Title: Model Multivariate Ordinal Responses Including Response Styles
Description: In the case of multivariate ordinal responses, parameter estimates can be severely biased if personal response styles are ignored. This packages provides methods to account for personal response styles and to explain the effects of covariates on the response style, as proposed by Schauberger and Tutz 2021 <doi:10.1177/1471082X20978034>. The method is implemented both for the multivariate cumulative model and the multivariate adjacent categories model.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between MultOrdRS versions 0.1-1 dated 2021-03-23 and 0.1-2 dated 2021-03-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- build/partial.rdb |binary src/cppMultOrd.cpp | 7 ++++++- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Single Cell Mapper
Description: The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.
Author: Dustin Sokolowski [aut, cre],
Mariela Faykoo-Martinez [aut],
Lauren Erdman [aut],
Houyun Hou [aut],
Cadia Chan [aut],
Helen Zhu [aut],
Melissa Holmes [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between scMappR versions 1.0.0 dated 2021-03-21 and 1.0.1 dated 2021-03-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/process_from_count.R | 2 +- inst/doc/scMappR_Vignette.html | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Download and Run Cargo, the Rust Package Manager
Description: Help is provided to run 'Cargo' <https://doc.rust-lang.org/cargo/> (the 'Rust' <https://www.rust-lang.org/> package manager).
Other packages based on Rust can declare 'LinkingTo: cargo' in their DESCRIPTION file and then use Cargo during the installation of
their source package.
Author: David B. Dahl [aut, cre] (<https://orcid.org/0000-0002-8173-1547>)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between cargo versions 0.1.28 dated 2021-03-17 and 0.1.29 dated 2021-03-29
cargo-0.1.28/cargo/man/is_available.Rd |only cargo-0.1.29/cargo/DESCRIPTION | 7 +-- cargo-0.1.29/cargo/MD5 | 11 ++--- cargo-0.1.29/cargo/NAMESPACE | 2 cargo-0.1.29/cargo/NEWS | 4 + cargo-0.1.29/cargo/R/cargo.R | 70 ++++++++++++++------------------- cargo-0.1.29/cargo/man/target.Rd | 6 +- 7 files changed, 48 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-26 1.5
2020-03-05 1.4
2018-05-22 1.2
2017-03-23 1.1
2017-03-07 1.0
2016-10-24 0.9-14
2016-06-29 0.9-12
2015-10-21 0.9-11
2015-07-10 0.9-10
2015-06-03 0.9-9
2014-11-13 0.9-8
2014-09-12 0.9-7
2014-07-15 0.9-6
2014-06-25 0.9-5
2014-06-16 0.9-3
2014-05-13 0.9-2
2014-03-27 0.9-1
2014-01-14 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-12 0.1.1
2015-04-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-06 1.6
2018-05-22 1.5
2017-04-12 1.4
2016-07-18 1.3-15
2016-01-11 1.3-14
2015-11-19 1.3-13
2015-09-10 1.3-11
2015-02-25 1.3-9
2015-02-04 1.3-8
2015-01-24 1.3-7
2014-05-09 1.3-6
2014-03-03 1.3-4
2014-01-07 1.3-3
2013-06-14 1.3-2
2013-06-11 1.3-1
2013-05-31 1.3
2013-01-23 1.01
2012-11-23 1.0
2012-07-20 0.9-7
2012-06-11 0.9-5
2012-05-30 0.9-4-2
2012-04-20 0.9-4
2012-03-26 0.9-3
2012-03-12 0.9-2
2011-12-09 0.9-1
2011-10-02 0.9-0
Title: Hazard Function Estimation in Survival Analysis
Description: Produces a smooth estimate of the hazard
function for censored data.
Author: S original by Kenneth Hess, <khess@odin.mdacc.tmc.edu> R port
by R. Gentleman
Maintainer: David Winsemius <dwinsemius@comcast.net>
Diff between muhaz versions 1.2.6.1 dated 2019-01-26 and 1.2.6.2 dated 2021-03-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ man/kphaz.plot.Rd | 2 +- man/muhaz.Rd | 2 +- man/pehaz.Rd | 2 +- man/plot.pehaz.Rd | 2 +- man/summary.muhaz.Rd | 4 ++-- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Complement to 'Modern Data Science with R'
Description: A complement to *Modern Data
Science with R*, both the first (ISBN: 978-1498724487, publisher URL:
<https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9781498724487>)
and second editions (ISBN: 978-0367191498, publisher URL:
<https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9780367191498>).
This package contains data and code to complete exercises and
reproduce examples from the text. It also facilitates connections
to the SQL database server used in the book. Both editions of the book are
supported by this package.
Author: Benjamin S. Baumer [aut, cre] (<https://orcid.org/0000-0002-3279-0516>),
Nicholas Horton [aut] (<https://orcid.org/0000-0003-3332-4311>),
Daniel Kaplan [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between mdsr versions 0.2.4 dated 2021-01-06 and 0.2.5 dated 2021-03-29
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/data.R | 10 ++++++++-- build/partial.rdb |binary man/Cherry.Rd | 10 ++++++++-- 6 files changed, 29 insertions(+), 12 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.3.4 dated 2021-02-10 and 2.3.5 dated 2021-03-29
DESCRIPTION | 9 -- MD5 | 16 +-- R/gjamHfunctions.R | 184 ++++++++++++++++++++++++++------------------- R/gjamPredict.r | 2 R/gjamPriorTemplate.R | 4 inst/doc/gjamVignette.Rmd | 2 inst/doc/gjamVignette.html | 47 ++++++----- man/gjam-package.Rd | 4 vignettes/gjamVignette.Rmd | 2 9 files changed, 157 insertions(+), 113 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut, ctb, cph],
Marco A. Aquino Lopez [aut],
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.5.2 dated 2021-03-11 and 2.5.3 dated 2021-03-29
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++------------- NEWS.md | 5 +++ R/Bacon.R | 25 +++++++++++----- R/MCMC.R | 6 +++ R/agedepth.R | 65 ++++++++++++++++++++++++------------------ R/calc.R | 7 ++-- R/calibrate.R | 7 +--- build/partial.rdb |binary man/agedepth.Rd | 11 ++++--- src/Matrix.cpp | 3 - src/Matrix.h | 34 ++++++++++------------ src/bacon.cpp | 30 +------------------ src/bacon.h | 83 ++++++++++++++++++++++++------------------------------ src/events.cpp | 18 ----------- src/input.cpp | 11 ++----- src/input.h | 42 +++++++++++++-------------- src/kernel.cpp | 14 ++++----- src/ranfun.cpp | 12 +++---- src/twalk.h | 14 +++------ src/vector.cpp | 42 ++++++++++++++++----------- 21 files changed, 229 insertions(+), 248 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
François Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>),
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid Keydana [ctb]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between keras versions 2.3.0.0 dated 2020-05-19 and 2.4.0 dated 2021-03-29
keras-2.3.0.0/keras/tests/testthat/utils.R |only keras-2.4.0/keras/DESCRIPTION | 10 keras-2.4.0/keras/MD5 | 307 ++++--- keras-2.4.0/keras/NAMESPACE | 5 keras-2.4.0/keras/NEWS.md | 46 - keras-2.4.0/keras/R/Layer.R |only keras-2.4.0/keras/R/applications.R | 4 keras-2.4.0/keras/R/backend.R | 24 keras-2.4.0/keras/R/callbacks.R | 14 keras-2.4.0/keras/R/constraints.R | 2 keras-2.4.0/keras/R/history.R | 7 keras-2.4.0/keras/R/initializers.R | 10 keras-2.4.0/keras/R/install.R | 25 keras-2.4.0/keras/R/layer-attention.R | 100 ++ keras-2.4.0/keras/R/layer-text_vectorization.R | 25 keras-2.4.0/keras/R/layers-convolutional.R | 76 + keras-2.4.0/keras/R/layers-core.R | 9 keras-2.4.0/keras/R/layers-embedding.R | 2 keras-2.4.0/keras/R/layers-noise.R | 2 keras-2.4.0/keras/R/layers-normalization.R | 68 + keras-2.4.0/keras/R/layers-recurrent.R | 26 keras-2.4.0/keras/R/losses.R | 31 keras-2.4.0/keras/R/metrics-callback.R | 11 keras-2.4.0/keras/R/model-legacy.R |only keras-2.4.0/keras/R/model-persistence.R | 5 keras-2.4.0/keras/R/model.R | 386 +++++----- keras-2.4.0/keras/R/optimizers.R | 6 keras-2.4.0/keras/R/package.R | 8 keras-2.4.0/keras/R/preprocessing.R | 122 ++- keras-2.4.0/keras/R/seed.R | 6 keras-2.4.0/keras/R/utils.R | 11 keras-2.4.0/keras/build/vignette.rds |binary keras-2.4.0/keras/inst/doc/applications.html | 26 keras-2.4.0/keras/inst/doc/custom_layers.R | 265 +++++- keras-2.4.0/keras/inst/doc/custom_layers.Rmd | 347 +++++++- keras-2.4.0/keras/inst/doc/custom_layers.html | 343 +++++++- keras-2.4.0/keras/inst/doc/custom_models.html | 26 keras-2.4.0/keras/inst/doc/faq.Rmd | 4 keras-2.4.0/keras/inst/doc/faq.html | 30 keras-2.4.0/keras/inst/doc/functional_api.Rmd | 4 keras-2.4.0/keras/inst/doc/functional_api.html | 30 keras-2.4.0/keras/inst/doc/guide_keras.html | 26 keras-2.4.0/keras/inst/doc/index.Rmd | 2 keras-2.4.0/keras/inst/doc/index.html | 28 keras-2.4.0/keras/inst/doc/saving_serializing.Rmd | 2 keras-2.4.0/keras/inst/doc/saving_serializing.html | 28 keras-2.4.0/keras/inst/doc/sequential_model.html | 26 keras-2.4.0/keras/inst/doc/training_callbacks.html | 26 keras-2.4.0/keras/inst/doc/training_visualization.Rmd | 6 keras-2.4.0/keras/inst/doc/training_visualization.html | 32 keras-2.4.0/keras/inst/python/kerastools/generator.py | 3 keras-2.4.0/keras/inst/python/kerastools/layer.py | 4 keras-2.4.0/keras/inst/python/kerastools/model.py | 32 keras-2.4.0/keras/inst/python/kerastools/wrapper.py | 4 keras-2.4.0/keras/man/KerasCallback.Rd | 4 keras-2.4.0/keras/man/KerasConstraint.Rd | 4 keras-2.4.0/keras/man/KerasLayer.Rd | 4 keras-2.4.0/keras/man/KerasWrapper.Rd | 4 keras-2.4.0/keras/man/Layer.Rd |only keras-2.4.0/keras/man/application_inception_resnet_v2.Rd | 2 keras-2.4.0/keras/man/application_inception_v3.Rd | 2 keras-2.4.0/keras/man/backend.Rd | 6 keras-2.4.0/keras/man/callback_remote_monitor.Rd | 2 keras-2.4.0/keras/man/callback_tensorboard.Rd | 6 keras-2.4.0/keras/man/constraints.Rd | 2 keras-2.4.0/keras/man/evaluate.keras.engine.training.Model.Rd | 4 keras-2.4.0/keras/man/fit.keras.engine.training.Model.Rd | 4 keras-2.4.0/keras/man/flow_images_from_dataframe.Rd | 7 keras-2.4.0/keras/man/get_file.Rd | 6 keras-2.4.0/keras/man/image_dataset_from_directory.Rd |only keras-2.4.0/keras/man/initializer_glorot_normal.Rd | 2 keras-2.4.0/keras/man/initializer_glorot_uniform.Rd | 2 keras-2.4.0/keras/man/initializer_he_normal.Rd | 2 keras-2.4.0/keras/man/initializer_he_uniform.Rd | 2 keras-2.4.0/keras/man/initializer_orthogonal.Rd | 2 keras-2.4.0/keras/man/install_keras.Rd | 4 keras-2.4.0/keras/man/keras_model.Rd | 4 keras-2.4.0/keras/man/layer_conv_1d.Rd | 1 keras-2.4.0/keras/man/layer_conv_1d_transpose.Rd |only keras-2.4.0/keras/man/layer_conv_2d.Rd | 1 keras-2.4.0/keras/man/layer_conv_2d_transpose.Rd | 2 keras-2.4.0/keras/man/layer_conv_3d.Rd | 1 keras-2.4.0/keras/man/layer_conv_3d_transpose.Rd | 2 keras-2.4.0/keras/man/layer_conv_lstm_2d.Rd | 5 keras-2.4.0/keras/man/layer_cropping_1d.Rd | 1 keras-2.4.0/keras/man/layer_cropping_2d.Rd | 1 keras-2.4.0/keras/man/layer_cropping_3d.Rd | 1 keras-2.4.0/keras/man/layer_cudnn_gru.Rd | 4 keras-2.4.0/keras/man/layer_cudnn_lstm.Rd | 8 keras-2.4.0/keras/man/layer_depthwise_conv_2d.Rd | 1 keras-2.4.0/keras/man/layer_embedding.Rd | 2 keras-2.4.0/keras/man/layer_gaussian_dropout.Rd | 2 keras-2.4.0/keras/man/layer_gru.Rd | 12 keras-2.4.0/keras/man/layer_input.Rd | 7 keras-2.4.0/keras/man/layer_layer_normalization.Rd |only keras-2.4.0/keras/man/layer_lstm.Rd | 18 keras-2.4.0/keras/man/layer_multi_head_attention.Rd |only keras-2.4.0/keras/man/layer_separable_conv_1d.Rd | 1 keras-2.4.0/keras/man/layer_separable_conv_2d.Rd | 1 keras-2.4.0/keras/man/layer_simple_rnn.Rd | 10 keras-2.4.0/keras/man/layer_text_vectorization.Rd | 2 keras-2.4.0/keras/man/layer_upsampling_1d.Rd | 1 keras-2.4.0/keras/man/layer_upsampling_2d.Rd | 1 keras-2.4.0/keras/man/layer_upsampling_3d.Rd | 1 keras-2.4.0/keras/man/layer_zero_padding_1d.Rd | 1 keras-2.4.0/keras/man/layer_zero_padding_2d.Rd | 1 keras-2.4.0/keras/man/layer_zero_padding_3d.Rd | 1 keras-2.4.0/keras/man/loss_binary_crossentropy.Rd |only keras-2.4.0/keras/man/loss_mean_squared_error.Rd | 5 keras-2.4.0/keras/man/multi_gpu_model.Rd | 13 keras-2.4.0/keras/man/optimizer_adagrad.Rd | 2 keras-2.4.0/keras/man/optimizer_adam.Rd | 2 keras-2.4.0/keras/man/optimizer_nadam.Rd | 2 keras-2.4.0/keras/man/predict.keras.engine.training.Model.Rd | 4 keras-2.4.0/keras/man/predict_on_batch.Rd | 4 keras-2.4.0/keras/man/predict_proba.Rd | 4 keras-2.4.0/keras/man/reexports.Rd | 4 keras-2.4.0/keras/man/save_model_hdf5.Rd | 3 keras-2.4.0/keras/man/save_model_tf.Rd | 3 keras-2.4.0/keras/man/serialize_model.Rd | 3 keras-2.4.0/keras/man/set_vocabulary.Rd | 5 keras-2.4.0/keras/man/skipgrams.Rd | 2 keras-2.4.0/keras/man/text_one_hot.Rd | 9 keras-2.4.0/keras/tests/testthat/helper-skips.R |only keras-2.4.0/keras/tests/testthat/helper-utils.R |only keras-2.4.0/keras/tests/testthat/test-Layer.R |only keras-2.4.0/keras/tests/testthat/test-activations.R | 2 keras-2.4.0/keras/tests/testthat/test-applications.R | 2 keras-2.4.0/keras/tests/testthat/test-backend.R | 2 keras-2.4.0/keras/tests/testthat/test-callbacks.R | 10 keras-2.4.0/keras/tests/testthat/test-constraints.R | 2 keras-2.4.0/keras/tests/testthat/test-custom-layers.R | 56 + keras-2.4.0/keras/tests/testthat/test-custom-models.R | 4 keras-2.4.0/keras/tests/testthat/test-custom_wrappers.R | 2 keras-2.4.0/keras/tests/testthat/test-datasets.R | 2 keras-2.4.0/keras/tests/testthat/test-examples.R | 2 keras-2.4.0/keras/tests/testthat/test-freeze.R | 2 keras-2.4.0/keras/tests/testthat/test-generators.R | 110 +- keras-2.4.0/keras/tests/testthat/test-history.R |only keras-2.4.0/keras/tests/testthat/test-initializers.R | 2 keras-2.4.0/keras/tests/testthat/test-layer-attention.R |only keras-2.4.0/keras/tests/testthat/test-layer-methods.R | 2 keras-2.4.0/keras/tests/testthat/test-layer-text_vectorization.R | 32 keras-2.4.0/keras/tests/testthat/test-layers-normalization.R |only keras-2.4.0/keras/tests/testthat/test-layers.R | 11 keras-2.4.0/keras/tests/testthat/test-losses.R | 18 keras-2.4.0/keras/tests/testthat/test-metrics.R | 4 keras-2.4.0/keras/tests/testthat/test-model-persistence.R | 2 keras-2.4.0/keras/tests/testthat/test-model.R | 79 +- keras-2.4.0/keras/tests/testthat/test-optimizers.R | 2 keras-2.4.0/keras/tests/testthat/test-preprocessing.R | 82 +- keras-2.4.0/keras/tests/testthat/test-regularizers.R | 2 keras-2.4.0/keras/tests/testthat/test-tfdatasets.R | 2 keras-2.4.0/keras/tests/testthat/test-timeseries.R | 8 keras-2.4.0/keras/tests/testthat/test-utils.R | 5 keras-2.4.0/keras/tests/testthat/test.h5 |binary keras-2.4.0/keras/vignettes/custom_layers.Rmd | 347 +++++++- keras-2.4.0/keras/vignettes/faq.Rmd | 4 keras-2.4.0/keras/vignettes/functional_api.Rmd | 4 keras-2.4.0/keras/vignettes/index.Rmd | 2 keras-2.4.0/keras/vignettes/saving_serializing.Rmd | 2 keras-2.4.0/keras/vignettes/training_visualization.Rmd | 6 162 files changed, 2858 insertions(+), 825 deletions(-)
Title: Converting Transport Data from GTFS Format to GPS-Like Records
Description: Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.
