Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MoEClust versions 1.3.1 dated 2020-05-12 and 1.3.2 dated 2020-11-17
DESCRIPTION | 22 - MD5 | 72 ++--- R/Functions.R | 596 ++++++++++++++++++++++++++++++++--------------- R/MoEClust.R | 28 +- R/Plotting_Functions.R | 94 ++++--- README.md | 8 build/vignette.rds |binary inst/CITATION | 13 - inst/NEWS.md | 26 ++ inst/doc/MoEClust.R | 18 - inst/doc/MoEClust.Rmd | 28 +- inst/doc/MoEClust.html | 598 ++++++++++++++++++++++++++++++++++-------------- man/MoEClust-package.Rd | 16 - man/MoE_Uncertainty.Rd | 2 man/MoE_clust.Rd | 10 man/MoE_compare.Rd | 18 - man/MoE_control.Rd | 42 ++- man/MoE_crit.Rd | 10 man/MoE_cstep.Rd | 2 man/MoE_dens.Rd | 2 man/MoE_estep.Rd | 2 man/MoE_gpairs.Rd | 14 - man/MoE_mahala.Rd | 2 man/MoE_plotCrit.Rd | 2 man/MoE_plotGate.Rd | 4 man/MoE_plotLogLik.Rd | 6 man/MoE_stepwise.Rd | 4 man/aitken.Rd | 2 man/as.Mclust.Rd | 12 man/drop_constants.Rd | 2 man/drop_levels.Rd | 2 man/expert_covar.Rd | 6 man/force_posiDiag.Rd | 8 man/noise_vol.Rd | 4 man/plot.MoEClust.Rd | 8 man/predict.MoEClust.Rd | 7 vignettes/MoEClust.Rmd | 28 +- 37 files changed, 1145 insertions(+), 573 deletions(-)
Title: Distributions Hermite Polynomial Approximation
Description: Multivariate conditional and marginal densities, moments, cumulative distribution functions as well as binary choice and sample selection models based on Hermite polynomial approximation which was proposed and described by A. Gallant and D. W. Nychka (1987) <doi:10.2307/1913241>.
Author: Potanin Bogdan
Maintainer: Potanin Bogdan <bogdanpotanin@gmail.com>
Diff between hpa versions 1.1.2 dated 2020-08-24 and 1.1.3 dated 2020-11-17
hpa-1.1.2/hpa/man/AIC.hpaBinary.Rd |only hpa-1.1.2/hpa/man/AIC.hpaML.Rd |only hpa-1.1.2/hpa/man/AIC.hpaSelection.Rd |only hpa-1.1.2/hpa/man/AIC_hpaBinary.Rd |only hpa-1.1.2/hpa/man/AIC_hpaML.Rd |only hpa-1.1.2/hpa/man/AIC_hpaSelection.Rd |only hpa-1.1.2/hpa/man/dhpa.Rd |only hpa-1.1.2/hpa/man/dhpaDiff.Rd |only hpa-1.1.2/hpa/man/dtrhpa.Rd |only hpa-1.1.2/hpa/man/ehpa.Rd |only hpa-1.1.2/hpa/man/etrhpa.Rd |only hpa-1.1.2/hpa/man/ihpa.Rd |only hpa-1.1.2/hpa/man/ihpaDiff.Rd |only hpa-1.1.2/hpa/man/itrhpa.Rd |only hpa-1.1.2/hpa/man/phpa.Rd |only hpa-1.1.2/hpa/man/printPolynomial.Rd |only hpa-1.1.3/hpa/DESCRIPTION | 12 hpa-1.1.3/hpa/MD5 | 105 +--- hpa-1.1.3/hpa/NAMESPACE | 68 +- hpa-1.1.3/hpa/R/RcppExports.R | 616 +++++++++++------------- hpa-1.1.3/hpa/R/hpaBinary_generics.R | 33 - hpa-1.1.3/hpa/R/hpaML_generics.R | 62 +- hpa-1.1.3/hpa/R/hpaSelection_generics.R | 35 - hpa-1.1.3/hpa/man/dnorm_parallel.Rd | 6 hpa-1.1.3/hpa/man/hpaBinary.Rd | 170 +++--- hpa-1.1.3/hpa/man/hpaDist.Rd |only hpa-1.1.3/hpa/man/hpaML.Rd | 734 ++++++++++++++--------------- hpa-1.1.3/hpa/man/hpaSelection.Rd | 263 ++++++---- hpa-1.1.3/hpa/man/logLik_hpaSelection.Rd | 3 hpa-1.1.3/hpa/man/normalMoment.Rd | 38 - hpa-1.1.3/hpa/man/plot.hpaML.Rd | 6 hpa-1.1.3/hpa/man/plot.hpaSelection.Rd | 2 hpa-1.1.3/hpa/man/plot_hpaSelection.Rd | 11 hpa-1.1.3/hpa/man/pnorm_parallel.Rd | 5 hpa-1.1.3/hpa/man/polynomialIndex.Rd | 101 ++- hpa-1.1.3/hpa/man/predict.hpaBinary.Rd | 2 hpa-1.1.3/hpa/man/predict.hpaML.Rd | 2 hpa-1.1.3/hpa/man/predict.hpaSelection.Rd | 2 hpa-1.1.3/hpa/man/predict_hpaBinary.Rd | 9 hpa-1.1.3/hpa/man/predict_hpaML.Rd | 2 hpa-1.1.3/hpa/man/predict_hpaSelection.Rd | 24 hpa-1.1.3/hpa/man/summary.hpaBinary.Rd | 2 hpa-1.1.3/hpa/man/summary.hpaML.Rd | 2 hpa-1.1.3/hpa/man/summary.hpaSelection.Rd | 2 hpa-1.1.3/hpa/man/summary_hpaBinary.Rd | 4 hpa-1.1.3/hpa/man/summary_hpaML.Rd | 2 hpa-1.1.3/hpa/man/summary_hpaSelection.Rd | 8 hpa-1.1.3/hpa/man/truncatedNormalMoment.Rd | 86 +-- hpa-1.1.3/hpa/src/ParallelFunctions.cpp | 21 hpa-1.1.3/hpa/src/RcppExports.cpp | 179 +++---- hpa-1.1.3/hpa/src/hpaBinary.cpp | 286 +++++------ hpa-1.1.3/hpa/src/hpaBinary.h | 5 hpa-1.1.3/hpa/src/hpaML.cpp | 276 ++++++---- hpa-1.1.3/hpa/src/hpaML.h | 23 hpa-1.1.3/hpa/src/hpaMain.cpp | 550 +++++++++++---------- hpa-1.1.3/hpa/src/hpaMain.h | 30 - hpa-1.1.3/hpa/src/hpaSelection.cpp | 550 ++++++++++++--------- hpa-1.1.3/hpa/src/hpaSelection.h | 5 hpa-1.1.3/hpa/src/hpaValidation.cpp |only hpa-1.1.3/hpa/src/hpaValidation.h |only hpa-1.1.3/hpa/src/normalMoments.cpp | 95 ++- hpa-1.1.3/hpa/src/polynomialIndex.cpp | 86 ++- hpa-1.1.3/hpa/src/polynomialIndex.h | 8 63 files changed, 2486 insertions(+), 2045 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 1.3 dated 2019-01-25 and 1.4 dated 2020-11-17
DESCRIPTION | 6 MD5 | 8 R/mams.R | 808 +++++++++++++++++++++++++++++----------------------------- R/tite.mams.R | 38 +- inst/NEWS | 14 + 5 files changed, 447 insertions(+), 427 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-06 0.1.1
2017-09-08 0.1.0
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05> and the package vignette.
Author: Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>),
Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 3.0.1 dated 2020-11-04 and 3.0.2 dated 2020-11-17
DESCRIPTION | 8 MD5 | 70 +-- NAMESPACE | 3 NEWS | 7 R/exports.R | 63 ++- R/util.R | 36 - R/utilities_svdraws.R | 25 - R/validation.R | 25 + R/wrappers.R | 70 ++- inst/doc/article2.R | 96 ---- inst/doc/article2.Rnw | 743 ++++++++++++++++++++----------------- inst/doc/article2.pdf |binary inst/examples/svsample_cpp.R |only inst/include/adaptation.hpp | 373 +++++++++++++++--- inst/include/expert.hpp |only inst/include/stochvol.h | 26 + inst/include/type_definitions.h | 293 -------------- inst/include/type_definitions.hpp |only man/expert_defaults.Rd |only man/sv_prior.Rd | 4 man/svsample_cpp.Rd | 100 +++- man/svsample_roll.Rd | 6 man/validate_and_process_expert.Rd | 10 src/sampling_latent_states.cc | 2 src/sampling_latent_states.h | 2 src/sampling_main.cc | 60 +- src/sampling_parameters.cc | 2 src/sampling_parameters.h | 2 src/single_update.cc | 2 src/single_update.h | 2 src/utils.h | 2 src/utils_main.cc | 75 +++ src/utils_main.h | 15 src/utils_parameters.cc | 2 src/utils_parameters.h | 2 tests/testthat/test-samplers.R | 31 - vignettes/article2.Rnw | 743 ++++++++++++++++++++----------------- vignettes/ref.bib | 103 +++-- 38 files changed, 1638 insertions(+), 1365 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The netgwas package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The package is
implemented the recent methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>
and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.12 dated 2020-10-21 and 1.13 dated 2020-11-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/netmap.R | 23 +++++++++++++---------- 3 files changed, 19 insertions(+), 16 deletions(-)
Title: Animal Tracker
Description: Utilities for spatial-temporal analysis and visualization of animal (e.g. cattle) tracking data. The core feature is a 'shiny' web application for customized processing of GPS logs, including features for data augmentation (e.g. elevation lookup), data selection, export, plotting, and statistical summaries. A data validation application allows for side-by-side comparison via time series plots and extreme value detection described by J.P. van Brakel <https://stackoverflow.com/questions/22583391/peak-signal-detection-in-realtime-timeseries-data/>.
Author: Joe Champion [aut, cre],
Thea Sukianto [aut]
Maintainer: Joe Champion <joechampion@boisestate.edu>
Diff between animaltracker versions 0.1.0 dated 2020-03-25 and 0.2.0 dated 2020-11-17
DESCRIPTION | 34 MD5 | 85 +- NEWS.md |only R/app.R | 61 - R/app_server.R | 1502 +++++++++++++++++++---------------------- R/app_ui.R | 331 ++++----- R/data.R | 95 +- R/data_analysis.R | 1200 ++++++++++++++++---------------- R/data_cleaning.R | 602 ++++++++-------- R/data_processing.R | 606 +++++++++------- R/data_storage.R | 662 +++++++++--------- R/inputs_module.R |only R/plots_module.R |only R/stats_module.R |only R/validation_app.R | 482 ++++++------- README.md |only data/demo_info.rda |binary data/demo_meta.rda |binary man/clean_location_data.Rd | 7 man/compare_flags.Rd | 21 man/compare_summarise_daily.Rd | 16 man/compare_summarise_data.Rd | 9 man/datePicker.Rd |only man/datePickerOutput.Rd |only man/demo.Rd | 4 man/demo_comparison.Rd | 4 man/demo_filtered.Rd | 4 man/demo_filtered_elev.Rd | 10 man/demo_info.Rd | 4 man/demo_meta.Rd | 4 man/demo_unfiltered.Rd | 4 man/demo_unfiltered_elev.Rd | 10 man/detect_peak_modz.Rd | 12 man/dev_add_to_gitignore.Rd | 2 man/get_meta.Rd | 6 man/join_summaries.Rd | 16 man/line_compare.Rd | 4 man/reactivePicker.Rd |only man/reactivePickerOutput.Rd |only man/reactivePlot.Rd |only man/reactivePlotOutput.Rd |only man/reactiveRange.Rd |only man/reactiveRangeOutput.Rd |only man/run_shiny_animaltracker.Rd | 6 man/run_validation_app.Rd | 6 man/staticPicker.Rd |only man/staticPickerOutput.Rd |only man/stats.Rd |only man/statsLabel.Rd |only man/statsLabelOutput.Rd |only man/statsOutput.Rd |only man/summarise_anidf.Rd | 23 man/time.Rd |only man/timeOutput.Rd |only 54 files changed, 2979 insertions(+), 2853 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.11.0 dated 2020-11-11 and 1.11.1 dated 2020-11-17
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 7 ++++++ tests/testthat/helper.R | 6 +++++ tests/testthat/test-datatransfer-vroom.R | 1 tests/testthat/test-dplyr-compute.R | 4 ++- tests/testthat/test-dplyr-copy_to.R | 4 ++- tests/testthat/test-dplyr-sql-trans-env.R | 6 +++-- tests/testthat/test-upload-file-parameter.R | 31 ++++++++++++++++++++-------- 9 files changed, 58 insertions(+), 23 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.9.0 dated 2020-11-11 and 1.9.1 dated 2020-11-17
DESCRIPTION | 6 ++-- MD5 | 20 ++++++------- NEWS.md | 18 ++++++++++++ R/Connection.R | 15 +++++++--- tests/testthat/helper.R | 6 ++++ tests/testthat/test-datatransfer-datatable.R | 39 ++++++++++++++++----------- tests/testthat/test-datatransfer-vroom.R | 1 tests/testthat/test-dplyr-compute.R | 4 ++ tests/testthat/test-dplyr-copy_to.R | 4 ++ tests/testthat/test-dplyr-sql-trans-env.R | 6 ++-- tests/testthat/test-upload-file-parameters.R | 31 +++++++++++++++------ 11 files changed, 105 insertions(+), 45 deletions(-)
Title: A Forward-Pipe Operator for R
Description: Provides a mechanism for chaining commands with a
new forward-pipe operator, %>%. This operator will forward a value, or
the result of an expression, into the next function call/expression.
