Title: Transcription Factor Binding Site Identification Tool
Description: Identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Ritika Ramani<rramani@cshl.edu>
Diff between rtfbs versions 0.3.9 dated 2018-01-30 and 0.3.15 dated 2020-01-21
ChangeLog | 4 - DESCRIPTION | 11 ++--- LICENSE | 2 MD5 | 66 +++++++++++++++---------------- NAMESPACE | 1 R/tfbs.R | 7 +-- inst/doc/vignette.pdf |binary man/build.mm.Rd | 2 man/calc.fdr.Rd | 2 man/groupByGC.ms.Rd | 2 man/makeFdrPlot.Rd | 3 + man/output.sites.Rd | 2 man/read.ms.Rd | 2 man/read.pwm.Rd | 1 man/rtfbs-package.Rd | 9 ++-- man/score.ms.Rd | 3 + man/simulate.ms.Rd | 2 src/Makevars.in | 104 ++++++++++++++++++++++++------------------------- src/Makevars.win | 104 ++++++++++++++++++++++++------------------------- src/bgc_hmm.c | 5 +- src/hmm.c | 4 + src/matrix.c | 26 +++++++++++- src/rph_init.c | 1 src/rph_tfbs.c | 34 ++++++---------- src/sufficient_stats.c | 2 tests/build_mm.R | 2 tests/calc_fdr.R | 2 tests/groupByGC_ms.R | 2 tests/makeFdrPlot.R | 3 + tests/output_sites.R | 2 tests/read_ms.R | 2 tests/read_pwm.R | 1 tests/score_ms.R | 3 + tests/simulate_ms.R | 2 34 files changed, 237 insertions(+), 181 deletions(-)
Title: Overfitting Bayesian Mixtures of Factor Analyzers with
Parsimonious Covariance and Unknown Number of Components
Description: Model-based clustering of multivariate continuous data using Bayesian mixtures of factor analyzers (Papastamoulis (2019) <DOI:10.1007/s11222-019-09891-z> (2018) <DOI:10.1016/j.csda.2018.03.007>). The number of clusters is estimated using overfitting mixture models (Rousseau and Mengersen (2011) <DOI:10.1111/j.1467-9868.2011.00781.x>): suitable prior assumptions ensure that asymptotically the extra components will have zero posterior weight, therefore, the inference is based on the ``alive'' components. A Gibbs sampler is implemented in order to (approximately) sample from the posterior distribution of the overfitting mixture. A prior parallel tempering scheme is also available, which allows to run multiple parallel chains with different prior distributions on the mixture weights. These chains run in parallel and can swap states using a Metropolis-Hastings move. Eight different parameterizations give rise to parsimonious representations of the covariance per cluster (following Mc Nicholas and Murphy (2008) <DOI:10.1007/s11222-008-9056-0>). The model parameterization and number of factors is selected according to the Bayesian Information Criterion. Identifiability issues related to label switching are dealt by post-processing the simulated output with the Equivalence Classes Representatives algorithm (Papastamoulis and Iliopoulos (2010) <https://www.jstor.org/stable/25703571>, Papastamoulis (2016) <DOI:10.18637/jss.v069.c01>).
Author: Panagiotis Papastamoulis [aut, cre]
(<https://orcid.org/0000-0001-9468-7613>)
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between fabMix versions 4.5 dated 2019-01-08 and 4.6 dated 2020-01-21
DESCRIPTION | 12 +++--- MD5 | 16 ++++---- NAMESPACE | 1 R/fabMix.R | 97 ++++++++++++++++++++++++------------------------- build/partial.rdb |binary inst/CITATION | 38 ++++++++++--------- man/fabMix-package.Rd | 4 +- man/fabMix.Rd | 4 +- man/waveDataset1500.Rd | 2 - 9 files changed, 91 insertions(+), 83 deletions(-)
Title: Czekanowski's Diagrams
Description: Allows for production of Czekanowski's Diagrams. See A. Vasterlund (2019) Master thesis, Linkoping University.
Author: Albin Vasterlund [aut],
Krzysztof Bartoszek [cre, aut, ths]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between RMaCzek versions 1.0.0 dated 2019-08-03 and 1.2.0 dated 2020-01-21
DESCRIPTION | 15 + MD5 | 25 +- NAMESPACE | 4 R/Um_factor.R | 62 ++++-- R/czek_matrix.R | 385 +++++++++++++++++++++++++++++-------------- R/seriate_ga.R | 7 data |only man/RMaCzek-internal.Rd | 1 man/RMaCzek.Rd | 4 man/Um_factor.Rd |only man/czek_matrix.Rd | 67 +++++++ man/internet_availability.Rd |only man/seals_similarities.Rd |only man/skulls_distances.Rd |only man/urns.Rd |only 15 files changed, 406 insertions(+), 164 deletions(-)
Title: Nonparametric Assessment Between Competing Risks Hazard Ratios
Description: Nonparametric cumulative-incidence based estimation of the ratios of sub-hazard ratios to cause-specific hazard ratios using the approach from Ng et al. (2020).
Author: Daniel Antiporta <dantiporta@jhu.edu>;
Matthew Matheson <mmathes4@jhu.edu>;
Derek Ng <dng@jhu.edu>;
Alvaro Munoz <amunoz@jhu.edu>
Maintainer: Daniel Antiporta <dantiporta@jhu.edu>
Diff between hrcomprisk versions 0.1.0 dated 2020-01-13 and 0.1.1 dated 2020-01-21
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/CRCumInc.R | 22 ++++++++++++---------- R/bootCRCumInc.R | 16 +++++++++------- R/data.R | 28 ++++++++++++++-------------- R/datcheck.R | 9 ++------- R/npcrest.R | 28 +++++++++++++++------------- R/plotCIF.R | 8 +++++--- README.md | 31 +++++++++++++++++-------------- man/CRCumInc.Rd | 31 ++++++++++++------------------- man/bootCRCumInc.Rd | 20 +++++++++----------- man/dat_ckid.Rd | 28 ++++++++++++++-------------- man/datcheck.Rd | 8 +------- man/npcrest.Rd | 31 ++++++++++++------------------- man/plotCIF.Rd | 10 +++++----- 15 files changed, 144 insertions(+), 160 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR)
model, quantile residual tests, graphical diagnostics, simulations, and forecasting.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.1.1 dated 2019-08-28 and 1.1.2 dated 2020-01-21
DESCRIPTION | 8 - MD5 | 201 +++++++++++++++++++-------------------- NAMESPACE | 2 NEWS.md | 8 + R/GMVARconstruction.R | 30 ++--- R/MAINest.R | 136 +++++++++++++++----------- R/argumentChecks.R | 58 +++++------ R/data.R | 2 R/diagnosticPlot.R | 205 +++++++++++++++++++++++++++++++++++++++- R/generateParams.R | 78 +++++++-------- R/geneticAlgorithm.R | 183 ++++++++++++++++++++++------------- R/gmvarkit.R | 4 R/loglikelihood.R | 81 ++++++++------- R/matcal.R | 17 +-- R/numericalDifferentiation.R | 19 ++- R/parameterReforms.R | 50 ++++----- R/pickParams.R | 41 +++----- R/plotMethods.R | 13 +- R/predictMethod.R | 25 ++-- R/printMethods.R | 36 +++---- R/quantileResidualTests.R | 19 +-- R/quantileResiduals.R | 39 +++---- R/simulateGMVAR.R | 10 - R/standardErrors.R | 29 ++++- R/uncondMoments.R | 22 ++-- README.md | 11 +- build/vignette.rds |binary inst/doc/intro-to-gmvarkit.Rmd | 2 inst/doc/intro-to-gmvarkit.html | 6 - man/GAfit.Rd | 84 ++++++++-------- man/GMVAR.Rd | 20 +-- man/add_data.Rd | 8 - man/all_pos_ints.Rd | 2 man/alt_gmvar.Rd | 8 - man/calc_gradient.Rd | 20 ++- man/change_parametrization.Rd | 14 +- man/change_regime.Rd | 14 +- man/check_constraints.Rd | 4 man/check_data.Rd | 2 man/check_null_data.Rd | 8 - man/check_pMd.Rd | 6 - man/check_parameters.Rd | 14 +- man/cond_moments.Rd | 12 +- man/diagnostic_plot.Rd | 12 +- man/dlogmultinorm.Rd | 2 man/eurusd.Rd | 2 man/fitGMVAR.Rd | 67 +++++++------ man/form_boldA.Rd | 6 - man/format_valuef.Rd | 2 man/get_IC.Rd | 8 + man/get_boldA_eigens.Rd | 4 man/get_minval.Rd |only man/get_omega_eigens.Rd | 6 - man/get_regime_autocovs.Rd | 6 - man/get_regime_autocovs_int.Rd | 12 +- man/get_regime_means.Rd | 4 man/get_regime_means_int.Rd | 33 +++--- man/get_test_Omega.Rd | 12 +- man/gmvarkit.Rd | 4 man/in_paramspace.Rd | 19 +-- man/in_paramspace_int.Rd | 8 - man/is_stationary.Rd | 37 +++---- man/iterate_more.Rd | 22 ++-- man/loglikelihood.Rd | 28 ++--- man/loglikelihood_int.Rd | 28 ++--- man/n_params.Rd | 4 man/pick_Am.Rd | 12 +- man/pick_Ami.Rd | 10 - man/pick_Omegas.Rd | 31 +++--- man/pick_allA.Rd | 31 +++--- man/pick_all_phi0_A.Rd | 33 +++--- man/pick_alphas.Rd | 35 +++--- man/pick_phi0.Rd | 33 +++--- man/pick_regime.Rd | 11 -- man/plot.gmvarpred.Rd | 2 man/predict.gmvar.Rd | 22 ++-- man/print.gmvarpred.Rd | 4 man/print_std_errors.Rd | 9 + man/profile_logliks.Rd |only man/quantile_residual_tests.Rd | 21 ++-- man/quantile_residuals.Rd | 6 - man/quantile_residuals_int.Rd | 16 +-- man/random_coefmats.Rd | 4 man/random_coefmats2.Rd | 17 +-- man/random_covmat.Rd | 10 - man/random_ind.Rd | 18 +-- man/random_ind2.Rd | 34 +++--- man/reform_constrained_pars.Rd | 12 +- man/regime_distance.Rd | 3 man/simulateGMVAR.Rd | 6 - man/smart_covmat.Rd | 9 - man/smart_ind.Rd | 56 +++++----- man/sort_components.Rd | 43 ++++---- man/standard_errors.Rd | 16 +-- man/swap_parametrization.Rd | 11 -- man/uncond_moments.Rd | 8 - man/uncond_moments_int.Rd | 18 +-- man/unvec.Rd | 6 - man/unvech.Rd | 4 man/vec.Rd | 2 man/vech.Rd | 5 tests/testthat/test_MAINest.R |only vignettes/intro-to-gmvarkit.Rmd | 2 103 files changed, 1391 insertions(+), 1046 deletions(-)
Title: Interactive 3D Scatter Plots, Networks and Globes
Description: Create interactive 3D scatter plots, network plots, and
globes using the 'three.js' visualization library (<https://threejs.org>).
