Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre],
Daniel Graeber [aut, ctb],
Stefan Preiner [ctb],
Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>
Diff between staRdom versions 1.1.11 dated 2020-04-23 and 1.1.14 dated 2020-07-28
DESCRIPTION | 20 MD5 | 22 - R/absorption_functions.R | 2 R/correction_functions.R | 2 R/parafac_functions.R | 69 ++- inst/doc/Basic_analysis_of_DOM_samples.html | 516 ++++++++++++------------ inst/doc/PARAFAC_analysis_of_EEM.html | 588 +++++++++++++++------------- man/A_missing.Rd | 2 man/eem2array.Rd | 2 man/eem_parafac.Rd | 5 man/parafac_conv.Rd | 19 man/splithalf.Rd | 5 12 files changed, 700 insertions(+), 552 deletions(-)
Title: Generate and Test for Prime Numbers
Description: Functions for dealing with prime numbers, such as testing whether a
number is prime and generating a sequence prime numbers. Additional functions
include finding prime factors and Ruth-Aaron pairs, finding next and previous
prime numbers in the series, finding or estimating the nth prime, estimating
the number of primes less than or equal to an arbitrary number, computing
primorials, and prime k-tuples (e.g., twin primes).
Author: Os Keyes [aut, cre],
Paul Egeler [aut] (<https://orcid.org/0000-0001-6948-9498>)
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between primes versions 0.2.0 dated 2020-07-26 and 1.0.0 dated 2020-07-28
primes-0.2.0/primes/R/primes.R |only primes-0.2.0/primes/src/primorial.cpp |only primes-0.2.0/primes/tests/testthat/test_primality.R |only primes-1.0.0/primes/DESCRIPTION | 24 +++-- primes-1.0.0/primes/MD5 | 53 ++++++++----- primes-1.0.0/primes/NAMESPACE | 4 primes-1.0.0/primes/R/RcppExports.R | 45 ++++++++--- primes-1.0.0/primes/R/data.R |only primes-1.0.0/primes/R/prime_count.R |only primes-1.0.0/primes/R/primes-package.R |only primes-1.0.0/primes/R/primorial.R | 23 ++++- primes-1.0.0/primes/R/ruth_aaron_pairs.R | 6 - primes-1.0.0/primes/R/sieve.R | 7 + primes-1.0.0/primes/README.md | 17 +++- primes-1.0.0/primes/data |only primes-1.0.0/primes/man/generate_primes.Rd | 15 ++- primes-1.0.0/primes/man/nth_prime.Rd |only primes-1.0.0/primes/man/prime_count.Rd |only primes-1.0.0/primes/man/primes.Rd | 20 +++- primes-1.0.0/primes/man/primorial.Rd | 10 -- primes-1.0.0/primes/man/ruth_aaron_pairs.Rd | 6 - primes-1.0.0/primes/src/RcppExports.cpp | 57 ++++++++------ primes-1.0.0/primes/src/generate_n_primes.cpp |only primes-1.0.0/primes/src/is_prime.cpp | 2 primes-1.0.0/primes/src/nth_prime.cpp |only primes-1.0.0/primes/src/prime_count.cpp | 17 +++- primes-1.0.0/primes/src/prime_factors.cpp | 3 primes-1.0.0/primes/src/primes.h | 5 - primes-1.0.0/primes/src/sieve.cpp | 2 primes-1.0.0/primes/tests/testthat/test_generate_primes.R |only primes-1.0.0/primes/tests/testthat/test_is_prime.R |only primes-1.0.0/primes/tests/testthat/test_k_tuple.R |only primes-1.0.0/primes/tests/testthat/test_next_prime.R |only primes-1.0.0/primes/tests/testthat/test_nth_prime.R |only primes-1.0.0/primes/tests/testthat/test_prime_count.R |only primes-1.0.0/primes/tests/testthat/test_prime_factors.R |only primes-1.0.0/primes/tests/testthat/test_primorial.R |only 37 files changed, 213 insertions(+), 103 deletions(-)
Title: Estimate Phenological Metrics using Presence-Only Data
Description: Generates Weibull-parameterized estimates of phenology for any percentile of
a distribution using the framework established in Cooke (1979)
<doi:10.1093/biomet/66.2.367>. Extensive testing against other
estimators suggest the weib_percentile() function is especially useful in
generating more accurate and less biased estimates of onset and offset
(Belitz et al. 2020 <doi.org:10.1111/2041-210X.13448>. Non-parametric
bootstrapping can be used to generate confidence intervals around those
estimates, although this is computationally expensive. Additionally, this
package offers an easy way to perform non-parametric bootstrapping to
generate confidence intervals for quantile estimates, mean estimates,
or any statistical function of interest.
