Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-01 1.1.0
2022-08-29 1.0.1
2022-06-06 1.0.0
Title: Efficient Plotting of Large-Sized Data
Description: A tool to plot data with large sample size using 'shiny' and 'plotly'.
Relatively small samples are chosen from the data using an appropriate algorithm according to a user-defined x range.
Jonas Van Der Donckt, Jeroen Van Der Donckt, Emiel Deprost (2022) <https://github.com/predict-idlab/plotly-resampler>.
Author: Junta Tagusari [aut, cre, cph],
Jonas Van Der Donckt [cph],
Jeroen Van Der Donckt [cph],
Emiel Deprost [cph]
Maintainer: Junta Tagusari <j.tagusari@eng.hokudai.ac.jp>
Diff between shinyHugePlot versions 0.2.0 dated 2022-10-26 and 0.2.1 dated 2022-11-16
shinyHugePlot-0.2.0/shinyHugePlot/R/apply_downsampler.R |only shinyHugePlot-0.2.0/shinyHugePlot/man/apply_downsampler.Rd |only shinyHugePlot-0.2.0/shinyHugePlot/tests/manual/test-wrappers.R |only shinyHugePlot-0.2.0/shinyHugePlot/tests/testthat/test-abstract-downsampler.R |only shinyHugePlot-0.2.0/shinyHugePlot/tests/testthat/test-utils.R |only shinyHugePlot-0.2.1/shinyHugePlot/DESCRIPTION | 6 shinyHugePlot-0.2.1/shinyHugePlot/MD5 | 86 +- shinyHugePlot-0.2.1/shinyHugePlot/NAMESPACE | 5 shinyHugePlot-0.2.1/shinyHugePlot/NEWS.md | 5 shinyHugePlot-0.2.1/shinyHugePlot/R/LTTB_aggregator.R | 49 + shinyHugePlot-0.2.1/shinyHugePlot/R/aggregator.R | 296 +++++----- shinyHugePlot-0.2.1/shinyHugePlot/R/custom_func_aggregator.R | 44 - shinyHugePlot-0.2.1/shinyHugePlot/R/custom_stat_aggregator.R | 29 shinyHugePlot-0.2.1/shinyHugePlot/R/downsampler.R | 125 +++- shinyHugePlot-0.2.1/shinyHugePlot/R/eLTTB_aggregator.R | 39 - shinyHugePlot-0.2.1/shinyHugePlot/R/globalVariables.R |only shinyHugePlot-0.2.1/shinyHugePlot/R/min_max_aggregator.R | 22 shinyHugePlot-0.2.1/shinyHugePlot/R/min_max_ovlp_aggregator.R | 19 shinyHugePlot-0.2.1/shinyHugePlot/R/nth_pnt_aggregator.R | 19 shinyHugePlot-0.2.1/shinyHugePlot/R/null_aggregator.R | 35 - shinyHugePlot-0.2.1/shinyHugePlot/R/plotly_build_light.R | 118 +-- shinyHugePlot-0.2.1/shinyHugePlot/R/plotly_datahandler.R | 277 +++++---- shinyHugePlot-0.2.1/shinyHugePlot/R/range_stat_aggregator.R | 31 - shinyHugePlot-0.2.1/shinyHugePlot/R/rng_aggregator.R | 104 ++- shinyHugePlot-0.2.1/shinyHugePlot/R/shiny_hugeplot.R | 105 ++- shinyHugePlot-0.2.1/shinyHugePlot/R/updatePlotlyH.R | 5 shinyHugePlot-0.2.1/shinyHugePlot/README.md | 49 - shinyHugePlot-0.2.1/shinyHugePlot/data/noise_fluct.rda |binary shinyHugePlot-0.2.1/shinyHugePlot/man/LTTB_aggregator.Rd | 188 +++--- shinyHugePlot-0.2.1/shinyHugePlot/man/aggregator.Rd | 255 ++++---- shinyHugePlot-0.2.1/shinyHugePlot/man/custom_func_aggregator.Rd | 212 +++---- shinyHugePlot-0.2.1/shinyHugePlot/man/custom_stat_aggregator.Rd | 191 +++--- shinyHugePlot-0.2.1/shinyHugePlot/man/downsampler.Rd | 37 + shinyHugePlot-0.2.1/shinyHugePlot/man/eLTTB_aggregator.Rd | 178 +++--- shinyHugePlot-0.2.1/shinyHugePlot/man/min_max_aggregator.Rd | 158 ++--- shinyHugePlot-0.2.1/shinyHugePlot/man/min_max_ovlp_aggregator.Rd | 157 ++--- shinyHugePlot-0.2.1/shinyHugePlot/man/nth_pnt_aggregator.Rd | 149 ++--- shinyHugePlot-0.2.1/shinyHugePlot/man/null_aggregator.Rd | 37 - shinyHugePlot-0.2.1/shinyHugePlot/man/plotly_build_light.Rd | 14 shinyHugePlot-0.2.1/shinyHugePlot/man/plotly_datahandler.Rd | 15 shinyHugePlot-0.2.1/shinyHugePlot/man/range_stat_aggregator.Rd | 