Author: B. W. Lewis [aut, cre, cph],
Three.js authors [cph] (three.js library),
jQuery Foundation [cph] (jQuery library),
Alexey Stukalov [ctb],
Yihui Xie [ctb],
Andreas Briese [ctb],
B. Thieurmel [ctb]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between threejs versions 0.3.1 dated 2017-08-13 and 0.3.3 dated 2020-01-21
threejs-0.3.1/threejs/inst/htmlwidgets/lib/threejs-85 |only threejs-0.3.3/threejs/DESCRIPTION | 23 - threejs-0.3.3/threejs/LICENSE | 10 threejs-0.3.3/threejs/MD5 | 62 ++-- threejs-0.3.3/threejs/NAMESPACE | 2 threejs-0.3.3/threejs/R/globe.R | 17 - threejs-0.3.3/threejs/R/graph.R | 64 +--- threejs-0.3.3/threejs/R/scatterplot.R | 131 +++++++--- threejs-0.3.3/threejs/R/utilities.R | 10 threejs-0.3.3/threejs/inst/htmlwidgets/globe.js | 33 -- threejs-0.3.3/threejs/inst/htmlwidgets/globe.yaml | 4 threejs-0.3.3/threejs/inst/htmlwidgets/lib/threejs-111 |only threejs-0.3.3/threejs/inst/htmlwidgets/scatterplotThree.js | 95 ++++--- threejs-0.3.3/threejs/inst/htmlwidgets/scatterplotThree.yaml | 4 threejs-0.3.3/threejs/man/LeMis.Rd | 1 threejs-0.3.3/threejs/man/ego.Rd | 1 threejs-0.3.3/threejs/man/flights.Rd | 1 threejs-0.3.3/threejs/man/gcol.Rd | 1 threejs-0.3.3/threejs/man/globejs.Rd | 31 +- threejs-0.3.3/threejs/man/graphjs.Rd | 32 ++ threejs-0.3.3/threejs/man/light_ambient.Rd |only threejs-0.3.3/threejs/man/light_directional.Rd |only threejs-0.3.3/threejs/man/lines3d.Rd | 1 threejs-0.3.3/threejs/man/points3d.Rd | 4 threejs-0.3.3/threejs/man/scatterplot3js.Rd | 62 +++- threejs-0.3.3/threejs/man/texture.Rd | 1 threejs-0.3.3/threejs/man/threejs-package.Rd | 3 threejs-0.3.3/threejs/man/threejs-shiny.Rd | 3 threejs-0.3.3/threejs/man/vertices-scatterplotThree-method.Rd | 2 29 files changed, 377 insertions(+), 221 deletions(-)
Title: Fluid Data Transformations
Description: Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases.
The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 .
This package introduces the idea of explicit control table specification of data transforms.
Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 1.1.4 dated 2020-01-08 and 1.1.5 dated 2020-01-21
DESCRIPTION | 10 ++--- MD5 | 37 +++++++++--------- NEWS.md | 5 ++ R/GeneralTransform.R | 65 ++++++++++++++++++--------------- R/RowsColsQ.R | 34 +++++++++++------ R/opspec.R | 64 ++++++++++++++++++++++---------- R/relops.R | 36 +++++++++++++++++- README.md | 3 + inst/doc/blocksrecs.html | 4 +- inst/doc/cdata.html | 4 +- inst/doc/control_table_keys.html | 4 +- inst/doc/design.html | 4 +- inst/doc/exercises.html | 4 +- inst/doc/general_transform.html | 8 ++-- inst/doc/operators.html | 6 +-- inst/unit_tests/test_complex_example.R |only man/blocks_to_rowrecs_q.Rd | 5 ++ man/convert_records.Rd | 4 +- man/layout_specification.Rd | 4 +- man/rowrecs_to_blocks_q.Rd | 7 ++- 20 files changed, 201 insertions(+), 107 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 1.2.2 dated 2019-11-29 and 1.2.3 dated 2020-01-21
DESCRIPTION | 10 +- MD5 | 136 +++++++++++++++++---------------- R/GetCross_references_Information.R | 3 R/GetExpression.R | 4 R/GetFamily_Domains.R | 3 R/GetGeneral_Information.R | 3 R/GetMiscellaneous.R | 3 R/GetNamesTaxa.R | 3 R/GetPTM_Processing.R | 3 R/GetPathology_Biotech.R | 3 R/GetProteinFunction.R | 3 R/GetProteinGOInfo.R | 3 R/GetProteinInteractions.R | 4 R/GetProteoAnnotator.R | 4 R/GetPublication.R | 4 R/GetSequences.R | 2 R/GetStructureInfo.R |only R/GetSubcellular_location.R | 4 R/GetTaxaidentifier.R | 3 R/GetTaxonomic_lineage.R | 3 R/GetproteinNetwork.R | 5 - R/PlotChromosomeInfo.R | 2 R/PlotPhyscochemical.R | 15 +++ R/PlotSummaryInfo.R |only R/PlotproteinScore.R | 1 R/UniprotR.r | 5 - build |only inst |only man/ConstructGenesTree.Rd | 38 ++++----- man/ConstructLocTree.Rd | 38 ++++----- man/ConvertID.Rd | 78 +++++++++--------- man/GetAccessionList.Rd | 40 ++++----- man/GetCross_references_Information.Rd | 66 ++++++++-------- man/GetExpression.Rd | 64 +++++++-------- man/GetFamily_Domains.Rd | 64 +++++++-------- man/GetGeneral_Information.Rd | 64 +++++++-------- man/GetMiscellaneous.Rd | 64 +++++++-------- man/GetNamesTaxa.Rd | 64 +++++++-------- man/GetPTM_Processing.Rd | 64 +++++++-------- man/GetPathology_Biotech.Rd | 64 +++++++-------- man/GetProteinAnnontate.Rd | 58 +++++++------- man/GetProteinFunction.Rd | 64 +++++++-------- man/GetProteinGOInfo.Rd | 64 +++++++-------- man/GetProteinInteractions.Rd | 64 +++++++-------- man/GetProteomeFasta.Rd | 44 +++++----- man/GetProteomeInfo.Rd | 44 +++++----- man/GetPublication.Rd | 64 +++++++-------- man/GetSequences.Rd | 64 +++++++-------- man/GetStructureInfo.Rd |only man/GetSubcellular_location.Rd | 56 ++++++------- man/GetTaxaidentifier.Rd | 64 +++++++-------- man/GetTaxonomic_lineage.Rd | 64 +++++++-------- man/GetpdbStructure.Rd | 40 ++++----- man/GetproteinNetwork.Rd | 42 +++++----- man/Goparse.Rd | 38 ++++----- man/HandleBadRequests.Rd | 52 ++++++------ man/PlotChromosomeInfo.Rd | 38 ++++----- man/PlotGoInfo.Rd | 38 ++++----- man/PlotPhysicochemical.Rd | 38 ++++----- man/PlotProteinGO_bio.Rd | 44 +++++----- man/PlotProteinGO_cel.Rd | 44 +++++----- man/PlotProteinGO_molc.Rd | 44 +++++----- man/PlotProteinTaxa.Rd | 38 ++++----- man/PlotSummaryInfo.Rd |only man/PlotproteinExist.Rd | 38 ++++----- man/PlotproteinScore.Rd | 38 ++++----- man/PlotproteinStatus.Rd | 38 ++++----- man/ProcessAcc.Rd | 34 ++++---- man/UniprotR.Rd | 124 +++++++++--------------------- man/plotGoannotation.Rd | 38 ++++----- vignettes |only 71 files changed, 1179 insertions(+), 1174 deletions(-)
Title: Particle Tracking and Demography
Description: Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in evolutionary and ecological studies.
Author: Marjolein Bruijning, Marco D. Visser, Caspar A. Hallmann, Eelke Jongejans
Maintainer: Marjolein Bruijning <mbruijning@princeton.edu>
Diff between trackdem versions 0.5 dated 2019-10-17 and 0.5.1 dated 2020-01-21
DESCRIPTION | 12 - MD5 | 42 ++--- NAMESPACE | 2 R/identifyFunctions.R | 298 +++++++++++++++++++++----------------- R/nnFunctions.R | 244 +++++++++++++++---------------- R/trackFunctions.R | 199 ++++++++++++------------- build/vignette.rds |binary inst/doc/tutorial.pdf |binary inst/tests/test_all.R | 10 - man/createBackground.Rd | 10 - man/createImageSeq.Rd | 34 ++-- man/findThreshold.Rd | 6 man/identifyParticles.Rd | 33 ++-- man/loadImages.Rd | 8 - man/manuallySelect.Rd | 8 - man/mergeTracks.Rd | 22 +- man/subtractBackground.Rd | 4 man/testNN.Rd | 8 - man/trackParticles.Rd | 16 +- man/update.particles.Rd | 14 - src/ConnectedComponentLabelling.c |only src/RcppExports.cpp | 5 src/patchstats.c |only 23 files changed, 504 insertions(+), 471 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for performing variation partitioning, calculating several measures of model discrimination and calibration, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots.
Author: Barbosa A.M., Brown J.A., Jimenez-Valverde A., Real R.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 1.3.2 dated 2016-07-15 and 2.0 dated 2020-01-21
DESCRIPTION | 14 ++-- MD5 | 75 ++++++++++++----------- NAMESPACE | 6 - NEWS | 158 ++++++++++++++++++++++++++++++++++++++++++++++++++ R/AUC.R | 143 +++++++++++++++++++++++++++++++-------------- R/MillerCalib.R | 18 ++--- R/RsqGLM.R | 6 - R/evaluate.R | 13 +++- R/modEvA-internal.R | 139 +------------------------------------------ R/modEvAmethods.R | 17 ++--- R/multModEv.R | 14 +++- R/optiPair.R | 37 ++++------- R/optiThresh.R | 3 R/plotGLM.R | 23 ++++--- R/predDensity.R |only R/threshMeasures.R | 23 ++----- R/varPart.R | 6 - data/rotif.mods.rda |binary inst |only man/AUC.Rd | 55 +++++++++++------ man/Dsquared.Rd | 8 +- man/HLfit.Rd | 25 ++++--- man/MESS.Rd | 4 - man/MillerCalib.Rd | 21 +++--- man/OA.Rd | 2 man/RsqGLM.Rd | 4 - man/evaluate.Rd | 9 +- man/getBins.Rd | 7 +- man/getModEqn.Rd | 3 man/modEvA-package.Rd | 11 +-- man/modEvAmethods.Rd | 2 man/multModEv.Rd | 28 ++++---- man/optiPair.Rd | 34 ++++++---- man/optiThresh.Rd | 35 ++++++----- man/plotGLM.Rd | 12 +-- man/predDensity.Rd |only man/rotif.mods.Rd | 4 - man/standard01.Rd | 4 - man/threshMeasures.Rd | 47 ++++++++------ man/varPart.Rd | 24 +++---- 40 files changed, 586 insertions(+), 448 deletions(-)
Title: Spatially- and Temporally-Explicit Population Simulator
Description: Software to simulate population change across space and time.