Author: Rafael H. M. Pereira [aut] (<https://orcid.org/0000-0003-2125-7465>),
Pedro R. Andrade [aut, cre] (<https://orcid.org/0000-0001-8675-4046>),
Joao Bazzo [aut] (<https://orcid.org/0000-0003-4536-5006>),
Marcin Stepniak [ctb],
Marcus Saraiva [ctb] (<https://orcid.org/0000-0001-6218-2338>),
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro R. Andrade <pedro.andrade@inpe.br>
Diff between gtfs2gps versions 1.3-2 dated 2020-11-05 and 1.4-0 dated 2021-03-29
DESCRIPTION | 13 MD5 | 72 NAMESPACE | 2 NEWS.md |only R/RcppExports.R | 6 R/filter_gtfs.R | 100 + R/gps_as_sflinestring.R | 45 R/gtfs2gps.R | 187 +- R/gtfs_as_sf.R | 3 R/merge_gtfs_feeds.R | 16 R/mod_updates.R | 27 R/read_gtfs.R | 3 R/write_gtfs.R | 10 R/zzz.R | 6 build/vignette.rds |binary inst/doc/intro_to_gtfs2gps.R | 4 inst/doc/intro_to_gtfs2gps.Rmd | 4 inst/doc/intro_to_gtfs2gps.html | 901 ++-------- inst/extdata/berlin.zip |only inst/extdata/saopaulo.zip |binary man/cpp_snap_points.Rd | 5 man/figures/gtfs2gps_hex.png |only man/filter_by_day.Rd |only man/filter_by_route_id.Rd | 5 man/filter_week_days.Rd | 3 man/gtfs2gps.Rd | 40 man/merge_gtfs_feeds.Rd | 2 man/remove_by_route_id.Rd |only src/RcppExports.cpp | 9 src/snap_points.cpp | 60 tests/testthat/test_filter_gtfs.R | 39 tests/testthat/test_gps_as_sflinestring.R | 5 tests/testthat/test_gtfs2gps.R | 62 tests/testthat/test_merge_gtfs_feeds.R | 13 tests/testthat/test_snap_points.R | 10 tests/testthat/test_write_gtfs.R | 4 vignettes/intro_to_gtfs2gps.Rmd | 4 vignettes/intro_to_gtfs2gps_files/figure-gfm/unnamed-chunk-6-1.png |binary vignettes/intro_to_gtfs2gps_files/figure-gfm/unnamed-chunk-7-1.png |binary vignettes/sao_small-DESKTOP-V07AVEN.zip |only 40 files changed, 735 insertions(+), 925 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.8.3 dated 2021-03-01 and 0.8.4 dated 2021-03-29
DESCRIPTION | 6 MD5 | 41 ++-- NEWS.md | 46 ++++ R/MiscFuns.R | 357 ++++++++++++++++++++++++++++++++----- R/etable.R | 205 ++++++++------------- R/etable_aliases.R |only R/fixest_env.R | 4 R/test_fun.R | 3 inst/doc/exporting_tables.R | 102 +++++----- inst/doc/exporting_tables.html | 116 +++++++++++- inst/doc/fixest_walkthrough.html | 252 +++++++++++++------------- inst/doc/multiple_estimations.html | 165 +++++++++-------- inst/doc/standard_errors.Rmd | 2 inst/doc/standard_errors.html | 6 man/aggregate.fixest.Rd | 4 man/etable.Rd | 113 ++++++----- man/fitstat.Rd | 4 man/fixest-deprecated.Rd | 14 - man/model.matrix.fixest.Rd | 22 +- man/setFixest_estimation.Rd | 3 tests/fixest_tests.R | 105 ++++------ vignettes/standard_errors.Rmd | 2 22 files changed, 990 insertions(+), 582 deletions(-)
Title: Sleep Cycle Detection
Description: Sleep cycles are largely detected according to the originally proposed criteria by Feinberg & Floyd (1979) <doi:10.1111/j.1469-8986.1979.tb02991.x> as described in Blume & Cajochen (2021) <doi:10.1016/j.mex.2021.101318>.
Author: Christine Blume [aut, cre] (<https://orcid.org/0000-0003-2328-9612>)
Maintainer: Christine Blume <christine.blume@sbg.ac.at>
Diff between SleepCycles versions 1.1.0 dated 2021-03-02 and 1.1.1 dated 2021-03-29
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md | 7 ++++++- README.md | 2 +- build/partial.rdb |binary inst/CITATION |only inst/doc/introduction.Rmd | 11 ++++++----- inst/doc/introduction.html | 21 ++++++++++++++------- vignettes/introduction.Rmd | 11 ++++++----- 9 files changed, 45 insertions(+), 30 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the seasonal adjustment
software by the US Census Bureau. It offers full access to almost all
options and outputs of X-13, including X-11 and SEATS, automatic ARIMA model
search, outlier detection and support for user defined holiday variables,
such as Chinese New Year or Indian Diwali. A graphical user interface can be
used through the 'seasonalview' package. Uses the X-13-binaries from the
'x13binary' package.
Author: Christoph Sax [aut, cre] (<https://orcid.org/0000-0002-7192-7044>),
Dirk Eddelbuettel [ctb] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 1.8.1 dated 2021-03-14 and 1.8.2 dated 2021-03-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/checkX13.R | 4 ++++ R/multi_seas.R | 4 ++++ build/partial.rdb |binary inst/doc/seas.pdf |binary tests/testthat/test-cran.R | 3 --- 8 files changed, 26 insertions(+), 14 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.4.2 dated 2021-03-19 and 0.5.0 dated 2021-03-29
modeltime-0.4.2/modeltime/man/metric_tweak.Rd |only modeltime-0.5.0/modeltime/DESCRIPTION | 14 modeltime-0.5.0/modeltime/MD5 | 45 modeltime-0.5.0/modeltime/NAMESPACE | 6 modeltime-0.5.0/modeltime/NEWS.md | 18 modeltime-0.5.0/modeltime/R/00_global_variables.R | 3 modeltime-0.5.0/modeltime/R/modeltime-accuracy.R | 80 - modeltime-0.5.0/modeltime/R/modeltime-forecast.R | 65 + modeltime-0.5.0/modeltime/R/modeltime-recursive.R | 462 ++++++++-- modeltime-0.5.0/modeltime/R/modeltime-refit.R | 90 + modeltime-0.5.0/modeltime/R/utils-parsnip-helpers.R | 6 modeltime-0.5.0/modeltime/README.md | 14 modeltime-0.5.0/modeltime/inst/doc/getting-started-with-modeltime.R | 1 modeltime-0.5.0/modeltime/inst/doc/getting-started-with-modeltime.Rmd | 11 modeltime-0.5.0/modeltime/inst/doc/getting-started-with-modeltime.html | 101 +- modeltime-0.5.0/modeltime/man/default_forecast_accuracy_metric_set.Rd | 35 modeltime-0.5.0/modeltime/man/panel_tail.Rd |only modeltime-0.5.0/modeltime/man/predict.recursive.Rd | 3 modeltime-0.5.0/modeltime/man/predict.recursive_panel.Rd |only modeltime-0.5.0/modeltime/man/recursive.Rd | 149 ++- modeltime-0.5.0/modeltime/man/summarize_accuracy_metrics.Rd | 1 modeltime-0.5.0/modeltime/tests/testthat/test-recursive.R | 400 ++++++-- modeltime-0.5.0/modeltime/tests/testthat/test-results-accuracy-tables.R | 4 modeltime-0.5.0/modeltime/vignettes/getting-started-with-modeltime.Rmd | 11 modeltime-0.5.0/modeltime/vignettes/recursive_panel_forecast.png |only modeltime-0.5.0/modeltime/vignettes/temp/recursive-forecasting.Rmd |only 26 files changed, 1145 insertions(+), 374 deletions(-)
Title: Tools to Support Relative Importance Analysis
Description: Provides tools that support relative importance analysis focusing
on dominance analysis. Dominance analysis is a methodology for
determining the relative importance of predictors/features/independent
variables (Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>;
Groemping, U. (2007) <doi:10.1198/000313007X188252>)
as well as parameter estimates (Luchman, J. N, Lei, X., & Kaplan, S.
(2020) <doi:10.47263/JASEM.4(2)02>).
These tools are intended to extend relative importance analysis to,
effectively, any statistical or machine learning function as defined or
desired by the user-especially those where the user wants to use custom
importance/fit metric or modeling function.
Author: Joseph Luchman [aut, cre] (<https://orcid.org/0000-0002-8886-9717>)
Maintainer: Joseph Luchman <jluchman@gmail.com>
Diff between domir versions 0.0.0 dated 2021-03-01 and 0.0.1 dated 2021-03-29
DESCRIPTION | 13 ++++++------- MD5 | 12 ++++++------ R/domin.r | 18 ++++++++++++------ R/domir-package.r | 4 ++-- man/domin.Rd | 4 ++-- man/domir-package.Rd | 4 ++-- man/print.domin.Rd | 2 +- 7 files changed, 31 insertions(+), 26 deletions(-)
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census Bureau provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and
X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau
offers both source and binary versions -- which this package integrates for
use by other R packages.
