Title: Event Prediction
Description: Predicts enrollment and events at the design or analysis stage using specified enrollment and time-to-event models through simulations.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between eventPred versions 0.1.4 dated 2023-05-27 and 0.1.5 dated 2023-06-04
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 10 + R/eventPred-package.R | 3 R/getPrediction.R | 16 +- R/predictEnrollment.R | 25 ++-- R/predictEvent.R | 275 +++++++++++++++++++++++++++++++++-------------- R/summarizeObserved.R | 22 ++- man/eventPred-package.Rd | 3 9 files changed, 260 insertions(+), 118 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.5 dated 2023-03-06 and 0.8.6 dated 2023-06-04
DESCRIPTION | 16 - MD5 | 42 +-- NAMESPACE | 9 NEWS | 8 R/asca.R | 2 R/asca_plots.R | 38 +- R/basic.R | 64 ++--- R/multiblock-package.R | 1 R/rosa.R | 9 R/rosaCV.R | 7 R/rosa_results.R | 40 ++- R/sopls.R | 5 R/supervised.R | 76 +++-- R/unsupervised.R | 434 +++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/vignette_B_basic.html | 2 inst/doc/vignette_C_unsupervised.html | 4 inst/doc/vignette_E_supervised.html | 20 - man/asca.Rd | 2 man/asca_plots.Rd | 3 man/jive.Rd | 8 man/rosa_results.Rd | 26 +- 22 files changed, 488 insertions(+), 328 deletions(-)
Title: Confidence Intervals
Description: Calculates classic and/or bootstrap confidence intervals for
many parameters such as the population mean, variance, interquartile
range (IQR), median absolute deviation (MAD), skewness, kurtosis,
Cramer's V, odds ratio, R-squared, quantiles (incl. median),
proportions, different types of correlation measures, difference in
means, quantiles and medians. Many of the classic confidence intervals
are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap
confidence intervals are calculated with the R package 'boot'. Both
one- and two-sided intervals are supported.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between confintr versions 1.0.1 dated 2023-05-12 and 1.0.2 dated 2023-06-04
DESCRIPTION | 6 - MD5 | 38 +++++----- NEWS.md | 133 ++++++++++++++++++++------------------ R/ci_cramersv.R | 2 R/ci_oddsratio.R | 3 R/ci_proportion.R | 2 R/ci_rsquared.R | 8 +- R/standard_errors.R | 8 -- build/vignette.rds |binary inst/doc/confintr.R | 8 +- inst/doc/confintr.Rmd | 12 +-- inst/doc/confintr.html | 36 +++++----- man/ci_cramersv.Rd | 2 man/ci_f_ncp.Rd | 2 man/ci_proportion.Rd | 2 man/ci_rsquared.Rd | 6 - man/oddsratio.Rd | 5 + man/se.Rd | 8 -- tests/testthat/test-ci_rsquared.R | 2 vignettes/confintr.Rmd | 12 +-- 20 files changed, 149 insertions(+), 146 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.3.9 dated 2023-01-26 and 1.4.0 dated 2023-06-04
DESCRIPTION | 12 MD5 | 60 - NEWS.md | 9 R/helpers.R | 8 R/plot_confusion_matrix.R | 87 + R/update_hyperparameters.R | 3 README.md | 508 ++++------ build/cvms.pdf |binary inst/doc/Creating_a_confusion_matrix.R | 1 inst/doc/Creating_a_confusion_matrix.Rmd | 1 inst/doc/Creating_a_confusion_matrix.html | 39 inst/doc/available_metrics.R | 1 inst/doc/available_metrics.Rmd | 1 inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.R | 1 inst/doc/cross_validating_custom_functions.Rmd | 1 inst/doc/cross_validating_custom_functions.html | 193 +-- inst/doc/evaluate_by_id.R | 1 inst/doc/evaluate_by_id.Rmd | 1 inst/doc/evaluate_by_id.html | 82 - inst/doc/picking_the_number_of_folds_for_cross-validation.R | 1 inst/doc/picking_the_number_of_folds_for_cross-validation.Rmd | 1 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 175 +-- man/plot_confusion_matrix.Rd | 54 - tests/testthat/test_cross_validate.R | 19 tests/testthat/test_validate_fn.R | 22 vignettes/Creating_a_confusion_matrix.Rmd | 1 vignettes/available_metrics.Rmd | 1 vignettes/cross_validating_custom_functions.Rmd | 1 vignettes/evaluate_by_id.Rmd | 1 vignettes/picking_the_number_of_folds_for_cross-validation.Rmd | 1 31 files changed, 699 insertions(+), 591 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis
of spectral data including nuclear magnetic resonance (NMR), infrared (IR),
Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy.
