Title: Ensemble Learning Algorithms Based on Support Vector Machines
Description: Three ensemble learning algorithms based on support vector machines.
They all train support vector machines on subset of data and combine the result.
Author: Tong He <hetong007@gmail.com>, Aydin Demircioglu <aydin.demircioglu@ini.ruhr-uni-bochum.de>
Maintainer: Tong He <hetong007@gmail.com>
Diff between SwarmSVM versions 0.1-2 dated 2016-08-19 and 0.1-4 dated 2018-04-18
DESCRIPTION | 11 MD5 | 94 - NAMESPACE | 58 - R/SwarmSVM.R | 36 R/alphasvm.R | 1940 +++++++++++++++++----------------- R/clusterSVM.R | 654 +++++------ R/compute.r | 66 - R/dcSVM.R | 812 +++++++------- R/gater.R | 134 +- R/gaterSVM.R | 514 ++++----- R/neuralnet.r | 1872 ++++++++++++++++---------------- R/prediction.r | 196 +-- R/utils.R | 390 +++--- R/zzz.R | 22 README.md |only build/vignette.rds |binary inst/benchmark/clustered_SVM.R | 314 ++--- inst/benchmark/clustered_SVM_Repeat.R | 540 ++++----- inst/benchmark/dc_SVM.R | 386 +++--- inst/benchmark/gater_SVM.R | 270 ++-- inst/benchmark/preprocess_data.R | 310 ++--- inst/benchmark/utils.R | 90 - inst/doc/SwarmSVM.html | 442 +++++-- man/SwarmSVM.Rd | 48 man/alphasvm.Rd | 387 +++--- man/cluster.fun.kkmeans.Rd | 37 man/cluster.fun.mlpack.old.Rd | 37 man/cluster.predict.kkmeans.Rd | 33 man/clusterSVM.Rd | 212 +-- man/csvmTransform.Rd | 43 man/dcSVM.Rd | 182 +-- man/eucliDist.Rd | 33 man/gater.Rd | 69 - man/gaterSVM.Rd | 141 +- man/kmeans.predict.Rd | 33 man/plot.alphasvm.Rd | 73 - man/predict.alphasvm.Rd | 55 man/predict.clusterSVM.Rd | 45 man/predict.dcSVM.Rd | 39 man/predict.gater.Rd | 39 man/predict.gaterSVM.Rd | 41 man/svmguide1.Rd | 31 man/write.alphasvm.Rd | 43 src/init.c |only tests/testthat.R | 8 tests/testthat/test_alphasvm.R | 110 - tests/testthat/test_clusterSVM.R | 262 ++-- tests/testthat/test_dcSVM.R | 82 - tests/testthat/test_gaterSVM.R | 134 +- 49 files changed, 5790 insertions(+), 5578 deletions(-)
Title: Project Management Tools
Description: Tools for data importation, recoding, and inspection that
are used at the University of Kansas Center for Research Methods
and Data Analysis. There are functions to create new project
folders, R code templates, create uniquely named output
directories, and to quickly obtain a visual summary for each
variable in a data frame. The main feature here is the systematic
implementation of the "variable key" framework for data
importation and recoding. We are eager to have community feedback
about the variable key and the vignette about it.
Author: Paul Johnson [aut, cre],
Benjamin Kite [aut],
Charles Redmon [aut],
Jared Harpole [ctb],
Kenna Whitley [ctb],
Po-Yi Chen [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>
Diff between kutils versions 1.34 dated 2018-01-10 and 1.39 dated 2018-04-18
DESCRIPTION | 8 - MD5 | 28 +++--- NAMESPACE | 1 R/factors.R | 26 +++++- R/semTable.R | 192 +++++++++++++++++++++++++++++++++++------------ R/utils.R | 23 ++++- R/variableKey.R | 11 +- build/vignette.rds |binary data/natlongsurv.RData |binary inst/ChangeLog | 31 +++++++ inst/doc/variablekey.pdf |binary man/deduper.Rd | 9 +- man/markupConvert.Rd | 10 +- man/reverse.Rd | 24 +++++ man/semTable.Rd | 83 ++++++++++++++------ 15 files changed, 340 insertions(+), 106 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 3.1-2 dated 2018-04-10 and 3.2-0 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/hergm.mcmc.diagnostics.R | 22 +++++++++++++++++++--- src/h_ergm.c | 3 +-- 4 files changed, 27 insertions(+), 12 deletions(-)
Title: Functional Linear Mixed Models for Densely Sampled Data
Description: Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
Author: Sonja Greven, Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@gmail.com>
Diff between denseFLMM versions 0.1.1 dated 2018-04-01 and 0.1.2 dated 2018-04-18
DESCRIPTION | 6 MD5 | 7 NEWS.md |only R/denseFLMM.R | 482 +++++++++++++++++++++++++++---------------------------- man/denseFLMM.Rd | 172 +++++++++---------- 5 files changed, 334 insertions(+), 333 deletions(-)
Title: White Matter Normalization for Magnetic Resonance Images using
WhiteStripe
Description: Shinohara (2014) <DOI:10.1016/j.nicl.2014.08.008>
introduced 'WhiteStripe', an intensity-based normalization of T1
and T2 images, where normal
appearing white matter performs well, but requires segmentation.
This method performs white matter mean and standard deviation
estimates on data that has been rigidly-registered to the 'MNI'
template and uses histogram-based methods.
Author: R. Taki Shinohara, John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between WhiteStripe versions 2.3.0 dated 2018-01-30 and 2.3.1 dated 2018-04-18
DESCRIPTION | 9 ++++--- MD5 | 16 ++++++------- R/t1.voi.R | 6 +++- build/vignette.rds |binary inst/doc/Running_WhiteStripe.R | 16 +++++++++---- inst/doc/Running_WhiteStripe.Rmd | 14 +++++++++-- inst/doc/Running_WhiteStripe.html | 46 +++++++++++++++++++------------------- man/t1.voi.hist.Rd | 6 +++- vignettes/Running_WhiteStripe.Rmd | 14 +++++++++-- 9 files changed, 80 insertions(+), 47 deletions(-)
Title: Estimation of Transition Probabilities for the Illness-Death
Model
Description: Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.
Author: Vanesa Balboa-Barreiro, Jacobo de Una-Alvarez <jacobo@uvigo.es>
and Luis Meira-Machado <lmachado@math.uminho.pt>
Maintainer: Vanesa Balboa-Barreiro <vanesa.balboa@uvigo.es>
Diff between TP.idm versions 1.4 dated 2018-03-23 and 1.5 dated 2018-04-18
DESCRIPTION | 8 - MD5 | 10 - R/TP.idm-internal.R | 251 ++++++++++++++++++++++++-------------------------- R/plot.TPidm.R | 20 +-- build/partial.rdb |binary man/TP.idm-package.Rd | 3 6 files changed, 146 insertions(+), 146 deletions(-)
Title: A Pipeline for Meta-Genome Wide Association
Description: Correlates variation within the meta-genome to target species
phenotype variations in meta-genome with association studies. Follows
the pipeline described in Chaston, J.M. et al. (2014) <doi:10.1128/mBio.01631-14>.
