Title: Gene Expression Datasets for the 'MM2S' Package
Description: Gene Expression datasets for the 'MM2S' package. Contains normalized expression data for Human Medulloblastoma ('GSE37418') as well as Mouse Medulloblastoma models ('GSE36594'). Deena Gendoo et al. (2015) <doi:10.1016/j.ygeno.2015.05.002>.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Diff between MM2Sdata versions 1.0.2 dated 2019-03-13 and 1.0.3 dated 2019-03-15
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- build/vignette.rds |binary inst/CITATION |only inst/doc/MM2Sdata.pdf |binary 5 files changed, 10 insertions(+), 9 deletions(-)
Title: 'Rosette' API
Description: 'Rosette' is an API for multilingual text analysis and information
extraction. More information can be found at <https://developer.rosette.com>.
Author: Chris Park [aut],
Sam Hausmann [aut],
Hannah Gaudet [ctb],
Ian Redpath [ctb],
Seth Gransky [ctb, cre],
Basis Technology Corp. [cph]
Maintainer: Seth Gransky <seth@basistech.com>
Diff between rosetteApi versions 1.9.0 dated 2018-01-19 and 1.12.1 dated 2019-03-15
DESCRIPTION | 22 ++-- MD5 | 18 +-- NEWS.md | 6 + R/Api.R | 218 +++++++++++++++++++++++++++------------------- README.md | 18 ++- inst/doc/my-vignette.Rmd | 4 inst/doc/my-vignette.html | 8 - man/api.Rd | 9 + tests/testthat/test_api.R | 23 ++-- vignettes/my-vignette.Rmd | 4 10 files changed, 196 insertions(+), 134 deletions(-)
Title: Performs Common Linear Algebra Operations Used in Quantum
Computing
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Contains all commonly used quantum gates, creates arbitrarily controlled versions of all gates, and can simulate complete or partial measurements of kets. Implements modular arithmetic commonly found in quantum algorithms and can convert functions into equivalent quantum gates. It can also simulate larger applications, including the Quantum Fourier Transform developed by Shor (1999), Shor's algorithm which factors numbers up to 21, Grover's algorithm (1996), the Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and the training of a quantum neural network developed by Schuld (2018) <arXiv:1804.00633> which can classify the MNIST dataset.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Diff between QuantumOps versions 2.4 dated 2019-02-15 and 2.5 dated 2019-03-15
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++++++++--- NAMESPACE | 7 +++++++ R/QAOA.R |only R/QAOA_example.R |only R/checkCases.R |only R/many.R |only R/mexp.R |only R/plotprobs.R |only R/single.R |only R/unitary.R | 2 +- man/QAOA.Rd |only man/QAOA_example.Rd |only man/checkCases.Rd |only man/many.Rd |only man/plotprobs.Rd |only man/single.Rd |only 17 files changed, 29 insertions(+), 9 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and 'purrr' that
formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrrlyr versions 0.0.4 dated 2019-02-15 and 0.0.5 dated 2019-03-15
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/dmap.R | 2 +- R/rows.R | 4 ++-- src/map.c | 2 ++ src/rows.cpp | 12 ++++++------ src/utils.cpp | 13 ++++++++++--- tests/testthat/test-rows.R | 8 ++++---- 9 files changed, 42 insertions(+), 29 deletions(-)
Title: Classification, Regression, Clustering with K Nearest Neighbors
Description: Classification, regression, and clustering with k nearest neighbors
algorithm. Implements several distance and similarity measures, covering
continuous and logical features. Outputs ranked neighbors. Most features of
this package are directly based on the PMML specification for KNN.
Author: Dmitriy Bolotov [aut, cre],
Zementis Inc [cph]
Maintainer: Dmitriy Bolotov <dmitriy.bolotov@softwareag.com>
Diff between neighbr versions 1.0.1 dated 2019-03-13 and 1.0.2 dated 2019-03-15
DESCRIPTION | 6 - MD5 | 14 ++-- NEWS.md | 4 + inst/doc/neighbr-help.html | 19 +++-- tests/testthat/test_comparison_measures.R | 50 --------------- tests/testthat/test_knn.R | 45 +++++++++---- tests/testthat/test_knn_input_check.R | 97 +++++++++++++++--------------- tests/testthat/test_utility_functions.R | 6 - 8 files changed, 108 insertions(+), 133 deletions(-)
Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), hierarchical and non-hierarchical cluster analysis, linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.0.4 dated 2019-02-24 and 2.0.5 dated 2019-03-15
DESCRIPTION | 8 - MD5 | 14 +- R/PP_Index_English.R | 28 ++++ R/PP_Optimizer_English.R | 6 man/MVar-package.Rd | 4 man/PP_Index_English.Rd | 1 man/PP_Optimizer_English.Rd | 1 src/PP_IndexC.c | 282 ++++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 327 insertions(+), 17 deletions(-)
Title: Miscellaneous Basic Functions
Description: A collection of miscellaneous functions for
copying objects to the clipboard ('Copy');
manipulating strings ('concat', 'mgsub', 'trim', 'verlan');
loading or showing packages ('library_with_dep', 'require_with_dep',
'sessionPackages');
creating or testing for named lists ('nlist', 'as.nlist', 'is.nlist'),
formulas ('is.formula'), empty objects ('as.empty', 'is.empty'),
whole numbers ('as.wholenumber', 'is.wholenumber');
testing for equality ('almost.equal', 'almost.zero') and computing
uniqueness ('almost.unique');
getting modified versions of usual functions ('rle2', 'sumNA');
making a pause or a stop ('pause', 'stopif');
converting into a function ('as.fun');
providing a C like ternary operator ('condition %?% true %:% false');
finding packages and functions ('get_all_pkgs', 'get_all_funs');
and others ('erase', '%nin%', 'unwhich', 'top', 'bot', 'normalize').
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between bazar versions 1.0.10 dated 2018-10-06 and 1.0.11 dated 2019-03-15
DESCRIPTION | 10 +++++----- MD5 | 27 ++++++++++++++------------- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/as.fun.R | 19 +++++++++++++++++-- R/find_files_containing.R |only R/get_all_funs.R | 12 ++++++++---- R/get_all_pkgs.R | 17 +++++++++++------ R/is.empty.R | 1 + man/Copy.Rd | 4 ++-- man/almost.unique.Rd | 3 ++- man/as.fun.Rd | 3 +++ man/get_all_pkgs.Rd | 10 ++++++---- man/is.empty.Rd | 1 + man/library_with_dep.Rd | 5 +++-- 15 files changed, 81 insertions(+), 39 deletions(-)
Title: Interim Monitoring Using Adaptively Weighted Log-Rank Test in
Clinical Trials
Description: For any spending function specified by the user, this
package provides corresponding boundaries for interim testing using
the adaptively weighted log-rank test developed by Yang and Prentice
(2010 <doi:10.1111/j.1541-0420.2009.01243.x>).
The package uses a re-sampling method to obtain stopping boundaries
at the interim looks.The output consists of stopping boundaries
and observed values of the test statistics at the interim looks,
along with nominal p-values defined as the probability of the test
exceeding the specific observed test statistic value or critical
value, regardless of the test behavior at other looks.
The asymptotic validity of the stopping boundaries is established
in Yang (2018 <doi:10.1002/sim.7958>).
Author: Daewoo Pak and Song Yang
Maintainer: Daewoo Pak <heavyrain.pak@gmail.com>
Diff between YPInterimTesting versions 1.0.0 dated 2018-11-26 and 1.0.1 dated 2019-03-15
DESCRIPTION | 6 MD5 | 8 NEWS.md | 11 - R/ypinterim.default.R | 431 +++++++++++++++++++++++++------------------------- src/resamf.cpp | 2 5 files changed, 234 insertions(+), 224 deletions(-)
More information about YPInterimTesting at CRAN
Permanent link
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.0.4 dated 2019-02-24 and 2.0.5 dated 2019-03-15
DESCRIPTION | 8 - MD5 | 14 +- R/PP_Index.R | 28 ++++ R/PP_Optimizer.R | 6 - man/MVar.pt-package.Rd | 4 man/PP_Index.Rd | 1 man/PP_Optimizer.Rd | 1 src/PP_IndexC.c | 282 +++++++++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 327 insertions(+), 17 deletions(-)
Title: Statistical Matching or Data Fusion
Description: Integration of two data sources referred to the same target population which share a number of variables. Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <mdo.statmatch@gmail.com>
Diff between StatMatch versions 1.2.5 dated 2017-01-09 and 1.3.0 dated 2019-03-15
StatMatch-1.2.5/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.R |only StatMatch-1.2.5/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.Rnw |only StatMatch-1.2.5/StatMatch/vignettes/Statistical_Matching_with_StatMatch.Rnw |only StatMatch-1.3.0/StatMatch/DESCRIPTION | 15 StatMatch-1.3.0/StatMatch/MD5 | 67 - StatMatch-1.3.0/StatMatch/NEWS | 215 ++-- StatMatch-1.3.0/StatMatch/R/Fbwidths.by.x.R | 179 ++- StatMatch-1.3.0/StatMatch/R/Frechet.bounds.cat.R | 242 ++-- StatMatch-1.3.0/StatMatch/R/NND.hotdeck.R | 22 StatMatch-1.3.0/StatMatch/R/RANDwNND.hotdeck.R | 18 StatMatch-1.3.0/StatMatch/R/SelMtc.by.unc.R |only StatMatch-1.3.0/StatMatch/R/fact2dummy.R | 20 StatMatch-1.3.0/StatMatch/R/gower.dist.R | 21 StatMatch-1.3.0/StatMatch/R/mixed.mtc.R | 4 StatMatch-1.3.0/StatMatch/R/pw.assoc.R | 149 ++ StatMatch-1.3.0/StatMatch/R/rankNND_hotdeck.R | 6 StatMatch-1.3.0/StatMatch/build/vignette.rds |binary StatMatch-1.3.0/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.pdf |binary StatMatch-1.3.0/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.pdf.asis |only StatMatch-1.3.0/StatMatch/man/Fbwidths.by.x.Rd | 72 - StatMatch-1.3.0/StatMatch/man/Frechet.bounds.cat.Rd | 396 +++---- StatMatch-1.3.0/StatMatch/man/NND.hotdeck.Rd | 399 +++---- StatMatch-1.3.0/StatMatch/man/RANDwNND.hotdeck.Rd | 434 ++++---- StatMatch-1.3.0/StatMatch/man/SelMtc.by.unc.Rd |only StatMatch-1.3.0/StatMatch/man/StatMatch-package.Rd | 4 StatMatch-1.3.0/StatMatch/man/comb.samples.Rd | 38 StatMatch-1.3.0/StatMatch/man/comp.prop.Rd | 291 ++--- StatMatch-1.3.0/StatMatch/man/create.fused.Rd | 200 +-- StatMatch-1.3.0/StatMatch/man/fact2dummy.Rd | 133 +- StatMatch-1.3.0/StatMatch/man/gower.dist.Rd | 239 ++-- StatMatch-1.3.0/StatMatch/man/harmonize.x.Rd | 33 StatMatch-1.3.0/StatMatch/man/mahalanobis.dist.Rd | 136 +- StatMatch-1.3.0/StatMatch/man/maximum.dist.Rd | 138 +- StatMatch-1.3.0/StatMatch/man/mixed.mtc.Rd | 536 +++++----- StatMatch-1.3.0/StatMatch/man/pBayes.Rd | 216 ++-- StatMatch-1.3.0/StatMatch/man/pw.assoc.Rd | 267 ++-- StatMatch-1.3.0/StatMatch/man/rankNND.hotdeck.Rd | 304 ++--- StatMatch-1.3.0/StatMatch/vignettes/Statistical_Matching_with_StatMatch.pdf.asis |only 38 files changed, 2554 insertions(+), 2240 deletions(-)
Title: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices.
The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use,
3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>
Diff between matrixTests versions 0.1.0 dated 2018-03-05 and 0.1.1 dated 2019-03-15
matrixTests-0.1.0/matrixTests/README.md |only matrixTests-0.1.1/matrixTests/DESCRIPTION | 8 - matrixTests-0.1.1/matrixTests/MD5 | 40 +++--- matrixTests-0.1.1/matrixTests/NEWS |only matrixTests-0.1.1/matrixTests/R/bartlett.R | 8 - matrixTests-0.1.1/matrixTests/R/cor.R | 8 - matrixTests-0.1.1/matrixTests/R/ievora.R | 36 ++--- matrixTests-0.1.1/matrixTests/R/kruskal.R | 8 - matrixTests-0.1.1/matrixTests/R/oneway.R | 14 +- matrixTests-0.1.1/matrixTests/R/ttest.R | 28 +++- matrixTests-0.1.1/matrixTests/man/bartlett.Rd | 8 - matrixTests-0.1.1/matrixTests/man/cortest.Rd | 8 - matrixTests-0.1.1/matrixTests/man/ievora.Rd | 8 - matrixTests-0.1.1/matrixTests/man/kruskalwallis.Rd | 8 - matrixTests-0.1.1/matrixTests/man/oneway.Rd | 14 +- matrixTests-0.1.1/matrixTests/man/ttest.Rd | 52 +++++--- matrixTests-0.1.1/matrixTests/tests/testthat/test-correct-cor_pearson.R | 6 matrixTests-0.1.1/matrixTests/tests/testthat/test-correct-ievora.R | 20 +-- matrixTests-0.1.1/matrixTests/tests/testthat/test-parameters-main-errors.R | 63 ++++++---- matrixTests-0.1.1/matrixTests/tests/testthat/test-parameters-optional-errors.R | 48 +++---- matrixTests-0.1.1/matrixTests/tests/testthat/test-parameters-special-cases.R | 32 ++--- matrixTests-0.1.1/matrixTests/tests/testthat/test-result-rownames.R | 10 - 22 files changed, 254 insertions(+), 173 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb],
Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between httpuv versions 1.4.5.1 dated 2018-12-18 and 1.5.0 dated 2019-03-15
httpuv-1.4.5.1/httpuv/man/WebSocket-class.Rd |only httpuv-1.4.5.1/httpuv/src/fixup.h |only httpuv-1.4.5.1/httpuv/src/libuv/Makefile.mingw |only httpuv-1.4.5.1/httpuv/src/libuv/android-configure |only httpuv-1.4.5.1/httpuv/src/libuv/checksparse.sh |only httpuv-1.4.5.1/httpuv/src/libuv/include/android-ifaddrs.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/pthread-barrier.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/stdint-msvc2008.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/tree.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-aix.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-bsd.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-darwin.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-errno.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-linux.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-os390.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-posix.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-sunos.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-threadpool.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-unix.