Author: Dirk Eddelbuettel and Christoph Sax
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 1.1.39-2 dated 2019-05-07 and 1.1.39-3 dated 2021-03-29
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 10 ++++++---- MD5 | 10 +++++----- R/checkX13binary.R | 3 ++- README.md | 9 +++++++-- configure | 25 ++++++++++++------------- 6 files changed, 47 insertions(+), 25 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 1.1.2 dated 2021-03-15 and 1.2.0 dated 2021-03-29
visvow-1.1.2/visvow/tests/testthat/data/Heeringa_Van_de_VeldeF.csv |only visvow-1.2.0/visvow/DESCRIPTION | 8 visvow-1.2.0/visvow/MD5 | 20 - visvow-1.2.0/visvow/R/visvow.R | 182 ++++++++-- visvow-1.2.0/visvow/build/partial.rdb |binary visvow-1.2.0/visvow/tests/testthat/data/BighamF.csv |only visvow-1.2.0/visvow/tests/testthat/data/ERB_Glasberg_Moore_1990.csv |only visvow-1.2.0/visvow/tests/testthat/data/ERB_Greenwood_1961.csv |only visvow-1.2.0/visvow/tests/testthat/data/ERB_Moore_Glasberg_1983.csv |only visvow-1.2.0/visvow/tests/testthat/data/Heeringa_Van_de_Velde_IF.csv |only visvow-1.2.0/visvow/tests/testthat/data/Heeringa_Van_de_Velde_IIF.csv |only visvow-1.2.0/visvow/tests/testthat/data/bark_Schroeder_et_al._1979.csv |only visvow-1.2.0/visvow/tests/testthat/data/bark_Traunmueller_1990.csv |only visvow-1.2.0/visvow/tests/testthat/data/bark_Zwicker_Terhardt_1980.csv |only visvow-1.2.0/visvow/tests/testthat/data/mel_Fant_1968.csv |only visvow-1.2.0/visvow/tests/testthat/data/mel_OShaughnessy_1987.csv |only visvow-1.2.0/visvow/tests/testthat/test.R | 4 17 files changed, 180 insertions(+), 34 deletions(-)
Title: Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and
'base' R Graphics
Description: Theme 'ggplot2', 'lattice', and 'base' graphics based on a few choices, including foreground color, background color, accent color,
and font family. Fonts that aren't available on the system, but are available via download on 'Google Fonts',
can be automatically downloaded, cached, and registered for use with the 'showtext' and 'ragg' packages.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
Joe Cheng [aut],
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between thematic versions 0.1.1 dated 2021-01-16 and 0.1.2 dated 2021-03-29
thematic-0.1.1/thematic/man/figures/README-unnamed-chunk-4-1.png |only thematic-0.1.1/thematic/tests/testthat/CairoPNG/tests/shinytest/mytest-current |only thematic-0.1.1/thematic/tests/testthat/agg_png/tests/shinytest/mytest-current |only thematic-0.1.1/thematic/tests/testthat/auto_theme_shiny/local_theme/tests/shinytest/mytest-current |only thematic-0.1.1/thematic/tests/testthat/auto_theme_shiny/with_theme/tests/shinytest/mytest-current |only thematic-0.1.1/thematic/tests/testthat/cairo_png/tests/shinytest/mytest-current |only thematic-0.1.1/thematic/tests/testthat/cairo_svg/tests/shinytest/mytest-current |only thematic-0.1.2/thematic/DESCRIPTION | 10 thematic-0.1.2/thematic/MD5 | 91 ++-- thematic-0.1.2/thematic/NEWS.md | 8 thematic-0.1.2/thematic/R/auto.R | 2 thematic-0.1.2/thematic/R/gfonts.R | 13 thematic-0.1.2/thematic/R/ggplot.R | 27 + thematic-0.1.2/thematic/R/hooks.R | 24 - thematic-0.1.2/thematic/R/onLoad.R | 4 thematic-0.1.2/thematic/R/sysdata.rda |binary thematic-0.1.2/thematic/R/thematic.R | 9 thematic-0.1.2/thematic/R/utils.R | 6 thematic-0.1.2/thematic/README.md | 203 ++++++---- thematic-0.1.2/thematic/man/figures/README-ggrepel-1.png |binary thematic-0.1.2/thematic/man/figures/README-ggrepel2-1.png |only thematic-0.1.2/thematic/man/figures/README-ggrepel3-1.png |only thematic-0.1.2/thematic/man/figures/README-unnamed-chunk-5-1.png |only thematic-0.1.2/thematic/man/figures/README-unnamed-chunk-6-1.png |only thematic-0.1.2/thematic/man/figures/auto-after.png |binary thematic-0.1.2/thematic/man/figures/auto-before.png |binary thematic-0.1.2/thematic/man/figures/logo.png |binary thematic-0.1.2/thematic/tests/testthat/CairoPNG/app.R | 5 thematic-0.1.2/thematic/tests/testthat/agg_png/app.R | 5 thematic-0.1.2/thematic/tests/testthat/agg_png/tests/shinytest/mytest-expected-linux/001.png |binary thematic-0.1.2/thematic/tests/testthat/agg_png/tests/shinytest/mytest-expected-mac/001.png |binary thematic-0.1.2/thematic/tests/testthat/agg_png/tests/shinytest/mytest-expected-win/001.png |binary thematic-0.1.2/thematic/tests/testthat/auto_theme_rmd/darkly_rmd/app.R | 18 thematic-0.1.2/thematic/tests/testthat/auto_theme_shiny/base/app.R | 3 thematic-0.1.2/thematic/tests/testthat/auto_theme_shiny/lattice/app.R | 3 thematic-0.1.2/thematic/tests/testthat/auto_theme_shiny/local_theme/tests/shinytest/mytest-expected-mac/001.json | 3 thematic-0.1.2/thematic/tests/testthat/auto_theme_shiny/with_theme/tests/shinytest/mytest-expected-mac/001.json | 3 thematic-0.1.2/thematic/tests/testthat/cairo_png/app.R | 5 thematic-0.1.2/thematic/tests/testthat/cairo_svg/app.R | 5 thematic-0.1.2/thematic/tests/testthat/cairo_svg/tests/shinytest/mytest-expected-linux/001.png |binary thematic-0.1.2/thematic/tests/testthat/pdf.Rmd | 8 thematic-0.1.2/thematic/tests/testthat/quartz_png/app.R | 5 thematic-0.1.2/thematic/tests/testthat/shiny_runtime/tests/shinytest/mytest-expected-win/001.json | 19 thematic-0.1.2/thematic/tests/testthat/template_device.Rmd | 6 thematic-0.1.2/thematic/tests/testthat/template_theme.Rmd | 6 thematic-0.1.2/thematic/tests/testthat/test-base.R | 6 thematic-0.1.2/thematic/tests/testthat/test-ggplot.R | 47 +- thematic-0.1.2/thematic/tests/testthat/test-lattice.R | 14 thematic-0.1.2/thematic/tests/testthat/test-shinytest.R | 21 - 49 files changed, 343 insertions(+), 236 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Werner Stahel [ctb] (Functions: compresid2way(), f.robftest(), last(),
p.scales(), p.dnorm()),
Andreas Ruckstuhl [ctb] (Functions: p.arrows(), p.profileTraces(),
p.res.2x()),
Christian Keller [ctb] (Functions: histBxp(), p.tachoPlot()),
Kjetil Halvorsen [ctb] (Functions: KSd(), ecdf.ksCI()),
Alain Hauser [ctb] (Functions: cairoSwd(), is.whole(),
toLatex.numeric()*),
Christoph Buser [ctb] (to function Duplicated()),
Lorenz Gygax [ctb] (to function p.res.2fact()),
Bill Venables [ctb] (Functions: empty.dimnames(), primes()),
Tony Plate [ctb] (to inv.seq()),
Isabelle Fl<fc>ckiger [ctb],
Marcel Wolbers [ctb],
Markus Keller [ctb],
Sandrine Dudoit [ctb],
Jane Fridlyand [ctb],
Greg Snow [ctb] (to loessDemo()),
Henrik Aa. Nielsen [ctb] (to loessDemo()),
Vincent Carey [ctb],
Ben Bolker [ctb],
Philippe Grosjean [ctb],
Fr<e9>d<e9>ric Ibanez [ctb],
Caterina Savi [ctb],
Charles Geyer [ctb],
Jens Oehlschl<e4>gel [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-9 dated 2021-03-23 and 1.1-10 dated 2021-03-29
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- R/sessionInfo-ext.R | 3 ++- inst/NEWS.Rd | 11 +++++++++++ 4 files changed, 23 insertions(+), 9 deletions(-)
Title: Mixture Models with Heterogeneous and (Partially) Missing Data
Description: Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with
heterogeneous data sets and partially missing data management.
It includes 8 models for real, categorical, counting, functional and ranking data.
Author: Vincent Kubicki [aut],
Christophe Biernacki [aut],
Quentin Grimonprez [aut],
Matthieu Marbac-Lourdelle [ctb],
Étienne Goffinet [ctb],
Serge Iovleff [ctb],
Julien Vandaele [ctb, cre]
Maintainer: Julien Vandaele <julien.vandaele@inria.fr>
Diff between RMixtComp versions 4.1.2 dated 2020-06-25 and 4.1.3 dated 2021-03-29
DESCRIPTION | 29 +++--- MD5 | 50 +++++------ NEWS | 6 + R/MIXTCOMP_datasets.R | 2 R/MIXTCOMP_hierarchical.R | 50 +++++++---- R/MIXTCOMP_methods.R | 8 - R/MIXTCOMP_mixtCompLearn.R | 50 +++++++---- R/PLOT_plotCrit.R | 11 +- R/RMixtComp-package.R | 2 build/vignette.rds |binary data/CanadianWeather.rda |binary data/prostate.rda |binary data/simData.rda |binary data/titanic.rda |binary inst/doc/ClusVis.html | 59 ++++++++----- inst/doc/MixtComp.html | 169 +++++++++++++++++++++------------------ inst/doc/dataFormat.html | 23 ++++- inst/doc/mixtCompObject.Rmd | 1 inst/doc/mixtCompObject.html | 15 +++ man/RMixtComp-package.Rd | 2 man/mixtCompLearn.Rd | 26 ++++-- man/plotCrit.Rd | 4 man/titanic.Rd | 2 tests/testthat/test.run.R | 2 tests/testthat/test.runWrapper.R | 12 +- vignettes/mixtCompObject.Rmd | 1 26 files changed, 322 insertions(+), 202 deletions(-)
Title: Iterative and Interactive Dashboards
Description: Create customized, web-based dashboards for data presentation, exploration and sharing. 'i2dash' integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts.
Author: Arsenij Ustjanzew [aut, cre, cph]
(<https://orcid.org/0000-0002-1014-4521>),
Jens Preussner [aut, cph] (<https://orcid.org/0000-0003-1927-3458>),
Mario Looso [aut, cph] (<https://orcid.org/0000-0003-1495-9530>)
Maintainer: Arsenij Ustjanzew <arsenij.ustjanzew@gmail.com>
Diff between i2dash versions 0.2.2 dated 2020-10-19 and 0.2.3 dated 2021-03-29
DESCRIPTION | 22 LICENSE | 4 MD5 | 123 - NAMESPACE | 29 R/AllGenerics.R | 174 - R/assemble.R | 278 +- R/colormap.R | 24 R/components.R | 548 ++-- R/get_set.R | 192 - R/i2dash-pkg.R |only R/i2dashboard.R | 210 - R/pages.R | 128 - R/reexports.R | 32 R/sidebar.R | 124 - R/vis_objects.R | 88 build/vignette.rds |binary inst/CITATION | 36 inst/doc/i2dash-extension.R |only inst/doc/i2dash-extension.Rmd |only inst/doc/i2dash-extension.html |only inst/doc/i2dash-intro.R | 44 inst/doc/i2dash-intro.Rmd | 66 inst/doc/i2dash-intro.html | 3017 --------------------------- inst/templates/component.Rmd | 8 inst/templates/global_sidebar.Rmd | 10 inst/templates/i2dash-global-setup.Rmd | 32 inst/templates/layout_2x2_grid.Rmd | 38 inst/templates/layout_default.Rmd | 22 inst/templates/layout_empty.Rmd | 8 inst/templates/layout_focal_left.Rmd | 36 inst/templates/layout_storyboard.Rmd | 12 inst/templates/local_sidebar.Rmd | 10 inst/templates/vis_object.Rmd | 64 man/add_vis_object.Rd | 50 man/assemble.Rd | 92 man/dot-add_component.Rd | 42 man/dot-create_page_name.Rd | 34 man/dot-render_page.Rd | 62 man/embed_var.Rd | 44 man/grapes-greater-than-grapes.Rd | 22 man/grapes-less-than-greater-than-grapes.Rd | 22 man/i2dash.Rd | 40 man/i2dashboard-class.Rd | 146 - man/i2dashboard-content.Rd | 310 +- man/i2dashboard-methods.Rd | 238 +- man/i2dashboard-pages.Rd | 110 man/render_image.Rd | 74 man/render_text.Rd | 42 tests/testthat.R | 10 tests/testthat/input-data/i2dashboard.Rmd | 74 tests/testthat/input-data/sample.txt | 2 tests/testthat/test-accessor-methods.R | 86 tests/testthat/test-add-content.R | 258 +- tests/testthat/test-assemble.R | 38 tests/testthat/test-i2dashboard-class.R | 28 tests/testthat/test-internal-functions.R | 98 tests/testthat/test-pages.R | 64 vignettes/i2dash-extension.Rmd |only vignettes/i2dash-intro.Rmd | 66 vignettes/images/RStudio_new_project.png |only vignettes/images/RStudio_new_project2.png |only vignettes/images/RStudio_new_project3.png |only vignettes/images/concept1.png |only vignettes/images/concept2.png |only vignettes/images/file_structure.png |only vignettes/images/lemur.jpg |binary vignettes/images/scatter3D_result_shiny.png |only vignettes/images/scatter3D_result_static.png |only vignettes/texts/lemurs.md | 7 69 files changed, 2371 insertions(+), 5067 deletions(-)
Title: Access Finnish Geospatial Data
Description: Tools for reading Finnish open geospatial data in R.