Author: Corinne Sexton [aut],
John Chaston [aut, cre],
Hayden Smith [ctb]
Maintainer: John Chaston <john_chaston@byu.edu>
Diff between MAGNAMWAR versions 2.0.2 dated 2018-01-24 and 2.0.3 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- R/AnalyzeOrthoMCL.R | 4 +++- R/PrintOGSeqs.R | 4 ++-- R/RASTtoGBK.R | 3 ++- R/SurvAppendMatrix.R | 3 ++- R/WriteMCL.R | 3 +++ R/graphics.R | 2 +- inst/doc/using_mag.html | 8 ++++---- 10 files changed, 35 insertions(+), 24 deletions(-)
Title: Probing Factor-Dependent Long-Range Contacts using Regression
with Higher-Order Interaction Terms
Description: We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
Diff between HiCglmi versions 1.1 dated 2017-06-07 and 1.3 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/HiCglmiModel.R | 24 ++++++++++++------------ R/HiCglmiProcData.R | 4 ++-- build/partial.rdb |binary data/dataExample.RData |binary 7 files changed, 25 insertions(+), 25 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports
the static site generator 'Hugo' (<https://gohugo.io>) best, and it also
supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Beilei Bian [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
JJ Allaire [ctb],
Kevin Ushey [ctb],
Leonardo Collado-Torres [ctb],
Xianying Tan [ctb],
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 0.5 dated 2018-01-24 and 0.6 dated 2018-04-18
DESCRIPTION | 16 ++++-- MD5 | 31 ++++++------ NEWS.md | 24 +++++++++ R/hugo.R | 71 +++++++++++++++++++--------- R/install.R | 45 ++++++++++++++--- R/render.R | 4 + R/serve.R | 15 ++++- R/utils.R | 6 +- inst/rstudio/addins.dcf | 5 + inst/rstudio/templates/project/skeleton.dcf | 2 inst/scripts/insert_image.R |only inst/scripts/new_post.R | 7 ++ inst/scripts/render_page.R | 6 +- man/build_site.Rd | 6 ++ man/hugo_cmd.Rd | 24 ++++++--- man/install_hugo.Rd | 14 +++++ man/install_theme.Rd | 14 +++-- 17 files changed, 220 insertions(+), 70 deletions(-)
Title: Nested and Crossed Block Designs for Factorial, Fractional
Factorial and Unstructured Treatment Sets
Description: The 'blocksdesign' package constructs nested block and
D-optimal factorial designs for any unstructured or factorial
treatment model of any size. The nested block designs can have repeated
nesting down to any required depth of nesting with either a simple set
of nested blocks or a crossed row-and-column blocks design at each level
of nesting. The block design at each level of nesting is optimized for
D-efficiency within the blocks of each preceding set of
blocks. Outputs include a table showing the allocation of
treatments to blocks, a plan layout showing the allocation of treatments
within blocks (unstructured treatment designs only) the achieved
D-efficiency factors for the block and treatment design
(factorial treatment designs only) and, where feasible,
an A-efficiency factor and A-efficiency upper bound for the block design
(unstructured treatment designs only).
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 2.7 dated 2017-09-11 and 2.8 dated 2018-04-18
blocksdesign-2.7/blocksdesign/man/factblocks.Rd |only blocksdesign-2.8/blocksdesign/DESCRIPTION | 18 blocksdesign-2.8/blocksdesign/MD5 | 22 blocksdesign-2.8/blocksdesign/NAMESPACE | 21 blocksdesign-2.8/blocksdesign/R/blocks.r | 1159 ++++----- blocksdesign-2.8/blocksdesign/R/blocksdesign-deprecated.R |only blocksdesign-2.8/blocksdesign/R/blocksdesign-package.r | 35 blocksdesign-2.8/blocksdesign/R/design.r |only blocksdesign-2.8/blocksdesign/R/factblocks.r | 1308 +++++------ blocksdesign-2.8/blocksdesign/man/blocks.Rd | 256 -- blocksdesign-2.8/blocksdesign/man/blocksdesign-deprecated.Rd |only blocksdesign-2.8/blocksdesign/man/blocksdesign-package.Rd | 119 - blocksdesign-2.8/blocksdesign/man/design.Rd |only blocksdesign-2.8/blocksdesign/man/factblocks-deprecated.Rd |only blocksdesign-2.8/blocksdesign/man/upper_bounds.Rd | 66 15 files changed, 1401 insertions(+), 1603 deletions(-)
Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>
Diff between WRSS versions 1.1 dated 2018-02-18 and 1.2 dated 2018-04-18
WRSS-1.1/WRSS/man/figures/Thumbs.db |only WRSS-1.2/WRSS/DESCRIPTION | 8 ++++---- WRSS-1.2/WRSS/MD5 | 15 ++++++++------- WRSS-1.2/WRSS/NAMESPACE | 2 +- WRSS-1.2/WRSS/R/rippl.R |only WRSS-1.2/WRSS/R/riverRouting.R | 6 +++--- WRSS-1.2/WRSS/man/WRSS-package.Rd | 8 +++++--- WRSS-1.2/WRSS/man/figures/Fig.pdf |binary WRSS-1.2/WRSS/man/figures/Fig.png |binary WRSS-1.2/WRSS/man/rippl.Rd |only 10 files changed, 21 insertions(+), 18 deletions(-)
Title: Spatial Temporal Analysis of Moving Polygons
Description: Perform spatial temporal analysis of moving polygons; a
longstanding analysis problem in Geographic Information Systems. Facilitates
directional analysis, shape analysis, and some other simple functionality for
examining spatial-temporal patterns of moving polygons.
Author: Jed Long and Colin Robertson
Maintainer: Colin Robertson <crobertson@wlu.ca>
Diff between stampr versions 0.1 dated 2017-01-12 and 0.2 dated 2018-04-18
DESCRIPTION | 13 ++-- MD5 | 39 ++++++------ R/stamp.group.summary.r | 2 R/stamp.r | 10 ++- R/stamp.stgroup.summary.r | 137 +++++++++++++++++++++---------------------- inst |only man/eyeshp.Rd | 1 man/fire1.Rd | 1 man/fire2.Rd | 1 man/glob.change.Rd | 1 man/katrina.Rd | 1 man/mpb.Rd | 1 man/stamp.Rd | 1 man/stamp.direction.Rd | 1 man/stamp.distance.Rd | 1 man/stamp.group.summary.Rd | 1 man/stamp.map.Rd | 1 man/stamp.multichange.Rd | 1 man/stamp.shape.Rd | 1 man/stamp.stgroup.summary.Rd | 1 man/stampr-package.Rd | 7 -- 21 files changed, 108 insertions(+), 114 deletions(-)
Title: Multiple Logistic Regression for 3D Chromatin Domain Border
Analysis
Description: We propose a multiple logistic regression model to assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
Diff between HiCfeat versions 1.2 dated 2016-09-25 and 1.3 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/BorderAnalysisFun.R | 4 ++-- build/partial.rdb |binary 4 files changed, 9 insertions(+), 9 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 1.3 dated 2018-03-27 and 1.4 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 +- build/partial.rdb |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl, Yan Yang, and Sharon Lohr
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.0-4 dated 2017-03-15 and 3.0-5 dated 2018-04-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 3 +++ R/GP.csh.R | 22 +++++++++++----------- R/GP.un.R | 22 +++++++++++----------- R/VP.CP.ZP.un.r | 20 ++++++++++---------- R/rGP.un.R | 22 +++++++++++----------- man/GPvam-package.Rd | 4 ++-- man/GPvam.Rd | 2 +- man/plot.Rd | 2 ++ 10 files changed, 65 insertions(+), 60 deletions(-)
Title: Classification of RNA Sequences using Complex Network Theory
Description: It makes the creation of networks from sequences of RNA, with this is done the abstraction of characteristics of these networks with a methodology of threshold for the purpose of making a classification between the classes of the sequences. There are two data present in the 'BASiNET' package, "sequences" and "sequences2" with 11 and 10 sequences respectively. These sequences were taken from the data set used in the article (LI, Aimin; ZHANG, Junying; ZHOU, Zhongyin, 2014) <doi:10.1186/1471-2105-15-311>. These sequences are used to run examples.
