Title: Generating Multi-State Survival Data
Description: Generation of survival data with one (binary)
time-dependent covariate. Generation of survival data arising
from a progressive illness-death model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>),
Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>),
Susana Faria [aut] (<https://orcid.org/0000-0001-8014-9902>)
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between genSurv versions 1.0.3 dated 2015-11-09 and 1.0.4 dated 2021-10-19
DESCRIPTION | 49 ++++++++++++++++++++------- MD5 | 32 ++++++++++------- NAMESPACE | 2 - R/dgBIV.R | 4 +- README.md |only build |only inst/CITATION | 30 ++++++++++------ inst/NEWS.Rd | 88 +++++++++++++++++++++++++------------------------ man/as.CMM.Rd | 15 +++++--- man/as.TDCM.Rd | 15 +++++--- man/as.THMM.Rd | 15 +++++--- man/genCMM.Rd | 25 ++++++++----- man/genCPHM.Rd | 7 +++ man/genSurv-package.Rd | 38 +++++++++++---------- man/genTDCM.Rd | 39 ++++++++++++--------- man/genTHMM.Rd | 25 ++++++++----- src/Makevars |only src/dgBIV.h |only src/genSurv-win.def |only src/init.c |only 20 files changed, 233 insertions(+), 151 deletions(-)
Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mañanes [aut, cre] (<https://orcid.org/0000-0001-7247-6794>),
Carlos Torroja [aut] (<https://orcid.org/0000-0001-8914-3400>),
Fatima Sanchez-Cabo [aut] (<https://orcid.org/0000-0003-1881-1664>)
Maintainer: Diego Mañanes <dmananesc@cnic.es>
Diff between digitalDLSorteR versions 0.1.0 dated 2021-10-08 and 0.1.1 dated 2021-10-19
DESCRIPTION | 8 ++-- MD5 | 34 +++++++++--------- NEWS.md | 9 ++++- R/dnnModel.R | 1 R/loadData.R | 1 R/simBulk.R | 4 +- R/simSingleCell.R | 70 ++++++++++++++++++++++----------------- R/utils.R | 1 README.md | 8 +++- build/partial.rdb |binary inst/doc/newModels.html | 66 ++++++++++++++++++------------------ man/estimateZinbwaveParams.Rd | 1 man/generateBulkCellMatrix.Rd | 1 man/loadSCProfiles.Rd | 1 man/showProbPlot.Rd | 1 man/simBulkProfiles.Rd | 1 man/simSCProfiles.Rd | 1 man/trainDigitalDLSorterModel.Rd | 1 18 files changed, 123 insertions(+), 86 deletions(-)
More information about digitalDLSorteR at CRAN
Permanent link
Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price
Sensitivity Meter in R, which is a survey-based approach
to analyze consumer price preferences and sensitivity
(van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>
Diff between pricesensitivitymeter versions 1.2.1 dated 2021-03-21 and 1.2.2 dated 2021-10-19
pricesensitivitymeter-1.2.1/pricesensitivitymeter/NEWS |only pricesensitivitymeter-1.2.2/pricesensitivitymeter/DESCRIPTION | 11 pricesensitivitymeter-1.2.2/pricesensitivitymeter/MD5 | 23 +- pricesensitivitymeter-1.2.2/pricesensitivitymeter/NEWS.md |only pricesensitivitymeter-1.2.2/pricesensitivitymeter/R/psm_plot.R | 10 pricesensitivitymeter-1.2.2/pricesensitivitymeter/README.md | 115 +++++----- pricesensitivitymeter-1.2.2/pricesensitivitymeter/build/vignette.rds |binary pricesensitivitymeter-1.2.2/pricesensitivitymeter/inst/doc/interpolation-in-small-samples.html | 8 pricesensitivitymeter-1.2.2/pricesensitivitymeter/inst/doc/using-weighted-data.Rmd | 2 pricesensitivitymeter-1.2.2/pricesensitivitymeter/inst/doc/using-weighted-data.html | 14 - pricesensitivitymeter-1.2.2/pricesensitivitymeter/inst/doc/visualizing-psm-results.html | 8 pricesensitivitymeter-1.2.2/pricesensitivitymeter/man/figures |only pricesensitivitymeter-1.2.2/pricesensitivitymeter/man/psm_plot.rd | 8 pricesensitivitymeter-1.2.2/pricesensitivitymeter/vignettes/using-weighted-data.Rmd | 2 14 files changed, 106 insertions(+), 95 deletions(-)
More information about pricesensitivitymeter at CRAN
Permanent link
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.
Author: Sacha Epskamp [aut, cre],
Eren Asena [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.2.4 dated 2020-10-23 and 0.3 dated 2021-10-19
DESCRIPTION | 15 ++++++++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS | 7 +++++++ R/Kappa.R | 8 ++++++-- R/Rothmana.R | 42 ++++++++++++++++++++++++++++++------------ R/dataPrep.R | 49 ++++++++++++++++++++++++++++++------------------- R/graphicalVAR.R | 12 ++++++++---- R/simMLgvar.R | 7 ++++--- man/graphicalVAR.Rd | 29 ++++++++++++++++++++--------- 10 files changed, 125 insertions(+), 63 deletions(-)
Title: Retrieving, Managing and Analysing Air Quality and Weather Data
for Lombardy (Italy) using ARPA Lombardia Open Database
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>).
Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network.
See the webpage <https://www.arpalombardia.it/Pages/ARPA_Home_Page.aspx> for further information on ARPA Lombardia's activities and history.
Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control.
The package makes available observations since 1989 (for weather) and 1996 (for air quality) and are updated with daily frequency by the regional agency.
Author: Paolo Maranzano [aut, cre, cph]
(<https://orcid.org/0000-0002-9228-2759>),
Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Diff between ARPALData versions 1.2.0 dated 2021-09-12 and 1.2.1 dated 2021-10-19
DESCRIPTION | 8 +- MD5 | 36 +++++------ R/ARPALdf_Summary_map.R | 2 R/Time_aggregate.R | 7 +- R/get_ARPA_Lombardia_AQ_data_1y.R | 20 +----- R/get_ARPA_Lombardia_AQ_municipal_registry.R | 2 R/get_ARPA_Lombardia_AQ_registry.R | 2 R/get_ARPA_Lombardia_W_data.R | 4 - R/get_ARPA_Lombardia_W_data_1y.R | 78 +++++++++++++----------- R/get_ARPA_Lombardia_W_registry.R | 2 R/registry_KNN_dist.R | 8 +- R/url_dataset_year.R | 2 man/ARPALdf_Summary_map.Rd | 2 man/Time_aggregate.Rd | 7 +- man/get_ARPA_Lombardia_AQ_municipal_registry.Rd | 2 man/get_ARPA_Lombardia_AQ_registry.Rd | 2 man/get_ARPA_Lombardia_W_data.Rd | 2 man/get_ARPA_Lombardia_W_registry.Rd | 2 man/registry_KNN_dist.Rd | 5 - 19 files changed, 101 insertions(+), 92 deletions(-)
Title: Computational Geometry
Description: R interface to (some of) cddlib
(<https://github.com/cddlib/cddlib>).
Converts back and forth between two representations of a convex polytope:
as solution of a set of linear equalities and inequalities and as
convex hull of set of points and rays.
Also does linear programming and redundant generator elimination
(for example, convex hull in n dimensions). All functions can use exact
infinite-precision rational arithmetic.
Author: Charles J. Geyer <charlie@stat.umn.edu> and
Glen D. Meeden <glen@stat.umn.edu>, incorporates code from
cddlib (ver 0.94f) written by Komei Fukuda <fukuda@ifor.math.ethz.ch>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between rcdd versions 1.2-2 dated 2019-04-22 and 1.4 dated 2021-10-19
DESCRIPTION | 15 +-- MD5 | 60 +++++++------- R/onAttach.R | 4 build/vignette.rds |binary inst/doc/vinny.R | 57 +++++++++++++ inst/doc/vinny.Rnw | 192 ++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/vinny.pdf |binary man/qgram.Rd | 10 +- man/scdd.Rd | 2 tests/allfaces.Rout.save | 9 -- tests/arith.Rout.save | 9 -- tests/bar-gmp.Rout.save | 9 -- tests/bar.Rout.save | 11 +- tests/bug.Rout.save | 9 -- tests/bug2.Rout.save | 9 -- tests/chull.Rout.save | 9 -- tests/chull2.Rout.save | 11 +- tests/convert.Rout.save | 9 -- tests/fred.Rout.save | 9 -- tests/lpcdd.Rout.save | 9 -- tests/make.Rout.save | 11 +- tests/oops.Rout.save | 9 -- tests/qgram.Rout.save | 9 -- tests/qmatmult.Rout.save | 9 -- tests/qux-gmp.Rout.save | 9 -- tests/qux.Rout.save | 9 -- tests/redund.Rout.save | 9 -- tests/sammy.Rout.save | 9 -- tests/subset.Rout.save | 9 -- tests/zero.Rout.save | 9 -- vignettes/vinny.Rnw | 192 ++++++++++++++++++++++++++++++++++++++++++++++- 31 files changed, 572 insertions(+), 155 deletions(-)
Title: Superfast Likelihood Inference for Stationary Gaussian Time
Series
Description: Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
Author: Yun Ling [aut],
Martin Lysy [aut, cre]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between SuperGauss versions 2.0.1 dated 2020-10-03 and 2.0.2 dated 2021-10-19
DESCRIPTION | 8 MD5 | 14 build/vignette.rds |binary configure | 731 ++++++++++++++++++++++++++++++++++++++ configure.ac | 12 inst/doc/SuperGauss-quicktut.html | 51 +- man/SuperGauss-package.Rd | 2 man/Toeplitz.Rd | 7 8 files changed, 789 insertions(+), 36 deletions(-)
Title: Fast Region-Based Association Tests on Summary Statistics
Description: An adaptation of classical region/gene-based association analysis
techniques to the use of summary statistics (P values and effect sizes)
and correlations between genetic variants as input. It is a tool to perform
the most popular and efficient gene-based tests using the results of genome-wide
association (meta-)analyses without having the original genotypes and
phenotypes at hand.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and
Gulnara R. Svishcheva <gulsvi@bionet.nsc.ru>
with contributions from:
Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method),
Minghui Wang, Yiyuan Liu, Shizhong Han (simpleM function),
Yaowu Liu (ACAT function), Thomas Lumley ('kuonen' method),
and James O. Ramsay (functional data analysis functions)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>
Diff between sumFREGAT versions 1.2.1 dated 2021-02-28 and 1.2.2 dated 2021-10-19
sumFREGAT-1.2.1/sumFREGAT/R/FFGAS.R |only sumFREGAT-1.2.1/sumFREGAT/R/MLR.R |only sumFREGAT-1.2.1/sumFREGAT/man/FFGAS.rd |only sumFREGAT-1.2.2/sumFREGAT/ChangeLog | 5 sumFREGAT-1.2.2/sumFREGAT/DESCRIPTION | 6 sumFREGAT-1.2.2/sumFREGAT/MD5 | 39 sumFREGAT-1.2.2/sumFREGAT/NAMESPACE | 2 sumFREGAT-1.2.2/sumFREGAT/R/ACAT.R | 2 sumFREGAT-1.2.2/sumFREGAT/R/ACATO.R | 5 sumFREGAT-1.2.2/sumFREGAT/R/BT.R | 11 sumFREGAT-1.2.2/sumFREGAT/R/FLM.R | 46 - sumFREGAT-1.2.2/sumFREGAT/R/KMTest_Optimal.R | 86 +- sumFREGAT-1.2.2/sumFREGAT/R/PCA.R | 178 ++-- sumFREGAT-1.2.2/sumFREGAT/R/SKAT.R | 48 - sumFREGAT-1.2.2/sumFREGAT/R/SKATO.R | 66 - sumFREGAT-1.2.2/sumFREGAT/R/check.R | 37 sumFREGAT-1.2.2/sumFREGAT/R/genewise.R | 28 sumFREGAT-1.2.2/sumFREGAT/R/get.sumstat.R | 557 +++++++------ sumFREGAT-1.2.2/sumFREGAT/R/sumSTAAR.R |only sumFREGAT-1.2.2/sumFREGAT/R/sumchi.R | 2 sumFREGAT-1.2.2/sumFREGAT/man/gene-based_test_functions.rd | 47 - sumFREGAT-1.2.2/sumFREGAT/man/sumFREGAT-package.rd | 2 sumFREGAT-1.2.2/sumFREGAT/man/sumSTAAR.rd |only 23 files changed, 622 insertions(+), 545 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre],
Giulio Costantini [aut],
Jonas Haslbeck [aut],
Adela Isvoranu [aut],
Angelique O. J. Cramer [ctb],
Lourens J. Waldorp [ctb],
Verena D. Schmittmann [ctb],
Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.6.9 dated 2021-01-28 and 1.9 dated 2021-10-19
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 16 ++++++++++++++++ R/centralityFunctions.R | 13 ++++++++++++- R/centralityPlot.R | 2 +- R/clusteringPlot.R | 2 +- R/cor_auto.R | 4 ++-- R/qgraph.R | 28 ++++++++++++++++++++++------ R/vein.R | 15 ++++++++++++++- man/CentAndClusfuns.Rd | 4 ++-- man/qgraph.Rd | 12 +----------- man/qgraph_loadings.Rd | 10 ++++++---- 12 files changed, 92 insertions(+), 44 deletions(-)
Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging,
weighted averaging, and stacking. These techniques are popular methods
to improve forecast accuracy and stability. Refer to papers such as
"Machine-Learning Models for Sales Time Series Forecasting" Pavlyshenko, B.M. (2019) <doi:10.3390>.
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime.ensemble versions 0.4.2 dated 2021-07-16 and 1.0.0 dated 2021-10-19
DESCRIPTION | 15 +++--- MD5 | 28 ++++++++---- NAMESPACE | 4 + NEWS.md | 14 ++++++ R/00_global_variables.R | 3 - R/nested_ensemble_average.R |only R/nested_ensemble_weighted.R |only R/utils-parallel_processing.R |only README.md | 6 +- build/vignette.rds |binary inst/doc/getting-started-with-modeltime-ensemble.html | 12 +---- inst/doc/nested-ensembles.R |only inst/doc/nested-ensembles.Rmd |only inst/doc/nested-ensembles.html |only inst/doc/recursive-ensembles.html | 12 ++--- man/ensemble_nested_average.Rd |only man/ensemble_nested_weighted.Rd |only tests/testthat/test-ensemble_model_spec.R | 42 +++++++----------- tests/testthat/test-nested-ensembles.R |only vignettes/nested-ensembles.Rmd |only 20 files changed, 77 insertions(+), 59 deletions(-)
More information about modeltime.ensemble at CRAN
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Title: Language Server Protocol
Description: An implementation of the Language Server Protocol
for R. The Language Server protocol is used by an editor client to
integrate features like auto completion. See
<https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre],
Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.11 dated 2021-07-22 and 0.3.12 dated 2021-10-19
languageserver-0.3.11/languageserver/man/document_code_action_reply.Rd |only languageserver-0.3.12/languageserver/DESCRIPTION | 17 - languageserver-0.3.12/languageserver/MD5 | 39 +- languageserver-0.3.12/languageserver/NEWS.md | 17 + languageserver-0.3.12/languageserver/R/completion.R | 14 languageserver-0.3.12/languageserver/R/definition.R | 8 languageserver-0.3.12/languageserver/R/document.R | 2 languageserver-0.3.12/languageserver/R/handlers-langfeatures.R | 4 languageserver-0.3.12/languageserver/R/hover.R | 15 languageserver-0.3.12/languageserver/R/namespace.R | 2 languageserver-0.3.12/languageserver/R/signature.R | 4 languageserver-0.3.12/languageserver/R/utils.R | 45 ++ languageserver-0.3.12/languageserver/R/workspace.R | 4 languageserver-0.3.12/languageserver/README.md | 34 +- languageserver-0.3.12/languageserver/tests/testthat/helper-utils.R | 95 +++--- languageserver-0.3.12/languageserver/tests/testthat/test-completion.R | 71 ++++ languageserver-0.3.12/languageserver/tests/testthat/test-definition.R | 74 ++++ languageserver-0.3.12/languageserver/tests/testthat/test-hover.R | 153 +++++++++- languageserver-0.3.12/languageserver/tests/testthat/test-link.R | 136 ++++++++ languageserver-0.3.12/languageserver/tests/testthat/test-signature.R | 19 + languageserver-0.3.12/languageserver/tests/testthat/test-workspace.R | 2 21 files changed, 650 insertions(+), 105 deletions(-)
More information about languageserver at CRAN
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Title: Fair Data Adaptation with Quantile Preservation
Description: An implementation of the fair data adaptation with quantile
preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>.
The adaptation procedure uses the specified causal graph to pre-process the
given training and testing data in such a way to remove the bias caused by
the protected attribute. The procedure uses tree ensembles for quantile
regression.
Author: Drago Plecko [aut, cre],
Nicolas Bennett [aut]
Maintainer: Drago Plecko <drago.plecko@stat.math.ethz.ch>
Diff between fairadapt versions 0.2.0 dated 2021-07-28 and 0.2.1 dated 2021-10-19
fairadapt-0.2.0/fairadapt/tests/PSCF |only fairadapt-0.2.0/fairadapt/tests/benchmarking |only fairadapt-0.2.0/fairadapt/tests/hidden |only fairadapt-0.2.0/fairadapt/tests/real-data |only fairadapt-0.2.0/fairadapt/vignettes/jss.fdb_latexmk |only fairadapt-0.2.0/fairadapt/vignettes/jss.fls |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/census-adapt-1.pdf |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/graph-semimarkov-1.pdf |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/log-and-graph-1.pdf |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/mat-1.pdf |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/resolving-graph-1.pdf |only fairadapt-0.2.0/fairadapt/vignettes/jss_files/figure-latex/vis-diff-1.pdf |only fairadapt-0.2.1/fairadapt/DESCRIPTION | 21 fairadapt-0.2.1/fairadapt/MD5 | 125 - fairadapt-0.2.1/fairadapt/NEWS.md | 5 fairadapt-0.2.1/fairadapt/R/checks.R | 18 fairadapt-0.2.1/fairadapt/R/data.R | 2 fairadapt-0.2.1/fairadapt/R/fairadapt.R | 6 fairadapt-0.2.1/fairadapt/R/generics.R | 15 fairadapt-0.2.1/fairadapt/R/graphs.R | 4 fairadapt-0.2.1/fairadapt/README.md | 4 fairadapt-0.2.1/fairadapt/build/vignette.rds |binary fairadapt-0.2.1/fairadapt/inst/doc/jss.R | 358 ++- fairadapt-0.2.1/fairadapt/inst/doc/jss.Rmd | 901 ++++++---- fairadapt-0.2.1/fairadapt/inst/doc/jss.pdf |binary fairadapt-0.2.1/fairadapt/man/fairTwins.Rd | 2 fairadapt-0.2.1/fairadapt/man/fairadapt.Rd | 5 fairadapt-0.2.1/fairadapt/man/gov_census.Rd | 2 fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/auto_cts.png |binary fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/auto_rf.png |binary fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/ftdef_cts.csv | 99 + fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/ftdef_lin.csv | 99 + fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/ftdef_rf.csv | 99 + fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/plot_cts.png |binary fairadapt-0.2.1/fairadapt/tests/testthat/_snaps/generics/plot_rf.png |binary fairadapt-0.2.1/fairadapt/tests/testthat/helpers.R | 9 fairadapt-0.2.1/fairadapt/tests/testthat/test-checks.R | 2 fairadapt-0.2.1/fairadapt/tests/testthat/test-generics.R | 6 fairadapt-0.2.1/fairadapt/vignettes/jss.Rmd | 901 ++++++---- fairadapt-0.2.1/fairadapt/vignettes/jss.bib | 297 ++- fairadapt-0.2.1/fairadapt/vignettes/jss_cache |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/before-adapt-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/census-graph-1.pdf |binary fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/census-tikz-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/census-tikz-1.png |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/fairtwin-plot-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/graph-plot-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/rel-edu-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/rel-edu-1.png |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/res-graph-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/semi-graph-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/semi-markov-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/semi-markov-1.png |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/uni-adm-1.pdf |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/uni-adm-1.png |only fairadapt-0.2.1/fairadapt/vignettes/jss_files/figure-latex/vis-adapt-1.pdf |binary 56 files changed, 1945 insertions(+), 1035 deletions(-)
Title: Build and Run Spatially Explicit Agent-Based Models
Description: Build and run spatially explicit
agent-based models using only the R platform. 'NetLogoR' follows the same
framework as the 'NetLogo' software
(Wilensky, 1999 <http://ccl.northwestern.edu/netlogo/>) and is a translation
in R of the structure and functions of 'NetLogo'.
'NetLogoR' provides new R classes to define model agents and functions to
implement spatially explicit agent-based models in the R environment.
This package allows benefiting of the fast and easy coding phase from the
highly developed 'NetLogo' framework, coupled with the versatility, power
and massive resources of the R software.
Examples of three models (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>,
Butterfly (Railsback and Grimm, 2012) and Wolf-Sheep-Predation
<http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>) written using
'NetLogoR' are available. The 'NetLogo' code of the original version of these
models is provided alongside.
A programming guide inspired from the 'NetLogo' Programming Guide
(<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary
of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>)
equivalences are also available.
NOTE: To increment 'time', these functions can use a for loop or can be
integrated with a discrete event simulator, such as 'SpaDES'
(<https://cran.r-project.org/package=SpaDES>).
The suggested package 'fastshp' can be installed with
'install.packages("fastshp", repos = "https://rforge.net", type = "source")'.
Author: Sarah Bauduin [aut] (<https://orcid.org/0000-0002-3252-5894>),
Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between NetLogoR versions 0.3.8 dated 2021-07-10 and 0.3.9 dated 2021-10-19
DESCRIPTION | 12 ++--- MD5 | 26 +++++------ NAMESPACE | 1 NEWS.md | 8 +++ R/NetLogoR-package.R | 10 +++- R/world-functions.R | 78 ++++++++++------------------------ R/worldNLR-classes-methods.R | 12 ++++- README.md | 7 +-- build/vignette.rds |binary inst/doc/ProgrammingGuide.html | 24 +++++----- man/projNowhere.Rd | 5 ++ man/raster2world.Rd | 23 +++++----- man/stackWorlds.Rd | 7 ++- tests/testthat/test-world-functions.R | 12 ++++- 14 files changed, 119 insertions(+), 106 deletions(-)
Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and
generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre],
Pedro G. Lind [aut],
David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>
Diff between Langevin versions 1.3.0 dated 2021-10-18 and 1.3.1 dated 2021-10-19
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/Langevin.pdf |binary src/Makevars | 6 ------ src/Makevars.win | 12 +----------- 6 files changed, 14 insertions(+), 26 deletions(-)
Title: Download, Edit and Include Wind and Sea Currents Data in
Ecological and Evolutionary Analysis
Description: Tools for download and manage surface wind and sea currents data from the Global Forecasting System <https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast> and to compute connectivity between locations.
Author: Javier Fernández-López [aut, cre],
Klaus Schliep [aut],
Yurena Arjona [aut]
Maintainer: Javier Fernández-López <jflopez.bio@gmail.com>
Diff between rWind versions 1.1.5 dated 2020-02-17 and 1.1.7 dated 2021-10-19
DESCRIPTION | 16 MD5 | 53 +- NEWS | 16 R/rWind-package.R | 14 R/wind_functions2.R | 869 +++++++++++++++++++++++-------------------- README.md | 122 +++++- build/vignette.rds |binary inst/WORDLIST |only inst/doc/Shortest_paths.R | 16 inst/doc/Shortest_paths.Rmd | 2 inst/doc/Shortest_paths.html | 258 ++++++++---- man/arrowDir.Rd | 11 man/flow.dispersion.Rd | 17 man/flow.dispersion_int.Rd | 16 man/rWind-package.Rd | 10 man/seaOscar.dl.Rd | 23 - man/tidy.rWind_series.Rd | 5 man/uv2ds.Rd | 11 man/wind.data.Rd | 9 man/wind.dl.Rd | 30 - man/wind.dl_2.Rd | 32 - man/wind.fit_int.Rd | 6 man/wind.mean.Rd | 10 man/wind.series.Rd | 8 man/wind2raster.Rd | 5 man/wind2raster_int.Rd | 4 tests/testthat/test_rWind.R | 31 - vignettes/Shortest_paths.Rmd | 2 28 files changed, 921 insertions(+), 675 deletions(-)
Title: Access, Retrieve, and Work with Canadian Census Data and
Geography
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer),
Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for
correspondence),
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.4.3 dated 2021-06-08 and 0.4.4 dated 2021-10-19
DESCRIPTION | 6 MD5 | 48 NEWS.md | 5 build/vignette.rds |binary inst/doc/Dwellings_by_document_type_cross_tabulation.html | 339 inst/doc/Making_maps_with_cancensus.R | 7 inst/doc/Making_maps_with_cancensus.Rmd | 7 inst/doc/Making_maps_with_cancensus.html | 5062 -------------- inst/doc/Taxfiler_Data.R | 8 inst/doc/Taxfiler_Data.Rmd | 8 inst/doc/Taxfiler_Data.html | 389 - inst/doc/cancensus.R | 9 inst/doc/cancensus.Rmd | 9 inst/doc/cancensus.html | 484 - inst/doc/data_discovery.R | 15 inst/doc/data_discovery.Rmd | 15 inst/doc/data_discovery.html | 1736 ---- inst/doc/intersecting_geometries.R | 8 inst/doc/intersecting_geometries.Rmd | 8 inst/doc/intersecting_geometries.html | 321 vignettes/Making_maps_with_cancensus.Rmd | 7 vignettes/Taxfiler_Data.Rmd | 8 vignettes/cancensus.Rmd | 9 vignettes/data_discovery.Rmd | 15 vignettes/intersecting_geometries.Rmd | 8 25 files changed, 745 insertions(+), 7786 deletions(-)
Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.
Author: Ozvan Bocher and Hervé Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>
Diff between Ravages versions 0.1.5 dated 2021-05-12 and 1.0.0 dated 2021-10-19
Ravages-0.1.5/Ravages/R/random_bed_matrix.r |only Ravages-0.1.5/Ravages/man/random.bed.matrix.Rd |only Ravages-1.0.0/Ravages/DESCRIPTION | 12 Ravages-1.0.0/Ravages/MD5 | 102 ++- Ravages-1.0.0/Ravages/NAMESPACE | 19 Ravages-1.0.0/Ravages/NEWS | 21 Ravages-1.0.0/Ravages/R/CAST.r | 16 Ravages-1.0.0/Ravages/R/RAVA_FIRST.r |only Ravages-1.0.0/Ravages/R/adjustedCADD_annotation.r |only Ravages-1.0.0/Ravages/R/burden.r | 6 Ravages-1.0.0/Ravages/R/burden_continuous.r | 25 Ravages-1.0.0/Ravages/R/burden_continuous_subscores.r |only Ravages-1.0.0/Ravages/R/burden_mlogit.r | 18 Ravages-1.0.0/Ravages/R/burden_mlogit_subscores.r |only Ravages-1.0.0/Ravages/R/burden_subscores.r |only Ravages-1.0.0/Ravages/R/filter_adjustedCADD.r |only Ravages-1.0.0/Ravages/R/filter_rare_variants.r | 19 Ravages-1.0.0/Ravages/R/genotypic.freq.r | 9 Ravages-1.0.0/Ravages/R/or_matrix_fix.r | 10 Ravages-1.0.0/Ravages/R/or_matrix_fix_same_variant.r | 10 Ravages-1.0.0/Ravages/R/random_bed_matrix_haplo.r | 30 - Ravages-1.0.0/Ravages/R/rbm_GRR.r |only Ravages-1.0.0/Ravages/R/rbm_GRR_power.r |only Ravages-1.0.0/Ravages/R/rbm_haplos_power.r |only Ravages-1.0.0/Ravages/R/set_CADDregions.r |only Ravages-1.0.0/Ravages/R/set_genomic_region.r | 19 Ravages-1.0.0/Ravages/R/set_genomic_region_subregion.r |only Ravages-1.0.0/Ravages/data/Subregions_LCT_example.RData |only Ravages-1.0.0/Ravages/data/datalist | 1 Ravages-1.0.0/Ravages/data/genes.b37.RData |binary Ravages-1.0.0/Ravages/data/genes.b38.RData |binary Ravages-1.0.0/Ravages/inst/doc/Ravages_Simulations_vignette.R | 72 -- Ravages-1.0.0/Ravages/inst/doc/Ravages_Simulations_vignette.Rmd | 139 ++--- Ravages-1.0.0/Ravages/inst/doc/Ravages_Simulations_vignette.html | 157 ++--- Ravages-1.0.0/Ravages/inst/doc/Ravages_vignette.R | 102 ++- Ravages-1.0.0/Ravages/inst/doc/Ravages_vignette.Rmd | 235 ++++++-- Ravages-1.0.0/Ravages/inst/doc/Ravages_vignette.html | 274 +++++++--- Ravages-1.0.0/Ravages/man/CAST.Rd | 7 Ravages-1.0.0/Ravages/man/GRR.matrix.Rd | 4 Ravages-1.0.0/Ravages/man/GnomADgenes.Rd | 2 Ravages-1.0.0/Ravages/man/Jaccard.Rd | 8 Ravages-1.0.0/Ravages/man/RAVA_FIRST.Rd |only Ravages-1.0.0/Ravages/man/SKAT.Rd | 9 Ravages-1.0.0/Ravages/man/adjustedCADD_annotation.Rd |only Ravages-1.0.0/Ravages/man/burden.Rd | 28 - Ravages-1.0.0/Ravages/man/burden.continuous.Rd | 15 Ravages-1.0.0/Ravages/man/burden.continuous.subscores.Rd |only Ravages-1.0.0/Ravages/man/burden.mlogit.Rd | 10 Ravages-1.0.0/Ravages/man/burden.mlogit.subscores.Rd |only Ravages-1.0.0/Ravages/man/burden.subscores.Rd |only Ravages-1.0.0/Ravages/man/burden.weighted.matrix.Rd | 2 Ravages-1.0.0/Ravages/man/filter.rare.variants.Rd | 19 Ravages-1.0.0/Ravages/man/filter_adjustedCADD.Rd |only Ravages-1.0.0/Ravages/man/genes.positions.Rd | 10 Ravages-1.0.0/Ravages/man/genotypic.freq.Rd | 9 Ravages-1.0.0/Ravages/man/rbm.GRR.Rd |only Ravages-1.0.0/Ravages/man/rbm.GRR.power.Rd |only Ravages-1.0.0/Ravages/man/rbm.haplos.power.Rd |only Ravages-1.0.0/Ravages/man/rbm.haplos.thresholds.Rd | 12 Ravages-1.0.0/Ravages/man/set.CADDregions.Rd |only Ravages-1.0.0/Ravages/man/set.genomic.region.Rd | 15 Ravages-1.0.0/Ravages/man/set.genomic.region.subregion.Rd |only Ravages-1.0.0/Ravages/man/subregions.LCT.Rd |only Ravages-1.0.0/Ravages/vignettes/Ravages_Simulations_vignette.Rmd | 139 ++--- Ravages-1.0.0/Ravages/vignettes/Ravages_vignette.Rmd | 235 ++++++-- 65 files changed, 1160 insertions(+), 660 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.0.6 dated 2021-07-25 and 1.0.7 dated 2021-10-19
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS.md | 4 + R/cox2.R | 4 - R/gee.R | 16 +++--- R/glmshow.R | 9 ++- R/lmer.R | 125 ++++++++++++++++++++++++-------------------------- R/svycox.R | 10 ++-- R/svyglm.R | 5 +- build/vignette.rds |binary inst/doc/jstable.html | 31 ++++++------ 11 files changed, 120 insertions(+), 112 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.8.0 dated 2021-06-09 and 0.9.0 dated 2021-10-19
ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggbarstats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggbetweenstats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggcorrmat.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggdotplotstats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_gghistostats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggpiestats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggscatterstats.R |only ggstatsplot-0.8.0/ggstatsplot/R/grouped_ggwithinstats.R |only ggstatsplot-0.8.0/ggstatsplot/R/helpers_ggcoefstats_graphics.R |only ggstatsplot-0.8.0/ggstatsplot/R/helpers_grouped_functions.R |only ggstatsplot-0.8.0/ggstatsplot/R/theme_ggstatsplot.R |only ggstatsplot-0.8.0/ggstatsplot/data/VR_dilemma.rdata |only ggstatsplot-0.8.0/ggstatsplot/data/movies_wide.rdata |only ggstatsplot-0.8.0/ggstatsplot/man/VR_dilemma.Rd |only ggstatsplot-0.8.0/ggstatsplot/man/figures/README-ggcoefstats2-1.png |only ggstatsplot-0.8.0/ggstatsplot/man/figures/README-ggscatterstats3-1.png |only ggstatsplot-0.8.0/ggstatsplot/man/figures/arguments.png |only ggstatsplot-0.8.0/ggstatsplot/man/figures/ggstatsverse.jpg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-archived.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-defunct.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-deprecated.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-experimental.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-maturing.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-questioning.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-stable.svg |only ggstatsplot-0.8.0/ggstatsplot/man/figures/lifecycle-superseded.svg |only ggstatsplot-0.8.0/ggstatsplot/man/ggcoefstats_label_maker.Rd |only ggstatsplot-0.8.0/ggstatsplot/man/movies_wide.Rd |only ggstatsplot-0.8.0/ggstatsplot/tests/README.md |only ggstatsplot-0.8.0/ggstatsplot/tests/testthat/Rplots.pdf |only ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/combine_plots.Rmd |only ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/effsize_interpretation.Rmd |only ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/other_resources.Rmd |only ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/session_info.Rmd |only ggstatsplot-0.9.0/ggstatsplot/DESCRIPTION | 24 ggstatsplot-0.9.0/ggstatsplot/MD5 | 316 +- ggstatsplot-0.9.0/ggstatsplot/NAMESPACE | 86 ggstatsplot-0.9.0/ggstatsplot/NEWS.md | 134 - 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ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 174 - ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggcoefstats.R | 142 - ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggcorrmat.R | 65 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggdotplotstats.R | 99 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-gghistostats.R | 140 - ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggpiestats.R | 303 +- ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggscatterstats.R | 274 +- ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-ggwithinstats.R | 327 +- ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggbarstats.R | 31 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggbetweenstats.R | 119 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggcorrmat.R | 96 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggdotplotstats.R | 23 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_gghistostats.R | 30 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggpiestats.R | 81 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggscatterstats.R | 170 - ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-grouped_ggwithinstats.R | 209 - ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-pairwise_caption_helpers.R |only ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-pairwise_comparisons_between.R |only ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-pairwise_comparisons_within.R |only ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-pairwise_ggsignif.R | 7 ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-vdiffr_figs.R | 247 +- ggstatsplot-0.9.0/ggstatsplot/tests/testthat/test-z_ggcoefstats_dataframes.R | 428 +-- ggstatsplot-0.9.0/ggstatsplot/vignettes/additional.Rmd | 77 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/benchmarking.Rmd | 4 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/dependencies.Rmd | 12 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/faq.Rmd | 99 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 134 - ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 266 +- ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 63 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 22 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 19 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 30 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 60 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 127 - ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/pairwise.Rmd |only ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/principles.Rmd | 48 ggstatsplot-0.9.0/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 340 +- 176 files changed, 6142 insertions(+), 6496 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute statistical tests and effect sizes if needed.
Author: Dan Chaltiel [aut, cre] (<https://orcid.org/0000-0003-3488-779X>),
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.2.1 dated 2021-03-08 and 0.2.2 dated 2021-10-19
crosstable-0.2.1/crosstable/R/summarise_survival.R |only crosstable-0.2.1/crosstable/R/summarize_categorical.R |only crosstable-0.2.1/crosstable/R/summarize_numeric.R |only crosstable-0.2.1/crosstable/man/body_add_table_legend.Rd |only crosstable-0.2.1/crosstable/man/str_wrap2.Rd |only crosstable-0.2.2/crosstable/DESCRIPTION | 21 crosstable-0.2.2/crosstable/MD5 | 197 - crosstable-0.2.2/crosstable/NAMESPACE | 27 crosstable-0.2.2/crosstable/NEWS.md | 31 crosstable-0.2.2/crosstable/R/burgled.R |only crosstable-0.2.2/crosstable/R/compact.R | 8 crosstable-0.2.2/crosstable/R/cross_by.R | 77 crosstable-0.2.2/crosstable/R/cross_categorical.R | 153 crosstable-0.2.2/crosstable/R/cross_numeric.R | 158 crosstable-0.2.2/crosstable/R/cross_survival.R | 126 crosstable-0.2.2/crosstable/R/crosstable-package.R | 1 crosstable-0.2.2/crosstable/R/crosstable.R | 334 + crosstable-0.2.2/crosstable/R/effect.R | 511 +-- crosstable-0.2.2/crosstable/R/flextable.R | 106 crosstable-0.2.2/crosstable/R/funs.R | 31 crosstable-0.2.2/crosstable/R/gt.R | 32 crosstable-0.2.2/crosstable/R/labels.R | 36 crosstable-0.2.2/crosstable/R/officer.R | 298 + crosstable-0.2.2/crosstable/R/openxlsx.R | 134 crosstable-0.2.2/crosstable/R/test.R | 35 crosstable-0.2.2/crosstable/R/utils.R | 95 crosstable-0.2.2/crosstable/README.md | 88 crosstable-0.2.2/crosstable/build/vignette.rds |binary crosstable-0.2.2/crosstable/inst/WORDLIST |only crosstable-0.2.2/crosstable/inst/doc/crosstable-install.Rmd | 23 crosstable-0.2.2/crosstable/inst/doc/crosstable-install.html | 73 crosstable-0.2.2/crosstable/inst/doc/crosstable-report.R | 27 crosstable-0.2.2/crosstable/inst/doc/crosstable-report.Rmd | 81 crosstable-0.2.2/crosstable/inst/doc/crosstable-report.html | 120 crosstable-0.2.2/crosstable/inst/doc/crosstable-selection.R | 35 crosstable-0.2.2/crosstable/inst/doc/crosstable-selection.Rmd | 58 crosstable-0.2.2/crosstable/inst/doc/crosstable-selection.html | 409 -- crosstable-0.2.2/crosstable/inst/doc/crosstable.R | 86 crosstable-0.2.2/crosstable/inst/doc/crosstable.Rmd | 210 - crosstable-0.2.2/crosstable/inst/doc/crosstable.html | 619 +-- crosstable-0.2.2/crosstable/man/apply_labels.Rd | 59 crosstable-0.2.2/crosstable/man/as_flextable.Rd | 197 - crosstable-0.2.2/crosstable/man/as_gt.Rd | 141 crosstable-0.2.2/crosstable/man/as_workbook.Rd | 16 crosstable-0.2.2/crosstable/man/body_add_crosstable.Rd | 94 crosstable-0.2.2/crosstable/man/body_add_crosstable_footnote.Rd | 39 crosstable-0.2.2/crosstable/man/body_add_gg2.Rd | 109 crosstable-0.2.2/crosstable/man/body_add_img2.Rd | 95 crosstable-0.2.2/crosstable/man/body_add_legend.Rd |only crosstable-0.2.2/crosstable/man/body_add_list.Rd | 104 crosstable-0.2.2/crosstable/man/body_add_normal.Rd | 84 crosstable-0.2.2/crosstable/man/body_add_title.Rd | 8 crosstable-0.2.2/crosstable/man/compact.Rd | 109 crosstable-0.2.2/crosstable/man/confint_numeric.Rd | 3 crosstable-0.2.2/crosstable/man/cross_summary.Rd | 57 crosstable-0.2.2/crosstable/man/crosstable-package.Rd | 4 crosstable-0.2.2/crosstable/man/crosstable.Rd | 42 crosstable-0.2.2/crosstable/man/crosstable_effect_args.Rd | 50 crosstable-0.2.2/crosstable/man/crosstable_options.Rd | 1 crosstable-0.2.2/crosstable/man/crosstable_test_args.Rd | 84 crosstable-0.2.2/crosstable/man/display_effect.Rd | 41 crosstable-0.2.2/crosstable/man/display_test.Rd | 45 crosstable-0.2.2/crosstable/man/docx_bookmarks2.Rd | 8 crosstable-0.2.2/crosstable/man/effect_summary.Rd | 106 crosstable-0.2.2/crosstable/man/effect_survival.Rd | 45 crosstable-0.2.2/crosstable/man/effect_tabular.Rd | 87 crosstable-0.2.2/crosstable/man/format_fixed.Rd | 7 crosstable-0.2.2/crosstable/man/generate_autofit_macro.Rd |only crosstable-0.2.2/crosstable/man/get_label.Rd | 3 crosstable-0.2.2/crosstable/man/import_labels.Rd | 7 crosstable-0.2.2/crosstable/man/peek.Rd | 43 crosstable-0.2.2/crosstable/man/remove_labels.Rd | 53 crosstable-0.2.2/crosstable/man/rename_dataframe_with_labels.Rd | 49 crosstable-0.2.2/crosstable/man/set_label.Rd | 10 crosstable-0.2.2/crosstable/man/summaryFunctions.Rd | 200 - crosstable-0.2.2/crosstable/man/test_correlation_auto.Rd | 3 crosstable-0.2.2/crosstable/man/test_summarize_auto.Rd | 46 crosstable-0.2.2/crosstable/man/test_survival_logrank.Rd | 40 crosstable-0.2.2/crosstable/man/test_tabular_auto.Rd | 46 crosstable-0.2.2/crosstable/tests/testthat/_snaps/1-crosstable.md | 1703 ---------- crosstable-0.2.2/crosstable/tests/testthat/_snaps/1-effects.md |only crosstable-0.2.2/crosstable/tests/testthat/_snaps/1-tests.md |only crosstable-0.2.2/crosstable/tests/testthat/_snaps/4-officer.md | 286 + crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_double_with_effects.docx |binary crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_double_with_effects_new.docx |only crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_helpers.docx |binary crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_simple.docx |binary crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_simple_new.docx |only crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_triple.docx |binary crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_crosstables_triple_new.docx |only crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_utils_functions.docx |binary crosstable-0.2.2/crosstable/tests/testthat/docx/4-officer/snap_utils_functions_new.docx |only crosstable-0.2.2/crosstable/tests/testthat/helper-init_dataset.R | 46 crosstable-0.2.2/crosstable/tests/testthat/test-1-crosstable.R | 448 -- crosstable-0.2.2/crosstable/tests/testthat/test-1-effects.R |only crosstable-0.2.2/crosstable/tests/testthat/test-1-tests.R |only crosstable-0.2.2/crosstable/tests/testthat/test-2-selection.R | 8 crosstable-0.2.2/crosstable/tests/testthat/test-3-compact.R | 18 crosstable-0.2.2/crosstable/tests/testthat/test-4-officer.R | 122 crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx1.xlsx |binary crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx2.xlsx |binary crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx3.xlsx |binary crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx4.xlsx |binary crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx5.xlsx |only crosstable-0.2.2/crosstable/tests/testthat/xlsx/test_openxlsx6.xlsx |only crosstable-0.2.2/crosstable/vignettes/crosstable-install.Rmd | 23 crosstable-0.2.2/crosstable/vignettes/crosstable-report.Rmd | 81 crosstable-0.2.2/crosstable/vignettes/crosstable-selection.Rmd | 58 crosstable-0.2.2/crosstable/vignettes/crosstable.Rmd | 210 - 109 files changed, 4440 insertions(+), 4938 deletions(-)
Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests on tidy data for
one-way analysis of variance for both between-subjects and
within-subjects designs. Currently, it supports only the most common
types of statistical analyses and tests: parametric (Welch's and
Student's t-test), nonparametric (Durbin-Conover and Dunn test),
robust (Yuen’s trimmed means test), and Bayes Factor (Student's
t-test).
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between pairwiseComparisons versions 3.1.6 dated 2021-06-01 and 3.2.0 dated 2021-10-19
pairwiseComparisons-3.1.6/pairwiseComparisons/R/data.R |only pairwiseComparisons-3.1.6/pairwiseComparisons/R/helpers.R |only pairwiseComparisons-3.1.6/pairwiseComparisons/data |only pairwiseComparisons-3.1.6/pairwiseComparisons/man/bugs_long.Rd |only pairwiseComparisons-3.1.6/pairwiseComparisons/man/movies_long.Rd |only pairwiseComparisons-3.1.6/pairwiseComparisons/man/movies_wide.Rd |only pairwiseComparisons-3.2.0/pairwiseComparisons/DESCRIPTION | 19 pairwiseComparisons-3.2.0/pairwiseComparisons/LICENSE | 4 pairwiseComparisons-3.2.0/pairwiseComparisons/MD5 | 59 pairwiseComparisons-3.2.0/pairwiseComparisons/NAMESPACE | 87 pairwiseComparisons-3.2.0/pairwiseComparisons/NEWS.md | 292 +- pairwiseComparisons-3.2.0/pairwiseComparisons/R/attach.R |only pairwiseComparisons-3.2.0/pairwiseComparisons/R/global_vars.R | 37 pairwiseComparisons-3.2.0/pairwiseComparisons/R/pairwise_comparisons.R | 767 +++--- pairwiseComparisons-3.2.0/pairwiseComparisons/R/reexports.R | 54 pairwiseComparisons-3.2.0/pairwiseComparisons/README.md | 1120 ++++------ pairwiseComparisons-3.2.0/pairwiseComparisons/inst/CITATION | 10 pairwiseComparisons-3.2.0/pairwiseComparisons/inst/WORDLIST | 69 pairwiseComparisons-3.2.0/pairwiseComparisons/man/figures/README-ggsignif-1.png |binary pairwiseComparisons-3.2.0/pairwiseComparisons/man/figures/README-ggsignif2-1.png |binary pairwiseComparisons-3.2.0/pairwiseComparisons/man/p_adjust_text.Rd | 48 pairwiseComparisons-3.2.0/pairwiseComparisons/man/pairwise_caption.Rd | 75 pairwiseComparisons-3.2.0/pairwiseComparisons/man/pairwise_comparisons.Rd | 443 +-- pairwiseComparisons-3.2.0/pairwiseComparisons/man/reexports.Rd | 46 pairwiseComparisons-3.2.0/pairwiseComparisons/tests/spelling.R | 12 pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat.R | 9 pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/_snaps/additional_args.md | 140 - pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/_snaps/pairwise_comparisons_between.md | 238 +- pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/_snaps/pairwise_comparisons_within.md | 294 +- pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/test-additional_args.R | 108 pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/test-pairwise_caption_helpers.R | 118 - pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/test-pairwise_comparisons_between.R | 612 ++--- pairwiseComparisons-3.2.0/pairwiseComparisons/tests/testthat/test-pairwise_comparisons_within.R | 408 +-- 33 files changed, 2517 insertions(+), 2552 deletions(-)
More information about pairwiseComparisons at CRAN
Permanent link
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The
functions are pipe-friendly and provide a consistent syntax to work
with tidy data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.1.0 dated 2021-05-30 and 1.2.0 dated 2021-10-19
statsExpressions-1.1.0/statsExpressions/R/bf_extractor.R |only statsExpressions-1.1.0/statsExpressions/data/VR_dilemma.rdata |only statsExpressions-1.1.0/statsExpressions/man/VR_dilemma.Rd |only statsExpressions-1.1.0/statsExpressions/man/bf_extractor.Rd |only statsExpressions-1.1.0/statsExpressions/man/tidy_model_effectsize.Rd |only statsExpressions-1.1.0/statsExpressions/tests/testthat/test-bf_extractor.R |only statsExpressions-1.2.0/statsExpressions/DESCRIPTION | 22 statsExpressions-1.2.0/statsExpressions/LICENSE | 4 statsExpressions-1.2.0/statsExpressions/MD5 | 193 - statsExpressions-1.2.0/statsExpressions/NAMESPACE | 145 statsExpressions-1.2.0/statsExpressions/NEWS.md | 740 ++-- statsExpressions-1.2.0/statsExpressions/R/centrality_description.R |only statsExpressions-1.2.0/statsExpressions/R/contingency_table.R | 495 +- statsExpressions-1.2.0/statsExpressions/R/corr_test.R | 184 - statsExpressions-1.2.0/statsExpressions/R/data.R | 286 - statsExpressions-1.2.0/statsExpressions/R/global_vars.R | 70 statsExpressions-1.2.0/statsExpressions/R/helpers_easystats.R | 121 statsExpressions-1.2.0/statsExpressions/R/helpers_expr_templates.R | 675 +-- statsExpressions-1.2.0/statsExpressions/R/long_to_wide_converter.R |only statsExpressions-1.2.0/statsExpressions/R/meta_analysis.R | 234 - statsExpressions-1.2.0/statsExpressions/R/one_sample_test.R | 379 +- statsExpressions-1.2.0/statsExpressions/R/oneway_anova.R | 677 +-- statsExpressions-1.2.0/statsExpressions/R/reexports.R | 106 statsExpressions-1.2.0/statsExpressions/R/statsExpressions-package.R | 65 statsExpressions-1.2.0/statsExpressions/R/tidy_model_expressions.R |only statsExpressions-1.2.0/statsExpressions/R/two_sample_test.R | 511 +- statsExpressions-1.2.0/statsExpressions/R/utils.R |only statsExpressions-1.2.0/statsExpressions/README.md | 1380 ++++---- statsExpressions-1.2.0/statsExpressions/build/vignette.rds |binary statsExpressions-1.2.0/statsExpressions/inst/CITATION | 28 statsExpressions-1.2.0/statsExpressions/inst/WORDLIST | 151 statsExpressions-1.2.0/statsExpressions/inst/doc/stats_details.R | 16 statsExpressions-1.2.0/statsExpressions/inst/doc/stats_details.Rmd | 499 +- statsExpressions-1.2.0/statsExpressions/inst/doc/stats_details.html | 1704 +++++----- statsExpressions-1.2.0/statsExpressions/man/bugs_long.Rd | 86 statsExpressions-1.2.0/statsExpressions/man/centrality_description.Rd |only statsExpressions-1.2.0/statsExpressions/man/contingency_table.Rd | 274 - 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statsExpressions-1.2.0/statsExpressions/tests/testthat/_snaps/two_sample_robust.md | 214 - statsExpressions-1.2.0/statsExpressions/tests/testthat/_snaps/z_meta_random_bayes.md | 20 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-centrality_description.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-contingency_table.R | 653 +-- statsExpressions-1.2.0/statsExpressions/tests/testthat/test-corr_test.R | 304 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-format_num.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-grouped_dataframes.R | 90 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-long_to_wide_converter.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-loop_execution.R | 105 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-loop_execution_bayes.R | 190 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-meta_random_parametric.R | 62 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-meta_random_robust.R | 60 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-one_sample.R | 350 +- statsExpressions-1.2.0/statsExpressions/tests/testthat/test-one_two_sample_dataframes.R | 205 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-oneway_anova_bayes.R | 391 +- statsExpressions-1.2.0/statsExpressions/tests/testthat/test-oneway_anova_nonparametric.R | 292 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-oneway_anova_parametric.R | 439 +- statsExpressions-1.2.0/statsExpressions/tests/testthat/test-oneway_anova_robust.R | 141 statsExpressions-1.2.0/statsExpressions/tests/testthat/test-stats_type_switch.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-tidy_model_expressions.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-tidy_model_expressions_F.R |only statsExpressions-1.2.0/statsExpressions/tests/testthat/test-two_sample_bayes.R | 281 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-two_sample_nonparametric.R | 288 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-two_sample_parametric.R | 332 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-two_sample_robust.R | 316 - statsExpressions-1.2.0/statsExpressions/tests/testthat/test-z_meta_random_bayes.R | 124 statsExpressions-1.2.0/statsExpressions/vignettes/stats_details.Rmd | 499 +- statsExpressions-1.2.0/statsExpressions/vignettes/web_only/dataframe_outputs.Rmd | 1168 +++--- 111 files changed, 10012 insertions(+), 10091 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Portfolio Management with R
Description: Functions and examples for 'Portfolio
Management with R': backtesting investment and
trading strategies, computing profit/loss and
returns, analysing trades, handling lists of
transactions, reporting, and more.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 0.16-1 dated 2021-09-18 and 0.17-0 dated 2021-10-19
PMwR-0.16-1/PMwR/tests/README |only PMwR-0.17-0/PMwR/ChangeLog | 50 +++++ PMwR-0.17-0/PMwR/DESCRIPTION | 8 PMwR-0.17-0/PMwR/MD5 | 64 +++---- PMwR-0.17-0/PMwR/NEWS | 20 ++ PMwR-0.17-0/PMwR/R/internal.R | 10 - PMwR-0.17-0/PMwR/R/is_valid_ISIN.R | 4 PMwR-0.17-0/PMwR/R/plot_trading_hours.R | 12 - PMwR-0.17-0/PMwR/R/rc.R |only PMwR-0.17-0/PMwR/R/rebalance.R | 34 +++ PMwR-0.17-0/PMwR/R/returns.R | 83 +++------ PMwR-0.17-0/PMwR/inst/CITATION | 4 PMwR-0.17-0/PMwR/inst/doc/An_overview_of_PMwR.R | 6 PMwR-0.17-0/PMwR/inst/doc/An_overview_of_PMwR.Rnw | 140 +++++++++++++--- PMwR-0.17-0/PMwR/inst/doc/An_overview_of_PMwR.pdf |binary PMwR-0.17-0/PMwR/inst/doc/Computing_returns.pdf |binary PMwR-0.17-0/PMwR/inst/doc/Drawdowns_streaks.pdf |binary PMwR-0.17-0/PMwR/inst/doc/FinTeX.pdf |binary PMwR-0.17-0/PMwR/inst/doc/pl_open_positions.pdf |binary PMwR-0.17-0/PMwR/inst/doc/q32.pdf |binary PMwR-0.17-0/PMwR/inst/tinytest/test_rc.R | 80 +++++++++ PMwR-0.17-0/PMwR/inst/tinytest/test_returns.R | 8 PMwR-0.17-0/PMwR/inst/tinytest/test_returns_dataframe.R | 7 PMwR-0.17-0/PMwR/inst/tinytest/test_returns_rebalance.R | 13 + PMwR-0.17-0/PMwR/man/PMwR-package.Rd | 2 PMwR-0.17-0/PMwR/man/instrument.Rd | 8 PMwR-0.17-0/PMwR/man/position.Rd | 18 +- PMwR-0.17-0/PMwR/man/quote32.Rd | 1 PMwR-0.17-0/PMwR/man/rc.Rd | 57 ++++-- PMwR-0.17-0/PMwR/man/returns.Rd | 11 - PMwR-0.17-0/PMwR/man/scale1.Rd | 6 PMwR-0.17-0/PMwR/man/trade-analysis.Rd | 2 PMwR-0.17-0/PMwR/man/valuation.Rd | 6 PMwR-0.17-0/PMwR/vignettes/An_overview_of_PMwR.Rnw | 140 +++++++++++++--- 34 files changed, 593 insertions(+), 201 deletions(-)
Title: Radiation and Photovoltaic Systems
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpiñán Lamigueiro [cre, aut]
(<https://orcid.org/0000-0002-4134-7196>)
Maintainer: Oscar Perpiñán Lamigueiro <oscar.perpinan@upm.es>
Diff between solaR versions 0.45 dated 2020-01-19 and 0.46 dated 2021-10-19
DESCRIPTION | 8 ++-- MD5 | 73 +++++++++++++++++++++---------------------- R/fSolD.R | 2 - README.md | 36 +++++++++++---------- build |only inst/CITATION | 26 +++++++-------- man/G0-class.Rd | 4 +- man/Gef-class.Rd | 4 +- man/HQCurve.Rd | 4 +- man/NmgSFB.Rd | 4 +- man/ProdGCPV-class.Rd | 4 +- man/ProdPVPS-class.Rd | 4 +- man/Shade-class.Rd | 6 +-- man/Sol-class.Rd | 4 +- man/calcG0.Rd | 4 +- man/calcGef.Rd | 4 +- man/calcShd.Rd | 4 +- man/calcSol.Rd | 8 ++-- man/compareLosses-methods.Rd | 4 +- man/defunct.Rd | 2 - man/fBTd.Rd | 4 +- man/fCompD.Rd | 4 +- man/fCompI.Rd | 4 +- man/fInclin.Rd | 4 +- man/fProd.Rd | 4 +- man/fPump.Rd | 4 +- man/fSolD.Rd | 8 ++-- man/fSolI.Rd | 8 ++-- man/fSombra.Rd | 4 +- man/fTemp.Rd | 4 +- man/fTheta.Rd | 4 +- man/local2UTC.Rd | 4 +- man/optimShd.Rd | 4 +- man/prodExample.Rd | 2 - man/prodGCPV.Rd | 4 +- man/prodPVPS.Rd | 4 +- man/pumpCoef.Rd | 6 +-- man/solaR-package.Rd | 5 ++ 38 files changed, 146 insertions(+), 140 deletions(-)
Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an
Rd file to a list, create the 'roxygen' documentation and update the original
R script (e.g. the one containing the definition of the function)
accordingly. This package also provides utilities that can help developers
build packages using 'roxygen' more easily. The 'formatR' package can be used
to reformat the R code in the examples sections so that the code will be
more readable.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between Rd2roxygen versions 1.11 dated 2020-06-24 and 1.12 dated 2021-10-19
Rd2roxygen-1.11/Rd2roxygen/NEWS |only Rd2roxygen-1.12/Rd2roxygen/DESCRIPTION | 8 Rd2roxygen-1.12/Rd2roxygen/MD5 | 18 - Rd2roxygen-1.12/Rd2roxygen/NEWS.md |only Rd2roxygen-1.12/Rd2roxygen/R/build.R | 2 Rd2roxygen-1.12/Rd2roxygen/R/utils.R | 23 - Rd2roxygen-1.12/Rd2roxygen/README.md | 4 Rd2roxygen-1.12/Rd2roxygen/build/vignette.rds |binary Rd2roxygen-1.12/Rd2roxygen/inst/doc/Rd2roxygen.Rmd | 6 Rd2roxygen-1.12/Rd2roxygen/inst/doc/Rd2roxygen.html | 330 +++----------------- Rd2roxygen-1.12/Rd2roxygen/vignettes/Rd2roxygen.Rmd | 6 11 files changed, 87 insertions(+), 310 deletions(-)
Title: R Commander Plug-in for Case 1 (Object Case) Best-Worst Scaling
Description: Adds menu items to the R Commander for implementing case 1 (object case) best-worst scaling (BWS1) from designing choice sets to measuring preferences for items. BWS1 is a question-based survey method that constructs various combinations of items (choice sets) using the experimental designs, asks respondents to select the best and worst items in each choice set, and then measures preferences for the items by analyzing the responses. For details on BWS1, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS1 versions 0.1-4 dated 2020-12-17 and 0.1-5 dated 2021-10-19
DESCRIPTION | 8 - MD5 | 10 - NEWS | 5 R/RcmdrPlugin.BWS1.R | 225 +++++++++++++--------------------------- inst/etc/menus.txt | 3 man/RcmdrPlugin.BWS1-package.Rd | 40 +++---- 6 files changed, 111 insertions(+), 180 deletions(-)
More information about RcmdrPlugin.BWS1 at CRAN
Permanent link
Title: A Lightweight, Modern and Flexible Logging Utility
Description: Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.
