Title: Time-Course Gene Set Analysis for RNA-Seq Data
Description: Analyze RNA-seq data with variance component score test accounting
for data heteroscedasticity through precision weights. Perform both gene-wise and gene set
analyses, and can deal with longitudinal data. Method is detailed in: Agniel D & Hejblum BP (2017)
Variance component score test for time-course gene set analysis of longitudinal RNA-seq data,
Biostatistics, 18(4):589-604.
Author: Denis Agniel [aut],
Boris P. Hejblum [aut, cre],
Marine Gauthier [aut]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between tcgsaseq versions 1.8.0 dated 2018-11-23 and 1.8.1 dated 2018-12-06
DESCRIPTION | 13 ++++--- MD5 | 34 ++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 13 +++++-- R/TcGSAseq-package.R | 4 +- R/dsFDR.R | 68 +++++++++++++++++++++++++++------------- R/perm_pe.R |only R/tcgsa_seq.R | 26 +++++---------- R/varseq.R | 7 +--- R/vc_score_perm.R | 3 + R/vc_test_asym.R | 16 ++++----- R/vc_test_perm.R | 44 ++++++++++++++++++------- man/dsFDR.Rd | 40 +++++++++++++++++------ man/perm_pe.Rd |only man/tcgsa_seq.Rd | 5 +- man/tcgsaseq.Rd | 4 +- man/varseq.Rd | 7 +--- man/vc_test_perm.Rd | 11 +++++- tests/testthat/test_tcgsa_seq.R | 7 ++-- 19 files changed, 189 insertions(+), 117 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package.
'pkgdown' converts your documentation, vignettes, 'README', and more to
'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 1.2.0 dated 2018-11-20 and 1.3.0 dated 2018-12-06
pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-index-template-md |only pkgdown-1.2.0/pkgdown/tests/testthat/assets/home-index-template-rmd |only pkgdown-1.3.0/pkgdown/DESCRIPTION | 6 pkgdown-1.3.0/pkgdown/MD5 | 44 ++--- pkgdown-1.3.0/pkgdown/NEWS.md | 22 ++ pkgdown-1.3.0/pkgdown/R/build-favicons.R |only pkgdown-1.3.0/pkgdown/R/build-home-index.R | 2 pkgdown-1.3.0/pkgdown/R/build-logo.R | 86 ---------- pkgdown-1.3.0/pkgdown/R/deploy-site.R | 18 +- pkgdown-1.3.0/pkgdown/R/html-tweak.R | 2 pkgdown-1.3.0/pkgdown/R/init.R | 1 pkgdown-1.3.0/pkgdown/README.md | 6 pkgdown-1.3.0/pkgdown/inst/assets/pkgdown.css | 2 pkgdown-1.3.0/pkgdown/inst/assets/pkgdown.js | 9 - pkgdown-1.3.0/pkgdown/inst/templates/content-home.html | 3 pkgdown-1.3.0/pkgdown/inst/templates/head.html | 1 pkgdown-1.3.0/pkgdown/man/build_favicon.Rd | 2 pkgdown-1.3.0/pkgdown/man/deploy_site_github.Rd | 10 - pkgdown-1.3.0/pkgdown/tests/testthat/test-build_home.R | 30 --- pkgdown-1.3.0/pkgdown/tests/testthat/test-html-tweak.R | 15 + pkgdown-1.3.0/pkgdown/vignettes/test/table.Rmd |only 21 files changed, 94 insertions(+), 165 deletions(-)
Title: 'Markdown' Rendering for R
Description: Provides R bindings to the 'Sundown' 'Markdown' rendering library
(<https://github.com/vmg/sundown>). 'Markdown' is a plain-text formatting
syntax that can be converted to 'XHTML' or other formats. See
<http://en.wikipedia.org/wiki/Markdown> for more information about 'Markdown'.
Author: JJ Allaire [aut],
Jeffrey Horner [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Henrik Bengtsson [ctb],
Jim Hester [ctb],
Yixuan Qiu [ctb],
Kohske Takahashi [ctb],
Adam November [ctb],
Nacho Caballero [ctb],
Jeroen Ooms [ctb],
Thomas Leeper [ctb],
Joe Cheng [ctb],
Andrzej Oles [ctb],
Vicent Marti [aut, cph] (The Sundown library),
Natacha Porte [aut, cph] (The Sundown library),
RStudio [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between markdown versions 0.8 dated 2017-04-20 and 0.9 dated 2018-12-06
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ README.md | 7 ++----- build/vignette.rds |binary src/autolink.c | 2 +- src/buffer.c | 3 --- tests/b64EncodeFile.R | 12 +++++++----- tests/tests.Rout.save | 9 +++------ 9 files changed, 36 insertions(+), 38 deletions(-)
Title: Pleiotropy Test for Multiple Traits on a Genetic Marker
Description: Perform tests for pleiotropy of multiple traits of various variable types on genotypes for a genetic marker.
Author: Daniel J Schaid
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pleio versions 1.5 dated 2017-06-27 and 1.6 dated 2018-12-06
DESCRIPTION | 9 +++++---- MD5 | 11 ++++++----- R/pleio.glm.fit.R | 9 ++++++--- build/vignette.rds |binary tests/test.pleio.glm.test.R | 9 ++++++++- tests/test.pleio.glm.test.Rout |only tests/test.pleio.glm.test.Rout.save | 26 +++++++++++++++++++++----- 7 files changed, 46 insertions(+), 18 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from this libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 1.1.5 dated 2018-06-25 and 2.0.0 dated 2018-12-06
multinet-1.1.5/multinet/NEWS |only multinet-1.1.5/multinet/build |only multinet-1.1.5/multinet/inst/extdata/florentine_families.mpx |only multinet-1.1.5/multinet/man/RandomWalkMeasures.Rd |only multinet-1.1.5/multinet/src/include/community |only multinet-1.1.5/multinet/src/include/community.h |only multinet-1.1.5/multinet/src/include/datastructures.h |only multinet-1.1.5/multinet/src/include/dtrace.h |only multinet-1.1.5/multinet/src/include/dynamics.h |only multinet-1.1.5/multinet/src/include/exceptions.h |only multinet-1.1.5/multinet/src/include/generation.h |only multinet-1.1.5/multinet/src/include/io.h |only multinet-1.1.5/multinet/src/include/layout.h |only multinet-1.1.5/multinet/src/include/measures.h |only multinet-1.1.5/multinet/src/include/multinet.h |only multinet-1.1.5/multinet/src/include/randomwalks.h |only multinet-1.1.5/multinet/src/include/transformation.h |only multinet-1.1.5/multinet/src/include/utils |only multinet-1.1.5/multinet/src/include/utils.h |only multinet-1.1.5/multinet/src/lib/dlib |only multinet-1.1.5/multinet/src/lib/spectra |only multinet-1.1.5/multinet/src/multinet/community |only multinet-1.1.5/multinet/src/multinet/datastructures |only multinet-1.1.5/multinet/src/multinet/dynamics |only multinet-1.1.5/multinet/src/multinet/exceptions |only multinet-1.1.5/multinet/src/multinet/generation |only multinet-1.1.5/multinet/src/multinet/io |only multinet-1.1.5/multinet/src/multinet/layout |only multinet-1.1.5/multinet/src/multinet/measures |only multinet-1.1.5/multinet/src/multinet/randomwalks |only multinet-1.1.5/multinet/src/multinet/transformation |only multinet-1.1.5/multinet/src/multinet/utils |only multinet-2.0.0/multinet/DESCRIPTION | 12 multinet-2.0.0/multinet/MD5 | 1990 +- multinet-2.0.0/multinet/NAMESPACE | 3 multinet-2.0.0/multinet/R/datasets.R |only multinet-2.0.0/multinet/R/deprecated.R |only multinet-2.0.0/multinet/R/functions.R | 130 multinet-2.0.0/multinet/inst/extdata/bankwiring.mpx |only multinet-2.0.0/multinet/inst/extdata/florentine.mpx |only multinet-2.0.0/multinet/inst/extdata/monastery.mpx |only multinet-2.0.0/multinet/inst/extdata/tailorshop.mpx |only multinet-2.0.0/multinet/man/Attributes.Rd | 64 multinet-2.0.0/multinet/man/Communities.Rd | 16 multinet-2.0.0/multinet/man/Conversion.Rd | 21 multinet-2.0.0/multinet/man/LayerMeasures.Rd | 4 multinet-2.0.0/multinet/man/Layout.Rd | 2 multinet-2.0.0/multinet/man/Manipulation.Rd | 45 multinet-2.0.0/multinet/man/Plot.Rd | 44 multinet-2.0.0/multinet/man/Predefined.Rd | 18 multinet-2.0.0/multinet/man/Properties.Rd | 40 multinet-2.0.0/multinet/man/Transformation.Rd | 14 