Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-4 dated 2016-03-10 and 0.1-5 dated 2016-06-14
DESCRIPTION | 10 +++---- MD5 | 36 +++++++++++++++++--------- NAMESPACE | 6 ++++ R/breeding.density.R | 19 +++++++------ R/daymet.point.R | 50 ++++++++++++++++++------------------ R/mwCorr.R |only R/nni.R | 17 +++++++----- R/polyPerimeter.R |only R/rasterCorrelation.R |only R/sample.transect.R |only R/shannons.R | 38 +++++++++++++++------------ R/stratified.random.R | 65 +++++++++++++++++++++++------------------------ R/trig.trans.R |only R/vrm.R |only inst/NEWS | 7 +++++ man/breeding.density.Rd | 16 ++++++----- man/daymet.point.Rd | 8 +++-- man/mwCorr.Rd |only man/nni.Rd | 4 +- man/polyPerimeter.Rd |only man/rasterCorrelation.Rd |only man/sampleTransect.Rd |only man/shannons.Rd | 16 ++++++----- man/trig.trans.Rd |only man/vrm.Rd |only 25 files changed, 166 insertions(+), 126 deletions(-)
Title: Qualitative Comparative Analysis
Description: Core functions to perform Qualitative Comparative Analysis.
Author: Adrian Dusa [aut, cre, cph],
Alrik Thiem [aut] (from version 1.0-0, up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 2.2 dated 2016-05-10 and 2.3 dated 2016-06-14
DESCRIPTION | 8 - MD5 | 24 +-- R/createString.R | 2 R/getSolution.R | 1 R/numeric.R | 3 R/prettyString.R | 19 -- R/sortVector.R | 3 R/specifics.R | 11 - R/string.R | 347 ++++++++++------------------------------------------- R/writePrimeimp.R | 4 R/writeSolution.R | 3 inst/ChangeLog | 4 man/QCA.package.Rd | 4 13 files changed, 96 insertions(+), 337 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from
'SPSS' or 'Stata' with 'haven' or 'foreign'.
Author: Joseph Larmarange [aut, cre],
Daniel Ludecke [ctb],
Hadley Wickham [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 0.2.1 dated 2016-06-01 and 0.2.2 dated 2016-06-14
labelled-0.2.1/labelled/R/to_labelled.r |only labelled-0.2.2/labelled/DESCRIPTION | 8 +++--- labelled-0.2.2/labelled/MD5 | 18 +++++++-------- labelled-0.2.2/labelled/NEWS.md | 6 +++++ labelled-0.2.2/labelled/R/to_character.R | 9 +++++-- labelled-0.2.2/labelled/R/to_factor.R | 20 ++++++++++++----- labelled-0.2.2/labelled/R/to_labelled.R |only labelled-0.2.2/labelled/README.md | 2 + labelled-0.2.2/labelled/man/to_factor.Rd | 6 +++-- labelled-0.2.2/labelled/man/to_labelled.Rd | 2 - labelled-0.2.2/labelled/tests/testthat/test-labelled.r | 8 ++++++ 11 files changed, 56 insertions(+), 23 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Future versions will include functionality for the Ar-Ar, Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, including isochrons, age spectra, ternary diagrams, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app at http://isoplotr.london-geochron.com. Offline access to this interface will be provided at a later point in time.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 0.3 dated 2016-05-24 and 0.4 dated 2016-06-14
IsoplotR-0.3/IsoplotR/data/UPb.rda |only IsoplotR-0.3/IsoplotR/man/I.R.Rd |only IsoplotR-0.3/IsoplotR/man/UPb.Rd |only IsoplotR-0.3/IsoplotR/man/concordia.age.Rd |only IsoplotR-0.3/IsoplotR/man/concordia.plot.Rd |only IsoplotR-0.3/IsoplotR/man/discordia.age.Rd |only IsoplotR-0.3/IsoplotR/man/read.matrix.Rd |only IsoplotR-0.4/IsoplotR/DESCRIPTION | 8 - IsoplotR-0.4/IsoplotR/MD5 | 50 ++++--- IsoplotR-0.4/IsoplotR/NAMESPACE | 22 ++- IsoplotR-0.4/IsoplotR/R/UPb.R | 125 ++++++++++++++++--- IsoplotR-0.4/IsoplotR/R/age.R |only IsoplotR-0.4/IsoplotR/R/botev.R |only IsoplotR-0.4/IsoplotR/R/cad.R |only IsoplotR-0.4/IsoplotR/R/concordia.R | 177 +++++++++++++++++++++++++--- IsoplotR-0.4/IsoplotR/R/constants.R | 29 ++-- IsoplotR-0.4/IsoplotR/R/discordia.R | 165 -------------------------- IsoplotR-0.4/IsoplotR/R/documentation.R | 31 +++- IsoplotR-0.4/IsoplotR/R/io.R | 57 +++++---- IsoplotR-0.4/IsoplotR/R/kde.R |only IsoplotR-0.4/IsoplotR/R/regression.R | 14 -- IsoplotR-0.4/IsoplotR/R/toolbox.R | 24 +++ IsoplotR-0.4/IsoplotR/data/examples.rda |only IsoplotR-0.4/IsoplotR/inst/DZ.csv |only IsoplotR-0.4/IsoplotR/inst/constants.json | 2 IsoplotR-0.4/IsoplotR/man/age.Rd |only IsoplotR-0.4/IsoplotR/man/botev.Rd |only IsoplotR-0.4/IsoplotR/man/cad.Rd |only IsoplotR-0.4/IsoplotR/man/concordia.Rd |only IsoplotR-0.4/IsoplotR/man/examples.Rd |only IsoplotR-0.4/IsoplotR/man/iratio.Rd |only IsoplotR-0.4/IsoplotR/man/kde.Rd |only IsoplotR-0.4/IsoplotR/man/lambda.Rd | 5 IsoplotR-0.4/IsoplotR/man/read.data.Rd | 26 ++-- IsoplotR-0.4/IsoplotR/man/settings.Rd | 2 IsoplotR-0.4/IsoplotR/man/yorkfit.Rd | 14 -- 36 files changed, 445 insertions(+), 306 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr versions 1.1.0 dated 2016-01-27 and 1.2.0 dated 2016-06-14
DESCRIPTION | 9 MD5 | 126 ++--- NAMESPACE | 2 NEWS.md | 55 ++ R/authenticate.r | 2 R/body.R | 19 R/cache.R | 1 R/config.r | 18 R/content-parse.r | 14 R/content.r | 8 R/handle-pool.r | 4 R/handle.r | 1 R/http-delete.r | 8 R/http-patch.r | 14 R/http-post.r | 21 R/http-put.r | 15 R/http-verb.R | 10 R/media-parse.r | 11 R/oauth-app.r | 1 R/oauth-cache.R | 32 - R/oauth-endpoint.r | 1 R/oauth-init.R | 11 R/oauth-listener.r | 11 R/oauth-refresh.R | 18 R/oauth-signature.r | 9 R/oauth-token.r | 4 R/progress.R | 14 R/proxy.r | 2 R/request.R | 10 R/response-status.r | 2 R/response-type.R |only R/response.r | 4 R/retry.R |only R/url.r | 6 R/write-function.R | 3 README.md | 6 build/vignette.rds |binary demo/00Index | 1 demo/oauth1-twitter.r | 2 demo/oauth2-azure.r | 4 demo/oauth2-facebook.r | 9 demo/oauth2-reddit.R |only inst/doc/api-packages.R | 249 ++++++---- inst/doc/api-packages.Rmd | 534 +++++++++++++++------ inst/doc/api-packages.html | 936 ++++++++++++++++++++------------------ inst/doc/quickstart.html | 56 +- man/DELETE.Rd | 31 + man/PATCH.Rd | 14 man/POST.Rd | 14 man/PUT.Rd | 14 man/RETRY.Rd |only man/VERB.Rd | 9 man/authenticate.Rd | 2 man/content.Rd | 8 man/http_type.Rd |only man/modify_url.Rd | 2 man/oauth1.0_token.Rd | 2 man/oauth2.0_token.Rd | 2 man/oauth_signature.Rd | 7 man/progress.Rd | 5 man/stop_for_status.Rd | 2 man/use_proxy.Rd | 2 man/write_stream.Rd | 3 tests/testthat/test-body.r | 5 tests/testthat/test-parse_media.R |only tests/testthat/test-url.r | 5 vignettes/api-packages.Rmd | 534 +++++++++++++++------ 67 files changed, 1835 insertions(+), 1089 deletions(-)
Title: Google Analytics API into R
Description: R library for interacting with the Google Analytics
Reporting API v3 and v4.
