Title: Truncated Harmonic Mean Estimator of the Marginal Likelihood
Description: Implements the truncated harmonic mean estimator (THAMES)
of the reciprocal marginal likelihood using posterior samples and
unnormalized log posterior values via reciprocal importance sampling.
Metodiev, Perrot-Dockès, Ouadah, Irons, & Raftery (2023) <arXiv:2305.08952>.
Author: Nicholas J. Irons [aut, cre] ,
Marie Perrot-Dockes [aut],
Martin Metodiev [aut]
Maintainer: Nicholas J. Irons <nicholasjonirons@gmail.com>
Diff between thames versions 0.1.0 dated 2023-10-18 and 0.1.1 dated 2023-10-27
DESCRIPTION | 17 +++++++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +-- R/bound_par_cor.R | 11 +++++++++-- R/thames.R | 1 + 5 files changed, 26 insertions(+), 14 deletions(-)
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection of gene trees,
primarily to make inferences about the species tree or network under the multi-species
coalescent model. These include quartet hypothesis tests for the model, as developed by
Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors
as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference
methods based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and
Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, and the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>. Software announcement by Rhodes et al. (2020)
<doi:10.1093/bioinformatics/btaa868>.
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
John Rhodes [aut, cre]
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 1.3.1 dated 2023-06-12 and 1.3.2 dated 2023-10-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/TreeQuartetHypTest.R | 2 +- build/partial.rdb |binary 4 files changed, 7 insertions(+), 7 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the new density and EM version
(Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>), censored observations,
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.3.0 dated 2023-01-05 and 2.4.0 dated 2023-10-27
DESCRIPTION | 9 MD5 | 38 - NAMESPACE | 1 R/data-preparation.R | 22 R/main.R | 359 +++++++--- R/zcurve-package.R | 1 R/zcurve_EM.R | 2 R/zcurve_density.R | 4 build/partial.rdb |binary man/control_EM.Rd | 2 man/control_density.Rd | 2 man/control_density_v1.Rd | 2 man/plot.zcurve.Rd | 7 man/zcurve.Rd | 2 man/zcurve_data.Rd | 12 man/zcurve_options.Rd | 54 - tests/testthat/_snaps/zcurve/z-curve-cens-em-ggplot.svg |only tests/testthat/_snaps/zcurve/z-curve-clustered-mixed-ggplot-1.svg |only tests/testthat/_snaps/zcurve/z-curve-clustered-mixed-ggplot-2.svg |only tests/testthat/_snaps/zcurve/z-curve-em-ggplot.svg |only tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg |only tests/testthat/_snaps/zcurve/z-curve-mixed-em-ggplot.svg |only tests/testthat/test-zcurve.R | 9 23 files changed, 378 insertions(+), 148 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Remi Theriault [ctb] ,
Martin Jullum [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.10.5 dated 2023-09-12 and 0.10.7 dated 2023-10-27
DESCRIPTION | 29 ++-- MD5 | 161 +++++++++++++------------ NAMESPACE | 6 NEWS.md | 37 +++++ R/binned_residuals.R | 99 +++++++++++++-- R/check_collinearity.R | 4 R/check_convergence.R | 40 ++---- R/check_distribution.R | 51 +++---- R/check_factorstructure.R | 23 ++- R/check_heteroscedasticity.R | 22 ++- R/check_homogeneity.R | 3 R/check_itemscale.R | 19 +- R/check_model.R | 53 +++----- R/check_model_diagnostics.R | 39 +++--- R/check_multimodal.R | 44 +++--- R/check_normality.R | 11 - R/check_outliers.R | 147 ++++++++++++---------- R/check_overdispersion.R | 4 R/check_predictions.R | 35 ++--- R/check_sphericity.R | 17 +- R/check_symmetry.R | 2 R/check_zeroinflation.R | 10 - R/compare_performance.R | 12 - R/icc.R | 44 +++--- R/logLik.R | 2 R/looic.R | 14 +- R/model_performance.bayesian.R | 51 ++++--- R/model_performance.lavaan.R | 111 ++++++++--------- R/model_performance.lm.R | 22 ++- R/model_performance.mixed.R | 8 - R/model_performance.rma.R | 23 ++- R/performance_rmse.R | 15 +- R/performance_score.R | 22 +-- R/r2.R | 89 ++++++------- R/r2_bayes.R | 33 +++-- R/r2_coxsnell.R | 20 +++ R/r2_loo.R | 19 +- R/r2_nagelkerke.R | 20 +++ R/r2_nakagawa.R | 14 -- R/r2_somers.R | 2 R/r2_tjur.R | 31 ++++ R/test_bf.R | 2 R/test_likelihoodratio.R | 2 R/test_performance.R | 2 R/test_vuong.R | 2 R/test_wald.R | 2 inst/WORDLIST | 25 ++- man/binned_residuals.Rd | 39 +++++- man/check_convergence.Rd | 40 ++---- man/check_distribution.Rd | 16 +- man/check_heteroscedasticity.Rd | 6 man/check_homogeneity.Rd | 3 man/check_itemscale.Rd | 13 -- man/check_model.Rd | 21 +-- man/check_multimodal.Rd | 44 +++--- man/check_normality.Rd | 11 - man/check_outliers.Rd | 16 +- man/check_overdispersion.Rd | 4 man/check_predictions.Rd | 30 ++-- man/check_sphericity.Rd | 15 +- man/check_symmetry.Rd | 2 man/check_zeroinflation.Rd | 10 - man/compare_performance.Rd | 12 - man/icc.Rd | 36 ++--- man/looic.Rd | 14 +- man/model_performance.lavaan.Rd | 26 ++-- man/model_performance.merMod.Rd | 8 - man/model_performance.rma.Rd | 23 ++- man/model_performance.stanreg.Rd | 43 +++--- man/performance_rmse.Rd | 15 +- man/performance_score.Rd | 22 +-- man/r2.Rd | 8 - man/r2_bayes.Rd | 29 +++- man/r2_loo.Rd | 19 ++ man/r2_nakagawa.Rd | 10 - man/r2_somers.Rd | 2 tests/testthat/_snaps/check_distribution.md |only tests/testthat/_snaps/nestedLogit.md |only tests/testthat/test-binned_residuals.R |only tests/testthat/test-check_autocorrelation.R |only tests/testthat/test-check_distribution.R |only tests/testthat/test-check_heterogeneity_bias.R |only tests/testthat/test-check_predictions.R |only tests/testthat/test-cronbachs_alpha.R | 8 - tests/testthat/test-logLik.R |only tests/testthat/test-nestedLogit.R |only 86 files changed, 1164 insertions(+), 824 deletions(-)
Title: Penalized Regression Calibration (PRC) for the Dynamic
Prediction of Survival
Description: Computes penalized regression calibration (PRC), a
statistical method for the dynamic prediction of survival when many
longitudinal predictors are available. PRC is described in Signorelli
et al. (2021) <doi:10.1002/sim.9178> and Signorelli (2023)
<doi:10.48550/arXiv.2309.15600>.