Author: Markus Kainu [aut, cre] (<https://orcid.org/0000-0003-1376-503X>),
Joona Lehtomaki [aut] (<https://orcid.org/0000-0002-7891-0843>),
Juuso Parkkinen [ctb] (<https://orcid.org/0000-0002-7818-5901>),
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>)
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.0 dated 2021-02-25 and 1.0.1 dated 2021-03-29
DESCRIPTION | 13 ++- MD5 | 52 +++++++-------- NEWS.md | 6 + R/data.R | 2 README.md | 19 ++--- build/vignette.rds |binary data/municipality_key.rda |binary data/municipality_key_2013.rda |binary data/municipality_key_2014.rda |binary data/municipality_key_2015.rda |binary data/municipality_key_2016.rda |binary data/municipality_key_2017.rda |binary data/municipality_key_2018.rda |binary data/municipality_key_2019.rda |binary data/municipality_key_2020.rda |binary data/municipality_key_2021.rda |binary inst/doc/geofi_datasets.html | 17 ++-- inst/doc/geofi_joining_attribute_data.html | 15 ++-- inst/doc/geofi_making_maps.html | 43 ++++++------ inst/doc/geofi_spatial_analysis.html | 31 ++++---- inst/doc/tricolore_tutorial.R | 16 ++-- inst/doc/tricolore_tutorial.Rmd | 24 ++++-- inst/doc/tricolore_tutorial.html | 100 +++++++++++++++-------------- man/figures/readme_map-1.png |binary man/municipality_key_2016.Rd | 2 tests/testthat/test-01-wfs.R | 3 vignettes/tricolore_tutorial.Rmd | 24 ++++-- 27 files changed, 201 insertions(+), 166 deletions(-)
Title: Data Correction and Imputation Using Deductive Methods
Description: Attempt to repair inconsistencies and missing values in
data records by using information from valid values and
validation rules restricting the data.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between deductive versions 0.1.3 dated 2019-04-10 and 1.0.0 dated 2021-03-29
deductive-0.1.3/deductive/tests/testthat |only deductive-0.1.3/deductive/tests/testthat.R |only deductive-1.0.0/deductive/DESCRIPTION | 23 +-- deductive-1.0.0/deductive/MD5 | 20 +-- deductive-1.0.0/deductive/NEWS | 13 ++ deductive-1.0.0/deductive/R/deductive-pkg.R | 4 deductive-1.0.0/deductive/R/linimpute.R | 162 ++++++++++++++----------- deductive-1.0.0/deductive/inst |only deductive-1.0.0/deductive/man/correct_typos.Rd | 4 deductive-1.0.0/deductive/man/deductive.Rd | 4 deductive-1.0.0/deductive/man/impute_lr.Rd | 16 ++ deductive-1.0.0/deductive/tests/tinytest.R |only 12 files changed, 151 insertions(+), 95 deletions(-)
Title: A 'Shiny' Application for Inspecting Structural Topic Models
Description: This app enables interactive validation, interpretation and visualization of structural topic models from the 'stm' package by Roberts and others (2014) <doi:10.1111/ajps.12103>. It also includes helper functions for model diagnostics and extracting data from effect estimates.
Author: Carsten Schwemmer [aut, cre] (<https://orcid.org/0000-0001-9084-946X>),
Jonne Guyt [ctb]
Maintainer: Carsten Schwemmer <c.schwem2er@gmail.com>
Diff between stminsights versions 0.3.0 dated 2018-11-24 and 0.4.1 dated 2021-03-29
DESCRIPTION | 23 - MD5 | 34 +- NEWS.md | 159 +++++++------ R/run_app.R | 15 - R/stm_diag.R | 16 - R/stm_effects.R | 19 - R/stm_network.R | 72 ++--- README.md | 52 +--- build/vignette.rds |binary inst/app/app.R | 595 +++++++++++++++++++++++++++++++++---------------- inst/doc/intro.R | 15 - inst/doc/intro.Rmd | 265 ++++++++++----------- inst/doc/intro.html | 163 +++++++++---- man/get_diag.Rd | 4 man/get_effects.Rd | 13 - man/get_network.Rd | 4 man/run_stminsights.Rd | 6 vignettes/intro.Rmd | 265 ++++++++++----------- 18 files changed, 1019 insertions(+), 701 deletions(-)
Title: Mann-Kendall Test, Seasonal and Regional Kendall Tests
Description: Contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.
Author: Aldo Marchetto
Maintainer: Aldo Marchetto <aldo.marchetto@cnr.it>
Diff between rkt versions 1.5 dated 2017-03-07 and 1.6 dated 2021-03-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/rkt-package.Rd | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Plackett-Luce Models for Rankings
Description: Functions to prepare rankings data and fit the Plackett-Luce model
jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce
(1959, ISBN:0486441369). The standard Plackett-Luce model is generalized
to accommodate ties of any order in the ranking. Partial rankings, in which
only a subset of items are ranked in each ranking, are also accommodated in
the implementation. Disconnected/weakly connected networks implied by the
rankings may be handled by adding pseudo-rankings with a hypothetical item.
Optionally, a multivariate normal prior may be set on the log-worth
parameters and ranker reliabilities may be incorporated as proposed by
Raman and Joachims (2014) <doi:10.1145/2623330.2623654>. Maximum a
posteriori estimation is used when priors are set. Methods are provided to
estimate standard errors or quasi-standard errors for inference as well as
to fit Plackett-Luce trees. See the package website or vignette for further
details.
Author: Heather Turner [aut, cre] (<https://orcid.org/0000-0002-1256-3375>),
Ioannis Kosmidis [aut] (<https://orcid.org/0000-0003-1556-0302>),
David Firth [aut] (<https://orcid.org/0000-0003-0302-2312>),
Jacob van Etten [ctb] (<https://orcid.org/0000-0001-7554-2558>)
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between PlackettLuce versions 0.3.2 dated 2021-01-04 and 0.4.0 dated 2021-03-29
DESCRIPTION | 12 MD5 | 56 NAMESPACE | 20 NEWS.md | 5 R/admm_log.R |only R/beans.R | 24 R/itempar.R | 324 +- R/logLik-PLADMM.R |only R/pladmm.R |only R/predict.R |only R/print.PLADMM.R |only R/summary.PLADMM.R |only R/utils.R |only R/vcov.PLADMM.R |only build/partial.rdb |only build/vignette.rds |binary data/beans.rda |binary inst/WORDLIST | 18 inst/doc/Overview.R | 902 +++---- inst/doc/Overview.html | 3778 +++++++++++++++---------------- inst/doc/PLADMM.R |only inst/doc/PLADMM.Rmd |only inst/doc/PLADMM.html |only man/beans.Rd | 24 man/itempar.PlackettLuce.Rd | 7 man/pladmm.Rd |only tests/testthat/outputs/print.coef.rds | 4 tests/testthat/outputs/print.rds | 10 tests/testthat/outputs/print.summary.rds | 24 tests/testthat/outputs/print.txt |only tests/testthat/outputs/print_PLADMM.txt |only tests/testthat/test-S3-methods-PLADMM.R |only tests/testthat/test-S3-methods.R | 2 tests/testthat/test-admm.R |only tests/testthat/test-itempar-PLADMM.R |only tests/testthat/test-predict-PLADMM.R |only vignettes/PLADMM.Rmd |only vignettes/plackettluce.bib | 307 +- vignettes/render.R | 7 39 files changed, 2807 insertions(+), 2717 deletions(-)
Title: R Interface for Apache Impala
Description: 'SQL' back-end to 'dplyr' for Apache Impala, the massively
parallel processing query engine for Apache 'Hadoop'. Impala enables
low-latency 'SQL' queries on data stored in the 'Hadoop' Distributed
File System '(HDFS)', Apache 'HBase', Apache 'Kudu', Amazon Simple
Storage Service '(S3)', Microsoft Azure Data Lake Store '(ADLS)',
and Dell 'EMC' 'Isilon'. See <https://impala.apache.org> for more
information about Impala.
Author: Ian Cook [aut, cre],
Cloudera [cph]
Maintainer: Ian Cook <ianmcook@gmail.com>
Diff between implyr versions 0.3.0 dated 2019-07-21 and 0.4.0 dated 2021-03-29
DESCRIPTION | 12 ++--- LICENSE | 2 MD5 | 59 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 8 +++ R/db-compute.R | 2 R/db-impala.R | 30 +++++++++++-- R/db-jdbc.R | 2 R/db-odbc.R | 2 R/schema.R | 2 R/sql-escape.R | 2 R/src_impala.R | 22 +++++---- R/tbl_impala.R | 4 - README.md | 40 ++++++++--------- man/compute.Rd | 20 ++++++-- man/copy_to.Rd | 31 ++++++++++--- man/dbDisconnect-src_impala-method.Rd | 1 man/dbExecute-src_impala-character-method.Rd | 1 man/dbGetQuery-src_impala-character-method.Rd | 1 man/impala_unnest.Rd | 2 tests/testthat/helper-src.R | 52 ++++++++++++++++++++++ tests/testthat/test-aggregate-functions.R | 4 - tests/testthat/test-cast.R | 3 + tests/testthat/test-complex.R | 6 +- tests/testthat/test-copy_to.R | 9 +++ tests/testthat/test-data.R | 12 ++--- tests/testthat/test-lubridate.R | 12 ++--- tests/testthat/test-numeric-functions.R | 9 +++ tests/testthat/test-readme.R | 12 +++-- tests/testthat/test-regex.R | 8 +-- tests/testthat/test-rowwise.R |only 31 files changed, 252 insertions(+), 120 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Romain François [ctb],
Benjamin Kietzman [ctb],
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between cpp11 versions 0.2.6 dated 2021-01-29 and 0.2.7 dated 2021-03-29
DESCRIPTION | 7 MD5 | 26 - NEWS.md | 4 README.md | 2 build/vignette.rds |binary inst/doc/converting.html | 9 inst/doc/cpp11.R | 344 +++++++++++------------ inst/doc/cpp11.html | 613 +++++++++++++++++++---------------------- inst/doc/internals.html | 9 inst/doc/motivations.R | 58 +-- inst/doc/motivations.Rmd | 2 inst/doc/motivations.html | 370 +----------------------- inst/include/cpp11/protect.hpp | 10 vignettes/motivations.Rmd | 2 14 files changed, 554 insertions(+), 902 deletions(-)
Title: Computerized Adaptive Testing and Decision Trees
Description: Implements the Merged Tree-CAT method (Javier Rodriguez-Cuadrado et al., 2020, <doi:10.1016/j.eswa.2019.113066>) to generate Computerized Adaptive Tests (CATs) based on a decision tree. The tree growth is controlled by merging branches with similar trait distributions and estimations. This package has the necessary tools for creating CATs and estimate the subject's ability level.
Author: Javier Rodriguez-Cuadrado [aut, cre],
Juan C. Laria [aut],
David Delgado-Gomez [aut]
Maintainer: Javier Rodriguez-Cuadrado <javierro@est-econ.uc3m.es>
Diff between cat.dt versions 0.2.0 dated 2020-04-23 and 0.3.0 dated 2021-03-29
DESCRIPTION | 8 MD5 | 93 +++++----- R/CAT_DT.R | 81 +++++---- R/CAT_ability_est.R | 42 ++-- R/CAT_ability_est_group.R | 9 - R/CAT_summary.R | 88 ++++----- R/Fisher_GRM.R | 2 R/Fisher_Inf.R | 3 R/Fisher_NRM.R | 2 R/a_posteriori.R | 2 R/ability_density.R | 2 R/allocate_sons.R | 10 - R/create_E_MEPV.R | 109 ++++++------ R/create_E_MFI.R | 68 +++---- R/create_last_level.R | 113 ++++++------ R/create_level_1.R | 137 +++++++-------- R/create_levels.R | 382 +++++++++++++++++++++++++------------------ R/create_node.R | 63 +++---- R/estimate.R | 10 - R/join_node.R | 220 ++++++++++++------------ R/plot_tree.R | 77 +++++--- README.md | 313 +++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/cat.R | 2 inst/doc/cat.Rmd | 6 inst/doc/cat.html | 312 ++++++++--------------------------- man/CAT_DT.Rd | 15 - man/CAT_ability_est.Rd | 7 man/CAT_ability_est_group.Rd | 7 man/Fisher_GRM.Rd | 2 man/Fisher_NRM.Rd | 2 man/a_posteriori.Rd | 2 man/ability_density.Rd | 2 man/allocate_sons.Rd | 2 man/create_E_MEPV.Rd | 2 man/create_E_MFI.Rd | 2 man/create_last_level.Rd | 4 man/create_level_1.Rd | 2 man/create_levels.Rd | 12 - man/create_node.Rd | 10 - man/estimate.Rd | 5 man/figures |only man/join_node.Rd | 2 man/plot_tree.Rd | 2 man/predict.cat.dt.Rd | 2 man/summary.cat.dt.Rd | 2 vignettes/cat.Rmd | 6 47 files changed, 1265 insertions(+), 979 deletions(-)
Title: Sampling from k-th Order Statistics of New Families of
Distributions
Description: Set of tools to generate samples of order statistics and others quantities of interest from new families of distributions.
The main references for this package are: Gentle, J. (2009), Computational Statistics, Springer-Verlag;
Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and
Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>.
The families of distributions are: Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions,
beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions,
exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions,
and exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distribution, Skew normal type 1 distributions, Skew student t distribution, Sinh-Arcsinh distribution, Sichel distribution and Zero inflated Poisson.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between orders versions 0.1.4 dated 2020-09-24 and 0.1.5 dated 2021-03-29
DESCRIPTION | 11 ++--- MD5 | 101 +++++++++++++++++++++++------------------------ NAMESPACE | 4 - R/aux_func.R |only R/order_beg.R | 29 +++++++------ R/order_betaexpg.R | 17 +++++-- R/order_betag.R | 22 ++++++---- R/order_eepg.R | 20 ++++++--- R/order_eg.R | 20 ++++++--- R/order_expg.R | 20 ++++++--- R/order_expkumg.R | 20 ++++++--- R/order_gammag.R | 20 ++++++--- R/order_gammag1.R | 20 ++++++--- R/order_gammag2.R | 21 ++++++--- R/order_gbg.R | 20 ++++++--- R/order_kumg.R | 20 ++++++--- R/order_loggammag1.R | 20 ++++++--- R/order_loggammag2.R | 20 ++++++--- R/order_mbetag.R | 20 ++++++--- R/order_mog.R | 20 ++++++--- R/order_pig.R | 21 ++++++--- R/order_sichel.R | 23 ++++++---- R/order_sinharcsinh.R | 20 ++++++--- R/order_snormal1.R | 20 ++++++--- R/order_sstudentt.R | 20 ++++++--- R/order_tessg.R | 20 ++++++--- R/order_weibullg.R | 20 ++++++--- R/order_zip.R | 23 ++++++---- man/order_beg.Rd | 21 +++++---- man/order_betaexpg.Rd | 10 ++-- man/order_betag.Rd | 13 +++--- man/order_eepg.Rd | 13 +++--- man/order_eg.Rd | 13 +++--- man/order_expg.Rd | 13 +++--- man/order_expkumg.Rd | 13 +++--- man/order_gammag.Rd | 13 +++--- man/order_gammag1.Rd | 13 +++--- man/order_gammag2.Rd | 13 +++--- man/order_gbg.Rd | 13 +++--- man/order_kumg.Rd | 13 +++--- man/order_loggammag1.Rd | 13 +++--- man/order_loggammag2.Rd | 13 +++--- man/order_mbetag.Rd | 13 +++--- man/order_mog.Rd | 13 +++--- man/order_pig.Rd | 13 +++--- man/order_sichel.Rd | 15 ++++-- man/order_sinharcsinh.Rd | 13 +++--- man/order_snormal1.Rd | 13 +++--- man/order_sstudentt.Rd | 13 +++--- man/order_tessg.Rd | 13 +++--- man/order_weibullg.Rd | 13 +++--- man/order_zip.Rd | 15 ++++-- 52 files changed, 570 insertions(+), 363 deletions(-)
Title: Multidimensional Scaling for Big Data
Description: MDS is a statistic tool for reduction of dimensionality, using as input a distance matrix of dimensions n × n.