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-version.h |only httpuv-1.4.5.1/httpuv/src/libuv/include/uv-win.h |only httpuv-1.4.5.1/httpuv/src/libuv/libuv.nsi |only httpuv-1.4.5.1/httpuv/src/libuv/src/unix/timer.c |only httpuv-1.4.5.1/httpuv/src/libuv/src/win/timer.c |only httpuv-1.5.0/httpuv/DESCRIPTION | 16 httpuv-1.5.0/httpuv/MD5 | 493 httpuv-1.5.0/httpuv/NAMESPACE | 12 httpuv-1.5.0/httpuv/NEWS.md | 21 httpuv-1.5.0/httpuv/R/RcppExports.R | 73 httpuv-1.5.0/httpuv/R/httpuv.R | 383 httpuv-1.5.0/httpuv/R/server.R |only httpuv-1.5.0/httpuv/R/static_paths.R |only httpuv-1.5.0/httpuv/R/utils.R | 23 httpuv-1.5.0/httpuv/man/PipeServer.Rd |only httpuv-1.5.0/httpuv/man/Server.Rd |only httpuv-1.5.0/httpuv/man/WebServer.Rd |only httpuv-1.5.0/httpuv/man/WebSocket.Rd |only httpuv-1.5.0/httpuv/man/encodeURI.Rd | 9 httpuv-1.5.0/httpuv/man/httpuv-package.Rd | 6 httpuv-1.5.0/httpuv/man/listServers.Rd |only httpuv-1.5.0/httpuv/man/runServer.Rd | 12 httpuv-1.5.0/httpuv/man/startDaemonizedServer.Rd | 4 httpuv-1.5.0/httpuv/man/startServer.Rd | 84 httpuv-1.5.0/httpuv/man/staticPath.Rd |only httpuv-1.5.0/httpuv/man/staticPathOptions.Rd |only httpuv-1.5.0/httpuv/man/stopAllServers.Rd | 4 httpuv-1.5.0/httpuv/man/stopDaemonizedServer.Rd | 6 httpuv-1.5.0/httpuv/man/stopServer.Rd | 10 httpuv-1.5.0/httpuv/src/Makevars | 6 httpuv-1.5.0/httpuv/src/Makevars.win | 8 httpuv-1.5.0/httpuv/src/RcppExports-legacy.cpp | 4 httpuv-1.5.0/httpuv/src/RcppExports.cpp | 113 httpuv-1.5.0/httpuv/src/base64/base64.hpp | 2 httpuv-1.5.0/httpuv/src/filedatasource-unix.cpp | 46 httpuv-1.5.0/httpuv/src/filedatasource-win.cpp | 56 httpuv-1.5.0/httpuv/src/filedatasource.h | 20 httpuv-1.5.0/httpuv/src/fs.h |only httpuv-1.5.0/httpuv/src/httprequest.cpp | 40 httpuv-1.5.0/httpuv/src/httprequest.h | 7 httpuv-1.5.0/httpuv/src/httpresponse.cpp | 7 httpuv-1.5.0/httpuv/src/httpresponse.h | 6 httpuv-1.5.0/httpuv/src/httpuv.cpp | 214 httpuv-1.5.0/httpuv/src/httpuv.h | 3 httpuv-1.5.0/httpuv/src/libuv/AUTHORS | 30 httpuv-1.5.0/httpuv/src/libuv/CMakeLists.txt |only httpuv-1.5.0/httpuv/src/libuv/CONTRIBUTING.md | 5 httpuv-1.5.0/httpuv/src/libuv/ChangeLog | 413 httpuv-1.5.0/httpuv/src/libuv/MAINTAINERS.md | 4 httpuv-1.5.0/httpuv/src/libuv/Makefile-libuv.mingw |only httpuv-1.5.0/httpuv/src/libuv/Makefile.am | 48 httpuv-1.5.0/httpuv/src/libuv/Makefile.in | 4984 +++++----- httpuv-1.5.0/httpuv/src/libuv/README.md | 104 httpuv-1.5.0/httpuv/src/libuv/SUPPORTED_PLATFORMS.md | 3 httpuv-1.5.0/httpuv/src/libuv/aclocal.m4 | 191 httpuv-1.5.0/httpuv/src/libuv/android-configure-arm |only httpuv-1.5.0/httpuv/src/libuv/android-configure-arm64 |only httpuv-1.5.0/httpuv/src/libuv/android-configure-x86 |only httpuv-1.5.0/httpuv/src/libuv/android-configure-x86_64 |only httpuv-1.5.0/httpuv/src/libuv/appveyor.yml | 7 httpuv-1.5.0/httpuv/src/libuv/ar-lib | 4 httpuv-1.5.0/httpuv/src/libuv/common.gypi | 14 httpuv-1.5.0/httpuv/src/libuv/compile | 8 httpuv-1.5.0/httpuv/src/libuv/config.guess | 559 - httpuv-1.5.0/httpuv/src/libuv/config.sub | 249 httpuv-1.5.0/httpuv/src/libuv/configure | 263 httpuv-1.5.0/httpuv/src/libuv/configure.ac | 9 httpuv-1.5.0/httpuv/src/libuv/depcomp | 8 httpuv-1.5.0/httpuv/src/libuv/docs/code/tty-gravity/main.c | 2 httpuv-1.5.0/httpuv/src/libuv/docs/code/tty/main.c | 2 httpuv-1.5.0/httpuv/src/libuv/docs/src/conf.py | 2 httpuv-1.5.0/httpuv/src/libuv/docs/src/errors.rst | 21 httpuv-1.5.0/httpuv/src/libuv/docs/src/fs.rst | 66 httpuv-1.5.0/httpuv/src/libuv/docs/src/fs_event.rst | 6 httpuv-1.5.0/httpuv/src/libuv/docs/src/guide/processes.rst | 4 httpuv-1.5.0/httpuv/src/libuv/docs/src/guide/utilities.rst | 8 httpuv-1.5.0/httpuv/src/libuv/docs/src/handle.rst | 43 httpuv-1.5.0/httpuv/src/libuv/docs/src/loop.rst | 14 httpuv-1.5.0/httpuv/src/libuv/docs/src/misc.rst | 38 httpuv-1.5.0/httpuv/src/libuv/docs/src/pipe.rst | 4 httpuv-1.5.0/httpuv/src/libuv/docs/src/process.rst | 11 httpuv-1.5.0/httpuv/src/libuv/docs/src/request.rst | 36 httpuv-1.5.0/httpuv/src/libuv/docs/src/signal.rst | 10 httpuv-1.5.0/httpuv/src/libuv/docs/src/stream.rst | 8 httpuv-1.5.0/httpuv/src/libuv/docs/src/tcp.rst | 11 httpuv-1.5.0/httpuv/src/libuv/docs/src/threading.rst | 11 httpuv-1.5.0/httpuv/src/libuv/docs/src/timer.rst | 2 httpuv-1.5.0/httpuv/src/libuv/docs/src/tty.rst | 11 httpuv-1.5.0/httpuv/src/libuv/docs/src/udp.rst | 19 httpuv-1.5.0/httpuv/src/libuv/gyp_uv.py | 23 httpuv-1.5.0/httpuv/src/libuv/include/uv |only httpuv-1.5.0/httpuv/src/libuv/include/uv.h | 104 httpuv-1.5.0/httpuv/src/libuv/install-sh | 45 httpuv-1.5.0/httpuv/src/libuv/libuv.pc.in | 3 httpuv-1.5.0/httpuv/src/libuv/m4/libuv-check-flags.m4 | 4 httpuv-1.5.0/httpuv/src/libuv/missing | 14 httpuv-1.5.0/httpuv/src/libuv/samples/socks5-proxy/main.c | 6 httpuv-1.5.0/httpuv/src/libuv/src/fs-poll.c | 4 httpuv-1.5.0/httpuv/src/libuv/src/inet.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/threadpool.c | 104 httpuv-1.5.0/httpuv/src/libuv/src/timer.c |only httpuv-1.5.0/httpuv/src/libuv/src/unix/aix-common.c | 26 httpuv-1.5.0/httpuv/src/libuv/src/unix/aix.c | 63 httpuv-1.5.0/httpuv/src/libuv/src/unix/android-ifaddrs.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/unix/async.c | 8 httpuv-1.5.0/httpuv/src/libuv/src/unix/bsd-ifaddrs.c | 6 httpuv-1.5.0/httpuv/src/libuv/src/unix/core.c | 183 httpuv-1.5.0/httpuv/src/libuv/src/unix/cygwin.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/unix/darwin-proctitle.c | 13 httpuv-1.5.0/httpuv/src/libuv/src/unix/darwin.c | 24 httpuv-1.5.0/httpuv/src/libuv/src/unix/freebsd.c | 82 httpuv-1.5.0/httpuv/src/libuv/src/unix/fs.c | 234 httpuv-1.5.0/httpuv/src/libuv/src/unix/fsevents.c | 28 httpuv-1.5.0/httpuv/src/libuv/src/unix/getaddrinfo.c | 11 httpuv-1.5.0/httpuv/src/libuv/src/unix/getnameinfo.c | 3 httpuv-1.5.0/httpuv/src/libuv/src/unix/ibmi.c | 5 httpuv-1.5.0/httpuv/src/libuv/src/unix/internal.h | 41 httpuv-1.5.0/httpuv/src/libuv/src/unix/kqueue.c | 12 httpuv-1.5.0/httpuv/src/libuv/src/unix/linux-core.c | 131 httpuv-1.5.0/httpuv/src/libuv/src/unix/linux-inotify.c | 12 httpuv-1.5.0/httpuv/src/libuv/src/unix/linux-syscalls.c | 133 httpuv-1.5.0/httpuv/src/libuv/src/unix/linux-syscalls.h | 34 httpuv-1.5.0/httpuv/src/libuv/src/unix/loop-watcher.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/unix/loop.c | 9 httpuv-1.5.0/httpuv/src/libuv/src/unix/netbsd.c | 55 httpuv-1.5.0/httpuv/src/libuv/src/unix/no-fsevents.c | 6 httpuv-1.5.0/httpuv/src/libuv/src/unix/no-proctitle.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/unix/openbsd.c | 60 httpuv-1.5.0/httpuv/src/libuv/src/unix/os390-syscalls.c | 100 httpuv-1.5.0/httpuv/src/libuv/src/unix/os390-syscalls.h | 5 httpuv-1.5.0/httpuv/src/libuv/src/unix/os390.c | 172 httpuv-1.5.0/httpuv/src/libuv/src/unix/pipe.c | 88 httpuv-1.5.0/httpuv/src/libuv/src/unix/poll.c | 7 httpuv-1.5.0/httpuv/src/libuv/src/unix/posix-poll.c | 18 httpuv-1.5.0/httpuv/src/libuv/src/unix/process.c | 57 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httpuv-1.5.0/httpuv/src/libuv/src/win/getaddrinfo.c | 16 httpuv-1.5.0/httpuv/src/libuv/src/win/getnameinfo.c | 48 httpuv-1.5.0/httpuv/src/libuv/src/win/handle-inl.h | 25 httpuv-1.5.0/httpuv/src/libuv/src/win/handle.c | 12 httpuv-1.5.0/httpuv/src/libuv/src/win/internal.h | 124 httpuv-1.5.0/httpuv/src/libuv/src/win/loop-watcher.c | 2 httpuv-1.5.0/httpuv/src/libuv/src/win/pipe.c | 1121 +- httpuv-1.5.0/httpuv/src/libuv/src/win/poll.c | 51 httpuv-1.5.0/httpuv/src/libuv/src/win/process-stdio.c | 59 httpuv-1.5.0/httpuv/src/libuv/src/win/process.c | 81 httpuv-1.5.0/httpuv/src/libuv/src/win/signal.c | 48 httpuv-1.5.0/httpuv/src/libuv/src/win/snprintf.c | 5 httpuv-1.5.0/httpuv/src/libuv/src/win/stream-inl.h | 10 httpuv-1.5.0/httpuv/src/libuv/src/win/stream.c | 36 httpuv-1.5.0/httpuv/src/libuv/src/win/tcp.c | 239 httpuv-1.5.0/httpuv/src/libuv/src/win/thread.c | 238 httpuv-1.5.0/httpuv/src/libuv/src/win/tty.c | 155 httpuv-1.5.0/httpuv/src/libuv/src/win/udp.c | 102 httpuv-1.5.0/httpuv/src/libuv/src/win/util.c | 277 httpuv-1.5.0/httpuv/src/libuv/src/win/winapi.c | 45 httpuv-1.5.0/httpuv/src/libuv/src/win/winapi.h | 58 httpuv-1.5.0/httpuv/src/libuv/src/win/winsock.c | 38 httpuv-1.5.0/httpuv/src/libuv/src/win/winsock.h | 3 httpuv-1.5.0/httpuv/src/libuv/test/benchmark-async-pummel.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/run-tests.c | 5 httpuv-1.5.0/httpuv/src/libuv/test/runner-unix.c | 13 httpuv-1.5.0/httpuv/src/libuv/test/runner-win.c | 4 httpuv-1.5.0/httpuv/src/libuv/test/runner.h | 13 httpuv-1.5.0/httpuv/src/libuv/test/task.h | 4 httpuv-1.5.0/httpuv/src/libuv/test/test-callback-stack.c | 15 httpuv-1.5.0/httpuv/src/libuv/test/test-condvar.c | 238 httpuv-1.5.0/httpuv/src/libuv/test/test-connect-unspecified.c |only httpuv-1.5.0/httpuv/src/libuv/test/test-connection-fail.c | 4 httpuv-1.5.0/httpuv/src/libuv/test/test-delayed-accept.c | 4 httpuv-1.5.0/httpuv/src/libuv/test/test-error.c | 6 httpuv-1.5.0/httpuv/src/libuv/test/test-fork.c | 21 httpuv-1.5.0/httpuv/src/libuv/test/test-fs-copyfile.c | 27 httpuv-1.5.0/httpuv/src/libuv/test/test-fs-event.c | 46 httpuv-1.5.0/httpuv/src/libuv/test/test-fs.c | 332 httpuv-1.5.0/httpuv/src/libuv/test/test-getters-setters.c |only httpuv-1.5.0/httpuv/src/libuv/test/test-handle-fileno.c | 6 httpuv-1.5.0/httpuv/src/libuv/test/test-hrtime.c | 6 httpuv-1.5.0/httpuv/src/libuv/test/test-ipc-heavy-traffic-deadlock-bug.c |only httpuv-1.5.0/httpuv/src/libuv/test/test-ipc-send-recv.c | 7 httpuv-1.5.0/httpuv/src/libuv/test/test-ipc.c | 15 httpuv-1.5.0/httpuv/src/libuv/test/test-list.h | 72 httpuv-1.5.0/httpuv/src/libuv/test/test-loop-close.c | 18 httpuv-1.5.0/httpuv/src/libuv/test/test-loop-handles.c | 16 httpuv-1.5.0/httpuv/src/libuv/test/test-ping-pong.c | 89 httpuv-1.5.0/httpuv/src/libuv/test/test-pipe-close-stdout-read-stdin.c | 3 httpuv-1.5.0/httpuv/src/libuv/test/test-pipe-set-fchmod.c | 28 httpuv-1.5.0/httpuv/src/libuv/test/test-poll.c | 5 httpuv-1.5.0/httpuv/src/libuv/test/test-process-priority.c |only httpuv-1.5.0/httpuv/src/libuv/test/test-process-title-threadsafe.c |only httpuv-1.5.0/httpuv/src/libuv/test/test-signal-multiple-loops.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-signal.c | 20 httpuv-1.5.0/httpuv/src/libuv/test/test-spawn.c | 25 httpuv-1.5.0/httpuv/src/libuv/test/test-tcp-bind-error.c | 42 httpuv-1.5.0/httpuv/src/libuv/test/test-tcp-oob.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-tcp-open.c | 125 httpuv-1.5.0/httpuv/src/libuv/test/test-tcp-write-queue-order.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-timer-again.c | 4 httpuv-1.5.0/httpuv/src/libuv/test/test-tty.c | 51 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-alloc-cb-fail.c | 3 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-ipv6.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-multicast-interface.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-multicast-join.c | 3 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-multicast-join6.c | 6 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-multicast-ttl.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-open.c | 17 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-options.c | 19 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-send-and-recv.c | 6 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-send-hang-loop.c | 2 httpuv-1.5.0/httpuv/src/libuv/test/test-udp-send-immediate.c | 3 httpuv-1.5.0/httpuv/src/libuv/test/test.gyp |only httpuv-1.5.0/httpuv/src/libuv/uv.gyp | 386 httpuv-1.5.0/httpuv/src/libuv/vcbuild.bat | 7 httpuv-1.5.0/httpuv/src/mime.cpp |only httpuv-1.5.0/httpuv/src/mime.h |only httpuv-1.5.0/httpuv/src/staticpath.cpp |only httpuv-1.5.0/httpuv/src/staticpath.h |only httpuv-1.5.0/httpuv/src/utils.h | 248 httpuv-1.5.0/httpuv/src/uvutil.h | 16 httpuv-1.5.0/httpuv/src/webapplication.cpp | 281 httpuv-1.5.0/httpuv/src/webapplication.h | 19 httpuv-1.5.0/httpuv/tests/testthat/apps |only httpuv-1.5.0/httpuv/tests/testthat/helper-app.R |only httpuv-1.5.0/httpuv/tests/testthat/sample_app.R | 10 httpuv-1.5.0/httpuv/tests/testthat/test-app.R |only httpuv-1.5.0/httpuv/tests/testthat/test-static-paths.R |only httpuv-1.5.0/httpuv/tests/testthat/test-traffic.R | 79 httpuv-1.5.0/httpuv/tests/testthat/test-utils.R | 77 httpuv-1.5.0/httpuv/tools |only 265 files changed, 10543 insertions(+), 6858 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Krzysiek G [ctb] (https://github.com/storaged),
Manuela Hummel [ctb] (https://github.com/hummelma),
Chase Clark [ctb] (https://github.com/chasemc),
Lucas Graybuck [ctb] (https://github.com/hypercompetent),
jdetribol [ctb] (https://github.com/jdetribol),
Ben Ho [ctb] (https://github.com/SplitInf)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.9.0 dated 2018-10-19 and 1.10.0 dated 2019-03-15
DESCRIPTION | 14 MD5 | 32 + NAMESPACE | 3 NEWS | 15 R/cutree.dendrogram.R | 19 + R/pvclust.R | 27 + inst/doc/Cluster_Analysis.html | 146 ++++---- inst/doc/FAQ.html | 60 +-- inst/doc/Quick_Introduction.html | 6 inst/doc/introduction.html | 537 ++++++++++++++++----------------- man/cutree-methods.Rd | 9 man/pvclust_edges.Rd |only tests/testthat/test-bk_method.R | 1 tests/testthat/test-cor_bakers_gamma.R | 1 tests/testthat/test-cor_cophenetic.R | 1 tests/testthat/test-pvclust_extract.R |only tests/testthat/test-set.dendrogram.R | 1 tests/testthat/test-untangle.R | 2 18 files changed, 477 insertions(+), 397 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff
Algorithm)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.2.1 dated 2019-01-18 and 0.2.2 dated 2019-03-15
DESCRIPTION | 7 +++---- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/run.R | 5 ++++- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Randomer Forest
Description: R-RerF (aka Randomer Forest (RerF) or Random Projection
Forests) is an algorithm developed by Tomita (2016) <arXiv:1506.03410v2>
which is similar to Random Forest - Random Combination (Forest-RC)
developed by Breiman (2001) <doi:10.1023/A:1010933404324>. Random
Forests create axis-parallel, or orthogonal trees. That is, the feature
space is recursively split along directions parallel to the axes of the
feature space. Thus, in cases in which the classes seem inseparable
along any single dimension, Random Forests may be suboptimal. To
address this, Breiman also proposed and characterized Forest-RC, which
uses linear combinations of coordinates rather than individual
coordinates, to split along. This package, 'rerf', implements RerF
which is similar to Forest-RC. The difference between the two
algorithms is where the random linear combinations occur: Forest-RC
combines features at the per tree level whereas RerF takes linear
combinations of coordinates at every node in the tree.
Author: Jesse Patsolic [ctb, cre],
Benjamin Falk [ctb],
Jaewon Chung [ctb],
James Browne [aut],
Tyler Tomita [aut],
Joshua Vogelstein [ths]
Maintainer: Jesse Patsolic <software@neurodata.io>
Diff between rerf versions 2.0.3 dated 2019-02-06 and 2.0.4 dated 2019-03-15
DESCRIPTION | 10 +-- MD5 | 10 +-- R/RandMat.R | 8 +- man/RandMatFRC.Rd | 8 +- tests/testthat/test-RandMat.R | 126 +++++++++++++++++++++++++++++++++++++- tests/testthat/test-predictions.R | 21 ++++-- 6 files changed, 157 insertions(+), 26 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrr versions 0.3.1 dated 2019-03-03 and 0.3.2 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ build/purrr.pdf |binary src/pluck.c | 3 +++ tests/testthat/test-compose.R | 2 +- 6 files changed, 17 insertions(+), 9 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] (Hash table implementation in src/pfhash.h),
R Core Team [cph] (Used/adapted several code snippets from R sources,
see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.6 dated 2018-08-15 and 0.2.7 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/alike.html | 20 ++++++++++---------- inst/doc/vetr.html | 10 +++++----- src/alike.c | 4 ++-- src/all-bw.c | 6 +++--- tests/run.R | 2 ++ 9 files changed, 38 insertions(+), 31 deletions(-)
Title: Regression Standardization
Description: Contains functionality for regression standardization.
Four general classes of models are allowed; generalized linear models,
Conditional generalized estimating equation models,
Cox proportional hazards models and shared frailty gamma-Weibull models. Sjolander, A. (2016) <doi:10.1007/s10654-016-0157-3>.
