Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins [aut, cre],
Bob Rudis [ctb] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.5.3 dated 2019-01-30 and 2.5.4 dated 2020-11-19
DESCRIPTION | 25 +- MD5 | 61 +++-- NAMESPACE | 4 NEWS.md | 120 ++++++----- R/a-rect.R |only R/data.R | 2 R/geom_treemap.R | 121 +++++++---- R/geom_treemap_subgroup_border.R | 42 +-- R/geom_treemap_subgroup_text.R | 62 +++-- R/geom_treemap_text.R | 61 ++--- R/treemapify.R | 29 +- R/utils.R |only README.md | 111 +++++----- build/vignette.rds |binary inst/WORDLIST |only inst/doc/introduction-to-treemapify.R | 10 inst/doc/introduction-to-treemapify.Rmd | 39 ++- inst/doc/introduction-to-treemapify.html | 204 ++++++++++++------- man/G20.Rd | 22 +- man/draw_key_rrect.Rd |only man/figures/README-basic_treemap-1.png |binary man/figures/README-complex_treemap-1.png |binary man/figures/README-geom_treemap_text-1.png |binary man/figures/README-multiple_subgrouped_treemap-1.png |binary man/figures/README-subgrouped_treemap-1.png |binary man/figures/animated_treemap.gif |binary man/geom_treemap.Rd | 78 ++++--- man/geom_treemap_subgroup_border.Rd | 66 +++--- man/geom_treemap_subgroup_text.Rd | 99 +++++---- man/geom_treemap_text.Rd | 86 ++++---- man/treemapify.Rd | 68 +++--- tests/spelling.R |only tests/testthat/test_plots.R | 26 ++ vignettes/introduction-to-treemapify.Rmd | 39 ++- 34 files changed, 814 insertions(+), 561 deletions(-)
Title: Advanced Tensor Arithmetic with Named Indices
Description: Provides convenience functions for advanced
linear algebra with tensors and computation with data sets of
tensors on a higher level abstraction. It includes Einstein and
Riemann summing conventions, dragging, co- and contravariate
indices, parallel computations on sequences of tensors.
Author: K. Gerald van den Boogaart <boogaart@uni-greifswald.de>
Maintainer: K. Gerald van den Boogaart <boogaart@math.tu-freiberg.de>
Diff between tensorA versions 0.36.1 dated 2018-07-29 and 0.36.2 dated 2020-11-19
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/TensorAx.R | 24 ++++++++++++------------ man/meantensor.Rd | 4 ++-- man/solvetensor.Rd | 2 +- src/tensora.c | 27 +++++++++++++++++++++++++++ 6 files changed, 54 insertions(+), 27 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses. For tutorial, please check Yan et al. (2020) <doi:10.18637/jss.v094.i13>.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.7.0 dated 2020-09-29 and 2.7.1 dated 2020-11-19
DESCRIPTION | 10 MD5 | 22 R/get.oc.R | 11 R/get.oc.comb.R | 2370 +++++++++++++++++++++++++------------------------ R/plot.boin.R | 2 R/select.mtd.R | 46 R/select.mtd.comb.R | 52 - R/summary.boin.R | 11 man/get.oc.Rd | 8 man/get.oc.comb.Rd | 11 man/select.mtd.Rd | 12 man/select.mtd.comb.Rd | 11 12 files changed, 1345 insertions(+), 1221 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.11 dated 2020-11-13 and 1.4.12 dated 2020-11-19
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 2 +- R/parse.R | 5 ++++- inst/doc/rmdhunks/intro.Rmd | 8 ++++---- inst/doc/u1_intro.html | 2 +- tests/testthat/testthat.parse.R | 19 ++++++++++++------- vignettes/rmdhunks/intro.Rmd | 8 ++++---- 8 files changed, 36 insertions(+), 28 deletions(-)
Title: A Framework for Investment Strategy Simulation
Description: Provides a framework for performing discrete (share-level) simulations of
investment strategies. Simulated portfolios optimize exposure to an input signal subject
to constraints such as position size and factor exposure. For background see L. Chincarini
and D. Kim (2010, ISBN:978-0-07-145939-6) "Quantitative Equity Portfolio Management".