Author: Casey Visintin [aut, cre],
Nick Golding [ctb],
Skipton Woolley [ctb],
John Baumgartner [ctb]
Maintainer: Casey Visintin <casey.visintin@unimelb.edu.au>
Diff between steps versions 0.2.1 dated 2019-04-02 and 1.0.0 dated 2020-01-21
steps-0.2.1/steps/data/egk_sink.rda |only steps-0.2.1/steps/data/egk_source.rda |only steps-0.2.1/steps/inst/doc/egk_vignette.R |only steps-0.2.1/steps/inst/doc/egk_vignette.Rmd |only steps-0.2.1/steps/inst/doc/egk_vignette.pdf |only steps-0.2.1/steps/man/dispersal_function.Rd |only steps-0.2.1/steps/man/simulation_results.Rd |only steps-0.2.1/steps/src/rcpp_dispersal_funs_v3.cpp |only steps-0.2.1/steps/vignettes/egk_vignette.Rmd |only steps-0.2.1/steps/vignettes/egk_vignette.html |only steps-1.0.0/steps/DESCRIPTION | 12 steps-1.0.0/steps/MD5 | 122 + steps-1.0.0/steps/NAMESPACE | 9 steps-1.0.0/steps/R/RcppExports.R | 16 steps-1.0.0/steps/R/data.R | 8 steps-1.0.0/steps/R/dispersal_kernel_functions-class.R | 29 steps-1.0.0/steps/R/dispersal_proportion_functions-class.R | 120 + steps-1.0.0/steps/R/growth_transition_functions-class.R | 185 +- steps-1.0.0/steps/R/habitat_dynamics-functions.R | 121 + steps-1.0.0/steps/R/landscape-class.R | 43 steps-1.0.0/steps/R/population_change-functions.R | 290 +++- steps-1.0.0/steps/R/population_density_dependence-functions.R | 60 steps-1.0.0/steps/R/population_dispersal-functions.R | 605 ++++++--- steps-1.0.0/steps/R/population_dynamics-class.R | 31 steps-1.0.0/steps/R/population_modification-functions.R | 136 +- steps-1.0.0/steps/R/simulation_results-class.R | 657 +++++++--- steps-1.0.0/steps/R/steps.R | 20 steps-1.0.0/steps/R/utils.R | 95 + steps-1.0.0/steps/build/vignette.rds |binary steps-1.0.0/steps/data/egk_destinations.rda |only steps-1.0.0/steps/data/egk_fire.rda |binary steps-1.0.0/steps/data/egk_hab.rda |binary steps-1.0.0/steps/data/egk_k.rda |binary steps-1.0.0/steps/data/egk_mat.rda |binary steps-1.0.0/steps/data/egk_mat_stoch.rda |binary steps-1.0.0/steps/data/egk_origins.rda |only steps-1.0.0/steps/data/egk_pop.rda |binary steps-1.0.0/steps/data/egk_road.rda |binary steps-1.0.0/steps/data/egk_sf.rda |binary steps-1.0.0/steps/inst/doc/custom_function_example.R |only steps-1.0.0/steps/inst/doc/custom_function_example.Rmd |only steps-1.0.0/steps/inst/doc/custom_function_example.pdf |only steps-1.0.0/steps/inst/doc/kangaroo_model_example.R |only steps-1.0.0/steps/inst/doc/kangaroo_model_example.Rmd |only steps-1.0.0/steps/inst/doc/kangaroo_model_example.pdf |only steps-1.0.0/steps/man/ceiling_density.Rd |only steps-1.0.0/steps/man/cellular_automata_dispersal.Rd |only steps-1.0.0/steps/man/compare_emp.Rd |only steps-1.0.0/steps/man/competition_density.Rd |only steps-1.0.0/steps/man/density_dependence_dispersing.Rd |only steps-1.0.0/steps/man/dispersal_kernel.Rd |only steps-1.0.0/steps/man/dispersal_proportion_function.Rd | 40 steps-1.0.0/steps/man/disturbance.Rd |only steps-1.0.0/steps/man/egk.Rd | 12 steps-1.0.0/steps/man/exponential_dispersal_kernel.Rd |only steps-1.0.0/steps/man/extract_spatial.Rd |only steps-1.0.0/steps/man/fast_dispersal.Rd |only steps-1.0.0/steps/man/fire_effects.Rd |only steps-1.0.0/steps/man/growth.Rd |only steps-1.0.0/steps/man/habitat_dynamics_functions.Rd | 46 steps-1.0.0/steps/man/kernel_dispersal.Rd |only steps-1.0.0/steps/man/landscape.Rd | 21 steps-1.0.0/steps/man/modified_transition.Rd |only steps-1.0.0/steps/man/mortality.Rd |only steps-1.0.0/steps/man/plot.simulation_results.Rd |only steps-1.0.0/steps/man/population_change_functions.Rd | 31 steps-1.0.0/steps/man/population_density_dependence_functions.Rd | 18 steps-1.0.0/steps/man/population_dispersal_functions.Rd | 93 - steps-1.0.0/steps/man/population_dynamics.Rd | 35 steps-1.0.0/steps/man/population_modification_functions.Rd | 34 steps-1.0.0/steps/man/set_proportion_dispersing.Rd |only steps-1.0.0/steps/man/simulation.Rd |only steps-1.0.0/steps/man/steps.Rd | 10 steps-1.0.0/steps/man/transition_function.Rd | 56 steps-1.0.0/steps/man/translocation.Rd |only steps-1.0.0/steps/src/RcppExports.cpp | 70 - steps-1.0.0/steps/src/rcpp_dispersal_funs_v4.cpp |only steps-1.0.0/steps/src/rcpp_utils_funs.cpp |only steps-1.0.0/steps/tests/testthat/test_simulation_results_class.R | 314 +++- steps-1.0.0/steps/vignettes/custom_function_example.Rmd |only steps-1.0.0/steps/vignettes/custom_function_example.html |only steps-1.0.0/steps/vignettes/kangaroo_model_example.Rmd |only steps-1.0.0/steps/vignettes/kangaroo_model_example.html |only steps-1.0.0/steps/vignettes/steps_diagram.png |only 84 files changed, 2131 insertions(+), 1208 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing as
described in "J. Polzehl and V. Spokoiny (2006)
<DOI:10.1007/s00440-005-0464-1>",
"J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>"
and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>",
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
Usage of the package is also described in
Polzehl and Tabelow (2019),
Magnetic Resonance Brain Imaging, Appendix A, Springer, Use R! Series.
<doi:10.1007/978-3-030-29184-6_6>.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.3-0 dated 2019-11-15 and 2.4-0 dated 2020-01-21
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Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>,
'Parameter estimation' vignettes),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>),
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.3.2.42 dated 2019-09-22 and 1.4.3.52 dated 2020-01-21
airGR-1.3.2.42/airGR/src/frun_cemaneige.f |only airGR-1.3.2.42/airGR/src/frun_gr1a.f |only airGR-1.3.2.42/airGR/src/frun_gr2m.f |only airGR-1.3.2.42/airGR/src/frun_gr4h.f |only airGR-1.3.2.42/airGR/src/frun_gr4j.f |only airGR-1.3.2.42/airGR/src/frun_gr5j.f |only airGR-1.3.2.42/airGR/src/frun_gr6j.f |only airGR-1.3.2.42/airGR/src/utils_D.f |only airGR-1.3.2.42/airGR/src/utils_H.f |only airGR-1.4.3.52/airGR/DESCRIPTION | 18 airGR-1.4.3.52/airGR/MD5 | 166 +- airGR-1.4.3.52/airGR/NAMESPACE | 4 airGR-1.4.3.52/airGR/NEWS.md | 44 airGR-1.4.3.52/airGR/R/Calibration_Michel.R | 8 airGR-1.4.3.52/airGR/R/CreateCalibOptions.R | 690 ++++++------ airGR-1.4.3.52/airGR/R/CreateIniStates.R | 41 airGR-1.4.3.52/airGR/R/CreateInputsCrit.R | 2 airGR-1.4.3.52/airGR/R/CreateInputsModel.R | 6 airGR-1.4.3.52/airGR/R/CreateRunOptions.R | 126 +- airGR-1.4.3.52/airGR/R/Imax.R |only airGR-1.4.3.52/airGR/R/RunModel_CemaNeigeGR4H.R | 1 airGR-1.4.3.52/airGR/R/RunModel_CemaNeigeGR4J.R | 1 airGR-1.4.3.52/airGR/R/RunModel_CemaNeigeGR5H.R |only airGR-1.4.3.52/airGR/R/RunModel_CemaNeigeGR5J.R | 3 airGR-1.4.3.52/airGR/R/RunModel_CemaNeigeGR6J.R | 3 airGR-1.4.3.52/airGR/R/RunModel_GR4H.R | 3 airGR-1.4.3.52/airGR/R/RunModel_GR4J.R | 3 airGR-1.4.3.52/airGR/R/RunModel_GR5H.R |only airGR-1.4.3.52/airGR/R/RunModel_GR5J.R | 3 airGR-1.4.3.52/airGR/R/RunModel_GR6J.R | 3 airGR-1.4.3.52/airGR/R/TransfoParam_GR1A.R | 1 airGR-1.4.3.52/airGR/R/TransfoParam_GR5H.R |only airGR-1.4.3.52/airGR/R/Utils.R | 19 airGR-1.4.3.52/airGR/R/plot.OutputsModel.R | 81 + airGR-1.4.3.52/airGR/README.md | 18 airGR-1.4.3.52/airGR/build/vignette.rds |binary airGR-1.4.3.52/airGR/inst/doc/V01_get_started.R | 24 airGR-1.4.3.52/airGR/inst/doc/V01_get_started.Rmd | 7 airGR-1.4.3.52/airGR/inst/doc/V01_get_started.html | 24 airGR-1.4.3.52/airGR/inst/doc/V02.1_param_optim.R | 26 airGR-1.4.3.52/airGR/inst/doc/V02.1_param_optim.html | 6 airGR-1.4.3.52/airGR/inst/doc/V02.2_param_mcmc.R | 22 