Author: Arvid Sjolander and Elisabeth Dahlqwist
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>
Diff between stdReg versions 3.2.0 dated 2019-03-14 and 3.3.0 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary inst/NEWS.Rd | 25 ++----------------------- 4 files changed, 9 insertions(+), 30 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <http://www.openstreetmap.org/>,
Bing Maps <http://www.bing.com/maps> and other tiled map sources. Use to create
basemaps quickly and add hillshade to vector-based maps.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
Timothée Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.2.2 dated 2017-04-07 and 0.2.4 dated 2019-03-15
rosm-0.2.2/rosm/inst/README_files |only rosm-0.2.2/rosm/tests/manual |only rosm-0.2.4/rosm/DESCRIPTION | 23 ++-- rosm-0.2.4/rosm/MD5 | 146 ++++++++++++++++++++++------ rosm-0.2.4/rosm/R/0_tilespec.R | 28 ++++- rosm-0.2.4/rosm/R/1_tiles.R | 4 rosm-0.2.4/rosm/R/bingmaps.R | 3 rosm-0.2.4/rosm/R/extract.R | 6 - rosm-0.2.4/rosm/R/osmplot.R | 8 - rosm-0.2.4/rosm/R/rosm-package.R | 30 ----- rosm-0.2.4/rosm/README.md | 119 ++-------------------- rosm-0.2.4/rosm/build |only rosm-0.2.4/rosm/inst/doc |only rosm-0.2.4/rosm/man/as.tile_source.Rd | 7 - rosm-0.2.4/rosm/man/bmaps.plot.Rd | 1 rosm-0.2.4/rosm/man/bmaps.types.Rd | 1 rosm-0.2.4/rosm/man/extract_bbox.Rd | 7 - rosm-0.2.4/rosm/man/figures |only rosm-0.2.4/rosm/man/osm.image.Rd | 10 - rosm-0.2.4/rosm/man/osm.lines.Rd | 1 rosm-0.2.4/rosm/man/osm.plot.Rd | 1 rosm-0.2.4/rosm/man/osm.points.Rd | 1 rosm-0.2.4/rosm/man/osm.polygon.Rd | 1 rosm-0.2.4/rosm/man/osm.segments.Rd | 4 rosm-0.2.4/rosm/man/osm.text.Rd | 5 rosm-0.2.4/rosm/man/osm.types.Rd | 1 rosm-0.2.4/rosm/man/register_tile_source.Rd | 3 rosm-0.2.4/rosm/man/rosm.Rd | 37 ------- rosm-0.2.4/rosm/man/set_default_cachedir.Rd | 3 rosm-0.2.4/rosm/tests/testthat |only rosm-0.2.4/rosm/tests/testthat.R |only rosm-0.2.4/rosm/vignettes |only 32 files changed, 206 insertions(+), 244 deletions(-)
Title: Heatmaps for Multiple Network Data
Description: Simplify the exploratory data analysis process for multiple network
data sets with the help of hierarchical clustering, consensus
clustering and heatmaps. Multiple network data consists of multiple
disjoint networks that have common variables (e.g. ego networks).
This package contains the necessary tools for exploring such data,
from the data pre-processing stage to the creation of dynamic
visualizations.
Author: Philippe Boileau [aut, cre]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between neatmaps versions 1.1.0 dated 2018-07-02 and 2.0.0 dated 2019-03-15
neatmaps-1.1.0/neatmaps/R/compactNodeAttr.R |only neatmaps-1.1.0/neatmaps/R/edgeData.R |only neatmaps-1.1.0/neatmaps/R/formatClusters.R |only neatmaps-1.1.0/neatmaps/R/netDataFrame.R |only neatmaps-1.1.0/neatmaps/R/networkAttr.R |only neatmaps-1.1.0/neatmaps/R/nodeAttr.R |only neatmaps-1.1.0/neatmaps/R/plotDendrogram.R |only neatmaps-1.1.0/neatmaps/inst |only neatmaps-1.1.0/neatmaps/man/compactNodeAttr.Rd |only neatmaps-1.1.0/neatmaps/man/edgeDF.Rd |only neatmaps-1.1.0/neatmaps/man/formatCluster.Rd |only neatmaps-1.1.0/neatmaps/man/networkAttrDF.Rd |only neatmaps-1.1.0/neatmaps/man/nodeAttrDF.Rd |only neatmaps-1.1.0/neatmaps/man/plotDendrogram.Rd |only neatmaps-2.0.0/neatmaps/DESCRIPTION | 33 +- neatmaps-2.0.0/neatmaps/MD5 | 71 +++-- neatmaps-2.0.0/neatmaps/NAMESPACE | 53 ++- neatmaps-2.0.0/neatmaps/R/aggNodeAttr.R |only neatmaps-2.0.0/neatmaps/R/calcICLNoPlots.R |only neatmaps-2.0.0/neatmaps/R/consClustResTable.R |only neatmaps-2.0.0/neatmaps/R/consensusChangeECDF.R |only neatmaps-2.0.0/neatmaps/R/consensusClusterNoPlots.R |only neatmaps-2.0.0/neatmaps/R/consensusECDF.R |only neatmaps-2.0.0/neatmaps/R/consensusMap.R |only neatmaps-2.0.0/neatmaps/R/createNetworks.R | 108 ++++---- neatmaps-2.0.0/neatmaps/R/edge_df.R |only neatmaps-2.0.0/neatmaps/R/getStructuralAttr.R | 96 +++---- neatmaps-2.0.0/neatmaps/R/hierarchy.R | 58 ++-- neatmaps-2.0.0/neatmaps/R/neatmap.R | 226 +++++++++-------- neatmaps-2.0.0/neatmaps/R/neatmaps.R |only neatmaps-2.0.0/neatmaps/R/netsDataFrame.R |only neatmaps-2.0.0/neatmaps/R/network_attr_df.R |only neatmaps-2.0.0/neatmaps/R/node_attr_df.R |only neatmaps-2.0.0/neatmaps/R/scaledColumns.R | 38 +- neatmaps-2.0.0/neatmaps/README.md | 108 ++++---- neatmaps-2.0.0/neatmaps/data/edgeTable.rda |binary neatmaps-2.0.0/neatmaps/data/networkAttr.rda |binary neatmaps-2.0.0/neatmaps/data/nodeAttr.rda |binary neatmaps-2.0.0/neatmaps/man/aggNodeAttr.Rd |only neatmaps-2.0.0/neatmaps/man/calcICLNoPlots.Rd |only neatmaps-2.0.0/neatmaps/man/consClustResTable.Rd |only neatmaps-2.0.0/neatmaps/man/consensusChangeECDF.Rd |only neatmaps-2.0.0/neatmaps/man/consensusClusterNoPlots.Rd |only neatmaps-2.0.0/neatmaps/man/consensusECDF.Rd |only neatmaps-2.0.0/neatmaps/man/consensusMap.Rd |only neatmaps-2.0.0/neatmaps/man/createNetworks.Rd | 49 +-- neatmaps-2.0.0/neatmaps/man/edge_df.Rd |only neatmaps-2.0.0/neatmaps/man/getStructureAttr.Rd | 38 +- neatmaps-2.0.0/neatmaps/man/hierarchy.Rd | 34 +- neatmaps-2.0.0/neatmaps/man/neatmap.Rd | 179 ++++++++----- neatmaps-2.0.0/neatmaps/man/neatmaps.Rd |only neatmaps-2.0.0/neatmaps/man/netsDataFrame.Rd | 100 +++---- neatmaps-2.0.0/neatmaps/man/network_attr_df.Rd |only neatmaps-2.0.0/neatmaps/man/node_attr_df.Rd |only neatmaps-2.0.0/neatmaps/man/scaleColumns.Rd | 38 +- 55 files changed, 675 insertions(+), 554 deletions(-)
Title: L-Moments and Quantile Mixtures
Description: Contains functions to estimate
L-moments and trimmed L-moments from the data. Also
contains functions to estimate the parameters of the normal
polynomial quantile mixture and the Cauchy polynomial quantile
mixture from L-moments and trimmed L-moments.
Author: Juha Karvanen [cre, aut],
Santeri Karppinen [aut]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>
Diff between Lmoments versions 1.2-3 dated 2016-02-22 and 1.3-1 dated 2019-03-15
DESCRIPTION | 21 +- MD5 | 19 +- NAMESPACE | 2 R/Lmoments.R | 457 +++++++++++++----------------------------------------- R/RcppExports.R |only inst/CITATION | 8 inst/News | 2 man/Lmoments.Rd | 169 +++++++++---------- man/t1lmoments.Rd | 103 ++++++------ src |only 10 files changed, 288 insertions(+), 493 deletions(-)
Title: Lazy (Non-Standard) Evaluation
Description: An alternative approach to non-standard evaluation using
formulas. Provides a full implementation of LISP style 'quasiquotation',
making it easier to generate code with other code.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between lazyeval versions 0.2.1 dated 2017-10-29 and 0.2.2 dated 2019-03-15
DESCRIPTION | 8 MD5 | 18 NEWS.md | 6 build/vignette.rds |binary inst/doc/lazyeval-old.html | 554 ++++++++++++++++++------- inst/doc/lazyeval.html | 988 ++++++++++++++++++++++++++++----------------- man/f_interp.Rd | 2 src/expr.c | 12 src/interp.c | 6 src/lazy.c | 12 10 files changed, 1057 insertions(+), 549 deletions(-)
Title: Compute Expected Shortfall and Value at Risk for Continuous
Distributions
Description: Compute expected shortfall (ES) and Value at Risk (VaR) from a
quantile function, distribution function, random number generator or
probability density function. ES is also known as Conditional Value at
Risk (CVaR). Virtually any continuous distribution can be specified.
The functions are vectorized over the arguments. The computations are
done directly from the definitions, see e.g. Acerbi and Tasche (2002)
<doi:10.1111/1468-0300.00091>. Some support for GARCH models is provided,
as well.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between cvar versions 0.3-0 dated 2018-10-06 and 0.4-0 dated 2019-03-15
DESCRIPTION | 10 ++++---- MD5 | 32 ++++++++++++++------------- NEWS.md | 10 ++++++++ R/VaR.R | 2 - R/garch.R | 41 +++++++++++++++++++++++++++-------- README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Guide_cvar.pdf |binary man/GarchModel.Rd | 13 +++++++++++ man/VaR.Rd | 2 - man/sim_garch1c1.Rd | 4 +-- tests/testthat/a.RDS |binary tests/testthat/a_before_6.0.RDS |only tests/testthat/a_pred.RDS |binary tests/testthat/a_pred_before_6.0.RDS |only tests/testthat/test-VaR.R | 2 + tests/testthat/test-garch.R | 15 +++++++++++- 18 files changed, 97 insertions(+), 36 deletions(-)
Title: Analysis of Codon Data under Stationarity using a Bayesian
Framework
Description: Is a collection of models to analyze genome scale codon
data using a Bayesian framework. Provides visualization
routines and checkpointing for model fittings. Currently
published models to analyze gene data for selection on codon
usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist
et al. (2015) <doi:10.1093/gbe/evv087>), and ROC with phi
(Wallace & Drummond (2013) <doi:10.1093/molbev/mst051>). In
addition 'AnaCoDa' contains three currently unpublished models.
The FONSE (First order approximation On NonSense Error) model
analyzes gene data for selection on codon usage against of
nonsense error rates. The PA (PAusing time) and PANSE (PAusing
time + NonSense Error) models use ribosome footprinting data to
analyze estimate ribosome pausing times with and without
nonsense error rate from ribosome footprinting data.
Author: Cedric Landerer [aut, cre],
Gabriel Hanas [ctb],
Jeremy Rogers [ctb],
Alex Cope [ctb],
Denizhan Pak [ctb]
Maintainer: Cedric Landerer <cedric.landerer@gmail.com>
Diff between AnaCoDa versions 0.1.2.2 dated 2019-03-04 and 0.1.2.3 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/mcmcObject.R | 6 +++--- R/modelObject.R | 2 +- R/parameterObject.R | 12 ++++++------ 5 files changed, 17 insertions(+), 17 deletions(-)
Title: The R Version of WebGestalt
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut],
Yuxing Liao [aut, cre]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>
Diff between WebGestaltR versions 0.3.0 dated 2019-01-18 and 0.3.1 dated 2019-03-15
DESCRIPTION | 8 +- MD5 | 70 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 2 R/WebGestaltR.R | 7 +- R/WebGestaltRGsea.R | 35 ++++++++--- R/WebGestaltRNta.R | 26 ++++++-- R/WebGestaltROra.R | 35 +++++++---- R/affinityPropagation.R | 3 + R/createNtaReport.R | 5 + R/createReport.R | 32 ++++++---- R/goSlimSummary.R | 31 ++++++---- R/gseaEnrichment.R | 25 +++++--- R/idMappingGene.R | 86 +++++++++++++++++++--------- R/idMappingPhosphosite.R | 107 ++++++++++++++++++++++-------------- R/idMappingUtils.R | 29 ++++++--- R/listGeneSet.R | 13 +++- R/listIdType.R | 12 ++-- R/listOrganism.R | 13 +++- R/listReferenceSet.R | 12 ++-- R/loadGeneList.R | 20 ++++-- R/loadGeneSet.R | 45 ++++++++++++--- R/oraEnrichment.R | 5 + R/randomWalkEnrichment.R | 38 ++++++++---- R/readGmt.R | 2 R/reportUtils.R | 33 ++++++++++- R/summaryDescription.R | 16 ++--- R/swGsea.R | 4 + R/weightedSetCover.R | 32 ++++++---- inst/templates/summaryGsea.mustache | 2 inst/templates/summaryOra.mustache | 2 man/WebGestaltR.Rd | 4 - man/keepRep.Rd |only man/loadGeneSet.Rd |only man/specificParameterSummaryGsea.Rd | 3 - man/specificParameterSummaryOra.Rd | 2 man/summaryDescription.Rd | 2 37 files changed, 506 insertions(+), 256 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' and other model objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models, mixed effects models and Bayesian models. However, some
of the functions also deal with other statistical measures,
like Cronbach's Alpha, Cramer's V, Phi etc.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.17.3 dated 2019-01-07 and 0.17.4 dated 2019-03-15
sjstats-0.17.3/sjstats/R/r2_helper.R |only sjstats-0.17.3/sjstats/R/typical.R |only sjstats-0.17.3/sjstats/man/typical_value.Rd |only sjstats-0.17.4/sjstats/DESCRIPTION | 22 sjstats-0.17.4/sjstats/MD5 | 149 - sjstats-0.17.4/sjstats/NAMESPACE | 41 sjstats-0.17.4/sjstats/NEWS.md | 28 sjstats-0.17.4/sjstats/R/HDI.R | 45 sjstats-0.17.4/sjstats/R/S3-methods.R | 198 +- sjstats-0.17.4/sjstats/R/check_model_assumptions.R | 2 sjstats-0.17.4/sjstats/R/colour_tools.R |only sjstats-0.17.4/sjstats/R/compute_variances.R |only sjstats-0.17.4/sjstats/R/converge_ok.R | 6 sjstats-0.17.4/sjstats/R/credint.R |only sjstats-0.17.4/sjstats/R/equi_test.R | 29 sjstats-0.17.4/sjstats/R/eta_sq.R | 16 sjstats-0.17.4/sjstats/R/gmd.R | 2 sjstats-0.17.4/sjstats/R/grpmean.R | 2 sjstats-0.17.4/sjstats/R/helpfunctions.R | 9 sjstats-0.17.4/sjstats/R/icc.R | 88 sjstats-0.17.4/sjstats/R/inequ_trends.R | 2 sjstats-0.17.4/sjstats/R/internal_consistency.R | 6 sjstats-0.17.4/sjstats/R/link_inverse.R |only sjstats-0.17.4/sjstats/R/mean_n.R | 2 sjstats-0.17.4/sjstats/R/mediation.R | 11 sjstats-0.17.4/sjstats/R/model_family.R |only sjstats-0.17.4/sjstats/R/model_frame.R |only sjstats-0.17.4/sjstats/R/mwu.R | 5 sjstats-0.17.4/sjstats/R/p_value.R | 19 sjstats-0.17.4/sjstats/R/pca.R | 5 sjstats-0.17.4/sjstats/R/pred_vars.R | 780 +------- sjstats-0.17.4/sjstats/R/r2.R | 163 - sjstats-0.17.4/sjstats/R/re_grp_var.R |only sjstats-0.17.4/sjstats/R/resp_val.R |only sjstats-0.17.4/sjstats/R/resp_var.R |only sjstats-0.17.4/sjstats/R/samplesize_lme.R | 10 sjstats-0.17.4/sjstats/R/std_b.R | 4 sjstats-0.17.4/sjstats/R/svy_scale_weights.R | 4 sjstats-0.17.4/sjstats/R/tidy_stan.R | 63 sjstats-0.17.4/sjstats/R/var_names.R |only sjstats-0.17.4/sjstats/R/weight.R | 5 sjstats-0.17.4/sjstats/build/partial.rdb |binary sjstats-0.17.4/sjstats/build/vignette.rds |binary sjstats-0.17.4/sjstats/inst/doc/anova-statistics.html | 404 +++- sjstats-0.17.4/sjstats/inst/doc/bayesian-statistics.R | 1 sjstats-0.17.4/sjstats/inst/doc/bayesian-statistics.Rmd | 3 sjstats-0.17.4/sjstats/inst/doc/bayesian-statistics.html | 1069 +++++++----- sjstats-0.17.4/sjstats/inst/doc/mixedmodels-statistics.html | 606 ++++-- sjstats-0.17.4/sjstats/man/cod.Rd | 6 sjstats-0.17.4/sjstats/man/converge_ok.Rd | 4 sjstats-0.17.4/sjstats/man/deff.Rd | 6 sjstats-0.17.4/sjstats/man/dot-badlink.Rd |only sjstats-0.17.4/sjstats/man/dot-collapse_cond.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_beta.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_dispersion.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_fixed.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_random.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_residual.Rd |only sjstats-0.17.4/sjstats/man/gmd.Rd | 2 sjstats-0.17.4/sjstats/man/hdi.Rd | 60 sjstats-0.17.4/sjstats/man/icc.Rd | 11 sjstats-0.17.4/sjstats/man/inequ_trend.Rd | 2 sjstats-0.17.4/sjstats/man/mean_n.Rd | 2 sjstats-0.17.4/sjstats/man/pca.Rd | 5 sjstats-0.17.4/sjstats/man/pred_vars.Rd | 53 sjstats-0.17.4/sjstats/man/re_var.Rd | 2 sjstats-0.17.4/sjstats/man/reexports.Rd | 3 sjstats-0.17.4/sjstats/man/reliab_test.Rd | 4 sjstats-0.17.4/sjstats/man/scale_weights.Rd | 4 sjstats-0.17.4/sjstats/man/smpsize_lmm.Rd | 4 sjstats-0.17.4/sjstats/man/std_beta.Rd | 4 sjstats-0.17.4/sjstats/man/tidy_stan.Rd | 10 sjstats-0.17.4/sjstats/tests/testthat/test-anova_stats.R | 124 - sjstats-0.17.4/sjstats/tests/testthat/test-equi_test.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-hdi.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-icc_bayes.R | 8 sjstats-0.17.4/sjstats/tests/testthat/test-icc_r2.R | 4 sjstats-0.17.4/sjstats/tests/testthat/test-icc_stan.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-mcse.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-neff.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-re_var-bayes.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-resp_val.R | 4 sjstats-0.17.4/sjstats/tests/testthat/test-se_icc.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-tidy_stan.R | 2 sjstats-0.17.4/sjstats/tests/testthat/test-wtd.R |only sjstats-0.17.4/sjstats/vignettes/bayesian-statistics.Rmd | 3 86 files changed, 2141 insertions(+), 1999 deletions(-)
More information about RblDataLicense at CRAN
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Title: Machine Learning Algorithms for Innovation in Tourism
Description: A collection of routines created in the collaboration framework in tourism innovation between
the Valencian Tourism Agency (AVT) <http://www.turisme.gva.es/opencms/opencms/turisme/es/index.jsp> and the Miguel Hernandez University.