Author: Gergely Daróczi [aut, cre] (<https://orcid.org/0000-0003-3149-8537>),
System1 [fnd]
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between logger versions 0.2.1 dated 2021-07-06 and 0.2.2 dated 2021-10-19
DESCRIPTION | 8 +-- MD5 | 30 ++++++------ NEWS.md | 6 ++ README.md | 2 build/vignette.rds |binary inst/doc/Intro.html | 16 +++--- inst/doc/anatomy.html | 12 ++-- inst/doc/customize_logger.Rmd | 2 inst/doc/customize_logger.html | 76 +++++++++++++++---------------- inst/doc/migration.R | 2 inst/doc/migration.Rmd | 2 inst/doc/migration.html | 46 +++++++++--------- inst/doc/r_packages.html | 2 tests/testthat/test-CRANSKIP-appenders.R | 2 vignettes/customize_logger.Rmd | 2 vignettes/migration.Rmd | 2 16 files changed, 108 insertions(+), 102 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.2.7 dated 2021-08-25 and 0.3.0 dated 2021-10-19
DESCRIPTION | 10 MD5 | 15 R/dplyr_methods.R | 2328 ++++++++++++++++++++++---------------------- R/zzz.R | 7 README.md | 1092 ++++++++++---------- build/tidyseurat.pdf |binary inst/CITATION |only inst/doc/introduction.html | 12 tests/testthat/test-dplyr.R | 298 ++--- 9 files changed, 1885 insertions(+), 1877 deletions(-)
Title: Linear Model with Breakpoint
Description: Exact significance tests for a changepoint in linear or multiple linear regression.
Confidence regions with exact coverage probabilities for the changepoint. Based on
Knowles, Siegmund and Zhang (1991) <doi:10.1093/biomet/78.1.15>.
Author: Marc Adams [aut, cre],
authors of R function 'lm' [ctb] (general interface),
authors of 'lm.gls' [ctb] (interface and R code for covariate weights),
U.S. NIST [ctb] (C++ code for TNT::Vector template)
Maintainer: Marc Adams <lm.br.pkg@gmail.com>
Diff between lm.br versions 2.9.3 dated 2017-04-27 and 2.9.4 dated 2021-10-19
DESCRIPTION | 16 +++--- MD5 | 24 +++++----- build/vignette.rds |binary demo/testscript.R | 2 inst/doc/lm.br.R | 122 ++++++++++++++++++++++++++--------------------------- inst/doc/lm.br.pdf |binary man/lm.br.Rd | 22 ++++----- src/gam_fs.cpp | 2 src/globals.h | 8 ++- src/pre_calc.cpp | 12 ++--- src/set_Sigma.cpp | 4 - src/set_sy.cpp | 4 - src/set_theta0.cpp | 4 - 13 files changed, 112 insertions(+), 108 deletions(-)
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative
signal is expected to be localized, a series of filters determine which peak
signals are characterized by an implausible spatial distribution. The filters
reduce the dataset dimensionality and increase its information vs noise ratio,
improving the quality of the unsupervised analysis results, reducing data
dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese@outlook.com>
Diff between SPUTNIK versions 1.3.3 dated 2021-05-17 and 1.4 dated 2021-10-18
SPUTNIK-1.3.3/SPUTNIK/README.md |only SPUTNIK-1.3.3/SPUTNIK/man/refAndROIimages.Rd |only SPUTNIK-1.4/SPUTNIK/DESCRIPTION | 11 SPUTNIK-1.4/SPUTNIK/MD5 | 62 ++- SPUTNIK-1.4/SPUTNIK/NAMESPACE | 17 - SPUTNIK-1.4/SPUTNIK/NEWS | 11 SPUTNIK-1.4/SPUTNIK/R/binary_refimg.R |only SPUTNIK-1.4/SPUTNIK/R/construct_funcs.R | 16 + SPUTNIK-1.4/SPUTNIK/R/continuous_refimg.R |only SPUTNIK-1.4/SPUTNIK/R/examples/filter_count.R | 9 SPUTNIK-1.4/SPUTNIK/R/examples/filter_global.R | 4 SPUTNIK-1.4/SPUTNIK/R/examples/graph_funcs.R | 6 SPUTNIK-1.4/SPUTNIK/R/examples/msImage_binOtsu.R | 2 SPUTNIK-1.4/SPUTNIK/R/examples/msImage_closeImage.R | 2 SPUTNIK-1.4/SPUTNIK/R/examples/msiDataset_binKmeans.R | 4 SPUTNIK-1.4/SPUTNIK/R/filter_csr.R | 138 ++++---- SPUTNIK-1.4/SPUTNIK/R/filter_global.R | 66 ++-- SPUTNIK-1.4/SPUTNIK/R/graph_funcs.R | 158 +--------- SPUTNIK-1.4/SPUTNIK/R/ms.image_class.R | 16 - SPUTNIK-1.4/SPUTNIK/R/ms.image_methods.R | 26 - SPUTNIK-1.4/SPUTNIK/R/msi.dataset_class.R | 14 SPUTNIK-1.4/SPUTNIK/R/msi.dataset_methods.R | 143 ++++++++- SPUTNIK-1.4/SPUTNIK/man/CSRPeaksFilter.Rd | 39 -- SPUTNIK-1.4/SPUTNIK/man/PCAImage-msi.dataset-method.Rd |only SPUTNIK-1.4/SPUTNIK/man/binKmeans-msi.dataset-method.Rd | 14 SPUTNIK-1.4/SPUTNIK/man/binOtsu-ms.image-method.Rd | 2 SPUTNIK-1.4/SPUTNIK/man/closeImage-ms.image-method.Rd | 2 SPUTNIK-1.4/SPUTNIK/man/countPixelsFilter.Rd | 9 SPUTNIK-1.4/SPUTNIK/man/globalPeaksFilter.Rd | 12 SPUTNIK-1.4/SPUTNIK/man/msi.dataset-class.Rd | 12 SPUTNIK-1.4/SPUTNIK/man/numDetectedMSI-msi.dataset-method.Rd |only SPUTNIK-1.4/SPUTNIK/man/plot.Rd | 3 SPUTNIK-1.4/SPUTNIK/man/refImageBinaryKmeans.Rd |only SPUTNIK-1.4/SPUTNIK/man/refImageBinaryKmeansMulti.Rd |only SPUTNIK-1.4/SPUTNIK/man/refImageBinaryOtsu.Rd |only SPUTNIK-1.4/SPUTNIK/man/refImageBinarySVM.Rd |only SPUTNIK-1.4/SPUTNIK/man/refImageContinuous.Rd |only SPUTNIK-1.4/SPUTNIK/man/totalIonCountMSI-msi.dataset-method.Rd |only 38 files changed, 426 insertions(+), 372 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] (Hash implementation based on Mike's xxhashlite),
Yann Collet [cph] (Author of the embedded xxHash library),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.4.11 dated 2021-04-30 and 0.4.12 dated 2021-10-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ README.md | 2 +- build/rlang.pdf |binary src/version.c | 2 +- tests/testthat/test-quo.R | 2 +- 7 files changed, 17 insertions(+), 12 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Søren Højsgaard [aut],
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik),
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-1995-6531>,
@vincentab),
Jeffrey Girard [ctb] (<https://orcid.org/0000-0002-7359-3746>,
@jeffreymgirard),
Christina Maimone [rev],
Niels Ohlsen [rev] (@Niels_Bremen)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.14.0 dated 2021-05-29 and 0.15.0 dated 2021-10-18
parameters-0.14.0/parameters/R/center.R |only parameters-0.14.0/parameters/R/check_multimodal.R |only parameters-0.14.0/parameters/R/ci_wald.R |only parameters-0.14.0/parameters/R/convert_data_to_numeric.R |only parameters-0.14.0/parameters/R/data_partition.R |only parameters-0.14.0/parameters/R/demean.R |only parameters-0.14.0/parameters/R/describe_distribution.R |only parameters-0.14.0/parameters/R/methods_FactorMineR.R |only parameters-0.14.0/parameters/R/methods_feis.R |only parameters-0.14.0/parameters/R/methods_glmmADMB.R |only parameters-0.14.0/parameters/R/methods_robustbase.R |only parameters-0.14.0/parameters/R/p_value_wald.R |only parameters-0.14.0/parameters/R/rescale_weights.R |only parameters-0.14.0/parameters/R/skewness_kurtosis.R |only parameters-0.14.0/parameters/R/smoothness.R |only parameters-0.14.0/parameters/R/standard_error_betwithin.R |only parameters-0.14.0/parameters/R/standard_error_ml1.R |only parameters-0.14.0/parameters/R/utils_values_aov.R |only parameters-0.14.0/parameters/man/center.Rd |only parameters-0.14.0/parameters/man/check_multimodal.Rd |only parameters-0.14.0/parameters/man/ci.merMod.Rd |only parameters-0.14.0/parameters/man/convert_data_to_numeric.Rd |only parameters-0.14.0/parameters/man/data_partition.Rd |only parameters-0.14.0/parameters/man/demean.Rd |only parameters-0.14.0/parameters/man/describe_distribution.Rd |only parameters-0.14.0/parameters/man/model_parameters.Mclust.Rd |only parameters-0.14.0/parameters/man/p_value.lmerMod.Rd |only parameters-0.14.0/parameters/man/p_value_wald.Rd |only parameters-0.14.0/parameters/man/rescale_weights.Rd |only parameters-0.14.0/parameters/man/skewness.Rd |only parameters-0.14.0/parameters/man/smoothness.Rd |only parameters-0.14.0/parameters/tests/testthat/test-center.R |only parameters-0.14.0/parameters/tests/testthat/test-describe_distribution.R |only parameters-0.14.0/parameters/tests/testthat/test-distributions.R |only parameters-0.14.0/parameters/tests/testthat/test-se_ml1R.R |only parameters-0.14.0/parameters/tests/testthat/test-skewness.R |only parameters-0.15.0/parameters/DESCRIPTION | 154 +- parameters-0.15.0/parameters/MD5 | 633 ++++------ parameters-0.15.0/parameters/NAMESPACE | 180 +- parameters-0.15.0/parameters/NEWS.md | 166 ++ parameters-0.15.0/parameters/R/1_model_parameters.R | 542 +++++--- parameters-0.15.0/parameters/R/2_ci.R | 92 + parameters-0.15.0/parameters/R/3_p_value.R | 48 parameters-0.15.0/parameters/R/4_standard_error.R | 43 parameters-0.15.0/parameters/R/5_simulate_model.R | 27 parameters-0.15.0/parameters/R/bootstrap_model-emmeans.R | 19 parameters-0.15.0/parameters/R/bootstrap_model.R | 86 - 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parameters-0.15.0/parameters/R/p_value_ml1.R | 22 parameters-0.15.0/parameters/R/p_value_satterthwaite.R | 17 parameters-0.15.0/parameters/R/parameters_type.R | 20 parameters-0.15.0/parameters/R/plot.R | 48 parameters-0.15.0/parameters/R/pool_parameters.R | 16 parameters-0.15.0/parameters/R/principal_components.R | 135 +- parameters-0.15.0/parameters/R/print.parameters_model.R | 169 +- parameters-0.15.0/parameters/R/print_html.R | 33 parameters-0.15.0/parameters/R/print_md.R | 55 parameters-0.15.0/parameters/R/random_parameters.R | 22 parameters-0.15.0/parameters/R/reduce_parameters.R | 30 parameters-0.15.0/parameters/R/reexports.R | 47 parameters-0.15.0/parameters/R/robust_estimation.R | 92 - parameters-0.15.0/parameters/R/select_parameters.R | 23 parameters-0.15.0/parameters/R/select_parameters.stanreg.R | 17 parameters-0.15.0/parameters/R/simulate_parameters.R | 16 parameters-0.15.0/parameters/R/utils_clustering.R |only parameters-0.15.0/parameters/R/utils_format.R | 489 +++++-- parameters-0.15.0/parameters/R/utils_model_parameters.R | 20 parameters-0.15.0/parameters/R/utils_pca_efa.R | 29 parameters-0.15.0/parameters/README.md | 57 parameters-0.15.0/parameters/build/partial.rdb |binary parameters-0.15.0/parameters/inst/WORDLIST | 67 - 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parameters-0.15.0/parameters/man/model_parameters.averaging.Rd | 39 parameters-0.15.0/parameters/man/model_parameters.befa.Rd | 16 parameters-0.15.0/parameters/man/model_parameters.cgam.Rd | 122 + parameters-0.15.0/parameters/man/model_parameters.default.Rd | 276 +++- parameters-0.15.0/parameters/man/model_parameters.glht.Rd | 6 parameters-0.15.0/parameters/man/model_parameters.htest.Rd | 9 parameters-0.15.0/parameters/man/model_parameters.kmeans.Rd | 155 ++ parameters-0.15.0/parameters/man/model_parameters.lavaan.Rd | 70 - parameters-0.15.0/parameters/man/model_parameters.merMod.Rd | 146 +- parameters-0.15.0/parameters/man/model_parameters.mira.Rd | 8 parameters-0.15.0/parameters/man/model_parameters.mlm.Rd | 54 parameters-0.15.0/parameters/man/model_parameters.principal.Rd | 39 parameters-0.15.0/parameters/man/model_parameters.rma.Rd | 33 parameters-0.15.0/parameters/man/model_parameters.stanreg.Rd | 168 +- parameters-0.15.0/parameters/man/model_parameters.t1way.Rd | 24 parameters-0.15.0/parameters/man/model_parameters.zcpglm.Rd | 99 + parameters-0.15.0/parameters/man/n_clusters.Rd | 192 ++- parameters-0.15.0/parameters/man/n_factors.Rd | 118 + parameters-0.15.0/parameters/man/p_value.BFBayesFactor.Rd | 2 parameters-0.15.0/parameters/man/p_value.DirichletRegModel.Rd | 2 parameters-0.15.0/parameters/man/p_value.Rd | 45 parameters-0.15.0/parameters/man/p_value.poissonmfx.Rd | 11 parameters-0.15.0/parameters/man/p_value.zcpglm.Rd | 16 parameters-0.15.0/parameters/man/p_value_betwithin.Rd | 18 parameters-0.15.0/parameters/man/p_value_kenward.Rd | 4 parameters-0.15.0/parameters/man/p_value_ml1.Rd | 24 parameters-0.15.0/parameters/man/p_value_satterthwaite.Rd | 2 parameters-0.15.0/parameters/man/parameters_type.Rd | 14 parameters-0.15.0/parameters/man/pool_parameters.Rd | 20 parameters-0.15.0/parameters/man/principal_components.Rd | 203 +-- parameters-0.15.0/parameters/man/print.parameters_model.Rd | 28 parameters-0.15.0/parameters/man/qol_cancer.Rd | 16 parameters-0.15.0/parameters/man/random_parameters.Rd | 64 - 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Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp],
Aidan Wright [csp],
Jonathan Park [ctb],
Sebastian Castro Alvarez [ctb]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-6 dated 2021-08-19 and 0.7-7 dated 2021-10-18
gimme-0.7-6/gimme/data/datalist |only gimme-0.7-7/gimme/DESCRIPTION | 13 gimme-0.7-7/gimme/MD5 | 41 +-- gimme-0.7-7/gimme/R/aggSEM.R | 26 + gimme-0.7-7/gimme/R/gimme.R | 22 - gimme-0.7-7/gimme/R/indSEM.R | 29 +- gimme-0.7-7/gimme/R/indiv.search.R | 4 gimme-0.7-7/gimme/R/indiv.search.ms.R | 6 gimme-0.7-7/gimme/R/search.paths.ms.R | 4 gimme-0.7-7/gimme/build/vignette.rds |binary gimme-0.7-7/gimme/data/HRFsim.rda |binary gimme-0.7-7/gimme/data/ms.fit.rda |binary gimme-0.7-7/gimme/data/simData.rda |binary gimme-0.7-7/gimme/data/simDataLV.rda |binary gimme-0.7-7/gimme/data/ts.rda |binary gimme-0.7-7/gimme/inst/doc/gimme_vignette.R | 2 gimme-0.7-7/gimme/inst/doc/gimme_vignette.html | 333 ++++++++++++++++++++----- gimme-0.7-7/gimme/man/aggSEM.Rd | 12 gimme-0.7-7/gimme/man/gimmeSEM.Rd | 2 gimme-0.7-7/gimme/man/indSEM.Rd | 6 gimme-0.7-7/gimme/man/indiv.search.Rd | 2 gimme-0.7-7/gimme/man/indiv.search.ms.Rd | 2 22 files changed, 384 insertions(+), 120 deletions(-)
Title: Tools to Create, Use, and Convert ecocomDP Data
Description: Work with the Ecological Community Data Design Pattern. 'ecocomDP'
is a flexible data model for harmonizing ecological community surveys, in a
research question agnostic format, from source data published across
repositories, and with methods that keep the derived data up-to-date as the
underlying sources change. Described in O'Brien et al. (2021),
<doi:10.1016/j.ecoinf.2021.101374>.
Author: Colin Smith [aut, cre, cph] (<https://orcid.org/0000-0003-2261-9931>),
Eric Sokol [aut] (<https://orcid.org/0000-0001-5923-0917>),
Margaret O'Brien [aut] (<https://orcid.org/0000-0002-1693-8322>),
Matt Bitters [ctb],
Melissa Chen [ctb],
Savannah Gonzales [ctb],
Matt Helmus [ctb],
Brendan Hobart [ctb],
Ruvi Jaimes [ctb],
Lara Janson [ctb],
Marta Jarzyna [ctb],
Michael Just [ctb],
Daijiang Li [ctb],
Wynne Moss [ctb],
Kari Norman [ctb],
Stephanie Parker [ctb],
Natalie Robinson [ctb],
Thilina Surasinghe [ctb],
Kyle Zollo-Venecek [ctb] (<https://orcid.org/0000-0002-1615-590X>)
Maintainer: Colin Smith <colin.smith@wisc.edu>
Diff between ecocomDP versions 1.1.0 dated 2021-07-31 and 1.2.0 dated 2021-10-18
ecocomDP-1.1.0/ecocomDP/man/view_descriptions.Rd |only ecocomDP-1.1.0/ecocomDP/man/view_diagram.Rd |only ecocomDP-1.2.0/ecocomDP/DESCRIPTION | 29 ecocomDP-1.2.0/ecocomDP/MD5 | 131 - ecocomDP-1.2.0/ecocomDP/NAMESPACE | 8 ecocomDP-1.2.0/ecocomDP/NEWS.md | 21 ecocomDP-1.2.0/ecocomDP/R/annotation_dictionary.R |only ecocomDP-1.2.0/ecocomDP/R/convert_to_dwca.R | 4 ecocomDP-1.2.0/ecocomDP/R/create_eml.R | 21 ecocomDP-1.2.0/ecocomDP/R/data.R | 12 ecocomDP-1.2.0/ecocomDP/R/flatten_data.R | 70 ecocomDP-1.2.0/ecocomDP/R/plot_taxa.R | 1250 ++++++++-- ecocomDP-1.2.0/ecocomDP/R/read_data.R | 146 - ecocomDP-1.2.0/ecocomDP/R/save_data.R | 91 ecocomDP-1.2.0/ecocomDP/R/search_data.R | 2 ecocomDP-1.2.0/ecocomDP/R/taxonomyCleanr.R | 170 - ecocomDP-1.2.0/ecocomDP/R/utilities.R | 222 + ecocomDP-1.2.0/ecocomDP/R/validate_arguments.R | 59 ecocomDP-1.2.0/ecocomDP/R/validate_data.R | 132 - ecocomDP-1.2.0/ecocomDP/R/zzz.R | 2 ecocomDP-1.2.0/ecocomDP/README.md | 15 ecocomDP-1.2.0/ecocomDP/build/vignette.rds |binary ecocomDP-1.2.0/ecocomDP/data/ants_L1.rda |binary ecocomDP-1.2.0/ecocomDP/inst/doc/convert.Rmd | 4 ecocomDP-1.2.0/ecocomDP/inst/doc/convert.html | 6 ecocomDP-1.2.0/ecocomDP/inst/doc/create.R | 18 ecocomDP-1.2.0/ecocomDP/inst/doc/create.Rmd | 20 ecocomDP-1.2.0/ecocomDP/inst/doc/create.html | 458 +-- ecocomDP-1.2.0/ecocomDP/inst/doc/model_overview.R |only ecocomDP-1.2.0/ecocomDP/inst/doc/model_overview.Rmd |only ecocomDP-1.2.0/ecocomDP/inst/doc/model_overview.html |only ecocomDP-1.2.0/ecocomDP/inst/doc/shared_practices_create.R |only ecocomDP-1.2.0/ecocomDP/inst/doc/shared_practices_create.Rmd |only ecocomDP-1.2.0/ecocomDP/inst/doc/shared_practices_create.html |only ecocomDP-1.2.0/ecocomDP/inst/doc/use.R | 55 ecocomDP-1.2.0/ecocomDP/inst/doc/use.Rmd | 98 ecocomDP-1.2.0/ecocomDP/inst/doc/use.html | 369 +- ecocomDP-1.2.0/ecocomDP/inst/extdata/ecocomDP/attributes_observation.txt | 11 ecocomDP-1.2.0/ecocomDP/inst/extdata/table_descriptions.txt | 10 ecocomDP-1.2.0/ecocomDP/man/annotation_dictionary.Rd |only ecocomDP-1.2.0/ecocomDP/man/ants_L1.Rd | 12 ecocomDP-1.2.0/ecocomDP/man/convert_to_dwca.Rd | 4 ecocomDP-1.2.0/ecocomDP/man/create_eml.Rd | 11 ecocomDP-1.2.0/ecocomDP/man/flatten_data.Rd | 19 ecocomDP-1.2.0/ecocomDP/man/plot_sample_space_time.Rd |only ecocomDP-1.2.0/ecocomDP/man/plot_sites.Rd |only ecocomDP-1.2.0/ecocomDP/man/plot_taxa_abund.Rd |only ecocomDP-1.2.0/ecocomDP/man/plot_taxa_accum_sites.Rd | 32 ecocomDP-1.2.0/ecocomDP/man/plot_taxa_accum_time.Rd | 32 ecocomDP-1.2.0/ecocomDP/man/plot_taxa_diversity.Rd | 44 ecocomDP-1.2.0/ecocomDP/man/plot_taxa_occur_freq.Rd |only ecocomDP-1.2.0/ecocomDP/man/plot_taxa_rank.Rd |only ecocomDP-1.2.0/ecocomDP/man/plot_taxa_sample_time.Rd | 13 ecocomDP-1.2.0/ecocomDP/man/plot_taxa_shared_sites.Rd | 33 ecocomDP-1.2.0/ecocomDP/man/read_data.Rd | 76 ecocomDP-1.2.0/ecocomDP/man/save_data.Rd | 22 ecocomDP-1.2.0/ecocomDP/man/search_data.Rd | 4 ecocomDP-1.2.0/ecocomDP/man/validate_data.Rd | 23 ecocomDP-1.2.0/ecocomDP/man/write_tables.Rd | 4 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_create_eml.R | 2 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_flatten_data.R | 22 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_plot_taxa.R | 12 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_read_data.R | 200 + ecocomDP-1.2.0/ecocomDP/tests/testthat/test_save_data.R | 71 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_utilities.R | 115 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_validate_arguments.R | 44 ecocomDP-1.2.0/ecocomDP/tests/testthat/test_validate_data.R | 214 - ecocomDP-1.2.0/ecocomDP/vignettes/LevelOfSurvey_final_long2.png |only ecocomDP-1.2.0/ecocomDP/vignettes/MLO_final_long2.png |only ecocomDP-1.2.0/ecocomDP/vignettes/convert.Rmd | 4 ecocomDP-1.2.0/ecocomDP/vignettes/coords_final_wide2.png |only ecocomDP-1.2.0/ecocomDP/vignettes/create.Rmd | 20 ecocomDP-1.2.0/ecocomDP/vignettes/deprecated.jpg |only ecocomDP-1.2.0/ecocomDP/vignettes/model.png |only ecocomDP-1.2.0/ecocomDP/vignettes/model_overview.Rmd |only ecocomDP-1.2.0/ecocomDP/vignettes/shared_practices_create.Rmd |only ecocomDP-1.2.0/ecocomDP/vignettes/use.Rmd | 98 ecocomDP-1.2.0/ecocomDP/vignettes/workflow.png |only 78 files changed, 3033 insertions(+), 1532 deletions(-)
Title: Tools for Customer Lifetime Value Estimation
Description: A set of state-of-the-art probabilistic modeling approaches to derive estimates of individual customer lifetime values (CLV).
Commonly, probabilistic approaches focus on modelling 3 processes, i.e. individuals' attrition, transaction, and spending process.
Latent customer attrition models, which are also known as "buy-'til-you-die models", model the attrition as well as the transaction process.
They are used to make inferences and predictions about transactional patterns of individual customers such as their future purchase behavior.
Moreover, these models have also been used to predict individuals’ long-term engagement in activities such as playing an online game or
posting to a social media platform. The spending process is usually modelled by a separate probabilistic model. Combining these results yields in
lifetime values estimates for individual customers.
This package includes fast and accurate implementations of various probabilistic models for non-contractual settings
(e.g., grocery purchases or hotel visits). All implementations support time-invariant covariates, which can be used to control for e.g.,
socio-demographics. If such an extension has been proposed in literature, we further provide the possibility to control for time-varying
covariates to control for e.g., seasonal patterns.
Currently, the package includes the following latent attrition models to model individuals' attrition and transaction process:
[1] Pareto/NBD model (Pareto/Negative-Binomial-Distribution),
[2] the Extended Pareto/NBD model (Pareto/Negative-Binomial-Distribution with time-varying covariates),
[3] the BG/NBD model (Beta-Gamma/Negative-Binomial-Distribution) and the
[4] GGom/NBD (Gamma-Gompertz/Negative-Binomial-Distribution).
Further, we provide an implementation of the Gamma/Gamma model to model the spending process of individuals.
Author: Patrick Bachmann [cre, aut],
Niels Kuebler [aut],
Markus Meierer [aut],
Jeffrey Naef [aut],
Elliot Oblander [aut],
Patrik Schilter [aut]
Maintainer: Patrick Bachmann <patrick.bachmann@business.uzh.ch>
Diff between CLVTools versions 0.8.0 dated 2021-03-23 and 0.8.1 dated 2021-10-18
DESCRIPTION | 15 +++++++-------- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/CLVTools.R | 1 + build/vignette.rds |binary inst/doc/CLVTools.pdf |binary src/RcppExports.cpp | 5 +++++ 8 files changed, 28 insertions(+), 15 deletions(-)
Title: R Interface to the A/B Street Transport System Simulation
Software
Description: Provides functions to convert origin-destination data,
represented as straight 'desire lines' in the 'sf' Simple Features
class system, into JSON files that can be directly imported into
A/B Street <https://www.abstreet.org>, a free and open source tool
for simulating urban transport systems and scenarios of change
<doi:10.1007/s10109-020-00342-2>.
Author: Nathanael Sheehan [aut, cre] (<https://orcid.org/0000-0002-2779-0976>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Trevor Nederlof [aut],
Lucas Dias [ctb],
Dustin Carlino [aut]
Maintainer: Nathanael Sheehan <nathanaelsheehan@gmail.com>
Diff between abstr versions 0.3.0 dated 2021-08-19 and 0.4.0 dated 2021-10-18
DESCRIPTION | 18 +- MD5 | 50 +++++-- NAMESPACE | 1 NEWS.md | 11 + R/ab_scenario.R | 159 ++++++++++++++++++---- R/sao_paulo_activity_df_20.R |only README.md | 127 ++++++++++++++---- build/vignette.rds |binary data/sao_paulo_activity_df_2.rda |only data/sao_paulo_activity_df_20.rda |only data/sao_paulo_activity_sf_2.rda |only data/sao_paulo_activity_sf_20.rda |only inst/doc/abstr.R | 161 +++++------------------ inst/doc/abstr.Rmd | 250 +++++++++++++----------------------- inst/doc/abstr.html | 245 ++++++++++++----------------------- inst/doc/activity.R |only inst/doc/activity.Rmd |only inst/doc/activity.html |only inst/doc/montlake.R |only inst/doc/montlake.Rmd |only inst/doc/montlake.html |only inst/doc/pct_to_abstr.R |only inst/doc/pct_to_abstr.Rmd |only inst/doc/pct_to_abstr.html |only inst/extdata |only man/ab_json.Rd | 24 ++- man/ab_sf.Rd |only man/figures/README-input-1.png |binary man/figures/README-outputplot-1.png |binary man/sao_paulo_activity_df_20.Rd |only man/sao_paulo_activity_sf_20.Rd |only vignettes/abstr.Rmd | 250 +++++++++++++----------------------- vignettes/activity.Rmd |only vignettes/montlake.Rmd |only vignettes/od-sketch.png |only vignettes/pct_to_abstr.Rmd |only 36 files changed, 632 insertions(+), 664 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>),
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.26 dated 2021-09-14 and 0.27 dated 2021-10-18
xfun-0.26/xfun/tests/test-all.R |only xfun-0.26/xfun/tests/testit |only xfun-0.27/xfun/DESCRIPTION | 6 xfun-0.27/xfun/MD5 | 60 +++-- xfun-0.27/xfun/NAMESPACE | 5 xfun-0.27/xfun/NEWS.md | 10 xfun-0.27/xfun/R/cache.R | 2 xfun-0.27/xfun/R/command.R | 4 xfun-0.27/xfun/R/cran.R | 2 xfun-0.27/xfun/R/github.R |only xfun-0.27/xfun/R/io.R | 56 ++--- xfun-0.27/xfun/R/markdown.R | 3 xfun-0.27/xfun/R/packages.R | 12 - xfun-0.27/xfun/R/paths.R | 2 xfun-0.27/xfun/R/revcheck.R | 372 +++++++++++++++++++++++++++++----- xfun-0.27/xfun/inst/doc/xfun.html | 6 xfun-0.27/xfun/man/base_pkgs.Rd |only xfun-0.27/xfun/man/crandalf_check.Rd |only xfun-0.27/xfun/man/github_releases.Rd | 2 xfun-0.27/xfun/man/read_utf8.Rd | 16 + xfun-0.27/xfun/man/rev_check.Rd | 12 - xfun-0.27/xfun/tests/test-ci |only xfun-0.27/xfun/tests/test-ci.R |only xfun-0.27/xfun/tests/test-cran |only xfun-0.27/xfun/tests/test-cran.R |only 25 files changed, 447 insertions(+), 123 deletions(-)
Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and
generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre],
Pedro G. Lind [aut],
David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>
Diff between Langevin versions 1.2.1 dated 2019-01-02 and 1.3.0 dated 2021-10-18
ChangeLog | 8 ++++ DESCRIPTION | 11 ++---- MD5 | 43 ++++++++++++------------- NAMESPACE | 1 R/Langevin-package.r | 3 + R/Langevin1D.r | 82 +++++++++++++++++++++++++++++++----------------- R/Langevin2D.r | 3 - R/print.Langevin.r | 4 +- R/summary.Langevin.r | 5 +- R/timeseries1D.r | 2 - R/timeseries2D.r | 2 - build/vignette.rds |binary inst/doc/Langevin.pdf |binary man/Langevin-package.Rd | 3 + man/Langevin1D.Rd | 81 +++++++++++++++++++++++++++++++---------------- man/Langevin2D.Rd | 14 ++++---- man/print.Langevin.Rd | 3 - man/summary.Langevin.Rd | 5 +- man/timeseries1D.Rd | 17 ++++++++- man/timeseries2D.Rd | 18 +++++++--- src/Makevars | 18 ++++------ src/RcppExports.cpp | 20 +++++++++++ src/kernel1D.cpp |only 23 files changed, 219 insertions(+), 124 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.6.3 dated 2021-09-26 and 1.6.4 dated 2021-10-18
pillar-1.6.3/pillar/inst/doc/digits.R |only pillar-1.6.4/pillar/DESCRIPTION | 6 pillar-1.6.4/pillar/MD5 | 49 +- pillar-1.6.4/pillar/NEWS.md | 17 pillar-1.6.4/pillar/R/multi.R | 47 -- pillar-1.6.4/pillar/R/num.R | 1 pillar-1.6.4/pillar/R/styles.R | 2 pillar-1.6.4/pillar/R/tbl-format.R | 40 - pillar-1.6.4/pillar/R/testthat.R | 1 pillar-1.6.4/pillar/build/vignette.rds |binary pillar-1.6.4/pillar/inst/doc/digits.Rmd | 131 ------ pillar-1.6.4/pillar/inst/doc/digits.html | 248 ----------- pillar-1.6.4/pillar/inst/doc/extending.html | 46 +- pillar-1.6.4/pillar/inst/doc/numbers.R | 437 ++++++++++++--------- pillar-1.6.4/pillar/inst/doc/numbers.Rmd | 140 ------ pillar-1.6.4/pillar/inst/doc/numbers.html | 369 ----------------- pillar-1.6.4/pillar/inst/doc/printing.html | 4 pillar-1.6.4/pillar/man/extra_cols.Rd | 3 pillar-1.6.4/pillar/man/format_tbl.Rd | 47 -- pillar-1.6.4/pillar/man/squeeze.Rd | 5 pillar-1.6.4/pillar/man/style_subtle.Rd | 2 pillar-1.6.4/pillar/tests/testthat/_snaps/multi.md | 222 ++++++---- pillar-1.6.4/pillar/tests/testthat/helper-output.R | 4 pillar-1.6.4/pillar/tests/testthat/test-multi.R | 6 pillar-1.6.4/pillar/vignettes/digits.Rmd | 131 ------ pillar-1.6.4/pillar/vignettes/numbers.Rmd | 140 ------ 26 files changed, 523 insertions(+), 1575 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.7 dated 2019-12-05 and 2.1.8 dated 2021-10-18
BAMMtools-2.1.7/BAMMtools/man/plot.bammdata.Rd |only BAMMtools-2.1.8/BAMMtools/DESCRIPTION | 12 - BAMMtools-2.1.8/BAMMtools/MD5 | 92 +++++----- BAMMtools-2.1.8/BAMMtools/NAMESPACE | 3 BAMMtools-2.1.8/BAMMtools/R/BAMMtools-package.R | 2 BAMMtools-2.1.8/BAMMtools/R/credibleShiftSet.R | 2 BAMMtools-2.1.8/BAMMtools/R/dtRates.R | 2 BAMMtools-2.1.8/BAMMtools/R/generateControlFile.R | 2 BAMMtools-2.1.8/BAMMtools/R/getBranchShiftPriors.R | 2 BAMMtools-2.1.8/BAMMtools/R/getCladeRates.R | 2 BAMMtools-2.1.8/BAMMtools/R/getCohortMatrix.R | 2 BAMMtools-2.1.8/BAMMtools/R/getEventData.R | 8 BAMMtools-2.1.8/BAMMtools/R/getMeanBranchLengthTree.R | 2 BAMMtools-2.1.8/BAMMtools/R/getRateThroughTimeMatrix.R | 19 +- BAMMtools-2.1.8/BAMMtools/R/marginalShiftProbsTree.R | 2 BAMMtools-2.1.8/BAMMtools/R/plot.bammdata.R | 12 - BAMMtools-2.1.8/BAMMtools/R/plot.bammshifts.R | 5 BAMMtools-2.1.8/BAMMtools/R/plot.credibleshiftset.R | 5 BAMMtools-2.1.8/BAMMtools/R/plotRateThroughTime.R | 124 ++++++-------- BAMMtools-2.1.8/BAMMtools/R/ratesHistogram.R | 2 BAMMtools-2.1.8/BAMMtools/R/samplingProbs.R | 2 BAMMtools-2.1.8/BAMMtools/R/speciesByRatesMatrix.R | 2 BAMMtools-2.1.8/BAMMtools/R/stepBF.R | 2 BAMMtools-2.1.8/BAMMtools/R/summary.bammdata.R | 2 BAMMtools-2.1.8/BAMMtools/R/summary.credibleshiftset.R | 2 BAMMtools-2.1.8/BAMMtools/R/testTimeVariableBranches.R | 2 BAMMtools-2.1.8/BAMMtools/R/traitDependentBAMM.R | 6 BAMMtools-2.1.8/BAMMtools/man/BAMMtools.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/ShiftProbsTree.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/credibleShiftSet.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/dtRates.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/generateControlFile.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/getBranchShiftPriors.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/getCladeRates.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/getCohortMatrix.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/getMeanBranchLengthTree.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/plot.Rd |only BAMMtools-2.1.8/BAMMtools/man/plot.bammshifts.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/plot.credibleshiftset.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/plotRateThroughTime.Rd | 38 ++-- BAMMtools-2.1.8/BAMMtools/man/ratesHistogram.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/samplingProbs.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/speciesByRatesMatrix.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/stepBF.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/summary.bammdata.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/summary.credibleshiftset.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/testTimeVariableBranches.Rd | 2 BAMMtools-2.1.8/BAMMtools/man/traitDependentBAMM.Rd | 2 48 files changed, 198 insertions(+), 196 deletions(-)
Title: R Implementation of Wordpiece Tokenization
Description: Apply 'Wordpiece' (<arXiv:1609.08144>) tokenization to input text,
given an appropriate vocabulary. The 'BERT' (<arXiv:1810.04805>) tokenization
conventions are used by default.
Author: Jonathan Bratt [aut, cre] (<https://orcid.org/0000-0003-2859-0076>),
Jon Harmon [aut] (<https://orcid.org/0000-0003-4781-4346>),
Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph]
Maintainer: Jonathan Bratt <jonathan.bratt@macmillan.com>
Diff between wordpiece versions 1.0.2 dated 2021-02-11 and 2.0.1 dated 2021-10-18
wordpiece-1.0.2/wordpiece/man/dot-apply_to_chars.Rd |only wordpiece-1.0.2/wordpiece/man/dot-clean_text.Rd |only wordpiece-1.0.2/wordpiece/man/dot-convert_to_unicode.Rd |only wordpiece-1.0.2/wordpiece/man/dot-is_chinese_char_cp.Rd |only wordpiece-1.0.2/wordpiece/man/dot-is_control.Rd |only wordpiece-1.0.2/wordpiece/man/dot-is_punctuation.Rd |only wordpiece-1.0.2/wordpiece/man/dot-is_whitespace.Rd |only wordpiece-1.0.2/wordpiece/man/dot-make_cache_filename.Rd |only wordpiece-1.0.2/wordpiece/man/dot-split_on_punc.Rd |only wordpiece-1.0.2/wordpiece/man/dot-strip_accents.Rd |only wordpiece-1.0.2/wordpiece/man/dot-tokenize_chinese_chars.Rd |only wordpiece-1.0.2/wordpiece/man/dot-tokenize_word.Rd |only wordpiece-1.0.2/wordpiece/man/dot-whitespace_tokenize.Rd |only wordpiece-1.0.2/wordpiece/man/get_cache_dir.Rd |only wordpiece-1.0.2/wordpiece/man/op-null-default.Rd |only wordpiece-2.0.1/wordpiece/DESCRIPTION | 20 wordpiece-2.0.1/wordpiece/MD5 | 59 - wordpiece-2.0.1/wordpiece/NAMESPACE | 7 wordpiece-2.0.1/wordpiece/NEWS.md | 7 wordpiece-2.0.1/wordpiece/R/imports.R |only wordpiece-2.0.1/wordpiece/R/tokenization.R | 229 ++-- wordpiece-2.0.1/wordpiece/R/utils.R | 497 ---------- wordpiece-2.0.1/wordpiece/R/vocab.R |only wordpiece-2.0.1/wordpiece/README.md | 57 - wordpiece-2.0.1/wordpiece/inst/doc/basic_usage.R | 20 wordpiece-2.0.1/wordpiece/inst/doc/basic_usage.Rmd | 92 + wordpiece-2.0.1/wordpiece/inst/doc/basic_usage.html | 70 + wordpiece-2.0.1/wordpiece/man/dot-infer_case_from_vocab.Rd | 2 wordpiece-2.0.1/wordpiece/man/dot-new_wordpiece_vocabulary.Rd | 2 wordpiece-2.0.1/wordpiece/man/dot-validate_wordpiece_vocabulary.Rd | 2 wordpiece-2.0.1/wordpiece/man/dot-wp_tokenize_single_string.Rd |only wordpiece-2.0.1/wordpiece/man/dot-wp_tokenize_word.Rd |only wordpiece-2.0.1/wordpiece/man/load_or_retrieve_vocab.Rd | 20 wordpiece-2.0.1/wordpiece/man/load_vocab.Rd | 2 wordpiece-2.0.1/wordpiece/man/prepare_vocab.Rd |only wordpiece-2.0.1/wordpiece/man/reexports.Rd |only wordpiece-2.0.1/wordpiece/man/set_wordpiece_cache_dir.Rd |only wordpiece-2.0.1/wordpiece/man/wordpiece_cache_dir.Rd |only wordpiece-2.0.1/wordpiece/man/wordpiece_tokenize.Rd | 25 wordpiece-2.0.1/wordpiece/tests/testthat/_snaps |only wordpiece-2.0.1/wordpiece/tests/testthat/test-tokenization.R | 124 -- wordpiece-2.0.1/wordpiece/tests/testthat/test-vocab.R |only wordpiece-2.0.1/wordpiece/vignettes/basic_usage.Rmd | 92 + 43 files changed, 450 insertions(+), 877 deletions(-)
Title: Efficient Estimation of the Causal Effects of Stochastic
Interventions
Description: Efficient estimation of the population-level causal effects of
stochastic interventions on a continuous-valued exposure. Both one-step and
targeted minimum loss estimators are implemented for the counterfactual mean
value of an outcome of interest under an additive modified treatment policy,
a stochastic intervention that may depend on the natural value of the
exposure. To accommodate settings with outcome-dependent two-phase
sampling, procedures incorporating inverse probability of censoring
weighting are provided to facilitate the construction of inefficient and
efficient one-step and targeted minimum loss estimators. The causal
parameter and its estimation were first described by Díaz and van der Laan
(2013) <doi:10.1111/j.1541-0420.2011.01685.x>, while the multiply robust
estimation procedure and its application to data from two-phase sampling
designs is detailed in NS Hejazi, MJ van der Laan, HE Janes, PB Gilbert,
and DC Benkeser (2020) <doi:10.1111/biom.13375>. The software package
implementation is described in NS Hejazi and DC Benkeser (2020)
<doi:10.21105/joss.02447>. Estimation of nuisance parameters may be
enhanced through the Super Learner ensemble model in 'sl3', available for
download from GitHub using 'remotes::install_github("tlverse/sl3")'.
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>),
David Benkeser [aut] (<https://orcid.org/0000-0002-1019-8343>),
Iván Díaz [ctb] (<https://orcid.org/0000-0001-9056-2047>),
Jeremy Coyle [ctb] (<https://orcid.org/0000-0002-9874-6649>),
Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>)
Maintainer: Nima Hejazi <nh@nimahejazi.org>
Diff between txshift versions 0.3.5 dated 2021-02-07 and 0.3.6 dated 2021-10-18
txshift-0.3.5/txshift/inst/doc/ipcw_txshift.R |only txshift-0.3.5/txshift/inst/doc/ipcw_txshift.Rmd |only txshift-0.3.5/txshift/inst/doc/ipcw_txshift.html |only txshift-0.3.5/txshift/vignettes/ipcw_txshift.Rmd |only txshift-0.3.6/txshift/DESCRIPTION | 48 - txshift-0.3.6/txshift/MD5 | 52 - txshift-0.3.6/txshift/NAMESPACE | 3 txshift-0.3.6/txshift/NEWS.md | 32 - txshift-0.3.6/txshift/R/eifs.R | 11 txshift-0.3.6/txshift/R/fit_mechanisms.R | 18 txshift-0.3.6/txshift/R/msm.R | 1 txshift-0.3.6/txshift/R/txshift.R | 51 - txshift-0.3.6/txshift/R/utils.R | 134 ++-- txshift-0.3.6/txshift/README.md | 185 ++---- txshift-0.3.6/txshift/build/vignette.rds |binary txshift-0.3.6/txshift/inst/CITATION | 4 txshift-0.3.6/txshift/inst/REFERENCES.bib | 113 +++ txshift-0.3.6/txshift/inst/doc/intro_txshift.R | 193 +++--- txshift-0.3.6/txshift/inst/doc/intro_txshift.Rmd | 365 ++++++----- txshift-0.3.6/txshift/inst/doc/intro_txshift.html | 367 ++++++------ txshift-0.3.6/txshift/man/est_g_exp.Rd | 4 txshift-0.3.6/txshift/man/print.txshift.Rd | 37 - txshift-0.3.6/txshift/man/txshift.Rd | 50 - txshift-0.3.6/txshift/tests/testthat/test-censoring_mech.R | 6 txshift-0.3.6/txshift/tests/testthat/test-estim_tmle_os.R | 13 txshift-0.3.6/txshift/tests/testthat/test-matches_tmle_ID.R | 7 txshift-0.3.6/txshift/tests/testthat/test-nuisance_est.R | 3 txshift-0.3.6/txshift/tests/testthat/test-tmle_comparison.R | 9 txshift-0.3.6/txshift/vignettes/intro_txshift.Rmd | 365 ++++++----- 29 files changed, 1166 insertions(+), 905 deletions(-)
Title: Missing Item Responses Imputation for Test and Assessment Data
Description: Functions for imputing missing item responses for dichotomous and
polytomous test and assessment data. This package enables missing imputation
methods that are suitable for test and assessment data, including:
listwise (LW) deletion (see De Ayala et al. 2001 <doi:10.1111/j.1745-3984.2001.tb01124.x>),
treating as incorrect (IN, see Lord, 1974 <doi: 10.1111/j.1745-3984.1974.tb00996.x>;
Mislevy & Wu, 1996 <doi: 10.1002/j.2333-8504.1996.tb01708.x>;
Pohl et al., 2014 <doi: 10.1177/0013164413504926>), person mean imputation (PM),
item mean imputation (IM), two-way (TW) and response function (RF) imputation,
(see Sijtsma & van der Ark, 2003 <doi: 10.1207/s15327906mbr3804_4>),
logistic regression (LR) imputation, predictive mean matching (PMM), and expectation–maximization (EM)
imputation (see Finch, 2008 <doi: 10.1111/j.1745-3984.2008.00062.x>).
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Diff between TestDataImputation versions 2.2 dated 2021-09-02 and 2.3 dated 2021-10-18
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + R/EMimpute.r | 12 ++++++++++-- R/ImputeTestData.r | 40 ++++++++++++++++++++++++++++++++-------- R/LogisticReg.r | 11 +++++++++-- R/micePMM.r |only man/EMimpute.Rd | 11 +++++++++-- man/ImputeTestData.Rd | 32 ++++++++++++++++++++++++-------- man/LogisticReg.Rd | 13 +++++++++++-- man/micePMM.Rd |only 11 files changed, 113 insertions(+), 39 deletions(-)
More information about TestDataImputation at CRAN
Permanent link
Title: R Interface to the Vowpal Wabbit
Description: The 'Vowpal Wabbit' project is a fast out-of-core learning
system sponsored by Microsoft Research (having started at Yahoo! Research)
and written by John Langford along with a number of contributors. This R
package does not include the distributed computing implementation of the
cluster/ directory of the upstream sources. Use of the software as a network
service is also not directly supported as the aim is a simpler direct call
from R for validation and comparison. Note that this package contains an
embedded older version of 'Vowpal Wabbit'. The package 'rvw' at the GitHub
repo <https://github.com/rvw-org/rvw-legacy> can provide an alternative using
an external 'Vowpal Wabbit' library installation.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RVowpalWabbit versions 0.0.15 dated 2020-08-07 and 0.0.16 dated 2021-10-18
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- README.md | 1 + configure | 35 +++++++++++++++++++---------------- configure.ac | 9 +++++---- man/vw.Rd | 2 +- src/v_array.h | 4 ++-- 8 files changed, 67 insertions(+), 36 deletions(-)
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute, summarize, and plot marginal effects, adjusted predictions, contrasts, and marginal means for a wide variety of models.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.1.0 dated 2021-09-29 and 0.2.0 dated 2021-10-18
marginaleffects-0.1.0/marginaleffects/R/get_dydx_categorical.R |only marginaleffects-0.1.0/marginaleffects/R/get_dydx_continuous.R |only marginaleffects-0.1.0/marginaleffects/man/get_dydx_and_se.Rd |only marginaleffects-0.1.0/marginaleffects/man/get_dydx_categorical.Rd |only marginaleffects-0.1.0/marginaleffects/man/get_dydx_continuous.Rd |only marginaleffects-0.1.0/marginaleffects/tests/testthat/helper-basic.R |only marginaleffects-0.1.0/marginaleffects/tests/testthat/test-plot_cmm.R |only marginaleffects-0.2.0/marginaleffects/DESCRIPTION | 39 - marginaleffects-0.2.0/marginaleffects/MD5 | 178 ++--- marginaleffects-0.2.0/marginaleffects/NAMESPACE | 5 marginaleffects-0.2.0/marginaleffects/NEWS.md | 31 marginaleffects-0.2.0/marginaleffects/R/complete_levels.R | 5 marginaleffects-0.2.0/marginaleffects/R/counterfactual_typical.R | 72 +- marginaleffects-0.2.0/marginaleffects/R/get_dydx.R |only marginaleffects-0.2.0/marginaleffects/R/get_dydx_and_se.R | 155 +--- marginaleffects-0.2.0/marginaleffects/R/get_dydx_se.R |only marginaleffects-0.2.0/marginaleffects/R/get_predict.R | 11 marginaleffects-0.2.0/marginaleffects/R/get_vcov.R | 8 marginaleffects-0.2.0/marginaleffects/R/marginaleffects.R | 61 - marginaleffects-0.2.0/marginaleffects/R/marginalmeans.R | 127 ++- marginaleffects-0.2.0/marginaleffects/R/methods_MASS.R | 10 marginaleffects-0.2.0/marginaleffects/R/methods_bife.R | 10 marginaleffects-0.2.0/marginaleffects/R/methods_crch.R | 4 marginaleffects-0.2.0/marginaleffects/R/methods_mgcv.R |only marginaleffects-0.2.0/marginaleffects/R/methods_ordinal.R |only marginaleffects-0.2.0/marginaleffects/R/plot_cap.R | 13 marginaleffects-0.2.0/marginaleffects/R/predictions.R | 46 - marginaleffects-0.2.0/marginaleffects/R/sanity.R | 7 marginaleffects-0.2.0/marginaleffects/R/sanity_model.R | 5 marginaleffects-0.2.0/marginaleffects/R/tidy.R | 5 marginaleffects-0.2.0/marginaleffects/R/utils.R | 2 marginaleffects-0.2.0/marginaleffects/README.md | 41 - marginaleffects-0.2.0/marginaleffects/data/supported_models.rda |binary marginaleffects-0.2.0/marginaleffects/inst/WORDLIST |only marginaleffects-0.2.0/marginaleffects/inst/doc/benchmark.html | 152 +--- marginaleffects-0.2.0/marginaleffects/inst/doc/contrasts.html | 159 +--- marginaleffects-0.2.0/marginaleffects/inst/doc/marginalmeans.R | 31 marginaleffects-0.2.0/marginaleffects/inst/doc/marginalmeans.Rmd | 48 + marginaleffects-0.2.0/marginaleffects/inst/doc/marginalmeans.html | 229 +++--- marginaleffects-0.2.0/marginaleffects/inst/doc/mfx.html | 341 ++++------ marginaleffects-0.2.0/marginaleffects/inst/doc/predictions.R | 14 marginaleffects-0.2.0/marginaleffects/inst/doc/predictions.Rmd | 18 marginaleffects-0.2.0/marginaleffects/inst/doc/predictions.html | 208 ++---- marginaleffects-0.2.0/marginaleffects/man/counterfactual.Rd | 8 marginaleffects-0.2.0/marginaleffects/man/figures/README-supported_models.png |binary marginaleffects-0.2.0/marginaleffects/man/get_coef.Rd | 5 marginaleffects-0.2.0/marginaleffects/man/get_group_names.Rd | 5 marginaleffects-0.2.0/marginaleffects/man/get_predict.Rd | 11 marginaleffects-0.2.0/marginaleffects/man/marginalmeans.Rd | 48 + marginaleffects-0.2.0/marginaleffects/man/plot_cap.Rd | 13 marginaleffects-0.2.0/marginaleffects/man/predictions.Rd | 13 marginaleffects-0.2.0/marginaleffects/man/typical.Rd | 8 marginaleffects-0.2.0/marginaleffects/tests/spelling.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/_snaps/plot_cap |only marginaleffects-0.2.0/marginaleffects/tests/testthat/_snaps/summary.md | 2 marginaleffects-0.2.0/marginaleffects/tests/testthat/helper-marginaleffects.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/helper-marginalmeans.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/helper-predictions.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/test-analytic.R | 6 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-complete_levels.R | 22 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-counterfactual.R | 12 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-marginalmeans.R | 29 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-AER.R | 17 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-MASS.R | 82 ++ marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-betareg.R | 29 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-bife.R | 13 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-brglm2.R | 20 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-crch.R | 40 - marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-estimatr.R | 23 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-fixest.R | 75 +- marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-gam.R | 25 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-geepack.R | 34 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-glmx.R | 18 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-ivreg.R | 26 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-lme4.R | 37 - marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-mgcv.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-nlme.R | 21 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-nnet.R | 48 + marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-ordinal.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-plm.R | 25 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-pscl.R | 41 - marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-quantreg.R | 25 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-rms.R | 20 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-robustbase.R | 24 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-speedglm.R | 4 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-stats.R | 55 + marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-survival.R | 6 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-pkg-truncreg.R | 5 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-plot.R | 5 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-plot_cap.R |only marginaleffects-0.2.0/marginaleffects/tests/testthat/test-plot_cme.R | 1 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-predictions.R | 12 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-summary.R | 4 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-tidy.R | 7 marginaleffects-0.2.0/marginaleffects/tests/testthat/test-typical.R | 2 marginaleffects-0.2.0/marginaleffects/vignettes/marginalmeans.Rmd | 48 + marginaleffects-0.2.0/marginaleffects/vignettes/predictions.Rmd | 18 97 files changed, 1816 insertions(+), 1211 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Do Multiple Imputation-Based Semi-Supervised and Unsupervised
Learning
Description: Algorithms for (i) unsupervised learning for dataset with
missing data and/or left-censored data, using multiple imputation and
consensus clustering ; (ii) semi-supervised learning with a survival
endpoint (right-censored) for complete or incomplete datasets, using
multiple imputation and consensus clustering in the latter case. The
methods are described in Faucheux et al. (2021)
<doi:10.1002/bimj.201900366> and Faucheux et al. (2021)
<doi:10.1002/bimj.202000365>, respectively.
Author: Lilith Faucheux [aut, cre],
Sylvie Chevret [ths],
Matthieu Resche-Rigon [ctb],
Marie Perrot-Dockès [ctb],
Eric Han [ctb]
Maintainer: Lilith Faucheux <lilith.faucheux@inserm.fr>
Diff between doMIsaul versions 1.0.0 dated 2021-08-05 and 1.0.1 dated 2021-10-18
DESCRIPTION | 12 +- MD5 | 30 +++--- NAMESPACE | 1 R/CH_index_functions.R | 27 ++++-- R/MI_imputation.R | 163 +++++++++++++++++++++++++++++++++++++- R/evaluate_partition_semisup.R | 16 ++- R/partition_generation.R | 2 R/unsupMI.R | 21 +++- man/CH.Rd | 5 - man/CH.sel.Rd | 5 - man/MImpute.Rd | 53 +++++++++++- man/evaluate_partition_semisup.Rd | 16 ++- man/unsupMI.Rd | 9 ++ tests/testthat/test-other.R | 35 ++++---- tests/testthat/test-seMIsupcox.R | 17 ++- tests/testthat/test-unsupMI.R | 46 +++++----- 16 files changed, 357 insertions(+), 101 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph] (Original author of included code for priority
heaps)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.2.11 dated 2021-10-07 and 0.2.12 dated 2021-10-18
DESCRIPTION | 9 +- MD5 | 32 ++++---- NEWS.md | 9 ++ R/compare-heaps.R | 77 ++++++++++++-------- README.md | 2 inst/doc/dists-categorical.html | 20 ++--- inst/doc/dodgr.R | 23 +++-- inst/doc/dodgr.Rmd | 23 +++-- inst/doc/dodgr.html | 123 +++++++++++--------------------- inst/doc/flows.html | 29 ++++--- inst/doc/times.html | 16 ++-- man/compare_heaps.Rd | 3 src/dgraph.h | 1 src/run_sp_categorical.cpp | 2 tests/testthat/test-dists-categorical.R | 4 - tests/testthat/test-graph-fns.R | 4 - vignettes/dodgr.Rmd | 23 +++-- 17 files changed, 202 insertions(+), 198 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Richard FitzJohn [ctb],
Brandon Bertelsen [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.13 dated 2021-10-15 and 0.0.14 dated 2021-10-18
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 7 +++ inst/doc/arkdb.html | 78 ++++++++++++++++++++++---------------------- tests/testthat/test-arkdb.R | 17 +++++++-- 5 files changed, 67 insertions(+), 49 deletions(-)
Title: Analysis of Oceanographic Argo Floats
Description: Supports the analysis of oceanographic data recorded by Argo autonomous drifting profiling floats. Functions are provided to (a) download and cache data files, (b) subset data in various ways, (c) handle quality-control flags and (d) plot the results according to oceanographic conventions. A shiny app is provided for easy exploration of datasets. The package is designed to work well with the 'oce' package, providing a wide range of processing capabilities that are particular to oceanographic analysis. See Kelley, Harbin, and Richards (2021) <doi:10.3389/fmars.2021.635922> for more on the scientific context and applications.