There is flexible support for the type of right-hand side expressions.
For more information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
Author: Stefan Milton Bache [aut, cph] (Original author and creator of
magrittr),
Hadley Wickham [aut],
Lionel Henry [cre],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between magrittr versions 1.5 dated 2014-11-22 and 2.0.1 dated 2020-11-17
magrittr-1.5/magrittr/R/first_type.R |only magrittr-1.5/magrittr/R/function_type.R |only magrittr-1.5/magrittr/R/is_something.R |only magrittr-1.5/magrittr/R/split_chain.R |only magrittr-1.5/magrittr/R/wrap_function.R |only magrittr-1.5/magrittr/man/magrittr.Rd |only magrittr-1.5/magrittr/tests/test-all.R |only magrittr-2.0.1/magrittr/DESCRIPTION | 55 magrittr-2.0.1/magrittr/LICENSE | 4 magrittr-2.0.1/magrittr/MD5 | 95 magrittr-2.0.1/magrittr/NAMESPACE | 87 magrittr-2.0.1/magrittr/NEWS.md |only magrittr-2.0.1/magrittr/R/aliases.R | 386 ++-- magrittr-2.0.1/magrittr/R/debug_pipe.R | 92 magrittr-2.0.1/magrittr/R/freduce.R | 49 magrittr-2.0.1/magrittr/R/functions.R | 66 magrittr-2.0.1/magrittr/R/getters.R | 50 magrittr-2.0.1/magrittr/R/magrittr.R | 90 magrittr-2.0.1/magrittr/R/pipe.R | 587 +++--- magrittr-2.0.1/magrittr/README.md | 287 +- magrittr-2.0.1/magrittr/build/vignette.rds |binary magrittr-2.0.1/magrittr/inst/doc/magrittr.R | 153 - magrittr-2.0.1/magrittr/inst/doc/magrittr.Rmd | 422 ++-- magrittr-2.0.1/magrittr/inst/doc/magrittr.html | 961 +++++----- magrittr-2.0.1/magrittr/inst/doc/tradeoffs.R |only magrittr-2.0.1/magrittr/inst/doc/tradeoffs.Rmd |only magrittr-2.0.1/magrittr/inst/doc/tradeoffs.html |only magrittr-2.0.1/magrittr/inst/logo-hex.png |only magrittr-2.0.1/magrittr/inst/logo-hex.svg |only magrittr-2.0.1/magrittr/inst/logo.png |only magrittr-2.0.1/magrittr/inst/logo.svg |only magrittr-2.0.1/magrittr/man/aliases.Rd | 172 - magrittr-2.0.1/magrittr/man/compound.Rd | 101 - magrittr-2.0.1/magrittr/man/debug_fseq.Rd | 46 magrittr-2.0.1/magrittr/man/debug_pipe.Rd | 36 magrittr-2.0.1/magrittr/man/exposition.Rd | 69 magrittr-2.0.1/magrittr/man/faq-pipe-gender.Rd |only magrittr-2.0.1/magrittr/man/figures |only magrittr-2.0.1/magrittr/man/freduce.Rd | 40 magrittr-2.0.1/magrittr/man/fseq.Rd | 48 magrittr-2.0.1/magrittr/man/functions.Rd | 36 magrittr-2.0.1/magrittr/man/magrittr-package.Rd |only magrittr-2.0.1/magrittr/man/pipe.Rd | 265 +- magrittr-2.0.1/magrittr/man/pipe_eager_lexical.Rd |only magrittr-2.0.1/magrittr/man/print.fseq.Rd | 38 magrittr-2.0.1/magrittr/man/tee.Rd | 63 magrittr-2.0.1/magrittr/src |only magrittr-2.0.1/magrittr/tests/testthat.R |only magrittr-2.0.1/magrittr/tests/testthat/test-aliases.R | 82 magrittr-2.0.1/magrittr/tests/testthat/test-anonymous-functions.r | 162 - magrittr-2.0.1/magrittr/tests/testthat/test-compound.R | 52 magrittr-2.0.1/magrittr/tests/testthat/test-freduce.R |only magrittr-2.0.1/magrittr/tests/testthat/test-fseq.r | 20 magrittr-2.0.1/magrittr/tests/testthat/test-multiple-arguments.r | 98 - magrittr-2.0.1/magrittr/tests/testthat/test-pipe.R |only magrittr-2.0.1/magrittr/tests/testthat/test-single-argument.r | 36 magrittr-2.0.1/magrittr/tests/testthat/test-tee.r | 22 magrittr-2.0.1/magrittr/vignettes/magrittr.Rmd | 422 ++-- magrittr-2.0.1/magrittr/vignettes/tradeoffs.Rmd |only 59 files changed, 2698 insertions(+), 2494 deletions(-)
Title: Retrieves Gene Expression Dataset and Gene Symbols from GEO Code
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optional) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between geneExpressionFromGEO versions 0.2 dated 2020-11-16 and 0.3 dated 2020-11-17
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/geneExpressionFromGEO.r | 13 ++++++------- man/getGeneExpressionFromGEO.Rd | 15 ++++----------- 4 files changed, 19 insertions(+), 26 deletions(-)
More information about geneExpressionFromGEO at CRAN
Permanent link
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] (Radix sort based on data.table's forder() and
their contribution to R's order()),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.3.4 dated 2020-08-29 and 0.3.5 dated 2020-11-17
DESCRIPTION | 15 LICENSE |only LICENSE.note |only MD5 | 132 +++--- NAMESPACE | 3 NEWS.md | 31 + R/compare.R | 80 --- R/complete.R |only R/equal.R | 4 R/fill.R |only R/order-radix.R |only R/order.R |only R/rep.R | 47 ++ R/runs.R |only R/translate.R | 8 R/type-vctr.R | 2 build/vctrs.pdf |binary build/vignette.rds |binary inst/doc/pillar.R | 38 - inst/doc/pillar.Rmd | 69 --- inst/doc/pillar.html | 103 ++-- inst/doc/s3-vector.html | 49 ++ inst/doc/stability.html | 55 ++ inst/doc/type-size.html | 49 ++ man/vctrs-package.Rd | 1 man/vec-rep.Rd | 40 + man/vec_fill_missing.Rd |only man/vec_identify_runs.Rd |only man/vec_order.Rd | 2 src/altrep-rle.c | 2 src/bind.c | 1 src/c-unchop.c | 8 src/c.c | 30 - src/compare.c | 41 - src/complete.c |only src/dictionary.c | 265 +----------- src/dictionary.h | 22 - src/equal.c | 729 +++++++++++++--------------------- src/equal.h | 341 +++++++++------ src/fill.c |only src/group.c | 11 src/hash.c | 4 src/init.c | 34 + src/lazy.h |only src/names.c | 29 + src/order-groups.c |only src/order-groups.h |only src/order-radix.c |only src/order-radix.h |only src/order-sortedness.c |only src/order-sortedness.h |only src/order-truelength.c |only src/order-truelength.h |only src/poly-op.c |only src/poly-op.h |only src/proxy.c | 47 ++ src/rep.c | 91 ++++ src/runs.c |only src/translate.c | 505 ++++++----------------- src/translate.h |only src/type-data-frame.c | 6 src/utils.c | 214 ++++++++- src/utils.h | 35 + src/vctrs.h | 71 +-- src/version.c | 2 tests/testthat/helper-order.R |only tests/testthat/test-bind.R | 5 tests/testthat/test-c.R | 18 tests/testthat/test-compare.R | 85 --- tests/testthat/test-complete.R |only tests/testthat/test-dictionary.R | 5 tests/testthat/test-equal.R | 31 - tests/testthat/test-fill.R |only tests/testthat/test-names.R | 21 tests/testthat/test-order-radix.R |only tests/testthat/test-order.R |only tests/testthat/test-rep.R | 47 ++ tests/testthat/test-runs.R |only tests/testthat/test-slice.R | 8 tests/testthat/test-translate.R | 210 ++------- tests/testthat/test-type-data-frame.R | 2 vignettes/pillar.Rmd | 69 --- 82 files changed, 1774 insertions(+), 1943 deletions(-)
Title: Boilerplate Code for 'Tidymodels' Analyses
Description: Code snippets to fit models using the tidymodels framework can be easily created for a given data set.
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>),
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between usemodels versions 0.0.1 dated 2020-09-22 and 0.1.0 dated 2020-11-17
DESCRIPTION | 13 ++++++----- MD5 | 13 ++++++----- NAMESPACE | 1 NEWS.md | 6 +++++ R/use.R | 44 ++++++++++++++++++++++++++++++++++++++++ man/templates.Rd | 10 +++++++++ tests/testthat/_snaps |only tests/testthat/test-templates.R | 2 - 8 files changed, 76 insertions(+), 13 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] (<https://orcid.org/0000-0003-0518-4710>),
Lorenz A. Kapsner [aut] (<https://orcid.org/0000-0003-1866-860X>),
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitätsklinikum Erlangen [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.0.4 dated 2020-06-03 and 0.0.6 dated 2020-11-17
DESCRIPTION | 38 ++-- MD5 | 63 +++---- NAMESPACE | 28 +-- NEWS.md |only R/clean_path_name.R | 38 ++-- R/close_all_connections.R | 10 - R/db_connection.R | 299 +++++++++++++++++++---------------- R/feedback.R | 20 +- R/firstup.R | 30 +-- R/get_config.R | 111 ++++++------ R/get_config_env.R | 150 ++++++++--------- R/global_env_hack.R | 56 +++--- R/notin.R | 52 ++---- R/query_database.R | 73 ++++---- R/set_env_vars.R | 6 README.md | 107 +++++++++++- man/clean_path_name.Rd | 50 ++--- man/cleanup_old_logfile.Rd | 52 ++---- man/close_all_connections.Rd | 58 +++--- man/db_connection.Rd | 129 +++++++-------- man/feedback.Rd | 175 ++++++++++---------- man/feedback_get_formatted_string.Rd | 80 ++++----- man/feedback_to_console.Rd | 104 ++++++------ man/feedback_to_logfile.Rd | 78 ++++----- man/feedback_to_logjs.Rd | 52 +++--- man/feedback_to_ui.Rd | 58 +++--- man/firstup.Rd | 44 ++--- man/get_config.Rd | 79 ++++----- man/get_config_env.Rd | 70 ++++---- man/global_env_hack.Rd | 66 +++---- man/grapes-notin-grapes.Rd | 50 ++--- man/query_database.Rd | 61 +++---- man/set_env_vars.Rd | 54 +++--- 33 files changed, 1240 insertions(+), 1101 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <arXiv:1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.7.1 dated 2020-10-12 and 0.7.2 dated 2020-11-17
DESCRIPTION | 8 +++--- MD5 | 24 +++++++++--------- NEWS.md | 9 ++++++ R/vinereg.R | 2 - README.md | 25 ++++++++++--------- build/vignette.rds |binary inst/doc/abalone-example.Rmd | 2 - inst/doc/abalone-example.html | 8 +++--- inst/doc/bike-rental.html | 40 +++++++++++++++---------------- man/figures/README-unnamed-chunk-1-1.png |binary man/vinereg.Rd | 2 - src/vinereg.cpp | 13 ++++++---- vignettes/abalone-example.Rmd | 2 - 13 files changed, 73 insertions(+), 62 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
treespaceServer().
