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 discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, 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 2.0.5 dated 2019-03-15 and 2.0.6 dated 2019-05-08
DESCRIPTION | 12 - MD5 | 26 ++-- NAMESPACE | 16 +- R/DA.R |only R/GrandTour.R | 309 ++++++++++++++++++++++++++++++++++++++----------- R/MDS.R | 148 ++++++++++++++++++----- R/Plot.PP.R | 86 +++++-------- man/Cluster.Rd | 2 man/DA.Rd |only man/GrandTour.Rd | 35 +++-- man/MDS.Rd | 40 +++--- man/MVar.pt-package.Rd | 6 man/PP_Index.Rd | 2 man/PP_Optimizer.Rd | 2 man/Plot.PP.Rd | 23 +-- 15 files changed, 483 insertions(+), 224 deletions(-)
Title: Plot Flow Charts According to the "PRISMA" Statement
Description: Plot a PRISMA <http://prisma-statement.org/> flow
chart describing the identification, screening, eligibility and
inclusion or studies in systematic reviews. The PRISMA statement
defines an evidence-based, minimal set of items for reporting in
systematic reviews and meta-analyses. PRISMA should be used for the
reporting of studies evaluating randomized clinical trials (RCT), and
is also for reporting on systematic reviews of other types of
research. There is also a function to generate flow charts describing
exclusions and inclusions for any kind of study.
Author: Jack O. Wasey [aut, cre, cph] (<https://orcid.org/0000-0003-3738-4637>)
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between PRISMAstatement versions 1.0.4 dated 2018-08-08 and 1.1.1 dated 2019-05-08
DESCRIPTION | 29 - MD5 | 43 + NAMESPACE | 4 NEWS.md | 12 R/flow-exclusions.r |only R/prisma.r | 118 ++++- README.md | 24 - build/vignette.rds |binary inst/JOSS |only inst/doc/PRISMA.R | 7 inst/doc/PRISMA.Rmd | 53 +- inst/doc/PRISMA.html | 825 +++++++++++++++++++------------------- inst/doc/exclusionflowcharts.R |only inst/doc/exclusionflowcharts.Rmd |only inst/doc/exclusionflowcharts.html |only man/flow_exclusions.Rd |only man/prisma.Rd | 40 + man/prisma_pdf.Rd | 17 tests/testthat/test-digraph.r |only vignettes/PRISMA.Rmd | 53 +- vignettes/PRISMA.bib | 211 +++++++++ vignettes/all.bib |only vignettes/exclusionflowcharts.Rmd |only vignettes/r.bib |only 24 files changed, 902 insertions(+), 534 deletions(-)
More information about PRISMAstatement at CRAN
Permanent link
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.12.0 dated 2019-03-08 and 1.13.0 dated 2019-05-08
DESCRIPTION | 6 MD5 | 100 ++++----- NEWS | 66 ++++++ R/ClusterFuture-class.R | 24 +- R/Future-class.R | 73 +++--- R/FutureRegistry.R | 14 - R/MulticoreFuture-class.R | 2 R/UniprocessFuture-class.R | 2 R/availableCores.R | 48 +--- R/availableWorkers.R | 14 + R/futureCall.R | 7 R/futureOf.R | 4 R/futures.R | 2 R/globals.R | 36 +-- R/makeClusterPSOCK.R | 92 +++++++- R/multicore.R | 18 - R/nbrOfWorkers.R | 2 R/options.R | 11 - R/resolve.R | 106 +++++---- R/signalEarly.R | 2 R/supportsMulticore.R |only R/tweak.R | 2 R/utils.R | 48 +++- R/values.R | 2 R/zzz.R | 30 +- R/zzz.plan.R | 22 +- build/vignette.rds |binary inst/doc/future-1-overview.html | 82 +++---- inst/doc/future-1-overview.md.rsp | 83 +++---- inst/doc/future-2-output.html | 16 - inst/doc/future-2-output.md.rsp | 16 - inst/doc/future-4-issues.html | 226 -------------------- inst/doc/future-4-issues.md.rsp | 230 --------------------- inst/doc/future-4-non-exportable-objects.html |only inst/doc/future-4-non-exportable-objects.md.rsp |only inst/vignettes-static/future-1-overview.md.rsp.rsp | 5 man/availableCores.Rd | 15 - man/availableWorkers.Rd | 9 man/future.options.Rd | 11 - man/futures.Rd | 2 man/makeClusterPSOCK.Rd | 82 +++---- man/multicore.Rd | 14 - man/nbrOfWorkers.Rd | 4 man/resolve.Rd | 9 man/supportsMulticore.Rd | 36 ++- man/tweak.Rd | 4 man/values.Rd | 2 tests/incl/start,load-only.R | 3 tests/utils.R | 11 - vignettes/future-1-overview.md.rsp | 83 +++---- vignettes/future-2-output.md.rsp | 16 - vignettes/future-4-issues.md.rsp | 230 --------------------- vignettes/future-4-non-exportable-objects.md.rsp |only 53 files changed, 741 insertions(+), 1181 deletions(-)
Title: Density Ratio Estimation
Description: Density ratio estimation.
The estimated density ratio function can be used in many applications such as
the inlier-based outlier detection, covariate shift adaptation and etc.
The implemented methods are uLSIF (Hido et al. (2011) <doi:10.1007/s10115-010-0283-2>)
and KLIEP (Sugiyama et al. (2007) <doi:10.1007/s10463-008-0197-x>).
Author: Koji Makiyama [aut, cre]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Diff between densratio versions 0.0.3 dated 2016-03-29 and 0.1.1 dated 2019-05-08
DESCRIPTION | 13 - LICENSE | 2 MD5 | 43 ++- NEWS.md |only R/KLIEP.R | 17 - R/KLIEP_compute_score.R | 18 + R/KLIEP_search_sigma.R | 14 - R/KLIEP_search_sigma_list.R | 16 - R/compute_kernel_Gaussian.R | 12 R/densratio.R | 40 ++- R/uLSIF.R | 15 - README.md |only build/vignette.rds |binary inst/doc/densratio.R | 37 +- inst/doc/densratio.Rmd | 105 +++++--- inst/doc/densratio.html | 508 +++++++++++++++++++++++++++++------------ man/KLIEP.Rd | 20 - man/densratio.Rd | 28 +- man/figures |only man/squared_euclid_distance.Rd |only man/uLSIF.Rd | 21 - tests |only vignettes/densratio.Rmd | 105 +++++--- 23 files changed, 666 insertions(+), 348 deletions(-)
Title: Estimation Methods for Gravity Models
Description: A wrapper of different standard estimation methods for gravity models.