Author: Dan Kelley [aut, cre, cph] (<https://orcid.org/0000-0001-7808-5911>),
Jaimie Harbin [aut] (<https://orcid.org/0000-0003-3774-3732>),
Dewey Dunnington [ctb] (<https://orcid.org/0000-0002-9415-4582>),
Clark Richards [ctb] (<https://orcid.org/0000-0002-7833-206X>)
Maintainer: Dan Kelley <dan.kelley@dal.ca>
Diff between argoFloats versions 1.0.2 dated 2021-09-15 and 1.0.3 dated 2021-10-18
DESCRIPTION | 6 MD5 | 24 - R/mapApp.R | 30 - R/plot.R | 3 R/subset.R | 2 README.md | 107 ++--- build/partial.rdb |binary inst/WORDLIST | 1 inst/doc/argoFloats.html | 4 inst/doc/qc.html | 4 inst/shiny/mapApp/app.R | 805 ++++++++++++++++++++++++++++------------ man/mapApp.Rd | 29 - man/subset-argoFloats-method.Rd | 2 13 files changed, 672 insertions(+), 345 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-8 dated 2020-09-21 and 1.4-9 dated 2021-10-18
DESCRIPTION | 6 +-- MD5 | 81 ++++++++++++++++++++--------------------- R/pairsplot.R | 3 + build/partial.rdb |only build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/CITATION | 4 +- inst/NEWS.Rd | 8 ++++ inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.pdf |binary man/assoc.Rd | 4 +- man/cotab_panel.Rd | 4 +- man/cotabplot.Rd | 5 +- man/doubledecker.Rd | 5 +- man/labeling_border.Rd | 4 +- man/labeling_cells_list.Rd | 4 +- man/legends.Rd | 4 +- man/mosaic.Rd | 4 +- man/pairs.table.Rd | 4 +- man/panel_pairs_diagonal.Rd | 2 + man/shadings.Rd | 5 +- man/sieve.Rd | 6 +-- man/spacings.Rd | 5 +- man/struc_assoc.Rd | 4 +- man/struc_mosaic.Rd | 5 +- man/struc_sieve.Rd | 4 +- man/strucplot.Rd | 6 +-- man/structable.Rd | 4 +- 42 files changed, 99 insertions(+), 82 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.0.0 dated 2021-09-14 and 1.1.0 dated 2021-10-18
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Title: Library of Research Designs
Description: A simple interface to build designs using the package 'DeclareDesign'.
In one line of code, users can specify the parameters of individual
designs and diagnose their properties. The designers can also be used
to compare performance of a given design across a range of combinations
of parameters, such as effect size, sample size, and assignment probabilities.
Author: Graeme Blair [aut],
Jasper Cooper [aut, cre],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Clara Bicalho [aut],
Neal Fultz [aut],
Lily Medina [aut]
Maintainer: Jasper Cooper <jjc2247@columbia.edu>
Diff between DesignLibrary versions 0.1.8 dated 2021-09-02 and 0.1.10 dated 2021-10-18
DESCRIPTION | 24 +++++++++++++----------- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/factorial_designer.R | 4 ++-- R/multi_arm_designer.R | 4 ++-- R/two_arm_covariate_designer.R | 2 +- man/two_arm_covariate_designer.Rd | 2 +- tests/testthat/test_diagnose_designers.R | 2 ++ 8 files changed, 32 insertions(+), 24 deletions(-)
Title: Coarsened Variable Modeling
Description: Extends R's implementation of categorical variables (factors)
to handle coarsened observations; implements log-linear models for
coarsened categorical data, including latent-class models. Detailed
information and examples are provided in the package vignettes.
Author: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Maintainer: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Diff between cvam versions 0.9.1 dated 2021-10-01 and 0.9.2 dated 2021-10-18
cvam-0.9.1/cvam/man/cvamLik.Rd |only cvam-0.9.2/cvam/ChangeLog | 89 cvam-0.9.2/cvam/DESCRIPTION | 12 cvam-0.9.2/cvam/LICENSE | 40 cvam-0.9.2/cvam/MD5 | 146 cvam-0.9.2/cvam/NAMESPACE | 156 cvam-0.9.2/cvam/NEWS | 29 cvam-0.9.2/cvam/R/coarsened.R | 634 cvam-0.9.2/cvam/R/cvamMlogit.R | 822 cvam-0.9.2/cvam/R/cvamModel.R | 6866 +-- cvam-0.9.2/cvam/R/miInference.R | 208 cvam-0.9.2/cvam/R/msgCvam.R | 236 cvam-0.9.2/cvam/R/sysdata.rda |binary cvam-0.9.2/cvam/build/partial.rdb |binary cvam-0.9.2/cvam/build/vignette.rds |binary cvam-0.9.2/cvam/data/abortion2000.rda |binary cvam-0.9.2/cvam/data/cig2019.rda |only cvam-0.9.2/cvam/data/crime.rda |binary cvam-0.9.2/cvam/data/hivtest.rda |binary cvam-0.9.2/cvam/data/microUCBAdmissions.rda |binary cvam-0.9.2/cvam/data/seatbelt.rda |binary cvam-0.9.2/cvam/inst/CITATION | 16 cvam-0.9.2/cvam/inst/doc/FittingLogLinearModelsInCvam.R | 1978 cvam-0.9.2/cvam/inst/doc/FittingLogLinearModelsInCvam.Rnw | 7838 +-- cvam-0.9.2/cvam/inst/doc/FittingLogLinearModelsInCvam.pdf |binary cvam-0.9.2/cvam/inst/doc/UnderstandingCoarsenedFactorsInCvam.R | 1230 cvam-0.9.2/cvam/inst/doc/UnderstandingCoarsenedFactorsInCvam.Rnw | 2716 - cvam-0.9.2/cvam/inst/doc/UnderstandingCoarsenedFactorsInCvam.pdf |binary cvam-0.9.2/cvam/man/abortion2000.Rd | 281 cvam-0.9.2/cvam/man/anova.cvam.Rd | 180 cvam-0.9.2/cvam/man/baseLevels.Rd | 150 cvam-0.9.2/cvam/man/cig2019.Rd |only cvam-0.9.2/cvam/man/coarsened.Rd | 350 cvam-0.9.2/cvam/man/crime.Rd | 86 cvam-0.9.2/cvam/man/cvam-package.Rd | 138 cvam-0.9.2/cvam/man/cvam.Rd | 409 cvam-0.9.2/cvam/man/cvamControl.Rd | 356 cvam-0.9.2/cvam/man/cvamEstimate.Rd | 234 cvam-0.9.2/cvam/man/cvamImpute.Rd | 164 cvam-0.9.2/cvam/man/cvamPredict.Rd | 158 cvam-0.9.2/cvam/man/cvamPrior.Rd | 206 cvam-0.9.2/cvam/man/cvamlik.Rd |only cvam-0.9.2/cvam/man/dropCoarseLevels.Rd | 116 cvam-0.9.2/cvam/man/get.coef.Rd | 526 cvam-0.9.2/cvam/man/hivtest.Rd | 92 cvam-0.9.2/cvam/man/is.naCoarsened.Rd | 112 cvam-0.9.2/cvam/man/latentFactor.Rd | 116 cvam-0.9.2/cvam/man/miInference.Rd | 290 cvam-0.9.2/cvam/man/microUCBAdmissions.Rd | 84 cvam-0.9.2/cvam/man/seatbelt.Rd | 130 cvam-0.9.2/cvam/man/summary.cvam.Rd | 98 cvam-0.9.2/cvam/src/cvam.f90 | 1682 cvam-0.9.2/cvam/src/cvam_engine.f90 |19921 +++++----- cvam-0.9.2/cvam/src/cvam_init.c | 4 cvam-0.9.2/cvam/src/dynalloc.f90 | 1760 cvam-0.9.2/cvam/src/error_handler.f90 | 1258 cvam-0.9.2/cvam/src/icodes_2.h | 20 cvam-0.9.2/cvam/src/icodes_3.h | 80 cvam-0.9.2/cvam/src/math_R.f90 | 4340 +- cvam-0.9.2/cvam/src/math_funcs.f90 | 510 cvam-0.9.2/cvam/src/matrix_methods.f90 | 2096 - cvam-0.9.2/cvam/src/program_constants.f90 | 84 cvam-0.9.2/cvam/src/quick_sort.f90 | 972 cvam-0.9.2/cvam/src/tabulate.f90 | 1610 cvam-0.9.2/cvam/tests/UCBAdmissionsTests.R | 174 cvam-0.9.2/cvam/tests/UCBAdmissionsTests.Rout.save | 44 cvam-0.9.2/cvam/tests/abortion2000Tests.R | 474 cvam-0.9.2/cvam/tests/abortion2000Tests.Rout.save | 60 cvam-0.9.2/cvam/tests/crimeTests.R | 224 cvam-0.9.2/cvam/tests/crimeTests.Rout.save | 38 cvam-0.9.2/cvam/tests/hivtestTests.R | 246 cvam-0.9.2/cvam/tests/hivtestTests.Rout.save | 44 cvam-0.9.2/cvam/vignettes/FittingLogLinearModelsInCvam.Rnw | 7838 +-- cvam-0.9.2/cvam/vignettes/UnderstandingCoarsenedFactorsInCvam.Rnw | 2716 - cvam-0.9.2/cvam/vignettes/apa.bst | 2260 - cvam-0.9.2/cvam/vignettes/cvamBibliography.bib | 1590 76 files changed, 40876 insertions(+), 36461 deletions(-)
Title: Boltzmann Entropy of a Landscape Gradient
Description: Calculates the Boltzmann entropy of a landscape gradient.
This package uses the analytical method created by Gao, P., Zhang, H.
and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019
(<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by
allowing calculations on data with missing values.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between belg versions 1.4.1 dated 2020-08-31 and 1.5.0 dated 2021-10-18
belg-1.4.1/belg/R/datasets.R |only belg-1.4.1/belg/data |only belg-1.4.1/belg/man/complex_land.Rd |only belg-1.4.1/belg/man/land_gradient1.Rd |only belg-1.4.1/belg/man/land_gradient2.Rd |only belg-1.4.1/belg/man/simple_land.Rd |only belg-1.5.0/belg/DESCRIPTION | 15 belg-1.5.0/belg/MD5 | 41 - belg-1.5.0/belg/NAMESPACE | 1 belg-1.5.0/belg/NEWS.md | 20 belg-1.5.0/belg/R/get_boltzmann.R | 13 belg-1.5.0/belg/README.md | 32 - belg-1.5.0/belg/build/vignette.rds |binary belg-1.5.0/belg/inst/doc/belg1.R | 2 belg-1.5.0/belg/inst/doc/belg1.Rmd | 2 belg-1.5.0/belg/inst/doc/belg1.html | 316 +++------------ belg-1.5.0/belg/inst/raster |only belg-1.5.0/belg/man/figures/README-unnamed-chunk-1-1.png |binary belg-1.5.0/belg/man/get_boltzmann.Rd | 13 belg-1.5.0/belg/src/RcppExports.cpp | 5 belg-1.5.0/belg/tests/testthat/test-raster-stars.R | 13 belg-1.5.0/belg/vignettes/belg1.Rmd | 2 22 files changed, 172 insertions(+), 303 deletions(-)
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Description: Functions, data sets, analyses and examples from the
third edition of the book
''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled ''An Introduction to R'',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides). The publishers web page is
'<http://www.crcpress.com/product/isbn/9781482204582>'.
Author: Torsten Hothorn and Brian S. Everitt
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR3 versions 1.0-11 dated 2021-04-07 and 1.0-12 dated 2021-10-18
DESCRIPTION | 8 - MD5 | 124 +++++++++++++------------- build/vignette.rds |binary data/BCG.rda |binary data/CYGOB1.rda |binary data/Lanza.rda |binary data/birthdeathrates.rda |binary data/bladdercancer.rda |binary data/epilepsy.rda |binary data/foster.rda |binary data/heptathlon.rda |binary data/meteo.rda |binary data/orallesions.rda |binary data/phosphate.rda |binary data/pistonrings.rda |binary data/planets.rda |binary data/plasma.rda |binary data/polyps.rda |binary data/rearrests.rda |binary data/roomwidth.rda |binary data/schizophrenia.rda |binary data/schizophrenia2.rda |binary data/smoking.rda |binary data/students.rda |binary data/suicides.rda |binary data/toothpaste.rda |binary data/voting.rda |binary data/water.rda |binary data/watervoles.rda |binary data/waves.rda |binary data/weightgain.rda |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_bayesian_inference.pdf |binary inst/doc/Ch_cluster_analysis.Rnw | 4 inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.Rnw | 10 +- inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.pdf |binary inst/doc/Ch_gam.pdf |binary inst/doc/Ch_graphical_display.Rnw | 4 inst/doc/Ch_graphical_display.pdf |binary inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_missing_values.pdf |binary inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_quantile_regression.Rnw | 10 +- inst/doc/Ch_quantile_regression.pdf |binary inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_simultaneous_inference.pdf |binary inst/doc/Ch_survival_analysis.pdf |binary vignettes/Ch_cluster_analysis.Rnw | 4 vignettes/Ch_density_estimation.Rnw | 10 +- vignettes/Ch_graphical_display.Rnw | 4 vignettes/Ch_quantile_regression.Rnw | 10 +- vignettes/tables/rec.tex | 14 +- 63 files changed, 111 insertions(+), 95 deletions(-)
Title: Extraction of Business Financial Information from 'XBRL'
Documents
Description: Functions to extract business financial information from
an Extensible Business Reporting Language ('XBRL') instance file and the
associated collection of files that defines its 'Discoverable' Taxonomy
Set ('DTS').
Author: Roberto Bertolusso
Maintainer: Roberto Bertolusso <rbertolusso@rice.edu>
Diff between XBRL versions 0.99.18 dated 2017-03-28 and 0.99.19 dated 2021-10-18
XBRL-0.99.18/XBRL/configure.in |only XBRL-0.99.19/XBRL/ChangeLog | 6 ++++++ XBRL-0.99.19/XBRL/DESCRIPTION | 8 ++++---- XBRL-0.99.19/XBRL/MD5 | 6 +++--- XBRL-0.99.19/XBRL/configure.ac |only 5 files changed, 13 insertions(+), 7 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between set6 versions 0.2.3 dated 2021-07-25 and 0.2.4 dated 2021-10-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/operation_setintersect.R | 4 +++- R/zzz.R | 2 ++ README.md | 2 +- inst/doc/set6.html | 4 ++-- man/set6-package.Rd | 2 +- src/RcppExports.cpp | 5 +++++ tests/testthat/test_operations_setintersect.R | 21 ++++++++++++--------- 11 files changed, 46 insertions(+), 28 deletions(-)
Title: Tests for Rotational Symmetry on the Hypersphere
Description: Implementation of the tests for rotational symmetry on the
hypersphere proposed in García-Portugués, Paindaveine and Verdebout (2020)
<doi:10.1080/01621459.2019.1665527>. The package also implements the
proposed distributions on the hypersphere, based on the tangent-normal
decomposition, and allows for the replication of the data application
considered in the paper.
Author: Eduardo García-Portugués [aut, cre]
(<https://orcid.org/0000-0002-9224-4111>),
Davy Paindaveine [aut],
Thomas Verdebout [aut]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Diff between rotasym versions 1.1.2 dated 2021-08-19 and 1.1.3 dated 2021-10-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/ACG.R | 2 +- build/partial.rdb |binary src/vMF.cpp | 2 +- 6 files changed, 17 insertions(+), 11 deletions(-)
Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical
Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] (<https://orcid.org/0000-0002-5818-6958>),
Sebastian Malkusch [aut] (<https://orcid.org/0000-0001-6766-140X>),
Alfred Ultsch [aut] (<https://orcid.org/0000-0002-7845-3283>)
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opdisDownsampling versions 0.6.1 dated 2021-10-11 and 0.7.0 dated 2021-10-18
DESCRIPTION | 10 +- MD5 | 8 - NAMESPACE | 10 +- R/opdisDownsampling.R | 208 ++++++++++++++++++++++++++--------------------- man/opdisDownsampling.Rd | 12 +- 5 files changed, 141 insertions(+), 107 deletions(-)
More information about opdisDownsampling at CRAN
Permanent link
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Mathilde Hagens [ctb],
Andreas Hofmann [ctb],
Jens-Daniel Mueller [ctb],
Aurélien Proye [ctb],
James Rae [ctb],
Karline Soetaert [ctb]
Maintainer: Jean-Pierre Gattuso <jean-pierre.gattuso@imev-mer.fr>
Diff between seacarb versions 3.2.16 dated 2021-02-22 and 3.3.0 dated 2021-10-18
seacarb-3.2.16/seacarb/R/sir.R |only seacarb-3.2.16/seacarb/R/sir_b.R |only seacarb-3.2.16/seacarb/R/sir_full.R |only seacarb-3.3.0/seacarb/ChangeLog | 8 seacarb-3.3.0/seacarb/DESCRIPTION | 14 seacarb-3.3.0/seacarb/MD5 | 31 seacarb-3.3.0/seacarb/NAMESPACE | 13 seacarb-3.3.0/seacarb/R/K1.R | 18 seacarb-3.3.0/seacarb/R/K2.R | 16 seacarb-3.3.0/seacarb/R/SIR.R |only seacarb-3.3.0/seacarb/R/SIR_b.R |only seacarb-3.3.0/seacarb/R/SIR_full.R |only seacarb-3.3.0/seacarb/R/calculate_carb.R |only seacarb-3.3.0/seacarb/R/carb.R | 924 --------------------------- seacarb-3.3.0/seacarb/R/carbb.R | 924 --------------------------- seacarb-3.3.0/seacarb/R/carbfull.R | 1042 ------------------------------- seacarb-3.3.0/seacarb/R/fCO2insi.R | 2 seacarb-3.3.0/seacarb/R/pCO2insi.R |only seacarb-3.3.0/seacarb/README.md | 2 seacarb-3.3.0/seacarb/man/fCO2insi.Rd | 2 seacarb-3.3.0/seacarb/man/pCO2insi.Rd |only 21 files changed, 82 insertions(+), 2914 deletions(-)
Title: Self-Drive Machine Learning Projects
Description: Implementing some of the pillars of an automated machine learning pipeline such as (i) Automated data preparation, (ii) Feature engineering, (iii) Model building in classification context that includes techniques such as (a) Regularised regression [1], (b) Logistic regression [2], (c) Random Forest [3], (d) Decision tree [4] and (e) Extreme Gradient Boosting (xgboost) [5], and finally, (iv) Model explanation (using lift chart and partial dependency plots). Accomplishes the above tasks by running the function instead of writing lengthy R codes. Also provides some additional features such as generating missing at random (MAR) variables and automated exploratory data analysis. Moreover, function exports the model results with the required plots in an HTML vignette report format that follows the best practices of the industry and the academia. [1] Gonzales G B and De Saeger (2018) <doi:10.1038/s41598-018-21851-7>, [2] Sperandei S (2014) <doi:10.11613/BM.2014.003>, [3] Breiman L (2001) <doi:10.1023/A:1010933404324>, [4] Kingsford C and Salzberg S (2008) <doi:10.1038/nbt0908-1011>, [5] Chen Tianqi and Guestrin Carlos (2016) <doi:10.1145/2939672.2939785>.
Author: Dayanand Ubrangala [aut, cre],
Sayan Putatunda [aut, ctb],
Kiran R [aut, ctb],
Ravi Prasad Kondapalli [aut, ctb]
Maintainer: Dayanand Ubrangala <daya6489@gmail.com>
Diff between DriveML versions 0.1.3 dated 2021-06-14 and 0.1.4 dated 2021-10-18
DESCRIPTION | 6 MD5 | 38 NEWS.md | 8 R/autoDataPrep.R | 12 R/autoFeature.R | 2 R/autoMAR.R | 2 R/predictDataprep.R | 7 R/utilis.R | 9 README.md | 23 inst/doc/DriveML.R | 42 inst/doc/DriveML.Rmd | 50 inst/doc/DriveML.html | 3186 ----------------------------------------- man/autoDataprep.Rd | 4 man/autoMLmodel.Rd | 1 man/autoPDP.Rd | 1 man/figures/dml_icon3.png |only man/figures/dml_logo.png |only man/figures/model-results.PNG |only man/figures/o10-1.png |only man/figures/o11-1.png |only man/figures/o12-1.png |only tests/testthat/test_dataprep.R | 2 vignettes/DriveML.Rmd | 50 23 files changed, 278 insertions(+), 3165 deletions(-)
Title: Analyzing Ecological Networks
Description: A collection of advanced tools, methods and models specifically designed for analyzing different types of ecological networks - especially antagonistic (food webs, host-parasite), mutualistic (plant-pollinator, plant-fungus, etc) and competitive networks, as well as their variability in time and space. Statistical models are developed to describe and understand the mechanisms that determine species interactions, and to decipher the organization of these ecological networks (Ohlmann et al. (2019) <doi:10.1111/ele.13221>, Gonzalez et al. (2020) <doi:10.1101/2020.04.02.021691>, Miele et al. (2021) submitted, Botella et al (2021) <doi:10.1111/2041-210X.13738>).
Author: Vincent Miele [aut, cre], Catherine Matias [ctb], Stephane Dray [ctb], Christophe Botella [ctb], Marc Ohlmann [aut], Giovanni Poggiato [ctb], Wilfried Thuiller [ctb]
Maintainer: Vincent Miele <vincent.miele@univ-lyon1.fr>
Diff between econetwork versions 0.5.1 dated 2021-03-02 and 0.6.0 dated 2021-10-18
DESCRIPTION | 12 ++++++------ MD5 | 14 ++++++++------ NAMESPACE | 1 + R/embedding.R |only man/disPairwise.Rd | 2 +- man/elgrin.Rd | 4 ++-- man/embedding.Rd |only src/EltonModel.cpp | 37 ++++++++++++++++++++++++++++++------- src/EnvironmentEffect.h | 2 +- 9 files changed, 49 insertions(+), 23 deletions(-)
Title: R Interface to API 'vk.com'
Description: Load data from vk.com api about your communiti users and views,
ads performance, post on user wall and etc. For more information
see API Documentation <https://vk.com/dev/first_guide>.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rvkstat versions 3.1.0 dated 2021-09-08 and 3.2.0 dated 2021-10-18
DESCRIPTION | 9 +++--- MD5 | 30 ++++++++++++++------- NAMESPACE | 6 +++- NEWS.md | 10 ++++++- R/api_version_checker.R |only R/vkAuth.R | 2 - R/vkGetAdStatistics.R | 62 +++++++++++++++++++++++++++----------------- R/vkGetDbMetroStations.R |only R/vkGetDbSchools.R |only R/vkGetDbUniversities.R |only R/vkGetGroupMembers.R |only R/vkGetGroupStat.R | 18 ++++++++---- R/vkGetUserWall.R | 7 ++-- R/vkLoadToken.R |only README.md | 7 ++-- build/partial.rdb |binary inst |only man/vkGetDbMetroStations.Rd |only man/vkGetDbSchools.Rd |only man/vkGetDbUniversities.Rd |only man/vkGetGroupMembers.Rd |only man/vkLoadToken.Rd |only 22 files changed, 99 insertions(+), 52 deletions(-)
Title: Geographically Weighted Panel Regression
Description: Geographically weighted panel regression is grounded in a branch of spatial statistics. Using geographically weights, the geographically weighted panel regression is try to solve the residuals from panel regression clustering spatially. To investigate whether the residuals cluster spatially, the Moran's I test is also improved. Furthermore, three local statistic tests are contained to help the users select model. The major references are Fotheringham et al. (2003, ISBN:978-0-470-85525-6) and Beenstock and Felsenstein (2019, ISBN:978-3-030-03614-0).
Author: Chao Li [aut, cre] (<https://orcid.org/0000-0002-6854-4456>),
Shunsuke Managi [aut] (<https://orcid.org/0000-0001-7883-1427>)
Maintainer: Chao Li <chaoli0394@gmail.com>
Diff between GWPR.light versions 0.1.0 dated 2021-10-12 and 0.1.1 dated 2021-10-18
DESCRIPTION | 8 +++--- MD5 | 46 ++++++++++++++++++------------------- R/AIC_A.R | 23 +++++++++++++++--- R/AIC_A_para.R | 23 +++++++++++++++--- R/AIC_F.R | 19 ++++++++++++--- R/AIC_F_para.R | 23 +++++++++++++++--- R/GWPR.R | 4 +-- R/GWPR.moran.test.R | 2 - R/GWPR.pFtest.R | 6 ++-- R/GWPR.phtest.R | 6 ++-- R/GWPR.plmtest.R | 2 - R/bw_GWPR.R | 12 ++++----- R/gwpr_A.R | 7 +++-- README.md | 36 ++++++++++++++++------------ build/vignette.rds |binary inst/doc/introduction_of_GWPR.Rmd | 2 - inst/doc/introduction_of_GWPR.html | 5 +--- man/GWPR.Rd | 4 +-- man/GWPR.moran.test.Rd | 2 - man/GWPR.pFtest.Rd | 6 ++-- man/GWPR.phtest.Rd | 8 +++--- man/GWPR.plmtest.Rd | 2 - man/bw.GWPR.Rd | 8 +++--- vignettes/introduction_of_GWPR.Rmd | 2 - 24 files changed, 158 insertions(+), 98 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering the GCV procedure), functions to compute
the multivariate skewness, kurtosis, Mahalanobis distance (checking the positive
defineteness) and the Wilson-Hilferty transformation of chi squared variables. Furthermore,
the package provides interfaces to C code callable by another C code from other R packages.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.3-819 dated 2021-05-08 and 0.3-8196 dated 2021-10-18
ChangeLog | 6 +++++ DESCRIPTION | 8 +++---- MD5 | 40 ++++++++++++++++++++++---------------- NAMESPACE | 12 +++++------ R/helmert.R |only R/mediancenter.R |only inst/CITATION | 4 +-- man/cov.MSSD.Rd | 2 - man/helmert.Rd |only man/mediancenter.Rd |only src/R_init_fastmatrix.c | 4 ++- src/blas_1.c | 2 - src/blas_2.c | 14 ++++++------- src/blas_3.c | 12 +++++------ src/fastmatrix.h | 12 ++++++++++- src/helmert.f |only src/linear_iterative.c | 4 +-- src/ls_API.c | 6 ++--- src/lu.c | 4 +-- src/matrix_API.c | 50 ++++++++++++++++++++++++------------------------ src/median_center.f |only src/norms.c | 6 ++--- src/ridge.c | 4 +-- src/stats_API.c | 1 24 files changed, 108 insertions(+), 83 deletions(-)
Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more.
Author: Michael Dumelle [aut, cre] (<https://orcid.org/0000-0002-3393-5529>),
Tom Kincaid [aut],
Tony Olsen [aut],
Marc Weber [aut],
Don Stevens [ctb],
Denis White [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spsurvey versions 4.1.4 dated 2020-09-18 and 5.0.0 dated 2021-10-18
spsurvey-4.1.4/spsurvey/NEWS.md |only spsurvey-4.1.4/spsurvey/R/FL_lakes.R |only spsurvey-4.1.4/spsurvey/R/IN_streams.R |only spsurvey-4.1.4/spsurvey/R/Luck_Ash_streams.R |only spsurvey-4.1.4/spsurvey/R/NE_lakes.R |only spsurvey-4.1.4/spsurvey/R/NLA_2007.R |only spsurvey-4.1.4/spsurvey/R/NRSA_2009.R |only spsurvey-4.1.4/spsurvey/R/SC_estuaries.R |only spsurvey-4.1.4/spsurvey/R/SpatialDesign_class.R |only spsurvey-4.1.4/spsurvey/R/SpatialDesign_methods.R |only spsurvey-4.1.4/spsurvey/R/UT_ecoregions.R |only spsurvey-4.1.4/spsurvey/R/aaa.R |only spsurvey-4.1.4/spsurvey/R/albersgeod.R |only spsurvey-4.1.4/spsurvey/R/ash1.wgt.R |only spsurvey-4.1.4/spsurvey/R/attrisk.analysis.R |only spsurvey-4.1.4/spsurvey/R/attrisk.est.R |only spsurvey-4.1.4/spsurvey/R/attrisk.var.R |only spsurvey-4.1.4/spsurvey/R/cat.analysis.R |only spsurvey-4.1.4/spsurvey/R/category.est.R |only spsurvey-4.1.4/spsurvey/R/catvar.prop.R |only spsurvey-4.1.4/spsurvey/R/catvar.size.R |only spsurvey-4.1.4/spsurvey/R/cdf.decon.R |only spsurvey-4.1.4/spsurvey/R/cdf.est.R |only spsurvey-4.1.4/spsurvey/R/cdf.nresp.R |only spsurvey-4.1.4/spsurvey/R/cdf.plot.R |only spsurvey-4.1.4/spsurvey/R/cdf.prop.R |only spsurvey-4.1.4/spsurvey/R/cdf.size.prop.R |only spsurvey-4.1.4/spsurvey/R/cdf.size.total.R |only spsurvey-4.1.4/spsurvey/R/cdf.test.R |only spsurvey-4.1.4/spsurvey/R/cdf.test.prop.R |only spsurvey-4.1.4/spsurvey/R/cdf.test.size.prop.R |only spsurvey-4.1.4/spsurvey/R/cdf.total.R |only spsurvey-4.1.4/spsurvey/R/cdfvar.prop.R |only spsurvey-4.1.4/spsurvey/R/cdfvar.size.prop.R |only spsurvey-4.1.4/spsurvey/R/cdfvar.size.total.R |only spsurvey-4.1.4/spsurvey/R/cdfvar.test.R |only spsurvey-4.1.4/spsurvey/R/cdfvar.total.R |only spsurvey-4.1.4/spsurvey/R/cell.wt.R |only spsurvey-4.1.4/spsurvey/R/cellWeight.R |only spsurvey-4.1.4/spsurvey/R/change.analysis.R |only spsurvey-4.1.4/spsurvey/R/change.est.R |only spsurvey-4.1.4/spsurvey/R/changevar.mean.R |only spsurvey-4.1.4/spsurvey/R/changevar.prop.R |only spsurvey-4.1.4/spsurvey/R/changevar.size.R |only spsurvey-4.1.4/spsurvey/R/constructAddr.R |only spsurvey-4.1.4/spsurvey/R/cont.analysis.R |only spsurvey-4.1.4/spsurvey/R/cont.cdfplot.R |only spsurvey-4.1.4/spsurvey/R/cont.cdftest.R |only spsurvey-4.1.4/spsurvey/R/cov.panel.dsgn.R |only spsurvey-4.1.4/spsurvey/R/dcdf.prop.R |only spsurvey-4.1.4/spsurvey/R/dcdf.size.prop.R |only spsurvey-4.1.4/spsurvey/R/dcdf.size.total.R |only spsurvey-4.1.4/spsurvey/R/dcdf.total.R |only spsurvey-4.1.4/spsurvey/R/dcdfvar.prop.R |only spsurvey-4.1.4/spsurvey/R/dcdfvar.size.prop.R |only spsurvey-4.1.4/spsurvey/R/dcdfvar.size.total.R |only spsurvey-4.1.4/spsurvey/R/dcdfvar.total.R |only spsurvey-4.1.4/spsurvey/R/decon_data.R |only spsurvey-4.1.4/spsurvey/R/dframe.check.R |only spsurvey-4.1.4/spsurvey/R/dsgnsum.R |only spsurvey-4.1.4/spsurvey/R/examine.R |only spsurvey-4.1.4/spsurvey/R/framesum.R |only spsurvey-4.1.4/spsurvey/R/geodalbers.R |only spsurvey-4.1.4/spsurvey/R/grtsarea.R |only spsurvey-4.1.4/spsurvey/R/grtslin.R |only spsurvey-4.1.4/spsurvey/R/grtspts.R |only spsurvey-4.1.4/spsurvey/R/input.check.R |only spsurvey-4.1.4/spsurvey/R/input.format.R |only spsurvey-4.1.4/spsurvey/R/interp.axis.R |only spsurvey-4.1.4/spsurvey/R/interp.cdf.R |only spsurvey-4.1.4/spsurvey/R/irsarea.R |only spsurvey-4.1.4/spsurvey/R/irslin.R |only spsurvey-4.1.4/spsurvey/R/irspts.R |only spsurvey-4.1.4/spsurvey/R/isotonic.R |only spsurvey-4.1.4/spsurvey/R/localmean.cov.R |only spsurvey-4.1.4/spsurvey/R/localmean.df.R |only spsurvey-4.1.4/spsurvey/R/localmean.var.R |only spsurvey-4.1.4/spsurvey/R/localmean.weight.R |only spsurvey-4.1.4/spsurvey/R/localmean.weight2.R |only spsurvey-4.1.4/spsurvey/R/make_grid.R |only spsurvey-4.1.4/spsurvey/R/marinus.R |only spsurvey-4.1.4/spsurvey/R/mdmarea.R |only spsurvey-4.1.4/spsurvey/R/mdmlin.R |only spsurvey-4.1.4/spsurvey/R/mdmpts.R |only spsurvey-4.1.4/spsurvey/R/numLevels.R |only spsurvey-4.1.4/spsurvey/R/panel_summary.R |only spsurvey-4.1.4/spsurvey/R/pickFiniteSamplePoints.R |only spsurvey-4.1.4/spsurvey/R/pickGridCells.R |only spsurvey-4.1.4/spsurvey/R/pickSamplePoints.R |only spsurvey-4.1.4/spsurvey/R/plot_powerpaneldesign.R |only spsurvey-4.1.4/spsurvey/R/power.dsgn.R |only spsurvey-4.1.4/spsurvey/R/ranho.R |only spsurvey-4.1.4/spsurvey/R/read.dbf.R |only spsurvey-4.1.4/spsurvey/R/read.sas.R |only spsurvey-4.1.4/spsurvey/R/read.shape.R |only spsurvey-4.1.4/spsurvey/R/relrisk.analysis.R |only spsurvey-4.1.4/spsurvey/R/relrisk.est.R |only spsurvey-4.1.4/spsurvey/R/relrisk.var.R |only spsurvey-4.1.4/spsurvey/R/sbcframe.R |only spsurvey-4.1.4/spsurvey/R/sbcsamp.R |only spsurvey-4.1.4/spsurvey/R/selectFeatureID.R |only spsurvey-4.1.4/spsurvey/R/selectframe.R |only spsurvey-4.1.4/spsurvey/R/selectpts.R |only spsurvey-4.1.4/spsurvey/R/simex.R |only spsurvey-4.1.4/spsurvey/R/sorted.R |only spsurvey-4.1.4/spsurvey/R/sp2shape.R |only 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Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] (<https://orcid.org/0000-0002-0750-061X>)
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.2.2 dated 2021-10-05 and 1.2.4 dated 2021-10-18
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Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation and initialization of the hidden hybrid Markov/semi-Markov model, introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>.
Author: Morteza Amini [aut, cre, cph],
Afarin Bayat [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>
Diff between hhsmm versions 0.2.0 dated 2021-10-13 and 0.2.1 dated 2021-10-18
DESCRIPTION | 8 +-- MD5 | 16 +++---- R/cov-miss-mix-wt.R | 2 R/initial-cluster.R | 10 ++-- R/plot-hhsmm-data.R | 9 +--- R/train-test-split.R | 99 +++++++++++++++++++++++++++++++----------------- man/cov.miss.mix.wt.Rd | 2 man/initial_cluster.Rd | 2 man/train_test_split.Rd | 20 +++++++-- 9 files changed, 103 insertions(+), 65 deletions(-)
Title: Geostatistics for Compositional Analysis
Description: Support for geostatistical analysis of multivariate data,
in particular data with restrictions, e.g. positive amounts data,
compositional data, distributional data, microstructural data, etc.
It includes descriptive analysis and modelling for such data, both
from a two-point Gaussian perspective and multipoint perspective.
The methods mainly follow Tolosana-Delgado, Mueller and van den
Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
Author: Raimon Tolosana-Delgado [aut] (<https://orcid.org/0000-0001-9847-0462>),
Ute Mueller [aut],
K. Gerald van den Boogaart [ctb, cre],
Hassan Talebi [ctb, cph],
Helmholtz-Zentrum Dresden-Rossendorf [cph],
Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmGeostats versions 0.10-9 dated 2021-09-17 and 0.11.0 dated 2021-10-18
DESCRIPTION | 10 +-- MD5 | 22 ++++---- NAMESPACE | 2 NEWS.md | 12 ++++ R/gmSpatialModel.R | 51 ++++++++++++++----- R/gstatCompatibility.R | 9 ++- inst/doc/register_new_layer_datatype.R | 27 +++++----- inst/doc/register_new_layer_datatype.Rmd | 31 ++++++----- inst/doc/register_new_layer_datatype.html | 80 +++++++++++++----------------- man/fit_lmc.Rd | 17 ++++++ man/predict_gmSpatialModel.Rd | 9 ++- vignettes/register_new_layer_datatype.Rmd | 31 ++++++----- 12 files changed, 180 insertions(+), 121 deletions(-)
Title: Detect the Language of Text
Description: With no external dependencies and
support for 335 languages; all languages spoken by
more than one million speakers. 'Franc' is a port
of the 'JavaScript' project of the same name,
see <https://github.com/wooorm/franc>.
Author: Gabor Csardi, Titus Wormer, Maciej Ceglowski, Jacob R. Rideout,
and Kent S. Johnson
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between franc versions 1.1.3 dated 2021-01-27 and 1.1.4 dated 2021-10-18
DESCRIPTION | 7 +++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/speakers.R | 4 ++-- R/trigrams.R | 7 ++++++- man/speakers.Rd | 4 ++-- tests/testthat.R | 2 +- 7 files changed, 24 insertions(+), 16 deletions(-)
Title: Spider Knowledge Online
Description: Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Author: Pedro Cardoso [aut, cre]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between spidR versions 1.0.1 dated 2021-04-19 and 1.0.2 dated 2021-10-18
DESCRIPTION | 12 +++++------ MD5 | 4 +-- R/spidR.R | 61 ++++++++++++++++++++---------------------------------------- 3 files changed, 29 insertions(+), 48 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Satu Helske [aut] (<https://orcid.org/0000-0003-0532-0153>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.1.1 dated 2021-08-13 and 1.2.0 dated 2021-10-18
DESCRIPTION | 10 MD5 | 16 NEWS | 366 - R/fit_model.R | 2486 +++++------ inst/doc/seqHMM.pdf | 5350 ++++++++++++++--------- inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf | 8525 ++++++++++++++++++++++++++++++++------ man/fit_model.Rd | 35 9 files changed, 12269 insertions(+), 4519 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.4.5 dated 2021-07-12 and 4.4.7 dated 2021-10-18
secr-4.4.5/secr/src/utils.cpp |only secr-4.4.7/secr/DESCRIPTION | 14 - secr-4.4.7/secr/MD5 | 138 ++++++++-------- secr-4.4.7/secr/NAMESPACE | 8 secr-4.4.7/secr/NEWS | 26 ++- secr-4.4.7/secr/R/DENSITY.R | 26 ++- secr-4.4.7/secr/R/RcppExports.R | 76 ++++----- secr-4.4.7/secr/R/addCovariates.R | 16 + secr-4.4.7/secr/R/addSightings.R | 1 secr-4.4.7/secr/R/autoini.R | 39 ++-- secr-4.4.7/secr/R/empirical.R | 55 +++--- secr-4.4.7/secr/R/esa.R | 34 ++-- secr-4.4.7/secr/R/fastsecrloglik.R | 62 +++---- secr-4.4.7/secr/R/fxi.R | 60 +++---- secr-4.4.7/secr/R/generalsecrloglik.R | 227 +++++++++++++++------------ secr-4.4.7/secr/R/loglikhelperfn.R | 41 +++- secr-4.4.7/secr/R/make.capthist.R | 28 ++- secr-4.4.7/secr/R/model.average.R | 38 ++++ secr-4.4.7/secr/R/pdot.R | 30 +-- secr-4.4.7/secr/R/plot.capthist.r | 12 + secr-4.4.7/secr/R/regionN.R | 75 ++------ secr-4.4.7/secr/R/score.test.R | 5 secr-4.4.7/secr/R/secr.fit.R | 10 - secr-4.4.7/secr/R/secr.make.newdata.R | 6 secr-4.4.7/secr/R/sim.popn.R | 134 ++++++++++----- secr-4.4.7/secr/R/sim.secr.R | 27 ++- secr-4.4.7/secr/R/snip.R | 37 ++-- secr-4.4.7/secr/R/suggest.buffer.R | 4 secr-4.4.7/secr/R/trap.builder.R | 28 ++- secr-4.4.7/secr/R/utility.R | 1 secr-4.4.7/secr/R/verify.R | 16 - secr-4.4.7/secr/inst/doc/secr-datainput.pdf |binary secr-4.4.7/secr/inst/doc/secr-overview.Rmd | 8 secr-4.4.7/secr/inst/doc/secr-overview.pdf |binary secr-4.4.7/secr/man/PG.Rd | 4 secr-4.4.7/secr/man/addCovariates.Rd | 2 secr-4.4.7/secr/man/details.Rd | 3 secr-4.4.7/secr/man/empirical.Rd | 4 secr-4.4.7/secr/man/extractMoves.Rd | 15 + secr-4.4.7/secr/man/make.capthist.Rd | 4 secr-4.4.7/secr/man/read.telemetry.Rd | 4 secr-4.4.7/secr/man/secr-defunct.Rd |only secr-4.4.7/secr/man/secr-deprecated.Rd |only secr-4.4.7/secr/man/secr-package.Rd | 4 secr-4.4.7/secr/man/smooths.Rd | 3 secr-4.4.7/secr/man/snip.Rd | 4 secr-4.4.7/secr/man/sort.Rd | 3 secr-4.4.7/secr/man/trap.builder.Rd | 5 secr-4.4.7/secr/man/turnover.Rd | 31 ++- secr-4.4.7/secr/src/RcppExports.cpp | 225 ++++++++++++++------------ secr-4.4.7/secr/src/autils.cpp |only secr-4.4.7/secr/src/autoini.cpp | 6 secr-4.4.7/secr/src/detectfn.cpp | 47 ++++- secr-4.4.7/secr/src/getdenom.cpp | 20 +- secr-4.4.7/secr/src/makegk.cpp | 31 ++- secr-4.4.7/secr/src/makegkpoly.cpp | 6 secr-4.4.7/secr/src/pdot.cpp | 21 +- secr-4.4.7/secr/src/poly.h | 12 - secr-4.4.7/secr/src/polygonN.cpp | 46 ++++- secr-4.4.7/secr/src/prwifastproximity.cpp | 8 secr-4.4.7/secr/src/prwipolygon.cpp | 17 +- secr-4.4.7/secr/src/prwipolygonfxi.cpp | 17 +- secr-4.4.7/secr/src/prwisignal.cpp | 20 +- secr-4.4.7/secr/src/prwisimple.cpp | 14 - secr-4.4.7/secr/src/prwisimplefxi.cpp | 8 secr-4.4.7/secr/src/secr.h | 102 +++++------- secr-4.4.7/secr/src/sighting.cpp | 60 ++++--- secr-4.4.7/secr/src/sightingchat.cpp | 13 - secr-4.4.7/secr/src/sightingexpectedmusk.cpp | 2 secr-4.4.7/secr/src/simsecr.cpp | 17 +- secr-4.4.7/secr/src/trapping.cpp | 7 secr-4.4.7/secr/vignettes/secr-overview.Rmd | 8 72 files changed, 1198 insertions(+), 877 deletions(-)
Title: Generalized Correlations and Various Causal Paths
Description: Since causal paths from data are important for all sciences, the
package provides many sophisticated functions. causeSummBlk()
gives easy-to-interpret causal paths. Let Z denote control variables and compare
two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X,Z)+e2. Our criterion Cr1
says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent"
than in Y and causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These
inequalities between many absolute values are quantified by four orders of
stochastic dominance. Our third criterion Cr3 for the causal path X to Y
requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|.
The function parcorVec() reports generalized partials between the first
variable and all others. The package provides several R functions including
get0outliers() for outlier detection, bigfp() for numerical integration by the
trapezoidal rule, stochdom2() for stochastic dominance, pillar3D() for 3D charts,
canonRho() for generalized canonical correlations, depMeas() measures nonlinear
dependence, and causeSummary(mtx) reports summary of causal paths among matrix columns
is easiest to use. Several functions whose names begin with 'boot' provide bootstrap
statistical inference including a new bootGcRsq() test for "Granger-causality"
allowing nonlinear relations. See five vignettes of the package for theory
and usage tips. See Vinod (2019) \doi{10.1080/03610918.2015.1122048}.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.1.8 dated 2020-12-02 and 1.1.9 dated 2021-10-18
DESCRIPTION | 15 +-- MD5 | 162 ++++++++++++++++++++----------------- NAMESPACE | 9 ++ NEWS | 3 R/GcRsqX12.R | 4 R/GcRsqX12c.R | 4 R/absBstdres.R | 2 R/absBstdresC.R | 2 R/abs_stdres.R | 2 R/abs_stdresC.R | 4 R/abs_stdrhserC.R | 2 R/causeAllPair.R |only R/causeSumNoP.R |only R/causeSummBlk.R | 41 ++++----- R/causeSummary.R | 47 +++++----- R/crosspLarge.R |only R/depMeas.R | 17 ++- R/generalCorrInfo.R | 105 ++++++++++++----------- R/kern.R | 2 R/kern2.R | 2 R/kern2ctrl.R | 2 R/kern_ctrl.R | 2 R/mag.R | 2 R/mag_ctrl.R | 2 R/parcorBMany.R | 5 - R/parcorHijk.R |only R/parcorVec.R |only R/parcorVecH.R |only R/pcause.R | 2 R/probSign.R | 2 R/siPairsBlk.R | 2 R/silentMtx.R | 2 R/silentMtx0.R | 6 - R/silentPairs.R | 2 R/silentPairs0.R | 2 R/some0Pairs.R | 2 R/someCPairs.R | 6 - R/someCPairs2.R | 6 - R/someMagPairs.R | 2 R/somePairs.R | 2 R/somePairs2.R | 2 R/stdres.R | 2 R/sudoCoefParcor.R |only R/sudoCoefParcorH.R |only R/symmze.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary inst/doc/generalCorr-vignette5.pdf |binary man/GcRsqX12.Rd | 6 - man/GcRsqX12c.Rd | 6 - man/absBstdres.Rd | 2 man/absBstdresC.Rd | 2 man/abs_stdres.Rd | 2 man/abs_stdresC.Rd | 4 man/abs_stdrhserC.Rd | 2 man/causeAllPair.Rd |only man/causeSumNoP.Rd |only man/causeSummBlk.Rd | 41 ++++----- man/causeSummary.Rd | 46 +++++----- man/depMeas.Rd | 16 ++- man/generalCorrInfo.Rd | 99 +++++++++++----------- man/kern.Rd | 2 man/kern2.Rd | 2 man/kern2ctrl.Rd | 2 man/kern_ctrl.Rd | 2 man/mag.Rd | 2 man/mag_ctrl.Rd | 2 man/parcorBMany.Rd | 5 - man/parcorHijk.Rd |only man/parcorVec.Rd |only man/parcorVecH.Rd |only man/pcause.Rd | 2 man/probSign.Rd | 2 man/siPairsBlk.Rd | 2 man/silentMtx.Rd | 2 man/silentMtx0.Rd | 4 man/silentPairs.Rd | 2 man/silentPairs0.Rd | 2 man/some0Pairs.Rd | 2 man/someCPairs.Rd | 4 man/someCPairs2.Rd | 4 man/someMagPairs.Rd | 2 man/somePairs.Rd | 2 man/somePairs2.Rd | 2 man/stdres.Rd | 2 man/sudoCoefParcor.Rd |only man/sudoCoefParcorH.Rd |only 90 files changed, 400 insertions(+), 355 deletions(-)
Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant
and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] (<https://orcid.org/0000-0001-5765-7060>),
Christopher McBride [ctb],
Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>
Diff between dycdtools versions 0.3.0 dated 2021-09-19 and 0.3.1 dated 2021-10-18
dycdtools-0.3.0/dycdtools/R/test.R |only dycdtools-0.3.1/dycdtools/DESCRIPTION | 6 dycdtools-0.3.1/dycdtools/MD5 | 45 ++--- dycdtools-0.3.1/dycdtools/NEWS.md | 3 dycdtools-0.3.1/dycdtools/R/Fun_Contour-plot_sim.R | 4 dycdtools-0.3.1/dycdtools/R/Fun_Extract-simulation.R | 3 dycdtools-0.3.1/dycdtools/R/Fun_Profile-plot.R | 2 dycdtools-0.3.1/dycdtools/R/Fun_Scatter-plot.R | 2 dycdtools-0.3.1/dycdtools/R/Fun_TS-plot.R | 2 dycdtools-0.3.1/dycdtools/man/calib.assist.Rd | 144 ++++++++-------- dycdtools-0.3.1/dycdtools/man/change_input_file.Rd | 36 ++-- dycdtools-0.3.1/dycdtools/man/delete.space.Rd | 28 +-- dycdtools-0.3.1/dycdtools/man/ext.output.Rd | 75 ++++---- dycdtools-0.3.1/dycdtools/man/hgt.to.dpt.Rd | 28 +-- dycdtools-0.3.1/dycdtools/man/interpol.Rd | 72 ++++---- dycdtools-0.3.1/dycdtools/man/objective.fun.Rd | 76 ++++---- dycdtools-0.3.1/dycdtools/man/obs_temp.Rd | 52 ++--- dycdtools-0.3.1/dycdtools/man/output_name.Rd | 48 ++--- dycdtools-0.3.1/dycdtools/man/plot_cont.Rd | 148 ++++++++-------- dycdtools-0.3.1/dycdtools/man/plot_cont_comp.Rd | 170 +++++++++---------- dycdtools-0.3.1/dycdtools/man/plot_prof.Rd | 148 ++++++++-------- dycdtools-0.3.1/dycdtools/man/plot_scatter.Rd | 146 ++++++++-------- dycdtools-0.3.1/dycdtools/man/plot_ts.Rd | 162 +++++++++--------- dycdtools-0.3.1/dycdtools/man/run.iteration.Rd | 32 +-- 24 files changed, 718 insertions(+), 714 deletions(-)
Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser.
Enables embedding a JB2 genome browser in a Shiny app or R Markdown
document. The browser can also be launched from an interactive R console.
The browser can be loaded with a variety of common genomics data types,
and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] (<https://orcid.org/0000-0003-2068-3366>),
the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>
Diff between JBrowseR versions 0.8.1 dated 2021-07-07 and 0.9.0 dated 2021-10-17
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NEWS.md | 10 ++++++-- R/wiggle.R | 4 +-- build/vignette.rds |binary inst/doc/JBrowseR.html | 1 inst/doc/creating-urls.html | 1 inst/doc/custom-browser-tutorial.html | 1 inst/doc/json-tutorial.html | 1 inst/htmlwidgets/JBrowseR.js | 41 +++++++++++++++++----------------- man/track_wiggle.Rd | 4 +-- 11 files changed, 51 insertions(+), 40 deletions(-)
Title: Geocoding Made Easy
Description: An intuitive interface for getting data from geocoding services.