For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Author: Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>),
Michelle Kendall [aut, cre] (<https://orcid.org/0000-0001-7344-7071>),
Jacob Almagro-Garcia [aut] (<https://orcid.org/0000-0002-0595-7333>),
Caroline Colijn [aut] (<https://orcid.org/0000-0001-6097-6708>)
Maintainer: Michelle Kendall <michelle.kendall@warwick.ac.uk>
Diff between treespace versions 1.1.3.2 dated 2019-12-08 and 1.1.4.0 dated 2020-11-17
treespace-1.1.3.2/treespace/inst/doc/DengueVignette.R |only treespace-1.1.3.2/treespace/inst/doc/TransmissionTreesVignette.R |only treespace-1.1.3.2/treespace/inst/doc/introduction.R |only treespace-1.1.3.2/treespace/inst/doc/tipCategories.R |only treespace-1.1.3.2/treespace/vignettes/construction.png |only treespace-1.1.3.2/treespace/vignettes/treespace3d.png |only treespace-1.1.3.2/treespace/vignettes/treespaceDensiTree.png |only treespace-1.1.3.2/treespace/vignettes/treespaceTree.png |only treespace-1.1.3.2/treespace/vignettes/vignettes |only treespace-1.1.4.0/treespace/DESCRIPTION | 28 treespace-1.1.4.0/treespace/MD5 | 72 treespace-1.1.4.0/treespace/NAMESPACE | 1 treespace-1.1.4.0/treespace/NEWS.md |only treespace-1.1.4.0/treespace/R/metrics.R | 3 treespace-1.1.4.0/treespace/R/servers.R | 2 treespace-1.1.4.0/treespace/R/transmissionTrees.R | 7 treespace-1.1.4.0/treespace/R/treespace.R | 44 treespace-1.1.4.0/treespace/README.md | 2 treespace-1.1.4.0/treespace/build/vignette.rds |binary treespace-1.1.4.0/treespace/inst/doc/DengueVignette.Rmd | 344 treespace-1.1.4.0/treespace/inst/doc/DengueVignette.html | 4623 ----- treespace-1.1.4.0/treespace/inst/doc/TransmissionTreesVignette.Rmd | 205 treespace-1.1.4.0/treespace/inst/doc/TransmissionTreesVignette.html | 383 treespace-1.1.4.0/treespace/inst/doc/introduction.Rmd | 379 treespace-1.1.4.0/treespace/inst/doc/introduction.html | 9032 ---------- treespace-1.1.4.0/treespace/inst/doc/tipCategories.Rmd | 315 treespace-1.1.4.0/treespace/inst/doc/tipCategories.html | 407 treespace-1.1.4.0/treespace/man/DengueBEASTMCC.Rd | 4 treespace-1.1.4.0/treespace/man/DengueSeqs.Rd | 4 treespace-1.1.4.0/treespace/man/DengueTrees.Rd | 4 treespace-1.1.4.0/treespace/man/fluTrees.Rd | 4 treespace-1.1.4.0/treespace/man/treespace.Rd | 21 treespace-1.1.4.0/treespace/man/treespaceServer.Rd | 2 treespace-1.1.4.0/treespace/man/woodmiceTrees.Rd | 4 treespace-1.1.4.0/treespace/tests/testthat/testbasics.R | 17 treespace-1.1.4.0/treespace/vignettes/DengueVignette.Rmd | 344 treespace-1.1.4.0/treespace/vignettes/TransmissionTreesVignette.Rmd | 205 treespace-1.1.4.0/treespace/vignettes/introduction.Rmd | 379 treespace-1.1.4.0/treespace/vignettes/tipCategories.Rmd | 315 39 files changed, 376 insertions(+), 16774 deletions(-)
Title: Perform Monothetic Clustering with Extensions to Circular Data
Description: Implementation of the Monothetic Clustering
algorithm (Chavent, 1998 <doi:10.1016/S0167-8655(98)00087-7>) on
continuous data sets. A lot of extensions are included in the package,
including applying Monothetic clustering on data sets with circular
variables, visualizations with the results, and permutation and
cross-validation based tests to support the decision on the number of
clusters.
Author: Tan Tran [aut, cre] (<https://orcid.org/0000-0001-9881-6339>),
Brian McGuire [aut],
Mark Greenwood [aut] (<https://orcid.org/0000-0001-6933-1201>)
Maintainer: Tan Tran <vinhtantran@gmail.com>
Diff between monoClust versions 1.0.0 dated 2020-11-06 and 1.1.0 dated 2020-11-17
monoClust-1.0.0/monoClust/data/arctic_2019.rda |only monoClust-1.0.0/monoClust/man/arctic_2019.Rd |only monoClust-1.0.0/monoClust/man/get_oper.Rd |only monoClust-1.1.0/monoClust/DESCRIPTION | 15 +- monoClust-1.1.0/monoClust/MD5 | 81 ++++++------- monoClust-1.1.0/monoClust/NAMESPACE | 2 monoClust-1.1.0/monoClust/NEWS.md | 23 +++ monoClust-1.1.0/monoClust/R/MonoClust.R | 35 ++++- monoClust-1.1.0/monoClust/R/cv.test.R | 3 monoClust-1.1.0/monoClust/R/data.R | 30 ---- monoClust-1.1.0/monoClust/R/ggcv.R | 1 monoClust-1.1.0/monoClust/R/ggpcp.R | 5 monoClust-1.1.0/monoClust/R/mono_utils.R | 106 +++++++++++------ monoClust-1.1.0/monoClust/R/perm.test.R | 17 +- monoClust-1.1.0/monoClust/R/plot.MonoClust.R | 2 monoClust-1.1.0/monoClust/R/plot.cv.MonoClust.R | 1 monoClust-1.1.0/monoClust/R/predict.MonoClust.R | 12 - monoClust-1.1.0/monoClust/R/print.MonoClust.R | 4 monoClust-1.1.0/monoClust/README.md | 10 + monoClust-1.1.0/monoClust/build/partial.rdb |only monoClust-1.1.0/monoClust/inst/doc/monoclust.Rmd | 3 monoClust-1.1.0/monoClust/inst/doc/monoclust.html | 130 ++++++++------------- monoClust-1.1.0/monoClust/man/MonoClust.Rd | 9 - monoClust-1.1.0/monoClust/man/MonoClust.object.Rd |only monoClust-1.1.0/monoClust/man/checkem.Rd | 2 monoClust-1.1.0/monoClust/man/circ_arith.Rd | 2 monoClust-1.1.0/monoClust/man/cluster_stats.Rd | 7 - monoClust-1.1.0/monoClust/man/create_labels.Rd | 2 monoClust-1.1.0/monoClust/man/cv.test.Rd | 3 monoClust-1.1.0/monoClust/man/find_split.Rd | 2 monoClust-1.1.0/monoClust/man/ggcv.Rd | 3 monoClust-1.1.0/monoClust/man/make_jump_table.Rd | 6 monoClust-1.1.0/monoClust/man/monoClust-package.Rd | 3 monoClust-1.1.0/monoClust/man/new_node.Rd | 8 - monoClust-1.1.0/monoClust/man/perm.test.Rd | 8 - monoClust-1.1.0/monoClust/man/plot.MonoClust.Rd | 2 monoClust-1.1.0/monoClust/man/plot.cv.MonoClust.Rd | 3 monoClust-1.1.0/monoClust/man/plot_tree.Rd | 2 monoClust-1.1.0/monoClust/man/print.MonoClust.Rd | 2 monoClust-1.1.0/monoClust/man/test_split.Rd | 3 monoClust-1.1.0/monoClust/man/to_deg_rad.Rd | 5 monoClust-1.1.0/monoClust/man/wind_sensit_2007.Rd | 6 monoClust-1.1.0/monoClust/man/wind_sensit_2008.Rd | 6 monoClust-1.1.0/monoClust/vignettes/monoclust.Rmd | 3 44 files changed, 309 insertions(+), 258 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing (rtciles()).
