Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre],
Matt Wand [ctb],
Jose Chacon [ctb],
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.11.4 dated 2019-02-20 and 1.11.5 dated 2019-05-20
CHANGELOG | 6 + DESCRIPTION | 17 +++- MD5 | 14 +-- R/kda.R | 207 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary inst/doc/kde.pdf |binary man/ks-package.Rd | 2 man/plot.kdde.Rd | 1 8 files changed, 128 insertions(+), 119 deletions(-)
Title: Detailed Statistics on Volleyball Matches
Description: Volleyball match statistics of the German volleyball first division league (seasons 2013/2014 to
2018/2019). The data has been collected from the official volleyball first division homepage
(<www.volleyball-bundesliga.de>) and contains information on teams, staff, sets, matches, and player-in-match
statistics (extracted automatically from the official match reports).
Author: Viktor Bozhinov [aut, cre]
Maintainer: Viktor Bozhinov <mail@viktor-bozhinov.de>
Diff between volleystat versions 0.1.0 dated 2019-02-26 and 0.2.0 dated 2019-05-20
DESCRIPTION | 13 +++-- MD5 | 48 ++++++++++++-------- NEWS.md | 6 ++ R/data.R | 64 ++++++++++++++++++++++----- R/volleystat.R | 21 ++++++--- README.md | 8 ++- build/vignette.rds |binary data/match_adresses.rda |only data/matches.rda |binary data/matchstats.rda |binary data/players.rda |binary data/sets.rda |binary data/staff.rda |binary data/team_adresses.rda |only inst/doc/Datasets-for-Seminars.R |only inst/doc/Datasets-for-Seminars.Rmd |only inst/doc/Datasets-for-Seminars.html |only inst/doc/Introduction-to-volleystat.Rmd | 2 inst/doc/Introduction-to-volleystat.html | 72 +++++++++++++++++-------------- man/match_adresses.Rd |only man/matches.Rd | 4 - man/matchstats.Rd | 6 +- man/players.Rd | 4 - man/sets.Rd | 4 - man/staff.Rd | 4 - man/team_adresses.Rd |only man/volleystat.Rd | 26 ++++++++--- vignettes/Datasets-for-Seminars.Rmd |only vignettes/Introduction-to-volleystat.Rmd | 2 29 files changed, 187 insertions(+), 97 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 6.500 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.1.14.4.1 dated 2019-05-13 and 0.1.15.0.1 dated 2019-05-20
ChangeLog | 13 +++++ DESCRIPTION | 6 +- MD5 | 22 +++++----- NEWS.md | 7 +++ inst/include/ensmallen.hpp | 1 inst/include/ensmallen_bits/adam/adam.hpp | 2 inst/include/ensmallen_bits/ens_version.hpp | 6 +- inst/include/ensmallen_bits/qhadam |only inst/include/ensmallen_bits/sgd/sgd.hpp | 2 inst/include/ensmallen_bits/sgd/update_policies/quasi_hyperbolic_update.hpp |only inst/include/ensmallen_bits/spsa/spsa.hpp | 9 ---- inst/include/ensmallen_bits/spsa/spsa_impl.hpp | 6 -- 12 files changed, 46 insertions(+), 28 deletions(-)
Title: Interacting with the PhenoCam Data and API
Description: A bundle to facilitate working with PhenoCam timeseries and data. The user would be able to obtain phenological time-series and site metadata from the PhenoCam network <https://phenocam.sr.unh.edu/webcam/>.
Author: Bijan Seyednasrollah
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Diff between phenocamapi versions 0.1.4 dated 2019-03-19 and 0.1.5 dated 2019-05-20
DESCRIPTION | 8 +++--- MD5 | 8 +++--- inst/doc/getting_started_phenocam_api.html | 36 ++++++++++++++--------------- inst/doc/phenocam_data_fusion.html | 14 +++++------ tests/testthat/testphenocamapi.R | 2 - 5 files changed, 34 insertions(+), 34 deletions(-)
Title: K-Sample Rank Tests and their Combinations
Description: Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests
with different rank score criteria, Steel's multiple comparison test, and the
Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact
P-values, all valid under randomization, with or without ties, or conditionally
under random sampling from populations, given the observed tie pattern. Except for
Steel's test and the JT test it also combines these tests across several blocks of
samples. Also analyzed are 2 x t contingency tables and their blocked combinations
using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous
confidence bounds for shift parameters. A plotting function compares tail probabilities
obtained under asymptotic approximation with those obtained via simulation or exact
calculations.
Author: Fritz Scholz [aut, cre],
Angie Zhu [aut]
Maintainer: Fritz Scholz <fscholz@u.washington.edu>
Diff between kSamples versions 1.2-8 dated 2018-06-03 and 1.2-9 dated 2019-05-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/listmake.R | 2 +- inst/NEWS.Rd | 10 ++++++++++ man/ad.test.Rd | 26 ++++++++++++++++++++++++++ 5 files changed, 45 insertions(+), 9 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between cmvnorm versions 1.0-5 dated 2018-08-16 and 1.0-6 dated 2019-05-20
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/complicator.Rnw | 14 +++++++++----- inst/doc/complicator.pdf |binary man/corr_complex.Rd | 29 +++++++++++++++-------------- vignettes/complex_gaussian.bib | 11 +++++++++++ vignettes/complicator.Rnw | 14 +++++++++----- 9 files changed, 59 insertions(+), 38 deletions(-)
Title: Retrieve Data from MacLeish Field Station
Description: Download data from the Ada and Archibald MacLeish Field
Station in Whately, MA. The Ada
and Archibald MacLeish Field Station is a 260-acre patchwork of
forest and farmland located in West Whately, MA that provides opportunities
for faculty and students to pursue environmental research, outdoor
education, and low-impact recreation
(see <http://www.smith.edu/ceeds/macleish.php> for more information).
This package contains
weather data over several years, and spatial data on various man-made and
natural structures.
