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Title: Wrapper for the SkyWatch API
Description: Query and download satellite imagery and climate/atmospheric datasets using the SkyWatch API.
Search datasets by wavelength (band), cloud cover, resolution, location, date, etc.
Get the query results as data frame and as HTML. To learn more about the SkyWatch API, see <https://github.com/skywatchspaceapps/api>.
Author: Ali Santacruz, SkyWatch API Developers
Maintainer: Ali Santacruz <amsantac@unal.edu.co>
Diff between SkyWatchr versions 0.5-0 dated 2016-12-04 and 0.5-1 dated 2017-01-08
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ R/downloadSW.R | 2 +- R/getPolygon.R |only R/querySW.R | 10 +++++++++- man/SkyWatchr-package.Rd | 4 ++-- man/downloadSW.Rd | 5 ++++- man/getPolygon.Rd |only man/querySW.Rd | 44 +++++++++++++++++++++++++------------------- 9 files changed, 53 insertions(+), 34 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.1.0 dated 2016-12-12 and 0.2.0 dated 2017-01-08
ChangeLog | 54 ++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 13 ++++++----- MD5 | 29 +++++++++++++++---------- R/RcppExports.R | 10 +++++++- R/init.R |only inst/NEWS.Rd | 25 ++++++++++++++++++---- inst/include/get_time.h |only man/RcppCCTZ-package.Rd | 17 +++++++++++---- man/formatDatetime.Rd | 10 ++++++++ src/Makevars.win |only src/RcppExports.cpp | 7 ++---- src/examples.cpp | 23 ++++++++++---------- src/time_zone_format.cc | 35 ++++++++++++++++++++++++------- src/time_zone_info.cc | 2 - src/time_zone_libc.cc | 3 ++ src/utilities.cpp | 18 +++++++++------- tests |only 17 files changed, 187 insertions(+), 59 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). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith' plots). Constructs Re-Os, Sm-Nd and Rb-Sr isochrons. Future versions will include functionality for Lu-Hf and U-series dating methods. 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 0.9 dated 2016-12-21 and 0.10 dated 2017-01-08
DESCRIPTION | 8 +- MD5 | 83 +++++++++++++------------- NAMESPACE | 20 +++++- R/ArAr.R | 18 ++++- R/PD.R |only R/RbSr.R | 161 +++++++++++++++++++------------------------------- R/ReOs.R | 56 +++++------------ R/SmNd.R |only R/age.R | 91 +++++++++++++++++++--------- R/agespectrum.R | 13 ++-- R/cad.R | 37 ++++++++++- R/concordia.R | 4 - R/constants.R | 51 ++++++++++----- R/documentation.R | 49 ++++++++++----- R/errorellipse.R | 5 - R/fissiontracks.R | 6 - R/helioplot.R | 3 R/io.R | 56 +++++++++++++++-- R/isochron.R | 59 +++++++++++++++--- R/kde.R | 69 ++++++++++++++++++--- R/peakfit.R | 128 +++++++++++++++++++++++----------------- R/radialplot.R | 166 +++++++++++++++++++++++++++++++++++----------------- R/regression.R | 25 ++++--- R/weightedmean.R | 146 +++++++++++++++++++++++++++++++-------------- data/examples.rda |binary inst/RbSr.csv | 25 +++++-- inst/ReOs.csv | 16 ++--- inst/SmNd.csv |only inst/constants.json | 18 ++++- man/age.Rd | 68 ++++++++++++++------- man/agespectrum.Rd | 8 ++ man/cad.Rd | 25 ++++++- man/concordia.Rd | 4 - man/ellipse.Rd | 6 + man/examples.Rd | 43 +++++++++---- man/helioplot.Rd | 4 + man/isochron.Rd | 20 +++++- man/kde.Rd | 39 ++++++++++-- man/peakfit.Rd | 52 +++++++++++----- man/radialplot.Rd | 30 +++++++-- man/read.data.Rd | 15 +++- man/settings.Rd | 51 ++++++++++----- man/weightedmean.Rd | 31 ++++++++- man/yorkfit.Rd | 21 +++--- 44 files changed, 1154 insertions(+), 576 deletions(-)
Title: R Interface to the Europe PubMed Central RESTful Web Service
Description: An R Client for the Europe PubMed Central RESTful Web Service. It
gives access to both metadata on life science literature and open access
full texts. Europe PMC indexes all PubMed content and other literature
sources including Agricola, a bibliographic database of citations to the
agricultural literature, or Biological Patents. In addition to bibliographic
metadata, the client allows users to fetch citations and reference lists.
Links between life-science literature and other EBI databases, including
ENA, PDB or ChEMBL are also accessible. No registration or API key is
required. See the vignettes for usage examples.
