Title: Models for Survival Analysis
Description: Implementations of classical and machine learning models for survival analysis, including deep neural networks via 'keras' and 'tensorflow'. Each model includes a separated fit and predict interface with consistent prediction types for predicting risk, survival probabilities, or survival distributions with 'distr6' <https://CRAN.R-project.org/package=distr6>. Models are either implemented from 'Python' via 'reticulate' <https://CRAN.R-project.org/package=reticulate>, from code in GitHub packages, or novel implementations using 'Rcpp' <https://CRAN.R-project.org/package=Rcpp>. Novel machine learning survival models wil be included in the package in near-future updates. Neural networks are implemented from the 'Python' package 'pycox' <https://github.com/havakv/pycox> and are detailed by Kvamme et al. (2019) <https://jmlr.org/papers/v20/18-424.html>. The 'Akritas' estimator is defined in Akritas (1994) <doi:10.1214/aos/1176325630>. 'DNNSurv' is defined in Zhao and Feng (2020) <arXiv:1908.02337>.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between survivalmodels versions 0.1.8 dated 2021-04-17 and 0.1.9 dated 2021-09-11
DESCRIPTION | 8 +- MD5 | 35 ++++++----- NEWS.md | 7 ++ R/akritas.R | 15 +---- R/dnnsurv.R | 12 +--- R/helpers.R | 4 - R/helpers_keras.R | 8 +- R/helpers_pycox.R | 120 +++++++++++++++++++++------------------- R/utils.R |only README.md | 7 ++ build/partial.rdb |binary man/get_pycox_activation.Rd | 14 ++-- man/install_keras.Rd | 8 ++ man/install_pycox.Rd | 11 ++- man/install_torch.Rd | 3 - man/pycox_prepare_train_data.Rd | 35 ++++++----- src/RcppExports.cpp | 5 + tests/testthat/helpers.R | 14 ++-- tests/testthat/test_pchazard.R | 16 ++--- 19 files changed, 177 insertions(+), 145 deletions(-)
More information about survivalmodels at CRAN
Permanent link
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package
and then attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgload versions 1.2.1 dated 2021-04-06 and 1.2.2 dated 2021-09-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.1.7 dated 2021-07-09 and 2.1.8 dated 2021-09-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Scatter.R | 1 + man/MVar.pt-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.1.7 dated 2021-07-09 and 2.1.8 dated 2021-09-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Scatter_English.R | 3 ++- man/MVar-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Geospatial Queries Using 'PyMongo'
Description: Utilizes methods of the 'PyMongo' 'Python' library to initialize, insert and query 'GeoJson' data (see <https://github.com/mongodb/mongo-python-driver> for more information on 'PyMongo'). Furthermore, it allows the user to validate 'GeoJson' objects and to use the console for 'MongoDB' (bulk) commands. The 'reticulate' package provides the 'R' interface to 'Python' modules, classes and functions.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between GeoMongo versions 1.0.2 dated 2021-05-07 and 1.0.3 dated 2021-09-11
DESCRIPTION | 8 MD5 | 20 NEWS.md | 5 R/package.R | 5 R/utils.R | 2 README.md | 19 build/vignette.rds |binary inst/doc/the_GeoMongo_package.Rmd | 2 inst/doc/the_GeoMongo_package.html | 1008 +++++++++++++++---------------------- man/mongodb_console.Rd | 2 vignettes/the_GeoMongo_package.Rmd | 2 11 files changed, 457 insertions(+), 616 deletions(-)
Title: Interface to the JavaScript Library 'amCharts 4'
Description: Creates JavaScript charts. The charts can be included in 'Shiny' apps and R markdown documents, or viewed from the R console and 'RStudio' viewer. Based on the JavaScript library 'amCharts 4' and the R packages 'htmlwidgets' and 'reactR'. Currently available types of chart are: vertical and horizontal bar chart, radial bar chart, stacked bar chart, vertical and horizontal Dumbbell chart, line chart, scatter chart, range area chart, gauge chart, boxplot chart, pie chart, and 100% stacked bar chart.
Author: Stéphane Laurent [aut, cre],
Antanas Marcelionis [ctb, cph] ('amCharts' library
(https://www.amcharts.com/)),
Terence Eden [ctb, cph] ('SuperTinyIcons' library
(https://github.com/edent/SuperTinyIcons/)),
Tom Alexander [ctb, cph] ('regression-js' library
(https://github.com/Tom-Alexander/regression-js))
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between rAmCharts4 versions 1.3.2 dated 2021-06-25 and 1.4.0 dated 2021-09-11
DESCRIPTION | 8 - MD5 | 12 + NAMESPACE | 1 NEWS.md | 93 +++++++------- R/amPercentageBarChart.R |only inst/htmlwidgets/amChart4.js | 259 ++++++++++++++++++++++++++++++++++++++- inst/htmlwidgets/amChart4.js.map | 2 man/amPercentageBarChart.Rd |only 8 files changed, 319 insertions(+), 56 deletions(-)
Title: Non Metric Space (Approximate) Library
