Title: Penalized Data Sharpening for Local Polynomial Regression
Description: Functions and data sets for penalized data sharpening.
Nonparametric regressions are computed subject to smoothness
and other kinds of penalties.
Author: W.J. Braun [aut],
D. Wang [aut, cre],
X.J. Hu [aut, ctb]
Maintainer: D. Wang <wdy@mail.ubc.ca>
Diff between sharpPen versions 1.7 dated 2021-03-06 and 1.8 dated 2022-06-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dpilc.R | 13 ++++++++----- 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.11.0 dated 2021-09-26 and 2.12.0 dated 2022-06-27
R.utils-2.11.0/R.utils/NEWS |only R.utils-2.12.0/R.utils/DESCRIPTION | 11 ++- R.utils-2.12.0/R.utils/MD5 | 46 ++++++++-------- R.utils-2.12.0/R.utils/NAMESPACE | 3 - R.utils-2.12.0/R.utils/NEWS.md |only R.utils-2.12.0/R.utils/R/006.fixVarArgs.R | 6 -- R.utils-2.12.0/R.utils/R/999.NonDocumentedObjects.R | 2 R.utils-2.12.0/R.utils/R/Assert.R | 5 - R.utils-2.12.0/R.utils/R/SmartComments.R | 10 +-- R.utils-2.12.0/R.utils/R/VComments.R | 42 +++++++------- R.utils-2.12.0/R.utils/R/queryRCmdCheck.R | 54 +++++++++++-------- R.utils-2.12.0/R.utils/R/tempvar.R | 35 +++++++++--- R.utils-2.12.0/R.utils/R/withCapture.R | 7 -- R.utils-2.12.0/R.utils/man/Assert.Rd | 1 R.utils-2.12.0/R.utils/man/Non-documented_objects.Rd | 2 R.utils-2.12.0/R.utils/man/R.utils-package.Rd | 1 R.utils-2.12.0/R.utils/man/SmartComments.Rd | 10 +-- R.utils-2.12.0/R.utils/man/VComments.Rd | 42 +++++++------- R.utils-2.12.0/R.utils/man/countLines.Rd | 2 R.utils-2.12.0/R.utils/man/displayCode.Rd | 4 - R.utils-2.12.0/R.utils/man/inheritsFrom.Assert.Rd | 4 - R.utils-2.12.0/R.utils/man/tempvar.Rd | 12 +++- R.utils-2.12.0/R.utils/man/withCapture.Rd | 4 - R.utils-2.12.0/R.utils/man/withTimeout.Rd | 8 +- R.utils-2.12.0/R.utils/tests/displayCode.R | 4 - 25 files changed, 162 insertions(+), 153 deletions(-)
Title: Moran Eigenvector-Based Spatial Regression Models
Description: Functions for estimating spatial varying coefficient models, mixed models, and other spatial regression models for Gaussian and non-Gaussian data. Moran eigenvectors are used to an approximate Gaussian process modeling which is interpretable in terms of the Moran coefficient. The GP is used for modeling the spatial processes in residuals and regression coefficients. For details see Murakami (2021) <arXiv:1703.04467>.
Author: Daisuke Murakami <dmuraka@ism.ac.jp>
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.2.2.3 dated 2022-04-28 and 0.2.2.4 dated 2022-06-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/resf_vc.R | 37 +++++++++++++++++++++---------------- man/besf_vc.Rd | 22 ++++------------------ man/resf_vc.Rd | 8 ++++---- 5 files changed, 37 insertions(+), 46 deletions(-)
Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.2.0.0 dated 2022-04-28 and 4.2.1.0 dated 2022-06-27
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 5 README.md | 158 +++---------------------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary 8 files changed, 35 insertions(+), 148 deletions(-)
Title: The Corset Plot
Description: Corset plots are a visualization technique used strictly to visualize repeat measures
at 2 time points (such as pre- and post- data). The distribution of measurements are visualized at
each time point, whilst the trajectories of individual change are visualized by connecting the pre-
and post- values linearly. These lines can be coloured to represent the magnitude of change, or
other user-defined value. This method of visualization is ideal for showing the heterogeneity of
data, including differences by sub-groups. The package relies on 'ggplot2' allowing for easy
integration so that users can customize their visualizations as required. Users can create corset
plots using data in either wide or long format using the functions gg_corset() or gg_corset_elongated(), respectively.
Author: Kyla Belisario
Maintainer: Kyla Belisario <kyla_belisario@protonmail.com>
Diff between ggcorset versions 0.2.0 dated 2022-05-29 and 0.3.0 dated 2022-06-27
ggcorset-0.2.0/ggcorset/man/ggcorset_theme.Rd |only ggcorset-0.2.0/ggcorset/vignettes/img |only ggcorset-0.3.0/ggcorset/DESCRIPTION | 8 ggcorset-0.3.0/ggcorset/LICENSE | 2 ggcorset-0.3.0/ggcorset/MD5 | 31 +- ggcorset-0.3.0/ggcorset/NAMESPACE | 1 ggcorset-0.3.0/ggcorset/R/gg_corset.R | 178 ++++++++++--- ggcorset-0.3.0/ggcorset/R/gg_corset_elongated.R | 207 +++++++++++----- ggcorset-0.3.0/ggcorset/R/utils.R | 4 ggcorset-0.3.0/ggcorset/build/vignette.rds |binary ggcorset-0.3.0/ggcorset/inst/doc/corset_plot_intro.R | 83 ++++++ ggcorset-0.3.0/ggcorset/inst/doc/corset_plot_intro.Rmd | 108 ++++++-- ggcorset-0.3.0/ggcorset/inst/doc/corset_plot_intro.html | 56 ++-- ggcorset-0.3.0/ggcorset/man/gg_corset.Rd | 9 ggcorset-0.3.0/ggcorset/man/gg_corset_elongated.Rd | 10 ggcorset-0.3.0/ggcorset/man/theme_ggcorset.Rd |only ggcorset-0.3.0/ggcorset/vignettes/corset_plot_intro.Rmd | 108 ++++++-- 17 files changed, 620 insertions(+), 185 deletions(-)
Title: Differential Pattern Analysis via Linear Modeling
Description: Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA' package). Using the framework of linear model-based differential expression comparisons ('limma' package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.
Author: Ryan C. Sartor <sartorry@gmail.com>, Kathleen Greenham <greenham@umn.edu>
Maintainer: Ryan C. Sartor <sartorry@gmail.com>
Diff between DiPALM versions 1.1 dated 2020-11-04 and 1.2 dated 2022-06-27
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- man/AdjustPvalue.Rd | 6 ++---- man/BlankPlot.Rd | 8 +++----- man/BuildLimmaLM.Rd | 6 ++---- man/BuildModMembership.Rd | 6 ++---- man/DiPALM-package.Rd | 6 ++---- man/PlotTCs.Rd | 6 ++---- man/PlotTCsRibbon.Rd | 6 ++---- man/exampleData.Rd | 6 ++---- man/ggPlotMultiDensities.Rd | 6 ++---- man/testData.Rd | 6 ++---- 12 files changed, 36 insertions(+), 56 deletions(-)
More information about RcppCensSpatial at CRAN
Permanent link
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
RStudio [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between pkgload versions 1.2.4 dated 2021-11-30 and 1.3.0 dated 2022-06-27
pkgload-1.2.4/pkgload/R/aaa.r |only pkgload-1.2.4/pkgload/R/dev-example.r |only pkgload-1.2.4/pkgload/R/dev-help.r |only pkgload-1.2.4/pkgload/R/dev-meta.r |only pkgload-1.2.4/pkgload/R/dev-topic.r |only pkgload-1.2.4/pkgload/R/file-cache.r |only pkgload-1.2.4/pkgload/R/imports-env.r |only pkgload-1.2.4/pkgload/R/inst.r |only pkgload-1.2.4/pkgload/R/load-code.r |only pkgload-1.2.4/pkgload/R/load-data.r |only pkgload-1.2.4/pkgload/R/load-depends.r |only pkgload-1.2.4/pkgload/R/load-dll.r |only pkgload-1.2.4/pkgload/R/load.r |only pkgload-1.2.4/pkgload/R/namespace-env.r |only pkgload-1.2.4/pkgload/R/package-deps.r |only pkgload-1.2.4/pkgload/R/package-env.r |only pkgload-1.2.4/pkgload/R/package.r |only pkgload-1.2.4/pkgload/R/remove-s4-class.r |only pkgload-1.2.4/pkgload/R/run-loadhooks.r |only pkgload-1.2.4/pkgload/R/shims.r |only pkgload-1.2.4/pkgload/R/source.r |only pkgload-1.2.4/pkgload/R/unload.r |only pkgload-1.2.4/pkgload/R/zzz.r |only pkgload-1.2.4/pkgload/tests/testthat/test-data.r |only pkgload-1.2.4/pkgload/tests/testthat/test-depend.r |only pkgload-1.2.4/pkgload/tests/testthat/test-description.r |only pkgload-1.2.4/pkgload/tests/testthat/test-dll.r |only pkgload-1.2.4/pkgload/tests/testthat/test-help.r |only pkgload-1.2.4/pkgload/tests/testthat/test-imports.r |only pkgload-1.2.4/pkgload/tests/testthat/test-load-collate.r |only pkgload-1.2.4/pkgload/tests/testthat/test-load-hooks.r |only pkgload-1.2.4/pkgload/tests/testthat/test-load.r |only pkgload-1.2.4/pkgload/tests/testthat/test-metadata.r |only pkgload-1.2.4/pkgload/tests/testthat/test-namespace.r |only pkgload-1.2.4/pkgload/tests/testthat/test-s4-export.r |only pkgload-1.2.4/pkgload/tests/testthat/test-s4-sort.r |only pkgload-1.2.4/pkgload/tests/testthat/test-s4-unload.r |only pkgload-1.2.4/pkgload/tests/testthat/test-shim.r |only pkgload-1.3.0/pkgload/DESCRIPTION | 24 - 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Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
Huijuan Xu [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Teun Post [ctb],
Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 2.0.6 dated 2022-05-24 and 2.0.7 dated 2022-06-27
DESCRIPTION | 17 - MD5 | 88 +++--- NAMESPACE | 3 NEWS.md | 15 + R/hardReexports.R | 310 +++++++++++------------ R/reexports.R | 8 R/utils.R | 19 + README.md | 205 +++++++++++---- inst/CITATION |only inst/doc/running_nlmixr.R | 18 - inst/doc/running_nlmixr.Rmd | 28 -- inst/doc/running_nlmixr.html | 403 ++++++++++++------------------ man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-10.png |binary man/figures/README-unnamed-chunk-2-11.png |binary man/figures/README-unnamed-chunk-2-12.png |binary man/figures/README-unnamed-chunk-2-13.png |binary man/figures/README-unnamed-chunk-2-14.png |binary man/figures/README-unnamed-chunk-2-15.png |binary man/figures/README-unnamed-chunk-2-16.png |binary man/figures/README-unnamed-chunk-2-17.png |binary man/figures/README-unnamed-chunk-2-18.png |binary man/figures/README-unnamed-chunk-2-19.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-2-20.png |binary man/figures/README-unnamed-chunk-2-21.png |binary man/figures/README-unnamed-chunk-2-22.png |binary man/figures/README-unnamed-chunk-2-23.png |binary man/figures/README-unnamed-chunk-2-24.png |binary man/figures/README-unnamed-chunk-2-25.png |binary man/figures/README-unnamed-chunk-2-26.png |binary man/figures/README-unnamed-chunk-2-27.png |binary man/figures/README-unnamed-chunk-2-28.png |binary man/figures/README-unnamed-chunk-2-3.png |binary man/figures/README-unnamed-chunk-2-4.png |binary man/figures/README-unnamed-chunk-2-5.png |binary man/figures/README-unnamed-chunk-2-6.png |binary man/figures/README-unnamed-chunk-2-7.png |binary man/figures/README-unnamed-chunk-2-8.png |binary man/figures/README-unnamed-chunk-2-9.png |binary man/nlmixr2.Rd |only man/reexports.Rd | 6 man/tableControl.Rd | 2 man/vpcSim.Rd | 13 tests/testthat/test-basic-nlmixr2.R | 4 vignettes/running_nlmixr.Rmd | 28 -- 46 files changed, 597 insertions(+), 570 deletions(-)
Title: Nonparametric Methods for Directional Data
Description: Nonparametric kernel density estimation, bandwidth selection,
and other utilities for analyzing directional data. Implements the estimator
in Bai, Rao and Zhao (1987) <doi:10.1016/0047-259X(88)90113-3>, the
cross-validation bandwidth selectors in Hall, Watson and Cabrera (1987)
<doi:10.1093/biomet/74.4.751> and the plug-in bandwidth selectors in
García-Portugués (2013) <doi:10.1214/13-ejs821>.
Author: Eduardo Garcia-Portugues [aut, cre]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between DirStats versions 0.1.7 dated 2021-01-10 and 0.1.8 dated 2022-06-27
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/bw-cv.R | 3 +-- R/bw-pi.R | 29 ++++++++++++++++++----------- R/kde.R | 5 ++--- R/vmf.R | 1 - build/partial.rdb |binary man/bw_dir_cv.Rd | 2 +- man/bw_dir_pi.Rd | 2 +- 10 files changed, 41 insertions(+), 33 deletions(-)
Title: Distance Covariance and Correlation for Time Series Analysis
Description: Computing and plotting the distance covariance and correlation function of a univariate or a multivariate time series. Both versions of biased and unbiased estimators of distance covariance and correlation are provided. Test statistics for testing pairwise independence are also implemented. Some data sets are also included. References include:
a) Edelmann Dominic, Fokianos Konstantinos and Pitsillou Maria (2019). An Updated Literature Review of Distance Correlation and Its Applications to Time Series. International Statistical Review, 87(2): 237--262. <doi:10.1111/insr.12294>.
b) Fokianos Konstantinos and Pitsillou Maria (2018). Testing independence for multivariate time series via the auto-distance correlation matrix. Biometrika, 105(2): 337--352. <doi:10.1093/biomet/asx082>.
c) Fokianos Konstantinos and Pitsillou Maria (2017). Consistent testing for pairwise dependence in time series. Technometrics, 59(2): 262--270. <doi:10.1080/00401706.2016.1156024>.
d) Pitsillou Maria and Fokianos Konstantinos (2016). dCovTS: Distance Covariance/Correlation for Time Series. R Journal, 8(2):324-340. <doi:10.32614/RJ-2016-049>.