Author: Mark Edmondson [aut, cre],
Artem Klevtsov [ctb],
Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAnalyticsR versions 0.1.1 dated 2016-05-24 and 0.2.0 dated 2016-06-14
googleAnalyticsR-0.1.1/googleAnalyticsR/inst/shiny/shiny-modules.R |only googleAnalyticsR-0.2.0/googleAnalyticsR/DESCRIPTION | 13 googleAnalyticsR-0.2.0/googleAnalyticsR/MD5 | 55 - googleAnalyticsR-0.2.0/googleAnalyticsR/NAMESPACE | 3 googleAnalyticsR-0.2.0/googleAnalyticsR/NEWS.md | 11 googleAnalyticsR-0.2.0/googleAnalyticsR/R/bigQuery.R |only googleAnalyticsR-0.2.0/googleAnalyticsR/R/data.R |only googleAnalyticsR-0.2.0/googleAnalyticsR/R/fetch_functions.R | 40 googleAnalyticsR-0.2.0/googleAnalyticsR/R/ga_v4_get.R | 49 - googleAnalyticsR-0.2.0/googleAnalyticsR/R/ga_v4_objects.R | 10 googleAnalyticsR-0.2.0/googleAnalyticsR/R/gadget.R |only googleAnalyticsR-0.2.0/googleAnalyticsR/R/getData.R | 84 - googleAnalyticsR-0.2.0/googleAnalyticsR/R/googleAnalyticsR.R | 26 googleAnalyticsR-0.2.0/googleAnalyticsR/R/parse_functions.R | 5 googleAnalyticsR-0.2.0/googleAnalyticsR/R/segments.R | 7 googleAnalyticsR-0.2.0/googleAnalyticsR/R/shiny-modules.R |only googleAnalyticsR-0.2.0/googleAnalyticsR/README.md | 467 ---------- googleAnalyticsR-0.2.0/googleAnalyticsR/build/vignette.rds |binary googleAnalyticsR-0.2.0/googleAnalyticsR/data |only googleAnalyticsR-0.2.0/googleAnalyticsR/inst/doc/googleAnalyticsR.Rmd | 200 ++++ googleAnalyticsR-0.2.0/googleAnalyticsR/inst/doc/googleAnalyticsR.html | 160 +++ googleAnalyticsR-0.2.0/googleAnalyticsR/inst/rstudio |only googleAnalyticsR-0.2.0/googleAnalyticsR/inst/shiny/ga4-example |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/googleAnalyticsR.Rd | 19 googleAnalyticsR-0.2.0/googleAnalyticsR/man/google_analytics.Rd | 6 googleAnalyticsR-0.2.0/googleAnalyticsR/man/google_analytics_bq.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/make_ga_4_req.Rd | 2 googleAnalyticsR-0.2.0/googleAnalyticsR/man/meta.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/order_type.Rd | 7 googleAnalyticsR-0.2.0/googleAnalyticsR/man/segmentBuilder.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/segmentBuilderUI.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/segmentChain.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/segmentChainUI.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/segmentElementUI.Rd |only googleAnalyticsR-0.2.0/googleAnalyticsR/man/segment_vector_sequence.Rd | 7 googleAnalyticsR-0.2.0/googleAnalyticsR/vignettes/googleAnalyticsR.Rmd | 200 ++++ 36 files changed, 785 insertions(+), 586 deletions(-)
More information about googleAnalyticsR at CRAN
Permanent link
Title: Tools for Geohash Creation and Manipulation
Description: Provides tools to encode lat/long pairs into geohashes, decode those geohashes,
and identify their neighbours.
Author: Oliver Keyes [aut, cre], G. Nagel [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between geohash versions 0.1.1 dated 2016-04-14 and 0.1.2 dated 2016-06-14
DESCRIPTION | 10 +- MD5 | 24 ++--- NEWS | 5 + R/RcppExports.R | 2 README.md | 8 - inst/doc/geohash.Rmd | 1 inst/doc/geohash.html | 164 +++++++++++++-------------------------- man/gh_decode.Rd | 2 src/geohash.cpp | 4 tests/testthat/test_decode.R | 14 +-- tests/testthat/test_encode.R | 16 +-- tests/testthat/test_neighbours.R | 36 ++++---- vignettes/geohash.Rmd | 1 13 files changed, 121 insertions(+), 166 deletions(-)
Title: ANES Raking Implementation
Description: Provides a comprehensive system for selecting
variables and weighting data to match the specifications of the American
National Election Studies. The package includes methods for identifying
discrepant variables, raking data, and assessing the effects of the raking
algorithm. It also allows automated re-raking if target variables fall
outside identified bounds and allows greater user specification than other
available raking algorithms. A variety of simple weighted statistics that
were previously in this package (version .55 and earlier) have been moved to
the package 'weights.'
