Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of
40 different coding schemes, convert between coding schemes, and
assign region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
CJ Yetman [ctb] (<https://orcid.org/0000-0001-5099-9500>),
Nils Enevoldsen [ctb] (<https://orcid.org/0000-0001-7195-4117>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.1.2 dated 2020-04-22 and 1.1.3 dated 2020-05-07
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 5 +++++ R/codelist.R | 1 + R/countrycode.R | 2 +- data/codelist.rda |binary data/codelist_panel.rda |binary man/codelist.Rd | 1 + 8 files changed, 20 insertions(+), 13 deletions(-)
Title: Bayesian Methods and Graphical Model Structures for Statistical
Modeling
Description: A set of frequently used Bayesian parametric and nonparametric model structures, as well as a set of tools for common analytical tasks. Structures include linear Gaussian systems, Gaussian and Normal-Inverse-Wishart conjugate structure, Gaussian and Normal-Inverse-Gamma conjugate structure, Categorical and Dirichlet conjugate structure, Dirichlet Process on positive integers, Dirichlet Process in general, Hierarchical Dirichlet Process ... Tasks include updating posteriors, sampling from posteriors, calculating marginal likelihood, calculating posterior predictive densities, sampling from posterior predictive distributions, calculating "Maximum A Posteriori" (MAP) estimates ... See <https://chenhaotian.github.io/Bayesian-Bricks/> to get started.
Author: Haotian Chen [aut, cre] (<https://orcid.org/0000-0001-9751-2093>)
Maintainer: Haotian Chen <chenhaotian.jtt@gmail.com>
Diff between bbricks versions 0.1.3 dated 2020-04-26 and 0.1.4 dated 2020-05-07
DESCRIPTION | 8 MD5 | 106 ++-- NAMESPACE | 3 NEWS.md | 25 - R/Bayesian_Bricks.r | 92 +-- R/Dirichlet_Process.r | 424 ++++++++++------- R/testData.r | 43 + build/vignette.rds |binary data/hmmData.RData |only inst/doc/bbricks-getting-started.R | 225 ++++++++- inst/doc/bbricks-getting-started.Rmd | 338 ++++++++++++- inst/doc/bbricks-getting-started.html | 328 +++++++++++-- man/CatHDP.Rd | 10 man/CatHDP2.Rd | 16 man/HDP.Rd | 10 man/HDP2.Rd | 16 man/bbricks-package.Rd | 2 man/dAllIndicators.HDP.Rd |only man/dAllIndicators.Rd |only man/dPosteriorPredictive.CatHDP.Rd | 8 man/dPosteriorPredictive.CatHDP2.Rd | 16 man/dPosteriorPredictive.HDP.Rd | 8 man/dPosteriorPredictive.HDP2.Rd | 14 man/farmadsData.Rd | 4 man/hlrData.Rd | 6 man/hmmData.Rd |only man/lrData.Rd | 4 man/mmhData.Rd | 4 man/mmhhData.Rd | 8 man/posterior.CatHDP.Rd | 8 man/posterior.CatHDP2.Rd | 14 man/posterior.DP.Rd | 2 man/posterior.HDP.Rd | 10 man/posterior.HDP2.Rd | 16 man/posterior.Rd | 18 man/posteriorDiscard.CatHDP.Rd | 8 man/posteriorDiscard.CatHDP2.Rd | 14 man/posteriorDiscard.DP.Rd | 2 man/posteriorDiscard.HDP.Rd | 10 man/posteriorDiscard.HDP2.Rd | 16 man/posteriorDiscard.Rd | 18 man/rPosteriorPredictive.CatHDP.Rd | 10 man/rPosteriorPredictive.CatHDP2.Rd | 16 man/rPosteriorPredictive.HDP.Rd | 8 man/rPosteriorPredictive.HDP2.Rd | 14 man/sufficientStatistics.HDP.Rd | 8 man/sufficientStatistics.HDP2.Rd | 14 man/sufficientStatistics.Rd | 18 man/sufficientStatistics_Weighted.HDP.Rd | 8 man/sufficientStatistics_Weighted.HDP2.Rd | 14 man/sufficientStatistics_Weighted.Rd | 18 vignettes/bbricks-getting-started.Rmd | 338 ++++++++++++- vignettes/notes_pictures/HDP.png |binary vignettes/notes_pictures/HDPHMM.png |only vignettes/notes_pictures/HMM.png |only vignettes/notes_pictures/hierarchicalMixtureModel.png |binary vignettes/notes_pictures/hierarchicalMixtureModel2.png |binary 57 files changed, 1735 insertions(+), 585 deletions(-)
Title: A Collection of Graphon Estimation Methods
Description: Provides a not-so-comprehensive list of methods for estimating graphon,
a symmetric measurable function, from a single or multiple of observed networks.
For a detailed introduction on graphon and popular estimation techniques,
see the paper by Orbanz, P. and Roy, D.M.(2014) <doi:10.1109/TPAMI.2014.2334607>.
It also contains several auxiliary functions for generating sample networks
using various network models and graphons.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between graphon versions 0.3.3 dated 2019-11-25 and 0.3.4 dated 2020-05-07
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 39 ++++++++++++++++++++------------------- NEWS.md | 30 ++++++++++++++++++------------ R/est.LG.R | 9 +++++---- R/est.SBA.R | 3 ++- R/est.USVT.R | 3 ++- R/est.completion.R | 3 ++- R/est.nbdsmooth.R | 3 ++- R/gmodel.ER.R | 19 +++++++++---------- R/gmodel.P.R | 10 ++++++---- R/gmodel.block.R | 6 +++--- build/partial.rdb |binary man/est.LG.Rd | 5 +++-- man/est.SBA.Rd | 3 ++- man/est.USVT.Rd | 3 ++- man/est.completion.Rd | 3 ++- man/est.nbdsmooth.Rd | 3 ++- man/gmodel.ER.Rd | 19 +++++++++---------- man/gmodel.P.Rd | 10 ++++++---- man/gmodel.block.Rd | 6 +++--- 21 files changed, 103 insertions(+), 84 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre],
Ignacio García Jurado [aut],
Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 1.2.4 dated 2020-01-15 and 1.3.1 dated 2020-05-07
DESCRIPTION | 12 ++++++------ MD5 | 14 ++++++++------ NAMESPACE | 9 +++++++-- R/ProjectManagement.R | 7 ++++--- R/function_dag.R |only R/function_pert_calendario.R | 9 ++++++++- R/function_pert_estocastico.R | 6 +++--- man/dag.plot.Rd |only man/stochastic.pert.Rd | 2 +- 9 files changed, 37 insertions(+), 22 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Fitting User-Specified Models with Group Lasso Penalty
Description: Fits user-specified (GLM-) models with group lasso penalty.
Author: Lukas Meier
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between grplasso versions 0.4-6 dated 2018-08-13 and 0.4-7 dated 2020-05-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/grplasso.R | 4 +++- build/partial.rdb |binary 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Create Visual Predictive Checks
Description: Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.
Author: Ron Keizer <ronkeizer@gmail.com>
Maintainer: Ron Keizer <ronkeizer@gmail.com>
Diff between vpc versions 1.1.0 dated 2018-08-27 and 1.2.0 dated 2020-05-07
DESCRIPTION | 10 +++--- MD5 | 59 ++++++++++++++++++------------------ NAMESPACE | 4 ++ NEWS.md |only R/add_stratification.R | 24 +++++++++----- R/binning.R | 77 ++++++++++++++++++++++++++++-------------------- R/compute_kaplan.R | 19 ++++++++++- R/plot_vpc.R | 2 - R/quantile_cens.R | 1 R/sim_data.R | 10 +++--- R/vpc.R | 74 ++++++++++++++++++++++++---------------------- R/vpc_cens.R | 4 +- R/vpc_tte.R | 33 ++++++++++++++------ man/auto_bin.Rd | 23 ++++++++++---- man/compute_kaplan.Rd | 10 +++++- man/pk_iv_1cmt.Rd | 11 +++++- man/pk_oral_1cmt.Rd | 3 - man/plot_vpc.Rd | 15 +++++++-- man/read_table_nm.Rd | 9 ++++- man/rtte_obs_nm.Rd | 4 +- man/rtte_sim_nm.Rd | 4 +- man/show_default.Rd | 4 +- man/show_default_tte.Rd | 4 +- man/sim_data.Rd | 16 +++++++-- man/simple_data.Rd | 4 +- man/vpc.Rd | 39 +++++++++++++++++++----- man/vpc_cat.Rd | 31 +++++++++++++++---- man/vpc_cens.Rd | 34 ++++++++++++++++----- man/vpc_tte.Rd | 41 ++++++++++++++++++++----- tests/test-vpc_cat.R | 2 - tests/test-vpc_cens.R | 15 ++++----- 31 files changed, 396 insertions(+), 190 deletions(-)
Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>,
a standalone 'C++' library for fast symbolic manipulation. The package has functionalities
for symbolic computation like calculating exact mathematical expressions, solving
systems of linear equations and code generation.