Author: Eric Augusto Ito
Maintainer: Eric Augusto Ito <ericaugustoito@hotmail.com>
Diff between BASiNET versions 0.0.2 dated 2017-12-18 and 0.0.3 dated 2018-04-18
BASiNET-0.0.2/BASiNET/R/createGraph3D.R |only BASiNET-0.0.2/BASiNET/inst/doc/vinheta.R |only BASiNET-0.0.2/BASiNET/inst/doc/vinheta.Rmd |only BASiNET-0.0.2/BASiNET/inst/doc/vinheta.html |only BASiNET-0.0.2/BASiNET/man/createGraph3D.Rd |only BASiNET-0.0.2/BASiNET/vignettes/3d.png |only BASiNET-0.0.2/BASiNET/vignettes/vinheta.Rmd |only BASiNET-0.0.3/BASiNET/DESCRIPTION | 15 BASiNET-0.0.3/BASiNET/MD5 | 45 +- BASiNET-0.0.3/BASiNET/NAMESPACE | 3 BASiNET-0.0.3/BASiNET/R/classification.R | 311 ++++++++++---------- BASiNET-0.0.3/BASiNET/R/createGraph2D.R | 27 - BASiNET-0.0.3/BASiNET/R/createNet.R | 4 BASiNET-0.0.3/BASiNET/R/measures.R | 4 BASiNET-0.0.3/BASiNET/R/minMax.R |only BASiNET-0.0.3/BASiNET/R/reschedule.R | 35 -- BASiNET-0.0.3/BASiNET/R/threshold.R | 23 - BASiNET-0.0.3/BASiNET/build/vignette.rds |binary BASiNET-0.0.3/BASiNET/inst/doc/BASiNET.R |only BASiNET-0.0.3/BASiNET/inst/doc/BASiNET.Rmd |only BASiNET-0.0.3/BASiNET/inst/doc/BASiNET.html |only BASiNET-0.0.3/BASiNET/inst/extdata/modelPredict.dat |only BASiNET-0.0.3/BASiNET/inst/extdata/predict.fasta |only BASiNET-0.0.3/BASiNET/man/classification.Rd | 47 +-- BASiNET-0.0.3/BASiNET/man/createGraph2D.Rd | 13 BASiNET-0.0.3/BASiNET/man/createNet.Rd | 4 BASiNET-0.0.3/BASiNET/man/measures.Rd | 4 BASiNET-0.0.3/BASiNET/man/minMax.Rd |only BASiNET-0.0.3/BASiNET/man/reschedule.Rd | 12 BASiNET-0.0.3/BASiNET/man/threshold.Rd | 4 BASiNET-0.0.3/BASiNET/vignettes/BASiNET.Rmd |only 31 files changed, 279 insertions(+), 272 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias Grenié [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.3 dated 2018-03-02 and 0.4.4 dated 2018-04-18
ggfortify-0.4.3/ggfortify/NEWS |only ggfortify-0.4.4/ggfortify/DESCRIPTION | 13 - ggfortify-0.4.4/ggfortify/MD5 | 78 +++--- ggfortify-0.4.4/ggfortify/NEWS.md |only ggfortify-0.4.4/ggfortify/R/fortify_stats.R | 2 ggfortify-0.4.4/ggfortify/R/plotlib.R | 29 +- ggfortify-0.4.4/ggfortify/inst/CITATION | 2 ggfortify-0.4.4/ggfortify/inst/doc/basics.R | 2 ggfortify-0.4.4/ggfortify/inst/doc/basics.Rmd | 2 ggfortify-0.4.4/ggfortify/inst/doc/basics.html | 40 +-- ggfortify-0.4.4/ggfortify/inst/doc/plot_dist.html | 10 ggfortify-0.4.4/ggfortify/inst/doc/plot_lm.html | 16 - ggfortify-0.4.4/ggfortify/inst/doc/plot_map.html | 14 - ggfortify-0.4.4/ggfortify/inst/doc/plot_pca.Rmd | 2 ggfortify-0.4.4/ggfortify/inst/doc/plot_pca.html | 44 +-- ggfortify-0.4.4/ggfortify/inst/doc/plot_surv.html | 12 ggfortify-0.4.4/ggfortify/inst/doc/plot_ts.html | 64 ++--- ggfortify-0.4.4/ggfortify/man/autoplot.pca_common.Rd | 2 ggfortify-0.4.4/ggfortify/man/ggbiplot.Rd | 10 ggfortify-0.4.4/ggfortify/man/ggmultiplot-class.Rd | 7 ggfortify-0.4.4/ggfortify/man/plot_label.Rd | 4 ggfortify-0.4.4/ggfortify/tests/testthat/Rplots.pdf |binary ggfortify-0.4.4/ggfortify/tests/testthat/test-MSwM.R | 1 ggfortify-0.4.4/ggfortify/tests/testthat/test-base-infer.R | 2 ggfortify-0.4.4/ggfortify/tests/testthat/test-base_ts.R | 13 - ggfortify-0.4.4/ggfortify/tests/testthat/test-changepoint.R | 9 ggfortify-0.4.4/ggfortify/tests/testthat/test-cluster.R | 2 ggfortify-0.4.4/ggfortify/tests/testthat/test-forecast.R | 58 ++++ ggfortify-0.4.4/ggfortify/tests/testthat/test-glmnet.R | 2 ggfortify-0.4.4/ggfortify/tests/testthat/test-maps.R | 4 ggfortify-0.4.4/ggfortify/tests/testthat/test-performance.R | 1 ggfortify-0.4.4/ggfortify/tests/testthat/test-raster.R | 4 ggfortify-0.4.4/ggfortify/tests/testthat/test-spatial.R | 12 ggfortify-0.4.4/ggfortify/tests/testthat/test-stats-lm.R | 148 ++++++------ ggfortify-0.4.4/ggfortify/tests/testthat/test-stats.R | 2 ggfortify-0.4.4/ggfortify/tests/testthat/test-surv.R | 63 +---- ggfortify-0.4.4/ggfortify/tests/testthat/test-ts.R | 90 +------ ggfortify-0.4.4/ggfortify/tests/testthat/test-tslib.R | 1 ggfortify-0.4.4/ggfortify/tests/testthat/test-vars.R | 6 ggfortify-0.4.4/ggfortify/vignettes/basics.Rmd | 2 ggfortify-0.4.4/ggfortify/vignettes/plot_pca.Rmd | 2 41 files changed, 386 insertions(+), 389 deletions(-)
Title: Handy File and String Manipulation
Description: Convenient functions for moving files, deleting directories,
and a variety of string operations that facilitate manipulating files
and extracting information from strings.
Author: Rory Nolan [aut, cre, cph],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 2.1.0 dated 2018-03-10 and 2.2.0 dated 2018-04-18
DESCRIPTION | 9 ++-- MD5 | 32 ++++++++-------- NEWS.md | 10 +++++ R/RcppExports.R | 16 ++++++++ R/files.R | 2 + R/strings.R | 42 ++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/files.html | 4 +- inst/doc/strings.html | 10 ++--- man/can_be_numeric.Rd | 4 +- man/locate_braces.Rd | 7 +-- man/nice_nums.Rd | 1 man/str_with_patterns.Rd | 4 ++ src/RcppExports.cpp | 50 +++++++++++++++++++++++++ src/strings.cpp | 81 ++++++++++++++++++++++++++++++++++++++++-- tests/testthat/test_strings.R | 9 ++-- 17 files changed, 223 insertions(+), 58 deletions(-)
Title: Weibull Analysis for Reliability Engineering
Description: Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586) <DOI:10.1002/0471725234>, William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986) <DOI:10.1002/9781118351994>.
Author: David Silkworth [aut],
Jurgen Symynck [aut],
Jacob Ormerod [cre],
OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
Diff between WeibullR versions 1.0.8 dated 2018-04-18 and 1.0.9 dated 2018-04-18
DESCRIPTION | 12 MD5 | 8 src/CallgetPvalue.cpp | 8 src/LSLR.cpp | 873 +++++++++++++++++++++++++------------------------- src/MLEmodel.cpp | 4 5 files changed, 453 insertions(+), 452 deletions(-)
Title: Estimating a Survival Distribution in the Presence of Dependent
Left Truncation and Right Censoring
Description: A structural transformation model for a latent, quasi-independent
truncation time as a function of the observed dependent truncation
time and the event time, and an unknown dependence parameter.
The dependence parameter is chosen to minimize the conditional
Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538>.
The marginal distribution for the truncation time and the event time are
completely left unspecified.
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between tranSurv versions 1.1-4 dated 2017-02-08 and 1.1-5 dated 2018-04-18
DESCRIPTION | 21 +++++++++++---------- MD5 | 11 ++++++----- NAMESPACE | 2 +- R/tranSurvfit.R | 23 ++++++++++++++--------- man/tranSurvfit.Rd | 4 +++- src/getKendall.c | 4 ++-- src/registerDynamicSymbol.c |only 7 files changed, 37 insertions(+), 28 deletions(-)
Title: Permutation Tests for General Dependent Truncation
Description: Implementations of permutation approach to hypothesis testing for quasi-independence of truncation time and failure time. The implemented approaches are powerful against non-monotone alternatives and thereby offer protection against erroneous assumptions of quasi-independence. The proposed tests use either a conditional or an unconditional method to evaluate the permutation p-value. The conditional method was first developed in Tsai (1980) <doi:10.2307/2336059> and Efron and Petrosian (1992) <doi:10.1086/171931>. The unconditional method provides a valid approximation to the conditional method, yet computationally simpler and does not hold fixed the size of each risk sets. Users also have an option to carry out the proposed permutation tests in a parallel computing fashion.