187 +++--- shinyHugePlot-0.2.1/shinyHugePlot/man/rng_aggregator.Rd | 29 shinyHugePlot-0.2.1/shinyHugePlot/man/shiny_hugeplot.Rd | 45 + shinyHugePlot-0.2.1/shinyHugePlot/man/updatePlotlyH.Rd | 5 shinyHugePlot-0.2.1/shinyHugePlot/tests/manual/test-addtrace.R | 23 shinyHugePlot-0.2.1/shinyHugePlot/tests/manual/test-shiny.R |only shinyHugePlot-0.2.1/shinyHugePlot/tests/testthat/test-aggregator.R | 105 +++ shinyHugePlot-0.2.1/shinyHugePlot/tests/testthat/test-downsampler.R |only 48 files changed, 1978 insertions(+), 1475 deletions(-)
Title: Sliding Window Functions
Description: Provides type-stable rolling window functions over any R data
type. Cumulative and expanding windows are also supported. For more
advanced usage, an index can be used as a secondary vector that
defines how sliding windows are to be created.
Author: Davis Vaughan [aut, cre],
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between slider versions 0.2.2 dated 2021-07-01 and 0.3.0 dated 2022-11-16
slider-0.2.2/slider/R/names.R |only slider-0.2.2/slider/src/names.c |only slider-0.2.2/slider/tests/testthat/output |only slider-0.3.0/slider/DESCRIPTION | 47 slider-0.3.0/slider/LICENSE | 4 slider-0.3.0/slider/MD5 | 228 ++-- slider-0.3.0/slider/NAMESPACE | 24 slider-0.3.0/slider/NEWS.md | 30 slider-0.3.0/slider/R/arithmetic.R |only slider-0.3.0/slider/R/conditions.R | 319 ++---- slider-0.3.0/slider/R/hop-common.R | 29 slider-0.3.0/slider/R/hop-index-common.R | 39 slider-0.3.0/slider/R/hop-index.R | 18 slider-0.3.0/slider/R/hop-index2.R | 28 slider-0.3.0/slider/R/hop.R | 10 slider-0.3.0/slider/R/hop2.R | 27 slider-0.3.0/slider/R/phop-index.R | 16 slider-0.3.0/slider/R/phop.R | 16 slider-0.3.0/slider/R/pslide-index.R | 22 slider-0.3.0/slider/R/pslide-period.R | 22 slider-0.3.0/slider/R/pslide.R | 21 slider-0.3.0/slider/R/slide-index-common.R | 91 + slider-0.3.0/slider/R/slide-index.R | 16 slider-0.3.0/slider/R/slide-index2.R | 21 slider-0.3.0/slider/R/slide-period-common.R | 48 slider-0.3.0/slider/R/slide-period.R | 16 slider-0.3.0/slider/R/slide-period2.R | 25 slider-0.3.0/slider/R/slide.R | 13 slider-0.3.0/slider/R/slide2.R | 22 slider-0.3.0/slider/R/slider-package.R | 7 slider-0.3.0/slider/R/summary-index.R | 33 slider-0.3.0/slider/R/summary-slide.R | 16 slider-0.3.0/slider/R/utils.R | 107 +- slider-0.3.0/slider/R/zzz.R | 2 slider-0.3.0/slider/README.md | 94 - slider-0.3.0/slider/build/vignette.rds |binary slider-0.3.0/slider/inst/doc/rowwise.html | 493 +++++++-- slider-0.3.0/slider/inst/doc/slider.html | 506 ++++++++-- slider-0.3.0/slider/inst/doc/tsibble.html | 396 ++++++- slider-0.3.0/slider/man/hop.Rd | 18 slider-0.3.0/slider/man/index-arithmetic.Rd |only slider-0.3.0/slider/man/slide.Rd | 32 slider-0.3.0/slider/man/slide2.Rd | 14 slider-0.3.0/slider/man/slide_index.Rd | 14 slider-0.3.0/slider/man/slide_index2.Rd | 14 slider-0.3.0/slider/man/slide_period.Rd | 14 slider-0.3.0/slider/man/slide_period2.Rd | 24 slider-0.3.0/slider/man/slider-package.Rd | 12 slider-0.3.0/slider/man/summary-index.Rd | 25 slider-0.3.0/slider/man/summary-slide.Rd | 10 slider-0.3.0/slider/src/hop.c | 2 slider-0.3.0/slider/src/index.c | 4 slider-0.3.0/slider/src/init.c | 8 slider-0.3.0/slider/src/params.c | 6 slider-0.3.0/slider/src/slide.c | 2 slider-0.3.0/slider/src/slider-vctrs-private.c | 4 slider-0.3.0/slider/src/slider-vctrs-private.h | 1 slider-0.3.0/slider/src/slider-vctrs-public.c | 2 slider-0.3.0/slider/src/summary-core-align.cpp | 4 slider-0.3.0/slider/src/summary-core-align.h | 4 slider-0.3.0/slider/src/summary-core.h | 4 slider-0.3.0/slider/src/utils.h | 8 slider-0.3.0/slider/tests/testthat/_snaps/block.md |only slider-0.3.0/slider/tests/testthat/_snaps/conditions.