Description: A Non-Metric Space Library ('NMSLIB' <https://github.com/nmslib/nmslib>) wrapper, which according to the authors "is an efficient cross-platform similarity search library and a toolkit for evaluation of similarity search methods. The goal of the 'NMSLIB' <https://github.com/nmslib/nmslib> Library is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods". The wrapper also includes Approximate Kernel k-Nearest-Neighbor functions based on the 'NMSLIB' <https://github.com/nmslib/nmslib> 'Python' Library.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
B. Naidan [cph] (Author of the Non-Metric Space Library (NMSLIB)),
L. Boytsov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
Yu. Malkov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
B. Frederickson [cph] (Author of the Non-Metric Space Library (NMSLIB)),
D. Novak [cph] (Author of the Non-Metric Space Library (NMSLIB))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between nmslibR versions 1.0.5 dated 2021-05-07 and 1.0.6 dated 2021-09-11
DESCRIPTION | 15 MD5 | 14 NEWS.md | 7 R/package.R | 5 README.md | 20 build/vignette.rds |binary inst/doc/the_nmslibR_package.html | 798 ++++++++++++++------------------------ src/RcppExports.cpp | 5 8 files changed, 354 insertions(+), 510 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] (<https://orcid.org/0000-0003-4092-8228>),
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] (<https://orcid.org/0000-0003-0532-4824>),
Ken Andersen [aut, cph] (<https://orcid.org/0000-0002-8478-3430>),
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.2.1 dated 2021-08-03 and 2.3.0 dated 2021-09-11
mizer-2.2.1/mizer/man/getPredKernel.Rd |only mizer-2.2.1/mizer/man/retune_erepro.Rd |only mizer-2.2.1/mizer/man/setLinetypes.Rd |only mizer-2.2.1/mizer/man/validEffortVector.Rd |only mizer-2.2.1/mizer/tests/testthat/Rplots.pdf |only mizer-2.3.0/mizer/DESCRIPTION | 28 mizer-2.3.0/mizer/MD5 | 291 +++++----- mizer-2.3.0/mizer/NAMESPACE | 46 + mizer-2.3.0/mizer/NEWS.md | 99 +++ mizer-2.3.0/mizer/R/MizerParams-class.R | 99 --- mizer-2.3.0/mizer/R/animateSpectra.R | 5 mizer-2.3.0/mizer/R/calibrate.R |only mizer-2.3.0/mizer/R/customFunction.R | 1 mizer-2.3.0/mizer/R/data.R | 35 - mizer-2.3.0/mizer/R/deprecated.R | 2 mizer-2.3.0/mizer/R/extension.R | 19 mizer-2.3.0/mizer/R/manipulate_species.R | 110 +-- mizer-2.3.0/mizer/R/match.R |only mizer-2.3.0/mizer/R/mizer-package.R | 5 mizer-2.3.0/mizer/R/newMultispeciesParams.R | 111 ++- mizer-2.3.0/mizer/R/plotBiomassObservedVsModel.R |only mizer-2.3.0/mizer/R/plotYieldObservedVsModel.R |only mizer-2.3.0/mizer/R/plots.R | 68 +- mizer-2.3.0/mizer/R/project.R | 7 mizer-2.3.0/mizer/R/project_methods.R | 18 mizer-2.3.0/mizer/R/rate_functions.R | 24 mizer-2.3.0/mizer/R/resource_dynamics.R | 15 mizer-2.3.0/mizer/R/saveParams.R |only mizer-2.3.0/mizer/R/setBevertonHolt.R | 62 +- mizer-2.3.0/mizer/R/setColours.R |only mizer-2.3.0/mizer/R/setExtMort.R | 96 ++- mizer-2.3.0/mizer/R/setFishing.R | 181 ++++-- mizer-2.3.0/mizer/R/setInitialValues.R | 6 mizer-2.3.0/mizer/R/setInteraction.R | 29 mizer-2.3.0/mizer/R/setMaxIntakeRate.R | 65 +- mizer-2.3.0/mizer/R/setMetabolicRate.R | 68 +- mizer-2.3.0/mizer/R/setMetadata.R |only mizer-2.3.0/mizer/R/setPredKernel.R | 113 ++- mizer-2.3.0/mizer/R/setReproduction.R | 99 ++- mizer-2.3.0/mizer/R/setResource.R | 139 +++- mizer-2.3.0/mizer/R/setSearchVolume.R | 62 +- mizer-2.3.0/mizer/R/species_params.R | 26 mizer-2.3.0/mizer/R/steady.R | 97 +-- mizer-2.3.0/mizer/R/summary_methods.R | 65 +- mizer-2.3.0/mizer/R/test-helpers.R |only mizer-2.3.0/mizer/R/upgrade.R | 15 mizer-2.3.0/mizer/R/wrapper_functions.R | 6 mizer-2.3.0/mizer/README.md | 35 - mizer-2.3.0/mizer/data/NS_interaction.RData |only mizer-2.3.0/mizer/data/NS_params.RData |binary mizer-2.3.0/mizer/data/NS_sim.rda |binary mizer-2.3.0/mizer/inst/WORDLIST | 25 mizer-2.3.0/mizer/inst/extdata |only mizer-2.3.0/mizer/man/MizerParams-class.Rd | 16 mizer-2.3.0/mizer/man/NS_interaction.Rd |only mizer-2.3.0/mizer/man/NS_params.Rd | 4 mizer-2.3.0/mizer/man/NS_sim.Rd | 4 mizer-2.3.0/mizer/man/NS_species_params.Rd | 4 mizer-2.3.0/mizer/man/NS_species_params_gears.Rd | 4 mizer-2.3.0/mizer/man/addSpecies.Rd | 71 +- mizer-2.3.0/mizer/man/calibrateBiomass.Rd |only mizer-2.3.0/mizer/man/calibrateYield.Rd |only mizer-2.3.0/mizer/man/customFunction.Rd | 1 mizer-2.3.0/mizer/man/emptyParams.Rd | 3 mizer-2.3.0/mizer/man/figures/Beverton-Holt-plot-1.png |binary mizer-2.3.0/mizer/man/figures/logo.png |binary mizer-2.3.0/mizer/man/figures/mizer.png |binary mizer-2.3.0/mizer/man/figures/mizer_twitter.jpeg |only mizer-2.3.0/mizer/man/figures/unnamed-chunk-4-1.png |binary mizer-2.3.0/mizer/man/gear_params.Rd | 20 mizer-2.3.0/mizer/man/getComponent.Rd | 6 mizer-2.3.0/mizer/man/getEGrowth.Rd | 2 mizer-2.3.0/mizer/man/getERepro.Rd | 2 mizer-2.3.0/mizer/man/getEReproAndGrowth.Rd | 2 mizer-2.3.0/mizer/man/getESpawning.Rd | 2 mizer-2.3.0/mizer/man/getFMort.Rd | 2 mizer-2.3.0/mizer/man/getFMortGear.Rd | 2 mizer-2.3.0/mizer/man/getFeedingLevel.Rd | 2 mizer-2.3.0/mizer/man/getM2.Rd | 2 mizer-2.3.0/mizer/man/getM2Background.Rd | 2 mizer-2.3.0/mizer/man/getMort.Rd | 2 mizer-2.3.0/mizer/man/getPhiPrey.Rd | 2 mizer-2.3.0/mizer/man/getPredMort.Rd | 2 mizer-2.3.0/mizer/man/getPredRate.Rd | 2 mizer-2.3.0/mizer/man/getRDD.Rd | 2 mizer-2.3.0/mizer/man/getRDI.Rd | 2 mizer-2.3.0/mizer/man/getResourceMort.Rd | 2 mizer-2.3.0/mizer/man/getZ.Rd | 2 mizer-2.3.0/mizer/man/get_size_range_array.Rd | 8 mizer-2.3.0/mizer/man/initial_effort.Rd |only mizer-2.3.0/mizer/man/inter.Rd | 10 mizer-2.3.0/mizer/man/matchBiomasses.Rd |only mizer-2.3.0/mizer/man/matchYields.Rd |only mizer-2.3.0/mizer/man/newMultispeciesParams.Rd | 126 +--- mizer-2.3.0/mizer/man/plotBiomassObservedVsModel.Rd |only mizer-2.3.0/mizer/man/plotFMort.Rd | 2 mizer-2.3.0/mizer/man/plotFeedingLevel.Rd | 2 mizer-2.3.0/mizer/man/plotGrowthCurves.Rd | 2 mizer-2.3.0/mizer/man/plotM2.Rd | 2 mizer-2.3.0/mizer/man/plotMizerSim.Rd | 4 mizer-2.3.0/mizer/man/plotPredMort.Rd | 2 mizer-2.3.0/mizer/man/plotSpectra.Rd | 2 mizer-2.3.0/mizer/man/plotYield.Rd | 4 mizer-2.3.0/mizer/man/plotYieldGear.Rd | 2 mizer-2.3.0/mizer/man/plotYieldObservedVsModel.Rd |only mizer-2.3.0/mizer/man/project.Rd | 3 mizer-2.3.0/mizer/man/renameSpecies.Rd | 5 mizer-2.3.0/mizer/man/resource_constant.Rd | 14 mizer-2.3.0/mizer/man/resource_params.Rd | 41 + mizer-2.3.0/mizer/man/resource_semichemostat.Rd | 19 mizer-2.3.0/mizer/man/saveParams.Rd |only mizer-2.3.0/mizer/man/scaleModel.Rd |only mizer-2.3.0/mizer/man/setBevertonHolt.Rd | 26 mizer-2.3.0/mizer/man/setColours.Rd | 48 + mizer-2.3.0/mizer/man/setExtMort.Rd | 50 + mizer-2.3.0/mizer/man/setFishing.Rd | 55 + mizer-2.3.0/mizer/man/setInteraction.Rd | 29 mizer-2.3.0/mizer/man/setMaxIntakeRate.Rd | 39 - mizer-2.3.0/mizer/man/setMetabolicRate.Rd | 43 - mizer-2.3.0/mizer/man/setMetadata.Rd |only mizer-2.3.0/mizer/man/setParams.Rd | 155 +---- mizer-2.3.0/mizer/man/setPredKernel.Rd | 47 - mizer-2.3.0/mizer/man/setReproduction.Rd | 51 - mizer-2.3.0/mizer/man/setResource.Rd | 47 + mizer-2.3.0/mizer/man/setRmax.Rd | 10 mizer-2.3.0/mizer/man/setSearchVolume.Rd | 36 - mizer-2.3.0/mizer/man/species_params.Rd | 10 mizer-2.3.0/mizer/man/steady.Rd | 13 mizer-2.3.0/mizer/man/validGearParams.Rd | 5 mizer-2.3.0/mizer/man/validSpeciesParams.Rd | 1 mizer-2.3.0/mizer/man/valid_species_arg.Rd | 3 mizer-2.3.0/mizer/tests/testthat/_snaps/plotBiomassObservedVsModel |only mizer-2.3.0/mizer/tests/testthat/_snaps/plotYieldObservedVsModel |only mizer-2.3.0/mizer/tests/testthat/_snaps/plots/plot-growth-curves-panel.svg | 268 ++++----- mizer-2.3.0/mizer/tests/testthat/_snaps/plots/plot-growth-curves.svg | 18 mizer-2.3.0/mizer/tests/testthat/_snaps/plots/plot-single-growth-curve.svg | 26 mizer-2.3.0/mizer/tests/testthat/test-MizerParams-class.R | 30 - mizer-2.3.0/mizer/tests/testthat/test-MizerSim-class.R | 2 mizer-2.3.0/mizer/tests/testthat/test-analytic_results.R | 172 ++--- mizer-2.3.0/mizer/tests/testthat/test-calibrate.R |only mizer-2.3.0/mizer/tests/testthat/test-extension.R | 3 mizer-2.3.0/mizer/tests/testthat/test-manipulate_species.R | 104 ++- mizer-2.3.0/mizer/tests/testthat/test-match.R |only mizer-2.3.0/mizer/tests/testthat/test-newMultispeciesParams.R | 2 mizer-2.3.0/mizer/tests/testthat/test-plotBiomassObservedVsModel.R |only mizer-2.3.0/mizer/tests/testthat/test-plotYieldObservedVsModel.R |only mizer-2.3.0/mizer/tests/testthat/test-resource_dynamics.R | 8 mizer-2.3.0/mizer/tests/testthat/test-setBevertonHolt.R | 12 mizer-2.3.0/mizer/tests/testthat/test-setColours.R |only mizer-2.3.0/mizer/tests/testthat/test-setExtMort.R | 61 +- mizer-2.3.0/mizer/tests/testthat/test-setFishing.R | 124 +++- mizer-2.3.0/mizer/tests/testthat/test-setInteraction.R | 4 mizer-2.3.0/mizer/tests/testthat/test-setMaxIntakeRate.R | 60 +- mizer-2.3.0/mizer/tests/testthat/test-setMetabolicRate.R | 54 + mizer-2.3.0/mizer/tests/testthat/test-setMetadata.R |only mizer-2.3.0/mizer/tests/testthat/test-setPredKernel.R | 56 + mizer-2.3.0/mizer/tests/testthat/test-setReproduction.R | 121 ++-- mizer-2.3.0/mizer/tests/testthat/test-setResource.R | 107 ++- mizer-2.3.0/mizer/tests/testthat/test-setSearchVolume.R | 55 + mizer-2.3.0/mizer/tests/testthat/test-species_params.R | 5 mizer-2.3.0/mizer/tests/testthat/test-steady.R | 58 - mizer-2.3.0/mizer/tests/testthat/test-summary_methods.R | 126 ++-- mizer-2.3.0/mizer/tests/testthat/test-upgrade.R | 8 163 files changed, 2891 insertions(+), 1848 deletions(-)
Title: Multidimensional Penalized Splines for Survival and Net Survival
Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for
multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics.