Author: Josh Pasek [aut, cre]
Maintainer: Josh Pasek <josh@joshpasek.com>
Diff between anesrake versions 0.70 dated 2011-05-26 and 0.75 dated 2016-06-14
DESCRIPTION | 35 ++--- MD5 |only NAMESPACE |only R/anesrake.R | 280 +++++++++++++++++++++++---------------------- R/anesrakefinder.R | 11 - R/discrep.default.R | 5 R/discrep.factor.R | 2 R/discrep.logical.R | 5 R/discrep.numeric.R | 5 R/rakelist.R | 7 - R/rakeonvar.default.R | 3 R/rakeonvar.factor.R | 3 R/rakeonvar.numeric.R | 3 R/summary.anesrake.R | 7 - R/weightassess.R | 86 ++++++------- man/anes04.Rd | 3 man/anesrake.Rd | 19 --- man/anesrakefinder.Rd | 17 -- man/discrep.Rd | 21 --- man/generaldesigneffect.Rd | 29 ---- man/rakelist.Rd | 17 -- man/weightassess.Rd | 23 --- 22 files changed, 236 insertions(+), 345 deletions(-)
Title: Accessing the Wordbank Database
Description: Tools for connecting to Wordbank, an open repository for
developmental vocabulary data.
Author: Mika Braginsky [aut, cre],
Daniel Yurovsky [ctb],
Michael Frank [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Diff between wordbankr versions 0.1 dated 2015-10-31 and 0.2.0 dated 2016-06-14
DESCRIPTION | 14 ++- MD5 | 31 ++++---- NAMESPACE | 2 NEWS.md |only R/wordbankr.R | 147 +++++++++++++++++++++++++---------------- README.md | 5 - build/vignette.rds |binary inst/doc/wordbankr.Rmd | 2 inst/doc/wordbankr.html | 110 +++++++++++++++--------------- man/connect_to_wordbank.Rd | 2 man/get_administration_data.Rd | 26 ++++--- man/get_common_table.Rd | 2 man/get_instrument_data.Rd | 2 man/get_instrument_table.Rd | 2 man/get_instruments.Rd | 2 man/get_item_data.Rd | 2 vignettes/wordbankr.Rmd | 2 17 files changed, 197 insertions(+), 154 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre],
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-34 dated 2016-05-04 and 0.1-35 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rollup.R | 40 ++++++++++++++++++++++++++++++---------- man/rollup.Rd | 15 ++++++++++----- tests/rollup.R | 7 +++++++ tests/rollup.Rout.save | 18 ++++++++++++++---- tests/util.R | 1 + tests/util.Rout.save | 14 ++++++++++---- 8 files changed, 82 insertions(+), 33 deletions(-)
Title: Environment for Assessing Recommender Systems
Description: Provides implementations of several popular recommendation systems. They can process standard recommendation datasets (user/item matrix) as input and generate rating predictions and recommendation lists. Standard algorithm implementations included in this package are: Global/Item/User-Average baselines, Item-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology for recommender systems using measures such as MAE, RMSE, Precision, Recall, AUC, NDCG, RankScore and coverage measures. The package is intended for rapid prototyping of recommendation algorithms and education purposes.
Author: Ludovik Çoba [aut, cre, cph],
Markus Zanker [ctb]
Maintainer: Ludovik Çoba <lcoba@unishk.edu.al>
Diff between rrecsys versions 0.9.5 dated 2016-05-31 and 0.9.5.1 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 3 ++- R/evalPred.R | 8 ++++---- man/getAUC.Rd | 4 ++-- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programming Kit.
GLPK is open source software for solving large-scale linear programming (LP),
mixed integer linear programming (MILP) and other related problems.
Author: Stefan Theussl [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb],
Heinrich Schuchardt [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between Rglpk versions 0.6-1 dated 2015-07-01 and 0.6-2 dated 2016-06-14
DESCRIPTION | 15 ++----- MD5 | 12 +++--- R/Rglpk_solve.R | 24 ++++++++++-- R/control.R | 12 +++++- inst/CHANGELOG | 6 +++ man/Rglpk_solve.Rd | 42 ++++++++++++++++----- src/Rglpk_solve.c | 102 ++++++++++++++++++++++++++++++++++++++--------------- 7 files changed, 155 insertions(+), 58 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.1.9 dated 2016-05-29 and 0.1.9.2 dated 2016-06-14
DESCRIPTION | 6 MD5 | 22 +- NAMESPACE | 3 R/ARMA_Regression.R | 17 +- R/Classifier.R | 350 ++++++++++++++++++++------------------------- R/Correlation.R | 10 - R/Feature_probability.R |only R/Partial_Moments.R | 10 - R/Partition_Map.R | 2 R/Regression.R | 58 ++++--- man/Feature.probability.Rd |only man/VN.class.Rd | 15 + man/VN.reg.Rd | 18 +- 13 files changed, 265 insertions(+), 246 deletions(-)
Title: Efficient Jonckheere-Terpstra Test Statistics
Description: The core of this 'Rcpp' based package is a function to compute standardized Jonckheere-Terpstra test statistics for large numbers of dependent and independent variables, e.g., genome-wide analysis. It implements 'OpenMP', allowing the option of computing on multiple threads. Supporting functions are also provided to calculate p-values and summarize results.
Author: Jiaxing Lin, Alexander Sibley, Ivo Shterev, and Kouros Owzar
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Diff between jtGWAS versions 1.1 dated 2016-06-13 and 1.2 dated 2016-06-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 6 +++++- inst/doc/jtGWAS.Rnw | 2 +- inst/doc/jtGWAS.pdf |binary man/jtGWAS-package.Rd | 4 ++-- src/jtGWAS.cpp | 13 +++++++++++-- src/jtGWASmp.cpp | 13 +++++++++++-- vignettes/jtGWAS.Rnw | 2 +- 9 files changed, 43 insertions(+), 21 deletions(-)
Title: Modeling Animal Movement with Continuous-Time Discrete-Space
Markov Chains
Description: Software to facilitates taking movement data in xyt format and pairing it with raster covariates within a continuous time Markov chain (CTMC) framework. As described in Hanks et al. (2015) <DOI:10.1214/14-AOAS803> , this allows flexible modeling of movement in response to covariates (or covariate gradients) with model fitting possible within a Poisson GLM framework.
Author: Ephraim Hanks
Maintainer: Ephraim Hanks <hanks@psu.edu>
Diff between ctmcmove versions 1.2.3 dated 2016-04-18 and 1.2.4 dated 2016-06-14
DESCRIPTION | 8 ++--- MD5 | 12 +++---- R/ctmc2glm.R | 31 ++++++++++++-------- data/seal.rda |binary man/ctmc2glm.Rd | 7 +++- man/mcmc.fmove.Rd | 18 +++++++---- man/seal.Rd | 82 ++++++++++++------------------------------------------ 7 files changed, 66 insertions(+), 92 deletions(-)
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.5.0 dated 2016-06-13 and 0.5.1 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 +++++- R/spread.R | 3 ++- inst/doc/tidy-data.html | 4 ++-- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Read Data Stored in DBC (Compressed DBF) Files
Description: Functions for reading and decompressing the DBC (compressed DBF) files. Please note that this is the file format used by the Brazilian Ministry of Health (DATASUS) to publish healthcare datasets. It is not related to the FoxPro or CANdb DBC file formats.
