Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-07 0.1.5
2018-04-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-07 0.1.13
2017-09-01 0.1.11
2017-08-21 0.1.10
2015-09-04 0.1.9
2014-08-04 0.1.8
2012-10-12 0.1.7
2012-01-04 0.1.5
2011-02-17 0.1.3
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>),
Carsten Schwemmer [ctb],
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>),
Amir Djalovski [ctb],
Johannes Titz [ctb] (<https://orcid.org/0000-0002-1102-5719>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.4 dated 2020-05-24 and 2.8.5 dated 2020-09-24
DESCRIPTION | 15 MD5 | 130 ++++---- NAMESPACE | 4 NEWS.md | 17 + R/html_print.R | 14 R/plot_grpfrq.R | 10 R/plot_model.R | 5 R/plot_models.R | 16 R/plot_stackfrq.R | 27 - R/plot_type_int.R | 12 R/sjPlotPearsonsChi2Test.R | 2 R/tab_itemscale.R | 2 R/tab_model.R | 148 ++++++--- R/tidiers.R | 11 README.md | 4 build/vignette.rds |binary inst/doc/blackwhitefigures.html | 136 +++++--- inst/doc/custplot.Rmd | 2 inst/doc/custplot.html | 304 ++++++++++-------- inst/doc/plot_interactions.Rmd | 2 inst/doc/plot_interactions.html | 124 +++++-- inst/doc/plot_likert_scales.html | 172 ++++++---- inst/doc/plot_marginal_effects.Rmd | 2 inst/doc/plot_marginal_effects.html | 142 +++++--- inst/doc/plot_model_estimates.Rmd | 2 inst/doc/plot_model_estimates.html | 298 ++++++++++-------- inst/doc/sjtitemanalysis.html | 82 +++-- inst/doc/tab_bayes.html | 284 +++++++++-------- inst/doc/tab_mixed.html | 129 ++++--- inst/doc/tab_model_estimates.html | 318 ++++++++++--------- inst/doc/tab_model_robust.html | 284 +++++++++++------ inst/doc/table_css.html | 272 +++++++++------- man/dist_chisq.Rd | 130 ++++---- man/dist_f.Rd | 122 +++---- man/dist_norm.Rd | 120 +++---- man/dist_t.Rd | 116 +++---- man/plot_frq.Rd | 4 man/plot_gpt.Rd | 286 ++++++++--------- man/plot_grid.Rd | 118 +++---- man/plot_grpfrq.Rd | 528 ++++++++++++++++---------------- man/plot_kfold_cv.Rd | 118 +++---- man/plot_model.Rd | 2 man/plot_residuals.Rd | 140 ++++---- man/plot_scatter.Rd | 308 +++++++++---------- man/plot_stackfrq.Rd | 278 ++++++++--------- man/plot_xtab.Rd | 462 ++++++++++++++-------------- man/save_plot.Rd | 124 +++---- man/set_theme.Rd | 582 ++++++++++++++++++------------------ man/sjPlot-package.Rd | 10 man/sjPlot-themes.Rd | 304 +++++++++--------- man/sjp.aov1.Rd | 234 +++++++------- man/sjp.chi2.Rd | 125 +++---- man/sjp.poly.Rd | 278 ++++++++--------- man/sjplot.Rd | 162 +++++----- man/tab_corr.Rd | 308 +++++++++---------- man/tab_df.Rd | 310 +++++++++---------- man/tab_fa.Rd | 268 ++++++++-------- man/tab_itemscale.Rd | 2 man/tab_model.Rd | 25 - man/tab_pca.Rd | 266 ++++++++-------- man/tab_xtab.Rd | 4 man/view_df.Rd | 298 +++++++++--------- vignettes/custplot.Rmd | 2 vignettes/plot_interactions.Rmd | 2 vignettes/plot_marginal_effects.Rmd | 2 vignettes/plot_model_estimates.Rmd | 2 66 files changed, 4758 insertions(+), 4252 deletions(-)
Title: Prediction Model Selection and Performance Evaluation in
Multiple Imputed Datasets
Description: Pooling, backward and forward selection of logistic and Cox regression models in
multiply imputed datasets. Backward and forward selection can be done
from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and
the median p-values method. This is also possible for Mixed models.
The models can contain continuous, dichotomous, categorical and restricted
cubic spline predictors and interaction terms between all these type of predictors.
The stability of the models can be evaluated using bootstrapping and cluster
bootstrapping. The package further contains functions to pool the model performance
as ROC/AUC, R-squares, scaled Brier score and calibration plots for logistic
regression models. Internal validation can be done with cross-validation or bootstrapping.
The adjusted intercept after shrinkage of pooled regression coefficients can be obtained.
Backward and forward selection as part of internal validation is possible.
Also a function to externally validate logistic prediction models in multiple imputed
datasets is available.
Eekhout (2017) <doi:10.1186/s12874-017-0404-7>.
Wiel (2009) <doi:10.1093/biostatistics/kxp011>.
Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut] (<https://orcid.org/0000-0002-3889-0921>),
Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>
Diff between psfmi versions 0.2.0 dated 2020-02-03 and 0.5.0 dated 2020-09-24
psfmi-0.2.0/psfmi/R/D1_cox.R |only psfmi-0.2.0/psfmi/R/D1_logistic.R |only psfmi-0.2.0/psfmi/R/psfmi_D3.R |only psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.R |only psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.Rmd |only psfmi-0.2.0/psfmi/inst/doc/psfmi-vignette.html |only psfmi-0.2.0/psfmi/man/D1_cox.Rd |only psfmi-0.2.0/psfmi/man/D1_logistic.Rd |only psfmi-0.2.0/psfmi/man/psfmi_D3.Rd |only psfmi-0.2.0/psfmi/vignettes/psfmi-vignette.Rmd |only psfmi-0.5.0/psfmi/DESCRIPTION | 67 - psfmi-0.5.0/psfmi/MD5 | 133 +- psfmi-0.5.0/psfmi/NAMESPACE | 128 +- psfmi-0.5.0/psfmi/NEWS.md | 19 psfmi-0.5.0/psfmi/R/MI_boot.R |only psfmi-0.5.0/psfmi/R/MI_cv_naive.R |only psfmi-0.5.0/psfmi/R/boot_MI.R |only psfmi-0.5.0/psfmi/R/bw_single.R |only psfmi-0.5.0/psfmi/R/clean_P.R |only psfmi-0.5.0/psfmi/R/cv_MI.R |only psfmi-0.5.0/psfmi/R/cv_MI_RR.R |only psfmi-0.5.0/psfmi/R/lbpmi_extval.R |only psfmi-0.5.0/psfmi/R/mean_auc_log.R |only psfmi-0.5.0/psfmi/R/miceImp.R |only psfmi-0.5.0/psfmi/R/mivalext_lr.R | 261 ++-- psfmi-0.5.0/psfmi/R/pool_auc.R |only psfmi-0.5.0/psfmi/R/pool_intadj.R | 6 psfmi-0.5.0/psfmi/R/pool_performance.R | 187 +-- psfmi-0.5.0/psfmi/R/psfmi_coxr.R | 936 +++++----------- psfmi-0.5.0/psfmi/R/psfmi_coxr_bw.R |only psfmi-0.5.0/psfmi/R/psfmi_coxr_fw.R |only psfmi-0.5.0/psfmi/R/psfmi_lr.R | 717 +++--------- psfmi-0.5.0/psfmi/R/psfmi_lr_bw.R |only psfmi-0.5.0/psfmi/R/psfmi_lr_fw.R |only psfmi-0.5.0/psfmi/R/psfmi_mm.R | 18 psfmi-0.5.0/psfmi/R/psfmi_perform.R | 737 +++--------- psfmi-0.5.0/psfmi/R/psfmi_stab.R | 244 ++-- psfmi-0.5.0/psfmi/R/rsq_nagel.R |only psfmi-0.5.0/psfmi/R/scaled_brier.R |only psfmi-0.5.0/psfmi/README.md | 139 +- psfmi-0.5.0/psfmi/build/vignette.rds |binary psfmi-0.5.0/psfmi/data/lbpmi_extval.rda |only psfmi-0.5.0/psfmi/inst/doc/MI_boot.R |only psfmi-0.5.0/psfmi/inst/doc/MI_boot.Rmd |only psfmi-0.5.0/psfmi/inst/doc/MI_boot.html |only psfmi-0.5.0/psfmi/inst/doc/MI_cv_naive.R |only psfmi-0.5.0/psfmi/inst/doc/MI_cv_naive.Rmd |only psfmi-0.5.0/psfmi/inst/doc/MI_cv_naive.html |only psfmi-0.5.0/psfmi/inst/doc/boot_MI.R |only psfmi-0.5.0/psfmi/inst/doc/boot_MI.Rmd |only psfmi-0.5.0/psfmi/inst/doc/boot_MI.html |only psfmi-0.5.0/psfmi/inst/doc/cv_MI.R |only psfmi-0.5.0/psfmi/inst/doc/cv_MI.Rmd |only psfmi-0.5.0/psfmi/inst/doc/cv_MI.html |only psfmi-0.5.0/psfmi/inst/doc/cv_MI_RR.R |only psfmi-0.5.0/psfmi/inst/doc/cv_MI_RR.Rmd |only psfmi-0.5.0/psfmi/inst/doc/cv_MI_RR.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_CoxModels.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_CoxModels.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_CoxModels.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_LogisticModels.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_LogisticModels.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_LogisticModels.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_StabilityAnalysis.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_StabilityAnalysis.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_StabilityAnalysis.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.html |only psfmi-0.5.0/psfmi/man/MI_boot.Rd |only psfmi-0.5.0/psfmi/man/MI_cv_naive.Rd |only psfmi-0.5.0/psfmi/man/boot_MI.Rd |only psfmi-0.5.0/psfmi/man/bw_single.Rd |only psfmi-0.5.0/psfmi/man/clean_P.Rd |only psfmi-0.5.0/psfmi/man/cv_MI.Rd |only psfmi-0.5.0/psfmi/man/cv_MI_RR.Rd |only psfmi-0.5.0/psfmi/man/figures |only psfmi-0.5.0/psfmi/man/lbpmi_extval.Rd |only psfmi-0.5.0/psfmi/man/mean_auc_log.Rd |only psfmi-0.5.0/psfmi/man/miceImp.Rd |only psfmi-0.5.0/psfmi/man/mivalext_lr.Rd | 19 psfmi-0.5.0/psfmi/man/pool_auc.Rd |only psfmi-0.5.0/psfmi/man/pool_intadj.Rd | 2 psfmi-0.5.0/psfmi/man/pool_performance.Rd | 10 psfmi-0.5.0/psfmi/man/psfmi_coxr.Rd | 169 +- psfmi-0.5.0/psfmi/man/psfmi_coxr_bw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_coxr_fw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_lr.Rd | 130 +- psfmi-0.5.0/psfmi/man/psfmi_lr_bw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_lr_fw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_mm.Rd | 4 psfmi-0.5.0/psfmi/man/psfmi_perform.Rd | 176 +-- psfmi-0.5.0/psfmi/man/psfmi_stab.Rd | 50 psfmi-0.5.0/psfmi/man/rsq_nagel.Rd |only psfmi-0.5.0/psfmi/man/scaled_brier.Rd |only psfmi-0.5.0/psfmi/vignettes/MI_boot.Rmd |only psfmi-0.5.0/psfmi/vignettes/MI_boot.png |only psfmi-0.5.0/psfmi/vignettes/MI_cv_naive.Rmd |only psfmi-0.5.0/psfmi/vignettes/MI_cv_naive.png |only psfmi-0.5.0/psfmi/vignettes/boot_MI.Rmd |only psfmi-0.5.0/psfmi/vignettes/boot_MI.png |only psfmi-0.5.0/psfmi/vignettes/cv_MI.Rmd |only psfmi-0.5.0/psfmi/vignettes/cv_MI.png |only psfmi-0.5.0/psfmi/vignettes/cv_MI_RR.Rmd |only psfmi-0.5.0/psfmi/vignettes/cv_mi_RR.png |only psfmi-0.5.0/psfmi/vignettes/psfmi_CoxModels.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_LogisticModels.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_StabilityAnalysis.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_mice.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_valext.Rmd |only 113 files changed, 1802 insertions(+), 2350 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.1.0 dated 2015-06-21 and 1.2.0 dated 2020-09-24
import-1.1.0/import/NEWS |only import-1.1.0/import/README |only import-1.1.0/import/man/make_import_call.Rd |only import-1.1.0/import/man/symbol_as_character.Rd |only import-1.1.0/import/man/symbol_list.Rd |only import-1.1.0/import/vignettes/import.md |only import-1.2.0/import/DESCRIPTION | 40 - import-1.2.0/import/LICENSE | 4 import-1.2.0/import/MD5 | 81 +- import-1.2.0/import/NAMESPACE | 10 import-1.2.0/import/NEWS.md |only import-1.2.0/import/R/detect_bad_recursion.R |only import-1.2.0/import/R/file_path.R |only import-1.2.0/import/R/from.R | 392 ++++++++---- import-1.2.0/import/R/here.R | 44 - import-1.2.0/import/R/import.R | 48 - import-1.2.0/import/R/import_aliases.R |only import-1.2.0/import/R/into.R | 42 - import-1.2.0/import/R/is_script.R | 33 - import-1.2.0/import/R/make_import_call.R | 45 - import-1.2.0/import/R/modified.R | 76 +- import-1.2.0/import/R/package_specs.R |only import-1.2.0/import/R/safe_assign.R |only import-1.2.0/import/R/scripts.R | 16 import-1.2.0/import/R/suppress_output.R | 2 import-1.2.0/import/R/symbol_as_character.R | 32 - import-1.2.0/import/R/symbol_list.R | 52 + import-1.2.0/import/R/zzz.R | 24 import-1.2.0/import/build/vignette.rds |binary import-1.2.0/import/inst/doc/import.R | 255 +++++-- import-1.2.0/import/inst/doc/import.Rmd | 792 +++++++++++++++++------- import-1.2.0/import/inst/doc/import.html | 800 ++++++++++++++++++------- import-1.2.0/import/man/examples |only import-1.2.0/import/man/import.Rd | 67 +- import-1.2.0/import/man/importfunctions.Rd | 221 ++++-- import-1.2.0/import/tests |only import-1.2.0/import/vignettes/import.Rmd | 792 +++++++++++++++++------- 37 files changed, 2631 insertions(+), 1237 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior
and predictions of any machine learning model. Implemented methods
are: Feature importance described by Fisher et al. (2018)
<arXiv:1801.01489>, accumulated local effects plots described by Apley
(2018) <arXiv:1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual
conditional expectation ('ice') plots described by Goldstein et al.
(2013) <doi:10.1080/10618600.2014.907095>, local models (variant of
'lime') described by Ribeiro et. al (2016) <arXiv:1602.04938>, the
Shapley Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Christoph Molnar [aut, cre],
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>
Diff between iml versions 0.10.0 dated 2020-03-26 and 0.10.1 dated 2020-09-24
DESCRIPTION | 20 MD5 | 31 - NAMESPACE | 2 NEWS.md | 30 - R/FeatureEffects.R | 2 R/FeatureImp.R | 4 R/Predictor.R | 5 R/iml.R | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/intro.html | 807 +++++++++++++++++++--------------------- inst/doc/parallel.html | 609 ++++++++++++------------------ tests/testthat/Rplots.pdf |binary tests/testthat/check-mlr3.R |only tests/testthat/helper.R | 6 tests/testthat/setup.R | 25 - tests/testthat/test-Predictor.R | 10 17 files changed, 743 insertions(+), 814 deletions(-)
Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Author: Hervé Perdry [cre, aut, cph],
Claire Dandine-Roulland [aut, cph],
Deepak Bandyopadhyay [cph] (C++ gzstream class),
Lutz Kettner [cph] (C++ gzstream class)
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.5.6 dated 2020-02-26 and 1.5.7 dated 2020-09-24
gaston-1.5.6/gaston/src/Parallel.h |only gaston-1.5.6/gaston/src/ai-reml-1k-covar.h |only gaston-1.5.6/gaston/src/ai-reml-1k.h |only gaston-1.5.6/gaston/src/ai-reml-logit-1k-covar.h |only gaston-1.5.6/gaston/src/ai-reml-logit-1k.h |only gaston-1.5.6/gaston/src/ai-reml-logit-nk-covar.h |only gaston-1.5.6/gaston/src/ai-reml-logit-nk.h |only gaston-1.5.6/gaston/src/ai-reml-nk-covar.h |only gaston-1.5.6/gaston/src/ai-reml-nk.h |only gaston-1.5.6/gaston/src/any.h |only gaston-1.5.6/gaston/src/diago2.h |only gaston-1.5.6/gaston/src/diago2_full.h |only gaston-1.5.6/gaston/src/diago2_full_nocovar.h |only gaston-1.5.6/gaston/src/diago2_nocovar.h |only gaston-1.5.6/gaston/src/flip_strand.h |only gaston-1.5.6/gaston/src/gzstream.h |only gaston-1.5.6/gaston/src/lmm_diago_min_max_h2.h |only gaston-1.5.6/gaston/src/logit_model.h |only gaston-1.5.6/gaston/src/loubar.h |only gaston-1.5.6/gaston/src/m4_kinship_type.h |only gaston-1.5.6/gaston/src/m4_ld.h |only gaston-1.5.6/gaston/src/matrix-varia.h |only gaston-1.5.6/gaston/src/matrix4.h |only gaston-1.5.6/gaston/src/optimize_2.h |only gaston-1.5.6/gaston/src/snp_hash.h |only gaston-1.5.7/gaston/DESCRIPTION | 8 gaston-1.5.7/gaston/MD5 | 81 +-- gaston-1.5.7/gaston/NEWS | 3 gaston-1.5.7/gaston/R/ld_plot.r | 2 gaston-1.5.7/gaston/R/logistic_mm_aireml.r | 16 gaston-1.5.7/gaston/TODO | 11 gaston-1.5.7/gaston/build/vignette.rds |binary gaston-1.5.7/gaston/inst/doc/gaston-faq.pdf |binary gaston-1.5.7/gaston/inst/doc/gaston.pdf |binary gaston-1.5.7/gaston/inst/include/gaston/Parallel.h |only gaston-1.5.7/gaston/inst/include/gaston/ai-reml-1k-covar.h | 3 gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-1k-covar.h | 28 - gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-1k.h | 32 + gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-nk-covar.h | 49 +- gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-nk.h | 48 +- gaston-1.5.7/gaston/inst/include/gaston/any_nan.h |only gaston-1.5.7/gaston/inst/include/gaston/flip_strand.h |only gaston-1.5.7/gaston/inst/include/gaston/gzstream.h |only gaston-1.5.7/gaston/inst/include/gaston/gzstream0.h |only gaston-1.5.7/gaston/inst/include/gaston/logit_model.h | 1 gaston-1.5.7/gaston/inst/include/gaston/loubar.h |only gaston-1.5.7/gaston/inst/include/gaston/m4_ld.h |only gaston-1.5.7/gaston/inst/include/gaston/snp_hash.h | 128 ++--- gaston-1.5.7/gaston/inst/include/gaston/string_equal.h |only gaston-1.5.7/gaston/man/logistic.mm.aireml.Rd | 11 gaston-1.5.7/gaston/src/Makevars | 2 gaston-1.5.7/gaston/src/export-aireml-logit-1k.cpp | 33 - gaston-1.5.7/gaston/src/export-aireml-logit-nk.cpp | 91 ++-- gaston-1.5.7/gaston/src/gaston_init.c | 218 ++++------ gaston-1.5.7/gaston/src/gwas_lmm_diago_lrt.cpp | 2 gaston-1.5.7/gaston/src/gwas_lmm_diago_wald.cpp | 2 gaston-1.5.7/gaston/src/gzstream.cpp | 167 ------- gaston-1.5.7/gaston/src/snp_match.cpp | 16 58 files changed, 423 insertions(+), 529 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-07 0.2.4
2019-12-17 0.2.3
2019-06-05 0.2.2
2017-09-25 0.2.1
2017-07-17 0.2.0
2017-03-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-18 0.1.1
2018-06-12 0.1.0
Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Description: Implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-6115.1252> and
a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described
in Zuber and Strimmer (2009) <DOI:10.1093/bioinformatics/btp460>.
It also offers a convenient interface to a number of other regularized
t-statistics commonly employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between st versions 1.2.5 dated 2015-07-08 and 1.2.6 dated 2020-09-24
DESCRIPTION | 24 ++++++++++++------------ MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/modt.R | 4 ++-- man/cst.stat.Rd | 4 ++-- man/diffmean.stat.Rd | 2 +- man/lait.stat.Rd | 2 +- man/regularizedt.Rd | 4 ++-- man/shrinkcat.stat.Rd | 4 ++-- man/shrinkt.stat.Rd | 4 ++-- man/st.package.Rd | 4 ++-- man/studentt.stat.Rd | 2 +- 12 files changed, 43 insertions(+), 38 deletions(-)
Title: Functions for Working with 'Eprime' Text Files
Description: 'Eprime' is a set of programs for administering
psychological experiments by computer. This package provides functions
for loading, parsing, filtering and exporting data in the text files
produced by 'Eprime' experiments.
Author: Tristan Mahr [aut, cre] (<https://orcid.org/0000-0002-8890-5116>)
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>
Diff between rprime versions 0.1.0 dated 2015-05-29 and 0.1.2 dated 2020-09-24
rprime-0.1.0/rprime/LICENSE |only rprime-0.1.0/rprime/R/rprime.R |only rprime-0.1.0/rprime/man/count_tabs.Rd |only rprime-0.1.0/rprime/man/make_filter.Rd |only rprime-0.1.0/rprime/man/make_ranges.Rd |only rprime-0.1.0/rprime/man/parse_chunks.Rd |only rprime-0.1.0/rprime/man/tidy.Rd |only rprime-0.1.2/rprime/DESCRIPTION | 36 rprime-0.1.2/rprime/MD5 | 73 - rprime-0.1.2/rprime/NAMESPACE | 7 rprime-0.1.2/rprime/NEWS.md |only rprime-0.1.2/rprime/R/extract.R | 10 rprime-0.1.2/rprime/R/filter.R | 5 rprime-0.1.2/rprime/R/frames.R | 11 rprime-0.1.2/rprime/R/load.R | 10 rprime-0.1.2/rprime/R/patterns.R | 1 rprime-0.1.2/rprime/R/rprime-package.R |only rprime-0.1.2/rprime/build/vignette.rds |binary rprime-0.1.2/rprime/inst/doc/multiple-files.R | 10 rprime-0.1.2/rprime/inst/doc/multiple-files.html | 462 ++++++++-- rprime-0.1.2/rprime/inst/doc/parsing-summary.R | 14 rprime-0.1.2/rprime/inst/doc/parsing-summary.Rmd | 10 rprime-0.1.2/rprime/inst/doc/parsing-summary.html | 484 ++++++++--- rprime-0.1.2/rprime/inst/doc/quick-start-demo.R | 30 rprime-0.1.2/rprime/inst/doc/quick-start-demo.Rmd | 41 rprime-0.1.2/rprime/inst/doc/quick-start-demo.html | 902 +++++++++++++-------- rprime-0.1.2/rprime/man/EprimeFrame.Rd | 3 rprime-0.1.2/rprime/man/FrameList.Rd | 35 rprime-0.1.2/rprime/man/as.EprimeFrame.Rd | 3 rprime-0.1.2/rprime/man/as.FrameList.Rd | 3 rprime-0.1.2/rprime/man/extract_chunks.Rd | 7 rprime-0.1.2/rprime/man/filter_in.Rd | 5 rprime-0.1.2/rprime/man/keep_levels.Rd | 5 rprime-0.1.2/rprime/man/list_functions.Rd | 7 rprime-0.1.2/rprime/man/listify.Rd | 3 rprime-0.1.2/rprime/man/preview_eprime.Rd | 5 rprime-0.1.2/rprime/man/read_eprime.Rd | 3 rprime-0.1.2/rprime/man/rprime.Rd | 21 rprime-0.1.2/rprime/man/to_data_frame.Rd | 3 rprime-0.1.2/rprime/tests/testthat/test-load.R | 4 rprime-0.1.2/rprime/vignettes/parsing-summary.Rmd | 10 rprime-0.1.2/rprime/vignettes/quick-start-demo.Rmd | 41 42 files changed, 1563 insertions(+), 701 deletions(-)
Title: Sampling from Order Statistics of New Families of Distributions
Description: Set of tools to generate samples of order statistics and others quantities of interest from new families of distributions.
The main references for this package are: Gentle, J. (2009), Computational Statistics, Springer-Verlag;
Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and
Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>.
The families of distributions are: Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions,
beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions,
exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions,
and exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distribution, Skew normal type 1 distributions, Skew student t distribution, Sinh-Arcsinh distribution, Sichel distribution and Zero inflated Poisson.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between orders versions 0.1.3 dated 2019-05-16 and 0.1.4 dated 2020-09-24
DESCRIPTION | 19 +++--- MD5 | 16 +++++ NAMESPACE | 130 ++++++++++++++++++++++++++--------------------- R/order_pig.R |only R/order_sichel.R |only R/order_sinharcsinh.R |only R/order_snormal1.R |only R/order_sstudentt.R |only R/order_zip.R |only man/order_pig.Rd |only man/order_sichel.Rd |only man/order_sinharcsinh.Rd |only man/order_snormal1.Rd |only man/order_sstudentt.Rd |only man/order_zip.Rd |only 15 files changed, 97 insertions(+), 68 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <DOI:10.1126/science.1132939>).
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.1 dated 2020-06-26 and 0.1.2 dated 2020-09-24
SubtypeDrug-0.1.1/SubtypeDrug/R/OCSSD.R |only SubtypeDrug-0.1.1/SubtypeDrug/R/plotDrugStructure.R |only SubtypeDrug-0.1.1/SubtypeDrug/man/OCSSD.Rd |only SubtypeDrug-0.1.1/SubtypeDrug/man/plotDrugStructure.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/DESCRIPTION | 6 SubtypeDrug-0.1.2/SubtypeDrug/MD5 | 48 ++--- SubtypeDrug-0.1.2/SubtypeDrug/NAMESPACE | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/AccumulateNormal.R | 2 SubtypeDrug-0.1.2/SubtypeDrug/R/Disease_drugs.R | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/PrioSubtypeDrug.R |only SubtypeDrug-0.1.2/SubtypeDrug/R/getDrugSpw.R | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/getDrugStructure.R |only SubtypeDrug-0.1.2/SubtypeDrug/R/plotDScoreHeatmap.R | 39 ++-- SubtypeDrug-0.1.2/SubtypeDrug/R/plotDSpwHeatmap.R | 25 +-- SubtypeDrug-0.1.2/SubtypeDrug/R/plotGlobalGraph.R | 19 +- SubtypeDrug-0.1.2/SubtypeDrug/build/vignette.rds |binary SubtypeDrug-0.1.2/SubtypeDrug/data/Colork.rda |binary SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.R | 5 SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.Rmd | 110 ++++++------- SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.html | 139 ++++++++--------- SubtypeDrug-0.1.2/SubtypeDrug/man/AccumulateNormal.Rd | 2 SubtypeDrug-0.1.2/SubtypeDrug/man/Disease_drugs.Rd | 4 SubtypeDrug-0.1.2/SubtypeDrug/man/PrioSubtypeDrug.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/man/getDrugStructure.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/man/plotDScoreHeatmap.Rd | 39 ++-- SubtypeDrug-0.1.2/SubtypeDrug/man/plotDSpwHeatmap.Rd | 6 SubtypeDrug-0.1.2/SubtypeDrug/man/plotGlobalGraph.Rd | 4 SubtypeDrug-0.1.2/SubtypeDrug/vignettes/references.bib | 33 ++++ SubtypeDrug-0.1.2/SubtypeDrug/vignettes/vignette.Rmd | 110 ++++++------- 29 files changed, 317 insertions(+), 286 deletions(-)
Title: R Script Visualization in Cytoscape
Description: Displays the content of a R script into the 'Cytoscape' network-visualization app <https://cytoscape.org/>.
Author: Raphael Bonnet [aut, cre], Marion Guernoté [ctb], Terry Gouin [ctb], Maxime Laurens [ctb], Thibault Meekel [ctb], Jean-François Peyron[aut,ths]
Maintainer: Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>
Diff between ScriptMapR versions 0.0.2 dated 2020-09-21 and 0.0.3 dated 2020-09-24
DESCRIPTION | 8 MD5 | 6 R/scriptmapr.R | 3613 ++++++++++++++++++++++++------------------------ README.md |only inst/extdata/parsed.RDS |only 5 files changed, 1842 insertions(+), 1785 deletions(-)
Title: Random Chuck Norris Facts
Description: R functions for generating and/or displaying random Chuck Norris
facts. Based on data from the 'Internet Chuck Norris database' ('ICNDb').
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between roundhouse versions 0.0.1 dated 2018-09-16 and 0.0.2 dated 2020-09-24
roundhouse-0.0.1/roundhouse/man/fetch_categories.Rd |only roundhouse-0.0.1/roundhouse/tests/testthat |only roundhouse-0.0.1/roundhouse/tests/testthat.R |only roundhouse-0.0.2/roundhouse/DESCRIPTION | 19 +-- roundhouse-0.0.2/roundhouse/MD5 | 29 +++-- roundhouse-0.0.2/roundhouse/NAMESPACE | 4 roundhouse-0.0.2/roundhouse/NEWS.md | 20 +++ roundhouse-0.0.2/roundhouse/R/facts.R |only roundhouse-0.0.2/roundhouse/R/kick.R | 6 - roundhouse-0.0.2/roundhouse/R/punch.R |only roundhouse-0.0.2/roundhouse/R/random_fact.R | 114 ++++---------------- roundhouse-0.0.2/roundhouse/R/suggest_new_fact.R |only roundhouse-0.0.2/roundhouse/data |only roundhouse-0.0.2/roundhouse/inst |only roundhouse-0.0.2/roundhouse/man/facts.Rd |only roundhouse-0.0.2/roundhouse/man/figures |only roundhouse-0.0.2/roundhouse/man/kick.Rd | 12 +- roundhouse-0.0.2/roundhouse/man/punch.Rd |only roundhouse-0.0.2/roundhouse/man/random_fact.Rd | 16 ++ roundhouse-0.0.2/roundhouse/man/suggest_new_fact.Rd |only roundhouse-0.0.2/roundhouse/tests/tinytest.R |only 21 files changed, 102 insertions(+), 118 deletions(-)
Title: The Lorentz Transform in Relativistic Physics
Description: The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Includes active and passive transforms and the ability to use units in which the speed of light is not one. For general relativity, see the
'schwarzschild' package.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between lorentz versions 1.0-2 dated 2019-03-21 and 1.0-5 dated 2020-09-24
lorentz-1.0-2/lorentz/tests/aaa.R |only lorentz-1.0-2/lorentz/tests/aab.R |only lorentz-1.0-5/lorentz/DESCRIPTION | 15 - lorentz-1.0-5/lorentz/MD5 | 71 ++++--- lorentz-1.0-5/lorentz/NAMESPACE | 10 - lorentz-1.0-5/lorentz/R/gyrogroup.R | 191 +++++++++++++------- lorentz-1.0-5/lorentz/R/nullvector.R | 10 - lorentz-1.0-5/lorentz/README.md |only lorentz-1.0-5/lorentz/build/partial.rdb |binary lorentz-1.0-5/lorentz/build/vignette.rds |binary lorentz-1.0-5/lorentz/inst/JOC |only lorentz-1.0-5/lorentz/inst/distributive_search.R | 40 +++- lorentz-1.0-5/lorentz/inst/doc/lorentz.R | 218 ++++++++++++++--------- lorentz-1.0-5/lorentz/inst/doc/lorentz.Rnw | 175 +++++++++++++----- lorentz-1.0-5/lorentz/inst/doc/lorentz.pdf |binary lorentz-1.0-5/lorentz/inst/mobius.Rmd |only lorentz-1.0-5/lorentz/man/3vel.Rd | 3 lorentz-1.0-5/lorentz/man/4mom.Rd | 36 ++- lorentz-1.0-5/lorentz/man/4vel.Rd | 28 +- lorentz-1.0-5/lorentz/man/Extract.Rd | 5 lorentz-1.0-5/lorentz/man/as.matrix.Rd |only lorentz-1.0-5/lorentz/man/boost.Rd | 55 +++-- lorentz-1.0-5/lorentz/man/c.Rd | 9 lorentz-1.0-5/lorentz/man/comm_fail.Rd | 12 - lorentz-1.0-5/lorentz/man/cosines.Rd |only lorentz-1.0-5/lorentz/man/galileo.Rd |only lorentz-1.0-5/lorentz/man/gam.Rd | 9 lorentz-1.0-5/lorentz/man/gyr.Rd | 5 lorentz-1.0-5/lorentz/man/r3vel.Rd | 28 ++ lorentz-1.0-5/lorentz/man/reflect.Rd | 30 ++- lorentz-1.0-5/lorentz/man/seq.Rd | 2 lorentz-1.0-5/lorentz/man/set.Rd | 13 - lorentz-1.0-5/lorentz/man/sol.Rd | 25 +- lorentz-1.0-5/lorentz/tests/testthat |only lorentz-1.0-5/lorentz/tests/testthat.R |only lorentz-1.0-5/lorentz/vignettes/f-002.pdf |only lorentz-1.0-5/lorentz/vignettes/lorentz.Rnw | 175 +++++++++++++----- lorentz-1.0-5/lorentz/vignettes/lorentz.bib | 5 38 files changed, 789 insertions(+), 381 deletions(-)
Title: Weighted Logrank Tests and NPMLE for Interval Censored Data
Description: Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between interval versions 1.1-0.1 dated 2014-01-22 and 1.1-0.7 dated 2020-09-24
DESCRIPTION | 10 ++--- MD5 | 25 +++++++------- NAMESPACE | 7 +++- NEWS | 12 ++++++ R/onLoad.R |only build/vignette.rds |binary inst/CITATION | 4 +- inst/doc/intervalCensoring.R | 70 ++++++++++++++++++++-------------------- inst/doc/intervalCensoring.Rnw | 1 inst/doc/intervalCensoring.pdf |binary man/icfit.Rd | 9 ++--- man/ictest.Rd | 6 +-- man/interval-package.Rd | 6 +-- vignettes/intervalCensoring.Rnw | 1 14 files changed, 84 insertions(+), 67 deletions(-)
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen, Nancy R. Zhang, Lynna Chu, and Hoseung Song
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 0.7 dated 2020-04-12 and 1.0 dated 2020-09-24
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++++----- NAMESPACE | 2 +- R/NNL.R |only R/gSeg_discrete.R |only man/gSeg-package.Rd | 34 ++++++++++++++++++++++++++++++---- man/gseg1.Rd | 4 +--- man/gseg1_discrete.Rd |only man/gseg2.Rd | 4 +--- man/gseg2_discrete.Rd |only man/nnl.Rd |only 11 files changed, 48 insertions(+), 21 deletions(-)
Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations
for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples.