Author: Najko Jahn [aut, cre, cph]
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between europepmc versions 0.1.1 dated 2017-01-06 and 0.1.2 dated 2017-01-08
DESCRIPTION | 8 +-- MD5 | 31 +++++++------ NAMESPACE | 4 + NEWS.md | 6 ++ R/epmc_ftxt.r | 3 - R/epmc_ftxt_book.r | 3 - R/epmc_profile.r |only R/europepmc.r | 6 +- R/utils.r | 38 +++++++++++++++- README.md | 58 +++++++++++++++++++----- inst/doc/introducing-europepmc.R | 3 + inst/doc/introducing-europepmc.Rmd | 61 +++++++++++-------------- inst/doc/introducing-europepmc.html | 83 ++++++++++++++++++++++++++--------- man/epmc_profile.Rd |only man/europepmc.Rd | 2 tests/testthat/test_epmc_ftxt_book.r | 21 ++++---- tests/testthat/test_epmc_profile.r |only vignettes/introducing-europepmc.Rmd | 61 +++++++++++-------------- 18 files changed, 253 insertions(+), 135 deletions(-)
Title: Big Data in-Database Analytics that Scales with Teradata Aster
Distributed Platform
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of parallel SQL, SQL-MR and
SQL-GR executing in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, networks, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most visualizations.
Author: Gregory Kanevsky [aut, cre]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.5.4 dated 2016-11-07 and 0.5.5 dated 2017-01-08
DESCRIPTION | 15 - MD5 | 50 ++--- NAMESPACE | 1 NEWS | 21 ++ R/computeGraph.R | 69 ++++++- R/computeGraphClusters.R | 4 R/computeKmeans.R | 62 ++++++- R/plotting.R | 3 R/plottingKmeans.R | 55 +++++- R/toaster.R | 2 R/utils.R | 24 +- R/validateGraph.R | 2 man/computeCanopy.Rd | 20 ++ man/computeClusterSample.Rd | 14 + man/computeGraph.Rd | 9 - man/createBubblechart.Rd | 2 man/createCentroidPlot.Rd | 25 +- man/isTable.Rd | 7 man/toaGraph.Rd | 17 + tests/testthat/test-computeGraph.R | 271 ++++++++++++++++++++++++++++++- tests/testthat/test-computeKmeans.R | 85 +++++++++ tests/testthat/test-createBoxplot.R | 6 tests/testthat/test-createClusterPlots.R | 30 +++ tests/testthat/test-createPopPyramid.R | 5 tests/testthat/test-showData.R | 4 tests/testthat/test-utils.R | 18 +- 26 files changed, 707 insertions(+), 114 deletions(-)
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The
source for the 'SQLite' engine (version 3.8.8.2) is included.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [cph],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 1.1-1 dated 2016-12-10 and 1.1-2 dated 2017-01-08
DESCRIPTION | 8 +- MD5 | 65 ++++++++--------- NEWS.md | 8 +- R/table.R | 4 + inst/doc/RSQLite.html | 20 +++-- man/SQLite.Rd | 1 man/SQLiteConnection-class.Rd | 1 man/SQLiteDriver-class.Rd | 1 man/SQLiteResult-class.Rd | 1 man/datasetsDb.Rd | 1 man/dbBeginTransaction.Rd | 1 man/dbDataType-SQLiteDriver-method.Rd | 1 man/dbExistsTable-SQLiteConnection-character-method.Rd | 1 man/dbGetInfo.Rd | 1 man/dbListFields-SQLiteConnection-character-method.Rd | 1 man/dbListResults-SQLiteConnection-method.Rd | 1 man/dbReadTable-SQLiteConnection-character-method.Rd | 13 +-- man/dbRemoveTable-SQLiteConnection-character-method.Rd | 1 man/dbWriteTable.Rd | 1 man/dummy-methods.Rd | 3 man/fetch-SQLiteResult-method.Rd | 1 man/initExtension.Rd | 2 man/isIdCurrent.Rd | 1 man/make.db.names-SQLiteConnection-character-method.Rd | 1 man/query-dep.Rd | 1 man/rsqliteVersion.Rd | 1 man/sqlite-meta.Rd | 1 man/sqlite-query.Rd | 13 +-- man/sqlite-transaction.Rd | 1 man/sqliteBuildTableDefinition.Rd | 1 man/sqliteCopyDatabase.Rd | 1 man/sqliteQuickColumn.Rd | 1 src/sqlite3/sqlite3.h.orig |only tests/testthat/helper-astyle.R | 9 +- 34 files changed, 82 insertions(+), 86 deletions(-)
Title: Nested and Crossed Block Designs for Unstructured and Factorial
Treatment Sets
Description: Constructs randomized nested row-and-column type block designs
with arbitrary depth of nesting for arbitrary factorial or fractional
factorial treatment designs. The treatment model can be defined
by a models.matrix formula which allows any feasible
combination of quantitative or qualitative model terms.