Author: Michael Belitz [aut, cre] (<https://orcid.org/0000-0002-8162-5998>),
Caitlin Campbell [ctb] (<https://orcid.org/0000-0002-8199-7775>),
Daijiang Li [ctb] (<https://orcid.org/0000-0002-0925-3421>)
Maintainer: Michael Belitz <mbelitz@ufl.edu>
Diff between phenesse versions 0.1.1 dated 2020-03-28 and 0.1.2 dated 2020-07-28
DESCRIPTION | 32 +++---- MD5 | 37 ++++---- NEWS.md | 13 +- R/mean_ci.R | 2 R/quantile_ci.R | 3 R/utils.R | 6 - R/weib_percentile.R | 181 ++++++++++++++++++++-------------------- R/weib_percentile_ci.R | 9 + README.md | 24 +++-- build/vignette.rds |binary inst/CITATION |only inst/doc/phenesse_vignette.R | 38 +++++--- inst/doc/phenesse_vignette.Rmd | 60 ++++++++----- inst/doc/phenesse_vignette.html | 134 +++++++++++++++++------------ man/estimate_ci.Rd | 8 - man/mean_ci.Rd | 2 man/quantile_ci.Rd | 3 man/weib_percentile.Rd | 8 - man/weib_percentile_ci.Rd | 155 +++++++++++++++++----------------- vignettes/phenesse_vignette.Rmd | 60 ++++++++----- 20 files changed, 440 insertions(+), 335 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean, see Pretis, Reade and Sucarrat (2018) <doi:10.18637/jss.v086.i03>.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut], Jonas Kurle [ctb], Moritz Schwarz [ctb]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.23 dated 2020-05-04 and 0.24 dated 2020-07-28
DESCRIPTION | 12 MD5 | 87 +++-- NAMESPACE | 28 - NEWS | 58 +++ R/arx.R | 431 ++++++++------------------- R/as.lm.R |only R/blocksFun.R |only R/coef.arx.R | 13 R/coef.gets.R | 3 R/diagnostics.R | 18 - R/dropvar.R | 2 R/eviews.R | 16 - R/gets-internal.R | 2 R/gets.arx.R |only R/getsFun.R | 210 ++++++++----- R/getsm.R | 710 +++++++++------------------------------------- R/getsv.R | 133 ++++---- R/isat.R | 14 R/ols.R | 75 ++++ R/paths.R | 2 R/plot.isat.R | 6 R/print.arx.R | 50 +-- R/print.gets.R | 151 ++++----- R/print.isat.R | 70 ++-- R/printtex.R | 40 +- R/regressorsMean.R | 37 +- R/regressorsVariance.R |only R/stata.R | 16 - R/terminals.R | 2 R/vcov.arx.R | 4 data/hpdata.rda |binary data/infldata.rda |binary data/so2data.rda |binary data/sp500data.rda |binary man/arx.Rd | 12 man/as.lm.Rd |only man/blocksFun.Rd |only man/coef.arx.Rd | 9 man/coef.gets.Rd | 10 man/diagnostics.Rd | 10 man/gets-package.Rd | 36 +- man/gets.Rd | 17 + man/getsFun.Rd | 79 ++--- man/getsm.Rd | 64 ++-- man/isat.Rd | 3 man/ols.Rd | 11 man/regressorsMean.Rd | 18 - man/regressorsVariance.Rd |only 48 files changed, 1082 insertions(+), 1377 deletions(-)
Title: Extension for 'DALEX' Package
Description: Provides wrapper of various machine learning models.
In applied machine learning, there
is a strong belief that we need to strike a balance
between interpretability and accuracy.
However, in field of the interpretable machine learning,
there are more and more new ideas for explaining black-box models,
that are implemented in 'R'.
'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models
including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library.
Important part of the package is Champion-Challenger analysis and innovative approach
to model performance across subsets of test data presented in Funnel Plot.
Third branch of 'DALEXtra' package is aspect importance analysis
that provides instance-level explanations for the groups of explanatory variables.
Author: Szymon Maksymiuk [aut, cre] (<https://orcid.org/0000-0002-3120-1601>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Katarzyna Pekala [aut],
Anna Kozak [ctb],
Hubert Baniecki [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between DALEXtra versions 1.3.1 dated 2020-07-16 and 1.3.2 dated 2020-07-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ tests/testthat/objects_for_tests.R | 5 +++++ tests/testthat/test_champion_challenger.R | 7 +++++-- tests/testthat/test_h2o_explain.R | 2 +- 6 files changed, 23 insertions(+), 11 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.17 dated 2020-05-26 and 0.18 dated 2020-07-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 10 ++++++++++ R/static.R | 4 ++-- R/utils.R | 2 +- README.md | 2 +- 6 files changed, 23 insertions(+), 13 deletions(-)
Title: Queries and Extracts Images from Extensible Neuroimaging Archive
Toolkit Public/Private Datasets
Description: Allows communication with Extensible Neuroimaging Archive Toolkit <https://www.xnat.org>.
'Rxnat' is using the 'XNAT' REST API to perform data queries and download images.
Author: Adi Gherman [aut, cre]
Maintainer: Adi Gherman <adig@jhu.edu>
Diff between Rxnat versions 1.0.8 dated 2020-04-17 and 1.0.12 dated 2020-07-28
DESCRIPTION | 10 +- MD5 | 21 +++-- NAMESPACE | 1 R/xnat_api.R | 15 +++- README.md | 10 ++ build/vignette.rds |binary inst/doc/rxnat.R | 2 inst/doc/rxnat.Rmd | 2 inst/doc/rxnat.html | 171 +++++++++++++++++++++++------------------------ man/download_xnat_dir.Rd | 6 + vignettes/refs.bib |only vignettes/rxnat.Rmd | 2 12 files changed, 135 insertions(+), 105 deletions(-)
Title: Historical Retail Data from the 'Trundler' API
Description: A wrapper around the 'Trundler' API, which gives
access to historical retail product and pricing data, and can be found
at <https://api.trundler.dev/>.
Author: Andrew B. Collier [aut, cre],
Megan Beckett [aut, pbl]
Maintainer: Andrew B. Collier <andrew@exegetic.biz>
Diff between trundler versions 0.1.17 dated 2020-07-20 and 0.1.19 dated 2020-07-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/http.R | 12 ++++++++++-- R/paginate.R | 14 ++++++++++++++ R/product.R | 4 ++-- R/retailer.R | 2 +- R/taxonomy.R | 2 +- R/trundler.R | 1 + tests/testthat/test-1-retail.R | 2 +- 10 files changed, 50 insertions(+), 26 deletions(-)
Title: Add Loading Animations to a 'shiny' Output While It's
Recalculating
Description: When a 'Shiny' output (such as a plot, table, map, etc.) is recalculating, it remains
visible but gets greyed out. Using 'shinycssloaders', you can add a loading animation ("spinner")
to outputs instead. By wrapping a 'Shiny' output in 'withSpinner()', a spinner will automatically
appear while the output is recalculating. See the demo online at
<https://daattali.com/shiny/shinycssloaders-demo/>.
