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 0.0.1 dated 2020-06-22 and 0.0.2 dated 2020-07-03
modeltime-0.0.1/modeltime/R/parsnip-fit_methods.R |only modeltime-0.0.1/modeltime/man/fit.modeltime.Rd |only modeltime-0.0.2/modeltime/DESCRIPTION | 18 - modeltime-0.0.2/modeltime/MD5 | 95 +++---- modeltime-0.0.2/modeltime/NAMESPACE | 9 modeltime-0.0.2/modeltime/NEWS.md | 16 + modeltime-0.0.2/modeltime/R/modeltime-forecast.R | 123 ++++++--- modeltime-0.0.2/modeltime/R/modeltime-refit.R | 2 modeltime-0.0.2/modeltime/R/parsnip-arima_boost.R | 34 -- modeltime-0.0.2/modeltime/R/parsnip-arima_boost_data.R | 23 + modeltime-0.0.2/modeltime/R/parsnip-arima_reg.R | 2 modeltime-0.0.2/modeltime/R/parsnip-arima_reg_data.R | 24 + modeltime-0.0.2/modeltime/R/parsnip-exp_smoothing.R | 2 modeltime-0.0.2/modeltime/R/parsnip-exp_smoothing_data.R | 12 modeltime-0.0.2/modeltime/R/parsnip-prophet_boost.R | 2 modeltime-0.0.2/modeltime/R/parsnip-prophet_boost_data.R | 20 + modeltime-0.0.2/modeltime/R/parsnip-prophet_reg.R | 2 modeltime-0.0.2/modeltime/R/parsnip-prophet_reg_data.R | 12 modeltime-0.0.2/modeltime/R/parsnip-seasonal_decomp.R | 2 modeltime-0.0.2/modeltime/R/parsnip-seasonal_decomp_data.R | 24 + modeltime-0.0.2/modeltime/R/tibble-type_sum.R | 2 modeltime-0.0.2/modeltime/R/utils-parsnip-helpers.R | 57 ++-- modeltime-0.0.2/modeltime/R/utils-xgboost.R |only modeltime-0.0.2/modeltime/inst/doc/extending-modeltime.R | 61 ++-- modeltime-0.0.2/modeltime/inst/doc/extending-modeltime.Rmd | 80 +++-- modeltime-0.0.2/modeltime/inst/doc/extending-modeltime.html | 134 +++++----- modeltime-0.0.2/modeltime/inst/doc/getting-started-with-modeltime.R | 23 + modeltime-0.0.2/modeltime/inst/doc/getting-started-with-modeltime.Rmd | 27 +- modeltime-0.0.2/modeltime/inst/doc/getting-started-with-modeltime.html | 99 ++++--- modeltime-0.0.2/modeltime/inst/doc/modeltime-model-list.html | 24 + modeltime-0.0.2/modeltime/man/arima_boost.Rd | 2 modeltime-0.0.2/modeltime/man/arima_reg.Rd | 2 modeltime-0.0.2/modeltime/man/exp_smoothing.Rd | 2 modeltime-0.0.2/modeltime/man/modeltime_forecast.Rd | 2 modeltime-0.0.2/modeltime/man/prophet_boost.Rd | 2 modeltime-0.0.2/modeltime/man/prophet_reg.Rd | 2 modeltime-0.0.2/modeltime/man/seasonal_decomp.Rd | 2 modeltime-0.0.2/modeltime/man/type_sum.mdl_time_tbl.Rd | 2 modeltime-0.0.2/modeltime/man/xgboost_impl.Rd |only modeltime-0.0.2/modeltime/man/xgboost_predict.Rd |only modeltime-0.0.2/modeltime/tests/testthat.R | 2 modeltime-0.0.2/modeltime/tests/testthat/test-algo-seasonal_decomp_arima.R | 2 modeltime-0.0.2/modeltime/tests/testthat/test-algo-seasonal_decomp_ets.R | 2 modeltime-0.0.2/modeltime/tests/testthat/test-developer-tools-constructor.R | 2 modeltime-0.0.2/modeltime/tests/testthat/test-developer-tools-xregs.R | 2 modeltime-0.0.2/modeltime/tests/testthat/test-modeltime_plot.R | 16 - modeltime-0.0.2/modeltime/tests/testthat/test-modeltime_table-forecast-accuracy-refitting.R | 30 +- modeltime-0.0.2/modeltime/tests/testthat/test-modeltime_table.R | 2 modeltime-0.0.2/modeltime/vignettes/extending-modeltime.Rmd | 80 +++-- modeltime-0.0.2/modeltime/vignettes/getting-started-with-modeltime.Rmd | 27 +- modeltime-0.0.2/modeltime/vignettes/model_fit.rds |only modeltime-0.0.2/modeltime/vignettes/refit_tbl.rds |only 52 files changed, 679 insertions(+), 431 deletions(-)
Title: Recurrent Neural Network
Description: Implementation of a Recurrent Neural Network architectures in native R, including Long Short-Term Memory (Hochreiter and Schmidhuber, <doi:10.1162/neco.1997.9.8.1735>), Gated Recurrent Unit (Chung et al., <arXiv:1412.3555>) and vanilla RNN.
Author: Bastiaan Quast [aut, cre],
Dimitri Fichou [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between rnn versions 0.9.8 dated 2019-05-27 and 1.4.0 dated 2020-07-03
rnn-0.9.8/rnn/NEWS |only rnn-1.4.0/rnn/DESCRIPTION | 8 rnn-1.4.0/rnn/MD5 | 35 - rnn-1.4.0/rnn/NEWS.md |only rnn-1.4.0/rnn/README.md | 25 - rnn-1.4.0/rnn/build/vignette.rds |binary rnn-1.4.0/rnn/inst/doc/GRU_units.R | 4 rnn-1.4.0/rnn/inst/doc/GRU_units.html | 416 ++++++++---------- rnn-1.4.0/rnn/inst/doc/LSTM_units.R | 4 rnn-1.4.0/rnn/inst/doc/LSTM_units.html | 415 ++++++++---------- rnn-1.4.0/rnn/inst/doc/basic_rnn.R | 12 rnn-1.4.0/rnn/inst/doc/basic_rnn.html | 730 +++++++++++++------------------- rnn-1.4.0/rnn/inst/doc/rnn.R | 30 - rnn-1.4.0/rnn/inst/doc/rnn.html | 750 ++++++++++++++++----------------- rnn-1.4.0/rnn/inst/doc/rnn_units.R | 4 rnn-1.4.0/rnn/inst/doc/rnn_units.html | 367 ++++++---------- rnn-1.4.0/rnn/inst/doc/sinus.R | 8 rnn-1.4.0/rnn/inst/doc/sinus.html | 536 +++++++++-------------- rnn-1.4.0/rnn/man/figures |only rnn-1.4.0/rnn/man/trainr.Rd | 25 - 20 files changed, 1525 insertions(+), 1844 deletions(-)
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 0.4.10-1 dated 2020-05-22 and 0.5.1 dated 2020-07-03
DESCRIPTION | 10 +-- MD5 | 74 +++++++++++++++----------- NAMESPACE | 8 ++ NEWS.md | 10 ++- R/appReset.R | 6 +- R/downloadFile.R | 17 ++--- R/downloadablePlot.R | 10 +-- R/downloadableTable.R | 3 - R/fw_helpers_external.R | 2 R/fw_helpers_internal.R | 18 +++--- R/generate_template.R | 34 ++++++++++- R/logger.R |only R/periscope.R | 13 ++++ R/ui_helpers.R | 2 README.md | 9 +++ build/vignette.rds |binary inst/doc/downloadFile-module.html | 4 - inst/doc/downloadablePlot-module.html | 4 - inst/doc/downloadableTable-module.html | 4 - inst/doc/new-application.R | 4 + inst/doc/new-application.Rmd | 15 ++++- inst/doc/new-application.html | 17 ++++- inst/fw_templ/server.R | 3 - man/bootstrapping.Rd |only man/create_new_application.Rd | 9 ++- man/downloadFile.Rd | 4 - man/downloadablePlot.Rd | 4 - man/downloadablePlotUI.Rd | 7 +- man/downloadableTable.Rd | 4 - man/getHandler.Rd |only man/getLogger.Rd |only man/handlers-management.Rd |only man/inbuilt-actions.Rd |only man/logging-entrypoints.Rd |only man/loglevels.Rd |only man/resetMsgComposer.Rd |only man/setLevel.Rd |only man/setMsgComposer.Rd |only man/set_app_parameters.Rd | 3 - man/updateOptions.Rd |only tests/testthat/sample_app/server.R | 3 - tests/testthat/sample_app_no_sidebar/server.R | 3 - tests/testthat/test_create_new_application.R | 36 ++++++++++++ vignettes/new-application.Rmd | 15 ++++- 44 files changed, 240 insertions(+), 115 deletions(-)
Title: A Tool for Processing and Analyzing Dendrometer Data
Description: There are various functions for managing and cleaning data before the application of different approaches. This includes identifying and erasing sudden jumps in dendrometer data not related to environmental change, identifying the time gaps of recordings, and changing the temporal resolution of data to different frequencies. Furthermore, the package calculates daily statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water. In addition, it identifies periods of consecutive days with user-defined climatic conditions in daily meteorological data, then check what trees are doing during that period.
Author: Sugam Aryal [aut, cre, dtc],
Martin Häusser [aut],
Jussi Grießinger [aut],
Ze-Xin Fan [aut],
Achim Bräuning [aut, dgs]
Maintainer: Sugam Aryal <sugam.aryal@fau.de>
Diff between dendRoAnalyst versions 0.1.0 dated 2020-06-04 and 0.1.1 dated 2020-07-03
DESCRIPTION | 14 ++++++++------ MD5 | 25 +++++++++++++++++-------- R/clim.twd.R | 2 +- R/jump.locator.R | 1 + R/nepa2.R |only R/phase.sc.R | 8 ++++---- R/phase.zg.R | 14 +++++++------- build |only data/gf_nepa17.rda |binary data/nepa2.rda |only inst |only man/nepa2.Rd |only man/phase.sc.Rd | 8 ++++---- man/phase.zg.Rd | 14 +++++++------- vignettes |only 15 files changed, 49 insertions(+), 37 deletions(-)
Title: Compute Viewshed in 3D Point Clouds of Ecosystems
Description: A set of tools to compute viewshed in 3D from Terrestrial Laser Scanner data and prepare the data prior to visibility estimation.