Author: Jeff Enos [cre, aut, cph],
David Kane [aut],
Ben Czekanski [ctb],
Robert Hoover [ctb],
Jack Luby [ctb],
Nils Wallin [ctb]
Maintainer: Jeff Enos <jeffrey.enos@gmail.com>
Diff between strand versions 0.1.3 dated 2020-05-26 and 0.2.0 dated 2020-11-19
DESCRIPTION | 51 MD5 | 95 NAMESPACE | 18 NEWS.md | 58 R/CrossSection.R | 26 R/PortOpt.R | 380 ++- R/Simulation.R | 1074 ++++++++-- R/StrategyConfig.R | 24 R/calculate_exposures.R |only R/data.R | 97 R/load_data_files.R |only R/reporting.R |only R/strand.R | 22 README.md | 33 build/vignette.rds |binary data/sample_inputs.RData |binary data/sample_pricing.RData |binary data/sample_secref.RData |binary inst/application/server.R | 595 ++++- inst/application/strategy_config.yaml | 43 inst/application/strategy_config_file_inputs.yaml | 45 inst/application/ui.R | 82 inst/doc/strand.R | 24 inst/doc/strand.Rmd | 128 - inst/doc/strand.html | 340 +-- inst/reports |only man/PortOpt.Rd |only man/Simulation.Rd | 290 ++ man/make_ft.Rd |only man/sample_inputs.Rd | 48 man/sample_pricing.Rd | 36 man/sample_secref.Rd | 18 man/show_best_worst.Rd |only man/show_config.Rd |only man/show_constraints.Rd |only man/show_monthly_returns.Rd |only man/show_stats.Rd |only man/strand-package.Rd | 9 tests/testthat/data/test_PortOpt_factor_constraint.RData |binary tests/testthat/data/test_PortOpt_factor_constraint.yaml | 4 tests/testthat/data/test_PortOpt_simple.RData |binary tests/testthat/data/test_PortOpt_simple.yaml | 4 tests/testthat/data/test_Simulation.RData |binary tests/testthat/data/test_Simulation.yaml | 4 tests/testthat/data/test_Simulation_overallReturnsByMonthDf.RData |only tests/testthat/data/test_Simulation_overallStatsDf.RData |only tests/testthat/data/test_Simulation_simple.yaml | 1 tests/testthat/data/test_input/inputs/inputs_20190102.feather |binary tests/testthat/data/test_input/inputs/inputs_20190103.feather |binary tests/testthat/data/test_input/inputs/inputs_20190104.feather |binary tests/testthat/data/test_input/inputs/inputs_20190107.feather |binary tests/testthat/data/test_input/inputs/inputs_20190108.feather |binary tests/testthat/test_Simulation.R | 380 +++ vignettes/sample.yaml | 27 vignettes/strand.Rmd | 128 - 55 files changed, 3109 insertions(+), 975 deletions(-)
Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph
parameter estimation, model selection based on the GIC (Graph Information
Criterion), statistical tests to discriminate two or more populations of
graphs (ANOGVA - Analysis of Graph Variability), correlation between
graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>,
Futija et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>,
Tang et al. (2017) <doi:10.3150/15-BEJ789>,
Tang et al. (2017) <doi:10.1080/10618600.2016.1193505>,
Ghoshdastidar et al. (2017) <arXiv:1705.06168>,
Ghoshdastidar et al. (2017) <arXiv:1707.00833>,
Cerqueira et al. (2017) <doi:10.1109/TNSE.2017.2674026>,
Fraiman and Fraiman (2018) <doi:10.1038/s41598-018-23152-5>,
Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Grover E. Castro Guzman [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 0.3.0 dated 2019-10-24 and 0.4.0 dated 2020-11-19
statGraph-0.3.0/statGraph/inst |only statGraph-0.4.0/statGraph/DESCRIPTION | 66 statGraph-0.4.0/statGraph/MD5 | 48 statGraph-0.4.0/statGraph/NAMESPACE | 5 statGraph-0.4.0/statGraph/R/statGraph-package.R | 6 statGraph-0.4.0/statGraph/R/statGraph.R | 1162 ++++++++--- statGraph-0.4.0/statGraph/build/partial.rdb |binary statGraph-0.4.0/statGraph/man/GIC.Rd | 50 statGraph-0.4.0/statGraph/man/anogva.Rd | 12 statGraph-0.4.0/statGraph/man/cerqueira.Rd | 22 statGraph-0.4.0/statGraph/man/fast.eigenvalue.probability.Rd |only statGraph-0.4.0/statGraph/man/fast.graph.param.estimator.Rd |only statGraph-0.4.0/statGraph/man/fast.spectral.density.Rd |only statGraph-0.4.0/statGraph/man/fraiman.Rd | 16 statGraph-0.4.0/statGraph/man/gCEM.Rd |only statGraph-0.4.0/statGraph/man/ghoshdastidar.Rd | 40 statGraph-0.4.0/statGraph/man/graph.acf.Rd | 6 statGraph-0.4.0/statGraph/man/graph.cluster.Rd | 18 statGraph-0.4.0/statGraph/man/graph.cor.test.Rd | 4 statGraph-0.4.0/statGraph/man/graph.entropy.Rd | 26 statGraph-0.4.0/statGraph/man/graph.model.selection.Rd | 28 statGraph-0.4.0/statGraph/man/graph.mult.scaling.Rd | 26 statGraph-0.4.0/statGraph/man/graph.param.estimator.Rd | 45 statGraph-0.4.0/statGraph/man/graph.test.Rd | 10 statGraph-0.4.0/statGraph/man/kmeans.graph.Rd |only statGraph-0.4.0/statGraph/man/sp.anogva.Rd | 44 statGraph-0.4.0/statGraph/man/statGraph-package.Rd | 6 statGraph-0.4.0/statGraph/man/tang.Rd | 33 28 files changed, 1230 insertions(+), 443 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Description: Methods and tools for Singular Spectrum Analysis including decomposition,
forecasting and gap-filling for univariate and multivariate time series.