The purpose of 'universals' is to reduce package dependencies and conflicts.
The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between universals versions 0.0.3 dated 2020-07-08 and 0.0.4 dated 2020-09-24
DESCRIPTION | 11 +++--- MD5 | 62 +++++++++++++++++----------------- NAMESPACE | 2 + NEWS.md | 4 ++ R/bind-iterations.R |only R/collapse-chains.R | 15 ++++++++ R/estimates.R | 6 --- R/nchains.R | 7 --- R/ndims.R | 1 R/niters.R | 5 -- R/npdims.R | 5 -- R/nsams.R | 9 ---- R/nsims.R | 5 -- R/nterms.R | 10 ----- R/pars.R | 4 -- R/pdims.R | 5 -- R/set-pars.R | 7 --- R/split-chains.R | 6 --- man/bind_chains.Rd | 1 man/bind_iterations.Rd |only man/collapse_chains.Rd | 4 ++ man/estimates.Rd | 10 ----- man/nchains.Rd | 10 ----- man/niters.Rd | 8 ---- man/npdims.Rd | 8 ---- man/nsams.Rd | 12 ------ man/nsims.Rd | 8 ---- man/nterms.Rd | 13 ------- man/pars.Rd | 7 --- man/pdims.Rd | 8 ---- man/set_pars.Rd | 10 ----- man/split_chains.Rd | 10 ----- tests/testthat/test-collapse-chains.R | 1 33 files changed, 67 insertions(+), 207 deletions(-)
Title: Time Series, Analysis and Application
Description: Accompanies the book Rainer Schlittgen and Cristina Sattarhoff (2020) <https://www.degruyter.com/view/title/575978> "Angewandte Zeitreihenanalyse mit R, 4. Auflage" . The package contains the time series and functions used therein. It was developed over many years teaching courses about time series analysis.
Author: Rainer Schlittgen
Maintainer: Rainer Schlittgen <R.Schlittgen@t-online.de>
Diff between tsapp versions 1.0.1 dated 2020-09-21 and 1.0.2 dated 2020-09-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/specialfun.r | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Score Optimal Probabilistic Forecast Reconciliation
Description: Training of reconciliation weights for probabilistic forecasts to optimise total energy (or variogram) score using Stochastic Gradient Descent with automatically differentiated gradients. See Panagiotelis, Gamakumara, Athanasopoulos and Hyndman, (2020) <https://www.monash.edu/business/ebs/research/publications/ebs/wp26-2020.pdf> for a description of the methods.
Author: Anastasios Panagiotelis [aut, cre]
(<https://orcid.org/0000-0001-8678-7294>)
Maintainer: Anastasios Panagiotelis <anastasios.panagiotelis@sydney.edu.au>
Diff between ProbReco versions 0.1.0 dated 2020-08-18 and 0.1.0.1 dated 2020-09-24
DESCRIPTION | 13 MD5 | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/ProbReco-with-fable.html | 575 +++++++++++++++++++++++++++----------- inst/doc/ProbReco.html | 472 ++++++++++++++++++++++--------- man/ProbReco-package.Rd | 2 man/inscoreopt.Rd | 22 + man/scoreopt.Rd | 19 - man/scoreopt.control.Rd | 16 - man/sim_hierarchy.Rd | 6 man/total_score.Rd | 9 12 files changed, 836 insertions(+), 320 deletions(-)
Title: Tools for Inference in the Presence of a Monotone Likelihood
Description: Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist. These difficulties are related to those arising from logistic and multinomial regression. References for methods are given in the separate function documents.
Author: John E. Kolassa and Juan Zhang
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between PHInfiniteEstimates versions 1.3 dated 2020-03-29 and 1.5 dated 2020-09-24
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 4 +--- R/convertmtol.R | 1 + R/testp.R | 8 ++++++-- R/voter.ml.R | 1 + build/partial.rdb |binary inst/REFERENCES.bib | 2 +- man/convertmtol.Rd | 1 + man/voter.ml.Rd | 1 + 10 files changed, 26 insertions(+), 20 deletions(-)
More information about PHInfiniteEstimates at CRAN
Permanent link
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.7.1 dated 2020-04-12 and 1.7.2 dated 2020-09-24
DESCRIPTION | 8 MD5 | 14 NEWS.md | 5 R/tools.R | 2 build/vignette.rds |binary inst/doc/An_Introduction_to_fakemake.html | 421 ++++++++++++++++++++++-------- inst/doc/Building_Packages.html | 371 ++++++++++++++++++++------ man/check_archive.Rd | 2 8 files changed, 625 insertions(+), 198 deletions(-)
Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Author: Samuel R. Borstein <sam@borstein.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between AnnotationBustR versions 1.2 dated 2018-04-09 and 1.3.0 dated 2020-09-24
DESCRIPTION | 14 - MD5 | 37 +-- NEWS.md | 8 R/AnnotationBust.R | 36 ++- R/FindLongestSeq.R | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/AnnotationBustR-vignette.R | 2 inst/doc/AnnotationBustR-vignette.Rmd | 29 ++ inst/doc/AnnotationBustR-vignette.html | 345 +++++++++++++++++++++++++++++---- man/AnnotationBust.Rd | 22 +- man/AnnotationBustR.Rd | 1 man/FindLongestSeq.Rd | 2 man/cpDNAterms.Rd | 6 man/mtDNAterms.Rd | 6 man/mtDNAtermsPlants.Rd | 6 man/rDNAterms.Rd | 6 tests/testthat/test_AnnotationBust.R | 11 - tests/testthat/test_FindLongestSeq.R | 18 + vignettes/AnnotationBustR-vignette.Rmd | 29 ++ 20 files changed, 465 insertions(+), 115 deletions(-)
More information about AnnotationBustR at CRAN
Permanent link
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>),
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>),
John Little [ctb],
Joselyn Chávez [ctb] (<https://orcid.org/0000-0002-4974-4591>),
Joseph Casillas [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Matthew Mark Strasiotto [ctb] (mstr3336),
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>),
Paul Lemmens [ctb],
Sean Lopp [ctb],
Yongfu Liao [ctb],
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.16 dated 2020-03-31 and 0.17 dated 2020-09-24
DESCRIPTION | 12 MD5 | 38 +- R/render.R | 39 +- README.md | 8 build/vignette.rds |binary inst/examples/ki-demo.Rmd | 2 inst/examples/uol-demo.Rmd | 2 inst/rmarkdown/templates/xaringan/resources/default.css | 2 inst/rmarkdown/templates/xaringan/resources/fc.css | 10 inst/rmarkdown/templates/xaringan/resources/ki-fonts.css | 2 inst/rmarkdown/templates/xaringan/resources/ki.css | 154 +++++----- inst/rmarkdown/templates/xaringan/resources/middlebury.css | 6 inst/rmarkdown/templates/xaringan/resources/robot.css | 2 inst/rmarkdown/templates/xaringan/resources/rutgers.css | 2 inst/rmarkdown/templates/xaringan/resources/uol.css | 2 inst/rmarkdown/templates/xaringan/resources/useR-fonts.css |only inst/rmarkdown/templates/xaringan/resources/useR.css |only inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 45 +- inst/rmarkdown/templates/xaringan_zh-CN/skeleton/skeleton.Rmd | 16 - man/inf_mr.Rd | 2 man/moon_reader.Rd | 19 - 21 files changed, 192 insertions(+), 171 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type
token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable
frequency analyses (supports Celex and Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For full functionality a local installation of
TreeTagger is recommended. It is also recommended to not load this package directly, but by loading one of the available language support packages from the
'l10n' repository <https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for
its basic features. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from <https://rkward.kde.org> (plugins are detected automatically). Due to some restrictions on CRAN, the full package sources
are only available from the project homepage. To ask for help, report bugs, request features, or discuss the development of the package, please subscribe to
the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.13-1 dated 2020-09-21 and 0.13-2 dated 2020-09-24
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/02_method_readTagged.R | 2 +- R/koRpus-package.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/doc/koRpus_vignette.html | 4 ++-- man/koRpus-package.Rd | 4 ++-- man/readTagged-methods.Rd | 2 +- tests/testthat/test_tokenizing_POS_tagging.R | 21 ++++++++++++++++----- 11 files changed, 47 insertions(+), 29 deletions(-)
Title: A Universal Foreach Parallel Adapter using the Future API of the
'future' Package
Description: Provides a '%dopar%' adapter such that any type of futures can
be used as backends for the 'foreach' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 0.9.0 dated 2020-01-11 and 0.10.0 dated 2020-09-24
doFuture-0.10.0/doFuture/DESCRIPTION | 14 - doFuture-0.10.0/doFuture/MD5 | 73 +++++----- doFuture-0.10.0/doFuture/NEWS | 23 ++- doFuture-0.10.0/doFuture/R/doFuture-package.R | 4 doFuture-0.10.0/doFuture/R/doFuture.R | 3 doFuture-0.10.0/doFuture/R/makeChunks.R |only doFuture-0.10.0/doFuture/R/registerDoFuture.R | 15 ++ doFuture-0.10.0/doFuture/R/utils.R | 23 +-- doFuture-0.10.0/doFuture/build/vignette.rds |binary doFuture-0.10.0/doFuture/inst/CITATION |only doFuture-0.10.0/doFuture/inst/doc/doFuture.html | 12 - doFuture-0.10.0/doFuture/inst/doc/doFuture.md.rsp | 12 - doFuture-0.10.0/doFuture/inst/tests2/NMF/manual.R | 2 doFuture-0.10.0/doFuture/inst/tests2/caret/examples.R | 2 doFuture-0.10.0/doFuture/inst/tests2/glmnet/examples.R | 2 doFuture-0.10.0/doFuture/inst/tests2/incl/utils.R | 30 ++-- doFuture-0.10.0/doFuture/man/doFuture.Rd | 17 +- doFuture-0.10.0/doFuture/man/makeChunks.Rd | 2 doFuture-0.10.0/doFuture/tests/DEPRECATED.R | 4 doFuture-0.10.0/doFuture/tests/doRNG,dorng.R | 5 doFuture-0.10.0/doFuture/tests/foreach,errors.R | 2 doFuture-0.10.0/doFuture/tests/foreach,globals.R | 2 doFuture-0.10.0/doFuture/tests/foreach.R | 45 ------ doFuture-0.10.0/doFuture/tests/incl/end.R | 3 doFuture-0.10.0/doFuture/tests/incl/start,load-only.R | 2 doFuture-0.10.0/doFuture/tests/makeChunks.R |only doFuture-0.10.0/doFuture/tests/registerDoFuture.R | 2 doFuture-0.10.0/doFuture/tests/times.R | 2 doFuture-0.10.0/doFuture/tests/utils.R |only doFuture-0.10.0/doFuture/tests/zzz,BiocParallel.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,NMF,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,TSP,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,caret,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,foreach,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,future.BatchJobs.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,future.batchtools.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,glmnet,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,plyr,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,plyr.R | 55 +++++-- doFuture-0.10.0/doFuture/vignettes/doFuture.md.rsp | 12 - doFuture-0.9.0/doFuture/R/chunks.R |only doFuture-0.9.0/doFuture/tests/future.BatchJobs.R |only doFuture-0.9.0/doFuture/tests/future.batchtools.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,NMF.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,TSP.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,caret.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,foreach.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,glmnet.R |only 48 files changed, 191 insertions(+), 177 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of
mapping functions to apply a function to each combination of elements
in a list of inputs. Also includes functions for automatically
detecting output type in mapping functions, finding every combination
of elements of lists or rows of data frames, and applying multiple
models to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.1.0 dated 2020-09-10 and 0.2.0 dated 2020-09-24
DESCRIPTION | 11 ++--- MD5 | 17 ++++---- NEWS.md |only R/cross_fit.R | 55 ++++++++++++++++++++++---- R/isFALSE.R | 12 ++--- README.md | 84 ++++++++++++++++++++-------------------- man/cross_fit.Rd | 11 ++++- man/cross_join.Rd | 4 - man/crossmap-package.Rd | 1 tests/testthat/test-cross_fit.R | 71 ++++++++++++++++++++++++++++----- 10 files changed, 185 insertions(+), 81 deletions(-)
Title: Reading and Saving DICOM Image Files
Description: This function provides an interface between 'Matlab' and 'R' in facilitating fast processing for reading and saving DICOM images.
Author: Shu Jiang [aut, cre] (<https://orcid.org/0000-0003-1464-4838>)
Maintainer: Shu Jiang <jiang.shu@wustl.edu>
Diff between DICOMread versions 0.0.0.1 dated 2020-09-01 and 0.0.0.2 dated 2020-09-24
DICOMread-0.0.0.1/DICOMread/R/save_mat.R |only DICOMread-0.0.0.1/DICOMread/man/form_mat_fun.Rd |only DICOMread-0.0.0.2/DICOMread/DESCRIPTION | 6 +++--- DICOMread-0.0.0.2/DICOMread/MD5 | 6 ++---- DICOMread-0.0.0.2/DICOMread/NAMESPACE | 1 - 5 files changed, 5 insertions(+), 8 deletions(-)
Title: An Extension of the Taylor Diagram to Two-Dimensional Vector
Data
Description: A new diagram for the verification of vector variables (wind, current, etc) generated by multiple models against a set of observations is presented in this package. It has been designed as a generalization of the Taylor diagram to two dimensional quantities. It is based on the analysis of the two-dimensional structure of the mean squared error matrix between model and observations. The matrix is divided into the part corresponding to the relative rotation and the bias of the empirical orthogonal functions of the data. The full set of diagnostics produced by the analysis of the errors between model and observational vector datasets comprises the errors in the means, the analysis of the total variance of both datasets, the rotation matrix corresponding to the principal components in observation and model, the angle of rotation of model-derived empirical orthogonal functions respect to the ones from observations, the standard deviation of model and observations, the root mean squared error between both datasets and the squared two-dimensional correlation coefficient. See the output of function UVError() in this package.
Author: Jon Sáenz [aut, cph] (<https://orcid.org/0000-0002-5920-7570>),
Sheila Carreno-Madinabeitia [aut, cph]
(<https://orcid.org/0000-0003-4625-6178>),
Santos J. González-Rojí [aut, cre, cph]
(<https://orcid.org/0000-0003-4737-0984>),
Ganix Esnaola [ctb, cph] (<https://orcid.org/0000-0001-9058-043X>),
Gabriel Ibarra-Berastegi [ctb, cph]
(<https://orcid.org/0000-0001-8681-3755>),
Alain Ulazia [ctb, cph] (<https://orcid.org/0000-0002-4124-2853>)
Maintainer: Santos J. González-Rojí <santosjose.gonzalez@ehu.eus>
Diff between SailoR versions 1.1.2 dated 2020-07-16 and 1.2 dated 2020-09-23
DESCRIPTION | 8 - MD5 | 6 NEWS.md | 5 R/UVError.R | 397 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 215 insertions(+), 201 deletions(-)
Title: Crawler and Data Scraper for Open Journal System ('OJS')
Description: Crawler for 'OJS' pages and scraper for meta-data from articles.
You can crawl 'OJS' archives, issues, articles, galleys, and search results.
You can scrape articles metadata from their head tag in html,
or from Open Archives Initiative ('OAI') records.
Most of these functions rely on 'OJS' routing conventions
(<https://docs.pkp.sfu.ca/dev/documentation/en/architecture-routes>).
Author: Gaston Becerra [aut, cre] (<https://orcid.org/0000-0001-9432-8848>)
Maintainer: Gaston Becerra <gaston.becerra@gmail.com>
Diff between ojsr versions 0.1.1 dated 2020-07-01 and 0.1.2 dated 2020-09-23
DESCRIPTION | 14 - MD5 | 34 +-- NEWS.md | 11 + R/ojsr.R | 7 R/scrapers.R | 201 +++++++++++--------- R/url_parsers.R | 4 README.md | 35 ++- inst/doc/ojsr-vignette.R | 79 ++++++- inst/doc/ojsr-vignette.Rmd | 195 +++++++++++-------- inst/doc/ojsr-vignette.html | 377 ++++++++++++++++++++------------------ man/get_articles_from_issue.Rd | 4 man/get_articles_from_search.Rd | 6 man/get_galleys_from_article.Rd | 4 man/get_html_meta_from_article.Rd | 4 man/get_issues_from_archive.Rd | 4 man/get_oai_meta_from_article.Rd | 4 man/ojsr.Rd | 7 vignettes/ojsr-vignette.Rmd | 195 +++++++++++-------- 18 files changed, 700 insertions(+), 485 deletions(-)
Title: Learning Causal or Non-Causal Graphical Models Using Information
Theory
Description: We report an information-theoretic method which learns a large
class of causal or non-causal graphical models from purely observational
data, while including the effects of unobserved latent variables, commonly
found in many datasets. Starting from a complete graph, the method
iteratively removes dispensable edges, by uncovering significant information
contributions from indirect paths, and assesses edge-specific confidences
from randomization of available data. The remaining edges are then oriented
based on the signature of causality in observational data. This approach can
be applied on a wide range of datasets and provide new biological insights
on regulatory networks from single cell expression data, genomic alterations
during tumor development and co-evolving residues in protein structures.
For more information you can refer to:
Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>,
Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre],
Honghao Li [aut],
Marcel Ribeiro Dantas [aut],
Nadir Sella [aut],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>
Diff between miic versions 1.5.1 dated 2020-09-18 and 1.5.2 dated 2020-09-23
DESCRIPTION | 6 MD5 | 34 R/miic.R | 2 man/miic.Rd | 2 src/computation_continuous.cpp | 1839 ++++++++++++++--------------------------- src/computation_continuous.h | 7 src/computation_discrete.cpp | 551 ++++-------- src/confidence_cut.cpp | 6 src/environment.h | 1 src/get_information.cpp | 8 src/linear_allocator.cpp | 19 src/linear_allocator.h | 6 src/mdl_pair_discretize.cpp | 48 - src/mutual_information.cpp | 294 ++---- src/mutual_information.h | 166 +-- src/skeleton.cpp | 14 src/structure.h | 22 src/utilities.cpp | 25 18 files changed, 1135 insertions(+), 1915 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@ab.mpg.de>
Maintainer: Damien R. Farine <dfarine@ab.mpg.de>
Diff between asnipe versions 1.1.12 dated 2019-08-19 and 1.1.13 dated 2020-09-23
DESCRIPTION | 10 ++++----- MD5 | 17 ++++++++------- R/network_permutation.R | 50 ++++++++++++++++++++++++++++++++------------- R/network_swap.R | 48 ++++++++++++++++++++++++++++++++----------- inst |only man/asnipe-package.Rd | 4 +-- man/mrqap.custom.null.Rd | 4 +-- man/mrqap.dsp.Rd | 4 +-- man/network_permutation.Rd | 10 ++++++++- man/network_swap.Rd | 13 ++++++++++- 10 files changed, 113 insertions(+), 47 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.9.6 dated 2020-06-11 and 3.9.7 dated 2020-09-23
lessR-3.9.6/lessR/R/corFA.Rmd.R |only lessR-3.9.7/lessR/DESCRIPTION | 8 lessR-3.9.7/lessR/MD5 | 115 +++++---- lessR-3.9.7/lessR/NAMESPACE | 2 lessR-3.9.7/lessR/NEWS | 58 ++++- lessR-3.9.7/lessR/R/ANOVA.R | 3 lessR-3.9.7/lessR/R/ANOVAz2.R | 93 +++++--- lessR-3.9.7/lessR/R/BarChart.R | 18 - lessR-3.9.7/lessR/R/Logit.R | 2 lessR-3.9.7/lessR/R/Plot.R | 11 lessR-3.9.7/lessR/R/Read.R | 22 + lessR-3.9.7/lessR/R/Regression.R | 290 +++++++++++++------------ lessR-3.9.7/lessR/R/Rescale.R |only lessR-3.9.7/lessR/R/corCFA.R | 27 +- lessR-3.9.7/lessR/R/corEFA.R | 23 + lessR-3.9.7/lessR/R/corFA_Rmd.R |only lessR-3.9.7/lessR/R/corProp.R | 19 - lessR-3.9.7/lessR/R/corReflect.R | 20 - lessR-3.9.7/lessR/R/corReorder.R | 104 +++++++- lessR-3.9.7/lessR/R/corScree.R | 37 ++- lessR-3.9.7/lessR/R/factors.R | 2 lessR-3.9.7/lessR/R/plt.zadd.R | 21 + lessR-3.9.7/lessR/R/plt.zbubble.R |only lessR-3.9.7/lessR/R/plt.zmain.R | 215 ++++++------------ lessR-3.9.7/lessR/R/reg.z1modelBasic.R | 3 lessR-3.9.7/lessR/R/reg.zKfold.R | 45 ++- lessR-3.9.7/lessR/R/style.R | 5 lessR-3.9.7/lessR/R/style.zshow.R | 2 lessR-3.9.7/lessR/R/zzz.R | 67 +++-- lessR-3.9.7/lessR/build/vignette.rds |binary lessR-3.9.7/lessR/inst/doc/BarChart.html | 78 +++--- lessR-3.9.7/lessR/inst/doc/Customize.html | 17 + lessR-3.9.7/lessR/inst/doc/Extract.html | 32 ++ lessR-3.9.7/lessR/inst/doc/FactorAnalysis.R |only lessR-3.9.7/lessR/inst/doc/FactorAnalysis.Rmd |only lessR-3.9.7/lessR/inst/doc/FactorAnalysis.html |only lessR-3.9.7/lessR/inst/doc/Histogram.html | 16 + lessR-3.9.7/lessR/inst/doc/Means.R | 21 + lessR-3.9.7/lessR/inst/doc/Means.Rmd | 65 +++-- lessR-3.9.7/lessR/inst/doc/Means.html | 210 +++++++++++------- lessR-3.9.7/lessR/inst/doc/Plot.R | 13 + lessR-3.9.7/lessR/inst/doc/Plot.Rmd | 24 +- lessR-3.9.7/lessR/inst/doc/Plot.html | 100 +++++++- lessR-3.9.7/lessR/inst/doc/Read.html | 16 + lessR-3.9.7/lessR/inst/doc/Regression.R | 5 lessR-3.9.7/lessR/inst/doc/Regression.Rmd | 11 lessR-3.9.7/lessR/inst/doc/Regression.html | 108 ++++++++- lessR-3.9.7/lessR/inst/doc/pivot.html | 16 + lessR-3.9.7/lessR/man/ANOVA.Rd | 7 lessR-3.9.7/lessR/man/Plot.Rd | 46 ++- lessR-3.9.7/lessR/man/Regression.Rd | 60 +++-- lessR-3.9.7/lessR/man/Rescale.Rd |only lessR-3.9.7/lessR/man/corCFA.Rd | 6 lessR-3.9.7/lessR/man/corEFA.Rd | 6 lessR-3.9.7/lessR/man/corProp.Rd | 2 lessR-3.9.7/lessR/man/corReflect.Rd | 2 lessR-3.9.7/lessR/man/corReorder.Rd | 23 + lessR-3.9.7/lessR/man/corScree.Rd | 4 lessR-3.9.7/lessR/man/style.Rd | 2 lessR-3.9.7/lessR/vignettes/FactorAnalysis.Rmd |only lessR-3.9.7/lessR/vignettes/Means.Rmd | 65 +++-- lessR-3.9.7/lessR/vignettes/Plot.Rmd | 24 +- lessR-3.9.7/lessR/vignettes/Regression.Rmd | 11 63 files changed, 1430 insertions(+), 772 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp]
Maintainer: KM Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-2 dated 2020-09-03 and 0.7-3 dated 2020-09-23
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/final.org.R | 6 +++--- inst/doc/gimme_vignette.html | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Description: Functions to compare two or more survival curves with:
a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>
Diff between FHtest versions 1.4 dated 2017-11-08 and 1.5 dated 2020-09-23
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/rcc.R | 2 +- R/rcp.R | 2 +- man/FHtest-package.Rd | 4 ++-- man/FHtesticp.Rd | 16 ++++++++-------- man/FHtestics.Rd | 10 +++++----- man/FHtestrcc.Rd | 8 ++++---- man/FHtestrcp.Rd | 14 +++++++------- man/illust3.Rd | 2 +- 10 files changed, 44 insertions(+), 44 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre],
Fanny Chow [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rsample versions 0.0.7 dated 2020-06-04 and 0.0.8 dated 2020-09-23
DESCRIPTION | 13 - MD5 | 116 +++++++------ NAMESPACE | 63 +++++++ NEWS.md | 8 R/apparent.R | 2 R/boot.R | 20 +- R/bootci.R | 20 +- R/compat-vctrs-helpers.R | 14 + R/compat-vctrs.R | 208 +++++++++++++++++++++++++ R/complement.R | 37 +++- R/data.R | 2 R/form_pred.R | 4 R/groups.R | 4 R/initial_split.R | 2 R/lables.R | 37 +++- R/loo.R | 2 R/manual.R |only R/mc.R | 22 +- R/misc.R | 4 R/nest.R | 2 R/pkg.R | 2 R/rolling_origin.R | 7 R/rset.R | 12 + R/rsplit.R | 4 R/slide.R |only R/validation_split.R | 4 R/vfold.R | 24 +- build/vignette.rds |binary inst/doc/Basics.html | 16 + inst/doc/Working_with_rsets.html | 68 +++++--- man/add_resample_id.Rd | 2 man/apparent.Rd | 2 man/bootstraps.Rd | 20 +- man/complement.Rd | 2 man/form_pred.Rd | 4 man/group_vfold_cv.Rd | 2 man/initial_split.Rd | 2 man/int_pctl.Rd | 9 - man/labels.rset.Rd | 2 man/manual_rset.Rd |only man/mc_cv.Rd | 20 +- man/nested_cv.Rd | 2 man/populate.Rd | 4 man/pretty.vfold_cv.Rd | 16 + man/rolling_origin.Rd | 8 man/rsample.Rd | 2 man/slide-resampling.Rd |only man/two_class_dat.Rd | 2 man/validation_split.Rd | 2 man/vfold_cv.Rd | 22 +- tests/testthat/test-manual.R |only tests/testthat/test-print-groups.txt | 10 - tests/testthat/test-slide.R |only tests/testthat/test_boot.R | 27 +-- tests/testthat/test_bootci.R | 35 +++- tests/testthat/test_for_pred.R | 8 tests/testthat/test_group.R | 44 ++--- tests/testthat/test_mc.R | 17 -- tests/testthat/test_rset.R | 4 tests/testthat/test_validation.R | 19 +- tests/testthat/test_vfold.R | 15 - vignettes/Applications/Recipes_and_rsample.Rmd | 2 62 files changed, 734 insertions(+), 287 deletions(-)
Title: Novel Statistical Test for Aberration Enrichment
Description: Testing for heterogeneous effects in a case-control setting.
The aim here to discover an association that is beyond a mean difference
between all cases and all controls. Instead, the signal of interest here
is present in only a proportion of the cases. This test should be more
powerful than a t-test or Wilcoxon test in this heterogeneous setting.
Please cite the corresponding paper: Mezlini et al. (2020)
<doi:10.1101/2020.03.23.002972>.