Author: Jialin Ma [cre, aut],
Isuru Fernando [aut],
Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>
Diff between symengine versions 0.1.2 dated 2020-05-02 and 0.1.3 dated 2020-05-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary configure | 50 ++++++++++++++++++++++++++++++++++++++------------ 4 files changed, 44 insertions(+), 18 deletions(-)
Title: Solver for Partially Observable Markov Decision Processes
(POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Processes (POMDP) models. The package includes pomdp-solve to solve POMDPs using a variety of exact and approximate value iteration algorithms. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Hossein Kamalzadeh [aut, cph, cre],
Michael Hahsler [aut, cph],
Anthony R. Cassandra [ctb, cph]
Maintainer: Hossein Kamalzadeh <hkamalzadeh@mail.smu.edu>
Diff between pomdp versions 0.9.2 dated 2019-12-16 and 0.99.0 dated 2020-05-07
pomdp-0.9.2/pomdp/R/plot.POMDP.R |only pomdp-0.9.2/pomdp/R/write_POMDP.R |only pomdp-0.9.2/pomdp/data/TigerProblem.rda |only pomdp-0.9.2/pomdp/inst/doc/POMDP.pdf |only pomdp-0.9.2/pomdp/man/TigerProblem.Rd |only pomdp-0.9.2/pomdp/man/model.Rd |only pomdp-0.9.2/pomdp/man/plot.POMDP.Rd |only pomdp-0.9.2/pomdp/man/solution.Rd |only pomdp-0.9.2/pomdp/man/solver_output.Rd |only pomdp-0.9.2/pomdp/src/Makevars.win |only pomdp-0.9.2/pomdp/src/alpha.c |only pomdp-0.9.2/pomdp/src/alpha.h |only pomdp-0.9.2/pomdp/src/associative-array.c |only pomdp-0.9.2/pomdp/src/associative-array.h |only pomdp-0.9.2/pomdp/src/belief-state.c |only pomdp-0.9.2/pomdp/src/belief-state.h |only pomdp-0.9.2/pomdp/src/belief.c |only pomdp-0.9.2/pomdp/src/belief.h |only pomdp-0.9.2/pomdp/src/cmd-line.c |only pomdp-0.9.2/pomdp/src/cmd-line.h |only pomdp-0.9.2/pomdp/src/command-line.c |only pomdp-0.9.2/pomdp/src/command-line.h |only pomdp-0.9.2/pomdp/src/common.c |only pomdp-0.9.2/pomdp/src/common.h |only pomdp-0.9.2/pomdp/src/config-file.c |only pomdp-0.9.2/pomdp/src/config-file.h |only pomdp-0.9.2/pomdp/src/cross-sum.c |only pomdp-0.9.2/pomdp/src/cross-sum.h |only pomdp-0.9.2/pomdp/src/double-vector.c |only pomdp-0.9.2/pomdp/src/double-vector.h |only pomdp-0.9.2/pomdp/src/enumeration.c |only pomdp-0.9.2/pomdp/src/enumeration.h |only pomdp-0.9.2/pomdp/src/fg-params.c |only pomdp-0.9.2/pomdp/src/fg-params.h |only pomdp-0.9.2/pomdp/src/finite-grid.c |only pomdp-0.9.2/pomdp/src/finite-grid.h |only pomdp-0.9.2/pomdp/src/global.c |only pomdp-0.9.2/pomdp/src/global.h |only pomdp-0.9.2/pomdp/src/inc-prune.c |only pomdp-0.9.2/pomdp/src/inc-prune.h |only pomdp-0.9.2/pomdp/src/index-list.c |only pomdp-0.9.2/pomdp/src/index-list.h |only pomdp-0.9.2/pomdp/src/laspack |only pomdp-0.9.2/pomdp/src/laspack-util.c |only pomdp-0.9.2/pomdp/src/laspack-util.h |only pomdp-0.9.2/pomdp/src/linear-support.c |only pomdp-0.9.2/pomdp/src/linear-support.h |only pomdp-0.9.2/pomdp/src/lp-interface.c |only pomdp-0.9.2/pomdp/src/lp-interface.h |only pomdp-0.9.2/pomdp/src/lp-solve |only pomdp-0.9.2/pomdp/src/main.c |only pomdp-0.9.2/pomdp/src/mcgs.c |only pomdp-0.9.2/pomdp/src/mcgs.h |only pomdp-0.9.2/pomdp/src/mdp |only pomdp-0.9.2/pomdp/src/neighbor.c |only pomdp-0.9.2/pomdp/src/neighbor.h |only pomdp-0.9.2/pomdp/src/params.c |only pomdp-0.9.2/pomdp/src/params.h |only pomdp-0.9.2/pomdp/src/parsimonious.c |only pomdp-0.9.2/pomdp/src/parsimonious.h |only pomdp-0.9.2/pomdp/src/pg-eval.c |only pomdp-0.9.2/pomdp/src/pg-eval.h |only pomdp-0.9.2/pomdp/src/pg.c |only pomdp-0.9.2/pomdp/src/pg.h |only pomdp-0.9.2/pomdp/src/pomdp-fg-main.c |only pomdp-0.9.2/pomdp/src/pomdp-fg-options.c |only pomdp-0.9.2/pomdp/src/pomdp-fg-options.h |only pomdp-0.9.2/pomdp/src/pomdp-fg.c |only pomdp-0.9.2/pomdp/src/pomdp-fg.h |only pomdp-0.9.2/pomdp/src/pomdp-solve-options.c |only pomdp-0.9.2/pomdp/src/pomdp-solve-options.h |only pomdp-0.9.2/pomdp/src/pomdp-solve.c |only pomdp-0.9.2/pomdp/src/pomdp-solve.h |only pomdp-0.9.2/pomdp/src/pomdp.c |only pomdp-0.9.2/pomdp/src/pomdp.h |only pomdp-0.9.2/pomdp/src/program-options.c |only pomdp-0.9.2/pomdp/src/program-options.h |only pomdp-0.9.2/pomdp/src/projection.c |only pomdp-0.9.2/pomdp/src/projection.h |only pomdp-0.9.2/pomdp/src/random.c |only pomdp-0.9.2/pomdp/src/random.h |only pomdp-0.9.2/pomdp/src/region.c |only pomdp-0.9.2/pomdp/src/region.h |only pomdp-0.9.2/pomdp/src/signal-handler.c |only pomdp-0.9.2/pomdp/src/signal-handler.h |only pomdp-0.9.2/pomdp/src/sim.c |only pomdp-0.9.2/pomdp/src/sim.h |only pomdp-0.9.2/pomdp/src/stats.c |only pomdp-0.9.2/pomdp/src/stats.h |only pomdp-0.9.2/pomdp/src/timing.c |only pomdp-0.9.2/pomdp/src/timing.h |only pomdp-0.9.2/pomdp/src/two-pass.c |only pomdp-0.9.2/pomdp/src/two-pass.h |only pomdp-0.9.2/pomdp/src/value-function.c |only pomdp-0.9.2/pomdp/src/value-function.h |only pomdp-0.9.2/pomdp/src/vertex-enum.c |only pomdp-0.9.2/pomdp/src/vertex-enum.h |only pomdp-0.9.2/pomdp/src/witness.c |only pomdp-0.9.2/pomdp/src/witness.h |only pomdp-0.9.2/pomdp/src/xalloc.c |only pomdp-0.9.2/pomdp/src/xalloc.h |only pomdp-0.9.2/pomdp/src/zlz_speedup.c |only pomdp-0.9.2/pomdp/src/zlz_speedup.h |only pomdp-0.9.2/pomdp/vignettes/POMDP_files |only pomdp-0.99.0/pomdp/DESCRIPTION | 42 - pomdp-0.99.0/pomdp/MD5 | 389 ++++++------ pomdp-0.99.0/pomdp/NAMESPACE | 67 +- pomdp-0.99.0/pomdp/NEWS.md | 88 +- pomdp-0.99.0/pomdp/R/AAAdatasets.R |only pomdp-0.99.0/pomdp/R/MDP.R |only pomdp-0.99.0/pomdp/R/POMDP.R | 446 ++++++++++---- pomdp-0.99.0/pomdp/R/colors.R |only pomdp-0.99.0/pomdp/R/optimal_action.R |only pomdp-0.99.0/pomdp/R/plot_belief_space.R |only pomdp-0.99.0/pomdp/R/plot_policy_graph.R |only pomdp-0.99.0/pomdp/R/plot_value_function.R |only pomdp-0.99.0/pomdp/R/policy.R |only pomdp-0.99.0/pomdp/R/policy_graph.R |only pomdp-0.99.0/pomdp/R/print.text.R |only pomdp-0.99.0/pomdp/R/read_write_POMDP.R |only pomdp-0.99.0/pomdp/R/read_write_pomdp_solve.R |only pomdp-0.99.0/pomdp/R/reward.R |only pomdp-0.99.0/pomdp/R/round_stochchastic.R |only pomdp-0.99.0/pomdp/R/sample_belief_space.R |only pomdp-0.99.0/pomdp/R/solve_POMDP.R | 821 ++++++++++++++++++-------- pomdp-0.99.0/pomdp/R/transition_matrix.R |only pomdp-0.99.0/pomdp/R/update_belief.R |only pomdp-0.99.0/pomdp/R/visNetwork.R |only pomdp-0.99.0/pomdp/README.md | 98 ++- pomdp-0.99.0/pomdp/build/vignette.rds |binary pomdp-0.99.0/pomdp/data/Three_doors.rda |only pomdp-0.99.0/pomdp/data/Tiger.rda |only pomdp-0.99.0/pomdp/inst/doc/POMDP.R | 300 ++++----- pomdp-0.99.0/pomdp/inst/doc/POMDP.Rmd | 772 ++++++++++++------------ pomdp-0.99.0/pomdp/inst/doc/POMDP.html |only pomdp-0.99.0/pomdp/man/MDP.Rd |only pomdp-0.99.0/pomdp/man/POMDP.Rd | 365 +++++++---- pomdp-0.99.0/pomdp/man/Tiger.Rd |only pomdp-0.99.0/pomdp/man/optimal_action.Rd |only pomdp-0.99.0/pomdp/man/plot_belief_space.Rd |only pomdp-0.99.0/pomdp/man/plot_policy_graph.Rd |only pomdp-0.99.0/pomdp/man/plot_value_function.Rd |only pomdp-0.99.0/pomdp/man/policy.Rd |only pomdp-0.99.0/pomdp/man/policy_graph.Rd | 99 +-- pomdp-0.99.0/pomdp/man/reward.Rd | 111 +-- pomdp-0.99.0/pomdp/man/round_stochastic.Rd |only pomdp-0.99.0/pomdp/man/sample_belief_space.Rd |only pomdp-0.99.0/pomdp/man/simulate_POMDP.Rd |only pomdp-0.99.0/pomdp/man/solve_POMDP.Rd | 398 +++++++++--- pomdp-0.99.0/pomdp/man/transition_matrix.Rd |only pomdp-0.99.0/pomdp/man/update_belief.Rd |only pomdp-0.99.0/pomdp/man/write_POMDP.Rd | 78 +- pomdp-0.99.0/pomdp/src/Makevars | 44 - pomdp-0.99.0/pomdp/src/install.libs.R |only pomdp-0.99.0/pomdp/src/pomdp-solve |only pomdp-0.99.0/pomdp/tests |only pomdp-0.99.0/pomdp/vignettes/POMDP.Rmd | 772 ++++++++++++------------ pomdp-0.99.0/pomdp/vignettes/bibliography.bib | 168 +++-- 158 files changed, 3083 insertions(+), 1975 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>),
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.3.42 dated 2017-07-28 and 0.3.56 dated 2020-05-07
HiveR-0.3.42/HiveR/inst/doc/HiveR.Rnw |only HiveR-0.3.42/HiveR/vignettes/HiveR.Rnw |only HiveR-0.3.42/HiveR/vignettes/graphics |only HiveR-0.3.56/HiveR/DESCRIPTION | 26 HiveR-0.3.56/HiveR/MD5 | 95 HiveR-0.3.56/HiveR/NAMESPACE | 2 HiveR-0.3.56/HiveR/NEWS.md |only HiveR-0.3.56/HiveR/R/Arroyo.R | 11 HiveR-0.3.56/HiveR/R/HEC.R | 120 HiveR-0.3.56/HiveR/R/HidingAnAxis.R | 183 HiveR-0.3.56/HiveR/R/HivePlotData.R | 11 HiveR-0.3.56/HiveR/R/HiveR-package.R | 9 HiveR-0.3.56/HiveR/R/adj2HPD.R | 239 - HiveR-0.3.56/HiveR/R/animateHive.R | 90 HiveR-0.3.56/HiveR/R/chkHPD.R | 139 HiveR-0.3.56/HiveR/R/dot2HPD.R | 388 +- HiveR-0.3.56/HiveR/R/drawHiveSpline.R | 408 +- HiveR-0.3.56/HiveR/R/edge2HPD.R | 97 HiveR-0.3.56/HiveR/R/manipAxis.R | 752 +-- HiveR-0.3.56/HiveR/R/mineHPD.R | 600 +-- HiveR-0.3.56/HiveR/R/plot3dHive.R | 596 +-- HiveR-0.3.56/HiveR/R/plotHive.R | 3954 ++++++++++----------- HiveR-0.3.56/HiveR/R/ranHiveData.R | 794 ++-- HiveR-0.3.56/HiveR/R/rcsr.R | 397 +- HiveR-0.3.56/HiveR/R/sph2cart.R | 28 HiveR-0.3.56/HiveR/R/sumHPD.R | 348 - HiveR-0.3.56/HiveR/build/vignette.rds |binary HiveR-0.3.56/HiveR/inst/doc/HiveR.R | 80 HiveR-0.3.56/HiveR/inst/doc/HiveR.Rmd |only HiveR-0.3.56/HiveR/inst/doc/HiveR.pdf |binary HiveR-0.3.56/HiveR/man/HEC.Rd | 85 HiveR-0.3.56/HiveR/man/HidingAnAxis.Rd | 125 HiveR-0.3.56/HiveR/man/HivePlotData.Rd | 1 HiveR-0.3.56/HiveR/man/adj2HPD.Rd | 15 HiveR-0.3.56/HiveR/man/animateHive.Rd | 4 HiveR-0.3.56/HiveR/man/dot2HPD.Rd | 11 HiveR-0.3.56/HiveR/man/edge2HPD.Rd | 16 HiveR-0.3.56/HiveR/man/manipAxis.Rd | 3 HiveR-0.3.56/HiveR/man/mineHPD.Rd | 3 HiveR-0.3.56/HiveR/man/plotHive.Rd | 134 HiveR-0.3.56/HiveR/man/ranHiveData.Rd | 20 HiveR-0.3.56/HiveR/man/rcsr.Rd | 159 HiveR-0.3.56/HiveR/man/sumHPD.Rd | 16 HiveR-0.3.56/HiveR/vignettes/Abbrev2ndCitation.tex |only HiveR-0.3.56/HiveR/vignettes/HiveR.Rmd |only HiveR-0.3.56/HiveR/vignettes/images |only 46 files changed, 5170 insertions(+), 4789 deletions(-)