This package provides estimation methods for log-log models and multiplicative models.
Author: Anna-Lena Woelwer [aut, cph],
Jan Pablo Burgard [aut, cph],
Joshua Kunst [aut, cph],
Mauricio Vargas [aut, cre, cph]
(<https://orcid.org/0000-0003-1017-7574>),
Romain Francois [ctb] (adapted parts of the code to use dplyr 0.8.0),
Lionel Henry [ctb] (simplified parts of the code),
Hrisyana Doytchinova [rev] (sent us different suggestions and bug
reports)
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between gravity versions 0.9.7 dated 2019-04-21 and 0.9.8 dated 2019-05-08
DESCRIPTION | 16 +++++++++++----- MD5 | 10 +++++----- R/ppml.R | 7 ++++++- build/partial.rdb |binary inst/doc/crash-course-on-gravity-models.html | 20 ++++++++++---------- inst/doc/creating-gravity-datasets.html | 4 ++-- 6 files changed, 34 insertions(+), 23 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions.
Author: Manos Papadakis, Michail Tsagris, Stefanos Fafalios and Marios Dimitriadis.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.0.1 dated 2019-03-22 and 0.0.2 dated 2019-05-08
DESCRIPTION | 8 +++---- MD5 | 23 ++++++++++++++++------ NAMESPACE | 2 - NEWS.md | 47 ++++++++++++++++++++++++++++++++++++++++++++++ R/gee.reg.R |only R/halfcauchy.mle.R |only R/kumar.mle.R |only R/powerlaw.mle.R |only R/reg.mle.lda.R |only R/walter.ci.R |only R/welch.tests.R | 51 +++++++++++++++++++++++++------------------------- man/Rfast2-package.Rd | 4 +-- man/gee.reg.Rd |only man/halfcauchy.mle.Rd |only man/kumar.mle.Rd |only man/reg.mle.lda.Rd |only man/walter.ci.Rd |only src/mmp_c.cpp | 13 ++++++------ 18 files changed, 104 insertions(+), 44 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.1.1 dated 2019-04-23 and 2.2.0 dated 2019-05-08
CHANGELOG | 5 +++- DESCRIPTION | 11 +++++----- MD5 | 48 ++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++++--- R/AgrMcDt.R | 24 +++++++++++++++++++++- R/ClasGenMetDef.R | 28 ++++++++++++++++++++++++++ R/IData.R | 24 +++++++++++++++------- R/IdtMclust_methods.R | 37 ++++++++++++++++++++++++++++++++++ R/Idtoutl_methods.R |only R/SNmle.R | 6 +++-- R/fasttle.R | 12 +++++++---- R/mle.R | 28 ++++++++++++++++++++++---- data/Abalone.RData |only man/Abalone.Rd |only man/IData-class.Rd | 7 ++++++ man/IDtOutl-class.Rd |only man/IdtE-class.Rd | 7 ++++++ man/IdtMANOVA-class.Rd | 1 man/IdtMclust-class.Rd | 39 ++++++++++++++++++++++++++++++++++++ man/IdtNDE-class.Rd | 1 man/IdtOutl-methods.Rd |only man/IdtSngNDRE-class.Rd | 2 - man/InfCrt-methods.Rd |only man/MAINT.Data-internal.Rd | 12 +++++++++++ man/MAINT.Data-package.Rd | 4 +-- man/fulltle-methods.Rd | 2 - man/logLik-methods.Rd |only man/mean-methods.Rd |only man/plot-methods.Rd | 2 - 29 files changed, 256 insertions(+), 53 deletions(-)
Title: Downloads, Unpacks and Tidies Legislative Data from the
Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and
Chamber of Deputies Application Programming Interfaces available at <http://
legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/>
respectively.
Author: Robert McDonnell [aut, cre],
Guilherme Jardim Duarte [aut],
Danilo Freire [aut],
Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>
Diff between congressbr versions 0.2.0 dated 2019-02-17 and 0.2.1 dated 2019-05-08
DESCRIPTION | 6 +-- MD5 | 22 ++++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/sen_commission_list.R | 32 ++++++++---------- R/sen_votes.R | 2 - R/util.R | 4 +- build/vignette.rds |binary inst/doc/chamber.html | 9 +++-- inst/doc/senate.html | 69 +++++++++++++++++++--------------------- man/sen_commission_positions.Rd | 2 - man/sen_votes.Rd | 2 - 12 files changed, 77 insertions(+), 76 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [aut], Sergii Babkin <babkin.sergii@gmail.com> [aut], Jonathan Stewart <jonathan.stewart@rice.edu> [aut], Duy Vu <duy.vu@unimelb.edu.au> [aut], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 4.1-1 dated 2019-05-01 and 4.1-2 dated 2019-05-08
DESCRIPTION | 8 +-- MD5 | 40 ++++++++-------- NAMESPACE | 2 R/auxiliary_functions.r | 8 ++- R/hergm.R | 11 +++- R/hergm.mcmc.R | 4 - R/hergm.preprocess.R | 13 ++--- R/hergm.simulate.R | 18 ++++++- R/zzz.R | 9 ++- man/bali.Rd | 3 - man/bunt.Rd | 3 - man/example.Rd | 4 - man/hergm.Rd | 103 ++++++++++++++++++++---------------------- man/hergm.gof.Rd | 2 man/hergm.mcmc.diagnostics.Rd | 2 man/hergm.plot.Rd | 3 - man/hergm.print.Rd | 5 -- man/hergm.simulate.Rd | 25 ++++++---- man/hergm.summary.Rd | 3 - man/hergm.terms.Rd | 58 ++++------------------- man/kapferer.Rd | 3 - 21 files changed, 163 insertions(+), 164 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 1.9-0 dated 2019-03-15 and 1.9-1 dated 2019-05-08
DESCRIPTION | 8 - MD5 | 24 ++--- R/g.getstarttime.R | 1 R/g.part4.R | 8 + R/g.part5.R | 6 - R/g.report.part5.R | 136 ++++++++++++++++---------------- build/vignette.rds |binary inst/NEWS.Rd | 9 ++ inst/doc/GGIR.R | 65 +++------------ inst/doc/GGIR.Rmd | 216 ++++++++++++++++++++++++++-------------------------- inst/doc/GGIR.html | 214 ++++++++++++++++++++++++++------------------------- man/GGIR-package.Rd | 4 vignettes/GGIR.Rmd | 216 ++++++++++++++++++++++++++-------------------------- 13 files changed, 450 insertions(+), 457 deletions(-)
Title: Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri', 'dwi'
Description: Defines the method extract and provides 'openMP' support as needed in several packages.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between awsMethods versions 1.1-0 dated 2018-02-01 and 1.1-1 dated 2019-05-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/methods.r | 6 ++++-- src/Makevars | 3 +-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Amazon Web Services Request Signatures
Description: Generates version 2 and version 4 request signatures for Amazon Web Services ('AWS') <https://aws.amazon.com/> Application Programming Interfaces ('APIs') and provides a mechanism for retrieving credentials from environment variables, 'AWS' credentials files, and 'EC2' instance metadata. For use on 'EC2' instances, users will need to install the suggested package 'aws.ec2metadata' <https://cran.r-project.org/package=aws.ec2metadata>.