Author: Aziz M. Mezlini [aut,cre,cph]
Maintainer: Aziz M. Mezlini <mmezlini@mgh.harvard.edu>
Diff between aziztest versions 0.1.0 dated 2020-04-01 and 0.2.0 dated 2020-09-23
DESCRIPTION | 6 +-- MD5 | 22 ++++++------ NAMESPACE | 2 + R/aziztest_description.R | 4 +- R/main.R | 77 +++++++++++++++++++++++++++++------------- R/post_analysis.R | 11 +++--- inst/CITATION | 4 +- man/aziz.test.Rd | 27 ++++++++++++-- man/aziztest.Rd | 4 +- man/calibrate_test.Rd | 21 +++++++++-- man/get_calibrated_pvalues.Rd | 12 ++++-- man/which_aberrant.Rd | 2 - 12 files changed, 134 insertions(+), 58 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-13 dated 2020-04-08 and 1.4-14 dated 2020-09-23
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary demo/Ch_Appl.R | 22 +++++++++++----------- demo/Ch_GLM.R | 2 +- demo/Ch_Misc.R | 21 ++++++++------------- inst/NEWS | 4 ++++ inst/doc/chfls1.R | 1 - inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.R | 1 - inst/doc/multcomp-examples.pdf |binary man/trees513.Rd | 2 +- tests/regtest-survival.Rout.save | 10 +++++----- 16 files changed, 49 insertions(+), 52 deletions(-)
More information about combinedevents at CRAN
Permanent link
Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and
without spatial components. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments developed
by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie J. Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Willem Kruijer [ctb] (<https://orcid.org/0000-0001-7179-1733>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenSTA versions 1.0.5 dated 2020-06-24 and 1.0.6 dated 2020-09-23
DESCRIPTION | 13 - MD5 | 101 ++++----- NAMESPACE | 3 NEWS.md | 12 + R/createExtract.R | 27 +- R/createSTA.R | 109 ++++++--- R/createTD.R | 396 +++++++++++++++++++++++++---------- R/data.R | 2 R/extract.R | 26 -- R/extractSTA.R |only R/fitTD.R | 123 +++++----- R/fitTDAsreml.R | 87 ++++--- R/fitTDLme4.R | 3 R/fitTDSpATS.R | 26 ++ R/outliers.R | 17 - R/statgenSTA.R | 21 + R/sysdata.rda |binary R/utils.R | 26 ++ README.md | 112 ++++++++- inst/doc/statgenSTA.R | 13 - inst/doc/statgenSTA.Rmd | 40 ++- inst/doc/statgenSTA.html | 356 +++++++++++++++---------------- inst/reports/modelReport.Rnw | 12 - man/STAtoCross.Rd | 150 ++++++------- man/STAtoTD.Rd | 134 +++++------ man/TD.Rd | 9 man/TDHeat05.Rd | 22 - man/TDMaize.Rd | 8 man/as.data.frame.extract.Rd | 44 +-- man/extract.Rd | 211 ++++++++---------- man/extractSTA.Rd |only man/figures |only man/fitTD.Rd | 404 ++++++++++++++++++------------------ man/getMeta.Rd | 162 +++++++------- man/outlierSTA.Rd | 140 ++++++------ man/plot.STA.Rd | 197 +++++++++-------- man/plot.TD.Rd | 73 ++++-- man/report.STA.Rd | 166 +++++++------- man/statgenSTA-package.Rd | 1 man/summary.STA.Rd | 122 +++++----- man/summary.TD.Rd | 156 ++++++------- man/wheatChl.Rd | 30 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-ExtractAsreml.R | 18 - tests/testthat/test-ExtractLme4.R | 18 - tests/testthat/test-ExtractSpATS.R | 27 +- tests/testthat/test-STA.R | 37 ++- tests/testthat/test-TD.R | 56 ++++ tests/testthat/test-TDplots.R | 45 +++- tests/testthat/test-extract.R | 47 ++-- vignettes/statgenSTA.Rmd | 40 ++- 51 files changed, 2197 insertions(+), 1645 deletions(-)
Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar
energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy
Resource) data are freely available global meteorology and surface solar
energy climatology data for download with a resolution of 1/2 by 1/2 arc
degree longitude and latitude and are funded through the 'NASA' Earth
Science Directorate Applied Science Program. For more on the data
themselves, a web-based data viewer and web access, please see
<https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>, Scott
Chamberlain reviewed nasapower for rOpenSci, see
https://github.com/ropensci/software-review/issues/155),
Hazel Kavili [rev] (Hazel Kavili reviewed nasapower for rOpenSci, see
https://github.com/ropensci/software-review/issues/155),
Alison Boyer [rev] (Alison Boyer reviewed nasapower for rOpenSci, see
https://github.com/ropensci/software-review/issues/155)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between nasapower versions 1.1.3 dated 2019-11-18 and 2.0.0 dated 2020-09-23
nasapower-1.1.3/nasapower/R/create_icasa.R |only nasapower-1.1.3/nasapower/R/create_met.R |only nasapower-1.1.3/nasapower/man/create_icasa.Rd |only nasapower-1.1.3/nasapower/man/nasapower.Rd |only nasapower-1.1.3/nasapower/tests/testthat/test-create_icasa.R |only nasapower-1.1.3/nasapower/tests/testthat/test-create_met.R |only nasapower-2.0.0/nasapower/DESCRIPTION | 57 - nasapower-2.0.0/nasapower/MD5 | 74 - nasapower-2.0.0/nasapower/NAMESPACE | 1 nasapower-2.0.0/nasapower/NEWS.md | 141 +- nasapower-2.0.0/nasapower/R/deprecated_create_met.R |only nasapower-2.0.0/nasapower/R/get_power.R | 41 nasapower-2.0.0/nasapower/R/internal_functions.R | 114 +- nasapower-2.0.0/nasapower/R/nasapower-package.R | 48 nasapower-2.0.0/nasapower/R/parameters_data.R | 107 + nasapower-2.0.0/nasapower/README.md | 67 - nasapower-2.0.0/nasapower/build/vignette.rds |binary nasapower-2.0.0/nasapower/data/parameters.rda |binary nasapower-2.0.0/nasapower/inst/doc/nasapower.Rmd | 368 ++---- nasapower-2.0.0/nasapower/inst/doc/nasapower.html | 544 ++++------ nasapower-2.0.0/nasapower/inst/doc/nasapower_states_example.Rmd | 330 +++--- nasapower-2.0.0/nasapower/inst/doc/nasapower_states_example.html | 524 +++++---- nasapower-2.0.0/nasapower/man/create_met.Rd | 26 nasapower-2.0.0/nasapower/man/get_power.Rd | 36 nasapower-2.0.0/nasapower/man/nasapower-package.Rd |only nasapower-2.0.0/nasapower/man/parameters.Rd | 109 +- nasapower-2.0.0/nasapower/tests/fixtures |only nasapower-2.0.0/nasapower/tests/testthat/helper-nasapower.R |only nasapower-2.0.0/nasapower/tests/testthat/test-get_power.R | 177 ++- nasapower-2.0.0/nasapower/tests/testthat/test-internal_functions.R | 353 +++--- nasapower-2.0.0/nasapower/vignettes/create-climatology-brick-1.png |binary nasapower-2.0.0/nasapower/vignettes/create-single-raster-1.png |binary nasapower-2.0.0/nasapower/vignettes/create_coords-1.png |binary nasapower-2.0.0/nasapower/vignettes/create_coords-2.png |binary nasapower-2.0.0/nasapower/vignettes/create_coords-3.png |binary nasapower-2.0.0/nasapower/vignettes/nasapower.Rmd | 368 ++---- nasapower-2.0.0/nasapower/vignettes/nasapower.Rmd.orig | 251 +--- nasapower-2.0.0/nasapower/vignettes/nasapower_states_example.Rmd | 330 +++--- nasapower-2.0.0/nasapower/vignettes/nasapower_states_example.Rmd.orig | 59 - nasapower-2.0.0/nasapower/vignettes/plot-fig1-1.png |binary nasapower-2.0.0/nasapower/vignettes/precompile.R | 4 41 files changed, 2122 insertions(+), 2007 deletions(-)
Title: Schedule R Scripts and Processes with the 'cron' Job Scheduler
Description: Create, edit, and remove 'cron' jobs on your unix-alike system. The package provides a set of easy-to-use wrappers
to 'crontab'. It also provides an RStudio add-in to easily launch and schedule your scripts.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Kevin Ushey [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between cronR versions 0.4.0 dated 2018-03-08 and 0.4.2 dated 2020-09-23
DESCRIPTION | 11 - MD5 | 14 +- R/cron_rscript.R | 17 ++ README.md | 5 build/vignette.rds |binary inst/doc/cronR.R | 8 - inst/doc/cronR.html | 343 +++++++++++++++++++++++++++++++++++++--------------- man/cron_rscript.Rd | 22 ++- 8 files changed, 297 insertions(+), 123 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>
Diff between schoRsch versions 1.7 dated 2019-11-12 and 1.8 dated 2020-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/anova_out.R | 8 ++++++-- man/schoRsch.Rd | 9 +++++---- 4 files changed, 18 insertions(+), 13 deletions(-)
More information about RSmallTelescopes at CRAN
Permanent link
Title: Cellwise Robust M-Regression and SPADIMO
Description: Method for fitting a cellwise robust linear M-regression model (CRM, Filzmoser et al. (2020) <DOI:10.1016/j.csda.2020.106944>) that yields both a map of cellwise outliers consistent with the linear model, and a vector of regression coefficients that is robust against vertical outliers and leverage points. As a by-product, the method yields an imputed data set that contains estimates of what the values in cellwise outliers would need to amount to if they had fit the model. The package also provides diagnostic tools for analyzing casewise and cellwise outliers using sparse directions of maximal outlyingness (SPADIMO, Debruyne et al. (2019) <DOI:10.1007/s11222-018-9831-5>).
Author: Peter Filzmoser [aut],
Sebastiaan Hoppner [aut, cre],
Irene Ortner [aut],
Sven Serneels [aut],
Tim Verdonck [aut]
Maintainer: Sebastiaan Hoppner <sebastiaan.hoppner@gmail.com>
Diff between crmReg versions 1.0.1 dated 2020-04-06 and 1.0.2 dated 2020-09-23
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/crmReg-package.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Non-Trivial Balance of Centrifuge Rotors
Description: Find the numbers of tubes that can be loaded in centrifuge
rotors in a single operation and show how to balance these tubes in
cases of equal or unequal masses. Refer to Pham (2020)
<doi:10.31224/osf.io/4xs38> for more information on package
functionality.
Author: Duy Nghia Pham [aut, cre] (<https://orcid.org/0000-0003-1349-1710>)
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between centrifugeR versions 0.1.4 dated 2020-04-17 and 0.1.5 dated 2020-09-23
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + R/centrifugeR-package.R | 5 +++-- R/rotorEqual.R | 6 +++++- R/rotorUnequal.R | 14 +++++++++----- R/rotorVerify.R |only R/zzz.R | 2 +- man/centrifugeR-package.Rd | 5 +++-- man/rotorEqual.Rd | 6 +++++- man/rotorUnequal.Rd | 6 +++++- man/rotorVerify.Rd |only 12 files changed, 47 insertions(+), 26 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of three replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated metabolomic data in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a Gaussian distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Author: Marie-Laure Delignette-Muller [aut],
Elise Billoir [aut],
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.1-2 dated 2020-09-22 and 2.1-3 dated 2020-09-23
DRomics-2.1-2/DRomics/DESCRIPTION |only DRomics-2.1-2/DRomics/MD5 |only DRomics-2.1-2/DRomics/R |only DRomics-2.1-2/DRomics/inst |only DRomics-2.1-2/DRomics/man |only DRomics-2.1-2/DRomics/tests |only DRomics-2.1-3/DRomics/data/Zhou_liver_pce.rda |binary 7 files changed
Title: Probabilistic Supervised Learning for 'mlr3'
Description: Provides extensions for probabilistic supervised
learning for 'mlr3'. This includes extending the regression task to
probabilistic and interval regression, adding a survival task, and
other specialized models, predictions, and measures. mlr3extralearners is available
from <https://github.com/mlr-org/mlr3extralearners>.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Nurul Ain Toha [ctb],
Andreas Bender [ctb] (<https://orcid.org/0000-0001-5628-8611>)
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between mlr3proba versions 0.2.1 dated 2020-08-28 and 0.2.2 dated 2020-09-23
mlr3proba-0.2.1/mlr3proba/build/vignette.rds |only mlr3proba-0.2.1/mlr3proba/inst/doc |only mlr3proba-0.2.1/mlr3proba/man/PipeOpCrankCompositor.Rd |only mlr3proba-0.2.1/mlr3proba/man/PipeOpDistrCompositor.Rd |only mlr3proba-0.2.1/mlr3proba/man/PipeOpProbregrCompositor.Rd |only mlr3proba-0.2.1/mlr3proba/vignettes |only mlr3proba-0.2.2/mlr3proba/DESCRIPTION | 21 - mlr3proba-0.2.2/mlr3proba/MD5 | 128 ++++------ mlr3proba-0.2.2/mlr3proba/NAMESPACE | 11 mlr3proba-0.2.2/mlr3proba/NEWS.md | 6 mlr3proba-0.2.2/mlr3proba/R/LearnerDensHistogram.R | 2 mlr3proba-0.2.2/mlr3proba/R/LearnerDensKDE.R | 7 mlr3proba-0.2.2/mlr3proba/R/LearnerSurvCoxPH.R | 4 mlr3proba-0.2.2/mlr3proba/R/LearnerSurvKaplan.R | 2 mlr3proba-0.2.2/mlr3proba/R/LearnerSurvRpart.R | 8 mlr3proba-0.2.2/mlr3proba/R/MeasureSurvCalibrationBeta.R | 13 - mlr3proba-0.2.2/mlr3proba/R/MeasureSurvSongAUC.R | 2 mlr3proba-0.2.2/mlr3proba/R/PipeOpCrankCompositor.R | 11 mlr3proba-0.2.2/mlr3proba/R/PipeOpDistrCompositor.R | 18 - mlr3proba-0.2.2/mlr3proba/R/PipeOpPredRegrSurv.R | 3 mlr3proba-0.2.2/mlr3proba/R/PipeOpPredSurvRegr.R | 3 mlr3proba-0.2.2/mlr3proba/R/PipeOpProbregrCompositor.R | 5 mlr3proba-0.2.2/mlr3proba/R/PipeOpSurvAvg.R | 11 mlr3proba-0.2.2/mlr3proba/R/PipeOpTaskRegrSurv.R | 3 mlr3proba-0.2.2/mlr3proba/R/PipeOpTaskSurvRegr.R | 17 - mlr3proba-0.2.2/mlr3proba/R/PredictionDataDens.R |only mlr3proba-0.2.2/mlr3proba/R/PredictionDataSurv.R |only mlr3proba-0.2.2/mlr3proba/R/PredictionDens.R | 78 +----- mlr3proba-0.2.2/mlr3proba/R/PredictionSurv.R | 128 ++-------- mlr3proba-0.2.2/mlr3proba/R/TaskGeneratorSimdens.R | 4 mlr3proba-0.2.2/mlr3proba/R/TaskGeneratorSimsurv.R | 8 mlr3proba-0.2.2/mlr3proba/R/integrated_scores.R | 2 mlr3proba-0.2.2/mlr3proba/R/pecs.R | 6 mlr3proba-0.2.2/mlr3proba/R/pipelines.R | 25 + mlr3proba-0.2.2/mlr3proba/R/plot.R | 2 mlr3proba-0.2.2/mlr3proba/R/zzz.R | 5 mlr3proba-0.2.2/mlr3proba/README.md | 1 mlr3proba-0.2.2/mlr3proba/build/partial.rdb |binary mlr3proba-0.2.2/mlr3proba/inst/references.bib | 16 - mlr3proba-0.2.2/mlr3proba/inst/testthat/helper_autotest.R | 29 +- mlr3proba-0.2.2/mlr3proba/man/PredictionDens.Rd | 9 mlr3proba-0.2.2/mlr3proba/man/PredictionSurv.Rd | 17 - mlr3proba-0.2.2/mlr3proba/man/mlr3proba-package.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_crankcompositor.Rd | 4 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_distrcompositor.Rd | 5 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_probregrcompositor.Rd | 3 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_survaverager.Rd | 4 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_survbagging.Rd | 4 mlr3proba-0.2.2/mlr3proba/man/mlr_graphs_survtoregr.Rd | 5 mlr3proba-0.2.2/mlr3proba/man/mlr_learners_dens.kde.Rd | 1 mlr3proba-0.2.2/mlr3proba/man/mlr_learners_surv.coxph.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_learners_surv.kaplan.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_compose_crank.Rd |only mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_compose_distr.Rd |only mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_compose_probregr.Rd |only mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_survavg.Rd | 5 mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_trafopred_regrsurv.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_trafopred_survregr.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_trafotask_regrsurv.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_pipeops_trafotask_survregr.Rd | 9 mlr3proba-0.2.2/mlr3proba/man/mlr_task_generators_simdens.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/mlr_task_generators_simsurv.Rd | 2 mlr3proba-0.2.2/mlr3proba/man/pecs.Rd | 4 mlr3proba-0.2.2/mlr3proba/man/plot.LearnerSurv.Rd | 2 mlr3proba-0.2.2/mlr3proba/tests/testthat/Rplots.pdf |binary mlr3proba-0.2.2/mlr3proba/tests/testthat/test_PredictionSurv.R | 2 mlr3proba-0.2.2/mlr3proba/tests/testthat/test_mlr_learners_density_kde.R | 3 mlr3proba-0.2.2/mlr3proba/tests/testthat/test_mlr_learners_surv_coxph.R | 2 mlr3proba-0.2.2/mlr3proba/tests/testthat/test_resample.R |only mlr3proba-0.2.2/mlr3proba/tests/testthat/test_single_step.R | 17 + 70 files changed, 336 insertions(+), 355 deletions(-)
Title: MArginal ePIstasis Test for Regions
Description: A genetic analysis tool and variance component
model for identifying marginal epistasis between pathways
and the rest of the genome. 'MAPITR' uses as input a matrix
of genotypes, a vector of phenotypes, and a list of
pathways. 'MAPITR' then iteratively tests each pathway for
epistasis between any variants within the pathway versus
any variants remaining in the rest of the genome. 'MAPITR'
returns results in the form of p-values for every pathway
indicating whether the null model of there being no
epistatic interactions between a pathway and the rest of
the genome can be rejected.
Author: Michael Turchin [aut, cre] (<https://orcid.org/0000-0003-3569-1529>),
Gregory Darnell [aut, ctb] (<https://orcid.org/0000-0003-0425-940X>),
Lorin Crawford [aut, ctb] (<https://orcid.org/0000-0003-0178-8242>),
Sohini Ramachandran [aut] (<https://orcid.org/0000-0002-9588-7964>),
Peter Carbonetto [ctb] (<https://orcid.org/0000-0003-1144-6780>)
Maintainer: Michael Turchin <michael_turchin@brown.edu>
Diff between MAPITR versions 1.0.5 dated 2020-09-17 and 1.1.1 dated 2020-09-23
DESCRIPTION | 16 +- MD5 | 26 +-- R/MAPITR.R | 65 ++++++-- R/RcppExports.R | 8 + R/RuntimeVersions.R | 30 ++++ README.md | 6 inst/doc/MAPITR.Intro.SimulatedData.R | 4 inst/doc/MAPITR.Intro.SimulatedData.Rmd | 26 ++- inst/doc/MAPITR.Intro.SimulatedData.html | 33 +++- man/MAPITR.Rd | 17 +- src/MAPITR.cpp | 229 ++++++++++++++++++++++++++++++- src/RcppExports.cpp | 29 +++ tests/testthat/test-MAPITR.R | 27 ++- vignettes/MAPITR.Intro.SimulatedData.Rmd | 26 ++- 14 files changed, 459 insertions(+), 83 deletions(-)
Title: Family of Bayesian EMM Algorithm for Item Response Models
Description: Applying the family of the Bayesian Expectation-Maximization-Maximization (BEMM) algorithm to estimate: (1) Three parameter logistic (3PL) model proposed by Birnbaum (1968, ISBN:9780201043105); (2) four parameter logistic (4PL) model proposed by Barton & Lord (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x>; (3) one parameter logistic guessing (1PLG) and (4) one parameter logistic ability-based guessing (1PLAG) models proposed by San Martín et al (2006) <doi:10.1177/0146621605282773>. The BEMM family includes (1) the BEMM algorithm for 3PL model proposed by Guo & Zheng (2019) <doi:10.3389/fpsyg.2019.01175>; (2) the BEMM algorithm for 1PLG model and (3) the BEMM algorithm for 1PLAG model proposed by Guo, Wu, Zheng, & Wang (2018) <https:www.ncme.org/news/past-meetings/2018-recap>; (4) the BEMM algorithm for 4PL model proposed by Zhang, Guo, & Zheng (2018) <https:www.ncme.org/news/past-meetings/2018-recap>; and (5) their maximum likelihood estimation versions proposed by Zheng, Meng, Guo, & Liu (2018) <doi:10.3389/fpsyg.2017.02302>. Thus, both Bayesian modal estimates and maximum likelihood estimates are available.
Author: Shaoyang Guo [aut, cre, cph],
Chanjin Zheng [aut],
Justin L Kern [aut]
Maintainer: Shaoyang Guo <syguo1992@outlook.com>
Diff between IRTBEMM versions 1.0.4 dated 2020-09-17 and 1.0.5 dated 2020-09-23
IRTBEMM-1.0.4/IRTBEMM/src |only IRTBEMM-1.0.5/IRTBEMM/DESCRIPTION | 8 IRTBEMM-1.0.5/IRTBEMM/MD5 | 35 - IRTBEMM-1.0.5/IRTBEMM/NAMESPACE | 2 IRTBEMM-1.0.5/IRTBEMM/NEWS.md | 5 IRTBEMM-1.0.5/IRTBEMM/R/BEMM.1PLAG.R | 555 ++++++++++++++++++++---- IRTBEMM-1.0.5/IRTBEMM/R/BEMM.1PLG.R | 443 +++++++++++++++---- IRTBEMM-1.0.5/IRTBEMM/R/BEMM.3PL.R | 520 ++++++++++++++++++----- IRTBEMM-1.0.5/IRTBEMM/R/BEMM.4PL.R | 623 ++++++++++++++++++++++------ IRTBEMM-1.0.5/IRTBEMM/R/ToolBox.R | 138 ++++-- IRTBEMM-1.0.5/IRTBEMM/build/partial.rdb |binary IRTBEMM-1.0.5/IRTBEMM/inst/CITATION | 5 IRTBEMM-1.0.5/IRTBEMM/man/BEMM.1PLAG.Rd | 7 IRTBEMM-1.0.5/IRTBEMM/man/BEMM.1PLG.Rd | 7 IRTBEMM-1.0.5/IRTBEMM/man/BEMM.3PL.Rd | 7 IRTBEMM-1.0.5/IRTBEMM/man/BEMM.4PL.Rd | 7 IRTBEMM-1.0.5/IRTBEMM/man/Input.Checking.Rd | 5 17 files changed, 1834 insertions(+), 533 deletions(-)
Title: Download and Augment the Corpus of Plenary Protocols of the
German Bundestag
Description: Data package to disseminate the 'GermaParl' corpus of parliamentary debates of
the German Bundestag prepared in the 'PolMine Project'. The package includes a small subset of
the corpus for demonstration and testing purposes. The package includes functionality to
download the full corpus and supplementary data from the open science repository 'Zenodo'.
Author: Andreas Blaette [aut, cre],
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between GermaParl versions 1.5.1 dated 2020-07-27 and 1.5.2 dated 2020-09-23
DESCRIPTION | 10 +++--- MD5 | 18 +++++----- NAMESPACE | 7 ++++ NEWS.md | 5 +++ R/lda.R | 79 +++++++++++++++++++++++++++++++++++------------- inst/doc/GermaParl.Rmd | 2 - inst/doc/GermaParl.html | 6 +-- man/germaparl_by_lp.Rd | 4 +- man/germaparl_topics.Rd | 15 +++------ vignettes/GermaParl.Rmd | 2 - 10 files changed, 98 insertions(+), 50 deletions(-)
Title: Correct Bias in DNA Methylation Analyses
Description: Implementation of the algorithms (with minor
modifications) to correct bias in quantitative DNA methylation
analyses as described by Moskalev et al. (2011)
<doi:10.1093/nar/gkr213>.
Author: Lorenz A. Kapsner [cre, aut, cph]
(<https://orcid.org/0000-0003-1866-860X>),
Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between rBiasCorrection versions 0.2.2 dated 2020-09-22 and 0.2.3 dated 2020-09-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/utils.R | 3 +++ README.md | 2 +- inst/doc/rBiasCorrection_benchmarking.html | 4 ++-- inst/doc/rBiasCorrection_howto.html | 8 ++++---- tests/testthat/test-create_aggregated.R | 11 ++++++++--- 7 files changed, 27 insertions(+), 19 deletions(-)
More information about rBiasCorrection at CRAN
Permanent link
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>),
Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>),
Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>),
Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>),
Jiong Wei Lua [aut],
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>),
Christian Müller [ctb],
Lori Young [dtc] (Lexicoder Sentiment Dictionary 2015),
Stuart Soroka [dtc] (Lexicoder Sentiment Dictionary 2015),
Ian Fellows [cph] (authored wordcloud C source code (modified)),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 2.1.1 dated 2020-07-27 and 2.1.2 dated 2020-09-23
DESCRIPTION | 6 - MD5 | 77 ++++++++-------- NEWS.md | 22 +++- R/RcppExports.R | 4 R/data-documentation.R | 6 - R/dictionaries.R | 24 ++--- R/fcm.R | 4 R/quanteda-documentation.R | 2 R/textstat_collocations.R | 3 R/textstat_keyness.R | 87 +++++++++++------- R/textstat_lexdiv.R | 2 R/textstat_readability.R | 51 +++++----- R/textstat_summary.R | 27 +++-- R/tokens_ngrams.R | 2 README.md | 13 +- inst/doc/quickstart.Rmd | 4 inst/doc/quickstart.html | 4 man/data_corpus_inaugural.Rd | 2 man/data_dictionary_LSD2015.Rd | 4 man/dictionary.Rd | 8 - man/fcm.Rd | 4 man/keyness.Rd | 2 man/quanteda-package.Rd | 2 man/read_dict_functions.Rd | 4 man/textstat_keyness.Rd | 14 +- man/textstat_lexdiv.Rd | 2 man/textstat_readability.Rd | 41 +++++--- man/textstat_summary.Rd | 27 +++-- man/tokens_ngrams.Rd | 2 man/valuetype.Rd | 2 src/RcppExports.cpp | 14 ++ src/collocations_mt_.cpp | 68 +++++++------- src/keyness_mt.cpp |only src/tokens_select_mt.cpp | 2 tests/testthat/test-dictionaries.R | 3 tests/testthat/test-spacyr-methods.R | 4 tests/testthat/test-textstat_keyness.R | 156 ++++++++++++++++----------------- tests/testthat/test-tokens.R | 5 + tests/testthat/test-tokens_recompile.R | 1 vignettes/quickstart.Rmd | 4 40 files changed, 395 insertions(+), 314 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-28 0.1.3.4
2019-08-05 0.1.3.3
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.9.4 dated 2020-08-28 and 0.9.6 dated 2020-09-22
DESCRIPTION | 8 - MD5 | 20 ++-- inst/doc/HTML.R | 6 + inst/doc/HTML.Rmd | 6 + inst/doc/HTML.html | 224 +++++++++++++++++++++++----------------------- inst/doc/knitrTables.R | 6 + inst/doc/knitrTables.Rmd | 6 + inst/doc/knitrTables.pdf |binary inst/doc/tables.pdf |binary vignettes/HTML.Rmd | 6 + vignettes/knitrTables.Rmd | 6 + 11 files changed, 162 insertions(+), 126 deletions(-)
Title: Display User Feedback in Shiny Apps
Description: Easily display user feedback in Shiny apps.
Author: Andy Merlino [aut, cre],
Patrick Howard [aut]
Maintainer: Andy Merlino <andy.merlino@tychobra.com>
Diff between shinyFeedback versions 0.2.0 dated 2020-04-29 and 0.3.0 dated 2020-09-22
DESCRIPTION | 10 MD5 | 40 +- NAMESPACE | 2 NEWS.md | 11 R/hideToast.R |only R/showToast.R | 63 ++- README.md | 10 build/vignette.rds |binary inst/assets/js/shinyfeedback.js | 462 ++++++++++------------------ inst/assets/toastr/js/shinytoastr.js | 13 inst/assets/toastr/js/toastr.js.map |only inst/doc/loading-button-and-toast.html | 4 inst/doc/shinyFeedback-intro.R | 2 inst/doc/shinyFeedback-intro.Rmd | 15 inst/doc/shinyFeedback-intro.html | 19 - inst/doc/valueBoxModule.html | 4 inst/examples/supported_inputs_app/server.R | 21 + inst/examples/supported_inputs_app/ui.R | 29 + inst/img/feedback_screenshot.png |only inst/img/shinyfeedback_hex_sticker.png |only man/hideToast.Rd |only man/showToast.Rd | 12 vignettes/feedback_screenshot.png |only vignettes/shinyFeedback-intro.Rmd | 15 24 files changed, 369 insertions(+), 363 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>),
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>),
Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Duncan Luguern [aut],
David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>,
dmkaplan2000),
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>),
Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>),
Alfredo Hernández [ctb] (<https://orcid.org/0000-0002-2660-4545>),
Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.15 dated 2020-08-26 and 0.16 dated 2020-09-22
rticles-0.15/rticles/README.md |only rticles-0.16/rticles/DESCRIPTION | 10 +- rticles-0.16/rticles/MD5 | 19 ++-- rticles-0.16/rticles/NEWS.md | 7 + rticles-0.16/rticles/R/article.R | 10 +- rticles-0.16/rticles/R/jss_article.R | 40 ++++------ rticles-0.16/rticles/R/rjournal_article.R | 21 ----- rticles-0.16/rticles/inst/rmarkdown/templates/ctex/skeleton/skeleton.Rmd | 1 rticles-0.16/rticles/inst/rmarkdown/templates/jss/skeleton/skeleton.Rmd | 4 + rticles-0.16/rticles/man/article.Rd | 8 +- rticles-0.16/rticles/tests/testit/test-formats.R | 1 11 files changed, 53 insertions(+), 68 deletions(-)
Title: Include Tables, Images and Graphs in Leaflet Pop-Ups
Description: Creates 'HTML' strings to embed tables, images or graphs in pop-ups
of interactive maps created with packages like 'leaflet' or 'mapview'. Handles
local images located on the file system or via remote URL. Handles graphs created
with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between leafpop versions 0.0.5 dated 2019-12-09 and 0.0.6 dated 2020-09-22
DESCRIPTION | 12 +++-- MD5 | 18 +++---- NEWS | 6 ++ NEWS.md | 6 ++ R/addPopupImages.R | 4 - R/brewRy.R | 89 +++++++++++++++++++++----------------- R/table.R | 93 +++++++++++++++++++++++++++++++++++++--- inst/htmlwidgets/popup.js | 4 - inst/templates/popup-graph.brew | 42 ++++++++++-------- man/popup.Rd | 71 ++++++++++++++++++++++++++++++ 10 files changed, 265 insertions(+), 80 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>),
James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.14 dated 2020-02-07 and 1.8.16 dated 2020-09-22
DESCRIPTION | 10 - MD5 | 42 ++--- NEWS | 10 + R/amiralandmarks-io.R | 2 R/neuron-io-fiji.R | 4 R/neuron-io-neuroml.R | 4 R/neuron-io.R | 58 ++++---- README.md | 14 - build/vignette.rds |binary inst/doc/Installation.Rmd | 2 inst/doc/Installation.html | 60 +++++--- inst/doc/neurons-intro.Rmd | 12 - inst/doc/neurons-intro.html | 282 ++++++++++++++++++++------------------- man/read.landmarks.Rd | 2 man/read.morphml.Rd | 2 man/read.neuron.Rd | 52 +++---- man/read.neuron.fiji.Rd | 4 man/read.neuron.neuroml.Rd | 2 man/read.neuron.swc.Rd | 2 tests/testthat/test-neuronlist.R | 2 vignettes/Installation.Rmd | 2 vignettes/neurons-intro.Rmd | 12 - 22 files changed, 313 insertions(+), 267 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Ellis Hughes [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.29 dated 2020-06-23 and 1.30 dated 2020-09-22
DESCRIPTION | 8 +- MD5 | 98 +++++++++++++++--------------- NAMESPACE | 9 ++ R/block.R | 3 R/citation.R | 28 ++++++-- R/defaults.R | 2 R/hooks-asciidoc.R | 8 ++ R/hooks-extra.R | 11 --- R/hooks-html.R | 28 +++++--- R/hooks-latex.R | 125 +++++++++++++++++++++++++++------------ R/hooks-md.R | 41 +++++++++--- R/hooks-rst.R | 11 ++- R/hooks-textile.R | 19 +++-- R/output.R | 4 - R/pandoc.R | 2 R/plot.R | 14 +++- R/table.R | 4 - R/themes.R | 2 R/utils-vignettes.R | 8 +- R/utils.R | 17 ++--- README.md | 4 - build/vignette.rds |binary inst/doc/datatables.Rmd | 2 inst/doc/datatables.html | 2 inst/doc/docco-classic.html | 2 inst/doc/docco-linear.Rmd | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.Rmd | 2 inst/doc/knit_expand.html | 6 - inst/doc/knit_print.html | 12 +-- inst/doc/knitr-intro.html | 14 ++-- inst/doc/knitr-markdown.Rmd | 2 inst/doc/knitr-markdown.html | 4 - inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-manual.bib | 2 inst/examples/knitr-packages.bib | 2 inst/misc/tweak_bib.csv | 24 +++---- man/chunk_hook.Rd | 11 --- man/image_uri.Rd | 2 man/knit.Rd | 4 - man/knit_theme.Rd | 2 man/opts_chunk.Rd | 2 man/output_hooks.Rd | 101 ++++++++++++++++++++++++------- man/pandoc.Rd | 2 man/plot_crop.Rd | 13 +++- man/write_bib.Rd | 5 + vignettes/datatables.Rmd | 2 vignettes/docco-linear.Rmd | 2 vignettes/knit_expand.Rmd | 2 vignettes/knitr-markdown.Rmd | 2 50 files changed, 427 insertions(+), 247 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.18.0 dated 2020-07-09 and 1.19.1 dated 2020-09-22
future-1.18.0/future/man/values.Rd |only future-1.19.1/future/DESCRIPTION | 8 future-1.19.1/future/MD5 | 100 +-- future-1.19.1/future/NAMESPACE | 1 future-1.19.1/future/NEWS | 96 +++ future-1.19.1/future/R/Future-class.R | 120 ---- future-1.19.1/future/R/FutureGlobals-class.R | 4 future-1.19.1/future/R/MulticoreFuture-class.R | 26 future-1.19.1/future/R/UniprocessFuture-class.R | 3 future-1.19.1/future/R/availableCores.R | 61 ++ future-1.19.1/future/R/availableWorkers.R | 20 future-1.19.1/future/R/future.R | 4 future-1.19.1/future/R/globals.R | 33 + future-1.19.1/future/R/makeClusterPSOCK.R | 272 ++++++---- future-1.19.1/future/R/options.R | 6 future-1.19.1/future/R/resolved.R | 5 future-1.19.1/future/R/tweakExpression.R | 8 future-1.19.1/future/R/utils.R | 2 future-1.19.1/future/R/value.R |only future-1.19.1/future/R/values.R | 92 --- future-1.19.1/future/inst/CITATION |only future-1.19.1/future/inst/WORDLIST | 127 ---- future-1.19.1/future/inst/doc/future-4-issues.html | 4 future-1.19.1/future/inst/doc/future-4-issues.md.rsp | 4 future-1.19.1/future/inst/doc/future-4-non-exportable-objects.html | 191 +++++-- future-1.19.1/future/inst/doc/future-4-non-exportable-objects.md.rsp | 181 ++++-- future-1.19.1/future/man/Future-class.Rd | 8 future-1.19.1/future/man/FutureGlobals.Rd | 4 future-1.19.1/future/man/availableCores.Rd | 10 future-1.19.1/future/man/availableWorkers.Rd | 5 future-1.19.1/future/man/cluster.Rd | 8 future-1.19.1/future/man/figures |only future-1.19.1/future/man/future.Rd | 12 future-1.19.1/future/man/future.options.Rd | 6 future-1.19.1/future/man/getGlobalsAndPackages.Rd | 2 future-1.19.1/future/man/grapes-seed-grapes.Rd | 8 future-1.19.1/future/man/makeClusterMPI.Rd | 4 future-1.19.1/future/man/makeClusterPSOCK.Rd | 39 + future-1.19.1/future/man/multicore.Rd | 8 future-1.19.1/future/man/multiprocess.Rd | 8 future-1.19.1/future/man/multisession.Rd | 8 future-1.19.1/future/man/pid_exists.Rd | 2 future-1.19.1/future/man/remote.Rd | 8 future-1.19.1/future/man/resolved.Rd | 5 future-1.19.1/future/man/sequential.Rd | 8 future-1.19.1/future/man/value.Rd | 54 + future-1.19.1/future/tests/availableCores.R | 11 future-1.19.1/future/tests/availableWorkers.R | 14 future-1.19.1/future/tests/dotdotdot.R | 17 future-1.19.1/future/tests/multicore,multithreading.R | 8 future-1.19.1/future/tests/tweak.R | 17 future-1.19.1/future/vignettes/future-4-issues.md.rsp | 4 future-1.19.1/future/vignettes/future-4-non-exportable-objects.md.rsp | 181 ++++-- 53 files changed, 1101 insertions(+), 726 deletions(-)
Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and
temporarily modified global state. Many of these functions were
originally a part of the 'devtools' package, this provides a simple
package with limited dependencies to provide access to these
functions.