Title: Time Series Forecasting with Machine Learning Methods
Description: The purpose of 'forecastML' is to simplify the process of multi-step-ahead forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
Author: Nickalus Redell
Maintainer: Nickalus Redell <nickalusredell@gmail.com>
Diff between forecastML versions 0.8.0 dated 2020-02-28 and 0.9.0 dated 2020-05-07
forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.R |only forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.Rmd |only forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.html |only forecastML-0.8.0/forecastML/vignettes/grouped_forecast_sequences.Rmd |only forecastML-0.9.0/forecastML/DESCRIPTION | 15 forecastML-0.9.0/forecastML/MD5 | 95 - forecastML-0.9.0/forecastML/NAMESPACE | 4 forecastML-0.9.0/forecastML/R/combine_forecasts.R | 112 - forecastML-0.9.0/forecastML/R/create_skeleton.R |only forecastML-0.9.0/forecastML/R/create_windows.R | 30 forecastML-0.9.0/forecastML/R/fill_gaps.R | 20 forecastML-0.9.0/forecastML/R/lagged_df.R | 181 +- forecastML-0.9.0/forecastML/R/return_error.R | 670 +++++++--- forecastML-0.9.0/forecastML/R/return_hyper.R | 22 forecastML-0.9.0/forecastML/R/train_model.R | 122 + forecastML-0.9.0/forecastML/R/zzz.R | 36 forecastML-0.9.0/forecastML/README.md | 26 forecastML-0.9.0/forecastML/build/vignette.rds |binary forecastML-0.9.0/forecastML/inst/doc/combine_forecasts.R |only forecastML-0.9.0/forecastML/inst/doc/combine_forecasts.Rmd |only forecastML-0.9.0/forecastML/inst/doc/combine_forecasts.html |only forecastML-0.9.0/forecastML/inst/doc/custom_functions.html | 79 - forecastML-0.9.0/forecastML/inst/doc/grouped_forecast.R | 10 forecastML-0.9.0/forecastML/inst/doc/grouped_forecast.Rmd | 10 forecastML-0.9.0/forecastML/inst/doc/grouped_forecast.html | 107 - forecastML-0.9.0/forecastML/inst/doc/lagged_features.html | 73 - forecastML-0.9.0/forecastML/inst/doc/package_overview.R | 62 forecastML-0.9.0/forecastML/inst/doc/package_overview.Rmd | 90 - forecastML-0.9.0/forecastML/inst/doc/package_overview.html | 329 ++-- forecastML-0.9.0/forecastML/man/combine_forecasts.Rd | 9 forecastML-0.9.0/forecastML/man/create_lagged_df.Rd | 346 ++--- forecastML-0.9.0/forecastML/man/create_skeleton.Rd |only forecastML-0.9.0/forecastML/man/data_buoy.Rd | 6 forecastML-0.9.0/forecastML/man/data_buoy_gaps.Rd | 6 forecastML-0.9.0/forecastML/man/data_seatbelts.Rd | 4 forecastML-0.9.0/forecastML/man/fill_gaps.Rd | 152 +- forecastML-0.9.0/forecastML/man/plot.forecast_error.Rd |only forecastML-0.9.0/forecastML/man/plot.forecast_model_hyper.Rd | 2 forecastML-0.9.0/forecastML/man/plot.validation_error.Rd | 9 forecastML-0.9.0/forecastML/man/return_error.Rd | 27 forecastML-0.9.0/forecastML/man/summary.lagged_df.Rd | 36 forecastML-0.9.0/forecastML/tests/testthat/test_combine_forecasts.R | 56 forecastML-0.9.0/forecastML/tests/testthat/test_create_lagged_df_grouped.R | 69 + forecastML-0.9.0/forecastML/tests/testthat/test_create_lagged_df_nongrouped.R | 8 forecastML-0.9.0/forecastML/tests/testthat/test_create_skeleton.R |only forecastML-0.9.0/forecastML/tests/testthat/test_create_windows.R | 10 forecastML-0.9.0/forecastML/tests/testthat/test_cv.R | 33 forecastML-0.9.0/forecastML/tests/testthat/test_fill_gaps.R | 18 forecastML-0.9.0/forecastML/tests/testthat/test_return_error.R | 239 +++ forecastML-0.9.0/forecastML/tests/testthat/test_train_model.R | 18 forecastML-0.9.0/forecastML/vignettes/combine_forecasts.Rmd |only forecastML-0.9.0/forecastML/vignettes/forecast_combination_1.png |only forecastML-0.9.0/forecastML/vignettes/forecast_combination_2.png |only forecastML-0.9.0/forecastML/vignettes/forecast_combination_3.png |only forecastML-0.9.0/forecastML/vignettes/grouped_forecast.Rmd | 10 forecastML-0.9.0/forecastML/vignettes/package_overview.Rmd | 90 - 56 files changed, 2047 insertions(+), 1194 deletions(-)
Title: Methods for Identification of Outliers in Environmental Data
Description: Three semi-parametric methods for detection of outliers in environmental data based on kernel regression and subsequent analysis of smoothing residuals. The first method (Campulova, Michalek, Mikuska and Bokal (2018) <DOI: 10.1002/cem.2997>) analyzes the residuals using changepoint analysis, the second method is based on control charts (Campulova, Veselik and Michalek (2017) <DOI: 10.1016/j.apr.2017.01.004>) and the third method (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>) analyzes the residuals using extreme value theory (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>).
Author: Martina Campulova [cre],
Martina Campulova [aut],
Roman Campula [ctb]
Maintainer: Martina Campulova <martina.campulova@mendelu.cz>
Diff between envoutliers versions 1.0.0 dated 2019-11-05 and 1.1.0 dated 2020-05-07
envoutliers-1.0.0/envoutliers/man/KRDetect.EV.plot.Rd |only envoutliers-1.0.0/envoutliers/man/KRDetect.changepoint.plot.Rd |only envoutliers-1.0.0/envoutliers/man/KRDetect.controlchart.plot.Rd |only envoutliers-1.1.0/envoutliers/DESCRIPTION | 6 envoutliers-1.1.0/envoutliers/MD5 | 53 envoutliers-1.1.0/envoutliers/NAMESPACE | 9 envoutliers-1.1.0/envoutliers/NEWS | 7 envoutliers-1.1.0/envoutliers/R/changepoint.R | 150 + envoutliers-1.1.0/envoutliers/R/controlchart.R | 100 - envoutliers-1.1.0/envoutliers/R/deprecated.R |only envoutliers-1.1.0/envoutliers/R/extremevalue.R | 928 +++++++++- envoutliers-1.1.0/envoutliers/R/generalFunctions.R | 341 ++- envoutliers-1.1.0/envoutliers/man/EV.plot.Rd |only envoutliers-1.1.0/envoutliers/man/KRDetect.outliers.EV.Rd | 121 + envoutliers-1.1.0/envoutliers/man/KRDetect.outliers.changepoint.Rd | 66 envoutliers-1.1.0/envoutliers/man/KRDetect.outliers.controlchart.Rd | 51 envoutliers-1.1.0/envoutliers/man/KRDetect.outliers.plot.Rd | 34 envoutliers-1.1.0/envoutliers/man/MRL.plot.Rd |only envoutliers-1.1.0/envoutliers/man/Moment.gpd.fit.Rd |only envoutliers-1.1.0/envoutliers/man/changepoint.Rd | 9 envoutliers-1.1.0/envoutliers/man/changepoint.plot.Rd |only envoutliers-1.1.0/envoutliers/man/control.limits.x.Rd | 8 envoutliers-1.1.0/envoutliers/man/controlchart.plot.Rd |only envoutliers-1.1.0/envoutliers/man/extremal.index.Kgaps.Rd |only envoutliers-1.1.0/envoutliers/man/extremal.index.censored.Rd |only envoutliers-1.1.0/envoutliers/man/extremal.index.gomes.Rd | 4 envoutliers-1.1.0/envoutliers/man/extremal.index.intervals.Rd |only envoutliers-1.1.0/envoutliers/man/extremal.index.runs.Rd |only envoutliers-1.1.0/envoutliers/man/extremal.index.sliding.blocks.Rd |only envoutliers-1.1.0/envoutliers/man/find.L.Rd | 2 envoutliers-1.1.0/envoutliers/man/plot.KRDetect.Rd |only envoutliers-1.1.0/envoutliers/man/return.level.est.Rd | 4 envoutliers-1.1.0/envoutliers/man/segment.length.control.Rd | 2 envoutliers-1.1.0/envoutliers/man/smoothing.Rd | 57 envoutliers-1.1.0/envoutliers/man/stability.plot.Rd |only envoutliers-1.1.0/envoutliers/man/summary.KRDetect.Rd |only 36 files changed, 1569 insertions(+), 383 deletions(-)
Title: An Interface to Specify Causal Graphs and Compute Bounds on
Causal Effects
Description: When causal quantities are not identifiable from the observed data, it still may be possible
to bound these quantities using the observed data. We outline a class of problems for which the
derivation of tight bounds is always a linear programming problem and can therefore, at least
theoretically, be solved using a symbolic linear optimizer. We extend and generalize the
approach of Balke and Pearl (1994) <doi:10.1016/B978-1-55860-332-5.50011-0> and we provide
a user friendly graphical interface for setting up such problems via directed acyclic
graphs (DAG), which only allow for problems within this class to be depicted. The user can
then define linear constraints to further refine their assumptions to meet their specific
problem, and then specify a causal query using a text interface. The program converts this
user defined DAG, query, and constraints, and returns tight bounds. The bounds can be
converted to R functions to evaluate them for specific datasets, and to latex code for
publication. The methods and proofs of tightness and validity of the bounds are described in
a preprint by Sachs, Gabriel, and Sjölander (2020)
<https://sachsmc.github.io/causaloptim/articles/CausalBoundsMethods.pdf>.