Author: Bastien Lecigne [aut, cre] (<https://orcid.org/0000-0002-1496-202X>),
Jan Eitel [aut]
Maintainer: Bastien Lecigne <lecignebastien@gmail.com>
Diff between viewshed3d versions 3.0.0 dated 2020-01-10 and 3.2.0 dated 2020-07-03
DESCRIPTION | 11 +++++------ MD5 | 26 ++++++++++++++------------ NAMESPACE | 1 + R/Denoise.R | 25 ++++++++++--------------- R/Downsample_scene.R |only R/reconstruct_ground.R | 10 +++++----- R/sample_scene.R | 2 +- R/viewsheds.R | 8 ++++---- R/visibility.R | 5 ++--- man/denoise_scene.Rd | 16 ++++++++-------- man/downsample_scene.Rd |only man/reconstruct_ground.Rd | 21 ++++++++++++++------- man/viewshed3d.Rd | 1 - man/viewsheds.Rd | 6 +++--- man/visibility.Rd | 5 ++--- 15 files changed, 69 insertions(+), 68 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrMisc versions 1.2.3 dated 2020-06-16 and 1.2.4 dated 2020-07-03
DESCRIPTION | 6 - MD5 | 20 +-- R/readVarColumns.R | 29 +++-- R/tableToPlot.R | 2 build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 25 ++-- inst/doc/wrMiscVignette1.Rmd | 62 +++++++---- inst/doc/wrMiscVignette1.html | 235 +++++++++++++++++++++++------------------- man/readVarColumns.Rd | 9 + man/tableToPlot.Rd | 2 vignettes/wrMiscVignette1.Rmd | 62 +++++++---- 11 files changed, 266 insertions(+), 186 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.5 dated 2020-04-06 and 0.3.8 dated 2020-07-03
spData-0.3.5/spData/data/datalist |only spData-0.3.8/spData/DESCRIPTION | 10 +++++----- spData-0.3.8/spData/MD5 | 11 +++++------ spData-0.3.8/spData/README.md | 6 ++++-- spData-0.3.8/spData/data/elect80.rda |binary spData-0.3.8/spData/data/house.rda |binary spData-0.3.8/spData/data/urban_agglomerations.rda |binary 7 files changed, 14 insertions(+), 13 deletions(-)
Title: Spatially Balanced Samples of Spatial Objects
Description: Routines for drawing samples from spatial objects, focused on spatially
balanced algorithms. Draws Halton Iterative Partition (HIP)
(Robertson et al., 2018; <doi:10.1007/s10651-018-0406-6>),
Balanced Acceptance Samples (BAS) (Robertson et al., 2013; <doi:10.1111/biom.12059>),
Generalized Random
Tessellation Stratified (GRTS) (Stevens and Olsen, 2004; <doi:10.1198/016214504000000250>),
Simple Systematic Samples (SSS) and
Simple Random Samples (SRS) from point, line, and polygon resources.
Frames are 'SpatialPoints', 'SpatialLines', or 'SpatialPolygons'
objects from package 'sp'.
Author: Trent McDonald [cre, aut],
Aidan McDonald [aut] (HIP sampling methods),
Michael Kleinsausser [ctb],
Stefan Emmons [ctb] (Auto testing and Travis)
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between SDraw versions 2.1.11 dated 2020-03-31 and 2.1.13 dated 2020-07-03
DESCRIPTION | 15 +++++---- MD5 | 54 +++++++++++++++++----------------- NEWS.md | 18 +++++++++++ R/voronoi.polygons.r | 2 - build/vignette.rds |binary data/HI.coast.rda |binary data/WA.cities.rda |binary data/WA.rda |binary data/WY.rda |binary inst/doc/BASPoints.pdf |binary inst/doc/HIPPoints.pdf |binary inst/doc/HIPPolygons.pdf |binary man/HI.coast.Rd | 6 ++- man/WA.Rd | 6 ++- man/WA.cities.Rd | 6 ++- man/WY.Rd | 6 ++- man/halton.frame.Rd | 3 - man/halton.indices.CRT.Rd | 10 +++++- man/halton.indices.Rd | 10 +++++- man/halton.indices.vector.Rd | 10 +++++- man/halton.lattice.Rd | 10 +++++- man/halton.lattice.polygon.Rd | 10 +++++- man/hip.plot.lattice.Rd | 3 - man/plotLattice.Rd | 3 - man/plotSample.Rd | 10 +++++- man/sss.polygon.Rd | 3 - man/voronoi.polygons.Rd | 2 - tests/testthat/test-bas.point.R | 62 ++++++++++++++++++++-------------------- 28 files changed, 154 insertions(+), 95 deletions(-)
Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.0.8 dated 2019-12-17 and 1.0.9 dated 2020-07-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/table.R | 13 +++++++++++-- man/dbConnect-MariaDBDriver-method.Rd | 2 +- src/MariaUtils.cpp | 6 +++++- 6 files changed, 32 insertions(+), 13 deletions(-)
Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc).
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between parsnip versions 0.1.1 dated 2020-05-06 and 0.1.2 dated 2020-07-03
parsnip-0.1.1/parsnip/man/convert_args.Rd |only parsnip-0.1.2/parsnip/DESCRIPTION | 12 parsnip-0.1.2/parsnip/MD5 | 231 +++--- parsnip-0.1.2/parsnip/NAMESPACE | 8 parsnip-0.1.2/parsnip/NEWS.md | 30 parsnip-0.1.2/parsnip/R/aaa.R | 30 parsnip-0.1.2/parsnip/R/aaa_models.R | 147 +++- parsnip-0.1.2/parsnip/R/arguments.R | 93 ++ parsnip-0.1.2/parsnip/R/boost_tree.R | 71 + parsnip-0.1.2/parsnip/R/boost_tree_data.R | 70 + parsnip-0.1.2/parsnip/R/contr_one_hot.R |only parsnip-0.1.2/parsnip/R/convert_data.R | 46 - parsnip-0.1.2/parsnip/R/decision_tree.R | 2 parsnip-0.1.2/parsnip/R/decision_tree_data.R | 61 + parsnip-0.1.2/parsnip/R/descriptors.R | 47 - parsnip-0.1.2/parsnip/R/fit.R | 2 parsnip-0.1.2/parsnip/R/fit_helpers.R | 53 - parsnip-0.1.2/parsnip/R/linear_reg.R | 14 parsnip-0.1.2/parsnip/R/linear_reg_data.R | 123 ++- parsnip-0.1.2/parsnip/R/logistic_reg.R | 12 parsnip-0.1.2/parsnip/R/logistic_reg_data.R | 81 +- parsnip-0.1.2/parsnip/R/mars_data.R | 30 parsnip-0.1.2/parsnip/R/misc.R | 16 parsnip-0.1.2/parsnip/R/mlp.R | 4 parsnip-0.1.2/parsnip/R/mlp_data.R | 46 + parsnip-0.1.2/parsnip/R/model_object_docs.R | 20 parsnip-0.1.2/parsnip/R/multinom_reg.R | 12 parsnip-0.1.2/parsnip/R/multinom_reg_data.R | 43 + parsnip-0.1.2/parsnip/R/nearest_neighbor_data.R | 22 parsnip-0.1.2/parsnip/R/nullmodel.R | 1 parsnip-0.1.2/parsnip/R/nullmodel_data.R | 22 parsnip-0.1.2/parsnip/R/predict.R | 14 parsnip-0.1.2/parsnip/R/rand_forest_data.R | 68 + parsnip-0.1.2/parsnip/R/repair_call.R |only parsnip-0.1.2/parsnip/R/req_pkgs.R |only parsnip-0.1.2/parsnip/R/surv_reg_data.R | 22 parsnip-0.1.2/parsnip/R/svm_poly_data.R | 34 parsnip-0.1.2/parsnip/R/svm_rbf_data.R | 58 + parsnip-0.1.2/parsnip/build/vignette.rds |binary parsnip-0.1.2/parsnip/inst/doc/parsnip_Intro.html | 16 parsnip-0.1.2/parsnip/man/C5.0_train.Rd | 2 parsnip-0.1.2/parsnip/man/boost_tree.Rd | 65 + parsnip-0.1.2/parsnip/man/contr_one_hot.Rd |only parsnip-0.1.2/parsnip/man/decision_tree.Rd | 25 parsnip-0.1.2/parsnip/man/descriptors.Rd | 30 parsnip-0.1.2/parsnip/man/linear_reg.Rd | 22 parsnip-0.1.2/parsnip/man/logistic_reg.Rd | 20 parsnip-0.1.2/parsnip/man/mars.Rd | 15 parsnip-0.1.2/parsnip/man/mlp.Rd | 18 parsnip-0.1.2/parsnip/man/model_spec.Rd | 20 parsnip-0.1.2/parsnip/man/multinom_reg.Rd | 20 parsnip-0.1.2/parsnip/man/nearest_neighbor.Rd | 8 parsnip-0.1.2/parsnip/man/other_predict.Rd | 6 parsnip-0.1.2/parsnip/man/predict.model_fit.Rd | 6 parsnip-0.1.2/parsnip/man/rand_forest.Rd | 28 parsnip-0.1.2/parsnip/man/reexports.Rd | 2 parsnip-0.1.2/parsnip/man/repair_call.Rd |only parsnip-0.1.2/parsnip/man/req_pkgs.Rd |only parsnip-0.1.2/parsnip/man/rmd/boost-tree.Rmd | 54 + parsnip-0.1.2/parsnip/man/rmd/decision-tree.Rmd | 25 parsnip-0.1.2/parsnip/man/rmd/linear-reg.Rmd | 19 parsnip-0.1.2/parsnip/man/rmd/logistic-reg.Rmd | 19 parsnip-0.1.2/parsnip/man/rmd/mars.Rmd | 22 parsnip-0.1.2/parsnip/man/rmd/mlp.Rmd | 20 parsnip-0.1.2/parsnip/man/rmd/multinom-reg.Rmd | 20 parsnip-0.1.2/parsnip/man/rmd/nearest-neighbor.Rmd | 16 parsnip-0.1.2/parsnip/man/rmd/one-hot.Rmd |only parsnip-0.1.2/parsnip/man/rmd/rand-forest.Rmd | 36 parsnip-0.1.2/parsnip/man/rmd/setup.Rmd |only parsnip-0.1.2/parsnip/man/rmd/surv-reg.Rmd | 19 parsnip-0.1.2/parsnip/man/rmd/svm-poly.Rmd | 20 parsnip-0.1.2/parsnip/man/rmd/svm-rbf.Rmd | 23 parsnip-0.1.2/parsnip/man/set_new_model.Rd | 39 + parsnip-0.1.2/parsnip/man/surv_reg.Rd | 7 parsnip-0.1.2/parsnip/man/svm_poly.Rd | 19 parsnip-0.1.2/parsnip/man/svm_rbf.Rd | 20 parsnip-0.1.2/parsnip/man/tidy.nullmodel.Rd | 1 parsnip-0.1.2/parsnip/man/xgb_train.Rd | 16 parsnip-0.1.2/parsnip/tests/testthat/helper-objects.R | 1 parsnip-0.1.2/parsnip/tests/testthat/mars_model.RData |only parsnip-0.1.2/parsnip/tests/testthat/test_adds.R | 10 parsnip-0.1.2/parsnip/tests/testthat/test_boost_tree.R | 6 parsnip-0.1.2/parsnip/tests/testthat/test_boost_tree_C50.R | 2 parsnip-0.1.2/parsnip/tests/testthat/test_boost_tree_spark.R | 24 parsnip-0.1.2/parsnip/tests/testthat/test_boost_tree_xgboost.R | 137 +++ parsnip-0.1.2/parsnip/tests/testthat/test_convert_data.R | 367 +++++++--- parsnip-0.1.2/parsnip/tests/testthat/test_decision_tree.R | 6 parsnip-0.1.2/parsnip/tests/testthat/test_descriptors.R | 91 +- parsnip-0.1.2/parsnip/tests/testthat/test_failed_models.R | 15 parsnip-0.1.2/parsnip/tests/testthat/test_fit_interfaces.R | 19 parsnip-0.1.2/parsnip/tests/testthat/test_linear_reg.R | 114 +-- parsnip-0.1.2/parsnip/tests/testthat/test_linear_reg_glmnet.R | 151 ++-- parsnip-0.1.2/parsnip/tests/testthat/test_linear_reg_keras.R | 41 - 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Title: Data Sets and Supplemental Functions from 'OpenIntro' Textbooks
and Labs
Description: Supplemental functions and data for 'OpenIntro' resources, which
includes open-source textbooks and resources for introductory statistics
(<https://www.openintro.org/>). The package contains data sets used in our
open-source textbooks along with custom plotting functions for reproducing
book figures. Note that many functions and examples include color
transparency; some plotting elements may not show up properly (or at all)
when run in some versions of Windows operating system.