Author: Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>),
Jonathan Stott [cre, aut]
Maintainer: Jonathan Stott <jonathan.stott@magairports.com>
Diff between aws.signature versions 0.4.4 dated 2018-07-27 and 0.5.0 dated 2019-05-08
aws.signature-0.4.4/aws.signature/man/credentials.Rd |only aws.signature-0.5.0/aws.signature/DESCRIPTION | 22 aws.signature-0.5.0/aws.signature/MD5 | 32 aws.signature-0.5.0/aws.signature/NEWS.md | 9 aws.signature-0.5.0/aws.signature/R/locate_credentials.R | 554 ++++------ aws.signature-0.5.0/aws.signature/R/read_credentials.R | 2 aws.signature-0.5.0/aws.signature/R/signature_v4.R | 25 aws.signature-0.5.0/aws.signature/R/utils.R |only aws.signature-0.5.0/aws.signature/R/v2.R | 45 aws.signature-0.5.0/aws.signature/R/v4.R | 67 - aws.signature-0.5.0/aws.signature/man/locate_credentials.Rd |only aws.signature-0.5.0/aws.signature/man/read_credentials.Rd | 2 aws.signature-0.5.0/aws.signature/man/signature_v2_auth.Rd | 11 aws.signature-0.5.0/aws.signature/man/signature_v4.Rd | 5 aws.signature-0.5.0/aws.signature/man/signature_v4_auth.Rd | 19 aws.signature-0.5.0/aws.signature/tests/testthat/test-utils.R |only aws.signature-0.5.0/aws.signature/tests/testthat/tests-locate_credentials.R | 40 aws.signature-0.5.0/aws.signature/tests/testthat/tests-read_credentials.R | 18 aws.signature-0.5.0/aws.signature/tests/testthat/tests.R | 12 19 files changed, 459 insertions(+), 404 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-01 18.4.17
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-20 0.3.1
Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn 2019). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.
Author: Jong Hee Park [aut,cre], Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between NetworkChange versions 0.4 dated 2018-10-10 and 0.5 dated 2019-05-08
NetworkChange-0.4/NetworkChange/R/Kmeans.R |only NetworkChange-0.4/NetworkChange/man/Kmeans.Rd |only NetworkChange-0.5/NetworkChange/DESCRIPTION | 19 ++-- NetworkChange-0.5/NetworkChange/MD5 | 44 ++++++----- NetworkChange-0.5/NetworkChange/NAMESPACE | 14 +++ NetworkChange-0.5/NetworkChange/R/BreakDiagnostic.R | 21 +++-- NetworkChange-0.5/NetworkChange/R/BreakPointLoss.R | 4 + NetworkChange-0.5/NetworkChange/R/MarginalCompare.R | 8 ++ NetworkChange-0.5/NetworkChange/R/NetworkChange.r | 10 -- NetworkChange-0.5/NetworkChange/R/NetworkStatic.R | 4 - NetworkChange-0.5/NetworkChange/R/Utils.R | 64 ++++++++++++++++ NetworkChange-0.5/NetworkChange/R/drawpostanalysis.R |only NetworkChange-0.5/NetworkChange/R/drawregimeraw.R |only NetworkChange-0.5/NetworkChange/R/kmeansU.R |only NetworkChange-0.5/NetworkChange/R/plotU.R | 15 +++ NetworkChange-0.5/NetworkChange/R/plotV.R | 46 +++++------ NetworkChange-0.5/NetworkChange/R/plotnetarray.R |only NetworkChange-0.5/NetworkChange/man/BreakDiagnostic.Rd | 5 + NetworkChange-0.5/NetworkChange/man/BreakPointLoss.Rd | 4 + NetworkChange-0.5/NetworkChange/man/MarginalCompare.Rd | 7 + NetworkChange-0.5/NetworkChange/man/NetworkChange.Rd | 15 +-- NetworkChange-0.5/NetworkChange/man/NetworkStatic.Rd | 10 +- NetworkChange-0.5/NetworkChange/man/drawPostAnalysis.Rd |only NetworkChange-0.5/NetworkChange/man/drawRegimeRaw.Rd |only NetworkChange-0.5/NetworkChange/man/kmeansU.Rd |only NetworkChange-0.5/NetworkChange/man/plotContour.Rd | 3 NetworkChange-0.5/NetworkChange/man/plotU.Rd | 2 NetworkChange-0.5/NetworkChange/man/plotnetarray.Rd |only 28 files changed, 206 insertions(+), 89 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds
has developed flexible code for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
www.ApolloChoiceModelling.com. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess,
S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview
of the field.
