Title: R as a Plotting Engine
Description: Generate basic charts either by custom applications, or from a small script launched from the system console, or within the R console. Two ASCII text files are necessary:
(1) The graph parameters file, which name is passed to the function 'rplotengine()'.
The user can specify the titles, choose the type of the graph, graph output formats
(e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend,
whether to show or not a grid at the background, etc.
(2) The data to be plotted, which name is specified as a parameter ('data_filename')
in the previous file. This data file has a tabulated format, with a single character
(e.g. tab) between each column, and a headers line located in the first row.
Optionally, the file could include data columns for showing confidence intervals.
Author: Pedro-Pablo Garrido Abenza [aut, cre]
Maintainer: Pedro-Pablo Garrido Abenza <pgarrido@umh.es>
Diff between rplotengine versions 1.0-6 dated 2016-11-01 and 1.0-7 dated 2018-08-07
DESCRIPTION | 8 - MD5 | 14 +-- R/rplotengine.R | 199 ++++++++++++++++++++++++++++------------------- inst/extdata/mydata.txt | 1 inst/extdata/mygraph.arg | 1 inst/mydata.txt | 1 inst/mygraph.arg | 1 man/rplotengine.Rd | 13 ++- 8 files changed, 145 insertions(+), 93 deletions(-)
Title: Gene Set Enrichment Analysis via Integration of Metabolic
Networks and RNA-Seq Data
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1101/200964>).
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Diff between metaboGSE versions 1.0.2 dated 2018-04-13 and 1.1.0 dated 2018-08-07
DESCRIPTION | 8 MD5 | 42 +- NAMESPACE | 2 R/addReactFixed.R | 16 R/metaboGSE.R | 219 ++++-------- R/rescue.R | 50 +- R/submnet.R | 793 +++++++++++++++++++++++++++++++---------------- R/weightReacts.R | 15 data/exprMaguire.RData |binary data/yarliGOdata.RData |binary data/yarliGSE.RData |binary data/yarliSubmnets.RData |binary inst/doc/metaboGSE.R | 64 +-- inst/doc/metaboGSE.Rmd | 64 +-- inst/doc/metaboGSE.pdf |binary man/bestRanking.Rd |only man/fitness.Rd |only man/metaboGSE.Rd | 15 man/scoreGeneDel.Rd | 11 man/simulateSubmnet.Rd | 16 man/submnet.Rd | 40 -- man/weightReacts.Rd | 2 vignettes/metaboGSE.Rmd | 64 +-- 23 files changed, 818 insertions(+), 603 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets,
also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.4.2 dated 2018-07-15 and 0.4.3 dated 2018-08-07
DESCRIPTION | 11 ++-- MD5 | 22 ++++----- NAMESPACE | 4 + NEWS.md | 13 ++++- R/overhaul.R | 99 +++++++++++++++++++++++++++++++++-------- R/pipe.R | 6 ++ R/utils.R | 15 +++--- README.md | 12 +--- man/edges.Rd | 7 ++ man/gt_graph.Rd | 2 man/reexports.Rd | 4 + tests/testthat/test_overhaul.R | 1 12 files changed, 145 insertions(+), 51 deletions(-)
Title: Statistical Inference for Unsupervised Learning
Description: Test for association between the observed data
and their systematic patterns of variations, that are often extracted by unsupervised learning.
Systematic patterns may be captured by latent variables using principal component analysis (PCA), factor analysis (FA), and related methods. This allows one to, for example, obtain principal components (PCs) and conduct rigorous statistical testing for association between observed variables and PCs. Similarly, unsupervised clustering, such as K-means clustering, partition around medoids (PAM), and other algorithms, finds subpopulations among the observed variables. The jackstraw test can estimate statistical significance of cluster membership, so that one can evaluate the strength of membership assignments. This package also includes several related methods to support statistical inference and probabilistic feature selection for unsupervised learning.
Author: Neo Christopher Chung <nchchung@gmail.com>, John D. Storey
<jstorey@princeton.edu>, Wei Hao <whao@princeton.edu>
Maintainer: Neo Christopher Chung <nchchung@gmail.com>
Diff between jackstraw versions 1.1.1 dated 2017-09-04 and 1.2 dated 2018-08-07
jackstraw-1.1.1/jackstraw/R/jackstraw_parametric.R |only jackstraw-1.1.1/jackstraw/R/permutationPA.R |only jackstraw-1.1.1/jackstraw/man/jackstraw.FUN.Rd |only jackstraw-1.1.1/jackstraw/man/jackstraw.LFA.Rd |only jackstraw-1.1.1/jackstraw/man/jackstraw.PCA.Rd |only jackstraw-1.1.1/jackstraw/man/jackstraw.parametric.Rd |only jackstraw-1.2/jackstraw/DESCRIPTION | 23 jackstraw-1.2/jackstraw/MD5 | 60 + jackstraw-1.2/jackstraw/NAMESPACE | 23 jackstraw-1.2/jackstraw/R/Jurkat293T.R |only jackstraw-1.2/jackstraw/R/find_k.R |only jackstraw-1.2/jackstraw/R/generic.R | 162 +++-- jackstraw-1.2/jackstraw/R/jackstraw.R | 478 --------------- jackstraw-1.2/jackstraw/R/jackstraw_MiniBatchKmeans.R |only jackstraw-1.2/jackstraw/R/jackstraw_cluster.R |only jackstraw-1.2/jackstraw/R/jackstraw_kmeans.R |only jackstraw-1.2/jackstraw/R/jackstraw_kmeanspp.R |only jackstraw-1.2/jackstraw/R/jackstraw_lfa.R |only jackstraw-1.2/jackstraw/R/jackstraw_pam.R |only jackstraw-1.2/jackstraw/R/jackstraw_pca.R |only jackstraw-1.2/jackstraw/R/jackstraw_subspace.R |only jackstraw-1.2/jackstraw/R/lfacorpcor.R | 115 ++- jackstraw-1.2/jackstraw/R/likelihood.R | 171 +++-- jackstraw-1.2/jackstraw/R/pip.R |only jackstraw-1.2/jackstraw/README.md |only jackstraw-1.2/jackstraw/build/vignette.rds |binary jackstraw-1.2/jackstraw/data |only jackstraw-1.2/jackstraw/inst/doc/jackstraw.R | 5 jackstraw-1.2/jackstraw/inst/doc/jackstraw.Rnw | 9 jackstraw-1.2/jackstraw/inst/doc/jackstraw.pdf |binary jackstraw-1.2/jackstraw/man/Jurkat293T.Rd |only jackstraw-1.2/jackstraw/man/dev.R.Rd | 2 jackstraw-1.2/jackstraw/man/find_k.Rd |only jackstraw-1.2/jackstraw/man/jackstraw.Rd | 95 -- jackstraw-1.2/jackstraw/man/jackstraw_MiniBatchKmeans.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_cluster.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_kmeans.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_kmeanspp.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_lfa.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_pam.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_pca.Rd |only jackstraw-1.2/jackstraw/man/jackstraw_subspace.Rd |only jackstraw-1.2/jackstraw/man/lfa.corpcor.Rd | 2 jackstraw-1.2/jackstraw/man/permutationPA.Rd | 2 jackstraw-1.2/jackstraw/man/pip.Rd |only jackstraw-1.2/jackstraw/vignettes/jackstraw.Rnw | 9 46 files changed, 396 insertions(+), 760 deletions(-)
Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides general features
which are used by other graphical modelling packages, in particular
by the packages 'gRain', 'gRim' and 'gRc'.
