Title: Delinate Region of Interests (ROI's) and Extract Time-Series
Data from Digital Repeat Photography Images
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Diff between xROI versions 0.1.1 dated 2018-03-28 and 0.1.2 dated 2018-04-11
DESCRIPTION | 6 ++-- MD5 | 64 ++++++++++++++++++++++---------------------- R/Launch.R | 10 ++++-- R/addMask.R | 10 +++--- R/drawPolygon.R | 10 +++--- R/extractCCC.R | 14 ++++----- R/extractCCCTimeSeries.R | 20 +++++++------ R/getCL.R | 3 +- R/getCLArray.R | 3 +- R/getServer.R | 50 ++++++++++++++++++++++------------ R/getUI.R | 16 +++++------ R/gettmpdir.R | 2 - R/parseROI.R | 3 +- R/plotCLArray.R | 5 ++- R/plotJPEG.R | 8 ++--- R/rasterizeROI.R | 11 ++++--- R/writeROI.R | 4 +- R/zzz.R | 13 +++++--- man/Launch.Rd | 11 +++++-- man/addMask.Rd | 10 +++--- man/drawPolygon.Rd | 11 ++++--- man/extractCCC.Rd | 10 +++--- man/extractCCCTimeSeries.Rd | 10 +++--- man/getCL.Rd | 5 ++- man/getCLArray.Rd | 5 ++- man/getServer.Rd | 5 ++- man/getUI.Rd | 3 ++ man/gettmpdir.Rd | 3 ++ man/parseROI.Rd | 5 ++- man/plotCLArray.Rd | 7 +++- man/plotJPEG.Rd | 8 ++--- man/rasterizeROI.Rd | 7 +++- man/writeROI.Rd | 4 +- 33 files changed, 207 insertions(+), 149 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package
evaluates the mass and charge balance, extracts all reactants, products, orphan
metabolites, metabolite names and compartments. Also are included some options
to characterize and write models in TSV and SBML formats.
Author: Daniel Osorio [aut, cre],
Janneth Gonzalez [aut, ths],
Andres Pinzon [aut, ths]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.8 dated 2017-06-05 and 0.8-1 dated 2018-04-11
DESCRIPTION | 8 ++-- MD5 | 65 ++++++++++++++++++------------------ NEWS.md | 6 +++ R/characterizeReactions.R | 2 - R/checkBalance.R | 4 +- R/compartments.R | 2 - R/downloadChEBI.R | 4 +- R/metabolites.R | 2 - R/orphanMetabolites.R | 2 - R/products.R | 2 - R/reactants.R | 2 - R/stoichiometricMatrix.R | 2 - R/validateSyntax.R | 2 - R/writeSBMLmod.R | 2 - R/writeTSVmod.R | 2 - build/vignette.rds |binary inst/CITATION |only inst/doc/MINVALintroduction.R | 10 ++--- inst/doc/MINVALintroduction.Rmd | 10 ++--- inst/doc/MINVALintroduction.html | 35 ++----------------- inst/doc/characterizeReactions.html | 6 +-- man/characterizeReactions.Rd | 2 - man/checkBalance.Rd | 2 - man/compartments.Rd | 2 - man/downloadChEBI.Rd | 2 - man/metabolites.Rd | 2 - man/orphanMetabolites.Rd | 2 - man/products.Rd | 2 - man/reactants.Rd | 2 - man/stoichiometricMatrix.Rd | 2 - man/validateSyntax.Rd | 2 - man/writeSBMLmod.Rd | 2 - man/writeTSVmod.Rd | 2 - vignettes/MINVALintroduction.Rmd | 10 ++--- 34 files changed, 92 insertions(+), 110 deletions(-)
Title: An HR Analytics Toolkit
Description: Manipulate, analyze, and visualize people data in meaningful ways.
This package is meant for practitioners of Human Resources analytics (often
referred to as talent analytics or people analytics).
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>
Diff between hR versions 0.1.1 dated 2018-02-14 and 0.1.3 dated 2018-04-11
hR-0.1.1/hR/R/idPad.R |only hR-0.1.1/hR/R/visRoleChanges.R |only hR-0.1.1/hR/man/idPad.Rd |only hR-0.1.1/hR/man/visRoleChanges.Rd |only hR-0.1.3/hR/DESCRIPTION | 14 +++++++------- hR-0.1.3/hR/MD5 | 16 ++++++---------- hR-0.1.3/hR/NAMESPACE | 3 --- hR-0.1.3/hR/R/hierarchyLong.R | 11 ++++++++--- hR-0.1.3/hR/R/hierarchyWide.R | 12 ++++++++---- hR-0.1.3/hR/man/hierarchyLong.Rd | 4 +++- hR-0.1.3/hR/man/hierarchyWide.Rd | 4 +++- 11 files changed, 35 insertions(+), 29 deletions(-)
More information about bigIntegerAlgos at CRAN
Permanent link
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.
Author: Charles Taragin and Michael Sandfort
Maintainer: Charles Taragin <charles.taragin@usdoj.gov>
Diff between antitrust versions 0.99.5 dated 2018-03-26 and 0.99.7 dated 2018-04-11
DESCRIPTION | 8 MD5 | 28 R/Antitrust.R | 408 ++++---- R/Bertrand.R | 33 R/Cournot.R | 1928 +++++++++++++++++++++--------------------- R/bert.R | 11 R/cesALM.R | 376 ++++---- R/logitALM.R | 400 ++++---- inst/antitrust_shiny/server.R | 226 ++++ inst/antitrust_shiny/ui.R | 106 -- inst/doc/manual.Rnw | 2 inst/doc/manual.pdf |binary man/Bertrand.Rd | 5 man/other-methods.Rd | 9 vignettes/manual.Rnw | 2 15 files changed, 1843 insertions(+), 1699 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters. Simulating and fitting models of trait evolution, and generating random trees using birth-death models. Dating trees, comparing two trees, and reading/writing trees to a file. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3.2 dated 2018-01-20 and 1.3.3 dated 2018-04-11
castor-1.3.2/castor/R/date_tree_PL.R |only castor-1.3.3/castor/DESCRIPTION | 10 castor-1.3.3/castor/MD5 | 34 castor-1.3.3/castor/NAMESPACE | 5 castor-1.3.3/castor/R/RcppExports.R | 36 castor-1.3.3/castor/R/auxiliary_routines.R | 163 + castor-1.3.3/castor/R/congruent_divergence_times.R |only castor-1.3.3/castor/R/date_tree_pl.R |only castor-1.3.3/castor/R/date_tree_red.R |only castor-1.3.3/castor/R/generate_tree_with_evolving_rates.R | 15 castor-1.3.3/castor/R/get_reds.R |only castor-1.3.3/castor/R/read_tree.R |only castor-1.3.3/castor/R/simulate_mk_model.R | 3 castor-1.3.3/castor/R/tree_distance.R |only castor-1.3.3/castor/man/congruent_divergence_times.Rd |only castor-1.3.3/castor/man/date_tree_red.Rd |only castor-1.3.3/castor/man/generate_random_tree.Rd | 4 castor-1.3.3/castor/man/generate_tree_with_evolving_rates.Rd | 20 castor-1.3.3/castor/man/get_reds.Rd |only castor-1.3.3/castor/man/read_tree.Rd |only castor-1.3.3/castor/man/tree_distance.Rd |only castor-1.3.3/castor/man/write_tree.Rd | 5 castor-1.3.3/castor/src/RcppExports.cpp | 135 + castor-1.3.3/castor/src/phylogenetics_cpp_routines.cpp | 988 ++++++++++- 24 files changed, 1375 insertions(+), 43 deletions(-)
Title: Human 'Connectome' Project Interface
Description: Downloads and reads data from Human 'Connectome' Project
<https://db.humanconnectome.org> using Amazon Web Services ('AWS')
'S3' buckets.
Author: John Muschelli [aut, cre],
Adi Gherman [ctb]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurohcp versions 0.7.3 dated 2018-02-01 and 0.8.0 dated 2018-04-11
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/bucketlist.R | 3 +++ R/download_hcp_dir.R | 4 ++++ R/get_hcp_file.R | 13 +++++++++---- R/parse_list_files.R | 7 ++++++- build/vignette.rds |binary inst/doc/hcp.html | 32 ++++++++++++++++---------------- man/parse_list_files.Rd | 3 ++- 10 files changed, 59 insertions(+), 35 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Mary C. Meyer (2013)<doi:10.1080/10485252.2013.797577> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.9 dated 2018-02-15 and 1.10 dated 2018-04-11
ChangeLog | 8 DESCRIPTION | 8 MD5 | 12 NAMESPACE | 11 R/cgam.R | 895 ++++++++++++++++++++++++++++++++++++++++------------ man/cgam.Rd | 5 man/predict.cgam.Rd | 46 ++ 7 files changed, 760 insertions(+), 225 deletions(-)
Title: Stochastic Gradient Markov Chain Monte Carlo
Description: Provides functions that performs popular stochastic gradient Markov chain Monte Carlo (SGMCMC) methods on user specified models. The required gradients are automatically calculated using 'TensorFlow' <https://www.tensorflow.org/>, an efficient library for numerical computation. This means only the log likelihood and log prior functions need to be specified. The methods implemented include stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian Monte Carlo (SGHMC), stochastic gradient Nose-Hoover thermostat (SGNHT) and their respective control variate versions for increased efficiency. References: M. Welling, Y. W. Teh (2011) <http://www.icml-2011.org/papers/398_icmlpaper.pdf>; T. Chen, E. B. Fox, C. E. Guestrin (2014) <arXiv:1402.4102>; N. Ding, Y. Fang, R. Babbush, C. Chen, R. D. Skeel, H. Neven (2014) <https://papers.nips.cc/paper/5592-bayesian-sampling-using-stochastic-gradient-thermostats>; J. Baker, P. Fearnhead, E. B. Fox, C. Nemeth (2017) <arXiv:1706.05439>.
