Title: Taxonomic Name Resolution Service
Description: Provides access to the Taxonomic Name Resolution Service <https://github.com/ojalaquellueva/tnrsapi> through R. The user supplies plant taxonomic names and the package returns resolved taxonomic names along with information on decisions. Optionally, the package can also be used to parse taxonomic names.
Author: Brian Maitner [aut, cre] ,
Brad Boyle [aut],
Paul Efren [ctb]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between TNRS versions 0.3.5 dated 2024-03-05 and 0.3.6 dated 2024-05-12
DESCRIPTION | 6 +-- MD5 | 48 ++++++++++++++++--------------- NAMESPACE | 1 NEWS | 14 +++++++++ R/TNRS_core.R | 2 - R/TNRS_synonyms.R |only inst/doc/TNRS_vignette.html | 6 +-- inst/doc/TNRS_vignette_spa.html | 6 +-- man/TNRS_synonyms.Rd |only tests/fixtures/tnrs_all.yml | 4 +- tests/fixtures/tnrs_base.yml | 4 +- tests/fixtures/tnrs_best.yml | 4 +- tests/fixtures/tnrs_character.yml | 4 +- tests/fixtures/tnrs_character_vector.yml | 4 +- tests/fixtures/tnrs_citations.yml | 4 +- tests/fixtures/tnrs_example.yml | 14 +++------ tests/fixtures/tnrs_high.yml | 4 +- tests/fixtures/tnrs_low.yml | 4 +- tests/fixtures/tnrs_parsed.yml | 4 +- tests/fixtures/tnrs_parsed_2.yml | 4 +- tests/fixtures/tnrs_resolved.yml | 4 +- tests/fixtures/tnrs_sources.yml | 4 +- tests/fixtures/tnrs_synonyms.yml |only tests/fixtures/tnrs_version.yml | 6 +-- tests/fixtures/tnrs_wcvp.yml | 4 +- tests/fixtures/tnrs_wfo.yml | 4 +- tests/testthat/test-TNRS_synonyms.R |only 27 files changed, 88 insertions(+), 71 deletions(-)
Title: Repeated Measurement Models for Discrete Times
Description: Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers"
taught by the section of Biostatistics of the University of Copenhagen.
It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, toeplitz, unstructured, ...).
Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite approximation of the degrees of freedom.
Normalized residuals are provided to assess model misspecification.
Statistical inference can be performed for arbitrary linear or non-linear combination(s) of model coefficients.
Predictions can be computed conditional to covariates only or also to outcome values.
Author: Brice Ozenne [aut, cre] ,
Julie Forman [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between LMMstar versions 1.0.1 dated 2024-01-11 and 1.1.0 dated 2024-05-12
LMMstar-1.0.1/LMMstar/R/addNA.R |only LMMstar-1.0.1/LMMstar/R/dummy.coef.R |only LMMstar-1.0.1/LMMstar/R/emmeans.R |only LMMstar-1.0.1/LMMstar/inst/doc-software |only LMMstar-1.0.1/LMMstar/man/LMMstar2emmeans.Rd |only LMMstar-1.0.1/LMMstar/man/dummy.coef.lmm.Rd |only LMMstar-1.0.1/LMMstar/tests/testthat/operator.R |only LMMstar-1.0.1/LMMstar/tests/testthat/test-auto-partial-residuals.R |only LMMstar-1.1.0/LMMstar/DESCRIPTION | 41 LMMstar-1.1.0/LMMstar/MD5 | 516 LMMstar-1.1.0/LMMstar/NAMESPACE | 296 LMMstar-1.1.0/LMMstar/NEWS | 31 LMMstar-1.1.0/LMMstar/R/0-onload.R | 59 LMMstar-1.1.0/LMMstar/R/BuyseTest_discreteRoot.R | 568 LMMstar-1.1.0/LMMstar/R/LMMstar-package.R | 123 LMMstar-1.1.0/LMMstar/R/LMMstar.options.R | 404 LMMstar-1.1.0/LMMstar/R/add.R | 84 LMMstar-1.1.0/LMMstar/R/anova.R | 1961 +- LMMstar-1.1.0/LMMstar/R/autoplot.R | 3351 +-- LMMstar-1.1.0/LMMstar/R/backtransform.R | 284 LMMstar-1.1.0/LMMstar/R/baselineAdjustment.R | 321 LMMstar-1.1.0/LMMstar/R/coef.R | 686 LMMstar-1.1.0/LMMstar/R/confint.R | 1734 - LMMstar-1.1.0/LMMstar/R/constrain.R | 116 LMMstar-1.1.0/LMMstar/R/df.R | 598 LMMstar-1.1.0/LMMstar/R/discreteRoot.R | 568 LMMstar-1.1.0/LMMstar/R/doc-data.R | 1460 - LMMstar-1.1.0/LMMstar/R/effects.R |only LMMstar-1.1.0/LMMstar/R/estimate.R | 1794 + LMMstar-1.1.0/LMMstar/R/findPatterns.R | 823 LMMstar-1.1.0/LMMstar/R/fitted.R | 583 LMMstar-1.1.0/LMMstar/R/formula.R | 600 LMMstar-1.1.0/LMMstar/R/iid.R | 210 LMMstar-1.1.0/LMMstar/R/information.R | 1023 - LMMstar-1.1.0/LMMstar/R/levels.R | 104 LMMstar-1.1.0/LMMstar/R/lmm.R | 2306 +- LMMstar-1.1.0/LMMstar/R/lmmCC.R | 746 LMMstar-1.1.0/LMMstar/R/logLik.R | 355 LMMstar-1.1.0/LMMstar/R/manifest.R | 250 LMMstar-1.1.0/LMMstar/R/mlmm.R | 718 LMMstar-1.1.0/LMMstar/R/model.frame.R | 270 LMMstar-1.1.0/LMMstar/R/model.matrix.R | 1935 +- LMMstar-1.1.0/LMMstar/R/model.tables.R | 261 LMMstar-1.1.0/LMMstar/R/moments.R | 585 LMMstar-1.1.0/LMMstar/R/mt.test.R | 320 LMMstar-1.1.0/LMMstar/R/multcomp.R | 103 LMMstar-1.1.0/LMMstar/R/namePatterns.R |only LMMstar-1.1.0/LMMstar/R/nobs.R | 121 LMMstar-1.1.0/LMMstar/R/operator.R | 52 LMMstar-1.1.0/LMMstar/R/partialCor.R | 1348 - LMMstar-1.1.0/LMMstar/R/plot.R | 180 LMMstar-1.1.0/LMMstar/R/precompute.R | 224 LMMstar-1.1.0/LMMstar/R/predict.R | 1329 - LMMstar-1.1.0/LMMstar/R/print.R | 756 LMMstar-1.1.0/LMMstar/R/profile.R | 501 LMMstar-1.1.0/LMMstar/R/proportion.R | 244 LMMstar-1.1.0/LMMstar/R/ranef.R | 753 LMMstar-1.1.0/LMMstar/R/rbind.R | 905 LMMstar-1.1.0/LMMstar/R/reformat.R | 223 LMMstar-1.1.0/LMMstar/R/remove.R | 82 LMMstar-1.1.0/LMMstar/R/reparametrize.R | 2089 +- LMMstar-1.1.0/LMMstar/R/resample.R | 1850 +- LMMstar-1.1.0/LMMstar/R/residuals.R | 1328 - LMMstar-1.1.0/LMMstar/R/restaureNA.R |only LMMstar-1.1.0/LMMstar/R/sampleRem.R | 289 LMMstar-1.1.0/LMMstar/R/scatterplot.R | 1477 - LMMstar-1.1.0/LMMstar/R/score.R | 573 LMMstar-1.1.0/LMMstar/R/sigma.R | 661 LMMstar-1.1.0/LMMstar/R/structure-calc_Omega.R | 425 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LMMstar-1.1.0/LMMstar/inst/dataTXT/amenorrhea.txt | 9210 +++++----- LMMstar-1.1.0/LMMstar/inst/dataTXT/bloodpressure.txt | 74 LMMstar-1.1.0/LMMstar/inst/dataTXT/calcium1.txt | 226 LMMstar-1.1.0/LMMstar/inst/dataTXT/ckdwide.txt | 104 LMMstar-1.1.0/LMMstar/inst/dataTXT/gastricbypass.txt | 42 LMMstar-1.1.0/LMMstar/inst/dataTXT/leprosy.txt | 62 LMMstar-1.1.0/LMMstar/inst/dataTXT/ncgs.txt | 208 LMMstar-1.1.0/LMMstar/inst/dataTXT/onycholysis.txt | 590 LMMstar-1.1.0/LMMstar/inst/dataTXT/pancreas_wide.txt | 26 LMMstar-1.1.0/LMMstar/inst/dataTXT/rabbit_long.txt | 74 LMMstar-1.1.0/LMMstar/inst/dataTXT/school.txt | 734 LMMstar-1.1.0/LMMstar/inst/dataTXT/swabs.txt | 182 LMMstar-1.1.0/LMMstar/inst/dataTXT/vasscores.txt | 64 LMMstar-1.1.0/LMMstar/inst/dataTXT/vitamin.txt | 22 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.aux | 50 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.fdb_latexmk | 522 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.fls | 3084 +-- LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.log | 2578 +- LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.org | 876 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.out | 6 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.soc | 2 LMMstar-1.1.0/LMMstar/inst/doc-covPattern/covariance-pattern.tex | 936 - LMMstar-1.1.0/LMMstar/inst/doc-overview |only LMMstar-1.1.0/LMMstar/inst/doc-partial-residuals |only LMMstar-1.1.0/LMMstar/inst/doc/overview.pdf |binary LMMstar-1.1.0/LMMstar/inst/doc/overview.pdf.asis | 1236 + LMMstar-1.1.0/LMMstar/inst/doc/partial-residuals.pdf |only LMMstar-1.1.0/LMMstar/inst/doc/partial-residuals.pdf.asis |only LMMstar-1.1.0/LMMstar/inst/todo/R-suggestions.aux | 12 LMMstar-1.1.0/LMMstar/inst/todo/R-suggestions.log | 1352 - LMMstar-1.1.0/LMMstar/inst/todo/R-suggestions.tex | 204 LMMstar-1.1.0/LMMstar/inst/todo/meeting-2021-03-26.org | 12 LMMstar-1.1.0/LMMstar/inst/todo/meeting-2021-07-07.org | 24 LMMstar-1.1.0/LMMstar/man/CS.Rd | 104 LMMstar-1.1.0/LMMstar/man/CUSTOM.Rd | 224 LMMstar-1.1.0/LMMstar/man/ID.Rd | 68 LMMstar-1.1.0/LMMstar/man/IND.Rd | 76 LMMstar-1.1.0/LMMstar/man/LMMstar-package.Rd | 132 LMMstar-1.1.0/LMMstar/man/LMMstar.options.Rd | 86 LMMstar-1.1.0/LMMstar/man/RE.Rd | 74 LMMstar-1.1.0/LMMstar/man/TOEPLITZ.Rd | 116 LMMstar-1.1.0/LMMstar/man/UN.Rd | 72 LMMstar-1.1.0/LMMstar/man/add.Rd | 50 LMMstar-1.1.0/LMMstar/man/anova.lmm.Rd | 223 LMMstar-1.1.0/LMMstar/man/autoplot.Wald_lmm.Rd | 150 LMMstar-1.1.0/LMMstar/man/autoplot.lmm.Rd | 253 LMMstar-1.1.0/LMMstar/man/autoplot.partialCor.Rd | 116 LMMstar-1.1.0/LMMstar/man/autoplot.profile_lmm.Rd | 124 LMMstar-1.1.0/LMMstar/man/autoplot.residuals_lmm.Rd | 158 LMMstar-1.1.0/LMMstar/man/autoplot.summarize.Rd | 134 LMMstar-1.1.0/LMMstar/man/autoplot.summarizeNA.Rd | 94 LMMstar-1.1.0/LMMstar/man/baselineAdjustment.Rd | 119 LMMstar-1.1.0/LMMstar/man/coef.lmm.Rd | 184 LMMstar-1.1.0/LMMstar/man/coef.mlmm.Rd | 48 LMMstar-1.1.0/LMMstar/man/confint.Wald_lmm.Rd | 124 LMMstar-1.1.0/LMMstar/man/confint.lmm.Rd | 186 LMMstar-1.1.0/LMMstar/man/confint.mlmm.Rd | 78 LMMstar-1.1.0/LMMstar/man/data-abetaL.Rd | 68 LMMstar-1.1.0/LMMstar/man/data-abetaW.Rd | 64 LMMstar-1.1.0/LMMstar/man/data-blandAltmanL.Rd | 48 LMMstar-1.1.0/LMMstar/man/data-blandAltmanW.Rd | 50 LMMstar-1.1.0/LMMstar/man/data-bloodpressureL.Rd | 58 LMMstar-1.1.0/LMMstar/man/data-calciumL.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-calciumW.Rd | 66 LMMstar-1.1.0/LMMstar/man/data-ckdL.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-ckdW.Rd | 60 LMMstar-1.1.0/LMMstar/man/data-gastricbypassL.Rd | 52 LMMstar-1.1.0/LMMstar/man/data-gastricbypassW.Rd | 60 LMMstar-1.1.0/LMMstar/man/data-ncgsL.Rd | 52 LMMstar-1.1.0/LMMstar/man/data-ncgsW.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-potassiumRepeatedL.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-potassiumSingleL.Rd | 58 LMMstar-1.1.0/LMMstar/man/data-potassiumSingleW.Rd | 62 LMMstar-1.1.0/LMMstar/man/data-schoolL.Rd | 40 LMMstar-1.1.0/LMMstar/man/data-swabsL.Rd | 50 LMMstar-1.1.0/LMMstar/man/data-swabsW.