General description of the methods with many examples can be found in the book
Golyandina (2018, <doi:10.1007/978-3-662-57380-8>).
See 'citation("Rssa")' for details.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between Rssa versions 1.0.2 dated 2020-02-28 and 1.0.3 dated 2020-11-19
DESCRIPTION | 15 ++++++++++----- MD5 | 30 +++++++++++++++--------------- R/capabilities.R | 13 +++++++++---- R/pssa.R | 2 +- R/wossa.R | 2 +- man/Barbara.rd | 2 +- man/Rssa-package.Rd | 6 +++--- man/autossa.Rd | 2 +- man/fossa.Rd | 2 +- man/gapfill.Rd | 2 +- man/iossa.Rd | 2 +- man/iossa.result.Rd | 2 +- man/owcor.Rd | 2 +- man/rforecast.Rd | 2 +- man/ssa.Rd | 10 +++++----- man/vforecast.Rd | 2 +- 16 files changed, 53 insertions(+), 43 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre] (<https://orcid.org/0000-0001-5537-637X>),
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.6.83 dated 2020-11-19 and 3.6.84 dated 2020-11-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/get_eurostat_geospatial.R | 10 ++++++---- README.md | 2 +- inst/doc/vignette.html | 4 ++-- man/get_eurostat_geospatial.Rd | 10 ++++++---- vignettes/website/maps.Rmd | 2 +- 7 files changed, 26 insertions(+), 22 deletions(-)
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2020. driveR: A Novel Method for Prioritizing Cancer
Driver Genes Using Somatic Genomics Data. bioRxiv
<doi:10.1101/2020.11.10.376707>.
Author: Ege Ulgen [aut, cre, cph] (<https://orcid.org/0000-0003-2090-3621>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.1.1 dated 2020-11-18 and 0.2.0 dated 2020-11-19
DESCRIPTION | 16 MD5 | 66 NEWS.md | 16 R/core_functions.R | 41 R/data.R | 4 R/driveR.R | 2 R/sysdata.rda |binary R/utility.R | 39 README.md | 15 build/vignette.rds |binary data/KEGG_cancer_pathways_descriptions.rda |binary data/MTL_submodel_descriptions.rda |binary data/example_cohort_features_table.rda |binary data/example_cohort_scna_table.rda |binary data/example_features_table.rda |binary data/example_scna_table.rda |binary data/specific_thresholds.rda |binary inst/CITATION | 4 inst/doc/how_to_use.R | 10 inst/doc/how_to_use.Rmd | 25 inst/doc/how_to_use.html | 168 inst/extdata/driver_workflow.png |binary inst/extdata/example.hg19_multianno.csv |22590 ++++++++++++------------- inst/extdata/example_cohort.hg19_multianno.csv | 202 man/KEGG_cancer_pathways.Rd | 2 man/KEGG_cancer_pathways_descriptions.Rd | 2 man/create_SCNA_score_df.Rd | 2 man/create_features_df.Rd | 8 man/create_noncoding_impact_score_df.Rd | 5 man/determine_double_hit_genes.Rd | 2 man/driveR.Rd | 2 man/predict_coding_impact.Rd | 9 tests/testthat/test-utility.R | 8 vignettes/how_to_use.Rmd | 25 34 files changed, 11666 insertions(+), 11597 deletions(-)
Title: Heatmap-Integrated Decision Tree Visualizations
Description: Creates interpretable decision tree visualizations
with the data represented as a heatmap at the tree's leaf nodes.
'treeheatr' utilizes the customizable 'ggparty' package for
drawing decision trees.