'gRbase' contains several data sets relevant for use in connection with
graphical models. Almost all data sets used in the book Graphical
Models with R (2012) are contained in 'gRbase'.
'gRbase' implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph
algorithms are:
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data. These features, however, are not maintained anymore and
remains in 'gRbase' only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The 'gRbase' Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE Proper functionality of 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8-3.1 dated 2018-07-16 and 1.8-3.4 dated 2018-08-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/gRbase-arrays.pdf |binary inst/doc/gRbase-graphs.pdf |binary 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Tsallis q-Exp Distribution
Description: Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Author: Cosma Shalizi [aut] (original R code), Christophe Dutang [cre] (R code packaging)
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between tsallisqexp versions 0.9-2 dated 2015-07-20 and 0.9-3 dated 2018-08-07
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++------- build/vignette.rds |binary inst/CITATION | 2 +- inst/NEWS | 5 +++++ inst/doc/qexpfamily.Rnw | 4 ++-- inst/doc/qexpfamily.pdf |binary vignettes/qexpfamily-concordance.tex |only vignettes/qexpfamily.Rnw | 4 ++-- vignettes/qexpfamily.tex |only 10 files changed, 22 insertions(+), 15 deletions(-)
Title: Side Effect Risks in Hospital : Simulation and Estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rhosp versions 1.07 dated 2015-07-20 and 1.10 dated 2018-08-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 6 +++--- inst/doc/rhosp.Rnw | 5 ++--- inst/doc/rhosp.pdf |binary vignettes/rhosp.Rnw | 5 ++--- 7 files changed, 16 insertions(+), 18 deletions(-)
Title: The Gumbel-Hougaard Copula
Description: Provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Anne-Lise Caillat [ctb], Christophe Dutang [aut,cre], Veronique Larrieu [ctb] and Triet Nguyen [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between gumbel versions 1.10-1 dated 2015-07-20 and 1.10-2 dated 2018-08-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/gumbel.Rnw | 27 ++++++++++++++++----------- inst/doc/gumbel.pdf |binary vignettes/gumbel-concordance.tex | 2 +- vignettes/gumbel.Rnw | 27 ++++++++++++++++----------- vignettes/gumbel.tex | 35 ++++++++++++++++++++--------------- 9 files changed, 66 insertions(+), 51 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight and simpler than both), tools
for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre],
Alex M Chubaty [aut],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.2 dated 2018-08-01 and 0.2.3 dated 2018-08-07
DESCRIPTION | 8 MD5 | 10 NEWS.md | 5 inst/doc/Intro-to-Cache.html | 1436 +++++++++++++++++------------------ tests/testthat/test-cacheArguments.R | 8 tests/testthat/test-prepInputs.R | 28 6 files changed, 755 insertions(+), 740 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library and the Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>.
Author: Lampros Mouselimis [aut, cre],
Sight Machine [cph] (findHOGFeatures function of the SimpleCV computer
vision platform),
Johannes Buchner [cph] (average_hash, dhash and phash functions of the
ImageHash python library),
Mohammad Haghighat [cph] (Gabor Feature Extraction)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.0.9 dated 2018-08-03 and 1.1.0 dated 2018-08-07
DESCRIPTION | 8 - MD5 | 22 +-- NEWS.md | 6 + R/RcppExports.R | 4 inst/doc/Gabor_Feature_Extraction.Rmd | 3 inst/doc/Gabor_Feature_Extraction.html | 7 - inst/doc/The_OpenImageR_package.html | 18 +-- src/RcppExports.cpp | 19 +++ src/init.c | 2 src/utils.cpp | 100 +++++++++-------- tests/testthat/test-gabor.R | 192 ++++++++++++++++++--------------- vignettes/Gabor_Feature_Extraction.Rmd | 3 12 files changed, 226 insertions(+), 158 deletions(-)
Title: Partitioned Symmetric Matrices
Description: A matrix-like class to represent a symmetric matrix partitioned
into file-backed blocks.