Author: Stephane Hess [aut],
David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>
Diff between apollo versions 0.0.6 dated 2019-03-13 and 0.0.7 dated 2019-05-08
DESCRIPTION | 38 +- MD5 | 125 +++++---- NAMESPACE | 6 R/apollo_addLog.R |only R/apollo_attach.R | 24 + R/apollo_avgInterDraws.R | 29 ++ R/apollo_avgIntraDraws.R | 77 ++++-- R/apollo_choiceAnalysis.R | 34 ++ R/apollo_cnl.R | 235 +++++++++++++----- R/apollo_combineModels.R | 15 + R/apollo_combineResults.R | 1 R/apollo_deltaMethod.R | 2 R/apollo_dft.R | 322 ++++++++++++++++++++----- R/apollo_el.R | 334 +++++++++++++++++--------- R/apollo_estimate.R | 495 +++++++++++++++++++++++++++++++++------ R/apollo_firstRow.R | 3 R/apollo_initialise.R | 2 R/apollo_lc.R | 59 +++- R/apollo_lcConditionals.R | 6 R/apollo_llCalc.R | 4 R/apollo_makeCluster.R | 23 + R/apollo_makeDraws.R | 71 ++++- R/apollo_makeLogLike.R | 13 - R/apollo_mdcev.R | 19 - R/apollo_mdcevInside.R | 181 +++++++++++--- R/apollo_mdcevOutside.R | 168 ++++++++++--- R/apollo_mdcnev.R | 212 ++++++++++++---- R/apollo_mnl.R | 186 ++++++++++---- R/apollo_modelOutput.R | 193 ++++++++------- R/apollo_nl.R | 400 +++++++++++++++++++------------ R/apollo_normalDensity.R | 76 +++-- R/apollo_ol.R | 87 ++++-- R/apollo_outOfSample.R | 29 ++ R/apollo_panelProd.R | 34 ++ R/apollo_prepareProb.R | 18 + R/apollo_printLog.R |only R/apollo_saveOutput.R | 43 +++ R/apollo_searchStart.R | 28 +- R/apollo_sharesTest.R | 15 + R/apollo_speedTest.R | 2 R/apollo_splitDataDraws.R | 14 - R/apollo_unconditionals.R | 4 R/apollo_validateControl.R | 54 ++-- R/apollo_validateData.R | 33 +- R/apollo_validateHBControl.R | 68 +++-- R/apollo_validateInputs.R | 23 + R/apollo_writeF12.R | 3 R/onAttach.R |only inst/CITATION |only inst/doc/apollofirstexample.R | 328 ++++++++++++------------- inst/doc/apollofirstexample.Rmd | 65 +++-- inst/doc/apollofirstexample.html | 229 +++++------------- man/apollo_addLog.Rd |only man/apollo_choiceAnalysis.Rd | 6 man/apollo_cnl.Rd | 4 man/apollo_dft.Rd | 7 man/apollo_estimate.Rd | 25 + man/apollo_normalDensity.Rd | 2 man/apollo_printLog.Rd |only man/apollo_validateControl.Rd | 1 man/apollo_validateData.Rd | 3 man/apollo_validateHBControl.Rd | 2 man/apollo_validateInputs.Rd | 1 man/dot-onAttach.Rd |only tests/testthat/test-mnl.R | 2 tests/testthat/test-multicore.R | 2 vignettes/apollofirstexample.Rmd | 65 +++-- 67 files changed, 3140 insertions(+), 1410 deletions(-)
Title: Inference Tool for Antibody Haplotype
Description: Infers V-D-J haplotypes and gene deletions from AIRR-seq data,
based on IGHJ, IGHD or IGHV as anchor, by adapting a Bayesian framework.
It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene.
Citation:
Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>.
Author: Ayelet Peres [aut, cre],
Moriah Gidoni [aut],
Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <peresay@biu.ac.il>
Diff between rabhit versions 0.1.0.0 dated 2019-04-09 and 0.1.1 dated 2019-05-08
rabhit-0.1.0.0/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_68741695ac497c71147f17338a1c3d7e.RData |only rabhit-0.1.0.0/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_68741695ac497c71147f17338a1c3d7e.rdb |only rabhit-0.1.0.0/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_68741695ac497c71147f17338a1c3d7e.rdx |only rabhit-0.1.1/rabhit/DESCRIPTION | 8 rabhit-0.1.1/rabhit/MD5 | 56 +++--- rabhit-0.1.1/rabhit/NAMESPACE | 4 rabhit-0.1.1/rabhit/NEWS.md | 7 rabhit-0.1.1/rabhit/R/functions.R | 64 ++---- rabhit-0.1.1/rabhit/R/graphic_functions.R | 60 +++--- rabhit-0.1.1/rabhit/R/internal_functions.R | 2 rabhit-0.1.1/rabhit/R/rabhit.R | 5 rabhit-0.1.1/rabhit/README.md | 8 rabhit-0.1.1/rabhit/inst/doc/RAbHIT-vignette.R | 31 +++ rabhit-0.1.1/rabhit/inst/doc/RAbHIT-vignette.Rmd | 92 ++++------ rabhit-0.1.1/rabhit/inst/doc/RAbHIT-vignette.pdf |binary rabhit-0.1.1/rabhit/man/rabhit.Rd | 2 rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette.Rmd | 92 ++++------ rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-12_ded83787596a509ff5e9d39c3b7b4fe9.RData |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_7feefaacda100e5bc8c0d5ab0e2e197a.RData |only rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_7feefaacda100e5bc8c0d5ab0e2e197a.rdb |only rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_7feefaacda100e5bc8c0d5ab0e2e197a.rdx |only rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-16_7985331a070cc9e8be2972e2f3db0191.RData |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-17_4a12901b7eaa05ed13d88577ae6dbb6c.RData |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-17_4a12901b7eaa05ed13d88577ae6dbb6c.rdb |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-17_4a12901b7eaa05ed13d88577ae6dbb6c.rdx |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-19_4357c1c46762e1ab592877e098eee4ff.RData |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-11-1.pdf |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-18-1.pdf |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-20-1.pdf |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-4-1.pdf |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-8-1.pdf |binary rabhit-0.1.1/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-9-1.pdf |binary 32 files changed, 229 insertions(+), 202 deletions(-)
Title: Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
Description: Parse dates automatically, without the need of
specifying a format. Currently it includes the git date parser.
It can also recognize and parse all ISO 8601 formats.