airGR-1.4.3.52/airGR/inst/doc/V02.2_param_mcmc.html | 10 airGR-1.4.3.52/airGR/inst/doc/V03_param_sets_GR4J.R | 28 airGR-1.4.3.52/airGR/inst/doc/V03_param_sets_GR4J.html | 13 airGR-1.4.3.52/airGR/inst/doc/V04_cemaneige_hysteresis.R | 30 airGR-1.4.3.52/airGR/inst/doc/V04_cemaneige_hysteresis.html | 6 airGR-1.4.3.52/airGR/man/BasinObs.Rd | 6 airGR-1.4.3.52/airGR/man/Calibration_Michel.Rd | 2 airGR-1.4.3.52/airGR/man/CreateIniStates.Rd | 22 airGR-1.4.3.52/airGR/man/CreateInputsCrit.Rd | 33 airGR-1.4.3.52/airGR/man/CreateInputsModel.Rd | 2 airGR-1.4.3.52/airGR/man/CreateRunOptions.Rd | 12 airGR-1.4.3.52/airGR/man/DataAltiExtrapolation_Valery.Rd | 2 airGR-1.4.3.52/airGR/man/ErrorCrit_KGE.Rd | 2 airGR-1.4.3.52/airGR/man/ErrorCrit_KGE2.Rd | 4 airGR-1.4.3.52/airGR/man/ErrorCrit_NSE.Rd | 2 airGR-1.4.3.52/airGR/man/ErrorCrit_RMSE.Rd | 10 airGR-1.4.3.52/airGR/man/Imax.Rd |only airGR-1.4.3.52/airGR/man/PE_Oudin.Rd | 2 airGR-1.4.3.52/airGR/man/RunModel_CemaNeige.Rd | 36 airGR-1.4.3.52/airGR/man/RunModel_CemaNeigeGR4H.Rd | 22 airGR-1.4.3.52/airGR/man/RunModel_CemaNeigeGR4J.Rd | 14 airGR-1.4.3.52/airGR/man/RunModel_CemaNeigeGR5H.Rd |only airGR-1.4.3.52/airGR/man/RunModel_CemaNeigeGR5J.Rd | 12 airGR-1.4.3.52/airGR/man/RunModel_CemaNeigeGR6J.Rd | 13 airGR-1.4.3.52/airGR/man/RunModel_GR1A.Rd | 10 airGR-1.4.3.52/airGR/man/RunModel_GR2M.Rd | 8 airGR-1.4.3.52/airGR/man/RunModel_GR4H.Rd | 36 airGR-1.4.3.52/airGR/man/RunModel_GR4J.Rd | 10 airGR-1.4.3.52/airGR/man/RunModel_GR5H.Rd |only airGR-1.4.3.52/airGR/man/RunModel_GR5J.Rd | 6 airGR-1.4.3.52/airGR/man/RunModel_GR6J.Rd | 8 airGR-1.4.3.52/airGR/man/SeriesAggreg.Rd | 4 airGR-1.4.3.52/airGR/man/TransfoParam.Rd | 2 airGR-1.4.3.52/airGR/man/airGR.Rd | 18 airGR-1.4.3.52/airGR/man/figures/diagramGR2M-EN.pdf |only airGR-1.4.3.52/airGR/man/figures/diagramGR2M-EN.png |only airGR-1.4.3.52/airGR/man/figures/diagramGR4J-EN.pdf |binary airGR-1.4.3.52/airGR/man/figures/diagramGR4J-EN.png |binary airGR-1.4.3.52/airGR/man/figures/diagramGR5J-EN.pdf |binary airGR-1.4.3.52/airGR/man/figures/diagramGR5J-EN.png |binary airGR-1.4.3.52/airGR/man/figures/diagramGR6J-EN.pdf |binary airGR-1.4.3.52/airGR/man/figures/diagramGR6J-EN.png |binary airGR-1.4.3.52/airGR/man/plot.OutputsModel.Rd | 8 airGR-1.4.3.52/airGR/src/airGR.c | 2 airGR-1.4.3.52/airGR/src/frun_CEMANEIGE.f90 |only airGR-1.4.3.52/airGR/src/frun_GR1A.f90 |only airGR-1.4.3.52/airGR/src/frun_GR2M.f90 |only airGR-1.4.3.52/airGR/src/frun_GR4H.f90 |only airGR-1.4.3.52/airGR/src/frun_GR4J.f90 |only airGR-1.4.3.52/airGR/src/frun_GR5H.f90 |only airGR-1.4.3.52/airGR/src/frun_GR5J.f90 |only airGR-1.4.3.52/airGR/src/frun_GR6J.f90 |only airGR-1.4.3.52/airGR/src/utils_D.f90 |only airGR-1.4.3.52/airGR/src/utils_H.f90 |only airGR-1.4.3.52/airGR/vignettes/V00_airgr_ref.bib | 28 airGR-1.4.3.52/airGR/vignettes/V01_get_started.Rmd | 7 98 files changed, 1066 insertions(+), 717 deletions(-)
Title: 'Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)'
Description: Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Author: Rene Locher [aut, cre],
Andreas Ruckstuhl [ctb]
Maintainer: Rene Locher <rene.locher@zhaw.ch>
Diff between IDPmisc versions 1.1.19 dated 2019-02-11 and 1.1.20 dated 2020-01-21
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/MS.rda |binary man/showColors.Rd | 1 - 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Interactive Studio with Explanations for ML Predictive Models
Description: Automate explanation of machine learning predictive models.
This package generates advanced interactive and animated model explanations in the form
of a serverless HTML site. It combines 'R' with 'D3.js' to produce plots and descriptions
for various local and global explanations. Tools for model exploration unite with
tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behaviour.
'modelStudio' is a fast and condensed way to get all the answers without much effort.
Break down your model and look into its ingredients with only a few lines of code.
Author: Hubert Baniecki [aut, cre] (<https://orcid.org/0000-0001-6661-5364>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>)
Maintainer: Hubert Baniecki <hbaniecki@gmail.com>
Diff between modelStudio versions 0.2.0 dated 2020-01-13 and 0.2.1 dated 2020-01-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/modelStudio.R | 2 +- R/prepare.R | 1 - inst/doc/vignette_modelStudio.html | 4 ++-- man/modelStudio.Rd | 2 +- 7 files changed, 16 insertions(+), 14 deletions(-)
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke
and Pearl and Extensions
Description: Implementation of the nonparametric bounds for the average causal
effect under an instrumental variable model by Balke and Pearl (Bounds on
Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92,
439, 1171-1176). The package can calculate bounds for a binary outcome, a
binary treatment/phenotype, and an instrument with either 2 or 3
categories. The package implements bounds for situations where these 3
variables are measured in the same dataset (trivariate data) or where the
outcome and instrument are measured in one study and the
treatment/phenotype and instrument are measured in another study
(bivariate data).
Author: Tom Palmer [aut, cre] (<https://orcid.org/0000-0003-4655-4511>),
Roland Ramsahai [aut] (<https://orcid.org/0000-0002-7349-1977>),
Vanessa Didelez [aut] (<https://orcid.org/0000-0001-8587-7706>),
Nuala Sheehan [aut] (<https://orcid.org/0000-0001-9094-2605>)
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between bpbounds versions 0.1.3 dated 2019-02-10 and 0.1.4 dated 2020-01-21
DESCRIPTION | 12 - MD5 | 26 +- NAMESPACE | 3 NEWS.md | 5 R/bpbounds.R | 1 README.md | 12 - build/vignette.rds |binary inst/doc/bpbounds.R | 22 +- inst/doc/bpbounds.Rmd | 2 inst/doc/bpbounds.html | 460 ++++++++++++++++++++++++------------------------ man/bpbounds-package.Rd | 42 ++-- man/bpbounds.Rd | 252 +++++++++++++------------- man/runExample.Rd | 36 +-- vignettes/bpbounds.Rmd | 2 14 files changed, 448 insertions(+), 427 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between spacetime versions 1.2-2 dated 2018-07-17 and 1.2-3 dated 2020-01-21
DESCRIPTION | 6 - MD5 | 62 ++++++------ R/Class-ST.R | 4 R/Class-xts.R | 12 ++ R/ST-methods.R | 4 R/STFDF-methods.R | 4 R/STIDF-methods.R | 14 +- R/STSDF-methods.R | 2 R/aggregate.R | 2 R/coerce.R | 4 R/stconstruct.R | 10 +- R/timematch.R | 2 build/vignette.rds |binary data/air.rda |binary data/fires.rda |binary demo/aggregate.R | 5 - inst/doc/jss816.R | 88 ++++++++--------- inst/doc/jss816.Rnw | 4 inst/doc/jss816.pdf |binary inst/doc/stgvis.html | 216 ++++++++++++++++++++++---------------------- inst/doc/sto.pdf |binary inst/doc/stpg.pdf |binary inst/doc/stsubs.pdf |binary man/stconstruct.Rd | 3 tests/rw.R | 21 ++-- tests/rw.Rout.save | 34 ++---- tests/stconstruct.R | 14 +- tests/stconstruct.Rout.save | 40 ++------ tests/subsetting.Rout.save | 114 +++++++---------------- tests/wind.R | 11 +- tests/wind.Rout.save | 28 +---- vignettes/jss816.Rnw | 4 32 files changed, 318 insertions(+), 390 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmap for Data Analysis
Description: Constructing hierarchical voronoi tessellations for a given data set and overlay heatmap for variables at various levels of the tessellations for in-depth data analysis. See <https://en.wikipedia.org/wiki/Voronoi_diagram> for more information. Credits to Mu Sigma for their continuous support throughout the development of the package.