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop-index-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop-index.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop-index2-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop-index2.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop.md |only slider-0.3.0/slider/tests/testthat/_snaps/hop2-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/phop-index-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/phop-index.md |only slider-0.3.0/slider/tests/testthat/_snaps/phop-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/phop.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide-index-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide-index.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide-period-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide-period.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/pslide.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-index-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-index.md | 258 ++++- slider-0.3.0/slider/tests/testthat/_snaps/slide-index2-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-index2.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-period-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-period.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-period2-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-period2.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide2-vec.md |only slider-0.3.0/slider/tests/testthat/_snaps/slide2.md |only slider-0.3.0/slider/tests/testthat/_snaps/summary-index.md |only slider-0.3.0/slider/tests/testthat/_snaps/summary-slide.md |only slider-0.3.0/slider/tests/testthat/helper-s3.R | 2 slider-0.3.0/slider/tests/testthat/test-arithmetic.R |only slider-0.3.0/slider/tests/testthat/test-block.R | 20 slider-0.3.0/slider/tests/testthat/test-conditions.R | 46 slider-0.3.0/slider/tests/testthat/test-hop-index-vec.R | 49 slider-0.3.0/slider/tests/testthat/test-hop-index.R | 54 - 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slider-0.3.0/slider/tests/testthat/test-slide-period.R | 137 +- slider-0.3.0/slider/tests/testthat/test-slide-period2-vec.R | 66 - slider-0.3.0/slider/tests/testthat/test-slide-period2.R | 22 slider-0.3.0/slider/tests/testthat/test-slide-vec.R | 55 - slider-0.3.0/slider/tests/testthat/test-slide.R | 54 - slider-0.3.0/slider/tests/testthat/test-slide2-vec.R | 24 slider-0.3.0/slider/tests/testthat/test-slide2.R | 7 slider-0.3.0/slider/tests/testthat/test-summary-index.R | 20 slider-0.3.0/slider/tests/testthat/test-summary-slide.R | 16 130 files changed, 2991 insertions(+), 1650 deletions(-)
Title: Spatial and Spatio-Temporal Semiparametric Regression Models
with Spatial Lags
Description: Estimation and inference of spatial and spatio-temporal
semiparametric models including spatial or spatio-temporal non-parametric
trends, parametric and non-parametric covariates and, possibly, a spatial
lag for the dependent variable and temporal correlation in the noise.