Author: Michail Tsagris [aut, cre],
Maria Pitsillou [aut, cph],
Konstantinos Fokianos [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between dCovTS versions 1.2 dated 2021-05-12 and 1.3 dated 2022-06-27
DESCRIPTION | 8 ++-- MD5 | 52 ++++++++++++++++---------------- NAMESPACE | 3 - R/OrdinaryBoot.R | 8 ++-- R/OrdinaryBoot1.R | 4 +- R/OrdinaryBoot2.R | 4 +- R/OrdinaryBootCV.R | 8 ++-- R/RbootCV.R | 1 R/SubsCV.R | 11 +++--- R/TstarBoot.R | 3 - R/TstarBoot2.R | 4 +- R/mADCFplot.R | 2 - R/mOrdinaryBootCV.R | 4 +- R/mRbootCV.R | 8 ++-- man/ADCF.Rd | 9 ++--- man/ADCFplot.Rd | 20 ++++++++---- man/ADCV.Rd | 79 ++++++++++++++++++++++++++++-------------------- man/MortTempPart.Rd | 19 ++++++----- man/UnivTest.Rd | 76 +++++++++++++++++++++++++++++----------------- man/dCovTS-package.Rd | 73 ++++++++++++++++++++++++++++----------------- man/ibmSp500.Rd | 36 ++++++++++++---------- man/kernelFun.Rd | 36 ++++++++++++---------- man/mADCF.Rd | 45 ++++++++++++++++----------- man/mADCFplot.Rd | 81 +++++++++++++++++++++++++++++++------------------- man/mADCFtest.Rd | 24 +++++++------- man/mADCV.Rd | 57 ++++++++++++++++++++--------------- man/mADCVtest.Rd | 30 +++++++++--------- 27 files changed, 407 insertions(+), 298 deletions(-)
Title: Make, Update, and Query Binary Causal Models
Description: Users can declare binary causal models, update beliefs about causal types given data and calculate arbitrary estimands. Model definition makes use of 'dagitty' functionality. Updating is implemented in 'stan'. The approach used in 'CausalQueries' is a generalization of the 'biqq' models described in "Mixing Methods: A Bayesian Approach" (Humphreys and Jacobs, 2015, <DOI:10.1017/S0003055415000453>). The conceptual extension makes use of work on probabilistic causal models described in Pearl's Causality (Pearl, 2009, <DOI:10.1017/CBO9780511803161>).
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut],
Till Tietz [aut, cre],
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut],
Julio Solis [ctb],
Georgiy Syunyaev [ctb]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between CausalQueries versions 0.0.3 dated 2020-06-03 and 0.1.0 dated 2022-06-27
CausalQueries-0.0.3/CausalQueries/R/make_confounds_df.R |only CausalQueries-0.0.3/CausalQueries/R/reveal_outcomes.R |only CausalQueries-0.0.3/CausalQueries/man/continue_names.Rd |only CausalQueries-0.0.3/CausalQueries/man/get_parameters.Rd |only CausalQueries-0.0.3/CausalQueries/man/get_priors.Rd |only CausalQueries-0.0.3/CausalQueries/man/make_confounds_df.Rd |only CausalQueries-0.0.3/CausalQueries/man/make_par_values_multiple.Rd |only CausalQueries-0.0.3/CausalQueries/man/make_parameters.Rd |only CausalQueries-0.0.3/CausalQueries/man/make_priors.Rd |only CausalQueries-0.0.3/CausalQueries/man/make_values_task_list.Rd |only CausalQueries-0.0.3/CausalQueries/man/set_confounds.Rd |only CausalQueries-0.0.3/CausalQueries/man/set_confounds_df.Rd |only CausalQueries-0.0.3/CausalQueries/man/set_parameters.Rd |only CausalQueries-0.0.3/CausalQueries/man/set_priors.Rd |only CausalQueries-0.0.3/CausalQueries/man/translate_dagitty.Rd |only CausalQueries-0.0.3/CausalQueries/tests/testthat/test_daggity.R |only CausalQueries-0.1.0/CausalQueries/DESCRIPTION | 22 CausalQueries-0.1.0/CausalQueries/LICENSE | 4 CausalQueries-0.1.0/CausalQueries/MD5 | 337 ++--- CausalQueries-0.1.0/CausalQueries/NAMESPACE | 190 +-- CausalQueries-0.1.0/CausalQueries/NEWS.md |only CausalQueries-0.1.0/CausalQueries/R/CausalQueries-package.R | 6 CausalQueries-0.1.0/CausalQueries/R/clean_params.R | 2 CausalQueries-0.1.0/CausalQueries/R/data_helpers.R | 21 CausalQueries-0.1.0/CausalQueries/R/draw_causal_type.R |only CausalQueries-0.1.0/CausalQueries/R/get_ambiguities_matrix.R | 6 CausalQueries-0.1.0/CausalQueries/R/get_event_prob.R | 86 + CausalQueries-0.1.0/CausalQueries/R/get_type_prob.R | 12 CausalQueries-0.1.0/CausalQueries/R/helpers.R | 53 CausalQueries-0.1.0/CausalQueries/R/internal_inherit_params.R | 2 CausalQueries-0.1.0/CausalQueries/R/make_data.R | 172 +- CausalQueries-0.1.0/CausalQueries/R/make_models.R | 23 CausalQueries-0.1.0/CausalQueries/R/make_par_values.R | 626 ++++----- CausalQueries-0.1.0/CausalQueries/R/map_query_to_causal_type.R | 6 CausalQueries-0.1.0/CausalQueries/R/parmap.R |only CausalQueries-0.1.0/CausalQueries/R/plot_dag.R | 129 +- CausalQueries-0.1.0/CausalQueries/R/prep_stan_data.R | 74 - CausalQueries-0.1.0/CausalQueries/R/query_model.R | 270 ++-- CausalQueries-0.1.0/CausalQueries/R/realise_outcomes.R |only CausalQueries-0.1.0/CausalQueries/R/set_confounds.R | 309 +--- CausalQueries-0.1.0/CausalQueries/R/set_parameter_matrix.R | 4 CausalQueries-0.1.0/CausalQueries/R/set_parameters.R | 245 ++- CausalQueries-0.1.0/CausalQueries/R/set_prior_distribution.R | 2 CausalQueries-0.1.0/CausalQueries/R/set_priors.R | 323 ++--- CausalQueries-0.1.0/CausalQueries/R/set_restrictions.R | 253 +++- CausalQueries-0.1.0/CausalQueries/R/simulate_events.R | 5 CausalQueries-0.1.0/CausalQueries/R/stanmodels.R | 2 CausalQueries-0.1.0/CausalQueries/R/update_model.R | 73 - CausalQueries-0.1.0/CausalQueries/README.md | 202 +-- CausalQueries-0.1.0/CausalQueries/configure.win | 8 CausalQueries-0.1.0/CausalQueries/inst/stan/CONTRIBUTING.md | 60 CausalQueries-0.1.0/CausalQueries/inst/stan/simplexes.stan | 82 + CausalQueries-0.1.0/CausalQueries/man/CausalQueries-package.Rd | 22 CausalQueries-0.1.0/CausalQueries/man/CausalQueries_internal_inherit_params.Rd | 106 - CausalQueries-0.1.0/CausalQueries/man/add_dots.Rd | 54 CausalQueries-0.1.0/CausalQueries/man/add_wildcard.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/all_data_types.Rd | 78 - CausalQueries-0.1.0/CausalQueries/man/causal_type_names.Rd | 52 CausalQueries-0.1.0/CausalQueries/man/check_string_input.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/clean_condition.Rd | 36 CausalQueries-0.1.0/CausalQueries/man/clean_param_vector.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/clean_params.Rd | 54 CausalQueries-0.1.0/CausalQueries/man/collapse_data.Rd | 129 +- CausalQueries-0.1.0/CausalQueries/man/collapse_nodal_types.Rd | 52 CausalQueries-0.1.0/CausalQueries/man/complements.Rd | 74 - CausalQueries-0.1.0/CausalQueries/man/data_to_data.Rd |only CausalQueries-0.1.0/CausalQueries/man/data_type_names.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/decreasing.Rd | 70 - CausalQueries-0.1.0/CausalQueries/man/default_stan_control.Rd | 46 CausalQueries-0.1.0/CausalQueries/man/democracy_data.Rd | 54 CausalQueries-0.1.0/CausalQueries/man/draw_causal_type.Rd |only CausalQueries-0.1.0/CausalQueries/man/drop_empty_families.Rd | 50 CausalQueries-0.1.0/CausalQueries/man/expand_data.Rd | 58 CausalQueries-0.1.0/CausalQueries/man/expand_nodal_expression.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/expand_wildcard.Rd | 72 - CausalQueries-0.1.0/CausalQueries/man/get_ambiguities_matrix.Rd | 46 CausalQueries-0.1.0/CausalQueries/man/get_causal_types.Rd | 42 CausalQueries-0.1.0/CausalQueries/man/get_data_families.Rd | 74 - CausalQueries-0.1.0/CausalQueries/man/get_event_prob.Rd | 67 - CausalQueries-0.1.0/CausalQueries/man/get_nodal_types.Rd | 62 CausalQueries-0.1.0/CausalQueries/man/get_param_dist.Rd | 50 CausalQueries-0.1.0/CausalQueries/man/get_parameter_matrix.Rd | 42 CausalQueries-0.1.0/CausalQueries/man/get_parameter_names.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/get_parents.Rd | 42 CausalQueries-0.1.0/CausalQueries/man/get_parmap.Rd |only CausalQueries-0.1.0/CausalQueries/man/get_prior_distribution.Rd | 60 CausalQueries-0.1.0/CausalQueries/man/get_query_types.Rd | 152 +- CausalQueries-0.1.0/CausalQueries/man/get_type_names.Rd | 44 CausalQueries-0.1.0/CausalQueries/man/get_type_prob.Rd | 58 CausalQueries-0.1.0/CausalQueries/man/get_type_prob_multiple.Rd | 75 - CausalQueries-0.1.0/CausalQueries/man/gsub_many.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/includes_var.Rd | 46 CausalQueries-0.1.0/CausalQueries/man/increasing.Rd | 70 - CausalQueries-0.1.0/CausalQueries/man/interacts.Rd | 78 - CausalQueries-0.1.0/CausalQueries/man/interpret_type.Rd | 66 - CausalQueries-0.1.0/CausalQueries/man/is_a_model.Rd |only CausalQueries-0.1.0/CausalQueries/man/is_improper.Rd |only CausalQueries-0.1.0/CausalQueries/man/list_non_parents.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/make_ambiguities_matrix.Rd | 46 CausalQueries-0.1.0/CausalQueries/man/make_data.Rd | 189 +-- CausalQueries-0.1.0/CausalQueries/man/make_data_single.Rd | 108 - CausalQueries-0.1.0/CausalQueries/man/make_events.Rd | 106 - CausalQueries-0.1.0/CausalQueries/man/make_model.Rd | 130 +- CausalQueries-0.1.0/CausalQueries/man/make_nodal_types.Rd | 52 CausalQueries-0.1.0/CausalQueries/man/make_par_values.Rd | 219 +-- CausalQueries-0.1.0/CausalQueries/man/make_parameter_matrix.Rd | 42 CausalQueries-0.1.0/CausalQueries/man/make_parmap.Rd |only CausalQueries-0.1.0/CausalQueries/man/make_prior_distribution.Rd | 58 CausalQueries-0.1.0/CausalQueries/man/minimal_data.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/minimal_event_data.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/n_check.Rd | 42 CausalQueries-0.1.0/CausalQueries/man/nodes_in_statement.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/non_decreasing.Rd | 70 - CausalQueries-0.1.0/CausalQueries/man/non_increasing.Rd | 70 - CausalQueries-0.1.0/CausalQueries/man/observe_data.Rd | 90 - CausalQueries-0.1.0/CausalQueries/man/parameter_setting.Rd |only CausalQueries-0.1.0/CausalQueries/man/perm.Rd | 46 CausalQueries-0.1.0/CausalQueries/man/plot_dag.Rd | 83 - CausalQueries-0.1.0/CausalQueries/man/prep_stan_data.Rd | 64 - CausalQueries-0.1.0/CausalQueries/man/prior_setting.Rd |only CausalQueries-0.1.0/CausalQueries/man/query_distribution.Rd | 128 +- CausalQueries-0.1.0/CausalQueries/man/query_model.Rd | 157 +- CausalQueries-0.1.0/CausalQueries/man/query_to_expression.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/realise_outcomes.Rd |only CausalQueries-0.1.0/CausalQueries/man/restrict_by_labels.Rd | 65 - CausalQueries-0.1.0/CausalQueries/man/restrict_by_query.Rd | 69 - CausalQueries-0.1.0/CausalQueries/man/reveal_outcomes.Rd | 51 CausalQueries-0.1.0/CausalQueries/man/set_ambiguities_matrix.Rd | 48 CausalQueries-0.1.0/CausalQueries/man/set_confound.Rd | 188 +- CausalQueries-0.1.0/CausalQueries/man/set_parameter_matrix.Rd | 52 CausalQueries-0.1.0/CausalQueries/man/set_parmap.Rd |only CausalQueries-0.1.0/CausalQueries/man/set_prior_distribution.Rd | 60 CausalQueries-0.1.0/CausalQueries/man/set_restrictions.Rd | 275 ++-- CausalQueries-0.1.0/CausalQueries/man/set_sampling_args.Rd | 58 CausalQueries-0.1.0/CausalQueries/man/simulate_data.Rd | 40 CausalQueries-0.1.0/CausalQueries/man/st_within.Rd | 76 - 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CausalQueries-0.1.0/CausalQueries/tests/testthat/test_set_restrictions.R | 67 - CausalQueries-0.1.0/CausalQueries/tests/testthat/test_simulate_data.R | 33 CausalQueries-0.1.0/CausalQueries/tests/testthat/test_type_helpers.R | 4 CausalQueries-0.1.0/CausalQueries/tests/testthat/test_update_model.R | 59 CausalQueries-0.1.0/CausalQueries/tests/testthat/testthat-problems.rds |only 186 files changed, 6017 insertions(+), 4887 deletions(-)
Title: Datasets for Categorical Data Analysis by Agresti
Description: Datasets used in the book "Categorical Data Analysis"
by Agresti (2012, ISBN:978-0-470-46363-5) but not printed in the book.
Datasets and help pages were automatically produced from the source
<https://users.stat.ufl.edu/~aa/cda/data.html> by the R script foo.R,
which can be found in the GitHub repository.