Author: Sangeet Moy Das [aut],
Zubin Dowlaty [aut],
Avinash Joshi [aut],
Meet Dave [ctb],
Shubhra Prakash [ctb],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between muHVT versions 1.0.0 dated 2020-01-16 and 1.0.1 dated 2020-01-21
DESCRIPTION | 16 MD5 | 6 README.md | 1833 +++++++--------------------------------------------- inst/doc/muHVT.html | 4 4 files changed, 271 insertions(+), 1588 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-06 1.2-8
2014-02-15 1.2-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-02 2.1.5
2017-10-07 1.5.2
2017-09-11 1.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-02 1.1.1
2014-10-01 1.1
2014-05-10 1.0
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 3.36 dated 2019-04-27 and 3.37 dated 2020-01-21
survey-3.36/survey/R/odbc.R |only survey-3.36/survey/tests/caleg.Rout.save |only survey-3.37/survey/DESCRIPTION | 10 - survey-3.37/survey/MD5 | 88 +++++----- survey-3.37/survey/NAMESPACE | 49 +---- survey-3.37/survey/R/DBI.R | 41 ---- survey-3.37/survey/R/dbiupdate.R | 11 - survey-3.37/survey/R/survey.R | 2 survey-3.37/survey/R/surveyrep.R | 52 ++++-- survey-3.37/survey/R/svyivreg.R |only survey-3.37/survey/R/svymi.R | 18 -- survey-3.37/survey/R/sysdata.rda |binary survey-3.37/survey/R/twophase.R | 10 - survey-3.37/survey/R/twophase2.R | 2 survey-3.37/survey/R/withPV.R | 2 survey-3.37/survey/THANKS | 3 survey-3.37/survey/build/vignette.rds |binary survey-3.37/survey/data/api.rda |binary survey-3.37/survey/data/crowd.rda |binary survey-3.37/survey/data/election.rda |binary survey-3.37/survey/data/fpc.rda |binary survey-3.37/survey/data/hospital.rda |binary survey-3.37/survey/data/mu284.rda |binary survey-3.37/survey/data/nhanes.rda |binary survey-3.37/survey/data/scd.rda |binary survey-3.37/survey/data/yrbs.rda |binary survey-3.37/survey/inst/NEWS | 33 +++ survey-3.37/survey/inst/doc/domain.pdf |binary survey-3.37/survey/inst/doc/epi.pdf |binary survey-3.37/survey/inst/doc/phase1.pdf |binary survey-3.37/survey/inst/doc/pps.pdf |binary survey-3.37/survey/inst/doc/survey.pdf |binary survey-3.37/survey/man/anova.svyglm.Rd | 4 survey-3.37/survey/man/dimnames.DBIsvydesign.Rd | 3 survey-3.37/survey/man/open.DBIsvydesign.Rd | 9 - survey-3.37/survey/man/paley.Rd | 5 survey-3.37/survey/man/svrepdesign.Rd | 43 +++-- survey-3.37/survey/man/svychisq.Rd | 4 survey-3.37/survey/man/svydesign.Rd | 9 - survey-3.37/survey/man/svyivreg.Rd |only survey-3.37/survey/man/svyquantile.Rd | 6 survey-3.37/survey/man/svyranktest.Rd | 6 survey-3.37/survey/man/update.survey.design.Rd | 2 survey-3.37/survey/tests/cigsw.rda |only survey-3.37/survey/tests/quantile.R | 28 +++ survey-3.37/survey/tests/quantile.Rout.save | 168 ++++++++++++++++++-- survey-3.37/survey/tests/svyivreg.R |only survey-3.37/survey/tests/testoutput/caleg.R |only survey-3.37/survey/tests/testoutput/caleg.Rout.save |only 49 files changed, 388 insertions(+), 220 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical measures,
which otherwise could only be calculated with additional effort
(like Cramer's V, Phi, or effect size statistics like Eta or Omega squared),
or for which currently no functions available. Second, another focus
lies on weighted variants of common statistical measures and tests
like weighted standard error, mean, t-test, correlation, and more.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.17.7 dated 2019-11-14 and 0.17.8 dated 2020-01-21
sjstats-0.17.7/sjstats/R/cohens_f.R |only sjstats-0.17.7/sjstats/R/robust.R |only sjstats-0.17.7/sjstats/R/std_beta.R |only sjstats-0.17.7/sjstats/man/grpmean.Rd |only sjstats-0.17.7/sjstats/man/overdisp.Rd |only sjstats-0.17.7/sjstats/man/robust.Rd |only sjstats-0.17.7/sjstats/man/std_beta.Rd |only sjstats-0.17.7/sjstats/man/wtd_sd.Rd |only sjstats-0.17.7/sjstats/man/xtab_statistics.Rd |only sjstats-0.17.7/sjstats/tests/testthat/test-tidy_stan.R |only sjstats-0.17.8/sjstats/DESCRIPTION | 16 sjstats-0.17.8/sjstats/MD5 | 194 ++--- sjstats-0.17.8/sjstats/NAMESPACE | 79 -- sjstats-0.17.8/sjstats/NEWS.md | 22 sjstats-0.17.8/sjstats/R/Deprecated.R | 153 ++-- sjstats-0.17.8/sjstats/R/S3-methods.R | 5 sjstats-0.17.8/sjstats/R/anova_stats.R | 338 ++++----- sjstats-0.17.8/sjstats/R/auto_prior.R | 314 ++++----- sjstats-0.17.8/sjstats/R/bootstrap.R | 226 +++--- sjstats-0.17.8/sjstats/R/confint_ncg.R | 224 +++--- sjstats-0.17.8/sjstats/R/cramer.R | 108 +-- sjstats-0.17.8/sjstats/R/cv_error.R | 156 ++-- sjstats-0.17.8/sjstats/R/design_effect.R | 72 +- sjstats-0.17.8/sjstats/R/epsilon_sq.R | 62 - sjstats-0.17.8/sjstats/R/find_beta.R | 380 +++++------ sjstats-0.17.8/sjstats/R/grpmean.R | 49 - sjstats-0.17.8/sjstats/R/is_prime.R | 48 - sjstats-0.17.8/sjstats/R/mediation.R | 364 +++++----- sjstats-0.17.8/sjstats/R/mwu.R | 409 ++++++------ sjstats-0.17.8/sjstats/R/omega_sq.R | 170 ++-- sjstats-0.17.8/sjstats/R/partial_eta_sq_ci.R | 120 +-- sjstats-0.17.8/sjstats/R/phi.R | 2 sjstats-0.17.8/sjstats/R/re-exports.R | 56 - sjstats-0.17.8/sjstats/R/samplesize_mixed.R | 180 ++--- sjstats-0.17.8/sjstats/R/se_ybar.R | 98 +- sjstats-0.17.8/sjstats/R/select_helpers.R | 72 +- sjstats-0.17.8/sjstats/R/svy_median.R | 49 - sjstats-0.17.8/sjstats/R/svy_scale_weights.R | 2 sjstats-0.17.8/sjstats/R/svyglmnb.R | 280 ++++---- sjstats-0.17.8/sjstats/R/svyglmzip.R | 258 +++---- sjstats-0.17.8/sjstats/R/tidy_stan.R | 2 sjstats-0.17.8/sjstats/R/weight.R | 194 ++--- sjstats-0.17.8/sjstats/R/wtd_chisqtest.R | 92 +- sjstats-0.17.8/sjstats/R/wtd_cor.R | 176 ++--- sjstats-0.17.8/sjstats/R/wtd_mean.R | 44 - sjstats-0.17.8/sjstats/R/wtd_median.R | 84 +- sjstats-0.17.8/sjstats/R/wtd_mwu.R | 132 +-- sjstats-0.17.8/sjstats/R/wtd_sd.R | 249 +++---- sjstats-0.17.8/sjstats/R/wtd_se.R | 64 - sjstats-0.17.8/sjstats/R/wtd_ttest.R | 368 +++++----- sjstats-0.17.8/sjstats/R/wtd_variance.R | 24 sjstats-0.17.8/sjstats/R/xtab_statistics.R | 20 sjstats-0.17.8/sjstats/README.md | 100 +- sjstats-0.17.8/sjstats/build/partial.rdb |binary sjstats-0.17.8/sjstats/build/vignette.rds |binary sjstats-0.17.8/sjstats/inst/doc/anova-statistics.R | 3 sjstats-0.17.8/sjstats/inst/doc/anova-statistics.Rmd | 9 sjstats-0.17.8/sjstats/inst/doc/anova-statistics.html | 73 -- sjstats-0.17.8/sjstats/inst/doc/bayesian-statistics.R | 29 sjstats-0.17.8/sjstats/inst/doc/bayesian-statistics.Rmd | 255 ++----- sjstats-0.17.8/sjstats/inst/doc/bayesian-statistics.html | 344 ++-------- sjstats-0.17.8/sjstats/inst/doc/mixedmodels-statistics.Rmd | 198 ++--- sjstats-0.17.8/sjstats/inst/doc/mixedmodels-statistics.html | 7 sjstats-0.17.8/sjstats/man/auto_prior.Rd | 174 ++--- sjstats-0.17.8/sjstats/man/boot_ci.Rd | 312 ++++----- sjstats-0.17.8/sjstats/man/bootstrap.Rd | 176 ++--- sjstats-0.17.8/sjstats/man/chisq_gof.Rd | 130 +-- sjstats-0.17.8/sjstats/man/crosstable_statistics.Rd |only sjstats-0.17.8/sjstats/man/cv.Rd | 82 +- sjstats-0.17.8/sjstats/man/cv_error.Rd | 98 +- sjstats-0.17.8/sjstats/man/design_effect.Rd | 86 +- sjstats-0.17.8/sjstats/man/efc.Rd | 24 sjstats-0.17.8/sjstats/man/eta_sq.Rd | 186 ++--- sjstats-0.17.8/sjstats/man/find_beta.Rd | 216 +++--- sjstats-0.17.8/sjstats/man/fish.Rd | 24 sjstats-0.17.8/sjstats/man/gmd.Rd | 76 +- sjstats-0.17.8/sjstats/man/inequ_trend.Rd | 140 ++-- sjstats-0.17.8/sjstats/man/is_prime.Rd | 48 - sjstats-0.17.8/sjstats/man/mean_n.Rd | 138 ++-- sjstats-0.17.8/sjstats/man/means_by_group.Rd |only sjstats-0.17.8/sjstats/man/mediation.Rd | 123 +-- sjstats-0.17.8/sjstats/man/mwu.Rd | 150 ++-- sjstats-0.17.8/sjstats/man/nhanes_sample.Rd | 30 sjstats-0.17.8/sjstats/man/odds_to_rr.Rd | 170 ++-- sjstats-0.17.8/sjstats/man/prop.Rd | 224 +++--- sjstats-0.17.8/sjstats/man/r2.Rd |only sjstats-0.17.8/sjstats/man/reexports.Rd | 60 - sjstats-0.17.8/sjstats/man/samplesize_mixed.Rd | 158 ++-- sjstats-0.17.8/sjstats/man/scale_weights.Rd | 148 ++-- sjstats-0.17.8/sjstats/man/se_ybar.Rd | 58 - sjstats-0.17.8/sjstats/man/svyglm.nb.Rd | 154 ++-- sjstats-0.17.8/sjstats/man/svyglm.zip.Rd | 114 +-- sjstats-0.17.8/sjstats/man/table_values.Rd | 74 +- sjstats-0.17.8/sjstats/man/tidy_stan.Rd | 214 +++--- sjstats-0.17.8/sjstats/man/var_pop.Rd | 78 +- sjstats-0.17.8/sjstats/man/weight.Rd | 114 +-- sjstats-0.17.8/sjstats/man/weighted_sd.Rd |only sjstats-0.17.8/sjstats/tests/testthat.R | 20 sjstats-0.17.8/sjstats/tests/testthat/test-anova_stats.R | 138 ++-- sjstats-0.17.8/sjstats/tests/testthat/test-autoprior.R | 64 - sjstats-0.17.8/sjstats/tests/testthat/test-grpmean.R | 58 - sjstats-0.17.8/sjstats/tests/testthat/test-wtd.R | 86 +- sjstats-0.17.8/sjstats/vignettes/anova-statistics.Rmd | 9 sjstats-0.17.8/sjstats/vignettes/bayesian-statistics.Rmd | 255 ++----- sjstats-0.17.8/sjstats/vignettes/mixedmodels-statistics.Rmd | 198 ++--- 105 files changed, 5625 insertions(+), 5955 deletions(-)
Title: Toolbox for WELL Random Number Generators
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky <savicky@cs.cas.cz>.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rngWELL versions 0.10-5 dated 2017-05-21 and 0.10-6 dated 2020-01-21
DESCRIPTION | 6 MD5 | 18 configure | 4804 +++++++++++++++++++++++--------------------------------- configure.ac | 2 inst/NEWS | 8 src/config.h | 7 src/config.h.in | 3 src/init.c | 15 src/rngWELL.h | 4 src/version.c | 2 10 files changed, 2068 insertions(+), 2801 deletions(-)
Title: Build Dependency Graphs using Projection
Description: Implements a general framework for creating dependency graphs using projection as introduced in Fan, Feng and Xia (2019)<arXiv:1501.01617>. Both lasso and sparse additive model projections are implemented. Both Pearson correlation and distance covariance options are available to generate the graph.