The spatio-temporal trend can be decomposed in ANOVA way including main and
interaction functional terms. Use of SAP algorithm to estimate the spatial
or spatio-temporal trend and non-parametric covariates. The methodology of
these models can be found in next references
Basile, R. et al. (2014), <doi:10.1016/j.jedc.2014.06.011>;
Rodriguez-Alvarez, M.X. et al. (2015) <doi:10.1007/s11222-014-9464-2> and,
particularly referred to the focus of the package, Minguez, R.,
Basile, R. and Durban, M. (2020) <doi:10.1007/s10260-019-00492-8>.
Author: Roman Minguez [aut, cre] ,
Roberto Basile [aut] ,
Maria Durban [aut] ,
Gonzalo Espana-Heredia [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between pspatreg versions 1.0.4 dated 2022-07-04 and 1.0.6 dated 2022-11-16
pspatreg-1.0.4/pspatreg/vignettes/plot2dpoints_anova_ames-4-vignetteB.png |only pspatreg-1.0.4/pspatreg/vignettes/unnamed-chunk-31-1-vignetteB.png |only pspatreg-1.0.4/pspatreg/vignettes/unnamed-chunk-31-2-vignetteB.png |only pspatreg-1.0.4/pspatreg/vignettes/unnamed-chunk-31-3-vignetteB.png |only pspatreg-1.0.6/pspatreg/DESCRIPTION | 24 pspatreg-1.0.6/pspatreg/MD5 | 83 pspatreg-1.0.6/pspatreg/NAMESPACE | 248 - pspatreg-1.0.6/pspatreg/R/impactsnopar.R | 18 pspatreg-1.0.6/pspatreg/R/methods_pspatreg.R | 18 pspatreg-1.0.6/pspatreg/R/package-pspatreg.R | 2 pspatreg-1.0.6/pspatreg/R/plot_impactsnopar.R | 17 pspatreg-1.0.6/pspatreg/R/plot_sp2d.R | 20 pspatreg-1.0.6/pspatreg/R/plot_terms.R | 18 pspatreg-1.0.6/pspatreg/R/pspatfit.R | 19 pspatreg-1.0.6/pspatreg/R/pspl_functions.R | 17 pspatreg-1.0.6/pspatreg/build/vignette.rds |binary pspatreg-1.0.6/pspatreg/demo/demo_impactsnopar.R | 10 pspatreg-1.0.6/pspatreg/demo/demo_plot_impactsnopar.R | 9 pspatreg-1.0.6/pspatreg/demo/demo_plot_sp2d.R | 9 pspatreg-1.0.6/pspatreg/demo/demo_plot_terms.R | 10 pspatreg-1.0.6/pspatreg/demo/demo_pspatfit.R | 10 pspatreg-1.0.6/pspatreg/demo/demo_pspl_pspt.R | 10 pspatreg-1.0.6/pspatreg/inst/doc/A_pspatregPackage.html | 172 - pspatreg-1.0.6/pspatreg/inst/doc/B_Examples_pspatreg_CS_data.Rmd | 1216 ++----- pspatreg-1.0.6/pspatreg/inst/doc/B_Examples_pspatreg_CS_data.html | 1524 +++------- pspatreg-1.0.6/pspatreg/inst/doc/C_Examples_pspatreg_Panel_data.Rmd | 2 pspatreg-1.0.6/pspatreg/inst/doc/C_Examples_pspatreg_Panel_data.html | 162 - pspatreg-1.0.6/pspatreg/man/impactsnopar.Rd | 18 pspatreg-1.0.6/pspatreg/man/methods_pspatreg.Rd | 18 pspatreg-1.0.6/pspatreg/man/plot_impactsnopar.Rd | 17 pspatreg-1.0.6/pspatreg/man/plot_sp2d.Rd | 20 pspatreg-1.0.6/pspatreg/man/plot_terms.Rd | 18 pspatreg-1.0.6/pspatreg/man/pspatfit.Rd | 19 pspatreg-1.0.6/pspatreg/man/pspl_terms.Rd | 17 pspatreg-1.0.6/pspatreg/vignettes/B_Examples_pspatreg_CS_data.Rmd | 1216 ++----- pspatreg-1.0.6/pspatreg/vignettes/B_Examples_pspatreg_CS_data.Rmd.orig | 122 pspatreg-1.0.6/pspatreg/vignettes/C_Examples_pspatreg_Panel_data.Rmd | 2 pspatreg-1.0.6/pspatreg/vignettes/plot2dpoints_anova_ames-1-vignetteB.png |binary pspatreg-1.0.6/pspatreg/vignettes/plot2dpoints_anova_ames-2-vignetteB.png |binary pspatreg-1.0.6/pspatreg/vignettes/plot2dpoints_anova_ames-3-vignetteB.png |binary pspatreg-1.0.6/pspatreg/vignettes/plot2dpoints_noanova_ames-1-vignetteB.png |binary pspatreg-1.0.6/pspatreg/vignettes/unnamed-chunk-29-1-vignetteB.png |only pspatreg-1.0.6/pspatreg/vignettes/unnamed-chunk-29-2-vignetteB.png |only pspatreg-1.0.6/pspatreg/vignettes/unnamed-chunk-29-3-vignetteB.png |only pspatreg-1.0.6/pspatreg/vignettes/unnamed-chunk-7-1-vignetteB.png |binary pspatreg-1.0.6/pspatreg/vignettes/unnamed-chunk-7-2-vignetteB.png |binary 46 files changed, 1847 insertions(+), 3238 deletions(-)
Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modelling mutations in pedigrees with
marker data, as used e.g. in likelihood computations with microsatellite data.
Implemented models include proportional and stepwise models, as well as random
models for experimental work, and custom models allowing the user to apply any
valid mutation matrix. Allele lumping is done following the lumpability criteria
of Kemeny and Snell (1976), ISBN:0387901922.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedmut versions 0.3.0 dated 2021-10-22 and 0.4.0 dated 2022-11-16
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS.md | 7 + R/model_properties.R | 12 +-- R/mutationMatrix.R | 22 +++-- R/mutationModel.R | 53 +++++++++----- README.md | 144 +++++++++++++++++++-------------------- man/figures/README-ex1-ped-1.png |binary man/mutationModel.Rd | 9 +- 9 files changed, 151 insertions(+), 120 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2019.12-10 dated 2019-12-15 and 2022.11-16 dated 2022-11-16
DESCRIPTION | 10 MD5 | 114 +++--- NAMESPACE | 17 NEWS | 18 R/AO.R | 34 - R/clm.R | 34 - R/clm.Thetamat.R | 34 - R/clm.anova.R | 34 - R/clm.fit.R | 34 - R/clm.fitter.R | 34 - R/clm.frames.R | 36 - R/clm.methods.R | 39 +- R/clm.nominal_test.R | 34 - R/clm.predict.R | 34 - R/clm.profile.R | 34 - R/clm.simple.R | 34 - R/clm.slice.R | 34 - R/clm.slice2D.R | 34 - R/clm.start.R | 47 +- R/clm2.R | 34 - R/clmm.R | 45 +- R/clmm.formula.R | 34 - R/clmm.methods.R | 84 ++-- R/clmm.ranef.R | 36 - R/clmm.ssr.R | 34 - R/clmm.start.R | 34 - R/clmm2.R | 34 - R/clmm2.utils.R | 34 - R/contrast_utils.R | 34 - R/control.R | 34 - R/convergence.R | 34 - R/derivatives.R | 34 - R/drop.coef.R | 34 - R/gdist.R | 34 - R/gumbel.R | 34 - R/lgamma.R | 34 - R/terms_utils.R | 34 - R/utils.R | 41 +- R/warning_functions.R | 34 - build/vignette.rds |binary inst/doc/clm_article.R | 258 ++++++++----- inst/doc/clm_article.Rnw | 705 ++++++++++++++++++++------------------ inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.pdf |binary man/VarCorr.Rd | 1 man/lgamma.Rd | 236 ++++++------ man/ranef.Rd | 3 src/get_fitted.c | 2 src/init.c | 2 src/links.c | 2 src/links.h | 2 src/utilityFuns.c | 21 - tests/clmm.R | 67 +-- tests/clmm.methods.R |only tests/ranef.loading.R |only tests/test.clm.flex.link.R | 13 tests/testthat/test-clm-formula.R | 12 vignettes/clm_article.Rnw | 705 ++++++++++++++++++++------------------ vignettes/clm_article_refs.bib | 219 ++++++++++- 59 files changed, 2058 insertions(+), 1629 deletions(-)
Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-
level treatments and individual-level outcomes using a network
optimization algorithm. Functions for checking balance at the
cluster and individual levels are also provided, as are methods
for permutation-inference-based outcome analysis. Details in
Pimentel et al. (2018) <doi:10.1214/17-AOAS1118>. The optmatch
package, which is useful for running many of the provided
functions, may be downloaded from Github at
<https://github.com/markmfredrickson/optmatch> if not available on
CRAN.
Author: Luke Keele [aut],
Luke Miratrix [aut],
Sam Pimentel [aut, cre],
Paul Rosenbaum [ctb]
Maintainer: Sam Pimentel <spi@berkeley.edu>
Diff between matchMulti versions 1.1.10 dated 2022-03-27 and 1.1.11 dated 2022-11-16
DESCRIPTION | 15 +++++---- MD5 | 22 ++++++------- NAMESPACE | 2 - R/balanceTable.R | 2 - R/matchMulti-internal.R | 12 +++++-- R/matchMulti.R | 60 +++++++++++++++++++++++++++++++------- build/matchMulti.pdf |binary inst/doc/multiMatch_vignette.R | 32 ++++++++++---------- inst/doc/multiMatch_vignette.pdf |binary man/matchMulti.Rd | 16 +++++++--- man/matchSchools.Rd | 8 ++++- tests/testthat/test-school_covs.R | 1 12 files changed, 114 insertions(+), 56 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of
functions. With its progressive approach, we can construct display tables
with a cohesive set of table parts. Table values can be formatted using any
of the included formatting functions. Footnotes and cell styles can be
precisely added through a location targeting system. The way in which 'gt'
handles things for you means that you don't often have to worry about the
fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Ellis Hughes [aut] ,
JooYoung Seo [aut] ,