Author: Benjamin S. Baumer [aut, cre],
Rose Goueth [aut],
Wencong Li [aut],
Weijia Zhang [aut],
Nicholas Horton [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between macleish versions 0.3.2 dated 2018-01-03 and 0.3.4 dated 2019-05-20
macleish-0.3.2/macleish/inst/doc/macleish_files |only macleish-0.3.4/macleish/DESCRIPTION | 12 macleish-0.3.4/macleish/MD5 | 40 - macleish-0.3.4/macleish/NAMESPACE | 8 macleish-0.3.4/macleish/NEWS.md | 5 macleish-0.3.4/macleish/R/data.R | 14 macleish-0.3.4/macleish/R/etl_extract.R | 45 - macleish-0.3.4/macleish/R/mass_gis.R | 23 macleish-0.3.4/macleish/README.md | 2 macleish-0.3.4/macleish/build/vignette.rds |binary macleish-0.3.4/macleish/data/datalist |only macleish-0.3.4/macleish/data/macleish_layers.rda |binary macleish-0.3.4/macleish/inst/doc/macleish.R | 5 macleish-0.3.4/macleish/inst/doc/macleish.Rmd | 18 macleish-0.3.4/macleish/inst/doc/macleish.html | 617 +++++++++++----- macleish-0.3.4/macleish/man/etl_extract.etl_macleish.Rd | 3 macleish-0.3.4/macleish/man/macleish_layers.Rd | 12 macleish-0.3.4/macleish/man/mass_gis.Rd | 10 macleish-0.3.4/macleish/man/whately_2015.Rd | 2 macleish-0.3.4/macleish/tests/testthat/test-macleish.R | 12 macleish-0.3.4/macleish/tests/testthat/test-mass-gis.R |only macleish-0.3.4/macleish/vignettes/macleish.Rmd | 18 22 files changed, 562 insertions(+), 284 deletions(-)
Title: Population Genetic Simulations & Numerical Analysis
Description: Conducts various numerical analyses and simulations in population genetics and evolutionary theory, primarily for the purpose of teaching (and learning about) key concepts in population & quantitative genetics, and evolutionary theory.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between learnPopGen versions 0.9.8 dated 2018-10-12 and 1.0.4 dated 2019-05-20
DESCRIPTION | 10 MD5 | 38 +-- NAMESPACE | 27 ++ R/evolution.R | 268 ++++++++++++++++++++++++-- R/games.R | 43 +++- R/popgen.R | 470 +++++++++++++++++++++++++++++++++++++++++----- R/rcd.R | 33 +-- man/clt.Rd | 28 ++ man/coalescent.plot.Rd | 14 + man/drift.selection.Rd | 8 man/founder.event.Rd | 8 man/freqdep.Rd | 11 - man/genetic.drift.Rd | 7 man/hawk.dove.Rd | 8 man/msd.Rd | 11 - man/mutation.selection.Rd | 6 man/phenotype.freq.Rd | 11 - man/rcd.Rd | 3 man/selection.Rd | 9 man/sexratio.Rd | 15 + 20 files changed, 890 insertions(+), 138 deletions(-)
Title: Input Output Analysis
Description: Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>, Ghosh, A. (1958) <doi:10.2307/2550694>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
Author: John Wade [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: John Wade <jjpwade2@illinois.edu>
Diff between ioanalysis versions 0.1.3 dated 2019-04-21 and 0.2.0 dated 2019-05-20
DESCRIPTION | 7 ++++--- MD5 | 14 +++++++++----- NAMESPACE | 5 ++++- R/as.inputoutput.R | 22 ++++++++++++++++++++++ R/f.influence.total.R |only R/heatmap.io.R |only man/as.inputoutput.Rd | 4 +++- man/f.influence.Rd | 3 ++- man/f.influence.total.Rd |only man/heatmap.io.Rd |only 10 files changed, 44 insertions(+), 11 deletions(-)
Title: Pricing Equity Derivatives with Extensions of Black-Scholes
Description: Algorithms to price American and European
equity options, convertible bonds and a
variety of other financial derivatives. It uses an
extension of the usual Black-Scholes model in which
jump to default may occur at a probability specified
by a power-law link between stock price and hazard
rate as found in the paper by Takahashi, Kobayashi,
and Nakagawa (2001) <doi:10.3905/jfi.2001.319302>. We
use ideas and techniques from Andersen and
Buffum (2002) <doi:10.2139/ssrn.355308> and
Linetsky (2006) <doi:10.1111/j.1467-9965.2006.00271.x>.
Author: Brian K. Boonstra
Maintainer: Brian K. Boonstra <ragtop@boonstra.org>
Diff between ragtop versions 1.0.0 dated 2018-12-15 and 1.1.0 dated 2019-05-20
DESCRIPTION | 10 +++---- MD5 | 17 ++++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/term_structures.R | 27 ++++++++++++++++++- inst/doc/ragtop_convertibles_in_r.R | 38 +++++++++++++++++++++++++++ inst/doc/ragtop_convertibles_in_r.Rmd | 46 +++++++++++++++++++++++++++++++-- inst/doc/ragtop_convertibles_in_r.pdf |binary man/detail_from_AnnivDates.Rd |only vignettes/ragtop_convertibles_in_r.Rmd | 46 +++++++++++++++++++++++++++++++-- 10 files changed, 171 insertions(+), 18 deletions(-)
Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics (2013, <doi: 10.1002/gepi.21727>).
