Title: Optimal Experimental Designs for Accelerated Life Testing
Description: Creates the optimal (D, U and I) designs for the accelerated life
testing with right censoring or interval censoring. It uses generalized
linear model (GLM) approach to derive the asymptotic variance-covariance
matrix of regression coefficients. The failure time distribution is assumed
to follow Weibull distribution with a known shape parameter and log-linear
link functions are used to model the relationship between failure time
parameters and stress variables. The acceleration model may have multiple
stress factors, although most ALTs involve only two or less stress factors.
ALTopt package also provides several plotting functions including contour plot,
Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space
(VDUS) plot. For more details, see Seo and Pan (2015) <doi:10.32614/RJ-2015-029>.
Author: Kangwon Seo [aut, cre],
Rong Pan [aut]
Maintainer: Kangwon Seo <seoka@missouri.edu>
Diff between ALTopt versions 0.1.1 dated 2015-08-27 and 0.1.2 dated 2019-12-12
DESCRIPTION | 15 +-- MD5 | 56 ++++++------ NAMESPACE | 3 R/ALTopt.R | 23 +++-- build/partial.rdb |binary man/ALTopt-package.Rd | 16 ++- man/Dobj.ic.Rd | 25 ++--- man/Dobj.rc.Rd | 25 ++--- man/ExtendedForm.Rd | 25 ++--- man/Iobj.ic.Rd | 25 ++--- man/Iobj.rc.Rd | 25 ++--- man/PreVar.Rd | 23 ++--- man/Uobj.ic.Rd | 25 ++--- man/Uobj.rc.Rd | 25 ++--- man/alteval.ic.Rd | 148 +++++++++++++++++--------------- man/alteval.rc.Rd | 143 ++++++++++++++++--------------- man/altopt.ic.Rd | 199 +++++++++++++++++++++++--------------------- man/altopt.rc.Rd | 194 ++++++++++++++++++++++-------------------- man/compare.fus.Rd | 89 +++++++++---------- man/compare.vdus.Rd | 89 +++++++++---------- man/convert.stress.level.Rd | 93 ++++++++++---------- man/design.plot.Rd | 73 +++++++--------- man/kmeansCls.Rd | 23 ++--- man/pv.contour.ic.Rd | 135 ++++++++++++++++------------- man/pv.contour.rc.Rd | 130 +++++++++++++++------------- man/pv.fus.ic.Rd | 118 +++++++++++++------------- man/pv.fus.rc.Rd | 113 +++++++++++++----------- man/pv.vdus.ic.Rd | 118 +++++++++++++------------- man/pv.vdus.rc.Rd | 113 +++++++++++++----------- 29 files changed, 1092 insertions(+), 997 deletions(-)
Title: Pipeline for Topological Data Analysis
Description: A comprehensive toolset for any
useR conducting topological data analysis, specifically via the
calculation of persistent homology in a Vietoris-Rips complex.
The tools this package currently provides can be conveniently split
into three main sections: (1) calculating persistent homology; (2)
conducting statistical inference on persistent homology calculations;
(3) visualizing persistent homology and statistical inference.
The published form of TDAstats can be found in Wadhwa et al. (2018)
<doi:10.21105/joss.00860>.
For a general background on computing persistent homology for
topological data analysis, see Otter et al. (2017)
<doi:10.1140/epjds/s13688-017-0109-5>.
To learn more about how the permutation test is used for
nonparametric statistical inference in topological data analysis,
read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>.
To learn more about how TDAstats calculates persistent homology,
you can visit the GitHub repository for Ripser, the software that
works behind the scenes at <https://github.com/Ripser/ripser>.
This package has been published as Wadhwa et al. (2018)
<doi:10.21105/joss.00860>.
Author: Raoul Wadhwa [aut, cre],
Andrew Dhawan [aut],
Drew Williamson [aut],
Jacob Scott [aut],
Jason Cory Brunson [ctb],
Shota Ochi [ctb]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Diff between TDAstats versions 0.4.0 dated 2018-11-05 and 0.4.1 dated 2019-12-12
TDAstats-0.4.0/TDAstats/tests/testthat/test_inputformat.R |only TDAstats-0.4.1/TDAstats/DESCRIPTION | 14 TDAstats-0.4.1/TDAstats/MD5 | 87 - TDAstats-0.4.1/TDAstats/NAMESPACE | 23 TDAstats-0.4.1/TDAstats/R/RcppExports.R | 14 TDAstats-0.4.1/TDAstats/R/TDAstats.R | 30 TDAstats-0.4.1/TDAstats/R/calculate.R | 203 +- TDAstats-0.4.1/TDAstats/R/data.R | 68 TDAstats-0.4.1/TDAstats/R/inference.R | 747 +++++---- TDAstats-0.4.1/TDAstats/R/utility.R | 74 TDAstats-0.4.1/TDAstats/R/visuals.R | 285 +-- TDAstats-0.4.1/TDAstats/R/zzz.R | 16 TDAstats-0.4.1/TDAstats/build/vignette.rds |binary TDAstats-0.4.1/TDAstats/inst/CITATION | 34 TDAstats-0.4.1/TDAstats/inst/doc/inference.R | 162 +- TDAstats-0.4.1/TDAstats/inst/doc/inference.Rmd | 444 ++--- TDAstats-0.4.1/TDAstats/inst/doc/inference.html | 801 ++++------ TDAstats-0.4.1/TDAstats/inst/doc/inputformat.R | 124 - TDAstats-0.4.1/TDAstats/inst/doc/inputformat.Rmd | 234 +- TDAstats-0.4.1/TDAstats/inst/doc/inputformat.html | 682 +++----- TDAstats-0.4.1/TDAstats/inst/doc/intro.R | 102 - TDAstats-0.4.1/TDAstats/inst/doc/intro.Rmd | 390 ++-- TDAstats-0.4.1/TDAstats/inst/doc/intro.html | 777 ++++----- TDAstats-0.4.1/TDAstats/man/TDAstats.Rd | 32 TDAstats-0.4.1/TDAstats/man/calculate_homology.Rd | 97 - TDAstats-0.4.1/TDAstats/man/circle2d.Rd | 36 TDAstats-0.4.1/TDAstats/man/figures/HexTDA.png |binary TDAstats-0.4.1/TDAstats/man/id_significant.Rd |only TDAstats-0.4.1/TDAstats/man/permutation_test.Rd | 84 - TDAstats-0.4.1/TDAstats/man/phom.dist.Rd | 54 TDAstats-0.4.1/TDAstats/man/plot_barcode.Rd | 88 - TDAstats-0.4.1/TDAstats/man/plot_persist.Rd | 92 - TDAstats-0.4.1/TDAstats/man/sphere3d.Rd | 36 TDAstats-0.4.1/TDAstats/man/unif2d.Rd | 36 TDAstats-0.4.1/TDAstats/man/unif3d.Rd | 36 TDAstats-0.4.1/TDAstats/tests/testthat.R | 8 TDAstats-0.4.1/TDAstats/tests/testthat/test_aaaload.R | 44 TDAstats-0.4.1/TDAstats/tests/testthat/test_calculate_errors.R | 80 TDAstats-0.4.1/TDAstats/tests/testthat/test_inference.R | 309 ++- TDAstats-0.4.1/TDAstats/tests/testthat/test_ioformat.R |only TDAstats-0.4.1/TDAstats/tests/testthat/test_plots.R | 134 - TDAstats-0.4.1/TDAstats/tests/testthat/test_ripser_accurate.R | 138 - TDAstats-0.4.1/TDAstats/tests/testthat/test_ripser_consistent.R | 168 +- TDAstats-0.4.1/TDAstats/vignettes/inference.Rmd | 444 ++--- TDAstats-0.4.1/TDAstats/vignettes/inputformat.Rmd | 234 +- TDAstats-0.4.1/TDAstats/vignettes/intro.Rmd | 390 ++-- 46 files changed, 3932 insertions(+), 3919 deletions(-)
Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly
Unrelated Regression (usually called SUR) models, with spatial structure, by maximum
likelihood and three-stage least squares. The package estimates the
most common spatial specifications, that is, SUR with Spatial Lag of
X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM),
SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM),
SUR with Spatial Durbin Error Model (called SUR-SDEM),
SUR with Spatial Autoregressive terms and Spatial Autoregressive
Disturbances (called SUR-SARAR) and SUR with Spatially Independent Model (called SUR-SIM).
The methodology of these models can be found in next references
Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443>
Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut],
Fernando A Lopez [aut],
Roman Minguez [aut, cre],
Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between spsur versions 1.0.0.3 dated 2019-03-23 and 1.0.0.4 dated 2019-12-12
DESCRIPTION | 10 MD5 | 69 +- NAMESPACE | 94 +-- R/aux_functions.R | 25 R/cov_spsur.R | 1244 +++++++++++++++++++++---------------------- R/dgp_spSUR.R | 754 +++++++++++++------------- R/fit_spsur.R | 763 +++++++++++++------------- R/fit_spsur_3sls.R | 7 R/impacts.R | 686 +++++++++++------------ R/lmtestspsur.R | 436 +++++++-------- R/lrtestspsur.R | 632 ++++++++++----------- R/spsur3sls.R | 610 ++++++++++----------- R/spsurml.R | 1032 +++++++++++++++++------------------ R/spsurtime.R | 500 ++++++++--------- R/summary.spsur.R | 2 build/vignette.rds |binary inst/doc/spsur-vignette.R | 84 +- inst/doc/spsur-vignette.html | 611 ++++++++++----------- man/NCOVR.Rd | 134 ++-- man/W.Rd | 54 - man/Wspc.Rd | 54 - man/dgp_spsur.Rd | 510 +++++++++-------- man/impacts.Rd | 290 ++++------ man/lmtestspsur.Rd | 377 ++++++------- man/lr_betas_spsur.Rd | 368 ++++++------ man/lrtestspsur.Rd | 389 ++++++------- man/print.summary.spsur.Rd | 67 +- man/spc.Rd | 76 +- man/spsur-package.Rd | 356 ++++++------ man/spsur3sls.Rd | 449 +++++++-------- man/spsurml.Rd | 685 ++++++++++++----------- man/spsurtime.Rd | 422 +++++++------- man/summary.spsur.Rd | 78 +- man/wald_betas.Rd | 220 +++---- man/wald_deltas.Rd | 252 ++++---- vignettes/rsconnect |only 36 files changed, 6170 insertions(+), 6170 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.1.1 dated 2019-10-03 and 3.1.2 dated 2019-12-12
Seurat-3.1.1/Seurat/man/MapQuery.Rd |only Seurat-3.1.1/Seurat/man/PairwiseIntegrateReference.Rd |only Seurat-3.1.2/Seurat/DESCRIPTION | 13 Seurat-3.1.2/Seurat/MD5 | 214 +-- Seurat-3.1.2/Seurat/NAMESPACE | 12 Seurat-3.1.2/Seurat/NEWS.md | 11 Seurat-3.1.2/Seurat/R/clustering.R | 58 Seurat-3.1.2/Seurat/R/differential_expression.R | 6 Seurat-3.1.2/Seurat/R/dimensional_reduction.R | 39 Seurat-3.1.2/Seurat/R/generics.R | 30 Seurat-3.1.2/Seurat/R/integration.R | 669 +++++----- Seurat-3.1.2/Seurat/R/objects.R | 629 ++++++--- Seurat-3.1.2/Seurat/R/preprocessing.R | 44 Seurat-3.1.2/Seurat/R/utilities.R | 121 + Seurat-3.1.2/Seurat/R/visualization.R | 37 Seurat-3.1.2/Seurat/README.md | 2 Seurat-3.1.2/Seurat/man/AddMetaData.Rd | 1 Seurat-3.1.2/Seurat/man/AddModuleScore.Rd | 18 Seurat-3.1.2/Seurat/man/Assay-class.Rd | 3 Seurat-3.1.2/Seurat/man/AverageExpression.Rd | 15 Seurat-3.1.2/Seurat/man/BuildClusterTree.Rd | 14 Seurat-3.1.2/Seurat/man/CalculateBarcodeInflections.Rd | 10 Seurat-3.1.2/Seurat/man/CellCycleScoring.Rd | 3 Seurat-3.1.2/Seurat/man/CellScatter.Rd | 12 Seurat-3.1.2/Seurat/man/CellsByIdentities.Rd |only Seurat-3.1.2/Seurat/man/CollapseEmbeddingOutliers.Rd | 10 Seurat-3.1.2/Seurat/man/CollapseSpeciesExpressionMatrix.Rd | 8 Seurat-3.1.2/Seurat/man/ColorDimSplit.Rd | 53 Seurat-3.1.2/Seurat/man/CreateDimReducObject.Rd | 17 Seurat-3.1.2/Seurat/man/CreateGeneActivityMatrix.Rd | 12 Seurat-3.1.2/Seurat/man/CreateSeuratObject.Rd | 13 Seurat-3.1.2/Seurat/man/DefaultAssay.Rd | 9 Seurat-3.1.2/Seurat/man/DietSeurat.Rd | 12 Seurat-3.1.2/Seurat/man/DimHeatmap.Rd | 21 Seurat-3.1.2/Seurat/man/DimPlot.Rd | 28 Seurat-3.1.2/Seurat/man/DimReduc-class.Rd | 14 Seurat-3.1.2/Seurat/man/DoHeatmap.Rd | 27 Seurat-3.1.2/Seurat/man/DotPlot.Rd | 19 Seurat-3.1.2/Seurat/man/ExpMean.Rd | 4 Seurat-3.1.2/Seurat/man/ExportToCellbrowser.Rd | 19 Seurat-3.1.2/Seurat/man/FeaturePlot.Rd | 34 Seurat-3.1.2/Seurat/man/FeatureScatter.Rd | 16 Seurat-3.1.2/Seurat/man/FindAllMarkers.Rd | 27 Seurat-3.1.2/Seurat/man/FindClusters.Rd | 49 Seurat-3.1.2/Seurat/man/FindConservedMarkers.Rd | 14 Seurat-3.1.2/Seurat/man/FindIntegrationAnchors.Rd | 24 Seurat-3.1.2/Seurat/man/FindMarkers.Rd | 61 Seurat-3.1.2/Seurat/man/FindNeighbors.Rd | 72 - Seurat-3.1.2/Seurat/man/FindTransferAnchors.Rd | 26 Seurat-3.1.2/Seurat/man/FindVariableFeatures.Rd | 59 Seurat-3.1.2/Seurat/man/GetResidual.Rd | 11 Seurat-3.1.2/Seurat/man/Graph-class.Rd | 8 Seurat-3.1.2/Seurat/man/HTODemux.Rd | 16 Seurat-3.1.2/Seurat/man/HTOHeatmap.Rd | 13 Seurat-3.1.2/Seurat/man/HVFInfo.Rd | 3 Seurat-3.1.2/Seurat/man/Idents.Rd | 13 Seurat-3.1.2/Seurat/man/IntegrateData.Rd | 21 Seurat-3.1.2/Seurat/man/IsGlobal.Rd |only Seurat-3.1.2/Seurat/man/JackStraw.Rd | 13 Seurat-3.1.2/Seurat/man/JackStrawPlot.Rd | 3 Seurat-3.1.2/Seurat/man/LabelClusters.Rd | 11 Seurat-3.1.2/Seurat/man/LabelPoints.Rd | 11 Seurat-3.1.2/Seurat/man/Loadings.Rd | 3 Seurat-3.1.2/Seurat/man/LocalStruct.Rd | 13 Seurat-3.1.2/Seurat/man/LogVMR.Rd | 4 Seurat-3.1.2/Seurat/man/MULTIseqDemux.Rd | 12 Seurat-3.1.2/Seurat/man/MetaFeature.Rd | 10 Seurat-3.1.2/Seurat/man/MixingMetric.Rd | 12 Seurat-3.1.2/Seurat/man/NormalizeData.Rd | 35 Seurat-3.1.2/Seurat/man/OldWhichCells.Rd | 30 Seurat-3.1.2/Seurat/man/PCASigGenes.Rd | 9 Seurat-3.1.2/Seurat/man/PercentageFeatureSet.Rd | 9 Seurat-3.1.2/Seurat/man/PolyDimPlot.Rd | 9 Seurat-3.1.2/Seurat/man/PolyFeaturePlot.Rd | 14 Seurat-3.1.2/Seurat/man/PrepSCTIntegration.Rd | 9 Seurat-3.1.2/Seurat/man/ProjectDim.Rd | 13 Seurat-3.1.2/Seurat/man/RenameAssays.Rd |only Seurat-3.1.2/Seurat/man/RenameCells.Rd | 9 Seurat-3.1.2/Seurat/man/RidgePlot.Rd | 19 Seurat-3.1.2/Seurat/man/RowMergeSparseMatrices.Rd |only Seurat-3.1.2/Seurat/man/RunALRA.Rd | 34 Seurat-3.1.2/Seurat/man/RunCCA.Rd | 34 Seurat-3.1.2/Seurat/man/RunICA.Rd | 56 Seurat-3.1.2/Seurat/man/RunLSI.Rd | 47 Seurat-3.1.2/Seurat/man/RunPCA.Rd | 64 Seurat-3.1.2/Seurat/man/RunTSNE.Rd | 67 - Seurat-3.1.2/Seurat/man/RunUMAP.Rd | 101 + Seurat-3.1.2/Seurat/man/SCTransform.Rd | 26 Seurat-3.1.2/Seurat/man/ScaleData.Rd | 69 - Seurat-3.1.2/Seurat/man/ScoreJackStraw.Rd | 16 Seurat-3.1.2/Seurat/man/SelectIntegrationFeatures.Rd | 10 Seurat-3.1.2/Seurat/man/SetAssayData.Rd | 3 Seurat-3.1.2/Seurat/man/SeuratCommand-class.Rd | 2 Seurat-3.1.2/Seurat/man/SeuratTheme.Rd | 10 Seurat-3.1.2/Seurat/man/SubsetData.Rd | 30 Seurat-3.1.2/Seurat/man/TopFeatures.Rd | 10 Seurat-3.1.2/Seurat/man/TransferData.Rd | 16 Seurat-3.1.2/Seurat/man/UpdateSymbolList.Rd | 18 Seurat-3.1.2/Seurat/man/VariableFeaturePlot.Rd | 10 Seurat-3.1.2/Seurat/man/VariableFeatures.Rd | 3 Seurat-3.1.2/Seurat/man/VizDimLoadings.Rd | 14 Seurat-3.1.2/Seurat/man/VlnPlot.Rd | 23 Seurat-3.1.2/Seurat/man/WhichCells.Rd | 19 Seurat-3.1.2/Seurat/man/as.Seurat.Rd | 27 Seurat-3.1.2/Seurat/man/as.loom.Rd | 15 Seurat-3.1.2/Seurat/man/as.sparse.Rd | 13 Seurat-3.1.2/Seurat/man/h5ad.Rd | 17 Seurat-3.1.2/Seurat/man/merge.Seurat.Rd | 13 Seurat-3.1.2/Seurat/man/print.DimReduc.Rd | 3 Seurat-3.1.2/Seurat/man/subset.Seurat.Rd | 3 Seurat-3.1.2/Seurat/tests/testthat/test_dimensional_reduction.R | 38 111 files changed, 2557 insertions(+), 1196 deletions(-)
Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre],
The Apache Software Foundation [aut, cph],
Julia Silge [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191),
David Gohel [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Diff between rtika versions 1.22 dated 2019-08-02 and 1.23 dated 2019-12-12
DESCRIPTION | 10 - LICENSE | 2 MD5 | 28 ++-- NEWS.md | 7 + R/install_tika.R | 8 - R/tika.R | 29 ++-- R/zzz.R | 2 README.md | 10 - build/vignette.rds |binary inst/doc/rtika_introduction.R | 30 ++-- inst/doc/rtika_introduction.html | 259 +++++++++++++++++++-------------------- man/install_tika.Rd | 17 +- man/rtika.Rd | 1 man/tika.Rd | 22 ++- man/tika_fetch.Rd | 9 + 15 files changed, 231 insertions(+), 203 deletions(-)
Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and statistical performance of 13 pre-defined
phylogenetic metrics and 11 null models, and of user-defined metrics
and null models, as detailed in Miller et al. (2017) <doi:10.1111/ecog.02070>.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>
Diff between metricTester versions 1.3.4 dated 2017-10-31 and 1.3.6 dated 2019-12-12
DESCRIPTION | 12 ++++----- MD5 | 38 ++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 8 ++++++ R/calcField.R | 4 +-- R/defineMetrics.R | 10 ++++++- R/utils.R | 7 +++++ man/betaLinker.Rd | 3 +- man/betaMetricSims.Rd | 3 +- man/betaMetricsNnulls.Rd | 4 +-- man/betaMultiLinker.Rd | 8 +++--- man/defineMetrics.Rd | 5 +++ man/dispersalNull.Rd | 4 +-- man/expectations.Rd | 4 +-- man/linker.Rd | 4 +-- man/metricsNnulls.Rd | 4 +-- man/multiLinker.Rd | 4 +-- man/sesTraitField.Rd | 4 +-- man/varyX.Rd | 4 +-- tests/testthat/test_calc_metric_null_sim.R | 2 - 20 files changed, 80 insertions(+), 53 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths],
Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
Diff between EpiILMCT versions 1.1.4 dated 2019-10-13 and 1.1.5 dated 2019-12-12
DESCRIPTION | 8 MD5 | 16 - R/datgen.r | 244 ++++++++++++------------ R/epictmcmc.r | 479 +++++++++++++++++++++++------------------------- R/epictmcmcsinr.r | 206 ++++++++++---------- R/epictmcmcsir.r | 164 ++++++++-------- R/epiplot.r | 142 +++++++------- R/loglikelihoodepiILM.r | 178 ++++++++--------- R/netdis.r | 53 ++--- 9 files changed, 745 insertions(+), 745 deletions(-)
Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList()
and caretStack(). caretList() is a convenience function for fitting multiple
caret::train() models to the same dataset. caretStack() will make linear or
non-linear combinations of these models, using a caret::train() model as a
meta-model, and caretEnsemble() will make a robust linear combination of
models using a GLM.