Author: Andras Sali [aut] (Original creator of shinycssloaders package),
Luke Hass [ctb, cph] (Author of included CSS loader code),
Dean Attali [aut, cre] (Maintainer of shinycssloaders since 2019)
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinycssloaders versions 0.3 dated 2020-01-16 and 1.0.0 dated 2020-07-28
shinycssloaders-0.3/shinycssloaders/inst/css-loaders |only shinycssloaders-0.3/shinycssloaders/inst/examples/app.R |only shinycssloaders-0.3/shinycssloaders/inst/examples/base_table |only shinycssloaders-0.3/shinycssloaders/inst/examples/plotly |only shinycssloaders-0.3/shinycssloaders/inst/examples/table |only shinycssloaders-1.0.0/shinycssloaders/DESCRIPTION | 29 - shinycssloaders-1.0.0/shinycssloaders/LICENSE |only shinycssloaders-1.0.0/shinycssloaders/MD5 | 74 +- shinycssloaders-1.0.0/shinycssloaders/NEWS.md | 22 shinycssloaders-1.0.0/shinycssloaders/R/globals.R | 3 shinycssloaders-1.0.0/shinycssloaders/R/shinycssloaders-package.r | 10 shinycssloaders-1.0.0/shinycssloaders/R/withSpinner.R | 257 +++++----- shinycssloaders-1.0.0/shinycssloaders/README.md | 100 ++- shinycssloaders-1.0.0/shinycssloaders/inst/assets/css-loaders.css |only shinycssloaders-1.0.0/shinycssloaders/inst/assets/spinner.css | 4 shinycssloaders-1.0.0/shinycssloaders/inst/assets/spinner.js | 54 +- shinycssloaders-1.0.0/shinycssloaders/inst/examples/demo |only shinycssloaders-1.0.0/shinycssloaders/inst/img |only shinycssloaders-1.0.0/shinycssloaders/inst/loaders-templates |only shinycssloaders-1.0.0/shinycssloaders/man/shinycssloaders.Rd | 13 shinycssloaders-1.0.0/shinycssloaders/man/withSpinner.Rd | 64 ++ 21 files changed, 370 insertions(+), 260 deletions(-)
More information about shinycssloaders at CRAN
Permanent link
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.2.1 dated 2018-11-10 and 0.2.2 dated 2020-07-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/utilities.R | 4 ++-- build/vignette.rds |binary inst/NEWS.Rd | 10 ++++++++++ inst/doc/jss2542.pdf |binary 6 files changed, 20 insertions(+), 10 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] (<https://orcid.org/0000-0003-4092-8228>),
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] (<https://orcid.org/0000-0003-0532-4824>),
Ken Andersen [aut, cph] (<https://orcid.org/0000-0002-8478-3430>),
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.0.2 dated 2020-06-08 and 2.0.3 dated 2020-07-28
mizer-2.0.2/mizer/R/help.R |only mizer-2.0.2/mizer/man/mizer.Rd |only mizer-2.0.3/mizer/DESCRIPTION | 10 mizer-2.0.3/mizer/MD5 | 162 +-- mizer-2.0.3/mizer/NEWS.md | 22 mizer-2.0.3/mizer/R/MizerParams-class.R | 15 mizer-2.0.3/mizer/R/MizerSim-class.R | 4 mizer-2.0.3/mizer/R/extension.R | 3 mizer-2.0.3/mizer/R/mizer-package.R |only mizer-2.0.3/mizer/R/plots.R | 22 mizer-2.0.3/mizer/R/pred_kernel_funcs.R | 1 mizer-2.0.3/mizer/R/project.R | 25 mizer-2.0.3/mizer/R/project_methods.R | 359 ++++++-- mizer-2.0.3/mizer/R/rate_functions.R | 416 +++------- mizer-2.0.3/mizer/R/setFishing.R | 58 + mizer-2.0.3/mizer/R/species_params.R | 31 mizer-2.0.3/mizer/R/summary_methods.R | 4 mizer-2.0.3/mizer/R/upgrade.R | 8 mizer-2.0.3/mizer/R/wrapper_functions.R | 2 mizer-2.0.3/mizer/README.md | 133 ++- mizer-2.0.3/mizer/inst/shiny/selectivity_effects/app.R | 10 mizer-2.0.3/mizer/inst/shiny/selectivity_effects/hake_mullet.RDS |binary mizer-2.0.3/mizer/inst/shiny/selectivity_effects/rsconnect |only mizer-2.0.3/mizer/man/getEGrowth.Rd | 34 mizer-2.0.3/mizer/man/getERepro.Rd | 25 mizer-2.0.3/mizer/man/getEReproAndGrowth.Rd | 37 mizer-2.0.3/mizer/man/getESpawning.Rd | 25 mizer-2.0.3/mizer/man/getEncounter.Rd | 31 mizer-2.0.3/mizer/man/getFMort.Rd | 14 mizer-2.0.3/mizer/man/getFMortGear.Rd | 17 mizer-2.0.3/mizer/man/getFeedingLevel.Rd | 40 mizer-2.0.3/mizer/man/getM2.Rd | 33 mizer-2.0.3/mizer/man/getM2Background.Rd | 29 mizer-2.0.3/mizer/man/getMort.Rd | 37 mizer-2.0.3/mizer/man/getPredMort.Rd | 33 mizer-2.0.3/mizer/man/getPredRate.Rd | 29 mizer-2.0.3/mizer/man/getRDD.Rd | 9 mizer-2.0.3/mizer/man/getRDI.Rd | 13 mizer-2.0.3/mizer/man/getResourceMort.Rd | 29 mizer-2.0.3/mizer/man/getZ.Rd | 37 mizer-2.0.3/mizer/man/get_time_elements.Rd | 12 mizer-2.0.3/mizer/man/idxFinalT.Rd | 4 mizer-2.0.3/mizer/man/indicator_functions.Rd | 2 mizer-2.0.3/mizer/man/mizer-package.Rd |only mizer-2.0.3/mizer/man/mizerEGrowth.Rd | 31 mizer-2.0.3/mizer/man/mizerERepro.Rd | 25 mizer-2.0.3/mizer/man/mizerEReproAndGrowth.Rd | 39 mizer-2.0.3/mizer/man/mizerEncounter.Rd | 30 mizer-2.0.3/mizer/man/mizerFMort.Rd | 17 mizer-2.0.3/mizer/man/mizerFMortGear.Rd | 6 mizer-2.0.3/mizer/man/mizerFeedingLevel.Rd | 33 mizer-2.0.3/mizer/man/mizerMort.Rd | 33 mizer-2.0.3/mizer/man/mizerPredMort.Rd | 23 mizer-2.0.3/mizer/man/mizerPredRate.Rd | 30 mizer-2.0.3/mizer/man/mizerRDI.Rd | 31 mizer-2.0.3/mizer/man/mizerRates.Rd | 8 mizer-2.0.3/mizer/man/mizerResourceMort.Rd | 24 mizer-2.0.3/mizer/man/newMultispeciesParams.Rd | 4 mizer-2.0.3/mizer/man/newTraitParams.Rd | 2 mizer-2.0.3/mizer/man/plotBiomass.Rd | 2 mizer-2.0.3/mizer/man/plotFMort.Rd | 2 mizer-2.0.3/mizer/man/plotFeedingLevel.Rd | 2 mizer-2.0.3/mizer/man/plotGrowthCurves.Rd | 2 mizer-2.0.3/mizer/man/plotM2.Rd | 2 mizer-2.0.3/mizer/man/plotMizerSim.Rd | 4 mizer-2.0.3/mizer/man/plotPredMort.Rd | 2 mizer-2.0.3/mizer/man/plotSpectra.Rd | 2 mizer-2.0.3/mizer/man/plotYield.Rd | 2 mizer-2.0.3/mizer/man/plotYieldGear.Rd | 2 mizer-2.0.3/mizer/man/plotting_functions.Rd | 2 mizer-2.0.3/mizer/man/project.Rd | 6 mizer-2.0.3/mizer/man/reexports.Rd | 2 mizer-2.0.3/mizer/man/setFishing.Rd | 4 mizer-2.0.3/mizer/man/setParams.Rd | 4 mizer-2.0.3/mizer/man/setRateFunction.Rd | 4 mizer-2.0.3/mizer/man/summary_functions.Rd | 2 mizer-2.0.3/mizer/man/validGearParams.Rd | 21 mizer-2.0.3/mizer/man/validSpeciesParams.Rd | 23 mizer-2.0.3/mizer/man/w.Rd | 20 mizer-2.0.3/mizer/tests/testthat/Rplots.pdf |binary mizer-2.0.3/mizer/tests/testthat/test-extension.R | 21 mizer-2.0.3/mizer/tests/testthat/test-project_methods.R | 29 mizer-2.0.3/mizer/tests/testthat/test-setFishing.R | 6 mizer-2.0.3/mizer/tests/testthat/test-summary_methods.R | 31 84 files changed, 1478 insertions(+), 830 deletions(-)
Title: Imputation for Proteomics
Description: Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Author: Quentin Giai Gianetto
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between imp4p versions 0.9 dated 2020-04-15 and 1.0 dated 2020-07-28