Author: Yang Feng [aut, cre],
Jianqing Fan [aut],
Lucy Xia [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>
Diff between pgraph versions 1.5 dated 2019-06-25 and 1.6 dated 2020-01-21
CHANGELOG | 3 +++ DESCRIPTION | 19 ++++++++++++------- MD5 | 16 ++++++++-------- R/pgraph.R | 4 ++-- R/projcore.R | 12 ++++++++---- R/projcov.R | 6 +++--- man/pgraph.Rd | 15 +++++++++++---- man/projcore.Rd | 12 +++++++++--- man/projcov.Rd | 15 ++++++++++++--- 9 files changed, 68 insertions(+), 34 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.10.0 dated 2019-04-05 and 0.10.1 dated 2020-01-21
networkDynamic-0.10.0/networkDynamic/src/spellfunctions.c |only networkDynamic-0.10.1/networkDynamic/ChangeLog | 3 networkDynamic-0.10.1/networkDynamic/DESCRIPTION | 11 networkDynamic-0.10.1/networkDynamic/MD5 | 25 - networkDynamic-0.10.1/networkDynamic/NAMESPACE | 3 networkDynamic-0.10.1/networkDynamic/R/tea_utils.R | 4 networkDynamic-0.10.1/networkDynamic/build/vignette.rds |binary networkDynamic-0.10.1/networkDynamic/inst/doc/networkDynamic.pdf |binary networkDynamic-0.10.1/networkDynamic/man/add.methods.networkDynamic.Rd | 6 networkDynamic-0.10.1/networkDynamic/man/networkDynamic-package.Rd | 2 networkDynamic-0.10.1/networkDynamic/man/networkDynamic.Rd | 2 networkDynamic-0.10.1/networkDynamic/man/persistent_ids.Rd | 6 networkDynamic-0.10.1/networkDynamic/man/tea_functions.Rd | 19 networkDynamic-0.10.1/networkDynamic/src/Rinit.c | 227 ++++++++++ 14 files changed, 270 insertions(+), 38 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015 for lassnags),
Bourdon Jean-François [ctb] (Implemented sensor_tracking)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.2.0 dated 2020-01-08 and 2.2.1 dated 2020-01-21
lidR-2.2.0/lidR/tests/testthat/test-catalog_apply.R |only lidR-2.2.0/lidR/tests/testthat/test-internal_quadtree.R |only lidR-2.2.1/lidR/DESCRIPTION | 38 ++-- lidR-2.2.1/lidR/MD5 | 85 +++++----- lidR-2.2.1/lidR/NAMESPACE | 1 lidR-2.2.1/lidR/NEWS.md | 34 ++++ lidR-2.2.1/lidR/R/algorithm-its.r | 56 +++--- lidR-2.2.1/lidR/R/catalog_apply.r | 17 +- lidR-2.2.1/lidR/R/catalog_merge_results.R | 40 ++++ lidR-2.2.1/lidR/R/clusters_apply.r | 17 +- lidR-2.2.1/lidR/R/grid_density.r | 10 - lidR-2.2.1/lidR/R/io_writeANY.r | 10 - lidR-2.2.1/lidR/R/io_writeLAS.r | 6 lidR-2.2.1/lidR/R/lasclip.r | 2 lidR-2.2.1/lidR/R/lasgenerator.R |only lidR-2.2.1/lidR/R/methods-LAScluster.r | 5 lidR-2.2.1/lidR/R/point_metrics.R | 14 + lidR-2.2.1/lidR/R/tree_hulls.r | 2 lidR-2.2.1/lidR/R/utils_geometry.r | 4 lidR-2.2.1/lidR/R/utils_misc.r | 25 -- lidR-2.2.1/lidR/R/utils_raster.r | 5 lidR-2.2.1/lidR/R/utils_threads.r | 18 +- lidR-2.2.1/lidR/README.md | 6 lidR-2.2.1/lidR/inst/doc/lidR-computation-speed-LAScatalog.html | 2 lidR-2.2.1/lidR/man/catalog_apply.Rd | 8 lidR-2.2.1/lidR/man/grid_density.Rd | 10 - lidR-2.2.1/lidR/man/point_metrics.Rd | 6 lidR-2.2.1/lidR/man/watershed.Rd | 11 - lidR-2.2.1/lidR/src/C_dalponte2016.cpp | 2 lidR-2.2.1/lidR/src/C_delaunay.cpp | 8 lidR-2.2.1/lidR/src/LAS.cpp | 75 +++++--- lidR-2.2.1/lidR/tests/testthat/Rplots.pdf |binary lidR-2.2.1/lidR/tests/testthat/test-catalog_apply-automerge.R |only lidR-2.2.1/lidR/tests/testthat/test-catalog_apply-generic.R |only lidR-2.2.1/lidR/tests/testthat/test-catalog_apply-ondisk.R |only lidR-2.2.1/lidR/tests/testthat/test-delaunay.R | 2 lidR-2.2.1/lidR/tests/testthat/test-grid_density.R | 9 + lidR-2.2.1/lidR/tests/testthat/test-internal_spatialindex.R |only lidR-2.2.1/lidR/tests/testthat/test-lasfilterdecimate.R | 15 + lidR-2.2.1/lidR/tests/testthat/test-lasindex.R |only lidR-2.2.1/lidR/tests/testthat/test-lasrangecorrection.R | 64 +++++++ lidR-2.2.1/lidR/tests/testthat/test-lassnags.R | 21 ++ lidR-2.2.1/lidR/tests/testthat/test-lastrees.R | 14 - lidR-2.2.1/lidR/tests/testthat/test-point_metrics.R | 8 lidR-2.2.1/lidR/tests/testthat/test-projection.R | 6 lidR-2.2.1/lidR/tests/testthat/test-utils_geometry.R | 31 +++ lidR-2.2.1/lidR/tests/testthat/test-utils_threads.R |only lidR-2.2.1/lidR/tests/testthat/test-writeLAS.R | 9 + 48 files changed, 472 insertions(+), 224 deletions(-)
Title: Latent Position and Cluster Models for Statistical Networks
Description: Fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Jake Fisher [ctb],
Jordan T. Bates [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between latentnet versions 2.9.0 dated 2018-08-25 and 2.10.1 dated 2020-01-21
DESCRIPTION | 20 ++-- LICENSE | 4 MD5 | 173 +++++++++++++++++++++--------------------- NEWS | 5 + R/InitErgmm.fixed.R | 6 - R/InitErgmm.latent.R | 6 - R/InitErgmm.random.R | 6 - R/P.alloc.R | 6 - R/bayesmbc.MCMC.C.R | 6 - R/bayesmbc.R | 6 - R/ergmm.MCMC.C.R | 16 +-- R/ergmm.R | 10 +- R/ergmm.defaults.R | 6 - R/ergmm.draw.utils.R | 10 +- R/ergmm.families.R | 6 - R/ergmm.geodesicmatrix.R | 6 - R/ergmm.get.model.R | 17 ++-- R/ergmm.initvals.R | 10 +- R/ergmm.latent.effects.R | 30 +++---- R/ergmm.par.R | 23 ++--- R/ergmm.permutation.R | 10 +- R/ergmm.probs.R | 40 ++++----- R/ergmm.statseval.R | 12 +- R/ergmm.tuner.R | 18 ++-- R/gof.ergmm.R | 24 ++--- R/label.switching.R | 18 ++-- R/latent.R | 6 - R/latentnet-package.R | 6 - R/mcmc.diagnostics.ergmm.R | 10 +- R/merge.ergmm.R | 6 - R/plot.ergmm.R | 14 +-- R/predict.ergmm.R | 14 +-- R/print.ergmm.R | 6 - R/print.ergmm.model.R | 6 - R/procrustes.R | 6 - R/simulate.ergmm.R | 12 +- R/summary.ergmm.R | 60 ++++++++------ R/utilities.R | 8 - R/zzz.R | 6 - data/davis.RData |binary inst/CITATION | 6 - man/as.mcmc.list.ergmm.Rd | 3 man/control.ergmm.Rd | 54 +++++++++---- man/ergmm.Rd | 19 +++- man/ergmm.drawpie.Rd | 3 man/gof.ergmm.Rd | 9 +- man/latentnet-package.Rd | 1 man/mcmc.diagnostics.ergmm.Rd | 11 +- man/plot.ergmm.Rd | 48 ++++++++--- man/simulate.ergmm.Rd | 3 man/summary.ergmm.Rd | 13 ++- src/P_alloc.c | 6 - src/P_alloc.h | 6 - src/ergmm_families.c | 14 +-- src/ergmm_families.h | 20 ++-- src/ergmm_latent_effects.c | 8 - src/ergmm_latent_effects.h | 10 +- src/ergmm_probs.c | 6 - src/ergmm_probs.h | 6 - src/ergmm_sampler.c | 10 +- src/ergmm_sampler.h | 6 - src/ergmm_structs.h | 6 - src/ergmm_updaters.c | 6 - src/ergmm_updaters.h | 6 - src/ergmm_utils.c | 6 - src/ergmm_utils.h | 6 - src/init.c | 10 +- src/kl_switch.c | 6 - src/kl_switch.h | 6 - src/matrix_utils.c | 6 - src/matrix_utils.h | 6 - src/mbc_sampler.c | 6 - src/mbc_sampler.h | 6 - src/mvnorm.c | 6 - src/mvnorm.h | 6 - src/post_predict.c | 6 - src/post_predict.h | 6 - src/procrustes.c | 6 - src/procrustes.h | 6 - src/wishart.c | 6 - src/wishart.h | 6 - tests/missing.R | 6 - tests/nofixed.R |only tests/nolatent.R | 7 - tests/nomcmc.R | 6 - tests/nomixing.R | 6 - tests/normal.R | 9 +- tests/onlymcmc.R | 6 - 88 files changed, 586 insertions(+), 494 deletions(-)
Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with
large-than-RAM datasets. Aims to lower the barrier-to-entry for
manipulating large datasets by adhering closely to popular and
familiar data manipulation paradigms like dplyr verbs and
data.table syntax.