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb],
Barbara Vreede [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 2.1.0 dated 2023-09-16 and 2.1.1 dated 2023-10-27
DESCRIPTION | 13 ++- MD5 | 102 +++++++++++++++--------------- R/datasets.R | 4 + R/draw_cluster_bootstrap.R | 110 +++++++++++++++++---------------- R/fit_lmms.R | 4 + R/fit_mlpmms.R | 4 + R/fit_prclmm.R | 4 + R/fit_prcmlpmm.R | 6 + R/getlmm.R | 4 + R/getmlpmm.R | 4 + R/pencox.R | 4 + R/performance_pencox.R | 4 + R/performance_prc.R | 4 + R/prepare_longdata.R | 140 +++++++++++++++++++++--------------------- R/print_prclmm.R | 14 +++- R/print_prcmlpmm.R | 14 +++- R/simulate_prclmm_data.R | 4 + R/simulate_prcmlpmm_data.R | 4 + R/simulate_t_weibull.R | 114 +++++++++++++++++----------------- R/summarize_lmms.R | 4 + R/summarize_mlpmms.R | 4 + R/summary_prclmm.R | 14 +++- R/summary_prcmlpmm.R | 14 +++- R/survpred_prclmm.R | 4 + R/survpred_prcmlpmm.R | 4 + inst/CITATION | 18 +++++ inst/NEWS.md | 9 ++ inst/doc/vignette.pdf |binary man/draw_cluster_bootstrap.Rd | 6 + man/fit_lmms.Rd | 4 + man/fit_mlpmms.Rd | 4 + man/fit_prclmm.Rd | 4 + man/fit_prcmlpmm.Rd | 4 + man/fitted_prclmm.Rd | 4 + man/getlmm.Rd | 4 + man/getmlpmm.Rd | 4 + man/pencox.Rd | 4 + man/performance_pencox.Rd | 4 + man/performance_prc.Rd | 4 + man/prepare_longdata.Rd | 4 + man/print.prclmm.Rd | 13 +++ man/print.prcmlpmm.Rd | 13 +++ man/simulate_prclmm_data.Rd | 4 + man/simulate_prcmlpmm_data.Rd | 4 + man/simulate_t_weibull.Rd | 4 + man/summarize_lmms.Rd | 4 + man/summarize_mlpmms.Rd | 4 + man/summary.prclmm.Rd | 13 +++ man/summary.prcmlpmm.Rd | 13 +++ man/survpred_prclmm.Rd | 4 + man/survpred_prcmlpmm.Rd | 4 + vignettes/pencal_vignette.pdf |binary 52 files changed, 498 insertions(+), 260 deletions(-)
Title: A Framework for Various Types of Mortality / Life Tables
Description: Classes to implement, analyze and plot cohort life tables
for actuarial calculations. Birth-year dependent cohort mortality
tables using a yearly trend to extrapolate from a base year are implemented,
as well as period life table, cohort life tables using an age shift, and
merged life tables. Additionally, several data sets from various countries
are included to provide widely-used tables out of the box.
Author: Reinhold Kainhofer [aut, cre, cph]
Maintainer: Reinhold Kainhofer <reinhold@kainhofer.com>
Diff between MortalityTables versions 2.0.4 dated 2023-10-19 and 2.0.5 dated 2023-10-27
DESCRIPTION | 19 MD5 | 369 NAMESPACE | 172 NEWS.md |only R/DocumentData.R | 28 R/ageShift.R | 92 R/ages.R | 76 R/baseTable.R | 52 R/baseYear.R | 52 R/commutationNumbers.R | 140 R/deathProbabilities.R | 178 R/fillAges.R | 76 R/getCohortTable.R | 58 R/getOmega.R | 64 R/getPeriodTable.R | 72 R/lifeTable.R | 108 R/makeQxDataFrame.R | 210 R/mortalityComparisonTable.R | 120 R/mortalityImprovement.R | 80 R/mortalityTable.MakehamGompertz.R | 130 R/mortalityTable.R | 90 R/mortalityTable.Weibull.R | 96 R/mortalityTable.ageShift.R | 102 R/mortalityTable.deMoivre.R | 84 R/mortalityTable.improvementFactors.R | 258 R/mortalityTable.joined.R | 72 R/mortalityTable.jointLives.R | 488 R/mortalityTable.mixed.R | 86 R/mortalityTable.observed.R | 240 R/mortalityTable.period.R | 198 R/mortalityTable.trendProjection.R | 132 R/mortalityTables.list.R | 104 R/mortalityTables.load.R | 166 R/pensionTable.R | 562 R/periodDeathProbabilities.R | 178 R/plot.mortalityTable.R | 148 R/plotMortalityTableComparisons.R | 204 R/plotMortalityTables.R | 232 R/plotMortalityTrend.R | 276 R/setLoading.R | 44 R/setModification.R | 70 R/undampenTrend.R | 50 R/utilityFunctions.R | 1882 - R/whittaker.mortalityTable.R | 304 README.md | 298 build/vignette.rds |binary inst/doc/international-mortality-tables-overview.R | 514 inst/doc/international-mortality-tables-overview.Rmd | 1438 - inst/doc/international-mortality-tables-overview.html | 2726 +- inst/doc/using-the-mortalityTables-package.R | 584 inst/doc/using-the-mortalityTables-package.Rmd | 1502 - inst/doc/using-the-mortalityTables-package.html | 2850 +- inst/extdata/Austria_Annuities_AVOe1996R.csv | 234 inst/extdata/Austria_Annuities_AVOe2005R.csv | 250 inst/extdata/Austria_Annuities_AVOe2005R_AVBasis.csv | 248 inst/extdata/Austria_Annuities_AVOe2005R_AVShifts.csv | 242 inst/extdata/Austria_Annuities_EROMF.csv | 208 inst/extdata/Austria_Annuities_EROMF_AV.csv | 108 inst/extdata/Austria_Annuities_RR67.csv | 206 inst/extdata/Austria_Census_Female.csv | 234 inst/extdata/Austria_Census_Male.csv | 234 inst/extdata/Austria_Census_Unisex.csv | 234 inst/extdata/Austria_Endowments_ADSt2426_2Lives.csv | 208 inst/extdata/Austria_Population_Forecast.csv | 208 inst/extdata/Austria_Population_MCMC2018.csv | 804 inst/extdata/Austria_Population_Observation_F.csv | 204 inst/extdata/Austria_Population_Observation_M.csv | 204 inst/extdata/Austria_Population_Observation_U.csv | 204 inst/extdata/Austria_Population_YearlyGraduated.csv |only inst/extdata/Germany_Annuities_DAV1994R.csv | 230 inst/extdata/Germany_Annuities_DAV1994R.test.csv | 230 inst/extdata/Germany_Annuities_DAV1994R_AV.csv | 232 inst/extdata/Germany_Annuities_DAV2004R.csv | 252 inst/extdata/Germany_Annuities_DAV2004R_AV.csv | 244 inst/extdata/Germany_Annuities_DAV2004R_AVBase.csv | 250 inst/extdata/Germany_Annuities_DAV2004R_Select.csv | 14 inst/extdata/Germany_Annuities_DAV2004R_Trends.csv | 252 inst/extdata/Germany_Endowments_DAV1994T.csv | 206 inst/extdata/Germany_Endowments_DAV2008T.csv | 254 inst/extdata/MortalityTables_Austria_Annuities.R | 6 inst/extdata/MortalityTables_Austria_Annuities_AVOe1996R.R | 224 inst/extdata/MortalityTables_Austria_Annuities_AVOe2005R.R | 342 inst/extdata/MortalityTables_Austria_Annuities_EROMF.R | 168 inst/extdata/MortalityTables_Austria_Annuities_RR67.R | 38 inst/extdata/MortalityTables_Austria_Census.R | 304 inst/extdata/MortalityTables_Austria_Endowments_ADSt2426_2Lives.R | 50 inst/extdata/MortalityTables_Austria_PopulationForecast.R | 100 inst/extdata/MortalityTables_Austria_PopulationMCMC.R | 174 inst/extdata/MortalityTables_Austria_PopulationObserved.R | 125 inst/extdata/MortalityTables_Austria_VUGesamtbestand_2012-16.R | 402 inst/extdata/MortalityTables_Germany_Annuities.R | 6 inst/extdata/MortalityTables_Germany_Annuities_DAV1994R.R | 150 inst/extdata/MortalityTables_Germany_Annuities_DAV2004R.R | 320 inst/extdata/MortalityTables_Germany_Census.R | 230 inst/extdata/MortalityTables_Germany_Endowments.R | 6 inst/extdata/MortalityTables_Germany_Endowments_DAV1994T.R | 118 inst/extdata/MortalityTables_Germany_Endowments_DAV2008T.R | 316 inst/extdata/MortalityTables_USA_Annuities.R | 6 inst/extdata/MortalityTables_USA_Annuities_1971IAM.R | 116 inst/extdata/MortalityTables_USA_Annuities_1983a.R | 114 inst/extdata/MortalityTables_USA_Annuities_1994GAR.R | 112 inst/extdata/MortalityTables_USA_Annuities_2012IAM.R | 110 inst/extdata/MortalityTables_USA_Annuities_Annuity2000.R | 114 inst/extdata/PensionTables_USA_PensionPlan_RP2014.R | 400 inst/extdata/PensionTables_USA_PensionPlans.R | 6 inst/extdata/USA_Annuities_1971IAM.csv | 230 inst/extdata/USA_Annuities_1983a_GAM.csv | 230 inst/extdata/USA_Annuities_1994GAR.csv | 248 inst/extdata/USA_Annuities_2012IAM.csv | 250 inst/extdata/USA_Annuities_Annuity2000.csv | 232 inst/extdata/USA_PensionPlans_MP2014_Female.csv | 206 inst/extdata/USA_PensionPlans_MP2014_Male.csv | 206 inst/extdata/USA_PensionPlans_RP2014.csv | 214 inst/extdata/VU_Gesamtbestand_Austria_Detail_2012-16.csv |13538 +++++----- inst/extdata/VU_Gesamtbestand_Austria_Storno_2012-16.csv | 248 inst/extdata/VU_Gesamtbestand_Austria_qx_2012-16.csv | 728 man/MortalityTables-package.Rd | 44 man/PopulationData.AT2017.Rd | 50 man/ageShift.Rd | 84 man/ages.Rd | 98 man/baseTable.Rd | 78 man/baseYear.Rd | 78 man/calculateImprovements.Rd | 74 man/commutationNumbers.Rd | 98 man/deathProbabilities.Rd | 166 man/deathProbabilitiesIndividual.Rd | 54 man/figures |only man/fillAges.Rd | 50 man/fitExpExtrapolation.Rd | 40 man/generateAgeShift.Rd | 46 man/getCohortTable.Rd | 68 man/getOmega.Rd | 88 man/getPeriodTable.Rd | 70 man/lifeTable.Rd | 100 man/mT.cleanup.Rd | 164 man/mT.extrapolateProbsExp.Rd | 74 man/mT.extrapolateTrendExp.Rd | 54 man/mT.fillAges.Rd | 50 man/mT.fitExtrapolationLaw.Rd | 126 man/mT.round.Rd | 142 man/mT.scaleProbs.Rd | 50 man/mT.setDimInfo.Rd | 68 man/mT.setName.Rd | 42 man/mT.setTrend.Rd | 84 man/mT.switchover.Rd | 90 man/mT.translate.Rd | 118 man/makeQxDataFrame.Rd | 62 man/mortalityComparisonTable.Rd | 78 man/mortalityImprovement.Rd | 76 man/mortalityTable-class.Rd | 62 man/mortalityTable.MakehamGompertz-class.Rd | 76 man/mortalityTable.NA.Rd | 32 man/mortalityTable.Weibull-class.Rd | 64 man/mortalityTable.ageShift-class.Rd | 52 man/mortalityTable.deMoivre-class.Rd | 54 man/mortalityTable.improvementFactors-class.Rd | 76 man/mortalityTable.jointLives-class.Rd | 56 man/mortalityTable.mixed-class.Rd | 74 man/mortalityTable.observed-class.Rd | 42 man/mortalityTable.once.Rd | 44 man/mortalityTable.onceAndFuture.Rd | 44 man/mortalityTable.period-class.Rd | 88 man/mortalityTable.trendProjection-class.Rd | 118 man/mortalityTable.zeroes.Rd | 32 man/mortalityTables.list.Rd | 66 man/mortalityTables.load.Rd | 74 man/pT.calculateTotalMortality.Rd | 88 man/pT.getSubTable.Rd | 86 man/pT.setDimInfo.Rd | 56 man/pensionTable-class.Rd | 128 man/pensionTables.list.Rd | 58 man/pensionTables.load.Rd | 50 man/periodDeathProbabilities.Rd | 188 man/periodDeathProbabilitiesIndividual.Rd | 54 man/periodTransitionProbabilities.Rd | 122 man/plot.mortalityTable.Rd | 140 man/plotMortalityTableComparisons.Rd | 146 man/plotMortalityTables.Rd | 154 man/plotMortalityTrend.Rd | 148 man/setLoading.Rd | 60 man/setModification.Rd | 86 man/transitionProbabilities.Rd | 136 man/undampenTrend.Rd | 64 man/whittaker.mortalityTable.Rd | 180 vignettes/international-mortality-tables-overview.Rmd | 1438 - vignettes/using-the-mortalityTables-package.Rmd | 1502 - 186 files changed, 26645 insertions(+), 26512 deletions(-)
More information about MortalityTables at CRAN
Permanent link
Title: Bindings to the 'Geospatial Data Abstraction Library' Raster API
Description: Interface to the Raster API of the 'Geospatial Data Abstraction
Library' ('GDAL') supporting manual creation of uninitialized datasets,
creation from existing raster as template, low level I/O, configuration of
virtual raster (VRT), coordinate transformation, and access to 'gdalwarp'
for reprojection. Includes several 'GDAL' algorithms and functions for
working with spatial reference systems. Calling signatures resemble the
native C, C++ and Python APIs provided by the 'GDAL' project
(<https://gdal.org>). Bindings are implemented via exposed C++ class
encapsulating a 'GDALDataset' and its associated 'GDALRasterBand' objects,
plus several stand-alone functions. Additional functionality includes:
class 'RunningStats' for efficient summary statistics on large data
streams; class 'CmbTable' for counting unique combinations of integers
with a hash table; raster 'combine()' to identify and count unique pixel
combinations across multiple input layers; raster 'calc()' to evaluate
an R ex [...truncated...]
Author: Chris Toney [aut, cre] ,
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <chris.toney@usda.gov>
Diff between gdalraster versions 1.5.0 dated 2023-09-25 and 1.6.0 dated 2023-10-27
DESCRIPTION | 12 MD5 | 98 +++-- NAMESPACE | 2 NEWS.md | 49 ++ R/RcppExports.R | 198 ++++++++++- R/display.R | 2 R/gdal_helpers.R |only R/gdal_rat.R |only R/gdalraster.R | 119 +++++- R/gdalraster_proc.R | 197 +++++------ R/running_stats.R | 13 README.md | 103 ++++- build/vignette.rds |binary configure | 26 - configure.ac | 8 inst/doc/raster-api-tutorial.R | 5 inst/doc/raster-api-tutorial.Rmd | 42 +- inst/doc/raster-api-tutorial.html | 106 +++-- inst/doc/raster-attribute-tables.R |only inst/doc/raster-attribute-tables.Rmd |only inst/doc/raster-attribute-tables.html |only man/GDALRaster-class.Rd | 127 +++++-- man/RunningStats-class.Rd | 14 man/buildRAT.Rd |only man/calc.Rd | 94 ++--- man/combine.Rd | 22 - man/copyDatasetFiles.Rd |only man/create.Rd | 6 man/createColorRamp.Rd | 4 man/createCopy.Rd | 4 man/deleteDataset.Rd |only man/displayRAT.Rd |only man/fillNodata.Rd | 12 man/gdal_formats.Rd |only man/gdalraster-package.Rd | 15 man/getCreationOptions.Rd |only man/rasterFromRaster.Rd | 14 man/rasterToVRT.Rd | 54 +-- man/read_ds.Rd | 2 man/renameDataset.Rd |only src/RcppExports.cpp | 76 ++++ src/cmb_table.cpp | 59 +-- src/cmb_table.h | 35 - src/gdal_exp.cpp | 377 +++++++++++++++++++-- src/gdalraster.cpp | 589 ++++++++++++++++++++++++--------- src/gdalraster.h | 83 ++++ src/geos_wkt.h | 1 src/rcpp_util.h | 2 src/running_stats.cpp | 28 - src/running_stats.h | 5 src/wkt_conv.cpp | 1 tests/testthat/test-GDALRaster-class.R | 53 ++ tests/testthat/test-gdal_exp.R | 72 ++++ tests/testthat/test-gdal_helpers.R |only tests/testthat/test-gdal_rat.R |only vignettes/qgis_rat_classify.png |only vignettes/raster-api-tutorial.Rmd | 42 +- vignettes/raster-attribute-tables.Rmd |only 58 files changed, 2094 insertions(+), 677 deletions(-)
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education S [...truncated...]