multinet-2.0.0/multinet/man/multinet-package.Rd | 20 multinet-2.0.0/multinet/src/Makevars | 12 multinet-2.0.0/multinet/src/Makevars.win | 10 multinet-2.0.0/multinet/src/RcppExports.cpp | 10 multinet-2.0.0/multinet/src/eclat/apriori/src/istree.c | 5130 +++--- multinet-2.0.0/multinet/src/eclat/apriori/src/istree.h | 244 multinet-2.0.0/multinet/src/eclat/eclat/src/eclat.c | 8444 ++++++---- multinet-2.0.0/multinet/src/eclat/eclat/src/eclat.cpp | 8444 ++++++---- multinet-2.0.0/multinet/src/eclat/eclat/src/eclat.h | 25 multinet-2.0.0/multinet/src/eclat/include |only multinet-2.0.0/multinet/src/eclat/math/src/chi2.c | 218 multinet-2.0.0/multinet/src/eclat/math/src/chi2.h | 21 multinet-2.0.0/multinet/src/eclat/math/src/gamma.c | 822 multinet-2.0.0/multinet/src/eclat/math/src/gamma.h | 39 multinet-2.0.0/multinet/src/eclat/math/src/ruleval.c | 853 - multinet-2.0.0/multinet/src/eclat/math/src/ruleval.h | 78 multinet-2.0.0/multinet/src/eclat/tract/src/clomax.c | 926 - multinet-2.0.0/multinet/src/eclat/tract/src/clomax.h | 136 multinet-2.0.0/multinet/src/eclat/tract/src/fim16.c | 2182 +- multinet-2.0.0/multinet/src/eclat/tract/src/fim16.h | 67 multinet-2.0.0/multinet/src/eclat/tract/src/patspec.c | 1945 +- multinet-2.0.0/multinet/src/eclat/tract/src/patspec.h | 112 multinet-2.0.0/multinet/src/eclat/tract/src/report.c | 5045 +++-- multinet-2.0.0/multinet/src/eclat/tract/src/report.h | 554 multinet-2.0.0/multinet/src/eclat/tract/src/tract.c | 8193 ++++++--- multinet-2.0.0/multinet/src/eclat/tract/src/tract.h | 706 multinet-2.0.0/multinet/src/eclat/util/src/arrays.c | 1645 + multinet-2.0.0/multinet/src/eclat/util/src/arrays.h | 627 multinet-2.0.0/multinet/src/eclat/util/src/error.h | 9 multinet-2.0.0/multinet/src/eclat/util/src/escape.c | 472 multinet-2.0.0/multinet/src/eclat/util/src/escape.h | 15 multinet-2.0.0/multinet/src/eclat/util/src/fntypes.h | 12 multinet-2.0.0/multinet/src/eclat/util/src/memsys.c | 318 multinet-2.0.0/multinet/src/eclat/util/src/memsys.h | 69 multinet-2.0.0/multinet/src/eclat/util/src/scanner.c | 2050 +- multinet-2.0.0/multinet/src/eclat/util/src/scanner.h | 129 multinet-2.0.0/multinet/src/eclat/util/src/symtab.c | 951 - multinet-2.0.0/multinet/src/eclat/util/src/symtab.h | 177 multinet-2.0.0/multinet/src/eclat/util/src/tabread.c | 560 multinet-2.0.0/multinet/src/eclat/util/src/tabread.h | 91 multinet-2.0.0/multinet/src/eclat/util/src/tabwrite.c | 259 multinet-2.0.0/multinet/src/eclat/util/src/tabwrite.h | 91 multinet-2.0.0/multinet/src/include/core |only multinet-2.0.0/multinet/src/include/mnet |only multinet-2.0.0/multinet/src/include/net |only multinet-2.0.0/multinet/src/include/tnet |only multinet-2.0.0/multinet/src/include/wnet |only multinet-2.0.0/multinet/src/include/xnet |only multinet-2.0.0/multinet/src/infomap |only multinet-2.0.0/multinet/src/init.cpp |only multinet-2.0.0/multinet/src/lib/eclat/arrays.h | 627 multinet-2.0.0/multinet/src/lib/eclat/chi2.h | 21 multinet-2.0.0/multinet/src/lib/eclat/clomax.h | 136 multinet-2.0.0/multinet/src/lib/eclat/eclat.h | 25 multinet-2.0.0/multinet/src/lib/eclat/error.h | 9 multinet-2.0.0/multinet/src/lib/eclat/escape.h | 15 multinet-2.0.0/multinet/src/lib/eclat/fim16.h | 67 multinet-2.0.0/multinet/src/lib/eclat/fntypes.h | 12 multinet-2.0.0/multinet/src/lib/eclat/gamma.h | 39 multinet-2.0.0/multinet/src/lib/eclat/istree.h | 244 multinet-2.0.0/multinet/src/lib/eclat/memsys.h | 69 multinet-2.0.0/multinet/src/lib/eclat/patspec.h | 112 multinet-2.0.0/multinet/src/lib/eclat/report.h | 554 multinet-2.0.0/multinet/src/lib/eclat/ruleval.h | 78 multinet-2.0.0/multinet/src/lib/eclat/scanner.h | 129 multinet-2.0.0/multinet/src/lib/eclat/symtab.h | 177 multinet-2.0.0/multinet/src/lib/eclat/tabread.h | 91 multinet-2.0.0/multinet/src/lib/eclat/tabwrite.h | 91 multinet-2.0.0/multinet/src/lib/eclat/tract.h | 706 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Cholesky/LDLT.h | 822 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Cholesky/LLT.h | 643 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Cholesky/LLT_LAPACKE.h | 2 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h | 657 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Array.h | 143 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/ArrayBase.h | 107 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/ArrayWrapper.h | 188 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Assign.h | 70 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/AssignEvaluator.h | 1296 - multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Assign_MKL.h | 52 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/BandMatrix.h | 399 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Block.h | 412 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/BooleanRedux.h | 175 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CommaInitializer.h | 210 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/ConditionEstimator.h | 238 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CoreEvaluators.h | 2846 +-- multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CoreIterators.h | 198 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CwiseBinaryOp.h | 175 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CwiseNullaryOp.h | 324 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CwiseTernaryOp.h | 291 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CwiseUnaryOp.h | 66 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/CwiseUnaryView.h | 102 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/DenseBase.h | 443 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/DenseCoeffsBase.h | 316 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/DenseStorage.h | 1029 - multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Diagonal.h | 168 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/DiagonalMatrix.h | 314 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/DiagonalProduct.h | 4 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Dot.h | 239 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/EigenBase.h | 224 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/ForceAlignedAccess.h | 83 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Fuzzy.h | 102 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/GeneralProduct.h | 680 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/GenericPacketMath.h | 667 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/GlobalFunctions.h | 244 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/IO.h | 244 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Inverse.h | 120 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Map.h | 78 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/MapBase.h | 204 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/MathFunctions.h | 1500 + multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/MathFunctionsImpl.h | 89 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/Matrix.h | 213 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/MatrixBase.h | 536 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/NestByValue.h | 74 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/NoAlias.h | 42 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/NumTraits.h | 325 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/PermutationMatrix.h | 538 multinet-2.0.0/multinet/src/lib/eigen3/Eigen/src/Core/PlainObjectBase.h | 1132 - 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multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h | 460 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SparseExtra/MarketIO.h | 519 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h | 447 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SparseExtra/RandomSetter.h | 333 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h | 42 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h | 283 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h | 70 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h | 2426 +- multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h | 63 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/SpecialFunctions/arch/CUDA/CudaSpecialFunctions.h | 130 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/Splines/Spline.h | 478 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/Splines/SplineFitting.h | 416 multinet-2.0.0/multinet/src/lib/eigen3/unsupported/Eigen/src/Splines/SplineFwd.h | 145 multinet-2.0.0/multinet/src/lib/infomap |only multinet-2.0.0/multinet/src/multinet/core |only multinet-2.0.0/multinet/src/multinet/mnet |only multinet-2.0.0/multinet/src/multinet/net |only multinet-2.0.0/multinet/src/multinet/tnet |only multinet-2.0.0/multinet/src/multinet/wnet |only multinet-2.0.0/multinet/src/multinet/xnet |only multinet-2.0.0/multinet/src/r_functions.cpp | 3158 ++- multinet-2.0.0/multinet/src/r_functions.h | 516 multinet-2.0.0/multinet/src/rcpp_module_definition.cpp | 217 multinet-2.0.0/multinet/src/rcpp_utils.cpp | 440 multinet-2.0.0/multinet/src/rcpp_utils.h | 93 550 files changed, 148730 insertions(+), 97891 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] (We have used the following software and made
minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT
license). We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genome Research Ltd (GRL) [cph],
Facebook, Inc [cph]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 6.1 dated 2018-08-02 and 6.7 dated 2018-12-06
ChangeLog | 5 DESCRIPTION | 38 ++++--- MD5 | 187 +++++++++++++++++++++++++++++++---- NAMESPACE | 4 R/seqminer.R | 112 ++++++++++++++++++++- README.md | 3 cleanup | 3 configure | 55 ++++++---- configure.ac | 25 +++- configure.win | 1 inst/bgen |only inst/doc/Manual.html | 2 man/annotateGene.Rd | 14 +- man/readBGENToListByGene.Rd |only man/readBGENToListByRange.Rd |only man/readBGENToMatrixByGene.Rd |only man/readBGENToMatrixByRange.Rd |only man/readVCFToListByGene.Rd | 4 man/readVCFToListByRange.Rd | 3 man/rvmeta.readDataByRange.Rd | 3 src/BGenFile.cpp |only src/BGenFile.h |only src/BGenIndex.cpp |only src/BGenIndex.h |only src/BGenVariant.cpp |only src/BGenVariant.h |only src/BitReader.h |only src/CommonFunction.h |only src/Indexer.h |only src/Makevars.in | 61 +++++++++++ src/Makevars.win | 54 ++++++++++ src/R_CPP_interface.cpp | 63 +++++++++++ src/R_CPP_interface.h | 12 ++ src/TypeConversion.h | 217 +++++++++++++++++++++++------------------ src/bgen2genoLoader.cpp |only src/bgen2genoLoader.h |only src/seqminer.c | 28 +++++ src/seqminer_init.c | 8 + src/sqlite |only src/zstd |only 40 files changed, 725 insertions(+), 177 deletions(-)
Title: Fit and Test Metaregression Models
Description: Fits and tests meta regression models and generates a
number of useful test statistics: next to t- and z-tests, the likelihood ratio,
bartlett corrected likelihood ratio and permutation tests are performed on
the model coefficients.
Author: Hilde M. Huizenga & Ingmar Visser
Maintainer: Ingmar Visser <i.visser@uva.nl>
Diff between metatest versions 1.0-4 dated 2013-01-25 and 1.0-5 dated 2018-12-06
DESCRIPTION | 21 +++++++++++---------- MD5 | 8 ++++---- NAMESPACE | 6 ++++++ NEWS | 3 +++ data/metadata.rda |binary 5 files changed, 24 insertions(+), 14 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.7.1 dated 2018-06-20 and 0.7.2 dated 2018-12-06
ChangeLog | 12 DESCRIPTION | 8 MD5 | 45 - NAMESPACE | 1 R/AAAClasses.R | 5 R/continuum_features.R | 28 R/continuum_features_properties.R | 4 R/nri_methods.R | 10 R/nri_plot.R | 43 - R/speclib_index.R | 7 R/sr.R |only R/vegindex.R | 1591 +++++++++++++++++++------------------- build/hsdar.pdf |binary inst/doc/Hsdar-intro.R | 224 ++--- inst/doc/Hsdar-intro.Rnw | 3 inst/doc/Hsdar-intro.pdf |binary inst/doc/References.pdf |binary man/plot.specfeat.Rd | 11 man/rededge.Rd | 2 man/simple.ratio.index.Rd |only man/specfeat.Rd | 10 man/vegindex.Rd | 5 src/recursiveSR.f90 |only vignettes/Hsdar-intro.Rnw | 3 vignettes/hsdar.bib | 2 25 files changed, 1037 insertions(+), 977 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.1.2 dated 2018-11-23 and 1.2.0 dated 2018-12-06
GenEst-1.1.2/GenEst/man/setkFix.Rd |only GenEst-1.2.0/GenEst/DESCRIPTION | 12 GenEst-1.2.0/GenEst/MD5 | 60 +- GenEst-1.2.0/GenEst/NAMESPACE | 3 GenEst-1.2.0/GenEst/R/GenEst.R | 1 GenEst-1.2.0/GenEst/R/app_download_functions.R | 3 GenEst-1.2.0/GenEst/R/app_msg_functions.R | 29 - GenEst-1.2.0/GenEst/R/app_panels.R | 12 GenEst-1.2.0/GenEst/R/app_server.R | 27 + GenEst-1.2.0/GenEst/R/app_update_input.R | 26 - GenEst-1.2.0/GenEst/R/app_update_output.R | 37 + GenEst-1.2.0/GenEst/R/app_update_rv.R | 101 ++-- GenEst-1.2.0/GenEst/R/app_utilities.R | 34 - GenEst-1.2.0/GenEst/R/app_widgets.R | 114 +---- GenEst-1.2.0/GenEst/R/carcass_persistence_functions.R | 2 GenEst-1.2.0/GenEst/R/detection_probability_figure_functions.R | 11 GenEst-1.2.0/GenEst/R/detection_probability_functions.R | 51 +- GenEst-1.2.0/GenEst/R/mortality_functions.R | 50 -- GenEst-1.2.0/GenEst/R/searcher_efficiency_functions.R | 12 GenEst-1.2.0/GenEst/R/utility_functions.R | 99 ++++ GenEst-1.2.0/GenEst/README.md | 2 GenEst-1.2.0/GenEst/inst/doc/GenEstGUI.html | 4 GenEst-1.2.0/GenEst/inst/doc/command-line-example.html | 132 +++--- GenEst-1.2.0/GenEst/inst/doc/solar-examples.html | 70 +-- GenEst-1.2.0/GenEst/inst/doc/wind-examples.html | 214 +++++----- GenEst-1.2.0/GenEst/man/GenEst.Rd | 1 GenEst-1.2.0/GenEst/man/defineUnitCol.Rd |only GenEst-1.2.0/GenEst/man/kFixedWidget.Rd | 2 GenEst-1.2.0/GenEst/man/modelSelectionWidget.Rd | 2 GenEst-1.2.0/GenEst/man/update_input.Rd | 2 GenEst-1.2.0/GenEst/man/update_rv.Rd | 4 GenEst-1.2.0/GenEst/tests/testthat/test-02-GUI-UI.R | 6 32 files changed, 588 insertions(+), 535 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei (Wayne) Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [ctb],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut],
Eric Dal Moro [aut],
Yuriy Krvavych [ctb],
Vincent Goulet [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.8 dated 2018-11-12 and 0.2.9 dated 2018-12-06
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- R/Triangles.R | 2 - THANKS | 2 - inst/doc/ChainLadder.pdf |binary inst/doc/NEWS.Rmd | 6 +++- inst/doc/NEWS.html | 60 +++++++++++++++++++++++++---------------------- vignettes/NEWS.Rmd | 6 +++- 8 files changed, 56 insertions(+), 42 deletions(-)
Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (www.mc-stan.org).