Author: Schaid Daniel [aut],
Visconti Alessia [ctb],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.9 dated 2015-10-09 and 3.1 dated 2019-05-20
DESCRIPTION | 18 ++- MD5 | 33 +++--- R/pedgene.R | 58 +++++------ build/vignette.rds |binary data/example.geno.RData |binary data/example.ped.RData |binary data/example.relation.RData |only inst/NEWS.Rd | 7 + inst/doc/pedgene.R | 2 inst/doc/pedgene.Rnw | 2 inst/doc/pedgene.pdf |binary man/example.geno.Rd | 21 +++- man/pedgene.Rd | 15 ++- tests/test.pedgene.R | 2 tests/test.pedgene.Rout.save | 25 ++--- tests/test.pedgene.expanded.R | 23 +++- tests/test.pedgene.expanded.Rout.save | 170 +++++++++++++++++++--------------- vignettes/pedgene.Rnw | 2 18 files changed, 223 insertions(+), 155 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Matthew Hutchinson <matthewhutchinson15@gmail.com>
Diff between paco versions 0.4.0 dated 2019-05-12 and 0.4.1 dated 2019-05-20
DESCRIPTION | 11 +++++++---- MD5 | 2 +- 2 files changed, 8 insertions(+), 5 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Bridge centrality, impact, & goldbricker.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <payton_jones@g.harvard.edu>
Diff between networktools versions 1.2.0 dated 2018-06-05 and 1.2.1 dated 2019-05-20
DESCRIPTION | 12 ++++---- MD5 | 58 ++++++++++++++++++++--------------------- NAMESPACE | 3 ++ NEWS.md | 5 +++ R/EIGENnet.R | 19 ++++++++++--- R/MDSnet.R | 19 ++++++++++--- R/PCAnet.R | 21 +++++++++++---- R/bridge.R | 64 ++++++++++++++++++++++++++++++++++++---------- R/edge_impact.R | 29 ++------------------ R/global_impact.R | 16 ++--------- R/goldbricker.R | 2 + R/hidden_functions.R | 19 +++++++++++++ R/impact.R | 12 ++++++++ R/imports.R | 3 ++ R/structure_impact.R | 19 ++----------- R/summary_print_plot.R | 8 ++--- build/vignette.rds |binary man/EIGENnet.Rd | 11 ++++++- man/MDSnet.Rd | 11 ++++++- man/PCAnet.Rd | 11 ++++++- man/bridge.Rd | 8 ++--- man/edge.impact.Rd | 39 +++++----------------------- man/global.impact.Rd | 25 +++++------------ man/impact.NCT.Rd | 6 ++-- man/impact.Rd | 16 ++++++++++- man/impact.boot.Rd | 4 +- man/plot.edge.impact.Rd | 4 +- man/plot.expectedInf.Rd | 4 +- man/plot.global.impact.Rd | 4 +- man/structure.impact.Rd | 28 +++++--------------- 30 files changed, 270 insertions(+), 210 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.1.1 dated 2019-04-02 and 3.1.2 dated 2019-05-20
geomorph-3.1.1/geomorph/NEWS |only geomorph-3.1.2/geomorph/DESCRIPTION | 8 geomorph-3.1.2/geomorph/MD5 | 75 +- geomorph-3.1.2/geomorph/NEWS.md |only geomorph-3.1.2/geomorph/R/bilat.symmetry.r | 4 geomorph-3.1.2/geomorph/R/build.template.r | 61 + geomorph-3.1.2/geomorph/R/combine.subsets.R | 4 geomorph-3.1.2/geomorph/R/digit.fixed.r | 38 - geomorph-3.1.2/geomorph/R/digitsurface.r | 30 geomorph-3.1.2/geomorph/R/editTemplate.r | 9 geomorph-3.1.2/geomorph/R/geomorph.support.code.r | 29 geomorph-3.1.2/geomorph/R/geomorph.utils.r | 4 geomorph-3.1.2/geomorph/R/globalIntegration.r | 2 geomorph-3.1.2/geomorph/R/morphol.disparity.r | 1 geomorph-3.1.2/geomorph/R/plotRefToTarget.r | 12 geomorph-3.1.2/geomorph/R/plotTangentSpace.r | 3 geomorph-3.1.2/geomorph/R/plotspec.r | 11 geomorph-3.1.2/geomorph/R/procD.lm.r | 43 - geomorph-3.1.2/geomorph/R/procD.pgls.r | 5 geomorph-3.1.2/geomorph/R/read.ply.r | 4 geomorph-3.1.2/geomorph/R/readland.tps.r | 18 geomorph-3.1.2/geomorph/R/shared.support.code.R | 17 geomorph-3.1.2/geomorph/R/warpRefMesh.r | 2 geomorph-3.1.2/geomorph/README.md | 4 geomorph-3.1.2/geomorph/build/vignette.rds |binary geomorph-3.1.2/geomorph/inst/doc/geomorph.assistance.html | 434 ++++++++++---- geomorph-3.1.2/geomorph/inst/doc/geomorph.digitize3D.R |only geomorph-3.1.2/geomorph/inst/doc/geomorph.digitize3D.Rmd |only geomorph-3.1.2/geomorph/inst/doc/geomorph.digitize3D.html |only geomorph-3.1.2/geomorph/inst/doc/geomorph.functions.R |only geomorph-3.1.2/geomorph/inst/doc/geomorph.functions.Rmd |only geomorph-3.1.2/geomorph/inst/doc/geomorph.functions.html |only geomorph-3.1.2/geomorph/man/buildtemplate.Rd | 59 + geomorph-3.1.2/geomorph/man/digit.fixed.Rd | 33 - geomorph-3.1.2/geomorph/man/digitsurface.Rd | 27 geomorph-3.1.2/geomorph/man/editTemplate.Rd | 9 geomorph-3.1.2/geomorph/man/globalIntegration.Rd | 2 geomorph-3.1.2/geomorph/man/plot.procD.lm.Rd | 4 geomorph-3.1.2/geomorph/man/plotTangentSpace.Rd | 2 geomorph-3.1.2/geomorph/man/readland.tps.Rd | 13 geomorph-3.1.2/geomorph/vignettes/figs |only geomorph-3.1.2/geomorph/vignettes/geomorph.digitize3D.Rmd |only geomorph-3.1.2/geomorph/vignettes/geomorph.functions.Rmd |only 43 files changed, 612 insertions(+), 355 deletions(-)
Title: Uncertainty Propagation for R Vectors
Description: Support for measurement errors in R vectors, matrices and arrays:
automatic uncertainty propagation and reporting.
Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
vignette; see 'citation("errors")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between errors versions 0.3.1 dated 2018-12-05 and 0.3.2 dated 2019-05-20
DESCRIPTION | 17 ++++++----- MD5 | 25 +++++++++++----- NEWS.md | 7 ++++ R/correl.R | 11 ++----- R/errors.R | 6 +++ README.md | 69 +++++++-------------------------------------- build |only inst |only man/errors-package.Rd | 5 +++ tests/testthat/test-math.R | 33 +++++++++++++-------- vignettes |only 11 files changed, 80 insertions(+), 93 deletions(-)
Title: The Unifed Distribution
Description: Probability functions and family for glm() of the unifed distribution (Quijano Xacur, 2018; <arXiv:1812.00251>).