Author: Paul Bailey [aut, cre] ,
Ahmad Emad [aut],
Huade Huo [aut] ,
Michael Lee [aut] ,
Yuqi Liao [aut] ,
Alex Lishinski [aut] ,
Trang Nguyen [aut] ,
Qingshu Xie [aut],
Jiao Yu [aut],
Ting Zhang [aut] ,
Eric Buehler [aut] ,
Sun-joo Lee [aut],
Blue Webb [aut [...truncated...]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 4.0.1 dated 2023-06-14 and 4.0.4 dated 2023-10-27
EdSurvey-4.0.1/EdSurvey/man/bind-methods.Rd |only EdSurvey-4.0.1/EdSurvey/man/subset.Rd |only EdSurvey-4.0.1/EdSurvey/tests/testthat/es_2pdf.rds |only EdSurvey-4.0.1/EdSurvey/tests/testthat/test-70-NHES.R |only EdSurvey-4.0.1/EdSurvey/tests/testthat/test-90-merge.R |only EdSurvey-4.0.1/EdSurvey/tests/testthat/test-95-parseScript_SPSS.R |only EdSurvey-4.0.4/EdSurvey/DESCRIPTION | 26 EdSurvey-4.0.4/EdSurvey/MD5 | 120 EdSurvey-4.0.4/EdSurvey/NAMESPACE | 5 EdSurvey-4.0.4/EdSurvey/R/achievementLevels.R | 2146 ++-- EdSurvey-4.0.4/EdSurvey/R/cbind.light.edsurvey.data.frame.R | 115 EdSurvey-4.0.4/EdSurvey/R/dim.edsurvey.data.frame.R | 166 EdSurvey-4.0.4/EdSurvey/R/downloadECLS_K.R | 294 EdSurvey-4.0.4/EdSurvey/R/downloadPIRLS.R | 262 EdSurvey-4.0.4/EdSurvey/R/drawPVs.sdf.R | 398 EdSurvey-4.0.4/EdSurvey/R/edsurvey.data.frame.R | 29 EdSurvey-4.0.4/EdSurvey/R/edsurveyTable.R | 1984 ++-- EdSurvey-4.0.4/EdSurvey/R/getData.R | 2 EdSurvey-4.0.4/EdSurvey/R/lm.sdf.R | 3076 +++--- EdSurvey-4.0.4/EdSurvey/R/mergev.R | 867 - EdSurvey-4.0.4/EdSurvey/R/mixed.sdf.R | 1388 +- EdSurvey-4.0.4/EdSurvey/R/mml.paramtabs.R | 1019 +- EdSurvey-4.0.4/EdSurvey/R/mml.scoreNAEP.R | 421 EdSurvey-4.0.4/EdSurvey/R/mml.scoreTIMSS.R | 196 EdSurvey-4.0.4/EdSurvey/R/mml.sdf.R | 1102 +- EdSurvey-4.0.4/EdSurvey/R/rbind.light.edsurvey.data.frame.R | 116 EdSurvey-4.0.4/EdSurvey/R/readHSTS.R | 1316 +- EdSurvey-4.0.4/EdSurvey/R/readICCS.R | 3926 ++++---- EdSurvey-4.0.4/EdSurvey/R/readNAEP.r | 41 EdSurvey-4.0.4/EdSurvey/R/readNAEP_XML.R | 1854 +-- EdSurvey-4.0.4/EdSurvey/R/readPIRLS.R | 2519 ++--- EdSurvey-4.0.4/EdSurvey/R/readTIMSS.R | 4766 +++++----- EdSurvey-4.0.4/EdSurvey/R/readTIMSSAdv.R | 1464 +-- EdSurvey-4.0.4/EdSurvey/R/read_ePIRLS.R | 1436 +-- EdSurvey-4.0.4/EdSurvey/R/rename.sdf.R | 512 - EdSurvey-4.0.4/EdSurvey/R/rq.sdf.R | 1506 +-- EdSurvey-4.0.4/EdSurvey/R/showCodebook.R | 264 EdSurvey-4.0.4/EdSurvey/R/subset.edsurvey.data.frame.list.R | 146 EdSurvey-4.0.4/EdSurvey/R/summary2.R | 775 - EdSurvey-4.0.4/EdSurvey/build/vignette.rds |binary EdSurvey-4.0.4/EdSurvey/inst/NEWS.Rd | 21 EdSurvey-4.0.4/EdSurvey/inst/doc/introduction.html | 4 EdSurvey-4.0.4/EdSurvey/man/cbind.light.edsurvey.data.frame.Rd |only EdSurvey-4.0.4/EdSurvey/man/downloadPIRLS.Rd | 6 EdSurvey-4.0.4/EdSurvey/man/getData.Rd | 2 EdSurvey-4.0.4/EdSurvey/tests/testthat/REF-0-main.R | 19 EdSurvey-4.0.4/EdSurvey/tests/testthat/helper-01-edsurveyHome.R |only EdSurvey-4.0.4/EdSurvey/tests/testthat/lm1.rds |binary EdSurvey-4.0.4/EdSurvey/tests/testthat/lm1re.rds |binary EdSurvey-4.0.4/EdSurvey/tests/testthat/lm1t.rds |binary EdSurvey-4.0.4/EdSurvey/tests/testthat/lm2.rds |binary EdSurvey-4.0.4/EdSurvey/tests/testthat/lm2t.rds |binary EdSurvey-4.0.4/EdSurvey/tests/testthat/test-10-main.R | 8 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-15-lesdf.R | 10 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-17-merge.R |only EdSurvey-4.0.4/EdSurvey/tests/testthat/test-25-mixed.R | 11 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-30-TIMSS.R | 14 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-35-piaac.R | 9 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-40-ELS.R | 11 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-45-HSLS.R | 11 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-50-pisa.R | 7 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-51-YAFS.R | 10 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-60-ECLS_K.R | 11 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-65-SSOCS.R | 9 EdSurvey-4.0.4/EdSurvey/tests/testthat/test-75-iccs.R | 4 EdSurvey-4.0.4/EdSurvey/tests/testthat/tst-80-NHES.R |only 66 files changed, 17190 insertions(+), 17234 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Emma Govan [cre, aut],
Andrew Parnell [aut]
Maintainer: Emma Govan <emma.govan.2021@mumail.ie>
Diff between simmr versions 0.5.1.215 dated 2023-10-13 and 0.5.1.216 dated 2023-10-27
DESCRIPTION | 6 +-- MD5 | 40 ++++++++++---------- R/RcppExports.R | 4 ++ R/combine_sources.R | 11 +++-- R/compare_groups.R | 6 +-- R/compare_sources.R | 4 +- R/plot.simmr_output.R | 2 - R/posterior_predictive.simmr_output.R | 3 - R/print.simmr_output.R | 4 +- R/prior_viz.simmr_output.R | 4 +- R/simmr_ffvb.R | 7 ++- R/simmr_mcmc.R | 4 +- R/summary.simmr_output.R | 4 +- inst/doc/advanced_plotting.html | 12 +++--- inst/doc/quick_start.html | 60 +++++++++++++++--------------- inst/doc/simmr.html | 68 +++++++++++++++++----------------- man/posterior_predictive.Rd | 3 - man/simmr_ffvb.Rd | 2 - src/RcppExports.cpp | 11 +++++ src/run_VB.cpp | 25 ++++++++++++ tests/testthat/test-simmr_ffvb.R | 4 +- 21 files changed, 162 insertions(+), 122 deletions(-)
Title: Armadillo Client for the Armadillo Service
Description: A set of functions to manage data shared on a
'MOLGENIS Armadillo' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