See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 1.5.1 dated 2020-09-25 and 1.5.2 dated 2021-09-11
survPen-1.5.1/survPen/R/survPenV1_51.r |only survPen-1.5.1/survPen/tests/compar_LAML_LCV.pdf |only survPen-1.5.1/survPen/tests/compar_several_mods.pdf |only survPen-1.5.1/survPen/tests/compar_tensor_tint.pdf |only survPen-1.5.1/survPen/tests/compar_total_excess.pdf |only survPen-1.5.1/survPen/tests/compar_total_excess_CI.pdf |only survPen-1.5.1/survPen/tests/compar_unpen_pen.pdf |only survPen-1.5.1/survPen/tests/output_tests_survPen.lis |only survPen-1.5.1/survPen/tests/test_survPen.r |only survPen-1.5.2/survPen/DESCRIPTION | 6 survPen-1.5.2/survPen/MD5 | 78 survPen-1.5.2/survPen/NEWS | 8 survPen-1.5.2/survPen/R/survPenV1_52.r |only survPen-1.5.2/survPen/inst/doc/survival_analysis_with_survPen.R | 2 survPen-1.5.2/survPen/inst/doc/survival_analysis_with_survPen.Rmd | 2 survPen-1.5.2/survPen/inst/doc/survival_analysis_with_survPen.html | 2816 +++------- survPen-1.5.2/survPen/man/NR.beta.Rd | 2 survPen-1.5.2/survPen/man/NR.rho.Rd | 2 survPen-1.5.2/survPen/man/constraint.Rd | 2 survPen-1.5.2/survPen/man/cor.var.Rd | 2 survPen-1.5.2/survPen/man/crs.FP.Rd | 2 survPen-1.5.2/survPen/man/crs.Rd | 2 survPen-1.5.2/survPen/man/datCancer.Rd | 2 survPen-1.5.2/survPen/man/design.matrix.Rd | 2 survPen-1.5.2/survPen/man/instr.Rd | 2 survPen-1.5.2/survPen/man/inv.repam.Rd | 2 survPen-1.5.2/survPen/man/model.cons.Rd | 2 survPen-1.5.2/survPen/man/predict.survPen.Rd | 2 survPen-1.5.2/survPen/man/print.summary.survPen.Rd | 2 survPen-1.5.2/survPen/man/rd.Rd | 2 survPen-1.5.2/survPen/man/repam.Rd | 2 survPen-1.5.2/survPen/man/smf.Rd | 2 survPen-1.5.2/survPen/man/smooth.cons.Rd | 2 survPen-1.5.2/survPen/man/smooth.cons.integral.Rd | 2 survPen-1.5.2/survPen/man/smooth.spec.Rd | 2 survPen-1.5.2/survPen/man/summary.survPen.Rd | 2 survPen-1.5.2/survPen/man/survPen.Rd | 2 survPen-1.5.2/survPen/man/survPen.fit.Rd | 2 survPen-1.5.2/survPen/man/survPenObject.Rd | 2 survPen-1.5.2/survPen/man/tensor.in.Rd | 2 survPen-1.5.2/survPen/man/tensor.prod.S.Rd | 2 survPen-1.5.2/survPen/man/tensor.prod.X.Rd | 2 survPen-1.5.2/survPen/src/Makevars | 4 survPen-1.5.2/survPen/src/Makevars.win | 3 survPen-1.5.2/survPen/vignettes/survival_analysis_with_survPen.Rmd | 2 45 files changed, 1003 insertions(+), 1970 deletions(-)
Title: Accessing 'SimFin' Data
Description: Through simfinapi, you can intuitively access the 'SimFin'
Web-API (<https://simfin.com/>) to make 'SimFin' data easily available
in R. To obtain an 'SimFin' API key (and thus to use this package),
you need to register at <https://simfin.com/login>.