Author: Gábor Csárdi, Linus Torvalds
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between parsedate versions 1.1.3 dated 2017-03-02 and 1.2.0 dated 2019-05-08
DESCRIPTION | 12 - MD5 | 24 +-- NAMESPACE | 1 R/parsedate-package.r | 285 ++++++++++++++++++++----------------- inst/NEWS.md | 11 + inst/README.Rmd | 11 + inst/README.md | 51 ++++-- man/parse_date.Rd | 22 ++ man/parse_iso_8601.Rd | 6 tests/testthat.R | 10 + tests/testthat/helper.R |only tests/testthat/test-corner-cases.R | 26 ++- tests/testthat/test-git.r | 3 tests/testthat/test-time-zones.R |only 14 files changed, 288 insertions(+), 174 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based
on the Clinical Scenario Evaluation (CSE) approach. The package supports a
broad class of data models (including clinical trials with continuous, binary,
survival-type and count-type endpoints as well as multivariate outcomes that are
based on combinations of different endpoints), analysis strategies and commonly
used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0.7 dated 2018-07-16 and 1.0.8 dated 2019-05-08
DESCRIPTION | 11 MD5 | 44 NEWS.md | 20 R/CreateTableOutcome.R | 12 R/MixtureGatekeepingAdj.R | 34 R/MultipleSequenceGatekeepingAdj.R | 2 R/ParallelGatekeepingAdj.R | 2 R/errorfrac.R | 9 README.md | 121 ++ build/vignette.rds |binary inst/doc/adjusted-pvalues.Rmd | 2 inst/doc/adjusted-pvalues.html | 491 +++++++--- inst/doc/case-studies.Rmd | 16 inst/doc/case-studies.html | 1755 ++++++++++++++++++++----------------- inst/doc/mediana.Rmd | 2 inst/doc/mediana.html | 1101 ++++++++++++++--------- inst/figures |only man/Mediana-package.Rd | 4 vignettes/adjusted-pvalues.Rmd | 2 vignettes/case-studies.Rmd | 16 vignettes/figures |only vignettes/mediana.Rmd | 2 22 files changed, 2226 insertions(+), 1420 deletions(-)
Title: Adaptive Smoothing of Digital Images
Description: Implements tools for manipulation of digital
images and the Propagation Separation approach
by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1>
for smoothing digital images, see Polzehl and Tabelow (2007)
<DOI:10.18637/jss.v019.i01>.
Author: Karsten Tabelow <tabelow@wias-berlin.de>,
Joerg Polzehl <polzehl@wias-berlin.de>
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between adimpro versions 0.8.2 dated 2016-09-15 and 0.9.0 dated 2019-05-08
adimpro-0.8.2/adimpro/R/io.R |only adimpro-0.9.0/adimpro/DESCRIPTION | 19 - adimpro-0.9.0/adimpro/MD5 | 41 +-- adimpro-0.9.0/adimpro/NAMESPACE | 8 adimpro-0.9.0/adimpro/R/aniso.r | 82 +++--- adimpro-0.9.0/adimpro/R/awsimage.r | 248 ++++++++++++-------- adimpro-0.9.0/adimpro/R/color.R | 106 ++++---- adimpro-0.9.0/adimpro/R/demosaic.r | 61 +--- adimpro-0.9.0/adimpro/R/edges.R | 66 ++--- adimpro-0.9.0/adimpro/R/io2.R |only adimpro-0.9.0/adimpro/R/misc.r | 123 ++++++--- adimpro-0.9.0/adimpro/R/rimage.r |only adimpro-0.9.0/adimpro/R/segment.r | 86 +++--- adimpro-0.9.0/adimpro/man/rimage.Rd |only adimpro-0.9.0/adimpro/src/aniso.f | 24 - adimpro-0.9.0/adimpro/src/awsimage.f | 421 +++++----------------------------- adimpro-0.9.0/adimpro/src/awspimage.f | 68 +---- adimpro-0.9.0/adimpro/src/demosaic.f | 82 +++--- adimpro-0.9.0/adimpro/src/edges.f | 40 +-- adimpro-0.9.0/adimpro/src/init.c |only adimpro-0.9.0/adimpro/src/misc.f | 8 adimpro-0.9.0/adimpro/src/segment.f | 77 ------ adimpro-0.9.0/adimpro/src/shrink.f | 46 ++- adimpro-0.9.0/adimpro/src/smsensor.f | 14 - 24 files changed, 669 insertions(+), 951 deletions(-)
More information about multilevelMatching at CRAN
Permanent link
Title: Methods for Dimension Reduction
Description: Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included. Xia (2002) <doi:10.1111/1467-9868.03411>; Xia (2007) <doi:10.1214/009053607000000352>; Wang (2008) <doi:10.1198/016214508000000418>.
Author: Hang Weiqiang<E0010758@u.nus.edu>, Xia Yingcun<staxyc@nus.edu.sg>
Maintainer: Hang Weiqiang<E0010758@u.nus.edu>
Diff between MAVE versions 1.3.8 dated 2018-05-20 and 1.3.9 dated 2019-05-08
DESCRIPTION | 12 - MD5 | 30 ++-- NAMESPACE | 50 +++---- build/vignette.rds |binary inst/doc/User_Guild_of_Package_MAVE.R | 170 ++++++++++++------------ inst/doc/User_Guild_of_Package_MAVE.pdf |binary man/Concrete.Rd | 108 +++++++-------- man/coef.mave.Rd | 80 +++++------ man/kc_house_data.Rd | 94 ++++++------- man/mave.Rd | 220 ++++++++++++++++---------------- man/mave.data.Rd | 60 ++++---- man/mave.dim.Rd | 80 +++++------ man/plot.mave.Rd | 74 +++++----- man/predict.mave.Rd | 122 ++++++++--------- man/spam.Rd | 48 +++--- src/CVfast_R.cpp | 6 16 files changed, 577 insertions(+), 577 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre] (<https://orcid.org/0000-0002-1027-3673>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Reto Stauffer [aut] (<https://orcid.org/0000-0002-3798-5507>)
Maintainer: ORPHANED
Diff between crch versions 1.0-2 dated 2019-04-22 and 1.0-3 dated 2019-05-08
DESCRIPTION | 16 +++---- MD5 | 18 ++++---- NEWS | 7 +++ R/crch.boost.R | 80 ++++++++++++++++++++++++++++++--------- build/partial.rdb |binary inst/doc/crch.pdf |binary man/crch.boost.Rd | 1 man/crch.stabsel.Rd | 1 tests/Examples/crch-Ex.Rout.save | 25 +++++------- vignettes/crch.Rout.save | 2 10 files changed, 99 insertions(+), 51 deletions(-)
More information about spectralGraphTopology at CRAN
Permanent link
Title: Import and Handling for Plain and Formatted Text Files
Description: Functions for importing and handling text files and formatted text
files with additional meta-data, such including '.csv', '.tab', '.json', '.xml',
'.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.