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between permDep versions 1.0-0 dated 2017-04-28 and 1.0-1 dated 2018-04-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- src/agfit4.c | 4 +++- src/permTest.c | 9 +++++---- 4 files changed, 17 insertions(+), 14 deletions(-)
Title: Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Bouveyron and Jacques, 2001, Schmutz et al., 2017) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Diff between funHDDC versions 1.0 dated 2014-09-08 and 2.0 dated 2018-04-18
funHDDC-1.0/funHDDC/R/funHDDC-internal.R |only funHDDC-2.0/funHDDC/DESCRIPTION | 22 funHDDC-2.0/funHDDC/MD5 | 26 funHDDC-2.0/funHDDC/NAMESPACE | 9 funHDDC-2.0/funHDDC/R/funHDDC.R | 1447 ++++++++++++++++++++++++++++- funHDDC-2.0/funHDDC/R/mfpca.R |only funHDDC-2.0/funHDDC/R/plot.mfpca.R |only funHDDC-2.0/funHDDC/R/predict.funHDDC.R |only funHDDC-2.0/funHDDC/R/slopeHeuristic.R |only funHDDC-2.0/funHDDC/data |only funHDDC-2.0/funHDDC/inst |only funHDDC-2.0/funHDDC/man/funHDDC-package.Rd | 52 - funHDDC-2.0/funHDDC/man/funHDDC.Rd | 211 +++- funHDDC-2.0/funHDDC/man/mfpca.Rd |only funHDDC-2.0/funHDDC/man/plot.mfpca.Rd |only funHDDC-2.0/funHDDC/man/predict.funHDDC.Rd |only funHDDC-2.0/funHDDC/man/slopeHeuristic.Rd |only funHDDC-2.0/funHDDC/man/triangle.Rd |only funHDDC-2.0/funHDDC/man/trigo.Rd |only 19 files changed, 1619 insertions(+), 148 deletions(-)
Title: Build Dirichlet Process Objects for Bayesian Modelling
Description: Perform nonparametric Bayesian analysis using Dirichlet
processes without the need to program the inference algorithms.
Utilise included pre-built models or specify custom
models and allow the dirichletprocess package to handle the
Markov chain Monte Carlo sampling.
Our Dirichlet process objects can act as building blocks for a variety
of statistical models including and not limited to: density estimation,
clustering and prior distributions in hierarchical models.
See Teh, Y. W. (2011)
<https://www.stats.ox.ac.uk/~teh/research/npbayes/Teh2010a.pdf>,
among many other sources.
Author: Gordon J. Ross [aut],
Dean Markwick [aut, cre]
Maintainer: Dean Markwick <dean.markwick@talk21.com>
Diff between dirichletprocess versions 0.2.0 dated 2018-01-29 and 0.2.1 dated 2018-04-18
DESCRIPTION | 28 +++- MD5 | 52 +++++---- NAMESPACE | 4 NEWS.md | 10 + R/beta_uniform_gamma.R | 26 ++++ R/cluster_component_update.R | 28 ++-- R/dirichlet_process_exponential.R |only R/dirichlet_process_hierarchical_beta.R | 13 -- R/dirichletprocess.R | 2 R/exponential_gamma.R |only R/hierarchical_beta.R | 17 +- R/metropolis_hastings.R | 12 +- R/mixing_distribution_penalised_likelihood.R |only R/mixing_distribution_posterior_draw.R | 6 - R/plot.R | 35 +----- R/plot_dirichletprocess.R |only R/update_concentration.R | 4 R/utilities.R | 10 + README.md | 14 +- build/vignette.rds |binary inst/doc/dirichletprocess.pdf |binary man/DirichletProcessExponential.Rd |only man/ExponentialMixtureCreate.Rd |only man/HierarchicalBetaCreate.Rd | 8 - man/plot.dirichletprocess.Rd | 10 + tests/testthat/test_beta_uniform_gamma.R | 59 +++++++--- tests/testthat/test_dirichlet_process_exponential.R |only tests/testthat/test_dirichlet_process_hierarchical_beta.R |only tests/testthat/test_exponential_gamma.R |only tests/testthat/test_mvnormal_normal_wishart.R | 4 tests/testthat/test_plot.R | 80 +++++++++++--- tests/testthat/test_plot_dirichletprocess.R |only 32 files changed, 283 insertions(+), 139 deletions(-)
More information about dirichletprocess at CRAN
Permanent link
Title: 'cpt-city' Colour Gradients
Description: Incorporates colour gradients from the 'cpt-city' web archive available at <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between cptcity versions 1.0.0 dated 2018-02-27 and 1.0.3 dated 2018-04-18
DESCRIPTION | 9 ++++++--- MD5 | 28 +++++++++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 21 ++++++++++++++++++++- R/cpt.R | 21 +++++++++++++-------- R/cpt_names.R | 2 +- R/cptcity.R | 18 +++--------------- R/find_cpt.R | 2 +- R/lucky.R |only man/cpt.Rd | 17 +++++++++-------- man/cpt_names.Rd | 2 +- man/cptcity.Rd | 19 +++---------------- man/find_cpt.Rd | 2 +- man/lucky.Rd |only tests |only 15 files changed, 77 insertions(+), 66 deletions(-)
Title: Analyze Clustered Data with Generalized Linear Models using the
Cluster Bootstrap
Description: Provides functionality for the analysis of clustered data using the cluster bootstrap.
Author: Mathijs Deen [aut, cre],
Mark de Rooij [aut]
Maintainer: Mathijs Deen <m.l.deen@fsw.leidenuniv.nl>
Diff between ClusterBootstrap versions 0.9.3 dated 2017-06-12 and 0.9.9 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++-------- NEWS |only R/additional_exports.R | 5 ++++- R/clusbootglm.R | 16 ++++++++-------- R/clusbootglm_s3_methods.R | 38 +++++++++++++++++++++++--------------- R/medication-data.R |only data/medication.rda |only man/clusbootglm.Rd | 4 ++-- man/coef.clusbootglm.Rd | 6 +++--- man/confint.clusbootglm.Rd | 6 +++--- man/medication.Rd |only man/summary.clusbootglm.Rd | 2 +- 13 files changed, 60 insertions(+), 45 deletions(-)
More information about ClusterBootstrap at CRAN
Permanent link
Title: Bayesian Inference for Differential Equations
Description: A Bayesian framework for parameter inference in differential equations.
This approach offers a rigorous methodology for parameter inference as well as
modeling the link between unobservable model states and parameters, and
observable quantities. Provides templates for the DE model, the
observation model and data likelihood, and the model parameters and their prior
distributions. A Markov chain Monte Carlo (MCMC) procedure processes these inputs
to estimate the posterior distributions of the parameters and any derived
quantities, including the model trajectories. Further functionality is provided
to facilitate MCMC diagnostics and the visualisation of the posterior distributions
of model parameters and trajectories.
Author: Philipp H Boersch-Supan [aut, cre]
(<https://orcid.org/0000-0001-6723-6833>),
Leah R Johnson [aut] (<https://orcid.org/0000-0002-9922-579X>),
Sadie J Ryan [aut] (<https://orcid.org/0000-0002-4308-6321>)
Maintainer: Philipp H Boersch-Supan <pboesu@gmail.com>
Diff between deBInfer versions 0.4.1 dated 2016-09-14 and 0.4.2 dated 2018-04-18
DESCRIPTION | 29 MD5 | 106 +- NAMESPACE | 87 +- R/data_doc.R | 60 - R/de_mcmc_rev.R | 987 +++++++++++++------------ R/de_solver.R | 233 ++--- R/debinfer_utils.R | 169 ++-- R/mcmc_plotting.R | 395 +++++----- R/setup_mcmc.R | 213 +++-- README.md | 32 build/vignette.rds |binary inst/CITATION | 43 - inst/doc/chytrid_dede_example.R | 357 ++++----- inst/doc/chytrid_dede_example.Rmd | 536 ++++++------- inst/doc/chytrid_dede_example.pdf |binary inst/doc/deBInfer_compiled_code.pdf |binary inst/doc/deBInfer_compiled_code.pdf.asis | 6 inst/doc/logistic_ode_example.R | 353 ++++---- inst/doc/logistic_ode_example.Rmd | 546 ++++++------- inst/doc/logistic_ode_example.pdf |binary man/chytrid.Rd | 39 man/de_mcmc.Rd | 103 +- man/debinfer_cov.Rd |only man/debinfer_par.Rd | 75 - man/deinits.Rd | 35 man/depars.Rd | 35 man/is.debinfer_parlist.Rd |only man/is.debinfer_result.Rd | 29 man/log_post_params.Rd | 53 - man/log_prior_params.Rd | 41 - man/logd_prior.Rd | 43 - man/logistic.Rd | 33 man/pairs.debinfer_result.Rd | 51 - man/plot.debinfer_result.Rd | 45 - man/plot.post_sim_list.Rd | 55 - man/post_prior_densplot.Rd | 51 - man/post_sim.Rd | 61 - man/prior_draw_rev.Rd | 37 man/propose_joint_rev.Rd | 41 - man/propose_single_rev.Rd | 33 man/reshape_post_sim.Rd | 29 man/setup_debinfer.Rd | 37 man/solve_de.Rd | 79 -- man/summary.debinfer_result.Rd | 39 man/update_sample_rev.Rd | 115 +- tests/testthat.R | 8 tests/testthat/test_debinfer_par.R | 24 tests/testthat/test_inference_logistic.R | 319 ++++---- tests/testthat/test_joint_inference.R |only tests/testthat/test_likelihood_eval.R | 26 tests/testthat/test_samplers.R |only vignettes/chytrid_dede_example.Rmd | 536 ++++++------- vignettes/deBInfer_compiled_code.pdf.asis | 6 vignettes/debinfer.bib | 779 +++++++++---------- vignettes/logistic_ode_example.Rmd | 546 ++++++------- vignettes/methods-in-ecology-and-evolution.csl | 370 ++++----- 56 files changed, 4044 insertions(+), 3881 deletions(-)
Title: Functions to Facilitate Power and Sensitivity Analyses for
Genetic Studies of Natural Populations
Description: Functions for sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for viewing pedigrees.