Author: Mine Çetinkaya-Rundel [aut, cre]
(<https://orcid.org/0000-0001-6452-2420>),
David Diez [aut],
Andrew Bray [aut],
Albert Kim [aut],
Ben Baumer [aut],
Chester Ismay [aut],
Christopher Barr [aut]
Maintainer: Mine Çetinkaya-Rundel <cetinkaya.mine@gmail.com>
Diff between openintro versions 1.7.1 dated 2017-09-07 and 2.0.0 dated 2020-07-03
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openintro-2.0.0/openintro/data/russian_influence_on_us_election_2016.rda |only openintro-2.0.0/openintro/data/sat_improve.rda |only openintro-2.0.0/openintro/data/satgpa.rda |only openintro-2.0.0/openintro/data/scotus_healthcare.rda |binary openintro-2.0.0/openintro/data/seattlepets.rda |only openintro-2.0.0/openintro/data/simulated_dist.rda |only openintro-2.0.0/openintro/data/simulated_normal.rda |only openintro-2.0.0/openintro/data/simulated_scatter.rda |only openintro-2.0.0/openintro/data/sinusitis.rda |binary openintro-2.0.0/openintro/data/sleep_deprivation.rda |only openintro-2.0.0/openintro/data/smallpox.rda |only openintro-2.0.0/openintro/data/smoking.rda |binary openintro-2.0.0/openintro/data/socialexp.rda |only openintro-2.0.0/openintro/data/solar.rda |only openintro-2.0.0/openintro/data/sp500.rda |only openintro-2.0.0/openintro/data/sp500_1950_2018.rda |only openintro-2.0.0/openintro/data/sp500_seq.rda |only openintro-2.0.0/openintro/data/speed_gender_height.rda |only openintro-2.0.0/openintro/data/starbucks.rda |binary openintro-2.0.0/openintro/data/stats_scores.rda |only openintro-2.0.0/openintro/data/stem_cell.rda |only openintro-2.0.0/openintro/data/stent30.rda |binary openintro-2.0.0/openintro/data/stent365.rda |binary openintro-2.0.0/openintro/data/stocks_18.rda |only openintro-2.0.0/openintro/data/student_housing.rda |only openintro-2.0.0/openintro/data/student_sleep.rda |only openintro-2.0.0/openintro/data/sulphinpyrazone.rda |binary openintro-2.0.0/openintro/data/supreme_court.rda |only openintro-2.0.0/openintro/data/teacher.rda |only openintro-2.0.0/openintro/data/textbooks.rda |binary openintro-2.0.0/openintro/data/thanksgiving_spend.rda |only openintro-2.0.0/openintro/data/tips.rda |binary openintro-2.0.0/openintro/data/toohey.rda |binary openintro-2.0.0/openintro/data/tourism.rda |binary openintro-2.0.0/openintro/data/toy_anova.rda |only openintro-2.0.0/openintro/data/transplant.rda |binary openintro-2.0.0/openintro/data/ucla_f18.rda 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Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.1.7 dated 2020-05-06 and 2.2.0 dated 2020-07-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 4 ++++ R/httpget_webhook.R | 3 +++ build/vignette.rds |binary inst/config/defaults.conf | 1 + inst/doc/opencpu-paper.pdf |binary 7 files changed, 17 insertions(+), 9 deletions(-)
Title: Test for Multivariate Normal Distribution Based on a
Characterization
Description: Provides a test of multivariate normality of an unknown sample
that does not require estimation of the nuisance parameters, the mean and covariance
matrix. Rather, a sequence of transformations removes these nuisance parameters and
results in a set of sample matrices that are positive definite. These matrices are
uniformly distributed on the space of positive definite matrices in the unit
hyper-rectangle if and only if the original data is multivariate normal. The package performs a
goodness of fit test of this hypothesis. In addition to the test, functions in the
package give visualizations of the support region of positive definite matrices for
bivariate samples.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between MVNtestchar versions 1.0.2 dated 2020-04-20 and 1.1.0 dated 2020-07-03
MVNtestchar-1.0.2/MVNtestchar/build/vignette.rds |only MVNtestchar-1.0.2/MVNtestchar/inst |only MVNtestchar-1.0.2/MVNtestchar/vignettes |only MVNtestchar-1.1.0/MVNtestchar/DESCRIPTION | 37 +++----- MVNtestchar-1.1.0/MVNtestchar/MD5 | 40 +++----- MVNtestchar-1.1.0/MVNtestchar/NAMESPACE | 8 - MVNtestchar-1.1.0/MVNtestchar/NEWS.md | 21 +++- MVNtestchar-1.1.0/MVNtestchar/R/maxv12.R | 68 +++++++-------- MVNtestchar-1.1.0/MVNtestchar/R/slice.v1.R | 63 ++++++------- MVNtestchar-1.1.0/MVNtestchar/R/slice.v12.R | 63 ++++++------- MVNtestchar-1.1.0/MVNtestchar/R/support.p2.R | 68 +++++++-------- MVNtestchar-1.1.0/MVNtestchar/R/testunknown.R | 23 +---- MVNtestchar-1.1.0/MVNtestchar/build/partial.rdb |binary MVNtestchar-1.1.0/MVNtestchar/man/MVNtestchar-package.Rd | 11 ++ MVNtestchar-1.1.0/MVNtestchar/man/maxv12.Rd | 25 ++--- MVNtestchar-1.1.0/MVNtestchar/man/slice.v1.Rd | 20 +--- MVNtestchar-1.1.0/MVNtestchar/man/slice.v12.Rd | 26 ++--- MVNtestchar-1.1.0/MVNtestchar/man/support.p2.Rd | 25 ++--- MVNtestchar-1.1.0/MVNtestchar/man/testunknown.Rd | 12 +- MVNtestchar-1.1.0/MVNtestchar/man/unknown.Bp2.Rd | 2 MVNtestchar-1.1.0/MVNtestchar/man/unknown.Bp4.Rd | 2 21 files changed, 232 insertions(+), 282 deletions(-)
Title: Multilevel Exponential-Family Random Graph Models
Description: Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.
Author: Jonathan Stewart [cre, aut],
Michael Schweinberger [ctb]
Maintainer: Jonathan Stewart <jonathan.stewart@rice.edu>
Diff between mlergm versions 0.5 dated 2020-01-08 and 0.6 dated 2020-07-03
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/helper_functions.R | 10 ++++++++-- R/is.inCH-3.9.R | 4 +--- build/vignette.rds |binary inst/doc/mlergm_tutorial.R | 22 +++++++++++----------- inst/doc/mlergm_tutorial.html | 4 ++-- man/classes.Rd | 4 +++- man/gof.mlergm.Rd | 3 +-- man/is.inCHv3.9.Rd | 4 +--- man/mlergm.Rd | 13 ++++++++++--- man/mlnet.Rd | 17 +++++++++++++---- man/plot.gof_mlergm.Rd | 31 ++++++++++++++++++++++++------- man/set_options.Rd | 24 +++++++++++++++++------- man/simulate_mlnet.Rd | 14 +++++++++++--- 15 files changed, 121 insertions(+), 67 deletions(-)
Title: Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Description: The 'midasml' estimation and prediction methods for high dimensional time series regression models under mixed data sampling data structures using structured-sparsity penalties and orthogonal polynomials. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2020) <arXiv:2005.14057>. Functions that compute MIDAS data structures were inspired by MIDAS 'Matlab' toolbox (v2.3) written by Eric Ghysels.