Author: Gustavo de los Campos [aut],
Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between symDMatrix versions 1.0.0 dated 2017-05-08 and 2.0.0 dated 2018-08-07
DESCRIPTION | 18 - MD5 | 53 ++- NAMESPACE | 6 NEWS.md |only R/package.R | 32 ++ R/symDMatrix.R | 443 +++++++++------------------------ README.md | 52 +-- inst/extdata/G.RData |binary inst/extdata/data_1_1.RData |only inst/extdata/data_1_1.bin |binary inst/extdata/data_1_2.RData |only inst/extdata/data_1_2.bin |binary inst/extdata/data_1_3.RData |only inst/extdata/data_1_3.bin |binary inst/extdata/data_2_2.RData |only inst/extdata/data_2_2.bin |binary inst/extdata/data_2_3.RData |only inst/extdata/data_2_3.bin |binary inst/extdata/data_3_3.RData |only inst/extdata/data_3_3.bin |binary man/as.symDMatrix.character.Rd | 10 man/as.symDMatrix.matrix.Rd | 6 man/examples/as.symDMatrix.character.R | 10 man/examples/as.symDMatrix.matrix.R | 17 - man/examples/initialize.R | 27 +- man/initialize-symDMatrix-method.Rd | 53 ++- man/load.symDMatrix.Rd | 5 man/nBlocks.Rd | 3 man/symDMatrix-class.Rd | 45 +-- man/symDMatrix-package.Rd | 26 + tests/testthat/test-symDMatrix.R | 126 ++------- 31 files changed, 348 insertions(+), 584 deletions(-)
Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4
classes and methods with a focus on Single Program/Multiple Data
('SPMD')
parallel programming style, which is intended for batch parallel
execution.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] (FreeBSD),
Brian Ripley [ctb] (Windows HPC Pack 2012),
R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.3-7 dated 2018-08-01 and 0.3-8 dated 2018-08-07
ChangeLog | 7 DESCRIPTION | 8 - MD5 | 18 +- NAMESPACE | 1 R/get_conf.r | 9 - R/util_execmpi.r | 16 +- configure | 416 ++++++++++++++++++++++++++++++++--------------------- configure.ac | 419 ++++++++++++++++++++++++++++++++++-------------------- man/uu_execmpi.Rd | 3 src/Makevars.in | 1 10 files changed, 560 insertions(+), 338 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Zonglin He [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2018.6-2 dated 2018-06-01 and 2018.7-25 dated 2018-08-07
ChangeLog | 22 +++++++- DESCRIPTION | 6 +- MD5 | 34 ++++++------- NAMESPACE | 4 - R/chngpt.test.2.R | 12 ++-- R/chngpt.test.R | 54 +++++++++++---------- R/chngptm.R | 73 +++++++++++++++------------- R/hinge.test.R | 4 - R/performance.R | 2 R/sim.chngpt.R | 47 ++++++++++-------- R/simulations.R | 4 - build/vignette.rds |binary inst/doc/chngpt-vignette.pdf |binary inst/unitTests/runit.chngpt.test.R | 20 +++---- man/chngpt.test.Rd | 8 ++- man/chngptm.Rd | 9 ++- man/sim.chngpt.Rd | 31 ++++++------ src/chnpgt_boot.cc | 94 ++++++++++++++++++++++++++++++++++++- 18 files changed, 280 insertions(+), 144 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: JJ Allaire [aut, cre],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Nick Golding [ctb, cph],
Tomasz Kalinowski [ctb, cph],
Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between tensorflow versions 1.8 dated 2018-06-14 and 1.9 dated 2018-08-07
DESCRIPTION | 8 - MD5 | 20 +- NAMESPACE | 7 - R/eager.R | 28 +++- R/extract.R | 7 - R/generics.R | 11 - R/install.R | 237 +++++++++++++++-------------------- R/utils.R | 4 man/install_tensorflow.Rd | 6 man/install_tensorflow_extras.Rd | 12 - tests/testthat/test-extract-syntax.R | 8 - 11 files changed, 172 insertions(+), 176 deletions(-)
Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre],
Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
Diff between archivist.github versions 0.2.2 dated 2016-08-30 and 0.2.6 dated 2018-08-07
archivist.github-0.2.2/archivist.github/README.md |only archivist.github-0.2.2/archivist.github/vignettes/README.md |only archivist.github-0.2.6/archivist.github/DESCRIPTION | 8 archivist.github-0.2.6/archivist.github/MD5 | 58 - archivist.github-0.2.6/archivist.github/NAMESPACE | 66 - archivist.github-0.2.6/archivist.github/NEWS.md | 88 - archivist.github-0.2.6/archivist.github/R/addHooksToPrintGitHub.R | 178 +-- archivist.github-0.2.6/archivist.github/R/agithub.R | 178 +-- archivist.github-0.2.6/archivist.github/R/archive.R | 284 ++--- archivist.github-0.2.6/archivist.github/R/archivist.github-package.R | 119 +- archivist.github-0.2.6/archivist.github/R/authoriseGitHub.R | 98 - archivist.github-0.2.6/archivist.github/R/cloneGitHubRepo.R | 198 +-- archivist.github-0.2.6/archivist.github/R/createGitHubRepo.R | 540 +++++----- archivist.github-0.2.6/archivist.github/R/deleteGitHubRepo.R | 230 ++-- archivist.github-0.2.6/archivist.github/R/push_pull_Repo.R | 228 ++-- archivist.github-0.2.6/archivist.github/R/zzz.R | 38 archivist.github-0.2.6/archivist.github/build/vignette.rds |binary archivist.github-0.2.6/archivist.github/inst/doc/archivist_and_GitHub_integration.R | 36 archivist.github-0.2.6/archivist.github/inst/doc/archivist_and_GitHub_integration.Rmd | 128 +- archivist.github-0.2.6/archivist.github/inst/doc/archivist_and_GitHub_integration.html | 392 +++---- archivist.github-0.2.6/archivist.github/man/addHooksToPrintGitHub.Rd | 131 +- archivist.github-0.2.6/archivist.github/man/archive.Rd | 215 +-- archivist.github-0.2.6/archivist.github/man/archivist-github-integration.Rd | 171 +-- archivist.github-0.2.6/archivist.github/man/archivist.github-package.Rd | 84 - archivist.github-0.2.6/archivist.github/man/authoriseGitHub.Rd | 95 - archivist.github-0.2.6/archivist.github/man/cloneGitHubRepo.Rd | 179 +-- archivist.github-0.2.6/archivist.github/man/createGitHubRepo.Rd | 267 ++-- archivist.github-0.2.6/archivist.github/man/deleteGitHubRepo.Rd | 159 +- archivist.github-0.2.6/archivist.github/man/pushGitHubRepo.Rd | 163 +-- archivist.github-0.2.6/archivist.github/vignettes/archivist_and_GitHub_integration.Rmd | 128 +- archivist.github-0.2.6/archivist.github/vignettes/ggsci.css | 430 +++---- 31 files changed, 2447 insertions(+), 2442 deletions(-)
More information about archivist.github at CRAN
Permanent link
Title: Find Free Versions of Scholarly Publications via Unpaywall
Description: This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly
oaDOI, a service finding free full-texts of academic papers by linking DOIs with
open access journals and repositories. It provides unified access to various data sources
for open access full-text links including Crossref and the Directory of Open Access
Journals (DOAJ). API usage is free and no registration is required.
Author: Najko Jahn [aut, cre],
Tuija Sonkkila [rev] (Tuija Sonkkila reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-6892-9305>),
Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-3520-2046>)
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between roadoi versions 0.5.1 dated 2018-05-21 and 0.5.2 dated 2018-08-07
DESCRIPTION | 20 +++-- MD5 | 26 +++---- NAMESPACE | 4 + NEWS | 7 ++ R/oadoiAddins.R | 24 ++++-- R/oadoi_fetch.r | 2 R/roadoi-package.r | 6 - R/utils.r | 4 - README.md | 180 ++++++++++++++++++++++++++-------------------------- inst/doc/intro.R | 6 - inst/doc/intro.Rmd | 6 - inst/doc/intro.html | 132 ++++++++++++++++++++------------------ man/oadoi_fetch.Rd | 2 vignettes/intro.Rmd | 6 - 14 files changed, 227 insertions(+), 198 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.1.0 dated 2018-07-29 and 0.1.1 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/RaceID.R | 6 ++++-- R/StemID.R | 4 +++- inst/doc/RaceID.html | 18 +++++++++--------- 5 files changed, 24 insertions(+), 20 deletions(-)
Title: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data
Description: Identifying labeled compounds in a 13C-tracer experiment in non-targeted fashion is a cumbersome process. This package facilitates such type of analyses
by providing high level quality control plots, deconvoluting and evaluating spectra and performing a multitude of tests in an automatic fashion.