Author: Oscar Alberto Quijano Xacur [aut,cre]
Maintainer: Oscar Alberto Quijano Xacur <oscar.quijano@use.startmail.com>
Diff between unifed versions 1.0.2 dated 2019-03-12 and 1.1.0 dated 2019-05-20
ChangeLog |only DESCRIPTION | 12 +- MD5 | 34 +++++--- NAMESPACE | 4 R/doc-unifed_stan.R |only R/dunifed.R | 54 ++++++++---- R/unifed.R | 59 ++++++++++++-- R/unifed.stan.path.R |only README.md | 6 - build/vignette.rds |binary inst/doc/introduction_unifed.R | 99 ++++++++++++++--------- inst/doc/introduction_unifed.Rmd | 150 ++++++++++++++++++++++++++++++------ inst/doc/introduction_unifed.html | 158 +++++++++++++++++++++++++++++++------- inst/stan |only man/dunifed.Rd | 10 ++ man/unifed.Rd | 31 ++++++- man/unifed.stan.Rd |only man/unifed.stan.path.Rd |only src/unifed_kappa.c | 8 - vignettes/introduction_unifed.Rmd | 150 ++++++++++++++++++++++++++++++------ vignettes/unifed_example.stan |only vignettes/unifed_test.r |only 22 files changed, 612 insertions(+), 163 deletions(-)
Title: Simple Imputation
Description: Easy to use interfaces to a number of imputation methods
that fit in the not-a-pipe operator of the 'magrittr' package.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between simputation versions 0.2.2 dated 2017-05-19 and 0.2.3 dated 2019-05-20
simputation-0.2.2/simputation/tests/testthat |only simputation-0.2.2/simputation/tests/testthat.R |only simputation-0.2.3/simputation/DESCRIPTION | 11 simputation-0.2.3/simputation/MD5 | 43 - simputation-0.2.3/simputation/NEWS | 6 simputation-0.2.3/simputation/R/proxy.R | 12 simputation-0.2.3/simputation/build/vignette.rds |binary simputation-0.2.3/simputation/inst/doc/intro.Rmd | 1 simputation-0.2.3/simputation/inst/doc/intro.html | 631 +++++++++++++------- simputation-0.2.3/simputation/inst/tinytest |only simputation-0.2.3/simputation/man/impute.Rd | 1 simputation-0.2.3/simputation/man/impute_hotdeck.Rd | 20 simputation-0.2.3/simputation/man/impute_lm.Rd | 4 simputation-0.2.3/simputation/man/impute_median.Rd | 4 simputation-0.2.3/simputation/man/impute_proxy.Rd | 8 simputation-0.2.3/simputation/man/impute_tree.Rd | 5 simputation-0.2.3/simputation/tests/tinytest.R |only simputation-0.2.3/simputation/vignettes/intro.Rmd | 1 18 files changed, 490 insertions(+), 257 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler [aut, cre, cph],
Giallanza Tyler [ctb],
Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.3-2 dated 2018-12-05 and 1.3-3 dated 2019-05-20
DESCRIPTION | 16 +- MD5 | 25 ++- NAMESPACE | 5 NEWS.md | 10 + R/paracoord.R | 23 +-- R/plotly.R | 15 +- R/shiny.R | 308 +++++++++++++++++++++++++----------------------- README.md | 13 +- build/vignette.rds |binary inst/CITATION |only inst/doc/arulesViz.Rnw | 2 inst/doc/arulesViz.pdf |binary vignettes/arulesViz.Rnw | 2 vignettes/arulesViz.bib | 12 + 14 files changed, 238 insertions(+), 193 deletions(-)
Title: Model-Based Estimation of Confounder-Adjusted Attributable
Fractions
Description: Estimates the attributable fraction in different sampling designs
adjusted for measured confounders using logistic regression (cross-sectional
and case-control designs), conditional logistic regression (matched case-control
design), Cox proportional hazard regression (cohort design with time-to-
event outcome), gamma-frailty model with a Weibull baseline hazard and instrumental variables analysis.
An exploration of the AF with a genetic exposure can be found in the package 'AFheritability' Dahlqwist E et al. (2019) <doi:10.1007/s00439-019-02006-8>.
Author: Elisabeth Dahlqwist and Arvid Sjolander
Maintainer: Elisabeth Dahlqwist <elisabeth.dahlqwist88@gmail.com>
Diff between AF versions 0.1.4 dated 2017-02-10 and 0.1.5 dated 2019-05-20
DESCRIPTION | 24 ++++------ MD5 | 20 +++++--- NAMESPACE | 3 + R/AFclogit.R | 23 +++++----- R/AFfunctions.R | 124 +++++++++++++++++++++++++++++++++++++++++++----------- R/AFgest.R |only R/AFglm.R | 2 R/AFivglm.R |only R/AFparfrailty.R | 3 - R/AFtsest.R |only man/AFivglm.Rd |only man/plot.AF.Rd | 8 +-- man/summary.AF.Rd | 2 13 files changed, 147 insertions(+), 62 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.2.3 dated 2019-04-12 and 0.3.1 dated 2019-05-20
hdme-0.2.3/hdme/R/fit_corrected_lasso.R |only hdme-0.2.3/hdme/R/fit_gds.R |only hdme-0.2.3/hdme/R/fit_gmu_lasso.R |only hdme-0.2.3/hdme/R/fit_gmus.R |only hdme-0.2.3/hdme/R/fit_mus.R |only hdme-0.2.3/hdme/man/fit_corrected_lasso.Rd |only hdme-0.2.3/hdme/man/fit_gds.Rd |only hdme-0.2.3/hdme/man/fit_gmu_lasso.Rd |only hdme-0.2.3/hdme/man/fit_gmus.Rd |only hdme-0.2.3/hdme/man/fit_mus.Rd |only hdme-0.2.3/hdme/src/fit_mu_lasso.cpp |only hdme-0.2.3/hdme/src/hdme_init.c |only hdme-0.3.1/hdme/DESCRIPTION | 10 hdme-0.3.1/hdme/MD5 | 102 +++-- hdme-0.3.1/hdme/NAMESPACE | 19 - hdme-0.3.1/hdme/NEWS.md | 25 + hdme-0.3.1/hdme/R/RcppExports.R | 4 hdme-0.3.1/hdme/R/coef_methods.R |only hdme-0.3.1/hdme/R/corrected_lasso.R |only hdme-0.3.1/hdme/R/corrected_lasso_glm.R | 1 hdme-0.3.1/hdme/R/cv_corrected_lasso.R | 14 hdme-0.3.1/hdme/R/gauss_loss.R | 12 hdme-0.3.1/hdme/R/gds.R |only hdme-0.3.1/hdme/R/gmu_lasso.R |only hdme-0.3.1/hdme/R/gmus.R |only hdme-0.3.1/hdme/R/mus.R |only hdme-0.3.1/hdme/R/mus_glm.R | 7 hdme-0.3.1/hdme/R/musalgorithm.R | 24 - hdme-0.3.1/hdme/R/plot.corrected_lasso.R | 19 - hdme-0.3.1/hdme/R/plot.gds.R | 4 