Author: Trang Le [aut, cre] (https://trang.page/),
Jason Moore [aut] (http://www.epistasisblog.org/),
University of Pennsylvania [cph]
Maintainer: Trang Le <grixor@gmail.com>
Diff between treeheatr versions 0.1.0 dated 2020-06-17 and 0.2.1 dated 2020-11-19
treeheatr-0.1.0/treeheatr/R/def_testing_data.R |only treeheatr-0.1.0/treeheatr/tests |only treeheatr-0.2.1/treeheatr/DESCRIPTION | 10 treeheatr-0.2.1/treeheatr/MD5 | 80 +-- treeheatr-0.2.1/treeheatr/NAMESPACE | 1 treeheatr-0.2.1/treeheatr/NEWS.md |only treeheatr-0.2.1/treeheatr/R/clust.R | 8 treeheatr-0.2.1/treeheatr/R/compute_tree.R | 120 +--- treeheatr-0.2.1/treeheatr/R/data.R | 1 treeheatr-0.2.1/treeheatr/R/draw_heat.R | 45 + treeheatr-0.2.1/treeheatr/R/draw_tree.R | 4 treeheatr-0.2.1/treeheatr/R/eval_tree.R | 30 - treeheatr-0.2.1/treeheatr/R/get_fit.R |only treeheatr-0.2.1/treeheatr/R/globals.R | 2 treeheatr-0.2.1/treeheatr/R/heat_tree.R | 66 +- treeheatr-0.2.1/treeheatr/R/treeheatr.R |only treeheatr-0.2.1/treeheatr/R/utils.R | 44 + treeheatr-0.2.1/treeheatr/README.md | 66 +- treeheatr-0.2.1/treeheatr/build/vignette.rds |binary treeheatr-0.2.1/treeheatr/data/diabetes.rda |binary treeheatr-0.2.1/treeheatr/data/test_covid.rda |binary treeheatr-0.2.1/treeheatr/data/train_covid.rda |binary treeheatr-0.2.1/treeheatr/inst/doc/explore.R | 93 +-- treeheatr-0.2.1/treeheatr/inst/doc/explore.Rmd | 192 +++---- treeheatr-0.2.1/treeheatr/inst/doc/explore.html | 313 +++++++----- treeheatr-0.2.1/treeheatr/man/align_plots.Rd |only treeheatr-0.2.1/treeheatr/man/clust_feat_func.Rd | 6 treeheatr-0.2.1/treeheatr/man/clust_samp_func.Rd | 2 treeheatr-0.2.1/treeheatr/man/compute_tree.Rd | 27 - treeheatr-0.2.1/treeheatr/man/diabetes.Rd | 1 treeheatr-0.2.1/treeheatr/man/draw_heat.Rd | 23 treeheatr-0.2.1/treeheatr/man/eval_tree.Rd | 11 treeheatr-0.2.1/treeheatr/man/figures/card.png |binary treeheatr-0.2.1/treeheatr/man/figures/unnamed-chunk-4-1.png |binary treeheatr-0.2.1/treeheatr/man/figures/unnamed-chunk-5-1.png |only treeheatr-0.2.1/treeheatr/man/get_cols.Rd | 5 treeheatr-0.2.1/treeheatr/man/get_disp_feats.Rd | 8 treeheatr-0.2.1/treeheatr/man/get_fit-methods.Rd |only treeheatr-0.2.1/treeheatr/man/heat_tree.Rd | 70 ++ treeheatr-0.2.1/treeheatr/man/position_nodes.Rd | 2 treeheatr-0.2.1/treeheatr/man/prediction_df.Rd | 8 treeheatr-0.2.1/treeheatr/man/prep_data.Rd | 24 treeheatr-0.2.1/treeheatr/man/term_node_pos.Rd | 2 treeheatr-0.2.1/treeheatr/vignettes/explore.Rmd | 192 +++---- 44 files changed, 800 insertions(+), 656 deletions(-)
Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize',
'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mg3901@columbia.edu>
Diff between statar versions 0.7.2 dated 2020-07-27 and 0.7.3 dated 2020-11-19
DESCRIPTION | 8 +- MD5 | 18 ++--- R/fill_gap.R | 10 +- R/stat_binmean.R | 15 +--- README.md | 157 +++++++++++++++++++++------------------------ inst/doc/data-frames.Rmd | 16 ++++ inst/doc/data-frames.html | 17 ++++ man/stat_binmean.Rd | 11 +-- tests/testthat/test_fill.R | 24 +++--- vignettes/data-frames.Rmd | 16 ++++ 10 files changed, 160 insertions(+), 132 deletions(-)
Title: State Space Modelling in 'R'
Description: A tool that makes estimating models in state space form
a breeze. See "Time Series Analysis by State Space Methods" by
Durbin and Koopman (2012, ISBN: 978-0-19-964117-8) for details
about the algorithms implemented.