Morris Swertz [aut]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between MolgenisArmadillo versions 2.0.0 dated 2023-02-23 and 2.1.2 dated 2023-10-27
DESCRIPTION | 11 - MD5 | 69 ++++---- NAMESPACE | 19 ++ NEWS.md | 6 R/names.R | 4 R/object.R | 4 R/package.R | 20 +- R/subset.R |only R/table.R | 2 R/utils.R | 11 - README.md | 19 -- inst/doc/MolgenisArmadillo.Rmd | 29 +-- inst/doc/MolgenisArmadillo.html | 191 ++++------------------- inst/doc/create_resources.Rmd | 57 +++--- inst/doc/create_resources.html | 95 ++++------- inst/doc/creating_data_subsets.Rmd | 252 +++++++++--------------------- inst/doc/creating_data_subsets.html | 254 ++++++++++++------------------- inst/doc/install_packages.Rmd | 19 -- inst/doc/install_packages.html | 33 ---- man/armadillo.subset.Rd |only man/armadillo.subset_definition.Rd |only tests/testthat.R | 1 tests/testthat/test-names.R | 16 + tests/testthat/test-object.R | 63 +++---- tests/testthat/test-package.R | 12 - tests/testthat/test-project.R | 5 tests/testthat/test-resource.R | 8 tests/testthat/test-subset.R |only tests/testthat/test-table.R | 8 vignettes/MolgenisArmadillo.Rmd | 29 +-- vignettes/MolgenisArmadillo.Rmd.orig | 2 vignettes/create_resources.Rmd | 57 +++--- vignettes/create_resources.Rmd.orig | 50 +++--- vignettes/creating_data_subsets.Rmd | 252 +++++++++--------------------- vignettes/creating_data_subsets.Rmd.orig | 137 +++++----------- vignettes/data/subset |only vignettes/install_packages.Rmd | 19 -- vignettes/pre-render.R | 22 +- 38 files changed, 655 insertions(+), 1121 deletions(-)
More information about MolgenisArmadillo at CRAN
Permanent link
Title: Aligning Ontology Annotation Across Single Cell Datasets with
'scOntoMatch'
Description: Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.
Author: Yuyao Song [aut, cre, ctb],
Irene Papatheodorou [aut, ths]
Maintainer: Yuyao Song <ysong@ebi.ac.uk>
Diff between scOntoMatch versions 0.1.0 dated 2022-06-27 and 0.1.1 dated 2023-10-27
DESCRIPTION | 17 - MD5 | 8 README.md | 4 build/vignette.rds |binary inst/doc/scOntoMatch_vignette.html | 603 +++++++++++++------------------------ 5 files changed, 230 insertions(+), 402 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] ,
Annabel Allison [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between rpsftm versions 1.2.7 dated 2020-04-24 and 1.2.8 dated 2023-10-27
DESCRIPTION | 15 MD5 | 71 NAMESPACE | 2 NEWS.md | 5 R/cox.zph.R | 54 R/data.R | 2 R/est_eqn.R | 80 - R/extract_z.R | 118 - R/plot.rpsftm.R | 78 - R/rand.R | 70 R/rpsftm.R | 694 ++++----- R/terms.inner.R | 59 R/uniroot_all.R | 84 - R/untreated.R | 96 - README.md | 117 - build/partial.rdb |only build/vignette.rds |binary inst/doc/rpsftm_vignette.Rmd | 592 +++---- inst/doc/rpsftm_vignette.html | 764 ++++++---- man/est_eqn.Rd | 80 - man/extract_z.Rd | 88 - man/immdef.Rd | 8 man/print.rand.Rd | 50 man/print.rpsftm.coxph.Rd | 38 man/print.rpsftm.summary.coxph.Rd | 52 man/print.rpsftm.summary.survreg.Rd | 38 man/print.rpsftm.survreg.Rd | 34 man/rand.Rd | 66 man/rpsftm.Rd | 222 +- man/terms.inner.Rd | 40 man/uniroot_all.Rd | 102 - man/untreated.Rd | 70 tests/testthat/test_errors.R | 526 +++--- vignettes/rpsftm_vignette.Rmd | 592 +++---- vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-7-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-9-1.png |binary 37 files changed, 2590 insertions(+), 2317 deletions(-)
Title: Basic Functions to Investigate Metabolomics Data Matrices
Description: A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between MetabolomicsBasics versions 1.4 dated 2023-01-30 and 1.4.3 dated 2023-10-27
DESCRIPTION | 18 +++++++++--------- MD5 | 25 ++++++++++++++----------- NAMESPACE | 3 +-- R/ClassificationCV.R | 5 +---- R/ClassificationWrapper.R | 5 +---- R/DeconvoluteSpectrum.R | 5 +---- R/FindMaxInt.R | 5 +---- R/Load_mzML.R | 7 +++---- R/ReplaceMissingValues.R | 3 ++- R/msconvert.R | 31 +++++++++++++++---------------- R/unique_subformula_masses.R | 5 ++--- R/verify_suggested.R |only README.md |only man/figures |only man/msconvert.Rd | 2 +- 15 files changed, 51 insertions(+), 63 deletions(-)
More information about MetabolomicsBasics at CRAN
Permanent link
Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 0.99.0 dated 2023-10-11 and 0.99.6 dated 2023-10-27
DESCRIPTION | 8 MD5 | 34 R/inferCSN.R | 10 R/sparse.regression.R | 38 README.md | 13 man/acc.calculate.Rd | 34 man/check.parameters.Rd | 122 man/coef.inferCSN.Rd | 60 man/contrast.networks.Rd | 72 man/figures/inferCSN.svg | 6750 +++++++++++++++++++++++------------------------ man/inferCSN-package.Rd | 30 man/inferCSN.Rd | 212 - man/inferCSN.fit.Rd | 212 - man/is.scalar.Rd | 34 man/network.heatmap.Rd | 136 man/predict.inferCSN.Rd | 74 man/print.inferCSN.Rd | 48 src/include/Params.h | 8 18 files changed, 3958 insertions(+), 3937 deletions(-)
Title: River Hydrograph Separation and Analysis
Description: River hydrograph separation and daily runoff time series analysis. Provides
various filters to separate baseflow and quickflow. Implements advanced separation
technique by Rets et al. (2022) <doi:10.1134/S0097807822010146> which involves
meteorological data to reveal genetic components of the runoff: ground, rain, thaw
and spring (seasonal thaw). High-performance C++17 computation, annually aggregated
variables, statistical testing and numerous plotting functions for high-quality
visualization.