Author: Jesse Cambon [aut, cre] (<https://orcid.org/0000-0001-6854-1514>),
Diego Hernangómez [aut] (<https://orcid.org/0000-0001-8457-4658>),
Christopher Belanger [aut] (<https://orcid.org/0000-0003-2070-5721>),
Daniel Possenriede [aut] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Jesse Cambon <jesse.cambon@gmail.com>
Diff between tidygeocoder versions 1.0.3 dated 2021-04-19 and 1.0.4 dated 2021-10-17
DESCRIPTION | 17 MD5 | 97 ++--- NAMESPACE | 2 NEWS.md | 57 ++- R/api_url.R | 19 - R/batch_geocoding.R | 43 +- R/data.R | 38 +- R/documentation.R | 23 + R/geo.R | 353 +++++++++++++------- R/geo_methods.R | 4 R/geocode.R | 12 R/geocode_combine.R |only R/global_variables.R | 12 R/input_handling.R | 7 R/query_factory.R | 2 R/results_processing.R | 41 +- R/reverse_batch_geocoding.R | 27 - R/reverse_geo.R | 205 +++++++---- R/reverse_geocode.R | 4 R/utils.R | 226 ++++++++++++- R/zzz.R |only README.md | 81 ++-- build/vignette.rds |binary data/api_info_reference.rda |binary data/api_key_reference.rda |binary data/api_parameter_reference.rda |binary data/min_time_reference.rda |binary inst/CITATION | 60 +-- inst/doc/tidygeocoder.R | 52 +-- inst/doc/tidygeocoder.Rmd | 103 +++-- inst/doc/tidygeocoder.html | 588 +++++++++++++++++++--------------- man/api_info_reference.Rd | 8 man/api_key_reference.Rd | 4 man/api_parameter_reference.Rd | 17 man/batch_limit_reference.Rd | 2 man/extract_results.Rd | 4 man/extract_reverse_results.Rd | 6 man/figures/README-usamap-1.png |binary man/figures/tidygeocoder_hex.png |binary man/geo.Rd | 155 +++++--- man/geo_census.Rd | 2 man/geo_combine.Rd |only man/geocode.Rd | 16 man/geocode_combine.Rd |only man/min_time_reference.Rd | 9 man/reverse_geo.Rd | 127 ++++--- man/reverse_geocode.Rd | 8 man/tidygeocoder-package.Rd | 2 tests/testthat/test-geocode-combine.R |only tests/testthat/test-geocode.R | 55 +-- tests/testthat/test-utils.R | 3 vignettes/tidygeocoder.Rmd | 103 +++-- 52 files changed, 1637 insertions(+), 957 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>),
Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>),
Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>),
Jeff Farrell [ctb],
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>),
Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>),
Patrick Roelli [ctb],
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>),
Karthik Shekhar [ctb],
Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>),
Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>),
Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>),
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between Seurat versions 4.0.4 dated 2021-08-20 and 4.0.5 dated 2021-10-17
DESCRIPTION | 8 ++-- MD5 | 44 +++++++++++++------------- NEWS.md | 7 ++++ R/data.R | 4 +- R/dimensional_reduction.R | 11 +----- R/generics.R | 8 +++- R/integration.R | 20 ++++++++++-- R/preprocessing.R | 6 ++- R/tree.R | 10 +++--- R/visualization.R | 20 ++++++------ README.md | 2 - build/partial.rdb |binary man/BuildClusterTree.Rd | 10 +++--- man/ColorDimSplit.Rd | 11 +++--- man/FindMarkers.Rd | 8 +++- man/IntegrateData.Rd | 68 ++++++++++++++++++++++++----------------- man/IntegrateEmbeddings.Rd | 16 ++++++++- man/Load10X_Spatial.Rd | 6 ++- man/PlotClusterTree.Rd | 9 +++-- man/RunSPCA.Rd | 1 man/cc.genes.Rd | 2 - man/cc.genes.updated.2019.Rd | 2 - tests/testthat/test_load_10X.R | 38 ++++++++++------------ 23 files changed, 184 insertions(+), 127 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.5.0 dated 2020-03-11 and 3.6.0 dated 2021-10-17
rcdk-3.5.0/rcdk/man/do.typing.Rd |only rcdk-3.6.0/rcdk/CHANGELOG | 28 rcdk-3.6.0/rcdk/DESCRIPTION | 12 rcdk-3.6.0/rcdk/MD5 | 88 - rcdk-3.6.0/rcdk/NAMESPACE | 4 rcdk-3.6.0/rcdk/NEWS | 3 rcdk-3.6.0/rcdk/R/atoms.R | 23 rcdk-3.6.0/rcdk/R/bonds.R | 29 rcdk-3.6.0/rcdk/R/deprecated_functions.R |only rcdk-3.6.0/rcdk/R/desc.R | 75 - rcdk-3.6.0/rcdk/R/fingerprint.R | 9 rcdk-3.6.0/rcdk/R/frags.R | 3 rcdk-3.6.0/rcdk/R/io.R | 2 rcdk-3.6.0/rcdk/R/molecule.R | 2 rcdk-3.6.0/rcdk/R/props.R | 11 rcdk-3.6.0/rcdk/R/rcdk.R | 47 rcdk-3.6.0/rcdk/R/smiles.R | 2 rcdk-3.6.0/rcdk/R/smsd.R | 2 rcdk-3.6.0/rcdk/R/visual.R | 10 rcdk-3.6.0/rcdk/build/vignette.rds |binary rcdk-3.6.0/rcdk/inst/cont/rcdk.jar |binary rcdk-3.6.0/rcdk/inst/doc/molform.Rmd | 2 rcdk-3.6.0/rcdk/inst/doc/molform.html | 545 +++------- rcdk-3.6.0/rcdk/inst/doc/using-rcdk.R | 4 rcdk-3.6.0/rcdk/inst/doc/using-rcdk.Rmd | 14 rcdk-3.6.0/rcdk/inst/doc/using-rcdk.html | 1068 +++++++------------- rcdk-3.6.0/rcdk/inst/molfiles/alanine.sdf |only rcdk-3.6.0/rcdk/inst/molfiles/glutamine.sdf |only rcdk-3.6.0/rcdk/inst/unitTests/runit.atoms.R | 2 rcdk-3.6.0/rcdk/inst/unitTests/runit.bonds.R |only rcdk-3.6.0/rcdk/inst/unitTests/runit.descs.R |only rcdk-3.6.0/rcdk/inst/unitTests/runit.fingerprints.R | 4 rcdk-3.6.0/rcdk/inst/unitTests/runit.frags.R | 6 rcdk-3.6.0/rcdk/inst/unitTests/runit.match.R | 6 rcdk-3.6.0/rcdk/inst/unitTests/runit.rcdk.R | 14 rcdk-3.6.0/rcdk/man/Atoms.Rd | 3 rcdk-3.6.0/rcdk/man/Molecule.Rd | 2 rcdk-3.6.0/rcdk/man/bpdata.Rd | 6 rcdk-3.6.0/rcdk/man/convert.implicit.to.explicit.Rd | 2 rcdk-3.6.0/rcdk/man/get.bond.order.Rd |only rcdk-3.6.0/rcdk/man/get.chem.object.builder.Rd | 4 rcdk-3.6.0/rcdk/man/get.desc.categories.Rd | 2 rcdk-3.6.0/rcdk/man/get.exhaustive.fragments.Rd | 2 rcdk-3.6.0/rcdk/man/get.volume.Rd | 2 rcdk-3.6.0/rcdk/man/rcdk-deprecated.Rd |only rcdk-3.6.0/rcdk/man/set.atom.types.Rd |only rcdk-3.6.0/rcdk/man/smiles.flavors.Rd | 2 rcdk-3.6.0/rcdk/man/view.table.Rd |only rcdk-3.6.0/rcdk/vignettes/molform.Rmd | 2 rcdk-3.6.0/rcdk/vignettes/using-rcdk.Rmd | 14 50 files changed, 878 insertions(+), 1178 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.24 dated 2020-12-18 and 0.28 dated 2021-10-17
qtl2-0.24/qtl2/tests/figs |only qtl2-0.28/qtl2/DESCRIPTION | 10 qtl2-0.28/qtl2/MD5 | 214 ++++++++-------- qtl2-0.28/qtl2/NAMESPACE | 3 qtl2-0.28/qtl2/NEWS.md | 66 ++++ qtl2-0.28/qtl2/R/CCcolors-data.R | 16 + qtl2-0.28/qtl2/R/calc_genoprob.R | 2 qtl2-0.28/qtl2/R/calc_genoprob2.R | 2 qtl2-0.28/qtl2/R/calc_het.R | 5 qtl2-0.28/qtl2/R/calc_kinship.R | 6 qtl2-0.28/qtl2/R/calc_raw_summaries.R | 8 qtl2-0.28/qtl2/R/create_gene_query_func.R | 2 qtl2-0.28/qtl2/R/create_snpinfo.R | 6 qtl2-0.28/qtl2/R/create_variant_query_func.R | 2 qtl2-0.28/qtl2/R/est_herit.R | 9 qtl2-0.28/qtl2/R/est_map.R | 1 qtl2-0.28/qtl2/R/find_ibd_segments.R | 2 qtl2-0.28/qtl2/R/find_index_snp.R | 2 qtl2-0.28/qtl2/R/fit1.R | 4 qtl2-0.28/qtl2/R/fit1_pg.R | 2 qtl2-0.28/qtl2/R/genoprob_to_snpprob.R | 2 qtl2-0.28/qtl2/R/index_snps.R | 2 qtl2-0.28/qtl2/R/plot_coef.R | 6 qtl2-0.28/qtl2/R/plot_genoprob.R | 2 qtl2-0.28/qtl2/R/plot_onegeno.R | 2 qtl2-0.28/qtl2/R/plot_sdp.R |only qtl2-0.28/qtl2/R/plot_snpasso.R | 28 +- qtl2-0.28/qtl2/R/plot_snpasso_and_genes.R | 7 qtl2-0.28/qtl2/R/plot_snpasso_and_sdp.R |only qtl2-0.28/qtl2/R/plot_snpasso_sdp_and_genes.R |only qtl2-0.28/qtl2/R/predict_snpgeno.R | 2 qtl2-0.28/qtl2/R/qtl2-package.R | 15 + qtl2-0.28/qtl2/R/qtl2version.R | 2 qtl2-0.28/qtl2/R/read_pheno.R | 4 qtl2-0.28/qtl2/R/recode_snps.R | 2 qtl2-0.28/qtl2/R/replace_ids.R | 20 + qtl2-0.28/qtl2/R/scan1_pg.R | 5 qtl2-0.28/qtl2/R/scan1coef.R | 2 qtl2-0.28/qtl2/R/scan1coef_pg.R | 2 qtl2-0.28/qtl2/R/scan1snps.R | 2 qtl2-0.28/qtl2/R/sim_geno.R | 6 qtl2-0.28/qtl2/R/sim_geno2.R | 6 qtl2-0.28/qtl2/R/summary_cross2.R | 6 qtl2-0.28/qtl2/R/top_snps.R | 2 qtl2-0.28/qtl2/R/viterbi.R | 6 qtl2-0.28/qtl2/R/viterbi2.R | 6 qtl2-0.28/qtl2/README.md | 23 + qtl2-0.28/qtl2/build |only qtl2-0.28/qtl2/data/CCaltcolors.RData |only qtl2-0.28/qtl2/data/CCcolors.RData |binary qtl2-0.28/qtl2/data/CCorigcolors.RData |binary qtl2-0.28/qtl2/inst/CITATION | 2 qtl2-0.28/qtl2/inst/extdata/ReadMe.md | 4 qtl2-0.28/qtl2/man/CCcolors.Rd | 6 qtl2-0.28/qtl2/man/calc_raw_founder_maf.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_geno_freq.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_het.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_maf.Rd | 2 qtl2-0.28/qtl2/man/create_gene_query_func.Rd | 2 qtl2-0.28/qtl2/man/create_snpinfo.Rd | 2 qtl2-0.28/qtl2/man/create_variant_query_func.Rd | 2 qtl2-0.28/qtl2/man/est_herit.Rd | 3 qtl2-0.28/qtl2/man/find_ibd_segments.Rd | 2 qtl2-0.28/qtl2/man/find_index_snp.Rd | 2 qtl2-0.28/qtl2/man/genoprob_to_snpprob.Rd | 2 qtl2-0.28/qtl2/man/index_snps.Rd | 2 qtl2-0.28/qtl2/man/plot_coef.Rd | 1 qtl2-0.28/qtl2/man/plot_genoprob.Rd | 2 qtl2-0.28/qtl2/man/plot_onegeno.Rd | 2 qtl2-0.28/qtl2/man/plot_sdp.Rd |only qtl2-0.28/qtl2/man/plot_snpasso.Rd | 14 - qtl2-0.28/qtl2/man/predict_snpgeno.Rd | 2 qtl2-0.28/qtl2/man/qtl2-package.Rd | 24 + qtl2-0.28/qtl2/man/read_pheno.Rd | 4 qtl2-0.28/qtl2/man/recode_snps.Rd | 2 qtl2-0.28/qtl2/man/replace_ids.Rd | 10 qtl2-0.28/qtl2/man/scan1snps.Rd | 2 qtl2-0.28/qtl2/man/top_snps.Rd | 2 qtl2-0.28/qtl2/src/RcppExports.cpp | 5 qtl2-0.28/qtl2/src/brent_fmin.cpp | 9 qtl2-0.28/qtl2/src/brent_fmin.h | 5 qtl2-0.28/qtl2/src/cross.cpp | 2 qtl2-0.28/qtl2/src/cross_genril.cpp | 2 qtl2-0.28/qtl2/src/cross_hsf1.cpp |only qtl2-0.28/qtl2/src/cross_hsf1.h |only qtl2-0.28/qtl2/src/hmm_util.cpp | 4 qtl2-0.28/qtl2/src/lmm.cpp | 7 qtl2-0.28/qtl2/tests/testthat/_snaps |only qtl2-0.28/qtl2/tests/testthat/test-basic_summaries.R | 2 qtl2-0.28/qtl2/tests/testthat/test-calc_raw_summaries.R | 2 qtl2-0.28/qtl2/tests/testthat/test-calcerrorlod.R | 2 qtl2-0.28/qtl2/tests/testthat/test-check_cross.R | 2 qtl2-0.28/qtl2/tests/testthat/test-create_snpinfo.R | 22 + qtl2-0.28/qtl2/tests/testthat/test-find_ibd_segments.R | 2 qtl2-0.28/qtl2/tests/testthat/test-find_peaks.R | 2 qtl2-0.28/qtl2/tests/testthat/test-fit1_binary.R | 2 qtl2-0.28/qtl2/tests/testthat/test-hmmbasic-hsf1.R |only qtl2-0.28/qtl2/tests/testthat/test-index_snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-plot_sdp.R |only qtl2-0.28/qtl2/tests/testthat/test-predict_snpgeno.R | 4 qtl2-0.28/qtl2/tests/testthat/test-recode_snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-replace_ids.R | 73 +++++ qtl2-0.28/qtl2/tests/testthat/test-scan1snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-snpprobs.R | 2 qtl2-0.28/qtl2/tests/testthat/test-top_snps.R | 4 105 files changed, 564 insertions(+), 219 deletions(-)
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman
filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in
BLAS and LAPACK. Due to the speed of the filter, the fitting of
high-dimensional linear state space models to large datasets
becomes possible. This package also contains a plot function
for the visualization of the state vector and graphical
diagnostics of the residuals.
Author: David Luethi [aut],
Philipp Erb [aut],
Simon Otziger [aut],
Daniel McDonald [aut],
Paul Smith [aut, cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between FKF versions 0.2.1 dated 2021-09-28 and 0.2.2 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 2 +- inst/doc/FKF.html | 20 ++++++++++---------- src/fkflib.c | 7 ++++--- 6 files changed, 28 insertions(+), 22 deletions(-)
Title: Automated Backtesting of Portfolios over Multiple Datasets
Description: Automated backtesting of multiple portfolios over multiple
datasets of stock prices in a rolling-window fashion. Intended for
researchers and practitioners to backtest a set of different portfolios,
as well as by a course instructor to assess the students in their portfolio
design in a fully automated and convenient manner, with results conveniently
formatted in tables and plots. Each portfolio design is easily defined as a
function that takes as input a window of the stock prices and outputs the
portfolio weights. Multiple portfolios can be easily specified as a list
of functions or as files in a folder. Multiple datasets can be conveniently
extracted randomly from different markets, different time periods, and
different subsets of the stock universe. The results can be later assessed
and ranked with tables based on a number of performance criteria (e.g.,
expected return, volatility, Sharpe ratio, drawdown, turnover rate, return
on investment, computational time, etc.), as well as plotted in a number of
ways with nice barplots and boxplots.
Author: Daniel P. Palomar [cre, aut],
Rui Zhou [aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between portfolioBacktest versions 0.3.0 dated 2021-09-21 and 0.3.1 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/CITATION | 4 ++-- tests/testthat/test-stockDataDownload.R | 2 +- 5 files changed, 17 insertions(+), 11 deletions(-)
More information about portfolioBacktest at CRAN
Permanent link
Title: Repeated Measurement Models for Discrete Times
Description: Companion R package for the course "Statistical analysis
of correlated and repeated measurements for health science
researchers" taught by the section of Biostatistics of the University
of Copenhagen. It provides functions for computing summary statistics
and obtaining graphical displays of longitudinal data, as well as for
statistical modeling and statistical inference using linear mixed model.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julie Forman [aut] (<https://orcid.org/0000-0001-7368-0869>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between LMMstar versions 0.3.2 dated 2021-10-05 and 0.3.3 dated 2021-10-17
DESCRIPTION | 8 - MD5 | 46 ++++----- R/estimate.R | 6 - R/fitted.R | 8 + R/model.matrix.R | 121 ++++++++++++++++++------- R/residuals.R | 70 ++++++++------ R/structure-skeleton.R | 13 +- inst/doc-software/figures/diag-correlation.pdf |binary inst/doc-software/figures/diag-scatterplot.pdf |binary inst/doc-software/figures/fit-autoplot.pdf |binary inst/doc-software/figures/fit-emmip.pdf |binary inst/doc-software/figures/gg-baseAdj.pdf |binary inst/doc-software/overview.aux | 92 +++++++++---------- inst/doc-software/overview.log | 102 ++++++++++----------- inst/doc-software/overview.org | 41 ++++++++ inst/doc-software/overview.pdf |binary inst/doc-software/overview.tex | 87 +++++++++++++---- inst/doc/overview.pdf |binary man/residuals.Rd | 3 tests/testthat.R | 1 tests/testthat/test-linear-regression.R | 29 +++-- tests/testthat/test-mixed-model.R | 14 +- tests/testthat/test-previous-bug.R | 50 +++++----- tests/testthat/test-ttest.R | 12 -- 24 files changed, 427 insertions(+), 276 deletions(-)
Title: Script Based 'NONMEM' Model Development
Description: Industrialisation of 'NONMEM'
<https://www.iconplc.com/innovation/nonmem/> via fully and rapidly reusable
model development 'workflows' entirely within 'RStudio'. Quickly get started
with new models by importing 'NONMEM' templates from the built-in code
library. Manipulate 'NONMEM' code from within R either via the tracked
'manual edit' interface or 'programmatically' via convenience functions.
Script 'workflows' by piping sequences of model building steps from control
file creation, to execution, to post-processing and evaluation. Run caching
makes 'workflows' R markdown friendly for easy documentation of thoughts and
modelling decisions alongside executable code. Share, reuse and recycle
'workflows' for new problems.
Author: Tarj Sahota [aut, cre, cph],
AstraZeneca [cph],
Nuria Buil Bruna [ctb],
Stein Schalkwijk [ctb]
Maintainer: Tarj Sahota <t.sahota0@gmail.com>
Diff between NMproject versions 0.6.5 dated 2021-09-02 and 0.6.7 dated 2021-10-17
DESCRIPTION | 11 MD5 | 83 +++-- NAMESPACE | 7 NEWS.md | 17 + R/NMproject-options.R | 15 + R/addin-apps.R | 5 R/apply_manual_edit.R | 17 - R/find-nonmem.R | 141 ++++++++-- R/make_project.R | 55 +-- R/manual-edit.R | 93 +++--- R/nm_render.R | 14 R/output_table.R | 10 R/run_nm.R | 49 ++- R/snippet_setup.R |only R/subroutine.R | 86 ++++-- R/with_temp_git_config.R |only R/zzz.R | 1 README.md | 2 inst/extdata/CodeLibrary/DerivedData |only inst/extdata/examples/theopp/Scripts/s02_model_log.Rmd | 12 inst/extdata/examples/theopp/Scripts/s04_covariate_modelling.Rmd | 4 inst/extdata/examples/theopp/Scripts/s05_advanced_usage.Rmd | 4 inst/extdata/r.snippets |only inst/rmarkdown/templates/basic_boot/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_boot/template.yaml | 1 inst/rmarkdown/templates/basic_gof/skeleton/skeleton.Rmd | 19 - inst/rmarkdown/templates/basic_gof/template.yaml | 1 inst/rmarkdown/templates/basic_ppc/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_ppc/template.yaml | 1 inst/rmarkdown/templates/basic_vpc/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_vpc/template.yaml | 1 inst/rmarkdown/templates/nm_general/skeleton/skeleton.Rmd | 10 inst/rmarkdown/templates/nm_general/template.yaml | 1 inst/rmarkdown/templates/nm_log/skeleton/skeleton.Rmd | 37 +- inst/rmarkdown/templates/nm_log/template.yaml | 1 inst/templates/README.Rmd | 2 man/find_nonmem.Rd | 7 man/psn_available.Rd |only man/psn_check.Rd |only man/setup_code_completion.Rd |only man/subroutine.Rd | 2 man/system_nm_available.Rd |only man/system_nm_intern.Rd |only man/temp_files.Rd | 13 tests/testthat/test-basic.R | 12 tests/testthat/test-manual_edit.R | 38 +- tests/testthat/test-theopp.R | 12 47 files changed, 550 insertions(+), 270 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Author: Fabio Demarqui [aut, cre],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between covid19br versions 0.1.2 dated 2021-10-08 and 0.1.3 dated 2021-10-17
covid19br-0.1.2/covid19br/data/ibgeCities.rda |only covid19br-0.1.2/covid19br/data/ibgeRegions.rda |only covid19br-0.1.2/covid19br/data/ibgeStates.rda |only covid19br-0.1.2/covid19br/data/mundi.rda |only covid19br-0.1.2/covid19br/man/ibgeCities.Rd |only covid19br-0.1.2/covid19br/man/ibgeRegions.Rd |only covid19br-0.1.2/covid19br/man/ibgeStates.Rd |only covid19br-0.1.2/covid19br/man/mundi.Rd |only covid19br-0.1.3/covid19br/DESCRIPTION | 8 covid19br-0.1.3/covid19br/MD5 | 56 +- covid19br-0.1.3/covid19br/NAMESPACE | 3 covid19br-0.1.3/covid19br/NEWS.md | 11 covid19br-0.1.3/covid19br/R/covid19br.R | 3 covid19br-0.1.3/covid19br/R/data_doc.R | 86 +-- covid19br-0.1.3/covid19br/R/downloadData.R | 37 + covid19br-0.1.3/covid19br/R/utils.R | 65 ++ covid19br-0.1.3/covid19br/build/vignette.rds |binary covid19br-0.1.3/covid19br/data/election2018Cities.rda |only covid19br-0.1.3/covid19br/data/election2018Regions.rda |only covid19br-0.1.3/covid19br/data/election2018States.rda |only covid19br-0.1.3/covid19br/inst/doc/covid19br.R | 3 covid19br-0.1.3/covid19br/inst/doc/covid19br.Rmd | 17 covid19br-0.1.3/covid19br/inst/doc/covid19br.html | 421 ++++++++--------- covid19br-0.1.3/covid19br/inst/doc/election2018.R |only covid19br-0.1.3/covid19br/inst/doc/election2018.Rmd |only covid19br-0.1.3/covid19br/inst/doc/election2018.html |only covid19br-0.1.3/covid19br/inst/doc/maps.R | 23 covid19br-0.1.3/covid19br/inst/doc/maps.Rmd | 32 + covid19br-0.1.3/covid19br/inst/doc/maps.html | 234 +++++---- covid19br-0.1.3/covid19br/man/add_epi_rates.Rd | 2 covid19br-0.1.3/covid19br/man/add_geo.Rd | 48 + covid19br-0.1.3/covid19br/man/downloadCovid19.Rd | 34 + covid19br-0.1.3/covid19br/man/election2018Cities.Rd |only covid19br-0.1.3/covid19br/man/election2018Regions.Rd |only covid19br-0.1.3/covid19br/man/election2018States.Rd |only covid19br-0.1.3/covid19br/vignettes/covid19br.Rmd | 17 covid19br-0.1.3/covid19br/vignettes/election2018.Rmd |only covid19br-0.1.3/covid19br/vignettes/maps.Rmd | 32 + 38 files changed, 673 insertions(+), 459 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>.
Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case
study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between MFPCA versions 1.3-8 dated 2021-08-09 and 1.3-9 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/UMPCA.R | 2 +- build/partial.rdb |binary configure | 18 +++++++++--------- configure.ac | 5 +++-- man/ttv.Rd | 2 +- 8 files changed, 31 insertions(+), 24 deletions(-)
Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with
utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description
of the package functionalities and its interplay with the MFPCA package for
multivariate functional principal component analysis
<https://CRAN.R-project.org/package=MFPCA>.
Author: Clara Happ-Kurz [aut, cre]
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between funData versions 1.3-7 dated 2021-08-03 and 1.3-8 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ README.md | 4 ++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Computation of Tree (Im)Balance Indices
Description: The aim of the 'R' package 'treebalance' is to provide functions for the computation of
a large variety of (im)balance indices for rooted trees. The package accompanies the manuscript
''Tree balance indices: a comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting,
L. Kuehn and K. Wicke (2021) <arXiv:2109.12281>, which gives a precise definition for the terms
'balance index' and 'imbalance index' (Section 3) and provides an overview of the terminology in
this manual (Section 2). For further information on (im)balance indices, see also
Fischer et al. (2021) <https://treebalance.wordpress.com>.
Considering both established and new (im)balance indices, 'treebalance' provides (among
others) functions for calculating the following 18 established indices: the average leaf depth,
the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal
weights Colless index, the family of Colless-like indices, the family of I-based indices, the
Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin
index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths.
Additionally, we include 5 tree shape statistics that satisfy the definition of an (im)balance
index but have not been thoroughly analyzed in terms of tree balance in the literature yet.
These are: the maximum width, the maximum difference in widths, the maximal depth, the
stairs1 and the stairs2 index.
As input, most functions of 'treebalance' require a rooted (phylogenetic) tree in 'phylo' format
(as introduced in 'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees
with no vertices of out-degree one. For further information on the format we kindly refer the
reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.
Author: Mareike Fischer [aut],
Lina Herbst [aut],
Sophie Kersting [aut],
Luise Kuehn [aut, cre],
Kristina Wicke [aut]
Maintainer: Luise Kuehn <treebalanceindices@gmail.com>
Diff between treebalance versions 1.0.0 dated 2021-09-22 and 1.1.0 dated 2021-10-17
DESCRIPTION | 18 ++++----- MD5 | 15 ++++--- NEWS.md |only R/colPlaLab.R | 97 +++++++++++++++++++++++++++++++++++---------------- R/colPlaLab_inv.R | 2 - R/furnasI_inv.R | 71 +++++++++++++++++-------------------- man/colPlaLab.Rd | 44 +++++++++++++++-------- man/colPlaLab_inv.Rd | 2 - man/furnasI_inv.Rd | 2 - 9 files changed, 151 insertions(+), 100 deletions(-)
Title: 'Dang' Associated New Goodies
Description: A collection of utility functions.
Author: Dirk Eddelbuettel with contributions by Brodie Gaslam, Kevin Denny,
Kabira Namit, Colin Gillespie, R Core, Josh Ulrich, Jordan Mark Barbone,
and others.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dang versions 0.0.13 dated 2021-02-17 and 0.0.14 dated 2021-10-17
ChangeLog | 86 ++++++++++++++++++++++++++++++++++++++++++++-- DESCRIPTION | 13 ++++-- MD5 | 26 +++++++++---- R/checkCRANStatus.R | 2 - R/datatable.R | 2 - R/intradayMarketMonitor.R | 11 ++++- R/readAndConvert.R |only R/rollMinMax.R |only R/wday.R |only README.md | 17 ++++----- inst/NEWS.Rd | 22 +++++++++++ man/readAndConvert.Rd |only man/rollMinMax.Rd |only man/wday.Rd |only src/checkNonAscii.cpp | 38 ++++++++++---------- src/init.c | 6 ++- src/readAndConvert.cpp |only src/rollMinMax.cpp |only 18 files changed, 174 insertions(+), 49 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Anthony North [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.7 dated 2021-10-07 and 0.1.8 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ inst/doc/osm-sf-translation.html | 4 ++-- inst/doc/osmdata-sc.html | 4 ++-- inst/doc/osmdata.R | 18 ++++++++++++++---- inst/doc/osmdata.Rmd | 12 +++++++++++- inst/doc/osmdata.html | 6 +++--- tests/testthat/test-getbb.R | 2 ++ vignettes/osmdata.Rmd | 12 +++++++++++- vignettes/osmdata.md |only 11 files changed, 66 insertions(+), 25 deletions(-)
Title: A Parametric Method for Generating Synthetic Data
Description: Builds synthetic data applicable across multiple domains. This package also provides flexibility to control data distribution to make it relevant to many industry examples.
Author: Sidharth Macherla [aut, cre] (<https://orcid.org/0000-0002-4825-2026>)
Maintainer: Sidharth Macherla <msidharthrasik@gmail.com>
Diff between conjurer versions 1.2.0 dated 2020-09-08 and 1.3.0 dated 2021-10-17
DESCRIPTION | 9 MD5 | 22 NAMESPACE | 1 NEWS.md | 15 R/buildHierarchy.R |only R/genTree.R |only R/treeDf.R |only inst/doc/introduction_to_conjurer.R | 35 + inst/doc/introduction_to_conjurer.Rmd | 88 ++- inst/doc/introduction_to_conjurer.html | 967 +++++++++++++++++++-------------- man/buildHierarchy.Rd |only man/genTree.Rd |only man/treeDf.Rd |only vignettes/bibliography.bib | 151 +++++ vignettes/introduction_to_conjurer.Rmd | 88 ++- 15 files changed, 908 insertions(+), 468 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.0.1 dated 2021-09-20 and 2.0.2 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 +++++++- R/check_data.R | 8 ++++---- README.md | 2 +- build/vignette.rds |binary tests/testthat/test-expand_classes.R | 4 ++-- tests/testthat/test-nec.R | 4 +++- 8 files changed, 27 insertions(+), 19 deletions(-)
Title: Color Manipulation Tools
Description: Manipulate and visualize colors in a intuitive,
low-dependency and functional way.
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between prismatic versions 1.0.0 dated 2021-01-05 and 1.1.0 dated 2021-10-17
prismatic-1.0.0/prismatic/R/0_imports.R |only prismatic-1.0.0/prismatic/tests/testthat/test-modify.R |only prismatic-1.1.0/prismatic/DESCRIPTION | 19 - prismatic-1.1.0/prismatic/MD5 | 43 +- prismatic-1.1.0/prismatic/NAMESPACE | 11 prismatic-1.1.0/prismatic/NEWS.md | 5 prismatic-1.1.0/prismatic/R/contrast_ratio.R | 10 prismatic-1.1.0/prismatic/R/extract.R |only prismatic-1.1.0/prismatic/R/prismatic-package.R |only prismatic-1.1.0/prismatic/README.md | 9 prismatic-1.1.0/prismatic/man/best_contrast.Rd |only prismatic-1.1.0/prismatic/man/clr_extract.Rd |only prismatic-1.1.0/prismatic/man/extract_hcl.Rd |only prismatic-1.1.0/prismatic/man/extract_hsl.Rd |only prismatic-1.1.0/prismatic/man/extract_rgb.Rd |only prismatic-1.1.0/prismatic/man/prismatic-package.Rd |only prismatic-1.1.0/prismatic/tests/testthat/Rplots.pdf |binary prismatic-1.1.0/prismatic/tests/testthat/helpers.R | 84 ----- prismatic-1.1.0/prismatic/tests/testthat/test-alpha.R | 31 +- prismatic-1.1.0/prismatic/tests/testthat/test-color-blindness.R | 119 ++++++- prismatic-1.1.0/prismatic/tests/testthat/test-color.R | 34 +- prismatic-1.1.0/prismatic/tests/testthat/test-extract.R |only prismatic-1.1.0/prismatic/tests/testthat/test-greyscale.R | 34 +- prismatic-1.1.0/prismatic/tests/testthat/test-lightness.R | 150 ++++++---- prismatic-1.1.0/prismatic/tests/testthat/test-mix.R | 43 ++ prismatic-1.1.0/prismatic/tests/testthat/test-negate.R | 17 - prismatic-1.1.0/prismatic/tests/testthat/test-rotate.R | 43 ++ prismatic-1.1.0/prismatic/tests/testthat/test-saturate.R | 81 ++++- 28 files changed, 457 insertions(+), 276 deletions(-)
Title: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 1.2.0 dated 2021-09-06 and 1.2.1 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/hs_mate_finder.R | 2 +- R/simulateGen.R | 1 + 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are
otherwise performed manually. This includes setting up unit testing,
test coverage, continuous integration, Git, 'GitHub', licenses,
'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
Malcolm Barrett [aut] (<https://orcid.org/0000-0003-0299-5825>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between usethis versions 2.0.1 dated 2021-02-10 and 2.1.0 dated 2021-10-16
usethis-2.0.1/usethis/inst/templates/data-table.R |only usethis-2.0.1/usethis/man/git_branch_default.Rd |only usethis-2.0.1/usethis/man/use_github_action.Rd |only usethis-2.0.1/usethis/tests/testthat/_snaps/pipe.md |only usethis-2.1.0/usethis/DESCRIPTION | 31 usethis-2.1.0/usethis/MD5 | 246 ++++--- usethis-2.1.0/usethis/NAMESPACE | 10 usethis-2.1.0/usethis/NEWS.md | 130 ++++ usethis-2.1.0/usethis/R/badge.R | 2 usethis-2.1.0/usethis/R/block.R | 30 usethis-2.1.0/usethis/R/browse.R | 2 usethis-2.1.0/usethis/R/ci.R | 12 usethis-2.1.0/usethis/R/code-of-conduct.R | 11 usethis-2.1.0/usethis/R/coverage.R | 16 usethis-2.1.0/usethis/R/data-table.R | 29 usethis-2.1.0/usethis/R/data.R | 5 usethis-2.1.0/usethis/R/description.R | 91 ++ usethis-2.1.0/usethis/R/edit.R | 40 - usethis-2.1.0/usethis/R/git-default-branch.R |only usethis-2.1.0/usethis/R/git.R | 222 ++---- usethis-2.1.0/usethis/R/github-actions.R | 254 +++---- usethis-2.1.0/usethis/R/github-labels.R | 22 usethis-2.1.0/usethis/R/github-pages.R | 39 - usethis-2.1.0/usethis/R/github.R | 42 + usethis-2.1.0/usethis/R/github_token.R | 219 +++++- usethis-2.1.0/usethis/R/helpers.R | 31 usethis-2.1.0/usethis/R/issue.R | 4 usethis-2.1.0/usethis/R/lifecycle.R | 15 usethis-2.1.0/usethis/R/logo.R | 5 usethis-2.1.0/usethis/R/make.R | 5 usethis-2.1.0/usethis/R/package.R | 12 usethis-2.1.0/usethis/R/pipe.R | 21 usethis-2.1.0/usethis/R/pkgdown.R | 138 ++-- usethis-2.1.0/usethis/R/pr.R | 325 +++++----- usethis-2.1.0/usethis/R/proj.R | 4 usethis-2.1.0/usethis/R/rcpp.R | 6 usethis-2.1.0/usethis/R/readme.R | 20 usethis-2.1.0/usethis/R/release.R | 267 ++++++-- usethis-2.1.0/usethis/R/roxygen.R | 36 - usethis-2.1.0/usethis/R/rprofile.R | 1 usethis-2.1.0/usethis/R/rstudio.R | 2 usethis-2.1.0/usethis/R/spelling.R | 2 usethis-2.1.0/usethis/R/template.R | 1 usethis-2.1.0/usethis/R/test.R | 8 usethis-2.1.0/usethis/R/tibble.R | 5 usethis-2.1.0/usethis/R/tidy-upkeep.R |only usethis-2.1.0/usethis/R/tidyverse.R | 101 +-- usethis-2.1.0/usethis/R/use_github_file.R |only usethis-2.1.0/usethis/R/use_import_from.R |only usethis-2.1.0/usethis/R/usethis-defunct.R | 45 + usethis-2.1.0/usethis/R/usethis-package.R | 6 usethis-2.1.0/usethis/R/utils-git.R | 82 +- usethis-2.1.0/usethis/R/utils-github.R | 28 usethis-2.1.0/usethis/R/utils-glue.R | 4 usethis-2.1.0/usethis/R/utils-ui.R |only usethis-2.1.0/usethis/R/utils.R | 50 + usethis-2.1.0/usethis/R/version.R | 2 usethis-2.1.0/usethis/README.md | 23 usethis-2.1.0/usethis/inst/WORDLIST | 11 usethis-2.1.0/usethis/inst/templates/CODE_OF_CONDUCT.md | 10 usethis-2.1.0/usethis/inst/templates/cran-comments.md | 5 usethis-2.1.0/usethis/inst/templates/package-README | 18 usethis-2.1.0/usethis/inst/templates/packagename-package.R | 2 usethis-2.1.0/usethis/inst/templates/project-README | 2 usethis-2.1.0/usethis/inst/templates/tidy-contributing.md | 2 usethis-2.1.0/usethis/inst/templates/tidy-eval.R | 140 +++- usethis-2.1.0/usethis/man/badges.Rd | 2 usethis-2.1.0/usethis/man/browse-this.Rd | 2 usethis-2.1.0/usethis/man/ci.Rd | 10 usethis-2.1.0/usethis/man/create_from_github.Rd | 4 usethis-2.1.0/usethis/man/create_package.Rd | 4 usethis-2.1.0/usethis/man/edit.Rd | 5 usethis-2.1.0/usethis/man/git-default-branch.Rd |only usethis-2.1.0/usethis/man/git_credentials.Rd | 2 usethis-2.1.0/usethis/man/git_vaccinate.Rd | 2 usethis-2.1.0/usethis/man/github-token.Rd | 17 usethis-2.1.0/usethis/man/github_actions.Rd | 118 +++ usethis-2.1.0/usethis/man/issue-this.Rd | 4 usethis-2.1.0/usethis/man/pull-requests.Rd | 11 usethis-2.1.0/usethis/man/tidyverse.Rd | 31 usethis-2.1.0/usethis/man/use_code_of_conduct.Rd | 5 usethis-2.1.0/usethis/man/use_data_table.Rd | 18 usethis-2.1.0/usethis/man/use_description.Rd | 6 usethis-2.1.0/usethis/man/use_github.Rd | 9 usethis-2.1.0/usethis/man/use_github_file.Rd |only usethis-2.1.0/usethis/man/use_github_labels.Rd | 16 usethis-2.1.0/usethis/man/use_github_links.Rd | 2 usethis-2.1.0/usethis/man/use_github_pages.Rd | 2 usethis-2.1.0/usethis/man/use_github_release.Rd | 23 usethis-2.1.0/usethis/man/use_import_from.Rd |only usethis-2.1.0/usethis/man/use_lifecycle.Rd | 14 usethis-2.1.0/usethis/man/use_pkgdown.Rd | 11 usethis-2.1.0/usethis/man/use_release_issue.Rd | 21 usethis-2.1.0/usethis/man/use_tibble.Rd | 2 usethis-2.1.0/usethis/man/usethis-defunct.Rd | 29 usethis-2.1.0/usethis/man/usethis-package.Rd | 6 usethis-2.1.0/usethis/tests/testthat/_snaps/course.md | 4 usethis-2.1.0/usethis/tests/testthat/_snaps/data-table.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/git-default-branch.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/github-actions.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/lifecycle.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/package.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/readme.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/release.md | 60 + usethis-2.1.0/usethis/tests/testthat/_snaps/tibble.md | 10 usethis-2.1.0/usethis/tests/testthat/_snaps/tidy-upkeep.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/tidyverse.md |only usethis-2.1.0/usethis/tests/testthat/_snaps/use_import_from.md |only usethis-2.1.0/usethis/tests/testthat/helper.R | 4 usethis-2.1.0/usethis/tests/testthat/setup.R | 12 usethis-2.1.0/usethis/tests/testthat/test-addin.R | 2 usethis-2.1.0/usethis/tests/testthat/test-badge.R | 9 usethis-2.1.0/usethis/tests/testthat/test-block.R |only usethis-2.1.0/usethis/tests/testthat/test-code-of-conduct.R | 2 usethis-2.1.0/usethis/tests/testthat/test-data-table.R | 25 usethis-2.1.0/usethis/tests/testthat/test-data.R | 2 usethis-2.1.0/usethis/tests/testthat/test-description.R | 71 ++ usethis-2.1.0/usethis/tests/testthat/test-edit.R | 13 usethis-2.1.0/usethis/tests/testthat/test-git-default-branch.R |only usethis-2.1.0/usethis/tests/testthat/test-git.R | 32 usethis-2.1.0/usethis/tests/testthat/test-github-actions.R | 158 ++-- usethis-2.1.0/usethis/tests/testthat/test-helpers.R | 45 - usethis-2.1.0/usethis/tests/testthat/test-lifecycle.R | 15 usethis-2.1.0/usethis/tests/testthat/test-package.R | 10 usethis-2.1.0/usethis/tests/testthat/test-pipe.R | 6 usethis-2.1.0/usethis/tests/testthat/test-pkgdown.R | 6 usethis-2.1.0/usethis/tests/testthat/test-proj.R | 11 usethis-2.1.0/usethis/tests/testthat/test-readme.R | 42 + usethis-2.1.0/usethis/tests/testthat/test-release.R | 112 ++- usethis-2.1.0/usethis/tests/testthat/test-tibble.R | 10 usethis-2.1.0/usethis/tests/testthat/test-tidy-upkeep.R |only usethis-2.1.0/usethis/tests/testthat/test-tidyverse.R | 14 usethis-2.1.0/usethis/tests/testthat/test-use_github_file.R |only usethis-2.1.0/usethis/tests/testthat/test-use_import_from.R |only usethis-2.1.0/usethis/tests/testthat/test-utils-github.R | 7 usethis-2.1.0/usethis/tests/testthat/test-utils.R | 14 usethis-2.1.0/usethis/tests/testthat/test-write.R | 75 ++ 137 files changed, 2581 insertions(+), 1458 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 1.0.1 dated 2021-07-26 and 1.0.2 dated 2021-10-16
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/html.R | 17 +++++++++-------- R/table.R | 5 +++++ R/utils.R | 1 - README.md | 28 ++++++++++++++-------------- inst/doc/rvest.html | 8 ++++---- man/html_attr.Rd | 17 +++++++++-------- man/rvest-package.Rd | 3 +-- tests/testthat/_snaps/table.md | 4 ++++ tests/testthat/test-encoding.R | 2 ++ tests/testthat/test-table.R | 6 ++++++ 13 files changed, 76 insertions(+), 53 deletions(-)
Title: Classify Occurrences by Confidence Levels in the Species ID
Description: Classify occurrence records based on confidence
levels of species identification. In addition, implement tools to filter
occurrence inside grid cells and to manually check for possibles errors with
an interactive shiny application.
Author: Arthur Vinicius Rodrigues [cre],
Gabriel Nakamura [aut],
Leandro Duarte [aut]
Maintainer: Arthur Vinicius Rodrigues <rodrigues.arthur.v@gmail.com>
Diff between naturaList versions 0.4.1 dated 2021-08-21 and 0.4.2 dated 2021-10-16
DESCRIPTION | 6 - MD5 | 42 ++++---- NEWS.md | 5 R/clean_eval.R | 138 +++++++++++---------------- R/create_spec_df.R | 11 -- R/data_description.R | 15 ++ R/define_env_space.R | 16 +-- README.md | 6 - build/partial.rdb |binary data/r.temp.prec.rda |only data/spec_names_ex.rda |only inst/doc/natutaList_clean_eval_vignette.R | 16 --- inst/doc/natutaList_clean_eval_vignette.Rmd | 18 +-- inst/doc/natutaList_clean_eval_vignette.html | 28 ++--- inst/doc/natutaList_vignette.R | 3 inst/doc/natutaList_vignette.Rmd | 5 inst/doc/natutaList_vignette.html | 5 man/clean_eval.Rd | 138 +++++++++++---------------- man/create_spec_df.Rd | 11 -- man/define_env_space.Rd | 14 -- man/r.temp.prec.Rd |only man/spec_names_ex.Rd |only vignettes/natutaList_clean_eval_vignette.Rmd | 18 +-- vignettes/natutaList_vignette.Rmd | 5 24 files changed, 223 insertions(+), 277 deletions(-)
Title: Causal Inference using Multivariate Generalized Propensity Score
Description: Methods for estimating and utilizing the multivariate generalized
propensity score (mvGPS) for multiple continuous exposures described in
Williams, J.R, and Crespi, C.M. (2020) <arxiv:2008.13767>. The methods allow
estimation of a dose-response surface relating the joint distribution of multiple
continuous exposure variables to an outcome. Weights are constructed assuming a
multivariate normal density for the marginal and conditional distribution of
exposures given a set of confounders. Confounders can be different for different
exposure variables. The weights are designed to achieve balance across all
exposure dimensions and can be used to estimate dose-response surfaces.
Author: Justin Williams [aut, cre] (<https://orcid.org/0000-0002-5045-2764>)
Maintainer: Justin Williams <williazo@ucla.edu>
Diff between mvGPS versions 1.1.1 dated 2021-04-28 and 1.2.1 dated 2021-10-16
DESCRIPTION | 19 +++++-- MD5 | 28 +++++----- NEWS | 6 ++ R/bal.R | 117 ++++++++++++++++++++++---------------------- R/gen_D.R | 97 +++++++++++++++++++++--------------- R/mvGPS.R | 2 build/partial.rdb |binary inst/doc/mvGPS-intro.R | 1 inst/doc/mvGPS-intro.Rmd | 1 inst/doc/mvGPS-intro.html | 4 - man/bal.Rd | 52 +++++++++---------- man/gen_D.Rd | 62 ++++++++++++----------- tests/testthat/test-bal.R | 10 --- tests/testthat/test-mvGPS.R | 1 vignettes/mvGPS-intro.Rmd | 1 15 files changed, 216 insertions(+), 185 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (University of Bonn),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting),
Katja Schiffers [aut] (University of Bonn),
Cory Whitney [aut] (University of Bonn),
Eduardo Fernandez [aut] (University of Bonn)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.107 dated 2021-10-16 and 1.108 dated 2021-10-16
DESCRIPTION | 6 - MD5 | 10 +-- R/scenario_mc.R | 3 build/partial.rdb |binary inst/doc/example_decision_function.html | 14 ++-- inst/doc/wildfire_example.html | 105 +++++++++++++++----------------- 6 files changed, 69 insertions(+), 69 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Data Only: The Correlates of State Policy Project Dataset
Description: Contains the Correlates of State Policy Project dataset (+ codebook) assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy> used by the 'cspp' package. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States.
Author: Caleb Lucas (https://caleblucas.com/) and Joshua McCrain (http://joshuamccrain.com/)
Maintainer: Caleb Lucas <calebjlucas@gmail.com>
Diff between csppData versions 0.1.3 dated 2021-06-07 and 0.1.4 dated 2021-10-16
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/codebook.R | 2 +- R/correlates.R | 2 +- R/zzz.R | 8 ++++---- README.md | 31 +++++++++++++++++-------------- data/codebook.rda |binary data/correlates.rda |binary man/codebook.Rd | 4 ++-- man/correlates.Rd | 4 ++-- 10 files changed, 40 insertions(+), 37 deletions(-)
Title: A Tool for the Correlates of State Policy Project Data
Description: A tool that imports, subsets, visualizes, and exports the Correlates of State Policy Project dataset assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy>. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States. Users with only a basic understanding of R can subset this data across multiple dimensions, export their search results, create map visualizations, export the citations associated with their searches, and more.
Author: Caleb Lucas (https://caleblucas.com/) and Joshua McCrain (http://joshuamccrain.com/)
Maintainer: Caleb Lucas <calebjlucas@gmail.com>
Diff between cspp versions 0.3.1 dated 2021-01-04 and 0.3.2 dated 2021-10-16
DESCRIPTION | 16 MD5 | 50 - NAMESPACE | 5 NEWS.md | 6 R/corr_plot.R |only R/generate_map.R | 8 R/get_cspp_data.R | 39 - R/get_network_data.R | 14 R/globals.R | 4 R/plot_panel.R | 18 R/zzz.R | 8 README.md | 529 ++++++++++-------- build/vignette.rds |binary inst/doc/cspp-vignette.R | 6 inst/doc/cspp-vignette.Rmd | 14 inst/doc/cspp-vignette.html | 846 +++++++++++------------------- man/corr_plot.Rd |only man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-26-1.png |only man/figures/README-unnamed-chunk-27-1.png |only man/generate_map.Rd | 4 man/plot_panel.Rd | 4 vignettes/cspp-vignette.Rmd | 14 28 files changed, 746 insertions(+), 839 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. Ordinary R vectors are unsuitable for working with values of
associative maps because elements of an R vector may be accessed by
reference to their location in the vector, but associative maps are
stored in arbitrary order. However, when associating keys with
values one needs both parts to be in 1-1 correspondence, so one
cannot dispense with the order entirely. The 'disordR' package
includes a single S4 class, disord. This class allows one to
perform only those operations appropriate for manipulating values of
associative maps and prevents any other operation (such as accessing
an element at a particular location). A useful heuristic is that
one is only allowed to access or modify a disord object using a
python list comprehension. The idea is to prevent ill-defined
operations on values (or keys) of associative maps, whose order is
undefined or at best implementation-specific, while allowing and
facilitating sensible operations. The package is needed for
development versions of 'mvp', 'hyper2', 'spray', 'clifford', and
'freealg'.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.0-7 dated 2021-08-05 and 0.0-8 dated 2021-10-16
DESCRIPTION | 6 ++-- MD5 | 17 ++++++----- R/disordR.R | 28 +++++++++++++------ README.md | 73 ++++++++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/disordR.Rmd | 10 ++++-- inst/doc/disordR.html | 54 ++++++++++++++++++------------------ man/figures |only man/misc.Rd | 6 ++++ vignettes/disordR.Rmd | 10 ++++-- 10 files changed, 121 insertions(+), 83 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-49 dated 2019-02-03 and 1.1-3 dated 2021-10-16
DESCRIPTION | 14 +-- MD5 | 71 ++++++++------- NAMESPACE | 6 + R/AAAClasses.R | 12 ++ R/ModisDownload.R | 154 ++++++++++++++++++++++----------- R/VHIdownload.R | 37 +++++-- R/apply.R | 157 ++++++++++++++++++++------------- R/cellFrom.R | 44 +++++++-- R/endpoints.R | 39 ++++---- R/extract.R | 175 ++++++++++++++++++++++++++++++++++--- R/index.R | 11 ++ R/period.R | 77 +++++++++++++--- R/plot.R | 23 ++++ R/rts.R | 166 ++++++++++++++++++++--------------- R/show.R | 165 +++++++++++++++++++++++------------ R/subset.R | 33 ++++++- R/utils.R |only R/writerts.R | 195 +++++++++++++++++++++++++++--------------- build |only inst/doc |only inst/external/ndvi/ndvi.grd | 52 +++++------ man/ModisDownload.Rd | 30 +++--- man/RasterStackBrick-class.Rd | 3 man/VHPdownload.Rd | 4 man/apply.monthly.Rd | 6 + man/cellFromXY.Rd | 26 +++-- man/endpoints.Rd | 2 man/extract.Rd | 4 man/extractIndex.Rd | 5 + man/index.Rd | 2 man/period.apply.Rd | 1 man/plot.Rd | 1 man/read.rts.Rd | 10 +- man/rts.Rd | 10 +- man/subset.Rd | 1 man/subsetIndex.Rd | 1 man/write.rts.Rd | 7 + vignettes |only 38 files changed, 1067 insertions(+), 477 deletions(-)
Title: R-Based Visualization Techniques for Task-Based Applications
Description: Performance analysis workflow that combines the power of the R
language (and the tidyverse realm) and many auxiliary tools to
provide a consistent, flexible, extensible, fast, and versatile
framework for the performance analysis of task-based applications
that run on top of the StarPU runtime (with its MPI (Message
Passing Interface) layer for multi-node support). Its goal is to
provide a fruitful prototypical environment to conduct performance
analysis hypothesis-checking for task-based applications that run
on heterogeneous (multi-GPU, multi-core) multi-node HPC
(High-performance computing) platforms.
Author: Lucas Mello Schnorr [aut, ths]
(<https://orcid.org/0000-0003-4828-9942>),
Vinicius Garcia Pinto [aut] (<https://orcid.org/0000-0002-6845-9358>),
Lucas Leandro Nesi [aut, cre] (<https://orcid.org/0000-0001-8874-1839>),
Marcelo Cogo Miletto [aut] (<https://orcid.org/0000-0002-1191-3863>),
Guilherme Alles [ctb],
Arnaud Legrand [ctb],
Luka Stanisic [ctb],
Rémy Drouilhet [ctb]
Maintainer: Lucas Leandro Nesi <lucas.nesi@inf.ufrgs.br>
Diff between starvz versions 0.5.0 dated 2021-03-25 and 0.6.0 dated 2021-10-16
DESCRIPTION | 8 ++-- MD5 | 46 +++++++++++++------------ R/RcppExports.R | 17 ++++++++- R/phase1.R | 56 ++++++++++++++++++++++--------- R/phase1_parse_csv.R | 49 +++++++++++++++++++-------- R/phase2.R | 11 ++++-- R/phase2_aggregation.R | 26 ++++++++++---- R/phase2_applications.R | 5 +- R/phase2_config.R | 7 ++- R/phase2_gaps.R | 2 + R/phase2_memory.R | 5 ++ R/phase2_states_chart.R | 20 +++++++---- R/phase2_util.R | 25 +++++++++++++- R/read_functions.R | 49 +++++++++++++++------------ R/write_functions.R | 29 ++++++++-------- inst/tools/phase1-workflow.sh | 75 +++++++++++++++++++++++++----------------- inst/tools/starvz | 4 +- man/panel_st_agg_dynamic.Rd | 5 ++ man/panel_st_agg_static.Rd | 6 +++ man/starvz_phase1.Rd | 2 - man/starvz_read_config.Rd | 6 ++- src/RcppExports.cpp | 42 +++++++++++++++++++++++ src/lastest.cpp |only src/separate_res.cpp |only tests/testthat/test_lu.R | 4 +- 25 files changed, 344 insertions(+), 155 deletions(-)
Title: Single Cell Mapper
Description: The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.
Author: Dustin Sokolowski [aut, cre],
Mariela Faykoo-Martinez [aut],
Lauren Erdman [aut],
Houyun Hou [aut],
Cadia Chan [aut],
Helen Zhu [aut],
Melissa Holmes [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between scMappR versions 1.0.2 dated 2021-05-14 and 1.0.7 dated 2021-10-16
DESCRIPTION | 6 +-- MD5 | 20 +++++------ R/compare_deconvolution_methods.R | 61 ++++++++++++++++++++++++++++++++--- R/cwFoldChange_evaluate.R | 12 +++++- R/process_dgTMatrix_lists.R | 3 + README.md | 2 - inst/doc/scMappR_Vignette.Rmd | 6 +++ inst/doc/scMappR_Vignette.html | 15 +++++++- man/compare_deconvolution_methods.Rd | 7 ++-- man/process_dgTMatrix_lists.Rd | 3 + vignettes/scMappR_Vignette.Rmd | 6 +++ 11 files changed, 113 insertions(+), 28 deletions(-)
Title: An Extended Mixed-Effects Framework for Meta-Analysis
Description: A collection of functions to perform various meta-analytical models
through a unified mixed-effects framework, including standard univariate
fixed and random-effects meta-analysis and meta-regression, and non-standard
extensions such as multivariate, multilevel, longitudinal, and dose-response
models.
Author: Antonio Gasparrini [aut, cre],
Francesco Sera [aut]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mixmeta versions 1.1.3 dated 2021-06-12 and 1.2.0 dated 2021-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/mixmeta.R | 2 +- inst/NEWS | 8 ++++++++ 5 files changed, 25 insertions(+), 9 deletions(-)
Title: The MBESS R Package
Description: Implements methods that are useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but MBESS became
more general and now contains methods applicable and used in a wide variety of fields and is an
orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has
greatly benefited from others, see <https://www3.nd.edu/~kkelley/site/MBESS.html> for a detailed
list of those that have contributed and other details.
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.8.0 dated 2020-08-05 and 4.8.1 dated 2021-10-16
DESCRIPTION | 25 +++++++++++++------------ MD5 | 6 +++--- R/ci.reliability.R | 18 +++++++++++------- man/MBESS-package.Rd | 20 ++++++++++---------- 4 files changed, 37 insertions(+), 32 deletions(-)
Title: R Bindings for the Hong Kong Legislative Council API
Description: Fetching data from Hong Kong Legislative Council's open data API in R.
Functions correspond to the data endpoints of the API.
Documentations of supported API databases:
<https://www.legco.gov.hk/odata/english/billsdb.html>,
<https://www.legco.gov.hk/odata/english/hansard-db.html>,
<https://www.legco.gov.hk/odata/english/attendance-db.html>,
<https://www.legco.gov.hk/odata/english/schedule-db.html> and
<https://www.legco.gov.hk/odata/english/vrdb.html>.