Author: Daniela Petruzalek [aut, cre]
Maintainer: Daniela Petruzalek <daniela.petruzalek@gmail.com>
Diff between read.dbc versions 1.0.3 dated 2016-06-13 and 1.0.4 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- README.md | 6 +++++- inst/CHANGELOG.md | 4 ++++ src/dbc2dbf.c | 15 +++++++++++---- 5 files changed, 27 insertions(+), 12 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 0.8 dated 2016-05-17 and 0.9 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/update_mams.R | 2 +- inst/NEWS | 5 +++++ 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.3.3 dated 2016-05-04 and 1.3.4 dated 2016-06-14
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS | 3 +++ R/kmciFunctions.R | 5 ++++- inst/doc/discreteBPCP.pdf |binary man/bpcp-package.Rd | 4 ++-- tests/abmmWarningTest.R |only 7 files changed, 19 insertions(+), 12 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Jason Becker [ctb],
Chung-hong Chan [aut],
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut, cre],
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.4.6 dated 2016-05-22 and 0.4.8 dated 2016-06-14
DESCRIPTION | 8 ++--- MD5 | 26 +++++++++---------- NAMESPACE | 3 -- NEWS | 9 ++++++ R/cleanup_haven.R | 18 ++++++------- R/import_methods.R | 53 +++++++++++++++++++-------------------- R/utils.R | 1 README.md | 2 - inst/doc/rio.Rmd | 2 - inst/doc/rio.html | 8 ++--- man/import.Rd | 2 - tests/testthat/test_format_csv.R | 15 +++++++++-- tests/testthat/test_format_sav.R | 7 ++--- vignettes/rio.Rmd | 2 - 14 files changed, 86 insertions(+), 70 deletions(-)
Title: Fast Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum, Nicolas Duforet-Frebourg
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 3.0 dated 2016-04-15 and 3.0.1 dated 2016-06-14
pcadapt-3.0.1/pcadapt/DESCRIPTION | 8 +- pcadapt-3.0.1/pcadapt/MD5 | 27 ++++--- pcadapt-3.0.1/pcadapt/NAMESPACE | 6 + pcadapt-3.0.1/pcadapt/R/pcadapt.R | 23 ++---- pcadapt-3.0.1/pcadapt/R/pcadaptClass.R | 17 ++-- pcadapt-3.0.1/pcadapt/R/pcadaptUtils.R | 66 ++++++++++++++++--- pcadapt-3.0.1/pcadapt/R/pcadaptggPlotting.R | 62 +++++++++-------- pcadapt-3.0.1/pcadapt/inst/extdata/geno3pops.pcadapt |only pcadapt-3.0.1/pcadapt/man/create.pcadapt.Rd | 2 pcadapt-3.0.1/pcadapt/man/get.pc.Rd |only pcadapt-3.0.1/pcadapt/man/get.pop.names.Rd |only pcadapt-3.0.1/pcadapt/man/pcadapt-package.Rd | 6 - pcadapt-3.0.1/pcadapt/man/pcadapt.Rd | 12 +-- pcadapt-3.0.1/pcadapt/man/read.pcadapt.Rd |only pcadapt-3.0.1/pcadapt/src/pcadapt.c | 11 --- pcadapt-3.0.1/pcadapt/vignettes/pcadapt.Rmd | 33 ++++++--- pcadapt-3.0/pcadapt/man/read4pcadapt.Rd |only 17 files changed, 168 insertions(+), 105 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 5.2.0 dated 2015-11-19 and 6.0.0 dated 2016-06-14
mixOmics-5.2.0/mixOmics/R/Mfold.R |only mixOmics-5.2.0/mixOmics/R/helpers.R |only mixOmics-5.2.0/mixOmics/R/ica.def.R |only mixOmics-5.2.0/mixOmics/R/ica.par.R |only mixOmics-5.2.0/mixOmics/R/loo.R |only mixOmics-5.2.0/mixOmics/R/map.R |only mixOmics-5.2.0/mixOmics/R/predict.R |only mixOmics-5.2.0/mixOmics/R/s.match.R |only mixOmics-5.2.0/mixOmics/R/srgcca.R |only mixOmics-5.2.0/mixOmics/R/tau.estim.R |only mixOmics-5.2.0/mixOmics/R/tune.splsdalevel1.R |only mixOmics-5.2.0/mixOmics/R/tune.splsdalevel2.R |only mixOmics-5.2.0/mixOmics/R/valid.R |only mixOmics-5.2.0/mixOmics/R/wrappers.R |only mixOmics-5.2.0/mixOmics/data/prostate.rda |only mixOmics-5.2.0/mixOmics/man/internal-functions.Rd |only mixOmics-5.2.0/mixOmics/man/prostate.Rd |only mixOmics-5.2.0/mixOmics/man/s.match.Rd |only mixOmics-5.2.0/mixOmics/man/wrappers.Rd |only mixOmics-6.0.0/mixOmics/DESCRIPTION | 29 mixOmics-6.0.0/mixOmics/MD5 | 263 + mixOmics-6.0.0/mixOmics/NAMESPACE | 127 mixOmics-6.0.0/mixOmics/NEWS | 65 mixOmics-6.0.0/mixOmics/R/LOGOCV.R |only mixOmics-6.0.0/mixOmics/R/MCVfold.R |only mixOmics-6.0.0/mixOmics/R/bin.color.R | 19 mixOmics-6.0.0/mixOmics/R/block.pls.R |only mixOmics-6.0.0/mixOmics/R/block.plsda.R |only mixOmics-6.0.0/mixOmics/R/block.spls.R |only mixOmics-6.0.0/mixOmics/R/block.splsda.R |only mixOmics-6.0.0/mixOmics/R/check_entry.R |only mixOmics-6.0.0/mixOmics/R/cim.R | 2325 +++++++--------- mixOmics-6.0.0/mixOmics/R/cimDiablo.R |only mixOmics-6.0.0/mixOmics/R/circosPlot.R |only mixOmics-6.0.0/mixOmics/R/color.GreenRed.R | 32 mixOmics-6.0.0/mixOmics/R/color.jet.R | 26 mixOmics-6.0.0/mixOmics/R/color.mixo.R | 41 mixOmics-6.0.0/mixOmics/R/color.spectral.R | 26 mixOmics-6.0.0/mixOmics/R/explained_variance.R |only mixOmics-6.0.0/mixOmics/R/ica.def.par.R |only mixOmics-6.0.0/mixOmics/R/image.tune.rcc.R | 16 mixOmics-6.0.0/mixOmics/R/imageMap.R | 32 mixOmics-6.0.0/mixOmics/R/imgCor.R | 38 mixOmics-6.0.0/mixOmics/R/internal_graphicModule.R |only mixOmics-6.0.0/mixOmics/R/internal_mint.block.R |only mixOmics-6.0.0/mixOmics/R/internal_mint.block_helpers.R |only mixOmics-6.0.0/mixOmics/R/internal_predict.DA.R |only mixOmics-6.0.0/mixOmics/R/internal_wrapper.mint.R |only mixOmics-6.0.0/mixOmics/R/internal_wrapper.mint.block.R |only mixOmics-6.0.0/mixOmics/R/ipca.R | 155 - mixOmics-6.0.0/mixOmics/R/mat.rank.R | 42 mixOmics-6.0.0/mixOmics/R/mint.block.pls.R |only mixOmics-6.0.0/mixOmics/R/mint.block.plsda.R |only mixOmics-6.0.0/mixOmics/R/mint.block.spls.R |only mixOmics-6.0.0/mixOmics/R/mint.block.splsda.R |only mixOmics-6.0.0/mixOmics/R/mint.pls.R |only mixOmics-6.0.0/mixOmics/R/mint.plsda.R |only mixOmics-6.0.0/mixOmics/R/mint.spls.R |only mixOmics-6.0.0/mixOmics/R/mint.splsda.R |only mixOmics-6.0.0/mixOmics/R/mixOmics.R |only mixOmics-6.0.0/mixOmics/R/multilevel.R | 263 + mixOmics-6.0.0/mixOmics/R/nearZeroVar.R | 67 mixOmics-6.0.0/mixOmics/R/network.R | 1630 +++++------ mixOmics-6.0.0/mixOmics/R/nipals.R | 176 - mixOmics-6.0.0/mixOmics/R/pca.R | 356 +- mixOmics-6.0.0/mixOmics/R/pcasvd.R | 81 mixOmics-6.0.0/mixOmics/R/perf.R | 929 ++---- mixOmics-6.0.0/mixOmics/R/perf.diablo.R |only mixOmics-6.0.0/mixOmics/R/perf.mint.splsda.R |only mixOmics-6.0.0/mixOmics/R/plot.pca.R | 29 mixOmics-6.0.0/mixOmics/R/plot.perf.R | 181 - mixOmics-6.0.0/mixOmics/R/plot.rcc.R | 30 mixOmics-6.0.0/mixOmics/R/plotArrow.R | 542 +-- mixOmics-6.0.0/mixOmics/R/plotContrib.R | 238 - mixOmics-6.0.0/mixOmics/R/plotDiablo.R |only mixOmics-6.0.0/mixOmics/R/plotIndiv.R | 1609 ++++------- mixOmics-6.0.0/mixOmics/R/plotIndiv.mint.R |only mixOmics-6.0.0/mixOmics/R/plotIndiv.pca.R |only mixOmics-6.0.0/mixOmics/R/plotIndiv.pls.R |only mixOmics-6.0.0/mixOmics/R/plotIndiv.sgcca.R |only mixOmics-6.0.0/mixOmics/R/plotLoadings.R |only mixOmics-6.0.0/mixOmics/R/plotLoadings.mint.spls.R |only mixOmics-6.0.0/mixOmics/R/plotLoadings.mint.splsda.R |only mixOmics-6.0.0/mixOmics/R/plotLoadings.spls.R |only mixOmics-6.0.0/mixOmics/R/plotLoadings.splsda.R |only mixOmics-6.0.0/mixOmics/R/plotVar.R | 1475 +++++----- mixOmics-6.0.0/mixOmics/R/pls.R | 398 -- mixOmics-6.0.0/mixOmics/R/plsda.R | 144 mixOmics-6.0.0/mixOmics/R/predict.mint.block.pls.R |only mixOmics-6.0.0/mixOmics/R/print.methods.R | 673 +++- mixOmics-6.0.0/mixOmics/R/rcc.R | 28 mixOmics-6.0.0/mixOmics/R/scatterutil.R | 29 mixOmics-6.0.0/mixOmics/R/selectVar.R | 100 mixOmics-6.0.0/mixOmics/R/sipca.R | 40 mixOmics-6.0.0/mixOmics/R/spca.R | 31 mixOmics-6.0.0/mixOmics/R/spls.R | 418 -- mixOmics-6.0.0/mixOmics/R/splsda.R | 156 - mixOmics-6.0.0/mixOmics/R/summary.R | 14 mixOmics-6.0.0/mixOmics/R/tune.R |only mixOmics-6.0.0/mixOmics/R/tune.mint.splsda.R |only mixOmics-6.0.0/mixOmics/R/tune.multilevel.R | 165 - mixOmics-6.0.0/mixOmics/R/tune.pca.R | 158 - mixOmics-6.0.0/mixOmics/R/tune.rcc.R | 96 mixOmics-6.0.0/mixOmics/R/tune.splsda.R |only mixOmics-6.0.0/mixOmics/R/tune.splslevel.R | 128 mixOmics-6.0.0/mixOmics/R/unmap.R | 84 mixOmics-6.0.0/mixOmics/R/vip.R | 33 mixOmics-6.0.0/mixOmics/R/withinVariation.R | 27 mixOmics-6.0.0/mixOmics/R/wrapper.ilr.R |only mixOmics-6.0.0/mixOmics/R/wrapper.rgcca.R |only mixOmics-6.0.0/mixOmics/R/wrapper.sgcca.R |only mixOmics-6.0.0/mixOmics/R/zzz.R | 22 mixOmics-6.0.0/mixOmics/README |only mixOmics-6.0.0/mixOmics/data/Koren.16S.rda |only mixOmics-6.0.0/mixOmics/data/breast.TCGA.rda |only mixOmics-6.0.0/mixOmics/data/breast.tumors.rda |binary mixOmics-6.0.0/mixOmics/data/datalist | 5 mixOmics-6.0.0/mixOmics/data/diverse.16S.rda |only mixOmics-6.0.0/mixOmics/data/linnerud.rda |binary mixOmics-6.0.0/mixOmics/data/liver.toxicity.rda |binary mixOmics-6.0.0/mixOmics/data/multidrug.rda |binary mixOmics-6.0.0/mixOmics/data/nutrimouse.rda |binary mixOmics-6.0.0/mixOmics/data/srbct.rda |binary mixOmics-6.0.0/mixOmics/data/stemcells.rda |only mixOmics-6.0.0/mixOmics/data/vac18.rda |binary mixOmics-6.0.0/mixOmics/data/vac18.simulated.rda |binary mixOmics-6.0.0/mixOmics/data/yeast.rda |binary mixOmics-6.0.0/mixOmics/man/Koren.16S.Rd |only mixOmics-6.0.0/mixOmics/man/block.pls.Rd |only mixOmics-6.0.0/mixOmics/man/block.plsda.Rd |only mixOmics-6.0.0/mixOmics/man/block.spls.Rd |only mixOmics-6.0.0/mixOmics/man/block.splsda.Rd |only mixOmics-6.0.0/mixOmics/man/breast.TCGA.Rd |only mixOmics-6.0.0/mixOmics/man/breast.tumors.Rd | 8 mixOmics-6.0.0/mixOmics/man/cim.Rd | 46 mixOmics-6.0.0/mixOmics/man/cimDiablo.Rd |only mixOmics-6.0.0/mixOmics/man/circosPlot.Rd |only mixOmics-6.0.0/mixOmics/man/diverse.16S.Rd |only mixOmics-6.0.0/mixOmics/man/explained_variance.Rd |only mixOmics-6.0.0/mixOmics/man/image.tune.rcc.Rd | 2 mixOmics-6.0.0/mixOmics/man/imgCor.Rd | 4 mixOmics-6.0.0/mixOmics/man/logratio.transfo.Rd |only mixOmics-6.0.0/mixOmics/man/map.Rd |only mixOmics-6.0.0/mixOmics/man/mint.block.pls.Rd |only mixOmics-6.0.0/mixOmics/man/mint.block.plsda.Rd |only mixOmics-6.0.0/mixOmics/man/mint.block.spls.Rd |only mixOmics-6.0.0/mixOmics/man/mint.block.splsda.Rd |only mixOmics-6.0.0/mixOmics/man/mint.pls.Rd |only mixOmics-6.0.0/mixOmics/man/mint.plsda.Rd |only mixOmics-6.0.0/mixOmics/man/mint.spls.Rd |only mixOmics-6.0.0/mixOmics/man/mint.splsda.Rd |only mixOmics-6.0.0/mixOmics/man/mixOmics.Rd |only mixOmics-6.0.0/mixOmics/man/multilevel.Rd | 87 mixOmics-6.0.0/mixOmics/man/pca.Rd | 58 mixOmics-6.0.0/mixOmics/man/perf.Rd | 269 + mixOmics-6.0.0/mixOmics/man/plot.perf.Rd | 7 mixOmics-6.0.0/mixOmics/man/plotArrow.Rd | 69 mixOmics-6.0.0/mixOmics/man/plotContrib.Rd | 29 mixOmics-6.0.0/mixOmics/man/plotDiablo.Rd |only mixOmics-6.0.0/mixOmics/man/plotIndiv.Rd | 168 - mixOmics-6.0.0/mixOmics/man/plotLoadings.Rd |only mixOmics-6.0.0/mixOmics/man/plotVar.Rd | 45 mixOmics-6.0.0/mixOmics/man/pls.Rd | 33 mixOmics-6.0.0/mixOmics/man/plsda.Rd | 44 mixOmics-6.0.0/mixOmics/man/predict.Rd | 127 mixOmics-6.0.0/mixOmics/man/scatterutil.Rd | 4 mixOmics-6.0.0/mixOmics/man/selectVar.Rd | 20 mixOmics-6.0.0/mixOmics/man/spls.Rd | 97 mixOmics-6.0.0/mixOmics/man/splsda.Rd | 117 mixOmics-6.0.0/mixOmics/man/stemcells.Rd |only mixOmics-6.0.0/mixOmics/man/study_split.Rd |only mixOmics-6.0.0/mixOmics/man/tune.Rd |only mixOmics-6.0.0/mixOmics/man/tune.mint.splsda.Rd |only mixOmics-6.0.0/mixOmics/man/tune.multilevel.Rd | 90 mixOmics-6.0.0/mixOmics/man/tune.pca.Rd | 30 mixOmics-6.0.0/mixOmics/man/tune.rcc.Rd | 14 mixOmics-6.0.0/mixOmics/man/tune.splsda.Rd |only mixOmics-6.0.0/mixOmics/man/unmap.Rd | 7 mixOmics-6.0.0/mixOmics/man/vac18.Rd | 8 mixOmics-6.0.0/mixOmics/man/withinVariation.Rd | 4 mixOmics-6.0.0/mixOmics/man/wrapper.rgcca.Rd |only mixOmics-6.0.0/mixOmics/man/wrapper.sgcca.Rd |only 182 files changed, 7831 insertions(+), 7147 deletions(-)
Title: Parameter Estimation and Inference in a Cointegrating Regression
Description: Cointegration methods are widely used in empirical macroeconomics
and empirical finance. It is well known that in a cointegrating
regression the ordinary least squares (OLS) estimator of the
parameters is super-consistent, i.e. converges at rate equal to the
sample size T. When the regressors are endogenous, the limiting
distribution of the OLS estimator is contaminated by so-called second
order bias terms, see e.g. Phillips and Hansen (1990) <DOI:10.2307/2297545>.
The presence of these bias terms renders inference difficult. Consequently,
several modifications to OLS that lead to zero mean Gaussian mixture
limiting distributions have been proposed, which in turn make
standard asymptotic inference feasible. These methods include
the fully modified OLS (FM-OLS) approach of Phillips and Hansen
(1990) <DOI:10.2307/2297545>, the dynamic OLS (D-OLS) approach of Phillips
and Loretan (1991) <DOI:10.2307/2298004>, Saikkonen (1991)
<DOI:10.1017/S0266466600004217> and Stock and Watson (1993)
<DOI:10.2307/2951763> and the new estimation approach called integrated
modified OLS (IM-OLS) of Vogelsang and Wagner (2014)
<DOI:10.1016/j.jeconom.2013.10.015>. The latter is based on an augmented
partial sum (integration) transformation of the regression model. IM-OLS is
similar in spirit to the FM- and D-OLS approaches, with the key difference
that it does not require estimation of long run variance matrices and avoids
the need to choose tuning parameters (kernels, bandwidths, lags). However,
inference does require that a long run variance be scaled out.
This package provides functions for the parameter estimation and inference
with all three modified OLS approaches. That includes the automatic
bandwidth selection approaches of Andrews (1991) <DOI:10.2307/2938229> and
of Newey and West (1994) <DOI:10.2307/2297912> as well as the calculation of
the long run variance.
Author: Philipp Aschersleben [aut, cre],
Martin Wagner [aut] (Author of underlying MATLAB code.)