Author: Michael C Sachs [aut, cre],
Erin E Gabriel [aut],
Arvid Sjölander [aut],
Alexander A Balke [ctb] ((C++ code)),
Colorado Reed [ctb] ((graph-creator.js))
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between causaloptim versions 0.6.5 dated 2020-03-25 and 0.7.1 dated 2020-05-07
causaloptim-0.6.5/causaloptim/vignettes/Linear_Optimization_of_Causal_Bounds.pdf |only causaloptim-0.7.1/causaloptim/DESCRIPTION | 10 causaloptim-0.7.1/causaloptim/MD5 | 57 +-- causaloptim-0.7.1/causaloptim/NAMESPACE | 4 causaloptim-0.7.1/causaloptim/NEWS.md | 13 causaloptim-0.7.1/causaloptim/R/response-functional.R | 177 ++++++++-- causaloptim-0.7.1/causaloptim/R/utils.R |only causaloptim-0.7.1/causaloptim/README.md | 2 causaloptim-0.7.1/causaloptim/build/vignette.rds |binary causaloptim-0.7.1/causaloptim/inst/doc/CausalBoundsMethods.Rmd | 4 causaloptim-0.7.1/causaloptim/inst/doc/CausalBoundsMethods.pdf |binary causaloptim-0.7.1/causaloptim/inst/doc/shinyapp.Rmd | 2 causaloptim-0.7.1/causaloptim/inst/doc/shinyapp.html | 16 causaloptim-0.7.1/causaloptim/inst/shiny/interface/server.R | 36 +- causaloptim-0.7.1/causaloptim/inst/shiny/interface/www/shinyapp.html | 37 -- causaloptim-0.7.1/causaloptim/man/analyze_graph.Rd | 6 causaloptim-0.7.1/causaloptim/man/btm_var.Rd |only causaloptim-0.7.1/causaloptim/man/const.to.sets.Rd | 30 - causaloptim-0.7.1/causaloptim/man/expand_cond.Rd | 30 - causaloptim-0.7.1/causaloptim/man/find_cycles.Rd | 32 - causaloptim-0.7.1/causaloptim/man/list_to_path.Rd |only causaloptim-0.7.1/causaloptim/man/pastestar.Rd | 26 - causaloptim-0.7.1/causaloptim/man/plot.linearcausalproblem.Rd |only causaloptim-0.7.1/causaloptim/man/plot_graphres.Rd | 32 - causaloptim-0.7.1/causaloptim/man/print.linearcausalproblem.Rd |only causaloptim-0.7.1/causaloptim/man/reduce.sets.Rd | 26 - causaloptim-0.7.1/causaloptim/man/shortentxt.Rd | 26 - causaloptim-0.7.1/causaloptim/man/symb.subtract.Rd | 30 - causaloptim-0.7.1/causaloptim/src/Makevars | 2 causaloptim-0.7.1/causaloptim/tests/test-graphs-for-known-bounds.R | 31 + causaloptim-0.7.1/causaloptim/vignettes/CausalBoundsMethods.Rmd | 4 causaloptim-0.7.1/causaloptim/vignettes/Linear_Optimization_of_Causal_Bounds_Draft.pdf |only causaloptim-0.7.1/causaloptim/vignettes/shinyapp.Rmd | 2 33 files changed, 411 insertions(+), 224 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC)
as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations,
and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring.
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints to estimate the probability that a random observation drawn from
one group performs better than a random observation drawn from the other group (Mann-Whitney parameter).
The net benefit and win ratio statistics,
i.e. the difference and ratio between the probabilities relative to the intervention and control groups,
can then also be estimated. Confidence intervals and p-values are obtained using permutations, a non-parametric bootstrap, or the asymptotic theory.
The software enables the use of thresholds of minimal importance difference,
stratification, non-prioritized endpoints (O'Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 2.1.0 dated 2020-04-26 and 2.1.3 dated 2020-05-07
DESCRIPTION | 8 +- MD5 | 31 +++++----- NEWS | 27 ++++++--- R/BuyseTest.R | 1 R/S4-BuyseTest-get.R | 1 R/auc.R | 5 - R/iid.prodlim.R | 5 - R/powerBuyseTest.R | 5 - R/simBuyseTest.R | 1 build/vignette.rds |binary inst/testthat2.R |only src/FCT_buyseTest.cpp | 72 ++++++++++++++---------- src/FCT_calcAllPairs.h | 82 ++++++++++++++-------------- src/FCT_calcOnePair.h | 43 +++++++------- tests/testthat.R | 26 ++++++++ tests/testthat/test-BuyseTest-engine.R | 5 + tests/testthat/test-BuyseTest-previousBug.R | 6 +- 17 files changed, 183 insertions(+), 135 deletions(-)
Title: Consistent Batch Means Estimation of Monte Carlo Standard Errors
Description: Provides consistent batch means estimation of Monte
Carlo standard errors.
Author: Murali Haran <mharan@stat.psu.edu> and John Hughes
<drjphughesjr@gmail.com>
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between batchmeans versions 1.0-3 dated 2016-07-04 and 1.0-4 dated 2020-05-07
COPYING | 2 +- DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/zzz.R | 6 +++--- inst/CITATION | 4 ++-- 5 files changed, 16 insertions(+), 16 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-20 1.4.0
2020-04-03 1.3.0
2020-03-15 1.2.1
2020-03-11 1.2.0
2020-03-01 1.1.0
2020-02-17 1.0.0
2019-12-06 0.19.0
2019-11-11 0.18.0
2019-10-30 0.16.0
2019-09-19 0.15.0
2019-05-28 0.14.0
2019-04-25 0.13.0
2018-11-05 0.12.0
2018-07-20 0.11.0
2018-06-25 0.10.0
2018-03-07 0.9.0
2018-01-31 0.7.0
2017-10-25 0.6.0
2017-10-10 0.5.0
2017-08-09 0.4.0
2017-06-20 0.3.0
2017-05-24 0.2.0
2017-04-26 0.1.0
Title: Manage 'tmux' Sessions, Windows, and Panes
Description: Create, control, and capture 'tmux' sessions, windows, and panes
using a pipeable API.
Author: Jeroen Janssens [aut, cre] (<https://orcid.org/0000-0002-5878-8924>),
Data Science Workshops [cph, fnd]
Maintainer: Jeroen Janssens <jeroen@datascienceworkshops.com>
Diff between tmuxr versions 0.2.2 dated 2020-05-02 and 0.2.3 dated 2020-05-07
DESCRIPTION | 10 +++--- MD5 | 58 ++++++++++++++++++++-------------------- NEWS.md | 9 +++++- R/layout.R | 2 + R/send.R | 18 ++++++++---- R/server.R | 2 + R/session.R | 2 + R/utils.R | 6 ++++ R/window.R | 2 + README.md | 13 ++++++-- man/display_message.Rd | 2 + man/new_session.Rd | 2 + man/new_window.Rd | 2 + man/prop.Rd | 2 + man/send_keys.Rd | 2 + man/send_prefix.Rd | 2 - man/style_convert.Rd | 2 + man/tmux_command.Rd | 2 + man/tmux_version.Rd | 2 + man/tmuxr-package.Rd | 2 - tests/testthat.R | 1 tests/testthat/setup-tmuxr.R | 15 ++++++---- tests/testthat/teardown-tmuxr.R | 4 ++ tests/testthat/test-pane.R | 29 +++++++++++--------- tests/testthat/test-select.R | 6 ++++ tests/testthat/test-send.R | 6 +++- tests/testthat/test-server.R | 7 ++++ tests/testthat/test-session.R | 11 ++++++- tests/testthat/test-utils.R | 6 ++++ tests/testthat/test-window.R | 16 +++++++++-- 30 files changed, 174 insertions(+), 69 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990's.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Werner Stahel [ctb] (Functions: compresid2way(), f.robftest(), last(),
p.scales(), p.dnorm()),
Andreas Ruckstuhl [ctb] (Functions: p.arrows(), p.profileTraces(),
p.res.2x()),
Christian Keller [ctb] (Functions: histBxp(), p.tachoPlot()),
Kjetil Halvorsen [ctb] (Functions: KSd(), ecdf.ksCI()),
Alain Hauser [ctb] (Functions: cairoSwd(), is.whole(),
toLatex.numeric()*),
Christoph Buser [ctb] (to function Duplicated()),
Lorenz Gygax [ctb] (to function p.res.2fact()),
Bill Venables [ctb] (Functions: empty.dimnames(), primes()),
Tony Plate [ctb] (to inv.seq()),
Isabelle Fl<fc>ckiger [ctb],
Marcel Wolbers [ctb],
Markus Keller [ctb],
Sandrine Dudoit [ctb],
Jane Fridlyand [ctb],
Greg Snow [ctb] (to loessDemo()),
Henrik Aa. Nielsen [ctb] (to loessDemo()),
Vincent Carey [ctb],
Ben Bolker [ctb],
Philippe Grosjean [ctb],
Fr<e9>d<e9>ric Ibanez [ctb],
Caterina Savi [ctb],
Charles Geyer [ctb],
Jens Oehlschl<e4>gel [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-6 dated 2020-04-06 and 1.1-7 dated 2020-05-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/misc-goodies.R | 10 ++++------ R/prettylab.R | 35 ++++++++++++++++++----------------- inst/NEWS.Rd | 18 ++++++++++++------ man/eaxis.Rd | 7 +++++-- 6 files changed, 48 insertions(+), 40 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.6-4 dated 2020-04-07 and 0.6-5 dated 2020-05-07
OncoBayes2-0.6-4/OncoBayes2/inst/sbc/sbc_report.html |only OncoBayes2-0.6-5/OncoBayes2/DESCRIPTION | 17 OncoBayes2-0.6-5/OncoBayes2/MD5 | 71 - OncoBayes2-0.6-5/OncoBayes2/NAMESPACE | 4 OncoBayes2-0.6-5/OncoBayes2/R/OncoBayes2-package.R | 1 OncoBayes2-0.6-5/OncoBayes2/R/blrm_exnex.R | 9 OncoBayes2-0.6-5/OncoBayes2/R/lodds.R |only OncoBayes2-0.6-5/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.6-5/OncoBayes2/R/zzz.R | 1 OncoBayes2-0.6-5/OncoBayes2/inst/NEWS | 6 OncoBayes2-0.6-5/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.6-5/OncoBayes2/inst/doc/introduction.R | 4 OncoBayes2-0.6-5/OncoBayes2/inst/doc/introduction.Rmd | 14 OncoBayes2-0.6-5/OncoBayes2/inst/doc/introduction.html | 451 ++++------ OncoBayes2-0.6-5/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.6-5/OncoBayes2/inst/sbc/make_reference_rankhist.R | 208 +++- OncoBayes2-0.6-5/OncoBayes2/inst/sbc/sbc_example_models.R | 36 OncoBayes2-0.6-5/OncoBayes2/inst/sbc/sbc_report.R | 9 OncoBayes2-0.6-5/OncoBayes2/inst/sbc/sbc_tools.R | 126 ++ OncoBayes2-0.6-5/OncoBayes2/man/OncoBayes2.Rd | 1 OncoBayes2-0.6-5/OncoBayes2/man/blrm_exnex.Rd | 33 OncoBayes2-0.6-5/OncoBayes2/man/blrm_trial.Rd | 28 OncoBayes2-0.6-5/OncoBayes2/man/codata_combo2.Rd | 7 OncoBayes2-0.6-5/OncoBayes2/man/dose_info_combo2.Rd | 11 OncoBayes2-0.6-5/OncoBayes2/man/drug_info_combo2.Rd | 13 OncoBayes2-0.6-5/OncoBayes2/man/example-combo2.Rd | 1 OncoBayes2-0.6-5/OncoBayes2/man/example-combo2_trial.Rd | 8 OncoBayes2-0.6-5/OncoBayes2/man/example-combo3.Rd | 1 OncoBayes2-0.6-5/OncoBayes2/man/example-single-agent.Rd | 2 OncoBayes2-0.6-5/OncoBayes2/man/hist_SA.Rd | 8 OncoBayes2-0.6-5/OncoBayes2/man/hist_combo2.Rd | 6 OncoBayes2-0.6-5/OncoBayes2/man/hist_combo3.Rd | 7 OncoBayes2-0.6-5/OncoBayes2/man/lodds.Rd |only OncoBayes2-0.6-5/OncoBayes2/man/posterior_linpred.blrmfit.Rd | 3 OncoBayes2-0.6-5/OncoBayes2/man/summary.blrm_trial.Rd | 9 OncoBayes2-0.6-5/OncoBayes2/man/summary.blrmfit.Rd | 3 OncoBayes2-0.6-5/OncoBayes2/tools/make-ds.R | 1 OncoBayes2-0.6-5/OncoBayes2/vignettes/introduction.Rmd | 14 38 files changed, 682 insertions(+), 437 deletions(-)
Title: Robust Partial Least Squares
Description: A robust Partial Least-Squares (PLS) method is implemented that is robust to outliers in the residuals as well as to leverage points. A specific weighting scheme is applied which avoids iterations, and leads to a highly efficient robust PLS estimator.