Author: Jack Baker [aut, cre, cph],
Christopher Nemeth [aut, cph],
Paul Fearnhead [aut, cph],
Emily B. Fox [aut, cph],
STOR-i [cph]
Maintainer: Jack Baker <j.baker1@lancaster.ac.uk>
Diff between sgmcmc versions 0.2.1 dated 2018-02-21 and 0.2.2 dated 2018-04-11
DESCRIPTION | 6 MD5 | 107 ++++---- NEWS.md | 4 R/sghmc.R | 4 R/sghmccv.R | 4 R/sgld.R | 4 R/sgldcv.R | 4 R/sgnht.R | 4 R/sgnhtcv.R | 4 R/storage.R | 2 R/update.R | 4 R/zzz.R |only build/vignette.rds |binary inst/doc/gaussMixture.R | 10 inst/doc/gaussMixture.Rmd | 14 - inst/doc/gaussMixture.html | 401 ++++++++++--------------------- inst/doc/logisticRegression.Rmd | 4 inst/doc/logisticRegression.html | 401 +++++++++---------------------- inst/doc/mvGauss.R | 4 inst/doc/mvGauss.Rmd | 8 inst/doc/mvGauss.html | 366 ++++++++-------------------- inst/doc/nn.R | 10 inst/doc/nn.Rmd | 12 inst/doc/nn.html | 493 +++++++++++++-------------------------- inst/doc/sgmcmc.R | 4 inst/doc/sgmcmc.Rmd | 6 inst/doc/sgmcmc.html | 371 ++++++++--------------------- man/getParams.Rd | 2 man/initSess.Rd | 2 man/sghmc.Rd | 2 man/sghmcSetup.Rd | 2 man/sghmccv.Rd | 2 man/sghmccvSetup.Rd | 2 man/sgld.Rd | 2 man/sgldSetup.Rd | 2 man/sgldcv.Rd | 2 man/sgldcvSetup.Rd | 2 man/sgmcmcStep.Rd | 2 man/sgnht.Rd | 2 man/sgnhtSetup.Rd | 2 man/sgnhtcv.Rd | 2 man/sgnhtcvSetup.Rd | 2 tests/testthat/test1dGauss.R | 4 tests/testthat/test3dGauss.R | 4 tests/testthat/testFloat64.R | 4 tests/testthat/testMatrixParam.R | 4 tests/testthat/testOptional.R | 2 tests/testthat/testSeeds.R | 2 tests/testthat/testSparse.R | 2 tests/testthat/testStepByStep.R | 4 vignettes/gaussMixture.Rmd | 14 - vignettes/logisticRegression.Rmd | 4 vignettes/mvGauss.Rmd | 8 vignettes/nn.Rmd | 12 vignettes/sgmcmc.Rmd | 6 55 files changed, 803 insertions(+), 1548 deletions(-)
Title: Geographic Information System Application
Description: A geographic information system (GIS) graphical user interface (GUI) that
provides data viewing, management, and analysis tools.
Author: Jason C. Fisher [aut, cre] (<https://orcid.org/0000-0001-9032-8912>)
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between RSurvey versions 0.9.2 dated 2017-11-23 and 0.9.3 dated 2018-04-11
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/BuildHistogram.R | 2 +- R/GetBitmapImage.R | 10 +++++----- R/LaunchGui.R | 27 +++++++++++++++------------ R/ManagePolygons.R | 9 ++++----- R/SetCrs.R | 2 +- man/BuildHistogram.Rd | 2 +- man/GetBitmapImage.Rd | 10 +++++----- man/ManagePolygons.Rd | 5 +++-- man/SetCrs.Rd | 2 +- 12 files changed, 57 insertions(+), 48 deletions(-)
Title: Tools for the Bayesian Discount Prior Function
Description: Functions for data augmentation using the
Bayesian discount prior function for 1 arm and 2 arm clinical trials.
Author: Shawn Balcome [cre],
Donnie Musgrove [aut],
Tarek Haddad [aut],
Christopher Jackson [ctb] (For the ppexp R code that was ported to
C++.)
Maintainer: Shawn Balcome <sbalcome@mdic.org>
Diff between bayesDP versions 1.3.0 dated 2017-12-07 and 1.3.1 dated 2018-04-11
DESCRIPTION | 8 - MD5 | 64 ++++----- NAMESPACE | 1 NEWS.md | 12 + R/bdpbinomial.R | 72 +++++----- R/bdplm.R | 77 +++++----- R/bdpnormal.R | 54 +++---- R/bdpsurvival.R | 261 ++++++++++++++++++++++++------------- R/print.R | 48 ++++++ R/summary.R | 242 ++++++++++++++-------------------- build/vignette.rds |binary inst/doc/bdpbinomial-vignette.R | 53 ++++--- inst/doc/bdpbinomial-vignette.Rmd | 102 +++++++------- inst/doc/bdpbinomial-vignette.html | 139 ++++++++++--------- inst/doc/bdplm-vignette.R | 91 ++++++------ inst/doc/bdplm-vignette.Rmd | 130 +++++++++--------- inst/doc/bdplm-vignette.html | 147 ++++++++++++-------- inst/doc/bdpnormal-vignette.R | 77 +++++----- inst/doc/bdpnormal-vignette.Rmd | 124 ++++++++--------- inst/doc/bdpnormal-vignette.html | 161 +++++++++++----------- inst/doc/bdpsurvival-vignette.R | 124 ++++++++--------- inst/doc/bdpsurvival-vignette.Rmd | 210 +++++++++++++---------------- inst/doc/bdpsurvival-vignette.html | 255 ++++++++++++++---------------------- man/bdpbinomial.Rd | 56 +++---- man/bdplm.Rd | 53 +++---- man/bdpnormal.Rd | 43 +++--- man/bdpsurvival.Rd | 140 ++++++++++--------- man/print-bdplm-method.Rd |only man/summary-bdpbinomial-method.Rd | 4 man/summary-bdplm-method.Rd |only vignettes/bdpbinomial-vignette.Rmd | 102 +++++++------- vignettes/bdplm-vignette.Rmd | 130 +++++++++--------- vignettes/bdpnormal-vignette.Rmd | 124 ++++++++--------- vignettes/bdpsurvival-vignette.Rmd | 210 +++++++++++++---------------- 34 files changed, 1697 insertions(+), 1617 deletions(-)
Title: 'AWS S3' Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple
Storage Service ('S3') 'REST' 'API' <https://aws.amazon.com/s3/>.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Boettiger Carl [ctb],
Andrew Martin [ctb],
Mark Thompson [ctb],
Tyler Hunt [ctb],
Steven Akins [ctb],
Bao Nguyen [ctb],
Thierry Onkelinx [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between aws.s3 versions 0.3.3 dated 2017-06-14 and 0.3.11 dated 2018-04-11
DESCRIPTION | 21 +++--- MD5 | 38 ++++++----- NAMESPACE | 19 +---- NEWS.md | 97 +++++++++++++++++++++--------- R/encryption.R |only R/get_object.R | 23 ++++--- R/print.R | 7 +- R/put_bucket.R | 14 +++- R/put_object.R | 5 - R/s3HTTP.R | 85 +++++++++++++++++--------- R/s3read_using.R | 2 R/s3source.R | 1 R/s3sync.R | 173 +++++++++++++++++++++++++++++++----------------------- R/utils.R | 6 + README.md | 36 ++++++----- man/encryption.Rd |only man/getobject.Rd | 5 + man/put_bucket.Rd | 2 man/put_object.Rd | 3 man/s3HTTP.Rd | 26 ++++---- man/sync.Rd | 13 +++- 21 files changed, 352 insertions(+), 224 deletions(-)
Title: Bi-Directional Interface Between 'R' and 'Scala' with Callbacks
Description: The 'Scala' <http://www.scala-lang.org/> interpreter is embedded in 'R' and callbacks to 'R' from the embedded interpreter are supported. Conversely, the 'R' interpreter is embedded in 'Scala'. 'Scala' versions in the 2.11.x and 2.12.x series are supported.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 2.5.1 dated 2018-02-11 and 2.5.3 dated 2018-04-11
rscala-2.5.1/rscala/inst/java/scala-2.11/rscala_2.11-2.5.1.jar |only rscala-2.5.1/rscala/inst/java/scala-2.12/rscala_2.12-2.5.1.jar |only rscala-2.5.3/rscala/DESCRIPTION | 8 +-- rscala-2.5.3/rscala/MD5 | 24 +++++----- rscala-2.5.3/rscala/NEWS | 9 +++ rscala-2.5.3/rscala/R/scala.R | 19 ++++--- rscala-2.5.3/rscala/R/scalaInstall.R | 18 +++++-- rscala-2.5.3/rscala/build/vignette.rds |binary rscala-2.5.3/rscala/inst/doc/article.Rnw | 4 - rscala-2.5.3/rscala/inst/doc/article.pdf |binary rscala-2.5.3/rscala/inst/java/scala-2.11/rscala_2.11-2.5.3.jar |only rscala-2.5.3/rscala/inst/java/scala-2.12/rscala_2.12-2.5.3.jar |only rscala-2.5.3/rscala/java/rscala-sources.jar |binary rscala-2.5.3/rscala/man/constructor.Rd | 5 -- rscala-2.5.3/rscala/vignettes/article.Rnw | 4 - 15 files changed, 53 insertions(+), 38 deletions(-)
Title: Downloading, Reading and Analysing PNADc Microdata
Description: Provides tools for download, read, and analyse the PNADc
household survey from Brazilian Institute of Geography and Statistics.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analyses must be made using package 'survey'.