Author: Jim Hester [aut, cre],
Kirill Müller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jennifer Bryan [ctb],
Richard Cotton [ctb],
RStudio [cph]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between withr versions 2.2.0 dated 2020-04-20 and 2.3.0 dated 2020-09-22
withr-2.2.0/withr/inst/doc/withr.R |only withr-2.2.0/withr/inst/doc/withr.Rmd |only withr-2.2.0/withr/inst/doc/withr.html |only withr-2.2.0/withr/vignettes/releases |only withr-2.2.0/withr/vignettes/withr.Rmd |only withr-2.3.0/withr/DESCRIPTION | 27 +-- withr-2.3.0/withr/MD5 | 94 +++++------ withr-2.3.0/withr/NAMESPACE | 3 withr-2.3.0/withr/NEWS.md | 23 ++ withr-2.3.0/withr/R/compat-defer.R |only withr-2.3.0/withr/R/defer.R | 70 +------- withr-2.3.0/withr/R/dir.R | 20 -- withr-2.3.0/withr/R/env.R | 5 withr-2.3.0/withr/R/file.R | 18 +- withr-2.3.0/withr/R/libpaths.R | 1 withr-2.3.0/withr/R/local_.R | 39 +++- withr-2.3.0/withr/R/locale.R | 8 withr-2.3.0/withr/R/makevars.R | 19 +- withr-2.3.0/withr/R/options.R | 5 withr-2.3.0/withr/R/par.R | 5 withr-2.3.0/withr/R/path.R | 1 withr-2.3.0/withr/R/seed.R | 33 +++ withr-2.3.0/withr/R/tempfile.R | 56 ++++++ withr-2.3.0/withr/R/utils.R | 7 withr-2.3.0/withr/R/with_.R | 6 withr-2.3.0/withr/README.md | 6 withr-2.3.0/withr/build/vignette.rds |binary withr-2.3.0/withr/inst/doc/changing-and-restoring-state.R |only withr-2.3.0/withr/inst/doc/changing-and-restoring-state.Rmd |only withr-2.3.0/withr/inst/doc/changing-and-restoring-state.html |only withr-2.3.0/withr/man/devices.Rd | 29 +-- withr-2.3.0/withr/man/with_.Rd | 2 withr-2.3.0/withr/man/with_collate.Rd | 2 withr-2.3.0/withr/man/with_dir.Rd | 8 withr-2.3.0/withr/man/with_envvar.Rd | 11 + withr-2.3.0/withr/man/with_file.Rd | 6 withr-2.3.0/withr/man/with_libpaths.Rd | 2 withr-2.3.0/withr/man/with_locale.Rd | 6 withr-2.3.0/withr/man/with_makevars.Rd | 19 +- withr-2.3.0/withr/man/with_options.Rd | 6 withr-2.3.0/withr/man/with_par.Rd | 11 + withr-2.3.0/withr/man/with_path.Rd | 2 withr-2.3.0/withr/man/with_seed.Rd | 8 withr-2.3.0/withr/man/with_sink.Rd | 4 withr-2.3.0/withr/man/with_tempfile.Rd | 31 +++ withr-2.3.0/withr/man/withr.Rd | 7 withr-2.3.0/withr/tests/testthat/test-defer.R | 19 ++ withr-2.3.0/withr/tests/testthat/test-file.R | 12 + withr-2.3.0/withr/tests/testthat/test-local.R | 6 withr-2.3.0/withr/tests/testthat/test-seed.R | 63 +++++++ withr-2.3.0/withr/tests/testthat/test-tempdir.R | 20 ++ withr-2.3.0/withr/tests/testthat/test-tempfile.R | 35 +++- withr-2.3.0/withr/vignettes/changing-and-restoring-state.Rmd |only 53 files changed, 527 insertions(+), 228 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.2.0 dated 2020-08-03 and 1.3.0 dated 2020-09-22
TreeTools-1.2.0/TreeTools/src/phangorn_bip.cpp |only TreeTools-1.2.0/TreeTools/src/renumber_tree.cpp |only TreeTools-1.2.0/TreeTools/src/types.h |only TreeTools-1.3.0/TreeTools/DESCRIPTION | 24 TreeTools-1.3.0/TreeTools/MD5 | 142 +++-- TreeTools-1.3.0/TreeTools/NAMESPACE | 16 TreeTools-1.3.0/TreeTools/NEWS.md | 22 TreeTools-1.3.0/TreeTools/R/Combinatorics.R | 2 TreeTools-1.3.0/TreeTools/R/RcppExports-manual.R |only TreeTools-1.3.0/TreeTools/R/RcppExports.R | 16 TreeTools-1.3.0/TreeTools/R/Splits.R | 34 - TreeTools-1.3.0/TreeTools/R/Stemwardness.R |only TreeTools-1.3.0/TreeTools/R/TreeNumber.R | 51 +- TreeTools-1.3.0/TreeTools/R/TreeTools-package.R | 6 TreeTools-1.3.0/TreeTools/R/data.R | 2 TreeTools-1.3.0/TreeTools/R/helper_functions.R | 1 TreeTools-1.3.0/TreeTools/R/mst.R |only TreeTools-1.3.0/TreeTools/R/parse_files.R | 2 TreeTools-1.3.0/TreeTools/R/split_analysis.R |only TreeTools-1.3.0/TreeTools/R/sysdata.rda |binary TreeTools-1.3.0/TreeTools/R/tree_generation.R | 26 - TreeTools-1.3.0/TreeTools/R/tree_rearrangement.R | 23 TreeTools-1.3.0/TreeTools/build/partial.rdb |binary TreeTools-1.3.0/TreeTools/inst/REFERENCES.bib | 20 TreeTools-1.3.0/TreeTools/inst/WORDLIST | 9 TreeTools-1.3.0/TreeTools/inst/doc/filesystem-navigation.html | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-data.html | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.R | 2 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.Rmd | 4 TreeTools-1.3.0/TreeTools/inst/doc/load-trees.html | 8 TreeTools-1.3.0/TreeTools/inst/extdata/tests/tnt-namedtree.tre | 4 TreeTools-1.3.0/TreeTools/inst/include |only TreeTools-1.3.0/TreeTools/man/ApeTime.Rd | 52 +- TreeTools-1.3.0/TreeTools/man/CladisticInfo.Rd | 1 TreeTools-1.3.0/TreeTools/man/Lobo.data.Rd | 50 +- TreeTools-1.3.0/TreeTools/man/MSTEdges.Rd |only TreeTools-1.3.0/TreeTools/man/MatrixToPhyDat.Rd | 76 +-- TreeTools-1.3.0/TreeTools/man/NJTree.Rd | 72 +- TreeTools-1.3.0/TreeTools/man/NPartitionPairs.Rd | 100 ++-- TreeTools-1.3.0/TreeTools/man/Neworder.Rd | 124 ++--- TreeTools-1.3.0/TreeTools/man/ReadTntTree.Rd | 242 +++++----- TreeTools-1.3.0/TreeTools/man/RightmostCharacter.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/RootTree.Rd | 3 TreeTools-1.3.0/TreeTools/man/SampleOne.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/Stemwardness.Rd |only TreeTools-1.3.0/TreeTools/man/Subsplit.Rd | 86 +-- TreeTools-1.3.0/TreeTools/man/TipsInSplits.Rd | 33 + TreeTools-1.3.0/TreeTools/man/TotalCopheneticIndex.Rd | 3 TreeTools-1.3.0/TreeTools/man/TreeTools-package.Rd | 4 TreeTools-1.3.0/TreeTools/man/TrivialSplits.Rd | 90 +-- TreeTools-1.3.0/TreeTools/man/UnshiftTree.Rd | 80 +-- TreeTools-1.3.0/TreeTools/man/as.Newick.Rd | 94 +-- TreeTools-1.3.0/TreeTools/man/brewer.Rd | 66 +- TreeTools-1.3.0/TreeTools/man/doubleFactorials.Rd | 52 +- TreeTools-1.3.0/TreeTools/man/figures |only TreeTools-1.3.0/TreeTools/man/logDoubleFactorials.Rd | 46 - TreeTools-1.3.0/TreeTools/man/nRootedShapes.Rd | 56 +- TreeTools-1.3.0/TreeTools/man/sapply64.Rd | 4 TreeTools-1.3.0/TreeTools/src/RcppExports-manual.cpp |only TreeTools-1.3.0/TreeTools/src/RcppExports.cpp | 45 - TreeTools-1.3.0/TreeTools/src/TreeTools-init.c | 8 TreeTools-1.3.0/TreeTools/src/ape_reorder.h | 8 TreeTools-1.3.0/TreeTools/src/int_to_tree.cpp | 2 TreeTools-1.3.0/TreeTools/src/splits.cpp | 4 TreeTools-1.3.0/TreeTools/src/tips_in_splits.cpp |only TreeTools-1.3.0/TreeTools/src/tree_shape.cpp | 2 TreeTools-1.3.0/TreeTools/tests/figs |only TreeTools-1.3.0/TreeTools/tests/testthat/test-Splits.R | 11 TreeTools-1.3.0/TreeTools/tests/testthat/test-Stemwardness.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-TreeNumber.R | 6 TreeTools-1.3.0/TreeTools/tests/testthat/test-combinatorics.R | 9 TreeTools-1.3.0/TreeTools/tests/testthat/test-int_to_tree.cpp.R | 8 TreeTools-1.3.0/TreeTools/tests/testthat/test-mst.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-parsers.R | 2 TreeTools-1.3.0/TreeTools/tests/testthat/test-root_tree.h.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-split_analysis.R |only TreeTools-1.3.0/TreeTools/tests/testthat/test-tree_generation.R | 6 TreeTools-1.3.0/TreeTools/tests/testthat/test-tree_properties.R | 6 TreeTools-1.3.0/TreeTools/vignettes/load-trees.Rmd | 4 79 files changed, 1057 insertions(+), 932 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.6 dated 2020-05-17 and 1.1.7 dated 2020-09-22
simTool-1.1.6/simTool/tests/testthat |only simTool-1.1.6/simTool/tests/testthat.R |only simTool-1.1.7/simTool/DESCRIPTION | 13 - simTool-1.1.7/simTool/MD5 | 32 +-- simTool-1.1.7/simTool/NAMESPACE | 1 simTool-1.1.7/simTool/R/bind_or_combine.R | 2 simTool-1.1.7/simTool/R/define_simulation.R | 3 simTool-1.1.7/simTool/R/eval_tibbles.R | 27 +- simTool-1.1.7/simTool/R/unnest_simulation.R | 3 simTool-1.1.7/simTool/build/vignette.rds |binary simTool-1.1.7/simTool/inst/doc/simTool.R | 298 ++++++++++++++-------------- simTool-1.1.7/simTool/inst/doc/simTool.html | 232 ++++++--------------- simTool-1.1.7/simTool/inst/tinytest |only simTool-1.1.7/simTool/tests/tinytest.R |only 14 files changed, 258 insertions(+), 353 deletions(-)
Title: Simulation of Diffusion Processes
Description: It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDE's. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
Author: Arsalane Chouaib Guidoum [cre, aut],
Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 4.6 dated 2020-05-04 and 4.7 dated 2020-09-22
DESCRIPTION | 8 MD5 | 80 ++-- R/utils.R | 24 - R/zzz.r | 4 README.md | 8 build/vignette.rds |binary inst/NEWS.Rd | 7 inst/doc/bridgesde.Rmd | 2 inst/doc/bridgesde.html | 504 +++++++++++++++++++-------- inst/doc/fitsde.Rmd | 4 inst/doc/fitsde.html | 713 +++++++++++++++++++++++++------------- inst/doc/fptsde.Rmd | 2 inst/doc/fptsde.html | 744 ++++++++++++++++++++++++++------------- inst/doc/mcmsde.Rmd | 2 inst/doc/mcmsde.html | 556 +++++++++++++++++++++-------- inst/doc/sdetotex.Rmd | 4 inst/doc/sdetotex.html | 494 ++++++++++++++++++++------ inst/doc/snssde.Rmd | 2 inst/doc/snssde.html | 820 +++++++++++++++++++++++++++----------------- man/HWV.Rd | 2 man/Sim.DiffProc-package.Rd | 4 man/TEX.sde.Rd | 2 man/bridgesde1d.Rd | 2 man/bridgesde2d.Rd | 2 man/bridgesde3d.Rd | 2 man/fitsde.Rd | 4 man/fptsde1d.Rd | 4 man/fptsde2d.Rd | 4 man/fptsde3d.Rd | 6 man/plot2d.Rd | 4 man/rsde1d.Rd | 8 man/rsde2d.Rd | 8 man/rsde3d.Rd | 8 man/snssde1d.Rd | 2 man/snssde3d.Rd | 2 vignettes/bridgesde.Rmd | 2 vignettes/fitsde.Rmd | 4 vignettes/fptsde.Rmd | 2 vignettes/mcmsde.Rmd | 2 vignettes/sdetotex.Rmd | 4 vignettes/snssde.Rmd | 2 41 files changed, 2759 insertions(+), 1299 deletions(-)
Title: Portable Address Space Mapping
Description: Portable '/proc/self/maps' as a data frame.
Determine which library or other region is mapped to a specific
address of a process. --
R packages can contain native code, compiled to shared libraries at build or
installation time.
When loaded, each shared library occupies a portion of the address space of
the main process.
When only a machine instruction pointer is available (e.g. from a backtrace
during error inspection or profiling), the address space map determines
which library this instruction pointer corresponds to.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
R Consortium [fnd],
Kostya Serebryany [ctb] (Bundled gperftools library),
Sanjay Ghemawat [ctb] (Bundled gperftools library),
Craig Silverstein [ctb] (Bundled gperftools library),
Google Inc. [cph] (Bundled gperftools library)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between procmaps versions 0.0.2 dated 2020-09-20 and 0.0.3 dated 2020-09-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ src/vendor/gperftools/src/base/sysinfo.cc | 14 +++++++++----- 4 files changed, 21 insertions(+), 12 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-11 dated 2020-08-16 and 2.6-12 dated 2020-09-22
DESCRIPTION | 8 +- MD5 | 10 +-- R/pcalg.R | 151 +++++++++++++++++++++++++++++----------------- inst/CITATION | 2 inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary 6 files changed, 106 insertions(+), 65 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class 'AutoFSelect'
provides a convenient way to perform nested resampling in combination
with 'mlr3'.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.2.1 dated 2020-09-10 and 0.3.0 dated 2020-09-22
DESCRIPTION | 10 ++--- MD5 | 44 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 6 +++ R/ArchiveFSelect.R |only R/AutoFSelect.R | 4 +- R/FSelectInstanceMultiCrit.R | 12 ++++-- R/FSelectInstanceSingleCrit.R | 12 ++++-- R/FSelector.R | 2 - R/FSelectorFromOptimizer.R | 2 - R/FSelectorRFE.R | 6 ++- R/ObjectiveFSelect.R | 25 +++++++++---- build/partial.rdb |binary man/ArchiveFSelect.Rd |only man/AutoFSelect.Rd | 4 +- man/FSelectInstanceMultiCrit.Rd | 9 ++-- man/FSelectInstanceSingleCrit.Rd | 9 ++-- man/FSelector.Rd | 2 - man/FSelectorFromOptimizer.Rd | 2 - man/ObjectiveFSelect.Rd | 17 +++++---- tests/testthat/helper.R | 8 ++-- tests/testthat/test_FSelectInstanceMultiCrit.R | 20 +++++++--- tests/testthat/test_FSelectInstanceSingleCrit.R | 27 +++++++++----- tests/testthat/test_ObjectiveFSelect.R | 10 +++-- 24 files changed, 140 insertions(+), 92 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of three replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated metabolomic data in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a Gaussian distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Author: Marie-Laure Delignette-Muller [aut],
Elise Billoir [aut],
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.0-1 dated 2019-09-16 and 2.1-2 dated 2020-09-22
DRomics-2.0-1/DRomics/inst/extdata/Zhou_kidney_pce.txt |only DRomics-2.1-2/DRomics/DESCRIPTION | 14 DRomics-2.1-2/DRomics/MD5 | 96 +-- DRomics-2.1-2/DRomics/NAMESPACE | 12 DRomics-2.1-2/DRomics/R/RNAseqdata.R | 116 ++- DRomics-2.1-2/DRomics/R/bmdboot.R | 10 DRomics-2.1-2/DRomics/R/bmdcalc.R | 19 DRomics-2.1-2/DRomics/R/bmdplotwithgradient.R |only DRomics-2.1-2/DRomics/R/continuousanchoringdata.R |only DRomics-2.1-2/DRomics/R/curvesplot.R | 41 + DRomics-2.1-2/DRomics/R/drcfit.R | 46 + DRomics-2.1-2/DRomics/R/ecdfplotwithCI.R | 14 DRomics-2.1-2/DRomics/R/ecdfquantileplot.R |only DRomics-2.1-2/DRomics/R/itemselect.R | 59 + DRomics-2.1-2/DRomics/R/metabolomicdata.R | 46 - DRomics-2.1-2/DRomics/R/microarraydata.R | 39 - DRomics-2.1-2/DRomics/R/targetplot.R |only DRomics-2.1-2/DRomics/R/util-plotfunc.R | 243 ++++--- DRomics-2.1-2/DRomics/data |only DRomics-2.1-2/DRomics/inst/CITATION | 2 DRomics-2.1-2/DRomics/inst/DRomics-shiny/global.R | 12 DRomics-2.1-2/DRomics/inst/DRomics-shiny/rinstall.txt | 23 DRomics-2.1-2/DRomics/inst/DRomics-shiny/server.R | 128 +++- DRomics-2.1-2/DRomics/inst/DRomics-shiny/ui.R | 221 ++++--- DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/Dromics_tutorial.pdf |binary DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/informations_datafile_input.txt | 6 DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/logodromics-dr.png |only DRomics-2.1-2/DRomics/inst/DRomics-shiny/www/logodromics.png |only DRomics-2.1-2/DRomics/inst/NEWS | 28 DRomics-2.1-2/DRomics/inst/extdata/apical_anchoring.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVcontigannot.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVcontigres.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVmetabannot.txt |only DRomics-2.1-2/DRomics/inst/extdata/triclosanSVmetabres.txt |only DRomics-2.1-2/DRomics/man/DRomics.Rd | 306 ++++++++-- DRomics-2.1-2/DRomics/man/RNAseqdata.Rd | 71 +- DRomics-2.1-2/DRomics/man/Scenedesmus.Rd |only DRomics-2.1-2/DRomics/man/Zhou.Rd |only DRomics-2.1-2/DRomics/man/bmdboot.Rd | 2 DRomics-2.1-2/DRomics/man/bmdcalc.Rd | 2 DRomics-2.1-2/DRomics/man/bmdplotwithgradient.Rd |only DRomics-2.1-2/DRomics/man/continuousanchoringdata.Rd |only DRomics-2.1-2/DRomics/man/curvesplot.Rd | 67 +- DRomics-2.1-2/DRomics/man/drcfit.Rd | 56 + DRomics-2.1-2/DRomics/man/ecdfplotwithCI.Rd | 72 +- DRomics-2.1-2/DRomics/man/ecdfquantileplot.Rd |only DRomics-2.1-2/DRomics/man/itemselect.Rd | 24 DRomics-2.1-2/DRomics/man/metabolomicdata.Rd | 45 + DRomics-2.1-2/DRomics/man/microarraydata.Rd | 28 DRomics-2.1-2/DRomics/man/targetplot.Rd |only DRomics-2.1-2/DRomics/tests/examplewithLprobit.R | 23 DRomics-2.1-2/DRomics/tests/examplewithRNAseq.R | 146 +++- DRomics-2.1-2/DRomics/tests/examplewithanchoringdata.R |only DRomics-2.1-2/DRomics/tests/examplewithmetabolomic.R | 60 + DRomics-2.1-2/DRomics/tests/examplewithmicroarray.R | 75 +- DRomics-2.1-2/DRomics/tests/testthat/test_drcfit.R | 9 56 files changed, 1609 insertions(+), 552 deletions(-)
Title: Interface to the 'Azure Machine Learning' 'SDK'
Description: Interface to the 'Azure Machine Learning' Software Development Kit
('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and
manage machine learning models on the 'Azure Machine Learning' service. To
learn more about 'Azure Machine Learning' visit the website:
<https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.