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-vasscoresL.Rd | 62 LMMstar-1.1.0/LMMstar/man/data-vasscoresW.Rd | 56 LMMstar-1.1.0/LMMstar/man/data-vitaminL.Rd | 60 LMMstar-1.1.0/LMMstar/man/data-vitaminW.Rd | 60 LMMstar-1.1.0/LMMstar/man/df.residual.lmm.Rd | 40 LMMstar-1.1.0/LMMstar/man/effects.lmm.Rd |only LMMstar-1.1.0/LMMstar/man/estfun.lmm.Rd | 72 LMMstar-1.1.0/LMMstar/man/estimate.lmm.Rd | 192 LMMstar-1.1.0/LMMstar/man/fitted.lmm.Rd | 258 LMMstar-1.1.0/LMMstar/man/iid.lmm.Rd | 90 LMMstar-1.1.0/LMMstar/man/information.lmm.Rd | 112 LMMstar-1.1.0/LMMstar/man/levels.lmm.Rd | 42 LMMstar-1.1.0/LMMstar/man/lmm.Rd | 332 LMMstar-1.1.0/LMMstar/man/lmmCC.Rd | 194 LMMstar-1.1.0/LMMstar/man/logLik.lmm.Rd | 58 LMMstar-1.1.0/LMMstar/man/manifest.lmm.Rd | 59 LMMstar-1.1.0/LMMstar/man/mlmm.Rd | 212 LMMstar-1.1.0/LMMstar/man/model.frame.lmm.Rd |only LMMstar-1.1.0/LMMstar/man/model.matrix.lmm.Rd |only 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Title: Discontinuous Regression and Image Processing
Description: A collection of functions that perform jump regression
and image analysis such as denoising, deblurring and
jump detection. The implemented methods are based on
the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>,
Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>,
Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>,
Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>,
Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>,
Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>,
Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.
Author: Yicheng Kang [aut, cre],
Peihua Qiu [aut, ctb]
Maintainer: Yicheng Kang <kangyicheng0527@gmail.com>
Diff between DRIP versions 1.9 dated 2024-02-05 and 2.0 dated 2024-05-12
DRIP-1.9/DRIP/man/diffLC2K.Rd |only DRIP-1.9/DRIP/man/diffLCK.Rd |only DRIP-1.9/DRIP/man/diffLL2K.Rd |only DRIP-1.9/DRIP/man/diffLLK.Rd |only DRIP-1.9/DRIP/man/stepEdgeLC2K.Rd |only DRIP-1.9/DRIP/man/stepEdgeLCK.Rd |only DRIP-1.9/DRIP/man/stepEdgeLL2K.Rd |only DRIP-1.9/DRIP/man/stepEdgeLLK.Rd |only DRIP-1.9/DRIP/man/stepEdgeParSelLC2K.Rd |only DRIP-1.9/DRIP/man/stepEdgeParSelLCK.Rd |only DRIP-1.9/DRIP/man/stepEdgeParSelLL2K.Rd |only DRIP-1.9/DRIP/man/stepEdgeParSelLLK.Rd |only DRIP-2.0/DRIP/DESCRIPTION | 17 +++- DRIP-2.0/DRIP/MD5 | 89 +++++++++++------------- DRIP-2.0/DRIP/NAMESPACE | 11 +-- DRIP-2.0/DRIP/R/JPLLK_surface.r | 4 - DRIP-2.0/DRIP/R/dKQ.r | 6 - DRIP-2.0/DRIP/R/modify1.r | 6 - DRIP-2.0/DRIP/R/modify2.r | 4 - DRIP-2.0/DRIP/R/roofEdge.r | 8 +- DRIP-2.0/DRIP/R/roofEdgeParSel.r | 8 +- DRIP-2.0/DRIP/R/stepDiff.R |only DRIP-2.0/DRIP/R/stepEdge.R |only DRIP-2.0/DRIP/R/stepEdgeParSel.R |only DRIP-2.0/DRIP/R/surfaceCluster.r | 16 ++-- DRIP-2.0/DRIP/R/surfaceCluster_bandwidth.r | 29 ++++---- DRIP-2.0/DRIP/R/threeStageParSel.r | 22 +++--- DRIP-2.0/DRIP/build |only DRIP-2.0/DRIP/data/brain.RData |binary DRIP-2.0/DRIP/data/circles.RData |binary DRIP-2.0/DRIP/data/kid.RData |binary DRIP-2.0/DRIP/data/sar.RData |binary DRIP-2.0/DRIP/man/JPLLK_surface.Rd | 57 ++++++++------- DRIP-2.0/DRIP/man/brain.Rd | 19 +++-- DRIP-2.0/DRIP/man/circles.Rd | 16 ++-- DRIP-2.0/DRIP/man/cv.jpex.Rd | 39 +++++----- DRIP-2.0/DRIP/man/dKQ.Rd | 27 +++---- DRIP-2.0/DRIP/man/jpex.Rd | 30 ++++---- DRIP-2.0/DRIP/man/kid.Rd | 22 +++--- DRIP-2.0/DRIP/man/lena.Rd | 13 +-- DRIP-2.0/DRIP/man/modify1.Rd | 57 ++++++++------- DRIP-2.0/DRIP/man/modify2.Rd | 56 +++++++-------- DRIP-2.0/DRIP/man/peppers.Rd | 18 +++- DRIP-2.0/DRIP/man/roofDiff.Rd | 60 +++++++--------- DRIP-2.0/DRIP/man/roofEdge.Rd | 94 +++++++++++++------------- DRIP-2.0/DRIP/man/roofEdgeParSel.Rd | 32 ++++---- DRIP-2.0/DRIP/man/sar.Rd | 23 +++--- DRIP-2.0/DRIP/man/stepDiff.Rd |only DRIP-2.0/DRIP/man/stepEdge.Rd |only DRIP-2.0/DRIP/man/stepEdgeParSel.Rd |only DRIP-2.0/DRIP/man/stopsign.Rd | 20 +++-- DRIP-2.0/DRIP/man/surfaceCluster.Rd | 71 +++++++++++++------ DRIP-2.0/DRIP/man/surfaceCluster_bandwidth.Rd | 88 +++++++++++++++++------- DRIP-2.0/DRIP/man/threeStage.Rd | 77 +++++++++++---------- DRIP-2.0/DRIP/man/threeStageParSel.Rd | 67 +++++++++++------- 55 files changed, 617 insertions(+), 489 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) is used to estimate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (nested) cross validation.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by defau [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-6 dated 2024-04-21 and 0.5-1 dated 2024-05-12
glmnetr-0.4-6/glmnetr/R/RandomForest_240322.R |only glmnetr-0.4-6/glmnetr/R/ann_tab_cv_240322.R |only glmnetr-0.4-6/glmnetr/R/calplot_240420.R |only glmnetr-0.4-6/glmnetr/R/cv.glmnetr_240412.R |only glmnetr-0.4-6/glmnetr/R/glmnetr_CIs_240410.R |only glmnetr-0.4-6/glmnetr/R/nested.glmnetr_240420.R |only glmnetr-0.4-6/glmnetr/R/plot.perf.glmnetr_240322.R |only glmnetr-0.4-6/glmnetr/R/predict_240322.R |only glmnetr-0.4-6/glmnetr/R/rederive_240322.R |only glmnetr-0.4-6/glmnetr/R/stepreg_240322.R |only glmnetr-0.4-6/glmnetr/R/summary.cv.glmnetr_240322.R |only glmnetr-0.4-6/glmnetr/R/summary.nested.glmnetr_240410.R |only glmnetr-0.4-6/glmnetr/R/tools_240322.R |only glmnetr-0.4-6/glmnetr/inst/doc/An_Overview_of_glmnetr_240420.pdf |only glmnetr-0.4-6/glmnetr/inst/doc/An_Overview_of_glmnetr_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/inst/doc/Calibration_240420.pdf |only glmnetr-0.4-6/glmnetr/inst/doc/Calibration_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/inst/doc/Using_ann_tab_cv_240420.pdf |only glmnetr-0.4-6/glmnetr/inst/doc/Using_ann_tab_cv_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/inst/doc/Using_stepreg_240420.pdf |only glmnetr-0.4-6/glmnetr/inst/doc/Using_stepreg_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/man/bsint.Rd |only glmnetr-0.4-6/glmnetr/man/calplot0.Rd |only glmnetr-0.4-6/glmnetr/man/dtstndrz.Rd |only glmnetr-0.4-6/glmnetr/man/getlamgam.Rd |only glmnetr-0.4-6/glmnetr/man/glmnetr.cis0.Rd |only glmnetr-0.4-6/glmnetr/man/glmnetr.compcv0.Rd |only glmnetr-0.4-6/glmnetr/man/glmnetr_devratio.Rd |only glmnetr-0.4-6/glmnetr/man/glmnetrll_1fold.Rd |only glmnetr-0.4-6/glmnetr/man/myaxis.Rd |only glmnetr-0.4-6/glmnetr/man/myrug.Rd |only glmnetr-0.4-6/glmnetr/man/predict_nested_rf.Rd |only glmnetr-0.4-6/glmnetr/man/predict_nested_xgb.Rd |only glmnetr-0.4-6/glmnetr/man/prednn_tl.Rd |only glmnetr-0.4-6/glmnetr/man/preds_1.Rd |only glmnetr-0.4-6/glmnetr/man/rf_xbhat.Rd |only glmnetr-0.4-6/glmnetr/man/rpart_xbhat.Rd |only glmnetr-0.4-6/glmnetr/man/wtlast.Rd |only glmnetr-0.4-6/glmnetr/man/wtmiddle.Rd |only glmnetr-0.4-6/glmnetr/man/wtzero.Rd |only glmnetr-0.4-6/glmnetr/man/xgb_xbhat.Rd |only glmnetr-0.4-6/glmnetr/vignettes/An_Overview_of_glmnetr_240420.Rmd |only