Author: Dai ZJ [aut, cre],
Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>
Diff between disk.frame versions 0.3.2 dated 2020-01-19 and 0.3.3 dated 2020-01-21
disk.frame-0.3.2/disk.frame/man/bloomfilter.Rd |only disk.frame-0.3.3/disk.frame/DESCRIPTION | 8 disk.frame-0.3.3/disk.frame/MD5 | 13 disk.frame-0.3.3/disk.frame/NAMESPACE | 3 disk.frame-0.3.3/disk.frame/NEWS.md | 3 disk.frame-0.3.3/disk.frame/R/bloom-filter.r | 394 ++++++------ disk.frame-0.3.3/disk.frame/README.md | 41 - disk.frame-0.3.3/disk.frame/inst/doc/data-table-syntax.html | 51 - 8 files changed, 268 insertions(+), 245 deletions(-)
Title: An Imperative Library for Data Manipulation
Description: Implements tools for manipulating data sets and performing regressions in a way that is familiar to users of a popular, but proprietary, statistical package commonly used in the social sciences. Loads a single dataset into memory and implements a set of imperative commands to modify that data and perform regressions and other analysis on the dataset. Offers an alternative to standard R's function-based approach to data manipulation.
Author: Zach Flynn [aut, cre]
Maintainer: Zach Flynn <zlflynn@gmail.com>
Diff between genvar versions 0.0.1.4 dated 2019-10-13 and 0.0.2.0 dated 2020-01-21
genvar-0.0.1.4/genvar/R/varlist.r |only genvar-0.0.1.4/genvar/man/estimates_print.Rd |only genvar-0.0.1.4/genvar/man/varlist.Rd |only genvar-0.0.2.0/genvar/DESCRIPTION | 9 - genvar-0.0.2.0/genvar/MD5 | 147 +++++++++++++------------ genvar-0.0.2.0/genvar/NAMESPACE | 14 ++ genvar-0.0.2.0/genvar/NEWS.md | 9 + genvar-0.0.2.0/genvar/R/capture.r | 4 genvar-0.0.2.0/genvar/R/collapse.r | 20 ++- genvar-0.0.2.0/genvar/R/convert.r | 39 ++---- genvar-0.0.2.0/genvar/R/count.r | 17 +- genvar-0.0.2.0/genvar/R/data.env.r | 1 genvar-0.0.2.0/genvar/R/describe.r | 10 + genvar-0.0.2.0/genvar/R/do.r | 26 ++-- genvar-0.0.2.0/genvar/R/drop.r | 46 ++----- genvar-0.0.2.0/genvar/R/estimates.r | 52 +++++++- genvar-0.0.2.0/genvar/R/fillin.r | 33 +++-- genvar-0.0.2.0/genvar/R/forval.r | 6 - genvar-0.0.2.0/genvar/R/forvar.r | 15 -- genvar-0.0.2.0/genvar/R/gen.r | 13 ++ genvar-0.0.2.0/genvar/R/getdata.r | 7 + genvar-0.0.2.0/genvar/R/gvcharexpr.r |only genvar-0.0.2.0/genvar/R/gvmerge.r |only genvar-0.0.2.0/genvar/R/gvplot.r | 10 - genvar-0.0.2.0/genvar/R/headdata.r | 6 + genvar-0.0.2.0/genvar/R/isloaded.r | 9 + genvar-0.0.2.0/genvar/R/lag.r | 6 - genvar-0.0.2.0/genvar/R/listif.r | 25 ++-- genvar-0.0.2.0/genvar/R/logit.r | 23 ++- genvar-0.0.2.0/genvar/R/pred.r | 4 genvar-0.0.2.0/genvar/R/reg.r | 46 +++++-- genvar-0.0.2.0/genvar/R/rename.r | 3 genvar-0.0.2.0/genvar/R/shape.r | 10 + genvar-0.0.2.0/genvar/R/structure_varlist.r |only genvar-0.0.2.0/genvar/R/subset.varlist.r | 3 genvar-0.0.2.0/genvar/R/summarize.r | 15 +- genvar-0.0.2.0/genvar/R/switchdata.r |only genvar-0.0.2.0/genvar/R/use.r | 11 - genvar-0.0.2.0/genvar/R/xtset.r | 12 +- genvar-0.0.2.0/genvar/README.md | 16 ++ genvar-0.0.2.0/genvar/man/L.Rd | 6 - genvar-0.0.2.0/genvar/man/assert_loaded.Rd | 4 genvar-0.0.2.0/genvar/man/collapse.Rd | 2 genvar-0.0.2.0/genvar/man/count.Rd | 6 - genvar-0.0.2.0/genvar/man/describe.Rd | 5 genvar-0.0.2.0/genvar/man/destring.Rd | 6 - genvar-0.0.2.0/genvar/man/do.Rd | 10 - genvar-0.0.2.0/genvar/man/dropif.Rd | 4 genvar-0.0.2.0/genvar/man/dropvar.Rd | 7 - genvar-0.0.2.0/genvar/man/estimates_get.Rd |only genvar-0.0.2.0/genvar/man/estimates_restore.Rd | 9 + genvar-0.0.2.0/genvar/man/estimates_save.Rd | 13 +- genvar-0.0.2.0/genvar/man/estimates_store.Rd | 9 + genvar-0.0.2.0/genvar/man/estimates_use.Rd | 9 + genvar-0.0.2.0/genvar/man/fillin.Rd | 11 + genvar-0.0.2.0/genvar/man/forval.Rd | 4 genvar-0.0.2.0/genvar/man/forvar.Rd | 6 - genvar-0.0.2.0/genvar/man/gen.Rd | 5 genvar-0.0.2.0/genvar/man/getdata.Rd | 9 + genvar-0.0.2.0/genvar/man/gvmerge.Rd |only genvar-0.0.2.0/genvar/man/gvplot.Rd | 8 - genvar-0.0.2.0/genvar/man/headdata.Rd | 4 genvar-0.0.2.0/genvar/man/is_loaded.Rd | 6 + genvar-0.0.2.0/genvar/man/keepif.Rd | 4 genvar-0.0.2.0/genvar/man/keepvar.Rd | 7 - genvar-0.0.2.0/genvar/man/listdata.Rd |only genvar-0.0.2.0/genvar/man/listif.Rd | 7 + genvar-0.0.2.0/genvar/man/logit.Rd | 10 + genvar-0.0.2.0/genvar/man/namedata.Rd |only genvar-0.0.2.0/genvar/man/pred.Rd | 4 genvar-0.0.2.0/genvar/man/probit.Rd | 2 genvar-0.0.2.0/genvar/man/reg.Rd | 18 ++- genvar-0.0.2.0/genvar/man/shape.Rd | 10 + genvar-0.0.2.0/genvar/man/structure_varlist.Rd |only genvar-0.0.2.0/genvar/man/subset.varlist.Rd | 2 genvar-0.0.2.0/genvar/man/summarize.Rd | 7 + genvar-0.0.2.0/genvar/man/switchdata.Rd |only genvar-0.0.2.0/genvar/man/taildata.Rd | 4 genvar-0.0.2.0/genvar/man/tostring.Rd | 4 genvar-0.0.2.0/genvar/man/use.Rd | 2 genvar-0.0.2.0/genvar/man/xtset.Rd | 10 - 81 files changed, 582 insertions(+), 319 deletions(-)
Title: Block Design for Response-Adaptive Randomization
Description: Computes power for response-adaptive randomization with a block design that captures both the time and treatment effect. T. Chandereng, R. Chappell (2019) <arXiv:1904.07758>.
Author: Thevaa Chandereng [aut, cre, cph]
(<https://orcid.org/0000-0003-4078-9176>),
Rick Chapppell [aut, cph]
Maintainer: Thevaa Chandereng <chandereng@wisc.edu>
Diff between blockRAR versions 1.0.1 dated 2019-09-08 and 1.0.2 dated 2020-01-21
blockRAR-1.0.1/blockRAR/tests/testthat/test_binomial.R |only blockRAR-1.0.2/blockRAR/DESCRIPTION | 8 blockRAR-1.0.2/blockRAR/MD5 | 27 blockRAR-1.0.2/blockRAR/NAMESPACE | 16 blockRAR-1.0.2/blockRAR/R/bdpbinomial.R |only blockRAR-1.0.2/blockRAR/R/binomialbayes.R | 83 ++ blockRAR-1.0.2/blockRAR/R/binomialfreq.R | 103 ++- blockRAR-1.0.2/blockRAR/README.md | 5 blockRAR-1.0.2/blockRAR/build/vignette.rds |binary blockRAR-1.0.2/blockRAR/inst/doc/blockRAR.Rmd | 4 blockRAR-1.0.2/blockRAR/inst/doc/blockRAR.html | 360 ++++++++---- blockRAR-1.0.2/blockRAR/man/bdpbinomial.Rd |only blockRAR-1.0.2/blockRAR/man/binomialbayes.Rd | 14 blockRAR-1.0.2/blockRAR/man/binomialfreq.Rd | 14 blockRAR-1.0.2/blockRAR/tests/testthat/test_binomialbayes.R |only blockRAR-1.0.2/blockRAR/tests/testthat/test_binomialfreq.R |only blockRAR-1.0.2/blockRAR/vignettes/blockRAR.Rmd | 4 17 files changed, 458 insertions(+), 180 deletions(-)
Title: Kernel Density Estimation and Selection of Optimum Bandwidth
Description: A collection of functions related to density estimation by using Chen's (2000) idea. Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull. For details see Chen (2000), Scaillet (2004) <doi:10.1080/10485250310001624819> and Khan and Akbar.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between AsyK versions 1.3.2 dated 2019-11-14 and 1.5.3 dated 2020-01-21
AsyK-1.3.2/AsyK/man/graphLap.Rd |only AsyK-1.3.2/AsyK/man/graphrig.Rd |only AsyK-1.3.2/AsyK/man/mselap.Rd |only AsyK-1.3.2/AsyK/man/mserig.Rd |only AsyK-1.5.3/AsyK/DESCRIPTION | 11 - AsyK-1.5.3/AsyK/MD5 | 25 +- AsyK-1.5.3/AsyK/NAMESPACE | 10 - AsyK-1.5.3/AsyK/R/AsyK.R | 342 ++++++++++++++++++++++++------------ AsyK-1.5.3/AsyK/man/AsyK-package.Rd |only AsyK-1.5.3/AsyK/man/Laplace.Rd |only AsyK-1.5.3/AsyK/man/NSR.Rd | 6 AsyK-1.5.3/AsyK/man/RIG.Rd |only AsyK-1.5.3/AsyK/man/compLR.Rd | 10 + AsyK-1.5.3/AsyK/man/laphcomp.Rd | 12 + AsyK-1.5.3/AsyK/man/mseLap.Rd |only AsyK-1.5.3/AsyK/man/mseRIG.Rd |only AsyK-1.5.3/AsyK/man/plot.Laplace.Rd |only AsyK-1.5.3/AsyK/man/plot.RIG.Rd |only AsyK-1.5.3/AsyK/man/righcomp.Rd | 12 + 19 files changed, 294 insertions(+), 134 deletions(-)
Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ubiquity versions 1.0.0 dated 2019-10-17 and 1.0.1 dated 2020-01-21