Author: Michael Morrissey
Maintainer: Michael Morrissey <michael.morrissey@st-andrews.ac.uk>
Diff between pedantics versions 1.6 dated 2018-03-09 and 1.7 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/pedantics.cc | 34 +++++++++++++++++----------------- 3 files changed, 23 insertions(+), 23 deletions(-)
Title: Uniform Design of Experiments
Description: Efficient procedures for constructing uniform design of experiments under various space-filling criteria. It is based on a stochastic and adaptive threshold accepting algorithm with flexible initialization, adaptive threshold, and stochastic evolution. The package may also construct the augmented uniform designs in a sequential manner.
Author: Aijun Zhang, Haoyu Li, Shijie Quan, Zebin Yang
Maintainer: Aijun Zhang <ajzhang@hku.hk>
Diff between UniDOE versions 1.0.1 dated 2017-12-08 and 1.0.2 dated 2018-04-18
DESCRIPTION | 12 ++++++------ MD5 | 48 ++++++++++++++++++++++++++++++------------------ NAMESPACE | 19 ++++++++++++------- R/LHD_CD2.R |only R/LHD_MD2.R |only R/R_Wrapper.R | 14 +++++++++++++- R/UD_CD2.R |only R/UD_MD2.R |only R/UniDOE_Ext.R |only man/DesignEval.Rd | 2 ++ man/DesignPairPlot.Rd |only man/DesignQuery.Rd |only man/GenAUD.Rd | 2 ++ man/GenAUD_MS.Rd |only man/GenLP.Rd | 2 ++ man/GenUD.Rd | 6 +++--- man/GenUD_MS.Rd |only man/LHD_CD2.Rd | 26 +++++++++++++------------- man/LHD_MD2.Rd | 28 ++++++++++++++-------------- man/UD_CD2.Rd | 28 ++++++++++++++-------------- man/UD_MD2.Rd | 28 ++++++++++++++-------------- man/UniTracePlot.Rd |only man/unidoe-internal.Rd | 6 ++++++ src/doe_Eval.cpp | 23 +++++++++++++++++++++++ src/doe_Eval.h | 1 + src/doe_MD2.cpp | 4 ++-- src/doe_WD2.cpp |only src/doe_WD2.h |only src/doe_criteria.cpp | 36 ++++++++++++++++++++++++++++++++++++ src/doe_search.cpp | 4 ++-- src/main.cpp | 7 +++---- 31 files changed, 198 insertions(+), 98 deletions(-)
Title: Association Rule Classification
Description: Implements the Classification-based on
Association Rules (CBA) (Bing Liu, Wynne Hsu, Yiming Ma (1999) <http://dl.acm.org/citation.cfm?id=3000292.3000305>) algorithm for association rule classification (ARC).
The package also contains several convenience methods that allow to automatically
set CBA parameters (minimum confidence, minimum support) and it also natively
handles numeric attributes by integrating a pre-discretization step.
The rule generation phase is handled by the 'arules' package.
To further decrease the size of the CBA models produced by the 'arc' package, postprocessing by the
'qCBA' package is suggested.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>
Diff between arc versions 1.1.4 dated 2018-03-05 and 1.2 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ R/cba.R | 13 +++++++++++-- R/m1prune.R | 23 +++++++++++++++-------- man/cba.Rd | 13 +++++++++++-- man/cba_manual.Rd | 2 +- man/prune.Rd | 5 ++++- 8 files changed, 59 insertions(+), 25 deletions(-)
Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Description: Fast Bayesian inference of marginal and conditional independence structures between variables from high-dimensional data (Leday and Richardson (2018) <arXiv:1803.08155>).
Author: Gwenael G.R. Leday [cre, aut],
Ilaria Speranza [aut],
Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@mrc-bsu.cam.ac.uk>
Diff between beam versions 1.0 dated 2018-03-23 and 1.0.1 dated 2018-04-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/beam-methods.r | 4 ++-- R/beam.select-methods.r | 16 ++++++++++++---- 4 files changed, 21 insertions(+), 13 deletions(-)
Title: Data Preparation During and After the Use of the Experience
Sampling Methodology (ESM)
Description: Support in preparing a raw ESM dataset for statistical analysis. Preparation includes the handling of errors (mostly due to technological reasons) and the generating of new variables that are necessary and/or helpful in meeting the conditions when statistically analyzing ESM data. The functions in 'esmprep' are meant to hierarchically lead from bottom, i.e. the raw (separated) ESM dataset(s), to top, i.e. a single ESM dataset ready for statistical analysis. This hierarchy evolved out of my personal experience in working with ESM data.
Author: Marcel Miché <esmprep@gmail.com>
Maintainer: Marcel Miché <esmprep@gmail.com>
Diff between esmprep versions 0.1.3 dated 2018-01-11 and 0.1.4 dated 2018-04-18
DESCRIPTION | 6 +- MD5 | 6 +- R/overallCounter.R | 66 +++++++++++----------- R/suggestShift.R | 159 ++++++++++++++++++++++++++--------------------------- 4 files changed, 120 insertions(+), 117 deletions(-)
Title: Genetic Rare Variants Tests
Description: A step-up test for genetic rare variants in a gene or in a pathway. The method determines an optimal grouping of rare variants analytically. The method has been described in Hoffmann TJ, Marini NJ, and Witte JS (2010) <doi:10.1371/journal.pone.0013584>.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between thgenetics versions 0.4-0 dated 2018-04-10 and 0.4-2 dated 2018-04-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- man/rareGeneTest.Rd | 2 -- src/raremethods.cpp | 13 +++++++------ 4 files changed, 16 insertions(+), 17 deletions(-)
Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-
Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures
the difference between two Lineage-Through-Time curves, where each curve is
normalised both in time and in number of lineages.