Author: Douglas Braga [aut, cre]
Maintainer: Douglas Braga <douglas.braga@ibge.gov.br>
Diff between PNADcIBGE versions 0.4.1 dated 2018-04-09 and 0.4.1.1 dated 2018-04-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/get_pnadc.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) <doi:10.1093/bioinformatics/btx835>). The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes (Drost et al. (2016) <doi:10.1101/051565>).
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between myTAI versions 0.6.0 dated 2017-07-03 and 0.7.0 dated 2018-04-11
myTAI-0.6.0/myTAI/tests/testthat/Rplots.pdf |only myTAI-0.7.0/myTAI/DESCRIPTION | 34 +++++---- myTAI-0.7.0/myTAI/MD5 | 77 +++++++++++----------- myTAI-0.7.0/myTAI/NAMESPACE | 1 myTAI-0.7.0/myTAI/NEWS.md | 19 ++++- myTAI-0.7.0/myTAI/R/EarlyConservationTest.R | 4 - myTAI-0.7.0/myTAI/R/FlatLineTest.R | 22 +++--- myTAI-0.7.0/myTAI/R/MatchMap.R | 20 ++--- myTAI-0.7.0/myTAI/R/PlotCIRatio.R |only myTAI-0.7.0/myTAI/R/PlotSignature.R | 3 myTAI-0.7.0/myTAI/R/RcppExports.R | 14 ++-- myTAI-0.7.0/myTAI/R/ReductiveHourglassTest.R | 8 +- myTAI-0.7.0/myTAI/R/TAI.R | 10 +- myTAI-0.7.0/myTAI/R/TDI.R | 10 +- myTAI-0.7.0/myTAI/R/TPI.R | 10 +- myTAI-0.7.0/myTAI/R/base.R | 3 myTAI-0.7.0/myTAI/R/bootMatrix.R | 6 - myTAI-0.7.0/myTAI/R/is.ExpressionSet.R | 30 ++++---- myTAI-0.7.0/myTAI/R/pMatrix.R | 8 +- myTAI-0.7.0/myTAI/R/pStrata.R | 2 myTAI-0.7.0/myTAI/README.md | 48 ++++++++++--- myTAI-0.7.0/myTAI/build/vignette.rds |binary myTAI-0.7.0/myTAI/inst/CITATION | 27 ++++--- myTAI-0.7.0/myTAI/inst/doc/Advanced.html | 14 ++-- myTAI-0.7.0/myTAI/inst/doc/Enrichment.html | 10 +- myTAI-0.7.0/myTAI/inst/doc/Expression.html | 46 ++++++------- myTAI-0.7.0/myTAI/inst/doc/Intermediate.html | 72 ++++++++++---------- myTAI-0.7.0/myTAI/inst/doc/Introduction.Rmd | 14 ++-- myTAI-0.7.0/myTAI/inst/doc/Introduction.html | 73 ++++++++++---------- myTAI-0.7.0/myTAI/inst/doc/Taxonomy.html | 4 - myTAI-0.7.0/myTAI/man/PlotCIRatio.Rd |only myTAI-0.7.0/myTAI/man/pMatrix.Rd | 2 myTAI-0.7.0/myTAI/src/RcppExports.cpp | 28 ++++---- myTAI-0.7.0/myTAI/tests/testthat/test-MatchMap.R | 4 - myTAI-0.7.0/myTAI/tests/testthat/test-REMatrix.R | 4 - myTAI-0.7.0/myTAI/tests/testthat/test-age.apply.R | 2 myTAI-0.7.0/myTAI/vignettes/Figures/Fig1.png |binary myTAI-0.7.0/myTAI/vignettes/Figures/Fig2.png |binary myTAI-0.7.0/myTAI/vignettes/Figures/Fig3.png |binary myTAI-0.7.0/myTAI/vignettes/Figures/Fig4.png |binary myTAI-0.7.0/myTAI/vignettes/Introduction.Rmd | 14 ++-- 41 files changed, 351 insertions(+), 292 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut],
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.2 dated 2017-09-25 and 8.3 dated 2018-04-11
forecast-8.2/forecast/R/baggedETS.R |only forecast-8.2/forecast/R/tsdiag.R |only forecast-8.2/forecast/man/baggedETS.Rd |only forecast-8.2/forecast/man/forecast.baggedETS.Rd |only forecast-8.2/forecast/tests/testthat/test-biasadj.R |only forecast-8.3/forecast/DESCRIPTION | 48 forecast-8.3/forecast/MD5 | 281 +- forecast-8.3/forecast/NAMESPACE | 25 forecast-8.3/forecast/NEWS.md | 16 forecast-8.3/forecast/R/DM2.R | 65 forecast-8.3/forecast/R/HoltWintersNew.R | 815 ++++---- forecast-8.3/forecast/R/acf.R | 455 ++-- forecast-8.3/forecast/R/adjustSeasonalSeeds.R | 314 +-- forecast-8.3/forecast/R/arfima.R | 532 ++--- forecast-8.3/forecast/R/arima.R | 951 ++++----- forecast-8.3/forecast/R/armaroots.R | 145 - forecast-8.3/forecast/R/attach.R | 7 forecast-8.3/forecast/R/baggedModel.R |only forecast-8.3/forecast/R/bats.R | 473 ++-- forecast-8.3/forecast/R/bootstrap.R | 67 forecast-8.3/forecast/R/calendar.R | 41 forecast-8.3/forecast/R/checkAdmissibility.R | 74 forecast-8.3/forecast/R/checkresiduals.R | 108 - forecast-8.3/forecast/R/clean.R | 184 + forecast-8.3/forecast/R/components.R | 138 - forecast-8.3/forecast/R/data.R | 43 forecast-8.3/forecast/R/dshw.r | 184 - forecast-8.3/forecast/R/errors.R | 261 +- forecast-8.3/forecast/R/ets.R | 1190 ++++++------ forecast-8.3/forecast/R/etsforecast.R | 314 +-- forecast-8.3/forecast/R/fitBATS.R | 411 ++-- forecast-8.3/forecast/R/fitTBATS.R | 416 ++-- forecast-8.3/forecast/R/forecast-package.R | 1 forecast-8.3/forecast/R/forecast.R | 751 +++---- forecast-8.3/forecast/R/forecast.varest.R | 84 forecast-8.3/forecast/R/forecast2.R | 469 ++-- forecast-8.3/forecast/R/forecastBATS.R | 314 +-- forecast-8.3/forecast/R/forecastTBATS.R | 353 +-- forecast-8.3/forecast/R/getResponse.R | 113 - forecast-8.3/forecast/R/ggplot.R | 1770 +++++++++--------- forecast-8.3/forecast/R/graph.R | 208 +- forecast-8.3/forecast/R/guerrero.R | 98 forecast-8.3/forecast/R/lm.R | 367 +-- forecast-8.3/forecast/R/makeMatrices.R | 590 ++---- forecast-8.3/forecast/R/makeParamVector.R | 502 ++--- forecast-8.3/forecast/R/mforecast.R | 87 forecast-8.3/forecast/R/mstl.R |only forecast-8.3/forecast/R/msts.R | 80 forecast-8.3/forecast/R/naive.R | 231 -- forecast-8.3/forecast/R/newarima2.R | 929 +++------ forecast-8.3/forecast/R/nnetar.R | 402 ++-- forecast-8.3/forecast/R/residuals.R | 140 - forecast-8.3/forecast/R/seasadj.R | 35 forecast-8.3/forecast/R/season.R | 675 +----- forecast-8.3/forecast/R/simulate.R | 645 +++--- forecast-8.3/forecast/R/spline.R | 272 +- forecast-8.3/forecast/R/subset.R | 158 - forecast-8.3/forecast/R/tbats.R | 1041 +++++----- forecast-8.3/forecast/R/theta.R | 93 forecast-8.3/forecast/R/tscv.R | 125 - forecast-8.3/forecast/R/unitRoot.R |only forecast-8.3/forecast/R/whichmodels.R | 26 forecast-8.3/forecast/R/wrangle.R | 40 forecast-8.3/forecast/README.md | 36 forecast-8.3/forecast/build/vignette.rds |binary forecast-8.3/forecast/inst/CITATION | 8 forecast-8.3/forecast/inst/doc/JSS2008.Rmd | 5 forecast-8.3/forecast/inst/doc/JSS2008.pdf |binary forecast-8.3/forecast/man/Arima.Rd | 12 forecast-8.3/forecast/man/BoxCox.Rd | 9 forecast-8.3/forecast/man/CVar.Rd | 26 forecast-8.3/forecast/man/accuracy.Rd | 7 forecast-8.3/forecast/man/arfima.Rd | 12 forecast-8.3/forecast/man/auto.arima.Rd | 34 forecast-8.3/forecast/man/autoplot.seas.Rd | 5 forecast-8.3/forecast/man/baggedModel.Rd |only forecast-8.3/forecast/man/croston.Rd | 4 forecast-8.3/forecast/man/dshw.Rd | 13 forecast-8.3/forecast/man/ets.Rd | 10 forecast-8.3/forecast/man/figures/logo.png |binary forecast-8.3/forecast/man/forecast.Arima.Rd | 13 forecast-8.3/forecast/man/forecast.HoltWinters.Rd | 12 forecast-8.3/forecast/man/forecast.Rd | 12 forecast-8.3/forecast/man/forecast.StructTS.Rd | 12 forecast-8.3/forecast/man/forecast.baggedModel.Rd |only forecast-8.3/forecast/man/forecast.ets.Rd | 13 forecast-8.3/forecast/man/forecast.lm.Rd | 12 forecast-8.3/forecast/man/forecast.mlm.Rd | 12 forecast-8.3/forecast/man/forecast.mts.Rd | 12 forecast-8.3/forecast/man/forecast.nnetar.Rd | 26 forecast-8.3/forecast/man/forecast.stl.Rd | 19 forecast-8.3/forecast/man/getResponse.Rd | 3 forecast-8.3/forecast/man/is.ets.Rd | 14 forecast-8.3/forecast/man/meanf.Rd | 19 forecast-8.3/forecast/man/mstl.Rd |only forecast-8.3/forecast/man/msts.Rd | 3 forecast-8.3/forecast/man/na.interp.Rd | 10 forecast-8.3/forecast/man/naive.Rd | 28 forecast-8.3/forecast/man/ndiffs.Rd | 44 forecast-8.3/forecast/man/nnetar.Rd | 15 forecast-8.3/forecast/man/nsdiffs.Rd |only forecast-8.3/forecast/man/ocsb.test.Rd |only forecast-8.3/forecast/man/plot.bats.Rd | 2 forecast-8.3/forecast/man/plot.forecast.Rd | 6 forecast-8.3/forecast/man/plot.mforecast.Rd | 6 forecast-8.3/forecast/man/residuals.forecast.Rd | 18 forecast-8.3/forecast/man/seasadj.Rd | 3 forecast-8.3/forecast/man/seasonplot.Rd | 6 forecast-8.3/forecast/man/ses.Rd | 18 forecast-8.3/forecast/man/simulate.ets.Rd | 7 forecast-8.3/forecast/man/splinef.Rd | 12 forecast-8.3/forecast/man/tbats.components.Rd | 4 forecast-8.3/forecast/man/tsCV.Rd | 10 forecast-8.3/forecast/man/tsclean.Rd | 12 forecast-8.3/forecast/man/tsdisplay.Rd | 6 forecast-8.3/forecast/man/tslm.Rd | 12 forecast-8.3/forecast/man/tsoutliers.Rd | 5 forecast-8.3/forecast/src/Makevars.win | 3 forecast-8.3/forecast/tests/testthat.R | 3 forecast-8.3/forecast/tests/testthat/test-accuracy.R | 69 forecast-8.3/forecast/tests/testthat/test-acf.R | 17 forecast-8.3/forecast/tests/testthat/test-arfima.R | 41 forecast-8.3/forecast/tests/testthat/test-arima.R | 165 - forecast-8.3/forecast/tests/testthat/test-armaroots.R | 19 forecast-8.3/forecast/tests/testthat/test-bats.R | 41 forecast-8.3/forecast/tests/testthat/test-boxcox.R |only forecast-8.3/forecast/tests/testthat/test-calendar.R | 37 forecast-8.3/forecast/tests/testthat/test-clean.R | 59 forecast-8.3/forecast/tests/testthat/test-dshw.R | 16 forecast-8.3/forecast/tests/testthat/test-ets.R | 97 forecast-8.3/forecast/tests/testthat/test-forecast.R | 37 forecast-8.3/forecast/tests/testthat/test-forecast2.R | 34 forecast-8.3/forecast/tests/testthat/test-ggplot.R | 41 forecast-8.3/forecast/tests/testthat/test-graph.R | 35 forecast-8.3/forecast/tests/testthat/test-hfitted.R | 33 forecast-8.3/forecast/tests/testthat/test-mforecast.R | 33 forecast-8.3/forecast/tests/testthat/test-msts.R | 11 forecast-8.3/forecast/tests/testthat/test-newarima2.R | 12 forecast-8.3/forecast/tests/testthat/test-nnetar.R | 119 - forecast-8.3/forecast/tests/testthat/test-refit.R | 114 - forecast-8.3/forecast/tests/testthat/test-season.R | 118 - forecast-8.3/forecast/tests/testthat/test-spline.R | 27 forecast-8.3/forecast/tests/testthat/test-subset.R | 83 forecast-8.3/forecast/tests/testthat/test-tbats.R | 11 forecast-8.3/forecast/tests/testthat/test-thetaf.R |only forecast-8.3/forecast/tests/testthat/test-tslm.R | 73 forecast-8.3/forecast/tests/testthat/test-wrangle.R | 35 forecast-8.3/forecast/vignettes/JSS2008.Rmd | 5 forecast-8.3/forecast/vignettes/jsslogo.jpg |binary 149 files changed, 10029 insertions(+), 10103 deletions(-)
Title: Data to Accompany Applied Linear Regression 3rd Edition
Description: Data files used in the textbook S. Weisberg (2005),
'Applied Linear Regression,' 3rd edition, Wiley are presented. It includes all the
data sets discussed in the book (except one), and a few functions that
are tailored to the methods discussed in the book. As of version 2.0.0,
this package depends on the car package. Many functions formerly
in alr3 have been renamed and now reside in car.
Data files have been lightly modified to make some data columns row labels.
Author: Sanford Weisberg <sandy@umn.edu>
Maintainer: Sanford Weisberg <sandy@umn.edu>
Diff between alr3 versions 2.0.5 dated 2011-10-27 and 2.0.7 dated 2018-04-11
alr3-2.0.5/alr3/NEWS |only alr3-2.0.7/alr3/DESCRIPTION | 20 +-- alr3-2.0.7/alr3/MD5 | 13 - alr3-2.0.7/alr3/NAMESPACE | 109 +++++++++------- alr3-2.0.7/alr3/R/alr3-deprecated.R | 216 ++++++++++++++++----------------- alr3-2.0.7/alr3/man/BigMac2003.Rd | 103 +++++++-------- alr3-2.0.7/alr3/man/alr3-deprecated.Rd | 186 ++++++++++++++-------------- alr3-2.0.7/alr3/man/alr3-package.Rd | 58 ++++---- 8 files changed, 358 insertions(+), 347 deletions(-)
Title: Functions to Compute Compositional Turnover Using Zeta Diversity
Description: Functions to compute compositional turnover using zeta-diversity,
the number of species shared by multiple assemblages. The package includes
functions to compute zeta-diversity for a specific number of
assemblages and to compute zeta-diversity for a range of numbers of
assemblages. It also includes functions to explain how zeta-diversity
varies with distance and with differences in environmental variables
between assemblages, using generalised linear models, linear models
with negative constraints, generalised additive models,shape
constrained additive models, and I-splines.
Author: Guillaume Latombe, Melodie A. McGeoch, David A. Nipperess, Cang Hui
Maintainer: Guillaume Latombe <latombe.guillaume@gmail.com>
Diff between zetadiv versions 1.0.1 dated 2017-06-06 and 1.1.0 dated 2018-04-11
DESCRIPTION | 10 MD5 | 66 NAMESPACE | 54 R/zetadiv.R | 8620 +++++++++++++++++++++------------------- man/Ispline.Rd | 77 man/Marion.env.Rd | 67 man/Marion.species.Rd | 67 man/Plot.ispline.Rd | 108 man/Plot.zeta.ddecay.Rd | 95 man/Plot.zeta.ddecays.Rd | 95 man/Plot.zeta.decline.Rd | 97 man/Plot.zeta.scale.min.dist.Rd | 97 man/Plot.zeta.scale.regular.Rd | 99 man/Predict.msgdm.Rd | 139 man/Zeta.ddecay.Rd | 204 man/Zeta.ddecays.Rd | 159 man/Zeta.decline.ex.Rd | 167 man/Zeta.decline.mc.Rd | 213 man/Zeta.msgdm.Rd | 288 - man/Zeta.order.ex.Rd | 121 man/Zeta.order.mc.Rd | 167 man/Zeta.sam.sensitivity.Rd | 169 man/Zeta.scale.min.dist.Rd | 159 man/Zeta.scale.regular.Rd | 137 man/Zeta.varpart.Rd | 203 man/bird.env.coarse.Rd | 89 man/bird.env.fine.Rd | 89 man/bird.spec.coarse.Rd | 61 man/bird.spec.fine.Rd | 61 man/glm.cons.Rd | 149 man/glm.fit.cons.Rd | 119 man/pie.neg.Rd | 115 man/rescale.min.dist.Rd | 109 man/rescale.regular.Rd | 89 34 files changed, 6620 insertions(+), 5939 deletions(-)
Title: Quality Control Metrics for Gene Signatures
Description: Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
Author: Andrew Dhawan [aut],
Alessandro Barberis [aut],
Wei-Chen Cheng [aut],
Francesca Buffa [aut, cre]
Maintainer: Francesca Buffa <francesca.buffa@oncology.ox.ac.uk>
Diff between sigQC versions 0.1.13 dated 2018-03-13 and 0.1.14 dated 2018-04-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/compare_metrics_loc.R | 14 +++++++++++++- R/make_all_plots.R | 28 +++++++++++++++++++++++++++- inst/doc/vignette.html | 4 ++-- man/make_all_plots.Rd | 2 +- 6 files changed, 51 insertions(+), 13 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.7.7 dated 2016-04-05 and 1.7.9 dated 2018-04-11
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 +- R/seqhap.q | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/manualHaploStats.pdf |binary src/haplo.stats_init.c |only src/seqhap.c | 4 ++-- 9 files changed, 23 insertions(+), 15 deletions(-)
Title: A GUI-Based Program to Compute Probabilities Regarding Group
Sequential Designs
Description: A graphical user interface to compute group sequential designs
based on normally distributed test statistics, particularly critical
boundaries, power, drift, and confidence intervals of such designs. All
computations are based on the alpha spending approach by Lan-DeMets with
various alpha spending functions being available to choose among.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between GroupSeq versions 1.3.4 dated 2017-02-03 and 1.3.5 dated 2018-04-11
GroupSeq-1.3.4/GroupSeq/R/stdDeviations.R |only GroupSeq-1.3.5/GroupSeq/DESCRIPTION | 17 + GroupSeq-1.3.5/GroupSeq/MD5 | 15 - GroupSeq-1.3.5/GroupSeq/R/calculateEqualBounds.R | 209 ++++++----------------- GroupSeq-1.3.5/GroupSeq/R/computeAlphaLevel.R | 193 ++++++--------------- GroupSeq-1.3.5/GroupSeq/R/computeBounds.R | 46 ++--- GroupSeq-1.3.5/GroupSeq/R/groupseq.R | 57 +++--- GroupSeq-1.3.5/GroupSeq/R/guiMode.R | 18 - GroupSeq-1.3.5/GroupSeq/tests |only 9 files changed, 201 insertions(+), 354 deletions(-)
Title: Preparing Genotypic Datasets in Order to Run Genomic Analysis
Description: Three functions to clean, summarize and prepare genomic datasets to Genome
Selection and Genome Association analysis and to estimate population genetic parameters.