Author: Diondra Peck [cre, aut],
Minna Xiao [aut],
AzureML R SDK Team [ctb],
Microsoft [cph, fnd],
Google Inc. [cph] (Examples and Tutorials),
The TensorFlow Authors [cph] (Examples and Tutorials),
RStudio Inc. [cph] (Examples and Tutorials)
Maintainer: Diondra Peck <Diondra.Peck@microsoft.com>
Diff between azuremlsdk versions 0.6.85 dated 2020-02-05 and 1.10.0 dated 2020-09-22
azuremlsdk-0.6.85/azuremlsdk/man/dot-create_run_details_plot.Rd |only azuremlsdk-0.6.85/azuremlsdk/man/generate_docker_file.Rd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/deploy-to-aks/deploy-to-aks.Rmd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/experiments-with-R |only azuremlsdk-0.6.85/azuremlsdk/vignettes/hyperparameter-tune-with-keras/hyperparameter-tune-with-keras.Rmd |only azuremlsdk-0.6.85/azuremlsdk/vignettes/train-and-deploy-to-aci |only azuremlsdk-0.6.85/azuremlsdk/vignettes/train-with-tensorflow/train-with-tensorflow.Rmd |only azuremlsdk-1.10.0/azuremlsdk/DESCRIPTION | 27 azuremlsdk-1.10.0/azuremlsdk/MD5 | 486 +- azuremlsdk-1.10.0/azuremlsdk/NAMESPACE | 325 - azuremlsdk-1.10.0/azuremlsdk/R/compute.R | 763 ++-- azuremlsdk-1.10.0/azuremlsdk/R/datasets.R | 1407 ++++--- azuremlsdk-1.10.0/azuremlsdk/R/datastore.R | 770 ++-- azuremlsdk-1.10.0/azuremlsdk/R/do_azureml_parallel.R |only azuremlsdk-1.10.0/azuremlsdk/R/environment.R | 579 +-- azuremlsdk-1.10.0/azuremlsdk/R/estimator.R | 266 - azuremlsdk-1.10.0/azuremlsdk/R/experiment.R | 248 - azuremlsdk-1.10.0/azuremlsdk/R/hyperdrive.R | 1387 +++---- azuremlsdk-1.10.0/azuremlsdk/R/install.R | 139 azuremlsdk-1.10.0/azuremlsdk/R/keyvault.R | 144 azuremlsdk-1.10.0/azuremlsdk/R/model.R | 1148 +++--- azuremlsdk-1.10.0/azuremlsdk/R/modules.R | 16 azuremlsdk-1.10.0/azuremlsdk/R/package.R | 90 azuremlsdk-1.10.0/azuremlsdk/R/run.R | 1850 +++++----- azuremlsdk-1.10.0/azuremlsdk/R/webservice-aci.R | 256 - azuremlsdk-1.10.0/azuremlsdk/R/webservice-aks.R | 558 +-- azuremlsdk-1.10.0/azuremlsdk/R/webservice-local.R | 176 azuremlsdk-1.10.0/azuremlsdk/R/webservice.R | 387 +- azuremlsdk-1.10.0/azuremlsdk/R/workspace.R | 761 ++-- azuremlsdk-1.10.0/azuremlsdk/README.md | 4 azuremlsdk-1.10.0/azuremlsdk/build/vignette.rds |binary azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.R | 35 azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.Rmd | 262 - azuremlsdk-1.10.0/azuremlsdk/inst/doc/configuration.html | 117 azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploy-to-aks.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/deploying-models.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/experiments-deep-dive.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/hyperparameter-tune-with-keras.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/installation.R | 17 azuremlsdk-1.10.0/azuremlsdk/inst/doc/installation.Rmd | 226 - azuremlsdk-1.10.0/azuremlsdk/inst/doc/installation.html | 139 azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-and-deploy-first-model.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-and-deploy-first-model.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-and-deploy-first-model.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-with-tensorflow.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-with-tensorflow.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/train-with-tensorflow.html |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/troubleshooting.R |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/troubleshooting.Rmd |only azuremlsdk-1.10.0/azuremlsdk/inst/doc/troubleshooting.html |only azuremlsdk-1.10.0/azuremlsdk/inst/widget/app.R | 130 azuremlsdk-1.10.0/azuremlsdk/man/aci_webservice_deployment_config.Rd | 162 azuremlsdk-1.10.0/azuremlsdk/man/aks_webservice_deployment_config.Rd | 319 - azuremlsdk-1.10.0/azuremlsdk/man/attach_aks_compute.Rd | 102 azuremlsdk-1.10.0/azuremlsdk/man/azureml.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/bandit_policy.Rd | 160 azuremlsdk-1.10.0/azuremlsdk/man/bayesian_parameter_sampling.Rd | 92 azuremlsdk-1.10.0/azuremlsdk/man/cancel_run.Rd | 34 azuremlsdk-1.10.0/azuremlsdk/man/choice.Rd | 45 azuremlsdk-1.10.0/azuremlsdk/man/complete_run.Rd | 40 azuremlsdk-1.10.0/azuremlsdk/man/container_registry.Rd | 60 azuremlsdk-1.10.0/azuremlsdk/man/convert_to_dataset_with_csv_files.Rd | 40 azuremlsdk-1.10.0/azuremlsdk/man/convert_to_dataset_with_parquet_files.Rd | 42 azuremlsdk-1.10.0/azuremlsdk/man/cran_package.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/create_aks_compute.Rd | 189 - azuremlsdk-1.10.0/azuremlsdk/man/create_aml_compute.Rd | 197 - azuremlsdk-1.10.0/azuremlsdk/man/create_child_run.Rd | 49 azuremlsdk-1.10.0/azuremlsdk/man/create_child_runs.Rd | 47 azuremlsdk-1.10.0/azuremlsdk/man/create_file_dataset_from_files.Rd | 45 azuremlsdk-1.10.0/azuremlsdk/man/create_tabular_dataset_from_delimited_files.Rd | 120 azuremlsdk-1.10.0/azuremlsdk/man/create_tabular_dataset_from_json_lines_files.Rd | 99 azuremlsdk-1.10.0/azuremlsdk/man/create_tabular_dataset_from_parquet_files.Rd | 85 azuremlsdk-1.10.0/azuremlsdk/man/create_tabular_dataset_from_sql_query.Rd | 90 azuremlsdk-1.10.0/azuremlsdk/man/create_workspace.Rd | 256 - azuremlsdk-1.10.0/azuremlsdk/man/data_path.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/data_type_bool.Rd | 28 azuremlsdk-1.10.0/azuremlsdk/man/data_type_datetime.Rd | 72 azuremlsdk-1.10.0/azuremlsdk/man/data_type_double.Rd | 28 azuremlsdk-1.10.0/azuremlsdk/man/data_type_long.Rd | 28 azuremlsdk-1.10.0/azuremlsdk/man/data_type_string.Rd | 28 azuremlsdk-1.10.0/azuremlsdk/man/dataset_consumption_config.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/define_timestamp_columns_for_dataset.Rd | 66 azuremlsdk-1.10.0/azuremlsdk/man/delete_compute.Rd | 50 azuremlsdk-1.10.0/azuremlsdk/man/delete_local_webservice.Rd | 47 azuremlsdk-1.10.0/azuremlsdk/man/delete_model.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/delete_secrets.Rd | 40 azuremlsdk-1.10.0/azuremlsdk/man/delete_webservice.Rd | 42 azuremlsdk-1.10.0/azuremlsdk/man/delete_workspace.Rd | 53 azuremlsdk-1.10.0/azuremlsdk/man/deploy_model.Rd | 156 azuremlsdk-1.10.0/azuremlsdk/man/detach_aks_compute.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/download_file_from_run.Rd | 59 azuremlsdk-1.10.0/azuremlsdk/man/download_files_from_run.Rd | 74 azuremlsdk-1.10.0/azuremlsdk/man/download_from_datastore.Rd | 61 azuremlsdk-1.10.0/azuremlsdk/man/download_from_file_dataset.Rd | 53 azuremlsdk-1.10.0/azuremlsdk/man/download_model.Rd | 64 azuremlsdk-1.10.0/azuremlsdk/man/drop_columns_from_dataset.Rd | 40 azuremlsdk-1.10.0/azuremlsdk/man/estimator.Rd | 234 - 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azuremlsdk-1.10.0/azuremlsdk/man/inference_config.Rd | 152 azuremlsdk-1.10.0/azuremlsdk/man/install_azureml.Rd | 60 azuremlsdk-1.10.0/azuremlsdk/man/interactive_login_authentication.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/invoke_webservice.Rd | 78 azuremlsdk-1.10.0/azuremlsdk/man/keep_columns_from_dataset.Rd | 50 azuremlsdk-1.10.0/azuremlsdk/man/list_nodes_in_aml_compute.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/list_secrets.Rd | 36 azuremlsdk-1.10.0/azuremlsdk/man/list_supported_vm_sizes.Rd | 42 azuremlsdk-1.10.0/azuremlsdk/man/list_workspaces.Rd | 50 azuremlsdk-1.10.0/azuremlsdk/man/load_dataset_into_data_frame.Rd | 46 azuremlsdk-1.10.0/azuremlsdk/man/load_workspace_from_config.Rd | 57 azuremlsdk-1.10.0/azuremlsdk/man/local_webservice_deployment_config.Rd | 54 azuremlsdk-1.10.0/azuremlsdk/man/log_accuracy_table_to_run.Rd | 152 azuremlsdk-1.10.0/azuremlsdk/man/log_confusion_matrix_to_run.Rd | 48 azuremlsdk-1.10.0/azuremlsdk/man/log_image_to_run.Rd | 59 azuremlsdk-1.10.0/azuremlsdk/man/log_list_to_run.Rd | 58 azuremlsdk-1.10.0/azuremlsdk/man/log_metric_to_run.Rd | 62 azuremlsdk-1.10.0/azuremlsdk/man/log_predictions_to_run.Rd | 82 azuremlsdk-1.10.0/azuremlsdk/man/log_residuals_to_run.Rd | 74 azuremlsdk-1.10.0/azuremlsdk/man/log_row_to_run.Rd | 86 azuremlsdk-1.10.0/azuremlsdk/man/log_table_to_run.Rd | 67 azuremlsdk-1.10.0/azuremlsdk/man/lognormal.Rd | 52 azuremlsdk-1.10.0/azuremlsdk/man/loguniform.Rd | 60 azuremlsdk-1.10.0/azuremlsdk/man/median_stopping_policy.Rd | 118 azuremlsdk-1.10.0/azuremlsdk/man/merge_results.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/mount_file_dataset.Rd | 54 azuremlsdk-1.10.0/azuremlsdk/man/normal.Rd | 54 azuremlsdk-1.10.0/azuremlsdk/man/package_model.Rd | 133 azuremlsdk-1.10.0/azuremlsdk/man/plot_run_details.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/primary_metric_goal.Rd | 46 azuremlsdk-1.10.0/azuremlsdk/man/promote_headers_behavior.Rd | 48 azuremlsdk-1.10.0/azuremlsdk/man/pull_model_package_image.Rd | 60 azuremlsdk-1.10.0/azuremlsdk/man/qlognormal.Rd | 62 azuremlsdk-1.10.0/azuremlsdk/man/qloguniform.Rd | 62 azuremlsdk-1.10.0/azuremlsdk/man/qnormal.Rd | 56 azuremlsdk-1.10.0/azuremlsdk/man/quniform.Rd | 60 azuremlsdk-1.10.0/azuremlsdk/man/r_environment.Rd | 244 - azuremlsdk-1.10.0/azuremlsdk/man/randint.Rd | 64 azuremlsdk-1.10.0/azuremlsdk/man/random_parameter_sampling.Rd | 84 azuremlsdk-1.10.0/azuremlsdk/man/random_split_dataset.Rd | 44 azuremlsdk-1.10.0/azuremlsdk/man/register_azure_blob_container_datastore.Rd | 177 azuremlsdk-1.10.0/azuremlsdk/man/register_azure_data_lake_gen2_datastore.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/register_azure_file_share_datastore.Rd | 141 azuremlsdk-1.10.0/azuremlsdk/man/register_azure_postgre_sql_datastore.Rd | 84 azuremlsdk-1.10.0/azuremlsdk/man/register_azure_sql_database_datastore.Rd | 111 azuremlsdk-1.10.0/azuremlsdk/man/register_dataset.Rd | 62 azuremlsdk-1.10.0/azuremlsdk/man/register_do_azureml_parallel.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/register_environment.Rd | 56 azuremlsdk-1.10.0/azuremlsdk/man/register_model.Rd | 146 azuremlsdk-1.10.0/azuremlsdk/man/register_model_from_run.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/reload_local_webservice_assets.Rd | 48 azuremlsdk-1.10.0/azuremlsdk/man/resource_configuration.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/save_model_package_files.Rd | 72 azuremlsdk-1.10.0/azuremlsdk/man/service_principal_authentication.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/set_default_datastore.Rd | 41 azuremlsdk-1.10.0/azuremlsdk/man/set_secrets.Rd | 58 azuremlsdk-1.10.0/azuremlsdk/man/skip_from_dataset.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/split_tasks.Rd |only azuremlsdk-1.10.0/azuremlsdk/man/start_logging_run.Rd | 93 azuremlsdk-1.10.0/azuremlsdk/man/submit_child_run.Rd | 42 azuremlsdk-1.10.0/azuremlsdk/man/submit_experiment.Rd | 94 azuremlsdk-1.10.0/azuremlsdk/man/take_from_dataset.Rd | 38 azuremlsdk-1.10.0/azuremlsdk/man/take_sample_from_dataset.Rd | 42 azuremlsdk-1.10.0/azuremlsdk/man/truncation_selection_policy.Rd | 135 azuremlsdk-1.10.0/azuremlsdk/man/uniform.Rd | 52 azuremlsdk-1.10.0/azuremlsdk/man/unregister_all_dataset_versions.Rd | 34 azuremlsdk-1.10.0/azuremlsdk/man/unregister_datastore.Rd | 36 azuremlsdk-1.10.0/azuremlsdk/man/update_aci_webservice.Rd | 109 azuremlsdk-1.10.0/azuremlsdk/man/update_aks_webservice.Rd | 243 - azuremlsdk-1.10.0/azuremlsdk/man/update_aml_compute.Rd | 58 azuremlsdk-1.10.0/azuremlsdk/man/update_local_webservice.Rd | 69 azuremlsdk-1.10.0/azuremlsdk/man/upload_files_to_datastore.Rd | 82 azuremlsdk-1.10.0/azuremlsdk/man/upload_files_to_run.Rd | 99 azuremlsdk-1.10.0/azuremlsdk/man/upload_folder_to_run.Rd | 89 azuremlsdk-1.10.0/azuremlsdk/man/upload_to_datastore.Rd | 61 azuremlsdk-1.10.0/azuremlsdk/man/wait_for_deployment.Rd | 56 azuremlsdk-1.10.0/azuremlsdk/man/wait_for_model_package_creation.Rd | 40 azuremlsdk-1.10.0/azuremlsdk/man/wait_for_provisioning_completion.Rd | 46 azuremlsdk-1.10.0/azuremlsdk/man/wait_for_run_completion.Rd | 43 azuremlsdk-1.10.0/azuremlsdk/man/write_workspace_config.Rd | 62 azuremlsdk-1.10.0/azuremlsdk/tests/testthat.R | 10 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/dummy_score.R | 36 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/helper-resources.R | 73 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/iris.csv | 302 - azuremlsdk-1.10.0/azuremlsdk/tests/testthat/teardown-resources.R | 12 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_compute.R | 90 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_datasets.R | 153 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_datastore.R | 150 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_environment.R | 145 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_estimator.R | 40 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_experiment.R | 304 - azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_hyperdrive.R | 120 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_keyvault.R | 44 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_model.R | 209 - azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_webservice.R | 112 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/test_workspace.R | 82 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/train_dummy.R | 14 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/train_hyperdrive_dummy.R | 18 azuremlsdk-1.10.0/azuremlsdk/tests/testthat/utils.R | 18 azuremlsdk-1.10.0/azuremlsdk/vignettes/README.md | 50 azuremlsdk-1.10.0/azuremlsdk/vignettes/configuration.Rmd | 262 - azuremlsdk-1.10.0/azuremlsdk/vignettes/deploy-to-aks.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/deploy-to-aks/score.R | 36 azuremlsdk-1.10.0/azuremlsdk/vignettes/deploying-models.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/experiments-deep-dive |only azuremlsdk-1.10.0/azuremlsdk/vignettes/experiments-deep-dive.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/hyperparameter-tune-with-keras.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/hyperparameter-tune-with-keras/Dockerfile |only azuremlsdk-1.10.0/azuremlsdk/vignettes/hyperparameter-tune-with-keras/cifar10_cnn.R | 245 - azuremlsdk-1.10.0/azuremlsdk/vignettes/installation.Rmd | 226 - azuremlsdk-1.10.0/azuremlsdk/vignettes/train-and-deploy-first-model |only azuremlsdk-1.10.0/azuremlsdk/vignettes/train-and-deploy-first-model.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/train-with-tensorflow.Rmd |only azuremlsdk-1.10.0/azuremlsdk/vignettes/train-with-tensorflow/Dockerfile |only azuremlsdk-1.10.0/azuremlsdk/vignettes/train-with-tensorflow/tf_mnist.R | 5 azuremlsdk-1.10.0/azuremlsdk/vignettes/troubleshooting.Rmd |only 264 files changed, 13962 insertions(+), 12823 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 1.1.0 dated 2020-09-15 and 1.1.1 dated 2020-09-22
DESCRIPTION | 10 MD5 | 20 + NAMESPACE | 9 NEWS.md | 6 R/ROC.R | 317 +++++++++++++++++++++++++---- inst/doc/lmExample.html | 4 inst/doc/sigrFormatting.html | 4 man/find_AUC_q.Rd | 5 man/find_ROC_matching_ab.Rd |only man/find_ROC_matching_ab1.Rd |only man/find_area_q.Rd |only man/fit_beta_shapes.Rd |only man/sensitivity_and_specificity_s12p12n.Rd |only man/sensitivity_from_specificity_q.Rd |only 14 files changed, 323 insertions(+), 52 deletions(-)
Title: NEON Data Store
Description: The National Ecological Observatory Network (NEON) provides access
to its numerous data products through its REST API,
<https://data.neonscience.org/data-api/>. This package provides a
high-level user interface for downloading and storing NEON data products.
While each of NEON data products consist of hundreds or thousands of individual
files. Unlike 'neonUtilities', this package will avoid repeated downloading,
provides persistent storage, and improves performance. This package does not
provide expose interactions with the individual low-level NEON API endpoints.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Quinn Thomas [aut] (<https://orcid.org/0000-0003-1282-7825>),
Christine Laney [aut] (<https://orcid.org/0000-0002-4944-2083>),
Claire Lunch [aut] (<https://orcid.org/0000-0001-8753-6593>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between neonstore versions 0.2.2 dated 2020-09-08 and 0.2.3 dated 2020-09-22
DESCRIPTION | 18 +++++++++++------- MD5 | 26 +++++++++++++------------- NEWS.md | 8 ++++++++ R/neon_download.R | 35 +++++++++++++++++++++++++++++------ R/neon_download_s3.R | 4 ++-- R/neon_export.R | 5 ++++- R/neon_filename_parser.R | 37 ++++++++++++++++++++++--------------- R/neon_index.R | 21 +++++++++++++++------ R/neon_read.R | 31 +++++++++++++++++-------------- inst/WORDLIST | 4 ++++ man/neon_download_s3.Rd | 2 +- man/neon_read.Rd | 5 +++++ tests/testthat/test-additional.R | 4 ++-- tests/testthat/test-store.R | 24 +++++++++++++++++++++--- 14 files changed, 154 insertions(+), 70 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny' apps and R markdown documents. A tree allows to represent hierarchical data (e.g. the contents of a directory). Similar to the 'shinyTree' package but offers more features and options, such as the grid extension, restricting the drag-and-drop behavior, and settings for the search functionality. It is possible to attach some data to the nodes of a tree and then to get these data in 'Shiny' when a node is selected. Also provides a 'Shiny' gadget allowing to manipulate one or more folders.
Author: Stéphane Laurent [aut, cre],
jQuery contributors [ctb, cph] (jQuery),
Ivan Bozhanov [ctb, cph] (jsTree),
Vedran Opacic [ctb, cph] (jsTree bootstrap theme),
Avi Deitcher [ctb, cph] (jsTreeGrid),
Terence Eden [ctb, cph] (SuperTinyIcons)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 0.1.0 dated 2020-08-31 and 1.0.0 dated 2020-09-22
DESCRIPTION | 12 LICENSE.note | 20 MD5 | 38 NAMESPACE | 14 NEWS.md | 17 R/folderGadget.R |only R/jstree.R | 45 R/zzz.R | 23 README.md | 29 inst/htmlwidgets/OtherIcons |only inst/htmlwidgets/SuperTinyIcons/SuperTinyIcons.json | 1225 ++++++++++++++++---- inst/htmlwidgets/jstree.js | 129 +- inst/htmlwidgets/jstree.yaml | 4 inst/htmlwidgets/lib/bootstrap-theme/style.min.css | 2 inst/rstudio |only man/folderGadget.Rd |only man/jstree-shiny.Rd | 33 man/jstree.Rd | 12 18 files changed, 1282 insertions(+), 321 deletions(-)
Title: Model for Semisupervised Text Analysis Based on Word Embeddings
Description: A word embeddings-based semisupervised models for document scaling Watanabe (2017) <doi:10.1177/0267323117695735>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 0.9.1 dated 2020-09-14 and 0.9.2 dated 2020-09-22
DESCRIPTION | 12 +++---- MD5 | 10 ++--- NEWS.md | 8 ++++ tests/testthat/test-textmodel.R | 68 +++++++++++++++++++--------------------- tests/testthat/test-textplot.R | 4 -- tests/testthat/test-utils.R | 6 ++- 6 files changed, 58 insertions(+), 50 deletions(-)
Title: Scenario Weights for Importance Measurement
Description: An efficient sensitivity analysis for stochastic models based on
Monte Carlo samples. Provides weights on simulated scenarios from a
stochastic model, such that stressed random variables fulfil given
probabilistic constraints (e.g. specified values for risk measures),
under the new scenario weights. Scenario weights are selected by
constrained minimisation of the relative entropy to the baseline model.
The 'SWIM' package is based on Pesenti S.M, Millossovich P., Tsanakas A.
(2019) "Reverse Sensitivity Testing: What does it take to break the model",
<openaccess.city.ac.uk/id/eprint/18896/>.
Author: Silvana M. Pesenti [aut, cre],
Alberto Bettini [aut],
Pietro Millossovich [aut],
Andreas Tsanakas [aut]
Maintainer: Silvana M. Pesenti <swimpackage@gmail.com>
Diff between SWIM versions 0.2.1 dated 2020-05-22 and 0.2.2 dated 2020-09-22
DESCRIPTION | 8 - MD5 | 66 +++++++------ NAMESPACE | 2 NEWS.md | 29 +++++ R/cdf.R | 1 R/class.R | 27 +++-- R/plot_cdf.R | 3 R/plot_hist.R | 3 R/plot_quantile.R |only R/plot_weights.R |only R/quantile.R | 2 R/stress_VaR_ES.R | 26 ++++- R/stress_moment.R | 52 ++++++++-- README.md | 23 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/REFERENCES.bib | 2 inst/WORDLIST | 5 + inst/doc/SWIM-vignette.R | 33 ++---- inst/doc/SWIM-vignette.Rmd | 42 +++----- inst/doc/SWIM-vignette.html | 165 ++++++++++++++++----------------- man/get_data.Rd | 181 +++++++++++++++++++------------------ man/plot_quantile.Rd |only man/plot_weights.Rd |only man/stress_VaR_ES.Rd | 8 + man/stress_mean.Rd | 8 + man/stress_mean_sd.Rd | 8 + man/stress_moment.Rd | 13 ++ man/summary.SWIM.Rd | 126 ++++++++++++------------- tests/testthat/testget_data.R | 5 - tests/testthat/testplot_cdf.R | 2 tests/testthat/testplot_quantile.R |only tests/testthat/testplot_weights.R |only tests/testthat/testsensitivity.R | 8 - vignettes/SWIM-vignette.Rmd | 42 +++----- vignettes/bibliography.bib | 2 37 files changed, 494 insertions(+), 400 deletions(-)
Title: Tools for Assessment the Association Between Two Spatial
Processes
Description: Tools to assess the association between two spatial processes. Currently,
several methodologies are implemented: A modified t-test to perform hypothesis testing
about the independence between the processes, a suitable nonparametric correlation
coefficient, the codispersion coefficient, and an F test for assessing the multiple
correlation between one spatial process and several others. Functions for image
processing and computing the spatial association between images are also provided.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Ronny Vallejos [aut] (<https://orcid.org/0000-0001-5519-0946>),
Francisco Cuevas [ctb],
Diego Mancilla [ctb]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between SpatialPack versions 0.3-819 dated 2020-06-21 and 0.3-8196 dated 2020-09-22
SpatialPack-0.3-819/SpatialPack/src/image.h |only SpatialPack-0.3-819/SpatialPack/src/similarity.h |only SpatialPack-0.3-819/SpatialPack/src/utils.c |only SpatialPack-0.3-819/SpatialPack/src/utils.h |only SpatialPack-0.3-8196/SpatialPack/ChangeLog | 5 + SpatialPack-0.3-8196/SpatialPack/DESCRIPTION | 22 +++--- SpatialPack-0.3-8196/SpatialPack/MD5 | 43 ++++++------- SpatialPack-0.3-8196/SpatialPack/NAMESPACE | 3 SpatialPack-0.3-8196/SpatialPack/R/codisp.R | 2 SpatialPack-0.3-8196/SpatialPack/R/image.R | 24 +++++-- SpatialPack-0.3-8196/SpatialPack/R/similarity.R | 4 - SpatialPack-0.3-8196/SpatialPack/data/wheat.rda |only SpatialPack-0.3-8196/SpatialPack/inst/CITATION | 20 +++--- SpatialPack-0.3-8196/SpatialPack/man/wheat.Rd |only SpatialPack-0.3-8196/SpatialPack/src/base.c | 1 SpatialPack-0.3-8196/SpatialPack/src/base.h | 17 +---- SpatialPack-0.3-8196/SpatialPack/src/codisp.c | 9 +- SpatialPack-0.3-8196/SpatialPack/src/denoise.f | 48 ++++++++++++--- SpatialPack-0.3-8196/SpatialPack/src/distn.c |only SpatialPack-0.3-8196/SpatialPack/src/image.c | 24 ++++++- SpatialPack-0.3-8196/SpatialPack/src/init.c | 67 ++++++++++++++------- SpatialPack-0.3-8196/SpatialPack/src/mod_ttest.c | 1 SpatialPack-0.3-8196/SpatialPack/src/similarity.c | 6 - SpatialPack-0.3-8196/SpatialPack/src/spatialpack.h | 19 ++++- SpatialPack-0.3-8196/SpatialPack/src/stats.c | 51 ++++----------- SpatialPack-0.3-8196/SpatialPack/src/stats.h | 12 +-- 26 files changed, 226 insertions(+), 152 deletions(-)
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@ec-nantes.fr>
Diff between SpatialExtremes versions 2.0-8 dated 2020-03-09 and 2.0-9 dated 2020-09-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/smith.R | 1 - build/vignette.rds |binary inst/doc/SpatialExtremesGuide.R | 1 - inst/doc/SpatialExtremesGuide.pdf |binary 6 files changed, 9 insertions(+), 11 deletions(-)
More information about SpatialExtremes at CRAN
Permanent link
Title: A Framework to Smooth L1 Penalized Regression Operators using
Nesterov Smoothing
Description: We provide full functionality to smooth L1 penalized regression operators and to compute regression estimates thereof. For this, the objective function of a user-specified regression operator is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified objective function with explicit gradients everywhere. The smoothed objective function and its gradient are minimized via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed objective functions as well as on their respective minimizers (see G. Hahn, S.M. Lutz, N. Laha, C. Lange (2020) <doi:10.1101/2020.09.17.301788>). A progressive smoothing approach is provided which iteratively smoothes the objective function, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between smoothedLasso versions 1.3 dated 2020-06-14 and 1.4 dated 2020-09-22
smoothedLasso-1.3/smoothedLasso/man/solveSmoothedLASSO.Rd |only smoothedLasso-1.3/smoothedLasso/man/solveSmoothedLASSOSequence.Rd |only smoothedLasso-1.3/smoothedLasso/man/solveUnsmoothedLASSO.Rd |only smoothedLasso-1.4/smoothedLasso/DESCRIPTION | 15 smoothedLasso-1.4/smoothedLasso/MD5 | 24 smoothedLasso-1.4/smoothedLasso/NAMESPACE | 10 smoothedLasso-1.4/smoothedLasso/R/smoothedLasso.r | 456 ++++++---- smoothedLasso-1.4/smoothedLasso/man/elasticNet.Rd |only smoothedLasso-1.4/smoothedLasso/man/fusedLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/graphicalLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/minimizeFunction.Rd |only smoothedLasso-1.4/smoothedLasso/man/minimizeSmoothedSequence.Rd |only smoothedLasso-1.4/smoothedLasso/man/objFunction.Rd | 26 smoothedLasso-1.4/smoothedLasso/man/objFunctionGradient.Rd | 28 smoothedLasso-1.4/smoothedLasso/man/objFunctionSmooth.Rd | 26 smoothedLasso-1.4/smoothedLasso/man/objFunctionSmoothGradient.Rd | 28 smoothedLasso-1.4/smoothedLasso/man/prsLasso.Rd |only smoothedLasso-1.4/smoothedLasso/man/standardLasso.Rd |only 18 files changed, 403 insertions(+), 210 deletions(-)
Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr'
with 'asciidoc'
(<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is
merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between rasciidoc versions 2.1.3 dated 2020-08-16 and 2.2.0 dated 2020-09-22
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 5 +++++ R/render.R | 41 ++++++++++++++++++++++++++++++++++++----- 4 files changed, 49 insertions(+), 13 deletions(-)
Title: Segment Images in Text Lines and Words
Description: Find text lines in scanned images and segment the lines into words.
Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>,
an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>,
and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital
Humanities [cph] (R wrapper),
Jeroen Ooms [ctb, cph] (More details in LICENSE.note file),
Arthur Flôr [ctb, cph] (More details in LICENSE.note file),
Saverio Meucci [ctb, cph] (More details in LICENSE.note file),
Yeara Kozlov [ctb, cph] (More details in LICENSE.note file),
Tino Weinkauf [ctb, cph] (More details in LICENSE.note file)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>
Diff between image.textlinedetector versions 0.1.1 dated 2020-09-21 and 0.1.2 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.win | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
More information about image.textlinedetector at CRAN
Permanent link
Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug
combinations in cancer cell lines (developed by the DrugLogics research group
in NTNU). It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set
of gold standard synergies and find the average activity difference per network
node between all model group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be found.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between emba versions 0.1.6 dated 2020-07-08 and 0.1.7 dated 2020-09-22
DESCRIPTION | 10 ++++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/input.R | 28 +++++++++++++++------------- README.md | 2 +- inst/doc/emba.html | 22 +++++++++++----------- man/get_fitness_from_models_dir.Rd | 3 ++- man/get_link_operators_from_models_dir.Rd | 5 ++--- man/get_model_names.Rd | 3 ++- man/get_node_names.Rd | 4 ++-- man/get_stable_state_from_models_dir.Rd | 5 +++-- 11 files changed, 60 insertions(+), 48 deletions(-)
More information about LifeInsuranceContracts at CRAN
Permanent link
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut],
Zhian N. Kamvar [aut] (<https://orcid.org/0000-0003-1458-7108>),
Rich FitzJohn [aut],
Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>),
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb],
Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 0.1.0 dated 2020-09-07 and 0.2.0 dated 2020-09-22
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++-------------- NAMESPACE | 1 NEWS.md | 11 +++++++ R/dplyr.R | 18 +++++++++++- R/incidence.R | 43 +++++++++++++----------------- R/make_incidence.R | 2 - R/plot.R | 41 ++++++++++++++++------------ R/scale_x_incidence.R | 12 ++++++-- build/vignette.rds |binary inst/doc/Introduction.html | 14 ++++----- inst/doc/customizing_incidence_plots.R | 8 ++--- inst/doc/customizing_incidence_plots.Rmd | 8 ++--- inst/doc/customizing_incidence_plots.html | 34 +++++++++++------------ inst/doc/handling_incidence_objects.R | 2 - inst/doc/handling_incidence_objects.Rmd | 2 - inst/doc/handling_incidence_objects.html | 28 +++++++++---------- man/plot.incidence2.Rd | 8 ++--- tests/testthat/test-incidence.R | 9 ++++++ vignettes/customizing_incidence_plots.Rmd | 8 ++--- vignettes/handling_incidence_objects.Rmd | 2 - 21 files changed, 171 insertions(+), 128 deletions(-)
More information about BayesianLaterality at CRAN
Permanent link
More information about testComplexity at CRAN
Permanent link
Title: L1 Constrained Estimation aka `lasso'
Description: Routines and documentation for solving regression problems
while imposing an L1 constraint on the estimates, based on
the algorithm of Osborne et al. (1998).
Author: Justin Lokhorst, Bill Venables and Berwin Turlach;
port to R, tests etc: Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Berwin Turlach <Berwin.Turlach@gmail.com>
Diff between lasso2 versions 1.2-20 dated 2018-11-27 and 1.2-21.1 dated 2020-09-22
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++-------- R/gl1ce.q | 2 +- R/l1ce.q | 2 +- build/vignette.rds |binary data/Prostate.rda |binary inst/doc/Manual-vignette.pdf |binary man/gl1ce.Rd | 6 ++---- man/l1ce.Rd | 2 +- 9 files changed, 18 insertions(+), 21 deletions(-)
Title: In-depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Description: Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
Maintainer: Steve Rozen <steverozen@gmail.com>
Diff between ICAMS versions 2.2.3 dated 2020-09-18 and 2.2.4 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only README.md | 6 +++--- tests/testthat/test_1TransformCatalog.R | 4 ++++ tests/testthat/test_discarded_variants.R | 8 ++++++++ 6 files changed, 23 insertions(+), 10 deletions(-)
Title: Sequence Manipulation Utilities
Description: Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between seqmagick versions 0.1.3 dated 2019-12-19 and 0.1.4 dated 2020-09-22
DESCRIPTION | 10 +-- MD5 | 18 +++-- R/NCBI.R | 2 build/vignette.rds |binary inst/doc/seqmagick.R | 14 ++-- inst/doc/seqmagick.Rmd | 6 - inst/doc/seqmagick.html | 145 +++++++++++++++++++++++++---------------------- inst/extdata/AB115403.fa |only inst/extdata/AB115403.gb |only man/download_genbank.Rd | 2 vignettes/seqmagick.Rmd | 6 - 11 files changed, 111 insertions(+), 92 deletions(-)
Title: Verbs and Nouns for Corpus Analysis
Description: Package for corpus analysis using the Corpus Workbench
('CWB', <http://cwb.sourceforge.net/>) as an efficient back end for indexing
and querying large corpora. The package offers functionality to flexibly create
subcorpora and to carry out basic statistical operations (count, co-occurrences
etc.). The original full text of documents can be reconstructed and inspected at
any time. Beyond that, the package is intended to serve as an interface to
packages implementing advanced statistical procedures. Respective data structures
(document-term matrices, term-co-occurrence matrices etc.) can be created based
on the indexed corpora.
Author: Andreas Blaette [aut, cre] (<https://orcid.org/0000-0001-8970-8010>),
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.8.4 dated 2020-07-22 and 0.8.5 dated 2020-09-22
DESCRIPTION | 10 +- MD5 | 37 ++++--- NEWS.md | 16 +++ R/as.markdown.R | 5 - R/corpus.R | 1 R/decode.R | 46 +++++++++ R/registry.R | 12 ++ R/stats.R | 2 R/templates.R | 14 +- R/utils.R | 1 inst/CITATION | 4 inst/doc/OpenCPU.html | 4 inst/doc/vignette.Rmd | 2 inst/doc/vignette.html | 169 +++++++++++++++++------------------- man/decode.Rd | 17 +++ man/ll.Rd | 2 man/registry_eval.Rd | 11 ++ man/templates.Rd | 10 +- tests/testthat/test_registry_eval.R |only vignettes/vignette.Rmd | 2 20 files changed, 233 insertions(+), 132 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Fernando Cagua [ctb],
Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.25 dated 2020-07-24 and 0.26 dated 2020-09-22
DESCRIPTION | 6 MD5 | 16 +- R/install.R | 317 +++++++++++++++++++++++++------------------------ R/latex.R | 12 + R/tlmgr.R | 80 +++++++++--- README.md | 8 - man/install_tinytex.Rd | 39 +++--- man/tl_pkgs.Rd | 11 + man/tl_sizes.Rd | 21 ++- 9 files changed, 293 insertions(+), 217 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Provides two approaches of comparison; the univariate and the multivariate analysis in two or more populations. Since the main obstacle of performing systematic comparisons in anthropological studies is the absence of raw data, the current package offer a solution for this problem by allowing the use of published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [aut] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bas12@fayoum.edu.eg>
Diff between TestDimorph versions 0.3.3 dated 2020-09-20 and 0.3.4 dated 2020-09-22
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 1 - R/V_to_R.R | 1 + R/index_D.R | 1 + R/to_parms.R | 2 +- R/to_symm_diag.R | 1 + R/van_Vark.R | 1 + man/V_to_R.Rd | 1 + man/index_D.Rd | 1 + man/to_params.Rd | 1 + man/van_Vark.Rd | 1 + 12 files changed, 23 insertions(+), 16 deletions(-)
More information about rBiasCorrection at CRAN
Permanent link
Title: Fractional Hot Deck and Fully Efficient Fractional Imputation
Description: Impute general multivariate missing data with the fractional hot deck imputation based on Jaekwang Kim (2011) <doi:10.1093/biomet/asq073>.
Author: Inho Cho [aut, cre],
Jaekwang Kim [aut],
Jongho Im [aut],
Yicheng Yang [aut]
Maintainer: Inho Cho <icho@iastate.edu>
Diff between FHDI versions 1.4.0 dated 2020-04-23 and 1.4.1 dated 2020-09-22
DESCRIPTION | 8 MD5 | 18 R/FHDI_CellMake.R | 25 R/FHDI_CellProb.R | 6 R/FHDI_Driver.R | 48 man/FHDI-package.Rd | 7 man/FHDI_CellMake.Rd | 35 man/FHDI_CellProb.Rd | 15 man/FHDI_Driver.Rd | 34 src/FHDI.cc | 9435 +++++++++++++++++++++++++++++++++++++++++++++++++-- 10 files changed, 9190 insertions(+), 441 deletions(-)
Title: Discontinuous Regression and Image Processing
Description: This is a collection of functions for discontinuous regression
analysis and image processing (DRIP). This version removes the
dependence on the GNU Scientific Library.
Author: Yicheng Kang <kangx276@umn.edu>
Maintainer: Yicheng Kang <kangx276@umn.edu>
Diff between DRIP versions 1.5 dated 2020-09-10 and 1.6 dated 2020-09-22
DESCRIPTION | 15 ++++++-------- MD5 | 8 +++---- NAMESPACE | 2 - R/jpex.R | 4 +-- src/JPEX0.c | 64 ++++++++++++++++++++++++++++++++++++++++-------------------- 5 files changed, 57 insertions(+), 36 deletions(-)
Title: Test for Parallel Regression Assumption
Description: Tests the parallel regression assumption wit the brant test by Brant (1990) <doi: 10.2307/2532457> for ordinal logit models generated with the function polr() from the package 'MASS'.
Author: Benjamin Schlegel [aut,cre], Marco Steenbergen [aut]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between brant versions 0.2-0 dated 2018-01-10 and 0.3-0 dated 2020-09-22
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 3 +- R/brant.R | 65 +++++++++++++++++++++++++------------------------- R/print.testresults.R | 2 - man/brant.Rd | 10 +++++-- 6 files changed, 53 insertions(+), 47 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-20 1.0.1
Title: Summarize Data for Scientific Publication
Description: Create and format tables and APA statistics for
scientific publication. This includes making a 'Table 1'
to summarize demographics across groups, correlation tables
with significance indicated by stars, and extracting formatted
statistical summarizes from simple tests for in-text notation.
The package also includes functions for Winsorizing data based
on a Z-statistic cutoff.