Author: Matthias Gomolka [aut, cre]
Maintainer: Matthias Gomolka <matthias.gomolka@posteo.de>
Diff between simfinapi versions 0.1.0 dated 2020-09-28 and 0.2.0 dated 2021-09-11
simfinapi-0.1.0/simfinapi/man/check_inputs.Rd |only simfinapi-0.1.0/simfinapi/man/sfa_get_info_.Rd |only simfinapi-0.1.0/simfinapi/man/sfa_get_shares_.Rd |only simfinapi-0.1.0/simfinapi/man/sfa_get_statement_.Rd |only simfinapi-0.2.0/simfinapi/DESCRIPTION | 37 simfinapi-0.2.0/simfinapi/MD5 | 68 - simfinapi-0.2.0/simfinapi/NAMESPACE | 15 simfinapi-0.2.0/simfinapi/NEWS.md |only simfinapi-0.2.0/simfinapi/R/call_api.R | 4 simfinapi-0.2.0/simfinapi/R/check_inputs.R | 245 +++-- simfinapi-0.2.0/simfinapi/R/param_doc.R |only simfinapi-0.2.0/simfinapi/R/sfa_get_entities.R | 20 simfinapi-0.2.0/simfinapi/R/sfa_get_info.R | 90 + simfinapi-0.2.0/simfinapi/R/sfa_get_prices.R | 132 +- simfinapi-0.2.0/simfinapi/R/sfa_get_ref.R |only simfinapi-0.2.0/simfinapi/R/sfa_get_shares.R | 144 +-- simfinapi-0.2.0/simfinapi/R/sfa_get_statement.R | 189 ++-- simfinapi-0.2.0/simfinapi/R/sfa_set_cache_dir.R | 1 simfinapi-0.2.0/simfinapi/R/sfa_set_sfplus.R |only simfinapi-0.2.0/simfinapi/R/utils.R | 89 + simfinapi-0.2.0/simfinapi/README.md | 81 + simfinapi-0.2.0/simfinapi/build/vignette.rds |binary simfinapi-0.2.0/simfinapi/inst/doc/simfinapi.html | 234 ----- simfinapi-0.2.0/simfinapi/man/figures/README-plot_data-1.png |binary simfinapi-0.2.0/simfinapi/man/figures/README-recreate_plot-1.png |binary simfinapi-0.2.0/simfinapi/man/param_doc.Rd |only simfinapi-0.2.0/simfinapi/man/set_clean_names.Rd |only simfinapi-0.2.0/simfinapi/man/sfa_get_info.Rd | 20 simfinapi-0.2.0/simfinapi/man/sfa_get_prices.Rd | 38 simfinapi-0.2.0/simfinapi/man/sfa_get_ref.Rd |only simfinapi-0.2.0/simfinapi/man/sfa_get_shares.Rd | 69 + simfinapi-0.2.0/simfinapi/man/sfa_get_statement.Rd | 36 simfinapi-0.2.0/simfinapi/man/sfa_set_sfplus.Rd |only simfinapi-0.2.0/simfinapi/tests/testthat/helper-options.R | 3 simfinapi-0.2.0/simfinapi/tests/testthat/test-call_api.R | 10 simfinapi-0.2.0/simfinapi/tests/testthat/test-check_inputs.R |only simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_get_entities.R | 4 simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_get_info.R | 122 +- simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_get_prices.R | 189 ++-- simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_get_shares.R | 136 ++ simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_get_statement.R | 458 ++++++++-- simfinapi-0.2.0/simfinapi/tests/testthat/test-sfa_set_sfplus.R |only 42 files changed, 1579 insertions(+), 855 deletions(-)
Title: Fuzzy String Matching
Description: Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
SeatGeek Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fuzzywuzzyR versions 1.0.4 dated 2021-05-07 and 1.0.5 dated 2021-09-11
DESCRIPTION | 8 MD5 | 12 NEWS.md | 5 R/package.R | 6 README.md | 20 build/vignette.rds |binary inst/doc/functionality_of_fuzzywuzzyR_package.html | 690 +++++++-------------- 7 files changed, 291 insertions(+), 450 deletions(-)
Title: Simulate Fantasy Football Seasons
Description: Uses bootstrap resampling to run fantasy football season
simulations supported by historical rankings and 'nflfastR' data,
calculating optimal lineups, and returning aggregated results.
Author: Tan Ho [aut, cre, cph] (<https://orcid.org/0000-0001-8388-5155>)
Maintainer: Tan Ho <tan@tanho.ca>
Diff between ffsimulator versions 1.0.0 dated 2021-07-20 and 1.1.0 dated 2021-09-11
ffsimulator-1.0.0/ffsimulator/man/dot-ff_apply_injury_model.Rd |only ffsimulator-1.0.0/ffsimulator/man/parse_raw_rds.Rd |only ffsimulator-1.1.0/ffsimulator/DESCRIPTION | 25 ffsimulator-1.1.0/ffsimulator/MD5 | 168 +- ffsimulator-1.1.0/ffsimulator/NAMESPACE | 16 ffsimulator-1.1.0/ffsimulator/NEWS.md | 30 ffsimulator-1.1.0/ffsimulator/R/0_ff_simulate.R | 167 ++ ffsimulator-1.1.0/ffsimulator/R/0_ff_simulate_week.R |only ffsimulator-1.1.0/ffsimulator/R/1_outcomes.R | 175 +- ffsimulator-1.1.0/ffsimulator/R/1_outcomes_week.R |only ffsimulator-1.1.0/ffsimulator/R/2_rankings.R | 113 - ffsimulator-1.1.0/ffsimulator/R/3_rosters.R | 231 ++- ffsimulator-1.1.0/ffsimulator/R/4_projections.R | 177 +- ffsimulator-1.1.0/ffsimulator/R/4_projections_week.R |only ffsimulator-1.1.0/ffsimulator/R/5_roster_scores.R | 111 - ffsimulator-1.1.0/ffsimulator/R/6_optimise.R | 323 ++--- ffsimulator-1.1.0/ffsimulator/R/7_schedule.R | 395 +++--- ffsimulator-1.1.0/ffsimulator/R/8_summaries.R | 391 +++--- ffsimulator-1.1.0/ffsimulator/R/9_autoplot.R | 348 ++--- ffsimulator-1.1.0/ffsimulator/R/9_autoplot_week.R |only ffsimulator-1.1.0/ffsimulator/R/template_copy.R |only ffsimulator-1.1.0/ffsimulator/R/utils-assert.R |only ffsimulator-1.1.0/ffsimulator/R/utils-data.R | 28 ffsimulator-1.1.0/ffsimulator/R/utils-ffscrapr.R | 175 +- ffsimulator-1.1.0/ffsimulator/R/utils.R | 119 - ffsimulator-1.1.0/ffsimulator/R/zzz.R | 3 ffsimulator-1.1.0/ffsimulator/README.md | 24 ffsimulator-1.1.0/ffsimulator/data/fp_injury_table.rda |binary ffsimulator-1.1.0/ffsimulator/data/fp_rankings_history_week.rda |only ffsimulator-1.1.0/ffsimulator/inst/cache/adp_outcomes.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/adp_outcomes_week.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/espn_franchises.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/espn_rosters.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/espn_scoring_history.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/fleaflicker_franchises.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/fleaflicker_rosters.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/fleaflicker_scoring_history.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/foureight_sim.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/foureight_sim_week.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/latest_rankings.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/latest_rankings_week.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/mfl_franchises.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/mfl_rosters.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/mfl_scoring_history.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/optimal_scores.