Author: Alan Agesti <aa@stat.ufl.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between CatDataAnalysis versions 0.1-3 dated 2020-11-18 and 0.1-5 dated 2022-06-27
DESCRIPTION | 14 +++++----- MD5 | 64 +++++++++++++++++++++++++------------------------- man/exercise_13.17.Rd | 4 +-- man/exercise_14.15.Rd | 4 +-- man/exercise_4.13.Rd | 4 +-- man/exercise_5.22.Rd | 4 +-- man/exercise_5.3.Rd | 4 +-- man/exercise_6.20.Rd | 4 +-- man/exercise_6.28.Rd | 4 +-- man/exercise_6.3.Rd | 4 +-- man/exercise_6.7.Rd | 4 +-- man/exercise_8.18.Rd | 4 +-- man/exercise_8.28.Rd | 4 +-- man/exercise_9.5.Rd | 4 +-- man/section_13.4.4.Rd | 4 +-- man/table_10.1.Rd | 4 +-- man/table_10.3.Rd | 4 +-- man/table_11.5.Rd | 4 +-- man/table_12.1.Rd | 4 +-- man/table_12.3.Rd | 4 +-- man/table_13.2.Rd | 4 +-- man/table_13.3.Rd | 4 +-- man/table_13.8.Rd | 4 +-- man/table_15.5.Rd | 4 +-- man/table_15.6.Rd | 4 +-- man/table_4.3.Rd | 4 +-- man/table_4.7.Rd | 4 +-- man/table_6.15.Rd | 4 +-- man/table_6.9.Rd | 4 +-- man/table_7.2.Rd | 4 +-- man/table_8.1.Rd | 4 +-- man/table_8.5.Rd | 4 +-- man/table_9.3.Rd | 4 +-- 33 files changed, 101 insertions(+), 101 deletions(-)
More information about CatDataAnalysis at CRAN
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Title: Statistical Tools for Quantitative Genetic Analyses
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.
Author: Peter Soerensen [aut, cre],
Palle Duun Rohde [aut],
Izel Fourie Soerensen [aut]
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Diff between qgg versions 1.0.4 dated 2020-06-29 and 1.1.0 dated 2022-06-27
qgg-1.0.4/qgg/R/compute_genotype_matrix.R |only qgg-1.0.4/qgg/R/multiple_marker_set_test.R |only qgg-1.0.4/qgg/inst/extdata/sample_21.bed |only qgg-1.0.4/qgg/inst/extdata/sample_21.bim |only qgg-1.0.4/qgg/inst/extdata/sample_21.fam |only qgg-1.0.4/qgg/inst/extdata/sample_22.bed |only qgg-1.0.4/qgg/inst/extdata/sample_22.bim |only qgg-1.0.4/qgg/inst/extdata/sample_22.fam |only qgg-1.0.4/qgg/man/getW.Rd |only qgg-1.0.4/qgg/man/lma.Rd |only qgg-1.0.4/qgg/src/bedfuncs.f90 |only qgg-1.1.0/qgg/DESCRIPTION | 15 qgg-1.1.0/qgg/MD5 | 108 - qgg-1.1.0/qgg/NAMESPACE | 35 qgg-1.1.0/qgg/NEWS.md | 2 qgg-1.1.0/qgg/R/RcppExports.R |only qgg-1.1.0/qgg/R/compute_grm.R | 96 + qgg-1.1.0/qgg/R/genomic_bayes.R | 1929 +++++++++++++++++++------- qgg-1.1.0/qgg/R/genomic_correlation.R |only qgg-1.1.0/qgg/R/genomic_matrix.R |only qgg-1.1.0/qgg/R/genomic_reml.R | 244 ++- qgg-1.1.0/qgg/R/genomic_score.R |only qgg-1.1.0/qgg/R/genomic_simulation.R |only qgg-1.1.0/qgg/R/genomic_solve.R | 458 +----- qgg-1.1.0/qgg/R/genomic_statistics.R |only qgg-1.1.0/qgg/R/multiple_marker_test.R |only qgg-1.1.0/qgg/R/qgg.R | 6 qgg-1.1.0/qgg/R/qgg_utility_functions.R | 268 ++- qgg-1.1.0/qgg/R/single_marker_test.R | 242 ++- qgg-1.1.0/qgg/inst/extdata/sample_chr1.bed |only qgg-1.1.0/qgg/inst/extdata/sample_chr1.bim |only qgg-1.1.0/qgg/inst/extdata/sample_chr1.fam |only qgg-1.1.0/qgg/inst/extdata/sample_chr2.bed |only qgg-1.1.0/qgg/inst/extdata/sample_chr2.bim |only qgg-1.1.0/qgg/inst/extdata/sample_chr2.fam |only qgg-1.1.0/qgg/man/acc.Rd |only qgg-1.1.0/qgg/man/adjLD.Rd | 18 qgg-1.1.0/qgg/man/adjLDStat.Rd |only qgg-1.1.0/qgg/man/adjStat.Rd |only qgg-1.1.0/qgg/man/auc.Rd |only qgg-1.1.0/qgg/man/computeROC.Rd |only qgg-1.1.0/qgg/man/gbayes.Rd | 206 ++ qgg-1.1.0/qgg/man/gblup.Rd | 1 qgg-1.1.0/qgg/man/getG.Rd |only qgg-1.1.0/qgg/man/getGRM.Rd | 1 qgg-1.1.0/qgg/man/getLD.Rd |only qgg-1.1.0/qgg/man/getLDsets.Rd |only qgg-1.1.0/qgg/man/getMarkers.Rd |only qgg-1.1.0/qgg/man/gfilter.Rd |only qgg-1.1.0/qgg/man/glma.Rd |only qgg-1.1.0/qgg/man/gprep.Rd | 47 qgg-1.1.0/qgg/man/greml.Rd | 51 qgg-1.1.0/qgg/man/grm.Rd | 10 qgg-1.1.0/qgg/man/gscore.Rd | 57 qgg-1.1.0/qgg/man/gsea.Rd | 14 qgg-1.1.0/qgg/man/gsim.Rd |only qgg-1.1.0/qgg/man/gsolve.Rd | 20 qgg-1.1.0/qgg/man/hwe.Rd |only qgg-1.1.0/qgg/man/ldsc.Rd |only qgg-1.1.0/qgg/man/mapStat.Rd |only qgg-1.1.0/qgg/man/mergeGRM.Rd | 1 qgg-1.1.0/qgg/man/mtadj.Rd |only qgg-1.1.0/qgg/man/plotBayes.Rd |only qgg-1.1.0/qgg/man/plotForest.Rd |only qgg-1.1.0/qgg/man/plotROC.Rd |only qgg-1.1.0/qgg/man/predict_auc_mt_cc.Rd |only qgg-1.1.0/qgg/man/predict_auc_mt_continous.Rd |only qgg-1.1.0/qgg/man/predict_auc_st.Rd |only qgg-1.1.0/qgg/man/predict_r2_mt.Rd |only qgg-1.1.0/qgg/man/predict_r2_st.Rd |only qgg-1.1.0/qgg/man/qcStat.Rd |only qgg-1.1.0/qgg/man/rnag.Rd |only qgg-1.1.0/qgg/src/Makevars | 6 qgg-1.1.0/qgg/src/Makevars.win | 9 qgg-1.1.0/qgg/src/RcppExports.cpp |only qgg-1.1.0/qgg/src/bedfunc.cpp |only qgg-1.1.0/qgg/src/bigreml.f90 | 325 ++++ qgg-1.1.0/qgg/src/gbayes.cpp |only qgg-1.1.0/qgg/src/grsbed.cpp |only qgg-1.1.0/qgg/src/mtgbayes.cpp |only qgg-1.1.0/qgg/src/qgg_init.c | 76 - qgg-1.1.0/qgg/src/solvebed.cpp |only qgg-1.1.0/qgg/src/sparseld.cpp |only qgg-1.1.0/qgg/src/utility.cpp |only 84 files changed, 2967 insertions(+), 1278 deletions(-)
Title: Sum of Single Effects Linear Regression
Description: Implements methods for variable selection in linear
regression based on the "Sum of Single Effects" (SuSiE) model, as
described in Wang et al (2020) <DOI:10.1101/501114> and Zou et al
(2021) <DOI:10.1101/2021.11.03.467167>. These methods provide
simple summaries, called "Credible Sets", for accurately
quantifying uncertainty in which variables should be selected.
The methods are motivated by genetic fine-mapping applications,
and are particularly well-suited to settings where variables are
highly correlated and detectable effects are sparse. The fitting
algorithm, a Bayesian analogue of stepwise selection methods
called "Iterative Bayesian Stepwise Selection" (IBSS), is simple
and fast, allowing the SuSiE model be fit to large data sets
(thousands of samples and hundreds of thousands of variables).
Author: Gao Wang [aut],
Yuxin Zou [aut],
Kaiqian Zhang [aut],
Peter Carbonetto [aut, cre],
Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between susieR versions 0.12.12 dated 2022-06-24 and 0.12.16 dated 2022-06-27
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/doc/finemapping.html | 6 +++--- inst/doc/finemapping_summary_statistics.html | 6 +++--- inst/doc/l0_initialization.html | 4 ++-- inst/doc/mwe.html | 6 +++--- inst/doc/sparse_susie_eval.html | 4 ++-- inst/doc/susie_refine.html | 6 +++--- inst/doc/susie_rss.html | 4 ++-- inst/doc/susierss_diagnostic.html | 6 +++--- inst/doc/trend_filtering.html | 4 ++-- inst/doc/trendfiltering_derivations.pdf |binary tests/testthat/test_prior_weights.R | 2 +- 14 files changed, 41 insertions(+), 41 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.7.1 dated 2022-06-10 and 2.7.2 dated 2022-06-27
soilDB-2.7.1/soilDB/R/get_component_from_LIMS.R |only soilDB-2.7.2/soilDB/DESCRIPTION | 6 soilDB-2.7.2/soilDB/MD5 | 113 ++++------ soilDB-2.7.2/soilDB/NAMESPACE | 27 ++ soilDB-2.7.2/soilDB/NEWS.md | 5 soilDB-2.7.2/soilDB/R/ROSETTA.R | 19 - soilDB-2.7.2/soilDB/R/fetchLDM.R | 6 soilDB-2.7.2/soilDB/R/fetchNASIS.R | 14 - soilDB-2.7.2/soilDB/R/fetchNASISWebReport.R | 14 + soilDB-2.7.2/soilDB/R/fetchNASIS_components.R | 76 +++--- soilDB-2.7.2/soilDB/R/fetchPedonPC.R | 1 soilDB-2.7.2/soilDB/R/fetchSCAN.R | 50 ++-- soilDB-2.7.2/soilDB/R/fetchSDA_spatial.R | 67 +++-- soilDB-2.7.2/soilDB/R/filter_KSSL.R | 88 +++---- soilDB-2.7.2/soilDB/R/getHzErrorsNASIS.R | 4 soilDB-2.7.2/soilDB/R/getHzErrorsPedonPC.R | 4 soilDB-2.7.2/soilDB/R/get_NASIS_table_key_by_name.R | 3 soilDB-2.7.2/soilDB/R/get_NASIS_table_name_by_purpose.R | 4 soilDB-2.7.2/soilDB/R/get_OSD.R | 2 soilDB-2.7.2/soilDB/R/get_RMF_from_NASIS_db.R | 100 ++++---- soilDB-2.7.2/soilDB/R/get_SDA_coecoclass.R | 6 soilDB-2.7.2/soilDB/R/get_component_data_from_NASIS_db.R | 2 soilDB-2.7.2/soilDB/R/get_component_from_GDB.R | 11 soilDB-2.7.2/soilDB/R/get_component_from_SDA.R | 38 ++- soilDB-2.7.2/soilDB/R/get_concentrations_from_NASIS_db.R | 2 soilDB-2.7.2/soilDB/R/get_cosoilmoist_from_LIMS.R | 5 soilDB-2.7.2/soilDB/R/get_cosoilmoist_from_SDA.R | 3 soilDB-2.7.2/soilDB/R/get_phfmp_from_NASIS_db.R | 2 soilDB-2.7.2/soilDB/R/get_soilseries_from_NASIS.R | 7 soilDB-2.7.2/soilDB/R/taxaExtent.R | 2 soilDB-2.7.2/soilDB/build/partial.rdb |binary soilDB-2.7.2/soilDB/man/fetchGDB.Rd | 32 ++ soilDB-2.7.2/soilDB/man/fetchNASIS.Rd | 25 +- soilDB-2.7.2/soilDB/man/fetchNASISWebReport.Rd | 17 + soilDB-2.7.2/soilDB/man/fetchPedonPC.Rd | 6 soilDB-2.7.2/soilDB/man/fetchSCAN.Rd | 2 soilDB-2.7.2/soilDB/man/fetchSDA.Rd | 12 - soilDB-2.7.2/soilDB/man/fetchSDA_spatial.Rd | 23 +- soilDB-2.7.2/soilDB/man/filter_geochem.Rd | 68 +++--- soilDB-2.7.2/soilDB/man/getHzErrorsNASIS.Rd | 4 soilDB-2.7.2/soilDB/man/get_NASIS_table_key_by_name.Rd | 2 soilDB-2.7.2/soilDB/man/get_OSD.Rd | 2 soilDB-2.7.2/soilDB/man/get_soilseries_from_NASIS.Rd | 4 soilDB-2.7.2/soilDB/man/metadata.Rd | 52 ++-- soilDB-2.7.2/soilDB/man/taxaExtent.Rd | 1 soilDB-2.7.2/soilDB/tests/testthat/test-fetchHenry.R | 3 soilDB-2.7.2/soilDB/tests/testthat/test-fetchKSSL.R | 68 ++++-- soilDB-2.7.2/soilDB/tests/testthat/test-fetchLDM.R | 7 soilDB-2.7.2/soilDB/tests/testthat/test-fetchNASISWebReport.R | 14 - soilDB-2.7.2/soilDB/tests/testthat/test-fetchOSD.R | 18 + soilDB-2.7.2/soilDB/tests/testthat/test-fetchSCAN.R | 9 soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_coecoclass.R | 12 + soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_cosurfmorph.R | 4 soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_hydric.R | 20 + soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_interpretation.R | 5 soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_muaggatt.R | 8 soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_pmgroupname.R | 19 + soilDB-2.7.2/soilDB/tests/testthat/test-get_SDA_property.R | 112 ++++++--- 58 files changed, 781 insertions(+), 449 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup
identification and personalized medicine / precision medicine under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies and is described in detail in Huling and Yu (2021)
<doi:10.18637/jss.v098.i05>.