Includes functions for plotting and inspecting spectra, peak alignment,
hierarchical cluster analysis (HCA), principal components analysis (PCA) and
model-based clustering. Robust methods appropriate for this type of
high-dimensional data are available. ChemoSpec is designed for structured
experiments, such as metabolomics investigations, where the samples fall into
treatment and control groups. Graphical output is formatted consistently for
publication quality plots. ChemoSpec is intended to be very user friendly and
to help you get usable results quickly. A vignette covering typical operations
is available.
Author: Bryan A. Hanson [aut, cre] ,
Mike Bostock [cph, ctb] ,
Matt Keinsley [ctb] ,
Tejasvi Gupta [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 6.1.4 dated 2022-10-21 and 6.1.8 dated 2023-06-04
ChemoSpec-6.1.4/ChemoSpec/inst/tinytest/test_cleanArgs.R |only ChemoSpec-6.1.4/ChemoSpec/inst/tinytest/test_evalClusters.R |only ChemoSpec-6.1.4/ChemoSpec/inst/tinytest/test_files2SpectraObject_JDX.R |only ChemoSpec-6.1.8/ChemoSpec/DESCRIPTION | 18 ChemoSpec-6.1.8/ChemoSpec/MD5 | 187 +++++----- ChemoSpec-6.1.8/ChemoSpec/NAMESPACE | 28 - ChemoSpec-6.1.8/ChemoSpec/NEWS.md | 12 ChemoSpec-6.1.8/ChemoSpec/R/ChemoSpec-package.R | 20 - ChemoSpec-6.1.8/ChemoSpec/R/DollarNames.R | 1 ChemoSpec-6.1.8/ChemoSpec/R/MUD.R | 2 ChemoSpec-6.1.8/ChemoSpec/R/Spectra.R | 29 - ChemoSpec-6.1.8/ChemoSpec/R/aovPCAloadings.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/aovPCAscores.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/aov_pcaSpectra.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/averageReplicates.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/avgFacLvls.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/baselineSpectra.R | 12 ChemoSpec-6.1.8/ChemoSpec/R/binData.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/binSpectra.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/c_pcaSpectra.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/cleanArgs.R | 56 ++ ChemoSpec-6.1.8/ChemoSpec/R/clupaSpectra.R | 40 +- ChemoSpec-6.1.8/ChemoSpec/R/coordProjCS.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/cv_pcaSpectra.R | 10 ChemoSpec-6.1.8/ChemoSpec/R/documentation_functions.R |only ChemoSpec-6.1.8/ChemoSpec/R/evalClusters.R | 72 --- ChemoSpec-6.1.8/ChemoSpec/R/files2SpectraObject.R | 2 ChemoSpec-6.1.8/ChemoSpec/R/hcaSpectra.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/hmapSpectra.R | 40 +- ChemoSpec-6.1.8/ChemoSpec/R/hypTestScores.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/irlba_pcaSpectra.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/isWholeNo.R | 3 ChemoSpec-6.1.8/ChemoSpec/R/labelExtremes3d.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/makeEllipsoid.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/mclust3dSpectra.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/mclustSpectra.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/normSpectra.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/normVec.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/pcaDiag.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/plot2Loadings.R | 10 ChemoSpec-6.1.8/ChemoSpec/R/plot3dScores.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/plotLoadings.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/plotSpectra.R | 10 ChemoSpec-6.1.8/ChemoSpec/R/plotSpectraDist.R | 27 - ChemoSpec-6.1.8/ChemoSpec/R/plotSpectraJS.R | 4 ChemoSpec-6.1.8/ChemoSpec/R/plotly3d.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/q2rPCA.R | 5 ChemoSpec-6.1.8/ChemoSpec/R/r_pcaSpectra.