hdme-0.3.1/hdme/R/plot.gmu_lasso.R | 4 hdme-0.3.1/hdme/R/plot.gmus.R | 6 hdme-0.3.1/hdme/R/print_methods.R |only hdme-0.3.1/hdme/README.md | 30 + hdme-0.3.1/hdme/build/partial.rdb |binary hdme-0.3.1/hdme/build/vignette.rds |binary hdme-0.3.1/hdme/inst/CITATION | 30 - hdme-0.3.1/hdme/inst/REFERENCES.bib | 8 hdme-0.3.1/hdme/inst/doc/hdme.R | 30 - hdme-0.3.1/hdme/inst/doc/hdme.Rmd | 60 +-- hdme-0.3.1/hdme/inst/doc/hdme.html | 266 ++++++++------- hdme-0.3.1/hdme/man/coef.corrected_lasso.Rd |only hdme-0.3.1/hdme/man/coef.gds.Rd |only hdme-0.3.1/hdme/man/coef.gmu_lasso.Rd |only hdme-0.3.1/hdme/man/coef.gmus.Rd |only hdme-0.3.1/hdme/man/corrected_lasso.Rd |only hdme-0.3.1/hdme/man/cv_corrected_lasso.Rd | 7 hdme-0.3.1/hdme/man/gds.Rd |only hdme-0.3.1/hdme/man/gmu_lasso.Rd |only hdme-0.3.1/hdme/man/gmus.Rd |only hdme-0.3.1/hdme/man/mus.Rd |only hdme-0.3.1/hdme/man/mus_glm.Rd | 5 hdme-0.3.1/hdme/man/musalgorithm.Rd | 2 hdme-0.3.1/hdme/man/plot.corrected_lasso.Rd | 9 hdme-0.3.1/hdme/man/plot.gds.Rd | 4 hdme-0.3.1/hdme/man/plot.gmu_lasso.Rd | 4 hdme-0.3.1/hdme/man/plot.gmus.Rd | 6 hdme-0.3.1/hdme/man/print.corrected_lasso.Rd |only hdme-0.3.1/hdme/man/print.cv_corrected_lasso.Rd |only hdme-0.3.1/hdme/man/print.gds.Rd |only hdme-0.3.1/hdme/man/print.gmu_lasso.Rd |only hdme-0.3.1/hdme/man/print.gmus.Rd |only hdme-0.3.1/hdme/src/RcppExports.cpp | 18 - hdme-0.3.1/hdme/src/mu_lasso.cpp |only hdme-0.3.1/hdme/tests/testthat/test_corrected_lasso.R | 144 ++++++-- hdme-0.3.1/hdme/tests/testthat/test_cv_corrected_lasso.R |only hdme-0.3.1/hdme/tests/testthat/test_gds.R |only hdme-0.3.1/hdme/tests/testthat/test_gmu_lasso.R |only hdme-0.3.1/hdme/tests/testthat/test_gmus.R | 195 ++++++++-- hdme-0.3.1/hdme/tests/testthat/test_plots.R |only hdme-0.3.1/hdme/vignettes/hdme.Rmd | 60 +-- 71 files changed, 750 insertions(+), 379 deletions(-)
Title: Data Package 'Frictionless Data'
Description: Work with 'Frictionless Data Packages' (<https://frictionlessdata.io/specs/data-package/>). Allows to load and validate any descriptor for a data package profile, create and modify descriptors and provides expose methods for reading and streaming data in the package. When a descriptor is a 'Tabular Data Package', it uses the 'Table Schema' package (<https://CRAN.R-project.org/package=tableschema.r>) and exposes its functionality, for each resource object in the resources field.
Author: Kleanthis Koupidis [aut, cre],
Lazaros Ioannidis [aut],
Charalampos Bratsas [aut],
Open Knowledge International [cph]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
Diff between datapackage.r versions 0.1.0 dated 2019-03-08 and 0.1.1 dated 2019-05-20
DESCRIPTION | 8 - MD5 | 36 +++---- NEWS.md | 6 + R/Package.R | 81 +++++++++++----- R/resource.R | 30 +++++ README.md | 17 +-- build/vignette.rds |binary inst/doc/creating_data_packages_in_r.html | 9 + inst/doc/using_data_packages_in_r.Rmd.html | 9 + inst/profiles/fiscal-data-package.json | 24 +++- inst/profiles/tabular-data-package.json | 12 +- inst/profiles/tabular-data-resource.json | 12 +- man/Package.load.Rd | 79 ++++++++++----- man/Resource.load.Rd | 30 +++++ tests/testthat/inst/profiles/fiscal-data-package.json | 24 +++- tests/testthat/inst/profiles/tabular-data-package.json | 12 +- tests/testthat/inst/profiles/tabular-data-resource.json | 12 +- tests/testthat/test-package.R | 13 ++ tests/testthat/test-resource.R | 13 ++ 19 files changed, 324 insertions(+), 103 deletions(-)
Title: Clonality Estimates in Tumor
Description: Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>.
Author: Davide Prandi [aut, cre],
Alessandro Romanel [ctb],
Tarcisio Fedrizzi [ctb]
Maintainer: Davide Prandi <davide.prandi@unitn.it>
Diff between CLONETv2 versions 2.0 dated 2019-04-05 and 2.1.0 dated 2019-05-20
CLONETv2-2.0/CLONETv2/inst/toy_sample.seg |only CLONETv2-2.0/CLONETv2/inst/toy_sample_normal_pileup.tsv.gz |only CLONETv2-2.0/CLONETv2/inst/toy_sample_snv_read_count.tsv |only CLONETv2-2.0/CLONETv2/inst/toy_sample_tumor_pileup.tsv.gz |only CLONETv2-2.1.0/CLONETv2/DESCRIPTION | 6 +- CLONETv2-2.1.0/CLONETv2/MD5 | 15 +++--- CLONETv2-2.1.0/CLONETv2/NEWS.md |only CLONETv2-2.1.0/CLONETv2/R/CLONETv2_compute_beta_table.R | 29 +++++++++++++ CLONETv2-2.1.0/CLONETv2/inst/sample.seg |only CLONETv2-2.1.0/CLONETv2/inst/sample_normal_pileup.tsv |only CLONETv2-2.1.0/CLONETv2/inst/sample_snv_read_count.tsv |only CLONETv2-2.1.0/CLONETv2/inst/sample_tumor_pileup.tsv |only CLONETv2-2.1.0/CLONETv2/man/compute_beta_table.Rd | 5 +- 13 files changed, 44 insertions(+), 11 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional kernel term and sampling techniques as described
by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Kyle Kocak, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.6.3 dated 2019-04-24 and 1.6.4 dated 2019-05-20
DESCRIPTION | 10 +- MD5 | 20 ++--- R/RcppExports.R | 4 + R/mix.R | 110 ++++++++++++--------------- demo/mixedmodel.R | 11 +- man/bWGR.Rd | 6 - man/mix.Rd | 14 ++- man/mvr.Rd | 14 ++- man/wgr.Rd | 6 - src/RcppExports.cpp | 13 +++ src/wgr20190410.cpp | 208 ++++++++++++++++++++++++++++++++++++++++++---------- 11 files changed, 283 insertions(+), 133 deletions(-)
Title: A Tidy Wrapper Around 'gtrendsR'
Description: Access Google Trends information. This package provides a tidy wrapper to the 'gtrendsR' package.