Author: Zachary A. Deane-Mayer [aut, cre],
Jared E. Knowles [aut]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>
Diff between caretEnsemble versions 2.0.0 dated 2016-02-07 and 2.0.1 dated 2019-12-12
DESCRIPTION | 25 LICENSE | 2 MD5 | 132 ++-- NAMESPACE | 7 R/S3GenericExtenstions.R | 8 R/caretEnsemble-package.R | 1 R/caretEnsemble.R | 2 R/caretList.R | 116 +++- R/caretStack.R | 23 R/helper_functions.R | 95 +++ README.md | 14 build/vignette.rds |binary inst/doc/caretEnsemble-intro.R | 9 inst/doc/caretEnsemble-intro.Rmd | 2 inst/doc/caretEnsemble-intro.html | 956 ++++++++++++++++++++++------------- man/as.caretList.Rd |only man/as.caretList.default.Rd |only man/as.caretList.list.Rd |only man/autoplot.Rd | 1 man/bestPreds.Rd | 1 man/c.caretList.Rd | 1 man/c.train.Rd | 1 man/caretEnsemble.Rd | 1 man/caretList.Rd | 1 man/caretModelSpec.Rd | 1 man/caretStack.Rd | 1 man/check_bestpreds_indexes.Rd | 1 man/check_bestpreds_obs.Rd | 1 man/check_bestpreds_preds.Rd | 1 man/check_bestpreds_resamples.Rd | 1 man/check_caretList_classes.Rd | 1 man/check_caretList_model_types.Rd | 1 man/data.Rd | 10 man/dotplot.caretStack.Rd | 1 man/extractBestPreds.Rd | 1 man/extractCaretTarget.Rd | 1 man/extractCaretTarget.default.Rd | 1 man/extractCaretTarget.formula.Rd | 1 man/extractModFrame.Rd | 1 man/extractModRes.Rd | 1 man/extractModelName.Rd |only man/extractModelTypes.Rd | 1 man/fortify.Rd | 1 man/getBinaryTargetLevel.Rd |only man/is.caretEnsemble.Rd | 1 man/is.caretList.Rd | 1 man/is.caretStack.Rd | 1 man/makePredObsMatrix.Rd | 1 man/methodCheck.Rd | 1 man/metrics.Rd | 3 man/multiResiduals.Rd | 1 man/plot.caretEnsemble.Rd | 1 man/plot.caretStack.Rd | 1 man/predict.caretList.Rd | 4 man/predict.caretStack.Rd | 5 man/print.caretStack.Rd | 1 man/residuals.caretEnsemble.Rd | 1 man/setBinaryTargetLevel.Rd |only man/sub-.caretList.Rd |only man/summary.caretEnsemble.Rd | 1 man/summary.caretStack.Rd | 1 man/trControlCheck.Rd | 1 man/tuneCheck.Rd | 1 man/validateBinaryTargetLevel.Rd |only man/validateCustomModel.Rd |only man/varImp.caretEnsemble.Rd | 1 man/wtd.sd.Rd | 1 tests/testthat/test-caretList.R | 13 tests/testthat/test-caretStack.R | 17 tests/testthat/test-classSelection.R |only tests/testthat/test-ensemble.R | 58 ++ vignettes/caretEnsemble-intro.Rmd | 2 72 files changed, 1018 insertions(+), 525 deletions(-)
Title: Interfacing with ProPublica's 'Congress' API
Description: A simple interface for interacting with ProPublica's 'Congress' API,
which provides data about current and former members of both chambers of the
U.S. Congress and can be found at the following URL: <https://projects.propublica.org/api-docs/congress-api/>.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>),
Lingshu Hu [ctb] (<https://orcid.org/0000-0003-0304-882X>),
Alieva Iuliia [ctb] (<https://orcid.org/0000-0001-6270-8985>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>
Diff between ppcong versions 0.0.1 dated 2019-11-28 and 0.0.2 dated 2019-12-12
DESCRIPTION | 14 ++++---- MD5 | 18 +++++------ NAMESPACE | 2 + NEWS.md | 5 +++ R/ppc_members.R | 74 ++++++++++++++++++++++++++++++++++++++++++---- R/utils.R | 6 +++ man/ppc_committees.Rd | 8 +++- man/ppc_members.Rd | 12 ++++--- man/ppc_votes.Rd | 3 - tests/testthat/test-ppc.R | 11 ++++++ 10 files changed, 123 insertions(+), 30 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut],
Roeland Voorrips [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.0.19 dated 2019-02-01 and 1.0.20 dated 2019-12-12
polymapR-1.0.19/polymapR/man/createMap.Rd |only polymapR-1.0.19/polymapR/vignettes/figures/map_diagnostics.png |only polymapR-1.0.20/polymapR/DESCRIPTION | 17 polymapR-1.0.20/polymapR/MD5 | 99 polymapR-1.0.20/polymapR/NAMESPACE | 2 polymapR-1.0.20/polymapR/R/aiding_functions.R | 16 polymapR-1.0.20/polymapR/R/exported_functions.R | 1493 ++-------- polymapR-1.0.20/polymapR/R/p4_functions.R | 52 polymapR-1.0.20/polymapR/R/r6_functions.R | 210 - polymapR-1.0.20/polymapR/R/roxygen_datasets.R | 7 polymapR-1.0.20/polymapR/data/datalist | 3 polymapR-1.0.20/polymapR/data/map1.rda |only polymapR-1.0.20/polymapR/data/map2.rda |only polymapR-1.0.20/polymapR/data/map3.rda |only polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.R | 19 polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.Rmd | 45 polymapR-1.0.20/polymapR/inst/doc/Vignette_polymapR.html | 71 polymapR-1.0.20/polymapR/man/MDSMap_from_list.Rd | 2 polymapR-1.0.20/polymapR/man/SNSN_LOD_deviations.Rd | 2 polymapR-1.0.20/polymapR/man/assign_linkage_group.Rd | 6 polymapR-1.0.20/polymapR/man/bridgeHomologues.Rd | 2 polymapR-1.0.20/polymapR/man/check_map.Rd | 16 polymapR-1.0.20/polymapR/man/cluster_SN_markers.Rd | 10 polymapR-1.0.20/polymapR/man/compare_maps.Rd |only polymapR-1.0.20/polymapR/man/consensus_LG_assignment.Rd | 6 polymapR-1.0.20/polymapR/man/convert_marker_dosages.Rd | 8 polymapR-1.0.20/polymapR/man/createTetraOriginInput.Rd | 3 polymapR-1.0.20/polymapR/man/create_phased_maplist.Rd | 3 polymapR-1.0.20/polymapR/man/finish_linkage_analysis.Rd | 6 polymapR-1.0.20/polymapR/man/get_markertype_combinations.Rd | 2 polymapR-1.0.20/polymapR/man/homologue_lg_assignment.Rd | 11 polymapR-1.0.20/polymapR/man/linkage.Rd | 8 polymapR-1.0.20/polymapR/man/map1.Rd |only polymapR-1.0.20/polymapR/man/map2.Rd |only polymapR-1.0.20/polymapR/man/map3.Rd |only polymapR-1.0.20/polymapR/man/marker_data_summary.Rd | 6 polymapR-1.0.20/polymapR/man/merge_homologues.Rd | 6 polymapR-1.0.20/polymapR/man/merge_marker_assignments.Rd | 2 polymapR-1.0.20/polymapR/man/orient_and_merge_maps.Rd | 8 polymapR-1.0.20/polymapR/man/overviewSNlinks.Rd | 8 polymapR-1.0.20/polymapR/man/parental_quantities.Rd | 3 polymapR-1.0.20/polymapR/man/phase_SN_diploid.Rd | 6 polymapR-1.0.20/polymapR/man/plot_phased_maplist.Rd | 4 polymapR-1.0.20/polymapR/man/screen_for_NA_values.Rd | 7 polymapR-1.0.20/polymapR/man/screen_for_duplicate_individuals.Rd | 6 polymapR-1.0.20/polymapR/man/split_linkage_info.Rd | 2 polymapR-1.0.20/polymapR/man/test_prefpairing.Rd | 3 polymapR-1.0.20/polymapR/man/write.TSNPM.Rd | 3 polymapR-1.0.20/polymapR/man/write.mct.Rd | 3 polymapR-1.0.20/polymapR/man/write.pwd.Rd | 3 polymapR-1.0.20/polymapR/man/write_nested_list.Rd | 3 polymapR-1.0.20/polymapR/man/write_pwd_list.Rd | 3 polymapR-1.0.20/polymapR/vignettes/Vignette_polymapR.Rmd | 45 polymapR-1.0.20/polymapR/vignettes/figures/LG1_check_map_plotA.png |only polymapR-1.0.20/polymapR/vignettes/figures/LG1_check_map_plotB.png |only polymapR-1.0.20/polymapR/vignettes/polymapR_vignette.RData |binary 56 files changed, 787 insertions(+), 1453 deletions(-)
Title: Glucose Variability Measures from Continuous Glucose Monitoring
Data
Description: Calculate different glucose variability measures,
including average measures of glycemia, measures of glycemic variability and
measures of glycemic risk, from continuous glucose monitoring data.
Boris P. Kovatchev, Erik Otto, Daniel Cox, Linda Gonder-Frederick, and William Clarke (2006) <doi:10.2337/dc06-1085>.
Jean-Pierre Le Floch, Philippe Escuyer, Eric Baudin, Dominique Baudon, and Leon Perlemuter (1990) <doi:10.2337/diacare.13.2.172>.
C.M. McDonnell, S.M. Donath, S.I. Vidmar, G.A. Werther, and F.J. Cameron (2005) <doi:10.1089/dia.2005.7.253>.
Everitt, Brian (1998) <doi:10.1111/j.1751-5823.2011.00149_2.x>.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) <doi:10.2307/2234167>.
Dougherty, R. L., Edelman, A. and Hyman, J. M. (1989) <doi:10.1090/S0025-5718-1989-0962209-1>.
Tukey, J. W. (1977) <doi:10.1016/0377-2217(86)90209-2>.
F. John Service (2013) <doi:10.2337/db12-1396>.
Edmond A. Ryan, Tami Shandro, Kristy Green, Breay W. Paty, Peter A. Senior, David Bigam, A.M. James Shapiro, and Marie-Christine Vantyghem (2004) <doi:10.2337/diabetes.53.4.955>.
Seniz Sevimer Tuncan, Mehmet Uzunlulu, Ozge telci caklili, Hasan Huseyin Mutlu, and Aytekin Oguz (2016) <doi:10.5152/cjms.2016.109>.
Sarah E. Siegelaar, Frits Holleman, Joost B. L. Hoekstra, and J. Hans DeVries (2010) <doi:10.1210/er.2009-0021>.
Gabor Marics, Zsofia Lendvai, Csaba Lodi, Levente Koncz, David Zakarias, Gyorgy Schuster, Borbala Mikos, Csaba Hermann, Attila J. Szabo, and Peter Toth-Heyn (2015) <doi:10.1186/s12938-015-0035-3>.
Author: Sergio Contador
Maintainer: Sergio Contador <scontador@ucm.es>
Diff between gluvarpro versions 1.0 dated 2019-04-09 and 2.0 dated 2019-12-12
DESCRIPTION | 13 +++++++------ MD5 | 46 +++++++++++++++++++++++++--------------------- NAMESPACE | 20 +++++++++++--------- R/avggvp.R |only R/mplotgvp.R |only R/plotgvp.R | 18 ++++++------------ man/adrrgvp.Rd | 4 ++-- man/aucgvp.Rd | 2 +- man/avggvp.Rd |only man/bgigvp.Rd | 4 ++-- man/congagvp.Rd | 2 +- man/cvgvp.Rd | 2 +- man/datagvp1.Rd | 2 +- man/datagvp2.Rd | 2 +- man/datagvp3.Rd | 2 +- man/fillgvp.Rd | 2 +- man/iqrgvp.Rd | 2 +- man/jigvp.Rd | 2 +- man/ligvp.Rd | 2 +- man/magegvp.Rd | 2 +- man/meangvp.Rd | 2 +- man/mplotgvp.Rd |only man/mvgvp.Rd | 2 +- man/plotgvp.Rd | 2 +- man/pstrgvp.Rd | 2 +- man/sdgvp.Rd | 2 +- 26 files changed, 69 insertions(+), 68 deletions(-)
Title: Analysis of Ecotoxicology
Description: A simple approach to using a probit or logit analysis to calculate
lethal concentration (LC) or time (LT) and the appropriate fiducial
confidence limits desired for selected LC or LT for
ecotoxicology studies (Finney 1971; Wheeler et al. 2006;
Robertson et al. 2007). The simplicity of 'ecotox' comes from the
syntax it implies within its functions which are similar to functions
like glm() and lm(). In addition to the simplicity of the syntax,
a comprehensive data frame is produced which gives the user a
predicted LC or LT value for the desired level and a suite of important
parameters such as fiducial confidence limits and slope.
Finney, D.J. (1971, ISBN: 052108041X);
Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>;
Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K.
(2007, ISBN: 0849323312).