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/projected_scores.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/projected_scores_week.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/roster_scores.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/schedules.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/sleeper_franchises.rds |only ffsimulator-1.1.0/ffsimulator/inst/cache/sleeper_rosters.rds |binary ffsimulator-1.1.0/ffsimulator/inst/cache/sleeper_scoring_history.rds |binary ffsimulator-1.1.0/ffsimulator/inst/doc/basic.R | 25 ffsimulator-1.1.0/ffsimulator/inst/doc/basic.Rmd | 44 ffsimulator-1.1.0/ffsimulator/inst/doc/basic.html | 306 +++- ffsimulator-1.1.0/ffsimulator/inst/doc/custom.R | 40 ffsimulator-1.1.0/ffsimulator/inst/doc/custom.Rmd | 50 ffsimulator-1.1.0/ffsimulator/inst/doc/custom.html | 75 - ffsimulator-1.1.0/ffsimulator/inst/simulation_template_season.R |only ffsimulator-1.1.0/ffsimulator/inst/simulation_template_week.R |only ffsimulator-1.1.0/ffsimulator/man/assert_columns.Rd |only ffsimulator-1.1.0/ffsimulator/man/autoplot.ff_simulation.Rd | 11 ffsimulator-1.1.0/ffsimulator/man/autoplot.ff_simulation_week.Rd |only ffsimulator-1.1.0/ffsimulator/man/dot-ff_apply_gp_model.Rd |only ffsimulator-1.1.0/ffsimulator/man/dot-ff_optimise_one_lineup.Rd | 2 ffsimulator-1.1.0/ffsimulator/man/espn_connect.Rd | 42 ffsimulator-1.1.0/ffsimulator/man/ff_simulate.Rd | 23 ffsimulator-1.1.0/ffsimulator/man/ff_simulate_week.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_adp_outcomes.Rd | 22 ffsimulator-1.1.0/ffsimulator/man/ffs_adp_outcomes_week.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_build_schedules.Rd | 14 ffsimulator-1.1.0/ffsimulator/man/ffs_copy_template.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_franchises.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_generate_projections.Rd | 8 ffsimulator-1.1.0/ffsimulator/man/ffs_generate_projections_week.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_latest_rankings.Rd | 8 ffsimulator-1.1.0/ffsimulator/man/ffs_optimise_lineups.Rd | 9 ffsimulator-1.1.0/ffsimulator/man/ffs_repeat_schedules.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_rosters.Rd | 2 ffsimulator-1.1.0/ffsimulator/man/ffs_schedule.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_score_rosters.Rd | 2 ffsimulator-1.1.0/ffsimulator/man/ffs_starter_positions.Rd |only ffsimulator-1.1.0/ffsimulator/man/ffs_summaries.Rd | 12 ffsimulator-1.1.0/ffsimulator/man/figures/README-unnamed-chunk-5-1.png |binary ffsimulator-1.1.0/ffsimulator/man/figures/ffsimulator_plot.png |only ffsimulator-1.1.0/ffsimulator/man/fleaflicker_connect.Rd | 42 ffsimulator-1.1.0/ffsimulator/man/fp_injury_table.Rd | 2 ffsimulator-1.1.0/ffsimulator/man/fp_rankings_history.Rd | 4 ffsimulator-1.1.0/ffsimulator/man/fp_rankings_history_week.Rd |only ffsimulator-1.1.0/ffsimulator/man/mfl_connect.Rd | 42 ffsimulator-1.1.0/ffsimulator/man/pipe.Rd | 40 ffsimulator-1.1.0/ffsimulator/man/sleeper_connect.Rd | 42 ffsimulator-1.1.0/ffsimulator/tests/testthat/_snaps/ffs_autoplot/points-plot.svg | 180 +- ffsimulator-1.1.0/ffsimulator/tests/testthat/_snaps/ffs_autoplot/rank-plot.svg | 632 ++++------ ffsimulator-1.1.0/ffsimulator/tests/testthat/_snaps/ffs_autoplot/weekly-luck-plot.svg |only ffsimulator-1.1.0/ffsimulator/tests/testthat/_snaps/ffs_autoplot/weekly-points-plot.svg |only ffsimulator-1.1.0/ffsimulator/tests/testthat/_snaps/ffs_autoplot/wins-plot.svg | 108 - ffsimulator-1.1.0/ffsimulator/tests/testthat/test-ffs_autoplot.R | 11 ffsimulator-1.1.0/ffsimulator/tests/testthat/test-ffs_components.R | 124 + ffsimulator-1.1.0/ffsimulator/tests/testthat/test-integration.R | 49 ffsimulator-1.1.0/ffsimulator/vignettes/basic.Rmd | 44 ffsimulator-1.1.0/ffsimulator/vignettes/custom.Rmd | 50 102 files changed, 2849 insertions(+), 2235 deletions(-)
Title: Rendering Math to HTML, 'MathML', or R-Documentation Format
Description: Convert latex math expressions to HTML and 'MathML' for use in
markdown documents or package manual pages. The rendering is done in
R using the V8 engine (i.e. server-side), which eliminates the need
for embedding the 'MathJax' library into your web pages. In addition
a 'math-to-rd' wrapper is provided to automatically render beautiful
math in R documentation files.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between katex versions 1.1.0 dated 2021-07-15 and 1.2.0 dated 2021-09-11
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS | 5 +++++ R/katex.R | 4 ++++ R/rd.R | 17 +++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/js/he.min.js |only man/math_to_rd.Rd | 11 ++++------- 9 files changed, 31 insertions(+), 27 deletions(-)
Title: Bayesian Generalized Linear Models with Time-Varying
Coefficients
Description: Bayesian generalized linear models with time-varying coefficients
as in Helske (2020, <arXiv:2009.07063>). Gaussian, Poisson, and binomial
observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, the package uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 1.0.2 dated 2021-04-06 and 1.0.3 dated 2021-09-11
DESCRIPTION | 15 MD5 | 37 - NAMESPACE | 1 R/rw.R | 24 R/test_args.R |only R/walker.R | 1216 +++++++++++++++++++++---------------------- README.md | 7 build/vignette.rds |binary configure | 2 configure.win | 12 inst/doc/walker.html | 18 inst/stan/walker_glm.stan | 743 +++++++++++++------------- inst/stan/walker_lm.stan | 490 ++++++++--------- man/walker.Rd | 30 + src/Makevars | 17 src/Makevars.win | 16 src/RcppExports.cpp | 5 src/stanExports_walker_glm.h | 323 +++++------ src/stanExports_walker_lm.h | 64 +- tests/testthat/tests.R | 6 20 files changed, 1547 insertions(+), 1479 deletions(-)
Title: Interface to the 'JWSACruncher' of 'JDemetra+'
Description: 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>) is the seasonal adjustment software officially recommended
to the members of the European Statistical System and the European System of Central Banks. Seasonal adjustment models performed
with 'JDemetra+' can be stored into workspaces. 'JWSACruncher' (<https://github.com/jdemetra/jwsacruncher/releases>) is a console tool that
re-estimates all the multi-processing defined in a workspace and to export the result. 'rjwsacruncher' allows to launch easily the 'JWSACruncher'.