Author: Dylan Beijers [aut, cre]
Maintainer: Dylan Beijers <dylanbeijers@gmail.com>
Diff between statespacer versions 0.3.0 dated 2020-09-15 and 0.4.0 dated 2020-11-19
DESCRIPTION | 14 +-- MD5 | 59 ++++++++------- NAMESPACE | 1 NEWS.md | 14 +++ R/GetSysMat.R | 6 + R/RcppExports.R | 58 +++++++++++++++ R/SimSmoother.R |only R/StateSpaceEval.R | 116 +++++++++++-------------------- R/predict.R | 60 +++++----------- R/statespacer.R | 14 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/boxjenkins.html | 60 ++++++++++++++-- inst/doc/dictionary.Rmd | 4 - inst/doc/dictionary.html | 52 +++++++++++++ inst/doc/intro.Rmd | 2 inst/doc/intro.html | 56 +++++++++++++- inst/doc/seatbelt.html | 66 +++++++++++++++-- inst/doc/selfspec.Rmd | 2 inst/doc/selfspec.html | 56 +++++++++++++- man/SimSmoother.Rd |only man/figures/README-unnamed-chunk-4-1.png |binary man/statespacer-package.Rd | 6 - man/statespacer.Rd | 2 src/ExtractComponentC.cpp |only src/FastSmootherC.cpp |only src/KalmanC.cpp | 79 +++++++++++++-------- src/LogLikC.cpp | 36 ++++++--- src/RcppExports.cpp | 57 +++++++++++++++ src/SimulateC.cpp |only vignettes/dictionary.Rmd | 4 - vignettes/intro.Rmd | 2 vignettes/selfspec.Rmd | 2 33 files changed, 596 insertions(+), 232 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-12 0.1.1
2019-10-13 0.1.0
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.4 dated 2020-05-19 and 1.0.5 dated 2020-11-19
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- R/getNOAA.bathy.R | 6 ++++++ build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/etopo.Rd | 2 +- man/getNOAA.bathy.Rd | 4 ++-- man/irregular.Rd | 2 +- man/marmap.Rd | 4 ++-- man/plot.bathy.Rd | 42 +++++++++++++++++++++--------------------- man/readGEBCO.bathy.Rd | 25 +++++++++++++------------ man/space.pies.Rd | 18 +++++++++--------- man/subsetBathy.Rd | 2 +- man/subsetSQL.Rd | 4 ++-- 22 files changed, 84 insertions(+), 77 deletions(-)
Title: Lattice-Based Space-Filling Designs
Description: Lattice-based space-filling designs with fill or separation distance properties including interleaved lattice-based minimax distance designs, interleaved lattice-based maximin distance designs, (sliced) rotated sphere packing designs, and densest packing-based maximum projections designs.
Author: Xu He [aut, cre]
Maintainer: Xu He <hexu@amss.ac.cn>
Diff between LatticeDesign versions 1.0-1 dated 2018-08-17 and 2.0-1 dated 2020-11-19
DESCRIPTION | 11 +++++------ MD5 | 40 ++++++++++++++++++++++++++++------------ NAMESPACE | 2 ++ R/InterleavedMaximinD.R | 2 +- R/InterleavedMinimaxD.r |only data/GMs2.rda |only data/GMs3.rda |only data/GMs4.rda |only data/GMs5.rda |only data/GMs6.rda |only data/GMs7.rda |only data/GMs8.rda |only man/AdaptiveRSPD.Rd | 2 +- man/DPMPD.Rd | 7 ++++++- man/GMs.Rd |only man/GeneratorMatrices.Rd | 6 +++--- man/InterleavedMaximinD.Rd | 4 ++-- man/InterleavedMinimaxD.Rd |only man/LRS.Rd |only man/LatticeDesign-package.Rd | 30 ++++++++++++++++++++---------- man/ProjSepD.Rd | 2 +- man/SlicedRSPD.Rd | 2 +- src/ProjSep.c | 4 ++-- src/init.c | 4 ++++ src/lrslib.c |only src/lrslib.h |only src/lrsmp.c |only src/lrsmp.h |only src/selectlss.c |only 29 files changed, 76 insertions(+), 40 deletions(-)
Title: Generalized Weighted Quantile Sum Regression
Description: Fits Weighted Quantile Sum (WQS) regressions for continuous, binomial, multinomial and count outcomes.
Author: Stefano Renzetti, Paul Curtin, Allan C Just, Ghalib Bello, Chris Gennings
Maintainer: Stefano Renzetti <stefano.renzetti88@gmail.com>
Diff between gWQS versions 3.0.0 dated 2020-06-23 and 3.0.1 dated 2020-11-19
DESCRIPTION | 8 - MD5 | 14 +- R/gwqs.R | 42 ++++--- R/wqs_helpers.R | 4 build/vignette.rds |binary inst/doc/gwqs-vignette.html | 253 +++++++++++++++++++++++++++++++++----------- man/main_functions.Rd | 6 - man/secondary_functions.Rd | 2 8 files changed, 236 insertions(+), 93 deletions(-)
Title: Algorithmic Fairness Metrics
Description: Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.