Author: Robert Kubinec [aut, cre],
Jonah Gabry [ctb],
Ben Goodrich [ctb],
Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>
Diff between idealstan versions 0.5.0 dated 2018-10-31 and 0.5.1 dated 2018-12-06
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/Estimate.R | 20 ++++++++++++-------- R/Generics.R | 2 +- R/Helpers.R | 12 +++++++++++- R/Plot.R | 30 ++++++++++++++++++++++++------ R/rstan_generics.R | 13 ++++++++++--- build/vignette.rds |binary src/stan_files/irt_standard.stan | 9 +-------- src/stan_files/irt_standard_noid.stan | 6 ------ vignettes/Package_Introduction.Rmd | 9 ++++++++- vignettes/Time_Series.Rmd | 4 ++-- 13 files changed, 93 insertions(+), 54 deletions(-)
Title: Identification of the Factors Affecting Species Richness
Description: It identifies the factors significantly related to species richness, and their relative contribution, using multiple regressions and support vector machine models. It uses an output file of 'ModestR' (<http://www.ipez.es/ModestR>) with data of richness of the species and environmental variables in a cell size defined by the user. The residuals of the support vector machine model are shown on a map. Negative residuals may be potential areas with undiscovered and/or unregistered species, or areas with decreased species richness due to the negative effect of anthropogenic factors.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between FactorsR versions 1.2 dated 2017-09-06 and 1.3 dated 2018-12-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- data/Sharks.RData |binary data/adworld.RData |binary man/Factors.Rd | 36 ++++++++++++++++++++++++------------ 5 files changed, 31 insertions(+), 19 deletions(-)
Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the
survey responses, but also the survey metadata, e.g. the original survey
questions and the answer options. The 'surveydata' package makes it easy to
keep track of this metadata, and to easily extract columns with
specific questions.
Author: Andrie de Vries [aut, cre, cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between surveydata versions 0.2.0 dated 2017-07-19 and 0.2.2 dated 2018-12-06
surveydata-0.2.0/surveydata/man/fixCommonEncodingProblems.Rd |only surveydata-0.2.0/surveydata/man/fixLevels01.Rd |only surveydata-0.2.0/surveydata/man/fixLevels01R.Rd |only surveydata-0.2.0/surveydata/man/fixLevels01SPSS.Rd |only surveydata-0.2.0/surveydata/man/hasDK.Rd |only surveydata-0.2.0/surveydata/man/lapplyNames.Rd |only surveydata-0.2.0/surveydata/man/leveltestR.Rd |only surveydata-0.2.0/surveydata/man/leveltestSPSS.Rd |only surveydata-0.2.0/surveydata/man/qOrder.Rd |only surveydata-0.2.0/surveydata/man/qText.Rd |only surveydata-0.2.0/surveydata/man/qTextCommon.Rd |only surveydata-0.2.0/surveydata/man/qTextUnique.Rd |only surveydata-0.2.0/surveydata/man/removeAllDK.Rd |only surveydata-0.2.0/surveydata/man/removeDK.Rd |only surveydata-0.2.0/surveydata/man/splitCommonUnique.Rd |only surveydata-0.2.2/surveydata/DESCRIPTION | 23 surveydata-0.2.2/surveydata/MD5 | 123 +- surveydata-0.2.2/surveydata/NAMESPACE | 39 surveydata-0.2.2/surveydata/NEWS | 58 + surveydata-0.2.2/surveydata/R/cleandata.R | 117 +- surveydata-0.2.2/surveydata/R/dplyr_verbs.R | 1 surveydata-0.2.2/surveydata/R/encoding.R | 15 surveydata-0.2.2/surveydata/R/extract.R | 2 surveydata-0.2.2/surveydata/R/merge.R | 2 surveydata-0.2.2/surveydata/R/opentext.R |only surveydata-0.2.2/surveydata/R/pattern.R | 2 surveydata-0.2.2/surveydata/R/plots.R |only surveydata-0.2.2/surveydata/R/questions.R | 63 + surveydata-0.2.2/surveydata/R/strings.R | 2 surveydata-0.2.2/surveydata/R/surveydata-deprecated.R |only surveydata-0.2.2/surveydata/R/surveydata-package.R | 28 surveydata-0.2.2/surveydata/R/surveydata.R | 12 surveydata-0.2.2/surveydata/R/tools.R | 6 surveydata-0.2.2/surveydata/R/varlabels.R | 2 surveydata-0.2.2/surveydata/build/vignette.rds |binary surveydata-0.2.2/surveydata/inst/doc/surveydata.R | 10 surveydata-0.2.2/surveydata/inst/doc/surveydata.Rmd | 2 surveydata-0.2.2/surveydata/inst/doc/surveydata.html | 430 +++++++--- surveydata-0.2.2/surveydata/inst/examples/example-asSurveydata.R | 12 surveydata-0.2.2/surveydata/inst/examples/example-plots.R |only surveydata-0.2.2/surveydata/inst/examples/example-questions.R | 6 surveydata-0.2.2/surveydata/inst/vignette_child/child.Rmd | 16 surveydata-0.2.2/surveydata/inst/vignette_child/child.html |only surveydata-0.2.2/surveydata/man/as.surveydata.Rd | 27 surveydata-0.2.2/surveydata/man/as_opentext_datatable.Rd |only surveydata-0.2.2/surveydata/man/dplyr-surveydata.Rd | 2 surveydata-0.2.2/surveydata/man/encToInt.Rd | 13 surveydata-0.2.2/surveydata/man/fix_common_encoding_problems.Rd |only surveydata-0.2.2/surveydata/man/fix_levels_01.Rd |only surveydata-0.2.2/surveydata/man/has_dont_know.Rd |only surveydata-0.2.2/surveydata/man/intToEnc.Rd | 12 surveydata-0.2.2/surveydata/man/lapply_names.Rd |only surveydata-0.2.2/surveydata/man/leveltest.Rd |only surveydata-0.2.2/surveydata/man/pattern.Rd | 2 surveydata-0.2.2/surveydata/man/print_opentext.Rd |only surveydata-0.2.2/surveydata/man/question_order.Rd |only surveydata-0.2.2/surveydata/man/question_text.Rd |only surveydata-0.2.2/surveydata/man/question_text_common.Rd |only surveydata-0.2.2/surveydata/man/question_text_unique.Rd |only surveydata-0.2.2/surveydata/man/questions.Rd | 14 surveydata-0.2.2/surveydata/man/remove_all_dont_know.Rd |only surveydata-0.2.2/surveydata/man/remove_dont_know.Rd |only surveydata-0.2.2/surveydata/man/split_common_unique.Rd |only surveydata-0.2.2/surveydata/man/strCommonUnique.Rd | 1 surveydata-0.2.2/surveydata/man/survey_plot_question.Rd |only surveydata-0.2.2/surveydata/man/survey_plot_satisfaction.Rd |only surveydata-0.2.2/surveydata/man/survey_plot_title.Rd |only surveydata-0.2.2/surveydata/man/survey_plot_yes_no.Rd |only surveydata-0.2.2/surveydata/man/surveydata-deprecated.Rd |only surveydata-0.2.2/surveydata/man/surveydata-package.Rd | 32 surveydata-0.2.2/surveydata/man/varlabels.Rd | 1 surveydata-0.2.2/surveydata/man/which.q.Rd | 14 surveydata-0.2.2/surveydata/tests/testthat/helper.R | 57 + surveydata-0.2.2/surveydata/tests/testthat/notest-9-gss.R | 2 surveydata-0.2.2/surveydata/tests/testthat/test-01-essentials.R | 41 surveydata-0.2.2/surveydata/tests/testthat/test-01-surveydata.R | 89 -- surveydata-0.2.2/surveydata/tests/testthat/test-02-whichq.R | 105 -- surveydata-0.2.2/surveydata/tests/testthat/test-05-questions.R | 60 - surveydata-0.2.2/surveydata/tests/testthat/test-10-cleandata.R | 34 surveydata-0.2.2/surveydata/tests/testthat/test-11-encoding.R | 26 surveydata-0.2.2/surveydata/tests/testthat/test-12-plots.R |only surveydata-0.2.2/surveydata/tests/testthat/test-13-opentext.R |only surveydata-0.2.2/surveydata/vignettes/surveydata.Rmd | 2 83 files changed, 942 insertions(+), 563 deletions(-)
Title: R Interface to the ClassyFire RESTful API
Description: Access to the ClassyFire RESTful API <http://classyfire.wishartlab.com>. Retrieve existing entity classifications and submit new entities for classification.