The main idea is to use changing intensity ratios of ion pairs from peak list generated with 'xcms' as candidates and evaluate those against
base peak chromatograms and spectra information within the raw measurement data automatically.
Author: Jan Lisec [aut, cre],
Friederike Hoffmann [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between HiResTEC versions 0.52 dated 2018-05-07 and 0.54 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/DeconvoluteSpectrum.R | 38 +++++++++++++++++++++++--------------- R/EvaluateCandidate.R | 12 +++++++----- R/EvaluateSpectrum.R | 2 +- R/plotMID.R | 8 +++++--- man/plotMID.Rd | 4 +++- 7 files changed, 49 insertions(+), 35 deletions(-)
Title: Tools for Grid-Based Survey Sampling Design
Description: Multi-stage cluster surveys of households are commonly performed by
governments and programmes to monitor population-level demographic, social,
economic, and health outcomes. Generally, communities are sampled from
subpopulations (strata) in a first stage, and then households are listed and
sampled in a second stage. In this typical two-stage design, sampled
communities are the Primary Sampling Units (PSUs) and households are the
Secondary Sampling Units (SSUs). Census data typically serve as the sample
frame from which PSUs are selected. However, if census data are outdated
inaccurate, or too geographically course, gridded population data (such as
<http://www.worldpop.org.uk>) can be used as a sample frame instead.
GridSample (<doi:10.1186/s12942-017-0098-4>) generates PSUs from
gridded population data according to user-specified complex survey design
characteristics and household sample size. In gridded population sampling,
like census sampling, PSUs are selected within each stratum using a
serpentine sampling method, and can be oversampled in urban or rural areas to
ensure a minimum sample size in each of these important sub-domains.
Furthermore, because grid cells are uniform in size and shape, gridded
population sampling allows for samples to be representative of both the
population and of space, which is not possible with a census sample frame.
Author: Dana R. Thomson [aut] (University of Southampton),
Nick Ruktanonchai [cre] (University of Southampton),
Forrest R. Stevens [aut] (University of Louisville),
Marcia Castro [aut] (Harvard University),
Andrew J. Tatem [aut] (University of Southampton),
Guilherme A. Zagatti [ctb] (Flowminder)
Maintainer: Nick Ruktanonchai <nrukt00@gmail.com>
Diff between gridsample versions 0.2.0 dated 2017-04-09 and 0.2.1 dated 2018-08-07
DESCRIPTION | 69 +- MD5 | 32 - NEWS | 13 R/data.R | 3 R/gs_mode.r | 39 - R/gs_rasterize.r | 66 +- R/gs_sample.r | 1392 ++++++++++++++++++++++++++++++------------------- R/gs_zonal_raster.r | 55 + build/vignette.rds |binary inst/doc/Rwanda.R |only inst/doc/Rwanda.Rmd | 91 +-- inst/doc/Rwanda.html | 246 +++++++- inst/extdata |only man/gs_mode.Rd | 15 man/gs_rasterize.Rd | 26 man/gs_sample.Rd | 265 ++++++--- man/gs_zonal_raster.Rd | 15 vignettes/Rwanda.Rmd | 91 +-- 18 files changed, 1547 insertions(+), 871 deletions(-)
Title: Forecast Combination Methods
Description: Provides geometric- and regression-based forecast
combination methods under a unified user interface for the packages 'ForecastCombinations'
and 'GeomComb'. Additionally, updated tools and convenience functions for data pre-processing are available in order to deal with
common problems in forecast combination (missingness, collinearity). For method details see Hsiao C, Wan SK (2014). <doi:10.1016/j.jeconom.2013.11.003>, Hansen BE (2007). <doi:10.1111/j.1468-0262.2007.00785.x>,
Elliott G, Gargano A, Timmermann A (2013). <doi:10.1016/j.jeconom.2013.04.017>,
and Clemen RT (1989). <doi:10.1016/0169-2070(89)90012-5>.
Author: Christoph E. Weiss, Gernot R. Roetzer, Eran Raviv
Maintainer: Christoph E. Weiss <info@ceweiss.com>
Diff between ForecastComb versions 1.2 dated 2018-05-17 and 1.3.1 dated 2018-08-07
DESCRIPTION | 6 MD5 | 46 +++-- NAMESPACE | 2 R/comb_BG.R | 192 +++++++++++------------ R/comb_CLS.R | 18 -- R/comb_CSR.R | 15 - R/comb_EIG1.R | 18 -- R/comb_EIG2.R | 22 +- R/comb_EIG3.R | 19 -- R/comb_EIG4.R | 26 +-- R/comb_InvW.R | 192 +++++++++++------------ R/comb_LAD.R | 19 -- R/comb_MED.R | 21 +- R/comb_NG.R | 214 +++++++++++++------------- R/comb_OLS.R | 23 +- R/comb_SA.R | 194 +++++++++++------------- R/comb_TA.R | 19 -- R/comb_WA.R | 19 -- R/foreccomb.R | 2 R/foreccomb_res.R |only R/predict.foreccomb_res.R | 40 ++++ R/rolling_combine.R | 290 +++++++++++++++++------------------- man/foreccomb_res.Rd |only man/predict.foreccomb_res.Rd |only tests/testthat/test-foreccomb.R | 20 +- tests/testthat/test-foreccomb_res.R |only 26 files changed, 701 insertions(+), 716 deletions(-)
Title: Quantification of Fate Bias in Multipotent Progenitors
Description: Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2017) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between FateID versions 0.1.3 dated 2018-07-27 and 0.1.4 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/FateID_functions.R | 18 ++++++++++++------ inst/doc/FateID.html | 20 ++++++++++---------- 4 files changed, 29 insertions(+), 23 deletions(-)
Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.2.6 dated 2018-06-21 and 1.3.0 dated 2018-08-07
DESCRIPTION | 13 +-- MD5 | 28 +++++--- NAMESPACE | 4 + NEWS.md | 4 + R/chr_uzemi.R |only R/lesy.R |only R/silnice.R |only R/zeleznice.R |only README.md | 5 + build/vignette.rds |binary inst/doc/vignette.R | 85 ++++++++++++++----------- inst/doc/vignette.Rmd | 81 ++++++++++++++++-------- inst/doc/vignette.html | 106 +++++++++++++++++++++----------- man/chr_uzemi.Rd |only man/lesy.Rd |only man/silnice.Rd |only man/zeleznice.Rd |only tests/testthat/test-1-data-structures.R | 62 ++++++++++++++++++ vignettes/vignette.Rmd | 81 ++++++++++++++++-------- 19 files changed, 325 insertions(+), 144 deletions(-)
Title: Multivariate Statistical Methods with R Applications
Description: Data sets in the book entitled "Multivariate Statistical Methods with R Applications", H.Bulut (2018).