glmnetr-0.4-6/glmnetr/vignettes/An_Overview_of_glmnetr_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/vignettes/Calibration_240420.Rmd |only glmnetr-0.4-6/glmnetr/vignettes/Calibration_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/vignettes/Using_ann_tab_cv_240420.Rmd |only glmnetr-0.4-6/glmnetr/vignettes/Using_ann_tab_cv_240420.pdf.asis |only glmnetr-0.4-6/glmnetr/vignettes/Using_stepreg_240420.Rmd |only glmnetr-0.4-6/glmnetr/vignettes/Using_stepreg_240420.pdf.asis |only glmnetr-0.5-1/glmnetr/DESCRIPTION | 13 glmnetr-0.5-1/glmnetr/MD5 | 169 ++++------ glmnetr-0.5-1/glmnetr/NAMESPACE | 10 glmnetr-0.5-1/glmnetr/R/ObliqueRandomForest_240508.R |only glmnetr-0.5-1/glmnetr/R/RandomForest_240323.R |only glmnetr-0.5-1/glmnetr/R/ann_tab_cv_240422.R |only glmnetr-0.5-1/glmnetr/R/calplot_240509.R |only glmnetr-0.5-1/glmnetr/R/cv.glmnetr_240422.R |only glmnetr-0.5-1/glmnetr/R/nested.cis_240510.R |only glmnetr-0.5-1/glmnetr/R/nested.compare_240510.R |only glmnetr-0.5-1/glmnetr/R/nested.glmnetr_240510.R |only glmnetr-0.5-1/glmnetr/R/perform_240510.R |only glmnetr-0.5-1/glmnetr/R/plot.perf.glmnetr_240422.R |only glmnetr-0.5-1/glmnetr/R/predict_240510.R |only glmnetr-0.5-1/glmnetr/R/predict_ann_tab_240322.R | 3 glmnetr-0.5-1/glmnetr/R/rederive_240508.R |only glmnetr-0.5-1/glmnetr/R/stepreg_240422.R |only glmnetr-0.5-1/glmnetr/R/summary.cv.glmnetr_240422.R |only glmnetr-0.5-1/glmnetr/R/summary.nested.glmnetr_240510.R |only glmnetr-0.5-1/glmnetr/R/tools_240423.R |only glmnetr-0.5-1/glmnetr/R/xgbm_tuned_240322.R | 10 glmnetr-0.5-1/glmnetr/build/vignette.rds |binary glmnetr-0.5-1/glmnetr/inst/doc/An_Overview_of_glmnetr_240510.pdf |only glmnetr-0.5-1/glmnetr/inst/doc/An_Overview_of_glmnetr_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/inst/doc/Calibration_240510.pdf |only glmnetr-0.5-1/glmnetr/inst/doc/Calibration_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/inst/doc/Using_ann_tab_cv_240510.pdf |only glmnetr-0.5-1/glmnetr/inst/doc/Using_ann_tab_cv_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/inst/doc/Using_stepreg_240510.pdf |only glmnetr-0.5-1/glmnetr/inst/doc/Using_stepreg_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/man/ann_tab_cv.Rd | 2 glmnetr-0.5-1/glmnetr/man/ann_tab_cv_best.Rd | 2 glmnetr-0.5-1/glmnetr/man/best.preds.Rd | 2 glmnetr-0.5-1/glmnetr/man/calceloss.Rd | 2 glmnetr-0.5-1/glmnetr/man/calplot.Rd | 6 glmnetr-0.5-1/glmnetr/man/cox.sat.dev.Rd | 2 glmnetr-0.5-1/glmnetr/man/cv.glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/devrat_.Rd | 2 glmnetr-0.5-1/glmnetr/man/diff_time.Rd | 4 glmnetr-0.5-1/glmnetr/man/diff_time1.Rd | 5 glmnetr-0.5-1/glmnetr/man/factor.foldid.Rd | 2 glmnetr-0.5-1/glmnetr/man/get.foldid.Rd | 2 glmnetr-0.5-1/glmnetr/man/glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/glmnetr.cis.Rd | 23 - glmnetr-0.5-1/glmnetr/man/glmnetr.compcv.Rd | 26 - glmnetr-0.5-1/glmnetr/man/glmnetr.simdata.Rd | 2 glmnetr-0.5-1/glmnetr/man/glmnetr_seed.Rd | 2 glmnetr-0.5-1/glmnetr/man/nested.cis.Rd |only glmnetr-0.5-1/glmnetr/man/nested.compare.Rd |only glmnetr-0.5-1/glmnetr/man/nested.glmnetr.Rd | 17 - glmnetr-0.5-1/glmnetr/man/orf_tune.Rd |only