Author: Italo Granato [aut, cre],
Roberto Fritsche-Neto [aut, ths]
Maintainer: Italo Granato <italo.granato@gmail.com>
Diff between snpReady versions 0.9.4 dated 2017-10-27 and 0.9.6 dated 2018-04-11
DESCRIPTION | 10 - MD5 | 24 ++-- NAMESPACE | 11 +- R/G.matrix.R | 92 ++++++++++-------- R/popgen.R | 204 ++++++++++++++++++++++++++++------------ R/raw.data.R | 202 +++++++++++++++++++++++++-------------- README.md | 6 - inst/doc/snpReady-vignette.Rmd | 56 ++++++---- inst/doc/snpReady-vignette.html | 198 ++++++++++++++++++++------------------ man/G.matrix.Rd | 12 +- man/popgen.Rd | 18 ++- man/raw.data.Rd | 16 +-- vignettes/snpReady-vignette.Rmd | 56 ++++++---- 13 files changed, 558 insertions(+), 347 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.0.0 dated 2017-11-20 and 1.1.0 dated 2018-04-11
DESCRIPTION | 16 - MD5 | 42 +-- NAMESPACE | 3 R/viewers.R | 15 - build/vignette.rds |binary data/Dark24.rda |binary data/Light24.rda |binary data/alphabet.rda |binary data/colorsafe.rda |only data/glasbey.rda |binary data/iscc.rda |binary data/palette36.rda |binary inst/doc/color-deficits.R |only inst/doc/color-deficits.Rmd | 10 inst/doc/color-deficits.html | 448 +++++++++++++++++----------------- inst/doc/creatingPalettes.R |only inst/doc/creatingPalettes.Rmd | 2 inst/doc/creatingPalettes.html | 526 ++++++++++++++++++++--------------------- inst/doc/polychrome.R |only inst/doc/polychrome.html | 290 +++++++++++----------- man/colorsafe.Rd |only man/getLUV.Rd |only man/viewers.Rd | 4 vignettes/color-deficits.Rmd | 10 vignettes/creatingPalettes.Rmd | 2 25 files changed, 689 insertions(+), 679 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.6-6 dated 2016-06-02 and 0.6-7 dated 2018-04-11
ChangeLog | 2 DESCRIPTION | 14 MD5 | 86 ++--- R/Rparutilities.R | 13 configure | 192 ++++++++---- configure.ac | 625 +++++++++++++++++++++-------------------- inst/CITATION | 2 inst/Rprofile | 15 inst/slavedaemon.R | 10 man/mpi.abort.Rd | 3 man/mpi.barrier.Rd | 3 man/mpi.bcast.Rd | 3 man/mpi.cart.coords.Rd | 3 man/mpi.cart.create.Rd | 3 man/mpi.cart.get.Rd | 3 man/mpi.cart.rank.Rd | 3 man/mpi.cart.shift.Rd | 3 man/mpi.cartdim.get.Rd | 3 man/mpi.comm.Rd | 3 man/mpi.comm.disconnect.Rd | 3 man/mpi.comm.free.Rd | 3 man/mpi.comm.inter.Rd | 3 man/mpi.comm.set.errhandler.Rd | 3 man/mpi.comm.spawn.Rd | 3 man/mpi.const.Rd | 2 man/mpi.dims.create.Rd | 3 man/mpi.finalize.Rd | 3 man/mpi.gather.Rd | 3 man/mpi.gather.Robj.Rd | 3 man/mpi.get.count.Rd | 3 man/mpi.get.processor.name.Rd | 3 man/mpi.get.sourcetag.Rd | 3 man/mpi.intercomm.merge.Rd | 2 man/mpi.probe.Rd | 3 man/mpi.realloc.Rd | 3 man/mpi.reduce.Rd | 3 man/mpi.scatter.Rd | 3 man/mpi.send.Rd | 3 man/mpi.send.Robj.Rd | 3 man/mpi.sendrecv.Rd | 3 man/mpi.universe.size.Rd | 3 man/mpi.wait.Rd | 3 src/Rmpi.h | 89 +++++ src/internal.c | 82 +++++ 44 files changed, 739 insertions(+), 488 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo. The approximation
uses Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors and for
the comparison of predictive errors between models. The package also
provides methods for using stacking and other model weighting techniques
to average Bayesian predictive distributions.
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Yuling Yao [aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 1.1.0 dated 2017-03-27 and 2.0.0 dated 2018-04-11
loo-1.1.0/loo/R/compare.R |only loo-1.1.0/loo/R/loo_expectation.R |only loo-1.1.0/loo/R/loo_package.R |only loo-1.1.0/loo/R/pareto_k.R |only loo-1.1.0/loo/inst/doc/loo-example.R |only loo-1.1.0/loo/inst/doc/loo-example.Rmd |only loo-1.1.0/loo/inst/doc/loo-example.html |only loo-1.1.0/loo/tests/testthat/E_loo_default_quantile_10_90.rds |only loo-1.1.0/loo/tests/testthat/test_helpers.R |only loo-1.1.0/loo/vignettes/loo-example.Rmd |only loo-2.0.0/loo/DESCRIPTION | 29 loo-2.0.0/loo/MD5 | 133 +- loo-2.0.0/loo/NAMESPACE | 53 loo-2.0.0/loo/NEWS.md | 55 loo-2.0.0/loo/R/E_loo.R |only loo-2.0.0/loo/R/compare_models.R |only loo-2.0.0/loo/R/datasets.R |only loo-2.0.0/loo/R/diagnostics.R |only loo-2.0.0/loo/R/effective_sample_sizes.R |only loo-2.0.0/loo/R/example_log_lik_array.R |only loo-2.0.0/loo/R/extract_log_lik.R | 61 loo-2.0.0/loo/R/gpdfit.R | 92 + loo-2.0.0/loo/R/helpers.R | 243 ++- loo-2.0.0/loo/R/kfold-helpers.R |only loo-2.0.0/loo/R/loo-package.R |only loo-2.0.0/loo/R/loo.R | 635 ++++++++-- loo-2.0.0/loo/R/loo_model_weights.R |only loo-2.0.0/loo/R/print.R | 132 +- loo-2.0.0/loo/R/psis.R |only loo-2.0.0/loo/R/psislw.R | 49 loo-2.0.0/loo/R/sysdata.rda |only loo-2.0.0/loo/R/waic.R | 143 +- loo-2.0.0/loo/R/zzz.R | 18 loo-2.0.0/loo/build/vignette.rds |binary loo-2.0.0/loo/data |only loo-2.0.0/loo/inst/CITATION | 23 loo-2.0.0/loo/inst/doc/loo2-example.R |only loo-2.0.0/loo/inst/doc/loo2-example.Rmd |only loo-2.0.0/loo/inst/doc/loo2-example.html |only loo-2.0.0/loo/inst/doc/loo2-weights.R |only loo-2.0.0/loo/inst/doc/loo2-weights.Rmd |only loo-2.0.0/loo/inst/doc/loo2-weights.html |only loo-2.0.0/loo/inst/doc/loo2-with-rstan.R |only loo-2.0.0/loo/inst/doc/loo2-with-rstan.Rmd |only loo-2.0.0/loo/inst/doc/loo2-with-rstan.html |only loo-2.0.0/loo/man/E_loo.Rd | 85 - loo-2.0.0/loo/man/compare.Rd | 21 loo-2.0.0/loo/man/example_loglik_array.Rd |only loo-2.0.0/loo/man/extract_log_lik.Rd | 30 loo-2.0.0/loo/man/gpdfit.Rd | 30 loo-2.0.0/loo/man/kfold-helpers.Rd |only loo-2.0.0/loo/man/loo-datasets.Rd |only loo-2.0.0/loo/man/loo-package.Rd | 187 -- loo-2.0.0/loo/man/loo.Rd | 333 +++-- loo-2.0.0/loo/man/loo_model_weights.Rd |only loo-2.0.0/loo/man/old-extractors.Rd |only loo-2.0.0/loo/man/pareto-k-diagnostic.Rd | 166 +- loo-2.0.0/loo/man/print.loo.Rd | 25 loo-2.0.0/loo/man/print_dims.Rd |only loo-2.0.0/loo/man/psis.Rd |only loo-2.0.0/loo/man/psislw.Rd | 77 - loo-2.0.0/loo/man/relative_eff.Rd |only loo-2.0.0/loo/man/waic.Rd | 112 + loo-2.0.0/loo/tests/testthat/E_loo_default_mean.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_default_quantile_10_50_90.rds |only loo-2.0.0/loo/tests/testthat/E_loo_default_quantile_50.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_default_var.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_matrix_mean.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_matrix_quantile_10_90.