The book will be published in Turkish and the original name of this book will be "R Uygulamalari ile Cok Degiskenli Istatistiksel Yontemler".
Author: Hasan BULUT
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Diff between MSMwRA versions 1.2 dated 2018-07-22 and 1.3 dated 2018-08-07
MSMwRA-1.2/MSMwRA/R/agriculture.R |only MSMwRA-1.2/MSMwRA/data/agriculture.rda |only MSMwRA-1.2/MSMwRA/man/agriculture.Rd |only MSMwRA-1.3/MSMwRA/DESCRIPTION | 8 ++++---- MSMwRA-1.3/MSMwRA/MD5 | 8 ++++---- MSMwRA-1.3/MSMwRA/R/Agriculture.R |only MSMwRA-1.3/MSMwRA/data/Agriculture.rda |only MSMwRA-1.3/MSMwRA/man/Agriculture.Rd |only 8 files changed, 8 insertions(+), 8 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis,
drake rebuilds intermediate data objects when their dependencies change,
and it skips work when the results are already up to date.
Not every execution starts from scratch,
and completed projects have tangible evidence
that they are reproducible.
Extensive documentation, from beginner-friendly tutorials
to practical examples and more, is available at the reference website
<https://ropensci.github.io/drake/> and the online manual
<https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre],
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 5.3.0 dated 2018-07-19 and 5.4.0 dated 2018-08-07
drake-5.3.0/drake/R/generate.R |only drake-5.3.0/drake/R/graph.R |only drake-5.3.0/drake/R/plan.R |only drake-5.3.0/drake/R/static_drake_graph.R |only drake-5.3.0/drake/inst/examples |only drake-5.3.0/drake/man/default_trigger.Rd |only drake-5.3.0/drake/tests/testthat/test-plan.R |only drake-5.4.0/drake/DESCRIPTION | 24 drake-5.4.0/drake/MD5 | 273 ++---- drake-5.4.0/drake/NAMESPACE | 25 drake-5.4.0/drake/NEWS.md | 13 drake-5.4.0/drake/R/Makefile.R | 6 drake-5.4.0/drake/R/build.R | 8 drake-5.4.0/drake/R/build_drake_graph.R |only drake-5.4.0/drake/R/cache_namespaces.R | 15 drake-5.4.0/drake/R/check.R | 11 drake-5.4.0/drake/R/clean.R | 28 drake-5.4.0/drake/R/color.R | 5 drake-5.4.0/drake/R/config.R | 29 drake-5.4.0/drake/R/console.R | 35 drake-5.4.0/drake/R/dependencies.R | 38 drake-5.4.0/drake/R/deprecate.R | 145 +++ drake-5.4.0/drake/R/drake_graph_info.R | 24 drake-5.4.0/drake/R/drake_graph_info_utils.R | 105 +- drake-5.4.0/drake/R/drake_plan.R |only drake-5.4.0/drake/R/drake_plan_class.R |only drake-5.4.0/drake/R/drake_plan_print.R |only drake-5.4.0/drake/R/envir.R | 32 drake-5.4.0/drake/R/examples.R | 74 + drake-5.4.0/drake/R/generate_plans.R |only drake-5.4.0/drake/R/ggraph.R |only drake-5.4.0/drake/R/igraph_utils.R |only drake-5.4.0/drake/R/knitr.R | 1 drake-5.4.0/drake/R/make.R | 2 drake-5.4.0/drake/R/mc_utils.R | 9 drake-5.4.0/drake/R/meta.R | 105 +- drake-5.4.0/drake/R/mtcars_example.R | 4 drake-5.4.0/drake/R/package.R | 14 drake-5.4.0/drake/R/read.R | 1 drake-5.4.0/drake/R/sanitize.R | 35 drake-5.4.0/drake/R/sankey_drake_graph.R | 35 drake-5.4.0/drake/R/staged.R | 4 drake-5.4.0/drake/R/store.R | 22 drake-5.4.0/drake/R/test.R | 12 drake-5.4.0/drake/R/test_scenarios.R | 1 drake-5.4.0/drake/R/triggers.R | 247 ++--- drake-5.4.0/drake/R/utils.R | 19 drake-5.4.0/drake/R/vis_drake_graph.R | 37 drake-5.4.0/drake/inst/doc/drake.Rmd | 9 drake-5.4.0/drake/inst/doc/drake.html | 198 ++++ drake-5.4.0/drake/inst/rmarkdown/mtcars.Rmd |only drake-5.4.0/drake/man/analysis_wildcard.Rd | 2 drake-5.4.0/drake/man/as_drake_plan.Rd |only drake-5.4.0/drake/man/bind_plans.Rd | 2 drake-5.4.0/drake/man/build_drake_graph.Rd | 10 drake-5.4.0/drake/man/built.Rd | 6 drake-5.4.0/drake/man/clean.Rd | 3 drake-5.4.0/drake/man/cleaned_namespaces.Rd | 3 drake-5.4.0/drake/man/dataset_wildcard.Rd | 2 drake-5.4.0/drake/man/dependency_profile.Rd | 2 drake-5.4.0/drake/man/deps_targets.Rd | 5 drake-5.4.0/drake/man/drake_build.Rd | 6 drake-5.4.0/drake/man/drake_cache_log.Rd | 5 drake-5.4.0/drake/man/drake_config.Rd | 34 drake-5.4.0/drake/man/drake_example.Rd | 34 drake-5.4.0/drake/man/drake_examples.Rd | 17 drake-5.4.0/drake/man/drake_ggraph.Rd |only drake-5.4.0/drake/man/drake_graph_info.Rd | 20 drake-5.4.0/drake/man/drake_plan.Rd | 2 drake-5.4.0/drake/man/drake_session.Rd | 6 drake-5.4.0/drake/man/evaluate_plan.Rd | 19 drake-5.4.0/drake/man/example_drake.Rd | 2 drake-5.4.0/drake/man/expand_plan.Rd | 2 drake-5.4.0/drake/man/file_in.Rd | 2 drake-5.4.0/drake/man/file_out.Rd | 2 drake-5.4.0/drake/man/gather_plan.Rd | 2 drake-5.4.0/drake/man/get_cache.Rd | 4 drake-5.4.0/drake/man/ignore.Rd | 2 drake-5.4.0/drake/man/imported.Rd | 4 drake-5.4.0/drake/man/in_progress.Rd | 6 drake-5.4.0/drake/man/knitr_in.Rd | 2 drake-5.4.0/drake/man/loadd.Rd | 7 drake-5.4.0/drake/man/make.Rd | 32 drake-5.4.0/drake/man/max_useful_jobs.Rd | 4 drake-5.4.0/drake/man/parallel_stages.Rd | 3 drake-5.4.0/drake/man/plan_analyses.Rd | 2 drake-5.4.0/drake/man/plan_summaries.Rd | 5 drake-5.4.0/drake/man/plot_graph.Rd | 17 drake-5.4.0/drake/man/predict_load_balancing.Rd | 8 drake-5.4.0/drake/man/predict_runtime.Rd | 4 drake-5.4.0/drake/man/progress.Rd | 4 drake-5.4.0/drake/man/prune_drake_graph.Rd | 2 drake-5.4.0/drake/man/rate_limiting_times.Rd | 6 drake-5.4.0/drake/man/read_config.Rd | 5 drake-5.4.0/drake/man/read_drake_config.Rd | 3 drake-5.4.0/drake/man/read_graph.Rd | 5 drake-5.4.0/drake/man/read_plan.Rd | 5 drake-5.4.0/drake/man/readd.Rd | 4 drake-5.4.0/drake/man/reduce_plan.Rd | 2 drake-5.4.0/drake/man/reexports.Rd | 7 drake-5.4.0/drake/man/render_drake_ggraph.Rd |only drake-5.4.0/drake/man/render_drake_graph.Rd | 20 drake-5.4.0/drake/man/render_sankey_drake_graph.Rd | 15 drake-5.4.0/drake/man/render_static_drake_graph.Rd | 28 drake-5.4.0/drake/man/rescue_cache.Rd | 4 drake-5.4.0/drake/man/sankey_drake_graph.Rd | 44 - drake-5.4.0/drake/man/session.Rd | 4 drake-5.4.0/drake/man/static_drake_graph.Rd | 42 drake-5.4.0/drake/man/target.Rd | 41 drake-5.4.0/drake/man/target_namespaces.Rd | 3 drake-5.4.0/drake/man/trigger.Rd |only drake-5.4.0/drake/man/triggers.Rd | 68 - drake-5.4.0/drake/man/vis_drake_graph.Rd | 55 - drake-5.4.0/drake/tests/testthat/test-console.R | 2 drake-5.4.0/drake/tests/testthat/test-dependencies.R | 11 drake-5.4.0/drake/tests/testthat/test-deprecate.R | 55 + drake-5.4.0/drake/tests/testthat/test-edge-cases.R | 1 drake-5.4.0/drake/tests/testthat/test-examples.R | 15 drake-5.4.0/drake/tests/testthat/test-graph.R | 182 ++++ drake-5.4.0/drake/tests/testthat/test-intermediate-file.R | 4 drake-5.4.0/drake/tests/testthat/test-knitr.R | 9 drake-5.4.0/drake/tests/testthat/test-other-features.R | 35 drake-5.4.0/drake/tests/testthat/test-plans.R |only drake-5.4.0/drake/tests/testthat/test-retry.R | 12 drake-5.4.0/drake/tests/testthat/test-triggers.R | 605 ++++++++++---- drake-5.4.0/drake/tests/testthat/test-visuals.R | 28 drake-5.4.0/drake/vignettes/drake.Rmd | 9 127 files changed, 2237 insertions(+), 1031 deletions(-)
Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js',
a re-usable easy interface JavaScript chart library, based on D3 v4+.
Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts.
All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between billboarder versions 0.2.2 dated 2018-05-29 and 0.2.3 dated 2018-08-07
billboarder-0.2.2/billboarder/inst/htmlwidgets/lib/billboard-1.3.0 |only billboarder-0.2.3/billboarder/DESCRIPTION | 8 billboarder-0.2.3/billboarder/MD5 | 54 ++-- billboarder-0.2.3/billboarder/NAMESPACE | 2 billboarder-0.2.3/billboarder/NEWS.md | 9 billboarder-0.2.3/billboarder/R/bb_add_style.R | 4 billboarder-0.2.3/billboarder/R/bb_helpers.R | 110 +++++++++ billboarder-0.2.3/billboarder/R/bb_utils.R | 45 +++ billboarder-0.2.3/billboarder/R/billboarder-data.R | 27 ++ billboarder-0.2.3/billboarder/R/billboarder-shiny.R | 2 billboarder-0.2.3/billboarder/build/vignette.rds |binary billboarder-0.2.3/billboarder/data/avengers.rda |only billboarder-0.2.3/billboarder/data/avengers_wide.rda |only billboarder-0.2.3/billboarder/inst/doc/billboarder-intro.html | 100 ++++---- billboarder-0.2.3/billboarder/inst/doc/billboarder-mapping.html | 46 ++-- billboarder-0.2.3/billboarder/inst/doc/billboarder-options.html | 86 +++---- billboarder-0.2.3/billboarder/inst/htmlwidgets/billboarder.js | 6 billboarder-0.2.3/billboarder/inst/htmlwidgets/billboarder.yaml | 4 billboarder-0.2.3/billboarder/inst/htmlwidgets/lib/billboard-1.5.1 |only billboarder-0.2.3/billboarder/man/avengers.Rd |only billboarder-0.2.3/billboarder/man/bb_barchart.Rd | 4 billboarder-0.2.3/billboarder/man/bb_linechart.Rd | 4 billboarder-0.2.3/billboarder/man/bb_proxy_data_names.Rd | 2 billboarder-0.2.3/billboarder/man/bb_proxy_tooltip.Rd | 4 billboarder-0.2.3/billboarder/man/bb_radar.Rd |only billboarder-0.2.3/billboarder/man/bb_radarchart.Rd |only billboarder-0.2.3/billboarder/man/billboarder.Rd | 4 billboarder-0.2.3/billboarder/man/cdc_prod_filiere.Rd | 2 billboarder-0.2.3/billboarder/man/equilibre_mensuel.Rd | 2 billboarder-0.2.3/billboarder/tests/testthat/test-mapping.R |only billboarder-0.2.3/billboarder/tests/testthat/test-readme.R | 115 +++++++++- 31 files changed, 469 insertions(+), 171 deletions(-)
Title: Nonnegative Integer Solutions of Linear Diophantine Equations
with Applications
Description: Routines for enumerating all existing nonnegative integer solutions of a linear Diophantine equation. The package provides routines for solving 0-1, bounded and unbounded knapsack problems; 0-1, bounded and unbounded subset sum problems; and a problem of additive partitioning of natural numbers.