Author: Jonas Striaukas [aut, cre]
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>
Diff between midasml versions 0.0.2 dated 2020-07-01 and 0.0.3 dated 2020-07-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/fit_sgl.R | 2 ++ build/partial.rdb |binary man/predict.panel_sgl.Rd | 2 ++ 5 files changed, 11 insertions(+), 7 deletions(-)
Title: Isotope Origin Clustering and Assignment Tools
Description: This resource provides tools to create, compare, and post-process
spatial isotope assignment models of animal origin. It generates
probability-of-origin maps for individuals based on user-provided tissue and
environment isotope values (e.g., as generated by IsoMAP, Bowen et al. [2013]
<doi:10.1111/2041-210X.12147>) using the framework established in Bowen et al.
(2010) <doi:10.1146/annurev-earth-040809-152429>). The package 'isocat' can then
quantitatively compare and cluster these maps to group individuals by
similar origin. It also includes techniques for applying four approaches
(cumulative sum, odds ratio, quantile only, and quantile simulation) with
which users can summarize geographic origins and probable distance traveled
by individuals. Campbell et al. [2020] establishes several of the functions
included in this package <doi:10.1515/ami-2020-0004>.
Author: Caitlin Campbell [aut, cre] (<https://orcid.org/0000-0002-8199-7775>)
Maintainer: Caitlin Campbell <caitjcampbell@gmail.com>
Diff between isocat versions 0.2.5 dated 2020-03-28 and 0.2.6 dated 2020-07-03
DESCRIPTION | 27 MD5 | 43 NEWS.md | 14 README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/isocat.R | 50 - inst/doc/isocat.Rmd | 4 inst/doc/isocat.html | 477 ++++------ man/isoscape.Rd | 4 man/isoscape_sd.Rd | 4 vignettes/isocat.Rmd | 4 vignettes/isocat_files/figure-html/Create_mean_aggregate_surfaces-1.png |binary vignettes/isocat_files/figure-html/clusterSimmatrix-1.png |binary vignettes/isocat_files/figure-html/eval_odds_ratio_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantile_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantsim_surface-1.png |binary vignettes/isocat_files/figure-html/example_surface-1.png |binary vignettes/isocat_files/figure-html/plot_cumulative_sum_surface-1.png |binary vignettes/isocat_files/figure-html/plot_isoscape_data-1.png |binary vignettes/isocat_files/figure-html/prob_of_orgin_surface-1.png |binary vignettes/isocat_files/figure-html/quantsim_values-1.png |binary vignettes/isocat_files/figure-html/summary_surface-1.png |binary 23 files changed, 327 insertions(+), 302 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
Hua Zhou [aut, ctb] (<https://orcid.org/0000-0003-1822-1306>),
Nicole Doudican [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>),
John Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>),
Adriana Heguy [aut, ctb],
Boris Reizis [aut, ctb] (<https://orcid.org/0000-0003-1140-7853>),
Aristotelis Tsirigos [aut, ctb]
(<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.5.1 dated 2020-06-17 and 1.5.4 dated 2020-07-03
DESCRIPTION | 13 ++--- MD5 | 42 ++++++++++------ NAMESPACE | 6 ++ R/F004.qc.stats.R | 32 +++++++++--- R/F005.stats.plot.R | 26 +++++++--- R/F020.cluster.plot.R | 2 R/F027.clust.stats.plot.R | 6 +- R/F031.gene.plot.R | 18 ++++--- R/RcppExports.R | 12 ---- R/Rphenograph.R |only R/cell.cycle.R | 114 +++++++++++++++++++++++++++++++++++++++++++++- R/clust.ord.R |only R/findKNN.R |only man/Rphenograph.Rd |only man/cell.cycle.Rd | 2 man/clust.ord.Rd |only man/cluster.plot.Rd | 2 man/demo.obj.Rd | 4 + man/find_neighbors.Rd |only man/g2m.phase.Rd | 4 + man/gene.plot.Rd | 11 ++-- man/qc.stats.Rd | 2 man/s.phase.Rd | 4 + man/stats.plot.Rd | 6 +- src |only 25 files changed, 230 insertions(+), 76 deletions(-)
Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides graphical modelling features
used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements
graph algorithms including (i) maximum cardinality search (for marked
and unmarked graphs).
(ii) moralization, (iii) triangulation, (iv) creation of junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data.
The facilities of the package are documented in the book by Højsgaard,
Edwards and Lauritzen (2012,
<doi:10.1007/978-1-4614-2299-0>) and in the paper by
Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>).
Please see 'citation("gRbase")' for citation details.
NOTICE 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8-6.6 dated 2020-06-14 and 1.8-6.7 dated 2020-07-03
gRbase-1.8-6.6/gRbase/R/api_setops_obsolete.R |only gRbase-1.8-6.6/gRbase/R/combnC-c.R |only gRbase-1.8-6.6/gRbase/man/combn_prim.Rd |only gRbase-1.8-6.6/gRbase/man/set-operations-obsolete.Rd |only gRbase-1.8-6.6/gRbase/src/_m_coerce-M2ftM.cpp |only gRbase-1.8-6.6/gRbase/src/_m_coerce-dense-sparse.cpp |only gRbase-1.8-6.6/gRbase/src/_m_coerce-list2M.cpp |only gRbase-1.8-6.6/gRbase/src/_m_colmat2list_etc.cpp |only gRbase-1.8-6.6/gRbase/src/_m_isadjMAT.cpp |only gRbase-1.8-6.6/gRbase/src/api_setops.cpp |only gRbase-1.8-6.6/gRbase/src/api_setops_obsolete1.c |only gRbase-1.8-6.6/gRbase/src/api_setops_obsolete2.cpp |only gRbase-1.8-6.6/gRbase/src/combnC.c |only gRbase-1.8-6.6/gRbase/src/combnPrimC.c |only gRbase-1.8-6.6/gRbase/src/combnPrimC.h |only gRbase-1.8-6.6/gRbase/src/f2c.h |only gRbase-1.8-6.7/gRbase/DESCRIPTION | 32 gRbase-1.8-6.7/gRbase/MD5 | 69 gRbase-1.8-6.7/gRbase/NAMESPACE | 7 gRbase-1.8-6.7/gRbase/NEWS | 15 gRbase-1.8-6.7/gRbase/R/RcppExports.R | 204 -- gRbase-1.8-6.7/gRbase/R/api_array_pct.R | 1 gRbase-1.8-6.7/gRbase/R/fastcombn.R |only gRbase-1.8-6.7/gRbase/R/xxx_downstream-depends.R | 25 gRbase-1.8-6.7/gRbase/inst/doc/arrays.pdf |binary gRbase-1.8-6.7/gRbase/inst/doc/graphs.pdf |binary gRbase-1.8-6.7/gRbase/inst/include/gRbase_RcppExports.h | 504 ++--- gRbase-1.8-6.7/gRbase/man/fastcombn.Rd |only gRbase-1.8-6.7/gRbase/src/RcppExports.cpp | 968 +++++----- gRbase-1.8-6.7/gRbase/src/api_matrix_coerce-M2ftM.cpp |only gRbase-1.8-6.7/gRbase/src/api_matrix_coerce-list2M.cpp |only gRbase-1.8-6.7/gRbase/src/api_matrix_coerce_dense_sparse.cpp |only gRbase-1.8-6.7/gRbase/src/api_matrix_colmat2list_etc.cpp |only gRbase-1.8-6.7/gRbase/src/api_matrix_isadjMAT.cpp |only gRbase-1.8-6.7/gRbase/src/api_set-operations.cpp |only gRbase-1.8-6.7/gRbase/src/combn-bristol |only gRbase-1.8-6.7/gRbase/src/fastcombn.cpp |only gRbase-1.8-6.7/gRbase/src/init.c | 30 gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-13-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-18-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-29-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-31-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-34-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-36-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-38-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-6-1.pdf |binary gRbase-1.8-6.7/gRbase/vignettes/fig/graphunnamed-chunk-9-1.pdf |binary 47 files changed, 945 insertions(+), 910 deletions(-)
Title: Sparse Matrix Format with Data on Disk
Description: Provides a sparse matrix format with data stored on disk, to be
used in both R and C++. This is intended for more efficient use of sparse
data in C++ and also when parallelizing, since data on disk does not need
copying. Only a limited number of features will be implemented. For now,
conversion can be performed from a 'dgCMatrix' of R package 'Matrix'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigsparser versions 0.2.2 dated 2020-06-29 and 0.2.3 dated 2020-07-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/write-indval.cpp | 17 ++++++++++------- 3 files changed, 15 insertions(+), 12 deletions(-)
Title: Plot Positive and Negative Predictive Values for Medical Tests
Description: Functions to plot and help understand positive and negative predictive values (PPV and NPV), and their relationship with sensitivity, specificity, and prevalence. See Akobeng, A.K. (2007) <doi:10.1111/j.1651-2227.2006.00180.x> for a theoretical overview of the technical concepts and Navarrete et al. (2015) for a practical explanation about the importance of their understanding <doi:10.3389/fpsyg.2015.01327>.