Any feasible design size can be defined and, where necessary,
a D-optimal swapping routine will find the best fraction for the required
design size. Blocks are nested hierarchically in successive strata and the
blocks model in any particular stratum will comprise either a simple nested blocks
design or a crossed row-and-column blocks design. Block sizes in any one stratum
are either all equal or differ, at most, by one plot. The design outputs
include a data frame showing the allocation of treatments to blocks, a table
showing block levels, the fractional design efficiency,
the achieved D-efficiency, the achieved A-efficiency
(unstructured treatments only) and A-efficiency upper bounds, where available,
for each stratum in the design. For designs with simple unstructured treatments,
a plan layout showing the allocation of treatments to blocks or to rows and
columns in the bottom stratum of the design is also given.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 2.3 dated 2016-12-09 and 2.4 dated 2017-01-08
DESCRIPTION | 28 +++-- MD5 | 6 - R/blocks.r | 276 ++++++++++++++++++++++++++++++++++++++++------------------ man/blocks.Rd | 137 ++++++++++++++++------------ 4 files changed, 287 insertions(+), 160 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.7-2 dated 2016-08-29 and 2.8-0 dated 2017-01-08
BiodiversityR-2.7-2/BiodiversityR/R/ensemble.test.R |only BiodiversityR-2.7-2/BiodiversityR/R/ensemble.test.gbm.R |only BiodiversityR-2.7-2/BiodiversityR/R/ensemble.test.nnet.R |only BiodiversityR-2.7-2/BiodiversityR/R/ensemble.test.splits.R |only BiodiversityR-2.7-2/BiodiversityR/R/ordihull.centroids.R |only BiodiversityR-2.7-2/BiodiversityR/R/ordispider.centroids.R |only BiodiversityR-2.8-0/BiodiversityR/DESCRIPTION | 17 BiodiversityR-2.8-0/BiodiversityR/MD5 | 116 BiodiversityR-2.8-0/BiodiversityR/NAMESPACE | 22 BiodiversityR-2.8-0/BiodiversityR/R/BiodiversityRGUI.R | 19 BiodiversityR-2.8-0/BiodiversityR/R/diversitycomp.R | 85 BiodiversityR-2.8-0/BiodiversityR/R/diversityresult.R | 145 - BiodiversityR-2.8-0/BiodiversityR/R/ensemble.VIF.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.analogue.R | 15 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.batch.R | 233 + BiodiversityR-2.8-0/BiodiversityR/R/ensemble.batch.presence.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.bioclim.R | 43 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.bioclim.graph.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.calibrate.models.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.calibrate.models.gbm.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.calibrate.models.nnet.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.calibrate.weights.R |only BiodiversityR-2.8-0/BiodiversityR/R/ensemble.centroids.R | 24 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.drop1.R | 629 ++++ BiodiversityR-2.8-0/BiodiversityR/R/ensemble.dummy.variables.R | 32 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.ecocrop.R | 21 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.formulae.R | 70 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.habitat.change.R | 14 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.mean.R | 124 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.novel.R | 31 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.plot.R | 79 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.raster.R | 1048 +++++-- BiodiversityR-2.8-0/BiodiversityR/R/ensemble.simplified.categories.R | 7 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.strategy.R | 23 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.threshold.R | 82 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.weights.R | 2 BiodiversityR-2.8-0/BiodiversityR/R/ensemble.zones.R | 11 BiodiversityR-2.8-0/BiodiversityR/R/evaluation.strip.data.R | 407 +-- BiodiversityR-2.8-0/BiodiversityR/R/evaluation.strip.plot.R | 100 BiodiversityR-2.8-0/BiodiversityR/R/rankabundance.R | 4 BiodiversityR-2.8-0/BiodiversityR/R/renyiaccumresult.R | 33 BiodiversityR-2.8-0/BiodiversityR/R/renyicomp.R | 23 BiodiversityR-2.8-0/BiodiversityR/R/renyiplot.R | 10 BiodiversityR-2.8-0/BiodiversityR/R/renyiresult.R | 27 BiodiversityR-2.8-0/BiodiversityR/R/stackcommunitydataset.R |only BiodiversityR-2.8-0/BiodiversityR/R/subsetcomm.R | 2 BiodiversityR-2.8-0/BiodiversityR/R/zzz.R | 