Author: Timofey Samsonov [aut, cre] ,
Ekaterina Retz [ctb] ,
Maria Kireeva [ctb]
Maintainer: Timofey Samsonov <tsamsonov@geogr.msu.ru>
Diff between grwat versions 0.0.2 dated 2022-05-18 and 0.0.4 dated 2023-10-27
DESCRIPTION | 40 - MD5 | 89 +-- NEWS.md | 15 R/locale.R | 5 R/plot.R | 162 +++---- R/process.R | 18 R/report.R | 11 R/separate.R | 71 +-- R/summarize.R | 18 R/test.R | 7 README.md | 70 ++- build/vignette.rds |binary inst/doc/baseflow.R | 2 inst/doc/baseflow.html | 253 +++++------ inst/doc/grwat.R | 6 inst/doc/grwat.html | 297 ++++++------ inst/doc/separation.R | 4 inst/doc/separation.html | 498 ++++++++++----------- inst/doc/summaries.R | 2 inst/doc/summaries.html | 804 +++++++++++++++++------------------ inst/examples/gr_kable_tests.R | 32 - inst/examples/gr_plot_minmonth.R | 4 inst/examples/gr_plot_periods.R | 4 inst/examples/gr_plot_sep.R | 15 inst/examples/gr_plot_tests.R | 6 inst/examples/gr_plot_vars.R | 21 inst/examples/gr_report.R | 34 - inst/examples/gr_set_locale.R | 14 inst/examples/gr_test_vars.R | 6 inst/reports/Report_HTML.Rmd | 27 - man/gr_baseflow.Rd | 4 man/gr_kable_tests.Rd | 36 - man/gr_plot_minmonth.Rd | 8 man/gr_plot_periods.Rd | 8 man/gr_plot_sep.Rd | 19 man/gr_plot_tests.Rd | 8 man/gr_plot_vars.Rd | 23 - man/gr_report.Rd | 32 - man/gr_set_locale.Rd | 14 man/gr_summarize.Rd | 10 man/gr_test_vars.Rd | 10 src/grwat_core.cpp | 31 - tests/testthat/Rplots.pdf |only tests/testthat/test-gr_plot_hori.R | 2 tests/testthat/test-gr_plot_matrix.R | 6 tests/testthat/test-gr_set_locale.R | 18 46 files changed, 1412 insertions(+), 1352 deletions(-)
Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto-grading check-fields and check-boxes for 'rmarkdown'
or 'quarto' HTML. It can be used in class, when teacher share materials
and tasks, so students can solve some problems and check their work. In
contrast to the 'learnr' package, the 'checkdown' package works serverlessly
without 'shiny'.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between checkdown versions 0.0.11 dated 2023-10-21 and 0.0.12 dated 2023-10-27
DESCRIPTION | 6 MD5 | 16 - NEWS | 3 R/check_question.R | 2 R/zzz.R | 11 - inst/doc/start_checkdown.Rmd | 12 + inst/doc/start_checkdown.html | 377 ++++++++++++++++++++++++------------------ man/check_question.Rd | 2 vignettes/start_checkdown.Rmd | 12 + 9 files changed, 266 insertions(+), 175 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via Markov chain Monte Carlo (MCMC) based on parallel
importance sampling type weighted estimators
(Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>),
particle MCMC, and its delayed acceptance version.
Gaussian, Poisson, binomial, negative binomial, and Gamma
observation densities and basic stochastic volatility models
with linear-Gaussian state dynamics, as well as general non-linear Gaussian
models and discretised diffusion models are supported.
See Helske and Vihola (2021, <doi:10.32614/RJ-2021-103>) for details.
Author: Jouni Helske [aut, cre] ,
Matti Vihola [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 2.0.1 dated 2022-05-03 and 2.0.2 dated 2023-10-27
bssm-2.0.1/bssm/NEWS |only bssm-2.0.2/bssm/DESCRIPTION | 14 bssm-2.0.2/bssm/MD5 | 230 - bssm-2.0.2/bssm/NAMESPACE | 3 bssm-2.0.2/bssm/NEWS.md |only bssm-2.0.2/bssm/R/as.data.frame.mcmc_output.R | 198 - bssm-2.0.2/bssm/R/as_bssm.R | 308 - bssm-2.0.2/bssm/R/as_draws.R | 220 - bssm-2.0.2/bssm/R/asymptotic_var.R | 342 - bssm-2.0.2/bssm/R/bootstrap_filter.R | 404 +- bssm-2.0.2/bssm/R/bssm-package.R | 451 +- bssm-2.0.2/bssm/R/check_arguments.R | 910 ++--- bssm-2.0.2/bssm/R/check_diagnostics.R | 182 - bssm-2.0.2/bssm/R/cpp_example_models.R | 1530 ++++---- bssm-2.0.2/bssm/R/expand_sample.R | 186 - bssm-2.0.2/bssm/R/fitted.R | 5 bssm-2.0.2/bssm/R/importance_sample.R | 144 bssm-2.0.2/bssm/R/init_mode.R | 62 bssm-2.0.2/bssm/R/loglik.R | 322 - bssm-2.0.2/bssm/R/model_type.R | 32 bssm-2.0.2/bssm/R/models.R | 4 bssm-2.0.2/bssm/R/particle_smoother.R | 582 +-- bssm-2.0.2/bssm/R/plot_mcmc.R |only bssm-2.0.2/bssm/R/post_correction.R | 24 bssm-2.0.2/bssm/R/predict.R | 38 bssm-2.0.2/bssm/R/print_mcmc.R | 96 bssm-2.0.2/bssm/R/priors.R | 524 +-- bssm-2.0.2/bssm/R/run_mcmc.R | 1714 +++++----- bssm-2.0.2/bssm/R/sim_smoother.R | 122 bssm-2.0.2/bssm/R/smoother.R | 316 - bssm-2.0.2/bssm/R/srr-stats-standards.R | 88 bssm-2.0.2/bssm/R/summary.R | 12 bssm-2.0.2/bssm/R/zzz.R | 6 bssm-2.0.2/bssm/README.md | 115 bssm-2.0.2/bssm/build/vignette.rds |binary bssm-2.0.2/bssm/inst/doc/bssm.R | 12 bssm-2.0.2/bssm/inst/doc/bssm.Rmd | 408 +- bssm-2.0.2/bssm/inst/doc/bssm.html | 273 - bssm-2.0.2/bssm/inst/doc/growth_model.R | 23 bssm-2.0.2/bssm/inst/doc/growth_model.Rmd | 23 bssm-2.0.2/bssm/inst/doc/growth_model.html | 198 - bssm-2.0.2/bssm/inst/doc/psi_pf.R | 67 bssm-2.0.2/bssm/inst/doc/psi_pf.Rmd | 55 bssm-2.0.2/bssm/inst/doc/psi_pf.html | 131 bssm-2.0.2/bssm/inst/doc/sde_model.R | 7 bssm-2.0.2/bssm/inst/doc/sde_model.Rmd | 5 bssm-2.0.2/bssm/inst/doc/sde_model.html | 164 bssm-2.0.2/bssm/man/ar1_lg.Rd | 122 bssm-2.0.2/bssm/man/ar1_ng.Rd | 162 bssm-2.0.2/bssm/man/as.data.frame.mcmc_output.Rd | 144 bssm-2.0.2/bssm/man/as_bssm.Rd | 76 bssm-2.0.2/bssm/man/as_draws-mcmc_output.Rd | 134 bssm-2.0.2/bssm/man/asymptotic_var.Rd | 128 bssm-2.0.2/bssm/man/bootstrap_filter.Rd | 178 - bssm-2.0.2/bssm/man/bsm_lg.Rd | 206 - bssm-2.0.2/bssm/man/bsm_ng.Rd | 318 - bssm-2.0.2/bssm/man/bssm.Rd | 171 bssm-2.0.2/bssm/man/bssm_prior.Rd | 237 - bssm-2.0.2/bssm/man/check_diagnostics.Rd | 100 bssm-2.0.2/bssm/man/cpp_example_model.Rd | 52 bssm-2.0.2/bssm/man/drownings.Rd | 66 bssm-2.0.2/bssm/man/ekf.Rd | 112 bssm-2.0.2/bssm/man/ekf_smoother.Rd | 118 bssm-2.0.2/bssm/man/ekpf_filter.Rd | 132 bssm-2.0.2/bssm/man/estimate_ess.Rd | 112 bssm-2.0.2/bssm/man/exchange.Rd | 64 bssm-2.0.2/bssm/man/expand_sample.Rd | 116 bssm-2.0.2/bssm/man/fitted.mcmc_output.Rd | 64 bssm-2.0.2/bssm/man/gaussian_approx.Rd | 124 bssm-2.0.2/bssm/man/iact.Rd | 68 bssm-2.0.2/bssm/man/importance_sample.Rd | 132 bssm-2.0.2/bssm/man/kfilter.Rd | 90 bssm-2.0.2/bssm/man/logLik_bssm.Rd | 248 - bssm-2.0.2/bssm/man/negbin_model.Rd | 78 bssm-2.0.2/bssm/man/negbin_series.Rd | 72 bssm-2.0.2/bssm/man/particle_smoother.Rd | 276 - bssm-2.0.2/bssm/man/plot.mcmc_output.Rd |only bssm-2.0.2/bssm/man/poisson_series.Rd | 50 bssm-2.0.2/bssm/man/post_correct.Rd | 266 - bssm-2.0.2/bssm/man/predict.mcmc_output.Rd | 300 - bssm-2.0.2/bssm/man/print.mcmc_output.Rd | 40 bssm-2.0.2/bssm/man/run_mcmc.Rd | 766 ++-- bssm-2.0.2/bssm/man/sim_smoother.Rd | 134 bssm-2.0.2/bssm/man/smoother.Rd | 106 bssm-2.0.2/bssm/man/ssm_mlg.Rd | 214 - bssm-2.0.2/bssm/man/ssm_mng.Rd | 278 - bssm-2.0.2/bssm/man/ssm_nlg.Rd | 230 - bssm-2.0.2/bssm/man/ssm_sde.Rd | 182 - bssm-2.0.2/bssm/man/ssm_ulg.Rd | 462 +- bssm-2.0.2/bssm/man/ssm_ung.Rd | 248 - bssm-2.0.2/bssm/man/suggest_N.Rd | 192 - bssm-2.0.2/bssm/man/summary.mcmc_output.Rd | 146 bssm-2.0.2/bssm/man/svm.Rd | 162 bssm-2.0.2/bssm/man/ukf.Rd | 122 bssm-2.0.2/bssm/tests/test_all.R | 2 bssm-2.0.2/bssm/tests/testthat/test_approx.R | 402 +- bssm-2.0.2/bssm/tests/testthat/test_as_bssm.R | 148 bssm-2.0.2/bssm/tests/testthat/test_as_data_frame.R | 96 bssm-2.0.2/bssm/tests/testthat/test_bootstrap_filter.R | 216 - bssm-2.0.2/bssm/tests/testthat/test_ekpf.R | 170 bssm-2.0.2/bssm/tests/testthat/test_is.R | 132 bssm-2.0.2/bssm/tests/testthat/test_mcmc.R | 1026 ++--- bssm-2.0.2/bssm/tests/testthat/test_models.R | 226 - bssm-2.0.2/bssm/tests/testthat/test_particle_smoother.R | 346 +- bssm-2.0.2/bssm/tests/testthat/test_post_correct.R | 230 - bssm-2.0.2/bssm/tests/testthat/test_predict.R | 594 +-- bssm-2.0.2/bssm/tests/testthat/test_priors.R | 40 bssm-2.0.2/bssm/tests/testthat/test_sde.R | 158 bssm-2.0.2/bssm/tests/testthat/test_sim_smoother.R | 62 bssm-2.0.2/bssm/vignettes/bssm.Rmd | 408 +- bssm-2.0.2/bssm/vignettes/bssm.bib | 962 ++--- bssm-2.0.2/bssm/vignettes/growth_model.Rmd | 23 bssm-2.0.2/bssm/vignettes/psi_pf.Rmd | 55 bssm-2.0.2/bssm/vignettes/psi_pf_experiments/ar_exp_model_functions.cpp | 240 - bssm-2.0.2/bssm/vignettes/psi_pf_experiments/growth_model_functions.cpp | 296 - bssm-2.0.2/bssm/vignettes/sde_model.Rmd | 5 bssm-2.0.2/bssm/vignettes/ssm_nlg_template.cpp | 322 - bssm-2.0.2/bssm/vignettes/ssm_sde_template.cpp | 160 118 files changed, 12442 insertions(+), 12225 deletions(-)
Title: High Dimensional Locally-Linear Mapping
Description: Provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <DOI:10.1016/j.jmva.2017.09.009>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <arXiv:1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).
Author: Emeline Perthame , Florence Forbes , Antoine Deleforge , Emilie Devijver , Melina Gallopin
Maintainer: Emeline Perthame <emeline.perthame@pasteur.fr>
Diff between xLLiM versions 2.2.1 dated 2023-09-11 and 2.3 dated 2023-10-27
DESCRIPTION | 9 ++- MD5 | 20 +++++--- NAMESPACE | 4 + R/Kfoldcv_xllim.R |only R/bllim.R | 6 +- R/compared_methods.R |only R/createFolds_xllim.R |only R/gllim.R | 93 ++++++++++++++++++++------------------- R/kmeans_probs.R |only R/preprocess_data.R |only README.md | 4 - man/data.xllim.trueparameters.Rd | 14 ++--- man/preprocess_data.Rd |only man/xLLiM-package.Rd | 7 ++ 14 files changed, 88 insertions(+), 69 deletions(-)
More information about RFlocalfdr.data at CRAN
Permanent link
Title: Utility Functions, Datasets and Extended Examples for Survival
Analysis
Description: Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Author: Annika Tillander [ctb],
Andreas Karlsson [aut],
Johan Zetterqvist [ctb],
Peter Strom [ctb],
Benedicte Delcoigne [ctb],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between biostat3 versions 0.1.8 dated 2022-11-06 and 0.1.9 dated 2023-10-27
DESCRIPTION | 8 - MD5 | 14 +- build/partial.rdb |binary inst/doc/labs/q22.Rmd | 2 inst/doc/q7.R | 1 inst/doc/solutions/q7.Rmd | 29 +++- inst/doc/solutions/q7.html | 269 ++++++++++++++++++++++++++++++++------------- inst/doc/solutions/q9.Rmd | 28 ++-- 8 files changed, 239 insertions(+), 112 deletions(-)
Title: The 'shiny' App for Test Analysis and Visualization
Description: This application enables exploratory factor analysis,
confirmatory factor analysis, classical measurement theory analysis,
unidimensional item response theory, multidimensional item response theory, and continuous item response
model analysis, through the 'shiny' interactive interface. It also facilitates the visualization
of the results. Users can easily download the analysis results from the
interactive interface. Additionally, users can download a concise report
about items and test quality on the interactive interface.