Author: Peter Filzmoser, Sukru Acitas, Birdal Senoglu and Maximilian Plattner
Maintainer: Peter Filzmoser <peter.filzmoser@tuwien.ac.at>
Diff between rpls versions 0.4.0 dated 2020-03-08 and 0.6.0 dated 2020-05-07
DESCRIPTION | 6 MD5 | 6 R/PRM.R | 767 +++++++++++++++++++++++++++++------------------------------- man/PRM.Rd | 8 4 files changed, 393 insertions(+), 394 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-210X.13270>,
and
Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc],
Autumn-Lynn Harrison [dtc],
Ronaldo G. Morato [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.9 dated 2020-03-23 and 0.5.10 dated 2020-05-07
DESCRIPTION | 8 - MD5 | 36 +++---- NAMESPACE | 7 + NEWS.md | 11 ++ R/1.R | 1 R/color.R | 14 +- R/covm.R | 16 +++ R/encounter.R | 7 + R/generic.R | 9 + R/kde.R | 48 +++++---- R/meta.R | 244 ++++++++++++++++++++++++++++++++++++++++++++++-- R/modes.R | 260 ++++++++++++++++++++++++++++++++++++++++------------ R/plot.telemetry.R | 2 R/telemetry.R | 112 +++++++++++++--------- TODO | 2 build/vignette.rds |binary data/jaguar.rda |binary man/bandwidth.Rd | 2 man/ctmm-package.Rd | 4 19 files changed, 612 insertions(+), 171 deletions(-)
Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care
Data and visualization of individual medication histories and adherence
patterns. The package implements a set of S3 classes and
functions consistent with current adherence guidelines and definitions.
It allows the computation of different measures of
adherence (as defined in the literature, but also several original ones),
their publication-quality plotting,
the estimation of event duration and time to initiation,
the interactive exploration of patient medication history and
the real-time estimation of adherence given various parameter settings.
It scales from very small datasets stored in flat CSV files to very large
databases and from single-thread processing on mid-range consumer
laptops to parallel processing on large heterogeneous computing clusters.
It exposes a standardized interface allowing it to be used from other
programming languages and platforms, such as Python.
Author: Dan Dediu [aut, cre],
Alexandra Dima [aut],
Samuel Allemann [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>
Diff between AdhereR versions 0.5 dated 2019-06-11 and 0.6.0 dated 2020-05-07
AdhereR-0.5/AdhereR/inst/interactivePlotShiny |only AdhereR-0.6.0/AdhereR/DESCRIPTION | 18 AdhereR-0.6.0/AdhereR/MD5 | 144 AdhereR-0.6.0/AdhereR/NAMESPACE | 160 AdhereR-0.6.0/AdhereR/NEWS.md |only AdhereR-0.6.0/AdhereR/R/adherer.R |18628 ++++------ AdhereR-0.6.0/AdhereR/R/matching_function.R | 4546 +- AdhereR-0.6.0/AdhereR/R/plotting.R |only AdhereR-0.6.0/AdhereR/R/polypharmacy.R |only AdhereR-0.6.0/AdhereR/build/vignette.rds |binary AdhereR-0.6.0/AdhereR/inst/CITATION | 56 AdhereR-0.6.0/AdhereR/inst/doc/AdhereR-overview.R | 658 AdhereR-0.6.0/AdhereR/inst/doc/AdhereR-overview.Rmd | 1798 AdhereR-0.6.0/AdhereR/inst/doc/AdhereR-overview.html | 3173 - AdhereR-0.6.0/AdhereR/inst/doc/adherer_with_databases.pdf.asis | 10 AdhereR-0.6.0/AdhereR/inst/doc/calling-AdhereR-from-python3.R | 10 AdhereR-0.6.0/AdhereR/inst/doc/calling-AdhereR-from-python3.Rmd | 2742 - AdhereR-0.6.0/AdhereR/inst/doc/calling-AdhereR-from-python3.html | 6147 +-- AdhereR-0.6.0/AdhereR/inst/html-templates |only AdhereR-0.6.0/AdhereR/inst/specialVignettes/adherer_with_databases.Rmd | 1900 - AdhereR-0.6.0/AdhereR/inst/specialVignettes/apa.csl | 1550 AdhereR-0.6.0/AdhereR/inst/specialVignettes/bibliography.bibtex | 28 AdhereR-0.6.0/AdhereR/inst/wrappers/python3/adherer.py | 6212 +-- AdhereR-0.6.0/AdhereR/man/CMA0.Rd | 409 AdhereR-0.6.0/AdhereR/man/CMA1.Rd | 496 AdhereR-0.6.0/AdhereR/man/CMA2.Rd | 496 AdhereR-0.6.0/AdhereR/man/CMA5.Rd | 504 AdhereR-0.6.0/AdhereR/man/CMA6.Rd | 504 AdhereR-0.6.0/AdhereR/man/CMA7.Rd | 496 AdhereR-0.6.0/AdhereR/man/CMA8.Rd | 532 AdhereR-0.6.0/AdhereR/man/CMA9.Rd | 516 AdhereR-0.6.0/AdhereR/man/CMA_per_episode.Rd | 581 AdhereR-0.6.0/AdhereR/man/CMA_polypharmacy.Rd |only AdhereR-0.6.0/AdhereR/man/CMA_sliding_window.Rd | 544 AdhereR-0.6.0/AdhereR/man/callAdhereR.Rd | 92 AdhereR-0.6.0/AdhereR/man/compute.event.int.gaps.Rd | 382 AdhereR-0.6.0/AdhereR/man/compute.treatment.episodes.Rd | 388 AdhereR-0.6.0/AdhereR/man/compute_event_durations.Rd | 501 AdhereR-0.6.0/AdhereR/man/cover_special_periods.Rd | 242 AdhereR-0.6.0/AdhereR/man/durcomp.dispensing.Rd | 76 AdhereR-0.6.0/AdhereR/man/durcomp.hospitalisation.Rd | 60 AdhereR-0.6.0/AdhereR/man/durcomp.prescribing.Rd | 88 AdhereR-0.6.0/AdhereR/man/get.event.plotting.area.Rd |only AdhereR-0.6.0/AdhereR/man/get.legend.plotting.area.Rd |only AdhereR-0.6.0/AdhereR/man/get.plotted.events.Rd |only AdhereR-0.6.0/AdhereR/man/get.plotted.partial.cmas.Rd |only AdhereR-0.6.0/AdhereR/man/getCMA.Rd | 92 AdhereR-0.6.0/AdhereR/man/getCallerWrapperLocation.Rd | 57 AdhereR-0.6.0/AdhereR/man/last.plot.get.info.Rd |only AdhereR-0.6.0/AdhereR/man/map.event.coords.to.plot.Rd |only AdhereR-0.6.0/AdhereR/man/med.events.Rd | 86 AdhereR-0.6.0/AdhereR/man/plot.CMA0.Rd | 460 AdhereR-0.6.0/AdhereR/man/plot.CMA1.Rd | 523 AdhereR-0.6.0/AdhereR/man/plot.CMA_per_episode.Rd | 672 AdhereR-0.6.0/AdhereR/man/plot_interactive_cma.Rd | 193 AdhereR-0.6.0/AdhereR/man/print.CMA0.Rd | 230 AdhereR-0.6.0/AdhereR/man/prune_event_durations.Rd | 204 AdhereR-0.6.0/AdhereR/man/time_to_initiation.Rd | 187 AdhereR-0.6.0/AdhereR/vignettes/AdhereR-overview.Rmd | 1798 AdhereR-0.6.0/AdhereR/vignettes/adherer_with_databases.pdf.asis | 10 AdhereR-0.6.0/AdhereR/vignettes/calling-AdhereR-from-python3.Rmd | 2742 - 61 files changed, 29794 insertions(+), 32147 deletions(-)
Title: Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Description: Rapid advancements in high-throughput gene sequencing
technologies have resulted in genome-scale time-series datasets.
Uncovering the underlying temporal sequence of gene regulatory events
in the form of time-varying gene regulatory networks demands
accurate and computationally efficient algorithms. Such an
algorithm is 'TGS'. It is proposed in Saptarshi Pyne, Alok Ranjan
Kumar, and Ashish Anand. Rapid reconstruction of time-varying
gene regulatory networks. IEEE/ACM Transactions on Computational
Biology and Bioinformatics, 17(1):278{291, Jan-Feb 2020. The TGS
algorithm is shown to consume only 29 minutes for a microarray
dataset with 4028 genes. This package provides an implementation
of the TGS algorithm and its variants.