The package provides a set of machine learning tools for pattern
detection, association and classification rules and feature selection
even under massive data environments. Almiñana, Escudero, Pérez-Martín, Rabasa, and Santamaría (2014) <doi:10.1007/s11750-012-0264-6>.
Author: Agustin Perez-Martin [aut] (<https://orcid.org/0000-0003-4994-3176>),
Agustin Perez-Torregrosa [cre, aut]
(<https://orcid.org/0000-0001-5658-4795>),
Alejandro Rabasa-Dolado [aut] (<https://orcid.org/0000-0002-6243-9831>),
Nuria Molla-Campello [aut] (<https://orcid.org/0000-0002-6448-7116>),
Jesus Javier Rodriguez-Sala [aut]
(<https://orcid.org/0000-0002-3796-0692>),
Agencia Valenciana de Turisme [ctb, cph, fnd],
Miguel Hernandez University [ctb, cph, fnd]
Maintainer: Agustin Perez-Torregrosa <agustin.perez01@goumh.umh.es>
Diff between MachineLearning versions 0.0.3 dated 2019-02-22 and 0.1.3 dated 2019-03-15
MachineLearning-0.0.3/MachineLearning/R/AsociationRules.R |only MachineLearning-0.0.3/MachineLearning/man/VariableSelector.Rd |only MachineLearning-0.1.3/MachineLearning/DESCRIPTION | 8 MachineLearning-0.1.3/MachineLearning/MD5 | 36 +-- MachineLearning-0.1.3/MachineLearning/NAMESPACE | 5 MachineLearning-0.1.3/MachineLearning/NEWS.md | 8 MachineLearning-0.1.3/MachineLearning/R/AssociationRules.R |only MachineLearning-0.1.3/MachineLearning/R/CART.R | 6 MachineLearning-0.1.3/MachineLearning/R/Clustering.R | 26 +- MachineLearning-0.1.3/MachineLearning/R/MLA.class-functions.R | 103 ++++++++-- MachineLearning-0.1.3/MachineLearning/R/VariablesSelector.R | 6 MachineLearning-0.1.3/MachineLearning/R/sampler.R | 9 MachineLearning-0.1.3/MachineLearning/man/AssociationRules.Rd | 14 - MachineLearning-0.1.3/MachineLearning/man/Clustering.Rd | 17 + MachineLearning-0.1.3/MachineLearning/man/EGATUR.Rd | 15 - MachineLearning-0.1.3/MachineLearning/man/VariableRanker.Rd |only MachineLearning-0.1.3/MachineLearning/man/plot.MLA.Rd |only MachineLearning-0.1.3/MachineLearning/man/plotCART.Rd |only MachineLearning-0.1.3/MachineLearning/tests/testthat/test-AsociationRules.R | 6 MachineLearning-0.1.3/MachineLearning/tests/testthat/test-CART.R |only MachineLearning-0.1.3/MachineLearning/tests/testthat/test-Clustering.R | 9 MachineLearning-0.1.3/MachineLearning/tests/testthat/test-VarRank.R | 7 MachineLearning-0.1.3/MachineLearning/tests/testthat/test-sampler.R |only 23 files changed, 199 insertions(+), 76 deletions(-)
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Title: One-Sided Dynamic Principal Components
Description: Functions to compute the one-sided dynamic
principal components ('odpc') introduced in Smucler, Peña and Yohai (2018)
<DOI:10.1080/01621459.2018.1520117>. 'odpc' is a novel dimension
reduction technique for multivariate time series, that is useful
for forecasting. These dynamic principal components are defined as
the linear combinations of the present and past values of the series
that minimize the reconstruction mean squared error.
Author: Daniel Peña <daniel.pena@uc3m.es>,
Ezequiel Smucler <ezequiels.90@gmail.com>,
Victor Yohai <vyohai@dm.uba.ar>
Maintainer: Ezequiel Smucler <ezequiels.90@gmail.com>
Diff between odpc versions 2.0.0 dated 2018-09-12 and 2.0.1 dated 2019-03-15
DESCRIPTION | 8 ++--- MD5 | 8 ++--- configure | 9 ++++- configure.ac | 5 +-- src/autoconfig.h.in | 83 +++++++++++++++++++++++++++++++++++++++------------- 5 files changed, 81 insertions(+), 32 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
David Wilson [ctb],
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 0.9.0 dated 2019-02-07 and 0.10.0 dated 2019-03-15
AlphaSimR-0.10.0/AlphaSimR/DESCRIPTION | 8 AlphaSimR-0.10.0/AlphaSimR/MD5 | 118 + AlphaSimR-0.10.0/AlphaSimR/NAMESPACE | 13 AlphaSimR-0.10.0/AlphaSimR/NEWS | 16 AlphaSimR-0.10.0/AlphaSimR/R/AlphaSimR.R | 2 AlphaSimR-0.10.0/AlphaSimR/R/Class-LociMap.R | 116 + AlphaSimR-0.10.0/AlphaSimR/R/Class-Pop.R | 3 AlphaSimR-0.10.0/AlphaSimR/R/Class-SimParam.R | 779 ++++++++++-- AlphaSimR-0.10.0/AlphaSimR/R/GS.R | 253 +++ AlphaSimR-0.10.0/AlphaSimR/R/RcppExports.R | 28 AlphaSimR-0.10.0/AlphaSimR/R/crossing.R | 13 AlphaSimR-0.10.0/AlphaSimR/R/founderPop.R | 82 - AlphaSimR-0.10.0/AlphaSimR/R/hybrids.R | 7 AlphaSimR-0.10.0/AlphaSimR/R/mergePops.R | 4 AlphaSimR-0.10.0/AlphaSimR/R/misc.R | 2 AlphaSimR-0.10.0/AlphaSimR/R/popSummary.R | 138 +- AlphaSimR-0.10.0/AlphaSimR/R/pullGeno.R | 159 ++ AlphaSimR-0.10.0/AlphaSimR/R/selection.R | 24 AlphaSimR-0.10.0/AlphaSimR/inst/doc/intro.R | 4 AlphaSimR-0.10.0/AlphaSimR/inst/doc/intro.Rmd | 14 AlphaSimR-0.10.0/AlphaSimR/inst/doc/intro.html | 21 AlphaSimR-0.10.0/AlphaSimR/man/RRBLUP_D2.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/RRDsol-class.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/SimParam.Rd | 8 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitA.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitAD.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitADE.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitADEG.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitADG.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitAE.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitAEG.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/SimParam_addTraitAG.Rd | 3 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_rescaleTraits.Rd | 19 AlphaSimR-0.10.0/AlphaSimR/man/TraitADE-class.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/TraitADEG-class.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/TraitAE-class.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/TraitAEG-class.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/aa.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/calcGCA.Rd | 3 AlphaSimR-0.10.0/AlphaSimR/man/fastRRBLUP.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/genParam.Rd | 8 AlphaSimR-0.10.0/AlphaSimR/man/genicVarAA.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/getQtlMap.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/getSnpMap.Rd |only AlphaSimR-0.10.0/AlphaSimR/man/hybridCross.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/pullIbdHaplo.Rd | 15 AlphaSimR-0.10.0/AlphaSimR/man/resetPop.Rd | 2 AlphaSimR-0.10.0/AlphaSimR/man/runMacs.Rd | 5 AlphaSimR-0.10.0/AlphaSimR/man/runMacs2.Rd | 8 AlphaSimR-0.10.0/AlphaSimR/man/sampleHaplo.Rd | 5 AlphaSimR-0.10.0/AlphaSimR/man/selectFam.Rd | 4 AlphaSimR-0.10.0/AlphaSimR/man/selectInd.Rd | 5 AlphaSimR-0.10.0/AlphaSimR/man/selectOP.Rd | 5 AlphaSimR-0.10.0/AlphaSimR/man/selectWithinFam.Rd | 4 AlphaSimR-0.10.0/AlphaSimR/man/varAA.Rd |only AlphaSimR-0.10.0/AlphaSimR/src/GEBV.cpp | 5 AlphaSimR-0.10.0/AlphaSimR/src/MME.cpp | 128 + AlphaSimR-0.10.0/AlphaSimR/src/RcppExports.cpp | 107 - AlphaSimR-0.10.0/AlphaSimR/src/calcGenParam.cpp |only AlphaSimR-0.10.0/AlphaSimR/src/getGv.cpp | 210 +-- AlphaSimR-0.10.0/AlphaSimR/src/init.c | 10 AlphaSimR-0.10.0/AlphaSimR/src/meiosis.cpp | 41 AlphaSimR-0.10.0/AlphaSimR/src/misc.cpp | 8 AlphaSimR-0.10.0/AlphaSimR/tests/testthat/test-crossing.R | 5 AlphaSimR-0.10.0/AlphaSimR/tests/testthat/test-editGenome.R | 5 AlphaSimR-0.10.0/AlphaSimR/tests/testthat/test-hybrids.R | 8 AlphaSimR-0.10.0/AlphaSimR/vignettes/intro.Rmd | 14 AlphaSimR-0.9.0/AlphaSimR/man/trackHaploPop.Rd |only AlphaSimR-0.9.0/AlphaSimR/src/tuneTraits.cpp |only 69 files changed, 1891 insertions(+), 558 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 0.3.1 dated 2019-01-23 and 1.0 dated 2019-03-15
DESCRIPTION | 10 MD5 | 999 ++--- NAMESPACE | 1775 +++++----- NEWS.md | 15 R/RcppExports.R | 202 - R/calculate_lsm.R | 76 R/check_landscape.R | 314 - R/construct_buffer.R | 276 - R/data.R | 254 - R/data_info.R |only R/extract_lsm.R | 724 ++-- R/get_adjacencies.R | 170 R/get_boundaries.R | 212 - R/get_circumscribingcircle.R | 152 R/get_lsm.R |only R/get_nearestneighbour.R | 156 R/get_patches.R | 582 +-- R/get_unique_values.R | 434 +- R/landscapemetrics-package.R | 106 R/list_lsm.R | 219 - R/lsm_c_ai.R | 319 - R/lsm_c_area_cv.R | 277 - R/lsm_c_area_mn.R | 279 - R/lsm_c_area_sd.R | 277 - R/lsm_c_ca.R | 51 R/lsm_c_cai_cv.R | 313 - R/lsm_c_cai_mn.R | 307 - R/lsm_c_cai_sd.R | 311 - R/lsm_c_circle_cv.R | 294 - R/lsm_c_circle_mn.R | 289 - R/lsm_c_circle_sd.R | 291 - R/lsm_c_clumpy.R | 360 +- R/lsm_c_cohesion.R | 337 + R/lsm_c_contig_cv.R | 293 - R/lsm_c_contig_mn.R | 292 - R/lsm_c_contig_sd.R | 295 - R/lsm_c_core_cv.R | 305 - R/lsm_c_core_mn.R | 300 - R/lsm_c_core_sd.R | 304 - R/lsm_c_cpland.R | 335 + R/lsm_c_dcad.R | 331 - R/lsm_c_dcore_cv.R | 313 - R/lsm_c_dcore_mn.R | 307 - R/lsm_c_dcore_sd.R | 317 - R/lsm_c_division.R | 291 - R/lsm_c_ed.R | 336 + R/lsm_c_enn_cv.R | 303 - R/lsm_c_enn_mn.R | 305 - R/lsm_c_enn_sd.R | 305 - R/lsm_c_frac_cv.R | 283 - R/lsm_c_frac_mn.R | 277 - R/lsm_c_frac_sd.R | 281 - R/lsm_c_gyrate_cv.R | 291 - R/lsm_c_gyrate_mn.R | 289 - R/lsm_c_gyrate_sd.R | 289 - R/lsm_c_iji.R | 330 - R/lsm_c_lpi.R | 282 - R/lsm_c_lsi.R | 329 + R/lsm_c_mesh.R | 297 - R/lsm_c_ndca.R | 310 - R/lsm_c_nlsi.R | 362 +- R/lsm_c_np.R | 283 - R/lsm_c_pafrac.R | 371 +- R/lsm_c_para_cv.R | 277 - R/lsm_c_para_mn.R | 277 - R/lsm_c_para_sd.R | 277 - R/lsm_c_pd.R | 295 - R/lsm_c_pladj.R | 276 - R/lsm_c_pland.R | 268 - R/lsm_c_shape_cv.R | 283 - R/lsm_c_shape_mn.R | 283 - R/lsm_c_shape_sd.R | 283 - R/lsm_c_split.R | 291 - R/lsm_c_tca.R | 303 - R/lsm_c_te.R | 458 +- R/lsm_l_ai.R | 280 - R/lsm_l_area_cv.R | 276 - R/lsm_l_area_mn.R | 280 - R/lsm_l_area_sd.R | 278 - R/lsm_l_cai_cv.R | 341 + R/lsm_l_cai_mn.R | 335 + R/lsm_l_cai_sd.R | 339 + R/lsm_l_circle_cv.R | 287 - R/lsm_l_circle_mn.R | 287 - R/lsm_l_circle_sd.R | 291 - R/lsm_l_cohesion.R | 311 - R/lsm_l_condent.R | 332 - R/lsm_l_contag.R | 336 + R/lsm_l_contig_cv.R | 292 - R/lsm_l_contig_mn.R | 290 - R/lsm_l_contig_sd.R | 292 - R/lsm_l_core_cv.R | 335 + R/lsm_l_core_mn.R | 331 - R/lsm_l_core_sd.R | 333 + R/lsm_l_dcad.R | 354 +- R/lsm_l_dcore_cv.R | 341 + R/lsm_l_dcore_mn.R | 335 + R/lsm_l_dcore_sd.R | 339 + R/lsm_l_division.R | 287 - R/lsm_l_ed.R | 327 - R/lsm_l_enn_cv.R | 297 - R/lsm_l_enn_mn.R | 297 - R/lsm_l_enn_sd.R | 297 - R/lsm_l_ent.R | 246 - R/lsm_l_frac_cv.R | 281 - R/lsm_l_frac_mn.R | 279 - R/lsm_l_frac_sd.R | 279 - R/lsm_l_gyrate_cv.R | 287 - R/lsm_l_gyrate_mn.R | 285 - R/lsm_l_gyrate_sd.R | 285 - R/lsm_l_iji.R | 334 + R/lsm_l_joinent.R | 316 - R/lsm_l_lpi.R | 275 - R/lsm_l_lsi.R | 325 + R/lsm_l_mesh.R | 285 - R/lsm_l_msidi.R | 286 - R/lsm_l_msiei.R | 276 - R/lsm_l_mutinf.R | 328 - R/lsm_l_ndca.R | 333 + R/lsm_l_np.R | 255 - R/lsm_l_pafrac.R | 360 +- R/lsm_l_para_cv.R | 275 - R/lsm_l_para_mn.R | 275 - R/lsm_l_para_sd.R | 275 - R/lsm_l_pd.R | 300 - R/lsm_l_pladj.R | 267 - R/lsm_l_pr.R | 232 - R/lsm_l_prd.R | 273 - R/lsm_l_rpr.R | 293 - R/lsm_l_shape_cv.R | 283 - R/lsm_l_shape_mn.R | 283 - R/lsm_l_shape_sd.R | 283 - R/lsm_l_shdi.R | 260 - R/lsm_l_shei.R | 260 - R/lsm_l_sidi.R | 269 - R/lsm_l_siei.R | 272 - R/lsm_l_split.R | 284 - R/lsm_l_ta.R | 259 - R/lsm_l_tca.R | 329 - R/lsm_l_te.R | 355 +- R/lsm_p_area.R | 326 - R/lsm_p_cai.R | 380 +- R/lsm_p_circle.R | 426 +- R/lsm_p_contig.R | 406 +- R/lsm_p_core.R | 453 +- R/lsm_p_enn.R | 536 +-- R/lsm_p_frac.R | 318 - R/lsm_p_gyrate.R | 380 +- R/lsm_p_ncore.R | 684 +-- R/lsm_p_para.R | 303 - R/lsm_p_perim.R | 408 +- R/lsm_p_shape.R | 328 + R/matrix_to_raster.R | 164 R/onUnload.R | 16 R/options_landscapemetrics.R | 64 R/pad_raster.R | 358 +- R/proj_info.R |only R/raster_to_points.R | 84 R/sample_lsm.R | 552 +-- R/show_cores.R | 568 +-- R/show_correlation.R | 470 +- R/show_lsm.R | 602 +-- R/show_patches.R | 445 +- R/window_lsm.R |only build/vignette.rds |binary inst/doc/getstarted.R | 190 - inst/doc/getstarted.Rmd | 364 +- inst/doc/getstarted.html | 1180 +++--- man/augusta_nlcd.Rd | 42 man/calculate_lsm.Rd | 248 - man/check_landscape.Rd | 94 man/construct_buffer.Rd | 98 man/data_info.Rd |only man/extract_lsm.Rd | 200 - man/figures/README-unnamed-chunk-1-1.png |binary man/fragstats_class_augusta_nlcd.Rd | 32 man/fragstats_class_landscape.Rd | 32 man/fragstats_class_podlasie.Rd | 32 man/fragstats_landscape_augusta_nlcd.Rd | 32 man/fragstats_landscape_landscape.Rd | 32 man/fragstats_landscape_podlasie.Rd | 32 man/fragstats_patch_augusta_nlcd.Rd | 32 man/fragstats_patch_landscape.Rd | 32 man/fragstats_patch_podlasie.Rd | 32 man/get_adjacencies.Rd | 110 man/get_boundaries.Rd | 80 man/get_circumscribingcircle.Rd | 90 man/get_lsm.Rd |only man/get_nearestneighbour.Rd | 80 man/get_patches.Rd | 184 - man/get_unique_values.Rd | 120 man/landscape.Rd | 36 man/landscapemetrics.Rd | 92 man/list_lsm.Rd | 104 man/lsm_abbreviations_names.Rd | 54 man/lsm_c_ai.Rd | 126 man/lsm_c_area_cv.Rd | 134 man/lsm_c_area_mn.Rd | 136 man/lsm_c_area_sd.Rd | 142 man/lsm_c_ca.Rd | 134 man/lsm_c_cai_cv.Rd | 166 man/lsm_c_cai_mn.Rd | 160 man/lsm_c_cai_sd.Rd | 164 man/lsm_c_circle_cv.Rd | 150 man/lsm_c_circle_mn.Rd | 146 man/lsm_c_circle_sd.Rd | 146 man/lsm_c_clumpy.Rd | 122 man/lsm_c_cohesion.Rd | 136 man/lsm_c_contig_cv.Rd | 156 man/lsm_c_contig_mn.Rd | 154 man/lsm_c_contig_sd.Rd | 156 man/lsm_c_core_cv.Rd | 158 man/lsm_c_core_mn.Rd | 154 man/lsm_c_core_sd.Rd | 156 man/lsm_c_cpland.Rd | 150 man/lsm_c_dcad.Rd | 156 man/lsm_c_dcore_cv.Rd | 164 man/lsm_c_dcore_mn.Rd | 158 man/lsm_c_dcore_sd.Rd | 164 man/lsm_c_division.Rd | 128 man/lsm_c_ed.Rd | 148 man/lsm_c_enn_cv.Rd | 158 man/lsm_c_enn_mn.Rd | 158 man/lsm_c_enn_sd.Rd | 158 man/lsm_c_frac_cv.Rd | 146 man/lsm_c_frac_mn.Rd | 138 man/lsm_c_frac_sd.Rd | 144 man/lsm_c_gyrate_cv.Rd | 148 man/lsm_c_gyrate_mn.Rd | 146 man/lsm_c_gyrate_sd.Rd | 146 man/lsm_c_iji.Rd | 132 man/lsm_c_lpi.Rd | 128 man/lsm_c_lsi.Rd | 134 man/lsm_c_mesh.Rd | 138 man/lsm_c_ndca.Rd | 158 man/lsm_c_nlsi.Rd | 132 man/lsm_c_np.Rd | 120 man/lsm_c_pafrac.Rd | 152 man/lsm_c_para_cv.Rd | 140 man/lsm_c_para_mn.Rd | 140 man/lsm_c_para_sd.Rd | 140 man/lsm_c_pd.Rd | 130 man/lsm_c_pladj.Rd | 114 man/lsm_c_pland.Rd | 126 man/lsm_c_shape_cv.Rd | 142 man/lsm_c_shape_mn.Rd | 142 man/lsm_c_shape_sd.Rd | 142 man/lsm_c_split.Rd | 134 man/lsm_c_tca.Rd | 156 man/lsm_c_te.Rd | 140 man/lsm_l_ai.Rd | 130 man/lsm_l_area_cv.Rd | 134 man/lsm_l_area_mn.Rd | 136 man/lsm_l_area_sd.Rd | 132 man/lsm_l_cai_cv.Rd | 166 man/lsm_l_cai_mn.Rd | 160 man/lsm_l_cai_sd.Rd | 164 man/lsm_l_circle_cv.Rd | 146 man/lsm_l_circle_mn.Rd | 144 man/lsm_l_circle_sd.Rd | 148 man/lsm_l_cohesion.Rd | 126 man/lsm_l_condent.Rd | 134 man/lsm_l_contag.Rd | 136 man/lsm_l_contig_cv.Rd | 156 man/lsm_l_contig_mn.Rd | 154 man/lsm_l_contig_sd.Rd | 156 man/lsm_l_core_cv.Rd | 160 man/lsm_l_core_mn.Rd | 156 man/lsm_l_core_sd.Rd | 158 man/lsm_l_dcad.Rd | 156 man/lsm_l_dcore_cv.Rd | 164 man/lsm_l_dcore_mn.Rd | 158 man/lsm_l_dcore_sd.Rd | 162 man/lsm_l_division.Rd | 134 man/lsm_l_ed.Rd | 148 man/lsm_l_enn_cv.Rd | 158 man/lsm_l_enn_mn.Rd | 158 man/lsm_l_enn_sd.Rd | 158 man/lsm_l_ent.Rd | 104 man/lsm_l_frac_cv.Rd | 146 man/lsm_l_frac_mn.Rd | 144 man/lsm_l_frac_sd.Rd | 144 man/lsm_l_gyrate_cv.Rd | 148 man/lsm_l_gyrate_mn.Rd | 146 man/lsm_l_gyrate_sd.Rd | 146 man/lsm_l_iji.Rd | 134 man/lsm_l_joinent.Rd | 128 man/lsm_l_lpi.Rd | 128 man/lsm_l_lsi.Rd | 134 man/lsm_l_mesh.Rd | 138 man/lsm_l_msidi.Rd | 132 man/lsm_l_msiei.Rd | 122 man/lsm_l_mutinf.Rd | 130 man/lsm_l_ndca.Rd | 158 man/lsm_l_np.Rd | 122 man/lsm_l_pafrac.Rd | 152 man/lsm_l_para_cv.Rd | 140 man/lsm_l_para_mn.Rd | 140 man/lsm_l_para_sd.Rd | 140 man/lsm_l_pd.Rd | 130 man/lsm_l_pladj.Rd | 114 man/lsm_l_pr.Rd | 110 man/lsm_l_prd.Rd | 120 man/lsm_l_rpr.Rd | 136 man/lsm_l_shape_cv.Rd | 142 man/lsm_l_shape_mn.Rd | 142 man/lsm_l_shape_sd.Rd | 142 man/lsm_l_shdi.Rd | 122 man/lsm_l_shei.Rd | 126 man/lsm_l_sidi.Rd | 132 man/lsm_l_siei.Rd | 132 man/lsm_l_split.Rd | 134 man/lsm_l_ta.Rd | 124 man/lsm_l_tca.Rd | 154 man/lsm_l_te.Rd | 124 man/lsm_p_area.Rd | 138 man/lsm_p_cai.Rd | 166 man/lsm_p_circle.Rd | 148 man/lsm_p_contig.Rd | 158 man/lsm_p_core.Rd | 164 man/lsm_p_enn.Rd | 158 man/lsm_p_frac.Rd | 146 man/lsm_p_gyrate.Rd | 142 man/lsm_p_ncore.Rd | 166 man/lsm_p_para.Rd | 140 man/lsm_p_perim.Rd | 118 man/lsm_p_shape.Rd | 144 man/matrix_to_raster.Rd | 80 man/options_landscapemetrics.Rd | 56 man/pad_raster.Rd | 110 man/podlasie_ccilc.Rd | 36 man/proj_info.Rd |only man/raster_to_points.Rd | 56 man/rcpp_cell_from_xy.Rd | 38 man/rcpp_create_neighborhood.Rd | 38 man/rcpp_get_nearest_neighbor.Rd | 44 man/rcpp_xy_from_matrix.Rd | 36 man/sample_lsm.Rd | 174 man/show_cores.Rd | 148 man/show_correlation.Rd | 62 man/show_lsm.Rd | 140 man/show_patches.Rd | 112 man/window_lsm.Rd |only tests/testthat.R | 9 tests/testthat/helper-brick.R | 8 tests/testthat/helper-landscapes.R | 34 tests/testthat/helper-points.R | 36 tests/testthat/test-calculate-lsm.R | 186 - tests/testthat/test-check-landscape.R | 71 tests/testthat/test-construct-buffer.R | 34 tests/testthat/test-extract-lsm.R | 66 tests/testthat/test-get-adjacencies.R | 75 tests/testthat/test-get-boundaries.R | 76 tests/testthat/test-get-circumscribungcircle.R | 89 tests/testthat/test-get-lsm.R |only tests/testthat/test-get-nearestneighbour.R | 36 tests/testthat/test-get-patches.R | 46 tests/testthat/test-get-unique-values.R | 166 tests/testthat/test-list-lsm.R | 92 tests/testthat/test-lsm-c-ai.R | 48 tests/testthat/test-lsm-c-area-cv.R | 48 tests/testthat/test-lsm-c-area-mn.R | 50 tests/testthat/test-lsm-c-area-sd.R | 48 tests/testthat/test-lsm-c-ca.R | 52 tests/testthat/test-lsm-c-cai-cv.R | 50 tests/testthat/test-lsm-c-cai-mn.R | 50 tests/testthat/test-lsm-c-cai-sd.R | 46 tests/testthat/test-lsm-c-circle-cv.R | 52 tests/testthat/test-lsm-c-circle-mn.R | 48 tests/testthat/test-lsm-c-circle-sd.R | 48 tests/testthat/test-lsm-c-clumpy.R | 48 tests/testthat/test-lsm-c-cohesion.R | 50 tests/testthat/test-lsm-c-contig-cv.R | 50 tests/testthat/test-lsm-c-contig-mn.R | 50 tests/testthat/test-lsm-c-contig-sd.R | 50 tests/testthat/test-lsm-c-core-cv.R | 46 tests/testthat/test-lsm-c-core-mn.R | 46 tests/testthat/test-lsm-c-core-sd.R | 46 tests/testthat/test-lsm-c-cpland.R | 48 tests/testthat/test-lsm-c-dcad.R | 48 tests/testthat/test-lsm-c-dcore_cv.R | 46 tests/testthat/test-lsm-c-dcore_mn.R | 46 tests/testthat/test-lsm-c-dcore_sd.R | 46 tests/testthat/test-lsm-c-division.R | 48 tests/testthat/test-lsm-c-ed.R | 48 tests/testthat/test-lsm-c-enn-cv.R | 46 tests/testthat/test-lsm-c-enn-mn.R | 46 tests/testthat/test-lsm-c-enn-sd.R | 46 tests/testthat/test-lsm-c-frac-cv.R | 46 tests/testthat/test-lsm-c-frac-mn.R | 46 tests/testthat/test-lsm-c-frac-sd.R | 46 tests/testthat/test-lsm-c-gyrate-cv.R | 46 tests/testthat/test-lsm-c-gyrate-mn.R | 46 tests/testthat/test-lsm-c-gyrate-sd.R | 46 tests/testthat/test-lsm-c-iji.R | 58 tests/testthat/test-lsm-c-lpi.R | 48 tests/testthat/test-lsm-c-lsi.R | 48 tests/testthat/test-lsm-c-mesh.R | 48 tests/testthat/test-lsm-c-ndca.R | 48 tests/testthat/test-lsm-c-nlsi.R | 48 tests/testthat/test-lsm-c-np.R | 48 tests/testthat/test-lsm-c-pafrac.R | 56 tests/testthat/test-lsm-c-para-cv.R | 46 tests/testthat/test-lsm-c-para-mn.R | 46 tests/testthat/test-lsm-c-para-sd.R | 46 tests/testthat/test-lsm-c-pd.R | 48 tests/testthat/test-lsm-c-pladj.R | 48 tests/testthat/test-lsm-c-pland.R | 48 tests/testthat/test-lsm-c-shape-cv.R | 46 tests/testthat/test-lsm-c-shape-mn.R | 46 tests/testthat/test-lsm-c-shape-sd.R | 46 tests/testthat/test-lsm-c-split.R | 48 tests/testthat/test-lsm-c-tca.R | 48 tests/testthat/test-lsm-c-te.R | 64 tests/testthat/test-lsm-l-ai.R | 48 tests/testthat/test-lsm-l-area-cv.R | 46 tests/testthat/test-lsm-l-area-mn.R | 50 tests/testthat/test-lsm-l-area-sd.R | 50 tests/testthat/test-lsm-l-cai-cv.R | 50 tests/testthat/test-lsm-l-cai-mn.R | 50 tests/testthat/test-lsm-l-cai-sd.R | 50 tests/testthat/test-lsm-l-circle-cv.R | 50 tests/testthat/test-lsm-l-circle-mn.R | 50 tests/testthat/test-lsm-l-circle-sd.R | 50 tests/testthat/test-lsm-l-cohesion.R | 48 tests/testthat/test-lsm-l-condent.R | 48 tests/testthat/test-lsm-l-contag.R | 56 tests/testthat/test-lsm-l-contig-cv.R | 46 tests/testthat/test-lsm-l-contig-mn.R | 46 tests/testthat/test-lsm-l-contig-sd.R | 46 tests/testthat/test-lsm-l-core-cv.R | 50 tests/testthat/test-lsm-l-core-mn.R | 50 tests/testthat/test-lsm-l-core-sd.R | 50 tests/testthat/test-lsm-l-dcad.R | 48 tests/testthat/test-lsm-l-dcore-cv.R | 50 tests/testthat/test-lsm-l-dcore-mn.R | 50 tests/testthat/test-lsm-l-dcore-sd.R | 50 tests/testthat/test-lsm-l-division.R | 48 tests/testthat/test-lsm-l-ed.R | 48 tests/testthat/test-lsm-l-enn-cv.R | 50 tests/testthat/test-lsm-l-enn-mn.R | 50 tests/testthat/test-lsm-l-enn-sd.R | 50 tests/testthat/test-lsm-l-ent.R | 48 tests/testthat/test-lsm-l-frac-cv.R | 46 tests/testthat/test-lsm-l-frac-mn.R | 46 tests/testthat/test-lsm-l-frac-sd.R | 46 tests/testthat/test-lsm-l-gyrate-cv.R | 46 tests/testthat/test-lsm-l-gyrate-mn.R | 46 tests/testthat/test-lsm-l-gyrate-sd.R | 48 tests/testthat/test-lsm-l-iji.R | 58 tests/testthat/test-lsm-l-joinent.R | 48 tests/testthat/test-lsm-l-lpi.R | 48 tests/testthat/test-lsm-l-lsi.R | 48 tests/testthat/test-lsm-l-mesh.R | 48 tests/testthat/test-lsm-l-msidi.R | 48 tests/testthat/test-lsm-l-msiei.R | 48 tests/testthat/test-lsm-l-mutinf.R | 48 tests/testthat/test-lsm-l-ndca.R | 48 tests/testthat/test-lsm-l-np.R | 48 tests/testthat/test-lsm-l-pafrac.R | 56 tests/testthat/test-lsm-l-para-cv.R | 46 tests/testthat/test-lsm-l-para-mn.R | 46 tests/testthat/test-lsm-l-para-sd.R | 46 tests/testthat/test-lsm-l-pd.R | 48 tests/testthat/test-lsm-l-pladj.R | 48 tests/testthat/test-lsm-l-pr.R | 48 tests/testthat/test-lsm-l-prd.R | 48 tests/testthat/test-lsm-l-rpr.R | 48 tests/testthat/test-lsm-l-shape-cv.R | 46 tests/testthat/test-lsm-l-shape-mn.R | 46 tests/testthat/test-lsm-l-shape-sd.R | 46 tests/testthat/test-lsm-l-shdi.R | 48 tests/testthat/test-lsm-l-shei.R | 48 tests/testthat/test-lsm-l-sidi.R | 48 tests/testthat/test-lsm-l-siei.R | 48 tests/testthat/test-lsm-l-split.R | 48 tests/testthat/test-lsm-l-ta.R | 48 tests/testthat/test-lsm-l-tca.R | 48 tests/testthat/test-lsm-l-te.R | 66 tests/testthat/test-lsm-p-area.R | 50 tests/testthat/test-lsm-p-cai.R | 46 tests/testthat/test-lsm-p-circle.R | 54 tests/testthat/test-lsm-p-contig.R | 50 tests/testthat/test-lsm-p-core.R | 68 tests/testthat/test-lsm-p-enn.R | 50 tests/testthat/test-lsm-p-frac.R | 50 tests/testthat/test-lsm-p-gyrate.R | 50 tests/testthat/test-lsm-p-nca.R | 50 tests/testthat/test-lsm-p-para.R | 50 tests/testthat/test-lsm-p-perim.R | 54 tests/testthat/test-lsm-p-shape.R | 48 tests/testthat/test-matrix-to-raster.R | 96 tests/testthat/test-options-landscapemetrics.R |only tests/testthat/test-pad-raster.R | 54 tests/testthat/test-raster-to-points.R | 32 tests/testthat/test-rcpp-get-coocurrence-matrix.R | 204 - tests/testthat/test-rcpp-get-entropy.R | 46 tests/testthat/test-sample-lsm.R | 102 tests/testthat/test-show-cores.R | 90 tests/testthat/test-show-correlation.R | 42 tests/testthat/test-show-lsm.R | 78 tests/testthat/test-show-patches.R | 70 tests/testthat/test-unique-values.R | 26 tests/testthat/test-window-lsm.R |only tests/testthat/test_fragstats.R | 3884 +++++++++++----------- vignettes/getstarted.Rmd | 364 +- 506 files changed, 44874 insertions(+), 42139 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: CUSUM Charts for Monitoring of Hospital Performance
Description: Provides functions for constructing and evaluating
CUSUM charts and RA-CUSUM charts with focus on false signal probability.