Author: Benjamin L Hlina [aut, cre]
Maintainer: Benjamin L Hlina <benjamin.hlina@gmail.com>
Diff between ecotox versions 1.4.0 dated 2019-03-26 and 1.4.1 dated 2019-12-12
DESCRIPTION | 13 +- MD5 | 44 +++---- NAMESPACE | 3 R/LCx.R | 180 +++++++++++++---------------- R/LTx.R | 30 +--- R/lampreytime.R | 2 R/lampreytox.R | 5 R/ratio_test.R | 72 +++++++---- README.md | 42 ++++++ data/lamprey_tox.rda |binary inst/CITATION | 21 +-- man/LC_logit.Rd | 237 +++++++++++++++++++-------------------- man/LC_probit.Rd | 232 +++++++++++++++++++------------------- man/LT_logit.Rd | 126 ++++++++++---------- man/LT_probit.Rd | 126 ++++++++++---------- man/lamprey_time.Rd | 58 ++++----- man/lamprey_tox.Rd | 58 ++++----- man/ratio_test.Rd | 127 ++++++++++---------- tests/testthat/test-LC_logit.R | 38 +++++- tests/testthat/test-LC_probit.R | 70 ++++++++--- tests/testthat/test-LT_logit.R | 27 ++++ tests/testthat/test-LT_probit.R | 28 ++++ tests/testthat/test-ratio_test.R | 160 +++++++++++++++++++++++--- 23 files changed, 976 insertions(+), 723 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Barret Schloerke [ctb],
Christophe Dervieux [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak lua filter),
Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 1.18 dated 2019-11-27 and 2.0 dated 2019-12-12
rmarkdown-1.18/rmarkdown/inst/rmd/latex/compact-title.tex |only rmarkdown-2.0/rmarkdown/DESCRIPTION | 10 rmarkdown-2.0/rmarkdown/MD5 | 111 +++++----- rmarkdown-2.0/rmarkdown/NAMESPACE | 1 rmarkdown-2.0/rmarkdown/NEWS.md | 28 ++ rmarkdown-2.0/rmarkdown/R/context_document.R |only rmarkdown-2.0/rmarkdown/R/html_dependencies.R | 13 + rmarkdown-2.0/rmarkdown/R/html_document.R | 4 rmarkdown-2.0/rmarkdown/R/html_document_base.R | 9 rmarkdown-2.0/rmarkdown/R/html_notebook.R | 6 rmarkdown-2.0/rmarkdown/R/html_resources.R | 32 +- rmarkdown-2.0/rmarkdown/R/md_document.R | 6 rmarkdown-2.0/rmarkdown/R/output_format.R | 109 +++------ rmarkdown-2.0/rmarkdown/R/params.R | 5 rmarkdown-2.0/rmarkdown/R/pdf_document.R | 47 ++-- rmarkdown-2.0/rmarkdown/R/powerpoint_presentation.R | 4 rmarkdown-2.0/rmarkdown/R/render.R | 72 ++---- rmarkdown-2.0/rmarkdown/R/render_site.R | 75 +++--- rmarkdown-2.0/rmarkdown/R/shiny.R | 55 +--- rmarkdown-2.0/rmarkdown/R/shiny_prerendered.R | 21 - rmarkdown-2.0/rmarkdown/R/slidy_presentation.R | 16 + rmarkdown-2.0/rmarkdown/R/util.R | 22 - rmarkdown-2.0/rmarkdown/inst/rmd/h/pandoc |only rmarkdown-2.0/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/theme/css/default.css | 6 rmarkdown-2.0/rmarkdown/inst/rmd/lua/pagebreak.lua | 5 rmarkdown-2.0/rmarkdown/inst/rmd/slidy/slidy_shiny.js |only rmarkdown-2.0/rmarkdown/man/all_output_formats.Rd | 4 rmarkdown-2.0/rmarkdown/man/beamer_presentation.Rd | 12 - rmarkdown-2.0/rmarkdown/man/context_document.Rd |only rmarkdown-2.0/rmarkdown/man/default_output_format.Rd | 4 rmarkdown-2.0/rmarkdown/man/find_external_resources.Rd | 2 rmarkdown-2.0/rmarkdown/man/github_document.Rd | 12 - rmarkdown-2.0/rmarkdown/man/html_document.Rd | 12 - rmarkdown-2.0/rmarkdown/man/html_fragment.Rd | 12 - rmarkdown-2.0/rmarkdown/man/html_vignette.Rd | 12 - rmarkdown-2.0/rmarkdown/man/ioslides_presentation.Rd | 12 - rmarkdown-2.0/rmarkdown/man/knit_params_ask.Rd | 2 rmarkdown-2.0/rmarkdown/man/md_document.Rd | 17 - rmarkdown-2.0/rmarkdown/man/output_format.Rd | 56 ++--- rmarkdown-2.0/rmarkdown/man/parse_html_notebook.Rd | 4 rmarkdown-2.0/rmarkdown/man/pdf_document.Rd | 12 - rmarkdown-2.0/rmarkdown/man/powerpoint_presentation.Rd | 12 - rmarkdown-2.0/rmarkdown/man/render.Rd | 3 rmarkdown-2.0/rmarkdown/man/render_site.Rd | 14 - rmarkdown-2.0/rmarkdown/man/resolve_output_format.Rd | 5 rmarkdown-2.0/rmarkdown/man/slidy_presentation.Rd | 12 - rmarkdown-2.0/rmarkdown/man/word_document.Rd | 12 - rmarkdown-2.0/rmarkdown/man/yaml_front_matter.Rd | 2 rmarkdown-2.0/rmarkdown/tests/rmd/raw-header.Rmd |only rmarkdown-2.0/rmarkdown/tests/rmd/two-authors.Rmd |only rmarkdown-2.0/rmarkdown/tests/rmd/yaml-r-code.Rmd |only rmarkdown-2.0/rmarkdown/tests/testrmd.R | 12 + rmarkdown-2.0/rmarkdown/tests/testthat/resources/file-exists.Rmd | 3 rmarkdown-2.0/rmarkdown/tests/testthat/site/PageD.R |only rmarkdown-2.0/rmarkdown/tests/testthat/site/_site.yml | 3 rmarkdown-2.0/rmarkdown/tests/testthat/test-formats.R | 1 rmarkdown-2.0/rmarkdown/tests/testthat/test-formats.Rmd | 1 rmarkdown-2.0/rmarkdown/tests/testthat/test-ioslides.R | 2 rmarkdown-2.0/rmarkdown/tests/testthat/test-lua-filters.R | 2 rmarkdown-2.0/rmarkdown/tests/testthat/test-notebook.R | 2 rmarkdown-2.0/rmarkdown/tests/testthat/test-site.R | 7 61 files changed, 479 insertions(+), 444 deletions(-)
Title: Learn Computer and Data Science using Algorithmic Trading
Description: Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading.
Main goal is to process information within "Decision Support System" to come up with analysis or predictions.
There are several utilities such as dynamic and adaptive risk management using reinforcement learning
and even functions to generate predictions of price changes using pattern recognition deep regression learning.
Author: Vladimir Zhbanko
Maintainer: Vladimir Zhbanko <vladimir.zhbanko@gmail.com>
Diff between lazytrade versions 0.3.7 dated 2019-12-03 and 0.3.8 dated 2019-12-12
DESCRIPTION | 8 - MD5 | 103 +++++++------- NAMESPACE | 3 NEWS.md | 7 + R/util_generate_password.R |only R/zzz.R | 3 README.md | 42 ++++-- man/DFR.Rd | 50 +++---- man/EURUSDM15X75.Rd | 34 ++-- man/TradeStatePolicy.Rd | 34 ++-- man/aml_collect_data.Rd | 158 +++++++++++----------- man/aml_make_model.Rd | 150 ++++++++++----------- man/aml_score_data.Rd | 177 +++++++++++++------------ man/aml_test_model.Rd | 186 +++++++++++++-------------- man/check_if_optimize.Rd | 137 ++++++++++--------- man/create_labelled_data.Rd | 104 +++++++-------- man/create_transposed_data.Rd | 84 ++++++------ man/data_trades.Rd | 46 +++--- man/decrypt_mykeys.Rd | 78 +++++------ man/evaluate_macroeconomic_event.Rd | 141 ++++++++++---------- man/evaluate_market_type.Rd | 106 +++++++-------- man/generate_RL_policy.Rd | 94 ++++++------- man/generate_RL_policy_mt.Rd | 84 ++++++------ man/get_profit_factorDF.Rd | 60 ++++---- man/import_data.Rd | 78 +++++------ man/import_data_mt.Rd | 75 +++++----- man/indicator_dataset.Rd | 34 ++-- man/load_asset_data.Rd | 108 ++++++++------- man/log_RL_progress.Rd | 76 +++++------ man/log_RL_progress_mt.Rd | 78 +++++------ man/macd_df.Rd | 32 ++-- man/opt_aggregate_results.Rd | 72 +++++----- man/opt_create_graphs.Rd | 86 ++++++------ man/policy_tr_systDF.Rd | 34 ++-- man/price_dataset.Rd | 34 ++-- man/profit_factor.Rd | 68 ++++----- man/profit_factorDF.Rd | 46 +++--- man/profit_factor_data.Rd | 46 +++--- man/record_policy.Rd | 95 +++++++------ man/record_policy_mt.Rd | 82 ++++++----- man/result_R.Rd | 34 ++-- man/result_prev.Rd | 32 ++-- man/self_learn_ai_R.Rd | 151 +++++++++++---------- man/test_data_pattern.Rd | 36 ++--- man/test_model.Rd | 90 ++++++------- man/to_m.Rd | 54 +++---- man/trading_systemDF.Rd | 50 +++---- man/util_generate_password.Rd |only man/writeCommandViaCSV.Rd | 98 +++++++------- man/write_command_via_csv.Rd | 99 +++++++------- man/write_control_parameters.Rd | 80 +++++------ man/write_control_parameters_mt.Rd | 84 ++++++------ man/x_test_model.Rd | 34 ++-- tests/testthat/test-util_generate_password.R |only 54 files changed, 1923 insertions(+), 1852 deletions(-)
Title: Models Spatially Continuous and Discrete Population Genetic
Structure
Description: A method for modeling genetic data as a combination of discrete
layers, within each of which relatedness may decay continuously with geographic
distance. This package contains code for running analyses (which are implemented
in the modeling language 'rstan') and visualizing and interpreting output. See the
paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@msu.edu>
Diff between conStruct versions 1.0.3 dated 2019-01-03 and 1.0.4 dated 2019-12-12
DESCRIPTION | 10 +++--- MD5 | 54 ++++++++++++++++++------------------ NEWS.md | 6 ++++ R/format.data.R | 18 ++++++++---- R/model.comparison.R | 19 ++++++++---- R/plot.output.R | 6 ++-- R/process.model.fit.R | 10 +++--- R/run.conStruct.R | 11 ++++--- R/zzz.R | 2 - build/vignette.rds |binary inst/doc/format-data.R | 18 ++++++------ inst/doc/format-data.Rmd | 5 ++- inst/doc/format-data.html | 30 ++++++++++++-------- inst/doc/model-comparison.R | 28 +++++++++--------- inst/doc/model-comparison.html | 34 +++++++++++++--------- inst/doc/run-conStruct.R | 14 ++++----- inst/doc/run-conStruct.html | 22 +++++++++----- inst/doc/visualize-results.R | 22 +++++++------- inst/doc/visualize-results.html | 18 ++++++++---- man/calculate.layer.contribution.Rd | 3 -- man/compare.two.runs.Rd | 10 +++++- man/conStruct.Rd | 16 ++++++++-- man/make.admix.pie.plot.Rd | 13 ++++++-- man/make.all.the.plots.Rd | 5 +-- man/make.structure.plot.Rd | 12 ++++++-- man/structure2conStruct.Rd | 22 ++++++++++---- man/x.validation.Rd | 20 ++++++++++--- vignettes/format-data.Rmd | 5 ++- 28 files changed, 268 insertions(+), 165 deletions(-)
Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and
A-bomb data binaries from ASCII sources and provides tools for estimating
SEER second cancer risks. Methods are described in <doi:10.1038/leu.2015.258>.
Author: Tomas Radivoyevitch [aut, cre],
R. Molenaar [ctb]
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>
Diff between SEERaBomb versions 2019.1 dated 2019-05-07 and 2019.2 dated 2019-12-12
DESCRIPTION | 8 ++--- MD5 | 31 +++++++++++----------- NAMESPACE | 2 - NEWS | 7 ++++ R/csd.R | 12 ++++++-- R/getE.R | 3 +- R/incidSEER.R | 2 - R/mk2D.R | 7 ++-- R/mkExcelCsd.R | 2 - R/pickFields.R | 12 ++++++++ R/simSeerSet.R | 4 +- inst/docs/examples/mkDataBinaries.R | 4 ++ inst/docs/papers/attic/leukemia2016/mkExcelDemo.R | 15 +++++++++- inst/docs/papers/attic/leukemia2016/tables.R | 4 +- inst/docs/papers/misc |only man/mkExcelCsd.Rd | 2 - man/simSeerSet.Rd | 2 - 17 files changed, 79 insertions(+), 38 deletions(-)
Title: Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait
data associated with the tips of a phylogenetic tree. Examples of such models
are Gaussian continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the
tips of the tree as an observed (final) state of a Markov process starting from
an initial state at the root and evolving along the branches of the tree. The
PCMBase R package provides a general framework for manipulating such models.
This framework consists of an application programming interface for specifying
data and model parameters, and efficient algorithms for simulating trait evolution
under a model and calculating the likelihood of model parameters for an assumed
model and trait data. The package implements a growing collection of models,
which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed
Gaussian models, in which different types of the above models can be associated
with different branches of the tree. The PCMBase package is limited to
trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic
models. The PCMFit package provides functionality for ML and Bayesian fit of
these models to tree and trait data. The package web-site
<https://venelin.github.io/PCMBase/>
provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph] (<a
href="https://venelin.github.io">venelin.github.io</a>),
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBase versions 1.2.10 dated 2019-09-11 and 1.2.11 dated 2019-12-12
PCMBase-1.2.10/PCMBase/man/UpperChol.Rd |only PCMBase-1.2.11/PCMBase/DESCRIPTION | 13 PCMBase-1.2.11/PCMBase/MD5 | 66 - PCMBase-1.2.11/PCMBase/NAMESPACE | 8 PCMBase-1.2.11/PCMBase/NEWS.md | 19 PCMBase-1.2.11/PCMBase/R/GaussianPCM.R | 35 PCMBase-1.2.11/PCMBase/R/MixedGaussian.R | 82 +- PCMBase-1.2.11/PCMBase/R/PCM.R | 400 +++++++++- PCMBase-1.2.11/PCMBase/R/PCMParam.R | 123 +-- PCMBase-1.2.11/PCMBase/R/PCMTree.R | 70 - PCMBase-1.2.11/PCMBase/R/Utilities.R | 60 - PCMBase-1.2.11/PCMBase/R/matrixparametrizations.R | 9 PCMBase-1.2.11/PCMBase/README.md | 23 PCMBase-1.2.11/PCMBase/inst/CITATION | 18 PCMBase-1.2.11/PCMBase/inst/doc/PCMBase.html | 46 - PCMBase-1.2.11/PCMBase/inst/doc/PCMCreateModel.html | 12 PCMBase-1.2.11/PCMBase/inst/doc/PCMParam.html | 8 PCMBase-1.2.11/PCMBase/inst/doc/PCMTracePruning.html | 8 PCMBase-1.2.11/PCMBase/man/MatchListMembers.Rd |only PCMBase-1.2.11/PCMBase/man/MixedGaussian.Rd | 42 - PCMBase-1.2.11/PCMBase/man/PCMAddToListAttribute.Rd |only PCMBase-1.2.11/PCMBase/man/PCMCombineListAttribute.Rd |only PCMBase-1.2.11/PCMBase/man/PCMGetAttribute.Rd |only PCMBase-1.2.11/PCMBase/man/PCMGetVecParamsRegimesAndModels.Rd | 4 PCMBase-1.2.11/PCMBase/man/PCMLik.Rd | 31 PCMBase-1.2.11/PCMBase/man/PCMListMembers.Rd |only PCMBase-1.2.11/PCMBase/man/PCMOptions.Rd | 2 PCMBase-1.2.11/PCMBase/man/PCMParamLocateInShortVector.Rd | 11 PCMBase-1.2.11/PCMBase/man/PCMParamSetByName.Rd | 4 PCMBase-1.2.11/PCMBase/man/PCMParseErrorMessage.Rd | 16 PCMBase-1.2.11/PCMBase/man/PCMSetAttribute.Rd |only PCMBase-1.2.11/PCMBase/man/PCMSim.Rd | 14 PCMBase-1.2.11/PCMBase/man/PCMTreeListCladePartitions.Rd | 6 PCMBase-1.2.11/PCMBase/man/PCMVar.Rd | 6 PCMBase-1.2.11/PCMBase/man/UpperTriFactor.Rd |only PCMBase-1.2.11/PCMBase/tests/testthat/test-PCMTree.R | 2 PCMBase-1.2.11/PCMBase/vignettes/REFERENCES-R.bib | 2 PCMBase-1.2.11/PCMBase/vignettes/REFERENCES.bib | 14 38 files changed, 753 insertions(+), 401 deletions(-)
Title: Another Multidimensional Analysis Package
Description: Tools for Clustering and Principal Component Analysis
(With robust methods, and parallelized functions).
Author: Antoine Lucas
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between amap versions 0.8-17 dated 2019-05-13 and 0.8-18 dated 2019-12-12
amap-0.8-17/amap/configure |only amap-0.8-17/amap/configure.ac |only amap-0.8-17/amap/src/distance_T.inl |only amap-0.8-17/amap/src/hclust_T.inl |only amap-0.8-18/amap/DESCRIPTION | 8 ++++---- amap-0.8-18/amap/MD5 | 27 ++++++++++++++------------- amap-0.8-18/amap/R/Kmeans.R | 2 +- amap-0.8-18/amap/R/dist.R | 2 +- amap-0.8-18/amap/R/hcluster.R | 2 +- amap-0.8-18/amap/build/vignette.rds |binary amap-0.8-18/amap/inst/doc/amap.pdf |binary amap-0.8-18/amap/inst/doc/vignettes |only amap-0.8-18/amap/inst/po/po |only amap-0.8-18/amap/src/Makevars.in | 4 +--- amap-0.8-18/amap/src/distance_T.h | 2 +- amap-0.8-18/amap/src/distance_T.h.h |only amap-0.8-18/amap/src/hclust_T.h | 2 +- amap-0.8-18/amap/src/hclust_T.h.h |only 18 files changed, 24 insertions(+), 25 deletions(-)
Title: Tree Structured Hidden Markov Model
Description: Used for Inference, Prediction and Parameter learning for tree structured Hidden Markov Model. The package propose a new architecture of Hidden Markov Model(HMM) known as Tree Structured HMM which could be used in various applications which involves graphs, trees etc.
Author: Prajwal Bende [aut, cre],
Russ Greiner [ths],
Pouria Ramazi [ths]
Maintainer: Prajwal Bende <pbende@ualberta.ca>
Diff between treeHMM versions 0.1.0 dated 2019-10-13 and 0.1.1 dated 2019-12-12
DESCRIPTION | 12 +++++++----- MD5 | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-)
Title: Multiple Imputation Using Weighted Quantile Sum Regression
Description: The `miWQS` package handles the uncertainty due to below the detection limit in a correlated component mixture problem. Researchers want to determine if a set/mixture of continuous and correlated components/chemicals is associated with an outcome and if so, which components are important in that mixture. These components share a common outcome but are interval-censored between zero and low thresholds, or detection limits, that may be different across the components. The `miWQS` package applies the multiple imputation (MI) procedure to the weighted quantile sum regression (WQS) methodology for continuous, binary, or count outcomes. The imputation models are: bootstrapping imputation (Lubin et.al (2004) <doi:10.1289/ehp.7199>) and Bayesian imputation.