DESCRIPTION | 18 MD5 | 109 - NAMESPACE | 4 R/ubiquity.r | 1495 ++++++++++++++++++++---- README.md | 4 inst/doc/Deployment.R | 1 inst/doc/Deployment.Rmd | 1 inst/doc/Deployment.html | 4 inst/doc/Estimation.R | 11 inst/doc/Estimation.Rmd | 39 inst/doc/Estimation.html | 212 +-- inst/doc/Language.Rmd | 44 inst/doc/Language.html | 34 inst/doc/NCA.R | 7 inst/doc/NCA.Rmd | 18 inst/doc/NCA.html | 121 + inst/doc/Reporting.R | 150 ++ inst/doc/Reporting.Rmd | 459 ++++++- inst/doc/Reporting.html | 416 +++++- inst/doc/Simulation.R | 16 inst/doc/Simulation.Rmd | 23 inst/doc/Simulation.html | 27 inst/doc/Titration.R | 1 inst/doc/Titration.Rmd | 9 inst/doc/Titration.html | 24 inst/ubinc/scripts/analysis_multiple.r | 5 inst/ubinc/scripts/analysis_nca_md.R | 21 inst/ubinc/scripts/analysis_nca_sd.R | 18 inst/ubinc/scripts/analysis_nca_sparse.R | 20 inst/ubinc/scripts/analysis_parent.r | 15 inst/ubinc/scripts/analysis_parent_metabolite.r | 15 inst/ubinc/scripts/make_report_Word.R |only inst/ubinc/scripts/ubiquity_fcns.R | 1495 ++++++++++++++++++++---- inst/ubinc/templates/org_functions.R | 76 + inst/ubinc/templates/r_analysis_estimation.R | 10 inst/ubinc/templates/r_components.R | 32 inst/ubinc/templates/r_gui_save.R | 1 inst/ubinc/templates/r_nca.R | 28 inst/ubinc/templates/r_simulation_driver.R | 16 inst/ubinc/templates/report.docx |binary inst/ubinc/templates/ubiquity_server.R | 13 inst/ubinc/templates/ubiquity_server_custom.R | 1 man/md_to_officer.Rd |only man/simulate_subjects.Rd | 9 man/system_define_cohort.Rd | 23 man/system_report_doc_add_content.Rd | 62 man/system_report_doc_format_section.Rd |only man/system_report_estimation.Rd | 2 man/system_report_nca.Rd | 2 man/system_report_ph_content.Rd | 2 vignettes/Deployment.Rmd | 1 vignettes/Estimation.Rmd | 39 vignettes/Language.Rmd | 44 vignettes/NCA.Rmd | 18 vignettes/Reporting.Rmd | 459 ++++++- vignettes/Simulation.Rmd | 23 vignettes/Titration.Rmd | 9 57 files changed, 4740 insertions(+), 966 deletions(-)
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez [cre],
Carlos Aguero [aut],
Olger Calderon [cph],
Roberto Zuniga [cph],
Jorge Arce [cph]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 3.0 dated 2019-10-22 and 3.0.1 dated 2020-01-21
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NAMESPACE | 1 R/RSDA.R | 4 +-- R/sym.predict.R | 19 ++++++++++++++++- R/sym_glm.R | 2 - inst/doc/introduction.html | 48 +++++++++++++++++++++------------------------ man/RSDA.Rd | 4 +-- man/sym.predict.Rd | 3 ++ 9 files changed, 62 insertions(+), 43 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. Handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. New fast interface using subsampling and confidence regions for variable importance.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.9.2 dated 2019-11-18 and 2.9.3 dated 2020-01-21
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 4 ++-- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS | 12 ++++++++++-- man/impute.rfsrc.Rd | 46 ++++++++++++++++++++++++++++++++++++++++++++++ src/randomForestSRC.c | 46 +++++++++++++++++++++++++--------------------- src/randomForestSRC.h | 2 -- 10 files changed, 107 insertions(+), 51 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.0-3 dated 2019-09-26 and 2.0-4 dated 2020-01-21
DESCRIPTION | 6 MD5 | 76 ++++---- R/krigeST.R | 18 +- build/vignette.rds |binary data/DE_RB_2005.rda |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/krigeST.Rd | 13 - man/variogram.Rd | 2 man/vv.Rd | 5 man/wind.Rd | 4 src/mtrx.c | 8 tests/allier.R | 2 tests/allier.Rout.save | 302 +++++++++++++++++------------------ tests/cv3d.R | 1 tests/cv3d.Rout.save | 51 ++--- tests/merge.Rout.save | 142 ++++++++-------- tests/stars.R | 16 - tests/stars.Rout.save | 36 +--- tests/unproj.R | 9 - tests/unproj.Rout.save | 70 +++----- tests/windst.R | 8 tests/windst.Rout.save | 21 -- 39 files changed, 376 insertions(+), 414 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@ucsd.edu>
Diff between bio3d versions 2.4-0 dated 2019-11-26 and 2.4-1 dated 2020-01-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/get.seq.R | 2 +- R/mktrj.pca.R | 19 ++++++------------- inst/doc/bio3d_vignettes.html | 9 ++++++++- man/bio3d.package.Rd | 4 ++-- man/write.pir.Rd | 2 +- 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. In addition, missing event types or left truncation are considered. We provide the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 3.0.0 dated 2019-12-09 and 3.0.1 dated 2020-01-21
DESCRIPTION | 14 ++++---- MD5 | 18 +++++------ R/bssmle.R | 70 -------------------------------------------- R/bssmle_aipw.R | 79 ++++---------------------------------------------- R/bssmle_se_aipw.R | 15 ++++++++- R/ciregic_aipw.R | 7 ++-- data/fit.RData |binary data/fit_aipw.RData |binary man/bssmle_se_aipw.Rd | 5 ++- man/ciregic_aipw.Rd | 5 ++- 10 files changed, 48 insertions(+), 165 deletions(-)
Title: Functions for Time Series Analysis and Forecasting
Description: Provides a set of tools for descriptive and predictive analysis of time series data. That includes functions for interactive visualization of time series objects and as well utility functions for automation time series forecasting.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between TSstudio versions 0.1.5 dated 2019-10-28 and 0.1.6 dated 2020-01-21
TSstudio-0.1.5/TSstudio/man/ts_acf.Rd |only TSstudio-0.1.5/TSstudio/man/ts_backtesting.Rd |only TSstudio-0.1.5/TSstudio/man/ts_pacf.Rd |only TSstudio-0.1.6/TSstudio/DESCRIPTION | 19 TSstudio-0.1.6/TSstudio/LICENSE | 2 TSstudio-0.1.6/TSstudio/MD5 | 39 TSstudio-0.1.6/TSstudio/NAMESPACE | 3 TSstudio-0.1.6/TSstudio/NEWS.md | 10 TSstudio-0.1.6/TSstudio/R/correlation_functions.R | 282 ---- TSstudio-0.1.6/TSstudio/R/forecast_tools.R | 4 TSstudio-0.1.6/TSstudio/R/train_functions.R | 814 ------------- TSstudio-0.1.6/TSstudio/R/util_functions.R | 24 TSstudio-0.1.6/TSstudio/README.md | 8 TSstudio-0.1.6/TSstudio/data/EURO_Brent.rda |binary TSstudio-0.1.6/TSstudio/data/Michigan_CS.rda |binary TSstudio-0.1.6/TSstudio/data/USUnRate.rda |binary TSstudio-0.1.6/TSstudio/data/USVSales.rda |binary TSstudio-0.1.6/TSstudio/data/US_indicators.rda |binary TSstudio-0.1.6/TSstudio/data/USgas.rda |binary TSstudio-0.1.6/TSstudio/inst/doc/Plotting_Time_Series.R | 32 TSstudio-0.1.6/TSstudio/inst/doc/Plotting_Time_Series.html | 162 +- TSstudio-0.1.6/TSstudio/man/ts_grid.Rd | 2 22 files changed, 223 insertions(+), 1178 deletions(-)
Title: Generalized Graded Unfolding Model
Description: An implementation of the generalized graded unfolding model (GGUM) in R, see Roberts, Donoghue, and Laughlin (2000) <doi:10.1177/01466216000241001>). It allows to simulate data sets based on the GGUM. It fits the GGUM and the GUM, and it retrieves item and person parameter estimates. Several plotting functions are available (item and test information functions; item and test characteristic curves; item category response curves). Additionally, there are some functions that facilitate the communication between R and 'GGUM2004'. Finally, a model-fit checking utility, MODFIT(), is also available.
Author: Jorge N. Tendeiro [aut, cre],
Sebastian Castro-Alvarez [aut]
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>
Diff between GGUM versions 0.3.3 dated 2018-10-04 and 0.4 dated 2020-01-21
DESCRIPTION | 8 MD5 | 68 +- NAMESPACE | 62 - R/Accessory.R | 1400 ++++++++++++++++++++++---------------------- R/GGUM.R | 758 +++++++++++------------ R/GGUM2004.R | 1160 ++++++++++++++++++------------------ R/GUM.R | 680 ++++++++++----------- R/GUM_internal.R | 300 ++++----- R/IRT_models.R | 256 ++++---- R/MODFIT.R | 712 +++++++++++----------- R/Methods.R | 90 +- R/Model4.R | 268 ++++---- R/Plots.R | 1082 +++++++++++++++++----------------- R/SanityChecks.R | 212 +++--- R/pkgname.R | 258 ++++---- README.md | 8 build/partial.rdb |binary inst/REFERENCES.bib | 146 ++-- man/GGUM-package.Rd | 296 ++++----- man/GGUM.Rd | 230 +++---- man/GUM.Rd | 180 ++--- man/GenData.GGUM.Rd | 170 ++--- man/MODFIT.Rd | 202 +++--- man/Theta.EAP.Rd | 128 ++-- man/export.GGUM2004.Rd | 114 +-- man/plotCRC.Rd | 117 +-- man/plotICC.Rd | 118 +-- man/plotIIF.Rd | 116 +-- man/plotTCC.Rd | 118 +-- man/plotTIF.Rd | 104 +-- man/probs.GGUM.Rd | 116 +-- man/read.item.GGUM2004.Rd | 106 +-- man/read.person.GGUM2004.Rd | 86 +- man/run.GGUM2004.Rd | 159 ++-- man/write.GGUM2004.Rd | 155 ++-- 35 files changed, 5020 insertions(+), 4963 deletions(-)