Author: Elgar Teo
Maintainer: Elgar Teo <elgarteo@connect.hku.hk>
Diff between legco versions 0.1.3 dated 2020-03-31 and 0.1.4 dated 2021-10-16
DESCRIPTION | 12 - MD5 | 92 +++++++----- NAMESPACE | 9 + NEWS.md |only R/addresses.R | 4 R/all_bills.R | 10 - R/attendance.R | 8 - R/bills.R | 6 R/committee.R | 8 - R/db-man.R | 23 +++ R/hansard.R | 2 R/legco-package.R | 10 - R/legco_api.R | 32 ++-- R/meeting.R | 8 - R/meeting_committee.R | 6 R/member.R | 4 R/member_term.R | 4 R/membership.R | 12 - R/motions.R | 6 R/petitions.R | 4 R/questions.R | 4 R/rundown.R | 10 - R/search_committee.R |only R/search_member.R |only R/search_question.R |only R/search_voting_record.R |only R/session.R | 6 R/speakers.R | 2 R/statements.R | 4 R/subjects.R | 6 R/summoning_bells.R | 6 R/term.R | 4 R/utils-misc.R | 20 +- R/voting_record.R | 24 +-- R/voting_results.R | 6 README.md | 15 -- build/vignette.rds |binary inst/doc/attn.html | 234 ++++---------------------------- inst/doc/bills.html | 228 +++---------------------------- inst/doc/hansard.html | 320 ++++++++++---------------------------------- inst/doc/introduction.html | 288 +++++++-------------------------------- inst/doc/schedule.html | 272 ++++++------------------------------- inst/doc/voting.Rmd | 4 inst/doc/voting.html | 248 +++++----------------------------- man/comp-fun.Rd |only man/legco-package.Rd | 15 +- man/rundown.Rd | 2 man/search_committee.Rd |only man/search_member.Rd |only man/search_question.Rd |only man/search_voting_record.Rd |only vignettes/voting.Rmd | 4 52 files changed, 498 insertions(+), 1484 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik),
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>),
Alex Hayes [rev] (<https://orcid.org/0000-0002-4985-5160>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.14.4 dated 2021-09-02 and 0.14.5 dated 2021-10-16
DESCRIPTION | 16 MD5 | 303 +++---- NAMESPACE | 18 NEWS.md | 46 + R/check_if_installed.R | 30 R/clean_names.R | 2 R/compute_variances.R | 2 R/find_predictors.R | 33 R/find_transformation.R |only R/find_variables.R | 27 R/format_table.R | 5 R/get_df.R | 60 + R/get_modelmatrix.R | 37 R/get_parameters_bayesian.R | 51 - R/get_parameters_emmeans.R | 4 R/get_predicted.R | 522 ++++++++++-- R/get_predicted_ci.R | 62 - R/get_predicted_methods.R | 15 R/get_priors.R | 58 - R/get_response.R | 22 R/get_statistic.R | 125 --- R/get_transformation.R |only R/get_varcov.R | 15 R/model_info.R | 151 +-- R/utils_get_data.R | 2 README.md | 4 build/partial.rdb |binary inst/doc/display.html | 144 +-- man/check_if_installed.Rd | 6 man/figures/logo.png |binary man/find_transformation.Rd |only man/find_variables.Rd | 25 man/get_df.Rd | 8 man/get_predicted.Rd | 45 - man/get_predicted_ci.Rd | 13 man/get_transformation.Rd |only man/model_info.Rd | 145 +-- tests/testthat/_snaps |only tests/testthat/helper-requiet.R |only tests/testthat/test-BayesFactorBF.R | 2 tests/testthat/test-FE-formula.R | 2 tests/testthat/test-GLMMadaptive.R | 2 tests/testthat/test-Gam2.R | 6 tests/testthat/test-LORgee.R | 6 tests/testthat/test-MCMCglmm.R | 6 tests/testthat/test-afex_aov.R | 2 tests/testthat/test-all_models_equal.R | 2 tests/testthat/test-aovlist.R | 6 tests/testthat/test-backticks.R | 2 tests/testthat/test-betabin.R | 2 tests/testthat/test-betareg.R | 6 tests/testthat/test-bife.R |only tests/testthat/test-bigglm.R | 4 tests/testthat/test-blmer.R | 6 tests/testthat/test-brms.R | 41 - tests/testthat/test-censReg.R | 8 tests/testthat/test-cgam.R | 6 tests/testthat/test-check_if_installed.R | 2 tests/testthat/test-clean_names.R | 2 tests/testthat/test-clm.R | 33 tests/testthat/test-clm2.R | 8 tests/testthat/test-clmm.R | 6 tests/testthat/test-coxme.R | 14 tests/testthat/test-coxph.R | 8 tests/testthat/test-cpglmm.R | 6 tests/testthat/test-crch.R | 6 tests/testthat/test-crq.R | 6 tests/testthat/test-data.frame.R | 2 tests/testthat/test-ellipses_info.R | 2 tests/testthat/test-emmeans.R |only tests/testthat/test-epiR.R | 6 tests/testthat/test-export_table.R | 2 tests/testthat/test-feis.R | 6 tests/testthat/test-felm.R | 6 tests/testthat/test-find_formula-data.R | 2 tests/testthat/test-find_predictor_nested_re.R | 2 tests/testthat/test-find_random.R | 2 tests/testthat/test-find_smooth.R | 6 tests/testthat/test-find_terms.R | 2 tests/testthat/test-fixest.R | 417 +++++----- tests/testthat/test-format.R | 2 tests/testthat/test-format_table_ci.R | 2 tests/testthat/test-formatting.R | 2 tests/testthat/test-gam.R | 28 tests/testthat/test-gamlss.R | 24 tests/testthat/test-gamm.R | 16 tests/testthat/test-gamm4.R | 2 tests/testthat/test-gbm.R | 2 tests/testthat/test-gee.R | 10 tests/testthat/test-geeglm.R | 6 tests/testthat/test-get_auxiliary.R | 2 tests/testthat/test-get_data.R | 2 tests/testthat/test-get_deviance.R | 2 tests/testthat/test-get_loglikelihood.R | 18 tests/testthat/test-get_predicted.R | 854 +++++++++++---------- tests/testthat/test-get_priors.R | 2 tests/testthat/test-get_residuals.R | 2 tests/testthat/test-get_variance.R | 2 tests/testthat/test-get_weights.R | 2 tests/testthat/test-glm.R | 6 tests/testthat/test-glmmTMB.R | 41 - tests/testthat/test-glmrob_base.R | 6 tests/testthat/test-gls.R | 6 tests/testthat/test-gmnl.R | 24 tests/testthat/test-has_intercept.R | 2 tests/testthat/test-htest.R | 2 tests/testthat/test-hurdle.R | 6 tests/testthat/test-is_nullmodel.R | 2 tests/testthat/test-iv_robust.R | 6 tests/testthat/test-ivreg.R | 6 tests/testthat/test-ivreg_AER.R | 6 tests/testthat/test-lm.R | 6 tests/testthat/test-lm_robust.R | 6 tests/testthat/test-lme.R | 8 tests/testthat/test-lmer.R | 6 tests/testthat/test-lmrob_base.R | 6 tests/testthat/test-lmtest.R | 6 tests/testthat/test-logistf.R | 6 tests/testthat/test-metaBMA.R | 2 tests/testthat/test-mixed.R | 8 tests/testthat/test-mlogit.R | 6 tests/testthat/test-model_data.R | 8 tests/testthat/test-model_info.R | 2 tests/testthat/test-multinom.R | 50 + tests/testthat/test-mvrstanarm.R | 6 tests/testthat/test-n_parameters_rank-deficiency.R | 2 tests/testthat/test-namespace.R | 6 tests/testthat/test-negbin.R | 2 tests/testthat/test-nlmer.R | 2 tests/testthat/test-offset.R | 6 tests/testthat/test-ols.R | 6 tests/testthat/test-panelr.R | 6 tests/testthat/test-plm.R | 2 tests/testthat/test-polr.R | 26 tests/testthat/test-proportion_response.R |only tests/testthat/test-psm.R | 2 tests/testthat/test-r3_4.R | 2 tests/testthat/test-response_data2.R | 6 tests/testthat/test-rlm.R |only tests/testthat/test-rlmer.R | 4 tests/testthat/test-rms.R | 6 tests/testthat/test-rq.R | 6 tests/testthat/test-rqss.R | 8 tests/testthat/test-rstanarm.R | 8 tests/testthat/test-spatial.R | 2 tests/testthat/test-speedglm.R | 8 tests/testthat/test-speedlm.R | 6 tests/testthat/test-standardize_names.R | 8 tests/testthat/test-survey.R | 6 tests/testthat/test-survfit.R | 6 tests/testthat/test-survreg.R | 6 tests/testthat/test-tidymodels.R | 6 tests/testthat/test-tobit.R | 2 tests/testthat/test-truncreg.R | 8 tests/testthat/test-vgam.R | 2 tests/testthat/test-vglm.R | 4 tests/testthat/test-zeroinfl.R | 6 157 files changed, 2369 insertions(+), 1671 deletions(-)
Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. 1 ) Computing the probability density function,
cumulative distribution function, random generation, and estimating the parameters
of the eleven mixture models. 2 ) Point estimation of the parameters of two -
parameter Weibull distribution using twelve methods and three - parameter Weibull
distribution using nine methods. 3 ) The Bayesian inference for the three -
parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter
Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to
grouped data using three methods including approximated maximum likelihood,
expectation maximization, and maximum likelihood. 5 ) Estimating the parameters
of the gamma, log-normal, and Weibull mixture models fitted to the grouped data
through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve
fitted to the height - diameter observation, 7 ) Estimating parameters, computing
probability density function, cumulative distribution function, and generating
realizations from gamma shape mixture model introduced by Venturini et al. (2008)
<doi:10.1214/07-AOAS156> , 8 ) The Bayesian inference, computing probability
density function, cumulative distribution function, and generating realizations
from four-parameter Johnson SB distribution, 9 ) Robust multiple linear regression
analysis when error term follows skewed t distribution, 10 ) Estimating
parameters of a given distribution fitted to grouped data using method of maximum
likelihood, and 11 ) Estimating parameters of the Johnson SB distribution through
the Bayesian, method of moment, conditional maximum likelihood, and two - percentile
method.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 0.7.1 dated 2021-02-06 and 1.2.3 dated 2021-10-16
ForestFit-0.7.1/ForestFit/data/DBH.txt |only ForestFit-0.7.1/ForestFit/data/HW.txt |only ForestFit-0.7.1/ForestFit/data/SW.txt |only ForestFit-1.2.3/ForestFit/DESCRIPTION | 14 - ForestFit-1.2.3/ForestFit/MD5 | 13 - ForestFit-1.2.3/ForestFit/R/ForestFit.R | 349 ++++++++++++++++++--------- ForestFit-1.2.3/ForestFit/data/DBH.txt.gz |only ForestFit-1.2.3/ForestFit/data/HW.txt.gz |only ForestFit-1.2.3/ForestFit/data/SW.txt.gz |only ForestFit-1.2.3/ForestFit/man/fitJSB.Rd |only ForestFit-1.2.3/ForestFit/man/fitbayesJSB.Rd | 6 11 files changed, 260 insertions(+), 122 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (University of Bonn),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting),
Katja Schiffers [aut] (University of Bonn),
Cory Whitney [aut] (University of Bonn),
Eduardo Fernandez [aut] (University of Bonn)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.106 dated 2021-03-01 and 1.107 dated 2021-10-16
DESCRIPTION | 12 MD5 | 29 - NAMESPACE | 1 R/decisionSupport-package.R | 2 R/plot_cashflow.R | 39 - R/plot_evpi.R | 20 R/scenario_mc.R |only README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/example_decision_function.html | 645 +++++++++--------------- inst/doc/wildfire_example.html | 837 ++++++++++++-------------------- man/decisionSupport-package.Rd | 2 man/plot_cashflow.Rd | 3 man/plsr.mcSimulation.Rd | 13 man/scenario_mc.Rd |only vignettes/decisionSupport.png |only 17 files changed, 643 insertions(+), 966 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Censored Spatial Models
Description: It fits linear regression models for censored spatial data. It provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. It also offers graphical tools for assessing the fitted model. More details can be found in Ordonez et al. (2018) <doi:10.1016/j.spasta.2017.12.001>.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between CensSpatial versions 2.58 dated 2020-05-04 and 2.59 dated 2021-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- man/localinfmeas.Rd | 2 +- man/summary.SAEMSpatialCens.Rd | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Functions to Calculate Optimal Fourth Down Decisions in the
National Football League
Description: A set of functions to estimate outcomes of fourth down
plays in the National Football League and obtain fourth down plays
from <https://www.nfl.com/> and <https://www.espn.com/>.
Author: Ben Baldwin [aut, cre, cph],
Sebastian Carl [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>
Diff between nfl4th versions 1.0.0 dated 2021-03-17 and 1.0.1 dated 2021-10-16
DESCRIPTION | 16 +- MD5 | 16 +- NEWS.md | 21 +-- R/helpers.R | 2 R/silence_tidy_eval_notes.R | 254 ++++++++++++++++++++++---------------------- R/wrapper.R | 40 +++++- README.md | 19 ++- man/load_4th_pbp.Rd | 4 man/nfl4th-package.Rd | 4 9 files changed, 201 insertions(+), 175 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>),
Joseph Larmarange [aut] (<https://orcid.org/0000-0001-7097-700X>),
Jessica Lavery [aut] (<https://orcid.org/0000-0002-2746-5647>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Xing Bai [ctb],
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Margie Hannum [ctb] (<https://orcid.org/0000-0002-2953-0449>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.4.2 dated 2021-07-13 and 1.5.0 dated 2021-10-16
DESCRIPTION | 48 MD5 | 295 NAMESPACE | 24 NEWS.md | 1494 - R/add_ci.R |only R/add_difference.R | 79 R/add_global_p.R | 84 R/add_n.R | 2 R/add_nevent.R | 2 R/add_overall.R | 101 R/add_p.R | 54 R/add_q.R | 24 R/add_significance_stars.R | 2 R/add_stat.R | 60 R/add_vif.R | 26 R/as_flex_table.R | 15 R/as_gt.R | 16 R/as_hux_table.R | 13 R/as_kable_extra.R | 11 R/assert_package.R |only R/combine_terms.R | 1 R/custom_tidiers.R | 109 R/deprecated.R | 45 R/inline_text.R | 171 R/modify.R | 5 R/modify_cols_merge.R |only R/modify_column_hide.R | 2 R/modify_fmt_fun.R | 2 R/plot.R | 18 R/print.R | 2 R/reexport.R | 5 R/separate_p_footnotes.R |only R/set_gtsummary_theme.R | 2 R/style_sigfig.R | 6 R/syntax.R |only R/sysdata.rda |binary R/tbl_butcher.R |only R/tbl_continuous.R |only R/tbl_cross.R | 2 R/tbl_custom_summary.R |only R/tbl_regression.R | 9 R/tbl_regression_methods.R | 6 R/tbl_split.R |only R/tbl_strata.R | 46 R/tbl_summary.R | 16 R/tbl_survfit.R | 36 R/tbl_svysummary.R | 2 R/tbl_uvregression.R | 1 R/tests.R | 14 R/theme_gtsummary.R | 2 R/utils-add_p.R | 21 R/utils-add_p_tests.R | 156 R/utils-misc.R | 33 R/utils-tbl_custom_summary.R |only R/utils-tbl_summary.R | 19 README.md | 81 build/gtsummary.pdf |30234 +++++++++++++++++----------- build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 8 inst/doc/gallery.R | 10 inst/doc/gallery.Rmd | 12 inst/doc/gallery.html | 1244 - inst/doc/gtsummary_definition.R | 95 inst/doc/gtsummary_definition.Rmd | 110 inst/doc/gtsummary_definition.html | 2782 ++ inst/doc/inline_text.html | 228 inst/doc/rmarkdown.Rmd | 4 inst/doc/rmarkdown.html | 289 inst/doc/tbl_regression.html | 608 inst/doc/tbl_summary.html | 1220 - inst/doc/themes.html | 461 man/add_ci.Rd |only man/add_difference.Rd | 2 man/add_glance.Rd | 2 man/add_global_p.Rd | 38 man/add_n.tbl_summary.Rd | 8 man/add_n.tbl_survfit.Rd | 4 man/add_nevent.tbl_survfit.Rd | 4 man/add_overall.Rd | 13 man/add_p.tbl_summary.Rd | 5 man/add_p.tbl_survfit.Rd | 6 man/add_p.tbl_svysummary.Rd | 5 man/add_q.Rd | 38 man/add_stat.Rd | 18 man/add_stat_label.Rd | 10 man/add_vif.Rd | 24 man/as_flex_table.Rd | 15 man/as_gt.Rd | 11 man/as_hux_table.Rd | 13 man/as_kable_extra.Rd | 11 man/assert_package.Rd |only man/bold_italicize_labels_levels.Rd | 11 man/combine_terms.Rd | 4 man/continuous_summary.Rd |only man/custom_tidiers.Rd | 57 man/deprecated.Rd | 21 man/figures/README-tbl_merge_ex1-1.png |binary man/figures/add_ci_ex1.png |only man/figures/add_ci_ex2.png |only man/figures/add_prop_ci_ex1.png |only man/figures/add_prop_ci_ex2.png |only man/figures/continuous_summary_ex1.png |only man/figures/modify_cols_merge_ex1.png |only man/figures/modify_cols_merge_ex2.png |only man/figures/proportion_summary_ex1.png |only man/figures/ratio_summary_ex1.png |only man/figures/separate_p_footnotes_ex1.png |only man/figures/tbl_continuous_ex1.png |only man/figures/tbl_continuous_ex2.png |only man/figures/tbl_custom_summary_ex1.png |only man/figures/tbl_custom_summary_ex2.png |only man/figures/tbl_custom_summary_ex3.png |only man/gtsummary-package.Rd | 18 man/inline_text.tbl_cross.Rd | 2 man/inline_text.tbl_regression.Rd | 4 man/inline_text.tbl_summary.Rd | 5 man/inline_text.tbl_survfit.Rd | 7 man/inline_text.tbl_uvregression.Rd | 2 man/modify.Rd | 16 man/modify_cols_merge.Rd |only man/modify_column_hide.Rd | 3 man/modify_fmt_fun.Rd | 3 man/modify_table_body.Rd | 1 man/modify_table_styling.Rd | 1 man/plot.Rd | 16 man/proportion_summary.Rd |only man/ratio_summary.Rd |only man/reexports.Rd | 3 man/separate_p_footnotes.Rd |only man/set_gtsummary_theme.Rd | 2 man/style_sigfig.Rd | 11 man/syntax.Rd |only man/tbl_butcher.Rd |only man/tbl_continuous.Rd |only man/tbl_custom_summary.Rd |only man/tbl_merge.Rd | 16 man/tbl_regression.Rd | 17 man/tbl_regression_methods.Rd | 2 man/tbl_split.Rd |only man/tbl_stack.Rd | 16 man/tbl_strata.Rd | 82 man/tbl_summary.Rd | 16 man/tbl_survfit.Rd | 8 man/tbl_survfit_errors.Rd | 6 man/tbl_svysummary.Rd | 11 man/tbl_uvregression.Rd | 17 man/tests.Rd | 14 man/theme_gtsummary.Rd | 2 tests/testthat/test-add_ci.R |only tests/testthat/test-add_difference.R | 76 tests/testthat/test-add_p.tbl_summary.R | 119 tests/testthat/test-as_flex_table.R | 4 tests/testthat/test-as_hux_table.R | 4 tests/testthat/test-as_kable.R | 4 tests/testthat/test-as_kable_extra.R | 4 tests/testthat/test-combine_terms.R | 1 tests/testthat/test-custom_tidiers.R | 9 tests/testthat/test-inline_text.R | 57 tests/testthat/test-separate_p_footnotes.R |only tests/testthat/test-tbl_continuous.R |only tests/testthat/test-tbl_custom_summary.R |only tests/testthat/test-tbl_split.R |only tests/testthat/test-tbl_summary.R | 17 tests/testthat/test-tbl_survfit.R | 5 tests/testthat/test-tbl_uvregression.R | 1 tests/testthat/test-vetted_models-survreg.R | 1 vignettes/gallery.Rmd | 12 vignettes/gtsummary_definition.Rmd | 110 vignettes/rmarkdown.Rmd | 4 170 files changed, 26551 insertions(+), 14965 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for audio manipulation and acoustic analysis, including pitch tracking,
spectral analysis, audio segmentation, pitch and formant shifting, etc.
Includes four interactive web apps for synthesizing and annotating audio,
manually correcting pitch contours, and measuring formant frequencies.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 2.3.0 dated 2021-09-06 and 2.4.0 dated 2021-10-16
soundgen-2.3.0/soundgen/R/soundgenShiny.R |only soundgen-2.4.0/soundgen/DESCRIPTION | 15 soundgen-2.4.0/soundgen/MD5 | 96 soundgen-2.4.0/soundgen/NAMESPACE | 3 soundgen-2.4.0/soundgen/NEWS | 17 soundgen-2.4.0/soundgen/R/apps.R |only soundgen-2.4.0/soundgen/R/duration.R |only soundgen-2.4.0/soundgen/R/filters.R | 15 soundgen-2.4.0/soundgen/R/shiftPitch.R | 13 soundgen-2.4.0/soundgen/R/soundgen.R | 6 soundgen-2.4.0/soundgen/R/spectrogram.R | 234 - soundgen-2.4.0/soundgen/R/surprisal.R | 8 soundgen-2.4.0/soundgen/R/timeStretch.R |only soundgen-2.4.0/soundgen/R/utilities_pitch_postprocessing.R | 4 soundgen-2.4.0/soundgen/README.md | 32 soundgen-2.4.0/soundgen/THANKS | 5 soundgen-2.4.0/soundgen/inst/doc/acoustic_analysis.Rmd | 3 soundgen-2.4.0/soundgen/inst/doc/acoustic_analysis.html | 123 soundgen-2.4.0/soundgen/inst/doc/sound_generation.html | 1343 +++++----- soundgen-2.4.0/soundgen/inst/shiny/annotation_app |only soundgen-2.4.0/soundgen/inst/shiny/formant_app/server.R | 176 - soundgen-2.4.0/soundgen/inst/shiny/formant_app/www/formant_app.js | 7 soundgen-2.4.0/soundgen/inst/shiny/pitch_app/server.R | 38 soundgen-2.4.0/soundgen/inst/shiny/pitch_app/www/pitch_app.js | 19 soundgen-2.4.0/soundgen/man/annotation_app.Rd |only soundgen-2.4.0/soundgen/man/bandpass.Rd | 6 soundgen-2.4.0/soundgen/man/dot-bandpass.Rd | 4 soundgen-2.4.0/soundgen/man/dot-getDuration.Rd |only soundgen-2.4.0/soundgen/man/dot-shiftPitch.Rd | 6 soundgen-2.4.0/soundgen/man/dot-timeStretch.Rd |only soundgen-2.4.0/soundgen/man/figures/README-analysis-1.png |binary soundgen-2.4.0/soundgen/man/figures/README-synthsesis-1.png |binary soundgen-2.4.0/soundgen/man/figures/s.mp3 |binary soundgen-2.4.0/soundgen/man/filled.contour.mod.Rd | 2 soundgen-2.4.0/soundgen/man/formant_app.Rd | 2 soundgen-2.4.0/soundgen/man/getDuration.Rd |only soundgen-2.4.0/soundgen/man/pitch_app.Rd | 2 soundgen-2.4.0/soundgen/man/plotSpec.Rd | 3 soundgen-2.4.0/soundgen/man/shiftPitch.Rd | 5 soundgen-2.4.0/soundgen/man/soundgen_app.Rd | 2 soundgen-2.4.0/soundgen/man/spectrogram.Rd | 5 soundgen-2.4.0/soundgen/man/timeStretch.Rd |only soundgen-2.4.0/soundgen/vignettes/acoustic_analysis.Rmd | 3 43 files changed, 1172 insertions(+), 1025 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 2.0.1 dated 2021-10-02 and 2.0.2 dated 2021-10-16
DESCRIPTION | 8 +-- MD5 | 6 +- R/rand_completeData.R | 114 ++++++++++---------------------------------------- inst/NEWS.Rd | 6 ++ 4 files changed, 37 insertions(+), 97 deletions(-)
Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] (<https://orcid.org/0000-0001-5411-1409>),
Cameron Smith [aut] (<https://orcid.org/0000-0003-0020-5607>),
George Sugihara [aut, ccp] (<https://orcid.org/0000-0002-2863-6946>),
Ethan Deyle [aut] (<https://orcid.org/0000-0001-8704-8434>),
Erik Saberski [ctb] (<https://orcid.org/0000-0002-6475-6187>),
Hao Ye [ctb] (<https://orcid.org/0000-0002-8630-1458>),
The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>
Diff between rEDM versions 1.9.2 dated 2021-09-16 and 1.9.3 dated 2021-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++-- src/cppEDM/src/CCM.cc | 26 ++++++++++++-------------- src/cppEDM/src/Parameter.cc | 2 +- vignettes/rEDM-tutorial.html | 16 ++++++++-------- 6 files changed, 32 insertions(+), 34 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.3.0 dated 2021-06-30 and 1.3.1 dated 2021-10-16
DESCRIPTION | 11 +++++----- MD5 | 34 ++++++++++++++++++-------------- NAMESPACE | 3 ++ NEWS.md | 10 +++++++++ R/VAT.R | 8 +++---- R/ggVAT.R | 8 +++---- R/register_GA.R | 4 +-- R/register_optics.R |only R/register_tsne.R |only R/register_umap.R |only R/seriate.R | 16 +++++++-------- README.md | 17 +++++++++------- build/partial.rdb |binary inst/CITATION | 51 +++++++++++++++++++++++++++++------------------- inst/doc/seriation.pdf |binary man/VAT.Rd | 11 ++++++---- man/register_DendSer.Rd | 2 - man/register_GA.Rd | 2 - man/register_optics.Rd |only man/register_tsne.Rd |only man/register_umap.Rd |only 21 files changed, 107 insertions(+), 70 deletions(-)
Title: Random Subspace Ensemble Classification and Variable Screening
Description: We propose a general ensemble classification framework, RaSE algorithm, for the sparse classification problem. In RaSE algorithm, for each weak learner, some random subspaces are generated and the optimal one is chosen to train the model on the basis of some criterion. To be adapted to the problem, a novel criterion, ratio information criterion (RIC) is put up with based on Kullback-Leibler divergence. Besides minimizing RIC, multiple criteria can be applied, for instance, minimizing extended Bayesian information criterion (eBIC), minimizing training error, minimizing the validation error, minimizing the cross-validation error, minimizing leave-one-out error. There are various choices of base classifier, for instance, linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbour, logistic regression, decision trees, random forest, support vector machines. RaSE algorithm can also be applied to do feature ranking, providing us the importance of each feature based on the selected percentage in multiple subspaces. RaSE framework can be extended to the general prediction framework, including both classification and regression. We can use the selected percentages of variables for variable screening. The latest version added the variable screening function for both regression and classification problems.
Author: Ye Tian [aut, cre] and Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Diff between RaSEn versions 2.2.0 dated 2021-08-19 and 3.0.0 dated 2021-10-16
DESCRIPTION | 8 MD5 | 34 ++- NAMESPACE | 2 NEWS | 12 + R/RaSubset.R | 252 +++++++++++++++++++++++---- R/RaSubsetsc_c.R | 36 +-- R/RaSubsetsc_rg.R | 24 +- R/Rase.R | 420 +++++++++++++++++++++++++++++++--------------- R/predict.RaSE.R | 24 +- R/predict.super_RaSE.R |only R/print.super_RaSE.R |only inst/doc/RaSEn-demo.R | 9 inst/doc/RaSEn-demo.Rmd | 21 ++ inst/doc/RaSEn-demo.pdf |binary man/Rase.Rd | 59 +++++- man/predict.RaSE.Rd | 13 - man/predict.super_RaSE.Rd |only man/print.super_RaSE.Rd |only vignettes/RaSEn-demo.Rmd | 21 ++ vignettes/reference.bib | 9 20 files changed, 700 insertions(+), 244 deletions(-)
Title: Visualize the Climate Scenario Alignment of a Financial
Portfolio
Description: Create plots to visualize the alignment of a corporate
lending financial portfolio to climate change scenarios based on
climate indicators (production and emission intensities) across key
climate relevant sectors of the 'PACTA' methodology (Paris Agreement
Capital Transition Assessment; <https://2degrees-investing.org/>).
Financial institutions use 'PACTA' to study how their capital
allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre]
(<https://orcid.org/0000-0002-3728-0646>),
Mauro Lepore [aut, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Alex Axthelm [aut, ctr] (<https://orcid.org/0000-0001-8579-8565>),
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>
Diff between r2dii.plot versions 0.1.0 dated 2021-06-29 and 0.2.0 dated 2021-10-16
r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-10-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-11-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-4-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-5-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-5-2.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-6-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-6-2.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-6-3.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-7-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-8-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-9-1.png |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/helper.R |only r2dii.plot-0.2.0/r2dii.plot/DESCRIPTION | 21 - r2dii.plot-0.2.0/r2dii.plot/MD5 | 84 ++-- r2dii.plot-0.2.0/r2dii.plot/NAMESPACE | 12 r2dii.plot-0.2.0/r2dii.plot/NEWS.md | 74 ++- r2dii.plot-0.2.0/r2dii.plot/R/imports.R | 8 r2dii.plot-0.2.0/r2dii.plot/R/plot_emission_intensity.R | 38 + r2dii.plot-0.2.0/r2dii.plot/R/plot_techmix.R | 49 +- r2dii.plot-0.2.0/r2dii.plot/R/plot_trajectory.R | 210 ++++++---- r2dii.plot-0.2.0/r2dii.plot/R/qplot_emission_intensity.R | 3 r2dii.plot-0.2.0/r2dii.plot/R/qplot_techmix.R | 19 r2dii.plot-0.2.0/r2dii.plot/R/qplot_trajectory.R | 16 r2dii.plot-0.2.0/r2dii.plot/R/scale_colour_r2dii.R |only r2dii.plot-0.2.0/r2dii.plot/R/scale_colour_r2dii_sector.R |only r2dii.plot-0.2.0/r2dii.plot/R/scale_colour_r2dii_tech.R |only r2dii.plot-0.2.0/r2dii.plot/R/theme_2dii.R | 1 r2dii.plot-0.2.0/r2dii.plot/R/to_title.R |only r2dii.plot-0.2.0/r2dii.plot/R/utils-tests.R |only r2dii.plot-0.2.0/r2dii.plot/R/utils.R | 93 ++-- r2dii.plot-0.2.0/r2dii.plot/README.md | 50 +- r2dii.plot-0.2.0/r2dii.plot/inst/WORDLIST | 5 r2dii.plot-0.2.0/r2dii.plot/man/figures/README-unnamed-chunk-2-1.png |binary r2dii.plot-0.2.0/r2dii.plot/man/figures/README-unnamed-chunk-3-1.png |binary r2dii.plot-0.2.0/r2dii.plot/man/plot_emission_intensity.Rd | 21 - r2dii.plot-0.2.0/r2dii.plot/man/plot_techmix.Rd | 32 + r2dii.plot-0.2.0/r2dii.plot/man/plot_trajectory.Rd | 30 + r2dii.plot-0.2.0/r2dii.plot/man/r2dii.plot-package.Rd | 9 r2dii.plot-0.2.0/r2dii.plot/man/scale_colour_r2dii.Rd |only r2dii.plot-0.2.0/r2dii.plot/man/scale_colour_r2dii_sector.Rd |only r2dii.plot-0.2.0/r2dii.plot/man/scale_colour_r2dii_tech.Rd |only r2dii.plot-0.2.0/r2dii.plot/man/to_title.Rd |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/_snaps/plot_techmix.md | 4 r2dii.plot-0.2.0/r2dii.plot/tests/testthat/_snaps/scale_colour_r2dii.md |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/_snaps/scale_colour_r2dii_sector.md |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/_snaps/scale_colour_r2dii_tech.md |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-plot_emission_intensity.R | 22 + r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-plot_techmix.R | 98 +++- r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-plot_trajectory.R | 72 +++ r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-qplot_emission_intensity.R | 5 r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-qplot_techmix.R | 3 r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-qplot_trajectory.R | 25 - r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-scale_colour_r2dii.R |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-scale_colour_r2dii_sector.R |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-scale_colour_r2dii_tech.R |only r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-theme_2dii.R | 3 r2dii.plot-0.2.0/r2dii.plot/tests/testthat/test-to_title.R |only 57 files changed, 701 insertions(+), 306 deletions(-)
Title: Frequency Distribution Tables, Histograms and Polygons
Description: Perform frequency distribution tables, associated histograms
and polygons from vector, data.frame and matrix objects for
numerical and categorical variables.
Author: Jos<e9> Cl<e1>udio Faria, Enio G. Jelihovschi and Ivan B. Allaman
Maintainer: Jos<e9> Cl<e1>udio Faria <joseclaudio.faria@gmail.com>
Diff between fdth versions 1.2-5 dated 2020-04-17 and 1.2-6 dated 2021-10-16
ChangeLog | 77 +++++++++-------- DESCRIPTION | 8 - INDEX | 5 - MD5 | 54 ++++++------ NAMESPACE | 2 R/fdt.data.frame.R | 10 +- R/fdt.default.R | 18 +++- R/fdt.matrix.R | 6 - R/fdt_cat.data.frame.R | 6 - R/fdt_cat.default.R | 2 R/fdt_cat.matrix.R | 2 R/make.fdt.multiple.R | 71 +++++++++++++++- README.md | 2 build/vignette.rds |binary inst/doc/latex_fdt.pdf |binary man/fdt.Rd | 146 +++++++++++++++++++-------------- man/fdt_cat.Rd | 48 +++++------ man/fdth-package.Rd | 140 ++++++++++++++++---------------- man/make.fdt.Rd | 54 ++++++------ man/mean.fdt.Rd | 4 man/median.fdt.Rd | 4 man/mfv.Rd | 14 +-- man/plot.Rd | 211 +++++++++++++++++++++++++------------------------ man/print.Rd | 84 ++++++++++--------- man/quantile.fdt.Rd | 27 +++++- man/sd.Rd | 4 man/summary.Rd | 82 +++++++++---------- man/var.Rd | 4 28 files changed, 611 insertions(+), 474 deletions(-)
Title: Evaluating Individualized Treatment Rules
Description: Provides various statistical methods for evaluating Individualized Treatment Rules under randomized data. The provided metrics include Population Average Value (PAV), Population Average Prescription Effect (PAPE), Area Under Prescription Effect Curve (AUPEC). It also provides the tools to analyze Individualized Treatment Rules under budget constraints. Detailed reference in Imai and Li (2019) <arXiv:1905.05389>.
Author: Michael Lingzhi Li [aut, cre],
Kosuke Imai [aut]
Maintainer: Michael Lingzhi Li <mlli@mit.edu>
Diff between evalITR versions 0.2.1 dated 2021-07-07 and 0.2.2 dated 2021-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/PAPDcv.R | 4 ++-- R/PAPEcv.R | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Generate Disease-Specific Response Signatures from the
LINCS-L1000 Data
Description: Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Marieke Kuijjer [aut] (<https://orcid.org/0000-0001-6280-3130>)
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between retriever versions 0.1.0 dated 2021-10-08 and 0.2.0 dated 2021-10-15
DESCRIPTION | 9 +-- MD5 | 4 - R/retriever.R | 165 +++++++++++++++++++++++++++++----------------------------- 3 files changed, 92 insertions(+), 86 deletions(-)
Title: Life History Metrics from Matrix Population Models
Description: Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>),
Danny Buss [ctb],
Pol Capdevila [aut] (<https://orcid.org/0000-0002-2842-4302>),
Hal Caswell [aut] (<https://orcid.org/0000-0003-4394-6894>),
Judy P. Che-Castaldo [aut] (<https://orcid.org/0000-0002-9118-9202>),
John Jackson [aut] (<https://orcid.org/0000-0002-4563-2840>),
Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>),
Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>),
Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>),
William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>),
Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>),
Caroline Schuette [ctb] (<https://orcid.org/0000-0002-2063-8736>),
Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>),
Chelsea C. Thomas [aut] (<https://orcid.org/0000-0002-8155-9353>)
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rage versions 1.1.0 dated 2021-07-09 and 1.2.0 dated 2021-10-15
Rage-1.1.0/Rage/R/Rage-package.R |only Rage-1.1.0/Rage/man/Rage-package.Rd |only Rage-1.2.0/Rage/DESCRIPTION | 8 Rage-1.2.0/Rage/MD5 | 182 ++++----- Rage-1.2.0/Rage/NAMESPACE | 2 Rage-1.2.0/Rage/NEWS.md | 9 Rage-1.2.0/Rage/R/entropy_d.R | 19 Rage-1.2.0/Rage/R/entropy_k.R | 6 Rage-1.2.0/Rage/R/gen_time.R | 14 Rage-1.2.0/Rage/R/life_expect.R | 19 Rage-1.2.0/Rage/R/lifetable_convert.R | 38 + Rage-1.2.0/Rage/R/longevity.R | 19 Rage-1.2.0/Rage/R/mature_.R | 22 - Rage-1.2.0/Rage/R/mpm_collapse.R | 22 - Rage-1.2.0/Rage/R/mpm_rearrange.R | 14 Rage-1.2.0/Rage/R/mpm_split.R | 16 Rage-1.2.0/Rage/R/mpm_standardize.R | 21 - Rage-1.2.0/Rage/R/mpm_to_.R | 62 +-- Rage-1.2.0/Rage/R/mpm_to_table.R | 278 +++++++++----- Rage-1.2.0/Rage/R/name_stages.R | 32 - Rage-1.2.0/Rage/R/net_repro_rate.R | 13 Rage-1.2.0/Rage/R/perturb_matrix.R | 11 Rage-1.2.0/Rage/R/perturb_stochastic.R | 6 Rage-1.2.0/Rage/R/perturb_trans.R | 25 - Rage-1.2.0/Rage/R/perturb_vr.R | 23 - Rage-1.2.0/Rage/R/plot_life_cycle.R | 10 Rage-1.2.0/Rage/R/pop_vectors.R | 13 Rage-1.2.0/Rage/R/qsd_converge.R | 60 +-- Rage-1.2.0/Rage/R/repro_stages.R | 19 Rage-1.2.0/Rage/R/shape_rep.R | 14 Rage-1.2.0/Rage/R/shape_surv.R | 59 +- Rage-1.2.0/Rage/R/standard_stages.R | 12 Rage-1.2.0/Rage/R/utils.R | 48 +- Rage-1.2.0/Rage/R/vital_rates.R | 30 - Rage-1.2.0/Rage/R/vr.R | 35 - Rage-1.2.0/Rage/R/vr_mat.R | 12 Rage-1.2.0/Rage/R/vr_vec.R | 10 Rage-1.2.0/Rage/README.md | 78 ++- Rage-1.2.0/Rage/build/vignette.rds |binary Rage-1.2.0/Rage/inst/WORDLIST | 11 Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.R | 19 Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.Rmd | 21 - Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.html | 141 ++----- Rage-1.2.0/Rage/inst/doc/a02_VitalRates.R | 10 Rage-1.2.0/Rage/inst/doc/a02_VitalRates.Rmd | 153 +------ Rage-1.2.0/Rage/inst/doc/a02_VitalRates.html | 15 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.R | 4 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.Rmd | 15 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.html | 39 + Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.R | 56 +- Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.Rmd | 57 +- Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.html | 79 ++- Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.R |only Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.Rmd |only Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.html |only Rage-1.2.0/Rage/man/age_from_stage.Rd | 62 +-- Rage-1.2.0/Rage/man/entropy_d.Rd | 16 Rage-1.2.0/Rage/man/entropy_k.Rd | 2 Rage-1.2.0/Rage/man/figures/unnamed-chunk-9-1.png |binary Rage-1.2.0/Rage/man/gen_time.Rd | 12 Rage-1.2.0/Rage/man/life_expect.Rd | 15 Rage-1.2.0/Rage/man/lifetable_convert.Rd | 38 + Rage-1.2.0/Rage/man/longevity.Rd | 16 Rage-1.2.0/Rage/man/mpm_collapse.Rd | 15 Rage-1.2.0/Rage/man/mpm_rearrange.Rd | 12 Rage-1.2.0/Rage/man/mpm_split.Rd | 16 Rage-1.2.0/Rage/man/mpm_standardize.Rd | 20 - Rage-1.2.0/Rage/man/mpm_to_table.Rd | 138 ++++-- Rage-1.2.0/Rage/man/name_stages.Rd | 16 Rage-1.2.0/Rage/man/net_repro_rate.Rd | 10 Rage-1.2.0/Rage/man/perturb_matrix.Rd | 4 Rage-1.2.0/Rage/man/perturb_trans.Rd | 14 Rage-1.2.0/Rage/man/perturb_vr.Rd | 16 Rage-1.2.0/Rage/man/plot_life_cycle.Rd | 6 Rage-1.2.0/Rage/man/pop_vectors.Rd | 10 Rage-1.2.0/Rage/man/qsd_converge.Rd | 46 +- Rage-1.2.0/Rage/man/repro_maturity.Rd | 19 Rage-1.2.0/Rage/man/repro_stages.Rd | 15 Rage-1.2.0/Rage/man/shape_rep.Rd | 4 Rage-1.2.0/Rage/man/shape_surv.Rd | 38 + Rage-1.2.0/Rage/man/standard_stages.Rd | 6 Rage-1.2.0/Rage/man/vital_rates.Rd | 10 Rage-1.2.0/Rage/man/vr.Rd | 35 - Rage-1.2.0/Rage/man/vr_mat.Rd | 8 Rage-1.2.0/Rage/man/vr_vec.Rd | 10 Rage-1.2.0/Rage/tests/testthat/test-mpm_to_.R | 12 Rage-1.2.0/Rage/tests/testthat/test-mpm_to_table.R | 1 Rage-1.2.0/Rage/tests/testthat/test-qsd_converge.R | 4 Rage-1.2.0/Rage/tests/testthat/test-vr.R | 4 Rage-1.2.0/Rage/tests/testthat/test-vr_vec.R | 4 Rage-1.2.0/Rage/vignettes/a01_GettingStarted.Rmd | 21 - Rage-1.2.0/Rage/vignettes/a02_VitalRates.Rmd | 153 +------ Rage-1.2.0/Rage/vignettes/a03_LifeHistoryTraits.Rmd | 15 Rage-1.2.0/Rage/vignettes/a04_AgeFromStage.Rmd | 57 +- Rage-1.2.0/Rage/vignettes/a05_SuggestedQualityControl.Rmd |only 95 files changed, 1427 insertions(+), 1354 deletions(-)
Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then
applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU.
The relevant papers are
a) Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>.
b) Tsagris M. (2021). The FEDHC Bayesian network learning algorithm. <arXiv:2012.00113>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 0.5 dated 2021-03-21 and 0.6 dated 2021-10-15
DESCRIPTION | 20 +++---- MD5 | 81 ++++++++++++++++------------- NAMESPACE | 9 +-- R/big_read.R | 2 R/corpairs.R |only R/fedhc.R | 2 R/fedhc.boot.R |only R/fedhc.skel.R | 102 ------------------------------------- R/fedhc.skel.boot.R | 9 +-- R/fedtabu.R | 2 R/fedtabu.boot.R |only R/mmhc.R | 4 - R/mmhc.boot.R |only R/mmhc.skel.R | 128 ----------------------------------------------- R/mmhc.skel.boot.R | 9 +-- R/mmtabu.R | 2 R/mmtabu.boot.R |only R/pchc.R | 2 R/pchc.boot.R |only R/pchc.skel.R | 2 R/pchc.skel.boot.R | 9 +-- R/pcor.R | 6 +- R/pctabu.R | 2 R/pctabu.boot.R |only man/auc.Rd | 4 - man/big_read.Rd | 2 man/bn.skel.utils.Rd | 2 man/bnplot.Rd | 2 man/conf.edge.lower.Rd | 2 man/cor.fbed.Rd | 2 man/corpairs.Rd |only man/correls.Rd | 2 man/cortest.Rd | 2 man/fedhc.Rd | 6 +- man/fedhc.boot.Rd |only man/fedhc.skel.Rd | 26 +++++---- man/g2test_univariate.Rd | 2 man/mmhc.Rd | 2 man/mmhc.boot.Rd |only man/mmhc.skel.Rd | 2 man/mmpc.Rd | 2 man/pc.sel.Rd | 2 man/pchc-package.Rd | 6 +- man/pchc.Rd | 6 +- man/pchc.boot.Rd |only man/rbn.Rd | 2 man/rbn2.Rd | 4 + 47 files changed, 125 insertions(+), 344 deletions(-)
Title: Downloading, Reading and Analysing POF Microdata
Description: Provides tools for downloading, reading and analysing the POF,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between POFIBGE versions 0.1.3 dated 2021-06-24 and 0.1.4 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/example.R | 3 ++- R/get_pof.R | 6 +++++- R/pof_deflator.R | 2 +- R/pof_design.R | 17 +++++++++-------- R/pof_labeller.R | 2 +- R/read_pof.R | 3 ++- README.md | 4 ++-- 9 files changed, 34 insertions(+), 27 deletions(-)
Title: Downloading, Reading and Analysing PNS Microdata
Description: Provides tools for downloading, reading and analysing the PNS,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between PNSIBGE versions 0.1.4 dated 2021-06-24 and 0.1.5 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get_pns.R | 6 +++++- R/pns_deflator.R | 2 +- R/pns_design.R | 17 +++++++++-------- R/pns_labeller.R | 2 +- R/read_pns.R | 3 ++- README.md | 4 ++-- 8 files changed, 31 insertions(+), 25 deletions(-)
Title: Read Stable Isotope Data Files
Description: Interface to the raw data file formats commonly encountered in scientific disciplines that make use of stable isotopes.
Author: Sebastian Kopf [aut, cre] (<https://orcid.org/0000-0002-2044-0201>),
Brett Davidheiser-Kroll [aut] (<https://orcid.org/0000-0002-6153-7851>),
Ilja Kocken [aut] (<https://orcid.org/0000-0003-2196-8718>)
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>
Diff between isoreader versions 1.3.0 dated 2021-02-16 and 1.3.1 dated 2021-10-15
DESCRIPTION | 11 MD5 | 42 - R/isoread.R | 1 build/vignette.rds |binary inst/doc/continuous_flow.R | 24 inst/doc/continuous_flow.Rmd | 6 inst/doc/continuous_flow.html | 1119 ++++++++++++++++-------------------------- inst/doc/development.html | 561 ++++++--------------- inst/doc/dual_inlet.R | 24 inst/doc/dual_inlet.Rmd | 6 inst/doc/dual_inlet.html | 971 +++++++++++++----------------------- inst/doc/operations.html | 899 ++++++++++++--------------------- inst/doc/quick_start.R | 18 inst/doc/quick_start.Rmd | 12 inst/doc/quick_start.html | 405 +++------------ inst/doc/scan.R | 24 inst/doc/scan.Rmd | 4 inst/doc/scan.html | 606 +++++++--------------- vignettes/continuous_flow.Rmd | 6 vignettes/dual_inlet.Rmd | 6 vignettes/quick_start.Rmd | 12 vignettes/scan.Rmd | 4 22 files changed, 1710 insertions(+), 3051 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.4 dated 2021-09-30 and 0.2.5 dated 2021-10-15
dm-0.2.4/dm/man/sql_schema_create.Rd |only dm-0.2.4/dm/man/sql_schema_drop.Rd |only dm-0.2.4/dm/man/sql_schema_exists.Rd |only dm-0.2.4/dm/man/sql_schema_list.Rd |only dm-0.2.5/dm/DESCRIPTION | 15 - dm-0.2.5/dm/MD5 | 158 +++++----- dm-0.2.5/dm/NAMESPACE | 46 +-- dm-0.2.5/dm/NEWS.md | 28 + dm-0.2.5/dm/R/db-helpers.R | 93 +++--- dm-0.2.5/dm/R/db-interface.R | 53 --- dm-0.2.5/dm/R/deprecated.R | 55 +++ dm-0.2.5/dm/R/dm-from-src.R | 1 dm-0.2.5/dm/R/dm.R | 19 - dm-0.2.5/dm/R/dplyr.R | 42 +- dm-0.2.5/dm/R/error-helpers.R | 13 dm-0.2.5/dm/R/foreign-keys.R | 32 +- dm-0.2.5/dm/R/global.R | 2 dm-0.2.5/dm/R/import.R | 4 dm-0.2.5/dm/R/learn.R | 5 dm-0.2.5/dm/R/paste.R | 28 + dm-0.2.5/dm/R/rows-db.R | 238 ++++++---------- dm-0.2.5/dm/R/schema.R | 208 ++++++++------ dm-0.2.5/dm/R/upgrade.R | 11 dm-0.2.5/dm/R/waldo.R |only dm-0.2.5/dm/R/zoom.R | 8 dm-0.2.5/dm/R/zzz.R | 27 + dm-0.2.5/dm/README.md | 2 dm-0.2.5/dm/inst/doc/dm.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-copy.html | 12 dm-0.2.5/dm/inst/doc/howto-dm-db.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-df.html | 16 - dm-0.2.5/dm/inst/doc/howto-dm-rows.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-theory.html | 16 - dm-0.2.5/dm/inst/doc/tech-dm-cdm.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-class.html | 28 - dm-0.2.5/dm/inst/doc/tech-dm-draw.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-filter.html | 22 - dm-0.2.5/dm/inst/doc/tech-dm-join.html | 18 - dm-0.2.5/dm/inst/doc/tech-dm-low-level.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-zoom.Rmd | 8 dm-0.2.5/dm/inst/doc/tech-dm-zoom.html | 3 dm-0.2.5/dm/man/db_schema_create.Rd |only dm-0.2.5/dm/man/db_schema_drop.Rd |only dm-0.2.5/dm/man/db_schema_exists.Rd |only dm-0.2.5/dm/man/db_schema_list.Rd |only dm-0.2.5/dm/man/deprecated.Rd | 15 + dm-0.2.5/dm/man/dm_add_fk.Rd | 12 dm-0.2.5/dm/man/dm_get_all_fks.Rd | 1 dm-0.2.5/dm/man/dplyr_table_manipulation.Rd | 11 dm-0.2.5/dm/tests/testthat/_snaps/add-tbl.md | 23 + dm-0.2.5/dm/tests/testthat/_snaps/bind.md | 45 ++- dm-0.2.5/dm/tests/testthat/_snaps/check_suggested.md | 19 - dm-0.2.5/dm/tests/testthat/_snaps/disambiguate.md | 8 dm-0.2.5/dm/tests/testthat/_snaps/dm.md | 24 - dm-0.2.5/dm/tests/testthat/_snaps/dplyr.md | 276 +++++++++---------- dm-0.2.5/dm/tests/testthat/_snaps/error-helpers.md | 8 dm-0.2.5/dm/tests/testthat/_snaps/filter-dm.md | 17 + dm-0.2.5/dm/tests/testthat/_snaps/foreign-keys.md | 100 ++++-- dm-0.2.5/dm/tests/testthat/_snaps/paste.md | 88 ++++-- dm-0.2.5/dm/tests/testthat/_snaps/primary-keys.md | 112 +++---- dm-0.2.5/dm/tests/testthat/_snaps/rows-db.md | 47 +-- dm-0.2.5/dm/tests/testthat/_snaps/select-tbl.md | 5 dm-0.2.5/dm/tests/testthat/_snaps/select.md | 62 ++-- dm-0.2.5/dm/tests/testthat/_snaps/tidyr.md | 112 +++---- dm-0.2.5/dm/tests/testthat/_snaps/upgrade.md |only dm-0.2.5/dm/tests/testthat/_snaps/waldo.md |only dm-0.2.5/dm/tests/testthat/_snaps/zoom.md | 38 +- dm-0.2.5/dm/tests/testthat/dm/v2.rds |only dm-0.2.5/dm/tests/testthat/dm/v2_zoomed.rds |only dm-0.2.5/dm/tests/testthat/helper-config-db.R | 3 dm-0.2.5/dm/tests/testthat/helper-src.R | 2 dm-0.2.5/dm/tests/testthat/test-bind.R | 4 dm-0.2.5/dm/tests/testthat/test-check_suggested.R | 11 dm-0.2.5/dm/tests/testthat/test-db-interface.R | 53 ++- dm-0.2.5/dm/tests/testthat/test-dplyr.R | 81 ++++- dm-0.2.5/dm/tests/testthat/test-error-helpers.R | 2 dm-0.2.5/dm/tests/testthat/test-foreign-keys.R | 19 + dm-0.2.5/dm/tests/testthat/test-learn.R | 4 dm-0.2.5/dm/tests/testthat/test-paste.R | 5 dm-0.2.5/dm/tests/testthat/test-rows-db.R | 140 ++++++--- dm-0.2.5/dm/tests/testthat/test-schema.R | 91 +++--- dm-0.2.5/dm/tests/testthat/test-upgrade.R | 58 +++ dm-0.2.5/dm/tests/testthat/test-validate.R | 2 dm-0.2.5/dm/tests/testthat/test-waldo.R |only dm-0.2.5/dm/tests/testthat/test-zoom.R | 7 dm-0.2.5/dm/tests/testthat/test-zzx-deprecated.R | 2 dm-0.2.5/dm/vignettes/tech-dm-zoom.Rmd | 8 87 files changed, 1649 insertions(+), 1101 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Richard FitzJohn [ctb],
Brandon Bertelsen [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.12 dated 2021-04-05 and 0.0.13 dated 2021-10-15
DESCRIPTION | 16 - MD5 | 27 +- NAMESPACE | 1 NEWS.md | 28 +- R/ark.R | 185 +++++++++++--- R/bulk_importers.R | 59 +++- R/streamable_table.R | 75 +++++- README.md | 123 ++++++++- build/vignette.rds |binary inst/doc/arkdb.html | 475 +++++++++++--------------------------- man/ark.Rd | 16 + man/arkdb-package.Rd | 1 man/streamable_parquet.Rd |only tests/testthat/test-arkdb.R | 194 +++++++++++++++ tests/testthat/test-bulk-import.R | 89 ++++--- 15 files changed, 807 insertions(+), 482 deletions(-)
Title: Utilities for using the 'COM(P)ADRE' Matrix Model Database
Description: Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>),
Danny Buss [aut],
Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>),
Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>),
William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>),
Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>),
Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>),
Julia Jones [aut] (<https://orcid.org/0000-0001-9223-1778>),
Gesa Römer [aut] (<https://orcid.org/0000-0002-4859-5870>),
Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>)
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rcompadre versions 1.0.0 dated 2021-04-30 and 1.1.0 dated 2021-10-15
DESCRIPTION | 23 +- MD5 | 119 +++++++------- NAMESPACE | 2 NEWS.md | 12 + R/cdb_build_cdb.R |only R/cdb_fetch.R | 11 + R/cdb_flag.R | 231 ++++++++++++++++++---------- R/cdb_id_studies.R | 6 README.md | 36 ++-- build/vignette.rds |binary data/Comadre.rda |binary data/Compadre.rda |binary data/CompadreLegacy.rda |binary inst/WORDLIST | 7 inst/doc/a01_GettingStarted.Rmd | 25 +-- inst/doc/a01_GettingStarted.html | 94 ++++++----- inst/doc/a02_RcompadreTidy.R | 20 +- inst/doc/a02_RcompadreTidy.Rmd | 52 +++--- inst/doc/a02_RcompadreTidy.html | 70 ++++---- inst/doc/a03_VectorisingRcompadre.R | 58 +++---- inst/doc/a03_VectorisingRcompadre.Rmd | 75 ++++----- inst/doc/a03_VectorisingRcompadre.html | 98 +++++++---- inst/doc/a04_ObtainingReferences.R | 4 inst/doc/a04_ObtainingReferences.Rmd | 8 inst/doc/a04_ObtainingReferences.html | 56 ++++-- inst/doc/a05_UsingYourOwnData.R |only inst/doc/a05_UsingYourOwnData.Rmd |only inst/doc/a05_UsingYourOwnData.html |only man/Compadre.Rd | 4 man/cdb_build_cdb.Rd |only man/cdb_fetch.Rd | 7 man/cdb_flag.Rd | 91 ++++++++--- man/cdb_id_studies.Rd | 6 man/cdb_metadata.Rd | 1 tests/testthat/test-ClassUnion.R | 2 tests/testthat/test-CompadreDB-Methods.R | 2 tests/testthat/test-CompadreDB-Subsetting.R | 2 tests/testthat/test-CompadreDB-Tidyverse.R | 4 tests/testthat/test-CompadreDB.R | 2 tests/testthat/test-CompadreMat.R | 2 tests/testthat/test-as_cdb.R | 2 tests/testthat/test-cdb_build_cdb.R |only tests/testthat/test-cdb_check_species.R | 2 tests/testthat/test-cdb_collapse.R | 2 tests/testthat/test-cdb_compare.R | 2 tests/testthat/test-cdb_fetch.R | 2 tests/testthat/test-cdb_flag.R | 2 tests/testthat/test-cdb_flatten.R | 2 tests/testthat/test-cdb_id.R | 2 tests/testthat/test-cdb_id_stages.R | 2 tests/testthat/test-cdb_id_studies.R | 2 tests/testthat/test-cdb_mean_matF.R | 2 tests/testthat/test-cdb_metadata.R | 2 tests/testthat/test-cdb_rbind.R | 2 tests/testthat/test-cdb_unflatten.R | 2 tests/testthat/test-cdb_unnest.R | 2 tests/testthat/test-mpm_mean.R | 6 tests/testthat/test-mpm_methods.R | 2 tests/testthat/test-string_representation.R | 2 vignettes/a01_GettingStarted.Rmd | 25 +-- vignettes/a02_RcompadreTidy.Rmd | 52 +++--- vignettes/a03_VectorisingRcompadre.Rmd | 75 ++++----- vignettes/a04_ObtainingReferences.Rmd | 8 vignettes/a05_UsingYourOwnData.Rmd |only 64 files changed, 761 insertions(+), 569 deletions(-)
Title: Creates Plots Accompanying Bayesian Diagnostic Test Accuracy
Meta-Analyses
Description: Function to create forest plots. Functions to use posterior samples from Bayesian bivariate meta-analysis model, Bayesian hierarchical summary receiver operating characteristic (HSROC) meta-analysis model or Bayesian latent class (LC) meta-analysis model to create Summary Receiver Operating Characteristic (SROC) plots using methods described by Harbord et al (2007)<doi:10.1093/biostatistics/kxl004>.
Author: Ian Schiller [aut, cre],
Nandini Dendukuri [ctb]
Maintainer: Ian Schiller <ian.schiller@rimuhc.ca>
Diff between DTAplots versions 1.0.2.4 dated 2021-03-17 and 1.0.2.5 dated 2021-10-15
DESCRIPTION | 8 - MD5 | 17 +- NEWS | 14 ++ R/Forest.R | 211 ++++++++++++++++++----------------- R/SROC_rjags.R | 8 - data/datalist |only data/posterior_samples_Bivariate.rda |binary data/posterior_samples_LC.rda |binary man/Forest.Rd | 56 ++++++--- man/SROC_rjags.Rd | 4 10 files changed, 181 insertions(+), 137 deletions(-)
Title: Downloading, Reading and Analysing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analysing the PNAD COVID19,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between COVIDIBGE versions 0.1.5 dated 2021-06-24 and 0.1.6 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/covid_deflator.R | 2 +- R/covid_design.R | 5 +++-- R/covid_labeller.R | 2 +- R/get_covid.R | 6 +++++- R/read_covid.R | 3 ++- README.md | 4 ++-- 8 files changed, 25 insertions(+), 19 deletions(-)
Title: Create Credit State Migration (Transition) Matrices
Description: Tools to help convert credit risk data at two time points
into traditional credit state migration (aka, "transition") matrices.
At a higher level, 'migrate' is intended to help an analyst understand
how risk moved in their credit portfolio over a time interval.
References to this methodology include:
1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>.
2. Perederiy, V. (2017) <arXiv:1708.00062>.
Author: Michael Thomas [aut, cre],
Brad Lindblad [ctb]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between migrate versions 0.3.0 dated 2020-12-07 and 0.4.0 dated 2021-10-15
DESCRIPTION | 10 - LICENSE | 2 MD5 | 28 +-- NAMESPACE | 1 NEWS.md | 30 +++ R/build_matrix.R | 203 +++++++++++++---------- R/migrate.R | 378 +++++++++++++++++++++++++------------------- README.md | 91 ++++++---- build/vignette.rds |binary inst/doc/migrate.R | 43 +++-- inst/doc/migrate.Rmd | 44 +++-- inst/doc/migrate.html | 424 ++++++++++++++------------------------------------ man/build_matrix.Rd | 34 ++-- man/migrate.Rd | 74 ++++---- vignettes/migrate.Rmd | 44 +++-- 15 files changed, 700 insertions(+), 706 deletions(-)
Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.3.1 dated 2021-06-16 and 1.4.0 dated 2021-10-15
DESCRIPTION | 8 +- MD5 | 105 +++++++++++++++++++++------- NAMESPACE | 51 +++++++++++-- NEWS | 15 ++++ R/S3methods_islasso.R | 35 ++++----- R/S3methods_islasso.path.R |only R/confint_and_auxiliary.R | 33 ++++++++ R/islasso.R | 58 +++++++++++---- R/islasso.path.R |only inst/doc/islasso.R | 74 +++++++++++++++----- inst/doc/islasso.Rmd | 109 ++++++++++++++++++++++------- inst/doc/islasso.pdf |binary man/GoF.islasso.path.Rd |only man/aic.islasso.Rd | 20 ++--- man/anova.islasso.Rd | 8 +- man/confint.islasso.Rd | 29 +++++++ man/is.control.Rd | 11 +- man/islasso-internal.Rd | 12 ++- man/islasso-package.Rd | 21 +++-- man/islasso.Rd | 16 ++-- man/islasso.path.Rd |only man/plot.islasso.Rd | 12 ++- man/plot.islasso.path.Rd |only man/predict.islasso.Rd | 15 ++-- man/predict.islasso.path.Rd |only man/summary.islasso.Rd | 9 ++ man/summary.islasso.path.Rd |only src/dev_grad_hess.f90 | 53 +++++++++++--- src/init.c | 8 -- src/islasso.h | 34 +++------ src/islasso2.f90 | 147 ++++++++++++++++++++++++--------------- src/islasso_glm.f90 | 162 +++++++++++++++++++++++++------------------- src/trace_islasso.c | 32 ++++++++ vignettes/islasso.Rmd | 109 ++++++++++++++++++++++------- vignettes/islasso_cache |only 35 files changed, 840 insertions(+), 346 deletions(-)
Title: Graphical User Interface ('shiny' App) for 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian
regression models using the package 'brms' which in turn relies on
'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'shiny'
app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>),
Thomas Park [ctb, cph] ('Bootswatch' theme "United"),
Twitter, Inc. [ctb, cph] ('Bootstrap' (basis for the 'Bootswatch' theme
"United")),
Google, LLC [ctb, cph] ("Open Sans" font)
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between shinybrms versions 1.5.1 dated 2021-03-06 and 1.5.2 dated 2021-10-15
DESCRIPTION | 16 MD5 | 40 NEWS.md | 344 ++---- R/launch_shinybrms.R | 8 README.md | 82 - inst/CITATION | 15 inst/shinybrms_app/app.R | 573 ++++------ inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/006.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/007.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/008.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/009.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/005.json | 4 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/006.json | 6 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/007.json | 8 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/008.json | 8 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/009.json | 14 man/launch_shinybrms.Rd | 3 tests/testthat/test-bacteria.R | 4 tests/testthat/test-interactions.R | 2 tests/testthat/test-priors.R | 6 tests/testthat/test-react.R | 77 - 21 files changed, 589 insertions(+), 629 deletions(-)
Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in
Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 2.6-0 dated 2021-10-08 and 2.6-1 dated 2021-10-15
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary data/MLT1Ylookup.rda |binary data/MLTlookup.rda |binary 6 files changed, 13 insertions(+), 9 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vincent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between arm versions 1.11-2 dated 2020-07-27 and 1.12-2 dated 2021-10-15
CHANGELOG | 17 +++++++++++++---- DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 ---- R/balance.R | 2 +- man/lalonde.Rd | 2 +- 6 files changed, 25 insertions(+), 20 deletions(-)
Title: Tools for Analysing and Visualising Workplace Analytics Data
Description: Opinionated functions that enable easier and faster
analysis of Workplace Analytics data. There are three main types of functions in 'wpa':
(i) Standard functions create a 'ggplot' visual or a summary table based on a specific
Workplace Analytics metric; (2) Report Generation functions generate HTML reports on
a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover
more specific applications (e.g. Subject Line text mining) of Workplace Analytics data.