2 BiodiversityR-2.8-0/BiodiversityR/inst/ChangeLog | 128 BiodiversityR-2.8-0/BiodiversityR/inst/etc/BiodiversityGUI.R | 514 ++- BiodiversityR-2.8-0/BiodiversityR/inst/etc/BiodiversityR-menus.txt | 13 BiodiversityR-2.8-0/BiodiversityR/inst/etc/Rcmdr-menus.txt | 14 BiodiversityR-2.8-0/BiodiversityR/man/BiodiversityRGUI.Rd | 1347 ---------- BiodiversityR-2.8-0/BiodiversityR/man/CAPdiscrim.Rd | 6 BiodiversityR-2.8-0/BiodiversityR/man/balanced.specaccum.Rd | 8 BiodiversityR-2.8-0/BiodiversityR/man/diversityresult.Rd | 61 BiodiversityR-2.8-0/BiodiversityR/man/ensemble.Rd | 285 +- BiodiversityR-2.8-0/BiodiversityR/man/ensemble.batch.Rd | 101 BiodiversityR-2.8-0/BiodiversityR/man/ensemble.bioclim.Rd |only BiodiversityR-2.8-0/BiodiversityR/man/ensemble.bioclim.graph.Rd |only BiodiversityR-2.8-0/BiodiversityR/man/ensemble.dummy.variables.Rd | 35 BiodiversityR-2.8-0/BiodiversityR/man/ensemble.ecocrop.Rd | 32 BiodiversityR-2.8-0/BiodiversityR/man/ensemble.novel.Rd | 70 BiodiversityR-2.8-0/BiodiversityR/man/ensemble.raster.Rd | 169 - BiodiversityR-2.8-0/BiodiversityR/man/ensemble.zones.Rd | 52 BiodiversityR-2.8-0/BiodiversityR/man/evaluation.strip.Rd | 81 BiodiversityR-2.8-0/BiodiversityR/man/makecommunitydataset.Rd | 18 BiodiversityR-2.8-0/BiodiversityR/man/renyiresult.Rd | 19 67 files changed, 3550 insertions(+), 2903 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing quantitative financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'quantmod' and 'TTR' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre]
Maintainer: Matt Dancho <mdancho@gmail.com>
Diff between tidyquant versions 0.1.0 dated 2016-12-31 and 0.2.0 dated 2017-01-08
DESCRIPTION | 20 - MD5 | 37 - NAMESPACE | 3 NEWS.md | 9 R/global_vars.R | 20 - R/tidyquant.R | 3 R/tq_get.R | 276 ++++++++------ R/tq_mutate.R | 185 +++++++-- R/tq_transform.R | 137 ++++--- README.md | 319 ++++++++++------ inst/doc/tidyquant.R | 84 +++- inst/doc/tidyquant.Rmd | 166 ++++++-- inst/doc/tidyquant.html | 617 ++++++++++++++++++-------------- man/tq_get.Rd | 32 + man/tq_mutate.Rd | 30 - man/tq_transform.Rd | 30 - tests/testthat/test_tq_get_key_ratios.R |only tests/testthat/test_tq_mutate.R | 66 ++- tests/testthat/test_tq_transform.R | 42 +- vignettes/tidyquant.Rmd | 166 ++++++-- 20 files changed, 1453 insertions(+), 789 deletions(-)
Title: A Toolbox for Systemic Risk
Description: A toolbox for systemic risk based on liabilities matrices. Contains
a Gibbs sampler for liabilities matrices where only row and column sums of the
liabilities matrix as well as some other fixed entries are observed. Includes models
for power law distribution on the degree distribution.
Author: Axel Gandy and Luitgard A.M. Veraart
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between systemicrisk versions 0.3 dated 2015-12-21 and 0.4 dated 2017-01-08
DESCRIPTION | 8 ++--- MD5 | 33 +++++++++++--------- NAMESPACE | 2 + R/AdjustableModels.R |only R/ExponentialFitnessLinkFun.R | 12 +++---- R/HierarchicalModels.R | 13 +++++--- R/RcppExports.R | 6 +-- inst/NEWS.Rd | 11 ++++++ inst/doc/HierarchicalModels.Rmd |binary inst/doc/HierarchicalModels.html | 56 ++++++++++++----------------------- inst/doc/Introduction.html | 14 ++++---- man/calibrate_ER.Rd |only man/calibrate_FitnessEmp.Rd |only man/findFeasibleMatrix.Rd | 4 +- man/findFeasibleMatrix_targetmean.Rd | 4 +- man/sample_HierarchicalModel.Rd | 5 ++- src/RcppExports.cpp | 22 ++++++------- src/lib_FeasibleMatrix.cpp | 6 +-- vignettes/HierarchicalModels.Rmd |binary 19 files changed, 100 insertions(+), 96 deletions(-)
Title: Estimation for Multivariate Normal and Student-t Data with
Monotone Missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is monotone.
Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions fail,
the package can handle a nearly arbitrary amount of missing data.
The current version supports maximum likelihood inference and
a full Bayesian approach employing scale-mixtures for Gibbs sampling.
Monotone data augmentation extends this
Bayesian approach to arbitrary missingness patterns.
A fully functional standalone interface to the Bayesian lasso
(from Park & Casella), Normal-Gamma (from Griffin & Brown),
Horseshoe (from Carvalho, Polson, & Scott), and ridge regression
with model selection via Reversible Jump, and student-t errors
(from Geweke) is also provided.