Author: David Pagliaccio [aut, cre] (<https://orcid.org/0000-0002-1214-1965>)
Maintainer: David Pagliaccio <david.pagliaccio@gmail.com>
Diff between scipub versions 1.1.0 dated 2020-06-04 and 1.2.0 dated 2020-09-22
DESCRIPTION | 14 ++--- MD5 | 14 +++-- NAMESPACE | 3 + NEWS.md | 4 + R/correltable.R | 69 +++----------------------- R/gg_groupplot.R |only build/vignette.rds |binary inst/doc/scipub_vignette.html | 108 +++++++++++++++++++++--------------------- man/gg_groupplot.Rd |only 9 files changed, 85 insertions(+), 127 deletions(-)
Title: Import and Handling for Plain and Formatted Text Files
Description: Functions for importing and handling text files and formatted text
files with additional meta-data, such including '.csv', '.tab', '.json', '.xml',
'.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.
Author: Kenneth Benoit [aut, cre, cph],
Adam Obeng [aut],
Kohei Watanabe [ctb],
Akitaka Matsuo [ctb],
Paul Nulty [ctb],
Stefan Müller [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between readtext versions 0.76 dated 2020-03-04 and 0.80 dated 2020-09-22
DESCRIPTION | 14 - MD5 | 31 +- NEWS.md | 5 R/data.R | 2 R/encoding.R | 4 R/get-functions.R | 2 R/utils.R | 2 README.md | 19 - build/vignette.rds |binary data/data_char_encodedtexts.rda |only inst/doc/readtext_vignette.Rmd | 8 inst/doc/readtext_vignette.html | 560 +++++++++++++++++++++------------------- man/data_char_encodedtexts.Rd | 6 man/encoding.Rd | 4 tests/testthat/test-readtext.R | 35 -- tests/testthat/test-utils.R | 2 vignettes/readtext_vignette.Rmd | 8 17 files changed, 369 insertions(+), 333 deletions(-)
Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb],
Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>
Diff between rdbnomics versions 0.6.2 dated 2020-07-06 and 0.6.3 dated 2020-09-22
DESCRIPTION | 10 - MD5 | 46 ++-- NAMESPACE | 2 NEWS.md | 8 R/rdb.R | 12 - R/rdb_rename_xts.R |only R/rdb_to_xts.R |only R/sysdata.rda |binary R/utils.R | 6 R/zzz.R | 2 README.md | 393 +-------------------------------------- inst/doc/rdbnomics.R | 2 inst/doc/rdbnomics.Rmd | 2 inst/doc/rdbnomics.html | 65 ++---- man/dbnomics.Rd | 70 +++---- man/rdb.Rd | 474 ++++++++++++++++++++++++------------------------ man/rdb_by_api_link.Rd | 306 +++++++++++++++--------------- man/rdb_datasets.Rd | 162 ++++++++-------- man/rdb_dimensions.Rd | 186 +++++++++--------- man/rdb_last_updates.Rd | 122 ++++++------ man/rdb_providers.Rd | 124 ++++++------ man/rdb_rename_xts.Rd |only man/rdb_series.Rd | 228 +++++++++++------------ man/rdb_to_xts.Rd |only man/rdbnomics.Rd | 18 - vignettes/rdbnomics.Rmd | 2 26 files changed, 946 insertions(+), 1294 deletions(-)
Title: Geospatial Kriging with Metropolis Sampling
Description: Estimates kriging models for geographical point-referenced data. Method is described in Gill (2020) <doi:10.1177/1532440020930197>.
Author: Jason S. Byers [aut, cre], Le Bao [aut], Jamie Carson [aut], Jeff Gill [aut]
Maintainer: Jason S. Byers <jaybyers55@gmail.com>
Diff between krige versions 0.5.6 dated 2020-06-20 and 0.5.7 dated 2020-09-22
DESCRIPTION | 12 ++++++------ MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 3 ++- R/krige.update.R |only man/NY_subset.Rd | 6 +++--- man/NYcity_subset.Rd | 6 +++--- man/WVwells.Rd | 7 +++---- man/congCombined.Rd | 4 ++-- man/geweke.Rd | 2 +- man/heidel.welch.Rd | 2 +- man/krige.posterior.Rd | 2 +- man/krige.pred.Rd | 2 +- man/krige.update.Rd |only man/lowerCombined.Rd | 2 +- man/metropolis.krige.Rd | 10 +++++----- man/stateCombined.Rd | 4 ++-- man/upperCombined.Rd | 4 ++-- src/Makevars |only 18 files changed, 50 insertions(+), 47 deletions(-)
Title: Simultaneous Penalized Linear Mixed Effects Models
Description: Contains functions that fit linear mixed-effects models
for high-dimensional data (p>>n) with penalty for both the fixed effects and random effects for variable selection.
The details of the algorithm can be found in Luoying Yang PhD thesis (available soon). The algorithm implementation
is based on the R package 'lmmlasso'.
Author: Luoying Yang, Tong Tong Wu
Maintainer: Luoying Yang <lyang19@u.rochester.edu>
Diff between splmm versions 1.0 dated 2020-09-21 and 1.1 dated 2020-09-21
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/RcppExports.R | 46 +++++++++++++++++++++++----------------------- build/partial.rdb |binary data/cognitive.rda |binary man/cognitive.Rd | 10 +++++----- man/plot.splmm.Rd | 7 ++++--- man/plot3D.splmm.Rd | 7 ++++--- man/print.splmm.Rd | 7 ++++--- man/splmm.Rd | 8 ++++---- man/splmmTuning.Rd | 7 ++++--- src/splmm_rcpp.cpp | 12 ++++++------ 12 files changed, 69 insertions(+), 65 deletions(-)
Title: The Metropolis Algorithm
Description: Learning and using the Metropolis algorithm for
Bayesian fitting of a generalized linear model. The package vignette
includes examples of hand-coding a logistic model using several
variants of the Metropolis algorithm. The package also contains R
functions for simulating posterior distributions of Bayesian
generalized linear model parameters using guided, adaptive,
guided-adaptive and random walk Metropolis algorithms. The random walk
Metropolis algorithm was originally described in Metropolis et al
(1953); <doi:10.1063/1.1699114>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between metropolis versions 0.1.5 dated 2020-01-23 and 0.1.8 dated 2020-09-21
DESCRIPTION | 14 - MD5 | 35 ++- NAMESPACE | 1 NEWS.md | 13 + R/base.R | 353 +++++++++++++++++++++++++------------- R/conversions.R |only R/data.R | 2 R/loglikelihoods.R |only R/transformations.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/metropolis-vignette.html | 6 man/as.mcmc.metropolis.samples.Rd | 8 man/expit.Rd | 6 man/logistic_ll.Rd | 2 man/magfields.Rd | 14 - man/metropolis.control.Rd | 6 man/metropolis_glm.Rd | 36 +-- man/normal_ll.Rd | 2 man/summary.metropolis.samples.Rd | 16 - tests/test_transformations.R |only 21 files changed, 324 insertions(+), 190 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type
token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable
frequency analyses (supports Celex and Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For full functionality a local installation of
TreeTagger is recommended. It is also recommended to not load this package directly, but by loading one of the available language support packages from the
'l10n' repository <https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for
its basic features. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from <https://rkward.kde.org> (plugins are detected automatically). Due to some restrictions on CRAN, the full package sources
are only available from the project homepage. To ask for help, report bugs, request features, or discuss the development of the package, please subscribe to
the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.11-5 dated 2018-10-28 and 0.13-1 dated 2020-09-21
koRpus-0.11-5/koRpus/R/01_class_01_kRp.tagged.R |only koRpus-0.11-5/koRpus/R/01_class_03_kRp.txt.freq.R |only koRpus-0.11-5/koRpus/R/01_class_04_kRp.txt.trans.R |only koRpus-0.11-5/koRpus/R/01_class_05_kRp.analysis.R |only koRpus-0.11-5/koRpus/R/01_class_06_kRp.corp.freq.R |only koRpus-0.11-5/koRpus/R/01_class_09_kRp.lang.R |only koRpus-0.11-5/koRpus/R/01_class_10_kRp.readability.R |only koRpus-0.11-5/koRpus/R/02_method_kRp.taggedText.R |only koRpus-0.11-5/koRpus/R/02_method_plot.kRp.tagged.R |only koRpus-0.11-5/koRpus/R/02_method_show.kRp.taggedText.R |only koRpus-0.11-5/koRpus/R/02_method_summary.kRp.tagged.R |only koRpus-0.11-5/koRpus/R/02_method_summary.kRp.txt.freq.R |only koRpus-0.11-5/koRpus/R/02_method_text.transform.R |only koRpus-0.11-5/koRpus/R/jumbleWords.R |only koRpus-0.11-5/koRpus/R/kRp.filter.wclass.R |only koRpus-0.11-5/koRpus/R/kRp.text.paste.R |only koRpus-0.11-5/koRpus/R/koRpus-internal.roxy.all.R |only koRpus-0.11-5/koRpus/R/read.tagged.R |only koRpus-0.11-5/koRpus/R/tokenize.R |only koRpus-0.11-5/koRpus/R/treetag.R |only koRpus-0.11-5/koRpus/man/jumbleWords.Rd |only koRpus-0.11-5/koRpus/man/kRp.analysis-class.Rd |only koRpus-0.11-5/koRpus/man/kRp.filter.wclass.Rd |only koRpus-0.11-5/koRpus/man/kRp.tagged-class.Rd |only koRpus-0.11-5/koRpus/man/kRp.taggedText-methods.Rd |only koRpus-0.11-5/koRpus/man/kRp.text.analysis.Rd |only koRpus-0.11-5/koRpus/man/kRp.text.paste.Rd |only koRpus-0.11-5/koRpus/man/kRp.txt.freq-class.Rd |only koRpus-0.11-5/koRpus/man/kRp.txt.trans-class.Rd |only koRpus-0.11-5/koRpus/man/read.tagged.Rd |only koRpus-0.11-5/koRpus/man/tokenize.Rd |only koRpus-0.11-5/koRpus/man/treetag.Rd |only koRpus-0.13-1/koRpus/ChangeLog | 145 koRpus-0.13-1/koRpus/DESCRIPTION | 107 koRpus-0.13-1/koRpus/MD5 | 309 +- koRpus-0.13-1/koRpus/NAMESPACE | 59 koRpus-0.13-1/koRpus/R/00_environment.R | 2 koRpus-0.13-1/koRpus/R/01_class_01_kRp.text.R |only koRpus-0.13-1/koRpus/R/01_class_03_kRp.corp.freq.R |only koRpus-0.13-1/koRpus/R/01_class_04_kRp.lang.R |only koRpus-0.13-1/koRpus/R/01_class_05_kRp.readability.R |only koRpus-0.13-1/koRpus/R/01_class_81_kRp.connection_union.R |only koRpus-0.13-1/koRpus/R/01_class_90_deprecated_classes.R |only koRpus-0.13-1/koRpus/R/02_method_cTest.R | 36 koRpus-0.13-1/koRpus/R/02_method_clozeDelete.R | 62 koRpus-0.13-1/koRpus/R/02_method_correct.R | 70 koRpus-0.13-1/koRpus/R/02_method_docTermMatrix.R |only koRpus-0.13-1/koRpus/R/02_method_filterByClass.R |only koRpus-0.13-1/koRpus/R/02_method_freq.analysis.R | 92 koRpus-0.13-1/koRpus/R/02_method_get_set_kRp.text.R |only koRpus-0.13-1/koRpus/R/02_method_hyphen.R | 66 koRpus-0.13-1/koRpus/R/02_method_jumbleWords.R |only koRpus-0.13-1/koRpus/R/02_method_lex.div.R | 139 koRpus-0.13-1/koRpus/R/02_method_pasteText.R |only koRpus-0.13-1/koRpus/R/02_method_plot.kRp.text.R |only koRpus-0.13-1/koRpus/R/02_method_query.R | 192 - koRpus-0.13-1/koRpus/R/02_method_read.corp.custom.R | 105 koRpus-0.13-1/koRpus/R/02_method_readTagged.R |only koRpus-0.13-1/koRpus/R/02_method_readability.R | 253 - koRpus-0.13-1/koRpus/R/02_method_show.kRp.TTR.R | 240 - koRpus-0.13-1/koRpus/R/02_method_show.kRp.corp.freq.R | 4 koRpus-0.13-1/koRpus/R/02_method_show.kRp.lang.R | 4 koRpus-0.13-1/koRpus/R/02_method_show.kRp.readability.R | 437 +- koRpus-0.13-1/koRpus/R/02_method_show.kRp.text.R |only koRpus-0.13-1/koRpus/R/02_method_split_by_doc_id.R |only koRpus-0.13-1/koRpus/R/02_method_summary.kRp.TTR.R | 58 koRpus-0.13-1/koRpus/R/02_method_summary.kRp.lang.R | 16 koRpus-0.13-1/koRpus/R/02_method_summary.kRp.readability.R | 545 +-- koRpus-0.13-1/koRpus/R/02_method_summary.kRp.text.R |only koRpus-0.13-1/koRpus/R/02_method_textTransform.R |only koRpus-0.13-1/koRpus/R/02_method_tokenize.R |only koRpus-0.13-1/koRpus/R/02_method_treetag.R |only koRpus-0.13-1/koRpus/R/02_method_types_tokens.R | 29 koRpus-0.13-1/koRpus/R/guess.lang.R | 4 koRpus-0.13-1/koRpus/R/kRp.POS.tags.R | 54 koRpus-0.13-1/koRpus/R/kRp.cluster.R | 12 koRpus-0.13-1/koRpus/R/kRp.text.analysis.R | 85 koRpus-0.13-1/koRpus/R/koRpus-internal.R | 384 -- koRpus-0.13-1/koRpus/R/koRpus-internal.freq.analysis.R | 198 + koRpus-0.13-1/koRpus/R/koRpus-internal.lexdiv.formulae.R | 9 koRpus-0.13-1/koRpus/R/koRpus-internal.rdb.formulae.R | 1489 ++++------ koRpus-0.13-1/koRpus/R/koRpus-internal.rdb.params.grades.R | 516 +++ koRpus-0.13-1/koRpus/R/koRpus-internal.read.corp.custom.R | 224 - koRpus-0.13-1/koRpus/R/koRpus-package.R | 6 koRpus-0.13-1/koRpus/R/read.BAWL.R | 4 koRpus-0.13-1/koRpus/R/read.corp.LCC.R | 4 koRpus-0.13-1/koRpus/R/readability.num.R | 62 koRpus-0.13-1/koRpus/R/textFeatures.R | 13 koRpus-0.13-1/koRpus/R/wrapper_functions_lex.div.R | 48 koRpus-0.13-1/koRpus/R/wrapper_functions_readability.R | 88 koRpus-0.13-1/koRpus/README.md | 27 koRpus-0.13-1/koRpus/build/partial.rdb |binary koRpus-0.13-1/koRpus/build/vignette.rds |binary koRpus-0.13-1/koRpus/inst/CITATION | 8 koRpus-0.13-1/koRpus/inst/NEWS.Rd | 171 + koRpus-0.13-1/koRpus/inst/doc/koRpus_vignette.R | 4 koRpus-0.13-1/koRpus/inst/doc/koRpus_vignette.Rmd | 24 koRpus-0.13-1/koRpus/inst/doc/koRpus_vignette.html | 594 ++- koRpus-0.13-1/koRpus/man/ARI.Rd | 2 koRpus-0.13-1/koRpus/man/C.ld.Rd | 5 koRpus-0.13-1/koRpus/man/CTTR.Rd | 5 koRpus-0.13-1/koRpus/man/DRP.Rd | 2 koRpus-0.13-1/koRpus/man/ELF.Rd | 2 koRpus-0.13-1/koRpus/man/FOG.Rd | 10 koRpus-0.13-1/koRpus/man/FORCAST.Rd | 10 koRpus-0.13-1/koRpus/man/HDD.Rd | 5 koRpus-0.13-1/koRpus/man/K.ld.Rd | 5 koRpus-0.13-1/koRpus/man/LIX.Rd | 2 koRpus-0.13-1/koRpus/man/MATTR.Rd | 5 koRpus-0.13-1/koRpus/man/MSTTR.Rd | 5 koRpus-0.13-1/koRpus/man/MTLD.Rd | 17 koRpus-0.13-1/koRpus/man/R.ld.Rd | 5 koRpus-0.13-1/koRpus/man/RIX.Rd | 2 koRpus-0.13-1/koRpus/man/S.ld.Rd | 5 koRpus-0.13-1/koRpus/man/SMOG.Rd | 10 koRpus-0.13-1/koRpus/man/TRI.Rd | 10 koRpus-0.13-1/koRpus/man/TTR.Rd | 5 koRpus-0.13-1/koRpus/man/U.ld.Rd | 5 koRpus-0.13-1/koRpus/man/available.koRpus.lang.Rd | 3 koRpus-0.13-1/koRpus/man/bormuth.Rd | 2 koRpus-0.13-1/koRpus/man/cTest-methods.Rd | 21 koRpus-0.13-1/koRpus/man/clozeDelete-methods.Rd | 15 koRpus-0.13-1/koRpus/man/coleman.Rd | 17 koRpus-0.13-1/koRpus/man/coleman.liau.Rd | 12 koRpus-0.13-1/koRpus/man/correct-methods.Rd | 34 koRpus-0.13-1/koRpus/man/dale.chall.Rd | 10 koRpus-0.13-1/koRpus/man/danielson.bryan.Rd | 10 koRpus-0.13-1/koRpus/man/dickes.steiwer.Rd | 10 koRpus-0.13-1/koRpus/man/docTermMatrix.Rd |only koRpus-0.13-1/koRpus/man/farr.jenkins.paterson.Rd | 10 koRpus-0.13-1/koRpus/man/filterByClass-methods.Rd |only koRpus-0.13-1/koRpus/man/flesch.Rd | 10 koRpus-0.13-1/koRpus/man/flesch.kincaid.Rd | 10 koRpus-0.13-1/koRpus/man/freq.analysis-methods.Rd | 75 koRpus-0.13-1/koRpus/man/fucks.Rd | 2 koRpus-0.13-1/koRpus/man/guess.lang.Rd | 13 koRpus-0.13-1/koRpus/man/harris.jacobson.Rd | 19 koRpus-0.13-1/koRpus/man/hyphen-methods.Rd | 73 koRpus-0.13-1/koRpus/man/install.koRpus.lang.Rd | 7 koRpus-0.13-1/koRpus/man/jumbleWords-methods.Rd |only koRpus-0.13-1/koRpus/man/kRp.POS.tags.Rd | 13 koRpus-0.13-1/koRpus/man/kRp.corp.freq-class.Rd | 4 koRpus-0.13-1/koRpus/man/kRp.lang-class.Rd | 2 koRpus-0.13-1/koRpus/man/kRp.readability-class.Rd | 4 koRpus-0.13-1/koRpus/man/kRp.text-class.Rd |only koRpus-0.13-1/koRpus/man/kRp.text_get-methods.Rd |only koRpus-0.13-1/koRpus/man/koRpus-deprecated.Rd | 114 koRpus-0.13-1/koRpus/man/koRpus-package.Rd | 6 koRpus-0.13-1/koRpus/man/lex.div-methods.Rd | 116 koRpus-0.13-1/koRpus/man/lex.div.num.Rd | 9 koRpus-0.13-1/koRpus/man/linsear.write.Rd | 10 koRpus-0.13-1/koRpus/man/maas.Rd | 5 koRpus-0.13-1/koRpus/man/nWS.Rd | 17 koRpus-0.13-1/koRpus/man/pasteText-methods.Rd |only koRpus-0.13-1/koRpus/man/plot-methods.Rd | 14 koRpus-0.13-1/koRpus/man/query-methods.Rd | 58 koRpus-0.13-1/koRpus/man/read.BAWL.Rd | 2 koRpus-0.13-1/koRpus/man/read.corp.LCC.Rd | 16 koRpus-0.13-1/koRpus/man/read.corp.celex.Rd | 9 koRpus-0.13-1/koRpus/man/read.corp.custom-methods.Rd | 53 koRpus-0.13-1/koRpus/man/readTagged-methods.Rd |only koRpus-0.13-1/koRpus/man/readability-methods.Rd | 232 - 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Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.12 dated 2020-08-26 and 0.1.13 dated 2020-09-21
freesurferformats-0.1.12/freesurferformats/R/nifti2mgh.R |only freesurferformats-0.1.12/freesurferformats/tests/testthat/test-nifti2mgh.R |only freesurferformats-0.1.13/freesurferformats/DESCRIPTION | 6 freesurferformats-0.1.13/freesurferformats/MD5 | 160 ++++++---- freesurferformats-0.1.13/freesurferformats/NAMESPACE | 24 + freesurferformats-0.1.13/freesurferformats/R/gifti_writer.R | 4 freesurferformats-0.1.13/freesurferformats/R/mghheader.R | 107 ++++++ freesurferformats-0.1.13/freesurferformats/R/nifti_common.R |only freesurferformats-0.1.13/freesurferformats/R/nifti_to_mgh.R |only freesurferformats-0.1.13/freesurferformats/R/optdata.R | 28 + freesurferformats-0.1.13/freesurferformats/R/read_fs_curv.R | 59 +++ freesurferformats-0.1.13/freesurferformats/R/read_fs_mgh.R | 11 freesurferformats-0.1.13/freesurferformats/R/read_fs_surface.R | 42 +- freesurferformats-0.1.13/freesurferformats/R/read_fs_transform.R | 5 freesurferformats-0.1.13/freesurferformats/R/read_nifti1.R |only freesurferformats-0.1.13/freesurferformats/R/read_nifti2.R |only freesurferformats-0.1.13/freesurferformats/R/write_fs_curv.R | 90 ++++- freesurferformats-0.1.13/freesurferformats/R/write_fs_surface.R | 33 +- freesurferformats-0.1.13/freesurferformats/R/write_nifti1.R |only freesurferformats-0.1.13/freesurferformats/R/write_nifti2.R |only freesurferformats-0.1.13/freesurferformats/inst/doc/freesurferformats.R | 7 freesurferformats-0.1.13/freesurferformats/inst/doc/freesurferformats.Rmd | 19 + freesurferformats-0.1.13/freesurferformats/inst/doc/freesurferformats.html | 12 freesurferformats-0.1.13/freesurferformats/man/fileopen.gz.or.not.Rd |only freesurferformats-0.1.13/freesurferformats/man/fs.get.morph.file.ext.for.format.Rd | 2 freesurferformats-0.1.13/freesurferformats/man/fs.get.morph.file.format.from.filename.Rd | 2 freesurferformats-0.1.13/freesurferformats/man/fwrite3.Rd | 2 freesurferformats-0.1.13/freesurferformats/man/gifti_xml.Rd | 4 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Title: Superfast Likelihood Inference for Stationary Gaussian Time
Series
Description: Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
Author: Yun Ling [aut],
Martin Lysy [aut, cre]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between SuperGauss versions 1.0.2 dated 2020-02-27 and 2.0.0 dated 2020-09-21
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Title: A Monte Carlo Based Heterogeneity Test for Meta-Analysis
Description: Implements a Monte Carlo Based Heterogeneity Test for standardized mean differences (d), Fisher-transformed Pearson's correlations (r), and natural-logarithm-transformed odds ratio (OR) in Meta-Analysis Studies. Depending on the presence of moderators, this Monte Carlo Based Test can be implemented in the random or mixed-effects model. This package uses rma() function from the R package 'metafor' to obtain parameter estimates and likelihood, so installation of R package 'metafor' is required. This approach refers to the studies of Hedges (1981) <doi:10.3102/10769986006002107>, Hedges & Olkin (1985, ISBN:978-0123363800), Silagy, Lancaster, Stead, Mant, & Fowler (2004) <doi:10.1002/14651858.CD000146.pub2>, Viechtbauer (2010) <doi:10.18637/jss.v036.i03>, and Zuckerman (1994, ISBN:978-0521432009).
Author: Han Du [aut],
Ge Jiang [aut, cre],
Zijun Ke [ctb]
Maintainer: Ge Jiang <gejiang2@illinois.edu>
Diff between mc.heterogeneity versions 0.1.1 dated 2020-06-24 and 0.1.2 dated 2020-09-21
DESCRIPTION | 10 - MD5 | 24 ++-- R/mc.d.R | 2 R/mc.fcor.R | 2 R/mc.lnOR.R | 4 build/vignette.rds |binary inst/doc/Supplementary_Materials.R | 8 - inst/doc/Supplementary_Materials.Rmd | 13 -- inst/doc/Supplementary_Materials.html | 184 +++++++++++++++++----------------- man/mc.d.Rd | 2 man/mc.fcor.Rd | 2 man/mc.lnOR.Rd | 4 vignettes/Supplementary_Materials.Rmd | 13 -- 13 files changed, 128 insertions(+), 140 deletions(-)
More information about mc.heterogeneity at CRAN
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-04 1.0-3
2019-06-27 1.0-2
2019-05-01 1.0-1
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 0.5.1 dated 2020-07-03 and 0.5.2 dated 2020-09-21
periscope-0.5.1/periscope/tests/testthat/sample_app_no_sidebar/program/ui_sidebar.R |only periscope-0.5.2/periscope/DESCRIPTION | 16 periscope-0.5.2/periscope/MD5 | 58 + periscope-0.5.2/periscope/NEWS.md | 4 periscope-0.5.2/periscope/R/convert_template.R | 10 periscope-0.5.2/periscope/R/downloadFile.R | 19 periscope-0.5.2/periscope/build/vignette.rds |binary periscope-0.5.2/periscope/inst/doc/downloadFile-module.html | 110 ++- periscope-0.5.2/periscope/inst/doc/downloadablePlot-module.html | 76 +- periscope-0.5.2/periscope/inst/doc/downloadableTable-module.html | 92 +-- periscope-0.5.2/periscope/inst/doc/new-application.html | 298 +++++----- periscope-0.5.2/periscope/tests/testthat/sample_app/program/fxn/plots.R | 1 periscope-0.5.2/periscope/tests/testthat/sample_app_both_sidebar |only periscope-0.5.2/periscope/tests/testthat/sample_app_no_sidebar/program/fxn/plots.R | 1 periscope-0.5.2/periscope/tests/testthat/sample_app_no_sidebar/program/server_local.R | 11 periscope-0.5.2/periscope/tests/testthat/sample_app_r_sidebar |only periscope-0.5.2/periscope/tests/testthat/test_convert_application.R | 55 + periscope-0.5.2/periscope/tests/testthat/test_create_new_application.R | 19 periscope-0.5.2/periscope/tests/testthat/test_ui_functions.R | 5 periscope-0.5.2/periscope/tests/testthat/test_ui_misc_functions.R | 8 20 files changed, 479 insertions(+), 304 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Øyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 0.4.0 dated 2019-10-17 and 0.5.0 dated 2020-09-21
SmallCountRounding-0.4.0/SmallCountRounding/R/noeFraKostraFiler.R |only SmallCountRounding-0.5.0/SmallCountRounding/DESCRIPTION | 15 SmallCountRounding-0.5.0/SmallCountRounding/MD5 | 59 +- SmallCountRounding-0.5.0/SmallCountRounding/NAMESPACE | 4 SmallCountRounding-0.5.0/SmallCountRounding/NEWS.md |only SmallCountRounding-0.5.0/SmallCountRounding/R/OldVersions.R | 54 - SmallCountRounding-0.5.0/SmallCountRounding/R/PLS2way.R | 2 SmallCountRounding-0.5.0/SmallCountRounding/R/PLSrounding.R | 16 SmallCountRounding-0.5.0/SmallCountRounding/R/RoundViaDummy.R | 186 +++++- SmallCountRounding-0.5.0/SmallCountRounding/R/SmallCountRounding-package.R | 2 SmallCountRounding-0.5.0/SmallCountRounding/build |only SmallCountRounding-0.5.0/SmallCountRounding/inst |only SmallCountRounding-0.5.0/SmallCountRounding/man/FindMaxDiff.Rd | 52 - SmallCountRounding-0.5.0/SmallCountRounding/man/HDutility.Rd | 88 +-- SmallCountRounding-0.5.0/SmallCountRounding/man/Lists2formula.Rd | 44 - SmallCountRounding-0.5.0/SmallCountRounding/man/MakeControl.Rd | 44 - SmallCountRounding-0.5.0/SmallCountRounding/man/ModelMatrix.Rd | 75 +- SmallCountRounding-0.5.0/SmallCountRounding/man/PLS2way.Rd | 67 +- SmallCountRounding-0.5.0/SmallCountRounding/man/PLSrounding.Rd | 242 ++++---- SmallCountRounding-0.5.0/SmallCountRounding/man/Round2.Rd | 119 ++-- SmallCountRounding-0.5.0/SmallCountRounding/man/RoundViaDummy.Rd | 279 +++++----- SmallCountRounding-0.5.0/SmallCountRounding/man/RoundViaDummy2.Rd | 74 +- SmallCountRounding-0.5.0/SmallCountRounding/man/SmallCountData.Rd | 68 +- SmallCountRounding-0.5.0/SmallCountRounding/man/SmallCountRounding-package.Rd | 50 - SmallCountRounding-0.5.0/SmallCountRounding/man/aggrtab.Rd | 66 +- SmallCountRounding-0.5.0/SmallCountRounding/man/makeroundtabs.Rd | 142 ++--- SmallCountRounding-0.5.0/SmallCountRounding/man/print.PLSrounded.Rd | 45 - SmallCountRounding-0.5.0/SmallCountRounding/man/redcube.Rd | 88 +-- SmallCountRounding-0.5.0/SmallCountRounding/man/roundcube.Rd | 86 +-- SmallCountRounding-0.5.0/SmallCountRounding/man/sosialFiktiv.Rd | 42 - SmallCountRounding-0.5.0/SmallCountRounding/tests |only SmallCountRounding-0.5.0/SmallCountRounding/vignettes |only 32 files changed, 1083 insertions(+), 926 deletions(-)
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Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see support list of insight; Lüdecke,
Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), this package
implements features like bootstrapping or simulating of parameters and
models, feature reduction (feature extraction and variable selection)
as well as functions to describe data and variable characteristics
(e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>),
Søren Højsgaard [aut],
Zen J. Lau [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.8.5 dated 2020-09-12 and 0.8.6 dated 2020-09-21
parameters-0.8.5/parameters/R/format_algorithm.R |only parameters-0.8.5/parameters/R/format_model.R |only parameters-0.8.5/parameters/man/format_algorithm.Rd |only parameters-0.8.5/parameters/man/format_model.Rd |only parameters-0.8.6/parameters/DESCRIPTION | 6 parameters-0.8.6/parameters/MD5 | 133 +- parameters-0.8.6/parameters/NAMESPACE | 5 parameters-0.8.6/parameters/NEWS.md | 139 -- parameters-0.8.6/parameters/R/check_factorstructure.R | 4 parameters-0.8.6/parameters/R/ci.R | 7 parameters-0.8.6/parameters/R/ci_betwithin.R | 20 parameters-0.8.6/parameters/R/ci_wald.R | 7 parameters-0.8.6/parameters/R/dof.R | 3 parameters-0.8.6/parameters/R/extract_parameters.R | 27 parameters-0.8.6/parameters/R/get_scores.R | 108 +- parameters-0.8.6/parameters/R/model_parameters.BFBayesFactor.R | 13 parameters-0.8.6/parameters/R/model_parameters_mixed.R | 21 parameters-0.8.6/parameters/R/print.parameters_model.R | 4 parameters-0.8.6/parameters/R/standard_error.R | 9 parameters-0.8.6/parameters/R/utils_cleaners.R | 4 parameters-0.8.6/parameters/README.md | 21 parameters-0.8.6/parameters/build/partial.rdb |binary parameters-0.8.6/parameters/inst/doc/demean.html | 506 +++++----- parameters-0.8.6/parameters/inst/doc/efa_cfa.html | 120 +- parameters-0.8.6/parameters/inst/doc/model_parameters.html | 332 +++--- parameters-0.8.6/parameters/inst/doc/model_parameters_mice.html | 84 - parameters-0.8.6/parameters/inst/doc/model_parameters_robust.html | 150 +- parameters-0.8.6/parameters/inst/doc/model_parameters_standardized.html | 48 parameters-0.8.6/parameters/inst/doc/parameters_reduction.html | 46 parameters-0.8.6/parameters/inst/doc/parameters_selection.html | 56 - parameters-0.8.6/parameters/man/bootstrap_model.Rd | 64 - parameters-0.8.6/parameters/man/bootstrap_parameters.Rd | 122 +- parameters-0.8.6/parameters/man/check_clusterstructure.Rd | 78 - parameters-0.8.6/parameters/man/check_multimodal.Rd | 100 - parameters-0.8.6/parameters/man/ci.merMod.Rd | 276 ++--- parameters-0.8.6/parameters/man/degrees_of_freedom.Rd | 3 parameters-0.8.6/parameters/man/demean.Rd | 392 +++---- parameters-0.8.6/parameters/man/describe_distribution.Rd | 142 +- parameters-0.8.6/parameters/man/format_order.Rd | 52 - parameters-0.8.6/parameters/man/model_parameters.BFBayesFactor.Rd | 148 +- parameters-0.8.6/parameters/man/model_parameters.Mclust.Rd | 46 parameters-0.8.6/parameters/man/model_parameters.default.Rd | 338 +++--- parameters-0.8.6/parameters/man/model_parameters.gam.Rd | 162 +-- parameters-0.8.6/parameters/man/model_parameters.lavaan.Rd | 170 +-- parameters-0.8.6/parameters/man/model_parameters.merMod.Rd | 266 ++--- parameters-0.8.6/parameters/man/model_parameters.mira.Rd | 120 +- parameters-0.8.6/parameters/man/model_parameters.mlm.Rd | 204 ++-- parameters-0.8.6/parameters/man/model_parameters.principal.Rd | 170 +-- parameters-0.8.6/parameters/man/model_parameters.rma.Rd | 132 +- parameters-0.8.6/parameters/man/model_parameters.zeroinfl.Rd | 116 +- parameters-0.8.6/parameters/man/p_value.Rd | 206 ++-- parameters-0.8.6/parameters/man/p_value_betwithin.Rd | 146 +- parameters-0.8.6/parameters/man/p_value_wald.Rd | 126 +- parameters-0.8.6/parameters/man/parameters_table.Rd | 102 +- parameters-0.8.6/parameters/man/principal_components.Rd | 216 ++-- parameters-0.8.6/parameters/man/print.Rd | 138 +- parameters-0.8.6/parameters/man/qol_cancer.Rd | 20 parameters-0.8.6/parameters/man/rescale_weights.Rd | 190 +-- parameters-0.8.6/parameters/man/select_parameters.Rd | 200 +-- parameters-0.8.6/parameters/man/simulate_model.Rd | 150 +- parameters-0.8.6/parameters/man/simulate_parameters.Rd | 208 ++-- parameters-0.8.6/parameters/man/standard_error.Rd | 232 ++-- parameters-0.8.6/parameters/tests/testthat/test-glmmTMB-2.R | 34 parameters-0.8.6/parameters/tests/testthat/test-glmmTMB.R | 36 parameters-0.8.6/parameters/tests/testthat/test-lmerTest.R | 50 parameters-0.8.6/parameters/tests/testthat/test-model_parameters.hurdle.R | 24 parameters-0.8.6/parameters/tests/testthat/test-model_parameters.truncreg.R | 40 parameters-0.8.6/parameters/tests/testthat/test-model_parameters_std.R | 44 parameters-0.8.6/parameters/tests/testthat/test-parameters_type.R |only parameters-0.8.6/parameters/tests/testthat/test-quantreg.R | 28 70 files changed, 3598 insertions(+), 3566 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-7 dated 2020-08-31 and 1.0-8 dated 2020-09-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.R | 20 ++++++++++++++++---- inst/doc/mlt.Rnw | 20 ++++++++++++++++---- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 20 ++++++++++++++++---- 7 files changed, 66 insertions(+), 22 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.6.0 dated 2020-08-27 and 2.7.0 dated 2020-09-21
DESCRIPTION | 8 MD5 | 85 - NAMESPACE | 287 ++-- NEWS.md | 291 ++-- R/copy_labels.R | 163 +- R/drop_unused_value_labels.R | 72 - R/labelled-package.R | 20 R/labelled.R | 32 R/lookfor.R | 480 +++---- R/na_values.R | 413 +++--- R/recode.R | 168 +- R/remove_attributes.R | 72 - R/remove_labels.R | 258 ++-- R/retrocompatibility.R | 140 +- R/tagged_na.R | 38 R/to_character.R | 86 - R/to_factor.R | 388 +++--- R/to_labelled.R | 452 +++---- R/to_na.R | 138 +- R/val_labels.R | 803 ++++++------ R/var_label.R | 290 ++-- README.md | 112 - build/vignette.rds |binary inst/doc/intro_labelled.R | 558 ++++---- inst/doc/intro_labelled.Rmd | 1072 ++++++++--------- inst/doc/intro_labelled.html | 2395 ++++++++++++++++++-------------------- inst/doc/look_for.R | 120 - inst/doc/look_for.Rmd | 280 ++-- inst/doc/look_for.html | 1220 ++++++++++--------- man/copy_labels.Rd | 12 man/figures/labelled.svg | 312 ++-- man/look_for.Rd | 250 +-- man/na_values.Rd | 179 +- man/names_prefixed_by_values.Rd | 60 man/nolabel_to_na.Rd | 36 man/reexports.Rd | 52 man/val_labels.Rd | 261 ++-- man/val_labels_to_na.Rd | 42 man/var_label.Rd | 169 +- tests/testthat.R | 6 tests/testthat/test-copy_labels.r |only tests/testthat/test-labelled.r | 889 +++++++------- vignettes/intro_labelled.Rmd | 1072 ++++++++--------- vignettes/look_for.Rmd | 280 ++-- 44 files changed, 7127 insertions(+), 6934 deletions(-)
Title: Segment Images in Text Lines and Words
Description: Find text lines in scanned images and segment the lines into words.
Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>,
an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>,
and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital
Humanities [cph] (R wrapper),
Jeroen Ooms [ctb, cph] (More details in LICENSE.note file),
Arthur Flôr [ctb, cph] (More details in LICENSE.note file),
Saverio Meucci [ctb, cph] (More details in LICENSE.note file),
Yeara Kozlov [ctb, cph] (More details in LICENSE.note file),
Tino Weinkauf [ctb, cph] (More details in LICENSE.note file)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>
Diff between image.textlinedetector versions 0.1.0 dated 2020-09-15 and 0.1.1 dated 2020-09-21
DESCRIPTION | 9 - MD5 | 18 +- NEWS.md |only R/RcppExports.R | 60 --------- configure | 1 src/LineSegmentation.cpp | 7 - src/Makevars.win | 8 + src/RcppExports.cpp | 179 +--------------------------- src/base.cpp | 268 +++++++++++++++++++++--------------------- src/rcpp-linelocalization.cpp | 4 src/sieve.cpp |only 11 files changed, 182 insertions(+), 372 deletions(-)
More information about image.textlinedetector at CRAN
Permanent link
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Description: Functions, data sets, analyses and examples from the
third edition of the book
''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled ''An Introduction to R'',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides). The publishers web page is
'<http://www.crcpress.com/product/isbn/9781482204582>'.
Author: Torsten Hothorn and Brian S. Everitt
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR3 versions 1.0-9 dated 2018-05-28 and 1.0-10 dated 2020-09-21
DESCRIPTION | 28 ++-- MD5 | 158 +++++++++++++------------- build/vignette.rds |binary data/BCG.rda |binary data/CYGOB1.rda |binary data/Lanza.rda |binary data/birthdeathrates.rda |binary data/bladdercancer.rda |binary data/epilepsy.rda |binary data/foster.rda |binary data/heptathlon.rda |binary data/meteo.rda |binary data/orallesions.rda |binary data/phosphate.rda |binary data/pistonrings.rda |binary data/planets.rda |binary data/plasma.rda |binary data/polyps.rda |binary data/rearrests.rda |binary data/roomwidth.rda |binary data/schizophrenia.rda |binary data/schizophrenia2.rda |binary data/smoking.rda |binary data/students.rda |binary data/suicides.rda |binary data/toothpaste.rda |binary data/voting.rda |binary data/water.rda |binary data/watervoles.rda |binary data/waves.rda |binary data/weightgain.rda |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.R | 1 inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.R | 1 inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.R | 1 inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_bayesian_inference.R | 1 inst/doc/Ch_bayesian_inference.pdf |binary inst/doc/Ch_cluster_analysis.R | 1 inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.R | 1 inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.R | 1 inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.R | 1 inst/doc/Ch_errata.pdf |binary inst/doc/Ch_gam.R | 1 inst/doc/Ch_gam.pdf |binary inst/doc/Ch_graphical_display.R | 7 - inst/doc/Ch_graphical_display.Rnw | 8 - inst/doc/Ch_graphical_display.pdf |binary inst/doc/Ch_introduction_to_R.R | 1 inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.R | 1 inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.R | 1 inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_missing_values.R | 1 inst/doc/Ch_missing_values.pdf |binary inst/doc/Ch_multidimensional_scaling.R | 1 inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.R | 1 inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.R | 1 inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_quantile_regression.R | 1 inst/doc/Ch_quantile_regression.pdf |binary inst/doc/Ch_recursive_partitioning.R | 1 inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.R | 1 inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_simultaneous_inference.R | 1 inst/doc/Ch_simultaneous_inference.pdf |binary inst/doc/Ch_survival_analysis.R | 1 inst/doc/Ch_survival_analysis.pdf |binary man/CHFLS.Rd | 2 man/Forbes2000.Rd | 2 vignettes/Ch_graphical_display.Rnw | 8 - 80 files changed, 110 insertions(+), 128 deletions(-)
Title: Flexible Tool for Bias Detection, Visualization, and Mitigation
Description: Measure fairness metrics in one place for many models. Check how big is model's bias towards different races, sex, nationalities etc. Use measures such as Statistical Parity, Equal odds to detect the discrimination against unprivileged groups. Visualize the bias using heatmap, radar plot, biplot, bar chart (and more!). There are various pre-processing and post-processing bias mitigation algorithms implemented.
Author: Jakub Wiśniewski [aut, cre],
Przemysław Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>)
Maintainer: Jakub Wiśniewski <jakwisn@gmail.com>
Diff between fairmodels versions 0.1.1 dated 2020-08-20 and 0.2.2 dated 2020-09-21
DESCRIPTION | 8 - MD5 | 103 ++++++++++++------------ NEWS.md | 16 +++ R/all_cutoffs.R | 2 R/calculate_group_fairness_metrics.R | 10 +- R/ceteris_paribus_cutoff.R | 2 R/fairness_check.R | 60 +++++++++---- R/fairness_pca.R | 4 R/fairness_radar.R | 11 +- R/group_metric.R | 1 R/helper_functions.R | 10 +- R/metric_scores.R | 4 R/plot_all_cutoffs.R | 2 R/plot_fairness_object.R | 51 ++++++++--- R/plot_stacked_metrics.R | 3 R/print.R | 28 ++++-- R/roc_pivot.R | 3 R/stack_metrics.R | 10 +- R/zzz.R |only README.md | 31 ++++--- inst/WORDLIST |only inst/doc/Advanced_tutorial.Rmd | 16 +-- inst/doc/Advanced_tutorial.html | 80 +++++++++--------- inst/doc/Basic_tutorial.R | 13 +-- inst/doc/Basic_tutorial.Rmd | 38 +++++--- inst/doc/Basic_tutorial.html | 86 ++++++++++---------- man/all_cutoffs.Rd | 2 man/ceteris_paribus_cutoff.Rd | 2 man/compas.Rd | 2 man/fairness_check.Rd | 28 ++++-- man/fairness_radar.Rd | 4 man/figures/class_diagram.png |binary man/figures/flowchart.png |binary man/figures/formulas/parity_loss.png |binary man/figures/logo.png |only man/figures/preview.gif |binary man/german.Rd | 2 man/group_metric.Rd | 1 man/metric_scores.Rd | 4 man/plot_fairness_object.Rd | 14 ++- man/plot_stacked_barplot.Rd | 4 man/print_fairness_object.Rd | 10 +- man/roc_pivot.Rd | 3 tests/testthat/test_ceteris_paribus_with_plot.R | 2 tests/testthat/test_fairness_check.R | 31 ++++++- tests/testthat/test_fairness_object.R | 7 + tests/testthat/test_fairness_radar_and_plot.R | 2 tests/testthat/test_helper_functions.R | 4 tests/testthat/test_metric_scores_with_plot.R | 20 +--- tests/testthat/test_pca_fairness_with_plot.R | 4 tests/testthat/test_performance_and_fairness.R | 14 +-- tests/testthat/test_plot_fairmodels.R | 4 vignettes/Advanced_tutorial.Rmd | 16 +-- vignettes/Basic_tutorial.Rmd | 38 +++++--- 54 files changed, 482 insertions(+), 328 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Description: This is the R Interface to the C API of IBM ILOG CPLEX. It necessarily depends on IBM ILOG CPLEX (>= 12.1).
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between cplexAPI versions 1.3.6 dated 2019-06-21 and 1.4.0 dated 2020-09-21
cplexAPI-1.3.6/cplexAPI/man/copyPartBaseCPLEX.Rd |only cplexAPI-1.4.0/cplexAPI/DESCRIPTION | 8 +-- cplexAPI-1.4.0/cplexAPI/MD5 | 59 +++++++++++------------ cplexAPI-1.4.0/cplexAPI/NAMESPACE | 1 cplexAPI-1.4.0/cplexAPI/R/cplex.R | 2 cplexAPI-1.4.0/cplexAPI/R/cplexAPI.R | 22 -------- cplexAPI-1.4.0/cplexAPI/R/cplexConst.R | 2 cplexAPI-1.4.0/cplexAPI/R/cplexErrorClass.R | 2 cplexAPI-1.4.0/cplexAPI/R/cplexPtrClass.R | 2 cplexAPI-1.4.0/cplexAPI/R/cplex_checkAPI.R | 2 cplexAPI-1.4.0/cplexAPI/R/cplex_longparamAPI.R | 2 cplexAPI-1.4.0/cplexAPI/R/generics.R | 2 cplexAPI-1.4.0/cplexAPI/R/zzz.R | 11 +++- cplexAPI-1.4.0/cplexAPI/build/vignette.rds |binary cplexAPI-1.4.0/cplexAPI/configure | 37 ++++++++------ cplexAPI-1.4.0/cplexAPI/configure.ac | 28 ++++++++-- cplexAPI-1.4.0/cplexAPI/inst/INSTALL | 16 +++--- cplexAPI-1.4.0/cplexAPI/inst/NEWS.Rd | 18 +++++++ cplexAPI-1.4.0/cplexAPI/inst/c2r.map | 1 cplexAPI-1.4.0/cplexAPI/inst/doc/cplexAPI.R | 1 cplexAPI-1.4.0/cplexAPI/inst/doc/cplexAPI.pdf |binary cplexAPI-1.4.0/cplexAPI/src/Makevars.win | 2 cplexAPI-1.4.0/cplexAPI/src/cplexAPI.c | 43 ++++------------ cplexAPI-1.4.0/cplexAPI/src/cplexAPI.h | 10 +-- cplexAPI-1.4.0/cplexAPI/src/cplexR.c | 2 cplexAPI-1.4.0/cplexAPI/src/cplexR.h | 2 cplexAPI-1.4.0/cplexAPI/src/cplex_checkAPI.c | 2 cplexAPI-1.4.0/cplexAPI/src/cplex_checkAPI.h | 2 cplexAPI-1.4.0/cplexAPI/src/cplex_longparamAPI.c | 2 cplexAPI-1.4.0/cplexAPI/src/cplex_longparamAPI.h | 2 cplexAPI-1.4.0/cplexAPI/src/init.c | 10 --- 31 files changed, 146 insertions(+), 147 deletions(-)
More information about colocalization at CRAN
Permanent link
Title: A Bootstrap-Based Heterogeneity Test for Meta-Analysis
Description: Implements a bootstrap-based heterogeneity test for standardized mean differences (d), Fisher-transformed Pearson's correlations (r), and natural-logarithm-transformed odds ratio (or) in meta-analysis studies. Depending on the presence of moderators, this Monte Carlo based test can be implemented in the random- or mixed-effects model. This package uses rma() function from the R package 'metafor' to obtain parameter estimates and likelihoods, so installation of R package 'metafor' is required. This approach refers to the studies of Anscombe (1956) <doi:10.2307/2332926>, Haldane (1940) <doi:10.2307/2332614>, Hedges (1981) <doi:10.3102/10769986006002107>, Hedges & Olkin (1985, ISBN:978-0123363800), Silagy, Lancaster, Stead, Mant, & Fowler (2004) <doi:10.1002/14651858.CD000146.pub2>, Viechtbauer (2010) <doi:10.18637/jss.v036.i03>, and Zuckerman (1994, ISBN:978-0521432009).
Author: Ge Jiang [aut, cre],
Han Du [aut],
Zijun Ke [ctb]
Maintainer: Ge Jiang <gejiang2@illinois.edu>
Diff between boot.heterogeneity versions 0.1.0 dated 2020-05-08 and 0.1.1 dated 2020-09-21
DESCRIPTION | 11 - MD5 | 26 +-- R/boot.d.R | 8 - R/boot.fcor.R | 6 R/boot.lnOR.R | 8 - build/vignette.rds |binary inst/doc/boot.heterogeneity.R | 2 inst/doc/boot.heterogeneity.Rmd | 4 inst/doc/boot.heterogeneity.html | 264 ++++++++++++++++++++------------------- man/boot.d.Rd | 8 - man/boot.fcor.Rd | 6 man/boot.lnOR.Rd | 8 - tests/testthat/test_bt.R | 2 vignettes/boot.heterogeneity.Rmd | 4 14 files changed, 179 insertions(+), 178 deletions(-)
More information about boot.heterogeneity at CRAN
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Title: Filter Covariance and Correlation Matrices with
Bootstrapped-Averaged Hierarchical Ansatz
Description: A method to filter correlation and covariance matrices by averaging
bootstrapped filtered hierarchical clustering and boosting. See Ch. Bongiorno and D. Challet,
Covariance matrix filtering with bootstrapped hierarchies (2020) <arXiv:2003.05807> and
Ch. Bongiorno and D. Challet, Reactive Global Minimum Variance Portfolios with k-BAHC covariance cleaning
(2020) <arXiv:2005.08703>.
Author: Christian Bongiorno and Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between bahc versions 0.2.0 dated 2020-05-15 and 0.3.0 dated 2020-09-21
DESCRIPTION | 16 +++++++++------- MD5 | 9 +++++---- NEWS |only R/main.R | 13 +++++++------ man/filterCorrelation.Rd | 6 ++++-- man/filterCovariance.Rd | 4 ++-- 6 files changed, 27 insertions(+), 21 deletions(-)
Title: Time Series, Analysis and Application
Description: Accompanies the book Rainer Schlittgen and Cristina Sattarhoff (2020) <https://www.degruyter.com/view/title/575978> "Angewandte Zeitreihenanalyse mit R, 4. Auflage" . The package contains the time series and functions used therein. It was developed over many years teaching courses about time series analysis.
Author: Rainer Schlittgen
Maintainer: Rainer Schlittgen <R.Schlittgen@t-online.de>
Diff between tsapp versions 1.0.0 dated 2020-03-20 and 1.0.1 dated 2020-09-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/frequdom.r | 6 +++--- R/series.r | 2 +- R/smaniplot.r | 21 ++++++++++++--------- R/specialfun.r | 17 ++++++++++------- data/HSV.RData |binary man/HSV.Rd | 2 +- man/LjungBoxPierceTest.Rd | 4 ++-- man/acfpacf.Rd | 6 ++++-- man/missar.Rd | 6 ++++-- man/missls.Rd | 10 +++++++--- man/specest.Rd | 2 +- 13 files changed, 61 insertions(+), 47 deletions(-)
Title: Multivariate Normal Variance Mixtures
Description: Functions for working with (grouped) multivariate normal variance mixture
distributions (evaluation of distribution functions and densities,
random number generation and parameter estimation), including
Student's t distribution for non-integer degrees-of-freedom as well as the grouped t
distribution and copula with multiple degrees-of-freedom parameters.
See Hintz, Hofert, Lemieux (2019) <arXiv:1911.03017> for more details.
Author: Marius Hofert [aut, cre],
Erik Hintz [aut],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between nvmix versions 0.0-4 dated 2020-06-12 and 0.0-5 dated 2020-09-21
DESCRIPTION | 20 - MD5 | 63 ++-- NAMESPACE | 16 + R/Student.R | 267 ++++++++++++++++- R/auxiliaries.R | 42 +- R/dgnvmix.R | 225 +++++++++++---- R/dnvmix.R | 13 R/fitnvmix.R | 454 +++++++++++++++++++++++------- R/pnvmix.R | 8 R/qnvmix.R | 23 - R/riskmeasures.R | 1 demo/00Index | 2 demo/grouped_mixtures.R |only demo/numerical_experiments.R | 4 inst/doc/nvmix_functionality.html | 570 +++++++++++++++++++------------------- inst/doc/nvmix_riskmeasures.html | 134 +++++--- man/copula.Rd | 73 ++++ man/dependencemeasures.Rd | 2 man/dgnvmix.Rd | 18 - man/dnvmix.Rd | 14 man/fitnvmix.Rd | 29 + man/gammamix.Rd | 2 man/get_set_param.Rd | 48 +-- man/numerical_experiments_data.Rd | 2 man/pgnvmix.Rd | 10 man/pnvmix.Rd | 11 man/qnvmix.rd | 4 man/qqplot_maha.Rd | 14 man/rgnvmix.Rd | 2 man/riskmeasures.Rd | 2 man/rnvmix.Rd | 11 src/eval_gdensmix_integrand.c |only src/eval_gdensmix_integrand.h |only src/init.c | 3 34 files changed, 1411 insertions(+), 676 deletions(-)
Title: Mining Rigs for Specialized Subset Sum, Multi-Subset Sum,
Multidimensional Subset Sum, Multidimensional Knapsack,
Generalized Assignment Problems
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. These solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value sets with predefined subset sum errors, and (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) an option of mapping real-domain problems to the integer domain with user-controlled precision loss, and those integers are further zipped non-uniformly in 64-bit buffers. Arithmetic on compressed integers is done by bit-manipulation and the design has virtually zero speed lag relative to normal integer arithmetic. Reduction in dimensionality from the compression may yield substantial acceleration; (e) distributed computing infrastructure for multidimensional subset sum. Compilation with g++ '-Ofast' is recommended. See package vignette (<arXiv:1612.04484v3>) for details. Functions prefixed with 'aux' (auxiliary) are or will be implementations of existing foundational or cutting-edge algorithms for solving optimization problems of interest.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 8.5.6 dated 2019-10-28 and 8.6.6 dated 2020-09-21
DESCRIPTION | 8 MD5 | 60 - NAMESPACE | 18 R/RcppExports.R | 8 R/rinterface.r | 244 ++++++ inst/NEWS.Rd | 8 man/FLSSSmultiset.Rd | 204 ++--- man/GAP.Rd | 322 ++++---- man/decomposeMflsss.Rd |only man/mFLSSSobjRun.Rd |only man/mFLSSSpar.Rd | 306 ++++---- man/mFLSSSparImposeBounds.Rd | 2 src/BaB01kp.cpp | 4 src/BaBgapMulthreadKPs.cpp | 4 src/BaBgapMulthreadNodes.cpp | 4 src/DP01kp.cpp | 4 src/DPgapMultithreadKPs.cpp | 4 src/DPgapMultithreadNodes.cpp | 4 src/GAP.cpp | 11 src/GAgap.cpp | 4 src/Gknapsack.cpp | 6 src/RcppExports.cpp | 40 + src/header/dnyTasking.hpp | 21 src/header/mflsssOBJ.hpp | 1002 ++++++++++++++++++++------- src/legacy/BaB01kpOld.cpp | 4 src/legacy/GAP.cpp | 4 src/mflsss.cpp | 35 src/mflsssComoPar.cpp | 48 + src/mflsssDecomp.cpp |only src/mflsssVariableTree.cpp | 5 tests/debugTests/FLSSSnumericIssue20190708.r | 8 tests/debugTests/test001.r |only tests/valgrindTest/valgrindTest.cpp | 54 - 33 files changed, 1630 insertions(+), 816 deletions(-)
Title: Relationship Matrices for Diploid and Autopolyploid Species
Description: Computation of A (pedigree), G (genomic-base), and H (A corrected
by G) relationship matrices for diploid and autopolyploid species. Several methods
are implemented considering additive and non-additive models.
Author: Rodrigo Amadeu [aut, cre],
Catherine Cellon [ctb],
Leticia Lara [ctb],
Marcio Resende [ctb],
Ivone Oliveira [ctb],
Luis Ferrao [ctb],
Patricio Munoz [ctb],
Augusto Garcia [ctb]
Maintainer: Rodrigo Amadeu <rramadeu@ufl.edu>
Diff between AGHmatrix versions 1.0.2 dated 2019-07-30 and 2.0.0 dated 2020-09-21
DESCRIPTION | 13 ++++---- MD5 | 29 ++++++++++--------- R/Gmatrix.R | 60 ++++++++++++++++++++++++++++------------ R/Hmatrix.R | 2 - build/vignette.rds |binary inst/doc/Tutorial_AGHmatrix.R | 36 ++++++++++++------------ inst/doc/Tutorial_AGHmatrix.pdf |binary inst/docs |only man/Amatrix.Rd | 11 ++++++- man/Gmatrix.Rd | 33 ++++++++++++++++------ man/Hmatrix.Rd | 16 ++++++++-- man/formatmatrix.Rd | 10 +++++- man/ped.mrode.Rd | 4 ++ man/ped.sol.Rd | 4 ++ man/snp.pine.Rd | 4 ++ man/snp.sol.Rd | 4 ++ 16 files changed, 150 insertions(+), 76 deletions(-)
Title: Informative Procrustean Matrix Correlation
Description: Estimates corrected Procrustean correlation between matrices for removing overfitting effect. Coissac Eric and Gonindard-Melodelima Christelle (2019) <bioarXiv:10.1101/842070>.
Author: Eric Coissac, Christelle Gonindard-Melodelima
Maintainer: Eric Coissac <eric.coissac@metabarcoding.org>
Diff between ProcMod versions 1.0.3 dated 2019-11-25 and 1.0.6 dated 2020-09-21
ProcMod-1.0.3/ProcMod/man/internal.var2cor.Rd |only ProcMod-1.0.6/ProcMod/DESCRIPTION | 13 ++- ProcMod-1.0.6/ProcMod/MD5 | 35 +++++----- ProcMod-1.0.6/ProcMod/NAMESPACE | 2 ProcMod-1.0.6/ProcMod/R/corls_test.R | 4 - ProcMod-1.0.6/ProcMod/R/covls.R | 76 +++-------------------- ProcMod-1.0.6/ProcMod/R/procmod.R | 1 ProcMod-1.0.6/ProcMod/build/partial.rdb |binary ProcMod-1.0.6/ProcMod/inst/REFERENCES.bib | 40 ++---------- ProcMod-1.0.6/ProcMod/man/as.data.frame.dist.Rd | 3 ProcMod-1.0.6/ProcMod/man/australia.Rd | 16 +++- ProcMod-1.0.6/ProcMod/man/corls_test.Rd | 9 +- ProcMod-1.0.6/ProcMod/man/names.procmod_corls.Rd | 2 ProcMod-1.0.6/ProcMod/man/names.procmod_varls.Rd | 2 ProcMod-1.0.6/ProcMod/man/print.procmod_corls.Rd | 2 ProcMod-1.0.6/ProcMod/man/print.procmod_varls.Rd | 2 ProcMod-1.0.6/ProcMod/man/procmod.Rd | 1 ProcMod-1.0.6/ProcMod/man/procmod_frame.Rd | 9 ++ ProcMod-1.0.6/ProcMod/man/varls.Rd | 23 ------ 19 files changed, 78 insertions(+), 162 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-18 1.2.2
Title: Import and Export Data
Description: Import and export data from the most common statistical formats by using
R functions that guarantee the least loss of the data information, giving special
attention to the date variables and the labelled ones.
Author: Roger Pros, Isaac Subirana, Joan Vila.