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/impute_mi.R | 2 +- R/impute_slsa.R | 37 +++++++++++++++++++++++++++---------- R/mi_mix.R | 1 + R/sim_data.R | 2 +- man/fast_sim.Rd | 2 +- man/imp4p-package.Rd | 12 ++++++++---- man/impute_mi.Rd | 10 +++++----- man/impute_mix.Rd | 10 +++++----- man/impute_slsa.Rd | 2 +- man/sim_data.Rd | 2 +- src/fast_apply_nb_na.cpp | 24 ++++++++++++------------ src/fast_apply_nb_not_na.cpp | 24 ++++++++++++------------ src/fast_apply_sd_na_rm_T.cpp | 24 ++++++++++++------------ src/fast_apply_sum_na_rm_T.cpp | 24 ++++++++++++------------ src/fast_sim.cpp | 19 ++++++++++++++++++- 17 files changed, 136 insertions(+), 97 deletions(-)
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with
'mlr3', e.g. Grid Search, Random Search, or Simulated Annealing.
Various termination criteria can be set and combined. The class
'AutoTuner' provides a convenient way to perform nested resampling in
combination with 'mlr3'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Daniel Schalk [aut] (<https://orcid.org/0000-0003-0950-1947>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.1.2 dated 2020-01-31 and 0.2.0 dated 2020-07-28
mlr3tuning-0.1.2/mlr3tuning/R/Terminator.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorClockTime.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorCombo.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorEvals.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorModelTime.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorNone.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorPerfReached.R |only mlr3tuning-0.1.2/mlr3tuning/R/TerminatorStagnation.R |only mlr3tuning-0.1.2/mlr3tuning/R/TuningInstance.R |only mlr3tuning-0.1.2/mlr3tuning/R/mlr_terminators.R |only mlr3tuning-0.1.2/mlr3tuning/man/Terminator.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/TuningInstance.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_clock_time.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_combo.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_evals.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_model_time.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_none.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_perf_reached.Rd |only mlr3tuning-0.1.2/mlr3tuning/man/mlr_terminators_stagnation.Rd |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorClockTime.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorCombo.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorEvals.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorModelTime.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorNone.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorPerfReached.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TerminatorStagnation.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_TuningInstance.R |only mlr3tuning-0.1.2/mlr3tuning/tests/testthat/test_mlr_terminators.R |only mlr3tuning-0.2.0/mlr3tuning/DESCRIPTION | 41 - mlr3tuning-0.2.0/mlr3tuning/MD5 | 118 ++-- mlr3tuning-0.2.0/mlr3tuning/NAMESPACE | 18 mlr3tuning-0.2.0/mlr3tuning/NEWS.md | 10 mlr3tuning-0.2.0/mlr3tuning/R/AutoTuner.R | 237 +++++---- mlr3tuning-0.2.0/mlr3tuning/R/ObjectiveTuning.R |only mlr3tuning-0.2.0/mlr3tuning/R/Tuner.R | 230 ++++----- mlr3tuning-0.2.0/mlr3tuning/R/TunerDesignPoints.R | 83 +-- mlr3tuning-0.2.0/mlr3tuning/R/TunerFromOptimizer.R |only mlr3tuning-0.2.0/mlr3tuning/R/TunerGenSA.R | 62 -- mlr3tuning-0.2.0/mlr3tuning/R/TunerGridSearch.R | 66 -- mlr3tuning-0.2.0/mlr3tuning/R/TunerNLoptr.R |only mlr3tuning-0.2.0/mlr3tuning/R/TunerRandomSearch.R | 53 -- mlr3tuning-0.2.0/mlr3tuning/R/TuningInstanceMulticrit.R |only mlr3tuning-0.2.0/mlr3tuning/R/TuningInstanceSingleCrit.R |only mlr3tuning-0.2.0/mlr3tuning/R/assertions.R | 9 mlr3tuning-0.2.0/mlr3tuning/R/helper.R | 18 mlr3tuning-0.2.0/mlr3tuning/R/mlr_tuners.R | 8 mlr3tuning-0.2.0/mlr3tuning/R/reexport.R |only mlr3tuning-0.2.0/mlr3tuning/R/sugar.R | 13 mlr3tuning-0.2.0/mlr3tuning/R/zzz.R | 4 mlr3tuning-0.2.0/mlr3tuning/README.md | 60 ++ mlr3tuning-0.2.0/mlr3tuning/build |only mlr3tuning-0.2.0/mlr3tuning/man/AutoTuner.Rd | 217 ++++++-- mlr3tuning-0.2.0/mlr3tuning/man/ObjectiveTuning.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/Tuner.Rd | 254 ++++++---- mlr3tuning-0.2.0/mlr3tuning/man/TunerFromOptimizer.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/TuningInstanceMultiCrit.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/TuningInstanceSingleCrit.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/mlr3tuning-package.Rd | 1 mlr3tuning-0.2.0/mlr3tuning/man/mlr_terminators.Rd | 38 - mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners.Rd | 20 mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners_design_points.Rd | 127 ++++- mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners_gensa.Rd | 122 +++- mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners_grid_search.Rd | 135 ++++- mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners_nloptr.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/mlr_tuners_random_search.Rd | 138 ++++- mlr3tuning-0.2.0/mlr3tuning/man/tnr.Rd | 23 mlr3tuning-0.2.0/mlr3tuning/man/trm.Rd |only mlr3tuning-0.2.0/mlr3tuning/man/trms.Rd |only mlr3tuning-0.2.0/mlr3tuning/tests/testthat/helper.R | 124 +++- mlr3tuning-0.2.0/mlr3tuning/tests/testthat/setup.R | 9 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/teardown.R | 3 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_AutoTuner.R | 125 +++- mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_ObjectiveTuning.R |only mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_Tuner.R | 132 ++++- mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TunerDesignPoints.R | 4 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TunerGenSA.R | 25 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TunerGridSearch.R | 10 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TunerNLoptr.R |only mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TuningInstanceMultiCrit.R |only mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_TuningInstanceSingleCrit.R |only mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_error_handling.R | 33 - mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_mlr_tuners.R | 5 mlr3tuning-0.2.0/mlr3tuning/tests/testthat/test_trafos.R | 34 - 83 files changed, 1638 insertions(+), 971 deletions(-)
Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data.
Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU),
and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters
can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized
in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>,
Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>,
Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>,
Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and
Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanovic [aut, cre]
Maintainer: Mladen Jovanovic <coach.mladen.jovanovic@gmail.com>
Diff between shorts versions 1.0.1 dated 2020-05-08 and 1.1.0 dated 2020-07-28
DESCRIPTION | 8 MD5 | 72 ++- NAMESPACE | 11 NEWS.md | 13 R/mixed_model_using_splits.R | 655 ++++++++++++++++++++++-------- R/model_using_radar.R | 384 +++++++++++++---- R/model_using_splits.R | 496 ++++++++++++++++------ R/predict_functions.R | 91 ++++ R/shorts_S3.R |only R/shorts_constructors.R |only R/shorts_model_fit.R |only README.md | 654 ++++++++++++++++++++++++----- build/vignette.rds |binary inst/CITATION | 4 inst/doc/sprint-corrections.R | 183 ++++++++ inst/doc/sprint-corrections.Rmd | 206 +++++++++ inst/doc/sprint-corrections.html | 291 ++++++++++++- man/coef.shorts_mixed_model.Rd |only man/coef.shorts_model.Rd |only man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |only man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-16-1.png |only man/figures/README-unnamed-chunk-17-1.png |only man/figures/README-unnamed-chunk-18-1.png |only man/figures/README-unnamed-chunk-19-1.png |only man/figures/README-unnamed-chunk-21-1.png |only man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-23-1.png |only man/figures/README-unnamed-chunk-24-1.png |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-7-1.png |binary man/mixed_model_split_times.Rd | 27 - man/mixed_model_using_radar.Rd | 16 man/model_split_times.Rd | 21 man/model_using_radar.Rd | 11 man/predict.shorts_mixed_model.Rd |only man/predict.shorts_model.Rd |only man/predict_kinematics.Rd | 10 man/print.shorts_mixed_model.Rd |only man/print.shorts_model.Rd |only man/residuals.shorts_mixed_model.Rd |only man/residuals.shorts_model.Rd |only man/summary.shorts_mixed_model.Rd |only man/summary.shorts_model.Rd |only vignettes/sprint-corrections.Rmd | 206 +++++++++ 49 files changed, 2758 insertions(+), 601 deletions(-)
Title: Virtual Machines in 'Azure'
Description: Functionality for working with virtual machines (VMs) in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/services/virtual-machines/>. Includes facilities to deploy, startup, shutdown, and cleanly delete VMs and VM clusters. Deployment configurations can be highly customised, and can make use of existing resources as well as creating new ones. A selection of predefined configurations is provided to allow easy deployment of commonly used Linux and Windows images, including Data Science Virtual Machines. With a running VM, execute scripts and install optional extensions. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureVM versions 2.1.1 dated 2020-02-06 and 2.2.0 dated 2020-07-28
DESCRIPTION | 11 MD5 | 71 ++- NAMESPACE | 22 + NEWS.md | 11 R/add_methods.R | 5 R/az_vm_resource.R | 8 R/az_vmss_resource.R | 5 R/img_centos.R |only R/img_debian.R |only R/img_dsvm.R |only R/img_rhel.R |only R/img_ubuntu.R |only R/img_windows.R |only R/vm_config.R | 127 ------ R/vm_resource_config.R | 44 ++ R/vmss_config.R | 173 --------- R/vmss_template_builders.R | 2 build/vignette.rds |binary inst/doc/intro.html | 22 - man/az_vm_resource.Rd | 82 ++-- man/az_vm_template.Rd | 178 ++++----- man/az_vmss_resource.Rd | 122 +++--- man/az_vmss_template.Rd | 202 +++++----- man/lb_config.Rd | 112 ++--- man/lb_rules.Rd | 184 +++++---- man/nsg_rules.Rd | 120 +++--- man/reexports.Rd | 34 - man/scaleset_options.Rd | 72 +-- man/vm_config.Rd | 486 +++++++++++++------------ man/vm_resource_config.Rd | 112 +++-- man/vmss_config.Rd | 491 ++++++++++++++------------ tests/testthat/setup.R |only tests/testthat/test01_vmconfig.R | 197 ---------- tests/testthat/test13_custom.R | 5 tests/testthat/test14_par.R | 4 tests/testthat/test15_disktype.R | 3 tests/testthat/test16_sshkeyres.R |only tests/testthat/test17a_ubuntu_presets.R |only tests/testthat/test17b_windows_presets.R |only tests/testthat/test17c_debian_presets.R |only tests/testthat/test17d_centos_presets.R |only tests/testthat/test17e_rhel_presets.R |only tests/testthat/test17f_linux_dsvm_presets.R |only tests/testthat/test17g_windows_dsvm_presets.R |only 44 files changed, 1361 insertions(+), 1544 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis, especially raster data. Methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. The package is similar to the 'raster' package; but 'terra' is simpler and faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Karl Forner [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 0.7-11 dated 2020-07-01 and 0.8-5 dated 2020-07-28