Author: Nikita Kozodoi [aut, cre],
Tibor V. Varga [aut] (<https://orcid.org/0000-0002-2383-699X>)
Maintainer: Nikita Kozodoi <n.kozodoi@icloud.com>
Diff between fairness versions 1.1.1 dated 2020-07-26 and 1.2.0 dated 2020-11-19
DESCRIPTION | 8 +++--- MD5 | 56 +++++++++++++++++++++--------------------- NEWS.md | 5 +++ R/acc_parity.R | 43 ++++++++++++++++++++++++-------- R/dem_parity.R | 55 +++++++++++++++++++++++++++++------------ R/equal_odds.R | 41 +++++++++++++++++++++++-------- R/fairness-package.R | 4 +-- R/fnr_parity.R | 39 ++++++++++++++++++++++------- R/fpr_parity.R | 37 ++++++++++++++++++++++------ R/mcc_parity.R | 39 ++++++++++++++++++++++------- R/npv_parity.R | 41 +++++++++++++++++++++++-------- R/pred_rate_parity.R | 39 ++++++++++++++++++++++------- R/prop_parity.R | 53 ++++++++++++++++++++++++++++------------ R/roc_parity.R | 63 +++++++++++++++++++++++++++++++----------------- R/spec_parity.R | 43 ++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/fairness.html | 40 ++++++++++++++++-------------- man/acc_parity.Rd | 7 +++-- man/dem_parity.Rd | 7 +++-- man/equal_odds.Rd | 7 +++-- man/fairness.Rd | 4 +-- man/fnr_parity.Rd | 7 +++-- man/fpr_parity.Rd | 7 +++-- man/mcc_parity.Rd | 7 +++-- man/npv_parity.Rd | 7 +++-- man/pred_rate_parity.Rd | 7 +++-- man/prop_parity.Rd | 7 +++-- man/roc_parity.Rd | 14 +++++++++- man/spec_parity.Rd | 7 +++-- 29 files changed, 488 insertions(+), 206 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut] (<https://orcid.org/0000-0002-7672-0712>)
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.12-1 dated 2020-07-29 and 2.12-2 dated 2020-11-19
DESCRIPTION | 16 +- MD5 | 32 ++-- NAMESPACE | 3 R/ensemble.chull.R | 32 ++-- R/ensemble.environmentalThin.R | 13 + R/ensemble.raster.R | 3 R/rankabuncomp.R | 20 ++ R/sites.long.R |only inst/ChangeLog | 48 ++++++ inst/etc/BiodiversityGUI.R | 313 ++++++++++++++++++++++++++++++++++++----- man/accumresult.Rd | 49 ++++++ man/ensemble.Rd | 1 man/ensemble.red.Rd | 2 man/ensemble.spatialThin.Rd | 4 man/faramea.Rd | 2 man/rankabundance.Rd | 66 ++++++++ man/renyiresult.Rd | 77 ++++++++++ man/sites.long.Rd |only 18 files changed, 600 insertions(+), 81 deletions(-)
Title: Basic Routing for Shiny Web Applications
Description: It is a simple router for your Shiny apps.
The router allows you to create dynamic web applications with real-time
User Interface and easily share url to pages within your Shiny apps.
Author: Filip Stachura [aut],
Dominik Krzemiński [cre, aut],
Krystian Igras [aut],
Appsilon [cph]
Maintainer: Dominik Krzemiński <dominik@appsilon.com>
Diff between shiny.router versions 0.1.1 dated 2018-09-18 and 0.2.0 dated 2020-11-19
shiny.router-0.1.1/shiny.router/README.md |only shiny.router-0.2.0/shiny.router/DESCRIPTION | 35 + shiny.router-0.2.0/shiny.router/MD5 | 51 +- shiny.router-0.2.0/shiny.router/NAMESPACE | 5 shiny.router-0.2.0/shiny.router/R/pages.R | 48 ++ shiny.router-0.2.0/shiny.router/R/paths.R | 43 +- shiny.router-0.2.0/shiny.router/R/router.R | 179 ++++++---- shiny.router-0.2.0/shiny.router/R/zzz.R |only shiny.router-0.2.0/shiny.router/inst/www/shiny.router.css |only shiny.router-0.2.0/shiny.router/inst/www/shiny.router.js | 15 shiny.router-0.2.0/shiny.router/man/PAGE_404_ROUTE.Rd | 4 shiny.router-0.2.0/shiny.router/man/attach_attribs.Rd |only shiny.router-0.2.0/shiny.router/man/callback_mapping.Rd | 13 shiny.router-0.2.0/shiny.router/man/change_page.Rd | 3 shiny.router-0.2.0/shiny.router/man/cleanup_hashpath.Rd | 3 shiny.router-0.2.0/shiny.router/man/disable_bootstrap_on_bookmark.Rd |only shiny.router-0.2.0/shiny.router/man/figures |only shiny.router-0.2.0/shiny.router/man/get_page.Rd | 8 shiny.router-0.2.0/shiny.router/man/get_query_param.Rd | 3 shiny.router-0.2.0/shiny.router/man/get_url_hash.Rd |only shiny.router-0.2.0/shiny.router/man/grapes-colon-colon-colon-grapes.Rd |only shiny.router-0.2.0/shiny.router/man/make_router.Rd | 14 shiny.router-0.2.0/shiny.router/man/page404.Rd | 6 shiny.router-0.2.0/shiny.router/man/parse_url_path.Rd | 6 shiny.router-0.2.0/shiny.router/man/route.Rd | 2 shiny.router-0.2.0/shiny.router/man/route_link.Rd | 4 shiny.router-0.2.0/shiny.router/man/router_server.Rd |only shiny.router-0.2.0/shiny.router/man/router_ui.Rd | 23 - shiny.router-0.2.0/shiny.router/tests/testthat/test-pages.R | 13 shiny.router-0.2.0/shiny.router/tests/testthat/test-paths.R | 33 + shiny.router-0.2.0/shiny.router/tests/testthat/test-router.R | 70 +++ 31 files changed, 410 insertions(+), 171 deletions(-)
Title: Import Air Quality Monitoring Data in a Fast and Easy Way
Description: A collection of tools to access prepared air quality monitoring
data files from web servers with ease and speed. Air quality data are
sourced from open and publicly accessible repositories and can be found in
these locations:
<https://www.eea.europa.eu/data-and-maps/data/airbase-the-european-air-quality-database-8>
and <https://discomap.eea.europa.eu/map/fme/AirQualityExport.htm>. The web
server space has been provided by Ricardo Energy & Environment.