glmnetr-0.5-1/glmnetr/man/plot_perf_glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/predict.cv.glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/predict.glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/predict.nested.glmnetr.Rd | 7 glmnetr-0.5-1/glmnetr/man/predict_ann_tab.Rd | 2 glmnetr-0.5-1/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/print.orf_tune.Rd |only glmnetr-0.5-1/glmnetr/man/print.rf_tune.Rd | 4 glmnetr-0.5-1/glmnetr/man/rederive_orf.Rd |only glmnetr-0.5-1/glmnetr/man/rederive_rf.Rd | 2 glmnetr-0.5-1/glmnetr/man/rederive_xgb.Rd | 12 glmnetr-0.5-1/glmnetr/man/rf_tune.Rd | 4 glmnetr-0.5-1/glmnetr/man/roundperf.Rd | 2 glmnetr-0.5-1/glmnetr/man/stepreg.Rd | 2 glmnetr-0.5-1/glmnetr/man/summary.cv.glmnetr.Rd | 2 glmnetr-0.5-1/glmnetr/man/summary.nested.glmnetr.Rd | 5 glmnetr-0.5-1/glmnetr/man/summary.orf_tune.Rd |only glmnetr-0.5-1/glmnetr/man/summary.rf_tune.Rd | 4 glmnetr-0.5-1/glmnetr/man/summary.stepreg.Rd | 2 glmnetr-0.5-1/glmnetr/man/xgb.simple.Rd | 2 glmnetr-0.5-1/glmnetr/man/xgb.tuned.Rd | 2 glmnetr-0.5-1/glmnetr/vignettes/An_Overview_of_glmnetr_240510.Rmd |only glmnetr-0.5-1/glmnetr/vignettes/An_Overview_of_glmnetr_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/vignettes/Calibration_240510.Rmd |only glmnetr-0.5-1/glmnetr/vignettes/Calibration_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/vignettes/Using_ann_tab_cv_240510.Rmd |only glmnetr-0.5-1/glmnetr/vignettes/Using_ann_tab_cv_240510.pdf.asis |only glmnetr-0.5-1/glmnetr/vignettes/Using_stepreg_240510.Rmd |only glmnetr-0.5-1/glmnetr/vignettes/Using_stepreg_240510.pdf.asis |only 129 files changed, 172 insertions(+), 198 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.19.10 dated 2024-03-22 and 0.19.11 dated 2024-05-12
insight-0.19.10/insight/tests/testthat/test-mhurdle.R |only insight-0.19.11/insight/DESCRIPTION | 22 - insight-0.19.11/insight/MD5 | 43 +-- insight-0.19.11/insight/NAMESPACE | 1 insight-0.19.11/insight/NEWS.md | 12 insight-0.19.11/insight/R/ellipsis_info.R | 91 +++--- insight-0.19.11/insight/R/format_bf.R | 26 - insight-0.19.11/insight/R/format_p.R | 40 +- insight-0.19.11/insight/R/format_pd.R | 4 insight-0.19.11/insight/R/format_table.R | 34 +- insight-0.19.11/insight/R/get_data.R | 3 insight-0.19.11/insight/R/get_df_residual.R | 6 insight-0.19.11/insight/R/get_loglikelihood.R | 6 insight-0.19.11/insight/R/get_priors.R | 63 ++-- insight-0.19.11/insight/R/get_varcov_sandwich.R | 29 +- insight-0.19.11/insight/R/helper_functions.R | 10 insight-0.19.11/insight/R/utils_get_data.R | 2 insight-0.19.11/insight/build/partial.rdb |binary insight-0.19.11/insight/build/vignette.rds |binary insight-0.19.11/insight/inst/WORDLIST | 1 insight-0.19.11/insight/inst/doc/display.html | 212 +++++++-------- insight-0.19.11/insight/tests/testthat/test-coxme.R | 37 ++ insight-0.19.11/insight/tests/testthat/test-get_varcov.R | 16 + 23 files changed, 378 insertions(+), 280 deletions(-)
Title: Tools for Assessing Estimability of Linear Predictions
Description: Provides tools for determining estimability of linear functions
of regression coefficients, and 'epredict' methods that handle
non-estimable cases correctly. Estimability theory is discussed in
many linear-models textbooks including Chapter 3 of Monahan, JF (2008),
"A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).