Maintainer: Philipp Aschersleben <aschersleben@statistik.tu-dortmund.de>
Diff between cointReg versions 0.1.0 dated 2016-06-06 and 0.2.0 dated 2016-06-14
DESCRIPTION | 8 ++--- MD5 | 31 ++++++++++++---------- R/cointReg-D-OLS.R | 2 - R/cointReg-FM-OLS.R | 4 +- R/cointReg.R | 17 +++--------- R/zzz.R | 3 +- inst/NEWS.md | 5 +++ inst/doc/cointReg.R | 6 +++- inst/doc/cointReg.Rmd | 10 +++++-- inst/doc/cointReg.html | 29 ++++++++++---------- man/cointReg-package.Rd | 17 +++--------- vignettes/cointReg.Rmd | 10 +++++-- vignettes/figures/vignette-unnamed-chunk-10-1.png |binary vignettes/figures/vignette-unnamed-chunk-11-1.png |only vignettes/figures/vignette-unnamed-chunk-5-1.png |only vignettes/figures/vignette-unnamed-chunk-7-1.png |binary vignettes/figures/vignette-unnamed-chunk-8-1.png |binary vignettes/figures/vignette-unnamed-chunk-9-1.png |only 18 files changed, 77 insertions(+), 65 deletions(-)
Title: Embedded JavaScript Engine for R
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 1.0.1 dated 2016-04-04 and 1.0.2 dated 2016-06-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ build/vignette.rds |binary vignettes/npm.Rmd | 2 +- 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-
products matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). The related 'candisc' package
provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.3-0 dated 2016-06-04 and 1.3-1 dated 2016-06-14
DESCRIPTION | 12 MD5 | 156 +-- NAMESPACE | 1 NEWS | 12 R/plot.robmlm.R |only build/vignette.rds |binary data/AddHealth.RData |binary data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/NeuroCog.RData |binary data/Oslo.RData |binary data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/SocialCog.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/doc/HE-examples.R | 1098 +++++++++++++-------------- inst/doc/HE-examples.Rnw | 12 inst/doc/HE-examples.pdf |binary inst/doc/repeated.R | 1266 ++++++++++++++++---------------- inst/doc/repeated.pdf |binary man/heplot-package.Rd | 4 man/plot.robmlm.Rd |only vignettes/HE-examples.Rnw | 10 vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 80 files changed, 1294 insertions(+), 1277 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. parallel processing and distributed processing on
compute clusters. The purpose of this package is to provide a lightweight
interface for using futures in R. Functions 'future()' and 'value()' exist for
creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(c(0.28,0), side=2) })' and 'v <- value(f)'.
The 'resolved()' function can be used to check if a future is resolved or not.
An infix assignment operator '%<-%' exists for creating futures whose values
are accessible by the assigned variables (as promises), e.g.
'v %<-% { mandelbrot(c(0.28,0), side=2) }'.
This package implements synchronous "lazy" and "eager" futures, and asynchronous
"multicore", "multisession" and ad hoc "cluster" futures.
Globals variables and functions are automatically identified and exported.
Required packages are attached in external R sessions whenever needed.
All types of futures are designed to behave the same such that the exact
same code work regardless of futures used or number of cores, background
sessions or cluster nodes available.
Additional types of futures are provided by other packages enhancing
this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.14.0 dated 2016-05-16 and 0.15.0 dated 2016-06-14
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Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer).
Author: Steven P. Millard <EnvStats@ProbStatInfo.com>
Maintainer: Steven P. Millard <EnvStats@ProbStatInfo.com>
Diff between EnvStats versions 2.1.0 dated 2016-04-18 and 2.1.1 dated 2016-06-14
DESCRIPTION | 8 MD5 | 504 +++++++++---------- NEWS | 52 + R/elnormAltMultiplyCensored.R | 8 R/elnormAltSinglyCensored.R | 9 R/elnormMultiplyCensored.R | 8 R/elnormSinglyCensored.R | 11 R/enormMultiplyCensored.R | 10 R/enormSinglyCensored.R | 13 R/stripChart.default.R | 110 ++-- R/summaryStats.default.R | 106 +++ data/ACE.13.TCE.df.rda |binary data/Air.df.rda |binary data/Benthic.df.rda |binary data/Distribution.df.rda |binary data/EPA.02d.Ex.2.ug.per.L.vec.rda |binary data/EPA.02d.Ex.4.mg.per.kg.vec.rda |binary data/EPA.02d.Ex.6.mg.per.kg.vec.rda |binary data/EPA.02d.Ex.9.mg.per.L.vec.rda |binary data/EPA.09.Ex.10.1.nickel.df.rda |binary data/EPA.09.Ex.11.1.arsenic.df.rda |binary data/EPA.09.Ex.12.1.ccl4.df.rda |binary data/EPA.09.Ex.12.4.naphthalene.df.rda |binary data/EPA.09.Ex.13.1.iron.df.rda |binary data/EPA.09.Ex.14.1.manganese.df.rda |binary data/EPA.09.Ex.14.3.alkalinity.df.rda |binary data/EPA.09.Ex.14.4.arsenic.df.rda |binary data/EPA.09.Ex.14.8.df.rda |binary data/EPA.09.Ex.15.1.manganese.df.rda |binary data/EPA.09.Ex.16.1.sulfate.df.rda |binary data/EPA.09.Ex.16.2.benzene.df.rda |binary data/EPA.09.Ex.16.4.copper.df.rda |binary data/EPA.09.Ex.16.5.PCE.df.rda |binary data/EPA.09.Ex.17.1.loglead.df.rda |binary data/EPA.09.Ex.17.2.toluene.df.rda |binary data/EPA.09.Ex.17.3.chrysene.df.rda |binary data/EPA.09.Ex.17.3.log.chrysene.df.rda |binary data/EPA.09.Ex.17.4.copper.df.rda |binary data/EPA.09.Ex.17.5.chloride.df.rda |binary data/EPA.09.Ex.17.6.sulfate.df.rda |binary data/EPA.09.Ex.17.7.sodium.df.rda |binary data/EPA.09.Ex.18.1.arsenic.df.rda |binary data/EPA.09.Ex.18.2.chrysene.df.rda |binary data/EPA.09.Ex.18.3.TCE.df.rda |binary data/EPA.09.Ex.18.4.xylene.df.rda |binary data/EPA.09.Ex.19.1.sulfate.df.rda |binary data/EPA.09.Ex.19.2.chloride.df.rda |binary data/EPA.09.Ex.19.5.mercury.df.rda |binary