Author: Lena Hubig [aut, cre] (<https://orcid.org/0000-0002-9454-1232>)
Maintainer: Lena Hubig <cs@lenahubig.de>
Diff between cusum versions 0.1.0 dated 2018-11-18 and 0.2.0 dated 2019-03-15
DESCRIPTION | 8 MD5 | 67 +- NAMESPACE | 24 NEWS.md |only R/cusum.R | 206 +++---- R/cusum_alpha_sim.R | 150 ++--- R/cusum_limit_sim.R | 146 ++--- R/data.R | 68 +- R/plot_cusum.R |only R/print_cusum.R |only R/racusum.R | 215 +++---- R/racusum_alpha_sim.R | 182 +++--- R/racusum_limit_sim.R | 179 +++--- README.md | 90 +-- build/vignette.rds |binary inst/doc/cusum.R | 250 ++++----- inst/doc/cusum.Rmd | 444 ++++++++-------- inst/doc/cusum.html | 867 +++++++++++++++++++------------- man/cusum.Rd | 94 +-- man/cusum_alpha_sim.Rd | 82 +-- man/cusum_example_data.Rd | 54 - man/cusum_limit_sim.Rd | 76 +- man/figures/README-example-1.png |binary man/plot.cusum.Rd |only man/racusum.Rd | 118 ++-- man/racusum_alpha_sim.Rd | 96 +-- man/racusum_example_data.Rd | 56 +- man/racusum_limit_sim.Rd | 90 +-- man/summary.cusum.Rd |only tests/testthat.R | 8 tests/testthat/test-cusum.R | 34 - tests/testthat/test-cusum_alpha_sim.R | 36 - tests/testthat/test-cusum_limit_sim.R | 34 - tests/testthat/test-racusum.R | 44 - tests/testthat/test-racusum_alpha_sim.R | 42 - tests/testthat/test_racusum_limit_sim.R | 40 - vignettes/cusum.Rmd | 444 ++++++++-------- 37 files changed, 2230 insertions(+), 2014 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.1.1 dated 2018-12-21 and 3.2.0 dated 2019-03-15
DESCRIPTION | 8 +++--- MD5 | 50 +++++++++++++++++++------------------- NEWS.md | 16 +++++++++++- R/eval-bg.R | 8 ++++-- R/eval.R | 10 ++++--- R/options.R | 9 ++++-- R/r-process.R | 9 +++--- R/r-session.R | 8 +++--- R/rcmd-bg.R | 8 ++++-- R/rcmd-process.R | 7 +++-- R/rcmd.R | 10 ++++++- R/rscript.R | 10 ++++--- R/run.R | 19 +++++++++++--- R/setup.R | 2 - inst/_pkgdown.yml | 2 - man/r.Rd | 12 +++++---- man/r_bg.Rd | 11 +++++--- man/rcmd.Rd | 12 ++++++--- man/rcmd_bg.Rd | 11 ++++++-- man/rscript.Rd | 10 ++++++- tests/testthat/fixtures/D1 |only tests/testthat/fixtures/script2.R |only tests/testthat/helper.R | 24 ++++++++++++++++++ tests/testthat/test-eval.R | 18 +++++++++++++ tests/testthat/test-r-session.R | 1 tests/testthat/test-rcmd.R | 35 ++++++++++++++++++++++++-- tests/testthat/test-rscript.R | 16 ++++++++++++ 27 files changed, 245 insertions(+), 81 deletions(-)
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (See White I.R., 2010
<http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between rsimsum versions 0.5.0 dated 2019-02-21 and 0.5.1 dated 2019-03-15
DESCRIPTION | 7 ++-- MD5 | 34 +++++++++++------------ NEWS.md | 6 ++++ R/dropbig.R | 4 +- R/performance.R | 4 +- R/simsum.R | 2 - R/sysdata.rda |binary README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.Rmd | 6 ++-- inst/doc/introduction.html | 59 +++++++++++++++++++++-------------------- inst/doc/plotting.html | 19 +++++++------ inst/doc/relhaz.html | 19 +++++++------ inst/doc/rsimsumtidyverse.html | 31 +++++++++++---------- man/multisimsum.Rd | 2 - man/simsum.Rd | 2 - vignettes/introduction.Rmd | 6 ++-- 18 files changed, 110 insertions(+), 93 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.6 dated 2019-01-26 and 0.3.7 dated 2019-03-15
ChangeLog | 27 ++++++++++- DESCRIPTION | 8 +-- MD5 | 30 ++++++------ build/vignette.rds |binary configure | 21 ++++---- configure.ac | 4 - inst/NEWS.Rd | 14 +++++ inst/doc/littler-examples.Rmd | 2 inst/doc/littler-examples.html | 18 +++++-- inst/doc/littler-faq.html | 18 +++++-- inst/examples/getRStudioDesktop.r | 3 - inst/examples/getRStudioServer.r | 2 inst/examples/install2.r | 20 +++++--- inst/examples/installGithub.r | 35 +++++++++++++- src/littler.c | 90 +++++++++++++++++++------------------- vignettes/littler-examples.Rmd | 2 16 files changed, 189 insertions(+), 105 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016), <doi:10.1177/1073191116656437>, generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [ctb]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 1.1.5 dated 2019-02-06 and 1.1.8 dated 2019-03-15
DESCRIPTION | 8 - MD5 | 46 ++++----- NEWS.md | 48 ++++++++- R/modelling.R | 190 ++++++++++++++++++++++++--------------- R/plot.R | 45 ++++++++- R/predict.R | 144 ++++++++++++++++++++--------- R/preparation.R | 80 ++++++++++++---- R/roots.R | 18 ++- README.md | 16 ++- build/vignette.rds |binary inst/doc/cNORM-Demo.Rmd | 6 - inst/doc/cNORM-Demo.html | 23 ++-- inst/shiny/server.R | 39 +++++--- inst/shiny/ui.R | 38 ++----- inst/shiny/www/introduction.html | 4 man/bestModel.Rd | 29 ++++- man/checkConsistency.Rd | 8 + man/cnorm.cv.Rd | 2 man/normTable.Rd | 2 man/prepareData.Rd | 9 + man/printSubset.Rd | 1 man/rankByGroup.Rd | 10 +- man/rankBySlidingWindow.Rd | 4 vignettes/cNORM-Demo.Rmd | 6 - 24 files changed, 516 insertions(+), 260 deletions(-)
Title: Fast Adaptive Spectral Clustering for Single and Multi-View Data
Description: A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in the graph. For integrating multi-view data and reducing noise a tensor product graph data integration and diffusion procedure is used. 'Spectrum' analyses eigenvector variance or distribution to determine the number of clusters. 'Spectrum' is well suited for a wide range of data, including both Gaussian and non-Gaussian structures.
Author: Christopher R John, David Watson
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between Spectrum versions 0.3 dated 2019-02-18 and 0.4 dated 2019-03-15
DESCRIPTION | 11 MD5 | 14 - NAMESPACE | 1 R/spectrum.R | 494 ++++++++++++++++++++-------------------- inst/doc/Spectrum_vignette.Rmd | 2 inst/doc/Spectrum_vignette.pdf |binary man/Spectrum.Rd | 29 +- vignettes/Spectrum_vignette.Rmd | 2 8 files changed, 290 insertions(+), 263 deletions(-)
Title: Basic Finance; NPV/IRR/Annuities/Bond-Pricing; Black Scholes
Description: Implements the basic financial analysis
functions similar to (but not identical to) what
is available in most spreadsheet software. This
includes finding the IRR and NPV of regularly
spaced cash flows and annuities. Bond pricing and
YTM calculations are included. In addition, Black
Scholes option pricing and Greeks are also
provided.
Author: Jayanth Varma [aut, cre]
Maintainer: Jayanth Varma <jrvarma@iima.ac.in>
Diff between jrvFinance versions 1.4.0 dated 2018-06-17 and 1.4.1 dated 2019-03-15
jrvFinance-1.4.0/jrvFinance/inst/doc/index.html |only jrvFinance-1.4.1/jrvFinance/DESCRIPTION | 8 jrvFinance-1.4.1/jrvFinance/MD5 | 25 - jrvFinance-1.4.1/jrvFinance/NEWS.md | 4 jrvFinance-1.4.1/jrvFinance/R/daycount.R | 6 jrvFinance-1.4.1/jrvFinance/build/vignette.rds |binary jrvFinance-1.4.1/jrvFinance/inst/doc/jrvFinance-demo.html | 197 +++++++------- jrvFinance-1.4.1/jrvFinance/man/GenBSImplied.Rd | 4 jrvFinance-1.4.1/jrvFinance/man/annuity.Rd | 35 +- jrvFinance-1.4.1/jrvFinance/man/bonds.Rd | 19 - jrvFinance-1.4.1/jrvFinance/man/coupons.Rd | 4 jrvFinance-1.4.1/jrvFinance/man/daycount.Rd | 7 jrvFinance-1.4.1/jrvFinance/man/irr.Rd | 8 jrvFinance-1.4.1/jrvFinance/man/irr.solve.Rd | 4 14 files changed, 165 insertions(+), 156 deletions(-)
Title: Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait
data associated with the tips of a phylogenetic tree. Examples of such models
are Gaussian continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the
tips of the tree as an observed (final) state of a Markov process starting from
an initial state at the root and evolving along the branches of the tree. The
PCMBase R package provides a general framework for manipulating such models.
This framework consists of an application programming interface for specifying
data and model parameters, and efficient algorithms for simulating trait evolution
under a model and calculating the likelihood of model parameters for an assumed
model and trait data. The package implements a growing collection of models,
which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed
Gaussian models, in which different types of the above models can be associated
with different branches of the tree. The PCMBase package is limited to
trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic
models. The PCMFit package provides functionality for ML and Bayesian fit of
these models to tree and trait data. The package web-site
<https://venelin.github.io/PCMBase/>
provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph],
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ctb]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBase versions 1.2.7 dated 2018-11-30 and 1.2.9 dated 2019-03-15
PCMBase-1.2.7/PCMBase/man/PCMTreeDtNodeRegimes.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeExtractBackboneRegimes.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeGetRegimeForNode.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeGetStartingNodesRegimes.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeGetTipsInRegime.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeMatchRegimesWithModel.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeMatrixNodesInSameRegime.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeMatrixTipsInSameRegime.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeNumUniqueRegimes.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeSetDefaultRegime.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeSetRegimes.Rd |only PCMBase-1.2.7/PCMBase/man/PCMTreeUniqueRegimes.Rd |only PCMBase-1.2.7/PCMBase/tests/testthat/testobjects.RData |only PCMBase-1.2.9/PCMBase/DESCRIPTION | 8 PCMBase-1.2.9/PCMBase/MD5 | 196 PCMBase-1.2.9/PCMBase/NAMESPACE | 309 + PCMBase-1.2.9/PCMBase/NEWS.md | 25 PCMBase-1.2.9/PCMBase/R/AutoGeneratedModelTypes.R |only PCMBase-1.2.9/PCMBase/R/BM.R | 54 PCMBase-1.2.9/PCMBase/R/DOU.R | 139 PCMBase-1.2.9/PCMBase/R/DefaultModelTypes.R |only PCMBase-1.2.9/PCMBase/R/GaussianPCM.R | 185 PCMBase-1.2.9/PCMBase/R/JOU.R | 114 PCMBase-1.2.9/PCMBase/R/MixedGaussian.R | 93 PCMBase-1.2.9/PCMBase/R/OU.R | 133 PCMBase-1.2.9/PCMBase/R/PCM.R | 597 ++ PCMBase-1.2.9/PCMBase/R/PCMBaseTestObjects.R |only PCMBase-1.2.9/PCMBase/R/PCMParam.R | 175 PCMBase-1.2.9/PCMBase/R/PCMTree.R | 2189 +++++++--- PCMBase-1.2.9/PCMBase/R/Utilities.R | 92 PCMBase-1.2.9/PCMBase/R/White.R | 10 PCMBase-1.2.9/PCMBase/R/zzz.R |only PCMBase-1.2.9/PCMBase/README.md | 30 PCMBase-1.2.9/PCMBase/data |only PCMBase-1.2.9/PCMBase/inst/CITATION | 14 PCMBase-1.2.9/PCMBase/inst/doc/PCMBase.R | 17 PCMBase-1.2.9/PCMBase/inst/doc/PCMBase.Rmd | 21 PCMBase-1.2.9/PCMBase/inst/doc/PCMBase.html | 85 PCMBase-1.2.9/PCMBase/inst/doc/PCMParam.html | 36 PCMBase-1.2.9/PCMBase/man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd |only PCMBase-1.2.9/PCMBase/man/Args_MixedGaussian_MGPMScalarOUType.Rd |only PCMBase-1.2.9/PCMBase/man/Args_MixedGaussian_MGPMSurfaceOUType.Rd |only PCMBase-1.2.9/PCMBase/man/MGPMScalarOUType.Rd |only PCMBase-1.2.9/PCMBase/man/MGPMSurfaceOUType.Rd |only PCMBase-1.2.9/PCMBase/man/MixedGaussian.Rd | 37 PCMBase-1.2.9/PCMBase/man/PCM.Rd | 13 PCMBase-1.2.9/PCMBase/man/PCMAbCdEf.Rd | 13 PCMBase-1.2.9/PCMBase/man/PCMBaseIsADevRelease.Rd | 9 PCMBase-1.2.9/PCMBase/man/PCMBaseTestObjects.Rd |only PCMBase-1.2.9/PCMBase/man/PCMCond.GaussianPCM.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMCond.Rd | 6 PCMBase-1.2.9/PCMBase/man/PCMCreateLikelihood.Rd | 27 PCMBase-1.2.9/PCMBase/man/PCMDefaultModelTypes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMGenerateModelTypes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMGenerateParameterizations.Rd | 7 PCMBase-1.2.9/PCMBase/man/PCMGetVecParamsRegimesAndModels.Rd | 2 PCMBase-1.2.9/PCMBase/man/PCMInfo.Rd | 17 PCMBase-1.2.9/PCMBase/man/PCMLik.Rd | 13 PCMBase-1.2.9/PCMBase/man/PCMLikDmvNorm.Rd |only PCMBase-1.2.9/PCMBase/man/PCMListParameterizations.Rd | 19 PCMBase-1.2.9/PCMBase/man/PCMLmr.Rd | 14 PCMBase-1.2.9/PCMBase/man/PCMMapModelTypesToRegimes.Rd | 29 PCMBase-1.2.9/PCMBase/man/PCMMean.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMMeanAtTime.Rd | 8 PCMBase-1.2.9/PCMBase/man/PCMModelTypes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMNumRegimes.Rd | 8 PCMBase-1.2.9/PCMBase/man/PCMParamCount.Rd | 15 PCMBase-1.2.9/PCMBase/man/PCMParamGetShortVector.Rd | 7 PCMBase-1.2.9/PCMBase/man/PCMParamRandomVecParams.Rd | 13 PCMBase-1.2.9/PCMBase/man/PCMParamSetByName.Rd | 12 PCMBase-1.2.9/PCMBase/man/PCMPlotTraitData2D.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMRegimes.Rd | 10 PCMBase-1.2.9/PCMBase/man/PCMSim.Rd | 11 PCMBase-1.2.9/PCMBase/man/PCMTrajectory.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTree.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeBackbonePartition.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeDropClade.Rd | 42 PCMBase-1.2.9/PCMBase/man/PCMTreeDtNodes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeEvalNestedEDxOnTree.Rd | 39 PCMBase-1.2.9/PCMBase/man/PCMTreeExtractClade.Rd | 35 PCMBase-1.2.9/PCMBase/man/PCMTreeGetPartNames.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetPartRegimes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetPartition.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetPartsForNodes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetRegimesForEdges.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetRegimesForNodes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeGetTipsInPart.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeInsertSingletons.Rd | 94 PCMBase-1.2.9/PCMBase/man/PCMTreeListAllPartitions.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeListCladePartitions.Rd | 9 PCMBase-1.2.9/PCMBase/man/PCMTreeLocateMidpointsOnBranches.Rd | 9 PCMBase-1.2.9/PCMBase/man/PCMTreeMatchLabels.Rd | 3 PCMBase-1.2.9/PCMBase/man/PCMTreeMatrixNodesInSamePart.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeNearestNodesToEpoch.Rd | 2 PCMBase-1.2.9/PCMBase/man/PCMTreeNodeTimes.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMTreeNumParts.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreePlot.Rd | 22 PCMBase-1.2.9/PCMBase/man/PCMTreePostorder.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMTreePreorder.Rd | 4 PCMBase-1.2.9/PCMBase/man/PCMTreeSetLabels.Rd | 47 PCMBase-1.2.9/PCMBase/man/PCMTreeSetPartRegimes.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeSetPartition.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeSetRegimesForEdges.Rd |only PCMBase-1.2.9/PCMBase/man/PCMTreeSplitAtNode.Rd | 29 PCMBase-1.2.9/PCMBase/man/PCMTreeTableAncestors.Rd | 3 PCMBase-1.2.9/PCMBase/man/PCMTreeToString.Rd | 5 PCMBase-1.2.9/PCMBase/man/PCMVar.Rd | 13 PCMBase-1.2.9/PCMBase/man/PCMVarAtTime.Rd | 13 PCMBase-1.2.9/PCMBase/man/TruePositiveRate.Rd |only PCMBase-1.2.9/PCMBase/man/is.PCMTree.Rd |only PCMBase-1.2.9/PCMBase/tests/testthat/Rplots.pdf |binary PCMBase-1.2.9/PCMBase/tests/testthat/test-MixedGaussian.R | 7 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCM.R | 2 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMLik-BM.R | 29 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMLik-DOU.R | 18 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMLik-OU.R | 9 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMParam.R |only PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMSim.R | 10 PCMBase-1.2.9/PCMBase/tests/testthat/test-PCMTree.R | 129 PCMBase-1.2.9/PCMBase/tests/testthat/test-Transformations.R | 2 PCMBase-1.2.9/PCMBase/vignettes/PCMBase.Rmd | 21 PCMBase-1.2.9/PCMBase/vignettes/REFERENCES-R.bib | 15 PCMBase-1.2.9/PCMBase/vignettes/REFERENCES.bib | 22 123 files changed, 3916 insertions(+), 1549 deletions(-)
Title: Generalized Weighted Quantile Sum Regression
Description: Fits Weighted Quantile Sum (WQS) regressions for continuous or binomial outcomes.