Author: Russell Lenth [aut, cre, cph]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between estimability versions 1.5 dated 2024-02-20 and 1.5.1 dated 2024-05-12
DESCRIPTION | 13 ++++++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS | 5 +++++ inst/doc/add-est-check.Rmd | 2 +- inst/doc/add-est-check.html | 4 ++-- man/epredict.lm.Rd | 13 +++++++------ vignettes/add-est-check.Rmd | 2 +- 8 files changed, 31 insertions(+), 22 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.8.1 dated 2024-05-11 and 10.8.2 dated 2024-05-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/NNS_meboot.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre]
,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Aaron Caldwell [ctb] ,
Jessica Burnett [rev] ,
Johan [...truncated...]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 0.8.7 dated 2024-04-01 and 0.8.8 dated 2024-05-12
DESCRIPTION | 12 +- MD5 | 13 +- NEWS.md | 10 + R/cohens_d.R | 29 ++--- R/common_language.R | 5 R/effectsize.htest.R | 215 ++++++++++++++++++++++++++------------- R/rank_diff.R | 2 tests/testthat/test-htest_data.R |only 8 files changed, 186 insertions(+), 100 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-04 0.1.2
2019-06-19 0.1.1
2019-03-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-21 2.1.0
2022-03-01 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-19 2.0.2
2024-02-17 2.0.1
Title: Simplify Connections to Database Sources
Description: Connecting to databases requires boilerplate code to specify
connection parameters and to set up sessions properly with the DBMS.
This package provides a simple tool to fill two purposes: abstracting
connection details, including secret credentials, out of your source
code and managing configuration for frequently-used database connections
in a persistent and flexible way, while minimizing requirements on the
runtime environment.
Author: Charles Bailey [aut, cre],
Hanieh Razzaghi [aut]
Maintainer: Charles Bailey <baileyc@chop.edu>
Diff between srcr versions 1.1.0 dated 2021-10-30 and 1.1.1 dated 2024-05-12
DESCRIPTION | 10 MD5 | 16 - NEWS.md | 5 R/create_src.R | 12 - R/srcr.R | 3 build/vignette.rds |binary inst/doc/Managing_data_sources.html | 378 +++++++++++++++++++++++++++++++++--- man/srcr.Rd | 19 + tests/testthat/test_src_create.R | 26 ++ 9 files changed, 423 insertions(+), 46 deletions(-)
Title: Simple, Consistent Package Options
Description: Simple mechanisms for defining and interpreting package options. Provides
helpers for interpreting environment variables, global options, defining
default values and more.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between options versions 0.1.0 dated 2024-01-29 and 0.2.0 dated 2024-05-12
DESCRIPTION | 8 +-- MD5 | 36 +++++++-------- NAMESPACE | 5 ++ NEWS.md | 19 +++++++ R/define_option.R | 53 ++++++++++++---------- R/options_env.R | 63 ++++++++++++++++++++++---- R/options_get.R | 64 ++++++++++++++++---------- R/options_spec.R | 86 +++++++++++++++++++++++++++++++----- R/utils.R | 20 ++++++-- build/vignette.rds |binary inst/doc/envvars.html | 4 - man/defining_options.Rd | 1 man/format_value.Rd | 3 + man/get_options_env.Rd |only man/opt.Rd | 5 +- man/option_spec.Rd | 47 +++++++++++++++++++ man/options_env.Rd | 15 +++--- tests/testthat/test-define-option.R | 25 ++++++++++ tests/testthat/test-options_env.R |only tests/testthat/test-output.R | 7 ++ 20 files changed, 356 insertions(+), 105 deletions(-)