When n is large, classical algorithms suffer from computational problems and MDS configuration can not be obtained.
With this package, we address these problems by means of three algorithms:
- Divide and Conquer MDS developed by Delicado and Pachon-Garcia, (2020) <arXiv:2007.11919>.
- Fast MDS, which is an implementation of Tynia, Y., L. Jinze, M. Leonard, and W. Wei, (2006).
- MDS based on Gower interpolation, which uses Gower interpolation formula as described in Gower, J.C. and D.J, Hand (1995, ISBN: 978-0-412-71630-0).
The main idea of these methods is based on partitioning the dataset into small pieces, where classical methods can work. In order to align all the solutions, it is used Procrustes formula as described in Borg, I. and Groenen, P. (2005, ISBN : 978-0-387-25150-9).
Author: Cristian Pachón García [aut, cre]
(<https://orcid.org/0000-0001-9518-4874>),
Pedro Delicado [aut] (<https://orcid.org/0000-0003-3933-4852>)
Maintainer: Cristian Pachón García <cc.pachon@gmail.com>
Diff between bigmds versions 0.0.1 dated 2021-01-18 and 1.0.0 dated 2021-03-29
DESCRIPTION | 28 +-- MD5 | 26 +- NEWS.md | 5 R/divide_conquer_mds.R | 226 ++++++++++++++++--------- R/fast_mds.R | 232 ++++++++++++++------------ R/gower_interpolation_mds.R | 171 ++++++++++++------- R/utils.R | 61 +++++- README.md | 115 ++++++++---- man/divide_conquer_mds.Rd | 61 +++++- man/fast_mds.Rd | 61 +++++- man/gower_interpolation_mds.Rd | 52 ++++- tests/testthat/test-divide_conquer_mds.R | 8 tests/testthat/test-fast_mds.R | 6 tests/testthat/test-gower_interpolation_mds.R | 10 - 14 files changed, 684 insertions(+), 378 deletions(-)
Title: Bayesian Reliability Estimation
Description: Functionality for the most common single test reliability estimates:
Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower bound and coefficient omega.
The Bayesian estimates are provided with credible intervals.
The frequentist estimates are provided with bootstrapped confidence intervals
The method for the Bayesian estimates, except for omega, is sampling from the posterior inverse 'Wishart'
for the covariance matrix based measures
(see 'Murphy', 2007, <https://www.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>.
In the case of omega it is 'Gibbs' Sampling from the joint conditional distributions of a single factor model
('Lee', 2007, <doi:10.1002/9780470024737>).
The glb method uses adjusted code from the 'Rcsdp' package by 'Hector Corrada Bravo',
<https://CRAN.R-project.org/package=Rcsdp>. This process applies a slightly adjusted solving algorithm
from the 'CSDP' library by 'Brian Borchers' <https://github.com/coin-or/Csdp/wiki>,
<doi:10.1080/10556789908805765>, but is wrapped in 'RcppArmadillo'.
Guttman's Lambda-4 is from 'Benton' (2015) <doi:10.1007/978-3-319-07503-7_19>.
The principal factor analysis for a version of frequentist omega is from 'Schlegel' (2017)
<https://www.r-bloggers.com/2017/03/iterated-principal-factor-method-of-factor-analysis-with-r/>.
The analytic confidence interval of alpha is from 'Bonett' and 'Wright' (2015) <doi:10.1002/job.1960>.
Author: Julius M. Pfadt [aut, cre],
Don van den Bergh [aut],
Joris Goosen [aut]
Maintainer: Julius M. Pfadt <julius.pfadt@gmail.com>
Diff between Bayesrel versions 0.7.0.3 dated 2021-01-07 and 0.7.0.7 dated 2021-03-29
DESCRIPTION | 6 +- MD5 | 32 +++++++-------- R/RcppExports.R | 4 - R/boot_apply_functions.R | 8 +-- R/glb_funs.R | 6 -- R/help_funs.R | 13 ++---- R/omegaUni_Gibbs.R | 4 - R/omega_freq.R | 90 ++++++++++++++++++++++++++++---------------- R/samplePrior.R | 3 - R/sysdata.rda |binary README.md | 9 +--- build/partial.rdb |binary src/BayesrelCpp.cpp | 5 +- src/RcppExports.cpp | 9 ++-- src/customsdp.h | 2 src/customsdpCpp.cpp | 37 +++++++++++------- tests/testthat/test_strel.R | 13 ++++++ 17 files changed, 140 insertions(+), 101 deletions(-)
Title: Multinomial Logit Models, with or without Random Effects or
Overdispersion
Description: Provides estimators for multinomial logit models in their
conditional logit and baseline logit variants, with or without random effects,
with or without overdispersion.
Random effects models are estimated using the PQL technique (based on a Laplace approximation)
or the MQL technique (based on a Solomon-Cox approximation). Estimates should be treated
with caution if the group sizes are small.
Author: Martin Elff
Maintainer: Martin Elff <mclogit@elff.eu>
Diff between mclogit versions 0.8.6.4 dated 2020-11-04 and 0.8.7.3 dated 2021-03-29
DESCRIPTION | 11 ++-- MD5 | 33 +++++++------- R/getSummary-mblogit.R | 110 ++++++++++++++++++++++++++++++++++++++++++++----- R/getSummary-mclogit.R | 69 +++++++++++++++++++----------- R/mblogit.R | 85 ++++++++++++++++++++++--------------- R/mclogit-fit.R | 4 - R/mclogit.R | 107 ++++++++++++++++++++++++++++++++++------------- R/mmclogit-fitPQLMQL.R | 50 ++++------------------ R/zzz.R | 5 +- build |only data/Transport.rda |binary data/electors.rda |binary inst/ChangeLog | 18 ++++++++ inst/NEWS.Rd | 12 ++++- man/dispersion.Rd | 4 - man/mblogit.Rd | 4 - man/mclogit.Rd | 6 +- man/mclogit.fit.Rd | 5 +- 18 files changed, 347 insertions(+), 176 deletions(-)
Title: An Interface for Image Recognition
Description: Provides an interface for image recognition using the 'Google Vision API' <https://cloud.google.com/vision/> . Converts API data for features such as object detection and optical character recognition to data frames. The package also includes functions for analyzing image annotations.
Author: Carsten Schwemmer [aut, cre] (<https://orcid.org/0000-0001-9084-946X>)
Maintainer: Carsten Schwemmer <c.schwem2er@gmail.com>
Diff between imgrec versions 0.1.0 dated 2019-07-12 and 0.1.2 dated 2021-03-29
DESCRIPTION | 21 +- MD5 | 33 ++-- NEWS.md | 13 + R/get_annotations.R | 2 R/save_json.R | 76 +++++----- README.md | 94 +++++++------ build/vignette.rds |binary inst/doc/intro.R | 48 ------ inst/doc/intro.Rmd | 298 ++++++++++++++++++++++-------------------- inst/doc/intro.html | 267 ++++++++++++++++++++----------------- inst/doc/label_tweets.R |only inst/doc/label_tweets.Rmd |only inst/doc/label_tweets.html |only man/figures/example_image.png |only man/get_annotations.Rd | 114 ++++++++-------- man/gvision_init.Rd | 52 +++---- man/parse_annotations.Rd | 106 +++++++------- man/save_json.Rd | 60 ++++---- vignettes/intro.Rmd | 298 ++++++++++++++++++++++-------------------- vignettes/label_tweets.Rmd |only 20 files changed, 770 insertions(+), 712 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' with support for SSH and
HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors
and data-frames) for their arguments and return values. User credentials are
shared with command line 'git' through the git-credential store and ssh keys
stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jennifer Bryan [ctb] (<https://orcid.org/0000-0002-6983-2759>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 1.2.0 dated 2021-02-14 and 1.3.0 dated 2021-03-29
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS | 3 +++ R/config.R | 4 ++++ R/init.R | 5 +++++ R/repository.R | 5 +++-- build/vignette.rds |binary configure | 1 + inst/doc/gert.html | 17 ++++++++--------- man/git_config.Rd | 5 +++++ man/git_repo.Rd | 4 +++- src/clone.c | 4 ++-- src/commit.c | 11 ++++++++--- src/init.c | 12 ++++++++---- src/version.c | 2 +- 15 files changed, 68 insertions(+), 39 deletions(-)
Title: Interface Package for the 'EpiGraphDB' Platform
Description: The interface package to access data from the
'EpiGraphDB' <https://epigraphdb.org> platform.
It provides easy access to the 'EpiGraphDB' platform with functions that
query the corresponding REST endpoints on the API <https://api.epigraphdb.org>
and return the response data in the 'tibble' data frame format.
Author: Yi Liu [cre, aut],
Valeriia Haberland [aut],
Marina Vabistsevits [aut],
Tom Gaunt [aut],
MRC IEU [cph]
Maintainer: Yi Liu <yi6240.liu@bristol.ac.uk>
Diff between epigraphdb versions 0.2.1 dated 2020-08-26 and 0.2.2 dated 2021-03-29
DESCRIPTION | 7 MD5 | 90 +- NEWS.md | 5 R/drugs.R | 2 R/meta.R | 6 R/request_and_response.R | 10 R/zzz.R | 16 README.md | 33 build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/about.html | 196 ---- inst/doc/case-1-pleiotropy.R | 6 inst/doc/case-1-pleiotropy.Rmd | 6 inst/doc/case-1-pleiotropy.html | 938 ++++++++------------- inst/doc/case-2-alt-drug-target.html | 508 +++-------- inst/doc/case-3-literature-triangulation.R | 59 - inst/doc/case-3-literature-triangulation.Rmd | 62 - inst/doc/case-3-literature-triangulation.html | 1036 +++++++++--------------- inst/doc/getting-started-with-epigraphdb-r.R |only inst/doc/getting-started-with-epigraphdb-r.Rmd |only inst/doc/getting-started-with-epigraphdb-r.html |only inst/doc/meta-functionalities.Rmd | 2 inst/doc/meta-functionalities.html | 978 ++++++++-------------- inst/doc/options.html | 215 ---- inst/doc/using-epigraphdb-api.html | 479 +++-------- inst/doc/using-epigraphdb-r-package.html | 391 ++------- man/drugs_risk_factors.Rd | 2 man/meta_nodes_search_node.Rd | 4 man/meta_rels_list_rel.Rd | 2 tests/testthat.R | 1 tests/testthat/test-confounder.R | 3 tests/testthat/test-cypher.R | 3 tests/testthat/test-drugs.R | 3 tests/testthat/test-genetic_cor.R | 3 tests/testthat/test-literature.R | 3 tests/testthat/test-mappings.R | 2 tests/testthat/test-meta.R | 12 tests/testthat/test-mr.R | 3 tests/testthat/test-obs_cor.R | 3 tests/testthat/test-ontology.R | 3 tests/testthat/test-pathway.R | 3 tests/testthat/test-pqtl.R | 12 tests/testthat/test-protein.R | 2 tests/testthat/test-xqtl.R | 6 vignettes/case-1-pleiotropy.Rmd | 6 vignettes/case-3-literature-triangulation.Rmd | 62 - vignettes/getting-started-with-epigraphdb-r.Rmd |only vignettes/meta-functionalities.Rmd | 2 48 files changed, 1846 insertions(+), 3344 deletions(-)
Title: Detection of Structural Changes in Climate and Environment Time
Series
Description: Tools for automatic model selection and diagnostics for Climate and Environmental data. In particular the envcpt() function does automatic model selection between a variety of trend, changepoint and autocorrelation models. The envcpt() function should be your first port of call.
Author: Rebecca Killick [aut, cre],
Claudie Beaulieu [aut],
Simon Taylor [aut],
Harjit Hullait [aut]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between EnvCpt versions 1.1.2 dated 2020-06-21 and 1.1.3 dated 2021-03-29
DESCRIPTION | 8 ++--- MD5 | 15 +++++----- NAMESPACE | 2 - NEWS | 7 ++++ R/diagnostics.R | 15 +++++++--- R/envcpt.R | 61 ++++++++++++++++++++++++++++++++++--------- man/envcpt-package.Rd | 4 +- man/plot.envcpt.Rd | 5 ++- tests/testthat/test-envcpt.R |only 9 files changed, 86 insertions(+), 31 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] (<https://orcid.org/0000-0003-1676-0197>),
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.4.6 dated 2020-12-04 and 4.5.1 dated 2021-03-29
DESCRIPTION | 8 MD5 | 32 +- NEWS.md | 9 R/compare.i.R | 4 R/compareGroups.R | 15 - R/compareGroups.fit.R | 6 R/descrTable.R | 2 R/export2md.R | 3 R/export2mdcbind.R | 3 build/vignette.rds |binary inst/doc/compareGroups_vignette.html | 389 ++++++++++++++++++++++++----------- man/compareGroups-internal.Rd | 4 man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 5 man/createTable.Rd | 2 man/descrTable.Rd | 5 man/export2md.Rd | 2 17 files changed, 332 insertions(+), 161 deletions(-)
Title: A GUI to Correct Measurement Bias in DNA Methylation Analyses
Description: A GUI to correct measurement bias in DNA methylation
analyses. The 'BiasCorrector' package just wraps the functions
implemented in the 'R' package 'rBiasCorrection' into a shiny web
application in order to make them more easily accessible.