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.1.0 dated 2020-10-22 and 0.1.1 dated 2020-11-17
inti-0.1.0/inti/inst/doc/inti.R |only inti-0.1.0/inti/inst/doc/inti.Rmd |only inti-0.1.0/inti/inst/doc/inti.html |only inti-0.1.0/inti/inst/rticles/setup.r |only inti-0.1.0/inti/inst/rticles/template/files/setup.r |only inti-0.1.0/inti/inst/tarpuy/setup.r |only inti-0.1.0/inti/inst/yupanapro/setup.r |only inti-0.1.0/inti/vignettes/files/setup.r |only inti-0.1.0/inti/vignettes/inti.Rmd |only inti-0.1.1/inti/DESCRIPTION | 18 inti-0.1.1/inti/LICENSE | 4 inti-0.1.1/inti/MD5 | 128 inti-0.1.1/inti/NAMESPACE | 4 inti-0.1.1/inti/NEWS.md | 34 inti-0.1.1/inti/R/H2cal.R | 2 inti-0.1.1/inti/R/fieldbook_design.R | 2 inti-0.1.1/inti/R/fieldbook_mvr.R | 77 inti-0.1.1/inti/R/fieldbook_report.R | 6 inti-0.1.1/inti/R/fieldbook_summary.R | 18 inti-0.1.1/inti/R/include_figure.R | 181 - inti-0.1.1/inti/R/include_table.R | 166 - inti-0.1.1/inti/R/info_figure.R |only inti-0.1.1/inti/R/info_table.R |only inti-0.1.1/inti/R/mean_comparison.R | 70 inti-0.1.1/inti/R/means_lm.R | 12 inti-0.1.1/inti/R/plot_smr.R | 2 inti-0.1.1/inti/R/rticles.R | 17 inti-0.1.1/inti/R/tarpuy.R | 17 inti-0.1.1/inti/R/web_table.R | 16 inti-0.1.1/inti/R/yupana.R | 17 inti-0.1.1/inti/README.md | 34 inti-0.1.1/inti/build/vignette.rds |binary inti-0.1.1/inti/inst/doc/apps.R |only inti-0.1.1/inti/inst/doc/apps.Rmd |only inti-0.1.1/inti/inst/doc/apps.html |only inti-0.1.1/inti/inst/doc/heritability.R | 10 inti-0.1.1/inti/inst/doc/heritability.Rmd | 29 inti-0.1.1/inti/inst/doc/heritability.html | 156 - inti-0.1.1/inti/inst/doc/policy.Rmd |only inti-0.1.1/inti/inst/doc/policy.html |only inti-0.1.1/inti/inst/rticles/rsconnect/shinyapps.io/flavjack/rticles.dcf | 6 inti-0.1.1/inti/inst/rticles/server.R | 46 inti-0.1.1/inti/inst/rticles/template/_output.yml | 4 inti-0.1.1/inti/inst/rticles/template/files/style_thesis.docx |binary inti-0.1.1/inti/inst/rticles/template/index.rmd | 158 - inti-0.1.1/inti/inst/rticles/ui.R | 33 inti-0.1.1/inti/inst/rticles/www/analytics.html | 4 inti-0.1.1/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 inti-0.1.1/inti/inst/tarpuy/server.R | 50 inti-0.1.1/inti/inst/tarpuy/ui.R | 102 inti-0.1.1/inti/inst/tarpuy/www/analytics.html | 14 inti-0.1.1/inti/inst/tarpuy/www/bootstrap_sandstone.css | 1 inti-0.1.1/inti/inst/yupanapro/rsconnect/shinyapps.io/flavjack/yupanapro.dcf | 6 inti-0.1.1/inti/inst/yupanapro/server.R | 210 + inti-0.1.1/inti/inst/yupanapro/ui.R | 145 - inti-0.1.1/inti/inst/yupanapro/www/analytics.html | 4 inti-0.1.1/inti/inst/yupanapro/www/bootstrap_sandstone.css | 1 inti-0.1.1/inti/man/fieldbook_design.Rd | 2 inti-0.1.1/inti/man/fieldbook_mvr.Rd | 12 inti-0.1.1/inti/man/fieldbook_summary.Rd | 8 inti-0.1.1/inti/man/figures/logo.png |binary inti-0.1.1/inti/man/include_figure.Rd | 40 inti-0.1.1/inti/man/include_table.Rd | 43 inti-0.1.1/inti/man/info_figure.Rd |only inti-0.1.1/inti/man/info_table.Rd |only inti-0.1.1/inti/man/mean_comparison.Rd | 22 inti-0.1.1/inti/man/plot_smr.Rd | 2 inti-0.1.1/inti/man/rticles.Rd | 5 inti-0.1.1/inti/man/tarpuy.Rd | 5 inti-0.1.1/inti/man/web_table.Rd | 2 inti-0.1.1/inti/man/yupana.Rd | 5 inti-0.1.1/inti/vignettes/apps.Rmd |only inti-0.1.1/inti/vignettes/files/book.bib | 1371 ---------- inti-0.1.1/inti/vignettes/heritability.Rmd | 29 inti-0.1.1/inti/vignettes/policy.Rmd |only 75 files changed, 1245 insertions(+), 2111 deletions(-)
Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between BatchGetSymbols versions 2.5.7 dated 2020-04-21 and 2.5.9 dated 2020-11-17
DESCRIPTION | 10 +- MD5 | 14 +- NEWS.md | 10 ++ R/BatchGetSymbols.R | 64 ++++++++++-- R/Utils.R | 4 build/vignette.rds |binary inst/doc/BatchGetSymbols-vignette.html | 164 ++++++++++++++++++++++----------- man/BatchGetSymbols.Rd | 3 8 files changed, 192 insertions(+), 77 deletions(-)
More information about BatchGetSymbols at CRAN
Permanent link
Title: Read and write TIFF images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between tiff versions 0.1-5 dated 2013-09-04 and 0.1-6 dated 2020-11-17
tiff-0.1-5/tiff/configure.win |only tiff-0.1-6/tiff/DESCRIPTION | 6 +++--- tiff-0.1-6/tiff/MD5 | 8 ++++---- tiff-0.1-6/tiff/NEWS | 3 +++ tiff-0.1-6/tiff/src/Makevars.win | 19 +++++++++++-------- tiff-0.1-6/tiff/tools |only 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate
ordinal regression models with composite likelihood methods. Methodological details are given in Hirk, Hornik, Vana (2020) <doi:10.18637/jss.v093.i04>.
Author: Rainer Hirk [aut, cre],
Kurt Hornik [aut],
Laura Vana [aut],
Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>
Diff between mvord versions 1.0.1 dated 2020-05-28 and 1.1.0 dated 2020-11-17
DESCRIPTION | 10 MD5 | 41 +-- NAMESPACE | 1 NEWS | 8 R/fit_fast.R |only R/mvord.R | 7 R/mvord_fit.R | 109 ++++++++- R/predict.R | 212 +++++++++--------- R/utilities.R | 154 ++++++++++--- inst/doc/vignette_mvord.pdf |binary inst/doc/vignette_mvord2.html | 408 +++++++++++++++++------------------ tests/check_toy_example.R | 325 ++++++++++++++++++++++++--- vignettes/mvord.bib | 2 vignettes/res1.rda |binary vignettes/res2.rda |binary vignettes/res_AR1_probit.rda |binary vignettes/res_cor_logit.rda |binary vignettes/res_cor_probit_2raters.rda |binary vignettes/res_cor_probit_3raters.rda |binary vignettes/res_cor_probit_simple.rda |binary vignettes/res_essay.rda |binary vignettes/res_srhs.rda |binary 22 files changed, 868 insertions(+), 409 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Combines a collection of metrics and proper scoring rules
(Tilmann Gneiting & Adrian E Raftery (2007)
<doi:10.1198/016214506000001437>) with an easy to
use wrapper that can be used to automatically evaluate predictions.
Apart from proper scoring rules functions are provided to assess bias,
sharpness and calibration (Sebastian Funk, Anton Camacho, Adam J. Kucharski,
Rachel Lowe, Rosalind M. Eggo, W. John Edmunds (2019)
<doi:10.1371/journal.pcbi.1006785>) of forecasts.
Several types of predictions can be evaluated:
probabilistic forecasts (generally
predictive samples generated by Markov Chain Monte Carlo procedures),
quantile forecasts or point forecasts. Observed values and predictions
can be either continuous, integer, or binary. Users can either choose
to apply these rules separately in a vector / matrix format that can
be flexibly used within other packages, or they can choose to do an
automatic evaluation of their forecasts. This is implemented with
'data.table' and provides a consistent and very efficient framework for
evaluating various types of predictions.
Author: Nikos Bosse [aut, cre] (<https://orcid.org/0000-0002-7750-5280>),
Sam Abbott [aut] (<https://orcid.org/0000-0001-8057-8037>),
Joel Hellewell [ctb] (<https://orcid.org/0000-0003-2683-0849>),
Sophie Meakins [ctb],
James Munday [ctb],
Katharine Sherratt [ctb],
Sebastian Funk [aut]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 0.1.0 dated 2020-06-14 and 0.1.4 dated 2020-11-17
scoringutils-0.1.0/scoringutils/README.md |only scoringutils-0.1.0/scoringutils/data/quantile_example_data.rda |only scoringutils-0.1.0/scoringutils/man/quantile_example_data.Rd |only scoringutils-0.1.4/scoringutils/DESCRIPTION | 11 scoringutils-0.1.4/scoringutils/MD5 | 97 + scoringutils-0.1.4/scoringutils/NAMESPACE | 57 - scoringutils-0.1.4/scoringutils/R/bias.R | 118 ++ scoringutils-0.1.4/scoringutils/R/data.R | 62 - scoringutils-0.1.4/scoringutils/R/eval_forecasts.R | 561 ++++++++-- scoringutils-0.1.4/scoringutils/R/interval_score.R | 39 scoringutils-0.1.4/scoringutils/R/metrics_point_forecasts.R | 38 scoringutils-0.1.4/scoringutils/R/pit.R | 88 + scoringutils-0.1.4/scoringutils/R/pivoting_functions.R |only scoringutils-0.1.4/scoringutils/R/plot.R |only scoringutils-0.1.4/scoringutils/R/scoringRules_wrappers.R | 9 scoringutils-0.1.4/scoringutils/R/scoringutils.R | 27 scoringutils-0.1.4/scoringutils/R/utils.R | 37 scoringutils-0.1.4/scoringutils/build/vignette.rds |binary scoringutils-0.1.4/scoringutils/data/binary_example_data.rda |binary scoringutils-0.1.4/scoringutils/data/continuous_example_data.rda |binary scoringutils-0.1.4/scoringutils/data/integer_example_data.rda |binary scoringutils-0.1.4/scoringutils/data/quantile_example_data_long.rda |only scoringutils-0.1.4/scoringutils/data/quantile_example_data_plain.rda |only scoringutils-0.1.4/scoringutils/data/quantile_example_data_wide.rda |only scoringutils-0.1.4/scoringutils/inst/doc/scoringutils.R | 113 +- scoringutils-0.1.4/scoringutils/inst/doc/scoringutils.Rmd | 213 ++- scoringutils-0.1.4/scoringutils/inst/doc/scoringutils.html | 438 ++++--- scoringutils-0.1.4/scoringutils/man/ae_median.Rd |only scoringutils-0.1.4/scoringutils/man/binary_example_data.Rd | 7 scoringutils-0.1.4/scoringutils/man/continuous_example_data.Rd | 7 scoringutils-0.1.4/scoringutils/man/correlation_plot.Rd |only scoringutils-0.1.4/scoringutils/man/crps.Rd | 3 scoringutils-0.1.4/scoringutils/man/dss.Rd | 3 scoringutils-0.1.4/scoringutils/man/eval_forecasts.Rd | 168 ++ scoringutils-0.1.4/scoringutils/man/figures |only scoringutils-0.1.4/scoringutils/man/hist_PIT.Rd | 6 scoringutils-0.1.4/scoringutils/man/hist_PIT_quantile.Rd |only scoringutils-0.1.4/scoringutils/man/integer_example_data.Rd | 7 scoringutils-0.1.4/scoringutils/man/interval_coverage.Rd |only scoringutils-0.1.4/scoringutils/man/interval_score.Rd | 19 scoringutils-0.1.4/scoringutils/man/logs.Rd | 3 scoringutils-0.1.4/scoringutils/man/pit.Rd | 6 scoringutils-0.1.4/scoringutils/man/plot_predictions.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_bias.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_coverage.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_example_data_long.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_example_data_plain.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_example_data_wide.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_to_long.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_to_range.Rd |only scoringutils-0.1.4/scoringutils/man/quantile_to_wide.Rd |only scoringutils-0.1.4/scoringutils/man/range_plot.Rd |only scoringutils-0.1.4/scoringutils/man/range_to_quantile.Rd |only scoringutils-0.1.4/scoringutils/man/sample_to_quantile.Rd |only scoringutils-0.1.4/scoringutils/man/sample_to_range.Rd |only scoringutils-0.1.4/scoringutils/man/score_heatmap.Rd |only scoringutils-0.1.4/scoringutils/man/score_table.Rd |only scoringutils-0.1.4/scoringutils/man/scoringutils.Rd | 27 scoringutils-0.1.4/scoringutils/man/wis_components.Rd |only scoringutils-0.1.4/scoringutils/vignettes/scoringutils.Rmd | 213 ++- 60 files changed, 1720 insertions(+), 657 deletions(-)
Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for lm() [linear model], glm() [general linear model], glm.nb() [negative binomial model],
polr() [ordinal logistic model], multinom() [multinomial model] and tobit() [tobit model] using Monte Carlo simulations or bootstrap. Reference: Bennet A. Zelner (2009) <doi:10.1002/smj.783>.
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 3.1-0 dated 2019-09-04 and 4.0-0 dated 2020-11-17
DESCRIPTION | 19 +++-- MD5 | 63 ++++++++++-------- NAMESPACE | 8 +- R/basepredict.R | 3 R/basepredict.glm.R | 152 ++++++++++++++++++++++++++++---------------- R/basepredict.lm.R | 80 +++++++++++++++++------ R/basepredict.multinom.R | 106 ++++++++++++++++++++---------- R/basepredict.polr.R | 103 +++++++++++++++++++---------- R/basepredict.tobit.R |only R/dc.R | 3 R/dc.glm.R | 133 +++++++++++++++++++------------------- R/dc.lm.R | 121 ++++++++++++++++++++--------------- R/dc.multinom.R | 115 ++++++++++++++++++++++----------- R/dc.polr.R | 117 ++++++++++++++++++++++----------- R/dc.tobit.R |only R/getBaseCombinations.R | 10 ++ R/getFactorCombinations.R | 4 - R/getValues.R | 47 +++++++++---- R/predicts.R | 58 ++++++++++++---- build |only inst |only man/basepredict.Rd | 17 +++- man/basepredict.glm.Rd | 13 ++- man/basepredict.lm.Rd | 13 ++- man/basepredict.multinom.Rd | 15 +++- man/basepredict.polr.Rd | 15 +++- man/basepredict.tobit.Rd |only man/dc.Rd | 21 +++--- man/dc.glm.Rd | 17 +++- man/dc.lm.Rd | 17 +++- man/dc.multinom.Rd | 19 +++-- man/dc.polr.Rd | 19 +++-- man/dc.tobit.Rd |only man/predicts.Rd | 14 +++- vignettes |only 35 files changed, 850 insertions(+), 472 deletions(-)
Title: Gaussian Process Models for Scalar and Functional Inputs
Description: Construction and smart selection of Gaussian process models
with emphasis on treatment of functional inputs. This package
offers: (i) flexible modeling of functional-input regression
problems through the fairly general Gaussian process model; (ii)
built-in dimension reduction for functional inputs; (iii)
heuristic optimization of the structural parameters of the model
(e.g., active inputs, kernel function, type of distance).