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/reviewAllSpectra.R | 8 ChemoSpec-6.1.8/ChemoSpec/R/sPlotSpectra.R | 10 ChemoSpec-6.1.8/ChemoSpec/R/s_pcaSpectra.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/seXy.R | 14 ChemoSpec-6.1.8/ChemoSpec/R/sgfSpectra.R | 41 +- ChemoSpec-6.1.8/ChemoSpec/R/splitSpectraGroups.R | 6 ChemoSpec-6.1.8/ChemoSpec/R/surveySpectra.R | 8 ChemoSpec-6.1.8/ChemoSpec/build/vignette.rds |binary ChemoSpec-6.1.8/ChemoSpec/inst/doc/ChemoSpec.Rmd | 6 ChemoSpec-6.1.8/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-6.1.8/ChemoSpec/inst/tinytest/test-cleanArgs.R |only ChemoSpec-6.1.8/ChemoSpec/inst/tinytest/test-evalClusters.R |only ChemoSpec-6.1.8/ChemoSpec/inst/tinytest/test-files2SpectraObject_JDX.R |only ChemoSpec-6.1.8/ChemoSpec/man/ChemoSpec-package.Rd | 3 ChemoSpec-6.1.8/ChemoSpec/man/Spectra.Rd | 30 - ChemoSpec-6.1.8/ChemoSpec/man/aovPCAloadings.Rd | 11 ChemoSpec-6.1.8/ChemoSpec/man/aovPCAscores.Rd | 22 - ChemoSpec-6.1.8/ChemoSpec/man/aov_pcaSpectra.Rd | 2 ChemoSpec-6.1.8/ChemoSpec/man/averageReplicates.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/baselineSpectra.Rd | 12 ChemoSpec-6.1.8/ChemoSpec/man/binSpectra.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/c_pcaSpectra.Rd | 6 ChemoSpec-6.1.8/ChemoSpec/man/clupaSpectra.Rd | 40 +- ChemoSpec-6.1.8/ChemoSpec/man/cv_pcaSpectra.Rd | 10 ChemoSpec-6.1.8/ChemoSpec/man/evalClusters.Rd | 65 --- ChemoSpec-6.1.8/ChemoSpec/man/files2SpectraObject.Rd | 32 - ChemoSpec-6.1.8/ChemoSpec/man/hcaSpectra.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/hmapSpectra.Rd | 40 +- ChemoSpec-6.1.8/ChemoSpec/man/hypTestScores.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/irlba_pcaSpectra.Rd | 6 ChemoSpec-6.1.8/ChemoSpec/man/mclust3dSpectra.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/mclustSpectra.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/metMUD1.Rd | 2 ChemoSpec-6.1.8/ChemoSpec/man/normSpectra.Rd | 56 +- ChemoSpec-6.1.8/ChemoSpec/man/pcaDiag.Rd | 13 ChemoSpec-6.1.8/ChemoSpec/man/plot2Loadings.Rd | 20 - ChemoSpec-6.1.8/ChemoSpec/man/plot3dScores.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/plotLoadings.Rd | 11 ChemoSpec-6.1.8/ChemoSpec/man/plotSpectra.Rd | 20 - ChemoSpec-6.1.8/ChemoSpec/man/plotSpectraDist.Rd | 32 - ChemoSpec-6.1.8/ChemoSpec/man/plotSpectraJS.Rd | 4 ChemoSpec-6.1.8/ChemoSpec/man/r_pcaSpectra.Rd | 6 ChemoSpec-6.1.8/ChemoSpec/man/reviewAllSpectra.Rd | 23 - ChemoSpec-6.1.8/ChemoSpec/man/sPlotSpectra.Rd | 22 - ChemoSpec-6.1.8/ChemoSpec/man/s_pcaSpectra.Rd | 6 ChemoSpec-6.1.8/ChemoSpec/man/sgfSpectra.Rd | 37 + ChemoSpec-6.1.8/ChemoSpec/man/splitSpectraGroups.Rd | 6 ChemoSpec-6.1.8/ChemoSpec/man/surveySpectra.Rd | 11 ChemoSpec-6.1.8/ChemoSpec/tests/tinytest.R | 5 ChemoSpec-6.1.8/ChemoSpec/vignettes/ChemoSpec.Rmd | 6 98 files changed, 643 insertions(+), 756 deletions(-)
Title: Spatial and Environmental Blocking for K-Fold and LOO
Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre] ,
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 3.1-2 dated 2023-05-20 and 3.1-3 dated 2023-06-04
DESCRIPTION | 12 ++++----- MD5 | 10 +++---- R/checks.R | 6 ++-- build/vignette.rds |binary inst/doc/tutorial_1.html | 60 +++++++++++++++++++++++------------------------ inst/doc/tutorial_2.html | 8 +++--- 6 files changed, 48 insertions(+), 48 deletions(-)
Title: Clustering of Functional Data via Mixtures of t-Distributions
Description: Extension of 'funHDDC' Schmutz et al. (2018)
<doi:10.1007/s00180-020-00958-4> for cases including
outliers by fitting t-distributions for robust groups. 'TFunHDDC' can cluster
univariate or multivariate data produced by the 'fda' package for data using
a b-splines or Fourier basis.