Author: Lorenz A. Kapsner [cre, aut, cph]
(<https://orcid.org/0000-0003-1866-860X>),
Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between BiasCorrector versions 0.1.3 dated 2021-03-01 and 0.1.4 dated 2021-03-29
DESCRIPTION | 18 MD5 | 18 R/app_omitnas_modal.R | 80 +-- R/app_render_regressionstatistics.R | 232 ++++----- R/app_requirements_error.R | 224 ++++---- R/app_utils.R | 44 - R/launch_app.R | 200 +++---- R/modulePlotting.R | 905 ++++++++++++++++++------------------ R/type2Files.R | 218 ++++---- inst/application/ui.R | 309 ++++++------ 10 files changed, 1124 insertions(+), 1124 deletions(-)
Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and
without spatial components. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments developed
by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://www.vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre]
(<https://orcid.org/0000-0002-8673-2514>),
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie J. Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Willem Kruijer [ctb] (<https://orcid.org/0000-0001-7179-1733>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenSTA versions 1.0.6 dated 2020-09-23 and 1.0.7 dated 2021-03-29
statgenSTA-1.0.6/statgenSTA/data/wheatChl.rda |only statgenSTA-1.0.6/statgenSTA/inst/extdata/F2maize_pheno.csv |only statgenSTA-1.0.6/statgenSTA/inst/extdata/SB_yield.csv |only statgenSTA-1.0.6/statgenSTA/inst/extdata/pheno_data2011.txt |only statgenSTA-1.0.6/statgenSTA/inst/extdata/pheno_data2012.txt |only statgenSTA-1.0.6/statgenSTA/man/wheatChl.Rd |only statgenSTA-1.0.6/statgenSTA/tests/testthat/test-TDplots.R |only statgenSTA-1.0.7/statgenSTA/DESCRIPTION | 16 statgenSTA-1.0.7/statgenSTA/MD5 | 120 - statgenSTA-1.0.7/statgenSTA/NEWS.md | 13 statgenSTA-1.0.7/statgenSTA/R/boxPlot.R |only statgenSTA-1.0.7/statgenSTA/R/corPlot.R |only statgenSTA-1.0.7/statgenSTA/R/createSTA.R | 63 statgenSTA-1.0.7/statgenSTA/R/createTD.R | 999 +------- statgenSTA-1.0.7/statgenSTA/R/data.R | 95 statgenSTA-1.0.7/statgenSTA/R/extractSTA.R | 106 statgenSTA-1.0.7/statgenSTA/R/fitTD.R | 80 statgenSTA-1.0.7/statgenSTA/R/layoutPlot.R |only statgenSTA-1.0.7/statgenSTA/R/mapPlot.R |only statgenSTA-1.0.7/statgenSTA/R/outliers.R | 15 statgenSTA-1.0.7/statgenSTA/R/scatterPlot.R |only statgenSTA-1.0.7/statgenSTA/R/sysdata.rda |binary statgenSTA-1.0.7/statgenSTA/R/utils.R | 42 statgenSTA-1.0.7/statgenSTA/README.md | 73 statgenSTA-1.0.7/statgenSTA/build/partial.rdb |only statgenSTA-1.0.7/statgenSTA/build/vignette.rds |binary statgenSTA-1.0.7/statgenSTA/data/TDHeat05.rda |binary statgenSTA-1.0.7/statgenSTA/data/TDMaize.rda |binary statgenSTA-1.0.7/statgenSTA/data/dropsRaw.rda |only statgenSTA-1.0.7/statgenSTA/inst/data-raw |only statgenSTA-1.0.7/statgenSTA/inst/doc/statgenSTA.R | 344 +-- statgenSTA-1.0.7/statgenSTA/inst/doc/statgenSTA.Rmd | 403 ++- statgenSTA-1.0.7/statgenSTA/inst/doc/statgenSTA.html | 1141 +++++----- statgenSTA-1.0.7/statgenSTA/man/STAtoCross.Rd | 13 statgenSTA-1.0.7/statgenSTA/man/STAtoTD.Rd | 13 statgenSTA-1.0.7/statgenSTA/man/TD.Rd | 36 statgenSTA-1.0.7/statgenSTA/man/TDMaize.Rd | 4 statgenSTA-1.0.7/statgenSTA/man/dropsRaw.Rd |only statgenSTA-1.0.7/statgenSTA/man/extractSTA.Rd | 54 statgenSTA-1.0.7/statgenSTA/man/figures/README-basePlot-1.png |binary statgenSTA-1.0.7/statgenSTA/man/figures/README-boxPlot-1.png |binary statgenSTA-1.0.7/statgenSTA/man/figures/README-layoutPlot-1.png |binary statgenSTA-1.0.7/statgenSTA/man/figures/README-mapPlot-1.png |only statgenSTA-1.0.7/statgenSTA/man/figures/README-scatterPlot-1.png |binary statgenSTA-1.0.7/statgenSTA/man/figures/README-spatialPlot-1.png |binary statgenSTA-1.0.7/statgenSTA/man/fitTD.Rd | 80 statgenSTA-1.0.7/statgenSTA/man/getMeta.Rd | 27 statgenSTA-1.0.7/statgenSTA/man/outlierSTA.Rd | 7 statgenSTA-1.0.7/statgenSTA/man/plot.STA.Rd | 17 statgenSTA-1.0.7/statgenSTA/man/plot.TD.Rd | 84 statgenSTA-1.0.7/statgenSTA/man/report.STA.Rd | 14 statgenSTA-1.0.7/statgenSTA/man/statgenSTA-package.Rd | 4 statgenSTA-1.0.7/statgenSTA/man/summary.STA.Rd | 6 statgenSTA-1.0.7/statgenSTA/man/summary.TD.Rd | 7 statgenSTA-1.0.7/statgenSTA/tests/testthat/Rplots.pdf |binary statgenSTA-1.0.7/statgenSTA/tests/testthat/test-ExtractAsreml.R | 175 - statgenSTA-1.0.7/statgenSTA/tests/testthat/test-ExtractLme4.R | 182 - statgenSTA-1.0.7/statgenSTA/tests/testthat/test-ExtractSpATS.R | 200 - statgenSTA-1.0.7/statgenSTA/tests/testthat/test-STA.R | 26 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-TD.R | 2 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-boxPlot.R |only statgenSTA-1.0.7/statgenSTA/tests/testthat/test-corPlot.R |only statgenSTA-1.0.7/statgenSTA/tests/testthat/test-fitTDAsreml.R | 20 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-fitTDLme4.R | 6 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-fitTDSpATS.R | 2 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-layoutPlot.R |only statgenSTA-1.0.7/statgenSTA/tests/testthat/test-mapPlot.R |only statgenSTA-1.0.7/statgenSTA/tests/testthat/test-outliers.R | 25 statgenSTA-1.0.7/statgenSTA/tests/testthat/test-scatterPlot.R |only statgenSTA-1.0.7/statgenSTA/tests/testthat/test-statisticalFunctions.R | 36 statgenSTA-1.0.7/statgenSTA/vignettes/bibliography.bib | 35 statgenSTA-1.0.7/statgenSTA/vignettes/statgenSTA.Rmd | 403 ++- 72 files changed, 2503 insertions(+), 2485 deletions(-)
Title: Violin Plot
Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Author: Daniel Adler [aut, cph],
S. Thomas Kelly [aut, cre],
Tom M. Elliott [ctb]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>
Diff between vioplot versions 0.3.5 dated 2020-06-15 and 0.3.6 dated 2021-03-29
DESCRIPTION | 12 +- MD5 | 24 ++-- NEWS.md | 6 + R/vioplot.R | 7 + build/vignette.rds |binary inst/CITATION | 4 inst/doc/violin_area.html | 192 ++++++++++++++++++++++------------ inst/doc/violin_customisation.html | 140 ++++++++++++++++++------- inst/doc/violin_formulae.html | 148 ++++++++++++++++++-------- inst/doc/violin_split.Rmd | 2 inst/doc/violin_split.html | 206 ++++++++++++++++++++++++------------- inst/doc/violin_ylog.html | 136 +++++++++++++++++------- vignettes/violin_split.Rmd | 2 13 files changed, 601 insertions(+), 278 deletions(-)
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 0.3.6 dated 2020-12-17 and 0.3.7 dated 2021-03-29
DESCRIPTION | 9 MD5 | 182 ++-- NAMESPACE | 1 NEWS.md | 28 R/compat-friendly-type.R | 9 R/complete.R | 41 - R/order-radix.R | 47 + R/order.R | 2 R/partial-factor.R | 3 R/partial-frame.R | 3 R/partial.R | 4 R/print-str.R | 3 R/ptype-abbr-full.R | 27 R/register-s3.R | 14 R/type-data-frame.R | 5 R/type-factor.R | 4 R/type.R | 11 README.md | 12 build/vignette.rds |binary inst/doc/pillar.html | 10 inst/doc/s3-vector.R | 26 inst/doc/s3-vector.Rmd | 27 inst/doc/s3-vector.html | 730 +++++++++---------- inst/doc/stability.html | 18 inst/doc/type-size.html | 22 man/faq-error-scalar-type.Rd | 2 man/howto-faq-fix-scalar-type-error.Rd | 4 man/maybe_lossy_cast.Rd | 2 man/new_partial.Rd | 2 man/new_vctr.Rd | 2 man/partial_factor.Rd | 2 man/partial_frame.Rd | 2 man/s3_register.Rd | 14 man/theory-faq-coercion.Rd | 2 man/vctrs-package.Rd | 2 man/vec_as_index.Rd | 2 man/vec_as_subscript.Rd | 2 man/vec_cbind_frame_ptype.Rd | 2 man/vec_data.Rd | 2 man/vec_detect_complete.Rd |only man/vec_empty.Rd | 2 man/vec_fill_missing.Rd | 2 man/vec_group.Rd | 2 man/vec_proxy.Rd | 4 man/vec_ptype.Rd | 7 man/vec_ptype_full.Rd | 13 man/vec_repeat.Rd | 2 man/vec_type.Rd | 2 src/complete.c | 149 +-- src/decl |only src/init.c | 24 src/order-radix.c | 174 +--- src/order-sortedness.c | 38 src/order-sortedness.h | 1 src/order-transform.c |only src/order-transform.h |only src/order-truelength.c | 3 src/order-truelength.h | 6 src/translate.c | 17 src/type-data-frame.c | 52 + src/type-data-frame.h | 1 src/type.c | 34 src/utils.c | 31 src/utils.h | 4 src/vctrs.h | 6 src/version.c | 2 tests/testthat/error/test-conditions.txt | 8 tests/testthat/error/test-type-asis.txt | 2 tests/testthat/error/test-type2.txt | 4 tests/testthat/helper-rational.R | 2 tests/testthat/test-assert-explanations.txt | 6 tests/testthat/test-bind.R | 16 tests/testthat/test-cast-error-nested.txt | 6 tests/testthat/test-complete.R | 94 +- tests/testthat/test-names.R | 8 tests/testthat/test-order-radix.R | 59 + tests/testthat/test-order.R | 9 tests/testthat/test-partial-factor-print-both.txt | 4 tests/testthat/test-partial-factor-print-learned.txt | 2 tests/testthat/test-partial-factor-print-partial.txt | 2 tests/testthat/test-ptype-abbr-full.R | 30 tests/testthat/test-recycle.R | 4 tests/testthat/test-runs.R | 10 tests/testthat/test-shape.R | 4 tests/testthat/test-slice-assign.R | 2 tests/testthat/test-slice-chop.R | 4 tests/testthat/test-type-data-frame.R | 16 tests/testthat/test-type-data-frame.txt | 2 tests/testthat/test-type-factor.R | 2 tests/testthat/test-type-list-of.R | 4 tests/testthat/test-type-table.R | 10 tests/testthat/test-type-unspecified.R | 5 tests/testthat/test-type.R | 7 vignettes/s3-vector.Rmd | 27 94 files changed, 1210 insertions(+), 995 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x> and
Gile and Handcock (2015) <doi:10.1111/rssa.12091>.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.9-2 dated 2019-12-14 and 0.9-3 dated 2021-03-29
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/bootstrap-intervals.R | 5 ++++- R/rds.interval.estimate.R | 2 +- inst/CITATION | 2 +- 5 files changed, 15 insertions(+), 12 deletions(-)
Title: Piece-Wise Exponential Additive Mixed Modeling Tools for
Survival Analysis
Description: The Piece-wise exponential (Additive Mixed) Model
(PAMM; Bender and others (2018) <doi: 10.1177/1471082X17748083>) is a
powerful model class for the analysis of survival (or time-to-event) data,
based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2019)), as well as support for left-truncated, competing risks and recurrent events data.
pammtools provides tidy workflow for survival analysis with PAMMs,
including data simulation, transformation and other functions for data
preprocessing and model post-processing as well as visualization.
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>),
Fabian Scheipl [aut] (<https://orcid.org/0000-0001-8172-3603>),
Philipp Kopper [aut] (<https://orcid.org/0000-0002-5037-7135>)
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>
Diff between pammtools versions 0.5.4 dated 2020-12-18 and 0.5.6 dated 2021-03-29
pammtools-0.5.4/pammtools/R/geom_hazard.R |only pammtools-0.5.6/pammtools/DESCRIPTION | 12 - pammtools-0.5.6/pammtools/MD5 | 44 ++-- pammtools-0.5.6/pammtools/NEWS.md | 5 pammtools-0.5.6/pammtools/R/as-ped.R | 5 pammtools-0.5.6/pammtools/R/convenience-plots.R | 9 pammtools-0.5.6/pammtools/R/data.R | 3 pammtools-0.5.6/pammtools/R/geom-hazard.R |only pammtools-0.5.6/pammtools/R/split-data.R | 9 pammtools-0.5.6/pammtools/R/tidyverse-methods.R | 4 pammtools-0.5.6/pammtools/R/zzz.R | 5 pammtools-0.5.6/pammtools/README.md | 1 pammtools-0.5.6/pammtools/inst/CITATION | 9 pammtools-0.5.6/pammtools/man/geom_hazard.Rd | 2 pammtools-0.5.6/pammtools/man/gg_re.Rd | 9 pammtools-0.5.6/pammtools/man/patient.Rd | 3 pammtools-0.5.6/pammtools/man/split_data.Rd | 8 pammtools-0.5.6/pammtools/man/split_data_recurrent.Rd | 8 pammtools-0.5.6/pammtools/tests/testthat/test-add-functions.R | 105 ++++------ pammtools-0.5.6/pammtools/tests/testthat/test-as-ped.R | 16 - pammtools-0.5.6/pammtools/tests/testthat/test-interval-functions.R | 24 +- pammtools-0.5.6/pammtools/tests/testthat/test-pamm-fit.R | 20 - pammtools-0.5.6/pammtools/tests/testthat/test-simple-transform.R | 72 +++--- pammtools-0.5.6/pammtools/tests/testthat/test-tidyverse-S3methods.R | 43 +++- 24 files changed, 206 insertions(+), 210 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.2 dated 2020-09-17 and 0.9.3 dated 2021-03-29
DESCRIPTION | 8 +++---- MD5 | 4 +-- R/metNOAA.R | 63 +++++++++++++++++++++++++++++++----------------------------- 3 files changed, 39 insertions(+), 36 deletions(-)
More information about utilityFunctionTools at CRAN
Permanent link
Title: Common Methods of Spectral Data Analysis
Description: On discrete data spectral analysis is performed by Fourier and Hilbert
transforms as well as with model based analysis called Lomb-Scargle method.