Author: Alain Quartier-la-Tente [aut, cre]
(<https://orcid.org/0000-0001-7890-3857>),
Institut national de la statistique et des études économiques [cph]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjwsacruncher versions 0.1.1 dated 2021-07-21 and 0.1.2 dated 2021-09-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 ++++++- R/param_file.R | 5 +++-- inst/doc/run_jwsacruncher.html | 6 +++--- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>),
RStudio [cph, fnd],
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>),
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>),
Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Duncan Luguern [aut],
David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>,
dmkaplan2000),
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>),
Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>),
Alfredo Hernández [ctb] (<https://orcid.org/0000-0002-2660-4545>),
Stefano Coretta [ctb] (<https://orcid.org/0000-0001-9627-5532>,
stefanocoretta),
Matthias Templ [ctb] (<https://orcid.org/0000-0002-8638-5276>,
matthias-da),
Alvaro Uzaheta [ctb] (auzaheta),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.20 dated 2021-06-23 and 0.21 dated 2021-09-11
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Title: PD-Clustering and Factor PD-Clustering
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different size. GPDC and TPDC uses a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high dimensional data sets.
Author: Cristina Tortora [aut, cre, cph], Noe Vidales [aut], Francesco Palumbo [aut], Tina Kalra [aut], and Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 1.4.1 dated 2020-01-28 and 2.0 dated 2021-09-11
FPDclustering-1.4.1/FPDclustering/R/PDclust.R |only FPDclustering-1.4.1/FPDclustering/data/ais.rdata |only FPDclustering-1.4.1/FPDclustering/man/PDclust.Rd |only FPDclustering-2.0/FPDclustering/DESCRIPTION | 14 FPDclustering-2.0/FPDclustering/MD5 | 43 FPDclustering-2.0/FPDclustering/NAMESPACE | 9 FPDclustering-2.0/FPDclustering/R/FPDC.R | 7 FPDclustering-2.0/FPDclustering/R/GPDC.R | 8 FPDclustering-2.0/FPDclustering/R/PDC.R |only FPDclustering-2.0/FPDclustering/R/PDQ.R | 555 +++++++---- FPDclustering-2.0/FPDclustering/R/Silh.R | 1 FPDclustering-2.0/FPDclustering/R/TPDC.R | 3 FPDclustering-2.0/FPDclustering/R/TuckerFactors.R | 2 FPDclustering-2.0/FPDclustering/R/s3.r |only FPDclustering-2.0/FPDclustering/data/ais.rda |only FPDclustering-2.0/FPDclustering/data/asymmetric20.rda |binary FPDclustering-2.0/FPDclustering/data/asymmetric3.rda |binary FPDclustering-2.0/FPDclustering/data/outliers.rda |binary FPDclustering-2.0/FPDclustering/man/FPDC.Rd | 20 FPDclustering-2.0/FPDclustering/man/GPDC.Rd | 12 FPDclustering-2.0/FPDclustering/man/PDC.Rd |only FPDclustering-2.0/FPDclustering/man/PDQ.Rd | 77 + FPDclustering-2.0/FPDclustering/man/TPDC.Rd | 13 FPDclustering-2.0/FPDclustering/man/TuckerFactors.Rd | 4 FPDclustering-2.0/FPDclustering/man/ais.Rd | 2 FPDclustering-2.0/FPDclustering/man/plot.FPDclustering.Rd |only FPDclustering-2.0/FPDclustering/man/summary.FPDclustering.Rd |only 27 files changed, 530 insertions(+), 240 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-10 0.9.2
2019-05-03 0.9.1
Title: Spatial Analysis of Vectra Immunoflourescent Data
Description: Visualization and analysis of Vectra Immunoflourescent
data. Options for calculating both the univariate and bivariate Ripley's K
are included. Calculations are performed using a permutation-based
approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Author: Jordan Creed [aut],
Ram Thapa [aut],
Christopher Wilson [aut],
Alex Soupir [aut],
Brooke Fridley [cph],
Fridley Lab [cre]
Maintainer: Fridley Lab <fridley.lab@moffitt.org>
Diff between spatialTIME versions 1.1.0 dated 2021-08-21 and 1.2.0 dated 2021-09-11
DESCRIPTION | 16 - MD5 | 41 ++-- R/create_mif.R | 11 + R/plot_immunoflo.R | 26 ++ R/ripleys_k.R | 157 +++++++++++++--- R/subset_mif.R | 25 ++ R/utils-helpers.R | 104 ++++++++-- README.md |only data/example_clinical.rda |binary data/example_spatial.rda |binary data/example_summary.rda |binary inst/doc/intro.R | 200 ++++++++++++++++---- inst/doc/intro.Rmd | 296 +++++++++++++++++++++++------- inst/doc/intro.html | 445 ++++++++++++++++++++++++++++++++-------------- man/NN_G.Rd | 34 +++ man/bi_NN_G.Rd | 31 +++ man/bi_ripleys_k.Rd | 30 ++- man/create_mif.Rd | 11 + man/plot_immunoflo.Rd | 20 ++ man/ripleys_k.Rd | 33 +++ man/subset_mif.Rd | 20 +- vignettes/intro.Rmd | 296 +++++++++++++++++++++++------- 22 files changed, 1387 insertions(+), 409 deletions(-)
Title: Computing Envelope Estimators
Description: Provides a general routine, envMU, which allows estimation of the M envelope of span(U) given root n consistent estimators of M and U. The routine envMU does not presume a model. This package implements response envelopes, partial response envelopes, envelopes in the predictor space, heteroscedastic envelopes, simultaneous envelopes, scaled response envelopes, scaled envelopes in the predictor space, groupwise envelopes, weighted envelopes, envelopes in logistic regression and envelopes in Poisson regression. For each of these model-based routines the package provides inference tools including bootstrap, cross validation, estimation and prediction, hypothesis testing on coefficients are included except for weighted envelopes. Tools for selection of dimension include AIC, BIC and likelihood ratio testing. Background is available at Cook, R. D., Forzani, L. and Su, Z. (2016) <doi:10.1016/j.jmva.2016.05.006>. Optimization is based on a clockwise coordinate descent algorithm.