Author: Robert B. Gramacy <rbg@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between monomvn versions 1.9-6 dated 2016-02-10 and 1.9-7 dated 2017-01-08
ChangeLog | 7 +++++++ DESCRIPTION | 12 ++++++------ MD5 | 40 ++++++++++++++++++++-------------------- R/monomvn.s3.R | 2 +- data/cement.rda |binary man/blasso.Rd | 2 +- man/blasso.s3.Rd | 2 +- man/bmonomvn.Rd | 2 +- man/default.QP.Rd | 2 +- man/metrics.Rd | 2 +- man/monomvn-package.Rd | 4 ++-- man/monomvn.Rd | 2 +- man/monomvn.s3.Rd | 2 +- man/monomvn.solve.QP.Rd | 2 +- man/plot.monomvn.Rd | 2 +- man/randmvn.Rd | 2 +- man/regress.Rd | 2 +- man/rmono.Rd | 2 +- src/blasso.cc | 2 +- src/nu.c | 2 +- src/ustructs.cc | 2 +- 21 files changed, 51 insertions(+), 44 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <jasson@toulouse.inra.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.5-12 dated 2014-07-28 and 0.5-13 dated 2017-01-08
gmp-0.5-12/gmp/Done |only gmp-0.5-13/gmp/ChangeLog | 22 +++++ gmp-0.5-13/gmp/DESCRIPTION | 9 +- gmp-0.5-13/gmp/MD5 | 45 +++++------- gmp-0.5-13/gmp/NAMESPACE | 33 ++++++-- gmp-0.5-13/gmp/R/AllClasses-etc.R | 2 gmp-0.5-13/gmp/R/biginteger.R | 46 ++++++------ gmp-0.5-13/gmp/R/bigq.R | 35 +++++++-- gmp-0.5-13/gmp/R/matrix-prods.R | 12 +-- gmp-0.5-13/gmp/TODO | 64 ++++++++--------- gmp-0.5-13/gmp/man/gcd.Rd | 14 ++- gmp-0.5-13/gmp/man/gcdex.Rd | 17 +--- gmp-0.5-13/gmp/man/matrix.Rd | 1 gmp-0.5-13/gmp/man/solve.Rd | 41 ++++++---- gmp-0.5-13/gmp/src/Rgmp.h | 2 gmp-0.5-13/gmp/src/apply.cc | 4 - gmp-0.5-13/gmp/src/bigintegerR.cc | 6 - gmp-0.5-13/gmp/src/bigmod.h | 2 gmp-0.5-13/gmp/src/matrix.cc | 10 ++ gmp-0.5-13/gmp/src/matrixq.h | 3 gmp-0.5-13/gmp/tests/arith-ex.R | 85 ++++++++++++++-------- gmp-0.5-13/gmp/tests/basic-ex.R | 64 +++++++++++++++-- gmp-0.5-13/gmp/tests/gmp-test.R | 15 ++-- gmp-0.5-13/gmp/tests/gmp-test.Rout.save | 120 ++++++++++++++------------------ 24 files changed, 401 insertions(+), 251 deletions(-)
Title: 'Lex' and 'Yacc'
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph], Yasutaka Tanaka [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.4.1 dated 2017-01-07 and 1.4.2 dated 2017-01-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/yacc.R | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the personality-project.org/r web page.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 1.6.9 dated 2016-09-17 and 1.6.12 dated 2017-01-08
DESCRIPTION | 10 - MD5 | 135 +++++++++-------- NAMESPACE | 7 R/Promax.R | 3 R/alpha.R | 7 R/correct.cor.R | 2 R/densityBy.r | 10 - R/errorCircles.r | 6 R/esem.R | 77 ++++++++-- R/fa.R | 17 +- R/fa.parallel.R | 12 - R/factor.scores.R | 20 ++ R/factor.stats.R | 8 - R/irt.fa.R | 2 R/kaiser.R | 6 R/kappa.R | 4 R/mediate.r | 57 +++++-- R/misc.R | 31 ++++ R/omega.R | 10 - R/omega.diagram.R | 8 - R/omega.sem.R | 38 +++-- R/omegaSem.R | 72 +++++++-- R/polychoric.R | 4 R/principal.R | 2 R/print.psych.fa.R | 2 R/print.psych.omega.R | 45 +++++ R/print.psych.vss.R | 21 ++ R/schmid.R | 60 ++++++- R/score.irt.r | 333 ++++++++++++++++++++++++++++++++------------ R/score.items.R | 41 +++-- R/structure.diagram.R | 16 +- R/summary.psych.R | 29 +++ data/Reise.rda |binary data/Thurstone.33.rda |binary data/Thurstone.rda |binary data/cattell.rda |only inst/CITATION | 4 inst/NEWS.Rd | 66 ++++++++ inst/doc/overview.R | 6 inst/doc/overview.Rnw | 6 inst/doc/overview.pdf |binary inst/doc/psych_for_sem.R | 10 - inst/doc/psych_for_sem.Rnw | 12 - inst/doc/psych_for_sem.pdf |binary man/KMO.Rd | 11 + man/Promax.Rd | 7 man/bifactor.Rd | 5 man/cattell.Rd |only man/cortest.bartlett.Rd | 4 man/densityBy.Rd | 5 man/deprecated.Rd |only man/dfOrder.Rd |only man/error.circles.Rd | 8 - man/esem.Rd | 25 +++ man/fa.Rd | 39 +---- man/fa.parallel.Rd | 5 man/factor.scores.Rd | 15 + man/irt.fa.Rd | 4 man/kaiser.Rd | 9 - man/kappa.Rd | 11 + man/misc.Rd | 10 + man/omega.Rd | 38 +++-- man/principal.Rd | 11 - man/read.clipboard.Rd | 12 + man/schmid.Rd | 2 man/score.irt.Rd | 10 - man/score.items.Rd | 13 + man/sim.hierarchical.Rd | 2 man/test.irt.Rd |only vignettes/overview.Rnw | 6 vignettes/psych_for_sem.Rnw | 12 - 71 files changed, 1071 insertions(+), 392 deletions(-)
Title: Low Memory Use Trimmed K-Means
Description: Performs the trimmed k-means clustering algorithm with lower memory use. It also provides a number of utility functions such as BIC calculations.