Author: Paul M. Hargarten [aut, cre],
David C. Wheeler [aut, rev, ths]
Maintainer: Paul M. Hargarten <hargartenp@vcu.edu>
Diff between miWQS versions 0.1.0 dated 2019-07-31 and 0.2.0 dated 2019-12-12
miWQS-0.1.0/miWQS/R/impute_multivariate_bayesian_mi_part.R |only miWQS-0.2.0/miWQS/DESCRIPTION | 34 miWQS-0.2.0/miWQS/MD5 | 96 - miWQS-0.2.0/miWQS/NAMESPACE | 6 miWQS-0.2.0/miWQS/NEWS.md | 52 miWQS-0.2.0/miWQS/R/analyze_individually.R | 6 miWQS-0.2.0/miWQS/R/check_miWQS_Functions.R | 604 +++++----- miWQS-0.2.0/miWQS/R/coef_wqs_helper.R | 3 miWQS-0.2.0/miWQS/R/combine_AIC.R | 7 miWQS-0.2.0/miWQS/R/do_many_wqs.R | 39 miWQS-0.2.0/miWQS/R/estimate_wqs_WQS.R | 238 +-- miWQS-0.2.0/miWQS/R/estimate_wqs_formula.R |only miWQS-0.2.0/miWQS/R/formatIQR.R | 2 miWQS-0.2.0/miWQS/R/formatZ.R | 37 miWQS-0.2.0/miWQS/R/head_array.R | 5 miWQS-0.2.0/miWQS/R/impute_Lubin.R | 121 -- miWQS-0.2.0/miWQS/R/impute_boot.R | 150 +- miWQS-0.2.0/miWQS/R/impute_multivariate_bayesian_part.R |only miWQS-0.2.0/miWQS/R/impute_sub.R | 14 miWQS-0.2.0/miWQS/R/impute_univariate_bayesian_imputation_stage1.R | 68 - miWQS-0.2.0/miWQS/R/is_integer.R | 50 miWQS-0.2.0/miWQS/R/make_quantile_matrix_WQS.R | 4 miWQS-0.2.0/miWQS/R/plot_wqs_ggplot2_helper.R | 40 miWQS-0.2.0/miWQS/R/pool_mi_stage3.R | 99 - miWQS-0.2.0/miWQS/R/print_wqs_helper.R | 2 miWQS-0.2.0/miWQS/R/simdata87.R | 6 miWQS-0.2.0/miWQS/R/specify_init_WQS.R | 3 miWQS-0.2.0/miWQS/R/wqs.pool.test_data.R | 6 miWQS-0.2.0/miWQS/build/vignette.rds |binary miWQS-0.2.0/miWQS/inst/WORDLIST | 11 miWQS-0.2.0/miWQS/inst/doc/README.R | 3 miWQS-0.2.0/miWQS/inst/doc/README.Rmd | 7 miWQS-0.2.0/miWQS/inst/doc/README.pdf |binary miWQS-0.2.0/miWQS/man/analyze.individually.Rd | 6 miWQS-0.2.0/miWQS/man/coef.wqs.Rd | 4 miWQS-0.2.0/miWQS/man/combine.AIC.Rd | 8 miWQS-0.2.0/miWQS/man/do.many.wqs.Rd | 26 miWQS-0.2.0/miWQS/man/estimate.wqs.Rd | 53 miWQS-0.2.0/miWQS/man/estimate.wqs.formula.Rd |only miWQS-0.2.0/miWQS/man/impute.Lubin.Rd | 41 miWQS-0.2.0/miWQS/man/impute.boot.Rd | 33 miWQS-0.2.0/miWQS/man/impute.multivariate.bayesian.Rd | 15 miWQS-0.2.0/miWQS/man/impute.sub.Rd | 19 miWQS-0.2.0/miWQS/man/impute.univariate.bayesian.mi.Rd | 24 miWQS-0.2.0/miWQS/man/make.quantile.matrix.Rd | 9 miWQS-0.2.0/miWQS/man/plot.wqs.Rd | 10 miWQS-0.2.0/miWQS/man/pool.mi.Rd | 24 miWQS-0.2.0/miWQS/man/print.wqs.Rd | 1 miWQS-0.2.0/miWQS/man/simdata87.Rd | 6 miWQS-0.2.0/miWQS/man/wqs.pool.test.Rd | 4 miWQS-0.2.0/miWQS/vignettes/README.Rmd | 7 51 files changed, 974 insertions(+), 1029 deletions(-)
Title: Interfaces for Loading Datasets
Description: Visual interface for loading datasets in RStudio from all installed (unloaded) packages, also includes command line interfaces.
Author: Bastiaan quast [aut, cre]
Maintainer: Bastiaan quast <bquast@gmail.com>
Diff between datasets.load versions 0.3.0 dated 2018-09-10 and 1.0.0 dated 2019-12-12
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam'
with 64-bit integers. Loading this package together with the R package
spam enables the sparse matrix class spam to handle huge sparse matrices
with more than 2^31-1 non-zero elements.
Documentation is provided in Gerber, Moesinger and Furrer (2017) <doi:10.1016/j.cageo.2016.11.015>.
Author: Reinhard Furrer [aut, cre],
Florian Gerber [aut],
Roman Flury [aut],
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Youcef Saad [ctb] (SPARSEKIT
http://www-users.cs.umn.edu/~saad/software/SPARSKIT/),
Esmond G. Ng [ctb] (Fortran Cholesky routines),
Barry W. Peyton [ctb] (Fortran Cholesky routines),
Joseph W.H. Liu [ctb] (Fortran Cholesky routines),
Alan D. George [ctb] (Fortran Cholesky routines),
Lehoucq B. Rich [ctb] (ARPACK),
Maschhoff Kristi [ctb] (ARPACK),
Sorensen C. Danny [ctb] (ARPACK),
Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam64 versions 2.4-0 dated 2019-11-02 and 2.5-1 dated 2019-12-12
spam64-2.4-0/spam64/src/dn_eigen.f |only spam64-2.4-0/spam64/src/ds_eigen.f |only spam64-2.4-0/spam64/src/stat.h |only spam64-2.5-1/spam64/DESCRIPTION | 10 spam64-2.5-1/spam64/MD5 | 35 - spam64-2.5-1/spam64/src/bckslvmodified.f | 16 spam64-2.5-1/spam64/src/cholmodified.f | 458 ++++++++++++------------ spam64-2.5-1/spam64/src/dgetv0.f | 64 --- spam64-2.5-1/spam64/src/dist.f | 184 ++++----- spam64-2.5-1/spam64/src/dn_ARPACK.f | 461 +++--------------------- spam64-2.5-1/spam64/src/dn_eigen64.f |only spam64-2.5-1/spam64/src/ds_ARPACK.f | 523 +++++---------------------- spam64-2.5-1/spam64/src/ds_eigen64.f |only spam64-2.5-1/spam64/src/fromsparsekit.f | 33 - spam64-2.5-1/spam64/src/init.c | 8 spam64-2.5-1/spam64/src/kronecker.f | 4 spam64-2.5-1/spam64/src/permutation.f | 290 +++++++-------- spam64-2.5-1/spam64/src/rowcolstats.f | 50 +- spam64-2.5-1/spam64/src/spamown.f | 586 +++++++++++++++---------------- spam64-2.5-1/spam64/src/spamown2.f | 54 +- spam64-2.5-1/spam64/src/xybind.f | 8 21 files changed, 1038 insertions(+), 1746 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre],
Florian Gerber [aut],
Roman Flury [aut],
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Youcef Saad [ctb] (SPARSEKIT
http://www-users.cs.umn.edu/~saad/software/SPARSKIT/),
Esmond G. Ng [ctb] (Fortran Cholesky routines),
Barry W. Peyton [ctb] (Fortran Cholesky routines),
Joseph W.H. Liu [ctb] (Fortran Cholesky routines),
Alan D. George [ctb] (Fortran Cholesky routines),
Lehoucq B. Rich [ctb] (ARPACK),
Maschhoff Kristi [ctb] (ARPACK),
Sorensen C. Danny [ctb] (ARPACK),
Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 2.5-0 dated 2019-12-06 and 2.5-1 dated 2019-12-12
spam-2.5-0/spam/src/compare.f |only spam-2.5-1/spam/DESCRIPTION | 8 +-- spam-2.5-1/spam/MD5 | 35 ++++++-------- spam-2.5-1/spam/NEWS.md | 7 ++ spam-2.5-1/spam/inst/doc/spam.R | 26 +++++----- spam-2.5-1/spam/inst/doc/spam.pdf |binary spam-2.5-1/spam/src/dist.f | 6 -- spam-2.5-1/spam/src/ds_ARPACK.f | 26 ++++++++++ spam-2.5-1/spam/src/ds_eigen.f | 16 ------ spam-2.5-1/spam/src/spamown.f | 10 +--- spam-2.5-1/spam/tests/demo_article-jss-example1.Rout.save | 4 - spam-2.5-1/spam/tests/demo_article-jss-example2.Rout.save | 6 +- spam-2.5-1/spam/tests/demo_article-jss.Rout.save | 4 - spam-2.5-1/spam/tests/demo_cholesky.Rout.save | 4 - spam-2.5-1/spam/tests/demo_jss15-BYM.Rout.save | 4 - spam-2.5-1/spam/tests/demo_jss15-Leroux.Rout.save | 4 - spam-2.5-1/spam/tests/demo_spam.Rout.save | 4 - spam-2.5-1/spam/tests/demo_timing.Rout.save | 4 - spam-2.5-1/spam/tests/jss_areal_counts.Rout.save | 4 - 19 files changed, 93 insertions(+), 79 deletions(-)
Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data
and optionally mark data. Includes also a function to plot holocentrics and its marks supporting
micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline
or to the right of karyotypes. It is possible to calculate
chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> ,
karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and
Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.9.1 dated 2019-11-29 and 1.11.1 dated 2019-12-12
DESCRIPTION | 8 MD5 | 91 +-- NEWS.md | 11 R/chrbasicdataHolo.R | 5 R/markdataholo.R | 4 R/plotIdiograms.R | 475 +++++++++++------- R/plotlabelsright.R | 55 +- README.md | 140 ++--- data/bigdfOfChrSize3Mb.rda |only data/bigdfOfMarks3Mb.rda |only inst/doc/AplotIdiogramsVig.R | 228 +++++--- inst/doc/AplotIdiogramsVig.Rmd | 246 +++++---- inst/doc/AplotIdiogramsVig.html | 764 +++++++++++++++++++++++------- inst/doc/BplotIdiogramsHoloVig.R | 154 ++---- inst/doc/BplotIdiogramsHoloVig.Rmd | 154 ++---- inst/doc/BplotIdiogramsHoloVig.html | 206 +++----- inst/doc/CgroupsVig.R | 70 -- inst/doc/CgroupsVig.Rmd | 71 -- inst/doc/CgroupsVig.html | 144 ++--- inst/doc/DphylogenyVig.R | 84 +-- inst/doc/DphylogenyVig.Rmd | 84 +-- inst/doc/DphylogenyVig.html | 220 ++++---- inst/doc/EhumanVig.R | 69 +- inst/doc/EhumanVig.Rmd | 72 +- inst/doc/EhumanVig.html | 161 +++--- inst/doc/index.R | 122 ++-- inst/doc/index.Rmd | 130 ++--- inst/doc/index.html | 183 +++---- man/chrbasicdataHolo.Rd | 5 man/figures/README-example-1.svg | 351 +++++++------ man/figures/README-example2-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/crandownload.svg | 4 man/figures/cranversion.svg | 4 man/figures/gitbadge.svg | 2 man/markdataholo.Rd | 5 man/plotIdiograms.Rd | 81 +-- vignettes/AplotIdiogramsVig.Rmd | 246 +++++---- vignettes/BplotIdiogramsHoloVig.Rmd | 154 ++---- vignettes/CgroupsVig.Rmd | 71 -- vignettes/DphylogenyVig.Rmd | 84 +-- vignettes/DphylogenyVig_files |only vignettes/EhumanVig.Rmd | 72 +- vignettes/index.Rmd | 130 ++--- 45 files changed, 2818 insertions(+), 2342 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 2.0.5 dated 2019-11-08 and 2.0.6 dated 2019-12-12
rpact-2.0.5/rpact/R/f_analysis.R |only rpact-2.0.5/rpact/R/f_analysis_means.R |only rpact-2.0.5/rpact/R/f_analysis_means_multiarmed.R |only rpact-2.0.5/rpact/R/f_analysis_rates.R |only rpact-2.0.5/rpact/R/f_analysis_survival.R |only rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_means.R |only rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_rates.R |only rpact-2.0.5/rpact/inst/tests/testthat/test-f_analysis_survival.R |only rpact-2.0.5/rpact/man/sub-TrialDesignSet-ANY-ANY-ANY-method.Rd |only rpact-2.0.5/rpact/tests/testthat/test-f_analysis_means.R |only rpact-2.0.5/rpact/tests/testthat/test-f_analysis_rates.R |only rpact-2.0.5/rpact/tests/testthat/test-f_analysis_survival.R |only rpact-2.0.6/rpact/DESCRIPTION | 16 rpact-2.0.6/rpact/MD5 | 302 +-- rpact-2.0.6/rpact/NAMESPACE | 2 rpact-2.0.6/rpact/NEWS.md | 11 rpact-2.0.6/rpact/R/class_analysis_dataset.R | 442 +++-- rpact-2.0.6/rpact/R/class_analysis_results.R | 79 rpact-2.0.6/rpact/R/class_analysis_stage_results.R | 218 ++ rpact-2.0.6/rpact/R/class_core_parameter_set.R | 84 rpact-2.0.6/rpact/R/class_design.R | 38 rpact-2.0.6/rpact/R/class_design_plan.R | 27 rpact-2.0.6/rpact/R/class_design_set.R | 2 rpact-2.0.6/rpact/R/class_simulation_results.R | 10 rpact-2.0.6/rpact/R/class_summary.R | 40 rpact-2.0.6/rpact/R/class_time.R | 14 rpact-2.0.6/rpact/R/f_analysis_base.R |only rpact-2.0.6/rpact/R/f_analysis_base_means.R |only rpact-2.0.6/rpact/R/f_analysis_base_rates.R |only rpact-2.0.6/rpact/R/f_analysis_base_survival.R |only rpact-2.0.6/rpact/R/f_core_assertions.R | 74 rpact-2.0.6/rpact/R/f_core_constants.R | 28 rpact-2.0.6/rpact/R/f_core_utilities.R | 63 rpact-2.0.6/rpact/R/f_design_group_sequential.R | 116 - rpact-2.0.6/rpact/R/f_design_sample_size_calculator.R | 83 rpact-2.0.6/rpact/inst/tests/testthat/helper-f_analysis_rates.R | 1 rpact-2.0.6/rpact/inst/tests/testthat/helper-f_analysis_survival.R | 2 rpact-2.0.6/rpact/inst/tests/testthat/test-class_analysis_dataset.R | 265 +++ rpact-2.0.6/rpact/inst/tests/testthat/test-class_summary.R | 225 +- rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_means.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_rates.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_analysis_base_survival.R |only rpact-2.0.6/rpact/inst/tests/testthat/test-f_core_assertions.R | 35 rpact-2.0.6/rpact/inst/tests/testthat/test-f_core_output_formats.R | 2 rpact-2.0.6/rpact/inst/tests/testthat/test-f_design_power_calculator.R | 100 - rpact-2.0.6/rpact/inst/tests/testthat/test-f_design_sample_size_calculator.R | 230 ++ rpact-2.0.6/rpact/inst/tests/testthat/test_generic_functions.R |only rpact-2.0.6/rpact/man/AccrualTime.Rd | 26 rpact-2.0.6/rpact/man/AnalysisResults.Rd | 38 rpact-2.0.6/rpact/man/AnalysisResultsFisher.Rd | 28 rpact-2.0.6/rpact/man/AnalysisResultsGroupSequential.Rd | 30 rpact-2.0.6/rpact/man/AnalysisResultsInverseNormal.Rd | 30 rpact-2.0.6/rpact/man/AnalysisResults_as.data.frame.Rd | 36 rpact-2.0.6/rpact/man/AnalysisResults_names.Rd | 35 rpact-2.0.6/rpact/man/Dataset.Rd | 58 rpact-2.0.6/rpact/man/DatasetMeans.Rd | 58 rpact-2.0.6/rpact/man/DatasetRates.Rd | 54 rpact-2.0.6/rpact/man/DatasetSurvival.Rd | 58 rpact-2.0.6/rpact/man/EventProbabilities.Rd | 26 rpact-2.0.6/rpact/man/FieldSet.Rd | 26 rpact-2.0.6/rpact/man/FieldSet_names.Rd | 30 rpact-2.0.6/rpact/man/FieldSet_print.Rd | 30 rpact-2.0.6/rpact/man/FrameSet_as.matrix.Rd | 30 rpact-2.0.6/rpact/man/NumberOfSubjects.Rd | 26 rpact-2.0.6/rpact/man/ParameterSet.Rd | 26 rpact-2.0.6/rpact/man/ParameterSet_as.data.frame.Rd | 41 rpact-2.0.6/rpact/man/ParameterSet_print.Rd | 44 rpact-2.0.6/rpact/man/ParameterSet_summary.Rd | 61 rpact-2.0.6/rpact/man/PiecewiseSurvivalTime.Rd | 26 rpact-2.0.6/rpact/man/PlotSettings.Rd | 108 - rpact-2.0.6/rpact/man/PowerAndAverageSampleNumberResult.Rd | 28 rpact-2.0.6/rpact/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd | 41 rpact-2.0.6/rpact/man/SimulationResults.Rd | 36 rpact-2.0.6/rpact/man/SimulationResultsMeans.Rd | 26 rpact-2.0.6/rpact/man/SimulationResultsRates.Rd | 26 rpact-2.0.6/rpact/man/SimulationResultsSurvival.Rd | 26 rpact-2.0.6/rpact/man/StageResults.Rd | 70 rpact-2.0.6/rpact/man/StageResultsMeans.Rd | 70 rpact-2.0.6/rpact/man/StageResultsRates.Rd | 70 rpact-2.0.6/rpact/man/StageResultsSurvival.Rd | 70 rpact-2.0.6/rpact/man/StageResults_as.data.frame.Rd | 42 rpact-2.0.6/rpact/man/StageResults_names.Rd | 30 rpact-2.0.6/rpact/man/TrialDesign.Rd | 36 rpact-2.0.6/rpact/man/TrialDesignCharacteristics.Rd | 38 rpact-2.0.6/rpact/man/TrialDesignCharacteristics_as.data.frame.Rd | 55 rpact-2.0.6/rpact/man/TrialDesignConditionalDunnett.Rd | 26 rpact-2.0.6/rpact/man/TrialDesignFisher.Rd | 34 rpact-2.0.6/rpact/man/TrialDesignGroupSequential.Rd | 36 rpact-2.0.6/rpact/man/TrialDesignInverseNormal.Rd | 36 rpact-2.0.6/rpact/man/TrialDesignPlan.Rd | 36 rpact-2.0.6/rpact/man/TrialDesignPlanMeans.Rd | 28 rpact-2.0.6/rpact/man/TrialDesignPlanRates.Rd | 28 rpact-2.0.6/rpact/man/TrialDesignPlanSurvival.Rd | 28 rpact-2.0.6/rpact/man/TrialDesignPlanSurvival_summary.Rd | 33 rpact-2.0.6/rpact/man/TrialDesignPlan_as.data.frame.Rd | 41 rpact-2.0.6/rpact/man/TrialDesignSet.Rd | 62 rpact-2.0.6/rpact/man/TrialDesignSet_as.data.frame.Rd | 45 rpact-2.0.6/rpact/man/TrialDesignSet_length.Rd | 30 rpact-2.0.6/rpact/man/TrialDesignSet_names.Rd | 30 rpact-2.0.6/rpact/man/TrialDesign_as.data.frame.Rd | 55 rpact-2.0.6/rpact/man/getAccrualTime.Rd | 558 +++--- rpact-2.0.6/rpact/man/getAnalysisResults.Rd | 227 +- rpact-2.0.6/rpact/man/getAvailablePlotTypes.Rd | 65 rpact-2.0.6/rpact/man/getConditionalPower.Rd | 94 - rpact-2.0.6/rpact/man/getConditionalRejectionProbabilities.Rd | 78 rpact-2.0.6/rpact/man/getData.Rd | 38 rpact-2.0.6/rpact/man/getDataset.Rd | 292 +-- rpact-2.0.6/rpact/man/getDesignCharacteristics.Rd | 58 rpact-2.0.6/rpact/man/getDesignFisher.Rd | 182 +- rpact-2.0.6/rpact/man/getDesignGroupSequential.Rd | 213 +- rpact-2.0.6/rpact/man/getDesignInverseNormal.Rd | 218 +- rpact-2.0.6/rpact/man/getDesignSet.Rd | 82 rpact-2.0.6/rpact/man/getEventProbabilities.Rd | 154 - rpact-2.0.6/rpact/man/getFinalConfidenceInterval.Rd | 170 - rpact-2.0.6/rpact/man/getFinalPValue.Rd | 48 rpact-2.0.6/rpact/man/getLogLevel.Rd | 42 rpact-2.0.6/rpact/man/getNumberOfSubjects.Rd | 78 rpact-2.0.6/rpact/man/getPiecewiseSurvivalTime.Rd | 235 +- rpact-2.0.6/rpact/man/getPowerAndAverageSampleNumber.Rd | 67 rpact-2.0.6/rpact/man/getPowerMeans.Rd | 155 - rpact-2.0.6/rpact/man/getPowerRates.Rd | 164 + rpact-2.0.6/rpact/man/getPowerSurvival.Rd | 477 ++--- rpact-2.0.6/rpact/man/getRawData.Rd | 44 rpact-2.0.6/rpact/man/getRepeatedConfidenceIntervals.Rd | 54 rpact-2.0.6/rpact/man/getRepeatedPValues.Rd | 54 rpact-2.0.6/rpact/man/getSampleSizeMeans.Rd | 154 - rpact-2.0.6/rpact/man/getSampleSizeRates.Rd | 159 - rpact-2.0.6/rpact/man/getSampleSizeSurvival.Rd | 525 +++--- rpact-2.0.6/rpact/man/getSimulationMeans.Rd | 404 ++-- rpact-2.0.6/rpact/man/getSimulationRates.Rd | 408 ++-- rpact-2.0.6/rpact/man/getSimulationSurvival.Rd | 854 +++++----- rpact-2.0.6/rpact/man/getStageResults.Rd | 124 - rpact-2.0.6/rpact/man/getTestActions.Rd | 44 rpact-2.0.6/rpact/man/plot.AnalysisResults.Rd | 205 +- rpact-2.0.6/rpact/man/plot.Dataset.Rd | 135 - rpact-2.0.6/rpact/man/plot.SimulationResults.Rd | 161 + rpact-2.0.6/rpact/man/plot.StageResults.Rd | 210 +- rpact-2.0.6/rpact/man/plot.TrialDesign.Rd | 195 +- rpact-2.0.6/rpact/man/plot.TrialDesignPlan.Rd | 172 +- rpact-2.0.6/rpact/man/plot.TrialDesignSet.Rd | 184 +- rpact-2.0.6/rpact/man/printCitation.Rd | 46 rpact-2.0.6/rpact/man/readDataset.Rd | 118 - rpact-2.0.6/rpact/man/readDatasets.Rd | 114 - rpact-2.0.6/rpact/man/resetLogLevel.Rd | 42 rpact-2.0.6/rpact/man/rpact.Rd | 114 - rpact-2.0.6/rpact/man/setLogLevel.Rd | 55 rpact-2.0.6/rpact/man/sub-TrialDesignSet-method.Rd | 31 rpact-2.0.6/rpact/man/testPackage.Rd | 87 - rpact-2.0.6/rpact/man/utilitiesForPiecewiseExponentialDistribution.Rd | 204 +- rpact-2.0.6/rpact/man/utilitiesForSurvivalTrials.Rd | 89 - rpact-2.0.6/rpact/man/writeDataset.Rd | 134 - rpact-2.0.6/rpact/man/writeDatasets.Rd | 132 - rpact-2.0.6/rpact/tests/testthat/helper-f_analysis_rates.R | 1 rpact-2.0.6/rpact/tests/testthat/helper-f_analysis_survival.R | 2 rpact-2.0.6/rpact/tests/testthat/test-class_analysis_dataset.R | 265 +++ rpact-2.0.6/rpact/tests/testthat/test-class_summary.R | 225 +- rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_means.R |only rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_rates.R |only rpact-2.0.6/rpact/tests/testthat/test-f_analysis_base_survival.R |only rpact-2.0.6/rpact/tests/testthat/test-f_core_assertions.R | 35 rpact-2.0.6/rpact/tests/testthat/test-f_core_output_formats.R | 2 rpact-2.0.6/rpact/tests/testthat/test-f_design_power_calculator.R | 100 - rpact-2.0.6/rpact/tests/testthat/test-f_design_sample_size_calculator.R | 230 ++ rpact-2.0.6/rpact/tests/testthat/test_generic_functions.R |only 164 files changed, 8016 insertions(+), 6437 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>. For the extreme value random fields see Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and Schlather (2002) <doi.org/10.1023/A:1020977924878>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.3.6 dated 2019-03-06 and 3.3.7 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/RMmodels-Methods-plots.R | 5 ++++- R/fitgauss.R | 3 +-- man/RMpoissonpoly.Rd | 2 +- man/RMtrafo.Rd | 4 ++-- src/InternalCov.cc | 2 +- src/Machine.h | 4 ++-- src/RF.h | 2 +- src/cubicsolver.cc | 2 +- src/questions.cc | 6 +++++- src/trend.cc | 2 +- src/variogramAndCo.cc | 2 +- src/variogramAndCo.h | 2 +- 14 files changed, 38 insertions(+), 32 deletions(-)
Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between
samples is based on a modified kriging method that
accepts a genetic distance matrix and generates a map of
probability of lineage presence. This package also offers
tools to generate a map of potential contact zones
between groups with user-defined thresholds in the tree
to account for old and recent divergence. Additionally,
it has functions for IDW interpolation using genetic data
and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>
Diff between phylin versions 2.0.1 dated 2019-11-19 and 2.0.2 dated 2019-12-12
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/gen.variogram.R | 8 ++++---- R/krig.R | 2 +- R/mtest.gv.R | 2 +- inst/CITATION | 8 +++++--- inst/doc/phylin_tutorial.pdf |binary inst/doc/resistance_tutorial.pdf |binary man/mtest.gv.Rd | 2 +- man/simul.gen.dist.Rd | 2 +- 10 files changed, 25 insertions(+), 23 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],
Andrew Bean [aut],
Lukas A. Widmer [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.5-4 dated 2019-11-19 and 0.5-8 dated 2019-12-12
DESCRIPTION | 16 MD5 | 43 - NAMESPACE | 1 R/blrm_exnex.R | 174 ++++--- R/blrm_trial.R | 31 + R/posterior_predict.R | 2 R/pp_data.R | 11 R/summary.R | 4 R/sysdata.rda |binary inst/NEWS | 23 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.html | 262 +++++----- inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 244 +++++----- inst/sbc/sbc_tools.R | 3 inst/stan/blrm_exnex.stan | 78 ++- man/blrm_exnex.Rd | 173 ++++--- man/log_inv_logit.Rd |only src/stanExports_blrm_exnex.h | 789 +++++++++++++++++---------------- tests/testthat/helper-sampling.R | 4 tests/testthat/helper-trial_examples.R | 67 +- tests/testthat/test-blrm_exnex.R | 37 + tests/testthat/test-blrm_trial.R | 96 +++- 23 files changed, 1204 insertions(+), 860 deletions(-)
Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions,
a procedure increasingly used in ecology to improve species distribution
models. This package integrates the existing methodological approaches with the
objective of generating virtual species distributions with increased ecological
realism.
Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between virtualspecies versions 1.5 dated 2019-05-06 and 1.5.1 dated 2019-12-12
DESCRIPTION | 13 MD5 | 58 +-- NAMESPACE | 2 NEWS | 8 R/convertToPA.R | 10 R/generateRandomSp.R | 9 R/generateSpFromFun.R | 2 R/limitDistribution.R | 12 R/plotSuitabilityToProba.R | 2 R/removeCollinearity.R | 9 R/sampleOccurrences.R | 24 - R/utilityFunctions.R | 4 man/betaFun.Rd | 114 +++---- man/convertToPA.Rd | 562 +++++++++++++++++++------------------- man/custnorm.Rd | 104 +++---- man/formatFunctions.Rd | 150 +++++----- man/generateRandomSp.Rd | 356 ++++++++++++------------ man/generateSpFromBCA.Rd | 330 +++++++++++----------- man/generateSpFromFun.Rd | 290 ++++++++++--------- man/generateSpFromPCA.Rd | 319 +++++++++++---------- man/limitDistribution.Rd | 281 +++++++++---------- man/linearFun.Rd | 70 ++-- man/logisticFun.Rd | 118 ++++---- man/plotResponse.Rd | 209 +++++++------- man/plotSuitabilityToProba.Rd | 136 ++++----- man/quadraticFun.Rd | 76 ++--- man/removeCollinearity.Rd | 191 ++++++------ man/sampleOccurrences.Rd | 619 +++++++++++++++++++++--------------------- man/synchroniseNA.Rd | 82 ++--- man/virtualspecies-package.Rd | 140 ++++----- 30 files changed, 2190 insertions(+), 2110 deletions(-)
More information about virtualspecies at CRAN
Permanent link
Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing
Parents
Description: Parentage assignment package.
Parentage assignment is performed based on observed average Mendelian transmission probability distributions.
The main function of this package is the function APIS(), which is the parentage assignment function.
Author: Ronan Griot, François Allal, Romain Morvezen, Sophie Brard-Fudulea, Pierrick Haffray, Florence Phocas and Marc Vandeputte
Maintainer: Ronan Griot <ronan.griot@gmail.com>
Diff between APIS versions 0.1.0 dated 2019-08-19 and 1.0.0 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/APIS_functions.R | 7 ++++--- inst/doc/APIS_vignette.html | 8 ++++---- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 1.9.7 dated 2019-11-24 and 1.9.8 dated 2019-12-12
Rfast-1.9.7/Rfast/R/source.R |only Rfast-1.9.8/Rfast/DESCRIPTION | 10 +- Rfast-1.9.8/Rfast/MD5 | 33 +++--- Rfast-1.9.8/Rfast/NEWS.md | 2 Rfast-1.9.8/Rfast/R/system_and_package.R | 51 ++++++++++ Rfast-1.9.8/Rfast/R/variable_selection.R | 16 ++- Rfast-1.9.8/Rfast/inst/include/Rfast/helpers.hpp | 1 Rfast-1.9.8/Rfast/inst/include/Rfast/matrix.hpp | 4 Rfast-1.9.8/Rfast/inst/include/Rfast/vector.hpp | 2 Rfast-1.9.8/Rfast/man/Rfast-package.Rd | 114 +++++++++++++---------- Rfast-1.9.8/Rfast/src/dir_knn.cpp | 35 ++++--- Rfast-1.9.8/Rfast/src/dists.cpp | 2 Rfast-1.9.8/Rfast/src/dists_vec.cpp | 21 ++-- Rfast-1.9.8/Rfast/src/init.c | 4 Rfast-1.9.8/Rfast/src/my_k_sorted_array.cpp | 42 +++++--- Rfast-1.9.8/Rfast/src/reg_lib.cpp | 35 ++++--- Rfast-1.9.8/Rfast/src/system_files.cpp | 2 Rfast-1.9.8/Rfast/src/topological_sort.cpp | 14 +- 18 files changed, 249 insertions(+), 139 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, a posteriori time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of
fossil taxa using stratigraphic data. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.
Author: David W. Bapst, Peter J. Wagner
Maintainer: David W. Bapst <dwbapst@gmail.com>
Diff between paleotree versions 3.3.0 dated 2019-06-04 and 3.3.25 dated 2019-12-12
CHANGELOG | 639 - DESCRIPTION | 23 MD5 | 376 NAMESPACE | 328 R/DiversityCurves.R | 1042 +- R/RaiaCopesRule.R | 543 - R/SamplingConv.R | 414 - R/SongZhangDicrano.R | 238 R/binTimeData.R | 406 - R/branchClasses.R | 211 R/cal3TimePaleoPhy.R | 3533 ++++----- R/cladogeneticTraitCont.R | 226 R/communityEcology.R | 562 - R/compareTimescaling.R | 498 - R/constrainParPaleo.R | 813 +- R/createMrBayesConstraints.R | 255 R/createMrBayesTipCalibrations.R | 839 +- R/createMrBayesTipDatingNexus.R | 2190 ++--- R/dateNodes.R | 179 R/dateTaxonTreePBDB.R | 787 +- R/degradeTree.R | 330 R/depthRainbow.R | 68 R/divCurveFossilRecordSim.R | 198 R/durationFreq.R | 824 +- R/equation2function.R | 134 R/exhaustationFunctions.R | 3916 +++++----- R/expandTaxonTree.R | 270 R/fixRootTime.R | 464 - R/footeValues.R | 492 - R/fourDateFunctions.R | 226 R/freqRat.R | 618 - R/getDataPBDB.R | 628 - R/getFixedAgesFromNexus.R | 176 R/graptDisparity.R | 430 - R/graptPBDB.R | 350 R/hidden.gettingPhyloPicFunctions.R | 405 - R/hidden.makePBDBtaxonTree.Functions.R | 1202 +-- R/hidden.modelExpressionModification.R | 254 R/hidden.plotTaxonStratDurations.R | 160 R/hidden.plottingPhyloPicFunctions.R | 576 - R/horizonSampRate.R | 256 R/inverseSurv.R | 985 +- R/isTimeListSequential.R | 54 R/kanto.R | 541 - R/macroperforateForam.R | 756 - R/makePBDBtaxonTree.R | 844 +- R/minBranchLength.R | 357 R/minCharChange.R | 1644 ++-- R/modelMethods.R | 683 - R/modifyTerminalBranches.R | 965 +- R/multiDiv.R | 1037 +- R/nearestNeighborDist.R | 205 R/nodeDates2branchLengths.R | 346 R/obtainDatedPosteriorTreesMrB.R | 1059 +- R/occData2timeList.R | 494 - R/optimPaleo.R | 80 R/paleotree-package.R | 225 R/parentChild2TaxonTree.R | 708 - R/parseNexusFile.R | 236 R/perCapitaRates.R | 532 - R/perfectParsCharTree.R | 156 R/plotOccData.R | 269 R/plotPhyloPicTree.R | 1444 +-- R/plotTraitgram.R | 292 R/pqr2Ps.R | 250 R/probAnc.R | 403 - R/resolveTreeChar.R | 792 +- R/retiolitinae.R | 174 R/reverseList.R | 90 R/rootSplit.R | 65 R/sampleRanges.R | 986 +- R/seqTimeList.R | 329 R/setRootAge.R | 240 R/simFossilRecord.R | 3294 ++++---- R/simFossilRecordInternal.R | 1227 +-- R/simFossilRecordMethods.R | 830 +- R/taxa2cladogram.R | 292 R/taxa2phylo.R | 750 + R/taxonSortPBDBocc.R | 824 +- R/taxonTable2TaxonTree.R | 331 R/termTaxa.R | 854 +- R/testEdgeMat.R | 584 - R/timeLadderTree.R | 274 R/timePaleoPhy.R | 2766 +++---- R/timeSliceTree.R | 318 R/tipDatingCompatabilitySummaryMrB.R | 269 R/treeContradiction.R | 393 - R/twoWayEcologyCluster.R | 546 - R/unitLengthTree.R | 95 R/writeSimpleSumtNexus.R | 120 README.md | 110 inst/CITATION | 22 inst/WORDLIST |only man/DiversityCurves.Rd | 525 - man/RaiaCopesRule.Rd | 537 - man/SamplingConv.Rd | 240 man/SongZhangDicrano.Rd | 238 man/binTimeData.Rd | 277 man/branchClasses.Rd | 139 man/cal3TimePaleoPhy.Rd | 1404 +-- man/cladogeneticTraitCont.Rd | 214 man/communityEcology.Rd | 362 man/compareTimescaling.Rd | 240 man/constrainParPaleo.Rd | 528 - man/createMrBayesConstraints.Rd | 154 man/createMrBayesTipCalibrations.Rd | 317 man/createMrBayesTipDatingNexus.Rd | 794 +- man/dateNodes.Rd | 151 man/dateTaxonTreePBDB.Rd | 337 man/degradeTree.Rd | 213 man/depthRainbow.Rd | 64 man/divCurveFossilRecordSim.Rd | 127 man/durationFreq.Rd | 410 - man/equation2function.Rd | 103 man/exhaustionFunctions.Rd | 395 - man/expandTaxonTree.Rd | 192 man/fixRootTime.Rd | 200 man/footeValues.Rd | 223 man/freqRat.Rd | 560 - man/getDataPBDB.Rd | 312 man/graptDisparity.Rd | 424 - man/graptPBDB.Rd | 352 man/horizonSampRate.Rd | 171 man/inverseSurv.Rd | 576 - man/kanto.Rd | 526 - man/macroperforateForam.Rd | 744 - man/makePBDBtaxonTree.Rd | 524 - man/minBranchLength.Rd | 227 man/minCharChange.Rd | 907 +- man/modelMethods.Rd | 369 man/modifyTerminalBranches.Rd | 607 - man/multiDiv.Rd | 497 - man/nearestNeighborDist.Rd | 168 man/nodeDates2branchLengths.Rd | 250 man/obtainDatedPosteriorTreesMrB.Rd | 480 - man/occData2timeList.Rd | 320 man/optimPaleo.Rd | 78 man/paleotree-package.Rd | 201 man/parentChild2taxonTree.Rd | 277 man/perCapitaRates.Rd | 291 man/perfectParsCharTree.Rd | 104 man/plotOccData.Rd | 170 man/plotPhyloPicTree.Rd | 737 - man/plotTraitgram.Rd | 166 man/pqr2Ps.Rd | 230 man/probAnc.Rd | 218 man/resolveTreeChar.Rd | 459 - man/retiolitinae.Rd | 166 man/reverseList.Rd | 89 man/rootSplit.Rd | 67 man/sampleRanges.Rd | 597 - man/seqTimeList.Rd | 206 man/setRootAge.Rd | 140 man/simFossilRecord.Rd | 2402 +++--- man/simFossilRecordMethods.Rd | 369 man/taxa2cladogram.Rd | 223 man/taxa2phylo.Rd | 230 man/taxonSortPBDBocc.Rd | 409 - man/taxonTable2taxonTree.Rd | 145 man/termTaxa.Rd | 579 - man/testEdgeMat.Rd | 136 man/timeLadderTree.Rd | 144 man/timeList2fourDate.Rd | 143 man/timePaleoPhy.Rd | 1516 +-- man/timeSliceTree.Rd | 218 man/tipDatingCompatabilitySummaryMrB.Rd | 243 man/treeContradiction.Rd | 281 man/twoWayEcologyCluster.Rd | 298 man/unitLengthTree.Rd | 104 tests/spelling.R |only tests/testthat.R | 8 tests/testthat/data/retio_dating.nex | 316 tests/testthat/data/retio_dating.run1.p | 206 tests/testthat/data/retio_dating.run1.t | 258 tests/testthat/data/retio_dating.run2.p | 206 tests/testthat/data/retio_dating.run2.t | 258 tests/testthat/references |only tests/testthat/test_Contradiction_05-25-17.R | 111 tests/testthat/test_cal3_dateTreatment_Armin.R | 589 - tests/testthat/test_cladogeneticTraitCont.R | 67 tests/testthat/test_inverseSurv.R | 58 tests/testthat/test_minBranchLength_check_10-09-15.R | 69 tests/testthat/test_obtainDatedPosteriorTreesMrB.R | 125 tests/testthat/test_simFossilRecord_countFinalTaxa_07-15-19.R |only tests/testthat/test_simFossilRecord_negative_dates_07-06-19.R |only tests/testthat/test_simFossilRecord_rejection.R |only tests/testthat/test_simFossilRecord_returnAllRuns_output.R |only tests/testthat/test_simFossilRecord_return_extant_taxa.R |only tests/testthat/test_simFossilRecord_return_extinct_taxa.R |only tests/testthat/test_simFossilRecord_simple.R |only tests/testthat/test_timeSlice_dropExtinct_shifts_root_age.R |only tests/testthat/test_timeSlice_tip_labels_differ.R |only 192 files changed, 45686 insertions(+), 41838 deletions(-)
Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>
Diff between mpr versions 1.0.4 dated 2016-10-12 and 1.0.5 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/print.summary.mpr.R | 8 +++++--- 3 files changed, 11 insertions(+), 9 deletions(-)
Title: Funnel Plots for Indirectly-Standardised Ratios
Description: An implementation of the Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for reporting standardised ratios, with overdispersion adjustment.
