultPrior.Rd | 11 mclust-5.4/mclust/man/dens.Rd | 9 mclust-5.4/mclust/man/densityMclust.Rd | 15 mclust-5.4/mclust/man/densityMclust.diagnostic.Rd | 10 mclust-5.4/mclust/man/em.Rd | 19 mclust-5.4/mclust/man/emControl.Rd | 10 mclust-5.4/mclust/man/emE.Rd | 19 mclust-5.4/mclust/man/estep.Rd | 10 mclust-5.4/mclust/man/estepE.Rd | 10 mclust-5.4/mclust/man/hc.Rd | 7 mclust-5.4/mclust/man/hcE.Rd | 7 mclust-5.4/mclust/man/hclass.Rd | 6 mclust-5.4/mclust/man/hypvol.Rd | 8 mclust-5.4/mclust/man/icl.Rd | 9 mclust-5.4/mclust/man/imputeData.Rd | 4 mclust-5.4/mclust/man/imputePairs.Rd | 9 mclust-5.4/mclust/man/logLik.Mclust.Rd | 11 mclust-5.4/mclust/man/logLik.MclustDA.Rd | 11 mclust-5.4/mclust/man/map.Rd | 14 mclust-5.4/mclust/man/mclust-package.Rd | 21 mclust-5.4/mclust/man/mclust.options.Rd | 28 mclust-5.4/mclust/man/mclust1Dplot.Rd | 18 mclust-5.4/mclust/man/mclust2Dplot.Rd | 17 mclust-5.4/mclust/man/mclustBIC.Rd | 31 mclust-5.4/mclust/man/mclustICL.Rd | 13 mclust-5.4/mclust/man/mclustModel.Rd | 10 mclust-5.4/mclust/man/mclustModelNames.Rd | 10 mclust-5.4/mclust/man/mclustVariance.Rd | 9 mclust-5.4/mclust/man/me.Rd | 18 mclust-5.4/mclust/man/me.weighted.Rd | 19 mclust-5.4/mclust/man/meE.Rd | 18 mclust-5.4/mclust/man/mstep.Rd | 9 mclust-5.4/mclust/man/mstepE.Rd | 10 mclust-5.4/mclust/man/mvn.Rd | 10 mclust-5.4/mclust/man/mvnX.Rd | 12 mclust-5.4/mclust/man/nMclustParams.Rd | 10 mclust-5.4/mclust/man/nVarParams.Rd | 2 mclust-5.4/mclust/man/plot.Mclust.Rd | 11 mclust-5.4/mclust/man/plot.MclustDA.Rd | 11 mclust-5.4/mclust/man/plot.MclustDR.Rd | 5 mclust-5.4/mclust/man/plot.densityMclust.Rd | 11 mclust-5.4/mclust/man/plot.mclustBIC.Rd | 10 mclust-5.4/mclust/man/plot.mclustICL.Rd | 7 mclust-5.4/mclust/man/predict.Mclust.Rd | 11 mclust-5.4/mclust/man/predict.MclustDA.Rd | 11 mclust-5.4/mclust/man/predict.MclustDR.Rd | 5 mclust-5.4/mclust/man/predict.densityMclust.Rd | 25 mclust-5.4/mclust/man/priorControl.Rd | 16 mclust-5.4/mclust/man/randProj.Rd | 18 mclust-5.4/mclust/man/randomPairs.Rd | 7 mclust-5.4/mclust/man/sigma2decomp.Rd | 9 mclust-5.4/mclust/man/sim.Rd | 9 mclust-5.4/mclust/man/simE.Rd | 13 mclust-5.4/mclust/man/summary.Mclust.Rd | 11 mclust-5.4/mclust/man/summary.MclustBootstrap.Rd | 6 mclust-5.4/mclust/man/summary.MclustDA.Rd | 11 mclust-5.4/mclust/man/summary.MclustDR.Rd | 3 mclust-5.4/mclust/man/summary.mclustBIC.Rd | 10 mclust-5.4/mclust/man/surfacePlot.Rd | 16 mclust-5.4/mclust/man/uncerPlot.Rd | 11 mclust-5.4/mclust/man/unmap.Rd | 10 mclust-5.4/mclust/man/wreath.Rd | 9 mclust-5.4/mclust/src/init.c | 7 mclust-5.4/mclust/src/mclustaddson.f | 16 mclust-5.4/mclust/vignettes/mclust.Rmd | 128 +- mclust-5.4/mclust/vignettes/vignette.css |only 110 files changed, 1197 insertions(+), 1940 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 1.1.4 dated 2017-10-23 and 1.2.0 dated 2017-11-22