Author: Thijs Janzen [aut, cre],
Richel Bilderbeek [aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between nLTT versions 1.3.1 dated 2016-10-11 and 1.4 dated 2018-04-18
nLTT-1.3.1/nLTT/README.md |only nLTT-1.3.1/nLTT/tests/testthat/test_abc_smc_nltt.R |only nLTT-1.3.1/nLTT/tests/testthat/test_calculate_weight.R |only nLTT-1.3.1/nLTT/tests/testthat/test_get_average_nltt.R |only nLTT-1.3.1/nLTT/tests/testthat/test_get_average_nltt_matrix.R |only nLTT-1.3.1/nLTT/tests/testthat/test_get_nltt_values.R |only nLTT-1.3.1/nLTT/tests/testthat/test_get_phylogeny_nltt_matrix.R |only nLTT-1.3.1/nLTT/tests/testthat/test_mcmc_nltt.R |only nLTT-1.3.1/nLTT/tests/testthat/test_stretch_nltt_matrix.R |only nLTT-1.3.1/nLTT/vignettes/vignette_get_nltt_values.Rmd |only nLTT-1.3.1/nLTT/vignettes/vignette_nltts_plot.Rmd |only nLTT-1.3.1/nLTT/vignettes/vignette_stretch_nltt_matrix.Rmd |only nLTT-1.4/nLTT/DESCRIPTION | 14 nLTT-1.4/nLTT/MD5 | 129 ++- nLTT-1.4/nLTT/NAMESPACE | 7 nLTT-1.4/nLTT/R/ABC_SMC.R | 105 +- nLTT-1.4/nLTT/R/get_average_nltt_matrix.R | 18 nLTT-1.4/nLTT/R/get_branching_times.R |only nLTT-1.4/nLTT/R/get_n_lineages.R |only nLTT-1.4/nLTT/R/get_nltt_values.R | 9 nLTT-1.4/nLTT/R/get_norm_brts.R |only nLTT-1.4/nLTT/R/get_norm_n.R |only nLTT-1.4/nLTT/R/nLTTDiff.R | 378 +++++++--- nLTT-1.4/nLTT/R/nltts_plot.R | 6 nLTT-1.4/nLTT/R/plot_nLTT.R | 35 nLTT-1.4/nLTT/R/stretch_nltt_matrix.R | 27 nLTT-1.4/nLTT/build/vignette.rds |binary nLTT-1.4/nLTT/inst/doc/get_nltt_values.R |only nLTT-1.4/nLTT/inst/doc/get_nltt_values.Rmd |only nLTT-1.4/nLTT/inst/doc/get_nltt_values.html |only nLTT-1.4/nLTT/inst/doc/nltt_diff.R |only nLTT-1.4/nLTT/inst/doc/nltt_diff.Rmd |only nLTT-1.4/nLTT/inst/doc/nltt_diff.html |only nLTT-1.4/nLTT/inst/doc/nltts_plot.R |only nLTT-1.4/nLTT/inst/doc/nltts_plot.Rmd |only nLTT-1.4/nLTT/inst/doc/nltts_plot.html |only nLTT-1.4/nLTT/inst/doc/stretch_nltt_matrix.R |only nLTT-1.4/nLTT/inst/doc/stretch_nltt_matrix.Rmd |only nLTT-1.4/nLTT/inst/doc/stretch_nltt_matrix.html |only nLTT-1.4/nLTT/inst/doc/trees_with_root_edge.R | 21 nLTT-1.4/nLTT/inst/doc/trees_with_root_edge.Rmd | 4 nLTT-1.4/nLTT/inst/doc/trees_with_root_edge.html | 44 - nLTT-1.4/nLTT/inst/doc/vignette_get_nltt_values.html | 8 nLTT-1.4/nLTT/inst/doc/vignette_nltts_plot.html | 8 nLTT-1.4/nLTT/inst/doc/vignette_stretch_nltt_matrix.html | 8 nLTT-1.4/nLTT/inst/doc/walkthrough.R | 67 - nLTT-1.4/nLTT/inst/doc/walkthrough.Rmd | 8 nLTT-1.4/nLTT/inst/doc/walkthrough.html | 72 - nLTT-1.4/nLTT/inst/extdata |only nLTT-1.4/nLTT/man/abc_smc_nltt.Rd | 56 - nLTT-1.4/nLTT/man/get_average_nltt_matrix.Rd | 10 nLTT-1.4/nLTT/man/get_branching_times.Rd |only nLTT-1.4/nLTT/man/get_n_lineages.Rd |only nLTT-1.4/nLTT/man/get_nltt_values.Rd | 10 nLTT-1.4/nLTT/man/get_norm_brts.Rd |only nLTT-1.4/nLTT/man/get_norm_n.Rd |only nLTT-1.4/nLTT/man/get_phylogeny_nltt_matrix.Rd | 1 nLTT-1.4/nLTT/man/nLTT-package.Rd | 9 nLTT-1.4/nLTT/man/nLTTstat.Rd | 19 nLTT-1.4/nLTT/man/nLTTstat_exact.Rd | 18 nLTT-1.4/nLTT/man/nltt_diff.Rd | 12 nLTT-1.4/nLTT/man/nltt_diff_exact.Rd | 10 nLTT-1.4/nLTT/man/nltt_diff_exact_brts.Rd |only nLTT-1.4/nLTT/man/nltt_diff_exact_norm_brts.Rd |only nLTT-1.4/nLTT/man/nltt_lines.Rd | 5 nLTT-1.4/nLTT/man/nltt_plot.Rd | 12 nLTT-1.4/nLTT/man/nltts_diff.Rd |only nLTT-1.4/nLTT/man/nltts_plot.Rd | 7 nLTT-1.4/nLTT/man/stretch_nltt_matrix.Rd | 8 nLTT-1.4/nLTT/tests/testthat/test-abc_smc_nltt.R |only nLTT-1.4/nLTT/tests/testthat/test-calculate_weight.R |only nLTT-1.4/nLTT/tests/testthat/test-get_average_nltt.R |only nLTT-1.4/nLTT/tests/testthat/test-get_average_nltt_matrix.R |only nLTT-1.4/nLTT/tests/testthat/test-get_branching_times.R |only nLTT-1.4/nLTT/tests/testthat/test-get_n_lineages.R |only nLTT-1.4/nLTT/tests/testthat/test-get_nltt_values.R |only nLTT-1.4/nLTT/tests/testthat/test-get_phylogeny_nltt_matrix.R |only nLTT-1.4/nLTT/tests/testthat/test-mcmc_nltt.R |only nLTT-1.4/nLTT/tests/testthat/test-nLTTstat.R | 32 nLTT-1.4/nLTT/tests/testthat/test-nLTTstat_exact.R | 39 - nLTT-1.4/nLTT/tests/testthat/test-nltt_diff.R |only nLTT-1.4/nLTT/tests/testthat/test-nltt_diff_exact.R |only nLTT-1.4/nLTT/tests/testthat/test-nltt_diff_exact_norm_brts.R |only nLTT-1.4/nLTT/tests/testthat/test-nltt_plot.R | 17 nLTT-1.4/nLTT/tests/testthat/test-nltts_diff.R |only nLTT-1.4/nLTT/tests/testthat/test-nltts_plot.R |only nLTT-1.4/nLTT/tests/testthat/test-stretch_nltt_matrix.R |only nLTT-1.4/nLTT/vignettes/get_nltt_values.Rmd |only nLTT-1.4/nLTT/vignettes/nltt_diff.Rmd |only nLTT-1.4/nLTT/vignettes/nltts_plot.Rmd |only nLTT-1.4/nLTT/vignettes/stretch_nltt_matrix.Rmd |only nLTT-1.4/nLTT/vignettes/trees_with_root_edge.Rmd | 4 nLTT-1.4/nLTT/vignettes/walkthrough.Rmd | 8 93 files changed, 790 insertions(+), 455 deletions(-)
Title: R Functions for Robust Statistics
Description: Locations problems, M-estimates of coefficients and scale
in linear regression, Weights for bounded influence regression,
Covariance matrix of the coefficient estimates, Asymptotic
relative efficiency of regression M-estimates, Robust testing
in linear models, High breakdown point regression, M-estimates
of covariance matrices, M-estimates for discrete generalized
linear models.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Diff between robeth versions 2.7 dated 2013-07-29 and 2.7-1 dated 2018-04-18
DESCRIPTION | 20 -- MD5 | 17 + NAMESPACE | 3 R/glmdev.R | 16 - R/gymain.R | 9 R/lrfctd.R |only R/probin.R | 15 - man/cirock.Rd | 2 man/lrfctd.Rd |only src/init.c |only src/robeth.f | 569 +++++++++++++++++++++++++++++++++++++++------------------- 11 files changed, 428 insertions(+), 223 deletions(-)
Title: Local Gaussian Process Model for Large-Scale Dynamic Computer
Experiments
Description: Fits localized GP model for dynamic computer experiments via singular value decomposition of the response matrix Y for large N (the number of observations) using the algorithm proposed by Zhang et al. (2018) <arXiv:1611.09488>. The current version only supports 64-bit version of R.
Author: Ru Zhang [aut, cre],
Chunfang Devon Lin [aut],
Pritam Ranjan [aut],
Robert B Gramacy [ctb],
Nicolas Devillard [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Peihuang Lu-Chen [ctb],
University of Chicago [cph],
University of California [cph]
Maintainer: Ru Zhang <heavenmarshal@gmail.com>
Diff between DynamicGP versions 1.0-1 dated 2018-04-13 and 1.0-2 dated 2018-04-18
DynamicGP-1.0-1/DynamicGP/src/Makevars.win |only DynamicGP-1.0-1/DynamicGP/src/genmaximinLHS.cpp |only DynamicGP-1.0-1/DynamicGP/src/include/CRandom.hpp |only DynamicGP-1.0-1/DynamicGP/src/include/CommonDefines.hpp |only DynamicGP-1.0-1/DynamicGP/src/include/arithmetic_ansi.h |only DynamicGP-1.0-1/DynamicGP/src/include/arithmetic_sse_double.h |only DynamicGP-1.0-1/DynamicGP/src/include/arithmetic_sse_float.h |only DynamicGP-1.0-1/DynamicGP/src/include/genmaximinLHS.h |only DynamicGP-1.0-1/DynamicGP/src/include/matrix.hpp |only DynamicGP-1.0-1/DynamicGP/src/include/order.hpp |only DynamicGP-1.0-1/DynamicGP/src/include/utilityLHS.hpp |only DynamicGP-1.0-1/DynamicGP/src/maximinLHS.cpp |only DynamicGP-1.0-1/DynamicGP/src/utilityLHS.cpp |only DynamicGP-1.0-2/DynamicGP/DESCRIPTION | 14 +-- DynamicGP-1.0-2/DynamicGP/MD5 | 37 +++------- DynamicGP-1.0-2/DynamicGP/R/knnsvdGP.r | 4 - DynamicGP-1.0-2/DynamicGP/R/lasvdGP.r | 4 - DynamicGP-1.0-2/DynamicGP/R/svdGP.r | 6 - DynamicGP-1.0-2/DynamicGP/inst/COPYRIGHTS | 25 ------ DynamicGP-1.0-2/DynamicGP/man/DynamicGP-package.Rd | 2 DynamicGP-1.0-2/DynamicGP/man/knnsvdGP.Rd | 2 DynamicGP-1.0-2/DynamicGP/man/lasvdGP.Rd | 2 DynamicGP-1.0-2/DynamicGP/src/include/maximinLHS.h |only DynamicGP-1.0-2/DynamicGP/src/include/random.h |only DynamicGP-1.0-2/DynamicGP/src/lasvdgpms.c | 2 DynamicGP-1.0-2/DynamicGP/src/lbfgsb_c.c | 2 DynamicGP-1.0-2/DynamicGP/src/maximinLHS.c |only DynamicGP-1.0-2/DynamicGP/src/random.c |only 28 files changed, 31 insertions(+), 69 deletions(-)
Title: Weibull Analysis for Reliability Engineering
Description: Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586) <DOI:10.1002/0471725234>, William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986) <DOI:10.1002/9781118351994>.