This package adheres to 'tidyverse' principles and works well with the pipe syntax.
'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for
simplicity.
Author: Martin Chan [aut, cre],
Carlos Morales [aut],
Mark Powers [ctb],
Ainize Cidoncha [ctb],
Rosamary Ochoa Vargas [ctb],
Tannaz Sattari [ctb],
Lucas Hogner [ctb],
Jasminder Thind [ctb],
Simone Liebal [ctb],
Aleksey Ashikhmin [ctb],
Ellen Trinklein [ctb],
Microsoft Corporation [cph]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between wpa versions 1.6.1 dated 2021-09-01 and 1.6.2 dated 2021-10-15
wpa-1.6.1/wpa/build |only wpa-1.6.1/wpa/inst/doc |only wpa-1.6.1/wpa/vignettes |only wpa-1.6.2/wpa/DESCRIPTION | 9 - wpa-1.6.2/wpa/MD5 | 51 +++----- wpa-1.6.2/wpa/NEWS.md | 6 wpa-1.6.2/wpa/R/em_data.R | 57 ++++++++- wpa-1.6.2/wpa/R/flex_index.R | 78 ++++-------- wpa-1.6.2/wpa/R/network_g2g.R | 5 wpa-1.6.2/wpa/R/network_p2p.R | 13 +- wpa-1.6.2/wpa/R/period_change.R | 2 wpa-1.6.2/wpa/R/plot_flex_index.R | 6 wpa-1.6.2/wpa/R/validation_report.R | 45 ++++++- wpa-1.6.2/wpa/R/workpatterns_area.R | 5 wpa-1.6.2/wpa/R/workpatterns_classify_bw.R | 3 wpa-1.6.2/wpa/R/workpatterns_rank.R | 182 +++++++++++++++-------------- wpa-1.6.2/wpa/R/workpatterns_report.R | 16 +- wpa-1.6.2/wpa/README.md | 10 + wpa-1.6.2/wpa/data/em_data.rda |binary wpa-1.6.2/wpa/man/em_data.Rd | 57 ++++++++- wpa-1.6.2/wpa/man/flex_index.Rd | 14 +- wpa-1.6.2/wpa/man/network_g2g.Rd | 5 wpa-1.6.2/wpa/man/network_p2p.Rd | 4 wpa-1.6.2/wpa/man/period_change.Rd | 2 wpa-1.6.2/wpa/man/validation_report.Rd | 4 wpa-1.6.2/wpa/man/workpatterns_area.Rd | 5 wpa-1.6.2/wpa/man/workpatterns_rank.Rd | 20 ++- 27 files changed, 403 insertions(+), 196 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.12.1 dated 2021-09-05 and 2.13.0 dated 2021-10-15
DESCRIPTION | 15 MD5 | 54 +- NAMESPACE | 3 R/generic.predict.rfsrc.R | 4 R/imbalanced.rfsrc.R | 17 R/impute.rfsrc.R | 51 +- R/partial.rfsrc.R | 1 R/rfsrc.R | 8 R/sidClustering.rfsrc.R | 1 R/utilities.R | 9 R/utilities.data.R | 400 +++++++++---------- R/utilities.factor.R | 4 R/utilities.imbalanced.R | 43 +- configure | 18 configure.ac | 2 inst/NEWS | 15 man/housing.Rd | 7 man/imbalanced.rfsrc.Rd | 78 ++- man/impute.rfsrc.Rd | 13 man/max.subtree.rfsrc.Rd | 10 man/nutrigenomic.Rd | 34 + man/predict.rfsrc.Rd | 6 man/randomForestSRC_package.Rd | 64 +-- man/rfsrc.Rd | 234 ++++++----- man/sidClustering.rfsrc.Rd | 6 src/R_init_randomForestSRC.c | 8 src/randomForestSRC.c | 859 ++++++++++++++++++++++++++++++++++++++--- src/randomForestSRC.h | 23 + 28 files changed, 1448 insertions(+), 539 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.4.1 dated 2021-07-13 and 0.4.2 dated 2021-10-15
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NEWS.md | 4 + README.md | 2 inst/doc/Tplyr.html | 13 ++--- inst/doc/count.html | 1 inst/doc/denom.html | 97 ++++++++++++++++++++--------------------- inst/doc/desc.html | 1 inst/doc/options.html | 1 inst/doc/shift.html | 1 inst/doc/table.html | 1 tests/testthat/test-pop_data.R | 2 12 files changed, 82 insertions(+), 71 deletions(-)
Title: Data Processing after Running 'GGIR' for Accelerometer Data
Description: Generate all necessary R/Rmd/shell files for data processing after running 'GGIR' (v2.4.0) for accelerometer data. In part 1, all csv files in the GGIR output directory were read, transformed and then merged. In part 2, the GGIR output files were checked and summarized in one excel sheet. In part 3, the merged data was cleaned according to the number of valid hours on each night and the number of valid days for each subject. In part 4, the cleaned activity data was imputed by the average Euclidean norm minus one (ENMO) over all the valid days for each subject. Finally, a comprehensive report of data processing was created using Rmarkdown, and the report includes few exploratory plots and multiple commonly used features extracted from minute level actigraphy data.
Author: Wei Guo [aut, cre],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between postGGIR versions 2.4.0 dated 2021-07-14 and 2.4.0.1 dated 2021-10-15
postGGIR-2.4.0.1/postGGIR/DESCRIPTION | 13 postGGIR-2.4.0.1/postGGIR/MD5 | 42 postGGIR-2.4.0.1/postGGIR/R/Time2.R | 6 postGGIR-2.4.0.1/postGGIR/R/part0_maincall.R | 25 postGGIR-2.4.0.1/postGGIR/R/part2_summary.pipeline.R | 13 postGGIR-2.4.0.1/postGGIR/inst/doc/features.dictionary.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.R | 101 - postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.Rmd | 379 ++-- postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.html | 880 +++++----- postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.output.description.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/doc/quickguide.postGGIR.txt |only postGGIR-2.4.0.1/postGGIR/inst/template/STUDYNAME_part0.maincall.txt | 100 - postGGIR-2.4.0.1/postGGIR/inst/template/features.dictionary.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/template/part5_postGGIR.report.Rmd | 7 postGGIR-2.4.0.1/postGGIR/inst/template/part6_postGGIR.NonWear.report.Rmd | 2 postGGIR-2.4.0.1/postGGIR/inst/template/part7a_JIVE_1_featureExtraction.Rmd | 34 postGGIR-2.4.0.1/postGGIR/inst/template/part7b_JIVE_2_featureMerge.Rmd | 6 postGGIR-2.4.0.1/postGGIR/inst/template/part7c_JIVE_3_runJIVE.Rmd |only postGGIR-2.4.0.1/postGGIR/inst/template/part7d_JIVE_4_somefeatures_weekday.Rmd |only postGGIR-2.4.0.1/postGGIR/man/afterggir.Rd | 6 postGGIR-2.4.0.1/postGGIR/vignettes/postGGIR.Rmd | 379 ++-- postGGIR-2.4.0.1/postGGIR/vignettes/postGGIR.output.description.xlsx |binary postGGIR-2.4.0/postGGIR/inst/template/part7c_JIVE_3_excelReport.Rmd |only postGGIR-2.4.0/postGGIR/inst/template/part7d_JIVE_4_runJive.Rmd |only postGGIR-2.4.0/postGGIR/inst/template/part7e_JIVE_5_somefeatures_weekday.Rmd |only 25 files changed, 1175 insertions(+), 818 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.7.0 dated 2021-07-30 and 1.8.0 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mice.impute.2l.2stage.bin.intern.R | 9 ++++----- R/mice.impute.2l.2stage.pois.intern.R | 9 ++++----- R/mice.impute.2l.glm.norm.R | 2 +- man/mice.par.Rd | 2 +- 6 files changed, 19 insertions(+), 21 deletions(-)
Title: Fit and Simulate Generalised Hypergeometric Ensembles of Graphs
Description: Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG).
To learn how to use it, check the vignettes for a quick tutorial.
Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300>
together with those relevant references from the one listed below.
The package is based on the research developed at the Chair of Systems Design, ETH Zurich.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>.
Casiraghi, G., (2017) <arXiv:1702.02048>
Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926>
Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>.
Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>.
Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.
Author: Giona Casiraghi [aut, cre] (<https://orcid.org/0000-0003-0233-5747>),
Vahan Nanumyan [aut] (<https://orcid.org/0000-0001-9054-3217>),
Laurence Brandenberger [ctb],
Giacomo Vaccario [ctb]
Maintainer: Giona Casiraghi <giona@ethz.ch>
Diff between ghypernet versions 1.0.1 dated 2020-10-21 and 1.1.0 dated 2021-10-15
ghypernet-1.0.1/ghypernet/man/ComputeXi.Rd |only ghypernet-1.0.1/ghypernet/man/linkSignificance.Rd |only ghypernet-1.1.0/ghypernet/DESCRIPTION | 21 ghypernet-1.1.0/ghypernet/MD5 | 90 ghypernet-1.1.0/ghypernet/NAMESPACE | 3 ghypernet-1.1.0/ghypernet/NEWS.md | 19 ghypernet-1.1.0/ghypernet/R/auxilliary.R | 11 ghypernet-1.1.0/ghypernet/R/blockmodel.R | 172 ghypernet-1.1.0/ghypernet/R/computexi.R | 4 ghypernet-1.1.0/ghypernet/R/data.R | 4 ghypernet-1.1.0/ghypernet/R/deprecated.R | 16 ghypernet-1.1.0/ghypernet/R/endogenousstats.R | 99 ghypernet-1.1.0/ghypernet/R/ghype.R | 4 ghypernet-1.1.0/ghypernet/R/igraphintegration.R | 2 ghypernet-1.1.0/ghypernet/R/logl.R | 2 ghypernet-1.1.0/ghypernet/R/nrm.R | 6 ghypernet-1.1.0/ghypernet/R/nrmSelection.R | 2 ghypernet-1.1.0/ghypernet/R/omega.R | 2 ghypernet-1.1.0/ghypernet/R/residuals.nrm.R | 2 ghypernet-1.1.0/ghypernet/R/stats.R | 2 ghypernet-1.1.0/ghypernet/R/tests.R | 41 ghypernet-1.1.0/ghypernet/README.md | 13 ghypernet-1.1.0/ghypernet/build/vignette.rds |binary ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.R | 4 ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.Rmd | 6 ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.html | 321 - ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.R | 83 ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.Rmd | 159 ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.html | 3024 +++++++-------- ghypernet-1.1.0/ghypernet/inst/doc/tutorial.html | 575 -- ghypernet-1.1.0/ghypernet/man/FitOmega.Rd | 2 ghypernet-1.1.0/ghypernet/man/bccm.Rd | 2 ghypernet-1.1.0/ghypernet/man/compute_xi.Rd |only ghypernet-1.1.0/ghypernet/man/contacts.adj.Rd | 2 ghypernet-1.1.0/ghypernet/man/get_zero_dummy.Rd |only ghypernet-1.1.0/ghypernet/man/highschool.multiplex.Rd | 2 ghypernet-1.1.0/ghypernet/man/homophily_stat.Rd | 16 ghypernet-1.1.0/ghypernet/man/link_significance.Rd |only ghypernet-1.1.0/ghypernet/man/logl.Rd | 2 ghypernet-1.1.0/ghypernet/man/mcfaddenR2.Rd | 2 ghypernet-1.1.0/ghypernet/man/nrm.Rd | 4 ghypernet-1.1.0/ghypernet/man/reciprocity_stat.Rd | 13 ghypernet-1.1.0/ghypernet/man/residuals.nrm.Rd | 2 ghypernet-1.1.0/ghypernet/man/sharedPartner_stat.Rd | 17 ghypernet-1.1.0/ghypernet/tests |only ghypernet-1.1.0/ghypernet/vignettes/Significantlinks.Rmd | 6 ghypernet-1.1.0/ghypernet/vignettes/Tutorial_NRM.Rmd | 159 47 files changed, 2295 insertions(+), 2621 deletions(-)
Title: Empirical Bayes Estimation of Dynamic Bayesian Networks
Description: Infer the adjacency matrix of a
network from time course data using an empirical Bayes
estimation procedure based on Dynamic Bayesian Networks.
Author: Andrea Rau <andrea.rau@inra.fr>
Maintainer: Andrea Rau <andrea.rau@inra.fr>
Diff between ebdbNet versions 1.2.5 dated 2016-11-21 and 1.2.6 dated 2021-10-15
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NAMESPACE | 2 +- NEWS | 8 ++++++++ R/ebdbn.R | 26 ++++++++++++++++++++------ src/RunWrapGen.c | 13 ++++++++++--- src/init.c |only 7 files changed, 51 insertions(+), 21 deletions(-)
Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the
illness-death model and or the three-state progressive model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>),
Javier Roca-Pardinas [aut] (<https://orcid.org/0000-0003-3107-4515>),
Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>)
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between TPmsm versions 1.2.4 dated 2021-10-09 and 1.2.5 dated 2021-10-15
TPmsm-1.2.4/TPmsm/LICENSE |only TPmsm-1.2.5/TPmsm/DESCRIPTION | 10 - TPmsm-1.2.5/TPmsm/MD5 | 95 +++++------ TPmsm-1.2.5/TPmsm/README.md | 130 +++++++-------- TPmsm-1.2.5/TPmsm/build/partial.rdb |binary TPmsm-1.2.5/TPmsm/inst/CITATION | 2 TPmsm-1.2.5/TPmsm/inst/NEWS.Rd | 218 +++++++++++++------------- TPmsm-1.2.5/TPmsm/inst/doc/TPmsm.pdf |binary TPmsm-1.2.5/TPmsm/man/TPmsm-package.Rd | 182 ++++++++++----------- TPmsm-1.2.5/TPmsm/man/TPmsmOut.Rd | 6 TPmsm-1.2.5/TPmsm/man/as.data.frame.survTP.Rd | 6 TPmsm-1.2.5/TPmsm/man/bladderTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/colonTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/contour.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/corrTP.Rd | 6 TPmsm-1.2.5/TPmsm/man/dgpTP.Rd | 10 - TPmsm-1.2.5/TPmsm/man/heartTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/image.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/lines.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/lines.TPmsm.Rd | 2 TPmsm-1.2.5/TPmsm/man/plot.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/plot.TPmsm.Rd | 2 TPmsm-1.2.5/TPmsm/man/setPackageSeedTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/setSeedTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/setThreadsTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/survTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/transAJ.Rd | 2 TPmsm-1.2.5/TPmsm/man/transIPCW.Rd | 8 TPmsm-1.2.5/TPmsm/man/transKMPW.Rd | 6 TPmsm-1.2.5/TPmsm/man/transKMW.Rd | 6 TPmsm-1.2.5/TPmsm/man/transLIN.Rd | 8 TPmsm-1.2.5/TPmsm/man/transLS.Rd | 10 - TPmsm-1.2.5/TPmsm/man/transPAJ.Rd | 6 TPmsm-1.2.5/TPmsm/src/BtoTPCmsm.c | 1 TPmsm-1.2.5/TPmsm/src/BtoTPmsm.c | 1 TPmsm-1.2.5/TPmsm/src/RngArray.c | 1 TPmsm-1.2.5/TPmsm/src/init.c | 2 TPmsm-1.2.5/TPmsm/src/logistic.c | 1 TPmsm-1.2.5/TPmsm/src/logistic.h | 1 TPmsm-1.2.5/TPmsm/src/toTPCmsm.c | 1 TPmsm-1.2.5/TPmsm/src/toTPmsm.c | 1 TPmsm-1.2.5/TPmsm/src/transAJ.c | 1 TPmsm-1.2.5/TPmsm/src/transIPCW1.c | 1 TPmsm-1.2.5/TPmsm/src/transKMPW1.c | 1 TPmsm-1.2.5/TPmsm/src/transKMPW2.c | 1 TPmsm-1.2.5/TPmsm/src/transKMW.c | 1 TPmsm-1.2.5/TPmsm/src/transLIN1.c | 1 TPmsm-1.2.5/TPmsm/src/transPAJ.c | 1 TPmsm-1.2.5/TPmsm/src/unload.c | 1 49 files changed, 386 insertions(+), 394 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] (Bundled PCRE2 code),
Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code),
University of Cambridge [cph] (Bundled PCRE2 code),
Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with
PCRE2),
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash
code)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.3 dated 2021-10-10 and 0.15.4 dated 2021-10-15
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 9 +++--- inst/doc/vignette.html | 2 - inst/icelandic_words_500_utf8.txt |only tests/tests.r | 54 ++++++++++++++++++++++++++++++-------- 6 files changed, 56 insertions(+), 20 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction
package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>;
Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains
the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness
Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636.
<doi:10.1029/2020JG005636>;
Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing
global MODIS EVI time series on the Google Earth Engine.
ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24;
Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology
on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013).
Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Diff between phenofit versions 0.2.7 dated 2020-04-02 and 0.3.2 dated 2021-10-15
phenofit-0.2.7/phenofit/R/S3_fFIT.R |only phenofit-0.2.7/phenofit/R/adjust_pos.R |only phenofit-0.2.7/phenofit/R/doubleLogistics.R |only phenofit-0.2.7/phenofit/R/fixYearBroken.R |only phenofit-0.2.7/phenofit/R/phenofit_plot.R |only phenofit-0.2.7/phenofit/R/season.R |only phenofit-0.2.7/phenofit/R/temp |only phenofit-0.2.7/phenofit/R/tidyFitPheno.R |only phenofit-0.2.7/phenofit/inst/examples/compare_other_pkgs.R |only phenofit-0.2.7/phenofit/inst/examples/ex-season.R |only phenofit-0.2.7/phenofit/man/check_season.Rd |only phenofit-0.2.7/phenofit/man/examples |only phenofit-0.2.7/phenofit/man/julia_init.Rd |only phenofit-0.2.7/phenofit/man/phenofit_plot.Rd |only phenofit-0.2.7/phenofit/man/tidyFitPheno.Rd |only phenofit-0.2.7/phenofit/man/tidy_MOD13.gee.Rd |only phenofit-0.2.7/phenofit/src/season.cpp |only phenofit-0.2.7/phenofit/tests/testthat/Rplots.pdf |only phenofit-0.2.7/phenofit/tests/testthat/test-season3y.R |only phenofit-0.3.2/phenofit/DESCRIPTION | 33 phenofit-0.3.2/phenofit/MD5 | 252 +++--- phenofit-0.3.2/phenofit/NAMESPACE | 65 + phenofit-0.3.2/phenofit/NEWS.md | 81 +- phenofit-0.3.2/phenofit/R/D.R | 54 - phenofit-0.3.2/phenofit/R/I_optim.R | 20 phenofit-0.3.2/phenofit/R/PhenoExtractMeth.R | 104 +- phenofit-0.3.2/phenofit/R/RcppExports.R | 6 phenofit-0.3.2/phenofit/R/S3_fFITs.R | 37 phenofit-0.3.2/phenofit/R/add_HeadTail.R | 15 phenofit-0.3.2/phenofit/R/backval.R | 29 phenofit-0.3.2/phenofit/R/check_input.R | 485 ++++++------- phenofit-0.3.2/phenofit/R/curvefit.R | 58 - phenofit-0.3.2/phenofit/R/curvefits.R | 189 +++-- phenofit-0.3.2/phenofit/R/data_MOD13A1.R | 16 phenofit-0.3.2/phenofit/R/deprecated_season.R |only phenofit-0.3.2/phenofit/R/derivs.R | 35 phenofit-0.3.2/phenofit/R/doubleLogistics_R.R |only phenofit-0.3.2/phenofit/R/doubleLogistics_fitting.R | 24 phenofit-0.3.2/phenofit/R/f_goal.R | 7 phenofit-0.3.2/phenofit/R/findpeaks.R | 68 + phenofit-0.3.2/phenofit/R/get_GOF.R | 37 phenofit-0.3.2/phenofit/R/get_fitting.R | 15 phenofit-0.3.2/phenofit/R/get_param.R | 6 phenofit-0.3.2/phenofit/R/get_pheno.R | 187 +++-- phenofit-0.3.2/phenofit/R/global.R | 11 phenofit-0.3.2/phenofit/R/init_lambda.R | 2 phenofit-0.3.2/phenofit/R/julia.R |only phenofit-0.3.2/phenofit/R/make_legend.R | 4 phenofit-0.3.2/phenofit/R/opt_FUN.R | 2 phenofit-0.3.2/phenofit/R/opt_nlminb.R | 12 phenofit-0.3.2/phenofit/R/optim_pheno.R | 35 phenofit-0.3.2/phenofit/R/options.R |only phenofit-0.3.2/phenofit/R/phenofit-package.R | 38 - phenofit-0.3.2/phenofit/R/plot_curvefits.R |only phenofit-0.3.2/phenofit/R/plot_input.R | 34 phenofit-0.3.2/phenofit/R/plot_phenofit.R | 151 +--- phenofit-0.3.2/phenofit/R/plot_season.R | 85 +- phenofit-0.3.2/phenofit/R/process_phenofit.R |only phenofit-0.3.2/phenofit/R/process_season.R |only phenofit-0.3.2/phenofit/R/season_RoughFitting.R |only phenofit-0.3.2/phenofit/R/season_find.R |only phenofit-0.3.2/phenofit/R/season_mov.R | 298 ++++--- phenofit-0.3.2/phenofit/R/season_tools.R |only phenofit-0.3.2/phenofit/R/smooth_wHANTS.R | 4 phenofit-0.3.2/phenofit/R/smooth_wSG.R | 2 phenofit-0.3.2/phenofit/R/smooth_wWHIT.R | 6 phenofit-0.3.2/phenofit/R/smooth_wWHIT_lambda.R | 178 ++-- phenofit-0.3.2/phenofit/R/tidy_MODIS.R | 34 phenofit-0.3.2/phenofit/R/tools.R | 81 +- phenofit-0.3.2/phenofit/README.md | 341 +-------- phenofit-0.3.2/phenofit/build |only phenofit-0.3.2/phenofit/data/CA_NS6.rda |only phenofit-0.3.2/phenofit/inst/doc |only phenofit-0.3.2/phenofit/inst/examples/ex-check_input.R | 29 phenofit-0.3.2/phenofit/inst/examples/ex-curvefits.R | 37 phenofit-0.3.2/phenofit/inst/examples/ex-visual.R | 17 phenofit-0.3.2/phenofit/inst/examples/phenofit_MOD13A1.R | 24 phenofit-0.3.2/phenofit/man/CA_NS6.Rd |only phenofit-0.3.2/phenofit/man/D.Rd | 21 phenofit-0.3.2/phenofit/man/FitDL.Rd | 173 ++-- phenofit-0.3.2/phenofit/man/GOF.Rd | 96 +- phenofit-0.3.2/phenofit/man/PhenoExtractMeth.Rd | 17 phenofit-0.3.2/phenofit/man/R2_sign.Rd | 56 - phenofit-0.3.2/phenofit/man/add_HeadTail.Rd | 83 +- phenofit-0.3.2/phenofit/man/backval.Rd | 110 +- phenofit-0.3.2/phenofit/man/check_GS_HeadTail.Rd |only phenofit-0.3.2/phenofit/man/check_input.Rd | 39 - phenofit-0.3.2/phenofit/man/curvefit.Rd | 2 phenofit-0.3.2/phenofit/man/curvefits.Rd | 144 +-- phenofit-0.3.2/phenofit/man/fFIT.Rd | 2 phenofit-0.3.2/phenofit/man/fFITs.Rd | 76 +- phenofit-0.3.2/phenofit/man/find_season.peaks.Rd |only phenofit-0.3.2/phenofit/man/getRealDate.Rd | 54 - phenofit-0.3.2/phenofit/man/get_GOF.Rd | 113 +-- phenofit-0.3.2/phenofit/man/get_fitting.Rd | 74 - phenofit-0.3.2/phenofit/man/get_param.Rd | 74 - phenofit-0.3.2/phenofit/man/get_pheno.Rd | 7 phenofit-0.3.2/phenofit/man/init_lambda.Rd | 52 - phenofit-0.3.2/phenofit/man/init_param.Rd | 72 - phenofit-0.3.2/phenofit/man/julia_setup.Rd |only phenofit-0.3.2/phenofit/man/kurtosis.Rd | 62 - phenofit-0.3.2/phenofit/man/lambda_vcurve.Rd |only phenofit-0.3.2/phenofit/man/logistic.Rd | 80 +- phenofit-0.3.2/phenofit/man/logistics.Rd | 109 +- phenofit-0.3.2/phenofit/man/melt_list.Rd |only phenofit-0.3.2/phenofit/man/movmean.Rd | 54 - phenofit-0.3.2/phenofit/man/opt_FUN.Rd | 200 ++--- phenofit-0.3.2/phenofit/man/opt_season.Rd |only phenofit-0.3.2/phenofit/man/optim_pheno.Rd | 19 phenofit-0.3.2/phenofit/man/phenofit.Rd | 4 phenofit-0.3.2/phenofit/man/plot_curvefits.Rd |only phenofit-0.3.2/phenofit/man/plot_input.Rd | 79 -- phenofit-0.3.2/phenofit/man/plot_phenofit.Rd | 86 -- phenofit-0.3.2/phenofit/man/plot_season.Rd | 15 phenofit-0.3.2/phenofit/man/process_phenofit.Rd |only phenofit-0.3.2/phenofit/man/process_season.Rd |only phenofit-0.3.2/phenofit/man/qcFUN.Rd | 178 ++-- phenofit-0.3.2/phenofit/man/qc_levels.Rd |only phenofit-0.3.2/phenofit/man/rcpp_season_filter.Rd |only phenofit-0.3.2/phenofit/man/rcpp_wSG.Rd | 64 - phenofit-0.3.2/phenofit/man/reexports.Rd |only phenofit-0.3.2/phenofit/man/removeClosedExtreme.Rd |only phenofit-0.3.2/phenofit/man/season.Rd | 250 ++++-- phenofit-0.3.2/phenofit/man/season_mov.Rd |only phenofit-0.3.2/phenofit/man/set_options.Rd |only phenofit-0.3.2/phenofit/man/smooth_wHANTS.Rd | 2 phenofit-0.3.2/phenofit/man/smooth_wSG.Rd | 2 phenofit-0.3.2/phenofit/man/smooth_wWHIT.Rd | 4 phenofit-0.3.2/phenofit/man/tidy_MOD13.Rd |only phenofit-0.3.2/phenofit/man/tidy_pheno.Rd |only phenofit-0.3.2/phenofit/man/v_curve.Rd | 14 phenofit-0.3.2/phenofit/man/whit2.Rd | 90 +- phenofit-0.3.2/phenofit/src/RcppExports.cpp | 21 phenofit-0.3.2/phenofit/src/register_routines.c | 31 phenofit-0.3.2/phenofit/src/season_filter.cpp |only phenofit-0.3.2/phenofit/src/smooth_wSG.cpp | 57 - phenofit-0.3.2/phenofit/src/smooth_whit.c | 6 phenofit-0.3.2/phenofit/src/wTSM.cpp | 2 phenofit-0.3.2/phenofit/tests/testthat/helper_MOD13A1.R | 42 - phenofit-0.3.2/phenofit/tests/testthat/test-PhenoExtract.R | 18 phenofit-0.3.2/phenofit/tests/testthat/test-curvefits.R | 19 phenofit-0.3.2/phenofit/tests/testthat/test-find_season.R |only phenofit-0.3.2/phenofit/tests/testthat/test-season.R | 6 phenofit-0.3.2/phenofit/tests/testthat/test-season_mov.R |only phenofit-0.3.2/phenofit/tests/testthat/test-v_curve.R | 2 phenofit-0.3.2/phenofit/vignettes |only 146 files changed, 3001 insertions(+), 3028 deletions(-)
Title: Helper Functions for Use with the 'ncdf4' Package
Description: Contains a collection of helper functions for dealing with
'NetCDF' files <https://www.unidata.ucar.edu/software/netcdf/>
opened using 'ncdf4', particularly 'NetCDF' files that conform to the
Climate and Forecast (CF) Metadata Conventions
<http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html>.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts
Consortium (PCIC)
Maintainer: Lee Zeman <lzeman@uvic.ca>
Diff between ncdf4.helpers versions 0.3-5 dated 2020-06-08 and 0.3-6 dated 2021-10-15
CHANGELOG | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- tests/testthat/test-file-functions.R | 12 +++++++----- 5 files changed, 19 insertions(+), 15 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamás Nepusz <ntamas@gmail.com>
Diff between igraph versions 1.2.6 dated 2020-10-06 and 1.2.7 dated 2021-10-15
igraph-1.2.6/igraph/src/AMD |only igraph-1.2.6/igraph/src/CHOLMOD |only igraph-1.2.6/igraph/src/COLAMD |only igraph-1.2.6/igraph/src/plfit/zeta.c |only igraph-1.2.6/igraph/src/plfit/zeta.h |only igraph-1.2.7/igraph/DESCRIPTION | 16 igraph-1.2.7/igraph/MD5 | 1196 - igraph-1.2.7/igraph/NAMESPACE | 2 igraph-1.2.7/igraph/NEWS.md |only igraph-1.2.7/igraph/R/adjacency.R | 2 igraph-1.2.7/igraph/R/auto.R | 25 igraph-1.2.7/igraph/R/bipartite.R | 15 igraph-1.2.7/igraph/R/centrality.R | 2 igraph-1.2.7/igraph/R/centralization.R | 8 igraph-1.2.7/igraph/R/cliques.R | 4 igraph-1.2.7/igraph/R/cocitation.R | 2 igraph-1.2.7/igraph/R/cohesive.blocks.R | 2 igraph-1.2.7/igraph/R/community.R | 648 igraph-1.2.7/igraph/R/data_frame.R | 11 igraph-1.2.7/igraph/R/degseq.R | 6 igraph-1.2.7/igraph/R/embedding.R | 4 igraph-1.2.7/igraph/R/fit.R | 2 igraph-1.2.7/igraph/R/flow.R | 10 igraph-1.2.7/igraph/R/foreign.R | 11 igraph-1.2.7/igraph/R/games.R | 30 igraph-1.2.7/igraph/R/hrg.R | 6 igraph-1.2.7/igraph/R/igraph-package.R | 6 igraph-1.2.7/igraph/R/indexing.R | 4 igraph-1.2.7/igraph/R/interface.R | 4 igraph-1.2.7/igraph/R/iterators.R | 6 igraph-1.2.7/igraph/R/layout.R | 30 igraph-1.2.7/igraph/R/make.R | 37 igraph-1.2.7/igraph/R/minimum.spanning.tree.R | 6 igraph-1.2.7/igraph/R/motifs.R | 2 igraph-1.2.7/igraph/R/nexus.R | 6 igraph-1.2.7/igraph/R/other.R | 37 igraph-1.2.7/igraph/R/palette.R | 4 igraph-1.2.7/igraph/R/par.R | 2 igraph-1.2.7/igraph/R/paths.R | 6 igraph-1.2.7/igraph/R/plot.R | 44 igraph-1.2.7/igraph/R/printr.R | 14 igraph-1.2.7/igraph/R/sir.R | 2 igraph-1.2.7/igraph/R/structural.properties.R | 81 igraph-1.2.7/igraph/R/test.R | 2 igraph-1.2.7/igraph/R/tkplot.R | 10 igraph-1.2.7/igraph/R/topology.R | 6 igraph-1.2.7/igraph/build |only igraph-1.2.7/igraph/cleanup | 5 igraph-1.2.7/igraph/cleanup.win |only igraph-1.2.7/igraph/configure | 3970 ++- igraph-1.2.7/igraph/configure.ac | 16 igraph-1.2.7/igraph/demo/hrg.R | 4 igraph-1.2.7/igraph/inst/AUTHORS | 5 igraph-1.2.7/igraph/inst/NEWS.md | 300 igraph-1.2.7/igraph/inst/README.md | 17 igraph-1.2.7/igraph/inst/my_html_library.tcl | 2 igraph-1.2.7/igraph/man/aaa-igraph-package.Rd | 6 igraph-1.2.7/igraph/man/all_simple_paths.Rd | 5 igraph-1.2.7/igraph/man/alpha_centrality.Rd | 2 igraph-1.2.7/igraph/man/arpack.Rd | 2 igraph-1.2.7/igraph/man/as.igraph.Rd | 2 igraph-1.2.7/igraph/man/betweenness.Rd | 10 igraph-1.2.7/igraph/man/canonical_permutation.Rd | 2 igraph-1.2.7/igraph/man/centr_betw_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_clo_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_degree_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_eigen_tmax.Rd | 2 igraph-1.2.7/igraph/man/cliques.Rd | 4 igraph-1.2.7/igraph/man/closeness.Rd | 8 igraph-1.2.7/igraph/man/cluster_edge_betweenness.Rd | 2 igraph-1.2.7/igraph/man/cluster_fast_greedy.Rd | 3 igraph-1.2.7/igraph/man/cluster_fluid_communities.Rd |only igraph-1.2.7/igraph/man/cluster_infomap.Rd | 6 igraph-1.2.7/igraph/man/cluster_label_prop.Rd | 5 igraph-1.2.7/igraph/man/cluster_leiden.Rd |only igraph-1.2.7/igraph/man/cluster_louvain.Rd | 5 igraph-1.2.7/igraph/man/cluster_optimal.Rd | 2 igraph-1.2.7/igraph/man/cluster_walktrap.Rd | 3 igraph-1.2.7/igraph/man/cocitation.Rd | 2 igraph-1.2.7/igraph/man/cohesive_blocks.Rd | 2 igraph-1.2.7/igraph/man/communities.Rd | 5 igraph-1.2.7/igraph/man/compare.Rd | 11 igraph-1.2.7/igraph/man/components.Rd | 2 igraph-1.2.7/igraph/man/consensus_tree.Rd | 2 igraph-1.2.7/igraph/man/count_isomorphisms.Rd | 2 igraph-1.2.7/igraph/man/diverging_pal.Rd | 2 igraph-1.2.7/igraph/man/embed_laplacian_matrix.Rd | 4 igraph-1.2.7/igraph/man/erdos.renyi.game.Rd | 5 igraph-1.2.7/igraph/man/fit_power_law.Rd | 2 igraph-1.2.7/igraph/man/get.edge.ids.Rd | 2 igraph-1.2.7/igraph/man/graph_from_data_frame.Rd | 7 igraph-1.2.7/igraph/man/handle_vertex_type_arg.Rd |only igraph-1.2.7/igraph/man/igraph-es-indexing.Rd | 2 igraph-1.2.7/igraph/man/igraph-vs-indexing.Rd | 4 igraph-1.2.7/igraph/man/igraph_options.Rd | 2 igraph-1.2.7/igraph/man/igraph_version.Rd | 2 igraph-1.2.7/igraph/man/incident.Rd | 2 igraph-1.2.7/igraph/man/is_degseq.Rd | 2 igraph-1.2.7/igraph/man/is_graphical.Rd | 4 igraph-1.2.7/igraph/man/is_min_separator.Rd | 2 igraph-1.2.7/igraph/man/knn.Rd | 29 igraph-1.2.7/igraph/man/layout_.Rd | 2 igraph-1.2.7/igraph/man/layout_as_tree.Rd | 2 igraph-1.2.7/igraph/man/layout_on_grid.Rd | 2 igraph-1.2.7/igraph/man/layout_with_graphopt.Rd | 2 igraph-1.2.7/igraph/man/layout_with_kk.Rd | 2 igraph-1.2.7/igraph/man/make_bipartite_graph.Rd | 2 igraph-1.2.7/igraph/man/make_chordal_ring.Rd | 4 igraph-1.2.7/igraph/man/make_graph.Rd | 8 igraph-1.2.7/igraph/man/make_lattice.Rd | 2 igraph-1.2.7/igraph/man/matching.Rd | 2 igraph-1.2.7/igraph/man/min_cut.Rd | 4 igraph-1.2.7/igraph/man/modularity.igraph.Rd | 11 igraph-1.2.7/igraph/man/motifs.Rd | 2 igraph-1.2.7/igraph/man/mst.Rd | 6 igraph-1.2.7/igraph/man/nexus.Rd | 6 igraph-1.2.7/igraph/man/plot.common.Rd | 2 igraph-1.2.7/igraph/man/plot_dendrogram.communities.Rd | 2 igraph-1.2.7/igraph/man/plot_dendrogram.igraphHRG.Rd | 2 igraph-1.2.7/igraph/man/printer_callback.Rd | 2 igraph-1.2.7/igraph/man/printr.Rd |only igraph-1.2.7/igraph/man/read_graph.Rd | 11 igraph-1.2.7/igraph/man/reciprocity.Rd | 2 igraph-1.2.7/igraph/man/sample_bipartite.Rd | 2 igraph-1.2.7/igraph/man/sample_degseq.Rd | 2 igraph-1.2.7/igraph/man/sample_dot_product.Rd | 2 igraph-1.2.7/igraph/man/sample_hierarchical_sbm.Rd | 2 igraph-1.2.7/igraph/man/sample_last_cit.Rd | 2 igraph-1.2.7/igraph/man/sample_pa.Rd | 2 igraph-1.2.7/igraph/man/sample_pa_age.Rd | 9 igraph-1.2.7/igraph/man/sample_pref.Rd | 2 igraph-1.2.7/igraph/man/sample_sbm.Rd | 2 igraph-1.2.7/igraph/man/sequential_pal.Rd | 2 igraph-1.2.7/igraph/man/sir.Rd | 2 igraph-1.2.7/igraph/man/st_min_cuts.Rd | 2 igraph-1.2.7/igraph/man/sub-sub-.igraph.Rd | 2 igraph-1.2.7/igraph/man/tkplot.Rd | 10 igraph-1.2.7/igraph/man/transitivity.Rd | 9 igraph-1.2.7/igraph/man/vertex_connectivity.Rd | 2 igraph-1.2.7/igraph/man/which_multiple.Rd | 2 igraph-1.2.7/igraph/man/which_mutual.Rd | 2 igraph-1.2.7/igraph/src/DensityGrid.cpp | 387 igraph-1.2.7/igraph/src/DensityGrid.h | 89 igraph-1.2.7/igraph/src/DensityGrid_3d.cpp | 431 igraph-1.2.7/igraph/src/DensityGrid_3d.h | 89 igraph-1.2.7/igraph/src/Makevars.in | 3 igraph-1.2.7/igraph/src/Makevars.win | 7 igraph-1.2.7/igraph/src/NetDataTypes.cpp | 264 igraph-1.2.7/igraph/src/NetDataTypes.h | 1129 - igraph-1.2.7/igraph/src/NetRoutines.cpp | 424 igraph-1.2.7/igraph/src/NetRoutines.h | 18 igraph-1.2.7/igraph/src/adjlist.c | 992 igraph-1.2.7/igraph/src/arpack.c | 2095 +- igraph-1.2.7/igraph/src/array.c | 10 igraph-1.2.7/igraph/src/array.pmt | 102 igraph-1.2.7/igraph/src/atlas-edges.h | 2528 +- igraph-1.2.7/igraph/src/atlas.c | 78 igraph-1.2.7/igraph/src/attributes.c | 650 igraph-1.2.7/igraph/src/basic_query.c | 36 igraph-1.2.7/igraph/src/bfgs.c | 341 igraph-1.2.7/igraph/src/bigint.c | 438 igraph-1.2.7/igraph/src/bigint.h | 52 igraph-1.2.7/igraph/src/bignum.c | 2486 +- igraph-1.2.7/igraph/src/bignum.h | 46 igraph-1.2.7/igraph/src/bipartite.c | 1613 - igraph-1.2.7/igraph/src/blas.c | 85 igraph-1.2.7/igraph/src/bliss.cc | 209 igraph-1.2.7/igraph/src/bliss/bignum.hh | 4 igraph-1.2.7/igraph/src/bliss/bliss_heap.cc | 6 igraph-1.2.7/igraph/src/bliss/defs.cc | 12 igraph-1.2.7/igraph/src/bliss/defs.hh | 7 igraph-1.2.7/igraph/src/bliss/graph.cc | 65 igraph-1.2.7/igraph/src/bliss/graph.hh | 16 igraph-1.2.7/igraph/src/bliss/orbit.cc | 4 igraph-1.2.7/igraph/src/bliss/partition.cc | 6 igraph-1.2.7/igraph/src/bliss/partition.hh | 6 igraph-1.2.7/igraph/src/bliss/uintseqhash.hh | 2 igraph-1.2.7/igraph/src/bliss/utils.cc | 2 igraph-1.2.7/igraph/src/bliss/utils.hh | 6 igraph-1.2.7/igraph/src/cattributes.c | 6522 +++--- igraph-1.2.7/igraph/src/centrality.c | 4892 ++-- igraph-1.2.7/igraph/src/cliquer/cliquer.c | 9 igraph-1.2.7/igraph/src/cliquer/cliquer_graph.c | 8 igraph-1.2.7/igraph/src/cliquer/reorder.c | 2 igraph-1.2.7/igraph/src/cliquer/set.h | 4 igraph-1.2.7/igraph/src/cliques.c | 1810 - igraph-1.2.7/igraph/src/clustertool.cpp | 981 igraph-1.2.7/igraph/src/cocitation.c | 587 igraph-1.2.7/igraph/src/cohesive_blocks.c | 1019 igraph-1.2.7/igraph/src/coloring.c | 49 igraph-1.2.7/igraph/src/community.c | 5617 ++--- igraph-1.2.7/igraph/src/community_leiden.c |only igraph-1.2.7/igraph/src/complex.c | 572 igraph-1.2.7/igraph/src/components.c | 1686 - igraph-1.2.7/igraph/src/config.h.in | 17 igraph-1.2.7/igraph/src/conversion.c | 1389 - igraph-1.2.7/igraph/src/cores.c | 220 igraph-1.2.7/igraph/src/decomposition.c | 756 igraph-1.2.7/igraph/src/degree_sequence.cpp |only igraph-1.2.7/igraph/src/distances.c | 265 igraph-1.2.7/igraph/src/dotproduct.c | 326 igraph-1.2.7/igraph/src/dqueue.c | 10 igraph-1.2.7/igraph/src/dqueue.pmt | 385 igraph-1.2.7/igraph/src/drl_Node.h | 64 igraph-1.2.7/igraph/src/drl_Node_3d.h | 64 igraph-1.2.7/igraph/src/drl_graph.cpp | 2024 - igraph-1.2.7/igraph/src/drl_graph.h | 178 igraph-1.2.7/igraph/src/drl_graph_3d.cpp | 1461 - igraph-1.2.7/igraph/src/drl_graph_3d.h | 162 igraph-1.2.7/igraph/src/drl_layout.cpp | 562 igraph-1.2.7/igraph/src/drl_layout.h | 62 igraph-1.2.7/igraph/src/drl_layout_3d.cpp | 86 igraph-1.2.7/igraph/src/drl_layout_3d.h | 62 igraph-1.2.7/igraph/src/drl_parse.cpp | 240 igraph-1.2.7/igraph/src/drl_parse.h | 74 igraph-1.2.7/igraph/src/eigen.c | 2669 +- igraph-1.2.7/igraph/src/embedding.c | 1703 - igraph-1.2.7/igraph/src/fast_community.c | 1666 - igraph-1.2.7/igraph/src/feedback_arc_set.c | 1046 - igraph-1.2.7/igraph/src/flow.c | 3469 +-- igraph-1.2.7/igraph/src/foreign-dl-header.h | 37 igraph-1.2.7/igraph/src/foreign-dl-lexer.c | 95 igraph-1.2.7/igraph/src/foreign-dl-lexer.l | 7 igraph-1.2.7/igraph/src/foreign-gml-header.h | 18 igraph-1.2.7/igraph/src/foreign-gml-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-gml-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-graphml.c | 3179 +-- igraph-1.2.7/igraph/src/foreign-lgl-header.h | 26 igraph-1.2.7/igraph/src/foreign-lgl-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-lgl-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-ncol-header.h | 24 igraph-1.2.7/igraph/src/foreign-ncol-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-ncol-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-pajek-header.h | 42 igraph-1.2.7/igraph/src/foreign-pajek-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-pajek-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-pajek-parser.c | 4 igraph-1.2.7/igraph/src/foreign-pajek-parser.y | 4 igraph-1.2.7/igraph/src/foreign.c | 5304 ++--- igraph-1.2.7/igraph/src/forestfire.c | 343 igraph-1.2.7/igraph/src/fortran_intrinsics.c | 38 igraph-1.2.7/igraph/src/games.c | 6785 +++--- igraph-1.2.7/igraph/src/gengraph_box_list.cpp | 119 igraph-1.2.7/igraph/src/gengraph_box_list.h | 82 igraph-1.2.7/igraph/src/gengraph_definitions.h | 119 igraph-1.2.7/igraph/src/gengraph_degree_sequence.cpp | 451 igraph-1.2.7/igraph/src/gengraph_degree_sequence.h | 111 igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.cpp | 1080 - igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.h | 311 igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.cpp | 2775 +- igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.h | 447 igraph-1.2.7/igraph/src/gengraph_hash.h | 342 igraph-1.2.7/igraph/src/gengraph_header.h | 85 igraph-1.2.7/igraph/src/gengraph_mr-connected.cpp | 196 igraph-1.2.7/igraph/src/gengraph_powerlaw.cpp | 356 igraph-1.2.7/igraph/src/gengraph_powerlaw.h | 86 igraph-1.2.7/igraph/src/gengraph_qsort.h | 718 igraph-1.2.7/igraph/src/gengraph_random.cpp | 60 igraph-1.2.7/igraph/src/gengraph_random.h | 54 igraph-1.2.7/igraph/src/gengraph_vertex_cover.h | 68 igraph-1.2.7/igraph/src/glet.c | 1404 - igraph-1.2.7/igraph/src/glpk_support.c | 87 igraph-1.2.7/igraph/src/gml_tree.c | 370 igraph-1.2.7/igraph/src/hacks.c | 13 igraph-1.2.7/igraph/src/heap.c | 1273 - igraph-1.2.7/igraph/src/heap.pmt | 326 igraph-1.2.7/igraph/src/hrg_dendro.h | 351 igraph-1.2.7/igraph/src/hrg_graph.h | 158 igraph-1.2.7/igraph/src/hrg_graph_simp.h | 134 igraph-1.2.7/igraph/src/hrg_rbtree.h | 148 igraph-1.2.7/igraph/src/hrg_splittree_eq.h | 180 igraph-1.2.7/igraph/src/igraph_arpack_internal.h | 310 igraph-1.2.7/igraph/src/igraph_blas_internal.h | 69 igraph-1.2.7/igraph/src/igraph_buckets.c | 210 igraph-1.2.7/igraph/src/igraph_cliquer.c | 124 igraph-1.2.7/igraph/src/igraph_cliquer.h | 16 igraph-1.2.7/igraph/src/igraph_error.c | 219 igraph-1.2.7/igraph/src/igraph_estack.c | 54 igraph-1.2.7/igraph/src/igraph_estack.h | 22 igraph-1.2.7/igraph/src/igraph_f2c.h | 286 igraph-1.2.7/igraph/src/igraph_fixed_vectorlist.c | 98 igraph-1.2.7/igraph/src/igraph_flow_internal.h | 25 igraph-1.2.7/igraph/src/igraph_glpk_support.h | 20 igraph-1.2.7/igraph/src/igraph_gml_tree.h | 74 igraph-1.2.7/igraph/src/igraph_grid.c | 832 igraph-1.2.7/igraph/src/igraph_hacks_internal.h | 32 igraph-1.2.7/igraph/src/igraph_handle_exceptions.h |only igraph-1.2.7/igraph/src/igraph_hashtable.c | 148 igraph-1.2.7/igraph/src/igraph_heap.c | 10 igraph-1.2.7/igraph/src/igraph_hrg.cc | 1549 - igraph-1.2.7/igraph/src/igraph_hrg_types.cc | 5912 ++--- igraph-1.2.7/igraph/src/igraph_interrupt_internal.h | 38 igraph-1.2.7/igraph/src/igraph_isoclasses.h |only igraph-1.2.7/igraph/src/igraph_lapack_internal.h | 280 igraph-1.2.7/igraph/src/igraph_marked_queue.c | 112 igraph-1.2.7/igraph/src/igraph_marked_queue.h | 28 igraph-1.2.7/igraph/src/igraph_math.h | 40 igraph-1.2.7/igraph/src/igraph_psumtree.c | 102 igraph-1.2.7/igraph/src/igraph_set.c | 250 igraph-1.2.7/igraph/src/igraph_stack.c | 32 igraph-1.2.7/igraph/src/igraph_strvector.c | 651 igraph-1.2.7/igraph/src/igraph_threading.h | 16 igraph-1.2.7/igraph/src/igraph_trie.c | 504 igraph-1.2.7/igraph/src/igraph_types_internal.h | 246 igraph-1.2.7/igraph/src/igraph_version.h | 20 igraph-1.2.7/igraph/src/include/igraph.h | 12 igraph-1.2.7/igraph/src/include/igraph_adjlist.h | 145 igraph-1.2.7/igraph/src/include/igraph_arpack.h | 114 igraph-1.2.7/igraph/src/include/igraph_array.h | 10 igraph-1.2.7/igraph/src/include/igraph_array_pmt.h | 46 igraph-1.2.7/igraph/src/include/igraph_attributes.h | 545 igraph-1.2.7/igraph/src/include/igraph_bipartite.h | 88 igraph-1.2.7/igraph/src/include/igraph_blas.h | 27 igraph-1.2.7/igraph/src/include/igraph_centrality.h | 242 igraph-1.2.7/igraph/src/include/igraph_cliques.h | 78 igraph-1.2.7/igraph/src/include/igraph_cocitation.h | 38 igraph-1.2.7/igraph/src/include/igraph_cohesive_blocks.h | 24 igraph-1.2.7/igraph/src/include/igraph_coloring.h | 24 igraph-1.2.7/igraph/src/include/igraph_community.h | 271 igraph-1.2.7/igraph/src/include/igraph_complex.h | 78 igraph-1.2.7/igraph/src/include/igraph_components.h | 39 igraph-1.2.7/igraph/src/include/igraph_constants.h | 211 igraph-1.2.7/igraph/src/include/igraph_constructors.h | 58 igraph-1.2.7/igraph/src/include/igraph_conversion.h | 37 igraph-1.2.7/igraph/src/include/igraph_datatype.h | 49 igraph-1.2.7/igraph/src/include/igraph_decls.h | 29 igraph-1.2.7/igraph/src/include/igraph_dqueue.h | 14 igraph-1.2.7/igraph/src/include/igraph_dqueue_pmt.h | 46 igraph-1.2.7/igraph/src/include/igraph_eigen.h | 132 igraph-1.2.7/igraph/src/include/igraph_embedding.h | 57 igraph-1.2.7/igraph/src/include/igraph_epidemics.h | 24 igraph-1.2.7/igraph/src/include/igraph_error.h | 373 igraph-1.2.7/igraph/src/include/igraph_flow.h | 156 igraph-1.2.7/igraph/src/include/igraph_foreign.h | 64 igraph-1.2.7/igraph/src/include/igraph_games.h | 287 igraph-1.2.7/igraph/src/include/igraph_graphlets.h | 30 igraph-1.2.7/igraph/src/include/igraph_heap.h | 10 igraph-1.2.7/igraph/src/include/igraph_heap_pmt.h | 42 igraph-1.2.7/igraph/src/include/igraph_hrg.h | 67 igraph-1.2.7/igraph/src/include/igraph_interface.h | 109 igraph-1.2.7/igraph/src/include/igraph_interrupt.h | 16 igraph-1.2.7/igraph/src/include/igraph_iterators.h | 208 igraph-1.2.7/igraph/src/include/igraph_lapack.h | 100 igraph-1.2.7/igraph/src/include/igraph_layout.h | 263 igraph-1.2.7/igraph/src/include/igraph_lsap.h | 10 igraph-1.2.7/igraph/src/include/igraph_matching.h | 28 igraph-1.2.7/igraph/src/include/igraph_matrix.h | 12 igraph-1.2.7/igraph/src/include/igraph_matrix_pmt.h | 286 igraph-1.2.7/igraph/src/include/igraph_memory.h | 14 igraph-1.2.7/igraph/src/include/igraph_microscopic_update.h | 38 igraph-1.2.7/igraph/src/include/igraph_mixing.h | 30 igraph-1.2.7/igraph/src/include/igraph_motifs.h | 48 igraph-1.2.7/igraph/src/include/igraph_neighborhood.h | 27 igraph-1.2.7/igraph/src/include/igraph_nongraph.h | 49 igraph-1.2.7/igraph/src/include/igraph_operators.h | 44 igraph-1.2.7/igraph/src/include/igraph_paths.h | 181 igraph-1.2.7/igraph/src/include/igraph_pmt.h | 186 igraph-1.2.7/igraph/src/include/igraph_pmt_off.h | 78 igraph-1.2.7/igraph/src/include/igraph_progress.h | 114 igraph-1.2.7/igraph/src/include/igraph_psumtree.h | 30 igraph-1.2.7/igraph/src/include/igraph_qsort.h | 16 igraph-1.2.7/igraph/src/include/igraph_random.h | 77 igraph-1.2.7/igraph/src/include/igraph_scan.h | 50 igraph-1.2.7/igraph/src/include/igraph_scg.h | 219 igraph-1.2.7/igraph/src/include/igraph_separators.h | 26 igraph-1.2.7/igraph/src/include/igraph_sparsemat.h | 464 igraph-1.2.7/igraph/src/include/igraph_spmatrix.h | 42 igraph-1.2.7/igraph/src/include/igraph_stack.h | 10 igraph-1.2.7/igraph/src/include/igraph_stack_pmt.h | 38 igraph-1.2.7/igraph/src/include/igraph_statusbar.h | 86 igraph-1.2.7/igraph/src/include/igraph_structural.h | 128 igraph-1.2.7/igraph/src/include/igraph_strvector.h | 68 igraph-1.2.7/igraph/src/include/igraph_threading.h.in | 16 igraph-1.2.7/igraph/src/include/igraph_topology.h | 293 igraph-1.2.7/igraph/src/include/igraph_transitivity.h | 60 igraph-1.2.7/igraph/src/include/igraph_types.h | 34 igraph-1.2.7/igraph/src/include/igraph_vector.h | 55 igraph-1.2.7/igraph/src/include/igraph_vector_pmt.h | 302 igraph-1.2.7/igraph/src/include/igraph_vector_ptr.h | 38 igraph-1.2.7/igraph/src/include/igraph_vector_type.h | 18 igraph-1.2.7/igraph/src/include/igraph_version.h.in | 18 igraph-1.2.7/igraph/src/include/igraph_visitor.h | 80 igraph-1.2.7/igraph/src/infomap.cc | 462 igraph-1.2.7/igraph/src/infomap_FlowGraph.cc | 637 igraph-1.2.7/igraph/src/infomap_FlowGraph.h | 68 igraph-1.2.7/igraph/src/infomap_Greedy.cc | 1077 - igraph-1.2.7/igraph/src/infomap_Greedy.h | 98 igraph-1.2.7/igraph/src/infomap_Node.cc | 87 igraph-1.2.7/igraph/src/infomap_Node.h | 43 igraph-1.2.7/igraph/src/init.c | 22 igraph-1.2.7/igraph/src/interrupt.c | 35 igraph-1.2.7/igraph/src/iterators.c | 2119 +- igraph-1.2.7/igraph/src/lad.c | 2940 +- igraph-1.2.7/igraph/src/lapack.c | 1311 - igraph-1.2.7/igraph/src/layout.c | 3804 +-- igraph-1.2.7/igraph/src/layout_dh.c | 673 igraph-1.2.7/igraph/src/layout_fr.c | 1143 - igraph-1.2.7/igraph/src/layout_gem.c | 375 igraph-1.2.7/igraph/src/layout_kk.c | 1098 - igraph-1.2.7/igraph/src/lsap.c | 753 igraph-1.2.7/igraph/src/matching.c | 1534 - igraph-1.2.7/igraph/src/math.c | 320 igraph-1.2.7/igraph/src/matrix.c | 120 igraph-1.2.7/igraph/src/matrix.pmt | 1366 - igraph-1.2.7/igraph/src/maximal_cliques.c | 607 igraph-1.2.7/igraph/src/maximal_cliques_template.h | 551 igraph-1.2.7/igraph/src/memory.c | 30 igraph-1.2.7/igraph/src/microscopic_update.c | 1100 - igraph-1.2.7/igraph/src/mixing.c | 372 igraph-1.2.7/igraph/src/motifs.c | 1651 - igraph-1.2.7/igraph/src/operators.c | 1891 - igraph-1.2.7/igraph/src/optimal_modularity.c | 345 igraph-1.2.7/igraph/src/other.c | 480 igraph-1.2.7/igraph/src/paths.c | 210 igraph-1.2.7/igraph/src/plfit/error.c | 11 igraph-1.2.7/igraph/src/plfit/error.h | 6 igraph-1.2.7/igraph/src/plfit/gss.c | 7 igraph-1.2.7/igraph/src/plfit/gss.h | 8 igraph-1.2.7/igraph/src/plfit/hzeta.c |only igraph-1.2.7/igraph/src/plfit/hzeta.h |only igraph-1.2.7/igraph/src/plfit/kolmogorov.c | 6 igraph-1.2.7/igraph/src/plfit/kolmogorov.h | 10 igraph-1.2.7/igraph/src/plfit/mt.c |only igraph-1.2.7/igraph/src/plfit/mt.h |only igraph-1.2.7/igraph/src/plfit/options.c | 31 igraph-1.2.7/igraph/src/plfit/platform.c |only igraph-1.2.7/igraph/src/plfit/platform.h | 25 igraph-1.2.7/igraph/src/plfit/plfit.c | 1037 igraph-1.2.7/igraph/src/plfit/plfit.h | 104 igraph-1.2.7/igraph/src/plfit/plfit.inc | 5 igraph-1.2.7/igraph/src/plfit/rbinom.c |only igraph-1.2.7/igraph/src/plfit/sampling.c |only igraph-1.2.7/igraph/src/plfit/sampling.h |only igraph-1.2.7/igraph/src/pottsmodel_2.cpp | 3914 +-- igraph-1.2.7/igraph/src/pottsmodel_2.h | 130 igraph-1.2.7/igraph/src/progress.c | 131 igraph-1.2.7/igraph/src/prpack.cpp | 24 igraph-1.2.7/igraph/src/prpack.h | 26 igraph-1.2.7/igraph/src/prpack/prpack_base_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_csc.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_csr.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_edge_list.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_igraph_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_ge_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_gs_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_scc_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_schur_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_result.h | 6 igraph-1.2.7/igraph/src/prpack/prpack_solver.cpp | 2 igraph-1.2.7/igraph/src/prpack/prpack_solver.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_utils.cpp | 2 igraph-1.2.7/igraph/src/prpack/prpack_utils.h | 2 igraph-1.2.7/igraph/src/pstdint.h | 1170 - igraph-1.2.7/igraph/src/qsort.c | 262 igraph-1.2.7/igraph/src/random.c | 2529 +- igraph-1.2.7/igraph/src/random_walk.c | 163 igraph-1.2.7/igraph/src/rinterface.c | 173 igraph-1.2.7/igraph/src/sbm.c | 974 igraph-1.2.7/igraph/src/scan.c | 1351 - igraph-1.2.7/igraph/src/scg.c | 3176 +-- igraph-1.2.7/igraph/src/scg_approximate_methods.c | 239 igraph-1.2.7/igraph/src/scg_exact_scg.c | 78 igraph-1.2.7/igraph/src/scg_headers.h | 86 igraph-1.2.7/igraph/src/scg_kmeans.c | 134 igraph-1.2.7/igraph/src/scg_optimal_method.c | 391 igraph-1.2.7/igraph/src/scg_utils.c | 115 igraph-1.2.7/igraph/src/separators.c | 1365 - igraph-1.2.7/igraph/src/sir.c | 362 igraph-1.2.7/igraph/src/spanning_trees.c | 566 igraph-1.2.7/igraph/src/sparsemat.c | 3936 +-- igraph-1.2.7/igraph/src/spectral_properties.c | 727 igraph-1.2.7/igraph/src/spmatrix.c | 996 igraph-1.2.7/igraph/src/st-cuts.c | 2575 +- igraph-1.2.7/igraph/src/stack.pmt | 276 igraph-1.2.7/igraph/src/statusbar.c | 88 igraph-1.2.7/igraph/src/structural_properties.c |10394 +++++----- igraph-1.2.7/igraph/src/structural_properties_internal.h | 31 igraph-1.2.7/igraph/src/structure_generators.c | 3288 +-- igraph-1.2.7/igraph/src/sugiyama.c | 1898 - igraph-1.2.7/igraph/src/topology.c | 4767 ++-- igraph-1.2.7/igraph/src/triangles.c | 1352 - igraph-1.2.7/igraph/src/triangles_template.h | 161 igraph-1.2.7/igraph/src/triangles_template1.h | 111 igraph-1.2.7/igraph/src/type_indexededgelist.c | 2204 +- igraph-1.2.7/igraph/src/types.c | 192 igraph-1.2.7/igraph/src/uuid/gen_uuid.c | 2 igraph-1.2.7/igraph/src/vector.c | 598 igraph-1.2.7/igraph/src/vector.pmt | 2575 +- igraph-1.2.7/igraph/src/vector_ptr.c | 453 igraph-1.2.7/igraph/src/version.c | 54 igraph-1.2.7/igraph/src/visitors.c | 811 igraph-1.2.7/igraph/src/walktrap.cpp | 155 igraph-1.2.7/igraph/src/walktrap_communities.cpp | 1479 - igraph-1.2.7/igraph/src/walktrap_communities.h | 202 igraph-1.2.7/igraph/src/walktrap_graph.cpp | 304 igraph-1.2.7/igraph/src/walktrap_graph.h | 66 igraph-1.2.7/igraph/src/walktrap_heap.cpp | 238 igraph-1.2.7/igraph/src/walktrap_heap.h | 117 igraph-1.2.7/igraph/src/zeroin.c | 277 igraph-1.2.7/igraph/tests/testthat.R | 2 igraph-1.2.7/igraph/tests/testthat/test-make_graph.R | 22 igraph-1.2.7/igraph/tests/testthat/test-make_lattice.R |only igraph-1.2.7/igraph/tests/testthat/test_add.edges.R | 2 igraph-1.2.7/igraph/tests/testthat/test_all.st.cuts.R | 6 igraph-1.2.7/igraph/tests/testthat/test_are.connected.R | 18 igraph-1.2.7/igraph/tests/testthat/test_arpack.R | 4 igraph-1.2.7/igraph/tests/testthat/test_as.directed.R | 4 igraph-1.2.7/igraph/tests/testthat/test_ba.game.R | 18 igraph-1.2.7/igraph/tests/testthat/test_bipartite.projection.R | 36 igraph-1.2.7/igraph/tests/testthat/test_bipartite.random.game.R | 20 igraph-1.2.7/igraph/tests/testthat/test_bug-1073705-indexing.R | 4 igraph-1.2.7/igraph/tests/testthat/test_cliques.R | 3 igraph-1.2.7/igraph/tests/testthat/test_communities.R | 5 igraph-1.2.7/igraph/tests/testthat/test_correlated.R | 8 igraph-1.2.7/igraph/tests/testthat/test_count.multiple.R | 2 igraph-1.2.7/igraph/tests/testthat/test_degree.sequence.game.R | 4 igraph-1.2.7/igraph/tests/testthat/test_delete.vertices.R | 2 igraph-1.2.7/igraph/tests/testthat/test_evcent.R | 3 igraph-1.2.7/igraph/tests/testthat/test_get.adjacency.R | 8 igraph-1.2.7/igraph/tests/testthat/test_get.adjlist.R | 7 igraph-1.2.7/igraph/tests/testthat/test_get.edge.R | 2 igraph-1.2.7/igraph/tests/testthat/test_get.edgelist.R | 2 igraph-1.2.7/igraph/tests/testthat/test_get.shortest.paths.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.adjacency.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.adjlist.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.atlas.R | 8 igraph-1.2.7/igraph/tests/testthat/test_graph.complementer.R | 2 igraph-1.2.7/igraph/tests/testthat/test_graph.compose.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.de.bruijn.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.edgelist.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.knn.R | 8 igraph-1.2.7/igraph/tests/testthat/test_graph.subisomorphic.lad.R | 10 igraph-1.2.7/igraph/tests/testthat/test_graph.subisomorphic.vf2.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graphNEL.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graphlets.R | 4 igraph-1.2.7/igraph/tests/testthat/test_hsbm.R | 12 igraph-1.2.7/igraph/tests/testthat/test_igraph.options.R | 4 igraph-1.2.7/igraph/tests/testthat/test_is.bipartite.R | 2 igraph-1.2.7/igraph/tests/testthat/test_layout.kk.R | 3 igraph-1.2.7/igraph/tests/testthat/test_layout.merge.R | 2 igraph-1.2.7/igraph/tests/testthat/test_leiden.R |only igraph-1.2.7/igraph/tests/testthat/test_minimum.size.separators.R | 2 igraph-1.2.7/igraph/tests/testthat/test_modularity_matrix.R | 15 igraph-1.2.7/igraph/tests/testthat/test_multilevel.community.R | 8 igraph-1.2.7/igraph/tests/testthat/test_neighborhood.R | 2 igraph-1.2.7/igraph/tests/testthat/test_operators.R | 10 igraph-1.2.7/igraph/tests/testthat/test_operators3.R | 22 igraph-1.2.7/igraph/tests/testthat/test_pajek.R | 4 igraph-1.2.7/igraph/tests/testthat/test_sbm.game.R | 3 igraph-1.2.7/igraph/tests/testthat/test_sphere.R | 10 igraph-1.2.7/igraph/tests/testthat/test_unfold.tree.R | 4 igraph-1.2.7/igraph/tests/testthat/test_watts.strogatz.game.R | 2 553 files changed, 103568 insertions(+), 95314 deletions(-)
Title: Genetic Algorithms
Description: Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e. a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between GA versions 3.2.1 dated 2021-04-21 and 3.2.2 dated 2021-10-15
DESCRIPTION | 8 ++-- MD5 | 27 ++++++++-------- NEWS.md | 4 ++ R/gade.R | 13 ++++++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 10 +++--- inst/doc/GA.R | 4 +- inst/doc/GA.Rmd | 8 ++-- inst/doc/GA.html | 86 ++++++++++++++++++++++++++-------------------------- man/GA-package.Rd | 5 +-- man/de.Rd | 6 ++- man/ga.Rd | 4 +- src/RcppExports.cpp | 5 +++ vignettes/GA.Rmd | 8 ++-- 15 files changed, 104 insertions(+), 84 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.1.5 dated 2021-09-06 and 1.1.7 dated 2021-10-15
DESCRIPTION | 24 MD5 | 136 - NAMESPACE | 83 NEWS.md | 8 R/absolute_map.R | 14 R/absolute_map_builder.R | 154 - R/anomaly_map.R | 16 R/calculate_climatology.R | 562 +++--- R/calculate_climatology_mean.R | 142 - R/calculate_climatology_outfile.R | 159 - R/check_infile_monitor_climate.R | 38 R/climatology_map.R | 20 R/cmsaf.diff.R | 9 R/cmsaf.hist.R | 202 +- R/cmsaf.hovmoller.R | 191 +- R/cmsaf.scatter.R | 8 R/cmsaf.side.by.side.R | 770 ++++---- R/cmsaf.time.series.R | 410 ++-- R/compare_grid.R | 90 - R/compare_spatial_range.R | 84 R/create_country_mask.R | 327 +-- R/extractFinalOutfile.R | 195 +- R/extractOutfile.R | 97 - R/extractOutfileMean.R | 88 R/extract_climate_files.R | 324 +-- R/fieldmean_and_anomaly_map.R | 10 R/fieldmean_clima.R | 108 - R/fieldmean_current.R | 162 - R/fieldmean_ensemble.R | 304 +-- R/fieldmean_plot.R | 15 R/getUserOptions.R | 83 R/get_basename.R |only R/monitor_climate.R | 5 R/parse_arguments.R | 32 R/plot_abs_map.R | 10 R/plot_abs_map_mean.R | 8 R/plot_time_series.R | 213 +- R/plot_trend.R | 1086 ++++++------ R/plot_warming_stripes.R | 5 R/quicklook.R | 268 ++- R/render_plot.R | 1271 +++++++------- R/render_plot_hovmoller.R | 118 - R/render_plot_side_by_side.R | 2654 +++++++++++++++--------------- R/render_region_plot.R | 507 ++--- R/reset_par.R |only R/time_series_plot.R | 384 ++-- R/trend_plot.R | 392 ++-- R/warming_stripes_plot.R | 10 build/partial.rdb |binary inst/extdata/CMSAF_NoName_Black_s.png |only inst/extdata/CMSAF_NoName_Colour_crop.png |binary inst/extdata/quicklook_config.yml | 869 +++++++++ man/absolute_map.Rd | 6 man/anomaly_map.Rd | 6 man/climatology_map.Rd | 6 man/cmsaf.diff.Rd | 10 man/cmsaf.hist.Rd | 10 man/cmsaf.hovmoller.Rd | 10 man/cmsaf.scatter.Rd | 10 man/cmsaf.side.by.side.Rd | 10 man/cmsaf.time.series.Rd | 10 man/fieldmean_and_anomaly_map.Rd | 6 man/fieldmean_plot.Rd | 6 man/get_basename.Rd |only man/monitor_climate.Rd | 6 man/quicklook.Rd | 9 man/render_plot_hovmoller.Rd | 10 man/render_region_plot.Rd | 6 man/time_series_plot.Rd | 6 man/trend_plot.Rd | 6 man/warming_stripes_plot.Rd | 6 71 files changed, 7033 insertions(+), 5771 deletions(-)
Title: Analysis of the Nigeria National Data Repository (NDR)
Description: The goal is to simplify routine analysis of the Nigeria National Data Repository (NDR) <https://ndr.shieldnigeriaproject.com> using the PEPFAR Monitoring, Evaluation, and Reporting (MER) indicators (see <https://datim.zendesk.com/hc/en-us/articles/360000084446-MER-Indicator-Reference-Guides>). It is designed to import in to R patient-level line-list downloaded as 'csv' file from the front-end of the NDR.