Author: Saptarshi Pyne [aut, cre] (<https://orcid.org/0000-0001-9710-6749>),
Manan Gupta [aut],
Alok Kumar [aut],
Ashish Anand [aut] (<https://orcid.org/0000-0002-0024-3358>)
Maintainer: Saptarshi Pyne <saptarshipyne01@gmail.com>
Diff between TGS versions 1.0.0 dated 2018-11-16 and 1.0.1 dated 2020-05-07
TGS-1.0.0/TGS/R/TGS.R |only TGS-1.0.0/TGS/inst/doc/TGS.ltx |only TGS-1.0.0/TGS/inst/doc/TGS.pdf |only TGS-1.0.0/TGS/man/CompareNet.Rd |only TGS-1.0.0/TGS/man/ComputEntropy.Rd |only TGS-1.0.0/TGS/man/ComputeCmiPcaCmi.Rd |only TGS-1.0.0/TGS/man/ConvertDinetToUndinet.Rd |only TGS-1.0.0/TGS/man/CountFeedFwdEdgesUndi.Rd |only TGS-1.0.0/TGS/man/GenTrueAdjMatrix.Rd |only TGS-1.0.0/TGS/man/LearnClr2NetMfi.Rd |only TGS-1.0.0/TGS/man/LearnClr3NetMfi.Rd |only TGS-1.0.0/TGS/man/LearnClrNetFromDiscrData.Rd |only TGS-1.0.0/TGS/man/LearnClrNetMfi.Rd |only TGS-1.0.0/TGS/man/LearnClrNetMfiVer2.1.Rd |only TGS-1.0.0/TGS/man/LearnDbnStructMo1Clr3Ser.Rd |only TGS-1.0.0/TGS/man/LearnMiNetStructClr.Rd |only TGS-1.0.0/TGS/man/LearnMiNetStructRowMedian.Rd |only TGS-1.0.0/TGS/man/LearnMiNetStructZstat.Rd |only TGS-1.0.0/TGS/man/Print.common.di.edges.Rd |only TGS-1.0.0/TGS/man/adjmxToSif.Rd |only TGS-1.0.0/TGS/man/calcPerfDiNet.Rd |only TGS-1.0.0/TGS/man/checkUnrolledDbn.Rd |only TGS-1.0.0/TGS/man/computeCmi.Rd |only TGS-1.0.0/TGS/man/discretizeData.2L.Tesla.Rd |only TGS-1.0.0/TGS/man/discretizeData.2L.wt.l.Rd |only TGS-1.0.0/TGS/man/discretizeData.2L.wt.le.Rd |only TGS-1.0.0/TGS/man/discretizeData.3L.wt.Rd |only TGS-1.0.0/TGS/man/discretizeData.5L.wt.Rd |only TGS-1.0.0/TGS/man/eval.wrt.known.gene.ias.Rd |only TGS-1.0.0/TGS/man/learnCmiNetStruct.Rd |only TGS-1.0.0/TGS/man/learnDbnStructLayer3dParDeg1.Rd |only TGS-1.0.0/TGS/man/learnDbnStructMo1Layer3dParDeg1.Rd |only TGS-1.0.0/TGS/man/learnDbnStructMo1Layer3dParDeg1_v2.Rd |only TGS-1.0.0/TGS/man/reachable.nodes.Rd |only TGS-1.0.0/TGS/man/rollDbn.Rd |only TGS-1.0.0/TGS/man/rollDbn_v2.Rd |only TGS-1.0.0/TGS/vignettes/TGS.ltx |only TGS-1.0.0/TGS/vignettes/images |only TGS-1.0.1/TGS/DESCRIPTION | 50 TGS-1.0.1/TGS/MD5 | 128 TGS-1.0.1/TGS/NAMESPACE | 50 TGS-1.0.1/TGS/NEWS.md | 7 TGS-1.0.1/TGS/R/CompareNet.R | 183 TGS-1.0.1/TGS/R/CondMutualInfo.R | 90 TGS-1.0.1/TGS/R/RDataToCytoscape.R | 112 TGS-1.0.1/TGS/R/TGS-package.R |only TGS-1.0.1/TGS/R/calcPerfDiNet.R | 513 - TGS-1.0.1/TGS/R/checkUnrolledDbn.R | 82 TGS-1.0.1/TGS/R/compute_cmi.R | 147 TGS-1.0.1/TGS/R/convert_dinet_to_undinet.R | 63 TGS-1.0.1/TGS/R/count_feed_fwd_edges_undi.R | 77 TGS-1.0.1/TGS/R/discretizeData.R | 615 - TGS-1.0.1/TGS/R/genTrueNetFunc.R | 94 TGS-1.0.1/TGS/R/graphFns.R | 114 TGS-1.0.1/TGS/R/learnCmiNetStruct.R | 240 TGS-1.0.1/TGS/R/learnDbnStruct3dParDeg1.R | 3118 ++++------ TGS-1.0.1/TGS/R/learn_TGS.R |only TGS-1.0.1/TGS/R/learn_mi_net_struct.R | 1743 ++--- TGS-1.0.1/TGS/R/rollDbn.R | 421 - TGS-1.0.1/TGS/README.md | 24 TGS-1.0.1/TGS/build/vignette.rds |binary TGS-1.0.1/TGS/inst/doc/chap_01_QuickStartGuide.R |only TGS-1.0.1/TGS/inst/doc/chap_01_QuickStartGuide.Rmd |only TGS-1.0.1/TGS/inst/doc/chap_01_QuickStartGuide.html |only TGS-1.0.1/TGS/inst/extdata/DREAM3GoldStandard_InSilicoSize10_Yeast1_TrueNet.RData |only TGS-1.0.1/TGS/inst/extdata/InSilicoSize10-Yeast1-null-mutants.tsv |only TGS-1.0.1/TGS/inst/extdata/InSilicoSize10-Yeast1-trajectories.tsv |only TGS-1.0.1/TGS/inst/extdata/Output_Ds10n |only TGS-1.0.1/TGS/inst/extdata/Output_Ed10n |only TGS-1.0.1/TGS/inst/extdata/Result_Ds10n.RData |only TGS-1.0.1/TGS/inst/extdata/Result_Ed10n.RData |only TGS-1.0.1/TGS/inst/extdata/edi-data-10n.tsv |only TGS-1.0.1/TGS/inst/extdata/edi.net.10.adj.mx.RData |only TGS-1.0.1/TGS/man/LearnTgs.Rd | 324 - TGS-1.0.1/TGS/man/TGS-package.Rd |only TGS-1.0.1/TGS/tests |only TGS-1.0.1/TGS/vignettes/chap_01_QuickStartGuide.Rmd |only 77 files changed, 4137 insertions(+), 4058 deletions(-)
Title: Gene Set Enrichment Analysis via Integration of Metabolic
Networks and RNA-Seq Data
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Diff between metaboGSE versions 1.2.3 dated 2020-01-07 and 1.2.4 dated 2020-05-07
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 - R/metaboGSE.R | 30 +++++++++++++++--------------- inst/NEWS.Rd | 7 +++++++ inst/doc/metaboGSE.pdf |binary 6 files changed, 33 insertions(+), 27 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic
and math common to Item Factor Analysis fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for more
specialized IRT packages to build upon. Complete access to optimized C
functions are made available with R_RegisterCCallable().
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 1.0.3 dated 2020-02-23 and 1.0.4 dated 2020-05-07
DESCRIPTION | 8 +++---- MD5 | 22 ++++++++++----------- R/util.R | 10 ++++----- build/rpf.pdf |binary build/vignette.rds |binary inst/doc/customitem.html | 2 - inst/doc/diagnostics.html | 44 +++++++++++++++++++++---------------------- inst/doc/flexmirt-plots.html | 6 ++--- man/EAPscores.Rd | 2 - man/sumScoreEAPTest.Rd | 8 +++---- src/Makevars | 2 + tools/rox | 2 - 12 files changed, 54 insertions(+), 52 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.9.3 dated 2020-03-06 and 3.9.4 dated 2020-05-07
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Title: Animated Graph Layout Viewer
Description: This is an 'R' interface to Alun Thomas's 'ViewGraph' 'Java' graph
viewing program.
It takes a graph specified as an incidence matrix, list of
edges, or in 'igraph' format and runs a graphical user interface that shows
an animation of a force directed algorithm positioning the vertices in two
dimensions. It works well for graphs of various structure of up to a few
thousand vertices. It's not fazed by graphs that comprise several
components. The coordinates can be read as an 'igraph' style layout
matrix at any time. The user can mess with the layout using a mouse,
preferably one with 3 buttons, and some keyed commands.
Author: Alun Thomas
Maintainer: Alun Thomas <Alun.Thomas@utah.edu>
Diff between rviewgraph versions 1.3.0 dated 2020-05-04 and 1.3.1 dated 2020-05-07
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- R/rViewGraph.R | 19 +++++++++++-------- man/rViewGraph.Rd | 46 +++++++++++++++++++++++++++++++++------------- man/rviewgraph-package.Rd | 4 ++-- 5 files changed, 56 insertions(+), 32 deletions(-)
Title: Moment Condition Based Estimation of Linear Dynamic Panel Data
Models
Description: Linear dynamic panel data modeling based on linear and
nonlinear moment conditions as proposed by
Holtz-Eakin, Newey, and Rosen (1988) <doi:10.2307/1913103>,
Ahn and Schmidt (1995) <doi:10.1016/0304-4076(94)01641-C>,
and Arellano and Bover (1995) <doi:10.1016/0304-4076(94)01642-D>.
Estimation of the model parameters relies on numerical optimization
and the computation of closed form solutions. For inference and specification
testing, Windmeijer (2005) <doi:10.1016/j.jeconom.2004.02.005>
corrected standard errors, serial correlation tests, tests for overidentification,
and Wald tests are available.
Author: Markus Fritsch [aut, cre],
Joachim Schnurbus [aut],
Andrew Adrian Yu Pua [aut]
Maintainer: Markus Fritsch <Markus.Fritsch@uni-Passau.de>
Diff between pdynmc versions 0.8.0 dated 2020-02-01 and 0.9.0 dated 2020-05-07
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Title: Group Sequential Design
Description: Derives group sequential designs and describes their properties.
Author: Keaven Anderson [aut, cre]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.0-1 dated 2016-02-01 and 3.1.1 dated 2020-05-07
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gsDesign-3.1.1/gsDesign/R/gsSpending.R | 2545 ++++++--- gsDesign-3.1.1/gsDesign/R/gsSurv.R | 2090 +++++-- gsDesign-3.1.1/gsDesign/R/gsSurvival.R | 481 + gsDesign-3.1.1/gsDesign/R/gsUtilities.R | 572 +- gsDesign-3.1.1/gsDesign/R/gsWTPT.R | 182 gsDesign-3.1.1/gsDesign/R/gsqplot.R | 1795 ++++-- gsDesign-3.1.1/gsDesign/R/hgraph.r |only gsDesign-3.1.1/gsDesign/R/nBinomial1Sample.r | 79 gsDesign-3.1.1/gsDesign/R/nEvents.R | 95 gsDesign-3.1.1/gsDesign/R/nNormal.R | 182 gsDesign-3.1.1/gsDesign/R/package.R |only gsDesign-3.1.1/gsDesign/R/sequentialPValue.r |only gsDesign-3.1.1/gsDesign/R/ssrCP.R | 947 ++- gsDesign-3.1.1/gsDesign/R/varBinomial.R | 375 + gsDesign-3.1.1/gsDesign/R/xtable.R | 171 gsDesign-3.1.1/gsDesign/README.md |only gsDesign-3.1.1/gsDesign/build/vignette.rds |binary gsDesign-3.1.1/gsDesign/inst/doc/SurvivalOverview.R |only gsDesign-3.1.1/gsDesign/inst/doc/SurvivalOverview.Rmd |only gsDesign-3.1.1/gsDesign/inst/doc/SurvivalOverview.html |only gsDesign-3.1.1/gsDesign/inst/doc/gsSurvBasicExamples.R |only gsDesign-3.1.1/gsDesign/inst/doc/gsSurvBasicExamples.Rmd |only gsDesign-3.1.1/gsDesign/inst/doc/gsSurvBasicExamples.html |only gsDesign-3.1.1/gsDesign/inst/doc/hGraph.R |only gsDesign-3.1.1/gsDesign/inst/doc/hGraph.Rmd |only gsDesign-3.1.1/gsDesign/inst/doc/hGraph.html |only gsDesign-3.1.1/gsDesign/inst/doc/nNormal.R |only gsDesign-3.1.1/gsDesign/inst/doc/nNormal.Rmd |only gsDesign-3.1.1/gsDesign/inst/doc/nNormal.html |only gsDesign-3.1.1/gsDesign/inst/doc/tests_and_coverage.R |only gsDesign-3.1.1/gsDesign/inst/doc/tests_and_coverage.Rmd |only gsDesign-3.1.1/gsDesign/inst/doc/tests_and_coverage.html |only gsDesign-3.1.1/gsDesign/inst/unitTests/runit.gsDesign-inputs.R | 252 gsDesign-3.1.1/gsDesign/inst/unitTests/runit.nBinomial-inputs.R | 140 gsDesign-3.1.1/gsDesign/inst/unitTests/runit.output.R | 4 gsDesign-3.1.1/gsDesign/inst/unitTests/runit.testBinomial-stress.R | 316 - gsDesign-3.1.1/gsDesign/man/Spending_Function_Overview.Rd |only gsDesign-3.1.1/gsDesign/man/checkScalar.Rd |only gsDesign-3.1.1/gsDesign/man/eEvents.Rd | 204 gsDesign-3.1.1/gsDesign/man/gsBinomialExact.Rd | 462 + gsDesign-3.1.1/gsDesign/man/gsBound.Rd |only gsDesign-3.1.1/gsDesign/man/gsBoundCP.Rd | 132 gsDesign-3.1.1/gsDesign/man/gsBoundSummary.Rd | 529 +- gsDesign-3.1.1/gsDesign/man/gsCP.Rd | 431 - gsDesign-3.1.1/gsDesign/man/gsDensity.Rd | 211 gsDesign-3.1.1/gsDesign/man/gsDesign-package-overview.Rd |only gsDesign-3.1.1/gsDesign/man/gsDesign.Rd | 486 + gsDesign-3.1.1/gsDesign/man/gsProbability.Rd | 237 gsDesign-3.1.1/gsDesign/man/hGraph.Rd |only gsDesign-3.1.1/gsDesign/man/nNormal.Rd | 185 gsDesign-3.1.1/gsDesign/man/nSurv.Rd | 734 +- gsDesign-3.1.1/gsDesign/man/nSurvival.Rd | 480 + gsDesign-3.1.1/gsDesign/man/normalGrid.Rd | 209 gsDesign-3.1.1/gsDesign/man/plot.binomialSPRT.Rd |only gsDesign-3.1.1/gsDesign/man/plot.gsDesign.Rd | 305 - gsDesign-3.1.1/gsDesign/man/sequentiaPValue.Rd |only gsDesign-3.1.1/gsDesign/man/sfDistribution.Rd |only gsDesign-3.1.1/gsDesign/man/sfExponential.Rd |only gsDesign-3.1.1/gsDesign/man/sfHSD.Rd | 161 gsDesign-3.1.1/gsDesign/man/sfLDOF.Rd |only gsDesign-3.1.1/gsDesign/man/sfLinear.Rd | 270 - 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Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between WorldFlora versions 1.5 dated 2020-03-28 and 1.6 dated 2020-05-07
DESCRIPTION | 8 ++-- MD5 | 17 +++++---- NAMESPACE | 2 - R/WFO.download.R |only R/WFO.match.R | 43 ++++++++++++++++++++---- R/WFO.prepare.R | 90 +++++++++++++++++++++++++++++++++++++++++++++++++--- R/WFO.remember.R |only R/zzz.R | 2 - man/WFO.match.Rd | 2 + man/WFO.prepare.Rd | 33 +++++++++++++++---- man/WFO.remember.Rd |only 11 files changed, 166 insertions(+), 31 deletions(-)
Title: Multivariate Version of the Diebold-Mariano Test
Description: Allows to perform the multivariate version of the Diebold-Mariano test for equal predictive ability of multiple forecast comparison. Main reference: Mariano, R.S., Preve, D. (2012) <doi:10.1016/j.jeconom.2012.01.014>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University
of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between multDM versions 1.1.1 dated 2020-03-28 and 1.1.2 dated 2020-05-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 8 ++++++++ R/MDM.test.R | 2 +- 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single value.