Author: David Silkworth [aut],
Jurgen Symynck [aut],
Jacob Ormerod [cre],
OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
Diff between WeibullR versions 1.0.6 dated 2018-04-17 and 1.0.8 dated 2018-04-18
WeibullR-1.0.6/WeibullR/README.md |only WeibullR-1.0.8/WeibullR/DESCRIPTION | 13 ++++++++----- WeibullR-1.0.8/WeibullR/MD5 | 7 +++---- WeibullR-1.0.8/WeibullR/src/CallgetCCC2.cpp | 2 +- WeibullR-1.0.8/WeibullR/src/CallgetPvalue.cpp | 8 ++++---- 5 files changed, 16 insertions(+), 14 deletions(-)
Title: Omnibus Test for Genetic Association Analysis using the Rank
Normal Transformation
Description: Implementation of genetic association tests based on the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two complementary INT-based approaches. In simulations against phenotypes with skewed and heavy tailed residual distributions, the omnibus test provided valid inference in the absence of a genotypic effect, and provided power comparable to the more powerful of the component methods in the presence of a genotypic effect. Under these settings, standard linear regression often failed to control the type I error.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Diff between RNOmni versions 0.2.2 dated 2018-04-16 and 0.3.0 dated 2018-04-18
RNOmni-0.2.2/RNOmni/man/FIINT.Rd |only RNOmni-0.2.2/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.RData |only RNOmni-0.2.2/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.rdb |only RNOmni-0.2.2/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.rdx |only RNOmni-0.3.0/RNOmni/DESCRIPTION | 8 RNOmni-0.3.0/RNOmni/MD5 | 46 +- RNOmni-0.3.0/RNOmni/NAMESPACE | 3 RNOmni-0.3.0/RNOmni/R/DataDesc.R | 4 RNOmni-0.3.0/RNOmni/R/InputCheck.R | 14 RNOmni-0.3.0/RNOmni/R/RankNormal.R | 177 +++++----- RNOmni-0.3.0/RNOmni/R/RcppExports.R | 3 RNOmni-0.3.0/RNOmni/data/G.rda |binary RNOmni-0.3.0/RNOmni/inst/doc/RNOmni.R | 2 RNOmni-0.3.0/RNOmni/inst/doc/RNOmni.Rmd | 18 - RNOmni-0.3.0/RNOmni/inst/doc/RNOmni.html | 66 +-- RNOmni-0.3.0/RNOmni/man/BAT.Rd | 12 RNOmni-0.3.0/RNOmni/man/DINT.Rd | 12 RNOmni-0.3.0/RNOmni/man/G.Rd | 4 RNOmni-0.3.0/RNOmni/man/IINT.Rd | 18 - RNOmni-0.3.0/RNOmni/man/IINT0.Rd |only RNOmni-0.3.0/RNOmni/man/RNOmni.Rd | 28 - RNOmni-0.3.0/RNOmni/man/fitNorm.Rd | 2 RNOmni-0.3.0/RNOmni/man/inCheck.Rd | 6 RNOmni-0.3.0/RNOmni/src/RNOmni.cpp | 10 RNOmni-0.3.0/RNOmni/vignettes/RNOmni.Rmd | 18 - RNOmni-0.3.0/RNOmni/vignettes/RNOmni_cache/html/A02_1cf186843e25729f987ed40207ff32b5.RData |only RNOmni-0.3.0/RNOmni/vignettes/RNOmni_cache/html/A02_1cf186843e25729f987ed40207ff32b5.rdb |only RNOmni-0.3.0/RNOmni/vignettes/RNOmni_cache/html/A02_1cf186843e25729f987ed40207ff32b5.rdx |only 28 files changed, 246 insertions(+), 205 deletions(-)
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 1.6.1 dated 2017-03-06 and 2018.04.18 dated 2018-04-18
prodlim-1.6.1/prodlim/src/declareRoutines.c |only prodlim-1.6.1/prodlim/tests/testthat/prodlim.R |only prodlim-2018.04.18/prodlim/DESCRIPTION | 8 prodlim-2018.04.18/prodlim/MD5 | 115 ++++---- prodlim-2018.04.18/prodlim/NAMESPACE | 1 prodlim-2018.04.18/prodlim/R/EventHistory.frame.R | 13 - prodlim-2018.04.18/prodlim/R/atRisk.R | 2 prodlim-2018.04.18/prodlim/R/checkCauses.R | 51 +-- prodlim-2018.04.18/prodlim/R/followup.R | 4 prodlim-2018.04.18/prodlim/R/jackknife.R | 24 + prodlim-2018.04.18/prodlim/R/leaveOneOut.R | 6 prodlim-2018.04.18/prodlim/R/plot.prodlim.R | 195 +++++++-------- prodlim-2018.04.18/prodlim/R/plotIntervals.R | 2 prodlim-2018.04.18/prodlim/R/predict.prodlim.R | 145 ++++++----- prodlim-2018.04.18/prodlim/R/print.quantile.prodlim.R | 64 +--- prodlim-2018.04.18/prodlim/R/prodlim.R | 35 ++ prodlim-2018.04.18/prodlim/R/quantile.prodlim.R | 25 + prodlim-2018.04.18/prodlim/R/summary.prodlim.R | 48 +-- prodlim-2018.04.18/prodlim/man/EventHistory.frame.Rd | 7 prodlim-2018.04.18/prodlim/man/Hist.Rd | 9 prodlim-2018.04.18/prodlim/man/List2Matrix.Rd | 1 prodlim-2018.04.18/prodlim/man/PercentAxis.Rd | 7 prodlim-2018.04.18/prodlim/man/SimCompRisk.Rd | 1 prodlim-2018.04.18/prodlim/man/SimSurv.Rd | 7 prodlim-2018.04.18/prodlim/man/SmartControl.Rd | 7 prodlim-2018.04.18/prodlim/man/atRisk.Rd | 7 prodlim-2018.04.18/prodlim/man/backGround.Rd | 1 prodlim-2018.04.18/prodlim/man/checkCauses.Rd |only prodlim-2018.04.18/prodlim/man/confInt.Rd | 7 prodlim-2018.04.18/prodlim/man/crModel.Rd | 1 prodlim-2018.04.18/prodlim/man/dimColor.Rd | 7 prodlim-2018.04.18/prodlim/man/getEvent.Rd | 7 prodlim-2018.04.18/prodlim/man/getStates.Rd | 1 prodlim-2018.04.18/prodlim/man/jackknife.Rd | 12 prodlim-2018.04.18/prodlim/man/leaveOneOut.Rd | 12 prodlim-2018.04.18/prodlim/man/markTime.Rd | 7 prodlim-2018.04.18/prodlim/man/meanNeighbors.Rd | 7 prodlim-2018.04.18/prodlim/man/model.design.Rd | 7 prodlim-2018.04.18/prodlim/man/neighborhood.Rd | 7 prodlim-2018.04.18/prodlim/man/parseSpecialNames.Rd | 7 prodlim-2018.04.18/prodlim/man/plot.Hist.Rd | 7 prodlim-2018.04.18/prodlim/man/plot.prodlim.Rd | 24 - prodlim-2018.04.18/prodlim/man/plotCompetingRiskModel.Rd | 7 prodlim-2018.04.18/prodlim/man/plotIllnessDeathModel.Rd | 7 prodlim-2018.04.18/prodlim/man/predict.prodlim.Rd | 26 +- prodlim-2018.04.18/prodlim/man/predictSurvIndividual.Rd | 7 prodlim-2018.04.18/prodlim/man/print.prodlim.Rd | 11 prodlim-2018.04.18/prodlim/man/prodlim.Rd | 10 prodlim-2018.04.18/prodlim/man/quantile.prodlim.Rd | 7 prodlim-2018.04.18/prodlim/man/redist.Rd | 7 prodlim-2018.04.18/prodlim/man/row.match.Rd | 7 prodlim-2018.04.18/prodlim/man/sindex.Rd | 1 prodlim-2018.04.18/prodlim/man/stopTime.Rd | 7 prodlim-2018.04.18/prodlim/man/strip.terms.Rd | 7 prodlim-2018.04.18/prodlim/man/summary.Hist.Rd | 7 prodlim-2018.04.18/prodlim/man/summary.prodlim.Rd | 7 prodlim-2018.04.18/prodlim/man/survModel.Rd | 1 prodlim-2018.04.18/prodlim/src/init.c |only prodlim-2018.04.18/prodlim/src/prodlim_comprisk.c | 19 - prodlim-2018.04.18/prodlim/src/prodlim_surv.c | 30 +- prodlim-2018.04.18/prodlim/tests/testthat/test-prodlim.R |only 61 files changed, 542 insertions(+), 524 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2.5.4 dated 2017-08-08 and 2018.04.18 dated 2018-04-18