Author: Stefano Renzetti, Paul Curtin, Allan C Just, Ghalib Bello, Chris Gennings
Maintainer: Stefano Renzetti <stefano.renzetti88@gmail.com>
Diff between gWQS versions 1.1.0 dated 2018-05-07 and 1.1.1 dated 2019-03-15
gWQS-1.1.0/gWQS/Summary_results.html |only gWQS-1.1.0/gWQS/Weights_table.html |only gWQS-1.1.1/gWQS/DESCRIPTION | 6 gWQS-1.1.1/gWQS/MD5 | 27 ++-- gWQS-1.1.1/gWQS/R/gwqs.R | 3 gWQS-1.1.1/gWQS/build/vignette.rds |binary gWQS-1.1.1/gWQS/inst/doc/gwqs-vignette.R | 31 ---- gWQS-1.1.1/gWQS/inst/doc/gwqs-vignette.Rmd | 5 gWQS-1.1.1/gWQS/inst/doc/gwqs-vignette.html | 172 +++++++++++++------------- gWQS-1.1.1/gWQS/vignettes/gwqs-vignette.Rmd | 5 gWQS-1.1.1/gWQS/vignettes/gwqs-vignette_cache |only gWQS-1.1.1/gWQS/vignettes/gwqs-vignette_files |only 12 files changed, 115 insertions(+), 134 deletions(-)
Title: Fitting Separable Nonlinear Models in Spectroscopy and
Microscopy
Description: A problem-solving environment (PSE) for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments; has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg <j.snellenburg@vu.nl>
Diff between TIMP versions 1.13.1 dated 2019-01-28 and 1.13.2 dated 2019-03-15
TIMP-1.13.1/TIMP/R/initModelClassTest.R |only TIMP-1.13.1/TIMP/src/init.c |only TIMP-1.13.1/TIMP/tests/_paramEst.txt |only TIMP-1.13.1/TIMP/tests/_selectedtraces.ps |only TIMP-1.13.1/TIMP/tests/_summary.ps |only TIMP-1.13.2/TIMP/DESCRIPTION | 16 ++++---- TIMP-1.13.2/TIMP/MD5 | 48 +++++++++++--------------- TIMP-1.13.2/TIMP/NAMESPACE | 4 ++ TIMP-1.13.2/TIMP/R/calcB.R | 2 - TIMP-1.13.2/TIMP/R/calcCirf.R | 12 +++--- TIMP-1.13.2/TIMP/R/compCoh.R | 4 +- TIMP-1.13.2/TIMP/R/compModelMass.R | 2 - TIMP-1.13.2/TIMP/R/convGausExp.R | 2 - TIMP-1.13.2/TIMP/R/fitModel.R | 10 ++++- TIMP-1.13.2/TIMP/R/getTheta.R | 6 +++ TIMP-1.13.2/TIMP/R/init.dat.R | 14 +++---- TIMP-1.13.2/TIMP/R/init.theta.R | 2 - TIMP-1.13.2/TIMP/R/rescomp.R | 7 +++ TIMP-1.13.2/TIMP/data/denS4.rda |binary TIMP-1.13.2/TIMP/data/denS5.rda |binary TIMP-1.13.2/TIMP/data/donorAcceptorTagged.rda |binary TIMP-1.13.2/TIMP/data/donorTagged.rda |binary TIMP-1.13.2/TIMP/data/mea_IRF.rda |binary TIMP-1.13.2/TIMP/data/target.rda |binary TIMP-1.13.2/TIMP/man/dat-class.Rd | 4 +- TIMP-1.13.2/TIMP/man/kin-class.Rd | 2 + TIMP-1.13.2/TIMP/src/TIMP_init.c |only TIMP-1.13.2/TIMP/src/ntr.c | 14 +++---- 28 files changed, 85 insertions(+), 64 deletions(-)
Title: Continuous Optimization using Memetic Algorithms with Local
Search Chains (MA-LS-Chains) in R
Description: An implementation of an algorithm family for continuous
optimization called memetic algorithms with local search chains
(MA-LS-Chains). Memetic algorithms are hybridizations of genetic
algorithms with local search methods. They are especially suited
for continuous optimization.
Author: Christoph Bergmeir [aut, cre, cph],
José M. Benítez [ths],
Daniel Molina [aut, cph],
Robert Davies [ctb, cph] (Developer of the matrix library newmat which
partly ships with this package),
Dirk Eddelbuettel [ctb, cph] (Developer of RcppDE from which code was
used in evaluate.h),
Nikolaus Hansen [ctb, cph] (Author of the original cmaes implementation
that ships with the package)
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between Rmalschains versions 0.2-4 dated 2018-04-28 and 0.2-5 dated 2019-03-15
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/Rmalschains-package.R | 11 ++++++----- man/Rmalschains-package.Rd | 6 +----- src/origcmaes.cc | 6 ++++++ 6 files changed, 25 insertions(+), 18 deletions(-)
Title: Extensible, Parallelizable Implementation of the Random Forest
Algorithm
Description: Scalable implementation of classification and regression forests, as described by Breiman (2001), <DOI:10.1023/A:1010933404324>.
Author: Mark Seligman
Maintainer: Mark Seligman <mseligman@suiji.org>
Diff between Rborist versions 0.1-15 dated 2019-03-14 and 0.1-16 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Rborist.default.R | 2 +- src/pretree.cc | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Mapping Fisheries Data and Spatial Analysis Tools
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include 'C++' code developed by Angus Johnson for the
'Clipper' library, data for a global shoreline, and other data sets in the
public domain. Under the user's R library directory '.libPaths()',
specifically in './PBSmapping/doc', a complete user's guide is offered and
should be consulted to use package functions effectively.
Author: Jon T. Schnute [aut],
Nicholas Boers [aut],
Rowan Haigh [aut, cre],
Alex Couture-Beil [ctb],
Denis Chabot [ctb],
Chris Grandin [ctb],
Angus Johnson [ctb],
Paul Wessel [ctb],
Franklin Antonio [ctb],
Nicholas J. Lewin-Koh [ctb],
Roger Bivand [ctb]
Maintainer: Rowan Haigh <rowan.haigh@dfo-mpo.gc.ca>
Diff between PBSmapping versions 2.70.5 dated 2018-06-06 and 2.72.1 dated 2019-03-15
PBSmapping-2.70.5/PBSmapping/R/extraCode.r |only PBSmapping-2.72.1/PBSmapping/DESCRIPTION | 12 PBSmapping-2.72.1/PBSmapping/MD5 | 172 PBSmapping-2.72.1/PBSmapping/NAMESPACE | 7 PBSmapping-2.72.1/PBSmapping/R/PBSmapping.r | 4417 +++++--------------- PBSmapping-2.72.1/PBSmapping/R/dotFuns.r |only PBSmapping-2.72.1/PBSmapping/R/extraFuns.r |only PBSmapping-2.72.1/PBSmapping/R/zzz.r | 1 PBSmapping-2.72.1/PBSmapping/inst/doc/ChangeLog.txt | 439 + PBSmapping-2.72.1/PBSmapping/man/EventData.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/LocationSet.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/PBSmapping.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/PBSprint.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/PolyData.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/PolySet.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/addBubbles.Rd | 4 PBSmapping-2.72.1/PBSmapping/man/addCompass.Rd | 6 PBSmapping-2.72.1/PBSmapping/man/addLabels.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/addLines.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/addPoints.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/addPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/addStipples.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/appendPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/bcBathymetry.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcArea.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcCentroid.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcConvexHull.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcGCdist.Rd | 6 PBSmapping-2.72.1/PBSmapping/man/calcLength.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcMidRange.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcSummary.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/calcVoronoi.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/clipLines.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/clipPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/closePolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/combineEvents.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/combinePolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/convCP.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/convDP.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/convLP.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/convUL.Rd | 4 PBSmapping-2.72.1/PBSmapping/man/dividePolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/extractPolyData.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/findCells.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/findPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/fixBound.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/fixPOS.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/importEvents.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/importGSHHS.Rd | 4 PBSmapping-2.72.1/PBSmapping/man/importLocs.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/importPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/importShapefile.Rd | 39 PBSmapping-2.72.1/PBSmapping/man/isConvex.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/isIntersecting.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/joinPolys.Rd | 6 PBSmapping-2.72.1/PBSmapping/man/locateEvents.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/locatePolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/makeGrid.Rd | 57 PBSmapping-2.72.1/PBSmapping/man/makeProps.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/makeTopography.Rd | 45 PBSmapping-2.72.1/PBSmapping/man/nepacLL.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/placeHoles.Rd | 75 PBSmapping-2.72.1/PBSmapping/man/plotLines.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/plotMap.Rd | 4 PBSmapping-2.72.1/PBSmapping/man/plotPoints.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/plotPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/print.Rd | 30 PBSmapping-2.72.1/PBSmapping/man/pythagoras.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/refocusWorld.Rd | 23 PBSmapping-2.72.1/PBSmapping/man/rotatePolys.Rd |only PBSmapping-2.72.1/PBSmapping/man/summary.Rd | 26 PBSmapping-2.72.1/PBSmapping/man/surveyData.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/thickenPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/thinPolys.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/towData.Rd | 5 PBSmapping-2.72.1/PBSmapping/man/towTracks.Rd | 5 PBSmapping-2.72.1/PBSmapping/src/PBSmapping.c | 21 PBSmapping-2.72.1/PBSmapping/src/PBSmapping.h | 2 PBSmapping-2.72.1/PBSmapping/src/clipperWrapper.cpp | 966 ++-- PBSmapping-2.72.1/PBSmapping/src/clipperWrapper.h | 3 PBSmapping-2.72.1/PBSmapping/src/convGSHHS.c | 392 - PBSmapping-2.72.1/PBSmapping/src/convGSHHS.h | 2 PBSmapping-2.72.1/PBSmapping/src/conversions.c | 3 PBSmapping-2.72.1/PBSmapping/src/conversions.h | 3 PBSmapping-2.72.1/PBSmapping/src/floating.h | 3 PBSmapping-2.72.1/PBSmapping/src/globals.h | 3 PBSmapping-2.72.1/PBSmapping/src/init.c | 30 PBSmapping-2.72.1/PBSmapping/src/polygons.c | 3 PBSmapping-2.72.1/PBSmapping/src/polygons.h | 3 89 files changed, 2938 insertions(+), 4133 deletions(-)
Title: Multiply Robust Methods for Missing Data Problems
Description: Multiply robust estimation for population mean (Han and Wang 2013) <doi:10.1093/biomet/ass087>, regression analysis (Han 2014) <doi:10.1080/01621459.2014.880058> (Han 2016) <doi:10.1111/sjos.12177> and quantile regression (Han et al. 2019) <doi:10.1111/rssb.12309>.
Author: Shixiao Zhang and Peisong Han
Maintainer: Shixiao Zhang <praetere@gmail.com>
Diff between MultiRobust versions 1.0.2 dated 2019-03-14 and 1.0.3 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/MI.glm.r | 11 +---------- R/MR.mean.r | 13 +++++++------ R/MR.quantile.r | 19 ++++++------------- R/MR.quantreg.r | 15 ++++++++------- R/MR.reg.r | 17 +++++++++-------- R/ext.names.r | 6 +++--- 8 files changed, 44 insertions(+), 57 deletions(-)
Title: Linear Regression with Non-Constant Variances
Description: Runs a linear-like regression with in which both the expected value and the variance can vary per observation. The expected values mu follows the standard linear model mu = X_mu * beta_mu. The standard deviation sigma follows the model log(sigma) = X_sigma * beta_sigma. The package comes with two vignettes: 'Intro' gives an introduction, 'Math' gives mathematical details.
Author: Posthuma Partners <info@posthuma-partners.nl>
Maintainer: Marco Nijmeijer <nijmeijer@posthuma-partners.nl>
Diff between lmvar versions 1.5.0 dated 2018-05-07 and 1.5.1 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ build/vignette.rds |binary inst/doc/Intro.html | 28 +++++++++++++++++++++++++--- inst/doc/Math.pdf |binary man/cv.lmvar.Rd | 4 ++-- man/predict.lmvar.Rd | 6 +++--- tests/testthat/helper.R | 1 + tests/testthat/test_fwbw.R | 5 +++++ tests/testthat/test_lmvar.R | 3 +++ 11 files changed, 59 insertions(+), 22 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation. References: Bürkner (2017)
<doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.7.0 dated 2018-12-17 and 2.8.0 dated 2019-03-15
brms-2.7.0/brms/R/kfold-helpers.R |only brms-2.7.0/brms/man/kfold.Rd |only brms-2.8.0/brms/DESCRIPTION | 24 brms-2.8.0/brms/MD5 | 303 +-- brms-2.8.0/brms/NAMESPACE | 20 brms-2.8.0/brms/NEWS.md | 53 brms-2.8.0/brms/R/brm.R | 60 brms-2.8.0/brms/R/brm_multiple.R | 163 + brms-2.8.0/brms/R/brms-package.R | 5 brms-2.8.0/brms/R/brmsfit-helpers.R | 51 brms-2.8.0/brms/R/brmsfit-methods.R | 332 ++-- brms-2.8.0/brms/R/brmsformula.R | 145 + brms-2.8.0/brms/R/data-helpers.R | 57 brms-2.8.0/brms/R/data-predictor.R | 168 +- brms-2.8.0/brms/R/datasets.R | 27 brms-2.8.0/brms/R/distributions.R | 561 ++++++ brms-2.8.0/brms/R/exclude_pars.R | 4 brms-2.8.0/brms/R/extract_draws.R | 367 ++-- brms-2.8.0/brms/R/families.R | 138 + brms-2.8.0/brms/R/family-lists.R | 121 + brms-2.8.0/brms/R/fitted.R | 95 - brms-2.8.0/brms/R/formula-helpers.R | 18 brms-2.8.0/brms/R/generics.R | 18 brms-2.8.0/brms/R/ggplot-themes.R | 4 brms-2.8.0/brms/R/hypothesis.R | 12 brms-2.8.0/brms/R/log_lik.R | 106 - brms-2.8.0/brms/R/loo-helpers.R | 857 +++++++--- brms-2.8.0/brms/R/make_stancode.R | 54 brms-2.8.0/brms/R/make_standata.R | 23 brms-2.8.0/brms/R/marginal_effects-helpers.R | 92 - 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brms-2.8.0/brms/tests/testthat/tests.misc.R | 19 brms-2.8.0/brms/tests/testthat/tests.predict.R | 35 brms-2.8.0/brms/tests/testthat/tests.priors.R | 4 brms-2.8.0/brms/tests/testthat/tests.rename_pars.R | 2 brms-2.8.0/brms/vignettes/brms_customfamilies.Rmd | 2 brms-2.8.0/brms/vignettes/brms_distreg.Rmd | 2 brms-2.8.0/brms/vignettes/brms_families.Rmd | 296 ++- brms-2.8.0/brms/vignettes/brms_missings.Rmd | 2 brms-2.8.0/brms/vignettes/brms_monotonic.Rmd | 2 brms-2.8.0/brms/vignettes/brms_multivariate.Rmd | 8 brms-2.8.0/brms/vignettes/brms_nonlinear.Rmd | 2 brms-2.8.0/brms/vignettes/brms_phylogenetics.Rmd | 2 160 files changed, 7244 insertions(+), 4080 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite.
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'.