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between gt versions 0.7.0 dated 2022-08-25 and 0.8.0 dated 2022-11-16
gt-0.7.0/gt/tests/performance-monitoring |only gt-0.7.0/gt/tests/testthat/test-cols_merge.R |only gt-0.7.0/gt/tests/testthat/test-fmt_bytes.R |only gt-0.7.0/gt/tests/testthat/test-fmt_currency.R |only gt-0.7.0/gt/tests/testthat/test-fmt_engineering.R |only gt-0.7.0/gt/tests/testthat/test-fmt_integer.R |only gt-0.7.0/gt/tests/testthat/test-fmt_markdown.R |only gt-0.7.0/gt/tests/testthat/test-fmt_number.R |only gt-0.7.0/gt/tests/testthat/test-fmt_partsper.R |only gt-0.7.0/gt/tests/testthat/test-fmt_passthrough.R |only gt-0.7.0/gt/tests/testthat/test-fmt_percent.R |only gt-0.7.0/gt/tests/testthat/test-fmt_scientific.R |only gt-0.7.0/gt/tests/testthat/test-rtf_page_options.R |only gt-0.8.0/gt/DESCRIPTION | 38 gt-0.8.0/gt/MD5 | 344 +-- gt-0.8.0/gt/NAMESPACE | 15 gt-0.8.0/gt/NEWS.md | 51 gt-0.8.0/gt/R/as_data_frame.R | 2 gt-0.8.0/gt/R/build_data.R | 1 gt-0.8.0/gt/R/data_color.R | 50 gt-0.8.0/gt/R/dt_boxhead.R | 8 gt-0.8.0/gt/R/dt_formats.R | 8 gt-0.8.0/gt/R/dt_groups_rows.R | 33 gt-0.8.0/gt/R/dt_options.R | 4 gt-0.8.0/gt/R/dt_stub_df.R | 124 - gt-0.8.0/gt/R/dt_substitutions.R |only gt-0.8.0/gt/R/dt_summary.R | 10 gt-0.8.0/gt/R/export.R | 268 ++ gt-0.8.0/gt/R/format_data.R | 1389 ++++++++++++--- gt-0.8.0/gt/R/format_vec.R | 1187 ++++++++++-- gt-0.8.0/gt/R/gt.R | 26 gt-0.8.0/gt/R/gt_preview.R | 10 gt-0.8.0/gt/R/helpers.R | 417 ++-- gt-0.8.0/gt/R/image.R | 2 gt-0.8.0/gt/R/info_tables.R | 210 +- gt-0.8.0/gt/R/modify_columns.R | 263 ++ gt-0.8.0/gt/R/modify_rows.R | 4 gt-0.8.0/gt/R/opts.R | 6 gt-0.8.0/gt/R/print.R | 8 gt-0.8.0/gt/R/render_as_html.R | 43 gt-0.8.0/gt/R/resolver.R | 63 gt-0.8.0/gt/R/substitution.R | 357 +++ gt-0.8.0/gt/R/summary_rows.R | 15 gt-0.8.0/gt/R/tab_create_modify.R | 107 - gt-0.8.0/gt/R/tab_info.R |only gt-0.8.0/gt/R/tab_remove.R |only gt-0.8.0/gt/R/tab_style_body.R |only gt-0.8.0/gt/R/text_transform.R | 2 gt-0.8.0/gt/R/utils.R | 284 +-- gt-0.8.0/gt/R/utils_color_contrast.R |only gt-0.8.0/gt/R/utils_formatters.R | 13 gt-0.8.0/gt/R/utils_general_str_formatting.R | 164 + gt-0.8.0/gt/R/utils_render_common.R | 86 gt-0.8.0/gt/R/utils_render_html.R | 286 ++- gt-0.8.0/gt/R/utils_render_latex.R | 14 gt-0.8.0/gt/R/utils_render_rtf.R | 221 +- gt-0.8.0/gt/R/utils_render_xml.R | 43 gt-0.8.0/gt/R/z_utils_render_footnotes.R | 50 gt-0.8.0/gt/R/zzz.R | 8 gt-0.8.0/gt/inst/css/gt_styles_default.scss | 6 gt-0.8.0/gt/man/adjust_luminance.Rd | 5 gt-0.8.0/gt/man/as_latex.Rd | 1 gt-0.8.0/gt/man/as_raw_html.Rd | 1 gt-0.8.0/gt/man/as_rtf.Rd | 1 gt-0.8.0/gt/man/as_word.Rd | 22 