Author: Andrew Thomas Jones, Hien Duy Nguyen
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between lowmemtkmeans versions 0.1.1 dated 2016-09-15 and 0.1.2 dated 2017-01-08
DESCRIPTION | 6 ++--- MD5 | 23 ++++++++++---------- NEWS.md | 4 +-- R/RcppExports.R | 2 - src/RcppExports.cpp | 34 +++++++++++++++--------------- src/tkmeans.cpp | 43 ++++++++++++++++++++++++++++++++------ tests/testthat/test_BIC_one.rds |binary tests/testthat/test_clust_one.rds |binary tests/testthat/test_four.rds |only tests/testthat/test_multi_one.rds |binary tests/testthat/test_one.rds |binary tests/testthat/test_three.rds |binary tests/testthat/test_two.rds |binary 13 files changed, 72 insertions(+), 40 deletions(-)
Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression
models, with the support of reproducible survival model building,
validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre],
Qingsong Xu [aut],
Miaozhu Li [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 4.5 dated 2016-12-25 and 4.6 dated 2017-01-08
hdnom-4.5/hdnom/R/1.hdnom.models.R |only hdnom-4.5/hdnom/R/10.hdnom.compare.calibrate.R |only hdnom-4.5/hdnom/R/11.hdnom.color.palette.R |only hdnom-4.5/hdnom/R/2.hdnom.nomogram.R |only hdnom-4.5/hdnom/R/3.hdnom.validate.R |only hdnom-4.5/hdnom/R/4.hdnom.calibrate.R |only hdnom-4.5/hdnom/R/5.hdnom.external.validate.R |only hdnom-4.5/hdnom/R/6.hdnom.external.calibrate.R |only hdnom-4.5/hdnom/R/7.hdnom.kmplot.R |only hdnom-4.5/hdnom/R/8.hdnom.logrank.R |only hdnom-4.5/hdnom/R/9.hdnom.compare.validate.R |only hdnom-4.5/hdnom/vignettes/aenetfit.rds |only hdnom-4.6/hdnom/DESCRIPTION | 20 - hdnom-4.6/hdnom/MD5 | 185 +++++----- hdnom-4.6/hdnom/NAMESPACE | 2 hdnom-4.6/hdnom/NEWS.md | 38 +- hdnom-4.6/hdnom/R/01-hdnom-models.R |only hdnom-4.6/hdnom/R/02-hdnom-nomogram.R |only hdnom-4.6/hdnom/R/03-hdnom-validate.R |only hdnom-4.6/hdnom/R/04-hdnom-calibrate.R |only hdnom-4.6/hdnom/R/05-hdnom-external-validate.R |only hdnom-4.6/hdnom/R/06-hdnom-external-calibrate.R |only hdnom-4.6/hdnom/R/07-hdnom-kmplot.R |only hdnom-4.6/hdnom/R/08-hdnom-logrank.R |only hdnom-4.6/hdnom/R/09-hdnom-compare-validate.R |only hdnom-4.6/hdnom/R/10-hdnom-compare-calibrate.R |only hdnom-4.6/hdnom/R/11-hdnom-color-palette.R |only hdnom-4.6/hdnom/R/hdnom-package.R | 6 hdnom-4.6/hdnom/README.md | 29 + hdnom-4.6/hdnom/build/vignette.rds |binary hdnom-4.6/hdnom/inst/doc/hdnom.R | 28 - hdnom-4.6/hdnom/inst/doc/hdnom.Rmd | 34 - hdnom-4.6/hdnom/inst/doc/hdnom.html | 38 -- hdnom-4.6/hdnom/man/glmnet.basesurv.Rd | 2 hdnom-4.6/hdnom/man/glmnet.calibrate.internal.pred.Rd | 2 hdnom-4.6/hdnom/man/glmnet.external.calibrate.internal.pred.Rd | 2 hdnom-4.6/hdnom/man/glmnet.external.validate.internal.Rd | 2 hdnom-4.6/hdnom/man/glmnet.survcurve.Rd | 4 hdnom-4.6/hdnom/man/glmnet.tune.alpha.Rd | 2 hdnom-4.6/hdnom/man/glmnet.validate.internal.Rd | 2 hdnom-4.6/hdnom/man/hdcox.aenet.Rd | 13 hdnom-4.6/hdnom/man/hdcox.alasso.Rd | 11 hdnom-4.6/hdnom/man/hdcox.enet.Rd | 13 hdnom-4.6/hdnom/man/hdcox.flasso.Rd | 52 ++ hdnom-4.6/hdnom/man/hdcox.lasso.Rd | 11 hdnom-4.6/hdnom/man/hdcox.mcp.Rd | 18 hdnom-4.6/hdnom/man/hdcox.mnet.Rd | 23 - hdnom-4.6/hdnom/man/hdcox.scad.Rd | 18 hdnom-4.6/hdnom/man/hdcox.snet.Rd | 23 - hdnom-4.6/hdnom/man/hdnom-package.Rd | 6 hdnom-4.6/hdnom/man/hdnom.calibrate.Rd | 25 - hdnom-4.6/hdnom/man/hdnom.calibrate.internal.true.Rd | 2 hdnom-4.6/hdnom/man/hdnom.compare.calibrate.Rd | 2 hdnom-4.6/hdnom/man/hdnom.compare.validate.Rd | 2 hdnom-4.6/hdnom/man/hdnom.external.calibrate.Rd | 8 hdnom-4.6/hdnom/man/hdnom.external.calibrate.internal.true.Rd | 2 hdnom-4.6/hdnom/man/hdnom.external.validate.Rd | 8 hdnom-4.6/hdnom/man/hdnom.kmplot.Rd | 14 hdnom-4.6/hdnom/man/hdnom.logrank.Rd | 14 hdnom-4.6/hdnom/man/hdnom.nomogram.Rd | 31 - hdnom-4.6/hdnom/man/hdnom.validate.Rd | 18 hdnom-4.6/hdnom/man/hdnom.varinfo.Rd | 8 hdnom-4.6/hdnom/man/kmplot.Rd | 2 hdnom-4.6/hdnom/man/ncvreg.basesurv.Rd | 2 hdnom-4.6/hdnom/man/ncvreg.calibrate.internal.pred.Rd | 2 hdnom-4.6/hdnom/man/ncvreg.external.calibrate.internal.pred.Rd | 2 hdnom-4.6/hdnom/man/ncvreg.external.validate.internal.Rd | 2 hdnom-4.6/hdnom/man/ncvreg.survcurve.Rd | 4 hdnom-4.6/hdnom/man/ncvreg.tune.gamma.Rd | 4 hdnom-4.6/hdnom/man/ncvreg.tune.gamma.alpha.Rd | 4 hdnom-4.6/hdnom/man/ncvreg.validate.internal.Rd | 2 hdnom-4.6/hdnom/man/palette.aaas.Rd | 4 hdnom-4.6/hdnom/man/palette.jco.Rd | 4 hdnom-4.6/hdnom/man/palette.lancet.Rd | 4 hdnom-4.6/hdnom/man/palette.npg.Rd | 4 hdnom-4.6/hdnom/man/penalized.basesurv.Rd | 2 hdnom-4.6/hdnom/man/penalized.calibrate.internal.pred.Rd | 4 hdnom-4.6/hdnom/man/penalized.external.calibrate.internal.pred.Rd | 2 hdnom-4.6/hdnom/man/penalized.external.validate.internal.Rd | 2 hdnom-4.6/hdnom/man/penalized.survcurve.Rd | 2 hdnom-4.6/hdnom/man/penalized.tune.lambda.Rd |only hdnom-4.6/hdnom/man/penalized.validate.internal.Rd | 4 hdnom-4.6/hdnom/man/plot.hdnom.calibrate.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.compare.calibrate.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.compare.validate.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.external.calibrate.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.external.validate.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.nomogram.Rd | 2 hdnom-4.6/hdnom/man/plot.hdnom.validate.Rd | 2 hdnom-4.6/hdnom/man/predict.hdcox.model.Rd | 10 hdnom-4.6/hdnom/man/print.hdcox.model.Rd | 6 hdnom-4.6/hdnom/man/print.hdnom.calibrate.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.compare.calibrate.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.compare.validate.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.external.calibrate.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.external.validate.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.nomogram.Rd | 2 hdnom-4.6/hdnom/man/print.hdnom.validate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.calibrate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.compare.calibrate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.compare.validate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.external.calibrate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.external.validate.Rd | 2 hdnom-4.6/hdnom/man/summary.hdnom.validate.Rd | 2 hdnom-4.6/hdnom/vignettes/fit.rds |only hdnom-4.6/hdnom/vignettes/hdnom.Rmd | 34 - 106 files changed, 473 insertions(+), 391 deletions(-)
Title: A Fancy Version of 'base::cut'
Description: Provides the function fancycut() which is like cut() except
you can mix left open and right open intervals with point values,
intervals that are closed on both ends and intervals that are open on both ends.
Author: Adam Rich [aut, cre]
Maintainer: Adam Rich <adamleerich@gmail.com>
Diff between fancycut versions 0.1.0 dated 2015-11-09 and 0.1.1 dated 2017-01-08
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 2 +- NEWS |only R/fancycut.R | 28 +++++++++++++++++++++++++++- man/fancycut.Rd | 31 +++++++++++++++++++++---------- 6 files changed, 58 insertions(+), 20 deletions(-)
Title: Generation of IRT Response Patterns under Computerized Adaptive
Testing
Description: Provides routines for the generation of response patterns under unidimensional dichotomous and polytomous computerized adaptive testing (CAT) framework. It holds many standard functions to estimate ability, select the first item(s) to administer and optimally select the next item, as well as several stopping rules. Options to control for item exposure and content balancing are also available (Magis and Raiche (2012) <doi:10.18637/jss.v048.i08>).