CHANGELOG | 11 ++++++- DESCRIPTION | 10 +++--- MD5 | 65 ++++++++++++++++++++++++------------------- NAMESPACE | 8 ++++- R/ClasGenMetDef.R | 21 ++++++++++++-- R/IData.R | 16 +++++----- R/IdtMclust_methods.R |only R/Idtmclust.R |only R/fasttle.R | 67 +++++++++++++++++++++++++++------------------ R/fulltle.R | 46 ++++++++++++++++-------------- R/mle.R | 3 ++ data/Cars.RData |binary man/EMControl-class.Rd |only man/EMControl.Rd |only man/IData-class.Rd | 3 -- man/IData.Rd | 4 -- man/IdtE-class.Rd | 6 +--- man/IdtMclust-class.Rd |only man/IdtMxNDRE-class.Rd | 3 -- man/IdtMxSNDE-class.Rd | 2 + man/IdtSngNDRE-class.Rd | 3 -- man/Idtmclust-methods.Rd |only man/MAINT.Data-package.Rd | 44 ++++++++++++++++++++++------- man/RepLOptim.Rd | 38 ++++++++++++------------- man/RobEstControl-class.Rd | 9 ++---- man/RobEstControl.Rd | 14 ++++----- man/RobMxtDEst-methods.Rd | 7 ++-- man/Robda-methods.Rd | 4 +- man/fasttle-methods.Rd | 6 ++-- man/fulltle-methods.Rd | 25 ++++------------ man/getIdtOutl.Rd | 8 +++-- man/lda-methods.Rd | 5 ++- man/mle-methods.Rd | 6 ++-- man/qda-methods.Rd | 2 + man/snda-methods.Rd | 2 + man/summary-methods.Rd |only man/vcov-methods.Rd | 5 ++- 37 files changed, 257 insertions(+), 186 deletions(-)
Title: Systematic Analysis of Architectural Proteins and Functional
Elements in Blocking Long-Range Contacts Between Loci
Description: Here we propose a model to systematically analyze the roles of architectural proteins and functional elements in blocking long-range contacts between loci. The proposed model does not rely on topologically associating domain (TAD) mapping from Hi-C data. Instead of testing the enrichment or influence of protein binding at TAD borders, the model directly estimates the blocking effect of proteins on long-range contacts between flanking loci, making the model intuitive and biologically meaningful.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
Diff between HiCblock versions 1.1 dated 2017-10-09 and 1.2 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/HiCblockModel.R | 1 + build/partial.rdb |binary man/HiCblock-package.Rd | 40 ++++++++++++++++++++++++++++++---------- man/HiCblockModel.Rd | 4 ++-- 6 files changed, 42 insertions(+), 21 deletions(-)
Title: NRI for Risk Prediction Models with Time to Event and Binary
Response Data
Description: Calculating the net reclassification improvement (NRI) for risk prediction models with time to event and binary data.
Author: Eisuke Inoue
Maintainer: Eisuke Inoue <eisuke.inoue@marianna-u.ac.jp>
Diff between nricens versions 1.4 dated 2017-06-27 and 1.5 dated 2017-11-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/nribin.count.main.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Calculate the RR for the GAM
Description: To calculate the relative risk (RR) for the generalized additive model.
Author: Zhicheng Du,Wangjian Zhang, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between gamRR versions 0.2.0 dated 2017-10-17 and 0.3.0 dated 2017-11-22
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 3 ++- R/gamRR.R | 1 - R/gamRR.boot.R |only man/gamRR.Rd | 38 +++++++++++++++++++++++++++----------- man/gamRR.boot.Rd |only 7 files changed, 40 insertions(+), 22 deletions(-)