terra-0.7-11/terra/R/extend.R |only terra-0.7-11/terra/man/classes.Rd |only terra-0.7-11/terra/man/extend.Rd |only terra-0.7-11/terra/man/extent.Rd |only terra-0.7-11/terra/src/memory.h |only terra-0.7-11/terra/src/spatMessages.h |only terra-0.7-11/terra/src/warp2.cpp |only terra-0.8-5/terra/DESCRIPTION | 16 - terra-0.8-5/terra/MD5 | 227 +++++++++-------- terra-0.8-5/terra/NAMESPACE | 13 - terra-0.8-5/terra/R/Agenerics.R | 28 +- terra-0.8-5/terra/R/RcppExports.R | 4 terra-0.8-5/terra/R/SpatDataSet.R | 53 +++- terra-0.8-5/terra/R/aggregate.R | 2 terra-0.8-5/terra/R/arith.R | 21 + terra-0.8-5/terra/R/cells.R | 4 terra-0.8-5/terra/R/coerce.R | 35 +- terra-0.8-5/terra/R/crs.R | 86 ++++-- terra-0.8-5/terra/R/dimensions.R | 4 terra-0.8-5/terra/R/expand.R |only terra-0.8-5/terra/R/extent.R | 46 +++ terra-0.8-5/terra/R/focalMat.R |only terra-0.8-5/terra/R/gdal.R | 12 terra-0.8-5/terra/R/generics.R | 77 ++++- terra-0.8-5/terra/R/geom.R | 7 terra-0.8-5/terra/R/image.R | 32 +- terra-0.8-5/terra/R/lapp.R | 17 + terra-0.8-5/terra/R/messages.R | 64 +--- terra-0.8-5/terra/R/options.R | 49 +-- terra-0.8-5/terra/R/pack.R | 9 terra-0.8-5/terra/R/plot.R | 4 terra-0.8-5/terra/R/plot2rasters.R | 17 - terra-0.8-5/terra/R/plotExtent.R | 20 - terra-0.8-5/terra/R/plotLegend.R | 22 - terra-0.8-5/terra/R/plotRGB.R | 2 terra-0.8-5/terra/R/plotRaster.R | 37 -- terra-0.8-5/terra/R/plotVector.R | 123 +++++---- terra-0.8-5/terra/R/plot_legend.R |only terra-0.8-5/terra/R/plot_raster.R |only terra-0.8-5/terra/R/plot_scale.R |only terra-0.8-5/terra/R/rast.R | 30 +- terra-0.8-5/terra/R/show.R | 22 + terra-0.8-5/terra/R/spatvec.R | 9 terra-0.8-5/terra/R/subset.R | 1 terra-0.8-5/terra/R/tempfiles.R | 51 +++ terra-0.8-5/terra/R/values.R | 8 terra-0.8-5/terra/R/vect.R | 10 terra-0.8-5/terra/R/xyRowColCell.R | 12 terra-0.8-5/terra/R/zonal.R | 20 + terra-0.8-5/terra/R/zzz.R | 31 +- terra-0.8-5/terra/man/app.Rd | 19 + terra-0.8-5/terra/man/area.Rd | 16 - terra-0.8-5/terra/man/classify.Rd | 7 terra-0.8-5/terra/man/coerce.Rd | 3 terra-0.8-5/terra/man/crop.Rd | 1 terra-0.8-5/terra/man/crs.Rd | 23 + terra-0.8-5/terra/man/dimensions.Rd | 6 terra-0.8-5/terra/man/expand.Rd |only terra-0.8-5/terra/man/ext.Rd |only terra-0.8-5/terra/man/factors.Rd | 9 terra-0.8-5/terra/man/fill.Rd |only terra-0.8-5/terra/man/focalMat.Rd |only terra-0.8-5/terra/man/freq.Rd | 11 terra-0.8-5/terra/man/gdal_info.Rd | 14 - terra-0.8-5/terra/man/global.Rd | 5 terra-0.8-5/terra/man/image.Rd |only terra-0.8-5/terra/man/isLonLat.Rd | 25 - terra-0.8-5/terra/man/lapp.Rd | 7 terra-0.8-5/terra/man/math.Rd | 10 terra-0.8-5/terra/man/plot.Rd | 121 +++------ terra-0.8-5/terra/man/plotVector.Rd |only terra-0.8-5/terra/man/rast.Rd | 8 terra-0.8-5/terra/man/resample.Rd | 2 terra-0.8-5/terra/man/scatter.Rd |only terra-0.8-5/terra/man/sds.Rd | 7 terra-0.8-5/terra/man/selectRange.Rd | 3 terra-0.8-5/terra/man/stretch.Rd |only terra-0.8-5/terra/man/subset.Rd | 1 terra-0.8-5/terra/man/terra-package.Rd | 26 +- terra-0.8-5/terra/man/terraOptions.Rd | 9 terra-0.8-5/terra/man/tmpFile.Rd | 16 - terra-0.8-5/terra/man/writeRaster.Rd | 24 + terra-0.8-5/terra/man/zonal.Rd | 7 terra-0.8-5/terra/src/RcppExports.cpp | 11 terra-0.8-5/terra/src/RcppModule.cpp | 69 +++-- terra-0.8-5/terra/src/aggregate.cpp | 24 + terra-0.8-5/terra/src/area.cpp | 10 terra-0.8-5/terra/src/categories.cpp | 4 terra-0.8-5/terra/src/cellnumber.cpp | 120 ++++----- terra-0.8-5/terra/src/crs.cpp | 88 ++++++ terra-0.8-5/terra/src/distRaster.cpp | 32 +- terra-0.8-5/terra/src/extent.cpp | 24 + terra-0.8-5/terra/src/extract.cpp | 57 ++++ terra-0.8-5/terra/src/file_utils.cpp | 9 terra-0.8-5/terra/src/file_utils.h | 1 terra-0.8-5/terra/src/focal.cpp | 24 - terra-0.8-5/terra/src/gdalio.cpp | 265 +++++++++++++++++++- terra-0.8-5/terra/src/gdalio.h | 204 --------------- terra-0.8-5/terra/src/memory.cpp | 50 ++- terra-0.8-5/terra/src/mosaic.cpp | 2 terra-0.8-5/terra/src/polygonize.cpp | 6 terra-0.8-5/terra/src/ram.cpp | 2 terra-0.8-5/terra/src/raster_coerce.cpp | 8 terra-0.8-5/terra/src/raster_methods.cpp | 374 ++++++++++++++++++++++++----- terra-0.8-5/terra/src/raster_stats.cpp | 111 +++++--- terra-0.8-5/terra/src/rasterize.cpp | 12 terra-0.8-5/terra/src/read.cpp | 38 +- terra-0.8-5/terra/src/read_gdal.cpp | 58 ++-- terra-0.8-5/terra/src/reclassify.cpp | 10 terra-0.8-5/terra/src/resample.cpp | 11 terra-0.8-5/terra/src/sources.cpp | 12 terra-0.8-5/terra/src/spatBase.h | 58 ++++ terra-0.8-5/terra/src/spatDataframe.h | 4 terra-0.8-5/terra/src/spatOptions.cpp | 34 ++ terra-0.8-5/terra/src/spatRaster.cpp | 42 ++- terra-0.8-5/terra/src/spatRaster.h | 120 +++++---- terra-0.8-5/terra/src/spatRasterMultiple.h | 11 terra-0.8-5/terra/src/spatVector.cpp | 10 terra-0.8-5/terra/src/spatVector.h | 5 terra-0.8-5/terra/src/terrain.cpp | 2 terra-0.8-5/terra/src/vecmath.h | 46 +++ terra-0.8-5/terra/src/vector_methods.cpp | 26 ++ terra-0.8-5/terra/src/warp.cpp |only terra-0.8-5/terra/src/write.cpp | 113 ++++++-- terra-0.8-5/terra/src/write_gdal.cpp | 117 ++++----- 125 files changed, 2433 insertions(+), 1396 deletions(-)
Title: Provenance Visualizer
Description: Displays provenance graphically for provenance collected by the 'rdt' or
'rdtLite' packages, or other tools providing compatible PROV JSON output. The exact
format of the JSON created by 'rdt' and 'rdtLite' is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about
rdtLite and associated tools is available at <https://github.com/End-to-end-provenance/>
and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Emery Boose [ctb],
Barbara Lerner [aut, cre],
Sofiya Taskova [aut],
Miruna Oprescu [aut],
Nikki Hoffler [aut],
Marios Dardas [aut],
Elizabeth Fong [ctb],
Thomas Pasquier [ctb],
Matthew Lau [ctb],
Aaron Ellison [res],
Margo Seltzer [res]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provViz versions 1.0.6 dated 2019-08-26 and 1.0.7 dated 2020-07-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 13 ++++++++++++- README.md | 21 ++++----------------- inst/java/DDGExplorer.jar |binary inst/testdata/prov.json | 42 ++++++++++++++++++++++-------------------- 6 files changed, 48 insertions(+), 48 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.4.7.1 dated 2020-05-11 and 1.4.8 dated 2020-07-28
ChangeLog | 13 +++++++++++ DESCRIPTION | 8 +++--- MD5 | 45 +++++++++++++++++++-------------------- NEWS | 6 +++++ R/aaa.R | 2 - R/altReferenceRelatedFucntions.R | 3 +- R/calculationFunctions.R | 3 ++ R/checkConfigFile.R | 14 +++++++++++- R/class_definition.R | 4 +++ R/demoConfig.R | 4 ++- R/demo_inspector.R | 2 - R/effect_size_ref_make.R |only R/effectsizePlotFunction.R | 6 ++--- R/excelReportFunctions.R | 23 ++++++++++++------- R/loggerFunctions.R | 8 ++++-- R/multiStudyPlots.R | 1 R/run_inspector.R | 33 ++++++++++++++++++---------- R/saveFilesFunctions.R | 17 +++++++++++++- R/setup_inspector.R | 2 + R/studyFunctions.R | 7 ++++++ R/terminationFunctions.R | 9 +++++-- inst/doc/GWASinspector.html | 4 +-- inst/extdata/config.ini | 23 ++++++++++++++++--- man/run.inspector.Rd | 6 +++-- 24 files changed, 173 insertions(+), 70 deletions(-)
Title: Badge for R Package
Description: Query information and generate badge for using in README and GitHub Pages.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
Gregor de Cillia [ctb],
Dirk Eddelbuettel [ctb],
Maëlle Salmon [ctb],
Robrecht Cannoodt [ctb] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Alexander Rossell Hayes [ctb] (<https://orcid.org/0000-0001-9412-0457>,
rossellhayes)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between badger versions 0.0.7 dated 2019-11-15 and 0.0.8 dated 2020-07-28
DESCRIPTION | 23 +++++++++-------- MD5 | 16 ++++++----- NAMESPACE | 2 + R/badge.R | 59 +++++++++++++++++++++++++++++++++++++++++--- R/utilities.R | 2 - man/badge_altmetric.Rd | 2 + man/badge_cran_download.Rd | 7 +++-- man/badge_github_actions.Rd |only man/badge_license.Rd |only man/badge_travis.Rd | 5 ++- 10 files changed, 91 insertions(+), 25 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>),
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.17-4 dated 2020-02-06 and 0.17-5 dated 2020-07-28
DESCRIPTION | 8 +-- MD5 | 38 +++++++++--------- R/cma.R | 71 +++++++++++++++-------------------- R/compare.R | 6 ++ R/crossval.pcr.R | 10 ++-- R/crossval.wa.R | 4 - R/distance.R | 16 +++---- R/plot.cma.R | 2 R/plot.mcarlo.R | 2 R/predict.wa.R | 32 +++------------ R/rdaFit.R | 2 R/roc.R | 2 R/summary.cma.R | 2 R/wa.R | 4 - README.md | 4 - build/vignette.rds |binary inst/NEWS | 18 ++++++-- inst/doc/analogue_methods.pdf |binary man/bootstrap.Rd | 4 + tests/Examples/analogue-Ex.Rout.save | 12 +++-- 20 files changed, 116 insertions(+), 121 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-13 0.2.0
2016-10-14 0.1.0
Title: Extend 'tinytest' with 'diffobj'
Description: The 'tinytest' package offers a light-weight zero-dependency unit-testing
framework to which this package adds support of the 'diffobj' package for 'diff'-style
comparison of R objects.