Author: Chris Bielow <chris.bielow@fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@fu-berlin.de>
Diff between PTXQC versions 0.92.4 dated 2019-02-08 and 0.92.5 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 3 +++ R/fcn_misc.R | 10 +++++++--- README.md | 1 + build/vignette.rds |binary inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 ++-- inst/doc/PTXQC-CustomizeReport.html | 4 ++-- inst/doc/PTXQC-DragNDrop.html | 4 ++-- inst/doc/PTXQC-FAQ.html | 4 ++-- inst/doc/PTXQC-Input_And_Output_Data.html | 4 ++-- inst/doc/PTXQC-ListOfMetrics.html | 4 ++-- tests/testthat/test_misc.R | 5 +++++ 13 files changed, 44 insertions(+), 31 deletions(-)
Title: Ordinal Regression for High-Dimensional Data
Description: Provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne, Amanda Gentry
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between ordinalgmifs versions 1.0.5 dated 2018-07-16 and 1.0.6 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/eyedisease.rda |binary data/hccframe.rda |binary inst/NEWS.Rd | 6 ++++++ inst/doc/ordinalgmifs.pdf |binary src/includes/do_matrix_sum.h | 1 + src/includes/do_row_products.h | 1 + src/includes/do_vector_sum.h | 1 + 11 files changed, 23 insertions(+), 14 deletions(-)
Title: Model-Based Sliced Inverse Regression
Description: An R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between msir versions 1.3.1 dated 2016-04-07 and 1.3.2 dated 2019-03-15
msir-1.3.1/msir/inst/NEWS |only msir-1.3.1/msir/man/msir.dir.Rd |only msir-1.3.2/msir/DESCRIPTION | 27 - msir-1.3.2/msir/MD5 | 47 +- msir-1.3.2/msir/NAMESPACE | 33 + msir-1.3.2/msir/NEWS.md |only msir-1.3.2/msir/R/dimsel.R |only msir-1.3.2/msir/R/msir.R | 462 ++++++--------------------- msir-1.3.2/msir/R/plot.R |only msir-1.3.2/msir/R/spinplot.R |only msir-1.3.2/msir/R/util.R |only msir-1.3.2/msir/R/zzz.R | 2 msir-1.3.2/msir/build |only msir-1.3.2/msir/inst/CITATION | 2 msir-1.3.2/msir/inst/doc |only msir-1.3.2/msir/man/loess.sd.Rd | 2 msir-1.3.2/msir/man/msir-internal.Rd | 7 msir-1.3.2/msir/man/msir-package.Rd | 2 msir-1.3.2/msir/man/msir.Rd | 63 +-- msir-1.3.2/msir/man/msir.bic.Rd | 25 - msir-1.3.2/msir/man/msir.nslices.Rd | 2 msir-1.3.2/msir/man/msir.permutation.test.Rd | 13 msir-1.3.2/msir/man/msir.regularizedSigma.Rd | 17 msir-1.3.2/msir/man/msir.slices.Rd | 2 msir-1.3.2/msir/man/plot.msir.Rd | 23 - msir-1.3.2/msir/man/predict.msir.Rd |only msir-1.3.2/msir/man/splinplot.Rd |only msir-1.3.2/msir/man/summary.msir.Rd | 2 msir-1.3.2/msir/vignettes |only 29 files changed, 256 insertions(+), 475 deletions(-)
Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>),
Andrew Clausen [ctb] (multimin functionality),
Duncan Murdoch [ctb] (qrng functions)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 1.9-10.3 dated 2017-01-05 and 2.1-5 dated 2019-03-15
gsl-1.9-10.3/gsl/src/multimin.c |only gsl-2.1-5/gsl/DESCRIPTION | 30 gsl-2.1-5/gsl/INSTALL | 5 gsl-2.1-5/gsl/MD5 | 91 - gsl-2.1-5/gsl/R/dilog.R | 2 gsl-2.1-5/gsl/R/ellint.R | 6 gsl-2.1-5/gsl/R/legendre.R | 246 ++ gsl-2.1-5/gsl/R/multimin.R | 13 gsl-2.1-5/gsl/build/partial.rdb |only gsl-2.1-5/gsl/build/vignette.rds |binary gsl-2.1-5/gsl/configure | 3073 ++++++++++++++++++------------------ gsl-2.1-5/gsl/configure.ac | 10 gsl-2.1-5/gsl/inst/CITATION | 7 gsl-2.1-5/gsl/inst/doc/gslpaper.pdf |binary gsl-2.1-5/gsl/man/Ellint.Rd | 4 gsl-2.1-5/gsl/man/Legendre.Rd | 35 gsl-2.1-5/gsl/man/Multimin.Rd | 6 gsl-2.1-5/gsl/man/Psi.Rd | 2 gsl-2.1-5/gsl/man/Transport.Rd | 2 gsl-2.1-5/gsl/man/gsl-deprecated.Rd |only gsl-2.1-5/gsl/man/gsl-package.Rd | 26 gsl-2.1-5/gsl/src/airy.c | 24 gsl-2.1-5/gsl/src/bessel.c | 110 - gsl-2.1-5/gsl/src/clausen.c | 2 gsl-2.1-5/gsl/src/coulomb.c | 28 gsl-2.1-5/gsl/src/coupling.c | 6 gsl-2.1-5/gsl/src/dawson.c | 2 gsl-2.1-5/gsl/src/debye.c | 8 gsl-2.1-5/gsl/src/dilog.c | 4 gsl-2.1-5/gsl/src/ellint.c | 27 gsl-2.1-5/gsl/src/elljac.c | 2 gsl-2.1-5/gsl/src/error.c | 12 gsl-2.1-5/gsl/src/expint.c | 26 gsl-2.1-5/gsl/src/fermi_dirac.c | 18 gsl-2.1-5/gsl/src/gamma.c | 46 gsl-2.1-5/gsl/src/gegenbauer.c | 10 gsl-2.1-5/gsl/src/hyperg.c | 20 gsl-2.1-5/gsl/src/laguerre.c | 8 gsl-2.1-5/gsl/src/lambert.c | 4 gsl-2.1-5/gsl/src/legendre.c | 123 + gsl-2.1-5/gsl/src/log.c | 10 gsl-2.1-5/gsl/src/poly.c | 2 gsl-2.1-5/gsl/src/pow_int.c | 2 gsl-2.1-5/gsl/src/psi.c | 12 gsl-2.1-5/gsl/src/synchrotron.c | 4 gsl-2.1-5/gsl/src/transport.c | 8 gsl-2.1-5/gsl/src/trig.c | 18 gsl-2.1-5/gsl/src/zeta.c | 14 48 files changed, 2235 insertions(+), 1873 deletions(-)
Title: Quantifying Systematic Heterogeneity in Meta-Analysis
Description: Quantifying systematic heterogeneity in meta-analysis using R.
The M statistic aggregates heterogeneity information across multiple
variants to, identify systematic heterogeneity patterns and their direction
of effect in meta-analysis. It's primary use is to identify outlier studies,
which either show "null" effects or consistently show stronger or weaker
genetic effects than average across, the panel of variants examined in a
GWAS meta-analysis. In contrast to conventional heterogeneity metrics
(Q-statistic, I-squared and tau-squared) which measure random heterogeneity
at individual variants, M measures systematic (non-random)
heterogeneity across multiple independently associated variants. Systematic
heterogeneity can arise in a meta-analysis due to differences in the study
characteristics of participating studies. Some of the differences may
include: ancestry, allele frequencies, phenotype definition, age-of-disease
onset, family-history, gender, linkage disequilibrium and quality control
thresholds. See <https://magosil86.github.io/getmstatistic/> for statistical
statistical theory, documentation and examples.
Author: Lerato E Magosi [aut],
Jemma C Hopewell [aut],
Martin Farrall [aut],
Lerato E Magosi [cre]
Maintainer: Lerato E Magosi <magosil86@gmail.com>
Diff between getmstatistic versions 0.1.1 dated 2017-06-08 and 0.2.0 dated 2019-03-15
getmstatistic-0.1.1/getmstatistic/vignettes/getmstatistic-tutorial.md |only getmstatistic-0.2.0/getmstatistic/DESCRIPTION | 16 getmstatistic-0.2.0/getmstatistic/MD5 | 21 getmstatistic-0.2.0/getmstatistic/build/vignette.rds |binary getmstatistic-0.2.0/getmstatistic/inst/doc/getmstatistic-tutorial.html | 284 +++++++--- getmstatistic-0.2.0/getmstatistic/man/draw_table.Rd | 2 getmstatistic-0.2.0/getmstatistic/man/getmstatistic.Rd | 6 getmstatistic-0.2.0/getmstatistic/man/heartgenes214.Rd | 1 getmstatistic-0.2.0/getmstatistic/tests/testthat/Histogram_Mstatistics_48studies_214snps.tif |binary getmstatistic-0.2.0/getmstatistic/tests/testthat/Mstatistics_vs_average_variant_effectsize_48studies_214snps.tif |binary getmstatistic-0.2.0/getmstatistic/tests/testthat/table_influential_studies.tif |binary getmstatistic-0.2.0/getmstatistic/tests/testthat/table_underperforming_studies.tif |binary 12 files changed, 231 insertions(+), 99 deletions(-)
Title: Shiny/R Wrapper for 'clipboard.js'
Description: Leverages the functionality of 'clipboard.js', a JavaScript library
for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com>
for more information), and provides a reactive copy-to-clipboard UI button
component, called 'rclipButton', for 'shiny' R applications.
Author: Sebastien Bihorel
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between rclipboard versions 0.1 dated 2017-07-29 and 0.1.1 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/rclipButton.R | 2 +- README.md | 15 ++++++++++----- inst/lib/clipboard.min.js | 6 +++--- 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Fast K-Mer Counting and Clustering for Biological Sequence
Analysis
Description: Contains tools for rapidly computing distance matrices
and clustering large sequence datasets using fast alignment-free
k-mer counting and recursive k-means partitioning.
See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005>
for a review of k-mer counting methods and applications for
biological sequence analysis.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between kmer versions 1.1.0 dated 2018-07-04 and 1.1.1 dated 2019-03-15
DESCRIPTION | 8 ++--- MD5 | 32 ++++++++++----------- R/cluster.R | 1 R/distance.R | 22 ++++++++++++--- R/internals.R | 47 +++++++++++++++++++++++++++++++- R/otu.R | 1 README.md | 2 + build/vignette.rds |binary inst/doc/kmer-vignette.R | 24 ++++++++-------- inst/doc/kmer-vignette.Rmd | 30 ++++++++++---------- inst/doc/kmer-vignette.html | 60 ++++++++++++++++++++++++++++------------- man/cluster.Rd | 1 man/kcount.Rd | 6 +++- man/mbed.Rd | 1 man/otu.Rd | 5 ++- tests/testthat/test_distance.R | 14 +++++++++ vignettes/kmer-vignette.Rmd | 30 ++++++++++---------- 17 files changed, 195 insertions(+), 89 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Joe Heywood [ctb],
Evgeny Mirkes [ctb],
Severine Sabia [ctb],
Joan Capdevila Pujol [ctb],
Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.8-1 dated 2019-01-11 and 1.9-0 dated 2019-03-15
DESCRIPTION | 8 +- MD5 | 30 +++++----- R/g.analyse.R | 129 +++++++++++++++++++------------------------ R/g.calibrate.R | 21 ++++--- R/g.part1.R | 54 +++++++++++++++--- R/g.part2.R | 35 +++++++++++ R/g.part3.R | 17 ++++- R/g.part4.R | 13 ++++ R/g.part5.R | 36 +++++++----- R/g.report.part2.R | 5 + R/g.report.part4.R | 5 + R/g.report.part5.R | 145 ++++++++++++++++++++++++++----------------------- R/getfolderstructure.R | 3 - inst/NEWS.Rd | 13 ++++ inst/doc/GGIR.html | 24 +++++++- man/GGIR-package.Rd | 4 - 16 files changed, 343 insertions(+), 199 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.3.1 dated 2018-11-10 and 1.3.2 dated 2019-03-15
DESCRIPTION | 8 +- MD5 | 46 +++++++-------- R/RcppExports.R | 32 +++++----- R/Viterbi.R | 3 - R/backward.R | 1 R/derivePHMM.R | 15 +++-- R/forward.R | 1 R/generate.R | 1 R/plot.R | 2 README.md | 1 build/vignette.rds |binary inst/CITATION | 16 ++--- inst/doc/aphid-vignette.R | 3 - inst/doc/aphid-vignette.Rmd | 9 +-- inst/doc/aphid-vignette.html | 126 ++++++++++++++++++++++++++----------------- man/Viterbi.Rd | 1 man/backward.Rd | 1 man/forward.Rd | 1 man/generate.Rd | 1 man/plot.HMM.Rd | 2 src/RcppExports.cpp | 108 ++++++++++++++++++------------------ src/ViterbiC.cpp | 2 tests/testthat/test_PHMM.R | 11 +++ vignettes/aphid-vignette.Rmd | 9 +-- 24 files changed, 228 insertions(+), 172 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-06 0.1.59
2010-02-05 0.1.58
2005-04-01 0.1.56
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-09 0.5-2
2018-11-19 0.5-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-17 0.5.9
2017-08-20 0.5.8
2017-07-09 0.5.7
Title: Ridge Regression with Automatic Selection of the Penalty
Parameter
Description: Linear and logistic ridge regression functions. Additionally includes special functions for
genome-wide single-nucleotide polymorphism (SNP) data.
Author: Steffen Moritz [aut, cre] (<https://orcid.org/0000-0002-0085-1804>),
Erika Cule [aut]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between ridge versions 2.3 dated 2018-07-26 and 2.4 dated 2019-03-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ R/linearRidge.R | 11 ++++++++++- R/logisticRidge.R | 11 ++++++++++- README.md | 2 +- configure | 4 ++-- configure.ac | 5 +++-- 8 files changed, 46 insertions(+), 18 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful
for quickly placing data summaries and formatted regression results into
'.Rnw' or '.Rmd' files. Functions for generating commonly used graphics,
such as receiver operating curves or Bland-Altman plots, are also provided
by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The
original version 'qwraps' was never submitted to CRAN but can be found at
<https://github.com/dewittpe/qwraps/>. The implementation and limited scope
of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is
fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.4.0 dated 2019-01-14 and 0.4.1 dated 2019-03-15
DESCRIPTION | 6 ++-- MD5 | 6 ++-- inst/doc/summary-statistics.html | 48 +++++++++++++++++---------------- tests/testthat/test-confusion_matrix.R | 36 ++++++++++++------------ 4 files changed, 49 insertions(+), 47 deletions(-)
Title: Dose Finding in Drug Combination Phase I Trials Using PO-CRM
Description: Provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) of Wages, Conaway and O'Quigley (2011) <doi:10.1177/1740774511408748> for use in Phase I trials of combinations of agents. Provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Varhegyi, Nikole E. (nev4g)" <nev4g@virginia.edu>
Diff between pocrm versions 0.11 dated 2018-03-02 and 0.12 dated 2019-03-15
DESCRIPTION | 8 +-- MD5 | 6 +- NAMESPACE | 2 R/pocrm.sim.R | 145 ++++++++++++++++++++++++++++++++++++++++++++++------------ 4 files changed, 125 insertions(+), 36 deletions(-)
Title: Tools for Writing MCMC
Description: Simplifies MCMC setup by automatically looping through sampling
functions and saving the results. Reduces the memory footprint of running
MCMC and saves samples to disk as the chain runs. Allows samples from the
chain to be analyzed while the MCMC is still running. Provides functions
for commonly performed operations such as calculating Metropolis acceptance
ratios and creating adaptive Metropolis samplers. References: Roberts and
Rosenthal (2009) <doi:10.1198/jcgs.2009.06134>.
Author: Kurtis Shuler [aut, cre]
Maintainer: Kurtis Shuler <kurtis.s.1122+CRAN@gmail.com>
Diff between overture versions 0.1-0 dated 2019-01-25 and 0.2-0 dated 2019-03-15
DESCRIPTION | 7 +- MD5 | 29 +++++---- NAMESPACE | 1 NEWS.md |only R/mcmc.R | 128 +++++++++++++++++++++++++++------------- R/utilities.R | 46 +++++++++----- README.md | 25 +++++-- build/partial.rdb |binary man/AcceptProp.Rd |only man/AcceptProposal.Rd | 12 --- man/Amwg.Rd | 42 +++++-------- man/InitMcmc.Rd | 43 ++++++++++++- man/LoadMcmc.Rd | 11 +-- man/Peek.Rd | 5 - tests/testthat/test-mcmc.R | 76 +++++++++++++++++++++++ tests/testthat/test-utilities.R | 49 ++++++++++++--- tools |only 17 files changed, 340 insertions(+), 134 deletions(-)
Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and
repository management web application gitlab. For many common tasks (repository
file access, issue assignment and status, commenting) convenience wrappers
are provided, and in addition the full API can be used by specifying request
locations. Gitlab is open-source software and can be self-hosted or used on
gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between gitlabr versions 0.9 dated 2017-04-25 and 1.1.6 dated 2019-03-15
gitlabr-0.9/gitlabr/man/iff.Rd |only gitlabr-0.9/gitlabr/man/pipe_into.Rd |only gitlabr-1.1.6/gitlabr/DESCRIPTION | 12 +- gitlabr-1.1.6/gitlabr/MD5 | 51 +++++------ gitlabr-1.1.6/gitlabr/NAMESPACE | 8 + gitlabr-1.1.6/gitlabr/NEWS.md | 5 + gitlabr-1.1.6/gitlabr/R/connect.R | 68 ++------------ gitlabr-1.1.6/gitlabr/R/gitlab_api.R | 35 ++----- gitlabr-1.1.6/gitlabr/R/issues.R | 4 gitlabr-1.1.6/gitlabr/R/legacy_headers.R | 4 gitlabr-1.1.6/gitlabr/R/magrittr_extensions.R | 74 ---------------- gitlabr-1.1.6/gitlabr/R/projects_and_repos.R | 33 +++---- gitlabr-1.1.6/gitlabr/R/shiny_module_login.R | 16 +-- gitlabr-1.1.6/gitlabr/README.md | 32 +++--- gitlabr-1.1.6/gitlabr/build/vignette.rds |binary gitlabr-1.1.6/gitlabr/inst/doc/quick-start-gitlabr.pdf |binary gitlabr-1.1.6/gitlabr/inst/doc_save |only gitlabr-1.1.6/gitlabr/man/branches.Rd | 6 - gitlabr-1.1.6/gitlabr/man/gitlab.Rd | 18 ++- gitlabr-1.1.6/gitlabr/man/gitlabci.Rd | 3 gitlabr-1.1.6/gitlabr/man/gitlabr-deprecated.Rd | 4 gitlabr-1.1.6/gitlabr/man/gl_connection.Rd | 37 ++------ gitlabr-1.1.6/gitlabr/man/gl_edit_issue.Rd | 3 gitlabr-1.1.6/gitlabr/man/gl_get_project_id.Rd | 3 gitlabr-1.1.6/gitlabr/man/gl_push_file.Rd | 4 gitlabr-1.1.6/gitlabr/man/gl_repository.Rd | 2 gitlabr-1.1.6/gitlabr/man/gl_shiny_login.Rd | 8 + gitlabr-1.1.6/gitlabr/vignettes/quick-start-gitlabr.Rmd | 44 ++++----- 28 files changed, 180 insertions(+), 294 deletions(-)
Title: Exploration and Graphics for RivEr Trends Confidence Intervals
Description: Collection of functions to evaluate uncertainty of results from
water quality analysis using the Weighted Regressions on Time Discharge and
Season (WRTDS) method. This package is an add-on to the EGRET package that
performs the WRTDS analysis. The WRTDS modeling
method was initially introduced and discussed in Hirsch et al. (2010) <doi:10.1111/j.1752-1688.2010.00482.x>,
and expanded in Hirsch and De Cicco (2015) <doi:10.3133/tm4A10>. The
paper describing the uncertainty and confidence interval calculations
is Hirsch et al. (2015) <doi:10.1016/j.envsoft.2015.07.017>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
Jennifer Murphy [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRETci versions 2.0.2 dated 2019-02-12 and 2.0.3 dated 2019-03-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/wBTCode.R | 1 + inst/doc/EGRETci.html | 2 +- tests/testthat/tests_boot_tests.R | 2 ++ 5 files changed, 11 insertions(+), 8 deletions(-)