Author: Kenneth Benoit [aut, cre, cph],
Adam Obeng [aut],
Kohei Watanabe [ctb],
Akitaka Matsuo [ctb],
Paul Nulty [ctb],
Stefan Müller [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between readtext versions 0.71 dated 2018-05-10 and 0.74 dated 2019-05-08
DESCRIPTION | 17 - MD5 | 45 +-- NEWS.md | 24 + R/encoding.R | 2 R/get-functions.R | 25 + R/nexis.R | 3 R/readtext.R | 27 + R/readtext_options.R | 3 R/utils.R | 19 - README.md | 79 +++-- build/vignette.rds |binary inst/doc/readtext_vignette.Rmd | 6 inst/doc/readtext_vignette.html | 557 ++++++++++++++++++++-------------------- man/cache_remote.Rd | 3 man/encoding.Rd | 2 man/get_nexis_html.Rd | 3 man/get_temp.Rd | 9 man/readtext.Rd | 25 + man/readtext_options.Rd | 3 tests/data/csv/data_onecol.csv |only tests/data/csv/data_twocol.csv |only tests/data/odt |only tests/data/rtf |only tests/testthat/test-readtext.R | 57 +++- vignettes/readtext_vignette.Rmd | 6 25 files changed, 525 insertions(+), 390 deletions(-)
More information about pvaluefunctions at CRAN
Permanent link
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.3 dated 2019-04-23 and 1.3.1 dated 2019-05-08
DESCRIPTION | 8 - MD5 | 53 +++---- R/MCAk.r | 32 +++- R/boot_clusmca.R | 258 ++++++++++++++++++++----------------- R/boot_cluspca.R | 50 +++++-- R/boot_cluspcamix.R | 29 ++-- R/clusCA.R | 22 ++- R/cluspca.R | 62 +++------ R/cluspcamix.R | 333 ++++++++++++++++++++++++------------------------- R/clusval.R | 4 R/global_bootclus.R | 7 - R/iFCB.r | 27 ++- R/local_bootclus.R | 2 R/outOfIndependence.r | 7 - R/plot.clusmca.R | 1 R/plot.cluspcamix.R | 98 +++++++------- R/print.tuneclus.R | 36 +++-- R/tab.disjonctif.R |only R/tune_clusmca.R | 10 + R/tune_cluspca.R | 9 + R/tune_cluspcamix.R | 7 - man/bribery.Rd | 2 man/cluspca.Rd | 4 man/cluspcamix.Rd | 8 - man/global_bootclus.Rd | 4 man/local_bootclus.Rd | 2 man/plot.clusmca.Rd | 10 - man/tuneclus.Rd | 7 - 28 files changed, 608 insertions(+), 484 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing as
described in "J. Polzehl and V. Spokoiny (2006)
<DOI:10.1007/s00440-005-0464-1>",
"J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>"
and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>",
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.2-0 dated 2018-07-30 and 2.2-1 dated 2019-05-08
DESCRIPTION | 12 - MD5 | 48 +++--- NAMESPACE | 2 R/aws.r | 2 R/awsgaussian.r | 2 R/awspropagation.r | 408 ++++++++++++++++++++++++++++++++++++++++++++++++++++ R/awssegment.r | 2 R/nlmean.r | 7 R/paws.r | 4 build/partial.rdb |binary man/TV_denoising.Rd | 2 man/aws-class.Rd | 25 +-- man/aws.Rd | 12 + man/aws.gaussian.Rd | 51 +++--- man/aws.segment.Rd | 27 +-- man/awstestprop.Rd | 25 ++- man/lpaws.Rd | 25 +-- man/nlmeans.Rd | 10 - man/paws.Rd | 13 + man/vaws.Rd | 2 man/vpaws.Rd | 2 src/init.c | 9 - src/misc.f | 34 ++++ src/pcaws.f | 81 ++++++---- src/pcaws2.f | 58 +++---- 25 files changed, 675 insertions(+), 188 deletions(-)
Title: Learn Text 'Embeddings' with 'Starspace'
Description: Wraps the 'StarSpace' library <https://github.com/facebookresearch/StarSpace>
allowing users to calculate word, sentence, article, document, webpage, link and entity 'embeddings'.
By using the 'embeddings', you can perform text based multi-label classification,
find similarities between texts and categories, do collaborative-filtering based recommendation
as well as content-based recommendation, find out relations between entities, calculate
graph 'embeddings' as well as perform semi-supervised learning and multi-task learning on plain text.
The techniques are explained in detail in the paper: 'StarSpace: Embed All The Things!' by Wu et al. (2017), available at <arXiv:1709.03856>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Facebook, Inc. [cph] (Starspace (BSD licensed))
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between ruimtehol versions 0.1.2 dated 2019-01-28 and 0.2 dated 2019-05-08
ruimtehol-0.1.2/ruimtehol/src/Starspace/examples/Thumbs.db |only ruimtehol-0.2/ruimtehol/DESCRIPTION | 6 ruimtehol-0.2/ruimtehol/MD5 | 30 +-- ruimtehol-0.2/ruimtehol/NAMESPACE | 3 ruimtehol-0.2/ruimtehol/NEWS.md | 12 + ruimtehol-0.2/ruimtehol/R/embed-all-the-things.R | 18 + ruimtehol-0.2/ruimtehol/R/pkg.R | 4 ruimtehol-0.2/ruimtehol/R/r-all-the-things.R | 97 +++++++-- ruimtehol-0.2/ruimtehol/R/utils.R | 43 ++++ ruimtehol-0.2/ruimtehol/build/vignette.rds |binary ruimtehol-0.2/ruimtehol/inst/doc/ground-control-to-ruimtehol.R | 71 +++++++ ruimtehol-0.2/ruimtehol/inst/doc/ground-control-to-ruimtehol.Rnw | 98 +++++++++- ruimtehol-0.2/ruimtehol/inst/doc/ground-control-to-ruimtehol.pdf |binary ruimtehol-0.2/ruimtehol/man/embed_entityrelationspace.Rd | 46 ++-- ruimtehol-0.2/ruimtehol/man/range.textspace.Rd |only ruimtehol-0.2/ruimtehol/src/rcpp_textspace.cpp | 42 +++- ruimtehol-0.2/ruimtehol/vignettes/ground-control-to-ruimtehol.Rnw | 98 +++++++++- 17 files changed, 488 insertions(+), 80 deletions(-)
Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction
techniques from R packages and a common
interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between dimRed versions 0.2.2 dated 2018-11-13 and 0.2.3 dated 2019-05-08
DESCRIPTION | 8 +++--- MD5 | 40 ++++++++++++++++--------------- NEWS.md | 3 ++ R/diffmap.R | 3 +- R/dimRedData-class.R | 2 + R/hlle.R | 2 + R/l1pca.R | 6 +++- R/nnmf.R | 20 +++++++-------- build/vignette.rds |binary inst/doc/dimensionality-reduction.pdf |binary man/PCA_L1-class.Rd | 2 + tests/testthat.R | 2 - tests/testthat/test_HLLE.R |only tests/testthat/test_NNMF.R | 8 ++++++ tests/testthat/test_PCA_L1.R | 13 ++++++---- tests/testthat/test_all.R | 3 +- tests/testthat/test_autoencoder.R | 30 +++++++++++++++++++---- tests/testthat/test_diffmap.R |only tests/testthat/test_dimRedMethod-class.R | 8 +++--- tests/testthat/test_dimRedResult.R | 5 +++ tests/testthat/test_quality.R | 8 +++--- tests/testthat/test_umap.R | 4 +-- 22 files changed, 111 insertions(+), 56 deletions(-)
Title: Read 'CEP' and Legacy 'CANOCO' Files
Description: Read Condensed Cornell Ecology Program ('CEP') and legacy
'CANOCO' files into R data frames.