Use four spaces when indenting paragraphs within the Description.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between trendyy versions 0.1.0 dated 2019-05-15 and 0.1.1 dated 2019-05-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/get_trends.R | 54 +++++++++++++++++++++++++++++++++++++++++++++++++----- R/zzz.R | 7 +++++-- man/trendy.Rd | 7 ++++++- 6 files changed, 70 insertions(+), 17 deletions(-)
More information about changepoint.np at CRAN
Permanent link
Title: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time
Analyses Estimates on Trees
Description: Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Author: Mark Puttick [aut,cre]
Maintainer: Mark Puttick <mark.puttick@bristol.ac.uk>
Diff between MCMCtreeR versions 0.1 dated 2019-03-24 and 1.0 dated 2019-05-20
DESCRIPTION | 11 ++-- MD5 | 73 +++++++++++++++------------ R/MCMC.tree.plot.R | 119 +++++++++++++++++++++++++++------------------ R/MCMCtreePhy.R | 14 ++--- R/estimateBound.R | 15 ++--- R/estimateCauchy.R | 17 +++--- R/estimateFixed.R | 18 +++--- R/estimateGamma.R | 33 +++++------- R/estimateSkewNormal.R | 24 ++++----- R/estimateSkewT.R | 29 +++++----- R/estimateUpper.R | 12 +--- R/nodeTimes.R | 3 - R/nodeToPhy.R | 16 ------ R/plotMCMCtree.R | 15 +---- R/priorPosterior.R | 65 +++++++++++++++++------- R/readMCMCtree.R | 5 + R/tipDes.R | 50 ++++++++++++------ build |only data/MCMCtree.output.RData |binary data/apeData.RData |binary inst |only man/MCMC.tree.plot.Rd | 21 ++++++- man/MCMCtreePhy.Rd | 14 ++--- man/estimateBound.Rd | 16 +++--- man/estimateCauchy.Rd | 21 +++---- man/estimateFixed.Rd | 20 +++---- man/estimateGamma.Rd | 33 ++++++------ man/estimateSkewNormal.Rd | 20 ++++--- man/estimateSkewT.Rd | 21 ++++--- man/estimateUpper.Rd | 14 ++--- man/nodeToPhy.Rd | 17 ------ man/plotMCMCtree.Rd | 17 ++---- man/priorPosterior.Rd | 12 +++- man/readMCMCtree.Rd | 5 + man/tipDes.Rd | 13 ++++ vignettes |only 36 files changed, 420 insertions(+), 343 deletions(-)
Title: The Calibration Simplex
Description: Generates the calibration simplex (a generalization of the reliability diagram) for three-category probability forecasts, as proposed by Wilks (2013) <doi:10.1175/WAF-D-13-00027.1>.
Author: Johannes Resin
Maintainer: Johannes Resin <johannes.resin@h-its.org>
Diff between CalSim versions 0.2.2 dated 2019-02-01 and 0.3.2 dated 2019-05-20
DESCRIPTION | 9 +- MD5 | 21 ++++-- NEWS.md |only R/calibration_simplex.R | 70 ++++++++++++++-------- R/calibration_simplex.default.R | 103 +++++++++++++++++++-------------- R/data.R |only R/error.calibration_simplex.R | 12 +-- R/make_forecasts.calibration_simplex.R | 18 ++--- R/plot.calibration_simplex.R | 16 +++-- README.md |only data |only man/calibration_simplex.Rd | 76 ++++++++++++++++-------- man/plot.calibration_simplex.Rd | 11 ++- man/ternary_forecast_example.Rd |only 14 files changed, 207 insertions(+), 129 deletions(-)
More information about mc.heterogeneity at CRAN
Permanent link
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb],
Robert Corty [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.4.5 dated 2019-01-10 and 0.4.6 dated 2019-05-20
hexSticker-0.4.5/hexSticker/NEWS |only hexSticker-0.4.5/hexSticker/man/hexagon.Rd |only hexSticker-0.4.6/hexSticker/DESCRIPTION | 12 - hexSticker-0.4.6/hexSticker/MD5 | 16 - hexSticker-0.4.6/hexSticker/NAMESPACE | 1 hexSticker-0.4.6/hexSticker/NEWS.md |only hexSticker-0.4.6/hexSticker/R/sticker.R | 120 +++++++--- hexSticker-0.4.6/hexSticker/README.md | 36 ++- hexSticker-0.4.6/hexSticker/inst/figures/ggplot2-google-font.png |only hexSticker-0.4.6/hexSticker/inst/figures/ggplot2.png |binary hexSticker-0.4.6/hexSticker/man/sticker.Rd | 16 + 11 files changed, 146 insertions(+), 55 deletions(-)
Title: Fast K-Mer Counting and Clustering for Biological Sequence
Analysis
Description: Contains tools for rapidly computing distance matrices
and clustering large sequence datasets using fast alignment-free
k-mer counting and recursive k-means partitioning.
See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005>
for a review of k-mer counting methods and applications for
biological sequence analysis.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between kmer versions 1.1.1 dated 2019-03-15 and 1.1.2 dated 2019-05-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/distance.R | 18 ++++++++++-------- README.md | 1 + build/vignette.rds |binary inst/doc/kmer-vignette.html | 9 ++++++--- 6 files changed, 25 insertions(+), 19 deletions(-)
Title: Redraw Base Graphics Using 'grid' Graphics
Description: Functions to convert a page of plots drawn with the
'graphics' package into identical output drawn with the 'grid' package.