Fragmented and irregularly spaced data can be processed in almost all methods. Both,
FFT as well as LOMB methods take multivariate data and return standardized PSD.
For didactic reasons an analytical approach for deconvolution of noise spectra and
sampling function is provided.
A user friendly interface helps to interpret the results.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <martin.seilmayer@gmail.com>
Diff between spectral versions 1.3 dated 2019-06-03 and 2.0 dated 2021-03-29
spectral-1.3/spectral/NEWS.md |only spectral-2.0/spectral/DESCRIPTION | 26 spectral-2.0/spectral/MD5 | 82 - spectral-2.0/spectral/NAMESPACE | 13 spectral-2.0/spectral/NEWS |only spectral-2.0/spectral/R/amax.R |only spectral-2.0/spectral/R/analyticFunction.R | 195 +- spectral-2.0/spectral/R/bandPass.R | 142 +- spectral-2.0/spectral/R/deconvolve.R |only spectral-2.0/spectral/R/envelope.R | 54 spectral-2.0/spectral/R/examples/Error_Behaviour_LS_FFT.R | 182 +- spectral-2.0/spectral/R/examples/Error_Behaviour_QDT.R | 18 spectral-2.0/spectral/R/examples/deconvolutionExample.R |only spectral-2.0/spectral/R/examples/lombExample.R | 29 spectral-2.0/spectral/R/examples/lombExample2.R | 78 - spectral-2.0/spectral/R/examples/specFFTExample.r | 311 ++-- spectral-2.0/spectral/R/examples/waterfallExample.r | 64 spectral-2.0/spectral/R/filterFFT.R | 128 + spectral-2.0/spectral/R/hilbert.R | 62 spectral-2.0/spectral/R/interpolationFFT.R | 156 +- spectral-2.0/spectral/R/plotFFT.R | 42 spectral-2.0/spectral/R/printFFT.R |only spectral-2.0/spectral/R/printLOMB.R |only spectral-2.0/spectral/R/specFFT.R | 58 spectral-2.0/spectral/R/specLOMB.R | 915 +++++++------- spectral-2.0/spectral/R/summaryFFT.R |only spectral-2.0/spectral/R/summaryLomb.R |only spectral-2.0/spectral/R/waterfall.R | 229 ++- spectral-2.0/spectral/R/windowfunctions.R | 208 ++- spectral-2.0/spectral/R/zzz.R |only spectral-2.0/spectral/man/BP.Rd | 67 - spectral-2.0/spectral/man/H.Rd | 4 spectral-2.0/spectral/man/Windowfunctions.Rd | 12 spectral-2.0/spectral/man/amax.Rd |only spectral-2.0/spectral/man/analyticFunction.Rd | 45 spectral-2.0/spectral/man/deconvolve.Rd |only spectral-2.0/spectral/man/envelope.Rd | 4 spectral-2.0/spectral/man/filter.fft.Rd | 22 spectral-2.0/spectral/man/filter.lomb.Rd | 9 spectral-2.0/spectral/man/interpolate.fft.Rd | 5 spectral-2.0/spectral/man/onAttach.Rd |only spectral-2.0/spectral/man/onDetach.Rd |only spectral-2.0/spectral/man/plot.lomb.Rd | 25 spectral-2.0/spectral/man/print.fft.Rd |only spectral-2.0/spectral/man/print.lomb.Rd |only spectral-2.0/spectral/man/spec.fft.Rd | 51 spectral-2.0/spectral/man/spec.lomb.Rd | 76 - spectral-2.0/spectral/man/summary.fft.Rd |only spectral-2.0/spectral/man/summary.lomb.Rd |only spectral-2.0/spectral/man/waterfall.Rd | 105 + spectral-2.0/spectral/man/win.hann.Rd |only spectral-2.0/spectral/man/win.nutt.Rd |only 52 files changed, 2016 insertions(+), 1401 deletions(-)
Title: Stellar CharactEristics Pisa Estimation gRid
Description: A pipeline for estimating the stellar
age, mass, and radius given observational
effective temperature, [Fe/H], and astroseismic
parameters. The results are obtained adopting a maximum likelihood
technique over a grid of pre-computed stellar models, as
described in Valle et al. (2014) <doi:10.1051/0004-6361/201322210>.
Author: Matteo Dell'Omodarme [aut, cre],
Giada Valle [aut]
Maintainer: Matteo Dell'Omodarme <mattdell@fastmail.fm>
Diff between SCEPtER versions 0.2-1 dated 2015-01-05 and 0.2-4 dated 2021-03-29
DESCRIPTION | 16 +++++++++------- MD5 | 2 +- 2 files changed, 10 insertions(+), 8 deletions(-)
Title: Estimating a Group-Effect in Latent Class Analysis
Description: Fits latent class analysis (LCA) including group variable and covariates.
The group variable can be handled either by multilevel LCA described in Vermunt (2003) <DOI:10.1111/j.0081-1750.2003.t01-1-00131.x> or standard LCA at each level of group variable.
The covariates can be incorporated in the form of logistic regression (Bandeen-Roche et al. (1997) <DOI:10.1080/01621459.1997.10473658>).
Author: Youngsun Kim [aut, cre],
Hwan Chung [aut]
Maintainer: Youngsun Kim <kim0sun@korea.ac.kr>
Diff between glca versions 1.2.1 dated 2021-03-09 and 1.2.2 dated 2021-03-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.glca.R | 2 +- build/partial.rdb |binary inst/CITATION | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Gerard Walsh [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.4.4 dated 2020-10-02 and 0.4.8 dated 2021-03-29
DESCRIPTION | 15 +++--- MD5 | 41 ++++++++++-------- NAMESPACE | 1 R/address.R | 30 +++++++++++-- R/attachment.R | 10 +--- R/mime.R | 46 +++++++++++++++++++- README.md | 89 ++++++++++++++++++++++++++++++++-------- inst/cats.jpg |only inst/hex/emayili-hex.R | 4 - inst/tiny-test-image.png |only man/attachment.Rd | 10 +--- man/bcc.Rd | 2 man/cc.Rd | 2 man/figures/emayili-hex.png |binary man/format.mime.Rd | 4 + man/from.Rd | 2 man/parameter_value_encode.Rd |only man/reply.Rd | 2 man/sender.Rd |only man/to.Rd | 2 tests/testthat/setup-files.R | 4 - tests/testthat/teardown-files.R | 2 tests/testthat/test-address.R | 6 ++ tests/testthat/test-mime.R |only 24 files changed, 197 insertions(+), 75 deletions(-)
Title: Compare Output and Run Time
Description: Quickly run experiments to compare the run time and output of
code blocks. The function mbc() can make fast comparisons of code,
and will calculate statistics comparing the resulting outputs.
It can be used to compare model fits to the same data or
see which function runs faster.
The R6 class ffexp$new() runs a function using all possible combinations
of selected inputs. This is useful for comparing the effect of
different parameter values. It can also run in parallel and
automatically save intermediate results, which is very useful
for long computations.
Author: Collin Erickson [aut, cre]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between comparer versions 0.2.1 dated 2020-03-25 and 0.2.2 dated 2021-03-29
DESCRIPTION | 16 - MD5 | 21 - NAMESPACE | 3 NEWS.md | 53 ++- R/ffexp.R | 587 +++++++++++++++++++++++++++++++++++----- R/hype.R |only build/vignette.rds |binary inst/doc/comparer.html | 511 ++++++++++++---------------------- man/ffexp.Rd | 279 ++++++++++++++++++- man/hype.Rd |only man/par_hype.Rd |only man/par_unif.Rd |only tests/testthat/test-test_hype.R |only tests/testthat/test_ffexp.R | 203 +++++++++++-- 14 files changed, 1201 insertions(+), 472 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare, David Loris
Maintainer: Davide Altomare <info@channelattribution.net>
Diff between ChannelAttribution versions 2.0.2 dated 2020-07-27 and 2.0.4 dated 2021-03-29
DESCRIPTION | 11 LICENSE | 64 ++-- MD5 | 27 - R/ChannelAttribution.R | 569 ++++++++++++++++++-------------------- build |only inst/COPYRIGHTS | 26 - man/ChannelAttribution-package.Rd | 102 +++--- man/Data.Rd | 36 +- man/auto_markov_model.Rd | 128 ++++---- man/choose_order.Rd | 128 ++++---- man/heuristic_models.Rd | 108 +++---- man/markov_model.Rd | 160 +++++----- man/transition_matrix.Rd | 112 +++---- src/ChannelAttribution.cpp | 4 src/ChannelAttribution.h | 2 15 files changed, 738 insertions(+), 739 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed
by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is
estimated such that it maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore, avoids an iteration
between model fitting and balance checking. The package also implements optimal
CBPS from Fan et al. (2016) <https://imai.fas.harvard.edu/research/CBPStheory.html>,
several extensions of the CBPS beyond the cross-sectional, binary treatment setting.
They include the CBPS for longitudinal settings so that it can be used in
conjunction with marginal structural models from Imai and Ratkovic (2015)
<DOI:10.1080/01621459.2014.956872>, treatments with three- and four-valued treatment
variables, continuous-valued treatments from Fong, Hazlett, and Imai (2018)
<DOI:10.1214/17-AOAS1101>, propensity score estimation with a large number of
covariates from Ning, Peng, and Imai (2018) <arXiv:1812.08683>, and the situation
with multiple distinct binary treatments administered simultaneously. In the future
it will be extended to other settings including the generalization of experimental
and instrumental variable estimates.
Author: Christian Fong [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut],
Chad Hazlett [ctb],
Xiaolin Yang [ctb],
Sida Peng [ctb]
Maintainer: Christian Fong <cjfong@umich.edu>
Diff between CBPS versions 0.21 dated 2019-08-21 and 0.22 dated 2021-03-29
CBPS-0.21/CBPS/data/Blackwell.tab.gz |only CBPS-0.21/CBPS/data/LaLonde.tab.gz |only CBPS-0.22/CBPS/ChangeLog | 3 ++- CBPS-0.22/CBPS/DESCRIPTION | 8 ++++---- CBPS-0.22/CBPS/MD5 | 12 ++++++------ CBPS-0.22/CBPS/R/CBMSM.R | 7 ++++--- CBPS-0.22/CBPS/R/CBPSMain.R | 10 +++++----- CBPS-0.22/CBPS/data/Blackwell.tab |only CBPS-0.22/CBPS/data/LaLonde.tab |only 9 files changed, 21 insertions(+), 19 deletions(-)
Title: Australian Government Bureau of Meteorology ('BOM') Data Client
Description: Provides functions to interface with Australian Government Bureau
of Meteorology ('BOM') data, fetching data and returning a data frame of
precis forecasts, historical and current weather data from stations,
agriculture bulletin data, 'BOM' 0900 or 1500 weather bulletins and
downloading and importing radar and satellite imagery files. Data (c)
Australian Government Bureau of Meteorology Creative Commons (CC)
Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See
<http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>),
James Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>),
Dean Marchiori [aut],
Paul Melloy [aut] (<https://orcid.org/0000-0003-4253-7167>),
Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>),
Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>),
Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>),
James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>),
Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>),
Western Australia Agriculture Authority [fnd, cph]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between bomrang versions 0.7.3 dated 2020-12-01 and 0.7.4 dated 2021-03-29
bomrang-0.7.3/bomrang/inst/extdata/current_stations_site_list.rda |only bomrang-0.7.4/bomrang/DESCRIPTION | 15 bomrang-0.7.4/bomrang/MD5 | 108 bomrang-0.7.4/bomrang/NEWS.md | 365 - bomrang-0.7.4/bomrang/R/get_ag_bulletin.R | 18 bomrang-0.7.4/bomrang/R/get_coastal_forecast.R | 34 bomrang-0.7.4/bomrang/R/get_current_weather.R | 2 bomrang-0.7.4/bomrang/R/get_historical_weather.R | 66 bomrang-0.7.4/bomrang/R/get_precis_forecast.R | 4 bomrang-0.7.4/bomrang/R/get_radar_imagery.R | 35 bomrang-0.7.4/bomrang/R/get_satellite_imagery.R | 43 bomrang-0.7.4/bomrang/R/get_weather_bulletins.R | 215 - bomrang-0.7.4/bomrang/R/internal_functions.R | 107 bomrang-0.7.4/bomrang/R/update_forecast_towns.R | 4 bomrang-0.7.4/bomrang/R/update_station_locations.R | 12 bomrang-0.7.4/bomrang/R/zzz.R | 4 bomrang-0.7.4/bomrang/README.md | 3 bomrang-0.7.4/bomrang/build/vignette.rds |binary bomrang-0.7.4/bomrang/inst/CITATION | 2 bomrang-0.7.4/bomrang/inst/doc/bomrang.Rmd | 1987 +++------ bomrang-0.7.4/bomrang/inst/doc/bomrang.html | 2116 +++------- bomrang-0.7.4/bomrang/inst/doc/use_case.html | 13 bomrang-0.7.4/bomrang/inst/extdata/AAC_code_changes.rda |only bomrang-0.7.4/bomrang/inst/extdata/AAC_codes.rda |binary bomrang-0.7.4/bomrang/inst/extdata/JSONurl_site_list.rda |binary bomrang-0.7.4/bomrang/inst/extdata/JSONurl_site_list_changes.rda |only bomrang-0.7.4/bomrang/inst/extdata/marine_AAC_code_changes.rda |only bomrang-0.7.4/bomrang/inst/extdata/marine_AAC_codes.rda |binary bomrang-0.7.4/bomrang/inst/extdata/radar_location_changes.rda |only bomrang-0.7.4/bomrang/inst/extdata/radar_locations.rda |binary bomrang-0.7.4/bomrang/inst/extdata/stations_site_list.rda |binary bomrang-0.7.4/bomrang/inst/extdata/stations_site_list_changes.rda |only bomrang-0.7.4/bomrang/man/bomrang-package.Rd | 1 bomrang-0.7.4/bomrang/man/get_historical_weather.Rd | 26 bomrang-0.7.4/bomrang/man/get_satellite_imagery.Rd | 7 bomrang-0.7.4/bomrang/man/update_forecast_towns.Rd | 4 bomrang-0.7.4/bomrang/man/update_station_locations.Rd | 10 bomrang-0.7.4/bomrang/tests/testthat/test-bomrang_tbl.R | 15 bomrang-0.7.4/bomrang/tests/testthat/test-file_caching.R | 13 bomrang-0.7.4/bomrang/tests/testthat/test-get_ag_bulletin.R | 4 bomrang-0.7.4/bomrang/tests/testthat/test-get_coastal_forecast.R | 4 bomrang-0.7.4/bomrang/tests/testthat/test-get_current_weather.R | 2 bomrang-0.7.4/bomrang/tests/testthat/test-get_historical.R | 16 bomrang-0.7.4/bomrang/tests/testthat/test-get_precis_forecast.R | 4 bomrang-0.7.4/bomrang/tests/testthat/test-get_radar_imagery.R | 4 bomrang-0.7.4/bomrang/tests/testthat/test-get_satellite_imagery.R | 4 bomrang-0.7.4/bomrang/tests/testthat/test-get_weather_bulletins.R | 9 bomrang-0.7.4/bomrang/tests/testthat/test-internal-functions.R | 1 bomrang-0.7.4/bomrang/tests/testthat/test-sweep_for_stations.R | 1 bomrang-0.7.4/bomrang/tests/testthat/test-update_forecast_towns.R | 2 bomrang-0.7.4/bomrang/tests/testthat/test-update_station_locations.R | 3 bomrang-0.7.4/bomrang/vignettes/bomrang.Rmd | 1987 +++------ bomrang-0.7.4/bomrang/vignettes/completeness_map-1.png |binary bomrang-0.7.4/bomrang/vignettes/plot_satellite-1.png |binary bomrang-0.7.4/bomrang/vignettes/precompile.R | 2 bomrang-0.7.4/bomrang/vignettes/station-locations-map-1.png |binary bomrang-0.7.4/bomrang/vignettes/vignettes/get_radar_imagery-1.gif |binary bomrang-0.7.4/bomrang/vignettes/years_available-1.png |binary 58 files changed, 2946 insertions(+), 4326 deletions(-)
Title: Statistical Tools for Filebacked Big Matrices
Description: Easy-to-use, efficient, flexible and scalable statistical tools.
Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping.
It provides for instance matrix operations, Principal Component Analysis,
sparse linear supervised models, utility functions and more
<doi:10.1093/bioinformatics/bty185>.
Author: Florian Privé [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigstatsr versions 1.3.1 dated 2020-11-06 and 1.5.0 dated 2021-03-29
DESCRIPTION | 15 -- MD5 | 69 ++++----- NEWS.md | 16 ++ R/FBM.R | 16 +- R/RcppExports.R | 16 +- R/SVD.R | 2 R/apply-parallelize.R | 1 R/biglasso.R | 6 R/colstats.R | 7 R/mult-vec.R | 10 - R/pcor.R | 12 + R/plot.R | 12 - R/randomSVD.R | 7 R/scaling.R | 9 - R/summary.R | 16 +- R/univLinReg.R | 27 +-- R/utils-assert.R | 15 ++ R/utils.R | 4 build |only inst/WORDLIST | 5 inst/include/bigstatsr/colstats.hpp | 20 +- inst/include/bigstatsr/prodMatVec.hpp | 75 ++++++---- inst/include/bigstatsr/univLinReg.hpp | 51 +++--- inst/testdata/old-mod.rds |only man/big_SVD.Rd | 240 ++++++++++++++++---------------- man/big_apply.Rd | 1 man/big_randomSVD.Rd | 253 ++++++++++++++++------------------ man/big_spLinReg.Rd | 6 man/big_spLogReg.Rd | 6 src/Makevars | 4 src/RcppExports.cpp | 36 ++-- src/colstats.cpp | 5 src/prodMatVec.cpp | 10 - src/univRegLin5.cpp | 5 tests/testthat/test-openmp.R |only tests/testthat/test-pcor.R | 34 ++++ tests/testthat/test-spLinReg.R | 10 + 37 files changed, 569 insertions(+), 452 deletions(-)
Title: Manipulate and Map Origin-Destination Data
Description: The aim of 'od' is to provide tools and example datasets for working with
origin-destination ('OD') datasets of the type used to describe aggregate
urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>.
The package builds on functions for working with 'OD' data in the package 'stplanr',
(Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational
efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>.
With few dependencies and a simple class system based on data frames,
the package is intended to facilitate efficient analysis of 'OD' datasets
and to provide a place for developing new functions.
The package enables the creation and analysis of geographic entities
representing large scale mobility patterns,
from daily travel between zones in cities to migration between countries.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
David Cooley [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between od versions 0.1.0 dated 2021-02-10 and 0.2.0 dated 2021-03-29
DESCRIPTION | 8 MD5 | 42 +- NAMESPACE | 3 NEWS.md | 7 R/aggregate.R | 150 ++++++-- README.md | 94 +++-- build/vignette.rds |binary data/od_data_buildings.rda |binary data/od_data_df.rda |binary data/od_data_df_medium.rda |binary data/od_data_network.rda |binary data/od_data_zones_min.rda |binary data/od_data_zones_small.rda |binary inst/doc/od.R | 314 +++++------------- inst/doc/od.Rmd | 460 ++++++++------------------ inst/doc/od.html | 536 +++++++++++++++++-------------- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-5-2.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-6-2.png |only man/od_aggregate.Rd |only man/od_disaggregate.Rd | 22 + vignettes/od.Rmd | 460 ++++++++------------------ vignettes/od.json |only 24 files changed, 913 insertions(+), 1183 deletions(-)
Title: Implementation of a Generic Adaptive Monte Carlo Markov Chain
Sampler
Description: Enables sampling from arbitrary distributions if the log density is known up to a constant; a common situation in the context of Bayesian inference. The implemented sampling algorithm was proposed by Vihola (2012) <DOI:10.1007/s11222-011-9269-5> and achieves often a high efficiency by tuning the proposal distributions to a user defined acceptance rate.
Author: Andreas Scheidegger, <andreas.scheidegger@eawag.ch>, <scheidegger.a@gmail.com>
Maintainer: Andreas Scheidegger <andreas.scheidegger@eawag.ch>
Diff between adaptMCMC versions 1.3 dated 2018-01-14 and 1.4 dated 2021-03-29
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- R/Adaptive_MCMC.R | 22 +++++++--------------- man/MCMC.Rd | 7 ++++--- man/genericMCMC-package.Rd | 4 ++-- 5 files changed, 23 insertions(+), 29 deletions(-)
Title: Plotting and Comparing Means with Violin Plots
Description: Produces violin plots with optional mean comparison with Tukey's honest significant difference and linear regression. This package aims to be a simple and quick visualization tool for comparing means and assessing trends of categorical factors.
Author: Jefferson Paril <jeffersonparil@gmail.com>
Maintainer: Jefferson Paril <jeffersonparil@gmail.com>
Diff between violinplotter versions 1.0.1 dated 2020-03-25 and 2.0.0 dated 2021-03-29
DESCRIPTION | 18 ++++--------- MD5 | 22 ++++++++-------- NAMESPACE | 2 + NEWS.md | 13 +++------ R/mean_comparison_HSD.R | 18 +++++++++++-- R/parse_formula.R | 14 ++++++---- R/plot_violin_1x.R | 64 +++++++++++++++++++++++++++++------------------- R/violinplotter.R | 51 +++++++++++++++++++++++++++++++++----- README.md | 15 +++++++++-- man/dummy_data.Rd | 6 +++- man/violinplotter.Rd | 12 ++++++--- tests/test1.R | 3 +- 12 files changed, 158 insertions(+), 80 deletions(-)
Title: Variable-Lag Time Series Causality Inference Framework
Description: A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2019) <arXiv:1912.10829> when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between VLTimeCausality versions 0.1.1 dated 2020-05-17 and 0.1.2 dated 2021-03-29
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 2 +- inst/doc/VLTimeCausality_demo.html | 6 +++--- 5 files changed, 17 insertions(+), 14 deletions(-)
More information about VLTimeCausality at CRAN
Permanent link
Title: An Implementation of Re-Sampling Approaches to Utility-Based
Learning for Both Classification and Regression Tasks
Description: Provides a set of functions that can be used to obtain better predictive performance on cost-sensitive and cost/benefits tasks (for both regression and classification). This includes re-sampling approaches that modify the original data set biasing it towards the user preferences.
Author: Paula Branco [aut, cre],
Rita Ribeiro [aut, ctb],
Luis Torgo [aut, ctb]
Maintainer: Paula Branco <paobranco@gmail.com>
Diff between UBL versions 0.0.6 dated 2017-07-13 and 0.0.7 dated 2021-03-29
CHANGES | 10 ++++++ DESCRIPTION | 10 +++--- MD5 | 60 ++++++++++++++++++++++++----------------- NAMESPACE | 24 +++++++++++++--- R/AdasynClassif.R | 11 ++++--- R/BaggingRegress.R |only R/ImpSampClassif.R | 9 +++--- R/ImpSampRegress.R | 14 ++++----- R/ReBaggRegress.R |only R/classDef.R |only R/methods.R |only R/smognClassif.R |only R/smognRegress.R |only man/AdasynClassif.Rd | 6 ++-- man/BagModel-class.Rd |only man/BaggingRegress.Rd |only man/CNNClassif.Rd | 17 +++++++++-- man/Distances.Rd | 2 - man/ImpSampClassif.Rd | 14 ++++----- man/ImpSampRegress.Rd | 23 ++++++++------- man/OSSClassif.Rd | 7 ++-- man/ReBagg.Rd |only man/SMOGNClassif.Rd |only man/SMOGNRegress.Rd |only man/TomekClassif.Rd | 8 +++-- man/UBL-package.Rd | 16 ++++++---- man/UtilOptimClassif.Rd | 2 - man/UtilOptimRegress.Rd | 9 ++++-- man/gaussNoiseClassif.Rd | 9 +++--- man/gaussNoiseRegress.Rd | 9 +++--- man/neighbours.Rd | 2 - man/predict-BagModel-method.Rd |only man/randOverClassif.Rd | 14 +++++---- man/randOverRegress.Rd | 8 ++--- man/randUnderClassif.Rd | 16 ++++++---- man/smoteClassif.Rd | 14 ++++----- src/neighbours.f90 | 16 +++++----- 37 files changed, 200 insertions(+), 130 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>),
Zachary Foster [ctb] (<https://orcid.org/0000-0002-5075-0948>),
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.2.0 dated 2020-10-07 and 0.2.1 dated 2021-03-29
DESCRIPTION | 12 - MD5 | 51 +++-- NAMESPACE | 1 NEWS.md | 16 + R/dissect_name.R | 30 +-- R/indented_list.R |only R/internal.R | 1 R/replace_x.R | 9 R/taxlist-class.R | 9 R/taxlist-package.R | 7 R/taxon_views.R | 2 build/partial.rdb |only build/vignette.rds |binary data/Easplist.rda |binary inst/cyperus/names.csv | 190 ++++++++++---------- inst/doc/taxlist-intro.html | 340 +++++++----------------------------- man/dissect_name.Rd | 22 +- man/figures/genera_bar-1.png |binary man/figures/taxlist_logo.png |only man/indented_list.Rd |only man/replace_x.Rd | 7 man/taxlist-class.Rd | 2 man/taxlist-package.Rd | 7 man/taxon_views.Rd | 2 man/tnrs.Rd | 6 tests/testthat/temp.rda |binary tests/testthat/temp_2020-10-18.rda |only tests/testthat/temp_2021-03-27.rda |only tests/testthat/test-dissect_name.R | 1 tests/testthat/test-indented_list.R |only 30 files changed, 280 insertions(+), 435 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-22 1.0.1
2020-03-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-22 1.2.0
2020-12-02 1.1.1
2016-04-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-12 0.0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-15 0.3.0
2021-03-15 0.3.1
Title: Bayesian Regression Models with Global-Local Shrinkage Priors
Description: Fits linear or generalized linear regression models using Bayesian global-local shrinkage prior hierarchies as described in Polson and Scott (2010) <doi:10.1093/acprof:oso/9780199694587.003.0017>. Provides an efficient implementation of ridge, lasso, horseshoe and horseshoe+ regression with logistic, Gaussian, Laplace, Student-t, Poisson or geometric distributed targets using the algorithms summarized in Makalic and Schmidt (2016) <arXiv:1611.06649>.
Author: Daniel F. Schmidt [aut, cph, cre]
(<https://orcid.org/0000-0002-1788-2375>),
Enes Makalic [aut, cph] (<https://orcid.org/0000-0003-3017-0871>)
Maintainer: Daniel F. Schmidt <daniel.schmidt@monash.edu>
Diff between bayesreg versions 1.1 dated 2019-06-03 and 1.2 dated 2021-03-29
DESCRIPTION | 23 - MD5 | 20 NAMESPACE | 1 R/bayesreg-package.R | 58 ++ R/bayesreg.R | 1078 +++++++++++++++++++++++++++++++++++++++++------- R/tempcode.R |only R/test.R |only man/bayesreg-package.Rd | 381 +++++++++------- man/bayesreg.Rd | 443 ++++++++++--------- man/predict.bayesreg.Rd | 344 ++++++++------- man/spambase.Rd | 156 +++--- man/summary.bayesreg.Rd | 178 ++++--- 12 files changed, 1835 insertions(+), 847 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-12 2.1.5
2019-02-24 2.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-26 2.45
2017-04-18 2.44
2016-10-11 2.43
2016-10-10 2.42
2014-03-09 2.40
2012-05-10 2.38
2012-04-08 2.37
2011-12-08 2.34
2011-10-08 2.31
2011-02-10 2.29
2011-02-10 2.30
2010-06-16 2.18
2010-01-21 2.13
2010-01-15 2.12
2009-09-28 2.11
2009-09-18 2.10
2009-06-26 2.05
2009-03-10 1.93
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-11 1.1
2016-06-15 1.0
2016-01-13 0.4.1
2015-12-28 0.3
2015-11-01 0.2
2015-10-23 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-25 2.7
2017-04-18 2.6
2016-10-11 2.5
2016-10-10 2.4
2015-03-09 2.3
2014-03-09 2.0
2012-04-08 1.7
2011-02-10 1.5
2011-02-10 1.6
2009-09-18 1.3
2009-03-06 0.9