Author: Jari Oksanen [aut, cre] (<https://orcid.org/0000-0001-7102-9626>),
Gavin L. Simpson [aut] (<https://orcid.org/0000-0002-9084-8413>)
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between cepreader versions 1.1-2 dated 2018-02-05 and 1.1-3 dated 2019-05-08
DESCRIPTION | 14 ++++++++------ LICENCE | 2 +- MD5 | 13 +++++++------ inst/NEWS.md |only man/readCEP.Rd | 12 ++++++------ src/Makefile | 2 +- src/Makefile.win | 4 ++-- tests/Examples/cepreader-Ex.Rout.save | 12 +++++++----- 8 files changed, 32 insertions(+), 27 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Damiano Oldoni [ctb] (<https://orcid.org/0000-0003-3445-7562>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 1.2.0 dated 2019-02-26 and 1.3.0 dated 2019-05-08
DESCRIPTION | 17 MD5 | 158 NEWS.md | 20 R/dataset_search.r | 4 R/dataset_suggest.r | 4 R/download_queue.R | 20 R/gbif_citation.R | 6 R/name_backbone.r | 2 R/name_lookup.r | 6 R/name_suggest.r | 4 R/name_usage.r | 8 R/occ_data.R | 21 R/occ_download.R | 87 R/occ_download_import.R | 4 R/occ_download_queue.R | 9 R/occ_facet.R | 2 R/occ_get.r | 4 R/occ_issues.r | 2 R/occ_search.r | 10 R/print_gbif.R | 2 R/zzz.r | 60 README.md | 151 build/vignette.rds |binary man/GbifQueue.Rd | 3 man/occ_data.Rd | 19 man/occ_download.Rd | 23 man/occ_download_import.Rd | 4 tests/fixtures/dataset_search_keyword.yml | 176 tests/fixtures/dataset_search_limit.yml | 55 tests/fixtures/dataset_suggest.yml | 367 - tests/fixtures/dataset_suggest_limit.yml | 50 tests/fixtures/enumeration.yml | 162 tests/fixtures/gbif_oai_get_records.yml | 33 tests/fixtures/gbif_oai_identify.yml | 23 tests/fixtures/gbif_oai_list_sets.yml | 16 tests/fixtures/installations_deleted.yml | 49 tests/fixtures/name_lookup.yml | 622 -- tests/fixtures/name_lookup_paging1.yml | 1687 ----- tests/fixtures/name_lookup_paging2.yml | 1706 ----- tests/fixtures/name_lookup_paging3.yml | 1687 ----- tests/fixtures/name_suggest.yml | 1096 --- tests/fixtures/name_usage.yml | 65 tests/fixtures/name_usage_data_children.yml | 116 tests/fixtures/name_usage_data_descriptions.yml | 55 tests/fixtures/name_usage_data_parents.yml | 44 tests/fixtures/name_usage_data_references.yml | 153 tests/fixtures/name_usage_return_data.yml | 21 tests/fixtures/occ_data.yml | 4418 --------------- tests/fixtures/occ_data_args_with_many_inputs.yml | 142 tests/fixtures/occ_data_catalog_number.yml | 36 tests/fixtures/occ_data_datasetkey.yml | 1045 --- tests/fixtures/occ_data_elevation.yml | 87 tests/fixtures/occ_data_key_gbifid_character_class.yml |only tests/fixtures/occ_get.yml | 357 - tests/fixtures/occ_get_other.yml | 86 tests/fixtures/occ_issues_type_many.yml | 920 --- tests/fixtures/occ_search.yml | 4418 --------------- tests/fixtures/occ_search_datasetkey.yml | 1047 --- tests/fixtures/occ_search_elevation.yml | 105 tests/fixtures/occ_search_hierarchy_data.yml | 167 tests/fixtures/occ_search_key_gbifid_character_class.yml |only tests/fixtures/occ_search_many_inputs.yml | 142 tests/fixtures/occ_search_taxonkey.yml | 4222 -------------- tests/fixtures/parsenames.yml | 72 tests/testthat/test-dataset_search.r | 6 tests/testthat/test-dataset_suggest.r | 4 tests/testthat/test-download_parsing.R | 37 tests/testthat/test-downloads.R | 13 tests/testthat/test-elevation.R | 4 tests/testthat/test-enumeration.r | 2 tests/testthat/test-installations.r | 2 tests/testthat/test-name_lookup.r | 8 tests/testthat/test-name_suggest.r | 2 tests/testthat/test-name_usage.r | 12 tests/testthat/test-oai.R | 6 tests/testthat/test-occ_data.R | 19 tests/testthat/test-occ_download_queue.R | 60 tests/testthat/test-occ_get.r | 27 tests/testthat/test-occ_issues.R | 2 tests/testthat/test-occ_search.r | 33 tests/testthat/test-parsenames.r | 2 81 files changed, 1332 insertions(+), 25004 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Ben Tupper [ctb],
Roy Mendelssohn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.5.0 dated 2019-02-01 and 0.6.0 dated 2019-05-08
DESCRIPTION | 14 MD5 | 38 NEWS.md | 17 R/grid.R | 10 R/info.R | 3 R/ncdf_helpers.R | 16 R/search.R | 4 R/search_adv.R | 2 R/table.R | 2 README.md | 72 build/vignette.rds |binary man/griddap.Rd | 40 tests/testthat/fixtures/7af7a26dfab11da2d682118beeb52e2f.nc |only tests/testthat/helper-rerddap.R | 1 tests/testthat/test-ed_search_adv.R | 2 tests/testthat/test-griddap.r | 22 tests/testthat/test-info.R | 6 tests/testthat/test-tabledap.R | 4 tests/vcr_cassettes/ed_search_adv_errors.yml | 51 tests/vcr_cassettes/griddap_north_south_latitude.yml |only tests/vcr_cassettes/tabledap_units_fails_well.yml | 882 ------------ 21 files changed, 201 insertions(+), 985 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background.