Metamodeling background is provided in
Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>.
The algorithm for structural parameter optimization is described
in <https://hal.archives-ouvertes.fr/hal-02532713>.
Author: Jose Betancourt [cre, aut],
François Bachoc [aut],
Thierry Klein [aut],
Deborah Idier [ctb],
Jeremy Rohmer [ctb]
Maintainer: Jose Betancourt <djbetancourt@uninorte.edu.co>
Diff between funGp versions 0.1.0 dated 2020-04-22 and 0.2.0 dated 2020-11-17
funGp-0.1.0/funGp/man/format4pred.Rd |only funGp-0.2.0/funGp/DESCRIPTION | 8 funGp-0.2.0/funGp/MD5 | 40 +- funGp-0.2.0/funGp/NAMESPACE | 2 funGp-0.2.0/funGp/NEWS.md | 28 + funGp-0.2.0/funGp/R/0_funGp_Doc.R | 6 funGp-0.2.0/funGp/R/1_Xfgpm_Class.R | 39 +- funGp-0.2.0/funGp/R/1_fgpm_Class.R | 10 funGp-0.2.0/funGp/R/3_ant_admin.R | 504 ++++++++++++++++++++++------ funGp-0.2.0/funGp/R/3_ant_search.R | 57 ++- funGp-0.2.0/funGp/R/3_training_F.R | 3 funGp-0.2.0/funGp/R/3_training_S.R | 3 funGp-0.2.0/funGp/R/3_training_SF.R | 4 funGp-0.2.0/funGp/R/7_checkingFunctions.R | 1 funGp-0.2.0/funGp/R/7_distanceFunctions.R | 1 funGp-0.2.0/funGp/R/7_plottingFunctions.R | 83 +++- funGp-0.2.0/funGp/README.md | 12 funGp-0.2.0/funGp/man/fgpm.Rd | 9 funGp-0.2.0/funGp/man/fgpm_factory.Rd | 15 funGp-0.2.0/funGp/man/funGp-package.Rd | 6 funGp-0.2.0/funGp/man/get_active_in.Rd |only funGp-0.2.0/funGp/man/package-deprecated.Rd |only funGp-0.2.0/funGp/man/which_on.Rd |only 23 files changed, 624 insertions(+), 207 deletions(-)
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains functions and
classes to be used in conjunction with other 'tidymodels' packages for
finding reasonable values of hyper-parameters in models, pre-processing
methods, and post-processing steps.
Author: Max Kuhn [aut, cre],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between tune versions 0.1.1 dated 2020-07-08 and 0.1.2 dated 2020-11-17
DESCRIPTION | 19 MD5 | 143 +++---- NAMESPACE | 46 +- NEWS.md | 37 + R/0_imports.R | 18 R/acquisition.R | 6 R/augment.R |only R/checks.R | 144 +++++-- R/collect.R | 50 +- R/conf_mat_resampled.R | 2 R/control.R | 66 +++ R/extract.R | 84 +++- R/finalize.R | 3 R/grid_code_paths.R | 740 ++++++++++++++----------------------- R/grid_helpers.R | 506 +++++++++++++++++++++---- R/grid_performance.R | 84 ++-- R/last_fit.R | 55 -- R/load_ns.R | 46 ++ R/logging.R | 103 +++-- R/min_grid.R | 120 ++++-- R/parallel.R | 2 R/plots.R | 36 + R/reexports.R |only R/resample.R | 384 ++----------------- R/select_best.R | 44 ++ R/symbol.R | 57 +- R/tunable.R | 181 --------- R/tune_bayes.R | 146 ++++--- R/tune_grid.R | 136 +++--- R/tune_results.R | 18 R/zzz.R | 1 README.md | 4 data/example_ames_knn.RData |binary inst/WORDLIST | 2 man/augment.tune_results.Rd |only man/collect_predictions.Rd | 15 man/control_bayes.Rd | 35 + man/control_grid.Rd | 32 + man/empty_ellipses.Rd | 2 man/fit_resamples.Rd | 11 man/message_wrap.Rd |only man/min_grid.Rd | 65 +++ man/reexports.Rd | 8 man/required_pkgs.Rd |only man/show_best.Rd | 2 man/tunable.Rd | 68 --- man/tune_bayes.Rd | 2 man/tune_grid.Rd | 20 - tests/testthat/Rplots.pdf |binary tests/testthat/knn_gp.rds |binary tests/testthat/knn_grid.rds |binary tests/testthat/knn_results.rds |binary tests/testthat/knn_set.rds |binary tests/testthat/lm_bayes.rds |binary tests/testthat/lm_resamples.rds |binary tests/testthat/message_wrap |only tests/testthat/rcv_results.rds |binary tests/testthat/svm_reg_results.rds |binary tests/testthat/svm_results.rds |binary tests/testthat/test-acquisition.R | 14 tests/testthat/test-augment.R |only tests/testthat/test-autoplot.R | 18 tests/testthat/test-bayes.R | 144 +++++-- tests/testthat/test-checks.R | 17 tests/testthat/test-compat-dplyr.R | 2 tests/testthat/test-event-level.R |only tests/testthat/test-extract.R | 21 - tests/testthat/test-grid.R | 106 ++++- tests/testthat/test-last-fit.R | 57 +- tests/testthat/test-logging.R | 42 ++ tests/testthat/test-min-grid.R | 32 - tests/testthat/test-misc.R | 7 tests/testthat/test-resample.R | 128 +++++- tests/testthat/test-symbol.R | 12 tests/testthat/test_objects.RData |binary 75 files changed, 2406 insertions(+), 1737 deletions(-)
Title: Music Notation Syntax, Manipulation, Analysis and Transcription
in R
Description: Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing and analyzing musical information in R.
The music notation framework facilitates creating and analyzing music data in notation form.
Music data can be viewed, manipulated and analyzed while in different forms of representation based around different data structures: strings and data frames.
Each representation offers advantages over the other for different use cases.
Music syntax can be entered directly and represented in character strings to minimize the formatting overhead of data entry by using simple data structures, for example when wanting to quickly enter and transcribe short pieces of music to sheet music or tablature.
The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation.
The same music data can also be organized in tidy data frames, allowing for a more familiar and powerful approach to the analysis of large amounts of structured music data.
Functions are available for mapping seamlessly between these data structures and their representations of musical information.
The package also provides API wrapper functions for transcribing musical representations in R into guitar tablature ("tabs") and basic sheet music using the 'LilyPond' backend (<http://lilypond.org>).
'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax.
The package generates 'LilyPond' files from R code and can pass them to 'LilyPond' to be rendered into sheet music pdf files.
The package offers nominal MIDI file output support in conjunction with rendering sheet music.
The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>
Diff between tabr versions 0.4.3 dated 2020-05-05 and 0.4.4 dated 2020-11-17
DESCRIPTION | 8 - MD5 | 27 ++--- NEWS.md | 4 R/snippet.R | 40 ++++---- README.md | 180 +++++++++++++++++++----------------- build/vignette.rds |binary inst/WORDLIST | 59 ++++++----- inst/doc/tabr-prog-chords.html | 76 ++++++++++++++- inst/doc/tabr-prog-music.html | 64 ++++++++++++ inst/doc/tabr-prog-noteinfo.html | 64 ++++++++++++ inst/doc/tabr-prog-notes.html | 64 ++++++++++++ inst/doc/tabr-prog-nw.html | 64 ++++++++++++ inst/doc/tabr-prog-scales.html | 64 ++++++++++++ man/figures/README-plot_music-1.png |only man/plot_music.Rd | 33 +++++- 15 files changed, 586 insertions(+), 161 deletions(-)
Title: Scaling with Ranked Subsampling
Description: Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is a popular method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. An alternative to rarefying is scaling with ranked subsampling (SRS). SRS consists of two steps. In the first step, the total counts for all OTUs (operational taxonomic units) or species in each sample are divided by a scaling factor chosen in such a way that the sum of the scaled counts Cscaled equals Cmin. In the second step, the non-integer Cscaled values are converted into integers by an algorithm that we dub ranked subsampling. The Cscaled value for each OTU or species is split into the integer part Cint (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or equal to Cmin, additional delta C = Cmin - the sum of Cint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches delta C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking delta C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement. See Beule & Karlovsky (2020) <doi:10.7717/peerj.9593> for details.