Author: Stephen Balogun [aut, cre] (<https://orcid.org/0000-0002-9928-3703>),
Scholastica Olanrewaju [ctb],
Oluwaseun Okunuga [ctb],
Temitope Kolade [ctb],
Geraldine Abone [ctb]
Maintainer: Stephen Balogun <stephentaiyebalogun@gmail.com>
Diff between tidyndr versions 0.1.0 dated 2021-03-23 and 0.1.1 dated 2021-10-15
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 11 R/disaggregate.R | 421 ++++++++++++++-------------- README.md | 341 +++++++---------------- build/vignette.rds |binary inst/doc/Augmenting-tidyndr.html | 4 inst/doc/tidyndr.html | 570 ++++++++++++--------------------------- man/disaggregate.Rd | 2 9 files changed, 536 insertions(+), 837 deletions(-)
Title: Obtain Unweighted Natural Strata that Balance Many Covariates
Description: Natural strata can be used in observational studies to balance
the distributions of many covariates across any number of treatment
groups and any number of comparisons. These strata have proportional
amounts of units within each stratum across the treatments, allowing
for simple interpretation and aggregation across strata. Within each
stratum, the units are chosen using randomized rounding of a linear
program that balances many covariates.
To solve the linear program, the 'Gurobi' commercial optimization software
is recommended, but not required. The 'gurobi' R package can be installed following the instructions
at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
Author: Katherine Brumberg [aut, cre]
Maintainer: Katherine Brumberg <kbrum@wharton.upenn.edu>
Diff between natstrat versions 1.0.0 dated 2021-05-26 and 2.0.0 dated 2021-10-15
DESCRIPTION | 20 - MD5 | 73 ++-- NAMESPACE | 4 NEWS.md | 29 + R/balance_LP.R | 81 +++- R/check_balance.R | 89 +++-- R/create_balance_matrices.R |only R/create_dist_matrix.R | 2 R/data.R | 40 ++ R/generate_constraints.R | 37 +- R/generate_qs.R | 132 +++++-- R/optimize_controls.R | 483 ++++++++++++++++++----------- R/randomized_rounding.R | 61 +-- R/randomized_rounding_expectation.R |only R/stand.R | 88 +---- R/verify_optimize_controls_inputs.R |only README.md | 20 - build/vignette.rds |binary data/nh0506_3groups.rda |only inst/doc/natstrat.R | 50 ++- inst/doc/natstrat.Rmd | 88 +++++ inst/doc/natstrat.html | 131 ++++++- man/balance_LP.Rd | 15 man/check_balance.Rd | 16 man/create_balance_matrices.Rd |only man/create_dist_matrix.Rd | 2 man/generate_constraints.Rd | 27 + man/generate_qs.Rd | 24 - man/get_stand_diffs.Rd | 16 man/nh0506_3groups.Rd |only man/optimize_controls.Rd | 125 ++++++- man/process_qs.Rd |only man/randomized_rounding.Rd | 25 - man/randomized_rounding_expectation.Rd |only man/stand.Rd | 33 - man/verify_inputs.Rd | 24 - man/verify_inputs_EMD.Rd | 15 man/verify_multi_comp_inputs.Rd |only tests/testthat/test-generate_constraints.R | 32 - tests/testthat/test-generate_qs.R | 2 tests/testthat/test-optimize_controls.R | 320 ++++++++++++++++--- vignettes/natstrat.Rmd | 88 +++++ 42 files changed, 1567 insertions(+), 625 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut, cre] (<https://orcid.org/0000-0002-1196-8012>),
Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Nikolas Kuschnig [ctb] (<https://orcid.org/0000-0002-6642-2543>)
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between ivreg versions 0.6-0 dated 2021-05-28 and 0.6-1 dated 2021-10-15
DESCRIPTION | 16 +- MD5 | 36 ++--- NEWS.md | 21 +++ R/ivreg.R | 13 + R/ivreg.fit.R | 6 R/ivregDiagnostics.R | 177 +++++++++++--------------- R/ivregMethods.R | 25 ++- build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.html | 27 +-- inst/doc/ivreg.Rmd | 4 inst/doc/ivreg.html | 25 ++- man/figures/README-effects-1.png |binary man/figures/README-influenceplot-1.png |binary man/figures/README-qqplot-1.png |binary man/ivreg.Rd | 9 + man/ivreg.fit.Rd | 2 man/ivregDiagnostics.Rd | 12 - man/ivregMethods.Rd | 2 vignettes/ivreg.Rmd | 4 19 files changed, 200 insertions(+), 179 deletions(-)
Title: Collect and Clean Hockey Stats
Description: Various functions to scrape hockey play-by-play data from the
<https://www.nhl.com/>. It also contains functions to scrape data from <https://www.hockey-reference.com/>,
including standings, player stats, and jersey number history.
Author: Daniel Morse [aut, cre]
Maintainer: Daniel Morse <danmorse8642@gmail.com>
Diff between hockeyR versions 0.1.0 dated 2021-09-20 and 0.1.1 dated 2021-10-15
DESCRIPTION | 12 MD5 | 48 NAMESPACE | 2 NEWS.md | 13 R/fix_player_columns.R | 64 R/get_game_ids.R | 196 +- R/get_game_info.R | 160 +- R/get_game_rosters.R | 62 R/get_game_shifts.R | 190 +- R/get_jersey_players.R | 172 +- R/get_player_stats_hr.R | 56 R/get_rosters.R | 312 +-- R/get_team_records.R | 206 +- R/load_pbp.R | 124 - R/scrape_day.R | 68 R/scrape_game.R | 1672 ++++++++++----------- R/scrape_season.R | 74 R/utils-pipe.R |only README.md | 38 inst/doc/hockey-ref-scrapers.R | 31 inst/doc/hockey-ref-scrapers.Rmd | 31 inst/doc/hockey-ref-scrapers.html | 42 man/pipe.Rd |only vignettes/hockey-ref-scrapers.Rmd | 31 vignettes/man/figures/vignettes-plot-example-1.png |binary vignettes/man/figures/vignettes-rosters-1.png |binary 26 files changed, 1821 insertions(+), 1783 deletions(-)
Title: Generalized Linear Models with Truncated Lasso Penalty
Description: Extremely efficient procedures for fitting regularization path with l0, l1, and truncated lasso penalty for linear regression and logistic regression models. This version is a completely new version compared with our previous version, which was mainly based on R. New core algorithms are developed and are now written in C++ and highly optimized.
Author: Chunlin Li [aut],
Yu Yang [aut, cre],
Chong Wu [aut]
Maintainer: Yu Yang <yang6367@umn.edu>
Diff between glmtlp versions 1.1 dated 2018-02-07 and 2.0.0 dated 2021-10-15
glmtlp-1.1/glmtlp/R/cvglmTLP.R |only glmtlp-1.1/glmtlp/R/glmTLP.R |only glmtlp-1.1/glmtlp/data/QuickStartExample.RData |only glmtlp-1.1/glmtlp/man/QuickStartExample.Rd |only glmtlp-1.1/glmtlp/man/cv.glmTLP.Rd |only glmtlp-1.1/glmtlp/man/glmTLP.Rd |only glmtlp-1.1/glmtlp/man/glmtlp-package.Rd |only glmtlp-1.1/glmtlp/man/x.Rd |only glmtlp-1.1/glmtlp/man/y.Rd |only glmtlp-2.0.0/glmtlp/DESCRIPTION | 36 +++++++++---- glmtlp-2.0.0/glmtlp/MD5 | 68 ++++++++++++++++++++----- glmtlp-2.0.0/glmtlp/NAMESPACE | 28 ++++++++-- glmtlp-2.0.0/glmtlp/NEWS.md |only glmtlp-2.0.0/glmtlp/R/cv.glmtlp.R |only glmtlp-2.0.0/glmtlp/R/data.R |only glmtlp-2.0.0/glmtlp/R/gaussian_l0_reg.R |only glmtlp-2.0.0/glmtlp/R/gaussian_l1_reg.R |only glmtlp-2.0.0/glmtlp/R/gaussian_tlp_reg.R |only glmtlp-2.0.0/glmtlp/R/glmtlp.R |only glmtlp-2.0.0/glmtlp/R/glmtlp_package.R |only glmtlp-2.0.0/glmtlp/R/lambda_names.R |only glmtlp-2.0.0/glmtlp/R/logistic_l0_reg.R |only glmtlp-2.0.0/glmtlp/R/logistic_l1_reg.R |only glmtlp-2.0.0/glmtlp/R/logistic_tlp_reg.R |only glmtlp-2.0.0/glmtlp/R/loss.R |only glmtlp-2.0.0/glmtlp/R/plot_cv_glmtlp.R |only glmtlp-2.0.0/glmtlp/R/plot_glmtlp.R |only glmtlp-2.0.0/glmtlp/R/predict.R |only glmtlp-2.0.0/glmtlp/R/predict_cv.R |only glmtlp-2.0.0/glmtlp/R/setup_lambda.R |only glmtlp-2.0.0/glmtlp/R/standardize.R |only glmtlp-2.0.0/glmtlp/README.md |only glmtlp-2.0.0/glmtlp/build |only glmtlp-2.0.0/glmtlp/data/bin_data.rda |only glmtlp-2.0.0/glmtlp/data/gau_data.rda |only glmtlp-2.0.0/glmtlp/inst |only glmtlp-2.0.0/glmtlp/man/bin_data.Rd |only glmtlp-2.0.0/glmtlp/man/cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/figures |only glmtlp-2.0.0/glmtlp/man/gau_data.Rd |only glmtlp-2.0.0/glmtlp/man/glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/plot.cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/plot.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/predict.cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/predict.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/src |only glmtlp-2.0.0/glmtlp/vignettes |only 47 files changed, 106 insertions(+), 26 deletions(-)
Title: Diewert and Fox's Method of Value Added Growth Decomposition
Description: Decomposing value added growth into explanatory factors.
A cost constrained value added function is defined to specify the
production frontier. Industry estimates can also be aggregated using
a weighted average approach.
Details about the methodology and data can be found in Diewert and Fox (2018)
<doi:10.1093/oxfordhb/9780190226718.013.19>
and Zeng, Parsons, Diewert and Fox (2018)
<https://www.business.unsw.edu.au/research-site/centreforappliedeconomicresearch-site/Documents/emg2018-6_SZeng_EMG-Slides.pdf>.
Author: Shipei Zeng
Maintainer: Shipei Zeng <shipei.zeng@unswalumni.com>
Diff between dfvad versions 0.3.0 dated 2020-03-05 and 0.3.6 dated 2021-10-15
dfvad-0.3.0/dfvad/man/figures/README-unnamed-chunk-5-1.png |only dfvad-0.3.6/dfvad/DESCRIPTION | 14 ++--- dfvad-0.3.6/dfvad/MD5 | 34 ++++++++++--- dfvad-0.3.6/dfvad/NAMESPACE | 3 + dfvad-0.3.6/dfvad/R/dynamics.R |only dfvad-0.3.6/dfvad/R/firms.R |only dfvad-0.3.6/dfvad/R/pb_index.R |only dfvad-0.3.6/dfvad/R/pm_index.R |only dfvad-0.3.6/dfvad/R/prices.R |only dfvad-0.3.6/dfvad/README.md | 19 ++++++- dfvad-0.3.6/dfvad/data/firms.rda |only dfvad-0.3.6/dfvad/data/prices.rda |only dfvad-0.3.6/dfvad/inst/doc/dfvad_vignette.html | 4 - dfvad-0.3.6/dfvad/inst/extdata |only dfvad-0.3.6/dfvad/man/dynamics.Rd |only dfvad-0.3.6/dfvad/man/figures/README-unnamed-chunk-7-1.png |only dfvad-0.3.6/dfvad/man/firms.Rd |only dfvad-0.3.6/dfvad/man/pb_index.Rd |only dfvad-0.3.6/dfvad/man/pm_index.Rd |only dfvad-0.3.6/dfvad/man/prices.Rd |only dfvad-0.3.6/dfvad/tests/testthat/test_dynamics.R |only dfvad-0.3.6/dfvad/tests/testthat/test_pb_index.R |only dfvad-0.3.6/dfvad/tests/testthat/test_pm_index.R |only dfvad-0.3.6/dfvad/tests/testthat/test_t_weight.R | 8 +++ dfvad-0.3.6/dfvad/tests/testthat/test_value_decom.R | 3 + 25 files changed, 68 insertions(+), 17 deletions(-)
Title: Person Fit
Description: Several person-fit statistics
(PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>)
are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>
Diff between PerFit versions 1.4.5 dated 2021-02-21 and 1.4.6 dated 2021-10-15
DESCRIPTION | 10 - MD5 | 8 R/Accessory.R | 446 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/PerFit-package.Rd | 1 5 files changed, 233 insertions(+), 232 deletions(-)
Title: Calculate and Predict the Low Density Lipoprotein Values
Description: A wide variety of ways to calculate (through equations) or predict (using 9 Machine learning methods as well as a stack algorithm combination of them all) the Low Density Lipoprotein values of patients based on the values of three other metrics as Total Cholesterol , Triglyceride and High Density Lipoprotein.
Author: Petros Paplomatas [aut, cre],
Kostas Anagnostopoulos [aut]
Maintainer: Petros Paplomatas <P.paplomatas@hotmail.com>
Diff between LDLcalc versions 1.0 dated 2021-09-30 and 1.1 dated 2021-10-15
DESCRIPTION | 17 ++++++++++------- MD5 | 24 ++++++++++++------------ R/9ML_models_functions.R | 6 +++--- R/All9Models.R | 2 +- R/Plot_functions.R | 2 +- R/SampleData.R | 2 +- R/Stacking_Algorith_Model_Functions.R | 3 ++- man/Corr_Plot.Rd | 2 +- man/LDL_ML_Main.Rd | 4 ++-- man/LDL_ML_Main_All_Models.Rd | 2 +- man/LDL_ML_Main_StackingAlgorithm.Rd | 2 +- man/LDL_ML_predict.Rd | 2 +- man/SampleData.Rd | 2 +- 13 files changed, 37 insertions(+), 33 deletions(-)
Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
Description: Complex graphical representations of data are best explored using interactive elements.
'parcats' adds interactive graphing capabilities to the 'easyalluvial' package.
The 'plotly.js' parallel categories diagrams offer a good framework for
creating interactive flow graphs that allow manual drag and drop sorting of dimensions
and categories, highlighting single flows and displaying mouse over information. The
'plotly.js' dependency is quite heavy and therefore is outsourced into a separate package.
Author: Bjoern Koneswarakantha [aut, cre]
(<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Diff between parcats versions 0.0.2 dated 2020-09-09 and 0.0.3 dated 2021-10-15
DESCRIPTION | 19 - MD5 | 30 +- NAMESPACE | 1 NEWS.md | 3 R/parcats.R | 25 + README.md | 50 ++- inst/WORDLIST | 9 inst/htmlwidgets/lib/plotly.js/LICENSE | 2 inst/htmlwidgets/lib/plotly.js/locales/plotly-locale-cs.js | 2 inst/htmlwidgets/lib/plotly.js/plotly.min.js | 33 +- inst/htmlwidgets/parcats.js | 2 inst/htmlwidgets/parcats.yaml | 2 inst/shiny/parcats/rsconnect |only inst/shiny/parcats/server.R | 59 ++++ inst/shiny/parcats/ui.R | 171 ++++++++++++- man/parcats.Rd | 2 man/parcats_demo.Rd |only 17 files changed, 327 insertions(+), 83 deletions(-)
Title: R Interface to 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying
feasible solutions out of a very large set of candidates, where the problem can be modeled in terms
of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language.
Constraint satisfaction and discrete optimization problems can be formulated in a high-level
modeling language. Models are compiled into an intermediate representation that is understood by a
wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users
can use the package to solve constraint programming problems without using 'MiniZinc' directly,
modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>
Diff between rminizinc versions 0.0.7 dated 2021-08-04 and 0.0.8 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 10 +++------- configure.win | 18 +++++++++--------- data/config.RData |binary data/proot.RData |binary data/slvbin.RData |binary src/RcppExports.cpp | 5 +++++ 10 files changed, 39 insertions(+), 38 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre],
Jarrett Byrnes [aut] (<https://orcid.org/0000-0002-9791-9472>)
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between coronavirus versions 0.3.30 dated 2021-09-19 and 0.3.31 dated 2021-10-15
coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.R |only coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.Rmd |only coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.html |only coronavirus-0.3.30/coronavirus/vignettes/update_dataset_function.Rmd |only coronavirus-0.3.31/coronavirus/DESCRIPTION | 6 coronavirus-0.3.31/coronavirus/MD5 | 28 - coronavirus-0.3.31/coronavirus/NEWS.md | 11 coronavirus-0.3.31/coronavirus/R/data.R | 8 coronavirus-0.3.31/coronavirus/R/refresh_coronvirus.R | 5 coronavirus-0.3.31/coronavirus/README.md | 177 +++++----- coronavirus-0.3.31/coronavirus/build/vignette.rds |binary coronavirus-0.3.31/coronavirus/data/coronavirus.rda |binary coronavirus-0.3.31/coronavirus/data/covid19_vaccine.rda |binary coronavirus-0.3.31/coronavirus/man/coronavirus.Rd | 8 coronavirus-0.3.31/coronavirus/man/figures/brazil_cases.svg | 2 coronavirus-0.3.31/coronavirus/man/figures/top20_countries.svg | 2 coronavirus-0.3.31/coronavirus/man/figures/treemap_conf.svg | 2 17 files changed, 141 insertions(+), 108 deletions(-)
Title: Arbitrary-Precision Integer and Floating-Point Mathematics
Description: Classes for storing and manipulating arbitrary-precision
integer vectors and high-precision floating-point vectors. These
extend the range and precision of the 'integer' and 'double' data
types found in R. This package utilizes the 'Boost.Multiprecision' C++
library. It is specifically designed to work well with the 'tidyverse'
collection of R packages.
Author: David Hall [aut, cre, cph] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between bignum versions 0.2.2 dated 2021-09-21 and 0.3.0 dated 2021-10-15
bignum-0.2.2/bignum/inst/doc/operations.R |only bignum-0.2.2/bignum/inst/doc/operations.Rmd |only bignum-0.2.2/bignum/inst/doc/operations.html |only bignum-0.2.2/bignum/vignettes/operations.Rmd |only bignum-0.3.0/bignum/DESCRIPTION | 10 - bignum-0.3.0/bignum/MD5 | 52 ++++----- bignum-0.3.0/bignum/NAMESPACE | 4 bignum-0.3.0/bignum/NEWS.md | 10 + bignum-0.3.0/bignum/R/biginteger.R | 2 bignum-0.3.0/bignum/R/conditions.R | 27 +++- bignum-0.3.0/bignum/R/cpp11.R | 24 ++++ bignum-0.3.0/bignum/R/seq.R |only bignum-0.3.0/bignum/R/vctrs-arith.R | 41 +++++++ bignum-0.3.0/bignum/R/vctrs-compare.R | 21 +++ bignum-0.3.0/bignum/R/vctrs-math.R | 107 +++++++++++++++++++ bignum-0.3.0/bignum/README.md | 2 bignum-0.3.0/bignum/build/vignette.rds |binary bignum-0.3.0/bignum/inst/doc/precision.html | 26 ++-- bignum-0.3.0/bignum/inst/doc/type-hierarchy.html | 57 +++++----- bignum-0.3.0/bignum/man/biginteger.Rd | 2 bignum-0.3.0/bignum/man/bignum-arith.Rd |only bignum-0.3.0/bignum/man/bignum-compare.Rd |only bignum-0.3.0/bignum/man/bignum-math.Rd |only bignum-0.3.0/bignum/man/bignum-package.Rd | 7 - bignum-0.3.0/bignum/man/bignum-special.Rd |only bignum-0.3.0/bignum/man/seq.bignum_vctr.Rd |only bignum-0.3.0/bignum/src/bigfloat_interface.cpp | 81 ++++++++++++++ bignum-0.3.0/bignum/src/biginteger_interface.cpp | 89 +++++++++++++++ bignum-0.3.0/bignum/src/cpp11.cpp | 54 +++++++++ bignum-0.3.0/bignum/tests/testthat/_snaps/seq.md |only bignum-0.3.0/bignum/tests/testthat/test-bigfloat.R | 8 - bignum-0.3.0/bignum/tests/testthat/test-seq.R |only bignum-0.3.0/bignum/tests/testthat/test-vctrs-math.R | 4 33 files changed, 540 insertions(+), 88 deletions(-)
Title: Time-Varying Effect Models
Description: Fits time-varying effect models (TVEM). These are a kind of application of varying-coefficient models in the context of longitudinal data, allowing the strength of linear, logistic, or Poisson regression relationships to change over time. These models are described further in Tan, Shiyko, Li, Li & Dierker (2012) <doi:10.1037/a0025814>. We thank Kaylee Litson, Patricia Berglund, and Yajnaseni Chakraborti for their valuable help with testing the package and documentation. The development of this package was part of a research project supported by National Institutes of Health grants P50 DA039838 from the National Institute of Drug Abuse and 1R01 CA229542-01 from the National Cancer Institute and the NIH Office of Behavioral and Social Science Research. Content is solely the responsibility of the authors and does not necessarily represent the official views of the funding institutions mentioned above. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Author: John J. Dziak [aut, cre] (<https://orcid.org/0000-0003-0762-5495>),
Donna L. Coffman [aut] (<https://orcid.org/0000-0001-6305-6579>),
Runze Li [aut] (<https://orcid.org/0000-0002-0154-2202>),
Kaylee Litson [aut] (<https://orcid.org/0000-0003-1296-4811>),
Yajnaseni Chakraborti [aut]
Maintainer: John J. Dziak <dziakj1@gmail.com>
Diff between tvem versions 1.3 dated 2021-08-05 and 1.3.1 dated 2021-10-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/tvem.r | 6 +++++- build/vignette.rds |binary inst/doc/vignette-tvem.Rmd | 4 ++-- inst/doc/vignette-tvem.html | 8 ++++---- man/tvem.Rd | 6 +++++- vignettes/vignette-tvem.Rmd | 4 ++-- 8 files changed, 29 insertions(+), 21 deletions(-)
Title: Text Plots
Description: Visualise complex relations in texts. This is done by providing functionalities for displaying
text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering and semantic text 'embeddings'.
Feel free to join the effort of providing interesting text visualisations.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Sacha Epskamp [ctb, cph] (code in R/matrix_reduction.R adapted from the
qgraph package version 1.4.0 which is GPL-2 licensed),
Ingo Feinerer and Kurt Hornik [ctb, cph] (partial code in
R/textplot_corlines.R adapted from the tm package version 0.4 which
is GPL-2 licensed)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textplot versions 0.2.0 dated 2021-08-18 and 0.2.1 dated 2021-10-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/textplot_biterms.R | 2 +- build/vignette.rds |binary inst/doc/textplot-examples.pdf |binary 6 files changed, 15 insertions(+), 10 deletions(-)
Title: The Ramer-Douglas-Peucker Algorithm
Description: Pretty fast implementation of the Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2D curve.
Urs Ramer (1972), "An iterative procedure for the polygonal approximation of plane curves" <doi:10.1016/S0146-664X(72)80017-0>.
David H. Douglas and Thomas K. Peucker (1973), "Algorithms for the Reduction of the Number of Points Required to Represent a Digitized Line or its Caricature" <doi:10.3138/FM57-6770-U75U-7727>.
Author: Robert Dahl Jacobsen [aut, cre]
Maintainer: Robert Dahl Jacobsen <cran@dahl-jacobsen.dk>
Diff between RDP versions 0.1.8 dated 2021-09-25 and 0.2.0 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/RcppExports.R | 3 +++ build/partial.rdb |binary man/RamerDouglasPeucker.Rd | 4 ++++ src/RamerDouglasPeucker.cpp | 1 - src/wrapper.cpp | 7 +++++-- tests/testthat/test-RamerDouglasPeucker.R | 12 +++++++++--- 8 files changed, 31 insertions(+), 16 deletions(-)
Title: Variance Function Program
Description: Variance function estimation for models proposed by W. Sadler in his variance function program
('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is
to fit multiple variance functions to a data set and consequently assess which function reflects
the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship
is of great importance when individual test-results are used for defining follow-up treatment of patients.
Author: Andre Schuetzenmeister [cre, aut],
Florian Dufey [aut],
Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VFP versions 1.3 dated 2020-06-16 and 1.3.1 dated 2021-10-14
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- build/vignette.rds |binary inst/doc/VFP_package_vignette.html | 53 +++++++++++++++++++--------- inst/doc/VFP_package_vignette.rmd | 38 ++++++++++---------- man/VFP-Package.Rd | 4 +- vignettes/VFP_package_vignette.rmd | 38 ++++++++++---------- vignettes/figures/deriveCx_examples_2-1.png |binary vignettes/figures/deriveCx_examples_3-1.png |binary vignettes/figures/deriveCx_examples_4-1.png |binary 10 files changed, 89 insertions(+), 70 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 10. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>.
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.1.9 dated 2021-10-05 and 0.2.0 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/All.R | 26 ++++++++++++++++++++++---- data/AMSP.RData |binary data/NRFAData.RData |binary data/QMEDData.RData |binary 6 files changed, 30 insertions(+), 12 deletions(-)
Title: Framework for Specifying and Simulating Individual Based Models
Description: A framework which provides users a set of useful primitive elements for
specifying individual based simulation models, with special attention models for
infectious disease epidemiology. Users build models by specifying variables for
each characteristic of individuals in the simulated population by using data
structures exposed by the package. The package provides efficient methods for
finding subsets of individuals based on these variables, or cohorts. Cohorts can
then be targeted for variable updates or scheduled for events. Variable updates
queued during a time step are executed at the end of a discrete time step, and
the code places no restrictions on how individuals are allowed to interact.
These data structures are designed to provide an intuitive way for users to turn
their conceptual model of a system into executable code, which is fast and
memory efficient.
Author: Giovanni Charles [aut, cre] (<https://orcid.org/0000-0002-7024-1200>),
Sean L. Wu [aut] (<https://orcid.org/0000-0002-5781-9493>),
Peter Winskill [aut] (<https://orcid.org/0000-0003-3001-4959>),
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <giovanni.charles@gmail.com>
Diff between individual versions 0.1.4 dated 2021-07-29 and 0.1.6 dated 2021-10-14
individual-0.1.4/individual/tests/testthat/helper-event.R |only individual-0.1.4/individual/tests/testthat/test-variables.R |only individual-0.1.6/individual/DESCRIPTION | 21 individual-0.1.6/individual/MD5 | 83 +- individual-0.1.6/individual/NEWS.md |only individual-0.1.6/individual/R/RcppExports.R | 16 individual-0.1.6/individual/R/bitset.R | 23 individual-0.1.6/individual/R/categorical_variable.R | 6 individual-0.1.6/individual/R/double_variable.R | 42 - individual-0.1.6/individual/R/integer_variable.R | 42 - individual-0.1.6/individual/R/targeted_event.R | 36 - individual-0.1.6/individual/README.md | 91 ++ individual-0.1.6/individual/inst/doc/API.Rmd | 2 individual-0.1.6/individual/inst/doc/API.html | 4 individual-0.1.6/individual/inst/doc/Contributing.Rmd | 2 individual-0.1.6/individual/inst/doc/Contributing.html | 2 individual-0.1.6/individual/inst/doc/Tutorial.R | 2 individual-0.1.6/individual/inst/doc/Tutorial.Rmd | 2 individual-0.1.6/individual/inst/doc/Tutorial.html | 4 individual-0.1.6/individual/inst/include/CategoricalVariable.h | 170 +++-- individual-0.1.6/individual/inst/include/DoubleVariable.h | 222 ++++--- individual-0.1.6/individual/inst/include/Event.h | 314 ++++++--- individual-0.1.6/individual/inst/include/IntegerVariable.h | 316 +++++----- individual-0.1.6/individual/inst/include/IterableBitset.h | 55 + individual-0.1.6/individual/inst/include/Variable.h | 2 individual-0.1.6/individual/man/Bitset.Rd | 16 individual-0.1.6/individual/man/IntegerVariable.Rd | 4 individual-0.1.6/individual/man/TargetedEvent.Rd | 5 individual-0.1.6/individual/man/figures |only individual-0.1.6/individual/src/RcppExports.cpp | 56 + individual-0.1.6/individual/src/bitset.cpp | 22 individual-0.1.6/individual/src/categorical_variable.cpp | 2 individual-0.1.6/individual/src/double_variable.cpp | 13 individual-0.1.6/individual/src/event.cpp | 25 individual-0.1.6/individual/src/integer_variable.cpp | 23 individual-0.1.6/individual/tests/testthat/helper-targetedevent.R |only individual-0.1.6/individual/tests/testthat/test-bitset.R | 79 +- individual-0.1.6/individual/tests/testthat/test-categoricalvariable.R |only individual-0.1.6/individual/tests/testthat/test-cpp.R | 5 individual-0.1.6/individual/tests/testthat/test-doublevariable.R |only individual-0.1.6/individual/tests/testthat/test-events.R | 176 ----- individual-0.1.6/individual/tests/testthat/test-integervariable.R |only individual-0.1.6/individual/tests/testthat/test-simulation-e2e.R | 2 individual-0.1.6/individual/tests/testthat/test-targetedevent.R |only individual-0.1.6/individual/vignettes/API.Rmd | 2 individual-0.1.6/individual/vignettes/Contributing.Rmd | 2 individual-0.1.6/individual/vignettes/Tutorial.Rmd | 2 47 files changed, 1135 insertions(+), 756 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.10 dated 2021-06-18 and 2.0.1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 5 ++++- inst/raster |only 3 files changed, 7 insertions(+), 4 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized
linear models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [cre, aut]
(<https://orcid.org/0000-0002-7182-1346>),
Anthony Williams [cph],
Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between parglm versions 0.1.6 dated 2020-08-10 and 0.1.7 dated 2021-10-14
DESCRIPTION | 15 +-- MD5 | 35 +++---- NEWS.md | 18 ++- R/parglm.R | 2 README.md | 2 build/vignette.rds |binary src/LAPACK_wrappers.cpp | 90 +++---------------- src/LAPACK_wrappers.h | 98 +++++++++++++++++++-- src/R_BLAS_LAPACK.cpp | 29 ++++++ src/R_BLAS_LAPACK.h | 4 src/RcppExports.cpp | 5 + src/constant.h |only src/family.cpp | 36 ++++--- src/family.h | 134 +++++++++++++++++------------ src/parallel_glm.cpp | 206 +++++++++++++++++++++++++++------------------ src/parallel_qr.cpp | 55 +++++++++--- src/parallel_qr.h | 7 + src/thread_pool.h | 12 ++ tests/testthat/test_misc.R | 2 19 files changed, 472 insertions(+), 278 deletions(-)
Title: Create, Modify and Visualize Multi-Layered Networks
Description: Allows the user to create graph with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized.
Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>.
More about multilayered graphs and their usage can be found in our review paper:
Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.
Author: Zaynab Hammoud
Maintainer: Zaynab Hammoud <zaynabhassanhammoud@gmail.com>
Diff between mully versions 2.1.33 dated 2021-06-02 and 2.1.34 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/mully_constructor.R | 2 ++ R/mully_import.R | 10 ++++------ R/mully_visualization.R | 18 ++++++++++++++---- inst/doc/mully-pdf.pdf |binary inst/doc/mully-vignette.html | 4 ++-- man/importGraphCSV.Rd | 2 +- 8 files changed, 33 insertions(+), 23 deletions(-)
Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Raffaella Piccarreta [ctb],
Isobel Claire Gormley [ctb] (<https://orcid.org/0000-0001-7713-681X>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MEDseq versions 1.3.0 dated 2021-07-15 and 1.3.1 dated 2021-10-14
DESCRIPTION | 12 - MD5 | 29 +-- NAMESPACE | 4 R/Functions.R | 382 +++++++++++++++++++++++++++++++++++++++++++------- R/Hidden_Functions.R | 34 ++++ R/MEDseq.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 16 +- inst/doc/MEDseq.html | 8 - man/MEDseq-package.Rd | 4 man/MEDseq_compare.Rd | 2 man/MEDseq_control.Rd | 8 - man/plot.MEDseq.Rd | 12 + man/wKModes.Rd |only vignettes/bio_mod.rda |binary 16 files changed, 430 insertions(+), 85 deletions(-)
Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of loss-based estimator selection to
identify the optimal estimator of the covariance matrix from among a
prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
(<https://orcid.org/0000-0002-4850-2507>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Brian Collica [aut] (<https://orcid.org/0000-0003-1127-2557>),
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>),
Sandrine Dudoit [ctb, ths] (<https://orcid.org/0000-0002-6069-8629>)
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 1.0.0 dated 2021-07-25 and 1.0.1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/estimators.R | 8 +++----- R/thresholdingFunctions.R | 31 +++++++++++++------------------ README.md | 25 ++++++++++++++++++++----- build/partial.rdb |binary inst/doc/using_cvCovEst.html | 12 ++++++------ 8 files changed, 57 insertions(+), 44 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Maximillian H.K. Hesselbarth [ctb] (Co-author of underlying C++ code
for get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Marco Sciaini [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Sebastian Hanss [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.9.1 dated 2021-04-19 and 0.9.2 dated 2021-10-14
DESCRIPTION | 6 +- MD5 | 18 +++---- README.md | 16 +++++- build/vignette.rds |binary inst/doc/coma.html | 4 - inst/doc/incoma.html | 4 - inst/doc/wecoma.html | 4 - inst/include/comat_RcppExports.h | 63 +++++++++++++++++++++++++ src/RcppExports.cpp | 98 +++++++++++++++++++++++++++++++++++---- src/create_neighborhood.cpp | 6 -- 10 files changed, 187 insertions(+), 32 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.72.4 dated 2021-05-13 and 0.72.5 dated 2021-10-14
DESCRIPTION | 12 ++-- MD5 | 20 +++--- NAMESPACE | 1 R/daylength.R | 4 - R/temperature_generation.R | 1 inst/doc/PhenoFlex.html | 61 ++++++++++---------- inst/doc/hourly_temperatures.html | 114 +++++++++++++++++++------------------- src/RcppExports.cpp | 5 + tests/testthat/test_PhenoFlex.R | 2 tests/testthat/test_chifull.R | 2 vignettes/Chilling_references.bib | 2 11 files changed, 115 insertions(+), 109 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537>, which can be generated by the citation function in R.
Author: David Bolin [cre, aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 0.6.2 dated 2021-02-23 and 0.6.3 dated 2021-10-14
rSPDE-0.6.2/rSPDE/R/factional.computations.R |only rSPDE-0.6.2/rSPDE/R/factional.operators.R |only rSPDE-0.6.2/rSPDE/vignettes/rspde.bib |only rSPDE-0.6.3/rSPDE/DESCRIPTION | 8 rSPDE-0.6.3/rSPDE/MD5 | 23 rSPDE-0.6.3/rSPDE/NEWS.md | 3 rSPDE-0.6.3/rSPDE/R/fractional.computations.R |only rSPDE-0.6.3/rSPDE/R/fractional.operators.R |only rSPDE-0.6.3/rSPDE/build/vignette.rds |binary rSPDE-0.6.3/rSPDE/inst/doc/rspde.Rmd | 36 + rSPDE-0.6.3/rSPDE/inst/doc/rspde.html | 710 +++++++++++--------------- rSPDE-0.6.3/rSPDE/man/fractional.operators.Rd | 2 rSPDE-0.6.3/rSPDE/man/matern.operators.Rd | 2 rSPDE-0.6.3/rSPDE/man/rSPDE.loglike.Rd | 9 rSPDE-0.6.3/rSPDE/vignettes/rspde.Rmd | 36 + 15 files changed, 396 insertions(+), 433 deletions(-)
Title: Projection Pursuit Classification Forest
Description: Implements projection pursuit forest algorithm for supervised classification.
Author: Natalia da Silva, Eun-Kyung Lee, Di Cook
Maintainer: Natalia da Silva <natalia.dasilva@fcea.edu.uy>
Diff between PPforest versions 0.1.1 dated 2018-06-11 and 0.1.2 dated 2021-10-14
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 6 R/PPforest.R | 40 ++- R/trees_pred.R | 15 - build/vignette.rds |binary inst/doc/PPforest-vignette.R | 30 +- inst/doc/PPforest-vignette.Rmd | 23 +- inst/doc/PPforest-vignette.html | 444 +++++++++++++++------------------------- man/PPforest.Rd | 7 man/trees_pred.Rd | 6 src/RcppExports.cpp | 5 vignettes/PPforest-vignette.Rmd | 23 +- 13 files changed, 276 insertions(+), 355 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Sido Haakma [aut, cre] (<https://orcid.org/0000-0003-1278-9144>),
Tommy de Boer [aut] (<https://orcid.org/0000-0002-4492-7225>),
Fleur Kelpin [aut] (<https://orcid.org/0000-0003-1527-5130>),
MOLGENIS org [cph, fnd]
Maintainer: Sido Haakma <s.haakma@rug.nl>
Diff between DSMolgenisArmadillo versions 1.3.6 dated 2021-10-12 and 1.3.7 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/ArmadilloResult.R | 3 ++- tests/testthat/test-ArmadilloResult.R | 22 ++++++++++++++++++++++ 5 files changed, 39 insertions(+), 8 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.2.0 dated 2021-09-06 and 1.2.1 dated 2021-10-14
DESCRIPTION | 19 MD5 | 609 +++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 4 R/arith_wrapper.R | 20 - R/arithc_wrapper.R | 226 +++++------ R/calc_field.R | 73 +-- R/calc_overlapping_time.R | 319 ++++++++-------- R/calc_timx_result.R | 14 R/calc_trend.R | 141 +++---- R/calc_trend_advanced.R | 251 ++++++------ R/check_infile.R | 18 R/cmsaf.abs.R | 298 +++++++-------- R/cmsaf.add.R | 8 R/cmsaf.addc.R | 6 R/cmsaf.adjust.two.files.R | 36 + R/cmsaf.detrend.R | 14 R/cmsaf.div.R | 8 R/cmsaf.divc.R | 6 R/cmsaf.mk.test.R | 13 R/cmsaf.mul.R | 8 R/cmsaf.mulc.R | 6 R/cmsaf.regres.R | 14 R/cmsaf.stats.R | 13 R/cmsaf.stats.station.data.R | 422 ++++++++++----------- R/cmsaf.sub.R | 8 R/cmsaf.sub.rel.R | 24 - R/cmsaf.subc.R | 6 R/cmsaf.transform.coordinate.system.R | 217 +++++------ R/dayavg.R | 130 +++--- R/daymax.R | 122 +++--- R/daymean.R | 130 +++--- R/daymin.R | 6 R/daypctl.R | 6 R/dayrange.R | 14 R/daysd.R | 6 R/daysum.R | 120 +++--- R/dayvar.R | 6 R/dayx_wrapper.R | 302 +++++++-------- R/divdpm.R | 6 R/extract.level.R | 15 R/extract.period.R | 15 R/fld_cor_covar_wrapper.R | 284 +++++++------- R/fldcor.R | 8 R/fldcovar.R | 8 R/fldmax.R | 6 R/fldmean.R | 6 R/fldmin.R | 6 R/fldrange.R | 6 R/fldsd.R | 124 +++--- R/fldsum.R | 6 R/fldx_wrapper.R | 210 +++++----- R/getTimeRange.R | 77 +-- R/get_basename.R |only R/get_climatology.R | 57 +- R/get_time_bnds_from_file.R | 16 R/gridboxmax.R | 6 R/gridboxmean.R | 6 R/gridboxmin.R | 6 R/gridboxrange.R | 6 R/gridboxsd.R | 6 R/gridboxsum.R | 6 R/gridboxvar.R | 6 R/gridboxx_wrapper.R | 556 ++++++++++++++-------------- R/hourmean.R | 122 +++--- R/hoursum.R | 6 R/hourx_wrapper.R | 237 ++++++------ R/is_url.R |only R/mermean.R | 6 R/merx_wrapper.R | 217 +++++------ R/mon.anomaly.R | 18 R/mon.anomaly.climatology.R | 355 +++++++++--------- R/mon_num_above.R | 6 R/mon_num_below.R | 6 R/mon_num_equal.R | 6 R/mon_num_wrapper.R | 11 R/monavg.R | 6 R/mondaymean.R | 393 ++++++++++---------- R/monmax.R | 6 R/monmean.R | 6 R/monmin.R | 6 R/monpctl.R | 6 R/monsd.R | 6 R/monsum.R | 6 R/monvar.R | 6 R/monx_wrapper.R | 340 ++++++++--------- R/muldpm.R | 6 R/multimonmean.R | 13 R/multimonsum.R | 13 R/ncinfo.R | 9 R/num_above.R | 6 R/num_below.R | 6 R/num_equal.R | 6 R/num_wrapper.R | 11 R/read_file.R | 161 ++++---- R/read_file_all.R | 143 +++---- R/read_ncvar.R | 13 R/remap.R | 21 - R/runmax.R | 6 R/runmean.R | 6 R/runmin.R | 128 +++--- R/runrange.R | 6 R/runsd.R | 6 R/runsum.R | 6 R/runx_wrapper.R | 309 +++++++-------- R/seas.anomaly.R | 14 R/seasmean.R | 6 R/seassd.R | 6 R/seassum.R | 6 R/seasvar.R | 128 +++--- R/seasx_wrapper.R | 321 ++++++++-------- R/sellonlatbox.R | 18 R/selmon.R | 15 R/selperiod.R | 353 +++++++++-------- R/selpoint.R | 20 - R/selpoint.multi.R | 29 - R/seltime.R | 15 R/selyear.R | 15 R/tim_cor_covar_wrapper.R | 20 - R/timavg.R | 6 R/timcor.R | 8 R/timcovar.R | 8 R/timcumsum.R | 25 - R/timmax.R | 6 R/timmean.R | 6 R/timmin.R | 6 R/timpctl.R | 6 R/timsd.R | 6 R/timselmean.R | 6 R/timselsum.R | 6 R/timselx_wrapper.R | 11 R/timsum.R | 6 R/timx_wrapper.R | 164 ++++---- R/trend.R | 10 R/trend_advanced.R | 16 R/wfldmean.R | 7 R/xdpm_wrapper.R | 243 ++++++------ R/ydaymax.R | 6 R/ydaymean.R | 14 R/ydaymin.R | 6 R/ydayrange.R | 6 R/ydaysd.R | 6 R/ydaysum.R | 6 R/ydayx_wrapper.R | 268 ++++++------- R/ydrunmean.R | 6 R/ydrunsd.R | 6 R/ydrunsum.R | 6 R/ydrunx_wrapper.R | 97 ++-- R/year.anomaly.R | 16 R/yearmax.R | 124 +++--- R/yearmean.R | 14 R/yearmin.R | 122 +++--- R/yearrange.R | 6 R/yearsd.R | 6 R/yearsum.R | 13 R/yearvar.R | 122 +++--- R/yearx_wrapper.R | 257 ++++++------- R/ymonmax.R | 6 R/ymonmean.R | 6 R/ymonmin.R | 6 R/ymonsd.R | 6 R/ymonsum.R | 6 R/ymonx_wrapper.R | 258 ++++++------- R/yseasmax.R | 6 R/yseasmean.R | 6 R/yseasmin.R | 6 R/yseassd.R | 6 R/yseasx_wrapper.R | 256 ++++++------- R/zonmean.R | 124 +++--- R/zonsum.R | 124 +++--- R/zonx_wrapper.R | 229 +++++------ build/partial.rdb |binary inst/WORDLIST | 1 man/calc_overlapping_time.Rd | 15 man/cmsaf.abs.Rd | 13 man/cmsaf.add.Rd | 10 man/cmsaf.addc.Rd | 6 man/cmsaf.adjust.two.files.Rd | 10 man/cmsaf.detrend.Rd | 6 man/cmsaf.div.Rd | 10 man/cmsaf.divc.Rd | 6 man/cmsaf.mk.test.Rd | 6 man/cmsaf.mul.Rd | 10 man/cmsaf.mulc.Rd | 6 man/cmsaf.regres.Rd | 6 man/cmsaf.stats.Rd | 10 man/cmsaf.stats.station.data.Rd | 12 man/cmsaf.sub.Rd | 10 man/cmsaf.sub.rel.Rd | 10 man/cmsaf.subc.Rd | 6 man/cmsaf.transform.coordinate.system.Rd | 5 man/dayavg.Rd | 13 man/daymax.Rd | 13 man/daymean.Rd | 13 man/daymin.Rd | 13 man/daypctl.Rd | 6 man/dayrange.Rd | 13 man/daysd.Rd | 13 man/daysum.Rd | 13 man/dayvar.Rd | 13 man/divdpm.Rd | 13 man/extract.level.Rd | 6 man/extract.period.Rd | 6 man/fldcor.Rd | 10 man/fldcovar.Rd | 10 man/fldmax.Rd | 13 man/fldmean.Rd | 13 man/fldmin.Rd | 13 man/fldrange.Rd | 13 man/fldsd.Rd | 13 man/fldsum.Rd | 13 man/get_basename.Rd |only man/gridboxmax.Rd | 6 man/gridboxmean.Rd | 6 man/gridboxmin.Rd | 6 man/gridboxrange.Rd | 6 man/gridboxsd.Rd | 6 man/gridboxsum.Rd | 6 man/gridboxvar.Rd | 6 man/hourmean.Rd | 13 man/hoursum.Rd | 13 man/mermean.Rd | 13 man/mon.anomaly.Rd | 13 man/mon.anomaly.climatology.Rd | 6 man/mon_num_above.Rd | 6 man/mon_num_below.Rd | 6 man/mon_num_equal.Rd | 6 man/monavg.Rd | 13 man/mondaymean.Rd | 13 man/monmax.Rd | 13 man/monmean.Rd | 13 man/monmin.Rd | 13 man/monpctl.Rd | 6 man/monsd.Rd | 13 man/monsum.Rd | 13 man/monvar.Rd | 13 man/muldpm.Rd | 13 man/multimonmean.Rd | 6 man/multimonsum.Rd | 6 man/ncinfo.Rd | 123 +++--- man/num_above.Rd | 6 man/num_below.Rd | 6 man/num_equal.Rd | 6 man/read_file.Rd | 5 man/read_ncvar.Rd | 5 man/remap.Rd | 10 man/runmax.Rd | 6 man/runmean.Rd | 6 man/runmin.Rd | 6 man/runrange.Rd | 6 man/runsd.Rd | 6 man/runsum.Rd | 6 man/seas.anomaly.Rd | 6 man/seasmean.Rd | 13 man/seassd.Rd | 13 man/seassum.Rd | 13 man/seasvar.Rd | 13 man/sellonlatbox.Rd | 6 man/selmon.Rd | 6 man/selperiod.Rd | 6 man/selpoint.Rd | 6 man/selpoint.multi.Rd | 6 man/seltime.Rd | 6 man/selyear.Rd | 6 man/timavg.Rd | 13 man/timcor.Rd | 10 man/timcovar.Rd | 10 man/timcumsum.Rd | 6 man/timmax.Rd | 13 man/timmean.Rd | 13 man/timmin.Rd | 13 man/timpctl.Rd | 6 man/timsd.Rd | 13 man/timselmean.Rd | 6 man/timselsum.Rd | 6 man/timsum.Rd | 13 man/trend.Rd | 6 man/trend_advanced.Rd | 10 man/wfldmean.Rd | 13 man/ydaymax.Rd | 13 man/ydaymean.Rd | 13 man/ydaymin.Rd | 13 man/ydayrange.Rd | 13 man/ydaysd.Rd | 13 man/ydaysum.Rd | 13 man/ydrunmean.Rd | 6 man/ydrunsd.Rd | 6 man/ydrunsum.Rd | 6 man/year.anomaly.Rd | 6 man/yearmax.Rd | 13 man/yearmean.Rd | 13 man/yearmin.Rd | 13 man/yearrange.Rd | 13 man/yearsd.Rd | 13 man/yearsum.Rd | 13 man/yearvar.Rd | 13 man/ymonmax.Rd | 13 man/ymonmean.Rd | 13 man/ymonmin.Rd | 13 man/ymonsd.Rd | 13 man/ymonsum.Rd | 13 man/yseasmax.Rd | 13 man/yseasmean.Rd | 13 man/yseasmin.Rd | 13 man/yseassd.Rd | 13 man/zonmean.Rd | 13 man/zonsum.Rd | 13 307 files changed, 7144 insertions(+), 5686 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.2.0 dated 2021-09-06 and 3.3.0 dated 2021-10-14
DESCRIPTION | 23 - MD5 | 14 NEWS.md | 4 build/partial.rdb |binary inst/toolbox/global.R | 2 inst/toolbox/server.R | 923 +++++++++++++++++++++++++++++++++++++++------ inst/toolbox/ui.R | 108 ++++- inst/toolbox/www/style.css | 532 ++++++++++++------------- 8 files changed, 1211 insertions(+), 395 deletions(-)
Title: Moment Condition Based Estimation of Linear Dynamic Panel Data
Models
Description: Linear dynamic panel data modeling based on linear and
nonlinear moment conditions as proposed by
Holtz-Eakin, Newey, and Rosen (1988) <doi:10.2307/1913103>,
Ahn and Schmidt (1995) <doi:10.1016/0304-4076(94)01641-C>,
and Arellano and Bover (1995) <doi:10.1016/0304-4076(94)01642-D>.