Author: Dirk Eddelbuettel and Alton Barbehenn
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between ttdo versions 0.0.5 dated 2020-05-09 and 0.0.6 dated 2020-07-28
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/expectations.R | 2 +- R/expectations_xl.R | 4 ++-- README.md | 8 ++++++++ inst/NEWS.Rd | 7 +++++++ man/expect_equal_with_diff.Rd | 2 +- man/expect_equal_xl.Rd | 2 +- 9 files changed, 39 insertions(+), 17 deletions(-)
Title: Estimating a Survival Distribution in the Presence of Dependent
Left Truncation and Right Censoring
Description: A latent, quasi-independent truncation time is assumed to be linked with the observed dependent truncation time, the event time, and an unknown transformation parameter via a structural transformation model. The transformation parameter is chosen to minimize the conditional Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538> or the regression coefficient estimates (Jones and Crowley, 1992) <doi:10.2307/2336782>. The marginal distribution for the truncation time and the event time are completely left unspecified. The methodology is applied to survival curve estimation and regression analysis.
Author: Sy Han (Steven) Chiou [aut, cre]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between tranSurv versions 1.2.0 dated 2019-05-24 and 1.2.1 dated 2020-07-28
tranSurv-1.2.0/tranSurv/man/condKendall.Rd |only tranSurv-1.2.1/tranSurv/DESCRIPTION | 12 tranSurv-1.2.1/tranSurv/MD5 | 52 ++- tranSurv-1.2.1/tranSurv/NAMESPACE | 23 + tranSurv-1.2.1/tranSurv/NEWS.md |only tranSurv-1.2.1/tranSurv/R/Surv.R |only tranSurv-1.2.1/tranSurv/R/gof.R |only tranSurv-1.2.1/tranSurv/R/kendalls.R | 33 - tranSurv-1.2.1/tranSurv/R/plot.trSurvfit.R |only tranSurv-1.2.1/tranSurv/R/pmcc.R | 6 tranSurv-1.2.1/tranSurv/R/summary.R | 74 ++++ tranSurv-1.2.1/tranSurv/R/trReg.R | 407 +++++++++++++++++++----- tranSurv-1.2.1/tranSurv/R/trSurv_pkg.R | 3 tranSurv-1.2.1/tranSurv/R/trSurvfit.R | 106 +++--- tranSurv-1.2.1/tranSurv/R/util.R | 1 tranSurv-1.2.1/tranSurv/R/wKendall.R | 9 tranSurv-1.2.1/tranSurv/inst/examples |only tranSurv-1.2.1/tranSurv/man/Surv.Rd |only tranSurv-1.2.1/tranSurv/man/cKendall.Rd |only tranSurv-1.2.1/tranSurv/man/gof.Rd |only tranSurv-1.2.1/tranSurv/man/kendall.Rd | 2 tranSurv-1.2.1/tranSurv/man/plot.trSurvfit.Rd |only tranSurv-1.2.1/tranSurv/man/pmcc.Rd | 1 tranSurv-1.2.1/tranSurv/man/trReg.Rd | 63 ++- tranSurv-1.2.1/tranSurv/man/trSurv.control.Rd | 7 tranSurv-1.2.1/tranSurv/man/trSurvfit.Rd | 92 +++-- tranSurv-1.2.1/tranSurv/man/tranSurv-package.Rd | 3 tranSurv-1.2.1/tranSurv/man/wKendall.Rd | 14 28 files changed, 657 insertions(+), 251 deletions(-)
Title: Interval Mapping for Quantitative Trait Loci Underlying Neighbor
Effects
Description: To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2020) <doi:10.1101/2020.05.20.089474>.
Author: Yasuhiro Sato [aut, cre] (<https://orcid.org/0000-0002-6466-723X>),
Kazuya Takeda [aut],
Atsushi J. Nagano [aut] (<https://orcid.org/0000-0001-7891-5049>)
Maintainer: Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>
Diff between rNeighborQTL versions 1.0.0 dated 2020-06-04 and 1.1.0 dated 2020-07-28
DESCRIPTION | 6 MD5 | 96 ++++---- NAMESPACE | 26 +- R/calc_neiprob.R | 81 +++--- R/calc_pve.R | 45 +-- R/decompose_genoprobs.R | 19 + R/eff_neighbor.R | 75 +++--- R/genoprobs2selfprobs.R | 19 - R/get_markers.R | 42 +-- R/int_neighbor.R | 43 +-- R/logLik_glm.R |only R/min_dist.R | 34 +- R/neiprob.R | 71 +++-- R/perm_neighbor.R | 10 R/plot_eff.R | 61 ++--- R/plot_nei.R | 93 +++---- R/rNeighborQTL-package.R | 48 ++-- R/scan_neighbor.R | 54 +--- R/selfprob.R | 40 +-- R/sim_nei_qtl.R | 7 inst/CITATION | 30 +- inst/ColKas_geno.csv | 256 ++++++++++----------- inst/ColKas_pheno.csv | 254 ++++++++++----------- inst/doc/rNeighborQTL.R | 160 ++++++------- inst/doc/rNeighborQTL.Rmd | 24 -- inst/doc/rNeighborQTL.html | 236 ++++++++++--------- inst/rNeighborQTL.Rmd | 358 +++++++++++++++--------------- man/calc_neiprob.Rd | 2 man/calc_pve.Rd | 11 man/decompose_genoprobs.Rd | 4 man/eff_neighbor.Rd | 11 man/genoprobs2selfprobs.Rd | 4 man/int_neighbor.Rd | 8 man/logLik_glm.fit.Rd |only man/perm_neighbor.Rd | 12 - man/plot_eff.Rd | 2 man/plot_nei.Rd | 2 man/scan_neighbor.Rd | 9 man/sim_nei_qtl.Rd | 11 tests/testthat.R | 8 tests/testthat/ColKas_geno.csv | 256 ++++++++++----------- tests/testthat/ColKas_pheno.csv | 254 ++++++++++----------- tests/testthat/test-calc_pve.R | 12 - tests/testthat/test-decompose_genoprobs.R | 12 - tests/testthat/test-eff_neighbor.R | 6 tests/testthat/test-int_neighbor.R | 9 tests/testthat/test-perm_neighbor.R | 12 - tests/testthat/test-plot_nei.R | 4 tests/testthat/test-scan_neighbor.R | 18 - vignettes/rNeighborQTL.Rmd | 24 -- 50 files changed, 1397 insertions(+), 1482 deletions(-)