Author: Lukas Beule [aut, cre],
Vitor Heidrich [aut],
Devon O'rourke [aut],
Petr Karlovsky [aut]
Maintainer: Lukas Beule <lukas.beule@agr.uni-goettingen.de>
Diff between SRS versions 0.2.0 dated 2020-11-14 and 0.2.1 dated 2020-11-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/SRS.R | 4 +++- R/SRScurve.R | 38 ++++++++++++++++++++++++++++++++------ 4 files changed, 41 insertions(+), 13 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>
Diff between scTenifoldNet versions 1.2.3 dated 2020-08-25 and 1.2.4 dated 2020-11-17
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- R/scTenifoldNet.R | 5 +++-- R/tensorDecomposition.R | 7 ++++--- README.md | 4 ++-- inst |only man/cpDecomposition.Rd | 3 +-- man/makeNetworks.Rd | 11 +++++++++-- man/pcNet.Rd | 10 ++++++++-- man/scQC.Rd | 9 +++++++-- man/scTenifoldNet.Rd | 26 +++++++++++++++++++++----- man/tensorDecomposition.Rd | 12 ++++++++++-- 12 files changed, 81 insertions(+), 37 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] (<https://orcid.org/0000-0003-4152-5308>),
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.5-1 dated 2020-01-28 and 0.6-0 dated 2020-11-17
DESCRIPTION | 16 - MD5 | 74 +++---- NAMESPACE | 10 NEWS | 21 + R/anchor.R | 101 +++++++-- R/gpcmodel.R | 9 R/graphics.R | 14 - R/mptmodel.R | 73 +++++- R/paircomp.R | 54 ++--- R/pcmodel.R | 4 R/plmodel.R | 9 R/raschmodel.R | 6 R/rsmodel.R | 6 build/partial.rdb |binary data/ConspiracistBeliefs2016.rda |binary data/FirstNames.rda |binary data/GermanParties2009.rda |binary data/MathExam14W.rda |binary data/MemoryDeficits.rda |binary data/PairClustering.rda |binary data/Sim3PL.rda |binary data/SoundQuality.rda |binary data/SourceMonitoring.rda |binary data/StereotypeThreat.rda |binary data/VerbalAggression.rda |binary data/YouthGratitude.rda |binary demo |only inst/CITATION | 104 +++------ man/FirstNames.Rd | 2 man/SoundQuality.Rd | 6 man/anchor.Rd | 22 +- man/plot.paircomp.Rd | 5 man/rgpcm.Rd |only man/rpcm.Rd |only man/rpl.Rd |only man/rrm.Rd |only man/rrsm.Rd |only src/esf.c | 1 tests/Examples/psychotools-Ex.Rout.save | 337 +++++++++++++++++++++++++++++++- 39 files changed, 672 insertions(+), 202 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],
Leonard Henckel [ctb],
Joris Mooij [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-12 dated 2020-09-22 and 2.7-0 dated 2020-11-17
DESCRIPTION | 14 MD5 | 45 - NAMESPACE | 11 R/dsepAM.R |only R/fci.R |only R/fciPlus.R |only R/pag2anc.R |only R/pag2conf.R |only R/pag2edge.R |only R/pcalg.R | 2018 +++++++++++++++++++++++----------------------- R/pdsep.R |only R/searchAM.R |only R/udag2pag.R |only build/vignette.rds |binary inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary man/dsep.Rd | 7 man/dsepAM.Rd |only man/dsepAMTest.Rd |only man/dsepTest.Rd | 3 man/fci.Rd | 215 +++- man/fciPlus.Rd | 104 ++ man/pag2anc.Rd |only man/pag2conf.Rd |only man/pag2edge.Rd |only man/pdsep.Rd | 11 man/searchAM.Rd |only man/udag2pag.Rd | 39 tests/test_dsepAM.R |only tests/test_dsepAMTest.R |only tests/test_pag2anc.R |only tests/test_pag2conf.R |only tests/test_pag2edge.R |only tests/test_searchAM.R |only 34 files changed, 1371 insertions(+), 1096 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS
Optimization
Description: Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the
'Scilab' optimization documentation located at
<https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukhah [ctb],
Dirk Eddelbuettel [ctb],
Bruno Jofret [ctb],
INRIA [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.1-9 dated 2020-07-02 and 6.0.1-10 dated 2020-11-17
n1qn1-6.0.1-10/n1qn1/DESCRIPTION | 20 ++-- n1qn1-6.0.1-10/n1qn1/MD5 | 28 ++---- n1qn1-6.0.1-10/n1qn1/R/n1qn1.R | 80 ++++++++++--------- n1qn1-6.0.1-10/n1qn1/src/Makevars |only n1qn1-6.0.1-10/n1qn1/src/Makevars.win |only n1qn1-6.0.1-10/n1qn1/src/RcppExpMod.cpp | 36 ++++---- n1qn1-6.0.1-10/n1qn1/src/ajour.c |only n1qn1-6.0.1-10/n1qn1/src/calmaj.c |only n1qn1-6.0.1-10/n1qn1/src/init.c | 30 +++---- n1qn1-6.0.1-10/n1qn1/src/n1qn1_all.c |only n1qn1-6.0.1-10/n1qn1/src/proj.c |only n1qn1-6.0.1-10/n1qn1/src/satur.c |only n1qn1-6.0.1-10/n1qn1/tests/testthat/test-banana.R | 90 +++++++++++----------- n1qn1-6.0.1-9/n1qn1/cleanup |only n1qn1-6.0.1-9/n1qn1/cleanup.win |only n1qn1-6.0.1-9/n1qn1/configure |only n1qn1-6.0.1-9/n1qn1/configure.ac |only n1qn1-6.0.1-9/n1qn1/configure.win |only n1qn1-6.0.1-9/n1qn1/src/Makevars.in |only n1qn1-6.0.1-9/n1qn1/src/ajour.f |only n1qn1-6.0.1-9/n1qn1/src/calmaj.f |only n1qn1-6.0.1-9/n1qn1/src/n1qn1_all.f |only n1qn1-6.0.1-9/n1qn1/src/proj.f |only n1qn1-6.0.1-9/n1qn1/src/satur.f |only 24 files changed, 143 insertions(+), 141 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.5.0 dated 2020-08-13 and 0.6.0 dated 2020-11-17
mlr3misc-0.5.0/mlr3misc/R/cite_bib.R |only mlr3misc-0.5.0/mlr3misc/inst |only mlr3misc-0.5.0/mlr3misc/man/cite_bib.Rd |only mlr3misc-0.6.0/mlr3misc/DESCRIPTION | 8 mlr3misc-0.6.0/mlr3misc/MD5 | 112 +++++----- mlr3misc-0.6.0/mlr3misc/NAMESPACE | 3 mlr3misc-0.6.0/mlr3misc/NEWS.md | 10 mlr3misc-0.6.0/mlr3misc/R/crate.R |only mlr3misc-0.6.0/mlr3misc/R/encapsulate.R | 24 +- mlr3misc-0.6.0/mlr3misc/R/insert_named.R | 14 - mlr3misc-0.6.0/mlr3misc/R/invoke.R | 12 - mlr3misc-0.6.0/mlr3misc/R/register_namespace_callback.R |only mlr3misc-0.6.0/mlr3misc/R/remove_named.R | 8 mlr3misc-0.6.0/mlr3misc/R/require_namespaces.R | 13 - mlr3misc-0.6.0/mlr3misc/README.md | 4 mlr3misc-0.6.0/mlr3misc/man/crate.Rd |only mlr3misc-0.6.0/mlr3misc/man/encapsulate.Rd | 7 mlr3misc-0.6.0/mlr3misc/man/invoke.Rd | 15 + mlr3misc-0.6.0/mlr3misc/man/register_namespace_callback.Rd |only mlr3misc-0.6.0/mlr3misc/man/require_namespaces.Rd | 6 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_Dictionary.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_as_factor.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_as_short_string.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_check_packages_installed.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_chunk.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_compose.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_crate.R |only mlr3misc-0.6.0/mlr3misc/tests/testthat/test_cross_join.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_distinct_values.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_encapsulate.R | 23 +- mlr3misc-0.6.0/mlr3misc/tests/testthat/test_extract_vars.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_formulate.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_get_seed.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_has_element.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_ids.R | 3 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_insert.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_invoke.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_is_scalar_na.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_keep_in_bounds.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_leanify.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_load_data.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_map.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_map_values.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_modify.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_named_list.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_named_vector.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_names2.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_nin.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_printf.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_rcbind.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_require_namespaces.R | 5 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_rowwise_table.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_seq.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_set_names.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_shuffle.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_str_trunc.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_topo_sort.R | 1 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_transpose.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_unnest.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_which_max.R | 2 mlr3misc-0.6.0/mlr3misc/tests/testthat/test_with_package.R | 2 61 files changed, 173 insertions(+), 167 deletions(-)
Title: Multilevel Exponential-Family Random Graph Models
Description: Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.
Author: Jonathan Stewart [cre, aut],
Michael Schweinberger [ctb]
Maintainer: Jonathan Stewart <jrstewart@fsu.edu>
Diff between mlergm versions 0.6 dated 2020-07-03 and 0.7 dated 2020-11-17
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/MCMC_sample.R | 4 ++-- R/compute_initial_estimate.R | 4 ++-- R/initialize_object.R | 2 ++ R/mlergm.R | 18 +++++++++--------- R/step_to_chull.R | 2 +- build/vignette.rds |binary inst/doc/mlergm_tutorial.html | 6 +++--- man/mlergm.Rd | 2 +- 10 files changed, 34 insertions(+), 32 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of
functions and use them to create shells (skeletons which must be
manually completed by the user) of test files to be tested with the
'testthat' package. Sort of like python 'doctests' for R.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Thomas Quinn [rev] (<https://orcid.org/0000-0003-0286-6329>),
Laurent Gatto [rev] (<https://orcid.org/0000-0002-1520-2268>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 1.6.1 dated 2020-04-15 and 1.6.2 dated 2020-11-17
DESCRIPTION | 22 ++++---- MD5 | 30 +++++------ NEWS.md | 6 ++ R/example-extraction.R | 19 +++---- R/exemplar.R | 10 +-- R/shell-creation.R | 2 R/utils.R | 36 ++++++++++---- build/vignette.rds |binary inst/doc/one-file-at-a-time.html | 78 +++++++++++++++++++++++++++++-- inst/doc/one-function-at-a-time.html | 70 +++++++++++++++++++++++++++ inst/doc/whole-package.html | 74 ++++++++++++++++++++++++++++- man/make-test-shells.Rd | 2 tests/testthat.R | 3 - tests/testthat/test-example-extraction.R | 18 ++++--- tests/testthat/test-files.R | 7 +- tests/testthat/test-utils.R | 26 +++++----- 16 files changed, 322 insertions(+), 81 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.3.13 dated 2020-01-09 and 0.3.14 dated 2020-11-17
DESCRIPTION | 17 MD5 | 166 ++- NAMESPACE | 46 + NEWS | 45 - R/EDA.R | 39 R/binning.R | 113 +- R/compare.R |only R/correlate.R | 68 + R/diagnose.R | 10 R/discribe.R | 12 R/dlookr.R | 10 R/imputation.R | 1356 +++++++++++++++---------------- R/missing.R |only R/normality.R | 28 R/target_by.R | 49 - R/tbl_dbi.R | 66 - R/transform.R | 22 R/univariate.R |only R/utils.R | 55 + build/vignette.rds |binary inst/doc/EDA.R | 26 inst/doc/EDA.Rmd | 131 +- inst/doc/EDA.html | 746 ++++++++--------- inst/doc/diagonosis.R | 41 inst/doc/diagonosis.Rmd | 192 +++- inst/doc/diagonosis.html | 519 +++++++---- inst/doc/introduce.R |only inst/doc/introduce.Rmd |only inst/doc/introduce.html |only inst/doc/transformation.R | 26 inst/doc/transformation.Rmd | 85 - inst/doc/transformation.html | 476 ++++++---- inst/report/DataDiagnosis_Report.Rnw | 2 inst/report/DataDiagnosis_Report_KR.Rnw | 2 inst/report/EDA_Report.Rnw | 2 inst/report/EDA_Report_KR.Rmd | 4 inst/report/EDA_Report_KR.Rnw | 2 inst/report/Transformation_Report.Rnw | 2 inst/report/Transformation_Report_KR.Rnw | 2 man/binning.Rd | 32 man/binning_by.Rd | 54 - man/compare_category.data.frame.Rd |only man/compare_numeric.data.frame.Rd |only man/correlate.data.frame.Rd | 17 man/correlate.tbl_dbi.Rd | 19 man/describe.data.frame.Rd | 4 man/describe.tbl_dbi.Rd | 4 man/diagnose_category.data.frame.Rd | 4 man/diagnose_category.tbl_dbi.Rd | 4 man/diagnose_outlier.data.frame.Rd | 2 man/diagnose_outlier.tbl_dbi.Rd | 2 man/diagnose_report.data.frame.Rd | 6 man/diagnose_report.tbl_dbi.Rd | 2 man/dlookr-package.Rd | 6 man/eda_report.data.frame.Rd | 37 man/eda_report.tbl_dbi.Rd | 18 man/find_class.Rd | 2 man/imputate_na.Rd | 16 man/imputate_outlier.Rd | 22 man/kurtosis.Rd |only man/normality.data.frame.Rd | 6 man/normality.tbl_dbi.Rd | 2 man/plot.bins.Rd | 4 man/plot.compare_category.Rd |only man/plot.compare_numeric.Rd |only man/plot.imputation.Rd | 10 man/plot.optimal_bins.Rd | 9 man/plot.relate.Rd | 4 man/plot.transform.Rd | 2 man/plot.univar_category.Rd |only man/plot.univar_numeric.Rd |only man/plot_correlate.data.frame.Rd | 6 man/plot_correlate.tbl_dbi.Rd | 13 man/plot_na_hclust.Rd |only man/plot_na_intersect.Rd |only man/plot_na_pareto.Rd |only man/plot_normality.data.frame.Rd | 4 man/plot_normality.tbl_dbi.Rd | 2 man/print.relate.Rd | 10 man/relate.Rd | 10 man/skewness.Rd |only man/summary.bins.Rd | 14 man/summary.compare_category.Rd |only man/summary.compare_numeric.Rd |only man/summary.imputation.Rd | 8 man/summary.transform.Rd | 4 man/summary.univar_category.Rd |only man/summary.univar_numeric.Rd |only man/target_by.data.frame.Rd | 4 man/transformation_report.Rd | 13 man/univar_category.data.frame.Rd |only man/univar_numeric.data.frame.Rd |only vignettes/EDA.Rmd | 131 +- vignettes/diagonosis.Rmd | 192 +++- vignettes/introduce.Rmd |only vignettes/transformation.Rmd | 85 - 96 files changed, 2880 insertions(+), 2264 deletions(-)
Title: Species Distribution Modeling
Description: Methods for species distribution modeling, that is, predicting the environmental similarity of any site to that of the locations of known occurrences of a species.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between dismo versions 1.3-2 dated 2020-11-13 and 1.3-3 dated 2020-11-17
dismo-1.3-2/dismo/src/dismo_init.c |only dismo-1.3-2/dismo/src/percRank.c |only dismo-1.3-3/dismo/DESCRIPTION | 18 +++++--- dismo-1.3-3/dismo/MD5 | 35 ++++++++-------- dismo-1.3-3/dismo/NAMESPACE | 4 - dismo-1.3-3/dismo/R/RcppExports.R |only dismo-1.3-3/dismo/R/bioclim.predict.R | 8 +-- dismo-1.3-3/dismo/R/circles.R | 18 ++++++++ dismo-1.3-3/dismo/R/gbm.plot.R | 2 dismo-1.3-3/dismo/R/maxent.R | 72 +++++++++++++++++----------------- dismo-1.3-3/dismo/R/maxent.predict.R | 4 - dismo-1.3-3/dismo/build/vignette.rds |binary dismo-1.3-3/dismo/inst/doc/brt.Rnw | 12 +---- dismo-1.3-3/dismo/inst/doc/brt.pdf |binary dismo-1.3-3/dismo/inst/doc/sdm.Rnw | 13 +----- dismo-1.3-3/dismo/inst/doc/sdm.pdf |binary dismo-1.3-3/dismo/man/maxent.Rd | 11 +++-- dismo-1.3-3/dismo/src/RcppExports.cpp |only dismo-1.3-3/dismo/src/percRank.cpp |only dismo-1.3-3/dismo/vignettes/brt.Rnw | 12 +---- dismo-1.3-3/dismo/vignettes/sdm.Rnw | 13 +----- 21 files changed, 112 insertions(+), 110 deletions(-)
Title: Composite Likelihood Inference and Diagnostics for Replicated
Spatial Ordinal Data
Description: Composite likelihood parameter estimate and asymptotic covariance matrix are calculated for the spatial ordinal data with replications, where spatial ordinal response with covariate and both spatial exponential covariance within subject and independent and identically distributed measurement error. Parameter estimation can be performed by either solving the gradient function or maximizing composite log-likelihood. Parametric bootstrapping is used to estimate the Godambe information matrix and hence the asymptotic standard error and covariance matrix with parallel processing option. Moreover, the proposed surrogate residual, which extends the results of Liu and Zhang (2017) <doi: 10.1080/01621459.2017.1292915>, can act as a useful tool for model diagnostics.