Author: Tom Wilson [aut, cre]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Diff between classyfireR versions 0.1.1 dated 2018-10-14 and 0.1.2 dated 2018-12-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- inst/classyfireR-manual.pdf |binary tests/testthat/test-submission.R | 6 ++---- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Some Algorithms for Mixed Models
Description: This program can be used to fit Gaussian linear mixed models (LMM). Univariate and multivariate response models, multiple variance components, as well as, certain correlation and covariance structures are supported. In many occasions, the user can pick one of the several mixed model fitting algorithms, which are explained further in the details section. Some algorithms are specific to certain types of models (univariate or multivariate, diagonal or non-diagonal residual, one or multiple variance components, etc,...).
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between SAMM versions 1.1 dated 2018-11-26 and 1.1.1 dated 2018-12-06
DESCRIPTION | 6 MD5 | 10 - NAMESPACE | 1 build/partial.rdb |binary man/SAMM.Rd | 111 +----------- src/SAMM.cpp | 479 ++++++++++++++++++++++++++---------------------------- 6 files changed, 260 insertions(+), 347 deletions(-)
Title: Estimation of the Relative Importance of Factors Affecting
Species Distribution Based on Stability Concept
Description: From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between SPEDInstabR versions 1.6 dated 2018-04-20 and 1.7 dated 2018-12-06
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- data/FishFC.RData |binary data/Instability.RData |binary data/VI.RData |binary data/adworld.RData |binary man/ContrBB.Rd | 4 ++-- man/PreExt.Rd | 4 ++-- man/Rmap.Rd | 3 ++- 9 files changed, 17 insertions(+), 16 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C implementation of the Vincenty Formula for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Jan Antala [ctb, cph] (Author of C code for Vincenty distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.2.2 dated 2018-09-29 and 0.2.4 dated 2018-12-06
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++++------ NAMESPACE | 2 ++ NEWS.md | 18 +++++++++++------- R/st_ellipse.R |only R/st_nn.R | 2 +- R/st_remove_holes.R |only inst/doc/intro.pdf |binary man/st_ellipse.Rd |only man/st_nn.Rd | 2 +- man/st_remove_holes.Rd |only 11 files changed, 30 insertions(+), 19 deletions(-)
Title: Variable-Group Methods for Agglomerative Hierarchical Clustering
Description: A collection of methods for agglomerative hierarchical clustering
strategies on a matrix of distances, implemented using the variable-group
approach introduced in Fernandez and Gomez (2008)
<doi:10.1007/s00357-008-9004-x>. Descriptive measures to analyze the resulting
hierarchical trees are also provided. In addition to the usual clustering
methods, two parameterized methods are provided to explore an infinite family
of hierarchical clustering strategies. When there are ties in proximity
values, the hierarchical trees obtained are unique and independent of the
order of the elements in the input matrix.
Author: Alberto Fernandez [aut, cre] (<https://orcid.org/0000-0002-1241-1646>),
Sergio Gomez [aut] (<https://orcid.org/0000-0003-1820-0062>)
Maintainer: Alberto Fernandez <alberto.fernandez@urv.cat>
Diff between mdendro versions 1.0.0 dated 2018-05-31 and 1.0.1 dated 2018-12-06
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/linkage.R | 2 ++ man/linkage.Rd | 4 ++-- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Classes and Methods for Trajectory Data
Description: Classes and methods for trajectory data, with support for nesting individual Track objects in track sets (Tracks) and track sets for different entities in collections of Tracks. Methods include selection, generalization, aggregation, intersection, simulation, and plotting.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Benedikt Klus [aut],
Benedikt Graeler [ctb],
Nikolai Gorte [ctb],
Mehdi Moradi [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between trajectories versions 0.2-0 dated 2018-09-25 and 0.2-1 dated 2018-12-06
trajectories-0.2-0/trajectories/man/density.Track.Rd |only trajectories-0.2-0/trajectories/man/uniqueTrack.Rd |only trajectories-0.2-1/trajectories/DESCRIPTION | 12 trajectories-0.2-1/trajectories/MD5 | 48 - trajectories-0.2-1/trajectories/NAMESPACE | 31 trajectories-0.2-1/trajectories/R/Tracks-methods.R | 10 trajectories-0.2-1/trajectories/R/Trackstat.R | 92 ++ trajectories-0.2-1/trajectories/R/compare-methods.R | 4 trajectories-0.2-1/trajectories/demo/00Index | 1 trajectories-0.2-1/trajectories/demo/A3.R |only trajectories-0.2-1/trajectories/inst/doc/article.R | 282 +++---- trajectories-0.2-1/trajectories/inst/doc/article.Rnw | 385 +++++----- trajectories-0.2-1/trajectories/inst/doc/article.pdf |binary trajectories-0.2-1/trajectories/man/A3.Rd | 39 - trajectories-0.2-1/trajectories/man/as.list.Tracks.Rd |only trajectories-0.2-1/trajectories/man/as.list.TracksCollection.Rd |only trajectories-0.2-1/trajectories/man/chimaps.Rd | 2 trajectories-0.2-1/trajectories/man/density.list.Rd |only trajectories-0.2-1/trajectories/man/dists.Rd | 4 trajectories-0.2-1/trajectories/man/plot.KTrack.Rd | 3 trajectories-0.2-1/trajectories/man/plot.gTrack.Rd | 3 trajectories-0.2-1/trajectories/man/range.Track.Rd |only trajectories-0.2-1/trajectories/man/unique.Track.Rd |only trajectories-0.2-1/trajectories/vignettes/article-003.pdf |only trajectories-0.2-1/trajectories/vignettes/article-016.pdf |only trajectories-0.2-1/trajectories/vignettes/article-017.pdf |only trajectories-0.2-1/trajectories/vignettes/article-018.pdf |only trajectories-0.2-1/trajectories/vignettes/article-019.pdf |only trajectories-0.2-1/trajectories/vignettes/article-020.pdf |only trajectories-0.2-1/trajectories/vignettes/article-021.pdf |only trajectories-0.2-1/trajectories/vignettes/article.Rnw | 385 +++++----- trajectories-0.2-1/trajectories/vignettes/article.tpt |only trajectories-0.2-1/trajectories/vignettes/refs.bib | 166 ++-- 33 files changed, 777 insertions(+), 690 deletions(-)