Author: Natalya Pya Arnqvist[aut, cre],
Vassilly Voinov [aut],
Yevgeniy Voinov [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Diff between nilde versions 1.1-1 dated 2018-06-19 and 1.1-2 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/nlde.R | 17 +++++++++++++++-- build/partial.rdb |binary man/print.partitions.Rd | 2 +- 5 files changed, 24 insertions(+), 11 deletions(-)
Title: Distance-Based k-Medoids
Description: Algorithms of distance-based k-medoids clustering:
simple and fast k-medoids (Park and Jun, 2009) <doi:10.1016/j.eswa.2008.01.039>,
ranked k-medoids (Zadegan et al., 2013) <doi:10.1016/j.knosys.2012.10.012>, and
step k-medoids (Yu et al., 2018) <doi:10.1016/j.eswa.2017.09.052>.
Calculate distances for mixed variable data such as
Gower (1971) <doi:10.2307/2528823>,
Wishart (2003) <doi:10.1007/978-3-642-55721-7_23>,
Podani (1999) <doi:10.2307/1224438>,
Huang (1997) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.9984&rep=rep1&type=pdf>,
Harikumar and PV (2015) <doi:10.1016/j.procs.2015.10.077>, and
Ahmad and Dey (2007) <doi:10.1016/j.datak.2007.03.016>.
Cluster validation applies bootstrap procedure producing a heatmap with a flexible
reordering matrix algorithm such as complete, ward, or average linkages.
Author: Weksi Budiaji
Maintainer: Weksi Budiaji <budiaji@untirta.ac.id>
Diff between kmed versions 0.0.1 dated 2018-02-12 and 0.1.0 dated 2018-08-07
kmed-0.0.1/kmed/R/coocurrence.R |only kmed-0.1.0/kmed/DESCRIPTION | 25 +++--- kmed-0.1.0/kmed/MD5 | 53 +++++++------ kmed-0.1.0/kmed/NAMESPACE | 3 kmed-0.1.0/kmed/NEWS.md |only kmed-0.1.0/kmed/R/clustboot.R | 2 kmed-0.1.0/kmed/R/clustheatmap.R | 2 kmed-0.1.0/kmed/R/consensusmatrix.R | 2 kmed-0.1.0/kmed/R/cooccur.R |only kmed-0.1.0/kmed/R/coocurance.R |only kmed-0.1.0/kmed/R/distNumeric.R | 2 kmed-0.1.0/kmed/R/distmix.R | 36 +++++--- kmed-0.1.0/kmed/R/fastkmed.R | 24 +++-- kmed-0.1.0/kmed/R/matching.R | 2 kmed-0.1.0/kmed/R/rankkmed.R |only kmed-0.1.0/kmed/R/stepkmed.R |only kmed-0.1.0/kmed/R/weightednum.R | 50 ++++++++++++ kmed-0.1.0/kmed/inst/doc/kmedoid.R | 29 ++++--- kmed-0.1.0/kmed/inst/doc/kmedoid.Rmd | 134 ++++++++++++++++++++++++++------- kmed-0.1.0/kmed/inst/doc/kmedoid.html | 129 ++++++++++++++++++++----------- kmed-0.1.0/kmed/man/clustboot.Rd | 2 kmed-0.1.0/kmed/man/clustheatmap.Rd | 2 kmed-0.1.0/kmed/man/consensusmatrix.Rd | 2 kmed-0.1.0/kmed/man/cooccur.Rd |only kmed-0.1.0/kmed/man/coocurance.Rd | 8 - kmed-0.1.0/kmed/man/distNumeric.Rd | 2 kmed-0.1.0/kmed/man/distmix.Rd | 15 ++- kmed-0.1.0/kmed/man/fastkmed.Rd | 15 +-- kmed-0.1.0/kmed/man/matching.Rd | 2 kmed-0.1.0/kmed/man/rankkmed.Rd |only kmed-0.1.0/kmed/man/stepkmed.Rd |only kmed-0.1.0/kmed/vignettes/kmedoid.Rmd | 134 ++++++++++++++++++++++++++------- 32 files changed, 483 insertions(+), 192 deletions(-)
Title: Integro-Difference Equation Spatio-Temporal Models
Description: The Integro-Difference Equation model is a linear, dynamical model used to model
phenomena that evolve in space and in time; see, for example, Cressie and Wikle (2011,
ISBN:978-0-471-69274-4) or Dewar et al. (2009) <doi:10.1109/TSP.2008.2005091>. At the
heart of the model is the kernel, which dictates how the process evolves from one time
point to the next. Both process and parameter reduction are used to facilitate computation,
and spatially-varying kernels are allowed. Data used to estimate the parameters are assumed
to be readings of the process corrupted by Gaussian measurement error. Parameters are fitted
by maximum likelihood, and estimation is carried out using an evolution algorithm.
Author: Andrew Zammit-Mangion [aut, cre]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
Diff between IDE versions 0.1.0 dated 2018-05-07 and 0.2.0 dated 2018-08-07
DESCRIPTION | 10 MD5 | 10 R/IDEfunctions.R | 1517 +++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/IDE_intro.pdf | 837 ++++++++------------------- man/simIDE.Rd | 4 6 files changed, 1070 insertions(+), 1308 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.2.13 dated 2018-07-27 and 1.2.14 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/onLoad.R | 9 +++++---- inst/doc/v85i12.pdf |binary 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Non-Standard ROC Curve Analysis
Description: Tools for estimating Receiver Operating Characteristic (ROC) curves,
building confidence bands, comparing several curves both for dependent and
independent data, estimating the cumulative-dynamic ROC curve in presence of
censored data, and performing meta-analysis studies, among others.