The result looks like the original 'graphics'-based plot, but consists
of 'grid' grobs and viewports that can then be manipulated with
'grid' functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut],
Zhijian Wen [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridGraphics versions 0.4-0 dated 2019-05-06 and 0.4-1 dated 2019-05-20
DESCRIPTION | 8 - MD5 | 8 - R/axis.R | 316 ++++++++++++++++++++++++++++++++++++++++++ R/mtext.R | 61 ++++++++ inst/test-scripts/test-axis.R | 61 ++++---- 5 files changed, 417 insertions(+), 37 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman [aut, cre],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut, cre],
Noah Simon [aut, ctb],
Balasubramanian Narasimhan [aut, ctb],
Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 2.0-16 dated 2018-04-02 and 2.0-18 dated 2019-05-20
glmnet-2.0-16/glmnet/inst/mortran/glmnet5dp.m |only glmnet-2.0-16/glmnet/src/glmnet5dp.f |only glmnet-2.0-18/glmnet/ChangeLog | 6 glmnet-2.0-18/glmnet/DESCRIPTION | 10 - glmnet-2.0-18/glmnet/MD5 | 32 ++-- glmnet-2.0-18/glmnet/R/cv.coxnet.R | 40 +++--- glmnet-2.0-18/glmnet/R/cv.elnet.R | 18 +- glmnet-2.0-18/glmnet/R/cv.fishnet.R | 18 +- glmnet-2.0-18/glmnet/R/cv.glmnet.R | 12 + glmnet-2.0-18/glmnet/R/cv.lognet.R | 24 ++- glmnet-2.0-18/glmnet/R/cv.mrelnet.R | 91 +++++++------ glmnet-2.0-18/glmnet/R/cv.multnet.R | 140 ++++++++++----------- glmnet-2.0-18/glmnet/build/vignette.rds |binary glmnet-2.0-18/glmnet/inst/doc/Coxnet.pdf |binary glmnet-2.0-18/glmnet/inst/doc/glmnet_beta.pdf |binary glmnet-2.0-18/glmnet/inst/mortran/glmnet5dpclean.m |only glmnet-2.0-18/glmnet/man/cv.glmnet.Rd | 27 ++-- glmnet-2.0-18/glmnet/man/glmnet.Rd | 2 glmnet-2.0-18/glmnet/src/glmnet5dpclean.f |only 19 files changed, 229 insertions(+), 191 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, and Kendon Bell.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.18 dated 2018-10-10 and 0.6.19 dated 2019-05-20
ChangeLog | 804 ++++++++++++++++++++++++--------------------- DESCRIPTION | 21 - MD5 | 32 + NAMESPACE | 3 R/digest.R | 56 ++- R/digest2int.R |only README.md | 9 build/vignette.rds |binary cleanup | 2 inst/doc/sha1.html | 43 +- man/digest.Rd | 53 ++ man/digest2int.Rd |only src/Makevars |only src/SpookyV2.cpp |only src/SpookyV2.h |only src/digest.c | 2 src/digest2int.c |only src/spooky_serialize.cpp |only tests/digest2intTest.R |only tests/digestTest.R | 86 ++++ tests/digestTest.Rout.save | 104 +++++ 21 files changed, 779 insertions(+), 436 deletions(-)
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Flavio Poletti [aut],
Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Mark Padgham [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.4.0 dated 2019-04-16 and 0.5.0 dated 2019-05-20
tidytransit-0.4.0/tidytransit/man/gt_as_dt.Rd |only tidytransit-0.4.0/tidytransit/man/import_gtfs.Rd |only tidytransit-0.4.0/tidytransit/man/routes_df_as_sf.Rd |only tidytransit-0.4.0/tidytransit/man/stops_df_as_sf.Rd |only tidytransit-0.5.0/tidytransit/DESCRIPTION | 12 tidytransit-0.5.0/tidytransit/MD5 | 58 + tidytransit-0.5.0/tidytransit/NAMESPACE | 9 tidytransit-0.5.0/tidytransit/R/frequencies.R | 4 tidytransit-0.5.0/tidytransit/R/import.R | 49 - tidytransit-0.5.0/tidytransit/R/joins.R | 8 tidytransit-0.5.0/tidytransit/R/raptor.R |only tidytransit-0.5.0/tidytransit/R/spatial.R | 35 - tidytransit-0.5.0/tidytransit/R/spec.R | 29 tidytransit-0.5.0/tidytransit/R/time.R | 33 - tidytransit-0.5.0/tidytransit/R/utils.R | 30 tidytransit-0.5.0/tidytransit/build/vignette.rds |binary tidytransit-0.5.0/tidytransit/inst/doc/frequency.R | 20 tidytransit-0.5.0/tidytransit/inst/doc/frequency.Rmd | 74 +- tidytransit-0.5.0/tidytransit/inst/doc/frequency.html | 232 ++++--- tidytransit-0.5.0/tidytransit/inst/doc/introduction.R | 27 tidytransit-0.5.0/tidytransit/inst/doc/introduction.Rmd | 53 - tidytransit-0.5.0/tidytransit/inst/doc/introduction.html | 153 +---- tidytransit-0.5.0/tidytransit/inst/doc/servicepatterns.html | 302 +++++----- tidytransit-0.5.0/tidytransit/inst/doc/timetable.Rmd | 2 tidytransit-0.5.0/tidytransit/inst/doc/timetable.html | 228 ++++--- tidytransit-0.5.0/tidytransit/inst/extdata/routing.zip |only tidytransit-0.5.0/tidytransit/man/filter_stop_times.Rd |only tidytransit-0.5.0/tidytransit/man/raptor.Rd |only tidytransit-0.5.0/tidytransit/man/travel_times.Rd |only tidytransit-0.5.0/tidytransit/man/write_gtfs.Rd |only tidytransit-0.5.0/tidytransit/tests/testthat/test-import-gtfs.R | 5 tidytransit-0.5.0/tidytransit/tests/testthat/test-raptor.R |only tidytransit-0.5.0/tidytransit/tests/testthat/test-utils.R |only tidytransit-0.5.0/tidytransit/vignettes/frequency.Rmd | 74 +- tidytransit-0.5.0/tidytransit/vignettes/introduction.Rmd | 53 - tidytransit-0.5.0/tidytransit/vignettes/timetable.Rmd | 2 36 files changed, 707 insertions(+), 785 deletions(-)
Title: Wavelet-Based Enhanced FDR for Detecting Signals from Complete
or Incomplete Spatially Aggregated Data
Description: Enhanced False Discovery Rate (EFDR) is a tool to detect anomalies
in an image. The image is first transformed into the wavelet domain in
order to decorrelate any noise components, following which the coefficients
at each resolution are standardised. Statistical tests (in a multiple
hypothesis testing setting) are then carried out to find the anomalies. The
power of EFDR exceeds that of standard FDR, which would carry out tests on
every wavelet coefficient: EFDR choose which wavelets to test based on a
criterion described in Shen et al. (2002). The package also provides
elementary tools to interpolate spatially irregular data onto a grid of the
required size. The work is based on Shen, X., Huang, H.-C., and Cressie, N.