Title: Chi-Square and Exact Tests for Model-Free Functional Dependency
Description: Statistical hypothesis testing methods for
model-free functional dependency using asymptotic
chi-square or exact distributions. Functional
chi-squares are asymmetric and functionally optimal,
unique from other related statistics. Tests in this package
reveal evidence for causality based on the
causality-by-functionality principle. They include
asymptotic functional chi-square tests, an exact functional
test, a comparative functional chi-square test, and also a
comparative chi-square test. The normalized non-constant
functional chi-square test was used by Best Performer
NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network
Inference Challenges. A function index derived from the
functional chi-square offers a new effect size measure for
the strength of function dependency, a better alternative
to conditional entropy in many aspects. For continuous
data, these tests offer an advantage over regression
analysis when a parametric functional form cannot be
assumed; for categorical data, they provide a novel means
to assess directional dependency not possible with
symmetrical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang [aut],
Hua Zhong [aut],
Ruby Sharma [aut],
Sajal Kumar [aut],
Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.4.5-2 dated 2018-10-23 and 2.4.5-3 dated 2018-12-06
FunChisq-2.4.5-2/FunChisq/inst/doc/fun.chisq.test.R |only FunChisq-2.4.5-3/FunChisq/DESCRIPTION | 29 FunChisq-2.4.5-3/FunChisq/MD5 | 45 - FunChisq-2.4.5-3/FunChisq/NAMESPACE | 11 FunChisq-2.4.5-3/FunChisq/NEWS | 32 + FunChisq-2.4.5-3/FunChisq/R/FunChisq.R | 9 FunChisq-2.4.5-3/FunChisq/R/plot_table.R | 100 ++- FunChisq-2.4.5-3/FunChisq/R/simulate_tables.R | 475 ++++++++------- FunChisq-2.4.5-3/FunChisq/build/vignette.rds |binary FunChisq-2.4.5-3/FunChisq/inst/doc/exact.fun.test.R | 14 FunChisq-2.4.5-3/FunChisq/inst/doc/exact.fun.test.Rmd | 16 FunChisq-2.4.5-3/FunChisq/inst/doc/exact.fun.test.html | 334 ++++++++-- FunChisq-2.4.5-3/FunChisq/inst/doc/fun.chisq.test.Rmd | 34 - FunChisq-2.4.5-3/FunChisq/inst/doc/fun.chisq.test.html | 298 +++++---- FunChisq-2.4.5-3/FunChisq/inst/doc/patterns.R |only FunChisq-2.4.5-3/FunChisq/inst/doc/patterns.Rmd |only FunChisq-2.4.5-3/FunChisq/inst/doc/patterns.html |only FunChisq-2.4.5-3/FunChisq/man/FunChisq-package.Rd | 16 FunChisq-2.4.5-3/FunChisq/man/fun.chisq.test.Rd | 4 FunChisq-2.4.5-3/FunChisq/man/plot_table.Rd | 46 + FunChisq-2.4.5-3/FunChisq/man/simulate_tables.Rd | 119 ++- FunChisq-2.4.5-3/FunChisq/tests/testthat/test_FunChisq.R | 2 FunChisq-2.4.5-3/FunChisq/tests/testthat/test_simulate.R | 50 - FunChisq-2.4.5-3/FunChisq/vignettes/exact.fun.test.Rmd | 16 FunChisq-2.4.5-3/FunChisq/vignettes/fun.chisq.test.Rmd | 34 - FunChisq-2.4.5-3/FunChisq/vignettes/patterns.Rmd |only 26 files changed, 1091 insertions(+), 593 deletions(-)
Title: Ecological Indicators
Description: Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between EcoIndR versions 1.2 dated 2017-09-01 and 1.4 dated 2018-12-06
EcoIndR-1.2/EcoIndR/man/figures/F1.jpg |only EcoIndR-1.4/EcoIndR/DESCRIPTION | 6 EcoIndR-1.4/EcoIndR/MD5 | 14 +- EcoIndR-1.4/EcoIndR/NAMESPACE | 2 EcoIndR-1.4/EcoIndR/R/DER.R | 35 +++++ EcoIndR-1.4/EcoIndR/data/Rotifers.RData |binary EcoIndR-1.4/EcoIndR/man/DER.Rd | 171 +++++++++++++++++++------- EcoIndR-1.4/EcoIndR/man/figures/EcoIndRF3.jpg |binary EcoIndR-1.4/EcoIndR/man/figures/EcoIndRF4.jpg |only 9 files changed, 174 insertions(+), 54 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al. (1991) <doi:10.1007/BF00116466>), the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>) and the localised model (Lee et al. (2015) <doi:10.1002/env.2348>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 5.1 dated 2018-09-10 and 5.1.1 dated 2018-12-06
DESCRIPTION | 8 +- MD5 | 84 +++++++++++++++---------------- R/binomial.MVlerouxCAR.R | 18 ++---- R/binomial.bymCAR.R | 18 ++---- R/binomial.dissimilarityCAR.R | 35 ++++++++----- R/binomial.glm.R | 16 ++--- R/binomial.lerouxCAR.R | 18 ++---- R/binomial.localisedCAR.R | 20 +++---- R/binomial.multilevelCAR.R | 18 ++---- R/common.functions.R | 113 ++++++++++-------------------------------- R/gaussian.MVlerouxCAR.R | 18 ++---- R/gaussian.dissimilarityCAR.R | 35 ++++++++----- R/gaussian.glm.R | 16 ++--- R/gaussian.lerouxCAR.R | 18 ++---- R/gaussian.multilevelCAR.R | 21 +++---- R/multinomial.MVlerouxCAR.R | 20 +++---- R/multinomial.glm.R | 18 ++---- R/poisson.MVlerouxCAR.R | 18 ++---- R/poisson.bymCAR.R | 18 ++---- R/poisson.dissimilarityCAR.R | 36 ++++++++----- R/poisson.glm.R | 17 ++---- R/poisson.lerouxCAR.R | 23 ++++---- R/poisson.localisedCAR.R | 20 +++---- R/poisson.multilevelCAR.R | 18 ++---- R/print.CARBayes.R | 3 - R/zip.bymCAR.R | 20 +++---- R/zip.glm.R | 17 ++---- R/zip.lerouxCAR.R | 18 ++---- inst/doc/CARBayes.Rnw | 6 +- inst/doc/CARBayes.pdf |binary man/CARBayes-package.Rd | 6 +- man/MVS.CARleroux.Rd | 5 + man/S.CARbym.Rd | 9 +-- man/S.CARdissimilarity.Rd | 7 +- man/S.CARleroux.Rd | 11 ++-- man/S.CARlocalised.Rd | 5 + man/S.glm.Rd | 6 +- man/coef.CARBayes.Rd | 2 man/fitted.CARBayes.Rd | 2 man/logLik.CARBayes.Rd | 3 - man/print.CARBayes.Rd | 7 +- man/residuals.CARBayes.Rd | 2 vignettes/CARBayes.Rnw | 6 +- 43 files changed, 360 insertions(+), 419 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.5.0 dated 2017-06-15 and 1.5.1 dated 2018-12-06
DESCRIPTION | 12 ++-- MD5 | 21 ++++--- NAMESPACE | 2 NEWS | 2 R/cutnumeric.R | 31 +++++++--- R/final.plot.R | 53 ++++++++++-------- R/overlap.R | 156 +++++++++++++++++++++++------------------------------- man/cutnumeric.Rd | 10 +-- man/final.plot.Rd | 11 --- man/overlap.Rd | 58 +++++++++++++------- tests |only 11 files changed, 181 insertions(+), 175 deletions(-)
Title: Finding Convergence Clubs
Description: Functions for clustering regions that form convergence clubs, according to the definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>.