Author: Chris Mainey [aut, cre] (<https://orcid.org/0000-0002-3018-6171>),
Matthew Bass [ctb]
Maintainer: Chris Mainey <chris.mainey@uhb.nhs.uk>
Diff between FunnelPlotR versions 0.2.1 dated 2019-10-09 and 0.2.2 dated 2019-12-12
DESCRIPTION | 8 - MD5 | 39 +++-- NAMESPACE | 2 NEWS.md | 6 R/build_limits_lookup.R | 6 R/draw_plot.R | 2 R/funnel_plot.R | 2 README.md | 2 inst/CITATION |only inst/doc/funnel_plots.R | 10 - inst/doc/funnel_plots.Rmd | 2 inst/doc/funnel_plots.html | 9 - man/OD_adjust_func.Rd | 59 ++++---- man/aggregate_func.Rd | 36 ++--- man/build_limits_lookup.Rd | 79 ++++++----- man/draw_plot.Rd | 95 +++++++------- man/figures/README-funnel1-1.png |binary man/figures/README-funnel2-1.png |binary man/funnel_plot.Rd | 199 +++++++++++++++--------------- tests/testthat/test-build_limits_lookup.R | 4 vignettes/funnel_plots.Rmd | 2 21 files changed, 301 insertions(+), 261 deletions(-)
Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis,
fixing data errors in numerical, factor and date variables and creating report
tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.4.32 dated 2019-04-19 and 0.4.40 dated 2019-12-12
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NAMESPACE | 2 ++ R/check_quality.R | 35 ++++++++++++++++++++++++++++++++++- R/descriptive.R | 9 +++++++-- R/report_model.R | 2 +- man/search_scripts.Rd | 2 +- man/workspace.Rd |only man/workspace_sapply.Rd |only 9 files changed, 56 insertions(+), 14 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 2.4 dated 2019-05-16 and 2.5 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/boxcoxlm.R | 2 +- inst/citation | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Domain-Specific Language for Building PLS Structural Equation
Models
Description: A powerful, easy to write and easy to modify syntax for
specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods
for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per
Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing
parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminr versions 1.0.0 dated 2019-09-27 and 1.0.1 dated 2019-12-12
DESCRIPTION | 14 +- MD5 | 8 - R/library.R | 4 build/vignette.rds |binary inst/doc/SEMinR.html | 344 +++++++++++++++++++++++++-------------------------- 5 files changed, 185 insertions(+), 185 deletions(-)
Title: A Parallel Analysis with Polychoric Correlation Matrices
Description: The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis.
Author: Fabio Presaghi [aut, cre],
Marta Desimoni [ctb]
Maintainer: Fabio Presaghi <fabio.presaghi@uniroma1.it>
Diff between random.polychor.pa versions 1.1.4-2 dated 2016-07-26 and 1.1.4-3 dated 2019-12-12
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/random.polychor.pa.r | 21 ++++++++++++++------- man/NEWS.Rd | 6 ++++++ man/random.polychor.pa-package.Rd | 8 +++++--- man/random.polychor.pa.Rd | 21 +++++++++++++++------ 6 files changed, 50 insertions(+), 26 deletions(-)
More information about random.polychor.pa at CRAN
Permanent link
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 1.2.1 dated 2019-04-08 and 1.2.3 dated 2019-12-12
DESCRIPTION | 8 - MD5 | 8 - R/function_mce.R | 254 +++++++++++++++++++++++------------------- R/function_pert_estocastico.R | 4 man/mce.Rd | 2 5 files changed, 157 insertions(+), 119 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.1.5 dated 2019-09-28 and 0.1.6 dated 2019-12-12
DESCRIPTION | 8 - MD5 | 39 +++--- NEWS.md | 6 + R/Dictionary.R | 89 +++++++-------- R/cite_bib.R | 42 ++++--- R/dictionary_sugar.R | 7 + README.md | 3 man/Dictionary.Rd | 257 ++++++++++++++++++++++++++++++++++++-------- man/cite_bib.Rd | 13 +- man/compat-map.Rd | 14 +- man/dictionary_sugar_get.Rd | 3 man/encapsulate.Rd | 12 +- man/figures |only man/invoke.Rd | 2 man/keep_in_bounds.Rd | 4 man/mlr3misc-package.Rd | 4 man/modify_if.Rd | 4 man/require_namespaces.Rd | 6 - man/set_names.Rd | 2 man/str_collapse.Rd | 3 man/str_indent.Rd | 5 21 files changed, 368 insertions(+), 155 deletions(-)
Title: Image Statistics Based on Processing Fluency
Description: Get image statistics based on processing fluency theory. The
functions provide scores for several basic aesthetic principles that
facilitate fluent cognitive processing of images: contrast,
complexity / simplicity, self-similarity, symmetry, and typicality.
See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr
(2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Author: Stefan Mayer [aut, cre] (<https://orcid.org/0000-0003-0034-7090>)
Maintainer: Stefan Mayer <stefan@mayer-de.com>
Diff between imagefluency versions 0.2.1 dated 2019-09-27 and 0.2.2 dated 2019-12-12
DESCRIPTION | 13 ++--- MD5 | 32 +++++++------ NEWS.md | 6 ++ R/self-similarity.R | 2 R/typicality.R | 6 -- R/utils.R | 4 - README.md | 7 ++ build/vignette.rds |binary inst/doc/imagefluency.R | 28 +++++------ inst/doc/imagefluency.html | 39 +++++++--------- man/figures |only man/imagefluency-package.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test_complexity.R | 51 ++++++++++++++++++++- tests/testthat/test_contrast.R | 17 ++++++- tests/testthat/test_self_similarity.R | 81 +++++++++++++++++++++++++++++++-- tests/testthat/test_symmetry.R | 71 ++++++++++++++++++++++++++--- tests/testthat/test_typicality.R | 82 +++++++++++++++++++++++++++++++++- 18 files changed, 361 insertions(+), 80 deletions(-)
Title: Downloads, Unpacks and Tidies Legislative Data from the
Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and
Chamber of Deputies Application Programming Interfaces available at <http://
legis.senado.gov.br/dadosabertos/> and <https://dadosabertos.camara.leg.br/>
respectively.
Author: Robert McDonnell [aut, cre],
Guilherme Jardim Duarte [aut],
Danilo Freire [aut],
Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>
Diff between congressbr versions 0.2.1 dated 2019-05-08 and 0.2.2 dated 2019-12-12
DESCRIPTION | 10 +- MD5 | 64 +++++++------- NAMESPACE | 4 NEWS.md | 4 R/cham_votes.R | 194 ++++++++++++++++++++++++++++++++++---------- R/sen_agenda.R | 6 - R/sen_various.R | 4 R/sen_votes.R | 84 ++++++++++++++++--- R/util.R | 4 README.md | 3 build/vignette.rds |binary inst/doc/chamber.R | 22 ++-- inst/doc/chamber.html | 168 +++++++++++++++++++------------------- inst/doc/senate.R | 32 +++---- inst/doc/senate.html | 178 +++++++++++++++++++--------------------- man/cham_bills.Rd | 21 +++- man/cham_votes.Rd | 4 man/cham_votes_year.Rd |only man/congressbr.Rd | 1 man/sen_agenda.Rd | 12 ++ man/sen_bill_search.Rd | 28 ++++-- man/sen_bills.Rd | 9 +- man/sen_bills_current.Rd | 10 +- man/sen_bills_passing.Rd | 9 +- man/sen_bills_updates.Rd | 10 +- man/sen_commissions_type.Rd | 3 man/sen_plenary_agenda.Rd | 3 man/sen_senator.Rd | 9 +- man/sen_senator_legis.Rd | 9 +- man/sen_senator_list.Rd | 3 man/sen_votes.Rd | 3 man/sen_votes_year.Rd | 10 +- man/sen_votes_year_file.Rd |only man/vote_to_rollcall.Rd | 3 34 files changed, 579 insertions(+), 345 deletions(-)
Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between BIOdry versions 0.6 dated 2019-05-28 and 0.7 dated 2019-12-12
DESCRIPTION | 8 ++--- MD5 | 38 +++++++++++++-------------- NEWS | 3 ++ R/anova.modelFrame.R | 23 ++++++++++------ R/frametoLme.R | 64 +++++++++++++++++++++++++--------------------- R/modelFrame.R | 25 ++++++++++------- R/muleMan.R | 33 +++++++++++++---------- R/plot.modelFrame.R | 15 +++++----- R/plot.muleMan.R | 35 ++++++++++++++----------- R/summary.modelFrame.R | 16 ++++++----- R/wlai.R | 2 - build/partial.rdb |binary man/anova.modelFrame.Rd | 23 ++++++++++------ man/frametoLme.Rd | 64 +++++++++++++++++++++++++--------------------- man/modelFrame.Rd | 55 ++++++++++++++++++++------------------- man/muleMan.Rd | 33 +++++++++++++---------- man/plot.modelFrame.Rd | 15 +++++----- man/plot.muleMan.Rd | 35 ++++++++++++++----------- man/summary.modelFrame.Rd | 16 ++++++----- man/wlai.Rd | 2 - 20 files changed, 281 insertions(+), 224 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] (<https://orcid.org/0000-0001-7656-8338>),
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL
Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-6 dated 2018-12-21 and 0.7-7 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/matrix.R | 14 +++++++++----- build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary src/copy.c | 3 ++- src/init.c | 2 +- src/tdm.cpp | 8 ++++++-- 11 files changed, 32 insertions(+), 23 deletions(-)
Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs, compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://bit.ly/35a3V3H>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>
Diff between graph4lg versions 0.1.1 dated 2019-07-23 and 0.2.0 dated 2019-12-12
DESCRIPTION | 17 +- MD5 | 173 ++++++++++++----------- NAMESPACE | 7 NEWS.md | 6 R/add_nodes_attr.R | 34 ++-- R/aux_25_09.R | 3 R/compar_r_fisher.R | 3 R/convert_cd.R | 43 +++-- R/data.R | 31 ++-- R/df_to_pw_mat.R |only R/dist_max_corr.R | 34 ++-- R/g_percol.R | 24 +-- R/gen_graph_indep.R | 77 ++++++---- R/gen_graph_thr.R | 5 R/gen_graph_topo.R | 11 - R/genepop_to_genind.R | 19 +- R/genind_to_genepop.R | 13 + R/graph_modul_compar.R | 124 ++++++++++------ R/graph_node_compar.R | 59 ++++---- R/graph_plan.R |only R/graph_plot_compar.R | 37 ++--- R/graph_to_df.R |only R/graph_to_shp.R | 58 ++++--- R/graph_topo_compar.R | 62 ++++---- R/graphab_to_igraph.R | 34 ++-- R/gstud_to_genind.R | 18 +- R/kernel_param.R |only R/loci_to_genind.R | 5 R/mat_gen_dist.R | 57 ++++--- R/mat_geo_dist.R | 28 ++- R/mat_pw_d_jost.R | 14 + R/mat_pw_dps.R | 8 - R/mat_pw_fst.R | 16 +- R/mat_pw_gst.R | 14 + R/plot_graph_lg.R | 99 +++++++------ R/plot_graph_modul.R | 162 ++++++++++++---------- R/plot_w_hist.R | 10 - R/pop_gen_index.R | 123 ++++++++++------ R/pw_mat_to_df.R |only R/reorder_mat.R | 15 +- R/scatter_dist.R | 13 - R/scatter_dist_g.R | 34 ++-- R/structure_to_genind.R | 47 +++--- build/partial.rdb |binary inst/doc/vignette_graph4lg.R | 88 +++++------ inst/doc/vignette_graph4lg.html | 102 ++++++------- man/add_nodes_attr.Rd | 157 +++++++++++---------- man/compar_r_fisher.Rd | 96 ++++++------- man/convert_cd.Rd | 184 ++++++++++++------------- man/data_pc_genind.Rd | 56 +++---- man/data_pc_gpop.Rd | 76 +++++----- man/data_pc_gstud.Rd | 80 +++++----- man/data_pc_loci.Rd | 68 ++++----- man/data_pc_str.Rd | 72 ++++----- man/data_simul_genind.Rd | 69 ++++----- man/data_tuto.Rd | 50 +++--- man/df_to_pw_mat.Rd |only man/dist_max_corr.Rd | 212 ++++++++++++++-------------- man/g_percol.Rd | 70 ++++----- man/gen_graph_indep.Rd | 263 ++++++++++++++++++----------------- man/gen_graph_thr.Rd | 105 +++++++------- man/gen_graph_topo.Rd | 125 ++++++++--------- man/genepop_to_genind.Rd | 111 +++++++-------- man/genind_to_genepop.Rd | 174 +++++++++++------------ man/graph_modul_compar.Rd | 294 +++++++++++++++++++++------------------- man/graph_node_compar.Rd | 188 +++++++++++++------------ man/graph_plan.Rd |only man/graph_plot_compar.Rd | 115 +++++++-------- man/graph_to_df.Rd |only man/graph_to_shp.Rd | 157 +++++++++++---------- man/graph_topo_compar.Rd | 211 ++++++++++++++-------------- man/graphab_to_igraph.Rd | 161 +++++++++++---------- man/gstud_to_genind.Rd | 87 +++++------ man/kernel_param.Rd |only man/loci_to_genind.Rd | 61 ++++---- man/mat_gen_dist.Rd | 164 +++++++++++----------- man/mat_geo_dist.Rd | 90 ++++++------ man/mat_pw_d_j.Rd | 122 ++++++++-------- man/mat_pw_dps.Rd | 98 ++++++------- man/mat_pw_fst.Rd | 120 ++++++++-------- man/mat_pw_gst.Rd | 120 ++++++++-------- man/plot_graph_lg.Rd | 134 +++++++++--------- man/plot_graph_modul.Rd | 213 +++++++++++++++------------- man/plot_w_hist.Rd | 62 ++++---- man/pop_gen_index.Rd | 109 +++++++------- man/pts_pop_pc.Rd | 78 +++++----- man/pts_pop_simul.Rd | 56 +++---- man/pw_mat_to_df.Rd |only man/reorder_mat.Rd | 72 ++++----- man/scatter_dist.Rd | 159 +++++++++++---------- man/scatter_dist_g.Rd | 175 ++++++++++++----------- man/structure_to_genind.Rd | 139 +++++++++--------- vignettes/data_gpop_test.txt |only 93 files changed, 3630 insertions(+), 3250 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including Bernardinelli et al. (1995) <doi:10.1002/sim.4780142112>, Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001> and Lee et al. (2016) <doi:10.1214/16-AOAS941>. Full details are given in the vignette accompanying this package. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 3.0.1 dated 2019-01-08 and 3.0.2 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/binomial.CARadaptive.R | 8 ++++---- R/common.functions.R | 8 ++++---- R/gaussian.CARadaptive.R | 8 ++++---- R/poisson.CARadaptive.R | 8 ++++---- build/vignette.rds |binary inst/doc/CARBayesST.Rnw | 8 ++++---- inst/doc/CARBayesST.pdf |binary man/CARBayesST-package.Rd | 4 ++-- vignettes/CARBayesST.Rnw | 8 ++++---- 11 files changed, 40 insertions(+), 40 deletions(-)
Title: Simulation of in Silico Multi-Omic Networks
Description: A tool for the simulation of gene expression profiles for in silico regulatory networks. The package generates gene regulatory networks, which include protein-coding and noncoding genes linked via different types of regulation: regulation of transcription, translation, RNA or protein decay, and post-translational modifications. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations, but is defined by the user. A choice of stochastic simulation algorithms allow us to simulate the expression profiles (RNA and if applicable protein abundance) of the genes in the in silico system for the different in silico individuals. A tutorial explaining how to use the package is available at <https://oliviaab.github.io/sismonr/>. Manuscript in preparation; see also Angelin-Bonnet O., Biggs P.J. and Vignes M. (2018) <doi:10.1109/BIBM.2018.8621131>. Note that sismonr relies on Julia code called internally by the functions. No knowledge of Julia is required in order to use sismonr, but Julia must be installed on the computer (instructions can be found in the tutorial, the GitHub page or the vignette of the package).