Author: Cristina Anton [aut, cre],
Iain Smith [aut],
Malcolm Nielsen [aut],
Jeffrey Andrews [ctb],
Jaymeson Wickins [ctb],
Nicholas Boers [ctb],
Paul McNicholas [ctb],
Amandine Schmutz [ctb],
Julien Jacques [ctb],
Charles Bouveyron [ctb]
Maintainer: Cristina Anton <popescuc@macewan.ca>
Diff between TFunHDDC versions 1.0.0 dated 2023-05-24 and 1.0.1 dated 2023-06-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/predict.tfunHDDC.Rd | 18 +++++++++++------- man/tfunHDDC.Rd | 12 ++++++------ tests/examples.R | 14 ++++++++------ 5 files changed, 33 insertions(+), 27 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.7.0 dated 2022-08-29 and 2.8.0 dated 2023-06-04
DESCRIPTION | 18 MD5 | 114 - NAMESPACE | 11 R/PGLS_fossil.R | 158 +- R/RRphylo.R | 67 R/angle.matrix.R | 6 R/colorbar.R |only R/cutPhylo.R | 2 R/getSis.R | 4 R/move.lineage.R |only R/namesCompare.R | 22 R/overfitRR.R | 25 R/plotRR.R |only R/plotRates.R | 4 R/plotShift.R | 74 - R/plotTrend.R | 2 R/random.evolvability.test.R | 2 R/rate.map.R | 3 R/rescaleRR.R | 2 R/scaleTree.R | 17 R/search.conv.R | 8 R/search.shift.R | 7 R/search.trend.R | 18 R/tree.merger.R | 259 ++- R/treeCompare.R | 5 build/vignette.rds |binary inst/CITATION | 196 +- inst/doc/Plotting-tools.Rmd | 56 inst/doc/Plotting-tools.html | 533 +++---- inst/doc/RRphylo.Rmd | 7 inst/doc/RRphylo.html | 134 - inst/doc/Tree-Manipulation.Rmd | 409 +++-- inst/doc/Tree-Manipulation.html | 2937 ++++++++++++++++++++++++++++++++++++---- inst/doc/overfitRR.html | 111 - inst/doc/search.conv.html | 1019 +++++++------ inst/doc/search.shift.Rmd | 7 inst/doc/search.shift.html | 111 - inst/doc/search.trend.html | 111 - inst/doc/swapONE.html | 111 - man/PGLS_fossil.Rd | 102 + man/RRphylo.Rd | 32 man/angle.matrix.Rd | 2 man/colorbar.Rd |only man/move.lineage.Rd |only man/namesCompare.Rd | 8 man/overfitRR.Rd | 16 man/plotRR.Rd |only man/plotRates.Rd | 2 man/plotShift.Rd | 28 man/plotTrend.Rd | 2 man/rate.map.Rd | 3 man/rescaleRR.Rd | 2 man/search.conv.Rd | 2 man/search.shift.Rd | 4 man/search.trend.Rd | 10 man/tree.merger.Rd | 41 vignettes/Plotting-tools.Rmd | 56 vignettes/RRphylo.Rmd | 7 vignettes/Tree-Manipulation.Rmd | 409 +++-- vignettes/plotting-data.Rda |binary vignettes/search.shift.Rmd | 7 61 files changed, 5290 insertions(+), 2013 deletions(-)
Title: Linear and Nonlinear Longitudinal Process in Structural Equation
Modeling Framework
Description: Provides computational tools for nonlinear longitudinal models, in particular the intrinsically nonlinear models, in four scenarios: (1) univariate longitudinal processes with growth factors, with or without covariates including time-invariant covariates (TICs) and time-varying covariates (TVCs); (2) multivariate longitudinal processes that facilitate the assessment of correlation or causation between multiple longitudinal variables; (3) multiple-group models for scenarios (1) and (2) to evaluate differences among manifested groups, and (4) longitudinal mixture models for scenarios (1) and (2), with an assumption that trajectories are from multiple latent classes. The methods implemented are introduced in Jin Liu (2023) <arXiv:2302.03237v2>.