Author: Youxiang Jiang [cre, aut] ,
Hongbo Wen [ctb, ths]
Maintainer: Youxiang Jiang <jiangyouxiang34@163.com>
Diff between TestAnaAPP versions 0.1.2 dated 2023-09-11 and 0.1.3 dated 2023-10-27
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- R/server.R | 9 +++++---- 3 files changed, 15 insertions(+), 14 deletions(-)
Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.3.2 dated 2023-09-04 and 0.3.2.1 dated 2023-10-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/zooroh.R | 7 +++++++ build/vignette.rds |binary inst/doc/zooroh-vignette.pdf |binary 5 files changed, 14 insertions(+), 7 deletions(-)
More information about metalite.table1 at CRAN
Permanent link
Title: Run R Scripts if Needed
Description: Automation tool to run R scripts if needed, based on last modified
time. Implemented in base R with no additional software requirements,
organizational overhead, or structural requirements. In short: run an R script
if underlying files have changed, otherwise do nothing.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between makeit versions 1.0.0 dated 2023-03-28 and 1.0.1 dated 2023-10-27
DESCRIPTION | 18 +++++++------ MD5 | 37 +++++++++++++++++++++++---- NEWS.md | 13 +++++++++ R/make.R | 47 +++++++++++++++++++++++++---------- build |only inst/doc |only inst/examples/dag_targets |only inst/examples/dag_targets.png |only inst/examples/dag_wikipedia |only inst/examples/dag_wikipedia.png |only inst/examples/four_minutes |only inst/examples/sequential/02_plots.R | 4 +- inst/examples/sequential/03_tables.R | 4 +- inst/examples/sequential/_make.R |only man/make.Rd | 24 +++++++++++------ vignettes |only 16 files changed, 107 insertions(+), 40 deletions(-)
Title: An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Description: A suite of tools to allow you to download all
publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from
the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting
the downloaded data.
Author: Mauricio van den Berg [aut, cre],
Sarah Connor [aut],
Daniel Pfeffer [aut] ,
Tim Lucas [aut] ,
Daniel May [aut] ,
Suzanne Keddie [aut] ,
Jen Rozier [aut] ,
Oliver Watson [aut] ,
Harry Gibson [aut] ,
Nick Golding [ctb],
David Smith [ctb]
Maintainer: Mauricio van den Berg <mauricio.vandenberg@telethonkids.org.au>
Diff between malariaAtlas versions 1.5.0 dated 2023-10-04 and 1.5.1 dated 2023-10-27
DESCRIPTION | 8 ++--- MD5 | 48 +++++++++++++++++------------------ NEWS.md | 6 ++++ R/autoplot.MAPraster.R | 2 - R/autoplot.MAPshp.R | 2 - R/autoplot.pr.points.R | 4 +- R/autoplot.sf.R | 2 - R/autoplot.vector.points.R | 4 +- R/autoplot_MAPraster.R | 4 +- R/fillDHScoordinates.R | 2 - R/getPR.R | 4 +- R/getRaster.R | 2 - R/getVecOcc.R | 4 +- R/isAvailable_pr.R | 48 +---------------------------------- R/isAvailable_vec.R | 51 +------------------------------------- inst/doc/overview.html | 4 +- man/autoplot.MAPraster.Rd | 2 - man/autoplot.MAPshp.Rd | 2 - man/autoplot.pr.points.Rd | 4 +- man/autoplot.sf.Rd | 2 - man/autoplot.vector.points.Rd | 4 +- man/autoplot_MAPraster.Rd | 4 +- man/getRaster.Rd | 2 - tests/testthat/test_getPR.R | 14 +++++----- tests/testthat/test_isAvailable.R | 4 +- 25 files changed, 74 insertions(+), 159 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adamblake@g.ucla.edu>
Diff between coursekata versions 0.14.0 dated 2023-10-12 and 0.14.1 dated 2023-10-27
DESCRIPTION | 10 +-- MD5 | 26 +++---- NEWS.md | 6 + R/coursekata_attach.R | 27 ++++++-- R/coursekata_install.R | 2 R/coursekata_packages.R | 22 ------ R/utils-pkg.R | 103 ++++++++----------------------- R/zzz.R | 6 + README.md | 42 ++++++------ man/coursekata_attach.Rd | 4 - man/figures/README-samp_dist_of_b1-1.png |binary man/figures/README-samp_dist_of_hp-1.png |binary tests/testthat/test-coursekata_attach.R | 13 ++- tests/testthat/test-utils-pkg.R | 37 +++-------- 14 files changed, 128 insertions(+), 170 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-19 1.0.0
2021-01-25 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-28 0.9.6
2022-07-11 0.9.5
2022-05-06 0.9.4
2022-03-30 0.9.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 0.7
Title: A Collection of Amended Histograms Designed for Teaching
Statistics
Description: Statistics students often have problems understanding
the relation between a random variable's true scale and its z-values.
To allow instructors to better better visualize histograms for these
students, the package provides histograms with two horizontal
axis containing z-values and the true scale of the variable.
The function TeachHistDens() provides a density histogram with two axis.
TeachHistCounts() and TeachHistRelFreq() are variations for count and
relative frequency histograms, respectively. TeachConfInterv() and
TeachHypTest() help instructors to visualize confidence levels
and the results of hypothesis tests.
Author: Carsten Lange [aut, cre]
Maintainer: Carsten Lange <clange@cpp.edu>
Diff between TeachHist versions 0.2.0 dated 2022-06-08 and 0.2.1 dated 2023-10-27
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 8 ++++---- R/TeachHist.R | 1 + man/TeachHist.Rd | 1 + 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.6.2 dated 2023-09-02 and 0.6.3 dated 2023-10-27
DESCRIPTION | 8 MD5 | 56 +- NAMESPACE | 2 NEWS.md | 19 R/design_noreps.R |only R/design_repblock.R | 37 - R/figure2qmd.R | 2 R/gdoc2qmd.R | 2 R/tarpuy_design.R | 67 +-- R/tarpuy_plex.R | 5 R/tarpuy_plotdesign.R | 10 R/tarpuy_traits.R | 10 inst/doc/apps.html | 2 inst/doc/heritability.R | 2 inst/doc/rticles.R | 2 inst/doc/rticles.html | 2 inst/rmarkdown/templates/rticles/skeleton/files/cover-unalm.Rmd | 2 inst/rmarkdown/templates/rticles/skeleton/files/style_unalm.docx |binary inst/rmarkdown/templates/rticles/skeleton/manuscript.qmd | 6 inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 4 inst/tarpuy/server.R | 11 inst/tarpuy/ui.R | 2 inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 4 man/design_noreps.Rd |only man/design_repblock.Rd | 13 man/figure2qmd.Rd | 2 man/tarpuy_design.Rd | 9 man/tarpuy_plex.Rd | 3 man/tarpuy_plotdesign.Rd | 2 man/tarpuy_traits.Rd | 198 +++++----- 30 files changed, 260 insertions(+), 222 deletions(-)
Title: Framework for the Visualization of Distributional Regression
Models
Description: Functions for visualizing distributional regression models fitted using the 'gamlss', 'bamlss' or 'betareg' R package. The core of the package consists of a 'shiny' application, where the model results can be interactively explored and visualized.
Author: Stanislaus Stadlmann [cre, aut]
Maintainer: Stanislaus Stadlmann <stanislaus@stadlmann.cm>
Diff between distreg.vis versions 1.7.4 dated 2023-05-26 and 1.7.5 dated 2023-10-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot_moments.R | 2 +- man/reshape_into_long.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: TERN AusPlots Australian Ecosystem Monitoring Data
Description: Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-land-observatory/ecosystem-surveillance-and-environmental-monitoring/>).
Author: Greg Guerin [aut, cre],
Tom Saleeba [aut],
Samantha Munroe [aut],
Bernardo Blanco-Martin [aut],
Irene Martin-Fores [aut],
Walid Al Naim [ctb],
Andrew Tokmakoff [aut]
Maintainer: Greg Guerin <ggueri01@gmail.com>
Diff between ausplotsR versions 2.0.3 dated 2023-07-03 and 2.0.4 dated 2023-10-27
DESCRIPTION | 8 +- MD5 | 12 +-- inst/doc/start_guide.R | 16 ++-- inst/doc/start_guide.html | 162 +++++++++++++++++++++++----------------------- man/ausplotsR-package.Rd | 4 - man/fractional_cover.Rd | 2 man/get_ausplots.Rd | 2 7 files changed, 103 insertions(+), 103 deletions(-)