Author: Jared Huling [aut, cre] ,
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.2.6 dated 2021-05-28 and 0.2.7 dated 2022-06-27
DESCRIPTION | 12 MD5 | 89 NAMESPACE | 8 R/calculate_treatment_effects.R | 25 R/data_prep_utils_split.R |only R/est_subgroup_effects.R | 2 R/fit_losses.R | 413 ---- R/fit_subgroup.R | 69 R/multiple_treatment_utils.R | 110 + R/plot_compare.R | 22 R/plot_subgroup_fitted.R | 6 R/plot_subgroup_validated.R | 31 R/predict_subgroup.R | 8 R/validate_subgroup.R | 6 R/weighted_svm.R | 18 R/xgboost_functions.R |only README.md | 29 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 4 inst/doc/efficiency_augmentation_personalized.R | 28 inst/doc/efficiency_augmentation_personalized.Rmd | 41 inst/doc/efficiency_augmentation_personalized.html | 383 +++- inst/doc/fitting_itrs_with_xgboost.R |only inst/doc/fitting_itrs_with_xgboost.Rmd |only inst/doc/fitting_itrs_with_xgboost.html |only inst/doc/multicategory_treatments_with_personalized.R | 16 inst/doc/multicategory_treatments_with_personalized.Rmd | 20 inst/doc/multicategory_treatments_with_personalized.html | 441 +++- inst/doc/usage_of_the_personalized_package.R | 35 inst/doc/usage_of_the_personalized_package.Rmd | 51 inst/doc/usage_of_the_personalized_package.html | 1356 ++++++++++----- man/fit.subgroup.Rd | 32 man/plot.Rd | 4 man/plotCompare.Rd | 8 man/predict.Rd | 8 man/treatment.effects.Rd | 13 man/validate.subgroup.Rd | 6 man/weighted.ksvm.Rd | 7 tests/testthat/test-fitsubgroup.R | 365 ++-- tests/testthat/test-plotandplotcompare.R | 8 tests/testthat/test-treatmenteffects.R | 80 tests/testthat/test-validatesubgroup.R | 35 vignettes/efficiency_augmentation_personalized.Rmd | 41 vignettes/fitting_itrs_with_xgboost.Rmd |only vignettes/multicategory_treatments_with_personalized.Rmd | 20 vignettes/usage_of_the_personalized_package.Rmd | 51 vignettes/usage_overview-1.png |binary vignettes/vis_val-1.png |binary 49 files changed, 2388 insertions(+), 1513 deletions(-)
Title: R Interface to 'Mapbox' Web Services
Description: Includes support for 'Mapbox' Navigation APIs, including directions,
isochrones, and route optimization; the Search API for forward and reverse geocoding;
the Maps API for interacting with 'Mapbox' vector tilesets and visualizing
'Mapbox' maps in R; and the 'tippecanoe' tile-generation utility.
See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Author: Kyle Walker [aut, cre],
Eli Pousson [ctb],
Anthony North [ctb, cph],
Miles McBain [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapboxapi versions 0.3.3 dated 2022-04-12 and 0.4 dated 2022-06-27
mapboxapi-0.3.3/mapboxapi/man/list_styles.Rd |only mapboxapi-0.4/mapboxapi/DESCRIPTION | 22 mapboxapi-0.4/mapboxapi/MD5 | 60 - mapboxapi-0.4/mapboxapi/NAMESPACE | 4 mapboxapi-0.4/mapboxapi/NEWS.md |only mapboxapi-0.4/mapboxapi/R/accounts.R | 57 + mapboxapi-0.4/mapboxapi/R/helpers.R | 165 +++- mapboxapi-0.4/mapboxapi/R/mapboxapi-package.R | 2 mapboxapi-0.4/mapboxapi/R/maps.R | 680 +++++++++++++------- mapboxapi-0.4/mapboxapi/R/navigation.R | 99 +- mapboxapi-0.4/mapboxapi/R/route.R | 169 +++- mapboxapi-0.4/mapboxapi/R/search.R | 61 + mapboxapi-0.4/mapboxapi/R/styles.R | 29 mapboxapi-0.4/mapboxapi/R/sysdata.rda |only mapboxapi-0.4/mapboxapi/R/tippecanoe.R | 51 + mapboxapi-0.4/mapboxapi/man/addMapboxTiles.Rd | 25 mapboxapi-0.4/mapboxapi/man/get_static_tiles.Rd | 27 mapboxapi-0.4/mapboxapi/man/get_style.Rd | 17 mapboxapi-0.4/mapboxapi/man/get_vector_tiles.Rd | 18 mapboxapi-0.4/mapboxapi/man/layer_static_mapbox.Rd | 128 ++- mapboxapi-0.4/mapboxapi/man/mb_access_token.Rd | 31 mapboxapi-0.4/mapboxapi/man/mb_directions.Rd | 112 ++- mapboxapi-0.4/mapboxapi/man/mb_geocode.Rd | 43 - mapboxapi-0.4/mapboxapi/man/mb_isochrone.Rd | 34 - mapboxapi-0.4/mapboxapi/man/mb_matrix.Rd | 17 mapboxapi-0.4/mapboxapi/man/mb_optimized_route.Rd | 81 +- mapboxapi-0.4/mapboxapi/man/prep_overlay_markers.Rd |only mapboxapi-0.4/mapboxapi/man/query_tiles.Rd | 36 - mapboxapi-0.4/mapboxapi/man/static_mapbox.Rd | 134 +-- mapboxapi-0.4/mapboxapi/man/tippecanoe.Rd | 41 - mapboxapi-0.4/mapboxapi/man/upload_tiles.Rd | 9 mapboxapi-0.4/mapboxapi/tests |only 32 files changed, 1428 insertions(+), 724 deletions(-)
Title: Simulation of Bird Flight Range
Description: Functions for range estimation in birds based on Pennycuick (2008)
and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008)
requires manual entry of birds which can be tedious when there are hundreds
of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975)
and time-marching computation methods as in Pennycuick (1998) and Pennycuick (2008).
See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>,
and Pennycuick (2008, ISBN:9780080557816).
Author: Brian Masinde [aut, cre],
Krzysztof Bartoszek [ctb, ths]
Maintainer: Brian Masinde <masindeb@live.com>
Diff between FlyingR versions 0.2.0 dated 2020-11-06 and 0.2.2 dated 2022-06-27
DESCRIPTION | 10 +- MD5 | 24 ++--- NEWS.md | 13 --- R/birds_documentation.R | 2 R/migrate.R | 4 README.md | 10 -- build/vignette.rds |binary inst/doc/documentation.Rmd | 2 inst/doc/documentation.html | 185 +++++++++++++++++++++----------------------- man/birds.Rd | 2 man/migrate.Rd | 4 src/RcppExports.cpp | 5 + vignettes/documentation.Rmd | 2 13 files changed, 129 insertions(+), 134 deletions(-)
Title: Gaussian Process Based Design and Analysis for the Active
Subspace Method
Description: The active subspace method is a sensitivity analysis technique that finds important linear combinations of input variables for a simulator. This package provides functions allowing estimation of the active subspace without gradient information using Gaussian processes as well as sequential experimental design tools to minimize the amount of data required to do so. Implements Wycoff et al. (2019) <arXiv:1907.11572>.
Author: Nathan Wycoff, Mickael Binois
Maintainer: Nathan Wycoff <nathan.wycoff@georgetown.edu>
Diff between activegp versions 1.0.6 dated 2021-11-30 and 1.1.0 dated 2022-06-27
DESCRIPTION | 17 MD5 | 42 - NAMESPACE | 4 NEWS | 7 R/RcppExports.R | 191 ++++++- R/activeC.R | 272 +++++++--- R/deprecated.R |only R/fun_test.R |only R/hetGP_funcs.R | 1 man/C_GP.Rd | 34 + man/C_GP_cpp.Rd | 16 man/C_var2.Rd | 2 man/Lt_GP.Rd |only man/W_kappa_lk.Rd |only man/activegp.Rd | 1 man/as.matrix.const_C.Rd |only man/plot.const_C.Rd | 3 man/quick_C.Rd |only src/C_GPcpp.cpp | 79 +-- src/RcppExports.cpp | 291 +++++++++-- src/kernelexps.cpp | 940 ++++++++++++++++++++++++++++---------- tests/testthat/test_C_est.R | 11 tests/testthat/test_grad_expr.R | 601 ++++++++++++++---------- tests/testthat/test_hyper_UQ.R | 4 tests/testthat/test_kernel_expr.R | 12 25 files changed, 1800 insertions(+), 728 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.5-15 dated 2022-01-22 and 3.5-21 dated 2022-06-27
DESCRIPTION | 8 +-- MD5 | 77 ++++++++++++++++---------------- R/aggregate_3d.R | 2 R/bands.R | 3 - R/blockSize.R | 2 R/brick.R | 2 R/buffer.R | 2 R/calc.R | 4 - R/canProcessInMemory.R | 10 ++++ R/cellStats.R | 10 ++-- R/clearValues.R | 2 R/coerce.R | 101 ++++++++++++++++++++++++++----------------- R/dataProperties.R | 23 +++++---- R/fasterize.R | 2 R/frbind.R | 2 R/getData.R | 6 ++ R/hdrRaster.R | 23 +++++---- R/inifile.R | 12 ++++- R/interpolate.R | 2 R/makeRasterList.R | 4 - R/mosaic.R | 2 R/netCDFutil.R | 14 +++-- R/notused.R | 2 R/predict.R | 2 R/progressBar.R | 8 +-- R/rasterFromRasterFile.R | 14 +++++ R/rasterOptions.R | 25 ++++++++++ R/rasterizePoints.R | 2 R/rasterizePolygons.R | 4 - R/setExtent.R | 4 - R/stackApply.R | 2 R/summary.R | 2 R/trim.R | 4 - R/writeRaster.R | 2 R/zonal.R | 4 - build/partial.rdb |binary inst/tinytest/test_wkt_grd.R |only man/rasterOptions.Rd | 7 +- src/clamp.cpp | 2 src/reclass.cpp | 10 ++-- 40 files changed, 251 insertions(+), 156 deletions(-)
Title: Weighted and Directed Networks
Description: Implementations of network analysis including
(1) assortativity coefficient of weighted and directed networks,
Yuan, Yan and Zhang (2021) <doi:10.1093/comnet/cnab017>,
(2) centrality measures for weighted and directed networks,
Opsahl, Agneessens and Skvoretz (2010) <doi:10.1016/j.socnet.2010.03.006>,
Zhang, Wang and Yan (2022) <doi:10.1016/j.physa.2021.126438>,
(3) clustering coefficient of weighted and directed networks,
Fagiolo (2007) <doi:10.1103/PhysRevE.76.026107> and
Clemente and Grassi (2018) <doi:10.1016/j.chaos.2017.12.007>,
(4) network rewiring,
(5) preferential attachment network generation.
Author: Yelie Yuan [aut, cre],
Tiandong Wang [aut],
Jun Yan [aut],
Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>
Diff between wdnet versions 0.0.3 dated 2022-06-23 and 0.0.4 dated 2022-06-27
wdnet-0.0.3/wdnet/man/fillWeight_cpp.Rd |only wdnet-0.0.3/wdnet/man/findNode_cpp.Rd |only wdnet-0.0.3/wdnet/man/findNode_undirected_cpp.Rd |only wdnet-0.0.3/wdnet/man/nodeStrength_cpp.Rd |only wdnet-0.0.3/wdnet/man/rpanet_cpp.Rd |only wdnet-0.0.3/wdnet/man/sampleNode_cpp.Rd |only wdnet-0.0.3/wdnet/src/rpanet.cpp |only wdnet-0.0.4/wdnet/DESCRIPTION | 8 - wdnet-0.0.4/wdnet/MD5 | 51 +++++------ wdnet-0.0.4/wdnet/NEWS.md |only wdnet-0.0.4/wdnet/R/RcppExports.R | 24 ++--- wdnet-0.0.4/wdnet/R/assortativity.R | 4 wdnet-0.0.4/wdnet/R/joint_dist.R | 2 wdnet-0.0.4/wdnet/R/panet_control.R | 10 -- wdnet-0.0.4/wdnet/R/rewire.R | 2 wdnet-0.0.4/wdnet/R/rpanet.R | 45 +++++++-- wdnet-0.0.4/wdnet/R/rpanet_general.R | 22 ---- wdnet-0.0.4/wdnet/R/rpanet_simple.R | 22 ++-- wdnet-0.0.4/wdnet/R/utils.R | 2 wdnet-0.0.4/wdnet/man/fill_weight_cpp.Rd |only wdnet-0.0.4/wdnet/man/find_node_cpp.Rd |only wdnet-0.0.4/wdnet/man/find_node_undirected_cpp.Rd |only wdnet-0.0.4/wdnet/man/node_strength_cpp.Rd |only wdnet-0.0.4/wdnet/man/rpactl.newedge.Rd | 7 - wdnet-0.0.4/wdnet/man/rpanet_nodelist_cpp.Rd |only wdnet-0.0.4/wdnet/man/sample_node_cpp.Rd |only wdnet-0.0.4/wdnet/src/RcppExports.cpp | 48 +++++----- wdnet-0.0.4/wdnet/src/init.c | 40 ++++---- wdnet-0.0.4/wdnet/src/rpanet_binary_directed.cpp | 96 ++++++++++----------- wdnet-0.0.4/wdnet/src/rpanet_binary_undirected.cpp | 72 +++++++-------- wdnet-0.0.4/wdnet/src/rpanet_naive_directed.cpp | 34 +++---- wdnet-0.0.4/wdnet/src/rpanet_naive_undirected.cpp | 14 +-- wdnet-0.0.4/wdnet/src/rpanet_nodelist.cpp |only wdnet-0.0.4/wdnet/src/utils.cpp | 10 +- 34 files changed, 257 insertions(+), 256 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 1.0.2 dated 2022-03-04 and 1.0.3 dated 2022-06-27