'Nonparametric hypothesis testing for a spatial signal.' Journal of the
American Statistical Association 97.460 (2002): 1122-1140.
Author: Andrew Zammit-Mangion [aut, cre],
Hsin-Cheng Huang [aut]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
Diff between EFDR versions 0.1.1 dated 2015-04-04 and 1.0 dated 2019-05-20
DESCRIPTION | 20 +- MD5 | 40 ++-- NAMESPACE | 19 ++ R/EFDR.R | 4 R/EFDR_condsim.R |only R/EFDR_functions.R | 18 +- build/vignette.rds |binary inst/doc/EFDR.Rmd | 4 inst/doc/EFDR.html | 354 ++++++++++++++++++++++--------------------- inst/doc/EFDR_SST.Rmd | 10 - inst/doc/EFDR_SST.html | 188 ++++++++++++---------- inst/doc/EFDR_documents.html | 186 +++------------------- man/EFDR.Rd | 4 man/df.to.mat.Rd | 10 - man/diagnostic.table.Rd | 8 man/fdrpower.Rd | 4 man/nei.efdr.Rd | 10 - man/regrid.Rd | 30 +-- man/test.efdr.condsim.Rd |only man/test_image.Rd | 6 man/wav_th.Rd | 8 man/wavelet-test.Rd | 24 +- 22 files changed, 445 insertions(+), 502 deletions(-)
Title: Create Contour Plots from Data or a Function
Description: Provides functions for making contour plots.
The contour plot can be created from grid data, a function,
or a data set. If non-grid data is given, then a Gaussian
process is fit to the data and used to create the contour plot.
Author: Collin Erickson [aut, cre]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between ContourFunctions versions 0.1.0 dated 2017-05-04 and 0.1.1 dated 2019-05-20
ContourFunctions-0.1.0/ContourFunctions/R/cf_grid1.R |only ContourFunctions-0.1.0/ContourFunctions/man/cf_grid1.Rd |only ContourFunctions-0.1.1/ContourFunctions/DESCRIPTION | 11 ContourFunctions-0.1.1/ContourFunctions/MD5 | 73 + ContourFunctions-0.1.1/ContourFunctions/NAMESPACE | 14 ContourFunctions-0.1.1/ContourFunctions/NEWS.md | 11 ContourFunctions-0.1.1/ContourFunctions/R/cf.R | 22 ContourFunctions-0.1.1/ContourFunctions/R/cf_4dim.R |only ContourFunctions-0.1.1/ContourFunctions/R/cf_csa.R | 24 ContourFunctions-0.1.1/ContourFunctions/R/cf_data.R | 28 ContourFunctions-0.1.1/ContourFunctions/R/cf_func.R | 63 - ContourFunctions-0.1.1/ContourFunctions/R/cf_grid_screen.R | 71 + ContourFunctions-0.1.1/ContourFunctions/R/cf_highdim.R |only ContourFunctions-0.1.1/ContourFunctions/R/cf_make_multicolor_title.R | 4 ContourFunctions-0.1.1/ContourFunctions/R/cm_colors_strong.R |only ContourFunctions-0.1.1/ContourFunctions/R/eval_over_grid_with_batch.R |only ContourFunctions-0.1.1/ContourFunctions/R/gcf.R |only ContourFunctions-0.1.1/ContourFunctions/R/gcf_data.R |only ContourFunctions-0.1.1/ContourFunctions/R/gcf_func.R |only ContourFunctions-0.1.1/ContourFunctions/R/gcf_grid.R |only ContourFunctions-0.1.1/ContourFunctions/R/text_plot.R |only ContourFunctions-0.1.1/ContourFunctions/README.md | 81 + ContourFunctions-0.1.1/ContourFunctions/build/vignette.rds |binary ContourFunctions-0.1.1/ContourFunctions/inst/doc/Introduction_to_the_cf_R_package.R | 20 ContourFunctions-0.1.1/ContourFunctions/inst/doc/Introduction_to_the_cf_R_package.Rmd | 57 + ContourFunctions-0.1.1/ContourFunctions/inst/doc/Introduction_to_the_cf_R_package.html | 424 ++++++++-- ContourFunctions-0.1.1/ContourFunctions/man/cf.Rd | 14 ContourFunctions-0.1.1/ContourFunctions/man/cf_4dim.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/cf_data.Rd | 17 ContourFunctions-0.1.1/ContourFunctions/man/cf_func.Rd | 11 ContourFunctions-0.1.1/ContourFunctions/man/cf_grid.Rd | 40 ContourFunctions-0.1.1/ContourFunctions/man/cf_highdim.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/cm.colors.strong.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/csa.Rd | 21 ContourFunctions-0.1.1/ContourFunctions/man/eval_over_grid_with_batch.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/gcf.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/gcf_data.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/gcf_func.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/gcf_grid.Rd |only ContourFunctions-0.1.1/ContourFunctions/man/multicolor.title.Rd | 3 ContourFunctions-0.1.1/ContourFunctions/man/text_plot.Rd |only ContourFunctions-0.1.1/ContourFunctions/tests |only ContourFunctions-0.1.1/ContourFunctions/tools/README-cf_4dim-1.png |only ContourFunctions-0.1.1/ContourFunctions/tools/README-cf_data-1.png |binary ContourFunctions-0.1.1/ContourFunctions/tools/README-cf_func-1.png |binary ContourFunctions-0.1.1/ContourFunctions/tools/README-cf_grid-1.png |binary ContourFunctions-0.1.1/ContourFunctions/tools/README-cf_highdim-1.png |only ContourFunctions-0.1.1/ContourFunctions/vignettes/Introduction_to_the_cf_R_package.Rmd | 57 + 48 files changed, 810 insertions(+), 256 deletions(-)
More information about ContourFunctions at CRAN
Permanent link
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. Additionally, 'grouped_' variants
of the generics provides a convenient way to execute functions across
a combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 0.0.2 dated 2019-04-03 and 0.0.3 dated 2019-05-20
DESCRIPTION | 10 +- MD5 | 20 ++--- NAMESPACE | 1 NEWS.md | 4 + R/grouped_augment.R | 15 +--- R/grouped_glance.R | 17 +--- R/grouped_tidy.R | 15 +--- README.md | 33 +++++---- build/broomExtra.pdf |binary inst/doc/available_methods.html | 138 ++++++++++++++++++++++----------------- inst/doc/tests_and_coverage.html | 2 11 files changed, 134 insertions(+), 121 deletions(-)