Author: Roberto Sichera [aut, cre, cph],
Pietro Pizzuto [aut]
Maintainer: Roberto Sichera <roberto.sichera@unipa.it>
Diff between ConvergenceClubs versions 1.4.1 dated 2018-06-25 and 1.4.2 dated 2018-12-06
ConvergenceClubs-1.4.1/ConvergenceClubs/data/countryGDP.rda |only ConvergenceClubs-1.4.1/ConvergenceClubs/man/countryGDP.Rd |only ConvergenceClubs-1.4.2/ConvergenceClubs/DESCRIPTION | 12 ConvergenceClubs-1.4.2/ConvergenceClubs/MD5 | 64 - ConvergenceClubs-1.4.2/ConvergenceClubs/NAMESPACE | 56 ConvergenceClubs-1.4.2/ConvergenceClubs/R/ConvergenceClubs.R | 5 ConvergenceClubs-1.4.2/ConvergenceClubs/R/club.R | 13 ConvergenceClubs-1.4.2/ConvergenceClubs/R/computeH.R | 132 +- ConvergenceClubs-1.4.2/ConvergenceClubs/R/coreG.R | 16 ConvergenceClubs-1.4.2/ConvergenceClubs/R/countryGDP.R | 39 ConvergenceClubs-1.4.2/ConvergenceClubs/R/dim.convergence.clubs.R | 40 ConvergenceClubs-1.4.2/ConvergenceClubs/R/estimateMod.R | 22 ConvergenceClubs-1.4.2/ConvergenceClubs/R/findClubs.R | 464 +++---- ConvergenceClubs-1.4.2/ConvergenceClubs/R/mergeClubs.R | 414 +++---- ConvergenceClubs-1.4.2/ConvergenceClubs/R/mergeDivergent.R | 80 - ConvergenceClubs-1.4.2/ConvergenceClubs/R/plot.convergence.clubs.R | 582 +++++----- ConvergenceClubs-1.4.2/ConvergenceClubs/R/print.convergence.clubs.R | 26 ConvergenceClubs-1.4.2/ConvergenceClubs/R/summary.convergence.clubs.R | 177 +-- ConvergenceClubs-1.4.2/ConvergenceClubs/README.md | 164 +- ConvergenceClubs-1.4.2/ConvergenceClubs/data/GDP.rda |only ConvergenceClubs-1.4.2/ConvergenceClubs/data/filteredGDP.rda |only ConvergenceClubs-1.4.2/ConvergenceClubs/man/ConvergenceClubs-package.Rd | 89 - ConvergenceClubs-1.4.2/ConvergenceClubs/man/GDP.Rd |only ConvergenceClubs-1.4.2/ConvergenceClubs/man/club.Rd | 91 - ConvergenceClubs-1.4.2/ConvergenceClubs/man/computeH.Rd | 100 - ConvergenceClubs-1.4.2/ConvergenceClubs/man/coreG.Rd | 118 +- ConvergenceClubs-1.4.2/ConvergenceClubs/man/dim.convergence.clubs.Rd | 40 ConvergenceClubs-1.4.2/ConvergenceClubs/man/estimateMod.Rd | 100 - ConvergenceClubs-1.4.2/ConvergenceClubs/man/filteredGDP.Rd |only ConvergenceClubs-1.4.2/ConvergenceClubs/man/findClubs.Rd | 210 +-- ConvergenceClubs-1.4.2/ConvergenceClubs/man/mergeClubs.Rd | 198 +-- ConvergenceClubs-1.4.2/ConvergenceClubs/man/mergeDivergent.Rd | 149 +- ConvergenceClubs-1.4.2/ConvergenceClubs/man/plot.convergence.clubs.Rd | 216 +-- ConvergenceClubs-1.4.2/ConvergenceClubs/man/print.convergence.clubs.Rd | 32 ConvergenceClubs-1.4.2/ConvergenceClubs/man/ps_andrews_hac.Rd | 56 ConvergenceClubs-1.4.2/ConvergenceClubs/man/summary.convergence.clubs.Rd | 32 36 files changed, 1911 insertions(+), 1826 deletions(-)
More information about ConvergenceClubs at CRAN
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Title: Variable Life Adjusted Display and Other Risk-Adjusted Quality
Control Charts
Description: Contains functions to set up risk-adjusted quality control charts
in health care. For the variable life adjusted display (VLAD) proposed by
Lovegrove et al. (1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules
derived in Wittenberg et al. (2018) <doi: 10.1002/sim.7647> are implemented.
Additionally, for the risk-adjusted cumulative sum chart based on log-likelihood
ratio statistic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441>
average run length and control limits can be computed.
Author: Philipp Wittenberg [aut, cre] (<https://orcid.org/0000-0001-7151-8243>),
Sven Knoth [aut, ths] (<https://orcid.org/0000-0002-9666-5554>)
Maintainer: Philipp Wittenberg <pwitten@hsu-hh.de>
Diff between vlad versions 0.1.0 dated 2018-03-06 and 0.2.0 dated 2018-12-06
vlad-0.1.0/vlad/man/figures/README-pressure-1.png |only vlad-0.1.0/vlad/src/eocusum_sim.h |only vlad-0.1.0/vlad/src/racusum_sim.h |only vlad-0.1.0/vlad/src/vlad.h |only vlad-0.1.0/vlad/tests/testthat/test-cusum_arl_sim.R |only vlad-0.1.0/vlad/tests/testthat/test-eocusum_adoc_sim.R |only vlad-0.1.0/vlad/tests/testthat/test-eocusum_arl_h_sim.R |only vlad-0.2.0/vlad/DESCRIPTION | 25 vlad-0.2.0/vlad/MD5 | 128 +- vlad-0.2.0/vlad/NAMESPACE | 13 vlad-0.2.0/vlad/NEWS.md | 20 vlad-0.2.0/vlad/R/RcppExports.R | 20 vlad-0.2.0/vlad/R/eocusum_sim.R | 407 +++----- vlad-0.2.0/vlad/R/misc.R |only vlad-0.2.0/vlad/R/package.R | 12 vlad-0.2.0/vlad/R/racusum_mc.R |only vlad-0.2.0/vlad/R/racusum_sim.R | 604 ++++++------ vlad-0.2.0/vlad/R/zzz.R |only vlad-0.2.0/vlad/README.md | 183 ++- vlad-0.2.0/vlad/build |only vlad-0.2.0/vlad/inst/CITATION | 2 vlad-0.2.0/vlad/inst/include |only vlad-0.2.0/vlad/man/QQ.Rd |only vlad-0.2.0/vlad/man/bcusum_arl_sim.Rd |only vlad-0.2.0/vlad/man/bcusum_crit_sim.Rd |only vlad-0.2.0/vlad/man/calceo.Rd | 36 vlad-0.2.0/vlad/man/cusum_arl_h_sim.Rd | 48 vlad-0.2.0/vlad/man/cusum_arl_sim.Rd | 27 vlad-0.2.0/vlad/man/ell.Rd |only vlad-0.2.0/vlad/man/eocusum_ad_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_adoc_sim.Rd | 73 - vlad-0.2.0/vlad/man/eocusum_arl_h_sim.Rd | 76 - vlad-0.2.0/vlad/man/eocusum_arl_sim.Rd | 92 - vlad-0.2.0/vlad/man/eocusum_arloc_h_sim.Rd | 99 + vlad-0.2.0/vlad/man/eocusum_arloc_sim.Rd | 34 vlad-0.2.0/vlad/man/eocusum_crit_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_scores.Rd |only vlad-0.2.0/vlad/man/figures/README-VLADS1-7-1.png |binary vlad-0.2.0/vlad/man/figures/README-vladS2-1.png |binary vlad-0.2.0/vlad/man/gettherisk.Rd | 104 +- vlad-0.2.0/vlad/man/llr_score.Rd | 93 + vlad-0.2.0/vlad/man/optimal_k.Rd | 67 - vlad-0.2.0/vlad/man/racusum_adoc_sim.Rd | 62 - vlad-0.2.0/vlad/man/racusum_arl_h_sim.Rd | 61 - vlad-0.2.0/vlad/man/racusum_arl_mc.Rd |only vlad-0.2.0/vlad/man/racusum_arl_sim.Rd | 43 vlad-0.2.0/vlad/man/racusum_arloc_h_sim.Rd | 93 + vlad-0.2.0/vlad/man/racusum_arloc_sim.Rd | 73 - vlad-0.2.0/vlad/man/racusum_crit_mc.Rd |only vlad-0.2.0/vlad/man/racusum_crit_sim.Rd |only vlad-0.2.0/vlad/man/racusum_scores.Rd |only vlad-0.2.0/vlad/man/search_delta.Rd |only vlad-0.2.0/vlad/man/trafo.Rd |only vlad-0.2.0/vlad/man/vlad-package.Rd | 14 vlad-0.2.0/vlad/src/Makevars | 5 vlad-0.2.0/vlad/src/Makevars.win | 16 vlad-0.2.0/vlad/src/RcppExports.cpp | 70 + vlad-0.2.0/vlad/src/eocusum_sim.cpp | 36 vlad-0.2.0/vlad/src/racusum_mc.cpp |only vlad-0.2.0/vlad/src/racusum_sim.cpp | 4 vlad-0.2.0/vlad/tests/testthat.R | 2 vlad-0.2.0/vlad/tests/testthat/helper-racusum_arloc_h_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-bcusum_arl_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-bcusum_crit_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-calceo.R | 105 +- vlad-0.2.0/vlad/tests/testthat/test-eocusum_ad_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-eocusum_arl_sim.R | 110 +- vlad-0.2.0/vlad/tests/testthat/test-eocusum_arloc_h_sim.R | 141 +- vlad-0.2.0/vlad/tests/testthat/test-eocusum_arloc_sim.R | 134 +- vlad-0.2.0/vlad/tests/testthat/test-eocusum_crit_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-gettherisk.R | 58 - vlad-0.2.0/vlad/tests/testthat/test-llr_score.R | 164 +-- vlad-0.2.0/vlad/tests/testthat/test-optimal_k.R | 78 + vlad-0.2.0/vlad/tests/testthat/test-racusum_adoc_sim.R | 145 +- vlad-0.2.0/vlad/tests/testthat/test-racusum_arl_mc.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_arl_sim.R | 112 +- vlad-0.2.0/vlad/tests/testthat/test-racusum_arloc_h_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_arloc_sim.R | 117 +- vlad-0.2.0/vlad/tests/testthat/test-racusum_crit_mc.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_crit_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_scores.R |only 81 files changed, 2105 insertions(+), 1701 deletions(-)
Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Compute CCT and the Planckian and daylight loci. Three different standard color difference metrics are included.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.0-2 dated 2018-11-26 and 1.0-4 dated 2018-12-06
DESCRIPTION | 8 MD5 | 45 +-- NEWS.md | 5 R/CCT.R | 577 ++++++++++++++++++++++++++----------------- R/adaptation.R | 3 R/basic.R | 81 +++--- R/datasets.R | 23 + R/daylight.R | 2 R/hooks.R | 34 +- R/locus.R |only R/quintic.R |only R/sysdata.rda |binary data |only inst/doc/isotherms.pdf |binary inst/doc/isotherms.rnw | 59 ++-- inst/extdata/ciexyz31_1.csv |only inst/extdata/illuminants.txt | 9 man/CCT.Rd | 129 ++++++--- man/PlanckianLoci.Rd |only man/daylight.Rd | 18 - man/fromXYZ.Rd | 2 man/standardXYZ.Rd | 5 man/toXYZ.Rd | 5 tests/test-CCT.R | 38 +- tests/test-DeltaE.R | 21 + vignettes/isotherms.rnw | 59 ++-- 26 files changed, 693 insertions(+), 430 deletions(-)
Title: Fast Computing Euclidean Minimum Spanning Trees
Description: Computes an Euclidean Minimum Spanning Tree using the Dual-Tree
Boruvka algorithm (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>)
implemented in 'mlpack' - the C++ Machine Learning library (Curtin, 2005,
<doi:10.21105/joss.00726>). 'emstreeR' works as a wrapper so that R users
can benefit from the fast C++ function for computing an Euclidean Minimum
Spanning Tree without touching the C++ code. The package also provides
functions and an S3 method for readily plotting the Minimum Spanning Trees
(MST) using either 'base' R, 'scatterplot3d' or 'ggplot2' style.
Author: Allan Quadros [aut, cre],
Andre Cancado [aut],
Pedro Brom [aut],
Eduardo Hellas [aut]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 2.0.0 dated 2018-12-03 and 2.1.0 dated 2018-12-06
DESCRIPTION | 24 ++++++++++---------- MD5 | 19 ++++++++-------- NEWS.md | 18 +++++---------- README.md | 18 ++++++++++++--- man/emstreeR-package.Rd | 4 --- man/figures/README-base-1.png |binary man/figures/README-ggplot_curved-1.png |only src/Makevars | 38 ++++++++++++++++++++++++++++++++- src/Makevars.win | 28 +++++++++++++++++++++++- src/RcppExports.cpp | 4 +-- src/mlpack_mst.cpp | 4 ++- 11 files changed, 111 insertions(+), 46 deletions(-)
Title: Composite Likelihood Inference and Diagnostics for Replicated
Spatial Ordinal Data
Description: Composite likelihood parameter estimate and asymptotic covariance matrix are calculated for the spatial ordinal data with replications, where spatial ordinal response with covariate and both spatial exponential covariance within subject and independent and identically distributed measurement error. Parameter estimation can be performed by either solving the gradient function or maximizing composite log-likelihood. Parametric bootstrapping is used to estimate the Godambe information matrix and hence the asymptotic standard error and covariance matrix with parallel processing option. Moreover, the proposed surrogate residual, which extends the results of Liu and Zhang (2017) <doi: 10.1080/01621459.2017.1292915>, can act as a useful tool for model diagnostics.
Author: Ting Fung (Ralph) Ma [cre, aut],
Pingping Wang [aut],
Jun Zhu [aut],
Dipankar Bandyopadhyay [ctb],
Yincai Tang [ctb]
Maintainer: Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>
Diff between clordr versions 1.3.0 dated 2018-04-19 and 1.5.0 dated 2018-12-06
DESCRIPTION | 18 +++++++++--------- MD5 | 8 +++++--- NAMESPACE | 4 +++- R/sur_residual.R |only man/sim.rord.Rd | 4 ++-- man/surrogate.residual.Rd |only 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.3.1 dated 2018-01-03 and 3.3.3 dated 2018-12-06
DESCRIPTION | 9 - MD5 | 6 R/CMplot.r | 343 ++++++++++++++++++++++++++++---------------------- man/CMplot-package.Rd | 10 - 4 files changed, 211 insertions(+), 157 deletions(-)
Title: R/Package Version Check
Description: Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
Author: Guangchuang Yu [aut, cre],
Chun-hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between rvcheck versions 0.1.1 dated 2018-09-27 and 0.1.3 dated 2018-12-06
DESCRIPTION | 20 +-- MD5 | 34 ++--- NAMESPACE | 41 +++---- NEWS | 40 +++--- R/check_pkg.R | 280 ++++++++++++++++++++++++------------------------ R/check_r.R | 78 ++++++------- R/update_all.R | 199 +++++++++++++++++++--------------- R/utilities.R | 148 ++++++++++++------------- man/check_bioc.Rd | 52 ++++---- man/check_cran.Rd | 52 ++++---- man/check_github.Rd | 52 ++++---- man/check_gitlab.Rd | 40 +++--- man/check_r.Rd | 46 +++---- man/get_aes_var.Rd | 44 +++---- man/get_fun_from_pkg.Rd | 44 +++---- man/o.Rd | 28 ++-- man/read.cb.Rd | 40 +++--- man/update_all.Rd | 50 ++++---- 18 files changed, 660 insertions(+), 628 deletions(-)
Title: Quality Control of Sequencing Data
Description: 'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data.
It produces, for each sample, an html report and a compressed file containing the raw data.
If you have hundreds of samples, you are not going to open up each 'HTML' page.
You need some way of looking at these data in aggregate.
'fastqcr' Provides helper functions to easily parse, aggregate and analyze
'FastQC' reports for large numbers of samples. It provides a convenient solution for building
a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between fastqcr versions 0.1.0 dated 2017-04-11 and 0.1.1 dated 2018-12-06
DESCRIPTION | 17 ++++++----- MD5 | 21 ++++++++------ NAMESPACE | 3 ++ NEWS.md | 28 ++++++++++++++++++ R/fastqc.R | 6 ++-- R/qc_plot_collection.R |only R/qc_read.R | 4 +- R/qc_read_collection.R |only R/qc_report.R | 3 ++ README.md | 68 ++++++++++++++++++++++++++-------------------- man/fastqc.Rd | 5 ++- man/qc_plot_collection.Rd |only man/qc_read_collection.Rd |only tools/fastqcr.png |only 14 files changed, 105 insertions(+), 50 deletions(-)