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_matrix_quantile_50.rds |binary loo-2.0.0/loo/tests/testthat/E_loo_matrix_var.rds |binary loo-2.0.0/loo/tests/testthat/compare_three_models.rds |only loo-2.0.0/loo/tests/testthat/compare_two_models.rds |only loo-2.0.0/loo/tests/testthat/function_method_stuff.R |only loo-2.0.0/loo/tests/testthat/gpdfit.rds |only loo-2.0.0/loo/tests/testthat/gpdfit_default_grid.rds |only loo-2.0.0/loo/tests/testthat/gpdfit_old.rds |only loo-2.0.0/loo/tests/testthat/loo.rds |only loo-2.0.0/loo/tests/testthat/mcse_loo.rds |only loo-2.0.0/loo/tests/testthat/model_weights_pseudobma.rds |only loo-2.0.0/loo/tests/testthat/model_weights_stacking.rds |only loo-2.0.0/loo/tests/testthat/test_0_helpers.R |only loo-2.0.0/loo/tests/testthat/test_E_loo.R | 192 +-- loo-2.0.0/loo/tests/testthat/test_compare.R | 93 - loo-2.0.0/loo/tests/testthat/test_deprecated_extractors.R |only loo-2.0.0/loo/tests/testthat/test_gpdfit.R | 24 loo-2.0.0/loo/tests/testthat/test_kfold_helpers.R |only loo-2.0.0/loo/tests/testthat/test_loo_and_waic.R | 213 ++- loo-2.0.0/loo/tests/testthat/test_model_weighting.R |only loo-2.0.0/loo/tests/testthat/test_print_plot.R | 179 ++ loo-2.0.0/loo/tests/testthat/test_psis.R |only loo-2.0.0/loo/tests/testthat/test_psislw.R | 63 loo-2.0.0/loo/tests/testthat/waic.rds |only loo-2.0.0/loo/vignettes/children |only loo-2.0.0/loo/vignettes/loo2-example.Rmd |only loo-2.0.0/loo/vignettes/loo2-weights.Rmd |only loo-2.0.0/loo/vignettes/loo2-with-rstan.Rmd |only 97 files changed, 2394 insertions(+), 1102 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: Provides the next iteration of the EMU Speech
Database Management System (EMU-SDMS) with database management, data
extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between emuR versions 0.2.3 dated 2017-07-03 and 1.0.0 dated 2018-04-11
emuR-0.2.3/emuR/vignettes/pics/autobuild_linkFromTimesGraph.fdb_latexmk |only emuR-0.2.3/emuR/vignettes/pics/autobuild_linkFromTimesGraph.log |only emuR-0.2.3/emuR/vignettes/pics/db_structure.aux |only emuR-0.2.3/emuR/vignettes/pics/db_structure.fdb_latexmk |only emuR-0.2.3/emuR/vignettes/pics/db_structure.log |only emuR-0.2.3/emuR/vignettes/pics/db_structure.pdf |only emuR-0.2.3/emuR/vignettes/pics/functionGraph.fdb_latexmk |only emuR-0.2.3/emuR/vignettes/pics/functionGraph.log |only emuR-0.2.3/emuR/vignettes/pics/functionGraph.synctex.gz |only emuR-0.2.3/emuR/vignettes/pics/msajc003.fdb_latexmk |only emuR-0.2.3/emuR/vignettes/pics/msajc003.log |only emuR-0.2.3/emuR/vignettes/pics/positionSimple.fdb_latexmk |only emuR-0.2.3/emuR/vignettes/pics/positionSimple.log |only emuR-1.0.0/emuR/DESCRIPTION | 15 emuR-1.0.0/emuR/MD5 | 143 - emuR-1.0.0/emuR/NAMESPACE | 3 emuR-1.0.0/emuR/NEWS.md | 43 emuR-1.0.0/emuR/R/emuR-autobuild.R | 3 emuR-1.0.0/emuR/R/emuR-autoproc_annots.R | 273 +++ emuR-1.0.0/emuR/R/emuR-bas_webservices.R | 67 emuR-1.0.0/emuR/R/emuR-bas_webservicesDBI.R | 156 +- emuR-1.0.0/emuR/R/emuR-change_labels.R |only emuR-1.0.0/emuR/R/emuR-convert_TextGridCollection.R | 6 emuR-1.0.0/emuR/R/emuR-convert_txtCollection.R | 2 emuR-1.0.0/emuR/R/emuR-create_seglists.R | 201 +- emuR-1.0.0/emuR/R/emuR-database.DBconfig.EMUwebAppConfig.R | 12 emuR-1.0.0/emuR/R/emuR-database.DBconfig.R | 158 +- emuR-1.0.0/emuR/R/emuR-database.R | 15 emuR-1.0.0/emuR/R/emuR-database.annotJSON.R | 126 - emuR-1.0.0/emuR/R/emuR-database.caching.R | 15 emuR-1.0.0/emuR/R/emuR-database.files.R | 7 emuR-1.0.0/emuR/R/emuR-emuDBhandle.R | 27 emuR-1.0.0/emuR/R/emuR-emuRsegs.R | 22 emuR-1.0.0/emuR/R/emuR-emuRtrackdata.R | 162 +- emuR-1.0.0/emuR/R/emuR-export_BPFCollection.R | 27 emuR-1.0.0/emuR/R/emuR-export_TextGridCollection.R | 10 emuR-1.0.0/emuR/R/emuR-get_trackdata.R | 137 + emuR-1.0.0/emuR/R/emuR-legacy.R | 59 emuR-1.0.0/emuR/R/emuR-legacy.template.R | 10 emuR-1.0.0/emuR/R/emuR-objDocs.R | 6 emuR-1.0.0/emuR/R/emuR-parse_TextGridDBI.R | 9 emuR-1.0.0/emuR/R/emuR-parser.BPF.R | 6 emuR-1.0.0/emuR/R/emuR-parser.esps.R | 4 emuR-1.0.0/emuR/R/emuR-parser.hlb.R | 4 emuR-1.0.0/emuR/R/emuR-query.database.R | 9 emuR-1.0.0/emuR/R/emuR-requery.database.R | 91 + emuR-1.0.0/emuR/R/emuR-server.R | 105 - emuR-1.0.0/emuR/README.md | 4 emuR-1.0.0/emuR/build/vignette.rds |binary emuR-1.0.0/emuR/inst/doc/EQL.html | 580 +++++-- emuR-1.0.0/emuR/inst/doc/emuDB.html | 734 ++++++---- emuR-1.0.0/emuR/inst/doc/emuR_intro.Rmd | 6 emuR-1.0.0/emuR/inst/doc/emuR_intro.html | 562 +++++-- emuR-1.0.0/emuR/inst/extdata/rawDemoData/annotationFiles/ae_DBconfig.json | 2 emuR-1.0.0/emuR/man/create_emuRtrackdata.Rd | 4 emuR-1.0.0/emuR/man/emuRtrackdata.Rd | 6 emuR-1.0.0/emuR/man/export_TextGridCollection.Rd | 8 emuR-1.0.0/emuR/man/get_trackdata.Rd | 16 emuR-1.0.0/emuR/man/normalize_length.Rd |only emuR-1.0.0/emuR/man/print.emuRsegs.Rd | 4 emuR-1.0.0/emuR/man/print.emuRtrackdata.Rd |only emuR-1.0.0/emuR/man/query.Rd | 2 emuR-1.0.0/emuR/man/requery_hier.Rd | 4 emuR-1.0.0/emuR/man/requery_seq.Rd | 2 emuR-1.0.0/emuR/man/runBASwebservice_all.Rd | 8 emuR-1.0.0/emuR/man/runBASwebservice_chunker.Rd | 7 emuR-1.0.0/emuR/man/runBASwebservice_g2pForPronunciation.Rd | 7 emuR-1.0.0/emuR/man/runBASwebservice_g2pForTokenization.Rd | 9 emuR-1.0.0/emuR/man/runBASwebservice_maus.Rd | 7 emuR-1.0.0/emuR/man/runBASwebservice_minni.Rd | 9 emuR-1.0.0/emuR/man/runBASwebservice_pho2sylCanonical.Rd | 9 emuR-1.0.0/emuR/man/runBASwebservice_pho2sylSegmental.Rd | 9 emuR-1.0.0/emuR/man/serve.Rd | 7 emuR-1.0.0/emuR/man/sort.emuRsegs.Rd |only emuR-1.0.0/emuR/tests/testthat/test_emuR-autobuild.R | 4 emuR-1.0.0/emuR/tests/testthat/test_emuR-autoproc_annots.R | 263 ++- emuR-1.0.0/emuR/tests/testthat/test_emuR-database.DBconfig.R | 46 emuR-1.0.0/emuR/tests/testthat/test_emuR-database.files.R | 2 emuR-1.0.0/emuR/tests/testthat/test_emuR-query.database.R | 5 emuR-1.0.0/emuR/tests/testthat/test_emuR-requery.database.R | 28 emuR-1.0.0/emuR/vignettes/emuR_intro.Rmd | 6 81 files changed, 2908 insertions(+), 1385 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and time-spans: fast and user
friendly parsing of date-time data, extraction and updating of components of
a date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package has
a consistent and memorable syntax that makes working with dates easy and
fun.
Parts of the 'CCTZ' source code, released under the Apache 2.0 License,
are included in this package. See <https://github.com/google/cctz> for more
details.