rlang-1.0.2/rlang/R/compat-friendly-type.R |only rlang-1.0.2/rlang/src/internal/arg.h |only rlang-1.0.3/rlang/DESCRIPTION | 8 rlang-1.0.3/rlang/MD5 | 329 +-- rlang-1.0.3/rlang/NAMESPACE | 4 rlang-1.0.3/rlang/NEWS.md | 128 + rlang-1.0.3/rlang/R/arg.R | 18 rlang-1.0.3/rlang/R/bytes.R | 73 rlang-1.0.3/rlang/R/c-lib.R | 7 rlang-1.0.3/rlang/R/call.R | 44 rlang-1.0.3/rlang/R/cnd-abort.R | 175 + rlang-1.0.3/rlang/R/cnd-entrace.R | 2 rlang-1.0.3/rlang/R/cnd-last.R | 21 rlang-1.0.3/rlang/R/cnd-message.R | 52 rlang-1.0.3/rlang/R/cnd-signal.R | 47 rlang-1.0.3/rlang/R/cnd.R | 161 + rlang-1.0.3/rlang/R/compat-cli.R | 55 rlang-1.0.3/rlang/R/compat-downstream-deps.R | 2 rlang-1.0.3/rlang/R/compat-obj-type.R |only rlang-1.0.3/rlang/R/compat-purrr.R | 32 rlang-1.0.3/rlang/R/compat-rlang.R | 2 rlang-1.0.3/rlang/R/compat-s3-register.R | 2 rlang-1.0.3/rlang/R/compat-sizes.R |only rlang-1.0.3/rlang/R/compat-vctrs.R | 2 rlang-1.0.3/rlang/R/deparse.R | 38 rlang-1.0.3/rlang/R/dots-ellipsis.R | 12 rlang-1.0.3/rlang/R/dots.R | 2 rlang-1.0.3/rlang/R/env-binding.R | 3 rlang-1.0.3/rlang/R/env-special.R | 24 rlang-1.0.3/rlang/R/env.R | 54 rlang-1.0.3/rlang/R/eval-tidy.R | 4 rlang-1.0.3/rlang/R/expr.R | 2 rlang-1.0.3/rlang/R/fn.R | 2 rlang-1.0.3/rlang/R/lifecycle-deprecated.R | 14 rlang-1.0.3/rlang/R/nse-defuse.R | 6 rlang-1.0.3/rlang/R/obj.R | 2 rlang-1.0.3/rlang/R/quo.R | 9 rlang-1.0.3/rlang/R/rlang.R | 2 rlang-1.0.3/rlang/R/session.R | 32 rlang-1.0.3/rlang/R/trace.R | 490 ++-- rlang-1.0.3/rlang/R/utils-cli-tree.R | 59 rlang-1.0.3/rlang/R/utils.R | 35 rlang-1.0.3/rlang/R/vec-new.R | 2 rlang-1.0.3/rlang/man/abort.Rd | 42 rlang-1.0.3/rlang/man/args_error_context.Rd | 13 rlang-1.0.3/rlang/man/as_box.Rd | 4 rlang-1.0.3/rlang/man/bytes-class.Rd | 2 rlang-1.0.3/rlang/man/call2.Rd | 18 rlang-1.0.3/rlang/man/call_standardise.Rd | 4 rlang-1.0.3/rlang/man/caller_arg.Rd | 2 rlang-1.0.3/rlang/man/check_dots_empty.Rd | 6 rlang-1.0.3/rlang/man/check_dots_used.Rd | 6 rlang-1.0.3/rlang/man/check_exclusive.Rd | 9 rlang-1.0.3/rlang/man/cnd_inherits.Rd | 8 rlang-1.0.3/rlang/man/defusing-advanced.Rd | 6 rlang-1.0.3/rlang/man/dot-data.Rd | 12 rlang-1.0.3/rlang/man/dyn-dots.Rd | 6 rlang-1.0.3/rlang/man/embrace-operator.Rd | 8 rlang-1.0.3/rlang/man/englue.Rd | 4 rlang-1.0.3/rlang/man/enquo.Rd | 4 rlang-1.0.3/rlang/man/env_cache.Rd | 2 rlang-1.0.3/rlang/man/env_clone.Rd | 49 rlang-1.0.3/rlang/man/env_get.Rd | 4 rlang-1.0.3/rlang/man/env_poke.Rd | 2 rlang-1.0.3/rlang/man/eval_tidy.Rd | 6 rlang-1.0.3/rlang/man/exprs_auto_name.Rd | 4 rlang-1.0.3/rlang/man/global_entrace.Rd | 6 rlang-1.0.3/rlang/man/glue-operators.Rd | 40 rlang-1.0.3/rlang/man/injection-operator.Rd | 20 rlang-1.0.3/rlang/man/last_error.Rd | 6 rlang-1.0.3/rlang/man/last_warnings.Rd | 16 rlang-1.0.3/rlang/man/local_error_call.Rd | 30 rlang-1.0.3/rlang/man/missing_arg.Rd | 54 rlang-1.0.3/rlang/man/ns_registry_env.Rd |only rlang-1.0.3/rlang/man/qq_show.Rd | 8 rlang-1.0.3/rlang/man/rlang-package.Rd | 2 rlang-1.0.3/rlang/man/rlang_backtrace_on_error.Rd | 1 rlang-1.0.3/rlang/man/scoped_interactive.Rd | 6 rlang-1.0.3/rlang/man/splice-operator.Rd | 54 rlang-1.0.3/rlang/man/splice.Rd | 12 rlang-1.0.3/rlang/man/topic-condition-customisation.Rd | 20 rlang-1.0.3/rlang/man/topic-condition-formatting.Rd | 24 rlang-1.0.3/rlang/man/topic-data-mask-ambiguity.Rd | 48 rlang-1.0.3/rlang/man/topic-data-mask-programming.Rd | 90 rlang-1.0.3/rlang/man/topic-data-mask.Rd | 40 rlang-1.0.3/rlang/man/topic-defuse.Rd | 52 rlang-1.0.3/rlang/man/topic-double-evaluation.Rd | 28 rlang-1.0.3/rlang/man/topic-embrace-constants.Rd | 20 rlang-1.0.3/rlang/man/topic-embrace-non-args.Rd | 8 rlang-1.0.3/rlang/man/topic-error-call.Rd | 76 rlang-1.0.3/rlang/man/topic-error-chaining.Rd | 66 rlang-1.0.3/rlang/man/topic-inject-out-of-context.Rd | 28 rlang-1.0.3/rlang/man/topic-inject.Rd | 40 rlang-1.0.3/rlang/man/topic-metaprogramming.Rd | 88 rlang-1.0.3/rlang/man/topic-multiple-columns.Rd | 48 rlang-1.0.3/rlang/man/topic-quosure.Rd | 36 rlang-1.0.3/rlang/man/try_fetch.Rd | 24 rlang-1.0.3/rlang/man/vector-construction.Rd | 2 rlang-1.0.3/rlang/src/Makevars | 1 rlang-1.0.3/rlang/src/internal/arg.c | 98 rlang-1.0.3/rlang/src/internal/cnd.c | 16 rlang-1.0.3/rlang/src/internal/decl/arg-decl.h | 7 rlang-1.0.3/rlang/src/internal/decl/dots-decl.h | 6 rlang-1.0.3/rlang/src/internal/dots.c | 63 rlang-1.0.3/rlang/src/internal/env.c | 5 rlang-1.0.3/rlang/src/internal/globals.c |only rlang-1.0.3/rlang/src/internal/globals.h |only rlang-1.0.3/rlang/src/internal/init.c | 9 rlang-1.0.3/rlang/src/internal/internal.c | 4 rlang-1.0.3/rlang/src/internal/internal.h | 3 rlang-1.0.3/rlang/src/internal/utils.c | 18 rlang-1.0.3/rlang/src/rlang/arg.c | 8 rlang-1.0.3/rlang/src/rlang/arg.h | 5 rlang-1.0.3/rlang/src/rlang/c-utils.h | 2 rlang-1.0.3/rlang/src/rlang/cnd.c | 17 rlang-1.0.3/rlang/src/rlang/cnd.h | 2 rlang-1.0.3/rlang/src/rlang/decl/env-decl.h | 33 rlang-1.0.3/rlang/src/rlang/env-binding.c | 10 rlang-1.0.3/rlang/src/rlang/env.c | 129 - rlang-1.0.3/rlang/src/rlang/env.h | 2 rlang-1.0.3/rlang/src/rlang/eval.c | 8 rlang-1.0.3/rlang/src/rlang/eval.h | 33 rlang-1.0.3/rlang/src/rlang/globals.c | 3 rlang-1.0.3/rlang/src/rlang/globals.h | 3 rlang-1.0.3/rlang/src/rlang/obj.c | 27 rlang-1.0.3/rlang/src/rlang/obj.h | 4 rlang-1.0.3/rlang/src/rlang/rlang-types.h | 5 rlang-1.0.3/rlang/src/rlang/rlang.c | 1 rlang-1.0.3/rlang/src/rlang/rlang.h | 4 rlang-1.0.3/rlang/src/rlang/session.c | 43 rlang-1.0.3/rlang/src/rlang/session.h | 1 rlang-1.0.3/rlang/src/version.c | 2 rlang-1.0.3/rlang/tests/testthat/_snaps/arg.md | 39 rlang-1.0.3/rlang/tests/testthat/_snaps/bytes.md | 9 rlang-1.0.3/rlang/tests/testthat/_snaps/cnd-abort.md | 469 ++-- rlang-1.0.3/rlang/tests/testthat/_snaps/cnd-entrace.md | 6 rlang-1.0.3/rlang/tests/testthat/_snaps/cnd-handlers.md | 98 rlang-1.0.3/rlang/tests/testthat/_snaps/cnd-message.md | 55 rlang-1.0.3/rlang/tests/testthat/_snaps/cnd-signal.md | 6 rlang-1.0.3/rlang/tests/testthat/_snaps/cnd.md | 232 +- rlang-1.0.3/rlang/tests/testthat/_snaps/current/cnd-abort.md | 116 - rlang-1.0.3/rlang/tests/testthat/_snaps/dots-ellipsis.md | 11 rlang-1.0.3/rlang/tests/testthat/_snaps/dots.md | 32 rlang-1.0.3/rlang/tests/testthat/_snaps/pre-3.6.0/cnd-abort.md | 116 - rlang-1.0.3/rlang/tests/testthat/_snaps/session.md | 11 rlang-1.0.3/rlang/tests/testthat/_snaps/trace.md | 1034 ++++++---- rlang-1.0.3/rlang/tests/testthat/fixtures/error-backtrace-conditionMessage.R | 2 rlang-1.0.3/rlang/tests/testthat/helper-cli.R | 25 rlang-1.0.3/rlang/tests/testthat/helper-performance.R |only rlang-1.0.3/rlang/tests/testthat/helper-rlang.R | 16 rlang-1.0.3/rlang/tests/testthat/helper-trace.R | 19 rlang-1.0.3/rlang/tests/testthat/test-arg.R | 21 rlang-1.0.3/rlang/tests/testthat/test-bytes.R | 41 rlang-1.0.3/rlang/tests/testthat/test-c-api.R | 12 rlang-1.0.3/rlang/tests/testthat/test-call.R | 19 rlang-1.0.3/rlang/tests/testthat/test-cnd-abort.R | 55 rlang-1.0.3/rlang/tests/testthat/test-cnd-message.R | 60 rlang-1.0.3/rlang/tests/testthat/test-cnd-signal.R | 17 rlang-1.0.3/rlang/tests/testthat/test-cnd.R | 20 rlang-1.0.3/rlang/tests/testthat/test-compat-cli.R | 35 rlang-1.0.3/rlang/tests/testthat/test-compat-obj-type.R |only rlang-1.0.3/rlang/tests/testthat/test-compat-purrr.R | 20 rlang-1.0.3/rlang/tests/testthat/test-dots-ellipsis.R | 10 rlang-1.0.3/rlang/tests/testthat/test-dots.R | 30 rlang-1.0.3/rlang/tests/testthat/test-env-binding.R | 8 rlang-1.0.3/rlang/tests/testthat/test-env.R | 51 rlang-1.0.3/rlang/tests/testthat/test-friendly-type.R | 88 rlang-1.0.3/rlang/tests/testthat/test-quo.R | 14 rlang-1.0.3/rlang/tests/testthat/test-session.R | 12 rlang-1.0.3/rlang/tests/testthat/test-trace.R | 161 + 170 files changed, 4636 insertions(+), 2076 deletions(-)
Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.44.0 dated 2020-07-09 and 0.45.0 dated 2022-06-27
R.rsp-0.44.0/R.rsp/NEWS |only R.rsp-0.45.0/R.rsp/DESCRIPTION | 13 -- R.rsp-0.45.0/R.rsp/MD5 | 62 +++++----- R.rsp-0.45.0/R.rsp/NAMESPACE | 1 R.rsp-0.45.0/R.rsp/NEWS.md |only R.rsp-0.45.0/R.rsp/R/HttpDaemon.R | 2 R.rsp-0.45.0/R.rsp/R/RspParser.R | 5 R.rsp-0.45.0/R.rsp/R/compileAsciiDoc.R | 3 R.rsp-0.45.0/R.rsp/R/compileAsciiDocNoweb.R | 3 R.rsp-0.45.0/R.rsp/R/findAsciiDoc.R | 9 - R.rsp-0.45.0/R.rsp/R/splitUrl.R | 2 R.rsp-0.45.0/R.rsp/build/vignette.rds |binary R.rsp-0.45.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary R.rsp-0.45.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.tex.rsp | 4 R.rsp-0.45.0/R.rsp/inst/doc/RSP_intro.html | 19 +-- R.rsp-0.45.0/R.rsp/inst/doc/RSP_refcard.pdf |binary R.rsp-0.45.0/R.rsp/inst/doc/RSP_refcard.tex.rsp | 3 R.rsp-0.45.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx | 3 R.rsp-0.45.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |binary R.rsp-0.45.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 12 - R.rsp-0.45.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary R.rsp-0.45.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.tex.rsp | 4 R.rsp-0.45.0/R.rsp/man/HttpDaemon.Rd | 2 R.rsp-0.45.0/R.rsp/man/R.rsp-package.Rd | 4 R.rsp-0.45.0/R.rsp/man/RspShSourceCode.Rd | 1 R.rsp-0.45.0/R.rsp/man/compileAsciiDoc.Rd | 3 R.rsp-0.45.0/R.rsp/man/compileAsciiDocNoweb.Rd | 3 R.rsp-0.45.0/R.rsp/man/splitUrl.Rd | 2 R.rsp-0.45.0/R.rsp/vignettes/Dynamic_document_creation_using_RSP.tex.rsp | 4 R.rsp-0.45.0/R.rsp/vignettes/RSP_refcard.tex.rsp | 3 R.rsp-0.45.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx | 3 R.rsp-0.45.0/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 12 - R.rsp-0.45.0/R.rsp/vignettes/R_packages-Vignettes_prior_to_R300.tex.rsp | 4 33 files changed, 98 insertions(+), 88 deletions(-)
Title: Heuristics for the Quadratic Assignment Problem (QAP)
Description: Implements heuristics for the Quadratic Assignment Problem (QAP). Although, the QAP was introduced as a combinatorial optimization problem for the facility location problem in operations research, it also has many applications in data analysis. The problem is NP-hard and the package implements a simulated annealing heuristic.
Author: Michael Hahsler [aut, cre, cph]
,
Franz Rendl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between qap versions 0.1-1 dated 2017-02-27 and 0.1-2 dated 2022-06-27
DESCRIPTION | 19 +++++----- MD5 | 13 +++---- NEWS.md | 12 ++++-- README.md | 98 +++++++++++++++++++++++++++++++++++++---------------- build |only man/qap.Rd | 29 +++++++++------ man/read_qaplib.Rd | 2 - src/qapsim.f | 23 +++++++----- 8 files changed, 127 insertions(+), 69 deletions(-)
Title: Given a List of Gene Symbols, Performs Differential Enrichment
Analysis
Description: Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) <doi: 10.1371/journal.pone.0198139>. Given a list of gene symbols, 'diffEnrich' will
perform differential enrichment analysis using the Kyoto Encyclopedia of Genes
and Genomes (KEGG) REST API. This package provides a number of functions that are
intended to be used in a pipeline. Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will
download and clean species specific ENTREZ gene IDs and map them to their respective
KEGG pathways by accessing KEGG's REST API. KEGG's API is used to guarantee the most up-to-date pathway data from KEGG. Next, the user will identify significantly
enriched pathways from two gene sets, and finally, the user will identify
pathways that are differentially enriched between the two gene sets. In addition to
the analysis pipeline, this package also provides a plotting function.