Author: Ting Fung (Ralph) Ma [cre, aut],
Pingping Wang [aut],
Jun Zhu [aut],
Dipankar Bandyopadhyay [ctb],
Yincai Tang [ctb]
Maintainer: Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>
Diff between clordr versions 1.5.0 dated 2018-12-06 and 1.6.0 dated 2020-11-17
clordr-1.5.0/clordr/R/sim_data.R |only clordr-1.6.0/clordr/DESCRIPTION | 14 - clordr-1.6.0/clordr/MD5 | 32 +-- clordr-1.6.0/clordr/NAMESPACE | 43 ++--- clordr-1.6.0/clordr/R/cl.R | 2 clordr-1.6.0/clordr/R/cl.rord.R | 2 clordr-1.6.0/clordr/R/cl_l.R | 2 clordr-1.6.0/clordr/R/cle.rord.R | 23 +- clordr-1.6.0/clordr/R/clic.R | 2 clordr-1.6.0/clordr/R/sim.rord.R |only clordr-1.6.0/clordr/R/sur_residual.R | 4 clordr-1.6.0/clordr/man/cl.Rd | 70 ++++---- clordr-1.6.0/clordr/man/cl.rord.Rd | 104 ++++++------ clordr-1.6.0/clordr/man/cl_l.Rd | 70 ++++---- clordr-1.6.0/clordr/man/cle.rord.Rd | 210 +++++++++++++------------- clordr-1.6.0/clordr/man/clic.Rd | 60 +++---- clordr-1.6.0/clordr/man/sim.rord.Rd | 135 ++++++++-------- clordr-1.6.0/clordr/man/surrogate.residual.Rd | 168 +++++++++++--------- 18 files changed, 489 insertions(+), 452 deletions(-)
Title: Population Assignment using Genetic, Non-Genetic or Integrated
Data in a Machine Learning Framework
Description: Use Monte-Carlo and K-fold cross-validation coupled with machine-
learning classification algorithms to perform population assignment, with
functionalities of evaluating discriminatory power of independent training
samples, identifying informative loci, reducing data dimensionality for genomic
data, integrating genetic and non-genetic data, and visualizing results.
Author: Kuan-Yu (Alex) Chen [aut, cre], Elizabeth A. Marschall [aut], Michael
G. Sovic [aut], Anthony C. Fries [aut], H. Lisle Gibbs [aut], Stuart A. Ludsin
[aut]
Maintainer: Kuan-Yu (Alex) Chen <alexkychen@gmail.com>
Diff between assignPOP versions 1.2.1 dated 2020-11-03 and 1.2.2 dated 2020-11-17
DESCRIPTION | 6 ++--- MD5 | 8 +++---- R/read.Genepop.R | 59 +++++++++++++++++++++++++++++++++++++++++------------ R/read.Structure.R | 14 ++++++++++-- README.md | 10 ++++++-- 5 files changed, 72 insertions(+), 25 deletions(-)
Title: Density, Cumulative and Quantile Functions of Quadratic Forms
Description: The computation of quadratic form (QF) distributions is often not trivial and it requires numerical routines. The package contains functions aimed at evaluating the exact distribution of quadratic forms (QFs) and ratios of QFs. In particular, we propose to evaluate density, quantile and distribution functions of positive definite QFs and ratio of independent positive QFs by means of an algorithm based on the numerical inversion of Mellin transforms.
Author: Aldo Gardini [aut, cre],
Fedele Greco [aut],
Carlo Trivisano [aut]
Maintainer: Aldo Gardini <aldo.gardini2@unibo.it>
Diff between QF versions 0.0.2 dated 2020-11-11 and 0.0.3 dated 2020-11-17
QF-0.0.2/QF/inst |only QF-0.0.3/QF/DESCRIPTION | 6 QF-0.0.3/QF/MD5 | 32 - QF-0.0.3/QF/R/RcppExports.R | 4 QF-0.0.3/QF/configure.ac | 2 QF-0.0.3/QF/src/Makevars.in | 3 QF-0.0.3/QF/src/Makevars.win | 2 QF-0.0.3/QF/src/Mellin_QF.cpp | 3 QF-0.0.3/QF/src/Mellin_QF_ratio.cpp | 2 QF-0.0.3/QF/src/RcppExports.cpp | 638 ++---------------------------- QF-0.0.3/QF/src/complex_sf.cpp | 14 QF-0.0.3/QF/src/compute_ak.cpp | 13 QF-0.0.3/QF/src/fun_distr_QF.cpp | 5 QF-0.0.3/QF/src/fun_distr_QF_depratio.cpp | 3 QF-0.0.3/QF/src/get_mellin_QF.cpp | 4 QF-0.0.3/QF/src/get_mellin_QF_ratio.cpp | 2 QF-0.0.3/QF/src/quant_QF.cpp | 2 17 files changed, 97 insertions(+), 638 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. 'neonstore' can also
construct a local 'duckdb' database of stacked tables, making it possible
to work with tables that are far to big to fit into memory.
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>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between neonstore versions 0.3.2 dated 2020-10-27 and 0.3.3 dated 2020-11-17
DESCRIPTION | 11 ++--- MD5 | 49 +++++++++++----------- NAMESPACE | 1 NEWS.md | 8 +++ R/connection_pane.R | 9 +--- R/neon_citation.R | 2 R/neon_db.R | 75 +++++++++++++++++++++++++++------- R/neon_dir.R | 27 ++++++++++++ R/neon_read.R | 7 ++- R/neon_store.R | 85 ++++++++++++++++++++++++++------------- R/neon_table.R | 8 +-- inst/examples/thelio_mirror.R | 27 +++++++----- man/neon_citation.Rd | 2 man/neon_db.Rd | 13 +++++ man/neon_db_dir.Rd |only man/neon_delete_db.Rd | 12 +---- man/neon_disconnect.Rd | 8 --- man/neon_read.Rd | 6 ++ man/neon_store.Rd | 9 +++- man/neon_table.Rd | 4 - tests/testthat/setup-tests.R | 1 tests/testthat/test-additional.R | 21 +++++---- tests/testthat/test-db.R | 34 ++++++++++----- tests/testthat/test-eddy.R | 1 tests/testthat/test-read.R | 3 - tests/testthat/test-utils.R | 3 + 26 files changed, 289 insertions(+), 137 deletions(-)
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two tissues.