Author: Olivia Angelin-Bonnet [aut, cre]
(<https://orcid.org/0000-0002-7708-2919>),
Patrick Biggs [aut] (<https://orcid.org/0000-0002-0285-4101>),
Matthieu Vignes [aut] (<https://orcid.org/0000-0001-8929-2975>),
John M. Chambers [ctb]
Maintainer: Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>
Diff between sismonr versions 1.1.4 dated 2019-07-21 and 2.0.0 dated 2019-12-12
DESCRIPTION | 10 MD5 | 74 +++--- NAMESPACE | 2 NEWS.md | 15 + R/args_classes.R | 19 - R/in_silico_population.R | 136 +++++++---- R/in_silico_system.R | 30 +- R/stochastic_simulation.R | 345 ++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/sismonr_vignette.R | 22 - inst/doc/sismonr_vignette.Rmd | 36 -- inst/doc/sismonr_vignette.html | 145 +++++------ inst/julia/stochastic_model.jl | 282 +++++++++++++++++++--- inst/julia/stochastic_simulation.jl | 46 ++- inst/julia/testModules.jl | 4 man/callJuliaStochasticSimulation.Rd | 4 man/createInSilicoPopulation.Rd | 31 +- man/createInSilicoSystem.Rd | 2 man/createIndividual.Rd | 32 ++ man/createStochSystem.Rd | 10 man/getRNAseqMatrix.Rd |only man/insilicoindividualargs.Rd | 6 man/insilicosystemargs.Rd | 4 man/mergeAlleleAbundance.Rd | 4 man/mergeComplexesAbundance.Rd | 4 man/mergePTMAbundance.Rd | 4 man/plotGRN.Rd | 4 man/plotHeatMap.Rd | 14 - man/plotMutations.Rd | 6 man/plotSimulation.Rd | 14 - man/sampleLibrarySize.Rd |only man/simulateInSilicoSystem.Rd | 4 man/simulateParallelInSilicoSystem.Rd | 4 man/steadyStateAbundance.Rd | 4 man/summariseSimulation.Rd | 6 tests/testthat/test-args_classes.R | 8 tests/testthat/test-in_silico_population.R | 53 +++- tests/testthat/test-stochastic_simulation.R | 101 +++++--- vignettes/sismonr_vignette.Rmd | 36 -- 39 files changed, 1077 insertions(+), 444 deletions(-)
Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date, using existing
registry data extended with Monte Carlo simulations.
Author: Stuart Lacy [cre, aut],
Simon Crouch [aut],
Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>
Diff between rprev versions 1.0.2 dated 2019-03-12 and 1.0.3 dated 2019-12-12
DESCRIPTION | 11 MD5 | 54 +- NAMESPACE | 2 NEWS.md | 4 build/vignette.rds |binary inst/doc/diagnostics.R | 38 - inst/doc/diagnostics.html | 517 +++++++++++++++++------- inst/doc/user_guide.R | 72 +-- inst/doc/user_guide.html | 745 ++++++++++++++++++++++------------- man/UKmortality.Rd | 48 +- man/counted_prevalence.Rd | 72 +-- man/draw_incident_population.Rd | 64 +-- man/extract_covars.Rd | 46 +- man/fixed_cure.Rd | 123 +++-- man/plot.incdiag.Rd | 80 +-- man/plot.survfit.prev.Rd | 80 +-- man/predict_survival_probability.Rd | 52 +- man/prevalence.Rd | 357 ++++++++-------- man/prevsim.Rd | 62 +- man/rprev.Rd | 61 +- man/sim_prevalence.Rd | 104 ++-- man/summary.survfit.prev.Rd | 96 ++-- man/survfit.prevalence.Rd | 58 +- man/test_homogeneity.Rd | 180 ++++---- man/test_prevalence_fit.Rd | 75 +-- man/validate_incidence_model.Rd | 56 +- man/validate_survival_model.Rd | 65 +-- tests/testthat/test_survival_model.R | 2 28 files changed, 1796 insertions(+), 1328 deletions(-)
Title: Preprocessing and Multivariate Analysis of Bidimensional Gas
Chromatography Data
Description: Toolbox for chemometrics analysis of bidimensional gas
chromatography data. This package import data for common scientific data
format (NetCDF) and fold it to 2D chromatogram. Then, it can perform
preprocessing and multivariate analysis. In the preprocessing algorithms,
baseline correction, smoothing, and peak alignment are available.
While in multivariate analysis, multiway principal component analysis is
incorporated.
Author: Cristian Quiroz-Moreno [aut, cre],
Guilherme L. Alexandrino [aut],
Noroska G.S. Mogollón [aut]
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>
Diff between RGCxGC versions 1.0.0 dated 2019-01-20 and 1.1.0 dated 2019-12-12
RGCxGC-1.0.0/RGCxGC/vignettes/bioinformatics.csl |only RGCxGC-1.0.0/RGCxGC/vignettes/images/basicWorkflow.png |only RGCxGC-1.1.0/RGCxGC/DESCRIPTION | 25 RGCxGC-1.1.0/RGCxGC/MD5 | 106 ++- RGCxGC-1.1.0/RGCxGC/NAMESPACE | 13 RGCxGC-1.1.0/RGCxGC/R/A_classes.R | 104 +-- RGCxGC-1.1.0/RGCxGC/R/MTBLS579.R | 6 RGCxGC-1.1.0/RGCxGC/R/Myrothecium.R |only RGCxGC-1.1.0/RGCxGC/R/baseline_corr.R | 32 - RGCxGC-1.1.0/RGCxGC/R/batchTwoDCOW.R | 147 ++-- RGCxGC-1.1.0/RGCxGC/R/dephase_chrom.R |only RGCxGC-1.1.0/RGCxGC/R/get_metadata.R |only RGCxGC-1.1.0/RGCxGC/R/import_mixOmics.R |only RGCxGC-1.1.0/RGCxGC/R/join_chromatograms.R | 39 - RGCxGC-1.1.0/RGCxGC/R/m_prcomp.R | 35 - RGCxGC-1.1.0/RGCxGC/R/make_loadings.R |only RGCxGC-1.1.0/RGCxGC/R/plot.R | 45 + RGCxGC-1.1.0/RGCxGC/R/plot_loading.R | 120 ++- RGCxGC-1.1.0/RGCxGC/R/print.R | 6 RGCxGC-1.1.0/RGCxGC/R/read_chrom.R | 106 ++- RGCxGC-1.1.0/RGCxGC/R/reference_chrom.R |only RGCxGC-1.1.0/RGCxGC/R/scores.R | 6 RGCxGC-1.1.0/RGCxGC/R/set_metadata.R |only RGCxGC-1.1.0/RGCxGC/R/twod_cow.R | 33 - RGCxGC-1.1.0/RGCxGC/R/unfold_chrom.R |only RGCxGC-1.1.0/RGCxGC/R/wsmooth.R | 16 RGCxGC-1.1.0/RGCxGC/build/partial.rdb |binary RGCxGC-1.1.0/RGCxGC/build/vignette.rds |binary RGCxGC-1.1.0/RGCxGC/data/MTBLS579.rda |binary RGCxGC-1.1.0/RGCxGC/data/Myrothecium.rda |only RGCxGC-1.1.0/RGCxGC/data/datalist |only RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.R | 80 +- RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.Rmd | 288 +++++---- RGCxGC-1.1.0/RGCxGC/inst/doc/Explanation.html | 469 ++++++++------- RGCxGC-1.1.0/RGCxGC/man/GCxGC-class.Rd | 14 RGCxGC-1.1.0/RGCxGC/man/MPCA-class.Rd | 18 RGCxGC-1.1.0/RGCxGC/man/MTBLS579.Rd | 6 RGCxGC-1.1.0/RGCxGC/man/Myrothecium.Rd |only RGCxGC-1.1.0/RGCxGC/man/PLSDA-class.Rd |only RGCxGC-1.1.0/RGCxGC/man/baseline_corr.Rd | 18 RGCxGC-1.1.0/RGCxGC/man/batch_2DCOW-class.Rd | 4 RGCxGC-1.1.0/RGCxGC/man/batch_2DCOW.Rd | 68 +- RGCxGC-1.1.0/RGCxGC/man/dephase_chrom-methods.Rd |only RGCxGC-1.1.0/RGCxGC/man/get_metadata-methods.Rd |only RGCxGC-1.1.0/RGCxGC/man/import_mixOmics-methods.Rd |only RGCxGC-1.1.0/RGCxGC/man/join_chromatograms.Rd | 13 RGCxGC-1.1.0/RGCxGC/man/joined_chrom-class.Rd | 12 RGCxGC-1.1.0/RGCxGC/man/m_prcomp.Rd | 22 RGCxGC-1.1.0/RGCxGC/man/make_loadings.Rd |only RGCxGC-1.1.0/RGCxGC/man/plot-methods.Rd | 23 RGCxGC-1.1.0/RGCxGC/man/plot_loading-methods.Rd | 20 RGCxGC-1.1.0/RGCxGC/man/preproc_GCxGC-class.Rd | 8 RGCxGC-1.1.0/RGCxGC/man/print-methods.Rd | 6 RGCxGC-1.1.0/RGCxGC/man/projected-class.Rd |only RGCxGC-1.1.0/RGCxGC/man/raw_GCxGC-class.Rd | 10 RGCxGC-1.1.0/RGCxGC/man/read_chrom.Rd | 41 - RGCxGC-1.1.0/RGCxGC/man/reference_chrom.Rd |only RGCxGC-1.1.0/RGCxGC/man/scores-methods.Rd | 6 RGCxGC-1.1.0/RGCxGC/man/set_metadata-methods.Rd |only RGCxGC-1.1.0/RGCxGC/man/twod_cow.Rd | 26 RGCxGC-1.1.0/RGCxGC/man/unfold_chrom.Rd |only RGCxGC-1.1.0/RGCxGC/man/wsmooth.Rd | 16 RGCxGC-1.1.0/RGCxGC/vignettes/Explanation.Rmd | 288 +++++---- RGCxGC-1.1.0/RGCxGC/vignettes/analitica-chimica-acta.csl |only RGCxGC-1.1.0/RGCxGC/vignettes/images/basicWorkflow.jpg |only RGCxGC-1.1.0/RGCxGC/vignettes/images/dataProcessing.png |binary 66 files changed, 1374 insertions(+), 921 deletions(-)
Title: Graphical Toolbox for Clustering and Classification of Data
Frames
Description: Graphical toolbox for clustering and classification of data frames.
It proposes a graphical interface to process clustering and classification methods on features
data-frames, and to view initial data as well as resulted cluster or classes. According to the
level of available labels, different approaches are proposed: unsupervised clustering,
semi-supervised clustering and supervised classification.
To assess the processed clusters or classes, the toolbox can import and show some supplementary
data formats: either profile/time series, or images.
These added information can help the expert to label clusters (clustering), or to constrain data
frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by
Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by
Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.
Author: Guillaume Wacquet [aut],
Pierre-Alexandre Hebert [aut, cre],
Emilie Poisson [aut],
Pierre Talon [aut]
Maintainer: Pierre-Alexandre Hebert <hebert@univ-littoral.fr>
Diff between RclusTool versions 0.91 dated 2019-11-06 and 0.91.1 dated 2019-12-12
DESCRIPTION | 10 +- MD5 | 148 +++++++++++++++++----------------- NAMESPACE | 3 R/RclusTool.R | 5 - R/batchTab.R | 2 R/importTab.R | 2 R/preprocessTab.R | 2 R/sampleBuilding.R | 1 R/sampleClustering.R | 1 R/sampleCompute.R | 9 +- R/sampleView.R | 17 +++ R/semisupTab.R | 2 R/supTab.R | 2 R/unsupTab.R | 2 man/ElbowPlot.Rd | 3 man/KmeansAutoElbow.Rd | 3 man/KwaySSSC.Rd | 10 +- man/MainWindow.Rd | 3 man/abdPlot.Rd | 27 +++--- man/abdPlotTabs.Rd | 3 man/addClustering.Rd | 3 man/analyzePlot.Rd | 13 ++ man/applyPreprocessing.Rd | 10 +- man/buildBatchTab.Rd | 3 man/buildImportTab.Rd | 3 man/buildPreprocessTab.Rd | 3 man/buildSemisupTab.Rd | 3 man/buildUnsupTab.Rd | 3 man/buildsupTab.Rd | 3 man/clusterDensity.Rd | 8 + man/clusterSummary.Rd | 9 +- man/computeCKmeans.Rd | 11 ++ man/computeCSC.Rd | 10 +- man/computeEM.Rd | 10 +- man/computeItemsGUI.Rd | 3 man/computeKmeans.Rd | 3 man/computePcaSample.Rd | 11 +- man/computeSampling.Rd | 11 ++ man/computeSemiSupervised.Rd | 22 +++-- man/computeSpectralEmbeddingSample.Rd | 12 ++ man/computeSupervised.Rd | 9 +- man/computeUnSupervised.Rd | 17 ++- man/cor.mtest.Rd | 6 + man/dot-logoFrame.Rd | 3 man/extractProtos.Rd | 9 +- man/featSpaceNameConvert.Rd | 7 + man/formatLabelSample.Rd | 9 +- man/guessFileEncoding.Rd | 2 man/importSample.Rd | 24 ++++- man/initBatchTab.Rd | 3 man/initImportTab.Rd | 6 - man/initPreprocessTab.Rd | 13 ++ man/initSemisupTab.Rd | 6 - man/initSupTab.Rd | 3 man/initUnsupTab.Rd | 3 man/itemsModel.Rd | 5 - man/listDerivableFeatureSpaces.Rd | 8 + man/loadSample.Rd | 3 man/makeFeatureSpaceOperations.Rd | 13 ++ man/plotDensity2D.Rd | 28 +++--- man/plotProfile.Rd | 16 ++- man/plotProfileExtract.Rd | 16 ++- man/plotSampleFeatures.Rd | 37 +++++--- man/purgeSample.Rd | 8 + man/readTrainSet.Rd | 8 + man/saveLogFile.Rd | 3 man/spectralClustering.Rd | 14 ++- man/tk2add.notetab.Rd | 3 man/tk2delete.notetab.Rd | 3 man/tk2draw.notetab.Rd | 3 man/tk2notetab.RclusTool.Rd | 3 man/tkrplot.RclusTool.Rd | 3 man/tkrreplot.RclusTool.Rd | 3 man/toStringDataFrame.Rd | 3 man/visualizeSampleClustering.Rd | 20 +++- 75 files changed, 515 insertions(+), 214 deletions(-)
Title: Fit Interpretable Machine Learning Models and Explain Blackbox
Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretability. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.25 dated 2019-12-12 and 0.1.24 dated 2019-12-12
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.19 dated 2019-03-09 and 0.20 dated 2019-12-12
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++++--------- build/vignette.rds |binary inst/doc/pritikin-schmidt.pdf |binary inst/itemModelExplorer/ui.R | 2 +- man/iccPlot.Rd | 3 +-- man/replicateModelBy.Rd | 14 +++++++++++--- man/uniquenessPrior.Rd | 3 +-- man/univariatePrior.Rd | 3 +-- tests/testthat/test-addExploratoryFactor.R | 24 ++++++++++++++++++++---- tools |only 11 files changed, 54 insertions(+), 28 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
Author: Søren Højsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Ekstrøm [ctb]
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.2-1 dated 2016-09-24 and 1.3-0 dated 2019-12-12
geepack-1.2-1/geepack/data/dietox.txt.gz |only geepack-1.2-1/geepack/data/koch.txt.gz |only geepack-1.2-1/geepack/data/ohio.txt.gz |only geepack-1.2-1/geepack/data/respdis.txt.gz |only geepack-1.2-1/geepack/data/respiratory.txt.gz |only geepack-1.2-1/geepack/data/seizure.txt.gz |only geepack-1.2-1/geepack/data/sitka89.txt.gz |only geepack-1.2-1/geepack/data/spruce.txt.gz |only geepack-1.2-1/geepack/man/DATA-dietox.Rd |only geepack-1.2-1/geepack/man/DATA-koch.Rd |only geepack-1.2-1/geepack/man/DATA-ohio.Rd |only geepack-1.2-1/geepack/man/DATA-respdis.Rd |only geepack-1.2-1/geepack/man/DATA-respiratory.Rd |only geepack-1.2-1/geepack/man/DATA-seizure.Rd |only geepack-1.2-1/geepack/man/DATA-sitka89.Rd |only geepack-1.2-1/geepack/man/DATA-spruce.Rd |only geepack-1.2-1/geepack/man/SHDgeese-internal.Rd |only geepack-1.2-1/geepack/man/geese-internal.Rd |only geepack-1.3-0/geepack/ChangeLog | 18 geepack-1.3-0/geepack/DESCRIPTION | 35 geepack-1.3-0/geepack/MD5 | 162 +- geepack-1.3-0/geepack/NAMESPACE | 17 geepack-1.3-0/geepack/R/data-geepack.R |only geepack-1.3-0/geepack/R/fixed2Zcor.R | 97 + geepack-1.3-0/geepack/R/geeglm-anova.R | 718 +++++------ geepack-1.3-0/geepack/R/geeglm.R | 1206 ++++++++++-------- geepack-1.3-0/geepack/R/geem-interface.R |only geepack-1.3-0/geepack/R/geepack-package.R |only geepack-1.3-0/geepack/R/geese.R | 732 +++++++---- geepack-1.3-0/geepack/R/internal.R | 164 +- geepack-1.3-0/geepack/R/ordgee.R | 410 +++--- geepack-1.3-0/geepack/R/qic.R |only geepack-1.3-0/geepack/R/rrr.R | 49 geepack-1.3-0/geepack/R/summary.R | 228 +-- geepack-1.3-0/geepack/R/zzz.R | 6 geepack-1.3-0/geepack/README.md |only geepack-1.3-0/geepack/build/vignette.rds |binary geepack-1.3-0/geepack/data/dietox.rda |only geepack-1.3-0/geepack/data/koch.RData |only geepack-1.3-0/geepack/data/muscatine.rda |only geepack-1.3-0/geepack/data/ohio.RData |only geepack-1.3-0/geepack/data/respdis.RData |only geepack-1.3-0/geepack/data/respiratory.RData |only geepack-1.3-0/geepack/data/seizure.RData |only geepack-1.3-0/geepack/data/sitka89.RData |only geepack-1.3-0/geepack/data/spruce.RData |only geepack-1.3-0/geepack/inst/CITATION | 4 geepack-1.3-0/geepack/inst/doc/geepack-manual.R | 22 geepack-1.3-0/geepack/inst/doc/geepack-manual.Rnw | 410 +++--- geepack-1.3-0/geepack/inst/doc/geepack-manual.pdf |binary geepack-1.3-0/geepack/inst/include/famstr.h | 282 ++-- geepack-1.3-0/geepack/inst/include/gee2.h | 164 +- geepack-1.3-0/geepack/inst/include/geese.h | 16 geepack-1.3-0/geepack/inst/include/geesubs.h | 502 +++---- geepack-1.3-0/geepack/inst/include/inter.h | 84 - 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geepack-1.3-0/geepack/man/genZcor.Rd | 140 +- geepack-1.3-0/geepack/man/koch.Rd |only geepack-1.3-0/geepack/man/muscatine.Rd |only geepack-1.3-0/geepack/man/ohio.Rd |only geepack-1.3-0/geepack/man/ordgee.Rd | 234 +-- geepack-1.3-0/geepack/man/respdis.Rd |only geepack-1.3-0/geepack/man/respiratory.Rd |only geepack-1.3-0/geepack/man/seizure.Rd |only geepack-1.3-0/geepack/man/sitka89.Rd |only geepack-1.3-0/geepack/man/spruce.Rd |only geepack-1.3-0/geepack/src/gee2.cc | 19 geepack-1.3-0/geepack/src/init.c |only geepack-1.3-0/geepack/src/inter.cc | 22 geepack-1.3-0/geepack/src/ordgee.cc | 9 geepack-1.3-0/geepack/vignettes/geepack-manual.Rnw | 410 +++--- 104 files changed, 10111 insertions(+), 9337 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al. (1991) <doi:10.1007/BF00116466>), the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>) and the localised model (Lee et al. (2015) <doi:10.1002/env.2348>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 5.1.2 dated 2019-06-21 and 5.1.3 dated 2019-12-12
DESCRIPTION | 8 MD5 | 24 R/binomial.MVlerouxCAR.R | 1014 ++++++++++++------------- R/binomial.dissimilarityCAR.R | 1063 +++++++++++++-------------- R/common.functions.R | 11 R/gaussian.MVlerouxCAR.R | 962 ++++++++++++------------ R/gaussian.dissimilarityCAR.R | 987 ++++++++++++------------- R/poisson.MVlerouxCAR.R | 956 ++++++++++++------------ R/poisson.dissimilarityCAR.R | 1029 +++++++++++++------------- inst/doc/CARBayes.Rnw | 1646 +++++++++++++++++++++--------------------- inst/doc/CARBayes.pdf |binary man/CARBayes-package.Rd | 6 vignettes/CARBayes.Rnw | 1646 +++++++++++++++++++++--------------------- 13 files changed, 4674 insertions(+), 4678 deletions(-)
Title: Compile and Preview Snippets of 'LaTeX'
Description: Compile snippets of 'LaTeX' directly into images from the R console
to view in the 'RStudio' viewer pane, Shiny apps and 'RMarkdown' documents.