Author: Harry Smith [aut, cre],
Laura Saba [aut]
Maintainer: Harry Smith <harry.smith@ucdenver.edu>
Diff between diffEnrich versions 0.1.1 dated 2019-11-21 and 0.1.2 dated 2022-06-27
diffEnrich-0.1.1/diffEnrich/man/figures/README-pressure-1.png |only diffEnrich-0.1.2/diffEnrich/DESCRIPTION | 14 diffEnrich-0.1.2/diffEnrich/MD5 | 27 diffEnrich-0.1.2/diffEnrich/NEWS.md | 7 diffEnrich-0.1.2/diffEnrich/R/diffEnrich.R | 6 diffEnrich-0.1.2/diffEnrich/R/get_kegg.R | 2 diffEnrich-0.1.2/diffEnrich/R/plotFoldEnrichment.R | 2 diffEnrich-0.1.2/diffEnrich/README.md | 1216 +--------- diffEnrich-0.1.2/diffEnrich/build/vignette.rds |binary diffEnrich-0.1.2/diffEnrich/inst/doc/diffenrich_vignette.R | 40 diffEnrich-0.1.2/diffEnrich/inst/doc/diffenrich_vignette.Rmd | 12 diffEnrich-0.1.2/diffEnrich/inst/doc/diffenrich_vignette.html | 1051 +++++++- diffEnrich-0.1.2/diffEnrich/man/figures/README-plotFoldEnrichment-1.png |binary diffEnrich-0.1.2/diffEnrich/man/figures/README-unnamed-chunk-1-1.png |binary diffEnrich-0.1.2/diffEnrich/vignettes/diffenrich_vignette.Rmd | 12 15 files changed, 1059 insertions(+), 1330 deletions(-)
Title: Classification and Visualization
Description: Miscellaneous functions for classification and visualization,
e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes,
an interface to 'svmlight' and stepclass() wrapper variable selection
for supervised classification, partimat() visualization of classification rules
and shardsplot() of cluster results as well as kmodes() clustering for categorical data,
corclust() variable clustering, variable extraction from different variable clustering models
and weight of evidence preprocessing.
Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero Szepannek, Marc Zentgraf, David Meyer
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between klaR versions 1.7-0 dated 2022-03-10 and 1.7-1 dated 2022-06-27
DESCRIPTION | 18 +++++++++--------- MD5 | 22 +++++++++++----------- NEWS | 10 ++++++++++ R/corclust.R | 6 +++--- R/kmodes.R | 12 ++++++++++-- R/level_shardsplot.R | 2 +- R/partimat.R | 22 +++++++++++++--------- R/predict.NaiveBayes.R | 15 +++++++++++++++ R/stepclass.R | 8 ++++---- data/B3.RData |binary data/countries.RData |binary man/kmodes.Rd | 2 +- 12 files changed, 77 insertions(+), 40 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with
remote database tables as if they are in-memory data frames. Basic
features works with any database that has a 'DBI' back end; more
advanced features require 'SQL' translation to be provided by the
package author.
Author: Hadley Wickham [aut, cre],
Maximilian Girlich [aut],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 2.2.0 dated 2022-06-05 and 2.2.1 dated 2022-06-27
DESCRIPTION | 6 +- MD5 | 34 ++++++------- NAMESPACE | 4 + NEWS.md | 29 +++++++---- R/backend-.R | 83 +++++++++++++++++++-------------- R/backend-mssql.R | 6 -- R/backend-oracle.R | 9 +++ R/backend-teradata.R | 4 - R/db-sql.R | 17 +++++- R/lazy-select-query.R | 8 ++- README.md | 2 build/dbplyr.pdf |binary inst/doc/dbplyr.html | 82 +++++++++++++++----------------- man/db-sql.Rd | 5 + tests/testthat/test-backend-.R | 32 ++++++++++++ tests/testthat/test-backend-mssql.R | 3 - tests/testthat/test-backend-oracle.R | 9 +++ tests/testthat/test-backend-teradata.R | 6 -- 18 files changed, 209 insertions(+), 130 deletions(-)
Title: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling
Description: A shiny app for accurate estimation of vaccine induced immunogenicity
with bivariate linear modeling. Method is detailed in: Lhomme, Hejblum, Lacabaratz,
Wiedemann, Lelievre, Levy, Thiebaut & Richert (2020). Journal of Immunological Methods,
477:112711. <doi:10.1016/j.jim.2019.112711>.
Author: Boris Hejblum [cre, aut],
Melanie Huchon [aut],
Clement Nerestan [aut]
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between vici versions 0.5.2 dated 2019-08-21 and 0.6.0 dated 2022-06-27
DESCRIPTION | 31 + MD5 | 65 ++- NAMESPACE | 36 + NEWS.md | 8 R/BW_functions.R |only R/app_server.R | 814 +++++--------------------------------------- R/app_ui.R | 160 -------- R/boxplot_VICI.R | 4 R/gls_ownfunctions.R |only R/heatmap_VICI.R | 2 R/interarm_fit.R | 73 ++- R/interarm_postprocessres.R | 16 R/intraarm_fit.R | 46 +- R/intraarm_postprocessres.R | 3 R/mod_modelfit.R |only R/mod_settings_pan.R |only R/mygls.R |only R/run_app.R | 2 R/update_vars.R | 8 R/utils.R |only README.md | 33 + inst/CITATION | 2 inst/app/tests |only man/ICS_ex.Rd | 6 man/boxplot_VICI.Rd | 10 man/compute_jaclist.Rd |only man/ddf_BW.Rd |only man/devfun_gls.Rd |only man/figures |only man/get_coefmat_gls.Rd |only man/interarm_fit.Rd | 6 man/intraarm_fit.Rd | 6 man/mod_modelfit.Rd |only man/mod_settings_pan.Rd |only man/mygls.Rd |only man/qform.Rd |only man/rbindall.Rd |only man/varBetafun_gls.Rd |only man/waldCI.Rd |only tests |only 40 files changed, 350 insertions(+), 981 deletions(-)
Title: Spatial Regression Models for Large Datasets using Nearest
Neighbor Gaussian Processes
Description: Fits univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Finley, Datta, Banerjee (2022) <doi:10.18637/jss.v103.i05>, Finley, Datta, Cook, Morton, Andersen, and Banerjee (2019) <doi:10.1080/10618600.2018.1537924>, and Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Andrew Finley [aut, cre],
Abhirup Datta [aut],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spNNGP versions 0.1.8 dated 2022-05-24 and 1.0.0 dated 2022-06-27
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- build/partial.rdb |binary inst |only man/spConjNNGP.Rd | 4 ++++ man/spDiag.Rd | 6 +++++- man/spNNGP.Rd | 4 ++++ 7 files changed, 24 insertions(+), 11 deletions(-)
Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut]
,
Juan Carlos Oliveros [aut, ctb]
,
Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>
Diff between Rgff versions 0.1.1 dated 2022-06-24 and 0.1.2 dated 2022-06-27
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NEWS.md | 4 ++++ inst/doc/Using_Rgff.R | 6 +++--- inst/doc/Using_Rgff.Rmd | 6 +++--- inst/doc/Using_Rgff.html | 16 ++++++++-------- inst/extdata/AthSmall.gff3.gene.ncRNA_gene.saf |only inst/extdata/AthSmall.gtf.gff3 |only vignettes/Using_Rgff.Rmd | 6 +++--- 9 files changed, 32 insertions(+), 26 deletions(-)
Title: Main Existing Human Datasets
Description: Shiny for Open Science to visualize, share, and inventory the
main existing human datasets for researchers.
Author: Etienne Camenen [aut, cre],
Baptiste Couvy-Duchesne [aut]
Maintainer: Etienne Camenen <etienne.camenen@gmail.com>
Diff between MainExistingDatasets versions 1.0.0 dated 2022-06-20 and 1.0.1 dated 2022-06-27
DESCRIPTION | 6 +-- MD5 | 18 +++++----- NEWS.md | 4 +- R/run_app.R | 2 - README.md | 15 +++++++- inst/doc/Tutorial.R | 5 -- inst/doc/Tutorial.Rmd | 13 +++++-- inst/doc/Tutorial.html | 84 +++++++++++++++++++++---------------------------- inst/golem-config.yml | 2 - vignettes/Tutorial.Rmd | 13 +++++-- 10 files changed, 85 insertions(+), 77 deletions(-)
More information about MainExistingDatasets at CRAN
Permanent link
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAstats versions 0.3.0 dated 2022-05-19 and 0.3.1 dated 2022-06-27
DQAstats-0.3.0/DQAstats/README.md |only DQAstats-0.3.1/DQAstats/DESCRIPTION | 14 DQAstats-0.3.1/DQAstats/MD5 | 89 DQAstats-0.3.1/DQAstats/R/DQA.R | 4 DQAstats-0.3.1/DQAstats/R/categorical_analysis.R | 104 DQAstats-0.3.1/DQAstats/R/completeness.R | 354 - DQAstats-0.3.1/DQAstats/R/conformance.R | 1931 +++++----- DQAstats-0.3.1/DQAstats/R/create_markdown.R | 5 DQAstats-0.3.1/DQAstats/R/dataloading.R | 6 DQAstats-0.3.1/DQAstats/R/datetime_restrictions.R | 1243 +++--- DQAstats-0.3.1/DQAstats/R/descriptive_results.R | 568 +- DQAstats-0.3.1/DQAstats/R/format_value_conformance_results.R | 2 DQAstats-0.3.1/DQAstats/R/mdr.R | 769 ++- DQAstats-0.3.1/DQAstats/R/plausibilities.R | 784 ++-- DQAstats-0.3.1/DQAstats/R/plausibility_results.R | 1432 +++---- DQAstats-0.3.1/DQAstats/R/report.R | 27 DQAstats-0.3.1/DQAstats/R/test_csv.R | 280 - DQAstats-0.3.1/DQAstats/R/utils.R | 434 +- DQAstats-0.3.1/DQAstats/inst/demo_data/utilities/MISC/sitenames.JSON |only DQAstats-0.3.1/DQAstats/inst/demo_data/utilities/RMD/DQA_report.Rmd | 416 +- DQAstats-0.3.1/DQAstats/inst/doc/DQAstats2SHIPdataset.R | 2 DQAstats-0.3.1/DQAstats/inst/doc/DQAstats2SHIPdataset.Rmd | 994 ++--- DQAstats-0.3.1/DQAstats/inst/doc/DQAstats2SHIPdataset.html | 21 DQAstats-0.3.1/DQAstats/man/apply_time_restriciton.Rd | 9 DQAstats-0.3.1/DQAstats/man/format_value_conformance_results.Rd | 322 - DQAstats-0.3.1/DQAstats/man/test_csv.Rd | 2 DQAstats-0.3.1/DQAstats/tests/testthat.R | 16 DQAstats-0.3.1/DQAstats/tests/testthat/_snaps/datetime_restrictions.md |only DQAstats-0.3.1/DQAstats/tests/testthat/test-DQA.R | 136 DQAstats-0.3.1/DQAstats/tests/testthat/test-MDR.R | 4 DQAstats-0.3.1/DQAstats/tests/testthat/test-check_date_restriction_requirements.R | 106 DQAstats-0.3.1/DQAstats/tests/testthat/test-completeness.R | 258 - DQAstats-0.3.1/DQAstats/tests/testthat/test-conformance.R | 310 - DQAstats-0.3.1/DQAstats/tests/testthat/test-dataloading.R | 324 - DQAstats-0.3.1/DQAstats/tests/testthat/test-datamap.R | 264 - DQAstats-0.3.1/DQAstats/tests/testthat/test-datetime_restrictions.R |only DQAstats-0.3.1/DQAstats/tests/testthat/test-descriptive_results.R | 636 +-- DQAstats-0.3.1/DQAstats/tests/testthat/test-etl_checks.R | 254 - DQAstats-0.3.1/DQAstats/tests/testthat/test-export.R | 552 +- DQAstats-0.3.1/DQAstats/tests/testthat/test-helper_vars.R | 4 DQAstats-0.3.1/DQAstats/tests/testthat/test-import.R | 4 DQAstats-0.3.1/DQAstats/tests/testthat/test-lints.R |only DQAstats-0.3.1/DQAstats/tests/testthat/test-plausibilities.R | 292 - DQAstats-0.3.1/DQAstats/tests/testthat/test-readme.R | 162 DQAstats-0.3.1/DQAstats/tests/testthat/test-reduce_cat.R | 258 - DQAstats-0.3.1/DQAstats/tests/testthat/test-render_conformance.R | 328 - DQAstats-0.3.1/DQAstats/tests/testthat/test-stats.R | 4 DQAstats-0.3.1/DQAstats/vignettes/DQAstats2SHIPdataset.Rmd | 994 ++--- 48 files changed, 7398 insertions(+), 7320 deletions(-)
Title: Bayesian Reliability Estimation
Description: Functionality for reliability estimates. For 'unidimensional' tests:
Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower
bound and coefficient omega_u ('unidimensional') in a Bayesian and a frequentist version.
For multidimensional tests: omega_t (total) and omega_h (hierarchical).
The results include confidence and credible intervals, the
probability of a coefficient being larger than a cutoff,
and a check for the factor models, necessary for the omega coefficients.
The method for the Bayesian 'unidimensional' estimates, except for omega_u,
is sampling from the posterior inverse 'Wishart' for the
covariance matrix based measures (see 'Murphy', 2007,
<https://groups.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>.
The Bayesian omegas (u, t, and h) are obtained by
'Gibbs' sampling from the conditional posterior distributions of
(1) the single factor model and (2) the second-order factor model
('Lee', 2007, <https://onlinelibrary.wiley.com/doi/book/10.1002/9780470024737>).
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 0.7.4.1 dated 2022-04-06 and 0.7.4.2 dated 2022-06-27
DESCRIPTION | 10 +++---- MD5 | 14 +++++------ R/bomegasMultiGibbs.R | 63 ++++++++++++++++++++++++++++++-------------------- R/bomegasMultiOut.R | 16 +++++------- R/helpFunsOmegas.R | 56 ++++++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary man/bomegas.Rd | 3 +- man/strel.Rd | 3 +- 8 files changed, 111 insertions(+), 54 deletions(-)
Title: Clean the R Console and Environment
Description: Small package to clean the R console and the R environment
with the call of just one function.