Author: Vitalie Spinu [aut, cre],
Garrett Grolemund [aut],
Hadley Wickham [aut],
Ian Lyttle [ctb],
Imanuel Constigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.7.3 dated 2018-02-27 and 1.7.4 dated 2018-04-11
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++------------- NEWS.md | 17 ++++++++++ R/POSIXt.r | 4 +- R/accessors-tz.r | 5 ++ R/coercion.r | 34 ++++++++++++++++---- R/intervals.r | 52 +++++++++++++++++++++++++++--- R/ops-modulo.r | 4 +- R/parse.r | 68 +++++++++++++++++++++++++--------------- R/round.r | 5 ++ R/time-zones.r | 6 +-- man/as.period.Rd | 2 - man/as_date.Rd | 3 + man/force_tz.Rd | 6 +-- man/within-interval.Rd | 24 +++++++++++--- man/ymd.Rd | 7 ++++ man/ymd_hms.Rd | 7 ++++ src/RcppExports.cpp | 8 ++-- src/tparse.c | 6 ++- src/update.cpp | 5 +- tests/testthat/test-intervals.R | 37 +++++++++++++++++++++ tests/testthat/test-parsers.R | 6 ++- tests/testthat/test-round.R | 9 +++++ 23 files changed, 277 insertions(+), 88 deletions(-)
Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.2.1 dated 2018-02-02 and 0.2.2 dated 2018-04-11
DESCRIPTION | 6 - MD5 | 18 ++-- NEWS.md | 4 + R/plotting.R | 55 ++++++++++++-- build/vignette.rds |binary inst/doc/detzrcr-vignette.html | 147 +++++++++++++++++++------------------- inst/shiny-apps/detzrcr_app/app.R | 78 ++++++++++++++++++-- man/plot_dens.Rd | 2 man/plot_dens_hist.Rd | 2 man/plot_hf.Rd | 15 +++ 10 files changed, 225 insertions(+), 102 deletions(-)
Title: Tools for Microscopy Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy.
Read and write TIFF stacks. Functions for segmentation, filtering and analysing 3D point patterns.
Author: Volker Schmid [aut, cre],
Priyanka Kukreja [ctb],
Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between bioimagetools versions 1.1.0 dated 2017-02-18 and 1.1.3 dated 2018-04-11
bioimagetools-1.1.0/bioimagetools/inst/doc/bioimagetools.Rmd |only bioimagetools-1.1.0/bioimagetools/vignettes/readwriteplot_cache |only bioimagetools-1.1.3/bioimagetools/DESCRIPTION | 14 bioimagetools-1.1.3/bioimagetools/MD5 | 39 - bioimagetools-1.1.3/bioimagetools/NEWS | 24 bioimagetools-1.1.3/bioimagetools/R/bwlabel3d.R | 108 +- bioimagetools-1.1.3/bioimagetools/R/intensity3d.R | 136 +-- bioimagetools-1.1.3/bioimagetools/README.md | 65 + bioimagetools-1.1.3/bioimagetools/TODO | 9 bioimagetools-1.1.3/bioimagetools/build/vignette.rds |binary bioimagetools-1.1.3/bioimagetools/inst/doc/readwriteplot.R | 14 bioimagetools-1.1.3/bioimagetools/inst/doc/readwriteplot.Rmd | 14 bioimagetools-1.1.3/bioimagetools/inst/doc/readwriteplot.html | 379 +++------- bioimagetools-1.1.3/bioimagetools/vignettes/readwriteplot.Rmd | 14 14 files changed, 348 insertions(+), 468 deletions(-)
Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for
mix-models, reducing the numbers of parameters to estimate using
Non-negative Matrix Factorization methods.
For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>
Diff between nmfem versions 1.0.0 dated 2017-11-17 and 1.0.1 dated 2018-04-11
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/NMFEM_for_travelers.R | 4 ++-- inst/doc/NMFEM_for_travelers.Rmd | 8 ++++---- inst/doc/NMFEM_for_travelers.html | 8 ++++---- vignettes/NMFEM_for_travelers.Rmd | 8 ++++---- 7 files changed, 23 insertions(+), 23 deletions(-)
Title: Generalized and Classical Blockmodeling of Valued Networks
Description: This is primarily meant as an implementation of Generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.
Author: Aleš Žiberna [aut, cre]
Maintainer: Aleš Žiberna <ales.ziberna@gmail.com>
Diff between blockmodeling versions 0.1.9 dated 2017-07-03 and 0.3.0 dated 2018-04-11
blockmodeling-0.1.9/blockmodeling/R/check.these.par.R |only blockmodeling-0.1.9/blockmodeling/R/crit.fun.R |only blockmodeling-0.1.9/blockmodeling/R/gen.crit.fun.R |only blockmodeling-0.1.9/blockmodeling/R/gen.opt.par.R |only blockmodeling-0.1.9/blockmodeling/R/opt.par.R |only blockmodeling-0.1.9/blockmodeling/R/opt.random.par.R |only blockmodeling-0.1.9/blockmodeling/R/opt.these.par.R |only blockmodeling-0.1.9/blockmodeling/R/savecluster.R |only blockmodeling-0.1.9/blockmodeling/R/savepajek.R |only blockmodeling-0.1.9/blockmodeling/man/check.these.par.Rd |only blockmodeling-0.1.9/blockmodeling/man/crit.fun.Rd |only blockmodeling-0.1.9/blockmodeling/man/opt.par.Rd |only blockmodeling-0.1.9/blockmodeling/man/opt.random.par.Rd |only blockmodeling-0.1.9/blockmodeling/src/init.c |only blockmodeling-0.1.9/blockmodeling/src/opt_par_ss_com.f90 |only blockmodeling-0.1.9/blockmodeling/src/opt_par_ss_com_twoMode.f90 |only blockmodeling-0.1.9/blockmodeling/src/opt_par_ss_com_twoMode_forMoreRel.f90 |only blockmodeling-0.1.9/blockmodeling/src/ss_blocks.f90 |only blockmodeling-0.3.0/blockmodeling/CHANGES | 138 -- blockmodeling-0.3.0/blockmodeling/DESCRIPTION | 31 blockmodeling-0.3.0/blockmodeling/MD5 | 152 +- blockmodeling-0.3.0/blockmodeling/NAMESPACE | 35 blockmodeling-0.3.0/blockmodeling/R/Cinterfaces.R |only blockmodeling-0.3.0/blockmodeling/R/IM.R | 4 blockmodeling-0.3.0/blockmodeling/R/REGE.FC.R | 1 blockmodeling-0.3.0/blockmodeling/R/REGE.FC.ow.R | 1 blockmodeling-0.3.0/blockmodeling/R/REGE.R | 1 blockmodeling-0.3.0/blockmodeling/R/REGE.ow.R | 3 blockmodeling-0.3.0/blockmodeling/R/REGE_for.R | 44 blockmodeling-0.3.0/blockmodeling/R/clu.R | 4 blockmodeling-0.3.0/blockmodeling/R/err.R | 4 blockmodeling-0.3.0/blockmodeling/R/find.cut.R | 2 blockmodeling-0.3.0/blockmodeling/R/find.m2.R | 2 blockmodeling-0.3.0/blockmodeling/R/fun.by.blocks.default.R | 44 blockmodeling-0.3.0/blockmodeling/R/genMatrixMult.r |only blockmodeling-0.3.0/blockmodeling/R/genRandomPar.R | 107 + blockmodeling-0.3.0/blockmodeling/R/gplot.R | 25 blockmodeling-0.3.0/blockmodeling/R/ircNorm.R | 10 blockmodeling-0.3.0/blockmodeling/R/loadmatrix.R | 6 blockmodeling-0.3.0/blockmodeling/R/loadnetwork.R | 50 blockmodeling-0.3.0/blockmodeling/R/loadnetwork2.R | 63 - blockmodeling-0.3.0/blockmodeling/R/loadnetwork3.R |only blockmodeling-0.3.0/blockmodeling/R/loadnetwork4.R |only blockmodeling-0.3.0/blockmodeling/R/loadpajek.R | 6 blockmodeling-0.3.0/blockmodeling/R/loadvector.R | 9 blockmodeling-0.3.0/blockmodeling/R/loadvector2.R | 2 blockmodeling-0.3.0/blockmodeling/R/onAttach.R |only blockmodeling-0.3.0/blockmodeling/R/plot.crit.fun.R | 2 blockmodeling-0.3.0/blockmodeling/R/plot.mat.R | 579 ++++++---- blockmodeling-0.3.0/blockmodeling/R/plot.mat.nm.R | 2 blockmodeling-0.3.0/blockmodeling/R/plot.opt.par.R | 16 blockmodeling-0.3.0/blockmodeling/R/savematrix.R | 6 blockmodeling-0.3.0/blockmodeling/R/savenetwork.R | 8 blockmodeling-0.3.0/blockmodeling/R/savevector.R | 4 blockmodeling-0.3.0/blockmodeling/R/sedist.R | 122 ++ blockmodeling-0.3.0/blockmodeling/R/usepos.R | 3 blockmodeling-0.3.0/blockmodeling/inst |only blockmodeling-0.3.0/blockmodeling/man/Pajek.Rd | 64 - blockmodeling-0.3.0/blockmodeling/man/REGE.Rd | 46 blockmodeling-0.3.0/blockmodeling/man/blockmodeling-package.Rd | 50 blockmodeling-0.3.0/blockmodeling/man/clu.Rd | 52 blockmodeling-0.3.0/blockmodeling/man/critFunC.Rd |only blockmodeling-0.3.0/blockmodeling/man/find.m.Rd | 2 blockmodeling-0.3.0/blockmodeling/man/formatA.Rd | 2 blockmodeling-0.3.0/blockmodeling/man/fun.by.blocks.Rd | 42 blockmodeling-0.3.0/blockmodeling/man/genMatrixMult.Rd |only blockmodeling-0.3.0/blockmodeling/man/genRandomPar.Rd | 7 blockmodeling-0.3.0/blockmodeling/man/gplot1.Rd | 19 blockmodeling-0.3.0/blockmodeling/man/ircNorm.Rd | 16 blockmodeling-0.3.0/blockmodeling/man/nkpartitions.Rd | 25 blockmodeling-0.3.0/blockmodeling/man/optRandomParC.Rd |only blockmodeling-0.3.0/blockmodeling/man/plot.mat.Rd | 320 +++-- blockmodeling-0.3.0/blockmodeling/man/recode.Rd | 4 blockmodeling-0.3.0/blockmodeling/man/reorderImage.Rd | 2 blockmodeling-0.3.0/blockmodeling/man/sedist.Rd | 34 blockmodeling-0.3.0/blockmodeling/man/two2one.Rd | 34 blockmodeling-0.3.0/blockmodeling/src/REGD_NE_R.f90 | 20 blockmodeling-0.3.0/blockmodeling/src/REGD_OW_NE_R.f90 | 28 blockmodeling-0.3.0/blockmodeling/src/REGD_OW_R.f90 | 28 blockmodeling-0.3.0/blockmodeling/src/REGD_R.f90 | 21 blockmodeling-0.3.0/blockmodeling/src/REGE_NE_R.f90 | 23 blockmodeling-0.3.0/blockmodeling/src/REGE_NM_DIAG_R.f90 | 18 blockmodeling-0.3.0/blockmodeling/src/REGE_NM_NE_R.f90 | 21 blockmodeling-0.3.0/blockmodeling/src/REGE_NM_R.f90 | 19 blockmodeling-0.3.0/blockmodeling/src/REGE_OWNM_DIAG_R.f90 | 15 blockmodeling-0.3.0/blockmodeling/src/REGE_OWNM_NE_R.f90 | 18 blockmodeling-0.3.0/blockmodeling/src/REGE_OWNM_R.f90 | 15 blockmodeling-0.3.0/blockmodeling/src/REGE_OW_NE_R.f90 | 24 blockmodeling-0.3.0/blockmodeling/src/REGE_OW_R.f90 | 20 blockmodeling-0.3.0/blockmodeling/src/REGE_R.f90 | 22 blockmodeling-0.3.0/blockmodeling/src/blockmodelingC.c |only 91 files changed, 1515 insertions(+), 982 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of subgroup
identification and personalized medicine models under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre],
Aaron Potvien [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.1.4 dated 2018-03-08 and 0.1.5 dated 2018-04-11
DESCRIPTION | 6 MD5 | 28 +- R/print_subgroup.R | 231 +++++++++++++++++------- R/validate_subgroup.R | 2 README.md | 2 inst/doc/usage_of_the_personalized_package.Rmd | 57 +++++ inst/doc/usage_of_the_personalized_package.html | 31 ++- man/figures |only man/print.Rd | 7 man/validate.subgroup.Rd | 2 tests/testthat/test-plotandplotcompare.R | 26 ++ tests/testthat/test-validatesubgroup.R | 8 vignettes/sticker.png |only vignettes/usage_of_the_personalized_package.Rmd | 57 +++++ vignettes/usage_overview-1.png |binary vignettes/vis_val-1.png |binary 16 files changed, 370 insertions(+), 87 deletions(-)
More information about neutralitytestr at CRAN
Permanent link
Title: Finding Heterogeneous Treatment Effects
Description: The heterogeneous treatment effect estimation procedure
proposed by Imai and Ratkovic (2013)<DOI: 10.1214/12-AOAS593>.
The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
The package also contains a class of functions, CausalANOVA,
which estimates the average marginal interaction effects (AMIEs)
by a regularized ANOVA as proposed by Egami and Imai (2016+).
It contains a variety of regularization techniques to facilitate
analysis of large factorial experiments.
Author: Naoki Egami <negami@princeton.edu>, Marc Ratkovic <ratkovic@princeton.edu>, Kosuke Imai <kimai@princeton.edu>,
Maintainer: Naoki Egami <negami@princeton.edu>
Diff between FindIt versions 1.1.3 dated 2018-01-21 and 1.1.4 dated 2018-04-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- R/SVMHet.R | 6 ++---- R/makeallway.R | 4 ++-- 5 files changed, 14 insertions(+), 16 deletions(-)
Title: Bayesian Analysis of Change Point Problems
Description: Provides an implementation of the Barry and Hartigan (1993) product
partition model for the normal errors change point problem using Markov Chain
Monte Carlo. It also extends the methodology to regression models on a connected
graph (Wang and Emerson, 2015); this allows estimation of change point models
with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0,
is currently not implemented.
Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
Maintainer: Xiaofei Wang <xiaofei.wang@yale.edu>
Diff between bcp versions 4.0.0 dated 2015-07-15 and 4.0.1 dated 2018-04-11
DESCRIPTION | 18 MD5 | 60 +- NAMESPACE | 2 R/RcppExports.R | 14 R/bcp.R | 27 - R/output.R | 3 data/QuebecRivers.rda |binary demo/bcpgraph.R | 4 inst/CITATION | 5 man/NewHavenHousing.Rd | 5 man/QuebecRivers.Rd | 9 man/RealInt.Rd | 9 man/bcp-package.Rd | 3 man/bcp.Rd | 51 +- man/coriell.Rd | 8 man/fitted.bcp.Rd | 10 man/interval.prob.Rd | 10 man/legacyplot.Rd | 12 man/lombard.Rd | 12 man/makeAdjGrid.Rd | 24 - man/plot.bcp.Rd | 16 man/residuals.bcp.Rd | 10 man/summary.bcp.Rd | 11 src/Cbcp.cpp | 624 ++++++++-------------------- src/CbcpM.cpp | 377 +++++------------ src/Cbcpgraph.cpp | 812 ++---------------------------------- src/CbcpgraphR.cpp | 1082 +++++-------------------------------------------- src/Graph.h |only src/HelperVariables.h |only src/MCMC.h |only src/Params.h |only src/RcppExports.cpp | 61 +- src/bcp.h |only src/utils.cpp |only 34 files changed, 696 insertions(+), 2583 deletions(-)
Title: Interface to the 'USGS' 'BISON' 'API'
Description: Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>)
'API', a 'database' for species occurrence data. Data comes from
species in the United States from participating data providers. You can get
data via 'taxonomic' and location based queries. A simple function
is provided to help visualize data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbison versions 0.5.4 dated 2017-04-10 and 0.6.0 dated 2018-04-11
DESCRIPTION | 17 - LICENSE | 2 MD5 | 62 ++--- NEWS.md | 13 + R/bison.R | 11 R/bison_solr.r | 190 +++++++++++----- R/citation_datause.R | 8 R/rbison-package.R | 20 + R/zzz.R | 12 + README.md | 172 +++++---------- build/vignette.rds |binary inst/doc/other_functions.Rmd | 445 +++++++++++++++++++++------------------ inst/doc/other_functions.html | 445 +++++++++++++++++++++------------------ inst/doc/rbison_vignette.Rmd | 202 ++++++++++------- inst/doc/rbison_vignette.html | 202 ++++++++++------- man/bison.Rd | 14 - man/bison_datause.Rd | 2 man/bison_solr.Rd | 139 +++++++++--- man/fips.Rd | 12 - man/rbison-package.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-bison.R | 3 tests/testthat/test-bison_solr.R | 44 +++ tests/testthat/test-bison_tax.R | 16 - tools/unnamed-chunk-10-1.png |binary tools/unnamed-chunk-13-1.png |binary tools/unnamed-chunk-14-1.png |binary tools/unnamed-chunk-15-1.png |binary tools/unnamed-chunk-19-1.png |binary tools/unnamed-chunk-7-1.png |binary vignettes/other_functions.Rmd | 445 +++++++++++++++++++++------------------ vignettes/rbison_vignette.Rmd | 202 ++++++++++------- 32 files changed, 1570 insertions(+), 1114 deletions(-)
Title: Deficit Index (DI)
Description: A set of utilities for calculating the Deficit (frailty) Index (DI) in gerontological studies.
The deficit index was first proposed by Arnold Mitnitski and Kenneth Rockwood
and represents a proxy measure of aging and also can be served as
a sensitive predictor of survival. For more information, see
(i)"Accumulation of Deficits as a Proxy Measure of Aging"
by Arnold B. Mitnitski et al. (2001),
The Scientific World Journal 1, <DOI:10.1100/tsw.2001.58>;
(ii) "Frailty, fitness and late-life mortality in relation to chronological and biological age"
by Arnold B Mitnitski et al. (2001),
BMC Geriatrics2002 2(1), <DOI:10.1186/1471-2318-2-1>.
Author: Ilya Y. Zhbannikov [aut, cre]
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between di versions 1.1.3 dated 2017-10-26 and 1.1.4 dated 2018-04-11
DESCRIPTION | 10 +++--- MD5 | 18 ++++++------ R/di.R | 66 +++++++++++++++++++++------------------------- build/vignette.rds |binary inst/NEWS | 7 ++-- inst/doc/di-vignette.R | 8 ++++- inst/doc/di-vignette.Rmd | 10 +++++- inst/doc/di-vignette.html | 26 +++++++++++------- man/di-di.Rd | 6 +++- vignettes/di-vignette.Rmd | 10 +++++- 10 files changed, 93 insertions(+), 68 deletions(-)