Broman et al. (2015) <doi:10.1534/g3.115.019778>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between lineup versions 0.37-11 dated 2019-03-06 and 0.38-3 dated 2020-11-17
lineup-0.37-11/lineup/data/datalist |only lineup-0.38-3/lineup/ChangeLog | 13 lineup-0.38-3/lineup/DESCRIPTION | 15 lineup-0.38-3/lineup/MD5 | 107 ++--- lineup-0.38-3/lineup/NAMESPACE | 1 lineup-0.38-3/lineup/R/calc.locallod.R | 30 - lineup-0.38-3/lineup/R/combinedist.R | 28 - lineup-0.38-3/lineup/R/corbetw2mat.R | 46 +- lineup-0.38-3/lineup/R/distee.R | 18 lineup-0.38-3/lineup/R/disteg.R | 69 +-- lineup-0.38-3/lineup/R/expr1-data.R | 4 lineup-0.38-3/lineup/R/f2cross-data.R | 6 lineup-0.38-3/lineup/R/find.gene.pseudomarker.R | 28 - lineup-0.38-3/lineup/R/findCommonID.R | 22 - lineup-0.38-3/lineup/R/fscale.R | 4 lineup-0.38-3/lineup/R/genepos-data.R | 4 lineup-0.38-3/lineup/R/omitdiag.R | 14 lineup-0.38-3/lineup/R/plot.lineupdist.R | 20 lineup-0.38-3/lineup/R/plot2dist.R | 21 - lineup-0.38-3/lineup/R/plotEGclass.R | 26 - lineup-0.38-3/lineup/R/pmap-data.R | 6 lineup-0.38-3/lineup/R/pulldiag.R | 10 lineup-0.38-3/lineup/R/subset.lineupdist.R | 8 lineup-0.38-3/lineup/R/summary.lineupdist.R | 18 lineup-0.38-3/lineup/README.md | 10 lineup-0.38-3/lineup/build/vignette.rds |binary lineup-0.38-3/lineup/data/expr1.rda |binary lineup-0.38-3/lineup/data/expr2.rda |binary lineup-0.38-3/lineup/data/f2cross.rda |binary lineup-0.38-3/lineup/data/genepos.rda |binary lineup-0.38-3/lineup/data/pmap.rda |binary lineup-0.38-3/lineup/inst/CITATION | 2 lineup-0.38-3/lineup/inst/doc/lineup.R | 46 +- lineup-0.38-3/lineup/inst/doc/lineup.Rmd | 4 lineup-0.38-3/lineup/inst/doc/lineup.html | 436 ++++++++++++++++----- lineup-0.38-3/lineup/man/calc.locallod.Rd | 31 - lineup-0.38-3/lineup/man/combinedist.Rd | 8 lineup-0.38-3/lineup/man/corbetw2mat.Rd | 12 lineup-0.38-3/lineup/man/distee.Rd | 15 lineup-0.38-3/lineup/man/disteg.Rd | 36 + lineup-0.38-3/lineup/man/expr-data.Rd | 6 lineup-0.38-3/lineup/man/f2cross.Rd | 8 lineup-0.38-3/lineup/man/find.gene.pseudomarker.Rd | 16 lineup-0.38-3/lineup/man/findCommonID.Rd | 6 lineup-0.38-3/lineup/man/fscale.Rd | 2 lineup-0.38-3/lineup/man/genepos.Rd | 8 lineup-0.38-3/lineup/man/omitdiag.Rd | 12 lineup-0.38-3/lineup/man/plot.lineupdist.Rd | 17 lineup-0.38-3/lineup/man/plot2dist.Rd | 32 + lineup-0.38-3/lineup/man/plotEGclass.Rd | 27 - lineup-0.38-3/lineup/man/pmap.Rd | 10 lineup-0.38-3/lineup/man/pulldiag.Rd | 10 lineup-0.38-3/lineup/man/subset.lineupdist.Rd | 8 lineup-0.38-3/lineup/man/summary.lineupdist.Rd | 21 - lineup-0.38-3/lineup/vignettes/lineup.Rmd | 4 55 files changed, 831 insertions(+), 474 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function that is estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Elena Hsieh [ctb] (<https://orcid.org/0000-0003-3969-6597>),
Debashis Ghosh [ctb] (<https://orcid.org/0000-0001-6618-1316>),
Lance A. Waller [ctb] (<https://orcid.org/0000-0001-5002-8886>),
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@nih.gov>
Diff between gateR versions 0.1.2 dated 2020-11-10 and 0.1.3 dated 2020-11-17
DESCRIPTION | 14 +-- MD5 | 35 ++++---- NEWS.md | 6 + R/gating.R | 41 +--------- R/lotrrs.R | 37 --------- R/package.R | 4 + R/randCyto.R |only R/rrs.R | 40 ---------- README.md | 30 +++++++ data |only inst/doc/vignette.html | 21 ++--- man/gateR-package.Rd | 4 + man/gating.Rd | 41 +--------- man/lotrrs.Rd | 37 --------- man/randCyto.Rd |only man/rrs.Rd | 38 --------- tests/testthat/test-gating.R | 172 ++++++++++++++++--------------------------- tests/testthat/test-lotrrs.R | 67 +++------------- tests/testthat/test-rrs.R | 68 +++-------------- vignettes/vignette.Rmd | 14 ++- 20 files changed, 195 insertions(+), 474 deletions(-)
Title: Parses LaTeX Documents for Errors
Description: Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between TeXCheckR versions 0.6.0 dated 2018-08-25 and 0.7.0 dated 2020-11-17
DESCRIPTION | 12 MD5 | 168 - NAMESPACE | 3 NEWS.md | 195 - R/TexCheckR-package.R | 3 R/any_bib_duplicates.R | 346 +- R/bib_parser.R | 636 ++--- R/check_biber.R | 208 - R/check_consecutive_words.R | 346 +- R/check_dashes.R | 354 +- R/check_footnote_typography.R | 865 +++---- R/check_labels.R | 328 +- R/check_sentence_ending_periods.R | 100 R/check_spelling.R | 1199 +++++----- R/check_unclosed_parentheses.R | 248 +- R/check_xrefs.R | 158 - R/combine_bib_fields.R | 148 - R/combine_lines.R | 26 R/extract_mandatory_LaTeX_argument.R | 474 +-- R/extract_optional_LaTeX_argument.R | 322 +- R/extract_valid_abbreviations.R | 14 R/fill_nth_LaTeX_argument.R | 67 R/locate_footcite_punctuation.R |only R/locate_mandatory_LaTeX_argument.R | 570 ++-- R/parse_tex.R | 432 +-- R/read_tex_document.R | 194 - R/report_error.R | 315 +- R/rm_editorial_square_brackets.R | 2 R/strip_comments.R | 36 R/utils.R | 28 R/validate_bibliography.R | 690 ++--- R/zzz.R | 50 README.md | 139 + man/CORRECTLY_SPELLED_WORDS_CASE_SENSITIVE.Rd | 4 man/argument_parsing.Rd | 23 man/bib_parser.Rd | 28 man/check_consecutive_words.Rd | 9 man/check_dashes.Rd | 9 man/check_footnote_typography.Rd | 10 man/check_spelling.Rd | 71 man/check_xrefs.Rd | 3 man/correctly_spelled_words.Rd | 4 man/extract_LaTeX_argument.Rd | 3 man/extract_mandatory_LaTeX_argument.Rd | 9 man/extract_optional_LaTeX_argument.Rd | 8 man/locate_mandatory_LaTeX_argument.Rd | 8 man/minimal_bib.Rd | 3 man/report_error.Rd | 31 man/split_report.Rd | 9 man/strip_comments.Rd | 2 man/valid_English_contractions.Rd | 4 man/validate_bibliography.Rd | 3 man/wrongly_spelled_words.Rd | 4 tests/testthat/fread-bib/citr-zotero-test.bib |only tests/testthat/fread-bib/issue-44.bib |only tests/testthat/locate_footcite_punctuation |only tests/testthat/minimal-bib/article-for-min-bib.bbl | 29 tests/testthat/minimal-bib/article-for-min-bib.bcf | 29 tests/testthat/minimal-bib/article-for-min-bib.blg | 30 tests/testthat/minimal-bib/article-for-min-bib.log | 256 +- tests/testthat/minimal-bib/article-for-min-bib.pdf |binary tests/testthat/spellcheck_multi_input/spellcheck_multi_input.tex | 4 tests/testthat/spelling/113.tex |only tests/testthat/spelling/abbrev/abbrev-defd-ok.tex | 13 tests/testthat/spelling/ignore_113.tex |only tests/testthat/spelling/input/nest.tex |only tests/testthat/spelling/input/nest1 |only tests/testthat/test-locate_latex_argument.R | 31 tests/testthat/test_check_biber.R | 82 tests/testthat/test_check_consecutive_words.R | 30 tests/testthat/test_check_dashes.R | 94 tests/testthat/test_check_labels.R | 186 - tests/testthat/test_check_sentence_ending_periods.R | 12 tests/testthat/test_check_xrefs.R | 44 tests/testthat/test_fill_nth_LaTeX_argument.R | 38 tests/testthat/test_footnote_typography.R | 199 - tests/testthat/test_fread_bib.R | 19 tests/testthat/test_lint_bib.R | 94 tests/testthat/test_locate_footcite_punctuation.R |only tests/testthat/test_minimal_bib.R | 60 tests/testthat/test_parse_tex.R | 90 tests/testthat/test_read_tex_document.R | 70 tests/testthat/test_rm_editorial_square_brackets.R | 6 tests/testthat/test_spellcheck.R | 412 +-- tests/testthat/test_spellcheck_0-6-2.R |only tests/testthat/test_spellcheck_0-7-0.R |only tests/testthat/test_strip_comments.R | 16 tests/testthat/test_utils.R | 11 tests/testthat/test_validate_bibliography.R | 31 89 files changed, 5736 insertions(+), 5071 deletions(-)
Title: Diversity Indices for Numerical Matrices
Description: Providing functions to calculate indices of diversity on numerical matrices based on information theory. The rationale behind the package is described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039>.
Author: Matteo Marcantonio [aut, cre],
Martina Iannacito [aut, ctb],
Elisa Marchetto [ctb],
Elisa Thouverai [aut, ctb],
Daniele Da Re [aut],
Clara Tattoni [aut],
Giovanni Bacaro [aut],
Saverio Vicario [aut, ctb],
Carlo Ricotta [aut],
Duccio Rocchini [aut, ctb]
Maintainer: Matteo Marcantonio <marcantoniomatteo@gmail.com>
Diff between rasterdiv versions 0.2-1 dated 2020-07-18 and 0.2-2 dated 2020-11-17
DESCRIPTION | 21 MD5 | 77 +-- NAMESPACE | 18 NEWS.md | 14 R/CRE.R | 118 ++--- R/Rao.R | 507 ----------------------- R/RenyiP.R | 33 - R/RenyiS.R | 27 - R/accRao.R | 31 + R/globals.R | 2 R/mdist.R |only R/mpaRaoP.R |only R/mpaRaoS.R | 178 ++------ R/paRao.R | 233 ++++++---- R/paRaoP.R | 232 +++++----- R/paRaoS.R | 143 +++--- build/vignette.rds |binary inst/WORDLIST |only inst/doc/rasterdiv_advanced_accRao.R | 41 - inst/doc/rasterdiv_advanced_accRao.Rmd | 50 +- inst/doc/rasterdiv_advanced_accRao.html | 56 +- inst/doc/rasterdiv_advanced_multimensionRao.R |only inst/doc/rasterdiv_advanced_multimensionRao.Rmd |only inst/doc/rasterdiv_advanced_multimensionRao.html |only inst/doc/rasterdiv_basics.R | 22 inst/doc/rasterdiv_basics.Rmd | 27 - inst/doc/rasterdiv_basics.html | 55 +- man/BergerParker.Rd | 2 man/CRE.Rd | 6 man/Hill.Rd | 2 man/Pielou.Rd | 2 man/Rao.Rd | 34 - man/Renyi.Rd | 4 man/RenyiP.Rd | 2 man/RenyiS.Rd | 2 man/Shannon.Rd | 2 man/accRao.Rd | 19 man/mpaRaoS.Rd | 10 man/paRao.Rd | 50 +- tests |only vignettes/rasterdiv_advanced_accRao.Rmd | 50 +- vignettes/rasterdiv_advanced_multimensionRao.Rmd |only vignettes/rasterdiv_basics.Rmd | 27 - 43 files changed, 797 insertions(+), 1300 deletions(-)
Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and
maintenance. Designed to work with a build system such as 'GNU make' or
package 'fakemake' to help you to conditionally work through the stages of
package development (such as spell checking, linting, testing, before
building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between packager versions 1.6.0 dated 2020-11-05 and 1.7.0 dated 2020-11-17
DESCRIPTION | 12 ++-- MD5 | 30 ++++++----- NAMESPACE | 3 + NEWS.md | 11 ++++ R/devtools_modified.R | 3 + R/git_hooks.R | 77 +++++++++++++++++++++++++++--- R/main.R | 11 ++++ R/submit.R | 17 +++++- R/tools.R | 8 +++ R/use_dev_version.R | 7 ++ inst/doc/An_Introduction_to_packager.html | 55 +++++++++++---------- inst/runit_tests/test_main.R | 23 +++++--- inst/runit_tests/test_submit.R |only man/submit.Rd | 18 ++++++- man/use_dev_version.Rd | 8 +++ man/use_git_check_version_not_tagged.Rd | 10 +++ man/use_git_pre_commit_script.Rd |only 17 files changed, 226 insertions(+), 67 deletions(-)
Title: Connect to Your 'Zendesk' Data
Description: Facilitates making a connection to the
'Zendesk' API and executing various queries. You can use it to
get ticket data and ticket metrics. The 'Zendesk' documentation is
available at <https://developer.zendesk.com/rest_api
/docs/support/introduction>. This package is not supported by
'Zendesk' (owner of the software).
Author: Chris Umphlett [aut, cre],
Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between zdeskR versions 0.0.1 dated 2020-08-24 and 0.1.0 dated 2020-11-17
DESCRIPTION | 10 +++---- MD5 | 12 ++++++--- NAMESPACE | 2 + R/get_custom_fields.R |only R/get_users.R |only man/from_8601.Rd | 44 +++++++++++++++++----------------- man/get_custom_fields.Rd |only man/get_users.Rd |only man/to_unixtime.Rd | 60 +++++++++++++++++++++++------------------------ 9 files changed, 67 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-09 0.1.1
2017-01-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-27 0.3.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-14 0.5.5
2019-10-09 0.5.4
2019-09-03 0.5.3
2018-10-09 0.5.2
2018-06-25 0.5.1
2018-06-07 0.5.0
2018-05-06 0.4.1
2017-11-17 0.4
2017-08-18 0.3.1
2017-07-03 0.3
2016-09-06 0.2
2015-12-04 0.1