Author: Stuart K. Grange [cre, aut] (<https://orcid.org/0000-0003-4093-3596>)
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>
Diff between saqgetr versions 0.2.0 dated 2020-06-03 and 0.2.1 dated 2020-11-19
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 4 ++++ R/get_saq_observations.R | 13 +++++-------- R/str_date_formatted.R | 2 +- man/get_saq_observations.Rd | 2 +- 6 files changed, 22 insertions(+), 21 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient greedy search procedure to obtain a clustering estimate based on a partition loss function. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. SALSO was first presented at the workshop "Bayesian Nonparametric Inference: Dependence Structures and their Applications" in Oaxaca, Mexico on December 6, 2017. See <https://www.birs.ca/events/2017/5-day-workshops/17w5060/schedule>.
Author: David B. Dahl [aut, cre],
Devin J. Johnson [aut],
Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.2.3 dated 2020-11-09 and 0.2.5 dated 2020-11-19
DESCRIPTION | 8 - INSTALL | 2 MD5 | 16 +-- NEWS | 4 R/salso.R | 27 +++-- man/salso.Rd | 13 +- src/rustlib/Cargo.lock | 224 ++++++++++++++++++++++++------------------------- src/rustlib/Cargo.toml | 2 tools/staticlib.R | 2 9 files changed, 153 insertions(+), 145 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.12.0 dated 2020-11-12 and 1.12.1 dated 2020-11-19
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.26.0 dated 2020-09-07 and 0.28.0 dated 2020-11-19
estimatr-0.26.0/estimatr/tests/testthat/test-zzz.R |only estimatr-0.28.0/estimatr/DESCRIPTION | 8 ++++---- estimatr-0.28.0/estimatr/MD5 | 5 ++--- estimatr-0.28.0/estimatr/NEWS.md | 4 ++++ 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Kernel Density Estimation using Lifetime Distributions
Description: A collection of asymmetrical kernels belong to lifetime distributions for kernel density estimation is presented.
Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull.
For details see Chen (2000a, b), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between DELTD versions 2.6.5 dated 2019-12-13 and 2.6.6 dated 2020-11-19
DELTD-2.6.5/DELTD/man/LN.Rd |only DELTD-2.6.5/DELTD/man/dencomb.Rd |only DELTD-2.6.5/DELTD/man/mseBS.Rd |only DELTD-2.6.5/DELTD/man/mseEr.Rd |only DELTD-2.6.5/DELTD/man/mseGamma.Rd |only DELTD-2.6.5/DELTD/man/mseLN.Rd |only DELTD-2.6.5/DELTD/man/plot.LN.Rd |only DELTD-2.6.6/DELTD/DESCRIPTION | 8 DELTD-2.6.6/DELTD/MD5 | 32 - DELTD-2.6.6/DELTD/NAMESPACE | 12 DELTD-2.6.6/DELTD/R/DELTD.R | 957 ++++++++++++++++----------------- DELTD-2.6.6/DELTD/man/BS.Rd | 62 +- DELTD-2.6.6/DELTD/man/Beta.Rd |only DELTD-2.6.6/DELTD/man/DELTD-package.Rd | 29 - DELTD-2.6.6/DELTD/man/Erlang.Rd | 57 + DELTD-2.6.6/DELTD/man/Gamma.Rd | 58 +- DELTD-2.6.6/DELTD/man/LogN.Rd |only DELTD-2.6.6/DELTD/man/mse.Rd |only DELTD-2.6.6/DELTD/man/plot.BS.Rd | 28 DELTD-2.6.6/DELTD/man/plot.Beta.Rd |only DELTD-2.6.6/DELTD/man/plot.Erlang.Rd | 26 DELTD-2.6.6/DELTD/man/plot.Gamma.Rd | 26 DELTD-2.6.6/DELTD/man/plot.LogN.Rd |only 23 files changed, 730 insertions(+), 565 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines. The description of the corresponding approach
could be found at Gagin and Levin (2014) <DOI:10.1107/S1600576714023796>.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between BBEST versions 0.1-7 dated 2020-10-26 and 0.1-8 dated 2020-11-19
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/guide.R | 4 ++-- R/interface.R | 7 ++++--- man/set.sigma.Rd | 2 +- 7 files changed, 27 insertions(+), 16 deletions(-)
Title: Annotated Data
Description: An R wrapper for the Python package 'anndata'.