Author: Jonathan Sidi [aut, cre],
Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>
Diff between texPreview versions 1.4.2 dated 2019-12-05 and 1.4.3 dated 2019-12-12
DESCRIPTION | 16 ++++----- MD5 | 28 ++++++++--------- NEWS.md | 3 + README.md | 6 ++- build/texPreview.pdf |binary inst/doc/classes.html | 10 +++--- inst/doc/kable.html | 4 +- inst/doc/rmarkdown.html | 8 ++-- inst/doc/slickr.html | 14 ++++---- inst/doc/tests_and_coverage.html | 2 - inst/doc/tex_packages.html | 4 +- inst/doc/tikz.html | 4 +- tests/README.md | 62 +++++++++++++++++++------------------- tests/testthat/helper-functions.R | 14 +++++++- tests/testthat/test-rmd.R | 12 +------ 15 files changed, 98 insertions(+), 89 deletions(-)
Title: Fit Interpretable Machine Learning Models and Explain Blackbox
Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.23 dated 2019-11-03 and 0.1.25 dated 2019-12-12
interpret-0.1.23/interpret/man/get_best_model_feature_combination.Rd |only interpret-0.1.23/interpret/man/get_current_model_feature_combination.Rd |only interpret-0.1.23/interpret/man/initialize_training_classification.Rd |only interpret-0.1.23/interpret/man/initialize_training_regression.Rd |only interpret-0.1.23/interpret/man/training_step.Rd |only interpret-0.1.23/interpret/src/core/EbmTrainingState.h |only interpret-0.1.23/interpret/src/core/Training.cpp |only interpret-0.1.25/interpret/DESCRIPTION | 13 interpret-0.1.25/interpret/MD5 | 61 - interpret-0.1.25/interpret/NAMESPACE | 12 interpret-0.1.25/interpret/R/interpret_core.R | 238 +--- interpret-0.1.25/interpret/R/native_booster.R |only interpret-0.1.25/interpret/R/native_interactions.R |only interpret-0.1.25/interpret/man/ebm_classify.Rd |only interpret-0.1.25/interpret/man/ebm_feature.Rd | 4 interpret-0.1.25/interpret/man/ebm_feature_combination.Rd | 4 interpret-0.1.25/interpret/man/ebm_predict_proba.Rd |only interpret-0.1.25/interpret/man/get_interaction_score.Rd | 2 interpret-0.1.25/interpret/man/initialize_interaction_classification.Rd | 10 interpret-0.1.25/interpret/man/initialize_interaction_regression.Rd | 4 interpret-0.1.25/interpret/src/Makevars | 2 interpret-0.1.25/interpret/src/core/Boosting.cpp |only interpret-0.1.25/interpret/src/core/CachedThreadResources.h | 14 interpret-0.1.25/interpret/src/core/DataSetByFeature.cpp | 7 interpret-0.1.25/interpret/src/core/DimensionMultiple.h | 114 +- interpret-0.1.25/interpret/src/core/DimensionSingle.h | 73 - interpret-0.1.25/interpret/src/core/EbmBoostingState.h |only interpret-0.1.25/interpret/src/core/EbmInteractionState.h | 2 interpret-0.1.25/interpret/src/core/EbmInternal.h | 70 + interpret-0.1.25/interpret/src/core/EbmStatistics.h | 49 interpret-0.1.25/interpret/src/core/HistogramBucket.h | 2 interpret-0.1.25/interpret/src/core/InitializeResiduals.h | 2 interpret-0.1.25/interpret/src/core/InteractionDetection.cpp | 27 interpret-0.1.25/interpret/src/core/RandomStream.h | 3 interpret-0.1.25/interpret/src/core/SegmentedTensor.h | 4 interpret-0.1.25/interpret/src/core/TreeNode.h | 2 interpret-0.1.25/interpret/src/core/inc/ebmcore.h | 64 - interpret-0.1.25/interpret/src/interpret_R.cpp | 494 +++++----- 38 files changed, 674 insertions(+), 603 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-10 0.9.1
2019-05-21 0.9.0
Title: Multi-Site Auto-Regressive Weather GENerator
Description: S3 and S4 functions are implemented for spatial multi-site
stochastic generation of daily time series of temperature and
precipitation. These tools make use of Vector AutoRegressive models (VARs).
The weather generator model is then saved as an object and is calibrated by
daily instrumental "Gaussianized" time series through the 'vars' package
tools. Once obtained this model, it can it can be used for weather
generations and be adapted to work with several climatic monthly time
series.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between RMAWGEN versions 1.3.6 dated 2019-11-15 and 1.3.7 dated 2019-12-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/extractmonths.R | 2 +- data/trentino.rda |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Agglomerative Partitioning Framework for Dimension Reduction
Description: A fast and flexible framework for agglomerative partitioning. 'partition' uses an approach
called Direct-Measure-Reduce to create new variables that maintain the
user-specified minimum level of information. Each reduced variable is also interpretable:
the original variables map to one and only one variable in the reduced data set. 'partition'
is flexible, as well: how variables are selected to reduce, how information loss is measured,
and the way data is reduced can all be customized.
Author: Joshua Millstein [aut],
Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between partition versions 0.1.0 dated 2019-05-17 and 0.1.1 dated 2019-12-12
DESCRIPTION | 14 +-- MD5 | 87 +++++++++++----------- NEWS.md |only R/mappings.R | 4 - R/metrics.R | 1 R/plot.R | 6 - README.md | 9 ++ build/vignette.rds |binary inst/WORDLIST | 7 + inst/doc/extending-partition.R | 26 +++--- inst/doc/extending-partition.html | 38 +++++---- inst/doc/introduction-to-partition.R | 28 +++---- inst/doc/introduction-to-partition.html | 98 +++++++++++++------------ man/as_director.Rd | 5 - man/as_measure.Rd | 22 +++-- man/as_partition_step.Rd | 16 +++- man/as_partitioner.Rd | 11 +- man/as_reducer.Rd | 14 ++- man/assign_partition.Rd | 2 man/direct_distance.Rd | 5 - man/direct_k_cluster.Rd | 15 ++- man/hits.Rd | 1 man/kmeans_helpers.Rd | 3 man/map_partition.Rd | 8 +- man/mapping_helpers.Rd | 11 ++ man/measure_icc.Rd | 11 +- man/measure_min_icc.Rd | 10 +- man/measure_min_r2.Rd | 10 +- man/measure_std_mutualinfo.Rd | 10 +- man/measure_variance_explained.Rd | 10 +- man/part_icc.Rd | 11 +- man/part_kmeans.Rd | 20 +++-- man/part_minr2.Rd | 11 +- man/part_pc1.Rd | 11 +- man/part_stdmi.Rd | 11 +- man/partition.Rd | 17 +++- man/plot_partitions.Rd | 41 +++++++--- man/plot_permutation.Rd | 12 ++- man/reduce_first_component.Rd | 7 + man/reduce_kmeans.Rd | 10 +- man/reduce_scaled_mean.Rd | 7 + man/replace_partitioner.Rd | 14 ++- man/simulate_block_data.Rd | 11 ++ man/test_permutation.Rd | 9 +- tests/testthat/test-mappings-and-scores-work.R | 2 45 files changed, 402 insertions(+), 274 deletions(-)
Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for
elasticnet regression, a method for cross-validating the alpha parameter,
and other quality-of-life tools.
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between glmnetUtils versions 1.1.3 dated 2019-11-18 and 1.1.4 dated 2019-12-12
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 4 ++ R/glmnetFormula.r | 2 - inst/doc/intro.html | 101 ++++------------------------------------------------ 5 files changed, 20 insertions(+), 101 deletions(-)
Title: Emoji and Font Awesome in Graphics
Description: An implementation of using emoji and fontawesome for using in both
base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
Claus Thorn Ekstrøm [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between emojifont versions 0.5.2 dated 2018-06-20 and 0.5.3 dated 2019-12-12
DESCRIPTION | 8 - MD5 | 18 +-- NEWS.md | 4 build/vignette.rds |binary inst/doc/emojifont.R | 18 +-- inst/doc/emojifont.Rmd | 12 -- inst/doc/emojifont.html | 287 +++++++++++++++++++++++++++++------------------- man/geom_emoji.Rd | 11 + man/geom_fontawesome.Rd | 10 + vignettes/emojifont.Rmd | 12 -- 10 files changed, 232 insertions(+), 148 deletions(-)
Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine.
Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate
models (counterfactual patient-level quantities, for example the individual treatment effect),
(3) subgroup identification models (find subsets of patients with similar treatment effects),
and (4) parameter estimation and inference (for the overall population and discovered subgroups).
These tools can directly feed into stratified medicine algorithms including PRISM
(patient response identifiers for stratified medicine; Jemielita and Mehrotra (2019)
<arXiv:1912.03337>. PRISM is a flexible and general framework which accepts
user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>
Diff between StratifiedMedicine versions 0.2.0 dated 2019-10-13 and 0.2.1 dated 2019-12-12
StratifiedMedicine-0.2.0/StratifiedMedicine/R/model_template.R |only StratifiedMedicine-0.2.0/StratifiedMedicine/man/model_template.Rd |only StratifiedMedicine-0.2.1/StratifiedMedicine/DESCRIPTION | 16 StratifiedMedicine-0.2.1/StratifiedMedicine/MD5 | 104 +-- StratifiedMedicine-0.2.1/StratifiedMedicine/NAMESPACE | 4 StratifiedMedicine-0.2.1/StratifiedMedicine/R/PRISM.R | 48 + StratifiedMedicine-0.2.1/StratifiedMedicine/R/PRISM_resamp.R | 1 StratifiedMedicine-0.2.1/StratifiedMedicine/R/generate_subgrp_data.R | 60 +- StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_dr.R | 32 - StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_ple.R | 5 StratifiedMedicine-0.2.1/StratifiedMedicine/R/param_rmst.R | 2 StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_bart.R | 181 ++++-- StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_ranger.R | 88 ++- StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_rfsrc.R |only StratifiedMedicine-0.2.1/StratifiedMedicine/R/ple_train.R | 3 StratifiedMedicine-0.2.1/StratifiedMedicine/R/plot.R | 154 ++++- StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_ctree.R | 11 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_glmtree.R |only StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_lmtree.R | 15 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_otr.R | 7 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_train.R | 3 StratifiedMedicine-0.2.1/StratifiedMedicine/R/submod_weibull.R | 15 StratifiedMedicine-0.2.1/StratifiedMedicine/R/utils.R | 103 +-- StratifiedMedicine-0.2.1/StratifiedMedicine/README.md | 80 +- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.R | 59 +- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.Rmd | 117 ++-- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_PRISM.html | 280 +++++----- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.R | 108 ++- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.Rmd | 110 ++- StratifiedMedicine-0.2.1/StratifiedMedicine/inst/doc/SM_User_Models.html | 150 +++-- StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM.Rd | 34 - StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM_resamp.Rd | 11 StratifiedMedicine-0.2.1/StratifiedMedicine/man/PRISM_train.Rd | 7 StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-1.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-2.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-3.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-4.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-5.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/figures/README-example-6.png |binary StratifiedMedicine-0.2.1/StratifiedMedicine/man/param_dr.Rd | 12 StratifiedMedicine-0.2.1/StratifiedMedicine/man/param_ple.Rd | 5 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_bart.Rd | 16 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_ranger.Rd | 13 StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_rfsrc.Rd |only StratifiedMedicine-0.2.1/StratifiedMedicine/man/ple_train.Rd | 3 StratifiedMedicine-0.2.1/StratifiedMedicine/man/plot.PRISM.Rd | 7 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_ctree.Rd | 11 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_glmtree.Rd |only StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_lmtree.Rd | 13 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_otr.Rd | 7 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_train.Rd | 3 StratifiedMedicine-0.2.1/StratifiedMedicine/man/submod_weibull.Rd | 12 StratifiedMedicine-0.2.1/StratifiedMedicine/tests/testthat/test-param_preds_plots.R | 2 StratifiedMedicine-0.2.1/StratifiedMedicine/tests/testthat/test-ple_preds_plots.R | 4 StratifiedMedicine-0.2.1/StratifiedMedicine/vignettes/SM_PRISM.Rmd | 117 ++-- StratifiedMedicine-0.2.1/StratifiedMedicine/vignettes/SM_User_Models.Rmd | 110 ++- 56 files changed, 1403 insertions(+), 740 deletions(-)
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Title: Phylogenetic Comparative Tools for Missing Data and
Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between Rphylopars versions 0.2.11 dated 2019-10-21 and 0.2.12 dated 2019-12-12
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/phylopars_main.R | 64 ++++++++++++++++++++++++++++------------------ R/phylopars_update.R | 52 ++++++++++++++++++------------------- man/Rphylopars-package.Rd | 4 +- 5 files changed, 75 insertions(+), 61 deletions(-)
Title: Back-Calculation of Fish Length
Description: Helps fisheries scientists collect measurements from calcified
structures and back-calculate estimated lengths at previous ages using
standard procedures and models. This is intended to replace much of the
functionality provided by the now out-dated 'fishBC' software
(<https://fisheries.org/bookstore/all-titles/software/70317/>).
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between RFishBC versions 0.2.2 dated 2019-05-02 and 0.2.3 dated 2019-12-12
DESCRIPTION | 10 - MD5 | 48 ++++---- NAMESPACE | 2 NEWS.md | 4 R/digitizeRadii.R | 2 R/getID.R | 2 man/FSA-internals.Rd | 46 +++---- man/RFBCoptions.Rd | 184 +++++++++++++++---------------- man/RFishBC.Rd | 17 +- man/SMBassWB1.Rd | 56 ++++----- man/SMBassWB2.Rd | 70 +++++------ man/StdIntLit.Rd | 54 ++++----- man/aStandard.Rd | 58 ++++----- man/addNote.Rd | 58 ++++----- man/addRadCap.Rd | 98 ++++++++-------- man/backCalc.Rd | 101 +++++++++-------- man/bcFuns.Rd | 144 ++++++++++++------------ man/combineData.Rd | 72 ++++++------ man/digitizeRadii.Rd | 269 +++++++++++++++++++++++++--------------------- man/findNotes.Rd | 54 ++++----- man/findScalingFactor.Rd | 110 ++++++++++-------- man/gConvert.Rd | 135 +++++++++++------------ man/getID.Rd | 146 ++++++++++++------------ man/listFiles.Rd | 76 ++++++------ man/showDigitizedImage.Rd | 147 +++++++++++++------------ 25 files changed, 1021 insertions(+), 942 deletions(-)
Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region for point-based and for transect-based surveys. Accommodates, without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>
Diff between MBHdesign versions 2.1.5 dated 2019-10-17 and 2.1.6 dated 2019-12-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/FunsForTransect8.R | 6 ++++-- R/MBHdesign4.R | 6 ++++-- inst/doc/MBHdesign.pdf |binary 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 2.0.0 dated 2019-10-28 and 2.0.1 dated 2019-12-12
DESCRIPTION | 10 - MD5 | 47 ++-- NAMESPACE | 16 - NEWS |only R/BHSBVAR-package.R |only R/BHSBVAR.R | 141 ++++++++------ R/RcppExports.R | 4 R/USLMData.R | 4 data/USLMData.rda |binary inst/doc/BHSBVAR.R | 12 - inst/doc/BHSBVAR.Rnw | 35 +-- inst/doc/BHSBVAR.pdf |binary man/BHSBVAR-package.Rd |only man/BH_SBVAR.Rd | 390 +++++++++++++++++++++-------------------- man/Dist_Plots.Rd | 269 ++++++++++++++-------------- man/HD_Plots.Rd | 297 ++++++++++++++++--------------- man/IRF_Plots.Rd | 271 ++++++++++++++-------------- man/USLMData.Rd | 50 ++--- src/BHSBVAR-init.c | 4 src/BHSBVAR.cpp | 143 +++++++-------- src/RcppExports.cpp | 10 - vignettes/BHSBVAR.Rnw | 35 +-- vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 26 files changed, 896 insertions(+), 842 deletions(-)