It can check if a background process is running; wait on a background
process to finish; get the exit status of finished processes; kill
background processes. It can read the standard output and error of
the processes, using non-blocking connections. 'processx' can poll
a process for standard output or error, with a timeout. It can also
poll several processes at once.
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 processx versions 3.3.0 dated 2019-03-10 and 3.3.1 dated 2019-05-08
processx-3.3.0/processx/src/win/cleanup.c |only processx-3.3.0/processx/src/win/iocp.c |only processx-3.3.1/processx/DESCRIPTION | 8 processx-3.3.1/processx/MD5 | 45 - processx-3.3.1/processx/NAMESPACE | 1 processx-3.3.1/processx/NEWS.md | 5 processx-3.3.1/processx/R/assertions.R | 3 processx-3.3.1/processx/R/initialize.R | 3 processx-3.3.1/processx/R/io.R | 2 processx-3.3.1/processx/R/on-load.R | 2 processx-3.3.1/processx/R/poll.R | 36 + processx-3.3.1/processx/man/curl_fds.Rd |only processx-3.3.1/processx/src/Makevars.win | 6 processx-3.3.1/processx/src/init.c | 4 processx-3.3.1/processx/src/poll.c | 39 - processx-3.3.1/processx/src/processx-connection.c | 444 +++++++++++----- processx-3.3.1/processx/src/processx-connection.h | 82 ++ processx-3.3.1/processx/src/processx.h | 10 processx-3.3.1/processx/src/unix/childlist.c | 2 processx-3.3.1/processx/src/unix/processx-unix.h | 3 processx-3.3.1/processx/src/unix/processx.c | 25 processx-3.3.1/processx/src/win/processx-win.h | 3 processx-3.3.1/processx/src/win/processx.c | 33 - processx-3.3.1/processx/src/win/thread.c |only processx-3.3.1/processx/tests/testthat/helper.R | 12 processx-3.3.1/processx/tests/testthat/test-poll-curl.R |only 26 files changed, 553 insertions(+), 215 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2017, <DOI:10.1007/978-3-319-52452-8>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <ISBN: 978-0367221096>.
Author: David Stoffer
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 1.8 dated 2017-12-15 and 1.9 dated 2019-05-08
DESCRIPTION | 17 +++---- MD5 | 122 +++++++++++++++++++++++++++++---------------------- NAMESPACE | 4 - R/Grid.r |only R/LagReg.R | 2 R/acf1.R | 37 ++++++++------- R/acf2.R | 37 +++++++-------- R/arma.spec.R | 6 +- R/ccf2.R | 2 R/lag1.plot.R | 4 - R/lag2.plot.R | 4 - R/mvspec.R | 10 ++-- R/sarima.R | 50 ++++++++++++-------- R/sarima.for.R | 14 ++--- R/ssm.R |only R/tsplot.R | 9 ++- data/Hare.rda |only data/Lynx.rda |only data/cardox.rda |only data/gdp.rda |only data/gtemp_land.rda |only data/gtemp_ocean.rda |only data/salmon.rda |only man/ARMAtoAR.Rd | 4 - man/EM0.Rd | 2 man/Grid.Rd |only man/Hare.Rd |only man/Lynx.Rd |only man/UnempRate.Rd | 2 man/acf1.Rd | 8 ++- man/acf2.Rd | 52 ++------------------- man/ar1miss.Rd | 12 ----- man/arf.Rd | 2 man/arma.spec.Rd | 57 +++-------------------- man/astsa-package.Rd | 12 +---- man/beamd.Rd | 2 man/birth.Rd | 2 man/blood.Rd | 2 man/cardox.Rd |only man/ccf2.Rd | 2 man/cmort.Rd | 2 man/cpg.Rd | 2 man/djia.Rd | 13 +---- man/flu.Rd | 2 man/fmri1.Rd | 2 man/gas.Rd | 5 +- man/gdp.Rd |only man/globtemp.Rd | 6 +- man/globtempl.Rd | 7 +- man/gnp.Rd | 14 ++--- man/gtemp.Rd | 4 - man/gtemp2.Rd | 4 - man/gtemp_land.Rd |only man/gtemp_ocean.Rd |only man/hor.Rd | 2 man/jj.Rd | 2 man/lag1.plot.Rd | 38 ++------------- man/lag2.plot.Rd | 53 +--------------------- man/lap.Rd | 8 --- man/mvspec.Rd | 12 +++-- man/oil.Rd | 6 +- man/rec.Rd | 8 +-- man/salmon.Rd |only man/sarima.Rd | 13 +++-- man/sarima.for.Rd | 7 +- man/soi.Rd | 2 man/ssm.Rd |only man/star.Rd | 2 man/sunspotz.Rd | 2 man/tsplot.Rd | 8 ++- man/varve.Rd | 2 71 files changed, 292 insertions(+), 411 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 1.3.2 dated 2019-03-15 and 1.3.3 dated 2019-05-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/posterior.R | 6 +++--- R/train.R | 6 +++--- README.md | 1 + build/vignette.rds |binary man/posterior.Rd | 2 +- 7 files changed, 17 insertions(+), 16 deletions(-)
Title: Tools for Fast Computing and Plotting Euclidean Minimum Spanning
Trees
Description: Computes Euclidean Minimum Spanning Trees (EMST) using the fast
Dual-Tree Boruvka algorithm (March, Ram, Gray, 2010,
<doi:10.1145/1835804.1835882>) implemented in 'mlpack' - the C++ Machine
Learning library (Curtin et al., 2013). 'emstreeR' heavily relies on
'RcppMLPACK' and 'Rcpp', working as a wrapper to the C++ fast EMST
algorithm. Thus, R users do not have to deal with the R-'Rcpp'-C++
integration. The package also provides functions and an S3 method for
readily plotting Minimum Spanning Trees (MST) using either 'base' R,
'scatterplot3d' or 'ggplot2' style.
Author: Allan Quadros [aut, cre],
Andre Cancado [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 2.1.2 dated 2019-03-17 and 2.2.0 dated 2019-05-08
DESCRIPTION | 10 ++--- MD5 | 12 +++--- NEWS.md | 14 +++++++ R/ComputeMST.R | 84 +++++++++++++++++++++++++++++++------------ README.md | 92 +++++++++++++----------------------------------- man/ComputeMST.Rd | 8 +++- man/emstreeR-package.Rd | 2 - 7 files changed, 117 insertions(+), 105 deletions(-)