Provides a scalable way of keeping track of data and learned
annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [aut] (<https://orcid.org/0000-0002-0369-2888>,
flying-sheep),
Alex Wolf [aut] (<https://orcid.org/0000-0002-8760-7838>, falexwolf),
Isaac Virshup [aut] (ivirshup),
Sergei Rybakov [aut] (Koncopd),
Robrecht Cannoodt [aut, ctb, cre, cph]
(<https://orcid.org/0000-0003-3641-729X>, rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between anndata versions 0.7.4 dated 2020-11-04 and 0.7.5 dated 2020-11-19
DESCRIPTION | 8 MD5 | 46 +- NAMESPACE | 3 NEWS.md |only R/AnnData.R | 617 +++++++++++++++++++++++--------------- R/concat.R | 6 R/install_anndata.R | 2 R/package.R | 3 R/read_csv.R | 8 R/read_excel.R | 8 R/read_h5ad.R | 8 R/read_hdf.R | 8 R/read_loom.R | 8 R/read_mtx.R | 8 R/read_text.R | 8 R/read_umi_tools.R | 8 R/reticulate_conversions.R | 46 +- README.md | 18 - man/AnnData.Rd | 42 ++ man/AnnDataHelpers.Rd | 3 man/all.equal.AnnDataR6.Rd |only man/anndata-package.Rd | 3 man/r-py-conversion.Rd | 3 tests/testthat/helper-gen_adata.R |only tests/testthat/test-anndata.R | 37 +- tests/testthat/test-base.R |only 26 files changed, 549 insertions(+), 352 deletions(-)
More information about EvidenceSynthesis at CRAN
Permanent link
More information about PortalHacienda at CRAN
Permanent link
Title: Obfuscation Game Designs
Description: When people make decisions, they may do so using a wide variety of decision rules. The package allows users to easily create obfuscation games to test the obfuscation hypothesis. It provides an easy to use interface and multiple options designed to vary the difficulty of the game and tailor it to the user's needs. For more detail: Chorus et al., 2021, Obfuscation maximization-based decision-making: Theory, methodology and first empirical evidence, Mathematical Social Sciences, 109, 28-44.
Author: Erlend Dancke Sandorf [aut, cre],
Caspar Chorus [aut],
Sander van Cranenburgh [aut]
Maintainer: Erlend Dancke Sandorf <erlend.dancke.sandorf@nmbu.no>
Diff between obfuscatoR versions 0.2.0 dated 2019-08-01 and 0.2.1 dated 2020-11-19
DESCRIPTION | 24 MD5 | 87 - NAMESPACE | 24 NEWS.md | 20 R/calc_entropy.R | 354 ++--- R/calc_payouts.R | 264 ++-- R/check_design_opt.R | 98 - R/construct_ra_mat.R | 270 ++-- R/extract_attr.R | 62 - R/generate_designs.R | 88 - R/misc.R | 36 R/obfuscatoR.R | 28 R/on_attach.R | 69 - R/print_methods.R | 318 ++--- R/save_design.R | 100 - build/vignette.rds |binary inst/CITATION |only inst/doc/vignette-obfuscatoR.R | 237 +--- inst/doc/vignette-obfuscatoR.Rmd | 706 +++++------ inst/doc/vignette-obfuscatoR.html | 1893 ++++++++++++++++---------------- man/calc_entropy.Rd | 62 - man/calc_payout_dm.Rd | 50 man/calc_payout_obs.Rd | 48 man/calc_pr_aj_rk.Rd | 40 man/calc_pr_guess.Rd | 52 man/calc_pr_rk_aj.Rd | 50 man/calculate_entropy.Rd | 82 - man/calculate_payouts.Rd | 75 - man/check_design_opt.Rd | 84 - man/construct_design.Rd | 46 man/dot-onAttach.Rd | 38 man/extract_attr.Rd | 62 - man/generate_designs.Rd | 58 man/last.Rd | 44 man/obfuscatoR.Rd | 27 man/print_design.Rd | 62 - man/print_entropy.Rd | 68 - man/print_payout.Rd | 38 man/save_design.Rd | 46 tests/testthat.R | 8 tests/testthat/test_calc_entropy.R | 30 tests/testthat/test_calculate_entropy.R | 94 - tests/testthat/test_payouts.R | 86 - vignettes/ref.bib | 37 vignettes/vignette-obfuscatoR.Rmd | 706 +++++------ 45 files changed, 3331 insertions(+), 3340 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-08 0.5.3
2016-03-23 0.5.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-09 1.0.3
2020-11-06 1.0.2
2020-11-05 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-05 1.1.1
2020-11-04 1.1.0
2020-10-30 1.0.1
2020-10-30 1.0.2
2020-10-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-15 0.9.2-1