Author: Sonia Perez Fernandez
Maintainer: Sonia Perez Fernandez <uo217889@uniovi.es>
Diff between nsROC versions 1.0 dated 2017-06-23 and 1.1 dated 2018-08-07
DESCRIPTION | 6 MD5 | 20 - R/ROCbands.R | 654 +++++++++++++++++++++++++++++--------------------------- R/cdROC.R | 422 ++++++++++++++++++------------------ R/gROC.R | 381 ++++++++++++++++++++------------ R/metaROC.R | 380 ++++++++++++++++---------------- R/plot.R | 187 ++++++++-------- R/print.R | 190 ++++++++-------- man/ROCbands.Rd | 290 ++++++++++++------------ man/gROC.Rd | 201 +++++++++-------- man/plot.Rd | 162 ++++++------- 11 files changed, 1532 insertions(+), 1361 deletions(-)
Title: Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre],
Krisztian Sebestyen [aut],
Jason Becker [ctb],
Bendix Carstensen [ctb],
Daryl Morris [ctb],
Josh Pasek [ctb],
Dennis Chao [ctb],
Andri Signorell [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between kyotil versions 2017.12-27 dated 2018-01-03 and 2018.7-16 dated 2018-08-07
ChangeLog | 12 - DESCRIPTION | 13 - MD5 | 41 +-- NAMESPACE | 6 R/DMHeatMap.R | 2 R/base.R | 64 ++++- R/kernel.R | 2 R/matrix.R | 2 R/misc.R | 71 ++---- R/na.approx.R |only R/plotting.R | 434 +++++++++++++++++++++++++++++++++++--- R/print.R | 58 ++--- R/regression.model.functions.R | 120 ++++++---- R/string.R | 8 man/base.Rd | 39 +++ man/get.sim.res.Rd | 12 - man/kyotil.Rd | 4 man/plotting.Rd | 15 - man/print.Rd | 21 - man/regression.model.functions.Rd | 8 man/string.Rd | 5 tests/doRUnit.R | 18 - 22 files changed, 730 insertions(+), 225 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese & Fleming (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in
Fleming et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
and
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.0 dated 2018-05-16 and 0.5.1 dated 2018-08-07
DESCRIPTION | 16 MD5 | 118 +++---- NEWS.md | 37 ++ R/acf.R | 39 +- R/anonymize.R |only R/ctmm.refit.R |only R/emulate.R | 168 +++++++--- R/generic.R | 7 R/kalman.R | 4 R/kde.R | 9 R/likelihood.R | 147 ++++++-- R/mean.R | 38 +- R/median.R | 73 ++-- R/numDeriv.R | 117 ++----- R/optim.R | 11 R/overlap.R | 28 + R/parameters.R | 8 R/plot.telemetry.R | 26 + R/plot.variogram.R | 47 -- R/select.R | 594 ++++++++++++++--------------------- R/speed.R | 91 +++-- R/stats.R | 27 + R/summary.ctmm.R |only R/telemetry.R | 175 +++++++--- R/uere.R | 178 +++++----- R/units.R | 53 ++- R/variogram.R | 18 - TODO | 14 build/vignette.rds |binary data/coati.rda |only data/datalist |only data/turtle.rda |binary inst/doc/akde.R | 88 ++--- inst/doc/akde.html | 476 ++++++++++++++++++++-------- inst/doc/error.R | 157 +++------ inst/doc/error.Rmd | 80 +--- inst/doc/error.html | 673 ++++++++++++++++++++++++---------------- inst/doc/periodogram.R | 101 +++--- inst/doc/periodogram.Rmd | 58 +-- inst/doc/periodogram.html | 655 ++++++++++++++++++++++++++------------- inst/doc/variogram.R | 186 +++++------ inst/doc/variogram.html | 762 +++++++++++++++++++++++++++++----------------- man/akde.Rd | 2 man/as.telemetry.Rd | 22 - man/bandwidth.Rd | 2 man/buffalo.Rd | 2 man/coati.Rd |only man/ctmm-FAQ.Rd | 2 man/ctmm-package.Rd | 16 man/ctmm.boot.Rd | 9 man/ctmm.fit.Rd | 5 man/gazelle.Rd | 2 man/occurrence.Rd | 2 man/plot.variogram.Rd | 6 man/residuals.Rd | 13 man/speed.Rd | 27 + man/summary.UD.Rd | 8 man/summary.ctmm.Rd | 19 - man/turtle.Rd | 6 man/uere.Rd | 46 +- man/wolf.Rd | 2 vignettes/error.Rmd | 80 +--- vignettes/periodogram.Rmd | 58 +-- 63 files changed, 3322 insertions(+), 2286 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 2.0 dated 2018-07-14 and 2.0-1 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/smooth_map.R | 6 +++--- R/to_raster.R | 18 ++++++------------ man/aggregate_map.Rd | 4 ++-- man/get_asp_ratio.Rd | 2 ++ 7 files changed, 26 insertions(+), 27 deletions(-)
Title: Translate Integers into English
Description: Allow numbers to be presented in an English language
version, one, two, three, ...
Author: John Fox, Bill Venables and Anthony Damico
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between english versions 1.1-3 dated 2018-05-19 and 1.1-4 dated 2018-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 34 +++++++++++++++++----------------- R/words.R |only man/english-package.Rd | 11 +++++++++-- man/words.Rd |only 6 files changed, 35 insertions(+), 26 deletions(-)
Title: Calculate Predicted Means for Linear Models
Description: Providing functions to diagnose
and make inferences from various linear models, such as those obtained from 'aov',
'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted
means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 0.99 dated 2014-09-22 and 1.0 dated 2018-08-07
predictmeans-0.99/predictmeans/R/permmodels.R |only predictmeans-0.99/predictmeans/inst |only predictmeans-0.99/predictmeans/man/permmodels.Rd |only predictmeans-1.0/predictmeans/DESCRIPTION | 19 predictmeans-1.0/predictmeans/MD5 | 45 - predictmeans-1.0/predictmeans/NAMESPACE | 31 predictmeans-1.0/predictmeans/R/CookD.R | 2 predictmeans-1.0/predictmeans/R/Kmatrix.R | 15 predictmeans-1.0/predictmeans/R/PMplot.R | 21 predictmeans-1.0/predictmeans/R/anovalmer.R |only predictmeans-1.0/predictmeans/R/contrastmeans.R | 2 predictmeans-1.0/predictmeans/R/covariatemeans.R | 44 - predictmeans-1.0/predictmeans/R/misc.R | 194 ++++ predictmeans-1.0/predictmeans/R/permanova.lmer.R |only predictmeans-1.0/predictmeans/R/permlmer.R |only predictmeans-1.0/predictmeans/R/predictmeans.R | 605 ++++++++------ predictmeans-1.0/predictmeans/R/residplot.R | 8 predictmeans-1.0/predictmeans/R/rsplot.gls.R | 4 predictmeans-1.0/predictmeans/R/rsplot.lme.R | 6 predictmeans-1.0/predictmeans/man/Kmatrix.Rd | 5 predictmeans-1.0/predictmeans/man/PMplot.Rd | 20 predictmeans-1.0/predictmeans/man/anovalmer.Rd |only predictmeans-1.0/predictmeans/man/covariatemeans.Rd | 16 predictmeans-1.0/predictmeans/man/permanova.lmer.Rd |only predictmeans-1.0/predictmeans/man/permlmer.Rd |only predictmeans-1.0/predictmeans/man/predictmeans-package.Rd | 4 predictmeans-1.0/predictmeans/man/predictmeans.Rd | 34 predictmeans-1.0/predictmeans/man/residplot.Rd | 6 28 files changed, 744 insertions(+), 337 deletions(-)