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between ImportExport versions 1.1 dated 2015-09-19 and 1.3 dated 2020-09-21
ImportExport-1.1/ImportExport/inst/doc |only ImportExport-1.3/ImportExport/DESCRIPTION | 14 ++-- ImportExport-1.3/ImportExport/MD5 | 34 +++------- ImportExport-1.3/ImportExport/NAMESPACE | 3 ImportExport-1.3/ImportExport/NEWS.md |only ImportExport-1.3/ImportExport/R/access_export.R | 2 ImportExport-1.3/ImportExport/R/access_import.R | 2 ImportExport-1.3/ImportExport/R/excel_export.R | 11 ++- ImportExport-1.3/ImportExport/build/partial.rdb |binary ImportExport-1.3/ImportExport/inst/Import_ExportApp/server.R | 11 ++- ImportExport-1.3/ImportExport/inst/Import_ExportApp/ui.R | 2 ImportExport-1.3/ImportExport/inst/Import_ExportApp/www/App-guide.html | 4 - ImportExport-1.3/ImportExport/inst/Import_ExportApp/www/excel_export.html | 32 ++------- ImportExport-1.3/ImportExport/man/ImportExport-package.Rd | 1 ImportExport-1.3/ImportExport/man/excel_export.Rd | 13 +-- 15 files changed, 55 insertions(+), 74 deletions(-)
Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Description: Functions, data sets, analyses and examples from the
second edition of the book
''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2008). The first chapter
of the book, which is entitled ''An Introduction to R'',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
the package contains Sweave code for producing slides for selected
chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR2 versions 1.1-17 dated 2017-08-20 and 1.1-18 dated 2020-09-21
DESCRIPTION | 12 +- MD5 | 146 +++++++++++++------------- build/vignette.rds |binary data/BCG.rda |binary data/CYGOB1.rda |binary data/Lanza.rda |binary data/birthdeathrates.rda |binary data/bladdercancer.rda |binary data/epilepsy.rda |binary data/foster.rda |binary data/heptathlon.rda |binary data/meteo.rda |binary data/orallesions.rda |binary data/phosphate.rda |binary data/pistonrings.rda |binary data/planets.rda |binary data/plasma.rda |binary data/polyps.rda |binary data/rearrests.rda |binary data/roomwidth.rda |binary data/schizophrenia.rda |binary data/schizophrenia2.rda |binary data/smoking.rda |binary data/students.rda |binary data/suicides.rda |binary data/toothpaste.rda |binary data/voting.rda |binary data/water.rda |binary data/watervoles.rda |binary data/waves.rda |binary data/weightgain.rda |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.R | 1 inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.R | 1 inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.R | 1 inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_cluster_analysis.R | 1 inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.R | 1 inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.R | 1 inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.R | 1 inst/doc/Ch_errata.pdf |binary inst/doc/Ch_gam.R | 1 inst/doc/Ch_gam.pdf |binary inst/doc/Ch_graphical_display.R | 7 - inst/doc/Ch_graphical_display.Rnw | 12 +- inst/doc/Ch_graphical_display.pdf |binary inst/doc/Ch_introduction_to_R.R | 1 inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.R | 1 inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.R | 1 inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_multidimensional_scaling.R | 1 inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.R | 1 inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.R | 1 inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_recursive_partitioning.R | 1 inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.R | 1 inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_simultaneous_inference.R | 1 inst/doc/Ch_simultaneous_inference.pdf |binary inst/doc/Ch_survival_analysis.R | 1 inst/doc/Ch_survival_analysis.pdf |binary man/CHFLS.Rd | 2 man/Forbes2000.Rd | 2 vignettes/Ch_graphical_display.Rnw | 12 +- 74 files changed, 100 insertions(+), 115 deletions(-)
More information about retroharmonize at CRAN
Permanent link
More information about SlidingWindows at CRAN
Permanent link
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-7 dated 2020-04-02 and 1.4-8 dated 2020-09-21
DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++-------------------- R/legends.R | 4 ++ build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/CITATION | 4 +- inst/NEWS.Rd | 20 ++++++++++---- inst/doc/residual-shadings.R | 2 - inst/doc/residual-shadings.Rnw | 6 ++-- inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.pdf |binary man/Bundesliga.Rd | 2 - man/legends.Rd | 4 ++ man/mosaic.Rd | 2 - vignettes/residual-shadings.Rnw | 6 ++-- 29 files changed, 64 insertions(+), 50 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following
mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package
is not available from CRAN; see <https://www.gurobi.com/downloads/>. See vignette for installing 'Rsymphony' package
on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.0.2 dated 2020-02-05 and 1.1.2 dated 2020-09-21
TestDesign-1.0.2/TestDesign/build/partial.rdb |only TestDesign-1.0.2/TestDesign/data/constraints_fatigue_raw.rda |only TestDesign-1.0.2/TestDesign/data/constraints_reading_raw.rda |only TestDesign-1.0.2/TestDesign/data/constraints_science_raw.rda |only TestDesign-1.0.2/TestDesign/data/itemattrib_fatigue_raw.rda |only TestDesign-1.0.2/TestDesign/data/itemattrib_reading_raw.rda |only TestDesign-1.0.2/TestDesign/data/itemattrib_science_raw.rda |only TestDesign-1.0.2/TestDesign/data/itemcontent_fatigue_raw.rda |only TestDesign-1.0.2/TestDesign/data/itempool_fatigue_raw.rda |only TestDesign-1.0.2/TestDesign/data/itempool_reading_raw.rda |only TestDesign-1.0.2/TestDesign/data/itempool_science_raw.rda |only TestDesign-1.0.2/TestDesign/data/resp_fatigue_raw.rda |only TestDesign-1.0.2/TestDesign/data/stimattrib_reading_raw.rda |only TestDesign-1.0.2/TestDesign/man/OAT.Rd |only TestDesign-1.0.2/TestDesign/man/addTrans.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_1pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_2pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_3pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_gpc.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_gr.Rd |only TestDesign-1.0.2/TestDesign/man/array_info_pc.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_1pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_2pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_3pl.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_gpc.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_gr.Rd |only TestDesign-1.0.2/TestDesign/man/array_p_pc.Rd |only TestDesign-1.0.2/TestDesign/man/calcDerivative-methods.Rd |only TestDesign-1.0.2/TestDesign/man/calcDerivative2-methods.Rd |only TestDesign-1.0.2/TestDesign/man/calcRP.Rd |only TestDesign-1.0.2/TestDesign/man/calc_info_matrix.Rd |only TestDesign-1.0.2/TestDesign/man/calc_likelihood_function.Rd |only TestDesign-1.0.2/TestDesign/man/calc_log_likelihood.Rd |only TestDesign-1.0.2/TestDesign/man/calc_log_likelihood_function.Rd |only TestDesign-1.0.2/TestDesign/man/eaparray-methods.Rd |only TestDesign-1.0.2/TestDesign/man/extract-methods.Rd |only TestDesign-1.0.2/TestDesign/man/info_1pl.Rd |only TestDesign-1.0.2/TestDesign/man/info_2pl.Rd |only TestDesign-1.0.2/TestDesign/man/info_3pl.Rd |only TestDesign-1.0.2/TestDesign/man/info_gpc.Rd |only TestDesign-1.0.2/TestDesign/man/info_gr.Rd |only TestDesign-1.0.2/TestDesign/man/info_pc.Rd |only TestDesign-1.0.2/TestDesign/man/item_1PL-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_2PL-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_3PL-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_GPC-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_GR-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_PC-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_attrib-class.Rd |only TestDesign-1.0.2/TestDesign/man/item_pool.operators.Rd |only TestDesign-1.0.2/TestDesign/man/makeItemPoolCluster.Rd |only TestDesign-1.0.2/TestDesign/man/mlearray-methods.Rd |only TestDesign-1.0.2/TestDesign/man/p_1pl.Rd |only TestDesign-1.0.2/TestDesign/man/p_2pl.Rd |only TestDesign-1.0.2/TestDesign/man/p_3pl.Rd |only TestDesign-1.0.2/TestDesign/man/p_gpc.Rd |only TestDesign-1.0.2/TestDesign/man/p_gr.Rd |only TestDesign-1.0.2/TestDesign/man/p_pc.Rd |only TestDesign-1.0.2/TestDesign/man/plotEligibilityStats.Rd |only TestDesign-1.0.2/TestDesign/man/plotExposureRateBySegment.Rd |only TestDesign-1.0.2/TestDesign/man/plotExposureRateFinal.Rd |only TestDesign-1.0.2/TestDesign/man/plotExposureRateFinalFlag.Rd |only TestDesign-1.0.2/TestDesign/man/plotInfoOverlay.Rd |only TestDesign-1.0.2/TestDesign/man/plotRMSE.Rd |only TestDesign-1.0.2/TestDesign/man/st_attrib-class.Rd |only TestDesign-1.0.2/TestDesign/man/subsetItemPool.Rd |only TestDesign-1.0.2/TestDesign/man/subsetTest.Rd |only TestDesign-1.0.2/TestDesign/man/theta_EB_single.Rd |only TestDesign-1.0.2/TestDesign/src/IRT_functions.cpp |only TestDesign-1.0.2/TestDesign/tests/testthat/test-examples.R |only TestDesign-1.0.2/TestDesign/tests/testthat/test-exposure.R |only TestDesign-1.0.2/TestDesign/tests/testthat/test-items.R |only TestDesign-1.0.2/TestDesign/tests/testthat/test-static.R |only TestDesign-1.1.2/TestDesign/DESCRIPTION | 45 TestDesign-1.1.2/TestDesign/MD5 | 343 TestDesign-1.1.2/TestDesign/NAMESPACE | 62 TestDesign-1.1.2/TestDesign/NEWS.md | 60 TestDesign-1.1.2/TestDesign/R/RcppExports.R | 495 - TestDesign-1.1.2/TestDesign/R/bayes_functions.R |only TestDesign-1.1.2/TestDesign/R/constraint_functions.R |only TestDesign-1.1.2/TestDesign/R/constraints_operators.R |only TestDesign-1.1.2/TestDesign/R/cpp_documents.R |only TestDesign-1.1.2/TestDesign/R/datasets.R | 162 TestDesign-1.1.2/TestDesign/R/eligibility_functions.R |only TestDesign-1.1.2/TestDesign/R/exposure_control_functions.R |only TestDesign-1.1.2/TestDesign/R/extensions.R |only TestDesign-1.1.2/TestDesign/R/helper_functions.R | 79 TestDesign-1.1.2/TestDesign/R/import.R | 85 TestDesign-1.1.2/TestDesign/R/item_attrib_operators.R |only TestDesign-1.1.2/TestDesign/R/item_class.R | 577 - TestDesign-1.1.2/TestDesign/R/item_functions.R | 1138 +-- TestDesign-1.1.2/TestDesign/R/item_pool_operators.R |only TestDesign-1.1.2/TestDesign/R/loading_functions.R | 1224 +-- TestDesign-1.1.2/TestDesign/R/other_functions.R |only TestDesign-1.1.2/TestDesign/R/plot_functions.R |only TestDesign-1.1.2/TestDesign/R/pool_cluster_operators.R |only TestDesign-1.1.2/TestDesign/R/print_functions.R |only TestDesign-1.1.2/TestDesign/R/runshiny.R | 42 TestDesign-1.1.2/TestDesign/R/shadow_class.R | 794 +- TestDesign-1.1.2/TestDesign/R/shadow_functions.R | 3505 +--------- TestDesign-1.1.2/TestDesign/R/show_functions.R |only TestDesign-1.1.2/TestDesign/R/solver_functions.R | 92 TestDesign-1.1.2/TestDesign/R/st_attrib_operators.R |only TestDesign-1.1.2/TestDesign/R/static_class.R | 144 TestDesign-1.1.2/TestDesign/R/static_functions.R | 263 TestDesign-1.1.2/TestDesign/R/summary_class.R |only TestDesign-1.1.2/TestDesign/R/summary_functions.R |only TestDesign-1.1.2/TestDesign/R/test_operators.R |only TestDesign-1.1.2/TestDesign/R/theta_functions.R |only TestDesign-1.1.2/TestDesign/R/xdata_functions.R |only TestDesign-1.1.2/TestDesign/build/vignette.rds |binary TestDesign-1.1.2/TestDesign/data/constraints_bayes.rda |only TestDesign-1.1.2/TestDesign/data/constraints_bayes_data.rda |only TestDesign-1.1.2/TestDesign/data/constraints_fatigue.rda |binary TestDesign-1.1.2/TestDesign/data/constraints_fatigue_data.rda |only TestDesign-1.1.2/TestDesign/data/constraints_reading.rda |binary TestDesign-1.1.2/TestDesign/data/constraints_reading_data.rda |only TestDesign-1.1.2/TestDesign/data/constraints_science.rda |binary TestDesign-1.1.2/TestDesign/data/constraints_science_data.rda |only TestDesign-1.1.2/TestDesign/data/itemattrib_bayes.rda |only TestDesign-1.1.2/TestDesign/data/itemattrib_bayes_data.rda |only TestDesign-1.1.2/TestDesign/data/itemattrib_fatigue.rda |binary TestDesign-1.1.2/TestDesign/data/itemattrib_fatigue_data.rda |only TestDesign-1.1.2/TestDesign/data/itemattrib_reading.rda |binary TestDesign-1.1.2/TestDesign/data/itemattrib_reading_data.rda |only TestDesign-1.1.2/TestDesign/data/itemattrib_science.rda |binary TestDesign-1.1.2/TestDesign/data/itemattrib_science_data.rda |only TestDesign-1.1.2/TestDesign/data/itemcontent_fatigue_data.rda |only TestDesign-1.1.2/TestDesign/data/itempool_bayes.rda |only TestDesign-1.1.2/TestDesign/data/itempool_bayes_data.rda |only TestDesign-1.1.2/TestDesign/data/itempool_fatigue.rda |binary TestDesign-1.1.2/TestDesign/data/itempool_fatigue_data.rda |only TestDesign-1.1.2/TestDesign/data/itempool_reading.rda |binary TestDesign-1.1.2/TestDesign/data/itempool_reading_data.rda |only TestDesign-1.1.2/TestDesign/data/itempool_science.rda |binary TestDesign-1.1.2/TestDesign/data/itempool_science_data.rda |only TestDesign-1.1.2/TestDesign/data/itempool_se_bayes_data.rda |only TestDesign-1.1.2/TestDesign/data/resp_fatigue_data.rda |only TestDesign-1.1.2/TestDesign/data/stimattrib_reading.rda |binary TestDesign-1.1.2/TestDesign/data/stimattrib_reading_data.rda |only TestDesign-1.1.2/TestDesign/inst/REFERENCES.bib | 11 TestDesign-1.1.2/TestDesign/inst/doc/constraints.R | 90 TestDesign-1.1.2/TestDesign/inst/doc/constraints.Rmd | 112 TestDesign-1.1.2/TestDesign/inst/doc/constraints.html | 1055 +-- TestDesign-1.1.2/TestDesign/inst/doc/rsymphony.Rmd | 41 TestDesign-1.1.2/TestDesign/inst/doc/rsymphony.html | 535 - TestDesign-1.1.2/TestDesign/inst/extdata/constraints_bayes_320.csv |only TestDesign-1.1.2/TestDesign/inst/extdata/example_datasets.R | 70 TestDesign-1.1.2/TestDesign/inst/extdata/itemattrib_bayes_320.csv |only TestDesign-1.1.2/TestDesign/inst/extdata/itemcontent_fatigue_95.csv | 6 TestDesign-1.1.2/TestDesign/inst/extdata/itempool_bayes_320.csv |only TestDesign-1.1.2/TestDesign/inst/extdata/itempool_se_bayes_320.csv |only TestDesign-1.1.2/TestDesign/inst/shiny/app.R | 53 TestDesign-1.1.2/TestDesign/inst/shiny/styles.css | 63 TestDesign-1.1.2/TestDesign/man/Shadow-methods.Rd | 55 TestDesign-1.1.2/TestDesign/man/Static-methods.Rd | 32 TestDesign-1.1.2/TestDesign/man/TestDesign.Rd |only TestDesign-1.1.2/TestDesign/man/TestDesign_alias.Rd |only TestDesign-1.1.2/TestDesign/man/buildConstraints.Rd | 58 TestDesign-1.1.2/TestDesign/man/calcEscore-methods.Rd | 86 TestDesign-1.1.2/TestDesign/man/calcFisher-methods.Rd | 86 TestDesign-1.1.2/TestDesign/man/calcHessian-methods.Rd | 75 TestDesign-1.1.2/TestDesign/man/calcJacobian-methods.Rd | 71 TestDesign-1.1.2/TestDesign/man/calcLocation-methods.Rd | 103 TestDesign-1.1.2/TestDesign/man/calcLogLikelihood-methods.Rd |only TestDesign-1.1.2/TestDesign/man/calcProb-methods.Rd | 101 TestDesign-1.1.2/TestDesign/man/calc_MI_FB.Rd | 4 TestDesign-1.1.2/TestDesign/man/calc_info.Rd | 103 TestDesign-1.1.2/TestDesign/man/calc_info_EB.Rd | 4 TestDesign-1.1.2/TestDesign/man/calc_info_FB.Rd | 4 TestDesign-1.1.2/TestDesign/man/calc_likelihood.Rd | 118 TestDesign-1.1.2/TestDesign/man/calc_posterior.Rd | 2 TestDesign-1.1.2/TestDesign/man/calc_posterior_function.Rd | 2 TestDesign-1.1.2/TestDesign/man/constraint-class.Rd | 21 TestDesign-1.1.2/TestDesign/man/constraints-class.Rd | 49 TestDesign-1.1.2/TestDesign/man/constraints-operators.Rd |only TestDesign-1.1.2/TestDesign/man/createShadowTestConfig.Rd | 132 TestDesign-1.1.2/TestDesign/man/createStaticTestConfig.Rd | 35 TestDesign-1.1.2/TestDesign/man/dataset_bayes.Rd |only TestDesign-1.1.2/TestDesign/man/dataset_fatigue.Rd | 54 TestDesign-1.1.2/TestDesign/man/dataset_reading.Rd | 48 TestDesign-1.1.2/TestDesign/man/dataset_science.Rd | 38 TestDesign-1.1.2/TestDesign/man/eap-methods.Rd | 55 TestDesign-1.1.2/TestDesign/man/find_segment.Rd | 22 TestDesign-1.1.2/TestDesign/man/getSolution-methods.Rd | 3 TestDesign-1.1.2/TestDesign/man/getSolutionAttributes.Rd |only TestDesign-1.1.2/TestDesign/man/info_item.Rd |only TestDesign-1.1.2/TestDesign/man/item-classes.Rd |only TestDesign-1.1.2/TestDesign/man/item_attrib-operators.Rd |only TestDesign-1.1.2/TestDesign/man/item_pool-class.Rd | 29 TestDesign-1.1.2/TestDesign/man/item_pool-operators.Rd |only TestDesign-1.1.2/TestDesign/man/loadConstraints.Rd | 47 TestDesign-1.1.2/TestDesign/man/loadItemAttrib.Rd | 40 TestDesign-1.1.2/TestDesign/man/loadItemPool.Rd | 47 TestDesign-1.1.2/TestDesign/man/loadStAttrib.Rd | 50 TestDesign-1.1.2/TestDesign/man/makeTest-methods.Rd | 2 TestDesign-1.1.2/TestDesign/man/mle-methods.Rd | 72 TestDesign-1.1.2/TestDesign/man/mlef-methods.Rd |only TestDesign-1.1.2/TestDesign/man/output_Shadow-class.Rd | 58 TestDesign-1.1.2/TestDesign/man/output_Shadow_all-class.Rd |only TestDesign-1.1.2/TestDesign/man/output_Static-class.Rd |only TestDesign-1.1.2/TestDesign/man/p_item.Rd |only TestDesign-1.1.2/TestDesign/man/plot-methods.Rd |only TestDesign-1.1.2/TestDesign/man/plotCAT-methods.Rd | 20 TestDesign-1.1.2/TestDesign/man/plotExposure-methods.Rd | 19 TestDesign-1.1.2/TestDesign/man/plotInfo-methods.Rd | 37 TestDesign-1.1.2/TestDesign/man/plotShadow-methods.Rd | 17 TestDesign-1.1.2/TestDesign/man/pool_cluster-class.Rd | 2 TestDesign-1.1.2/TestDesign/man/pool_cluster-operators.Rd |only TestDesign-1.1.2/TestDesign/man/print-methods.Rd |only TestDesign-1.1.2/TestDesign/man/runAssembly.Rd | 6 TestDesign-1.1.2/TestDesign/man/show-methods.Rd |only TestDesign-1.1.2/TestDesign/man/showConstraints.Rd | 6 TestDesign-1.1.2/TestDesign/man/simResp-methods.Rd | 72 TestDesign-1.1.2/TestDesign/man/st_attrib-operators.Rd |only TestDesign-1.1.2/TestDesign/man/summary-classes.Rd |only TestDesign-1.1.2/TestDesign/man/summary-methods.Rd |only TestDesign-1.1.2/TestDesign/man/test-class.Rd | 16 TestDesign-1.1.2/TestDesign/man/test_cluster-class.Rd | 10 TestDesign-1.1.2/TestDesign/man/test_operators.Rd |only TestDesign-1.1.2/TestDesign/man/theta_EAP.Rd | 2 TestDesign-1.1.2/TestDesign/man/theta_EAP_matrix.Rd | 4 TestDesign-1.1.2/TestDesign/man/theta_EB.Rd | 111 TestDesign-1.1.2/TestDesign/man/theta_FB.Rd | 2 TestDesign-1.1.2/TestDesign/man/theta_FB_single.Rd | 2 TestDesign-1.1.2/TestDesign/man/toggleConstraints.Rd |only TestDesign-1.1.2/TestDesign/man/updateConstraints.Rd | 15 TestDesign-1.1.2/TestDesign/src/RcppExports.cpp | 589 - TestDesign-1.1.2/TestDesign/src/info_array_functions.cpp |only TestDesign-1.1.2/TestDesign/src/info_array_functions.h |only TestDesign-1.1.2/TestDesign/src/item_functions.cpp |only TestDesign-1.1.2/TestDesign/src/item_functions.h |only TestDesign-1.1.2/TestDesign/src/other_functions.cpp |only TestDesign-1.1.2/TestDesign/src/posterior_functions.cpp |only TestDesign-1.1.2/TestDesign/src/posterior_functions.h |only TestDesign-1.1.2/TestDesign/src/theta_functions.cpp |only TestDesign-1.1.2/TestDesign/src/theta_functions.h |only TestDesign-1.1.2/TestDesign/tests/testthat/test-refresh-methods.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test-selection-methods.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test-theta-methods.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcEscore_typecast.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcEscore_value.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcFisher_typecast.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcFisher_value.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcProb_typecast.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_calcProb_value.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_constraints.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_deprecated.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_examples.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_exposure_methods.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_item_exclusion.R |only TestDesign-1.1.2/TestDesign/tests/testthat/test_static.R |only TestDesign-1.1.2/TestDesign/vignettes/constraints.Rmd | 112 TestDesign-1.1.2/TestDesign/vignettes/rsymphony.Rmd | 41 254 files changed, 5995 insertions(+), 7940 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-30 0.99.2
Title: Safety Diagnostics for Dose-Escalation Trial Designs
Description: Enhances various R packages that support the design and simulation
of phase 1 dose-escalation trials, adding diagnostics to examine
the safety characteristics of these designs in light of expected
inter-individual variation in pharmacokinetics and pharmacodynamics.
See Norris (2020), "Retrospective analysis of a fatal dose-finding
trial" <arXiv:2004.12755>.
Author: David C. Norris [aut, cre, cph]
(<https://orcid.org/0000-0001-9593-6343>)
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between precautionary versions 0.1-3 dated 2020-09-13 and 0.1-4 dated 2020-09-21
DESCRIPTION | 8 MD5 | 18 + NEWS.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 13 + inst/doc/FDA-proactive.R |only inst/doc/FDA-proactive.Rmd |only inst/doc/FDA-proactive.html |only inst/doc/Intro.html | 358 +++++++++++++++++++++++++++--------- vignettes/FDA-proactive.Rmd |only vignettes/precautionary-package.bib | 25 ++ 12 files changed, 329 insertions(+), 99 deletions(-)
Title: Data Package for 'pathfindR'
Description: This is a data-only package, containing data needed to run the CRAN
package 'pathfindR', a package for enrichment analysis utilizing active
subnetworks. This package contains protein-protein interaction network data,
data related to gene sets and example input/output data.
Author: Ege Ulgen [cre, cph] (<https://orcid.org/0000-0003-2090-3621>),
Ozan Ozisik [aut] (<https://orcid.org/0000-0001-5980-8002>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR.data versions 1.0.0 dated 2020-06-04 and 1.1.0 dated 2020-09-21
DESCRIPTION | 8 +-- MD5 | 80 ++++++++++++++++---------------- NEWS.md | 16 ++++++ R/data.R | 90 ++++++++++++++++++------------------- R/sysdata.rda |binary data/RA_clustered.rda |binary data/RA_comparison_output.rda |binary data/RA_output.rda |binary data/biocarta_descriptions.rda |binary data/biocarta_genes.rda |binary data/cell_markers_descriptions.rda |binary data/cell_markers_gsets.rda |binary data/custom_result.rda |binary data/go_all_genes.rda |binary data/kegg_descriptions.rda |binary data/kegg_genes.rda |binary data/mmu_kegg_descriptions.rda |binary data/mmu_kegg_genes.rda |binary data/myeloma_output.rda |binary data/reactome_descriptions.rda |binary data/reactome_genes.rda |binary man/GO_all_terms_df.Rd | 4 - man/RA_clustered.Rd | 11 +--- man/RA_comparison_output.Rd | 4 - man/RA_output.Rd | 4 - man/biocarta_descriptions.Rd | 4 - man/biocarta_genes.Rd | 4 - man/biogrid_adj_list.Rd | 7 +- man/cell_markers_descriptions.Rd | 2 man/cell_markers_gsets.Rd | 2 man/custom_result.Rd | 2 man/go_all_genes.Rd | 4 - man/intact_adj_list.Rd | 7 +- man/kegg_adj_list.Rd | 7 +- man/kegg_descriptions.Rd | 4 - man/kegg_genes.Rd | 4 - man/mmu_kegg_descriptions.Rd | 4 - man/mmu_kegg_genes.Rd | 4 - man/myeloma_output.Rd | 4 - man/reactome_descriptions.Rd | 4 - man/reactome_genes.Rd | 4 - 41 files changed, 150 insertions(+), 134 deletions(-)
More information about pathfindR.data at CRAN
Permanent link
Title: Common Analysis with Remote Sensing Data
Description: A collection of functions used in remote sensing analysis (e.g., conversion from digital numbers to radiance, reflectance, and temperature). It includes several algorithms to calculate the albedo: Liang (2000) <doi:10.1016/S0034-4257(00)00205-4>, Silva et al. (2016) <doi:10.32614/RJ-2016-051>, Tasumi et al. (2008) <doi:10.1061/(ASCE)1084-0699(2008)13:2(51)>, among others; and include functions to derive several spectral indices. Although the current version implements basic functions, it will be expandable to a more robust tool for water cycle modeling (e.g., to include surface runoff and evapotranspiration calculations) in the near future.
This package is under development at the Institute about Natural Resources Research (INIRENA) from the Universidad Michoacana de San Nicolas de Hidalgo.
Author: Rafael Hernandez-Guzman [aut, cre]
(<https://orcid.org/0000-0002-2711-9015>)
Maintainer: Rafael Hernandez-Guzman <rhernandez.g@gmail.com>
Diff between nightmares versions 0.0.1 dated 2020-09-09 and 0.0.2 dated 2020-09-21
DESCRIPTION | 8 ++--- MD5 | 65 ++++++++++++++++++++++++++++++++++++++---------- NAMESPACE | 19 ++++++++++++++ NEWS |only R/AVI.R |only R/BSI.R |only R/ETo56_miss.R |only R/EVI.R |only R/GCI.R |only R/LAI.R |only R/MNDWI.R |only R/MSAVI.R |only R/NBR.R |only R/NBR2.R |only R/NDMI.R |only R/NDVI.R |only R/NDWI.R |only R/NPCRI.R |only R/SAVI.R |only R/SI.R |only R/alb_oli.R | 2 - R/atm_pressure.R |only R/dsi_oli.R |only R/rad_oli.R | 2 - R/ref_oli.R | 2 - R/solrad.R |only R/thermal_oli.R | 4 +- inst/doc/vignettes.Rmd | 54 ++++++++++++++++++++++++++++++++++++--- inst/doc/vignettes.html | 59 ++++++++++++++++++++++++++++++++++++------- man/AVI.Rd |only man/BSI.Rd |only man/ETo56_miss.Rd |only man/EVI.Rd |only man/GCI.Rd |only man/LAI.Rd |only man/MNDWI.Rd |only man/MSAVI.Rd |only man/NBR.Rd |only man/NBR2.Rd |only man/NDMI.Rd |only man/NDVI.Rd |only man/NDWI.Rd |only man/NPCRI.Rd |only man/SAVI.Rd |only man/SI.Rd |only man/alb_oli.Rd | 2 - man/atm_pressure.Rd |only man/dsi_oli.Rd |only man/rad_oli.Rd | 2 - man/ref_oli.Rd | 2 - man/solrad.Rd |only man/thermal_oli.Rd | 2 - vignettes/vignettes.Rmd | 54 ++++++++++++++++++++++++++++++++++++--- 53 files changed, 232 insertions(+), 45 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-08 1.0.17
2020-09-04 1.0.16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-03 1.0.4
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre], Robert Ness [ctb]
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 4.6 dated 2020-09-15 and 4.6.1 dated 2020-09-21
Changelog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/data.preprocessing.R | 5 +++++ R/frontend-data.R | 2 +- 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Ensemble Methods for Survival Data with Time-Varying Covariates
Description: Implements the conditional inference forest and random survival forest
algorithm to modeling left-truncated right-censored data with time-invariant
covariates, and (left-truncated) right-censored survival data with time-varying
covariates. It also provides functions to tune the parameters and evaluate the
model fit. See Yao et al. (2020) <arXiv:2006.00567>.
Author: Weichi Yao [aut, cre],
Halina Frydman [aut],
Denis Larocque [aut],
Jeffrey S. Simonoff [aut]
Maintainer: Weichi Yao <wy635@stern.nyu.edu>
Diff between LTRCforests versions 0.5.0 dated 2020-07-03 and 0.5.1 dated 2020-09-20
LTRCforests-0.5.0/LTRCforests/R/ltrcrsf.R |only LTRCforests-0.5.0/LTRCforests/R/tune.ltrcrsf.R |only LTRCforests-0.5.0/LTRCforests/man/ltrcrsf.Rd |only LTRCforests-0.5.0/LTRCforests/man/tune.ltrcrsf.Rd |only LTRCforests-0.5.1/LTRCforests/DESCRIPTION | 8 LTRCforests-0.5.1/LTRCforests/MD5 | 42 LTRCforests-0.5.1/LTRCforests/NAMESPACE | 8 LTRCforests-0.5.1/LTRCforests/R/LTRCforests-package.R | 36 LTRCforests-0.5.1/LTRCforests/R/LTRCforests.news.R | 1 LTRCforests-0.5.1/LTRCforests/R/data.utilities.R | 12 LTRCforests-0.5.1/LTRCforests/R/generic.predict.ltrcrfsrc.R | 71 - LTRCforests-0.5.1/LTRCforests/R/ltrccf.R | 2 LTRCforests-0.5.1/LTRCforests/R/ltrcrfsrc.R | 596 +++++------- LTRCforests-0.5.1/LTRCforests/R/ltrcrrf.R |only LTRCforests-0.5.1/LTRCforests/R/predictProb.R | 234 ++-- LTRCforests-0.5.1/LTRCforests/R/print.R | 22 LTRCforests-0.5.1/LTRCforests/R/tune.ltrccf.R | 4 LTRCforests-0.5.1/LTRCforests/R/tune.ltrcrrf.R |only LTRCforests-0.5.1/LTRCforests/man/LTRCforests-package.Rd | 37 LTRCforests-0.5.1/LTRCforests/man/ltrccf.Rd | 2 LTRCforests-0.5.1/LTRCforests/man/ltrcrrf.Rd |only LTRCforests-0.5.1/LTRCforests/man/predictProb.Rd | 14 LTRCforests-0.5.1/LTRCforests/man/print.Rd | 12 LTRCforests-0.5.1/LTRCforests/man/tune.ltrccf.Rd | 4 LTRCforests-0.5.1/LTRCforests/man/tune.ltrcrrf.Rd |only LTRCforests-0.5.1/LTRCforests/src/splitCustom.c | 15 26 files changed, 589 insertions(+), 531 deletions(-)
Title: Dive Analysis and Calibration
Description: Utilities to represent, visualize, filter, analyse, and summarize
time-depth recorder (TDR) data. Miscellaneous functions for
handling location data are also provided.
Author: Sebastian P. Luque <spluque@gmail.com>
Maintainer: Sebastian P. Luque <spluque@gmail.com>
Diff between diveMove versions 1.5.1 dated 2020-09-12 and 1.5.2 dated 2020-09-20
diveMove-1.5.1/diveMove/vignettes/auto |only diveMove-1.5.1/diveMove/vignettes/tcltk.png |only diveMove-1.5.2/diveMove/DESCRIPTION | 10 diveMove-1.5.2/diveMove/MD5 | 19 diveMove-1.5.2/diveMove/NEWS | 6 diveMove-1.5.2/diveMove/inst/doc/diveMove.R | 58 diveMove-1.5.2/diveMove/inst/doc/diveMove.Rmd | 83 diveMove-1.5.2/diveMove/inst/doc/diveMove.html | 1957 -------------- diveMove-1.5.2/diveMove/inst/tinytest/test_calibrations.R | 42 diveMove-1.5.2/diveMove/vignettes/diveMove.Rmd | 83 diveMove-1.5.2/diveMove/vignettes/figs |only 11 files changed, 237 insertions(+), 2021 deletions(-)
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic
factor analysis is a dimension reduction tool for multivariate time series.
'bayesdfa' extends conventional dynamic factor models in several ways.
First, extreme events may be estimated in the latent trend by modeling
process error with a student-t distribution. Second, autoregressive and
moving average components can be optionally included. Third, the estimated
dynamic factors can be analyzed with hidden Markov models to evaluate
support for latent regimes.
Author: Eric J. Ward [aut, cre],
Sean C. Anderson [aut],
Luis A. Damiano [aut],
Mary E. Hunsicker, [ctb],
Mike A. Litzow [ctb],
Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between bayesdfa versions 0.1.5 dated 2020-09-02 and 0.1.6 dated 2020-09-20
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/fit_regimes.R | 4 +++- inst/doc/bayesdfa.R | 22 +++++++++++----------- inst/doc/bayesdfa.Rmd | 6 +++--- inst/doc/bayesdfa.html | 16 ++-------------- tests/testthat/test-fit.R | 30 +++++++++++++++--------------- vignettes/bayesdfa.Rmd | 6 +++--- 9 files changed, 54 insertions(+), 60 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 Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.9.5 dated 2020-09-07 and 0.9.6 dated 2020-09-20
DESCRIPTION | 6 - MD5 | 34 +++++------ NAMESPACE | 1 NEWS.md | 15 ++++ R/clean_names.R | 27 +++++++- R/format_bf.R | 40 +++++++++---- R/format_value.R | 4 - R/get_data.R | 7 ++ R/get_parameters.R | 20 ++++++ R/get_priors.R | 25 ++++++-- build/partial.rdb |binary man/clean_names.Rd | 110 +++++++++++++++++++----------------- man/format_bf.Rd | 64 +++++++++++--------- man/get_parameters.Rd | 10 +++ tests/testthat/test-BayesFactorBF.R | 40 ++++++++++++- tests/testthat/test-clean_names.R | 5 + tests/testthat/test-mixed.R | 7 +- tests/testthat/test-namespace.R | 2 18 files changed, 286 insertions(+), 131 deletions(-)