Author: Jonathan M. Mang [aut, cre] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between cleaR versions 0.0.2 dated 2022-04-26 and 0.0.3 dated 2022-06-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/clear.R | 16 ++++++++++++---- man/clear.Rd | 6 +++++- 4 files changed, 24 insertions(+), 12 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between voluModel versions 0.1.5 dated 2022-06-05 and 0.1.6 dated 2022-06-27
DESCRIPTION | 10 MD5 | 77 ++--- NAMESPACE | 2 NEWS.md | 5 R/BackgroundSamplingFunctions.R | 4 R/inputProcessingUtilties.R | 1 R/marineBackground.R | 4 R/visualizations.R | 34 +- R/xyzSample.R | 3 inst/doc/a_Introduction.R | 88 +++--- inst/doc/a_Introduction.Rmd | 58 ++-- inst/doc/a_Introduction.html | 35 +- inst/doc/b_RasterProcessing.R | 116 ++++---- inst/doc/b_RasterProcessing.Rmd | 49 ++- inst/doc/b_RasterProcessing.html | 42 +-- inst/doc/c_DataSampling.R | 56 +--- inst/doc/c_DataSampling.Rmd | 56 +--- inst/doc/c_DataSampling.html | 292 ++++++++++----------- inst/doc/d_Visualization.R | 17 - inst/doc/d_Visualization.Rmd | 17 - inst/doc/d_Visualization.html | 16 - inst/doc/e_GLMWorkflow.R | 31 +- inst/doc/e_GLMWorkflow.Rmd | 20 + inst/doc/e_GLMWorkflow.html | 401 ++++++++++++++--------------- inst/extdata/backgroundSamplingRegions.rds |only man/downsample.Rd | 1 man/mSampling2D.Rd | 1 man/mSampling3D.Rd | 3 man/oneRasterPlot.Rd | 5 man/pointCompMap.Rd | 4 man/pointMap.Rd | 2 man/xyzSample.Rd | 3 vignettes/AOUInterpAndSmooth.png |only vignettes/OxygenTopBottom.png |only vignettes/PointsAndTrainingRegion.png |only vignettes/TemperatureTopBottom.png |only vignettes/a_Introduction.Rmd | 58 ++-- vignettes/b_RasterProcessing.Rmd | 49 ++- vignettes/c_DataSampling.Rmd | 56 +--- vignettes/clipToOceanDemo-1.png |binary vignettes/d_Visualization.Rmd | 17 - vignettes/e_GLMWorkflow.Rmd | 20 + 42 files changed, 825 insertions(+), 828 deletions(-)
Title: Scalable Bayesian Disease Mapping Models for High-Dimensional
Data
Description: Implements several spatial and spatio-temporal scalable disease mapping models for high-dimensional count data using the INLA technique for approximate Bayesian inference in latent Gaussian models (Orozco-Acosta et al., 2021 <doi:10.1016/j.spasta.2021.100496> and Orozco-Acosta et al., 2022 <arXiv:2201.08323>). The creation and develpment of this package has been supported by Project MTM2017-82553-R (AEI/FEDER, UE) and Project PID2020-113125RB-I00/MCIN/AEI/10.13039/501100011033. It has also been partially funded by the Public University of Navarra (project PJUPNA2001).
Author: Aritz Adin [aut, cre] ,
Erick Orozco-Acosta [aut] ,
Maria Dolores Ugarte [aut]
Maintainer: Aritz Adin <aritz.adin@unavarra.es>
Diff between bigDM versions 0.4.1 dated 2022-02-08 and 0.4.2 dated 2022-06-27
DESCRIPTION | 12 +++--- MD5 | 24 ++++++------ NAMESPACE | 1 NEWS | 4 ++ R/CAR_INLA.R | 64 +++++++++++++++++++++++++-------- R/STCAR_INLA.R | 104 +++++++++++++++++++++++++++++++++++++++++++++--------- R/mergeINLA.R | 99 +++++++++++++++++++++++++++++++++------------------ README.md | 14 +++++-- build/partial.rdb |binary inst/CITATION | 6 +-- man/CAR_INLA.Rd | 17 +++++--- man/STCAR_INLA.Rd | 19 +++++---- man/mergeINLA.Rd | 17 +++++--- 13 files changed, 271 insertions(+), 110 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided. For details and tutorial, see Gramacy (2016 <doi:10.18637/jss.v072.i01>.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5-6 dated 2022-04-03 and 1.5-7 dated 2022-06-27
ChangeLog | 8 +++ DESCRIPTION | 10 ++-- MD5 | 34 ++++++++-------- NAMESPACE | 4 - build/vignette.rds |binary demo/calib.R | 4 - inst/doc/laGP.R | 107 ++++++++++++++++++++++++++++++++-------------------- inst/doc/laGP.Rnw | 54 +++++++++++++++++++------- inst/doc/laGP.pdf |binary man/aGP.Rd | 71 +++++++++++++++++----------------- man/blhs.Rd | 9 ++-- man/darg.Rd | 13 +++--- man/laGP.Rd | 6 +- man/llikGP.Rd | 37 +++++++++-------- man/mleGP.Rd | 59 ++++++++++++++-------------- man/newGP.Rd | 29 +++++++------- man/optim.auglag.Rd | 11 +++-- vignettes/laGP.Rnw | 54 +++++++++++++++++++------- 18 files changed, 306 insertions(+), 204 deletions(-)
Title: Australian Tax Policy Analysis
Description: Utilities to cost and evaluate Australian tax policy, including fast
projections of personal income tax collections, high-performance tax and
transfer calculators, and an interface to common indices from the Australian
Bureau of Statistics. Written to support Grattan Institute's Australian
Perspectives program, and related projects. Access to the Australian Taxation
Office's sample files of personal income tax returns is assumed.
Author: Hugh Parsonage [aut, cre],
Tim Cameron [aut],
Brendan Coates [aut],
Matthew Katzen [aut],
William Young [aut],
Ittima Cherastidtham [dtc],
W. Karsten [ctb],
M. Enrique Garcia [ctb],
Matt Cowgill [aut]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattan versions 1.9.0.10 dated 2022-01-09 and 2.0.0.0 dated 2022-06-27
grattan-1.9.0.10/grattan/R/RcppExports.R |only grattan-1.9.0.10/grattan/R/age_pension.R |only grattan-1.9.0.10/grattan/R/carer_payment.R |only grattan-1.9.0.10/grattan/R/carers_allowance.R |only grattan-1.9.0.10/grattan/R/child_care_subsidy.R |only grattan-1.9.0.10/grattan/R/disability_pension.R |only grattan-1.9.0.10/grattan/R/energy_supplement.R |only grattan-1.9.0.10/grattan/R/family_tax_benefit.R |only grattan-1.9.0.10/grattan/R/income_tax_sapto.R |only grattan-1.9.0.10/grattan/R/model_child_care_subsidy.R |only grattan-1.9.0.10/grattan/R/model_income_tax2122.R |only grattan-1.9.0.10/grattan/R/model_rent_assistance.R |only grattan-1.9.0.10/grattan/R/new_income_tax.R |only grattan-1.9.0.10/grattan/R/new_medicare_levy.R |only grattan-1.9.0.10/grattan/R/new_sapto.R |only grattan-1.9.0.10/grattan/R/newstart_allowance.R |only grattan-1.9.0.10/grattan/R/pension_supplement.R |only grattan-1.9.0.10/grattan/R/population_forecast.R |only grattan-1.9.0.10/grattan/R/rent_assistance.R |only grattan-1.9.0.10/grattan/R/sapto_rcpp.R |only grattan-1.9.0.10/grattan/R/student_repayment.R |only grattan-1.9.0.10/grattan/R/unemployment_benefit.R |only grattan-1.9.0.10/grattan/R/youth_allowance.R |only grattan-1.9.0.10/grattan/R/youth_unemployment.R |only grattan-1.9.0.10/grattan/man/IncomeTax.Rd |only grattan-1.9.0.10/grattan/man/MedicareLevy.Rd |only grattan-1.9.0.10/grattan/man/Offset.Rd |only grattan-1.9.0.10/grattan/man/age_pension.Rd |only grattan-1.9.0.10/grattan/man/carer_payment.Rd |only grattan-1.9.0.10/grattan/man/carers_allowance.Rd |only grattan-1.9.0.10/grattan/man/child_care_subsidy.Rd |only grattan-1.9.0.10/grattan/man/disability_pension.Rd |only grattan-1.9.0.10/grattan/man/energy_supplement.Rd |only grattan-1.9.0.10/grattan/man/family_tax_benefit.Rd |only grattan-1.9.0.10/grattan/man/income_tax_sapto.Rd |only grattan-1.9.0.10/grattan/man/model_child_care_subsidy.Rd |only grattan-1.9.0.10/grattan/man/model_rent_assistance.Rd |only grattan-1.9.0.10/grattan/man/new_income_tax.Rd |only grattan-1.9.0.10/grattan/man/new_medicare_levy.Rd |only grattan-1.9.0.10/grattan/man/new_sapto.Rd |only grattan-1.9.0.10/grattan/man/newstart_allowance.Rd |only grattan-1.9.0.10/grattan/man/pension_supplement.Rd |only grattan-1.9.0.10/grattan/man/rent_assistance.Rd |only grattan-1.9.0.10/grattan/man/sapto_rcpp.Rd |only grattan-1.9.0.10/grattan/man/sapto_rcpp_singleton.Rd |only grattan-1.9.0.10/grattan/man/sapto_rcpp_yr.Rd |only grattan-1.9.0.10/grattan/man/student_repayment.Rd |only grattan-1.9.0.10/grattan/man/unemployment_benefit.Rd |only grattan-1.9.0.10/grattan/man/youth_allowance.Rd |only grattan-1.9.0.10/grattan/man/youth_unemployment.Rd |only grattan-1.9.0.10/grattan/src/IncomeTax.cpp |only grattan-1.9.0.10/grattan/src/Medicare.h |only grattan-1.9.0.10/grattan/src/MedicareLevySingle.cpp |only grattan-1.9.0.10/grattan/src/Offset.cpp |only grattan-1.9.0.10/grattan/src/Offset.h |only grattan-1.9.0.10/grattan/src/Person.h |only grattan-1.9.0.10/grattan/src/RcppExports.cpp |only grattan-1.9.0.10/grattan/src/Sapto.cpp |only grattan-1.9.0.10/grattan/src/Sapto.h |only grattan-1.9.0.10/grattan/src/constants.cpp |only grattan-1.9.0.10/grattan/src/do_income_tax.cpp |only grattan-1.9.0.10/grattan/src/do_lito.cpp |only grattan-1.9.0.10/grattan/src/grattanMedicareLevy.h |only grattan-1.9.0.10/grattan/src/medicare_levies.cpp |only grattan-1.9.0.10/grattan/src/sapto_rcpp.cpp |only grattan-1.9.0.10/grattan/src/sapto_rcpp_singleton.cpp |only grattan-1.9.0.10/grattan/src/sapto_rcpp_yr.cpp |only grattan-1.9.0.10/grattan/src/yrs |only grattan-1.9.0.10/grattan/tests/testthat/test_age_pension.R |only grattan-1.9.0.10/grattan/tests/testthat/test_carer_payment.R |only grattan-1.9.0.10/grattan/tests/testthat/test_carers_allowance.R |only grattan-1.9.0.10/grattan/tests/testthat/test_child_care_subsidy.R |only grattan-1.9.0.10/grattan/tests/testthat/test_disability_pension.R |only grattan-1.9.0.10/grattan/tests/testthat/test_energy_supplement.R |only grattan-1.9.0.10/grattan/tests/testthat/test_family_tax_benefit.R |only grattan-1.9.0.10/grattan/tests/testthat/test_model_child_care_subsidy.R |only grattan-1.9.0.10/grattan/tests/testthat/test_model_rent_assistance.R |only grattan-1.9.0.10/grattan/tests/testthat/test_new_income_tax.R |only grattan-1.9.0.10/grattan/tests/testthat/test_newstart_allowance.R |only grattan-1.9.0.10/grattan/tests/testthat/test_pension_supplement.R |only grattan-1.9.0.10/grattan/tests/testthat/test_rent_assistance.R |only grattan-1.9.0.10/grattan/tests/testthat/test_student_repayment.R |only grattan-1.9.0.10/grattan/tests/testthat/test_youth_allowance.R |only grattan-2.0.0.0/grattan/DESCRIPTION | 23 grattan-2.0.0.0/grattan/MD5 | 339 +- grattan-2.0.0.0/grattan/NAMESPACE | 34 grattan-2.0.0.0/grattan/NEWS.md | 52 grattan-2.0.0.0/grattan/R/CG_inflator.R | 6 grattan-2.0.0.0/grattan/R/LITO.R | 124 - grattan-2.0.0.0/grattan/R/Offset.R |only grattan-2.0.0.0/grattan/R/SysDate.R |only grattan-2.0.0.0/grattan/R/System.R |only grattan-2.0.0.0/grattan/R/age_grouper.R | 160 - grattan-2.0.0.0/grattan/R/age_pension_age.R | 266 +- grattan-2.0.0.0/grattan/R/cpi_inflator.R | 375 +-- grattan-2.0.0.0/grattan/R/cpi_inflator_quarters.R | 180 - grattan-2.0.0.0/grattan/R/decode_age_range.R |only grattan-2.0.0.0/grattan/R/fy.year.R | 1 grattan-2.0.0.0/grattan/R/grattan-package.R | 4 grattan-2.0.0.0/grattan/R/income_tax.R | 973 ------- grattan-2.0.0.0/grattan/R/lf_inflator.R | 596 ++-- grattan-2.0.0.0/grattan/R/medicare_levy.R | 50 grattan-2.0.0.0/grattan/R/model_income_tax.R | 1239 ++-------- grattan-2.0.0.0/grattan/R/rN.R |only grattan-2.0.0.0/grattan/R/residential_property_prices.R | 24 grattan-2.0.0.0/grattan/R/sapto.R | 67 grattan-2.0.0.0/grattan/R/small_business_tax_offset.R | 298 +- grattan-2.0.0.0/grattan/R/utils.R | 3 grattan-2.0.0.0/grattan/R/validate_date.R | 246 - grattan-2.0.0.0/grattan/R/validate_per.R | 122 grattan-2.0.0.0/grattan/R/wage_inflator.R | 530 ++-- grattan-2.0.0.0/grattan/R/zzz.R | 184 - grattan-2.0.0.0/grattan/man/System.Rd |only grattan-2.0.0.0/grattan/man/age_pension_age.Rd | 2 grattan-2.0.0.0/grattan/man/cpi_inflator.Rd | 8 grattan-2.0.0.0/grattan/man/cpi_inflator_quarters.Rd | 2 grattan-2.0.0.0/grattan/man/income_tax.Rd | 18 grattan-2.0.0.0/grattan/man/lito.Rd | 28 grattan-2.0.0.0/grattan/man/model_income_tax.Rd | 323 +- grattan-2.0.0.0/grattan/man/sapto.Rd | 3 grattan-2.0.0.0/grattan/man/set_offset.Rd |only grattan-2.0.0.0/grattan/man/small_business_tax_offset.Rd | 6 grattan-2.0.0.0/grattan/man/validate_date.Rd | 64 grattan-2.0.0.0/grattan/src/1984.c |only grattan-2.0.0.0/grattan/src/1985.c |only grattan-2.0.0.0/grattan/src/1986.c |only grattan-2.0.0.0/grattan/src/1987.c |only grattan-2.0.0.0/grattan/src/1988.c |only grattan-2.0.0.0/grattan/src/1989.c |only grattan-2.0.0.0/grattan/src/1990.c |only grattan-2.0.0.0/grattan/src/1991.c |only grattan-2.0.0.0/grattan/src/1992.c |only grattan-2.0.0.0/grattan/src/1993.c |only grattan-2.0.0.0/grattan/src/1994.c |only grattan-2.0.0.0/grattan/src/1995.c |only grattan-2.0.0.0/grattan/src/1996.c |only grattan-2.0.0.0/grattan/src/1997.c |only grattan-2.0.0.0/grattan/src/1998.c |only grattan-2.0.0.0/grattan/src/1999.c |only grattan-2.0.0.0/grattan/src/2000.c |only grattan-2.0.0.0/grattan/src/2001.c |only grattan-2.0.0.0/grattan/src/2002.c |only grattan-2.0.0.0/grattan/src/2003.c |only grattan-2.0.0.0/grattan/src/2004.c |only grattan-2.0.0.0/grattan/src/2005.c |only grattan-2.0.0.0/grattan/src/2006.c |only grattan-2.0.0.0/grattan/src/2007.c |only grattan-2.0.0.0/grattan/src/2008.c |only grattan-2.0.0.0/grattan/src/2009.c |only grattan-2.0.0.0/grattan/src/2010.c |only grattan-2.0.0.0/grattan/src/2011.c |only grattan-2.0.0.0/grattan/src/2012.c |only grattan-2.0.0.0/grattan/src/2013.c |only grattan-2.0.0.0/grattan/src/2014.c |only grattan-2.0.0.0/grattan/src/2015.c |only grattan-2.0.0.0/grattan/src/2016.c |only grattan-2.0.0.0/grattan/src/2017.c |only grattan-2.0.0.0/grattan/src/2018.c |only grattan-2.0.0.0/grattan/src/2019.c |only grattan-2.0.0.0/grattan/src/2020.c |only grattan-2.0.0.0/grattan/src/2021.c |only grattan-2.0.0.0/grattan/src/2022.c |only grattan-2.0.0.0/grattan/src/Cdecode_age_range.c |only grattan-2.0.0.0/grattan/src/Cdo_rn.c |only grattan-2.0.0.0/grattan/src/Cincome_tax.c |only grattan-2.0.0.0/grattan/src/Crebate_income.c |only grattan-2.0.0.0/grattan/src/Makevars |only grattan-2.0.0.0/grattan/src/Offset.c |only grattan-2.0.0.0/grattan/src/age.c |only grattan-2.0.0.0/grattan/src/errif.c |only grattan-2.0.0.0/grattan/src/getListElement.c |only grattan-2.0.0.0/grattan/src/grattan.h | 304 ++ grattan-2.0.0.0/grattan/src/hazName.c |only grattan-2.0.0.0/grattan/src/init.c |only grattan-2.0.0.0/grattan/src/isEquiInt.c |only grattan-2.0.0.0/grattan/src/lito.c |only grattan-2.0.0.0/grattan/src/medicare.c |only grattan-2.0.0.0/grattan/src/minmax.c |only grattan-2.0.0.0/grattan/src/omp_diagnose.c |only grattan-2.0.0.0/grattan/src/sapto.c |only grattan-2.0.0.0/grattan/src/starts_with_medicare.c |only grattan-2.0.0.0/grattan/src/starts_with_sapto.c |only grattan-2.0.0.0/grattan/src/tax-system.c |only grattan-2.0.0.0/grattan/tests/testthat.R | 38 grattan-2.0.0.0/grattan/tests/testthat/test-income_tax2.R | 55 grattan-2.0.0.0/grattan/tests/testthat/test_0sysdata.R | 124 - grattan-2.0.0.0/grattan/tests/testthat/test_CG_inflators.R | 18 grattan-2.0.0.0/grattan/tests/testthat/test_LITO.R | 75 grattan-2.0.0.0/grattan/tests/testthat/test_Offset.R | 88 grattan-2.0.0.0/grattan/tests/testthat/test_System.R |only grattan-2.0.0.0/grattan/tests/testthat/test_age_grouper.R | 8 grattan-2.0.0.0/grattan/tests/testthat/test_aus_pop_qtr.R | 170 - grattan-2.0.0.0/grattan/tests/testthat/test_bto.R | 34 grattan-2.0.0.0/grattan/tests/testthat/test_check_TF.R | 68 grattan-2.0.0.0/grattan/tests/testthat/test_compare_avg_tax_rates.R | 164 - grattan-2.0.0.0/grattan/tests/testthat/test_cpi.R | 750 +++--- grattan-2.0.0.0/grattan/tests/testthat/test_differentially_uprate_wage.R | 31 grattan-2.0.0.0/grattan/tests/testthat/test_financialfunctions.R | 26 grattan-2.0.0.0/grattan/tests/testthat/test_generic_inflator.R | 52 grattan-2.0.0.0/grattan/tests/testthat/test_gni.R | 72 grattan-2.0.0.0/grattan/tests/testthat/test_incomeTaxCollections.R | 7 grattan-2.0.0.0/grattan/tests/testthat/test_incometax_dotsATO.R | 21 grattan-2.0.0.0/grattan/tests/testthat/test_incometax_dotsATO_sfa.R | 98 grattan-2.0.0.0/grattan/tests/testthat/test_incometax_single.R | 248 +- grattan-2.0.0.0/grattan/tests/testthat/test_inflator.R | 7 grattan-2.0.0.0/grattan/tests/testthat/test_install_taxstats.R | 22 grattan-2.0.0.0/grattan/tests/testthat/test_inverse_average_rate.R | 438 +-- grattan-2.0.0.0/grattan/tests/testthat/test_inverse_income.R | 148 - grattan-2.0.0.0/grattan/tests/testthat/test_lf_inflator.R | 484 +-- grattan-2.0.0.0/grattan/tests/testthat/test_medicare_levy.R | 245 - grattan-2.0.0.0/grattan/tests/testthat/test_modelCJ.R | 98 grattan-2.0.0.0/grattan/tests/testthat/test_model_income_tax.R |only grattan-2.0.0.0/grattan/tests/testthat/test_mutate_ntile.R | 16 grattan-2.0.0.0/grattan/tests/testthat/test_progressivity.R | 28 grattan-2.0.0.0/grattan/tests/testthat/test_rN.R |only grattan-2.0.0.0/grattan/tests/testthat/test_sapto.R |only grattan-2.0.0.0/grattan/tests/testthat/test_small_business_tax_offset.R | 252 +- grattan-2.0.0.0/grattan/tests/testthat/test_super_vars.R | 566 ++-- grattan-2.0.0.0/grattan/tests/testthat/test_total_receipts.R | 116 grattan-2.0.0.0/grattan/tests/testthat/test_utils.R | 318 +- grattan-2.0.0.0/grattan/tests/testthat/test_verify_date.R | 142 - grattan-2.0.0.0/grattan/tests/testthat/test_wage_inflator.R | 436 +-- grattan-2.0.0.0/grattan/tests/testthat/test_wout_taxstats.R | 46 grattan-2.0.0.0/grattan/tests/testthat/test_zbenchmark.R | 94 224 files changed, 5457 insertions(+), 6800 deletions(-)
Title: Pie, Donut and Rose Pie Plots
Description: Create pie, donut and rose pie plot with 'ggplot2'.
Author: Yabing Song [aut, cre]
Maintainer: Yabing Song <songyb0519@gmail.com>
Diff between ggpie versions 0.2.1 dated 2022-06-09 and 0.2.2 dated 2022-06-27
DESCRIPTION | 7 - MD5 | 44 +++++----- R/utils.R | 11 ++ README.md | 2 inst/CITATION | 4 inst/doc/ggpie.html | 44 +++++----- man/figures/README-donut_horizon_in-1.png |binary man/figures/README-donut_horizon_in_no_split-1.png |binary man/figures/README-donut_horizon_out-1.png |binary man/figures/README-donut_horizon_out_no_split-1.png |binary man/figures/README-donut_threashold_horizon_in-1.png |binary man/figures/README-donut_threashold_horizon_in_no_split-1.png |binary man/figures/README-nested_pie_blank_inner_outer-1.png |binary man/figures/README-nested_pie_inner_outer_horizon_out_remove-1.png |binary man/figures/README-nested_pie_inner_outer_remove_horizon_in_remove-1.png |binary man/figures/README-pie3d-1.png |binary man/figures/README-pie_horizon_in_no_split-1.png |binary man/figures/README-pie_horizon_in_split-1.png |binary man/figures/README-pie_horizon_out_no_split-1.png |binary man/figures/README-pie_threashold_horizon_in-1.png |binary man/figures/README-rose_pie_no_tick-1.png |binary man/figures/README-rose_pie_with_tick-1.png |binary man/figures/README-rose_pie_with_tick_specific_break-1.png |binary 23 files changed, 62 insertions(+), 50 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package development
infrastructure inside the data integration centers ('DIZ') to
standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2022-06-27
DESCRIPTION | 9 - MD5 | 38 ++-- NAMESPACE | 20 +- R/check_if_table_exists.R | 126 +++++++-------- R/close_connection.R | 90 +++++------ R/combine_stats.R | 316 +++++++++++++++++++-------------------- R/db_connection.R | 36 ++++ R/get_config_env.R | 344 +++++++++++++++++++++---------------------- R/get_db_systems.R | 66 ++++---- R/query_database.R | 204 ++++++++++++------------- README.md | 1 man/check_if_table_exists.Rd | 54 +++--- man/close_connection.Rd | 64 ++++---- man/combine_stats.Rd | 62 +++---- man/db_connection.Rd | 156 +++++++++---------- man/get_config_env.Rd | 112 +++++++------- man/get_db_systems.Rd | 44 ++--- man/query_database.Rd | 118 +++++++------- man/xml_2_json.Rd | 34 ++-- tests/testthat/test-lints.R | 66 ++++---- 20 files changed, 999 insertions(+), 961 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.9 dated 2022-06-20 and 2.1.0 dated 2022-06-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/iterativeMCMC.R | 6 +++++- R/orderMCMCmain.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Bioclimatic Analysis and Classification
Description: Using numeric or raster data, this package contains functions to
calculate: complete water balance, bioclimatic balance, bioclimatic
intensities, reports for individual locations, multi-layered rasters for
spatial analysis.
Author: Roberto Serrano-Notivoli
Maintainer: Roberto Serrano-Notivoli <roberto.serrano@uam.es>
Diff between bioclim versions 0.2.0 dated 2022-02-18 and 0.3.0 dated 2022-06-27
DESCRIPTION | 10 ++-- MD5 | 47 +++++++++--------- NAMESPACE | 1 R/f_biobal.R | 25 ++++++---- R/f_biobal_raster.R | 23 ++++----- R/f_bioint.R | 36 +++++++------- R/f_bioint_raster.R | 104 ++++++++++++++++++++---------------------- R/f_biotype_raster.R | 7 +- R/f_ith.R | 8 +-- R/f_ith_raster.R | 19 +++---- R/f_plot_biobal.R | 37 ++++++++++---- R/f_plot_watbal.R | 14 ++--- R/f_postemp.R | 2 R/f_thermind.R | 4 - R/f_watbal.R | 4 + R/f_watbal_raster.R | 13 ++--- R/globals.R | 3 - data/biobalrast.rda |binary data/prerast.rda |binary data/temprast.rda |binary data/watbalrast.rda |binary inst/rmd/bc_template.Rmd | 10 +--- inst/rmd/bioclim_Mariquit.pdf |only man/biobal.Rd | 2 man/bioint.Rd | 5 +- 25 files changed, 202 insertions(+), 172 deletions(-)
Title: Interface to 'NetCDF' Datasets
Description: An interface to the 'NetCDF' file formats designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
Most capabilities of 'NetCDF' version 4 are supported. Optional conversions
of time units are enabled by 'UDUNITS' version 2, also from Unidata.
Author: Pavel Michna [aut],
Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>
Diff between RNetCDF versions 2.5-2 dated 2021-08-20 and 2.6-1 dated 2022-06-27
DESCRIPTION | 8 +++---- INSTALL | 4 +-- LICENSE | 2 - MD5 | 46 ++++++++++++++++++++-------------------- NEWS | 3 ++ R/RNetCDF.R | 58 +++++++++++++++++++++++++-------------------------- configure | 18 +++++++-------- configure.ac | 2 - src/Makevars.win | 22 ++++++++++++++++--- src/RNetCDF.h | 4 +-- src/attribute.c | 4 +-- src/common.c | 4 +-- src/common.h | 4 +-- src/convert.c | 4 +-- src/convert.h | 4 +-- src/dataset.c | 4 +-- src/dimension.c | 4 +-- src/group.c | 4 +-- src/init.c | 4 +-- src/type.c | 4 +-- src/udunits.c | 4 +-- src/variable.c | 4 +-- tests/RNetCDF-test.R | 4 +-- tools/convert.m4 | 4 +-- 24 files changed, 121 insertions(+), 102 deletions(-)
Title: Spherical Plotting
Description: Various functions for creating spherical coordinate system plots via extensions to rgl.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between sphereplot versions 1.5 dated 2013-10-22 and 1.5.1 dated 2022-06-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 4 ++++ man/rgl.sphMW.Rd | 1 - 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Statistical Significance of Clustering
Description: SigClust is a statistical method for testing the
significance of clustering results. SigClust can be applied to
assess the statistical significance of splitting a data set
into two clusters. For more than two clusters, SigClust can be
used iteratively.
Author: Hanwen Huang, Yufeng Liu & J. S. Marron
Maintainer: Hanwen Huang <hanwenh.unc@gmail.com>
Diff between sigclust versions 1.1.0 dated 2014-01-23 and 1.1.0.1 dated 2022-06-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: Robust Correlations
Description: Robust pairwise correlations based on estimates of scale,
particularly on "FastQn" one-step M-estimate.
Author: Paul Smirnov
Maintainer: Paul Smirnov <s.paul@mail.ru>
Diff between robcor versions 0.1-6 dated 2014-01-06 and 0.1-6.1 dated 2022-06-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 3 +++ R/psdcor.R | 6 ++---- R/robcor.R | 8 ++++---- 5 files changed, 16 insertions(+), 15 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.7 dated 2022-05-23 and 0.8.8 dated 2022-06-27
DESCRIPTION | 22 ++++---- MD5 | 30 +++++------ NEWS.md | 21 ++++++++ R/bruceR-stats_1_basic.R | 91 +++++++++++++++++++++++++---------- R/bruceR-stats_3_manova.R | 10 +-- R/bruceR-stats_4_regress.R | 115 +++++++++++++++++++++------------------------ R/bruceR-stats_5_advance.R | 5 - R/bruceR.R | 36 +++++++++++--- R/bruceR_utils.R | 12 +--- README.md | 6 -- man/EMMEANS.Rd | 10 +-- man/HLM_ICC_rWG.Rd | 18 +++---- man/PROCESS.Rd | 5 - man/TTEST.Rd | 28 +++++++++- man/model_summary.Rd | 99 ++++++++++++++++++-------------------- man/regress.Rd | 4 - 16 files changed, 297 insertions(+), 215 deletions(-)