Author: Jin Liu [aut, cre]
Maintainer: Jin Liu <Veronica.Liu0206@gmail.com>
Diff between nlpsem versions 0.1.0 dated 2023-05-29 and 0.1.1 dated 2023-06-04
DESCRIPTION | 10 + MD5 | 231 ++++++++++++++++++++++------------------ R/FitFig.helper.R | 2 R/LCSM.mxModel_helper.R | 2 R/LCSM.output_helper.R | 2 R/LGCM.mxModel_helper.R | 2 R/LGCM.output_helper.R | 2 R/MED.Initial_helper.R | 2 R/MED.loading_helper.R | 2 R/MED.mxModel_helper.R | 2 R/MED.output_helper.R | 2 R/MGM.mxModel_helper.R | 2 R/MGM.output_helper.R | 2 R/MGroup.SUBMODEL.LCSM_helper.R | 2 R/MGroup.SUBMODEL.LGCM_helper.R | 2 R/MGroup.SUBMODEL.MED_helper.R | 2 R/MGroup.SUBMODEL.MGM_helper.R | 2 R/MGroup.SUBMODEL.TVC_helper.R | 2 R/MGroup.initial_helper.R | 3 R/MGroup.mxModel_helper.R | 2 R/MGroup.output_helper.R | 2 R/MIX.SUBMODEL.LCSM_helper.R | 2 R/MIX.SUBMODEL.LGCM_helper.R | 2 R/MIX.SUBMODEL.MED_helper.R | 2 R/MIX.SUBMODEL.MGM_helper.R | 2 R/MIX.SUBMODEL.TVC_helper.R | 2 R/MIX.initial_helper.R | 2 R/MIX.mxModel_helper.R | 2 R/MIX.output_helper.R | 2 R/MIX_MED.loading_helper.R | 2 R/MIX_MULTI.addpara_helper.R | 2 R/MIX_MULTI.loading_helper.R | 2 R/MIX_TVC.info_helper.R | 2 R/MIX_UNI.addpara_helper.R | 2 R/MIX_UNI.loading_helper.R | 2 R/MULTI.addpara_helper.R | 2 R/MULTI.initial_helper.R | 2 R/MULTI.loading_helper.R | 2 R/TVC.info_helper.R | 2 R/TVC.initial_helper.R | 2 R/TVC.mxModel_helper.R | 2 R/TVC.output_helper.R | 2 R/UNI.GF_helper.R | 2 R/UNI.addpara_helper.R | 4 R/UNI.initial_helper.R | 2 R/UNI.loading_helper.R | 2 R/getFigure.R | 6 - R/getMGM.R | 10 - R/getMGroup.R | 10 - R/getMIX.R | 10 - R/getMediation.R | 3 R/getTVCmodel.R | 25 ++-- build/vignette.rds |only inst |only man/getFigure.Rd | 6 - man/getFitFig.Rd | 1 man/getLCSM.mxModel.Rd | 1 man/getLCSM.output.Rd | 1 man/getLGCM.mxModel.Rd | 1 man/getLGCM.output.Rd | 1 man/getMED.initial.Rd | 1 man/getMED.loadings.Rd | 1 man/getMED.mxModel.Rd | 1 man/getMED.output.Rd | 1 man/getMGM.Rd | 10 - man/getMGM.mxModel.Rd | 1 man/getMGM.output.Rd | 1 man/getMGroup.Rd | 6 - man/getMGroup.initial.Rd | 1 man/getMGroup.mxModel.Rd | 1 man/getMGroup.output.Rd | 1 man/getMIX.Rd | 6 - man/getMIX.initial.Rd | 1 man/getMIX.mxModel.Rd | 1 man/getMIX.output.Rd | 1 man/getMIX_MED.loadings.Rd | 1 man/getMIX_MULTI.addpara.Rd | 1 man/getMIX_MULTI.loadings.Rd | 1 man/getMIX_TVC.info.Rd | 1 man/getMIX_UNI.addpara.Rd | 1 man/getMIX_UNI.loadings.Rd | 1 man/getMULTI.addpara.Rd | 1 man/getMULTI.initial.Rd | 1 man/getMULTI.loadings.Rd | 1 man/getTVC.info.Rd | 1 man/getTVC.initial.Rd | 1 man/getTVC.mxModel.Rd | 1 man/getTVC.output.Rd | 1 man/getTVCmodel.Rd | 25 ++-- man/getUNI.GF.Rd | 1 man/getUNI.addpara.Rd | 1 man/getUNI.initial.Rd | 1 man/getUNI.loadings.Rd | 1 man/getsub.LCSM_l.Rd | 1 man/getsub.LCSM_m.Rd | 1 man/getsub.LGCM_l.Rd | 1 man/getsub.LGCM_m.Rd | 1 man/getsub.MED_l.Rd | 1 man/getsub.MED_m.Rd | 1 man/getsub.MGM_l.Rd | 1 man/getsub.MGM_m.Rd | 1 man/getsub.TVC_l.Rd | 1 man/getsub.TVC_m.Rd | 1 vignettes |only 104 files changed, 330 insertions(+), 163 deletions(-)
Title: Accelerated Functional Failure Time Model with
Error-Contaminated Survival Times
Description: We aim to deal with data with measurement error in the response and misclassification censoring status under an AFT model. This package primarily contains three functions, which are used to generate artificial data, correction for error-prone data and estimate the functional covariates for an AFT model.