Author: Minji Lee, Zhihua Su
Maintainer: Minji Lee <mlee9@ufl.edu>
Diff between Renvlp versions 2.9 dated 2020-11-15 and 3.0 dated 2021-09-11
DESCRIPTION | 8 +-- MD5 | 8 +-- R/logit.envMU.R | 121 ++++++++++++++++++++++++++----------------------- R/pois.envMU.R | 137 +++++++++++++++++++++++++++++--------------------------- man/Renvlp.Rd | 4 - 5 files changed, 148 insertions(+), 130 deletions(-)
Title: Reconstruction of Transmission Chains from Surveillance Data
Description: Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. 2020 <doi:10.1098/rsif.2020.0084>).
Author: Alexis Robert [aut, cre, cph] (<https://orcid.org/0000-0002-4516-2965>),
Sebastian Funk [aut] (<https://orcid.org/0000-0002-2842-3406>),
Adam J Kucharski [aut] (<https://orcid.org/0000-0001-8814-9421>),
Thibaut Jombart [ctb]
Maintainer: Alexis Robert <alexis.robert@lshtm.ac.uk>
Diff between o2geosocial versions 1.0.1 dated 2020-09-25 and 1.1.0 dated 2021-09-11
DESCRIPTION | 6 MD5 | 63 ++++--- NAMESPACE | 3 NEWS.md | 25 +++ R/RcppExports.R | 12 + R/create_config.R | 65 +++++--- R/create_param.R | 18 -- R/custom_likelihoods.R | 15 + R/outbreaker.R | 4 R/outbreaker_data.R | 59 +------ R/outbreaker_find_imports.R | 35 +++- R/outbreaker_move.R | 15 - R/plot_importation.R |only R/pre_clustering.R | 12 + README.md | 13 + build/vignette.rds |binary inst/doc/o2geosocial.html | 75 ++++----- inst/include/o2geosocial_RcppExports.h | 50 +++++- man/create_config.Rd | 3 man/custom_likelihoods.Rd | 2 man/custom_moves.Rd | 160 ++++++++++---------- man/custom_priors.Rd | 182 +++++++++++----------- man/outbreaker_chains.Rd | 262 ++++++++++++++++----------------- man/outbreaker_data.Rd | 4 man/pre_clustering.Rd | 56 +++---- man/toy_outbreak_long.Rd | 86 +++++----- src/RcppExports.cpp | 101 +++++++++++- src/internals.cpp | 165 ++++++-------------- src/internals.h | 8 - src/likelihoods.cpp | 55 +++++- src/moves.cpp | 187 +++++++++++++++-------- tests/testthat/test_likelihood.R | 14 - tests/testthat/test_outbreaker.R | 6 33 files changed, 998 insertions(+), 763 deletions(-)
Title: Analyzing Remotely Sensed Forest Data
Description: Provides tools for analyzing remotely sensed forest data, including functions for detecting treetops from canopy models, outlining tree crowns, calculating textural metrics and generating spatial statistics.
Author: Andrew Plowright, Jean-Romain Roussel
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between ForestTools versions 0.2.4 dated 2021-04-18 and 0.2.5 dated 2021-09-11
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/glcm.R | 34 +++++++++++++++++++++++++++++++++- README.md | 4 ++-- inst/doc/inventory_attributes.html | 4 ++-- inst/doc/polygonal_crowns.html | 4 ++-- inst/doc/treetop_analysis.html | 6 +++--- man/dot-calcGLCM.Rd | 2 +- man/glcm_img.Rd |only tests/testthat/test_glcm.R | 21 +++++++++++++++++++++ tests/testthat/test_glcm_internal.R | 28 ++++++++++++++-------------- 13 files changed, 99 insertions(+), 40 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.3.8 dated 2021-05-18 and 0.4.0 dated 2021-09-11
DESCRIPTION | 6 - MD5 | 26 ++--- R/RcppExports.R | 4 R/plot.R | 229 ++++++++++++++++++++++++++++++++++++---------------- build/partial.rdb |binary man/BEAST_null.Rd | 58 ++++++++----- man/BET.Rd | 35 ++++--- man/BETs.Rd | 29 +++--- man/Beast.Rd | 66 ++++++++------ man/bet.plot.Rd | 8 - man/star.Rd | 2 man/symm.Rd | 20 +--- src/BET3.cpp | 105 +++++++++-------------- src/RcppExports.cpp | 11 -- 14 files changed, 345 insertions(+), 254 deletions(-)