pec-2.5.4/pec/R/wallyPlot.R |only pec-2.5.4/pec/data/GBSG2.csv.gz |only pec-2.5.4/pec/data/Pbc3.csv.gz |only pec-2.5.4/pec/data/threecity.csv.gz |only pec-2.5.4/pec/man/wallyPlot.Rd |only pec-2.5.4/pec/src/declareRoutines.c |only pec-2018.04.18/pec/DESCRIPTION | 6 - pec-2018.04.18/pec/MD5 | 26 ++--- pec-2018.04.18/pec/NAMESPACE | 1 pec-2018.04.18/pec/R/cindex.R | 13 +- pec-2018.04.18/pec/R/pec.R | 127 +++++++++++++--------------- pec-2018.04.18/pec/R/predictEventProb.R | 53 ----------- pec-2018.04.18/pec/R/predictLifeYearsLost.R | 60 +++++-------- pec-2018.04.18/pec/data/GBSG2.csv |only pec-2018.04.18/pec/data/Pbc3.csv |only pec-2018.04.18/pec/data/threecity.csv |only pec-2018.04.18/pec/man/cindex.Rd | 13 +- pec-2018.04.18/pec/man/pec.Rd | 4 pec-2018.04.18/pec/src/init.c |only 19 files changed, 117 insertions(+), 186 deletions(-)
Title: Drug Repurposing: Integration and Systematic Investigation of
Genomic High Throughput Data
Description: This is a connectivity mapping-based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs.
Author: Jinyan Chan [aut, cre], Jinghua Gu [aut]
Maintainer: Jinyan Chan <Jinyan_Chan@baylor.edu>
Diff between DrInsight versions 0.1.0 dated 2018-04-17 and 0.1.1 dated 2018-04-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/readin.cmap.R | 5 +---- inst/doc/my-vignette.R | 3 ++- inst/doc/my-vignette.Rmd | 6 ++++-- inst/doc/my-vignette.html | 9 +++++---- man/get.cmap.ref.Rd | 4 ++-- vignettes/my-vignette.Rmd | 6 ++++-- 8 files changed, 28 insertions(+), 25 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre],
Hugh Chipman [aut],
Robert McCulloch [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-1 dated 2018-03-05 and 0.9-3 dated 2018-04-18
dbarts-0.9-1/dbarts/tests/testthat/test-14-predict.R |only dbarts-0.9-3/dbarts/DESCRIPTION | 10 dbarts-0.9-3/dbarts/MD5 | 72 +- dbarts-0.9-3/dbarts/NAMESPACE | 5 dbarts-0.9-3/dbarts/R/A_class.R | 20 dbarts-0.9-3/dbarts/R/bart.R | 39 - dbarts-0.9-3/dbarts/R/dbarts.R | 38 - dbarts-0.9-3/dbarts/R/rbart.R |only dbarts-0.9-3/dbarts/R/sliceSample.R |only dbarts-0.9-3/dbarts/R/xbart.R | 34 - dbarts-0.9-3/dbarts/configure | 18 dbarts-0.9-3/dbarts/configure.ac | 2 dbarts-0.9-3/dbarts/inst/NEWS.Rd | 9 dbarts-0.9-3/dbarts/inst/include/dbarts/bartFit.hpp | 1 dbarts-0.9-3/dbarts/inst/include/dbarts/control.hpp | 12 dbarts-0.9-3/dbarts/inst/include/dbarts/state.hpp | 17 dbarts-0.9-3/dbarts/man/bart.Rd | 33 - dbarts-0.9-3/dbarts/man/dbartsControl.Rd | 13 dbarts-0.9-3/dbarts/man/rbart.Rd |only dbarts-0.9-3/dbarts/man/xbart.Rd | 58 +- dbarts-0.9-3/dbarts/src/R_interface.cpp | 2 dbarts-0.9-3/dbarts/src/R_interface_common.cpp | 217 +++++--- dbarts-0.9-3/dbarts/src/R_interface_crossvalidate.cpp | 90 ++- dbarts-0.9-3/dbarts/src/R_interface_crossvalidate.hpp | 4 dbarts-0.9-3/dbarts/src/R_interface_sampler.cpp | 12 dbarts-0.9-3/dbarts/src/config.hpp.win | 4 dbarts-0.9-3/dbarts/src/crossvalidate.cpp | 287 +++++++++-- dbarts-0.9-3/dbarts/src/crossvalidate.hpp | 15 dbarts-0.9-3/dbarts/src/dbarts/bartFit.cpp | 448 ++++++++---------- dbarts-0.9-3/dbarts/src/dbarts/binaryIO.cpp | 54 +- dbarts-0.9-3/dbarts/src/dbarts/config.hpp.win | 4 dbarts-0.9-3/dbarts/src/dbarts/node.cpp | 18 dbarts-0.9-3/dbarts/src/dbarts/node.hpp | 2 dbarts-0.9-3/dbarts/src/dbarts/state.cpp | 254 +++++----- dbarts-0.9-3/dbarts/src/external/adaptiveRadixTree.c | 13 dbarts-0.9-3/dbarts/src/external/config.h.win | 4 dbarts-0.9-3/dbarts/tests/testthat/test-08-xbart.R | 71 ++ dbarts-0.9-3/dbarts/tests/testthat/test-09-predict.R |only dbarts-0.9-3/dbarts/tests/testthat/test-13-bart2.R | 2 dbarts-0.9-3/dbarts/tests/testthat/test-14-rbart.R |only 40 files changed, 1151 insertions(+), 731 deletions(-)
Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.1.2 dated 2018-03-19 and 0.1.4 dated 2018-04-18
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NAMESPACE | 3 +++ NEWS.md | 9 +++++++++ R/geom_image.R | 8 ++++---- R/ggbackground.R |only README.md | 2 +- inst/doc/ggimage.html | 4 ++-- man/ggbackground.Rd |only 9 files changed, 30 insertions(+), 16 deletions(-)
Title: Easy Dockerfile Creation from R
Description: Build a Dockerfile straight from your R session. 'dockerfiler' allows
you to create step by step a Dockerfile, and provide convenient tools to wrap
R code inside this Dockerfile.
Author: Colin Fay [cre, aut]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between dockerfiler versions 0.1.0 dated 2018-03-01 and 0.1.1 dated 2018-04-18
DESCRIPTION | 12 - MD5 | 14 - R/add.R | 4 R/dockerfile.R | 57 +++--- build/vignette.rds |binary inst/doc/dockerfiler.html | 392 ++++++++++------------------------------------ man/Dockerfile.Rd | 50 ++--- tests/testthat/test-r6.R | 5 8 files changed, 165 insertions(+), 369 deletions(-)
Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scatterpie versions 0.0.9 dated 2018-03-19 and 0.1.0 dated 2018-04-18
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 +++- R/geom_scatterpie.R | 10 +++++++--- README.md | 2 +- inst/doc/scatterpie.html | 13 +++++++------ 6 files changed, 28 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-26 1.0.2
2018-03-17 1.0.1
2018-03-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-27 0.1.2
2015-08-26 0.1.1
2015-08-21 0.1