data/EPA.09.Ex.20.1.nickel.df.rda |binary data/EPA.09.Ex.21.1.aldicarb.df.rda |binary data/EPA.09.Ex.21.2.benzene.df.rda |binary data/EPA.09.Ex.21.5.beryllium.df.rda |binary data/EPA.09.Ex.21.6.nitrate.df.rda |binary data/EPA.09.Ex.21.7.TCE.df.rda |binary data/EPA.09.Ex.22.1.VC.df.rda |binary data/EPA.09.Ex.22.2.Specific.Conductance.df.rda |binary data/EPA.09.Ex.6.3.sulfate.df.rda |binary data/EPA.09.Ex.7.1.arsenic.df.rda |binary data/EPA.09.Table.9.1.TCE.df.rda |binary data/EPA.09.Table.9.3.df.rda |binary data/EPA.09.Table.9.4.nickel.vec.rda |binary data/EPA.89b.aldicarb1.df.rda |binary data/EPA.89b.aldicarb2.df.rda |binary data/EPA.89b.benzene.df.rda |binary data/EPA.89b.cadmium.df.rda |binary data/EPA.89b.chlordane1.df.rda |binary data/EPA.89b.chlordane2.df.rda |binary data/EPA.89b.edb.df.rda |binary data/EPA.89b.lead.df.rda |binary data/EPA.89b.loglead.df.rda |binary data/EPA.89b.manganese.df.rda |binary data/EPA.89b.sulfate.df.rda |binary data/EPA.89b.t29.df.rda |binary data/EPA.89b.toc.vec.rda |binary data/EPA.92c.arsenic1.df.rda |binary data/EPA.92c.arsenic2.df.rda |binary data/EPA.92c.arsenic3.df.rda |binary data/EPA.92c.benzene1.df.rda |binary data/EPA.92c.benzene2.df.rda |binary data/EPA.92c.ccl4.df.rda |binary data/EPA.92c.chrysene.df.rda |binary data/EPA.92c.copper1.df.rda |binary data/EPA.92c.copper2.df.rda |binary data/EPA.92c.lognickel1.df.rda |binary data/EPA.92c.nickel1.df.rda |binary data/EPA.92c.nickel2.df.rda |binary data/EPA.92c.toluene.df.rda |binary data/EPA.92c.zinc.df.rda |binary data/EPA.92d.chromium.df.rda |binary data/EPA.92d.chromium.vec.rda |binary data/EPA.94b.lead.df.rda |binary data/EPA.94b.tccb.df.rda |binary data/EPA.97.cadmium.111.df.rda |binary data/Environmental.df.rda |binary data/Gibbons.et.al.09.Alkilinity.vec.rda |binary data/Gibbons.et.al.09.Vinyl.Chloride.vec.rda |binary data/Graham.et.al.75.etu.df.rda |binary data/Helsel.Cohn.88.app.b.df.rda |binary data/Helsel.Cohn.88.silver.df.rda |binary data/Helsel.Hirsch.02.Mayfly.df.rda |binary data/Lin.Evans.80.df.rda |binary data/Millard.Deverel.88.df.rda |binary data/Modified.TcCB.df.rda |binary data/NIOSH.89.air.lead.vec.rda |binary data/Olympic.NH4.df.rda |binary data/Ozone.NE.df.rda |binary data/Refinery.CO.df.rda |binary data/Skagit.NH3_N.df.rda |binary data/Total.P.df.rda |binary inst/doc/EnvStats-manual.pdf |binary man/EVD.Rd | 2 man/Empirical.Rd | 5 man/EnvStats-package.Rd | 4 man/Lognormal3.Rd | 2 man/LognormalMixAlt.Rd | 8 man/boxcoxCensored.Rd | 19 man/cdfCompare.Rd | 44 - 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Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for
Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>
Diff between TipDatingBeast versions 1.0-3 dated 2016-06-06 and 1.0-4 dated 2016-06-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TaxaOut.R | 4 ++-- R/TaxonOut.R | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
More information about TipDatingBeast at CRAN
Permanent link
Title: Trimmed Elemental Estimation for Linear Models
Description: For fitting multiple linear regressions, the ordinary least squares approach is sensitive to outliers and/or violations of model assumptions. The trimmed elemental estimators are more robust to such situations. This package contains functions for computing the trimmed elemental estimates, as well as for creating the bias-corrected and accelerated bootstrap confidence intervals based on elemental regressions.
Author: Wei Jiang and Matthew S. Mayo
Maintainer: Wei Jiang <wjiang@kumc.edu>
Diff between TEEReg versions 1.0 dated 2014-10-07 and 1.1 dated 2016-06-14
DESCRIPTION | 11 +- MD5 | 16 +-- NAMESPACE | 6 + R/TEE.BCa.R | 217 +++++++++++++++++++++--------------------- R/TEE.R | 257 +++++++++++++++++++++++++------------------------- data/telephone.rda |binary man/TEE.BCa.Rd | 2 man/TEEReg-package.Rd | 8 - man/telephone.Rd | 2 9 files changed, 264 insertions(+), 255 deletions(-)
Title: Perform JIVE Decompositions for Multi-Source Data
Description: Performs the JIVE decompositions on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data. It provides two methods of rank selection when the rank is unknown, a permutation test and a BIC selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.
Author: Michael J. O'Connell and Eric F. Lock
Maintainer: Michael J. O'Connell <oconn725@umn.edu>
Diff between r.jive versions 1.4 dated 2016-04-10 and 1.5 dated 2016-06-14
DESCRIPTION | 8 +++---- MD5 | 30 +++++++++++++-------------- inst/doc/BRCA_Example.Rmd | 49 ++++++++++++++++++++++++--------------------- inst/doc/BRCA_Example.html | 45 ++++++++++++++++++++++------------------- man/Data.Rd | 2 + man/SimData.Rd | 2 + man/SimResults.Rd | 2 + man/jive.Rd | 2 + man/plot.jive.Rd | 2 + man/r.jive-package.Rd | 7 +++--- man/show.image.Rd | 2 + man/showHeatmaps.Rd | 2 + man/showVarExplained.Rd | 2 + man/summary.jive.Rd | 2 + vignettes/BRCA_Example.Rmd | 34 +++++++++++++++---------------- vignettes/rjive_bib.bib | 13 +++++++++++ 16 files changed, 121 insertions(+), 83 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.6 dated 2016-03-30 and 1.7 dated 2016-06-14
DESCRIPTION | 14 - MD5 | 35 ++- NAMESPACE | 3 R/hisse.R | 72 +++++--- R/hisseNull4.R | 55 ++++-- R/marginRecon.R | 8 R/plotHisse.R | 3 R/simulateHisse.R | 7 R/supportRegion.R | 458 +++++++++++++++++++++++++++++++-------------------- build/vignette.rds |binary man/hisse.Rd | 12 + man/hisseNull4.Rd | 14 + man/marginRecon.Rd | 2 man/plotHisse.Rd | 4 man/simToPhylo.Rd | 2 man/simulateHisse.Rd | 2 man/supportRegion.Rd | 2 tests |only 18 files changed, 447 insertions(+), 246 deletions(-)