Author: Hsiao-Ting Huang <nikkihuang309700034@gmail.com> [cre,aut]
Li-Pang Chen <lchen723@nccu.edu.tw> [aut]
Maintainer: Hsiao-Ting Huang <nikkihuang309700034@gmail.com>
Diff between AFFECT versions 0.1.0 dated 2023-06-01 and 0.1.1 dated 2023-06-04
AFFECT-0.1.0/AFFECT/man/AFFECCT.Rd |only AFFECT-0.1.1/AFFECT/DESCRIPTION | 11 +++------- AFFECT-0.1.1/AFFECT/MD5 | 20 +++++++++---------- AFFECT-0.1.1/AFFECT/NAMESPACE | 2 - AFFECT-0.1.1/AFFECT/R/AFTER.R | 2 - AFFECT-0.1.1/AFFECT/R/boosting.R | 4 +-- AFFECT-0.1.1/AFFECT/R/data_generation.R | 2 - AFFECT-0.1.1/AFFECT/R/measurement_error_correction.R | 1 AFFECT-0.1.1/AFFECT/man/AFFECT.Rd |only AFFECT-0.1.1/AFFECT/man/Boosting.Rd | 2 - AFFECT-0.1.1/AFFECT/man/ME_correction.Rd | 1 AFFECT-0.1.1/AFFECT/man/data_gen.Rd | 1 12 files changed, 21 insertions(+), 25 deletions(-)
Title: A Service for Tidy Transcriptomics Software Suite
Description: It provides generic methods that are used by more than one package, avoiding conflicts. This package will be imported by 'tidySingleCellExperiment' and 'tidyseurat'.
Author: Stefano Mangiola [aut, cre]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between ttservice versions 0.2.2 dated 2022-06-24 and 0.3.5 dated 2023-06-04
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NAMESPACE | 1 + R/methods.R | 33 ++++++++++++++++++++++++++++++--- man/aggregate_cells.Rd |only man/join_features.Rd | 4 ++-- 6 files changed, 43 insertions(+), 14 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.2-0 dated 2023-06-02 and 1.2-1 dated 2023-06-04
mvtnorm-1.2-0/mvtnorm/inst/NEWS |only mvtnorm-1.2-1/mvtnorm/DESCRIPTION | 6 +- mvtnorm-1.2-1/mvtnorm/MD5 | 24 +++++------ mvtnorm-1.2-1/mvtnorm/build/partial.rdb |binary mvtnorm-1.2-1/mvtnorm/inst/NEWS.Rd |only mvtnorm-1.2-1/mvtnorm/inst/doc/MVT_Rnews.pdf |binary mvtnorm-1.2-1/mvtnorm/inst/doc/lmvnorm_src.R | 10 ++-- mvtnorm-1.2-1/mvtnorm/inst/doc/lmvnorm_src.Rnw | 38 +++++++++--------- mvtnorm-1.2-1/mvtnorm/inst/doc/lmvnorm_src.pdf |binary mvtnorm-1.2-1/mvtnorm/inst/include/mvtnorm.h | 5 -- mvtnorm-1.2-1/mvtnorm/src/lpmvnorm.c | 12 ++--- mvtnorm-1.2-1/mvtnorm/src/mvtnorm.h | 5 -- mvtnorm-1.2-1/mvtnorm/vignettes/lmvnorm_src.Rnw | 38 +++++++++--------- mvtnorm-1.2-1/mvtnorm/vignettes/lmvnorm_src.Rout.save | 14 +++--- 14 files changed, 78 insertions(+), 74 deletions(-)