'tidyr' contains tools for changing the shape (pivoting) and hierarchy
(nesting and 'unnesting') of a dataset, turning deeply nested lists
into rectangular data frames ('rectangling'), and extracting values out
of string columns. It also includes tools for working with missing values
(both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 1.0.2 dated 2020-01-24 and 1.0.3 dated 2020-05-07
DESCRIPTION | 8 MD5 | 52 - NEWS.md | 9 R/chop.R | 8 R/separate-rows.R | 5 R/utils.R | 2 build/tidyr.pdf |binary inst/doc/in-packages.html | 76 +- inst/doc/nest.html | 37 - inst/doc/pivot.R | 11 inst/doc/pivot.Rmd | 13 inst/doc/pivot.html | 1353 +++++++++++++++++++-------------------- inst/doc/rectangle.html | 152 ++-- inst/doc/tidy-data.html | 37 - man/billboard.Rd | 6 man/chop.Rd | 8 man/construction.Rd | 6 man/fish_encounters.Rd | 6 man/relig_income.Rd | 6 man/smiths.Rd | 4 man/table1.Rd | 14 man/us_rent_income.Rd | 6 man/who.Rd | 8 man/world_bank_pop.Rd | 6 tests/testthat/test-pivot-long.R | 9 tests/testthat/test-rectangle.R | 2 vignettes/pivot.Rmd | 13 27 files changed, 937 insertions(+), 920 deletions(-)
Title: A Tidy Implementation of Heatmap
Description: This is a tidy implementation for heatmap. At the
moment it is based on the (great) package 'ComplexHeatmap'. The goal
of this package is to interface a tidy data frame with this powerful
tool. Some of the advantages are: Row and/or columns colour
annotations are easy to integrate just specifying one parameter
(column names). Custom grouping of rows is easy to specify providing
a grouped tbl. For example: df %>% group_by(...). Labels size
adjusted by row and column total number. Default use of Brewer and
Viridis palettes.
Author: Stefano Mangiola [aut, cre]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyHeatmap versions 0.99.9 dated 2020-02-23 and 0.99.18 dated 2020-05-07
DESCRIPTION | 53 - MD5 | 46 - NAMESPACE | 6 R/functions.R | 394 +++++--- R/methods.R | 289 ++++-- R/utilities.R | 1732 +++++++++++++++++++++------------------ R/validation.R |only README.md | 217 ++-- build/tidyHeatmap.pdf |only data/pasilla.rda |binary inst/doc/introduction.R | 59 - inst/doc/introduction.Rmd | 197 ++-- inst/doc/introduction.html | 582 ++++++++----- man/N52.Rd | 30 man/check_if_counts_is_na.Rd |only man/check_if_duplicated_genes.Rd |only man/check_if_wrong_input.Rd |only man/figures |only man/heatmap.Rd | 131 +- man/pasilla.Rd | 30 man/plot_heatmap.Rd | 16 tests/testthat/tests.R | 484 +++++++--- vignettes/introduction.Rmd | 197 ++-- 23 files changed, 2684 insertions(+), 1779 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.5.2). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.5.1.1.0 dated 2019-11-26 and 0.5.2.1.0 dated 2020-05-07
DESCRIPTION | 10 MD5 | 196 ++--- NAMESPACE | 1 NEWS.md | 25 R/bicop.R | 2 R/bicop_methods.R | 6 R/bicop_plot.R | 2 R/family_sets.R | 4 R/rosenblatt.R | 2 R/rvine_structure.R | 30 R/rvinecopulib.R | 2 R/vinecop.R | 6 R/vinecop_plot.R | 26 README.md | 69 - inst/include/vinecopulib.hpp | 2 inst/include/vinecopulib/bicop/abstract.hpp | 8 inst/include/vinecopulib/bicop/archimedean.hpp | 4 inst/include/vinecopulib/bicop/bb1.hpp | 4 inst/include/vinecopulib/bicop/bb6.hpp | 4 inst/include/vinecopulib/bicop/bb7.hpp | 4 inst/include/vinecopulib/bicop/bb8.hpp | 4 inst/include/vinecopulib/bicop/class.hpp | 14 inst/include/vinecopulib/bicop/clayton.hpp | 4 inst/include/vinecopulib/bicop/elliptical.hpp | 4 inst/include/vinecopulib/bicop/family.hpp | 4 inst/include/vinecopulib/bicop/fit_controls.hpp | 16 inst/include/vinecopulib/bicop/frank.hpp | 4 inst/include/vinecopulib/bicop/gaussian.hpp | 4 inst/include/vinecopulib/bicop/gumbel.hpp | 4 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 14 inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 4 inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb6.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb8.ipp | 2 inst/include/vinecopulib/bicop/implementation/class.ipp | 282 ++++--- inst/include/vinecopulib/bicop/implementation/clayton.ipp | 2 inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 2 inst/include/vinecopulib/bicop/implementation/family.ipp | 10 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 99 +- inst/include/vinecopulib/bicop/implementation/frank.ipp | 2 inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 2 inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 2 inst/include/vinecopulib/bicop/implementation/indep.ipp | 2 inst/include/vinecopulib/bicop/implementation/joe.ipp | 2 inst/include/vinecopulib/bicop/implementation/kernel.ipp | 2 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 14 inst/include/vinecopulib/bicop/implementation/student.ipp | 2 inst/include/vinecopulib/bicop/implementation/tll.ipp | 13 inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 8 inst/include/vinecopulib/bicop/indep.hpp | 4 inst/include/vinecopulib/bicop/joe.hpp | 4 inst/include/vinecopulib/bicop/kernel.hpp | 4 inst/include/vinecopulib/bicop/parametric.hpp | 6 inst/include/vinecopulib/bicop/student.hpp | 4 inst/include/vinecopulib/bicop/tll.hpp | 4 inst/include/vinecopulib/bicop/tools_select.hpp | 2 inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 44 - inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 44 - inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 34 inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 67 - inst/include/vinecopulib/misc/tools_batch.hpp | 3 inst/include/vinecopulib/misc/tools_bobyqa.hpp | 2 inst/include/vinecopulib/misc/tools_constants.hpp | 2 inst/include/vinecopulib/misc/tools_eigen.hpp | 2 inst/include/vinecopulib/misc/tools_integration.hpp | 2 inst/include/vinecopulib/misc/tools_interface.hpp | 2 inst/include/vinecopulib/misc/tools_interpolation.hpp | 2 inst/include/vinecopulib/misc/tools_optimization.hpp | 4 inst/include/vinecopulib/misc/tools_serialization.hpp | 14 inst/include/vinecopulib/misc/tools_stats.hpp | 20 inst/include/vinecopulib/misc/tools_stats_ghalton.hpp | 4 inst/include/vinecopulib/misc/tools_stats_sobol.hpp | 2 inst/include/vinecopulib/misc/tools_stl.hpp | 12 inst/include/vinecopulib/misc/tools_thread.hpp | 18 inst/include/vinecopulib/misc/triangular_array.hpp | 50 - inst/include/vinecopulib/version.hpp | 6 inst/include/vinecopulib/vinecop/class.hpp | 53 - inst/include/vinecopulib/vinecop/fit_controls.hpp | 57 - inst/include/vinecopulib/vinecop/implementation/class.ipp | 370 +++++----- inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 110 +- inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 182 ++-- inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 130 +-- inst/include/vinecopulib/vinecop/rvine_structure.hpp | 42 - inst/include/vinecopulib/vinecop/tools_select.hpp | 2 man/bicop.Rd | 2 man/bicop_methods.Rd | 2 man/plot.bicop_dist.Rd | 2 man/plot.rvine_structure.Rd | 14 man/plot.vinecop_dist.Rd | 6 man/predict_bicop.Rd | 2 man/rosenblatt.Rd | 2 man/rvine_structure.Rd | 5 man/rvinecopulib.Rd | 2 man/vinecop.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test_bicop_dist.R | 4 tests/testthat/test_rvine_structure.R | 27 tests/testthat/test_vinecop_dist.R | 1 99 files changed, 1262 insertions(+), 1055 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers
needed to build R packages on various platforms and ensures the PATH is
configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
RStudio [cph]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgbuild versions 1.0.7 dated 2020-04-25 and 1.0.8 dated 2020-05-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/build-tools.R | 4 +++- R/rtools-cache.R | 5 +++-- R/rtools-config.R | 6 +++++- R/rtools-metadata.R | 10 +++++----- R/rtools.R | 50 ++++++++++++++++++++++++++++++++------------------ README.md | 7 ++++--- 9 files changed, 67 insertions(+), 41 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) Use of CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.4.5 dated 2019-09-27 and 0.4.7 dated 2020-05-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/BestSlope.R | 6 +++++- R/tblNCA.R | 4 ++-- inst/NEWS.Rd | 10 ++++++++++ inst/doc/NonCompart-manual.pdf |binary man/tblNCA.Rd | 5 +++-- 7 files changed, 30 insertions(+), 15 deletions(-)
Title: Fast Extraction from Raster Datasets using Polygons
Description: Provides a replacement for the 'extract' function from the 'raster' package
that is suitable for extracting raster values using 'sf' polygons.
Author: Daniel Baston [aut, cre],
ISciences, LLC [cph]
Maintainer: Daniel Baston <dbaston@isciences.com>
Diff between exactextractr versions 0.2.1 dated 2020-03-21 and 0.3.0 dated 2020-05-07
DESCRIPTION | 8 +- MD5 | 28 ++++---- NEWS.md | 7 ++ R/coverage_fraction.R | 2 R/exact_extract.R | 38 +++++++++-- README.md | 20 ++--- configure | 18 ++--- man/exact_extract.Rd | 27 ++++++-- src/exact_extract.cpp | 21 +++--- src/exactextract/src/grid.h | 8 +- src/exactextract/src/raster_stats.h | 65 ++++++++++++++++++- src/exactextract/test/test_grid.cpp | 4 + src/exactextract/test/test_stats.cpp | 31 ++++++++- tests/testthat/test_coverage_fraction.R | 11 +++ tests/testthat/test_exact_extract.R | 107 ++++++++++++++++++++++++++++++-- 15 files changed, 327 insertions(+), 68 deletions(-)
Title: Generate Alluvial Plots with a Single Line of Code
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data
over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in
Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694>
Their graphical grammar however is a bit more complex then that of a regular x/y
plots. The 'ggalluvial' package made a great job of translating that grammar into
'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial
plot, however there still remains a multi-layered complexity that makes it difficult
to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple
interface to this package that allows you to produce a decent alluvial plot from any
dataframe in either long or wide format from a single line of code while also handling
continuous data. It is meant to allow a quick visualisation of entire dataframes
with a focus on different colouring options that can make alluvial plots a great
tool for data exploration.