Estimation of the model parameters relies on the Generalized
Method of Moments (GMM), numerical optimization (when nonlinear
moment conditions are employed) and the computation of closed
form solutions (when estimation is based on linear moment
conditions). One-step, two-step and iterated estimation is
available. of closed form solutions. For inference and specification
testing, Windmeijer (2005) <doi:10.1016/j.jeconom.2004.02.005>
and doubly corrected standard errors
(Hwang, Kang, Lee, 2021 <doi:10.1016/j.jeconom.2020.09.010>)
are available. Additionally, serial correlation tests, tests for
overidentification, and Wald tests are provided. Functions for
visualizing panel data structures and modeling results obtained
from GMM estimation are also available. The plot methods include
functions to plot unbalanced panel structure, coefficient ranges
and coefficient paths across GMM iterations (the latter is
implemented according to the plot shown in
Hansen and Lee, 2021 <doi:10.3982/ECTA16274>).
Author: Markus Fritsch [aut, cre],
Joachim Schnurbus [aut],
Andrew Adrian Yu Pua [aut]
Maintainer: Markus Fritsch <Markus.Fritsch@uni-Passau.de>
Diff between pdynmc versions 0.9.5 dated 2021-08-13 and 0.9.6 dated 2021-10-14
DESCRIPTION | 16 MD5 | 72 +-- NAMESPACE | 124 ++--- NEWS.md | 30 + R/pdynmc_estFct.R | 136 ++++-- R/pdynmc_specTestFcst.R | 53 +- README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 2 inst/doc/pdynmc-intro.pdf |binary inst/doc/pdynmc-introLong.pdf |binary inst/doc/pdynmc-pres-in-a-nutshell.pdf |binary inst/tests/arguments_for_StepByStepFunctionChecksABdata.R | 6 inst/tests/arguments_for_StepByStepFunctionChecksMaxG.R |only man/case.names.pdynmc.Rd | 152 +++--- man/coef.pdynmc.Rd | 150 +++--- man/data.info.Rd | 102 ++-- man/dummy.coef.pdynmc.Rd | 150 +++--- man/fitted.pdynmc.Rd | 164 +++---- man/model.matrix.pdynmc.Rd | 152 +++--- man/mtest.fct.Rd | 14 man/ninst.Rd | 146 +++--- man/ninst.pdynmc.Rd | 146 +++--- man/optimIn.Rd | 152 +++--- man/optimIn.pdynmc.Rd | 158 +++---- man/pdynmc.Rd | 14 man/plot.pdynmc.Rd | 310 +++++++------- man/print.pdynmc.Rd | 152 +++--- man/print.summary.pdynmc.Rd | 166 +++---- man/residuals.pdynmc.Rd | 164 +++---- man/summary.pdynmc.Rd | 146 +++--- man/variable.names.pdynmc.Rd | 148 +++--- man/vcov.pdynmc.Rd | 156 +++---- man/wald.fct.Rd | 8 man/wmat.Rd | 148 +++--- man/wmat.pdynmc.Rd | 156 +++---- tests/testthat/test-stdErr.R |only 38 files changed, 1804 insertions(+), 1694 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>),
Kirill Koncha [ctb] (<https://orcid.org/0000-0003-0676-2658>),
Mikhail Leonov [ctb],
Anna Smirnova [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.5 dated 2021-05-15 and 1.1.6 dated 2021-10-14
DESCRIPTION | 10 +- MD5 | 110 +++++++++++++------------ NAMESPACE | 4 NEWS | 15 ++- R/aff.lang.R | 4 R/area.lang.R | 4 R/bantu.R |only R/bantu.feature.R |only R/country.lang.R |only R/eurasianphonology.R | 2 R/eurasianphonology.feature.R | 2 R/glottolog.R | 12 +- R/gltc.lang.R | 2 R/is.glottolog.R | 2 R/iso.lang.R | 2 R/lang.aff.R | 2 R/lang.gltc.R | 2 R/lang.iso.R | 2 R/lat.lang.R | 4 R/long.lang.R | 4 R/soundcomparisons.feature.R | 3 R/subc.lang.R |only R/url.lang.R | 3 build/vignette.rds |binary data/bantu.RData |only data/glottolog.RData |binary inst/doc/lingtypology_creating_maps.Rmd | 4 inst/doc/lingtypology_creating_maps.html | 8 - inst/doc/lingtypology_db_API.html | 4 inst/doc/lingtypology_dplyr.html | 4 inst/doc/lingtypology_glottolog_functions.R | 11 ++ inst/doc/lingtypology_glottolog_functions.Rmd | 32 ++++++- inst/doc/lingtypology_glottolog_functions.html | 41 +++++++-- inst/doc/lingtypology_intro.Rmd | 2 inst/doc/lingtypology_intro.html | 6 - man/aff.lang.Rd | 4 man/area.lang.Rd | 4 man/bantu.Rd |only man/bantu.feature.Rd |only man/country.lang.Rd |only man/eurasianphonology.Rd | 2 man/eurasianphonology.feature.Rd | 2 man/glottolog.Rd | 12 +- man/gltc.lang.Rd | 2 man/is.glottolog.Rd | 2 man/iso.lang.Rd | 2 man/lang.aff.Rd | 2 man/lang.gltc.Rd | 2 man/lang.iso.Rd | 2 man/lat.lang.Rd | 4 man/long.lang.Rd | 4 man/subc.lang.Rd |only man/url.lang.Rd | 5 - tests/testthat/test-aff-lang.R | 4 tests/testthat/test-bantu-feature.R |only tests/testthat/test-country-lang.R |only tests/testthat/test-lang-aff.R | 15 +-- tests/testthat/test-mapfeature.R | 1 tests/testthat/test-subc-lang.R |only vignettes/lingtypology_creating_maps.Rmd | 4 vignettes/lingtypology_glottolog_functions.Rmd | 32 ++++++- vignettes/lingtypology_intro.Rmd | 2 62 files changed, 260 insertions(+), 148 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>),
Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>),
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.0.2 dated 2021-06-04 and 1.0.3 dated 2021-10-14
DESCRIPTION | 8 MD5 | 246 ++--- NAMESPACE | 58 - NEWS.md | 283 +++--- R/BayesMallows.R | 64 - R/RcppExports.R | 386 ++++----- R/all_topological_sorts.R | 44 - R/assess_convergence.R | 396 ++++----- R/assign_cluster.R | 164 +-- R/compute_consensus.R | 414 ++++----- R/compute_mallows.R | 848 ++++++++++---------- R/compute_mallows_mixtures.R | 90 +- R/compute_posterior_intervals.R | 256 +++--- R/data.R | 62 - R/estimate_partition_function.R | 214 ++--- R/expected_dist.R | 108 +- R/generate_constraints.R | 162 +-- R/generate_initial_ranking.R | 312 +++---- R/generate_transitive_closure.R | 214 ++--- R/label_switching.R | 42 R/lik_db_mix.R | 146 +-- R/misc.R | 144 +-- R/misc_expected_dist.R | 222 ++--- R/misc_likelihood.R | 151 +-- R/obs_freq.R | 24 R/plot.BayesMallows.R | 282 +++--- R/plot_elbow.R | 134 +-- R/plot_top_k.R | 168 +-- R/predict_top_k.R | 126 +- R/print.BayesMallows.R | 52 - R/print.BayesMallowsMixtures.R | 58 - R/rank_conversion.R | 178 ++-- R/rank_distance.R | 80 - R/rank_freq_distr.R | 56 - R/sample_mallows.R | 284 +++--- R/tidy_mcmc.R | 506 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/REFERENCES.bib | 552 ++++++------- inst/doc/BayesMallows.pdf.asis | 4 inst/examples/compute_consensus_example.R | 128 +-- inst/examples/compute_mallows_example.R | 240 ++--- inst/examples/compute_mallows_mixtures_example.R | 122 +- inst/examples/compute_posterior_intervals_example.R | 56 - inst/examples/estimate_partition_function_example.R | 130 +-- inst/examples/expected_dist_example.R | 12 inst/examples/generate_constraints_example.R | 42 inst/examples/generate_initial_ranking_example.R | 148 +-- inst/examples/generate_transitive_closure_example.R | 106 +- inst/examples/label_switching_example.R | 150 +-- inst/examples/lik_db_mix_example.R | 96 +- inst/examples/obs_freq_example.R | 230 ++--- inst/examples/plot.BayesMallows_example.R | 98 +- inst/examples/plot_top_k_example.R | 42 inst/examples/rank_distance_example.R | 30 inst/examples/rank_freq_distr_example.R | 12 inst/examples/sample_mallows_example.R | 98 +- man/BayesMallows.Rd | 66 - man/assess_convergence.Rd | 76 - man/assign_cluster.Rd | 90 +- man/asymptotic_partition_function.Rd | 82 - man/beach_preferences.Rd | 38 man/compute_consensus.Rd | 214 ++--- man/compute_importance_sampling_estimate.Rd | 56 - man/compute_mallows.Rd | 726 ++++++++--------- man/compute_mallows_mixtures.Rd | 180 ++-- man/compute_posterior_intervals.Rd | 154 +-- man/dot-generate_transitive_closure.Rd | 32 man/estimate_partition_function.Rd | 270 +++--- man/expected_dist.Rd | 58 - man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/generate_constraints.Rd | 112 +- man/generate_initial_ranking.Rd | 310 +++---- man/generate_transitive_closure.Rd | 204 ++-- man/get_partition_function.Rd | 76 - man/get_rank_distance.Rd | 68 - man/label_switching.Rd | 198 ++-- man/lik_db_mix.Rd | 190 ++-- man/log_expected_dist.Rd | 50 - man/obs_freq.Rd | 260 +++--- man/plot.BayesMallows.Rd | 162 +-- man/plot_elbow.Rd | 188 ++-- man/plot_top_k.Rd | 116 +- man/potato_true_ranking.Rd | 38 man/potato_visual.Rd | 42 man/potato_weighing.Rd | 42 man/predict_top_k.Rd | 64 - man/print.BayesMallows.Rd | 34 man/print.BayesMallowsMixtures.Rd | 34 man/rank_conversion.Rd | 120 +- man/rank_distance.Rd | 106 +- man/rank_freq_distr.Rd | 60 - man/rmallows.Rd | 94 +- man/run_mcmc.Rd | 218 ++--- man/sample_mallows.Rd | 238 ++--- man/sushi_rankings.Rd | 40 man/validate_permutation.Rd | 36 src/RcppExports.cpp | 5 src/run_mcmc.cpp | 3 tests/testthat.R | 10 tests/testthat/test_assess_convergence.R | 28 tests/testthat/test_compute_consensus.R | 325 +++---- tests/testthat/test_compute_mallows.R | 357 ++++---- tests/testthat/test_distance_function.R | 224 ++--- tests/testthat/test_estimate_partition_function.R | 88 +- tests/testthat/test_expected_dist.R | 30 tests/testthat/test_generate_ranking.R | 136 +-- tests/testthat/test_lik_db_mix.R | 122 +- tests/testthat/test_mcmc_function.R | 80 - tests/testthat/test_misc_cpp.R | 102 +- tests/testthat/test_misc_functions.R | 46 - tests/testthat/test_partition_function.R | 242 ++--- tests/testthat/test_plot.R | 20 tests/testthat/test_plot_elbow.R | 24 tests/testthat/test_plot_top_k.R | 166 +-- tests/testthat/test_print.R | 40 tests/testthat/test_random_number_seed.R | 100 +- tests/testthat/test_rank_conversion.R | 52 - tests/testthat/test_rank_freq_distr.R | 122 +- tests/testthat/test_sample_mallows.R | 68 - tests/testthat/test_transitive_closure.R | 100 +- vignettes/BayesMallows.pdf.asis | 4 124 files changed, 8457 insertions(+), 8487 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Shengyu Zhang <syzhang@uw.edu>,
Douglas Martin <doug@amath.washington.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEIF versions 1.2.3 dated 2021-06-09 and 1.2.4 dated 2021-10-14
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 3 +++ README.md | 2 +- build/vignette.rds |binary 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangómez [aut, cre, cph]
(<https://orcid.org/0000-0001-8457-4658>, rOpenSpain)
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.3.1 dated 2021-09-10 and 0.4.0 dated 2021-10-14
DESCRIPTION | 49 ++--- MD5 | 159 +++++++++--------- NAMESPACE | 2 NEWS.md | 32 ++- R/addProviderEspTiles.R | 8 R/data.R | 12 - R/esp_cache.R | 20 +- R/esp_cache_clear.R | 8 R/esp_check_access.R |only R/esp_getTiles.R | 174 +++++++++++++------- R/esp_get_can_box.R | 59 +++--- R/esp_get_capimun.R | 22 +- R/esp_get_ccaa.R | 47 +---- R/esp_get_country.R | 12 + R/esp_get_gridmap.R | 2 R/esp_get_hydrobasin.R | 29 +-- R/esp_get_hypsobath.R | 55 ++++-- R/esp_get_munic.R | 40 ++-- R/esp_get_nuts.R | 75 +++----- R/esp_get_prov.R | 39 +++- R/esp_get_railway.R | 32 ++- R/esp_get_rivers.R | 34 ++- R/esp_get_roads.R | 25 +- R/layer_spatraster.R |only R/utils_siane.R | 198 ++++++++++------------- R/utils_tiles.R | 82 +++++---- README.md | 155 +++++++++--------- inst/WORDLIST | 4 inst/doc/mapSpain.R | 198 ++++++++++++----------- inst/doc/mapSpain.Rmd | 222 +++++++++++++------------- inst/doc/mapSpain.html | 256 +++++++++++++++--------------- inst/examples/esp_get_gridmap.R | 68 ++++--- inst/examples/esp_munic_sf.R | 37 ++-- inst/examples/esp_nuts_sf.R | 33 +-- man/addProviderEspTiles.Rd | 1 man/esp_check_access.Rd |only man/esp_clear_cache.Rd | 2 man/esp_codelist.Rd | 4 man/esp_getTiles.Rd | 20 +- man/esp_get_can_box.Rd | 59 +++--- man/esp_get_capimun.Rd | 26 +-- man/esp_get_ccaa.Rd | 33 +-- man/esp_get_country.Rd | 12 + man/esp_get_gridmap.Rd | 87 ++++------ man/esp_get_hydrobasin.Rd | 29 +-- man/esp_get_hypsobath.Rd | 55 ++++-- man/esp_get_munic.Rd | 40 ++-- man/esp_get_nuts.Rd | 77 ++++----- man/esp_get_prov.Rd | 39 +++- man/esp_get_railway.Rd | 32 ++- man/esp_get_rivers.Rd | 34 ++- man/esp_get_roads.Rd | 25 +- man/esp_munic.sf.Rd | 37 ++-- man/esp_nuts.sf.Rd | 33 +-- man/figures/lifecycle-experimental.svg |only man/layer_spatraster.Rd |only man/leaflet.providersESP.df.Rd | 7 man/mapSpain-package.Rd | 2 man/pobmun19.Rd | 4 tests/testthat.R | 8 tests/testthat/test-addProviderEspTiles.R | 3 tests/testthat/test-esp_cache.R |only tests/testthat/test-esp_getTiles.R | 184 ++++++++++++++++----- tests/testthat/test-esp_get_capimun.R | 7 tests/testthat/test-esp_get_ccaa.R | 17 + tests/testthat/test-esp_get_country.R | 4 tests/testthat/test-esp_get_gridmap.R | 40 ++-- tests/testthat/test-esp_get_hydrobasin.R | 56 +++--- tests/testthat/test-esp_get_hypsobath.R | 50 ++--- tests/testthat/test-esp_get_munic.R | 13 + tests/testthat/test-esp_get_nuts.R | 108 ++++++------ tests/testthat/test-esp_get_prov.R | 15 + tests/testthat/test-esp_get_railway.R | 32 +-- tests/testthat/test-esp_get_rivers.R | 64 +++---- tests/testthat/test-esp_get_roads.R | 33 +-- tests/testthat/test-layer_spatraster.R |only vignettes/basic-1.png |binary vignettes/basic-2.png |binary vignettes/basic-3.png |binary vignettes/choro-1.png |binary vignettes/giscoR-1.png |binary vignettes/mapSpain.Rmd | 222 +++++++++++++------------- vignettes/thematic-1.png |binary vignettes/tile-1.png |binary 84 files changed, 2009 insertions(+), 1693 deletions(-)
Title: Plotting, Smoothing and Growth Trait Extraction for Longitudinal
Data
Description: Assists in producing longitudinal or profile plots of measured
traits. These allow checks to be made for anomalous data and growth patterns
in the data to be explored. Smoothing of growth trends for individual plants
using smoothing splines is available for removing transient effects. There
are tools for diagnosing the adequacy of trait smoothing, either using this
package or other packages, such as those that fit nonlinear growth models.
A range of per-unit (pot, plant, plot) growth traits can be extracted from
longitudinal data, including single time-point smoothed trait values and
their growth rates, interval growth rates and other growth statistics, such
as maximum growth. The package is particularly suited to preparing data from
high-throughput phenotyping facilities, such as imaging data from a Lemna-Tec Scananalyzer 3D
(see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more
information). The package 'growthPheno' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 1.0-30 dated 2020-12-12 and 1.0-34 dated 2021-10-14
growthPheno-1.0-30/growthPheno/R/PVA.v2.r |only growthPheno-1.0-30/growthPheno/tests/testthat/testthat-problems.rds |only growthPheno-1.0-34/growthPheno/DESCRIPTION | 8 growthPheno-1.0-34/growthPheno/MD5 | 55 ++-- growthPheno-1.0-34/growthPheno/R/PVA.v3.r |only growthPheno-1.0-34/growthPheno/R/S3methodsDeprecations.r | 38 +-- growthPheno-1.0-34/growthPheno/R/dataLongi_v9.r | 117 ++-------- growthPheno-1.0-34/growthPheno/build/partial.rdb |binary growthPheno-1.0-34/growthPheno/build/vignette.rds |binary growthPheno-1.0-34/growthPheno/data/RiceRaw.dat.rda |binary growthPheno-1.0-34/growthPheno/data/cart.dat.rda |binary growthPheno-1.0-34/growthPheno/data/exampleData.rda |binary growthPheno-1.0-34/growthPheno/data/tomato.dat.rda |binary growthPheno-1.0-34/growthPheno/inst/News.Rd | 24 +- growthPheno-1.0-34/growthPheno/inst/doc/Rice.pdf |binary growthPheno-1.0-34/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-1.0-34/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-1.0-34/growthPheno/man/RiceRaw.dat.Rd | 4 growthPheno-1.0-34/growthPheno/man/getTimesSubset.Rd | 9 growthPheno-1.0-34/growthPheno/man/growthPheno-deprecated.Rd | 12 + growthPheno-1.0-34/growthPheno/man/growthPheno-pkg.Rd | 2 growthPheno-1.0-34/growthPheno/man/longitudinalPrime.Rd | 2 growthPheno-1.0-34/growthPheno/man/plotAnom.Rd | 4 growthPheno-1.0-34/growthPheno/man/plotCorrmatrix.Rd | 50 ++-- growthPheno-1.0-34/growthPheno/man/plotDeviationsBoxes.Rd | 12 - growthPheno-1.0-34/growthPheno/man/plotImagetimes.Rd | 11 growthPheno-1.0-34/growthPheno/man/plotLongitudinal.Rd | 7 growthPheno-1.0-34/growthPheno/man/plotMedianDeviations.Rd | 16 + growthPheno-1.0-34/growthPheno/tests/testthat/testCorrPlot.r | 3 growthPheno-1.0-34/growthPheno/tests/testthat/testProbeSmooth.r | 61 +++-- 30 files changed, 222 insertions(+), 213 deletions(-)
Title: R Bindings for Gtk 2.8.0 and Above
Description: Facilities in the R language for programming
graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence <michafla@gene.com> and Duncan Temple Lang <duncan@wald.ucdavis.edu>
Maintainer: ORPHANED
Diff between RGtk2 versions 2.20.36.1 dated 2021-10-11 and 2.20.36.2 dated 2021-10-14
RGtk2-2.20.36.1/RGtk2/configure.in |only RGtk2-2.20.36.2/RGtk2/DESCRIPTION | 8 +++++--- RGtk2-2.20.36.2/RGtk2/MD5 | 4 ++-- RGtk2-2.20.36.2/RGtk2/configure.ac |only 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Description: Standard and extensible Eddy-Covariance data post-processing
(Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>)
includes
uStar-filtering, gap-filling, and flux-partitioning.
The Eddy-Covariance (EC) micrometeorological technique quantifies continuous
exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere.
It is important for understanding ecosystem dynamics and upscaling exchange fluxes.
(Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>).
This package inputs pre-processed (half-)hourly data and supports further processing.
First, a quality-check and filtering is performed based on the relationship between
measured flux and friction
velocity (uStar) to discard biased data
(Papale et al. (2006) <doi:10.5194/bg-3-571-2006>).
Second, gaps in the data are filled based on information from environmental conditions
(Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>).
Third, the net flux of carbon dioxide is partitioned
into its gross fluxes in and out of the ecosystem by night-time
based and day-time based approaches
(Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
Author: Department for Biogeochemical Integration at MPI-BGC, Jena, Germany
[cph],
Thomas Wutzler [aut, cre],
Markus Reichstein [aut],
Antje Maria Moffat [aut, trl],
Olaf Menzer [ctb],
Mirco Migliavacca [aut],
Kerstin Sickel [ctb, trl],
Ladislav <U+0160>igut [ctb]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between REddyProc versions 1.2.2 dated 2020-03-18 and 1.3.0 dated 2021-10-14
DESCRIPTION | 21 MD5 | 311 +++-- NAMESPACE | 22 NEWS.md | 29 R/CheckVal.R | 38 R/DataFunctions.R | 21 R/EddyPartitioning.R | 37 R/EddyPlotting.R | 2 R/EddyUStarFilterChangePointDetection.R | 70 - R/EddyUStarFilterDP.R | 58 - R/FileHandling.R | 19 R/FileHandlingFormats.R | 217 ++++ R/GeoFunctions.R | 2 R/LRC_base.R | 44 R/PartitioningLasslop10.R | 23 R/PartitioningLasslop10Nighttime.R | 1 R/aEddy.R | 45 R/estimate_vpd_from_dew.R |only R/imports.R | 13 R/variableNames.R | 6 build/vignette.rds |binary inst/WORDLIST | 292 ++--- inst/doc/DEGebExample.R | 26 inst/doc/DEGebExample.html | 60 - inst/doc/aggUncertainty.Rmd | 211 +++- inst/doc/aggUncertainty.html | 278 +++-- inst/doc/bigleaf.Rmd | 1 inst/doc/bigleaf.html | 103 + inst/doc/gapFilling.R | 10 inst/doc/gapFilling.html | 30 inst/doc/uStarCases.R | 26 inst/doc/uStarCases.html | 68 - inst/doc/useCase.Rmd | 14 inst/doc/useCase.html | 187 +-- inst/genData/REddyProc-package.Rd | 214 ++-- inst/genData/deleteRdList.txt | 5 man/BerkeleyJulianDateToPOSIXct.Rd | 6 man/LightResponseCurveFitter_computeCost.Rd | 2 man/LightResponseCurveFitter_computeLRCGradient.Rd | 2 man/LightResponseCurveFitter_fitLRC.Rd | 4 man/LightResponseCurveFitter_getOptimizedParameterPositions.Rd | 2 man/LightResponseCurveFitter_getParameterInitials.Rd | 2 man/LightResponseCurveFitter_getParameterNames.Rd | 2 man/LightResponseCurveFitter_getPriorLocation.Rd | 2 man/LightResponseCurveFitter_getPriorScale.Rd | 2 man/LightResponseCurveFitter_isParameterInBounds.Rd | 2 man/LightResponseCurveFitter_optimLRC.Rd | 2 man/LightResponseCurveFitter_optimLRCBounds.Rd | 8 man/LightResponseCurveFitter_optimLRCOnAdjustedPrior.Rd | 2 man/LightResponseCurveFitter_predictGPP.Rd | 2 man/LightResponseCurveFitter_predictLRC.Rd | 2 man/LogisticSigmoidLRCFitter_predictGPP.Rd | 2 man/NonrectangularLRCFitter_getParameterNames.Rd | 2 man/NonrectangularLRCFitter_predictGPP.Rd | 2 man/POSIXctToBerkeleyJulianDate.Rd | 6 man/REddyProc-package.Rd | 214 ++-- man/RectangularLRCFitter_predictGPP.Rd | 2 man/estimate_vpd_from_dew.Rd |only man/extract_FN15.Rd |only man/fCalcAVPfromVMFandPress.Rd | 2 man/fCalcETfromLE.Rd | 2 man/fCalcExtRadiation.Rd | 2 man/fCalcPotRadiation.Rd | 2 man/fCalcRHfromAVPandTair.Rd | 2 man/fCalcSVPfromTair.Rd | 2 man/fCalcVPDfromRHandTair.Rd | 2 man/fCheckHHTimeSeries.Rd | 2 man/fConvertCtoK.Rd | 2 man/fConvertGlobalToVisible.Rd | 2 man/fConvertKtoC.Rd | 2 man/fConvertTimeToPosix.Rd | 2 man/fConvertVisibleWm2toPhotons.Rd | 2 man/fLloydTaylor.Rd | 2 man/fLoadEuroFlux16.Rd | 2 man/fLoadFluxnet15.Rd |only man/fLoadTXTIntoDataframe.Rd | 2 man/fWriteDataframeToFile.Rd | 2 man/filterLongRuns.Rd | 2 man/filterLongRunsInVector.Rd | 2 man/getAmerifluxToBGC05VariableNameMapping.Rd | 2 man/getBGC05ToAmerifluxVariableNameMapping.Rd | 2 man/getExamplePath.Rd | 2 man/getFilledExampleDETha98Data.Rd | 2 man/getREddyProcExampleDir.Rd | 2 man/getTZone.Rd | 2 man/get_timestep_hours.Rd |only man/partGLControl.Rd | 11 man/partGLControlLasslopCompatible.Rd | 2 man/partGLExtractStandardData.Rd | 2 man/partitionNEEGL.Rd | 8 man/read_from_fluxnet15.Rd |only man/renameVariablesInDataframe.Rd | 2 man/sEddyProc_initialize.Rd | 10 man/sEddyProc_sApplyUStarScen.Rd | 9 man/sEddyProc_sCalcPotRadiation.Rd | 2 man/sEddyProc_sEstUstarThold.Rd | 2 man/sEddyProc_sEstUstarThreshold.Rd | 2 man/sEddyProc_sEstUstarThresholdDistribution.Rd | 2 man/sEddyProc_sEstimateUstarScenarios.Rd | 6 man/sEddyProc_sExportData.Rd | 2 man/sEddyProc_sExportResults.Rd | 2 man/sEddyProc_sFillInit.Rd | 2 man/sEddyProc_sFillLUT.Rd | 2 man/sEddyProc_sFillMDC.Rd | 2 man/sEddyProc_sFillVPDFromDew.Rd |only man/sEddyProc_sGLFluxPartition.Rd | 2 man/sEddyProc_sGLFluxPartitionUStarScens.Rd | 17 man/sEddyProc_sGetData.Rd | 2 man/sEddyProc_sGetEstimatedUstarThresholdDistribution.Rd | 2 man/sEddyProc_sGetUstarScenarios.Rd | 2 man/sEddyProc_sGetUstarSuffixes.Rd |only man/sEddyProc_sMDSGapFill.Rd | 2 man/sEddyProc_sMDSGapFillAfterUStarDistr.Rd | 2 man/sEddyProc_sMDSGapFillAfterUstar.Rd | 2 man/sEddyProc_sMDSGapFillUStarScens.Rd | 2 man/sEddyProc_sMRFluxPartition.Rd | 2 man/sEddyProc_sMRFluxPartitionUStarScens.Rd | 2 man/sEddyProc_sPlotDailySums.Rd | 2 man/sEddyProc_sPlotDailySumsY.Rd | 2 man/sEddyProc_sPlotDiurnalCycle.Rd | 2 man/sEddyProc_sPlotFingerprint.Rd | 2 man/sEddyProc_sPlotFingerprintY.Rd | 2 man/sEddyProc_sPlotHHFluxes.Rd | 2 man/sEddyProc_sPlotHHFluxesY.Rd | 2 man/sEddyProc_sPlotNEEVersusUStarForSeason.Rd | 2 man/sEddyProc_sSetLocationInfo.Rd | 2 man/sEddyProc_sSetUStarSeasons.Rd | 2 man/sEddyProc_sSetUstarScenarios.Rd | 2 man/sEddyProc_sTKFluxPartition.Rd | 2 man/sEddyProc_sTKFluxPartitionUStarScens.Rd | 2 man/sEddyProc_update_ustarthreshold_columns.Rd |only man/sEddyProc_useAnnualUStarThresholds.Rd | 2 man/sEddyProc_useSeaonsalUStarThresholds.Rd | 2 man/usControlUstarEst.Rd | 2 man/usControlUstarSubsetting.Rd | 2 man/usCreateSeasonFactorMonth.Rd | 2 man/usCreateSeasonFactorMonthWithinYear.Rd | 2 man/usCreateSeasonFactorYday.Rd | 2 man/usCreateSeasonFactorYdayYear.Rd | 2 man/usEstUstarThreshold.Rd | 7 man/usEstUstarThresholdSingleFw1Binned.Rd | 2 man/usEstUstarThresholdSingleFw2Binned.Rd | 2 man/usGetAnnualSeasonUStarMap.Rd | 2 man/usGetSeasonalSeasonUStarMap.Rd | 2 man/usGetYearOfSeason.Rd | 2 src/RcppExports.cpp | 5 src/whichValueGreaterEqualC.cpp | 3 tests/testthat/test_FileHandlingFormats.R |only tests/testthat/test_LightResponseCurveFitter.R | 187 +++ tests/testthat/test_UStarFilter.R | 120 +- tests/testthat/test_binWithEqualValues.R | 46 tests/testthat/test_checkval.R |only tests/testthat/test_estimate_vpd_from_dew.R |only tests/testthat/test_fConvertTimeToPosix.R | 9 tests/testthat/test_gapfilling.R | 1 tests/testthat/test_partGL.R | 36 tests/testthat/test_plotFingerprint.R | 12 tests/testthat/test_sEddyProc.R | 526 +++++----- tests/testthat/test_sEddyProc_Partitioning.R | 286 ++--- vignettes/aggUncertainty.Rmd | 211 +++- vignettes/bigleaf.Rmd | 1 vignettes/plots |only vignettes/useCase.Rmd | 14 163 files changed, 2831 insertions(+), 1614 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut],
Nicolas Lambert [aut],
Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.3.0 dated 2021-01-20 and 0.4.0 dated 2021-10-14
MTA-0.3.0/MTA/data |only MTA-0.4.0/MTA/DESCRIPTION | 13 MTA-0.4.0/MTA/MD5 | 75 MTA-0.4.0/MTA/NAMESPACE | 2 MTA-0.4.0/MTA/NEWS | 12 MTA-0.4.0/MTA/R/bidev.R | 5 MTA-0.4.0/MTA/R/gdev.R | 52 MTA-0.4.0/MTA/R/map_bidev.R | 56 MTA-0.4.0/MTA/R/map_mst.R | 65 MTA-0.4.0/MTA/R/mas.R | 9 MTA-0.4.0/MTA/R/mst.R | 6 MTA-0.4.0/MTA/R/package.R | 19 MTA-0.4.0/MTA/R/plot_bidev.R | 7 MTA-0.4.0/MTA/R/plot_mst.R | 3 MTA-0.4.0/MTA/R/sdev.R | 31 MTA-0.4.0/MTA/R/tdev.R | 72 MTA-0.4.0/MTA/build/vignette.rds |binary MTA-0.4.0/MTA/inst/cardist.txt |only MTA-0.4.0/MTA/inst/doc/MTA.R | 6 MTA-0.4.0/MTA/inst/doc/MTA.Rmd | 20 MTA-0.4.0/MTA/inst/doc/MTA.html | 479 +++--- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.R | 637 +++----- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.Rmd | 641 +++----- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.html | 2334 ++++++++++++++----------------- MTA-0.4.0/MTA/inst/metroparis.gpkg |only MTA-0.4.0/MTA/man/bidev.Rd | 5 MTA-0.4.0/MTA/man/cardist.Rd | 5 MTA-0.4.0/MTA/man/com.Rd | 4 MTA-0.4.0/MTA/man/ept.Rd | 3 MTA-0.4.0/MTA/man/gdev.Rd | 50 MTA-0.4.0/MTA/man/map_bidev.Rd | 38 MTA-0.4.0/MTA/man/map_mst.Rd | 64 MTA-0.4.0/MTA/man/mas.Rd | 5 MTA-0.4.0/MTA/man/mst.Rd | 6 MTA-0.4.0/MTA/man/plot_bidev.Rd | 3 MTA-0.4.0/MTA/man/plot_mst.Rd | 3 MTA-0.4.0/MTA/man/sdev.Rd | 30 MTA-0.4.0/MTA/man/tdev.Rd | 50 MTA-0.4.0/MTA/vignettes/MTA.Rmd | 20 MTA-0.4.0/MTA/vignettes/MTA_Scenario.Rmd | 641 +++----- 40 files changed, 2583 insertions(+), 2888 deletions(-)
Title: Simple 'ggplot2' Visualisation with Less Brainpower
Description: Wrapper functions to make 'ggplot2' and 'leaflet' visualisation easier with less brainpower required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 4.5.0 dated 2021-08-06 and 4.6.0 dated 2021-10-14
simplevis-4.5.0/simplevis/R/internal.R |only simplevis-4.5.0/simplevis/inst/shiny/template1/www/js/iframe-resizer.js |only simplevis-4.5.0/simplevis/inst/shiny/template2/www/js/iframe-resizer.js |only simplevis-4.5.0/simplevis/man/bin_cuts_to_interval_labels.Rd |only simplevis-4.5.0/simplevis/man/sv_interval_breaks_to_interval_labels.Rd |only simplevis-4.5.0/simplevis/man/sv_max_dp.Rd |only simplevis-4.5.0/simplevis/man/theme_x_gridlines.Rd |only simplevis-4.5.0/simplevis/man/theme_xy_gridlines.Rd |only simplevis-4.5.0/simplevis/man/theme_y_gridlines.Rd |only simplevis-4.6.0/simplevis/DESCRIPTION | 10 simplevis-4.6.0/simplevis/MD5 | 168 +++---- simplevis-4.6.0/simplevis/NAMESPACE | 9 simplevis-4.6.0/simplevis/NEWS.md | 19 simplevis-4.6.0/simplevis/R/density_max.R |only simplevis-4.6.0/simplevis/R/font_size.R |only simplevis-4.6.0/simplevis/R/gg_bar.R | 230 +++++----- simplevis-4.6.0/simplevis/R/gg_boxplot.R | 102 +--- simplevis-4.6.0/simplevis/R/gg_density.R | 56 +- simplevis-4.6.0/simplevis/R/gg_hbar.R | 229 +++++---- simplevis-4.6.0/simplevis/R/gg_line.R | 60 +- simplevis-4.6.0/simplevis/R/gg_point.R | 175 +++---- simplevis-4.6.0/simplevis/R/gg_sf.R | 176 ++++--- simplevis-4.6.0/simplevis/R/gg_tile.R | 172 ++++--- simplevis-4.6.0/simplevis/R/imports.R | 1 simplevis-4.6.0/simplevis/R/interval_labels.R |only simplevis-4.6.0/simplevis/R/leaflet_sf.R | 169 ++----- simplevis-4.6.0/simplevis/R/max_digits.R |only simplevis-4.6.0/simplevis/R/numeric_breaks.R |only simplevis-4.6.0/simplevis/R/pal.R | 2 simplevis-4.6.0/simplevis/R/run_app.R | 2 simplevis-4.6.0/simplevis/R/theme.R | 59 +- simplevis-4.6.0/simplevis/R/zero_adjust.R |only simplevis-4.6.0/simplevis/inst/doc/simplevis.html | 99 ++-- simplevis-4.6.0/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-4.6.0/simplevis/inst/shiny/template1/global.R | 7 simplevis-4.6.0/simplevis/inst/shiny/template1/server.R | 25 - 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simplevis-4.6.0/simplevis/man/gg_sf_col.Rd | 55 -- simplevis-4.6.0/simplevis/man/gg_sf_col_facet.Rd | 57 -- simplevis-4.6.0/simplevis/man/gg_sf_facet.Rd | 38 - simplevis-4.6.0/simplevis/man/gg_tile_col.Rd | 74 --- simplevis-4.6.0/simplevis/man/gg_tile_col_facet.Rd | 83 +-- simplevis-4.6.0/simplevis/man/interval_labels.Rd |only simplevis-4.6.0/simplevis/man/leaflet_sf.Rd | 16 simplevis-4.6.0/simplevis/man/leaflet_sf_col.Rd | 29 - simplevis-4.6.0/simplevis/man/nz.Rd | 4 simplevis-4.6.0/simplevis/man/run_template.Rd | 2 simplevis-4.6.0/simplevis/man/sv_density_max.Rd | 13 simplevis-4.6.0/simplevis/man/sv_density_max_col.Rd | 15 simplevis-4.6.0/simplevis/man/sv_density_max_col_facet.Rd | 50 +- simplevis-4.6.0/simplevis/man/sv_density_max_facet.Rd | 15 simplevis-4.6.0/simplevis/man/sv_font_size_body.Rd | 2 simplevis-4.6.0/simplevis/man/sv_font_size_title.Rd | 2 simplevis-4.6.0/simplevis/man/sv_interval_labels_chr.Rd |only simplevis-4.6.0/simplevis/man/sv_interval_labels_num.Rd |only simplevis-4.6.0/simplevis/man/sv_max_digits.Rd |only simplevis-4.6.0/simplevis/man/sv_numeric_breaks_h.Rd | 12 simplevis-4.6.0/simplevis/man/sv_numeric_breaks_v.Rd | 11 simplevis-4.6.0/simplevis/man/sv_x_zero_adjust.Rd | 2 simplevis-4.6.0/simplevis/man/sv_y_zero_adjust.Rd | 2 simplevis-4.6.0/simplevis/man/theme_h_gridlines.Rd |only simplevis-4.6.0/simplevis/man/theme_hv_gridlines.Rd |only simplevis-4.6.0/simplevis/man/theme_map.Rd | 10 simplevis-4.6.0/simplevis/man/theme_no_gridlines.Rd | 11 simplevis-4.6.0/simplevis/man/theme_v_gridlines.Rd |only 96 files changed, 1596 insertions(+), 2528 deletions(-)
Title: Analysis of Geostatistical Count Data using Gaussian Copulas
Description: Provides a variety of functions to analyze and model
geostatistical count data with Gaussian copulas, including
1) data simulation and visualization;
2) correlation structure assessment (here also known as the Normal To Anything);
3) calculate multivariate normal rectangle probabilities;
4) likelihood inference and parallel prediction at predictive locations.
Description of the method is available from: Han and DeOliveira (2018) <doi:10.18637/jss.v087.i13>.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>
Diff between gcKrig versions 1.1.6 dated 2021-06-22 and 1.1.7 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary inst/NEWS.txt | 5 +++++ man/marginal.gc.Rd | 3 ++- 5 files changed, 14 insertions(+), 8 deletions(-)
Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of
Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
regression models, partially linear instrumental variable regression models,
interactive regression models and interactive instrumental variable
regression models. 'DoubleML' allows estimation of the nuisance parts in
these models by machine learning methods and computation of the Neyman
orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
the 'R6' package is very flexible.
Author: Philipp Bach [aut],
Victor Chernozhukov [aut],
Malte S. Kurz [aut, cre],
Martin Spindler [aut]
Maintainer: Malte S. Kurz <malte.simon.kurz@uni-hamburg.de>
Diff between DoubleML versions 0.3.1 dated 2021-08-02 and 0.4.0 dated 2021-10-14
DESCRIPTION | 11 MD5 | 149 - NAMESPACE | 2 R/datasets.R | 173 + R/double_ml.R | 653 +++++-- R/double_ml_data.R | 418 +++- R/double_ml_iivm.R | 29 R/double_ml_irm.R | 22 R/double_ml_pliv.R | 35 R/helper.R | 37 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_DoubleML.html | 4 man/DoubleML.Rd | 5 man/DoubleMLClusterData.Rd |only man/DoubleMLData.Rd | 2 man/double_ml_data_from_data_frame.Rd | 9 man/double_ml_data_from_matrix.Rd | 4 man/make_pliv_multiway_cluster_CKMS2021.Rd |only tests/testthat/helper-01-helper_functions.R | 6 tests/testthat/helper-03-dgp.R | 18 tests/testthat/helper-04-simdata.R | 65 tests/testthat/helper-05-ml-learner.R | 20 tests/testthat/helper-08-dml_plr.R | 234 +- tests/testthat/helper-09-dml_pliv.R | 105 - tests/testthat/helper-10-dml_irm.R | 118 - tests/testthat/helper-11-dml_iivm.R | 123 - tests/testthat/helper-13-dml_pliv_partial_x.R | 118 - tests/testthat/helper-14-dml_pliv_partial_z.R | 89 tests/testthat/helper-15-dml_pliv_partial_xz.R | 129 - tests/testthat/helper-16-dml_cluster.R |only tests/testthat/print_outputs |only tests/testthat/test-double_ml_active_bindings.R | 99 - tests/testthat/test-double_ml_cluster_not_implemented.R |only tests/testthat/test-double_ml_data.R | 931 +++++----- tests/testthat/test-double_ml_data_active_bindings.R | 563 +++--- tests/testthat/test-double_ml_datasets.R | 21 tests/testthat/test-double_ml_iivm.R | 18 tests/testthat/test-double_ml_iivm_parameter_passing.R | 221 +- tests/testthat/test-double_ml_iivm_trim.R | 36 tests/testthat/test-double_ml_iivm_tuning.R | 2 tests/testthat/test-double_ml_iivm_user_score.R | 2 tests/testthat/test-double_ml_irm.R | 20 tests/testthat/test-double_ml_irm_loaded_mlr3learner.R | 8 tests/testthat/test-double_ml_irm_parameter_passing.R | 180 - tests/testthat/test-double_ml_irm_trim.R | 32 tests/testthat/test-double_ml_irm_tuning.R | 2 tests/testthat/test-double_ml_irm_user_score.R | 8 tests/testthat/test-double_ml_pliv.R | 16 tests/testthat/test-double_ml_pliv_multi_z_parameter_passing.R | 274 +- tests/testthat/test-double_ml_pliv_one_way_cluster.R |only tests/testthat/test-double_ml_pliv_parameter_passing.R | 295 +-- tests/testthat/test-double_ml_pliv_partial_functional_initializer.R | 46 tests/testthat/test-double_ml_pliv_partial_x.R | 47 tests/testthat/test-double_ml_pliv_partial_xz.R | 46 tests/testthat/test-double_ml_pliv_partial_xz_parameter_passing.R | 303 +-- tests/testthat/test-double_ml_pliv_partial_z.R | 37 tests/testthat/test-double_ml_pliv_partial_z_parameter_passing.R | 189 +- tests/testthat/test-double_ml_pliv_tuning.R | 2 tests/testthat/test-double_ml_pliv_two_way_cluster.R |only tests/testthat/test-double_ml_pliv_user_score.R | 8 tests/testthat/test-double_ml_plr.R | 26 tests/testthat/test-double_ml_plr_classifier.R | 85 tests/testthat/test-double_ml_plr_exception_handling.R | 10 tests/testthat/test-double_ml_plr_export_preds.R | 2 tests/testthat/test-double_ml_plr_loaded_mlr3learner.R | 10 tests/testthat/test-double_ml_plr_multitreat.R | 32 tests/testthat/test-double_ml_plr_nocrossfit.R | 27 tests/testthat/test-double_ml_plr_nonorth.R | 2 tests/testthat/test-double_ml_plr_p_adjust.R | 2 tests/testthat/test-double_ml_plr_parameter_passing.R | 292 +-- tests/testthat/test-double_ml_plr_rep_cross_fit.R | 40 tests/testthat/test-double_ml_plr_set_samples.R | 6 tests/testthat/test-double_ml_plr_tuning.R | 2 tests/testthat/test-double_ml_plr_user_score.R | 2 tests/testthat/test-double_ml_print.R |only tests/testthat/test-double_ml_set_sample_splitting.R | 356 ++- 78 files changed, 4044 insertions(+), 2836 deletions(-)
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as well as
diversity indices for pathotypes. This package is meant to be a direct
replacement for Herrmann, Löwer and Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] (<https://orcid.org/0000-0003-2483-4184>),
Zachary Noel [aut, ccp] (<https://orcid.org/0000-0001-6375-8300>),
Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Martin Chilvers [aut, ths] (<https://orcid.org/0000-0001-8832-1666>),
Zhian N. Kamvar [ctb, rev] (<https://orcid.org/0000-0003-1458-7108>),
Michigan Soybean Promotion Committee [fnd],
Project GREEEN [fnd],
North Central Soybean Research Program [fnd],
GRDC Project DAQ00186 [fnd]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between hagis versions 3.1.2 dated 2021-09-30 and 3.1.3 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 14 ++++++++++++++ R/calculate_diversities.R | 4 ++-- README.md | 37 ++++++++++++++++++++++++------------- inst/CITATION | 9 +++++---- inst/WORDLIST | 4 ++++ inst/doc/betadiversity.html | 8 ++++---- inst/doc/hagis.html | 4 ++-- 9 files changed, 66 insertions(+), 36 deletions(-)
Title: Evaluation Metrics for Implicit-Feedback Recommender Systems
Description: Calculates evaluation metrics for implicit-feedback recommender systems
that are based on low-rank matrix factorization models, given the fitted model
matrices and data, thus allowing to compare models from a variety of libraries.
Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k),
AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k),
Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from
which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the
receiver-operating characteristic curve), and PR-AUC (area under the
precision-recall curve).
These are calculated on a per-user basis according to the ranking of items induced
by the model, using efficient multi-threaded routines. Also provides functions
for creating train-test splits for model fitting and evaluation.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between recometrics versions 0.1.5 dated 2021-09-02 and 0.1.5-2 dated 2021-10-14
DESCRIPTION | 6 MD5 | 14 configure | 1271 +++++++++++++++++---------- configure.ac | 6 inst/doc/Evaluating_recommender_systems.html | 254 ++--- src/Makevars.in | 4 src/Makevars.win | 2 src/recometrics.h | 11 8 files changed, 979 insertions(+), 589 deletions(-)
Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM'
Formats
Description: Read and write labelled sparse matrices in text format as used by
software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM',
and others. Supports labelled data for regression, classification (binary, multi-class, multi-label),
and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between readsparse versions 0.1.5 dated 2021-09-07 and 0.1.5-1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- configure | 6 +++--- configure.ac | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Pattern-Oriented Modeling Framework for Coupled Niche-Population
Paleo-Climatic Models
Description: This extension of the poems pattern-oriented modeling (POM) framework
provides a collection of modules and functions customized for paleontological
time-scales, and optimized for single-generation transitions and large populations,
across multiple generations.
Author: Sean Haythorne [aut],
Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>),
Stuart Brown [aut] (<https://orcid.org/0000-0002-0669-1418>),
Damien Fordham [aut] (<https://orcid.org/0000-0003-2137-5592>)
Maintainer: Julia Pilowsky <julia.pilowsky@adelaide.edu.au>
Diff between paleopop versions 2.1.1 dated 2021-04-23 and 2.1.2 dated 2021-10-14
DESCRIPTION | 26 ++++++++++++++++---------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/PaleoPopModel.R | 2 +- build/vignette.rds |binary inst/doc/bison_example.html | 4 ++-- man/PaleoPopModel.Rd | 2 +- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks,
predictions, resample results or benchmark results via the autoplot()
generic of 'ggplot2'. The returned 'ggplot' objects are intended to
provide sensible defaults, yet can easily be customized to create
camera-ready figures. Visualizations include barplots, boxplots,
histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Raphael Sonabend [aut] (<https://orcid.org/0000-0001-9225-4654>),
Marc Becker [aut] (<https://orcid.org/0000-0002-8115-0400>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.5.6 dated 2021-09-14 and 0.5.7 dated 2021-10-14
DESCRIPTION | 24 ++- MD5 | 39 ++++-- NAMESPACE | 3 NEWS.md | 4 R/OptimInstanceSingleCrit.R |only R/TuningInstanceSingleCrit.R | 159 +------------------------ build/partial.rdb |binary man/autoplot.OptimInstanceSingleCrit.Rd |only man/autoplot.TuningInstanceSingleCrit.Rd | 12 + man/mlr3viz-package.Rd | 8 - tests/testthat/_snaps/OptimInstanceSingleCrit |only tests/testthat/test_OptimInstanceSingleCrit.R |only tests/testthat/test_PredictionClust.R | 2 tests/testthat/test_TuningInstanceSingleCrit.R | 5 14 files changed, 77 insertions(+), 179 deletions(-)
Title: Functions to Fit Mixtures of Regressions
Description: Fits mixtures of (possibly multivariate) regressions
(which has been described as doing ANCOVA when you don't
know the levels). Turner (2000) <doi:10.1111/1467-9876.00198>.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between mixreg versions 0.0-6 dated 2018-03-31 and 2.0-10 dated 2021-10-14
mixreg-0.0-6/mixreg/R/bootSam.R |only mixreg-0.0-6/mixreg/R/bootcomp.R |only mixreg-0.0-6/mixreg/R/covmix.R |only mixreg-0.0-6/mixreg/R/plot.mresid.R |only mixreg-0.0-6/mixreg/R/residMix.R |only mixreg-0.0-6/mixreg/R/simmix.R |only mixreg-0.0-6/mixreg/inst/aphids.R |only mixreg-0.0-6/mixreg/inst/aphids.dat |only mixreg-0.0-6/mixreg/man/bootcomp.Rd |only mixreg-0.0-6/mixreg/man/covmix.Rd |only mixreg-0.0-6/mixreg/man/plot.mresid.Rd |only mixreg-0.0-6/mixreg/man/residMix.Rd |only mixreg-2.0-10/mixreg/ChangeLog | 320 ++++++++++++++++++++++++++- mixreg-2.0-10/mixreg/DESCRIPTION | 12 - mixreg-2.0-10/mixreg/MD5 | 86 ++++--- mixreg-2.0-10/mixreg/NAMESPACE | 12 - mixreg-2.0-10/mixreg/R/First.R | 18 + mixreg-2.0-10/mixreg/R/cband.R | 123 +++++----- mixreg-2.0-10/mixreg/R/cint.R |only mixreg-2.0-10/mixreg/R/covMix.R |only mixreg-2.0-10/mixreg/R/covMixMC.R |only mixreg-2.0-10/mixreg/R/distFuns.R |only mixreg-2.0-10/mixreg/R/gfun.R | 17 - mixreg-2.0-10/mixreg/R/hatfun.R | 1 mixreg-2.0-10/mixreg/R/info1.R | 3 mixreg-2.0-10/mixreg/R/info2.R | 3 mixreg-2.0-10/mixreg/R/initRand.R | 7 mixreg-2.0-10/mixreg/R/mixreg.R | 227 +++++++++---------- mixreg-2.0-10/mixreg/R/mixregEngine.R |only mixreg-2.0-10/mixreg/R/ncMcTest.R |only mixreg-2.0-10/mixreg/R/plot.cband.R | 158 ++++++++++--- mixreg-2.0-10/mixreg/R/plot.cint.R |only mixreg-2.0-10/mixreg/R/plot.mixreg.R |only mixreg-2.0-10/mixreg/R/plot.mixresid.R |only mixreg-2.0-10/mixreg/R/qqMix.R | 73 +++--- mixreg-2.0-10/mixreg/R/residuals.mixreg.R |only mixreg-2.0-10/mixreg/R/rmixreg.R |only mixreg-2.0-10/mixreg/R/rmixreg.default.R |only mixreg-2.0-10/mixreg/R/rmixreg.mixreg.R |only mixreg-2.0-10/mixreg/R/stepPlot.R |only mixreg-2.0-10/mixreg/R/visualFit.R |only mixreg-2.0-10/mixreg/build |only mixreg-2.0-10/mixreg/data/aphids.rda |binary mixreg-2.0-10/mixreg/data/kilnAfull.rda |only mixreg-2.0-10/mixreg/data/kilnAoneOut.rda |only mixreg-2.0-10/mixreg/data/kilnAsubset.rda |only mixreg-2.0-10/mixreg/data/kilnB.rda |only mixreg-2.0-10/mixreg/inst/doc |only mixreg-2.0-10/mixreg/man/aphids.Rd | 38 +-- mixreg-2.0-10/mixreg/man/cband.Rd | 134 +++++++---- mixreg-2.0-10/mixreg/man/covMix.Rd |only mixreg-2.0-10/mixreg/man/kilns.Rd |only mixreg-2.0-10/mixreg/man/mixreg-internal.Rd | 19 + mixreg-2.0-10/mixreg/man/mixreg.Rd | 320 ++++++++++++++++++--------- mixreg-2.0-10/mixreg/man/ncMcTest.Rd |only mixreg-2.0-10/mixreg/man/plot.cband.Rd | 93 +++++-- mixreg-2.0-10/mixreg/man/plot.cint.Rd |only mixreg-2.0-10/mixreg/man/plot.mixreg.Rd |only mixreg-2.0-10/mixreg/man/plot.mixresid.Rd |only mixreg-2.0-10/mixreg/man/qqMix.Rd | 85 ++++--- mixreg-2.0-10/mixreg/man/residuals.mixreg.Rd |only mixreg-2.0-10/mixreg/man/rmixreg.Rd |only mixreg-2.0-10/mixreg/man/stepPlot.Rd |only mixreg-2.0-10/mixreg/man/visualFit.Rd |only mixreg-2.0-10/mixreg/vignettes |only 65 files changed, 1227 insertions(+), 522 deletions(-)