Author: Gorka Navarrete [aut, cre] (<https://orcid.org/0000-0001-7678-8656>)
Maintainer: Gorka Navarrete <gorkang@gmail.com>
Diff between BayesianReasoning versions 0.3.1 dated 2020-06-30 and 0.3.2 dated 2020-07-03
DESCRIPTION | 13 MD5 | 53 - NEWS.md | 13 R/PPV_diagnostic_vs_screening.R | 8 R/PPV_heatmap.R | 52 - R/helper_functions.R | 322 +++------- R/min_possible_prevalence.R | 32 README.md | 9 build/vignette.rds |binary inst/doc/PPV_NPV.R |only inst/doc/PPV_NPV.Rmd |only inst/doc/PPV_NPV.html |only inst/doc/introduction.html | 16 man/dot-createPPVmatrix.Rd | 9 man/dot-get_point_ppv_npv.Rd | 12 man/dot-number_decimals_plot_axis.Rd | 6 man/dot-plot_creation.Rd | 2 man/dot-plot_overlay_area.Rd | 10 man/dot-plot_overlay_line.Rd | 13 man/dot-translate_labels.Rd | 4 man/figures/PPV_heatmap/NPV_800_1000_80_5_en.png |binary man/figures/PPV_heatmap/PPV_1_1000_100_2_en.png |binary man/figures/PPV_heatmap/PPV_1_1200_81_5_area_en.png |binary man/figures/PPV_heatmap/PPV_1_1200_81_5_line_en.png |binary man/figures/PPV_heatmap/PPV_1_1800_90_15_line_en.png |binary man/figures/diagnostic_vs_screening/FP_10_sens_100_screening_1000_diagnostic_2.png |binary man/figures/logo.png |only tests/testthat/test-PPV_diagnostic_vs_screening.R | 19 tests/testthat/test-PPV_heatmap.R | 191 +++++ vignettes/PPV_NPV.Rmd |only 30 files changed, 443 insertions(+), 341 deletions(-)
More information about BayesianReasoning at CRAN
Permanent link
Title: Applied Statistical Hypothesis Tests
Description: Gives some hypothesis test functions (sign test, median and other quantile tests, Wilcoxon signed rank test, coefficient of variation test, test of normal variance, test on weighted sums of Poisson [see Fay and Kim <doi:10.1002/bimj.201600111>], sample size for t-tests with different variances and non-equal n per arm, Behrens-Fisher test, nonparametric ABC intervals, Wilcoxon-Mann-Whitney test [with effect estimates and confidence intervals, see Fay and Malinovsky <doi:10.1002/sim.7890>], two-sample melding tests [see Fay, Proschan, and Brittain <doi:10.1111/biom.12231>], one-way ANOVA allowing var.equal=FALSE [see Brown and Forsythe, 1974, Biometrics]), prevalence confidence intervals that adjust for sensitivity and specificity [see Lang and Reiczigel, 2014 <doi:10.1016/j.prevetmed.2013.09.015>]). The focus is on hypothesis tests that have compatible confidence intervals, but some functions only have confidence intervals (e.g., prevSeSp).
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between asht versions 0.9.5 dated 2020-06-20 and 0.9.6 dated 2020-07-03
DESCRIPTION | 10 +-- MD5 | 10 +-- R/signTest.R | 160 +++++++++++++++++++++++++++++++++++++++++++--------- inst/NEWS.Rd | 14 +++- man/asht-package.Rd | 4 - man/signTest.Rd | 80 +++++++++++++++++++++----- 6 files changed, 223 insertions(+), 55 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.2-2 dated 2019-05-29 and 2.3-0 dated 2020-07-03
DESCRIPTION | 10 MD5 | 76 - NAMESPACE | 64 + R/Nmix.gof.test.R | 322 ++++- R/aictab.R | 366 ++++++ R/anovaOD.R | 598 +++++++++++ R/bictab.R | 261 ++++ R/countDist.R | 701 ++++++++++++- R/countHist.R | 904 +++++++++++++--- R/detHist.R | 338 ++++++ R/detTime.R |only R/extractX.R | 663 ++++++++++++ R/importance.R | 682 ++++++++++-- R/mb.gof.test.R | 172 ++- R/modavg.R | 1643 +++++++++++++++++++++++++++++- R/modavgEffect.R | 2350 ++++++++++++++++++++++++++++++++++++++++--- R/modavgPred.R | 2478 +++++++++++++++++++++++++++++++++++++++++----- R/modavgShrink.R | 1114 ++++++++++++++++++++ R/summaryOD.R | 240 ++++ R/xtable.R | 231 +++- inst/NEWS | 16 man/AICcmodavg-package.Rd | 6 man/Nmix.gof.test.Rd | 14 man/aictab.Rd | 16 man/anovaOD.Rd | 16 man/bictab.Rd | 16 man/countDist.Rd | 57 - man/countHist.Rd | 22 man/detHist.Rd | 46 man/detTime.Rd |only man/extractX.Rd | 59 - man/importance.Rd | 82 - man/mb.gof.test.Rd | 11 man/modavg.Rd | 92 + man/modavgEffect.Rd | 92 + man/modavgPred.Rd | 80 + man/modavgShrink.Rd | 79 - man/predictSE.Rd | 2 man/summaryOD.Rd | 19 man/xtable.Rd | 29 40 files changed, 12697 insertions(+), 1270 deletions(-)
Title: Logging for 'dplyr' and 'tidyr' Functions
Description: Provides feedback about 'dplyr' and 'tidyr' operations.
Author: Benjamin Elbers [aut, cre] (<https://orcid.org/0000-0001-5392-3448>),
Damiano Oldoni [ctb] (<https://orcid.org/0000-0003-3445-7562>)
Maintainer: Benjamin Elbers <elbersb@gmail.com>
Diff between tidylog versions 1.0.1 dated 2020-04-17 and 1.0.2 dated 2020-07-03
DESCRIPTION | 9 +- MD5 | 134 +++++++++++++++++++++++-------------------- NAMESPACE | 7 ++ NEWS.md | 8 ++ R/filter.R | 25 ++++++++ R/mutate.R | 2 R/rename.R | 5 + R/select.R | 5 + README.md | 38 ++++++------ build |only inst |only man/add_count.Rd | 6 - man/add_tally.Rd | 6 - man/anti_join.Rd | 10 +-- man/distinct.Rd | 6 - man/distinct_all.Rd | 6 - man/distinct_at.Rd | 6 - man/distinct_if.Rd | 6 - man/filter_all.Rd | 6 - man/filter_at.Rd | 6 - man/filter_if.Rd | 6 - man/full_join.Rd | 10 +-- man/group_by.Rd | 6 - man/group_by_all.Rd | 6 - man/group_by_at.Rd | 6 - man/group_by_if.Rd | 6 - man/inner_join.Rd | 10 +-- man/left_join.Rd | 10 +-- man/mutate.Rd | 6 - man/mutate_all.Rd | 6 - man/mutate_at.Rd | 6 - man/mutate_if.Rd | 6 - man/relocate.Rd |only man/rename.Rd | 6 - man/rename_all.Rd | 6 - man/rename_at.Rd | 6 - man/rename_if.Rd | 6 - man/rename_with.Rd |only man/right_join.Rd | 10 +-- man/sample_frac.Rd | 6 - man/sample_n.Rd | 6 - man/select_all.Rd | 6 - man/select_at.Rd | 6 - man/select_if.Rd | 6 - man/semi_join.Rd | 10 +-- man/slice.Rd | 6 - man/slice_head.Rd |only man/slice_max.Rd |only man/slice_min.Rd |only man/slice_sample.Rd |only man/slice_tail.Rd |only man/summarise.Rd | 6 - man/summarise_all.Rd | 6 - man/summarise_at.Rd | 6 - man/summarise_if.Rd | 6 - man/summarize.Rd | 6 - man/summarize_all.Rd | 6 - man/summarize_at.Rd | 6 - man/summarize_if.Rd | 6 - man/tally.Rd | 6 - man/top_frac.Rd | 6 - man/top_n.Rd | 6 - man/transmute.Rd | 6 - man/transmute_all.Rd | 6 - man/transmute_at.Rd | 6 - man/transmute_if.Rd | 6 - man/ungroup.Rd | 6 - tests/testthat/test_filter.R | 55 +++++++++++++++-- tests/testthat/test_mutate.R | 16 ++++- tests/testthat/test_rename.R | 7 ++ tests/testthat/test_select.R | 15 ++++ vignettes |only 72 files changed, 391 insertions(+), 253 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 1.0.1 dated 2020-04-21 and 1.0.2 dated 2020-07-03
DESCRIPTION | 14 MD5 | 65 - NAMESPACE | 5 NEWS.md | 5 R/check_recode.R | 3 R/coefficient_plot.R | 7 R/ff_glimpse.R | 2 R/ff_label.R | 72 + R/ff_permute.R | 4 R/finalfit.R | 19 R/finalfit_internal_functions.R | 88 +- R/fit2df.R | 59 + R/hr_plot.R | 7 R/missing_compare.R | 24 R/missing_glimpse.R | 2 R/or_plot.R | 5 R/summaryfactorlist.R | 5 inst/doc/all_tables_examples.R | 22 inst/doc/all_tables_examples.Rmd | 4 inst/doc/all_tables_examples.html | 1648 +++++++++++++++++--------------------- inst/doc/bootstrap.html | 179 ++-- inst/doc/data_prep.html | 212 ++-- inst/doc/export.html | 184 ++-- inst/doc/finalfit.html | 232 ++--- inst/doc/missing.html | 606 ++++++------- inst/doc/survival.html | 394 ++++----- man/check_recode.Rd | 3 man/extract_fit.Rd | 29 man/ff_permute.Rd | 4 man/finalfit.Rd | 19 man/fit2df.Rd | 12 man/labels_to_column.Rd |only man/labels_to_level.Rd |only man/rm_duplicates.Rd |only vignettes/all_tables_examples.Rmd | 4 35 files changed, 1970 insertions(+), 1968 deletions(-)
Title: A Tool Kit for Working with Time Series in R
Description: Easy visualization, wrangling, and preprocessing of time series data for
forecasting and machine learning prediction.
Methods discussed herein are commonplace in machine learning, and have been cited
in various literature. Refer to "Calendar Effects" in papers such as
Taieb, Souhaib Ben. "Machine learning strategies for multi-step-ahead time series
forecasting." Universit Libre de Bruxelles, Belgium (2014): 75-86.