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.11 dated 2016-11-16 and 3.12 dated 2017-01-08
DESCRIPTION | 10 - MD5 | 65 ++++---- NEWS | 45 ++++++ R/randomCAT.R | 196 ++++++++++++++++---------- R/simulateRespondents.R | 2 R/startItems.R | 64 ++++++-- R/testList.R | 331 +++++++++++++++++++++++---------------------- build |only inst/CITATION | 38 ++++- man/EPV.Rd | 11 - man/GDI.Rd | 7 man/Ii.Rd | 5 man/Ji.Rd | 6 man/KL.Rd | 9 - man/MEI.Rd | 11 - man/MWI.Rd | 13 - man/OIi.Rd | 7 man/Pi.Rd | 14 + man/breakBank.Rd | 4 man/checkStopRule.Rd | 4 man/eapEst.Rd | 7 man/eapSem.Rd | 6 man/genDichoMatrix.Rd | 5 man/genPattern.Rd | 5 man/genPolyMatrix.Rd | 15 +- man/nextItem.Rd | 29 ++- man/randomCAT.Rd | 57 ++++--- man/semTheta.Rd | 12 - man/simulateRespondents.Rd | 26 +-- man/startItems.Rd | 31 +++- man/tcals.Rd | 8 - man/test.cbList.Rd | 4 man/testList.Rd | 4 man/thetaEst.Rd | 18 +- 34 files changed, 646 insertions(+), 423 deletions(-)
Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>.
Author: Hana Sevcikova, Adrian Raftery, Jennifer Chunn
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesLife versions 3.0-3 dated 2016-12-02 and 3.0-4 dated 2017-01-08
ChangeLog | 14 +++++++++++--- DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ R/mcmc_estimate.R | 25 ++++++++++--------------- R/run_mcmc.R | 12 ++++++------ inst/ex-data/last.dump.rda |only man/bayesLife-package.Rd | 4 ++-- man/run.e0.mcmc.Rd | 4 +++- 8 files changed, 43 insertions(+), 37 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 3.0.0 dated 2016-12-01 and 3.1.0 dated 2017-01-08
DESCRIPTION | 18 MD5 | 128 +- NAMESPACE | 1 R/DBA.R | 420 +++---- R/GAK.R | 18 R/NCCc.R | 62 - R/SBD.R | 4 R/TADPole.R | 640 +++++------ R/all-cent.R | 526 ++++----- R/compute-envelop.R |only R/create-dtwclust.R | 2 R/cvi.R | 330 ++--- R/ddist.R | 4 R/dtw-basic.R | 39 R/dtw-lb.R | 466 ++++---- R/dtw2.R | 118 +- R/dtwclust-classes.R | 5 R/dtwclust-methods.R | 8 R/dtwclust.R | 1797 ++++++++++++++++---------------- R/fuzzy.R | 2 R/lb-improved.R | 532 ++++----- R/lb-keogh.R | 516 ++++----- R/partitional.R | 13 R/pkg.R | 361 +++--- R/reinterpolate.R | 92 - R/shape-extraction.R | 272 ++-- R/uciCT.R | 56 R/utils.R | 28 R/zscore.R | 110 - inst/NEWS.Rd | 21 inst/doc/dtwclust.Rnw | 34 inst/doc/dtwclust.pdf |binary inst/dtwclust-examples.R | 322 ++--- man/DBA.Rd | 9 man/GAK.Rd | 2 man/SBD.Rd | 4 man/TADPole.Rd | 2 man/compute_envelop.Rd |only man/dtw_basic.Rd | 9 man/dtw_lb.Rd | 23 man/dtwclust-class.Rd | 4 man/dtwclust-package.Rd | 7 man/dtwclust.Rd | 30 man/dtwclustFamily-class.Rd | 1 man/lb_improved.Rd | 6 man/lb_keogh.Rd | 10 man/shape_extraction.Rd | 4 src/dtw-basic.c | 134 +- src/logGAK.c | 6 tests/testthat.R | 26 tests/testthat/acceptance/dtwb.R | 164 +- tests/testthat/acceptance/gak.R | 138 +- tests/testthat/acceptance/lbs.R | 148 +- tests/testthat/integration/families.R | 662 ++++++----- tests/testthat/integration/proxy.R | 172 +-- tests/testthat/regression/clusterings.R | 148 +- tests/testthat/regression/dtwb.R | 54 tests/testthat/regression/proxy.R | 96 - tests/testthat/system/fuzzy.R | 137 +- tests/testthat/system/invalid-inputs.R | 389 +++--- tests/testthat/test-06-parallel.R | 128 +- tests/testthat/unit/cvis.R | 202 +-- tests/testthat/unit/distances.R | 324 ++--- tests/testthat/unit/methods.R | 130 +- vignettes/REFERENCES.bib | 21 vignettes/dtwclust.Rnw | 34 66 files changed, 5182 insertions(+), 4987 deletions(-)