Author: Bjoern Koneswarakantha [aut, cre]
(<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Diff between easyalluvial versions 0.2.2 dated 2019-12-09 and 0.2.3 dated 2020-05-07
easyalluvial-0.2.2/easyalluvial/inst/logo/logo_easyalluvial.png |only easyalluvial-0.2.2/easyalluvial/man/use_e1071.Rd |only easyalluvial-0.2.2/easyalluvial/tests/figs |only easyalluvial-0.2.3/easyalluvial/DESCRIPTION | 11 easyalluvial-0.2.3/easyalluvial/MD5 | 152 easyalluvial-0.2.3/easyalluvial/NAMESPACE | 128 easyalluvial-0.2.3/easyalluvial/NEWS.md | 83 easyalluvial-0.2.3/easyalluvial/R/alluvial_long.R | 928 ++--- easyalluvial-0.2.3/easyalluvial/R/alluvial_model_response.R | 1555 +++++----- easyalluvial-0.2.3/easyalluvial/R/alluvial_wide.R | 798 ++--- easyalluvial-0.2.3/easyalluvial/R/data.R | 150 easyalluvial-0.2.3/easyalluvial/R/manip.R | 499 +-- easyalluvial-0.2.3/easyalluvial/R/palette.R | 546 +-- easyalluvial-0.2.3/easyalluvial/R/plot_condensation.R | 342 +- easyalluvial-0.2.3/easyalluvial/R/plot_imp.R | 344 +- easyalluvial-0.2.3/easyalluvial/R/plot_marginal_hist.R | 1187 +++---- easyalluvial-0.2.3/easyalluvial/README.md | 453 +- easyalluvial-0.2.3/easyalluvial/inst/logo/logo.R | 108 easyalluvial-0.2.3/easyalluvial/inst/logo/logo.png |only easyalluvial-0.2.3/easyalluvial/man/add_imp_plot.Rd | 4 easyalluvial-0.2.3/easyalluvial/man/add_marginal_histograms.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/alluvial_long.Rd | 10 easyalluvial-0.2.3/easyalluvial/man/alluvial_model_response.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/alluvial_model_response_caret.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/alluvial_wide.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/figures/README-plot_long-1.png |binary easyalluvial-0.2.3/easyalluvial/man/figures/README-unnamed-chunk-3-1.png |binary easyalluvial-0.2.3/easyalluvial/man/figures/README-unnamed-chunk-5-1.png |only easyalluvial-0.2.3/easyalluvial/man/figures/README-wide_plot-1.png |binary easyalluvial-0.2.3/easyalluvial/man/figures/logo.png |only easyalluvial-0.2.3/easyalluvial/man/get_data_space.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/get_pdp_predictions.Rd | 4 easyalluvial-0.2.3/easyalluvial/man/manip_bin_numerics.Rd | 4 easyalluvial-0.2.3/easyalluvial/man/manip_factor_2_numeric.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/mtcars2.Rd | 8 easyalluvial-0.2.3/easyalluvial/man/palette_filter.Rd | 10 easyalluvial-0.2.3/easyalluvial/man/palette_increase_length.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/palette_plot_intensity.Rd | 6 easyalluvial-0.2.3/easyalluvial/man/palette_plot_rgp.Rd | 6 easyalluvial-0.2.3/easyalluvial/man/palette_qualitative.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/plot_all_hists.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/plot_condensation.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/plot_hist.Rd | 4 easyalluvial-0.2.3/easyalluvial/man/plot_imp.Rd | 4 easyalluvial-0.2.3/easyalluvial/man/quarterly_flights.Rd | 8 easyalluvial-0.2.3/easyalluvial/man/quarterly_sunspots.Rd | 8 easyalluvial-0.2.3/easyalluvial/man/tidy_imp.Rd | 2 easyalluvial-0.2.3/easyalluvial/man/titanic.Rd | 8 easyalluvial-0.2.3/easyalluvial/tests/testthat.R | 8 easyalluvial-0.2.3/easyalluvial/tests/testthat/Rplots.pdf |binary easyalluvial-0.2.3/easyalluvial/tests/testthat/test_alluvial_long.R | 244 - easyalluvial-0.2.3/easyalluvial/tests/testthat/test_alluvial_model_response.R | 696 ++-- easyalluvial-0.2.3/easyalluvial/tests/testthat/test_alluvial_wide.R | 288 - easyalluvial-0.2.3/easyalluvial/tests/testthat/test_manip.R | 312 +- easyalluvial-0.2.3/easyalluvial/tests/testthat/test_palette.R | 94 easyalluvial-0.2.3/easyalluvial/tests/testthat/test_plot_condensation.R | 110 easyalluvial-0.2.3/easyalluvial/tests/testthat/test_plot_imp.R | 92 easyalluvial-0.2.3/easyalluvial/tests/testthat/test_plot_marginal_histograms.R | 319 +- 58 files changed, 4785 insertions(+), 4768 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 0.1.1 dated 2020-03-21 and 1.0 dated 2020-05-07
carat-0.1.1/carat/R/RealData.R |only carat-0.1.1/carat/R/Rfunction.R |only carat-0.1.1/carat/R/Sequentially.R |only carat-0.1.1/carat/R/SimData.R |only carat-0.1.1/carat/R/carandom.R |only carat-0.1.1/carat/R/carcomp.R |only carat-0.1.1/carat/R/careval.R |only carat-0.1.1/carat/R/carseq.R |only carat-0.1.1/carat/R/compRand.R |only carat-0.1.1/carat/R/evalRand.R |only carat-1.0/carat/DESCRIPTION | 12 carat-1.0/carat/MD5 | 91 ++-- carat-1.0/carat/NAMESPACE | 2 carat-1.0/carat/R/RcppExports.R | 598 +++++++++++++------------- carat-1.0/carat/R/class_carandom.R |only carat-1.0/carat/R/class_carcomp.R |only carat-1.0/carat/R/class_careval.R |only carat-1.0/carat/R/class_carseq.R |only carat-1.0/carat/R/rand_CLI.R |only carat-1.0/carat/R/rand_compRand.R |only carat-1.0/carat/R/rand_completeData.R |only carat-1.0/carat/R/rand_evalRand.R |only carat-1.0/carat/R/rand_generatingData.R |only carat-1.0/carat/R/test_Rfunction.R |only carat-1.0/carat/data |only carat-1.0/carat/inst |only carat-1.0/carat/man/AdjBCD.Rd | 22 carat-1.0/carat/man/AdjBCD.sim.Rd | 14 carat-1.0/carat/man/AdjBCD.ui.Rd | 10 carat-1.0/carat/man/CompPower.Rd | 96 ++-- carat-1.0/carat/man/DoptBCD.Rd | 161 +++---- carat-1.0/carat/man/DoptBCD.sim.Rd | 12 carat-1.0/carat/man/DoptBCD.ui.Rd | 10 carat-1.0/carat/man/HuHuCAR.Rd | 171 +++---- carat-1.0/carat/man/HuHuCAR.sim.Rd | 16 carat-1.0/carat/man/HuHuCAR.ui.Rd | 12 carat-1.0/carat/man/PocSimMIN.Rd | 178 +++---- carat-1.0/carat/man/PocSimMIN.sim.Rd | 18 carat-1.0/carat/man/PocSimMIN.ui.Rd | 14 carat-1.0/carat/man/StrBCD.Rd | 176 +++---- carat-1.0/carat/man/StrBCD.sim.Rd | 16 carat-1.0/carat/man/StrBCD.ui.Rd | 12 carat-1.0/carat/man/StrPBR.Rd | 132 ++--- carat-1.0/carat/man/StrPBR.sim.Rd | 14 carat-1.0/carat/man/StrPBR.ui.Rd | 12 carat-1.0/carat/man/boot.test.Rd | 37 - carat-1.0/carat/man/carat-package.Rd | 75 +-- carat-1.0/carat/man/compRand.Rd | 159 +++---- carat-1.0/carat/man/corr.test.Rd | 14 carat-1.0/carat/man/evalPower.Rd | 125 ++--- carat-1.0/carat/man/evalRand.Rd | 37 - carat-1.0/carat/man/evalRand.sim.Rd | 28 - carat-1.0/carat/man/getData.Rd | 30 - carat-1.0/carat/man/pats.Rd |only carat-1.0/carat/man/print.carandom.Rd | 88 --- carat-1.0/carat/man/rand.test.Rd | 156 +++--- carat-1.0/carat/src/All.cpp | 720 +++++++++++++++++--------------- carat-1.0/carat/src/RcppExports.cpp | 108 ++-- 58 files changed, 1699 insertions(+), 1677 deletions(-)
Title: A Dirichlet Process Mixture Model for Clustering Longitudinal
Gene Expression Data
Description: Many clustering methods have been proposed, but
most of them cannot work for longitudinal gene expression data.
'BClustLonG' is a package that allows us to perform clustering analysis for
longitudinal gene expression data. It adopts a linear-mixed effects framework
to model the trajectory of genes over time, while clustering is jointly
conducted based on the regression coefficients obtained from all genes.
To account for the correlations among genes and alleviate the
high dimensionality challenges, factor analysis models are adopted
for the regression coefficients. The Dirichlet process prior distribution
is utilized for the means of the regression coefficients to induce clustering.
This package allows users to specify which variables to use for clustering
(intercepts or slopes or both) and whether a factor analysis model is desired.
More details about this method can be found in Jiehuan Sun, et al. (2017) <doi:10.1002/sim.7374>.
Author: Jiehuan Sun [aut, cre], Jose D. Herazo-Maya[aut], Naftali Kaminski[aut], Hongyu Zhao [aut], and Joshua L. Warren [aut],
Maintainer: Jiehuan Sun <jiehuan.sun@gmail.com>
Diff between BClustLonG versions 0.1.1 dated 2017-12-15 and 0.1.3 dated 2020-05-07
BClustLonG-0.1.1/BClustLonG/src/init.c |only BClustLonG-0.1.3/BClustLonG/DESCRIPTION | 8 ++-- BClustLonG-0.1.3/BClustLonG/MD5 | 24 ++++++------ BClustLonG-0.1.3/BClustLonG/NAMESPACE | 2 - BClustLonG-0.1.3/BClustLonG/R/RcppExports.R | 18 ++++----- BClustLonG-0.1.3/BClustLonG/build/vignette.rds |binary BClustLonG-0.1.3/BClustLonG/inst/doc/BClustLonG.pdf |binary BClustLonG-0.1.3/BClustLonG/man/BClustLonG.Rd | 14 +++++-- BClustLonG-0.1.3/BClustLonG/man/data.Rd | 3 + BClustLonG-0.1.3/BClustLonG/src/Makevars | 1 BClustLonG-0.1.3/BClustLonG/src/Makevars.win | 1 BClustLonG-0.1.3/BClustLonG/src/RcppExports.cpp | 36 +++++++++++++----- BClustLonG-0.1.3/BClustLonG/src/sparseFactor.cpp | 10 ++--- BClustLonG-0.1.3/BClustLonG/vignettes/BClustLonG.html |only 14 files changed, 73 insertions(+), 44 deletions(-)