<http://souhaib-bentaieb.com/pdf/2014_phd.pdf>.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timetk versions 2.0.0 dated 2020-05-31 and 2.1.0 dated 2020-07-03
timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.R |only timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.Rmd |only timetk-2.0.0/timetk/inst/doc/TK07_Time_Series_Data_Wrangling.html |only timetk-2.0.0/timetk/vignettes/TK07_Time_Series_Data_Wrangling.Rmd |only timetk-2.1.0/timetk/DESCRIPTION | 16 timetk-2.1.0/timetk/MD5 | 151 - timetk-2.1.0/timetk/NAMESPACE | 5 timetk-2.1.0/timetk/NEWS.md | 38 timetk-2.1.0/timetk/R/00_global_vars.R | 2 timetk-2.1.0/timetk/R/diagnostics-tk_acf_diagnostics.R | 27 timetk-2.1.0/timetk/R/diagnostics-tk_summary_diagnostics.R | 39 timetk-2.1.0/timetk/R/dplyr-filter_by_time.R | 31 timetk-2.1.0/timetk/R/dplyr-summarise_by_time.R | 59 timetk-2.1.0/timetk/R/make-tk_make_holiday_sequences.R | 2 timetk-2.1.0/timetk/R/make-tk_make_timeseries_future.R | 6 timetk-2.1.0/timetk/R/plot-acf_diagnostics.R | 45 timetk-2.1.0/timetk/R/plot-anomaly_diagnostics.R | 38 timetk-2.1.0/timetk/R/plot-seasonal_diagnostics.R | 22 timetk-2.1.0/timetk/R/plot-stl_diagnostics.R | 18 timetk-2.1.0/timetk/R/plot-time_series.R | 62 timetk-2.1.0/timetk/R/plot-time_series_regression.R |only timetk-2.1.0/timetk/R/recipes-step_box_cox.R | 22 timetk-2.1.0/timetk/R/recipes-step_diff.R | 10 timetk-2.1.0/timetk/R/recipes-step_fourier.R | 12 timetk-2.1.0/timetk/R/recipes-step_holiday_signature.R | 12 timetk-2.1.0/timetk/R/recipes-step_slidify.R | 10 timetk-2.1.0/timetk/R/recipes-step_smooth.R | 10 timetk-2.1.0/timetk/R/recipes-step_timeseries_signature.R | 10 timetk-2.1.0/timetk/R/recipes-step_ts_clean.R | 2 timetk-2.1.0/timetk/R/recipes-step_ts_impute.R | 10 timetk-2.1.0/timetk/R/recipes-step_ts_pad.R | 10 timetk-2.1.0/timetk/R/rsample-time_series_cv.R | 7 timetk-2.1.0/timetk/R/rsample-time_series_split.R |only timetk-2.1.0/timetk/R/rsample-tk_time_series_cv_plan.R | 20 timetk-2.1.0/timetk/R/utils-tidy-eval.R | 14 timetk-2.1.0/timetk/R/vec-fourier.R | 10 timetk-2.1.0/timetk/README.md | 14 timetk-2.1.0/timetk/build/vignette.rds |binary timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.R | 219 -- timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.Rmd | 290 +-- timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.html | 887 ++++++---- timetk-2.1.0/timetk/inst/doc/TK04_Plotting_Time_Series.R | 7 timetk-2.1.0/timetk/inst/doc/TK04_Plotting_Time_Series.Rmd | 12 timetk-2.1.0/timetk/inst/doc/TK04_Plotting_Time_Series.html | 56 timetk-2.1.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.R | 4 timetk-2.1.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.Rmd | 4 timetk-2.1.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.html | 60 timetk-2.1.0/timetk/man/figures/README-unnamed-chunk-4-1.png |binary timetk-2.1.0/timetk/man/figures/README-unnamed-chunk-5-1.png |binary timetk-2.1.0/timetk/man/figures/README-unnamed-chunk-6-1.png |binary timetk-2.1.0/timetk/man/figures/README-unnamed-chunk-7-1.png |only timetk-2.1.0/timetk/man/filter_by_time.Rd | 5 timetk-2.1.0/timetk/man/plot_acf_diagnostics.Rd | 17 timetk-2.1.0/timetk/man/plot_anomaly_diagnostics.Rd | 11 timetk-2.1.0/timetk/man/plot_seasonal_diagnostics.Rd | 4 timetk-2.1.0/timetk/man/plot_stl_diagnostics.Rd | 4 timetk-2.1.0/timetk/man/plot_time_series.Rd | 30 timetk-2.1.0/timetk/man/plot_time_series_regression.Rd |only timetk-2.1.0/timetk/man/step_box_cox.Rd | 30 timetk-2.1.0/timetk/man/step_diff.Rd | 10 timetk-2.1.0/timetk/man/step_fourier.Rd | 12 timetk-2.1.0/timetk/man/step_holiday_signature.Rd | 12 timetk-2.1.0/timetk/man/step_slidify.Rd | 10 timetk-2.1.0/timetk/man/step_smooth.Rd | 10 timetk-2.1.0/timetk/man/step_timeseries_signature.Rd | 10 timetk-2.1.0/timetk/man/step_ts_clean.Rd | 20 timetk-2.1.0/timetk/man/step_ts_impute.Rd | 26 timetk-2.1.0/timetk/man/step_ts_pad.Rd | 10 timetk-2.1.0/timetk/man/summarise_by_time.Rd | 66 timetk-2.1.0/timetk/man/tidyeval.Rd | 14 timetk-2.1.0/timetk/man/time_series_cv.Rd | 7 timetk-2.1.0/timetk/man/time_series_split.Rd |only timetk-2.1.0/timetk/man/tk_acf_diagnostics.Rd | 14 timetk-2.1.0/timetk/man/tk_make_holiday_sequence.Rd | 2 timetk-2.1.0/timetk/man/tk_summary_diagnostics.Rd | 16 timetk-2.1.0/timetk/vignettes/TK03_Forecasting_Using_Time_Series_Signature.Rmd | 290 +-- timetk-2.1.0/timetk/vignettes/TK04_Plotting_Time_Series.Rmd | 12 timetk-2.1.0/timetk/vignettes/TK05_Plotting_Seasonality_and_Correlation.Rmd | 4 timetk-2.1.0/timetk/vignettes/temp_archive/TK01_Working_With_Time_Series_Index.Rmd | 2 timetk-2.1.0/timetk/vignettes/temp_archive/TK06_Automatic_Frequency_And_Trend_Selection.Rmd | 2 timetk-2.1.0/timetk/vignettes/temp_archive/TK07_Time_Series_Data_Wrangling.Rmd |only timetk-2.1.0/timetk/vignettes/timetk_version_2.jpg |only 82 files changed, 1605 insertions(+), 1318 deletions(-)
Title: Read, Write, Manipulate, Explore Chess PGN Files and R API to
UCI Chess Engines
Description: Provides functions for reading *.PGN files with more than one game, including large files without copying it into RAM (using 'ff' package or 'RSQLite' package). Handle chess data and chess aggregated data, count figure moves statistics, create player profile, plot winning chances, browse openings. Set of functions of R API to communicate with UCI-protocol based chess engines.
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>
Diff between bigchess versions 1.7.1 dated 2020-04-03 and 1.9.0 dated 2020-07-03
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++-------- NAMESPACE | 4 +--- R/analyze_game.R |only R/analyze_position.R | 2 +- R/read.pgn.db.R | 9 ++++----- R/read.pgn.ff.R | 6 ++---- R/write.pgn.R |only man/analyze_game.Rd |only man/analyze_position.Rd | 2 +- man/read.pgn.db.Rd | 2 +- man/read.pgn.ff.Rd | 2 +- man/write.pgn.Rd |only 13 files changed, 30 insertions(+), 31 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and high-performance
2D drawing library. The 'ragg' package provides a set of graphic devices
based on AGG to use as alternative to the raster devices provided through
the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Maxim Shemanarev [aut, cph] (Author of AGG),
Tony Juricic [ctb, cph] (Contributor to AGG),
Milan Marusinec [ctb, cph] (Contributor to AGG),
Spencer Garrett [ctb] (Contributor to AGG),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between ragg versions 0.3.0 dated 2020-06-24 and 0.3.1 dated 2020-07-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ src/init_device.h | 7 ++++--- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity.
The great features are :
- Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology).
- Create interactive maps through zoom and pop-up ('leaflet' technology).
- Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut],
Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut],
SED - DR Hauts-de-France - INSEE [ctb],
PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb],
PSAR-EEP - DR Occitanie - INSEE [ctb],
SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>
Diff between oceanis versions 1.7.3 dated 2020-06-02 and 1.7.4 dated 2020-07-03
DESCRIPTION | 10 MD5 | 30 NEWS | 13 R/leaflet_ronds_classes.R | 8 R/oceanis-package.R | 71 +- R/plot_classes.R | 92 +- R/plot_classes_ronds.R | 124 ++- R/plot_joignantes.R | 64 + R/plot_ronds.R | 63 + R/plot_ronds_classes.R | 126 ++- R/plot_saphirs.R | 66 + R/plot_typo.R | 54 - R/plot_typo_symboles.R | 61 + inst/doc/integration_shiny.html | 1298 +++++++++++++++++++++--------------- inst/doc/oceanis.html | 1407 ++++++++++++++++++++++------------------ man/plot_.Rd | 77 +- 16 files changed, 2135 insertions(+), 1429 deletions(-)
Title: Methods for Visualization of Computer Experiments Design and
Surrogate
Description: View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Author: Yann Richet, Yves Deville, Clement Chevalier
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between DiceView versions 1.3-2 dated 2018-01-11 and 2.0-0 dated 2020-07-03
DiceView-1.3-2/DiceView/man/contourview.fun.Rd |only DiceView-1.3-2/DiceView/man/contourview.km.Rd |only DiceView-1.3-2/DiceView/man/contourview.list.Rd |only DiceView-1.3-2/DiceView/man/sectionview.fun.Rd |only DiceView-1.3-2/DiceView/man/sectionview.km.Rd |only DiceView-1.3-2/DiceView/man/sectionview.list.Rd |only DiceView-1.3-2/DiceView/man/sectionview3d.fun.Rd |only DiceView-1.3-2/DiceView/man/sectionview3d.km.Rd |only DiceView-1.3-2/DiceView/man/sectionview3d.list.Rd |only DiceView-1.3-2/DiceView/man/view.Rd |only DiceView-2.0-0/DiceView/CHANGELOG | 27 +- DiceView-2.0-0/DiceView/DESCRIPTION | 21 +- DiceView-2.0-0/DiceView/MD5 | 68 ++++-- DiceView-2.0-0/DiceView/NAMESPACE | 67 +++++- DiceView-2.0-0/DiceView/R/Utils.R | 45 ++-- DiceView-2.0-0/DiceView/R/contourview.fun.R | 106 ++++++---- DiceView-2.0-0/DiceView/R/contourview.km.R | 130 ++++++------- DiceView-2.0-0/DiceView/R/contourview.list.R | 8 DiceView-2.0-0/DiceView/R/function.R |only DiceView-2.0-0/DiceView/R/mesh_set.R |only DiceView-2.0-0/DiceView/R/sectionview.fun.R | 77 ++++--- DiceView-2.0-0/DiceView/R/sectionview.km.R | 111 ++++++----- DiceView-2.0-0/DiceView/R/sectionview.list.R | 10 - DiceView-2.0-0/DiceView/R/sectionview3d.fun.R | 98 ++++++---- DiceView-2.0-0/DiceView/R/sectionview3d.km.R | 151 ++++++++------- DiceView-2.0-0/DiceView/R/sectionview3d.list.R | 13 + DiceView-2.0-0/DiceView/R/wrapper.R | 214 +++++++++++++++++----- DiceView-2.0-0/DiceView/README.md | 6 DiceView-2.0-0/DiceView/man/Apply.fun.Rd |only DiceView-2.0-0/DiceView/man/Memoize.fun.Rd |only DiceView-2.0-0/DiceView/man/Vectorize.funD.Rd |only DiceView-2.0-0/DiceView/man/are_in.mesh.Rd |only DiceView-2.0-0/DiceView/man/combn.design.Rd |only DiceView-2.0-0/DiceView/man/contourview.Rd | 33 --- DiceView-2.0-0/DiceView/man/function-methods.Rd |only DiceView-2.0-0/DiceView/man/is_in.mesh.Rd |only DiceView-2.0-0/DiceView/man/is_in.p.Rd |only DiceView-2.0-0/DiceView/man/km-methods.Rd |only DiceView-2.0-0/DiceView/man/list-methods.Rd |only DiceView-2.0-0/DiceView/man/mesh_exsets.Rd |only DiceView-2.0-0/DiceView/man/mesh_roots.Rd |only DiceView-2.0-0/DiceView/man/min_dist.Rd |only DiceView-2.0-0/DiceView/man/plot2d_mesh.Rd |only DiceView-2.0-0/DiceView/man/plot3d_mesh.Rd |only DiceView-2.0-0/DiceView/man/plot_mesh.Rd |only DiceView-2.0-0/DiceView/man/points_in.mesh.Rd |only DiceView-2.0-0/DiceView/man/points_out.mesh.Rd |only DiceView-2.0-0/DiceView/man/root.Rd |only DiceView-2.0-0/DiceView/man/roots.Rd |only DiceView-2.0-0/DiceView/man/sectionview.Rd | 38 --- DiceView-2.0-0/DiceView/man/sectionview3d.Rd | 43 +--- 51 files changed, 759 insertions(+), 507 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories
(also known as a Sankey diagram), flow charts by extending the grid package,
a method for variable selection based on the SVD, Bézier lines with arrows
complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.10.0 dated 2020-05-06 and 1.11.0 dated 2020-07-03
Gmisc-1.10.0/Gmisc/R/boxGrobs.R |only Gmisc-1.11.0/Gmisc/DESCRIPTION | 20 Gmisc-1.11.0/Gmisc/MD5 | 233 - Gmisc-1.11.0/Gmisc/NAMESPACE | 10 Gmisc-1.11.0/Gmisc/NEWS | 12 Gmisc-1.11.0/Gmisc/R/Gmisc.R | 4 Gmisc-1.11.0/Gmisc/R/assert.R | 33 Gmisc-1.11.0/Gmisc/R/bezierArrowGradient.R | 246 + Gmisc-1.11.0/Gmisc/R/bezierArrowSmpl.R | 204 - Gmisc-1.11.0/Gmisc/R/bezier_private_functions.R | 442 +-- Gmisc-1.11.0/Gmisc/R/boxGrob_prConvert2Coords.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_S3_fns.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_align.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_boxGrob.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_boxPropGrob.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_connect.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_coords.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_distance.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_move.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_prCreateBoxCoordinates.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_print.Gmisc_list_of_boxes.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_private_helpers.R |only Gmisc-1.11.0/Gmisc/R/boxGrobs_spread.R |only Gmisc-1.11.0/Gmisc/R/convertShowMissing.R | 36 Gmisc-1.11.0/Gmisc/R/copyAllNewAttributes.R | 4 Gmisc-1.11.0/Gmisc/R/deprecated.R | 2 Gmisc-1.11.0/Gmisc/R/descGetMissing.R | 24 Gmisc-1.11.0/Gmisc/R/descriptionStats.R | 461 +-- Gmisc-1.11.0/Gmisc/R/docx_document.R | 84 Gmisc-1.11.0/Gmisc/R/fastDoCall.R | 28 Gmisc-1.11.0/Gmisc/R/figCaptionNo.R | 37 Gmisc-1.11.0/Gmisc/R/getDescriptionStatsBy.R | 527 ++- Gmisc-1.11.0/Gmisc/R/getPval.R | 49 Gmisc-1.11.0/Gmisc/R/getSvdMostInfluential.R | 62 Gmisc-1.11.0/Gmisc/R/insertRowAndKeepAttr.R | 24 Gmisc-1.11.0/Gmisc/R/mergeDesc.R | 195 - Gmisc-1.11.0/Gmisc/R/mergeLists.R | 100 Gmisc-1.11.0/Gmisc/R/pathJoin.R | 13 Gmisc-1.11.0/Gmisc/R/private_functions.R | 160 - Gmisc-1.11.0/Gmisc/R/retrieve_and_has.R | 31 Gmisc-1.11.0/Gmisc/R/time2spanTxt.R | 30 Gmisc-1.11.0/Gmisc/R/transitionClass.R | 1177 ++++---- Gmisc-1.11.0/Gmisc/R/transitionClass_helpers.R | 484 ++- Gmisc-1.11.0/Gmisc/R/transitionPlot.R | 668 ++-- Gmisc-1.11.0/Gmisc/R/transitionPlot_helpers.R | 734 ++--- Gmisc-1.11.0/Gmisc/R/yamlDump.R | 12 Gmisc-1.11.0/Gmisc/build/vignette.rds |binary Gmisc-1.11.0/Gmisc/inst/doc/Descriptives.R | 21 Gmisc-1.11.0/Gmisc/inst/doc/Descriptives.Rmd | 30 Gmisc-1.11.0/Gmisc/inst/doc/Descriptives.html | 394 +- Gmisc-1.11.0/Gmisc/inst/doc/Grid-based_flowcharts.R | 571 +++- Gmisc-1.11.0/Gmisc/inst/doc/Grid-based_flowcharts.Rmd | 675 +++- Gmisc-1.11.0/Gmisc/inst/doc/Grid-based_flowcharts.html | 854 ++++-- Gmisc-1.11.0/Gmisc/inst/doc/Transition-class.html | 219 - Gmisc-1.11.0/Gmisc/inst/doc/transitionPlot.Rmd | 2 Gmisc-1.11.0/Gmisc/inst/doc/transitionPlot.html | 250 + Gmisc-1.11.0/Gmisc/inst/examples/alignBox_ex.R |only Gmisc-1.11.0/Gmisc/inst/examples/bezierArrowGradient_example.R | 52 Gmisc-1.11.0/Gmisc/inst/examples/bezierArrowSmpl_example.R | 34 Gmisc-1.11.0/Gmisc/inst/examples/connectGrob_example.R | 10 Gmisc-1.11.0/Gmisc/inst/examples/data-SCB_example.R | 2 Gmisc-1.11.0/Gmisc/inst/examples/getDescriptionStatsBy_example.R | 30 Gmisc-1.11.0/Gmisc/inst/examples/getSvdMostInfluential_example.R | 144 - Gmisc-1.11.0/Gmisc/inst/examples/mergeLists_example.R | 6 Gmisc-1.11.0/Gmisc/inst/examples/moveBox_ex.R |only Gmisc-1.11.0/Gmisc/inst/examples/spreadBox_ex.R |only Gmisc-1.11.0/Gmisc/inst/examples/transitionClass_example.R | 41 Gmisc-1.11.0/Gmisc/inst/extdata/Full_test_suite.Rmd | 46 Gmisc-1.11.0/Gmisc/man/Gmisc-package.Rd | 2 Gmisc-1.11.0/Gmisc/man/Transition-class.Rd | 57 Gmisc-1.11.0/Gmisc/man/align.Rd |only Gmisc-1.11.0/Gmisc/man/assert.Rd | 2 Gmisc-1.11.0/Gmisc/man/bezierArrowGradient.Rd | 8 Gmisc-1.11.0/Gmisc/man/bezierArrowSmpl.Rd | 9 Gmisc-1.11.0/Gmisc/man/box.Rd | 51 Gmisc-1.11.0/Gmisc/man/boxPropGrob.Rd | 23 Gmisc-1.11.0/Gmisc/man/connect.Rd | 23 Gmisc-1.11.0/Gmisc/man/convertShowMissing.Rd | 2 Gmisc-1.11.0/Gmisc/man/coords.Rd | 17 Gmisc-1.11.0/Gmisc/man/descGetMissing.Rd | 4 Gmisc-1.11.0/Gmisc/man/describeFactors.Rd | 18 Gmisc-1.11.0/Gmisc/man/describeMean.Rd | 5 Gmisc-1.11.0/Gmisc/man/describeMedian.Rd | 3 Gmisc-1.11.0/Gmisc/man/describeProp.Rd | 3 Gmisc-1.11.0/Gmisc/man/distance.Rd | 56 Gmisc-1.11.0/Gmisc/man/figCapNo.Rd | 14 Gmisc-1.11.0/Gmisc/man/figCapNoLast.Rd | 4 Gmisc-1.11.0/Gmisc/man/figCapNoNext.Rd | 6 Gmisc-1.11.0/Gmisc/man/getDescriptionStatsBy.Rd | 35 Gmisc-1.11.0/Gmisc/man/getPval.Rd | 12 Gmisc-1.11.0/Gmisc/man/getSvdMostInfluential.Rd | 146 - Gmisc-1.11.0/Gmisc/man/insertRowAndKeepAttr.Rd | 7 Gmisc-1.11.0/Gmisc/man/mergeDesc.Rd | 52 Gmisc-1.11.0/Gmisc/man/mergeLists.Rd | 4 Gmisc-1.11.0/Gmisc/man/moveBox.Rd |only Gmisc-1.11.0/Gmisc/man/pathJoin.Rd | 5 Gmisc-1.11.0/Gmisc/man/prBuildSubLabel.Rd |only Gmisc-1.11.0/Gmisc/man/prConvert2Coords.Rd |only Gmisc-1.11.0/Gmisc/man/prCreateBoxCoordinates.Rd |only Gmisc-1.11.0/Gmisc/man/prGridPlotTitle.Rd | 2 Gmisc-1.11.0/Gmisc/man/prTpGetColors.Rd | 2 Gmisc-1.11.0/Gmisc/man/prTpPlotBoxes.Rd | 2 Gmisc-1.11.0/Gmisc/man/print.Gmisc_list_of_boxes.Rd |only Gmisc-1.11.0/Gmisc/man/retrieve.Rd | 2 Gmisc-1.11.0/Gmisc/man/spread.Rd |only Gmisc-1.11.0/Gmisc/man/time2spanTxt.Rd | 4 Gmisc-1.11.0/Gmisc/man/transitionPlot.Rd | 49 Gmisc-1.11.0/Gmisc/man/yamlDump.Rd | 6 Gmisc-1.11.0/Gmisc/tests/cpp_tests/visual_line_debugging.R | 101 Gmisc-1.11.0/Gmisc/tests/testthat/Rplots.pdf |binary Gmisc-1.11.0/Gmisc/tests/testthat/test-boxGrob_move.R |only Gmisc-1.11.0/Gmisc/tests/testthat/test-boxGrob_spread.R |only Gmisc-1.11.0/Gmisc/tests/testthat/test-boxGrobs.R | 38 Gmisc-1.11.0/Gmisc/tests/testthat/test-boxPropGrobs.R |only Gmisc-1.11.0/Gmisc/tests/testthat/test-copyAllAttributes.R | 60 Gmisc-1.11.0/Gmisc/tests/testthat/test-descriptionStats.R | 296 +- Gmisc-1.11.0/Gmisc/tests/testthat/test-docx_document.R | 302 +- Gmisc-1.11.0/Gmisc/tests/testthat/test-fastDoCall.R | 73 Gmisc-1.11.0/Gmisc/tests/testthat/test-getDescriptionStats.R | 1380 ++++++---- Gmisc-1.11.0/Gmisc/tests/testthat/test-insertRowAndKeepAttr.R | 20 Gmisc-1.11.0/Gmisc/tests/testthat/test-mergeLists.R | 133 Gmisc-1.11.0/Gmisc/tests/testthat/test-transitionClass.R | 218 - Gmisc-1.11.0/Gmisc/tests/visual_tests/FTP_test/Setup_and_munge.R | 51 Gmisc-1.11.0/Gmisc/tests/visual_tests/bezierArrowRcpp_vtests.R | 93 Gmisc-1.11.0/Gmisc/tests/visual_tests/bezierArrowSmpl_vtests.R | 142 - Gmisc-1.11.0/Gmisc/tests/visual_tests/tansitionPlot_vtests.R | 298 +- Gmisc-1.11.0/Gmisc/tests/visual_tests/test-bezier-adjustment.R | 224 - Gmisc-1.11.0/Gmisc/tests/visual_tests/transitionClass_vtest.R | 79 Gmisc-1.11.0/Gmisc/vignettes/Descriptives.Rmd | 30 Gmisc-1.11.0/Gmisc/vignettes/Grid-based_flowcharts.Rmd | 675 +++- Gmisc-1.11.0/Gmisc/vignettes/transitionPlot.Rmd | 2 131 files changed, 8806 insertions(+), 5571 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.12-0 dated 2020-05-04 and 4.13-0 dated 2020-07-03
meta-4.12-0/meta/man/baujat.Rd |only meta-4.12-0/meta/man/bubble.Rd |only meta-4.12-0/meta/man/forest.Rd |only meta-4.12-0/meta/man/funnel.Rd |only meta-4.13-0/meta/DESCRIPTION | 14 - meta-4.13-0/meta/MD5 | 47 ++--- meta-4.13-0/meta/NAMESPACE | 9 - meta-4.13-0/meta/NEWS.md | 14 + meta-4.13-0/meta/R/baujat.R | 12 - meta-4.13-0/meta/R/bubble.R | 24 +- meta-4.13-0/meta/R/forest-internal.R | 38 ++-- meta-4.13-0/meta/R/forest.R | 271 ++------------------------------ meta-4.13-0/meta/R/forest.metabind.R |only meta-4.13-0/meta/R/funnel.R | 136 ---------------- meta-4.13-0/meta/R/labbe.R | 225 ++++++++++++-------------- meta-4.13-0/meta/R/lm2or.R |only meta-4.13-0/meta/R/meta-package.R | 22 +- meta-4.13-0/meta/R/metabias.R | 128 +++++++-------- meta-4.13-0/meta/R/radial.R | 135 +++++++-------- meta-4.13-0/meta/R/trimfill.R | 159 ++++++++---------- meta-4.13-0/meta/man/baujat.meta.Rd |only meta-4.13-0/meta/man/bubble.metareg.Rd |only meta-4.13-0/meta/man/forest.meta.Rd |only meta-4.13-0/meta/man/forest.metabind.Rd |only meta-4.13-0/meta/man/funnel.meta.Rd |only meta-4.13-0/meta/man/labbe.Rd | 56 +++--- meta-4.13-0/meta/man/meta-package.Rd | 17 +- meta-4.13-0/meta/man/metabias.Rd | 32 +-- meta-4.13-0/meta/man/radial.Rd | 22 +- meta-4.13-0/meta/man/trimfill.Rd | 74 ++++---- 30 files changed, 528 insertions(+), 907 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 3.0.9 dated 2020-04-29 and 3.1.8 dated 2020-07-03
DESCRIPTION | 20 MD5 | 94 +- NAMESPACE | 38 NEWS.md | 6 R/CNVScopeserver.R | 60 - R/GRanges_to_underscored_pos.R | 34 R/calcCNVKernelProbDist.R | 297 +++---- R/calcVecLMs.R | 107 +- R/createChromosomalMatrixSet.R | 101 +- R/downsample_genomic_matrix.R | 105 +- R/formSampleMatrixFromRawGDCData.R | 8 R/freadGDCfile.R | 143 +-- R/getAnnotationMatrix.R | 6 R/getAsymmetricBlockIndices.R | 2 R/getBlockAverageMatrixFromBreakpoints.R | 236 +++--- R/getInterchromosomalInteractivePlot.R | 146 +-- R/importBreakpointBed.R | 62 - R/postProcessLinRegMatrix.R | 97 +- R/rebinGenomicInteractions.R | 8 R/runCNVScopeShiny.R | 38 R/signedRescale.R | 192 ++-- R/underscored_pos_to_GRanges.R | 54 - R/writeAsymmetricMeltedMatrixToDisk.R | 388 +++++----- R/writeMeltedChromosomalMatrixToDisk.R | 366 ++++----- build/vignette.rds |binary data/nbl_result_matrix_sign_small.rda |binary inst/doc/additonal_examples.R | 7 inst/doc/additonal_examples.Rmd | 7 inst/doc/additonal_examples.html | 12 inst/doc/create_input_matrix.R | 16 inst/doc/create_input_matrix.Rmd | 23 inst/doc/create_input_matrix.html | 14 inst/doc/create_output_matrix.Rmd | 194 ++--- inst/doc/create_output_matrix.html | 20 inst/extdata/ensembl_gene_tx_table_prot.rda |binary vignettes/NBL_custom_sample_matched_input_matrix_1e5binsize_parallel.rds |binary vignettes/NBL_custom_sample_matched_input_matrix_1e7binsize.rds |binary vignettes/NBL_custom_sample_matched_input_matrix_1e8binsize.rds |binary vignettes/NBL_custom_sample_matched_input_matrix_2.5e5binsize_parallel.rds |binary vignettes/NBL_sample_matched_input_matrix.rds |binary vignettes/additonal_examples.Rmd | 7 vignettes/aml_sample_matched_input_matrix.rds |binary vignettes/blca_sample_matched_input_matrix.rds |binary vignettes/create_input_matrix.Rmd | 23 vignettes/create_output_matrix.Rmd | 194 ++--- vignettes/nbl_result_matrix_small.rds |binary vignettes/nbl_slurm_object_test_zero_removed.rds |binary vignettes/skcm_sample_matched_input_matrix.rds |binary 48 files changed, 1570 insertions(+), 1555 deletions(-)
Title: Extracts the Backbone from Weighted Graphs
Description: Provides methods for extracting from a weighted graph
a binary or signed backbone that retains only the significant edges.
The user may input a weighted graph, or a bipartite graph
from which a weighted graph is first constructed via projection.
Backbone extraction methods include the stochastic degree sequence model (Neal, Z. P. (2014). <doi:10.1016/j.socnet.2014.06.001>),
hypergeometric model (Neal, Z. (2013). <doi:10.1007/s13278-013-0107-y>),
the fixed degree sequence model (Zweig, K. A., and Kaufmann, M. (2011). <doi:10.1007/s13278-011-0021-0>),
as well as a universal threshold method.
Author: Rachel Domagalski [aut, cre],
Zachary Neal [aut],
Bruce Sagan [aut]
Maintainer: Rachel Domagalski <domagal9@msu.edu>
Diff between backbone versions 1.2.0 dated 2020-05-15 and 1.2.1 dated 2020-07-03
DESCRIPTION | 11 ++--- MD5 | 39 +++++++++--------- NAMESPACE | 2 NEWS.md | 6 ++ R/RcppExports.R |only R/backbone.R | 4 + R/backbone.extract.R | 64 ++++++++++++++++++++++++----- R/fdsm.R | 39 +++++++++--------- R/hyperg.R | 33 +++++++++------ R/model.helpers.R | 42 ++++++++++++++----- R/sdsm.R | 70 ++++++++++++++++++-------------- R/universal.R | 26 +++++++----- README.md | 8 +-- inst/CITATION | 4 - inst/doc/backbone.R | 24 +++++------ inst/doc/backbone.Rmd | 42 ++++++++++--------- inst/doc/backbone.html | 53 ++++++++++++------------ man/backbone.extract.Rd | 91 +++++++++++++++++++++--------------------- man/sdsm.Rd | 104 ++++++++++++++++++++++++------------------------ src |only vignettes/backbone.Rmd | 42 ++++++++++--------- 21 files changed, 407 insertions(+), 297 deletions(-)