gt-0.8.0/gt/man/cell_borders.Rd | 5 gt-0.8.0/gt/man/cell_fill.Rd | 5 gt-0.8.0/gt/man/cell_text.Rd | 5 gt-0.8.0/gt/man/cells_body.Rd | 5 gt-0.8.0/gt/man/cells_column_labels.Rd | 5 gt-0.8.0/gt/man/cells_column_spanners.Rd | 5 gt-0.8.0/gt/man/cells_footnotes.Rd | 5 gt-0.8.0/gt/man/cells_grand_summary.Rd | 5 gt-0.8.0/gt/man/cells_row_groups.Rd | 5 gt-0.8.0/gt/man/cells_source_notes.Rd | 5 gt-0.8.0/gt/man/cells_stub.Rd | 5 gt-0.8.0/gt/man/cells_stub_grand_summary.Rd | 5 gt-0.8.0/gt/man/cells_stub_summary.Rd | 5 gt-0.8.0/gt/man/cells_stubhead.Rd | 5 gt-0.8.0/gt/man/cells_summary.Rd | 5 gt-0.8.0/gt/man/cells_title.Rd | 5 gt-0.8.0/gt/man/cols_align.Rd | 7 gt-0.8.0/gt/man/cols_align_decimal.Rd |only gt-0.8.0/gt/man/cols_hide.Rd | 3 gt-0.8.0/gt/man/cols_label.Rd | 3 gt-0.8.0/gt/man/cols_merge.Rd | 3 gt-0.8.0/gt/man/cols_merge_n_pct.Rd | 3 gt-0.8.0/gt/man/cols_merge_range.Rd | 3 gt-0.8.0/gt/man/cols_merge_uncert.Rd | 3 gt-0.8.0/gt/man/cols_move.Rd | 3 gt-0.8.0/gt/man/cols_move_to_end.Rd | 3 gt-0.8.0/gt/man/cols_move_to_start.Rd | 3 gt-0.8.0/gt/man/cols_unhide.Rd | 3 gt-0.8.0/gt/man/cols_width.Rd | 3 gt-0.8.0/gt/man/currency.Rd | 5 gt-0.8.0/gt/man/data_color.Rd | 17 gt-0.8.0/gt/man/default_fonts.Rd | 5 gt-0.8.0/gt/man/escape_latex.Rd | 5 gt-0.8.0/gt/man/extract_cells.Rd |only gt-0.8.0/gt/man/extract_summary.Rd | 1 gt-0.8.0/gt/man/fmt.Rd | 24 gt-0.8.0/gt/man/fmt_bytes.Rd | 22 gt-0.8.0/gt/man/fmt_currency.Rd | 20 gt-0.8.0/gt/man/fmt_date.Rd | 145 + gt-0.8.0/gt/man/fmt_datetime.Rd | 809 +++++++- gt-0.8.0/gt/man/fmt_duration.Rd | 22 gt-0.8.0/gt/man/fmt_engineering.Rd | 23 gt-0.8.0/gt/man/fmt_fraction.Rd | 23 gt-0.8.0/gt/man/fmt_integer.Rd | 20 gt-0.8.0/gt/man/fmt_markdown.Rd | 9 gt-0.8.0/gt/man/fmt_number.Rd | 20 gt-0.8.0/gt/man/fmt_partsper.Rd | 20 gt-0.8.0/gt/man/fmt_passthrough.Rd | 13 gt-0.8.0/gt/man/fmt_percent.Rd | 20 gt-0.8.0/gt/man/fmt_roman.Rd |only gt-0.8.0/gt/man/fmt_scientific.Rd | 20 gt-0.8.0/gt/man/fmt_time.Rd | 125 + gt-0.8.0/gt/man/google_font.Rd | 3 gt-0.8.0/gt/man/grand_summary_rows.Rd | 7 gt-0.8.0/gt/man/gt-package.Rd | 1 gt-0.8.0/gt/man/gt.Rd | 8 gt-0.8.0/gt/man/gt_latex_dependencies.Rd | 5 gt-0.8.0/gt/man/gtsave.Rd | 1 gt-0.8.0/gt/man/html.Rd | 3 gt-0.8.0/gt/man/info_date_style.Rd | 5 gt-0.8.0/gt/man/info_time_style.Rd | 5 gt-0.8.0/gt/man/md.Rd | 3 gt-0.8.0/gt/man/opt_footnote_marks.Rd | 2 gt-0.8.0/gt/man/pct.Rd | 3 gt-0.8.0/gt/man/px.Rd | 3 gt-0.8.0/gt/man/random_id.Rd | 5 gt-0.8.0/gt/man/rm_caption.Rd |only gt-0.8.0/gt/man/rm_footnotes.Rd |only gt-0.8.0/gt/man/rm_header.Rd |only gt-0.8.0/gt/man/rm_source_notes.Rd |only gt-0.8.0/gt/man/rm_spanners.Rd |only gt-0.8.0/gt/man/rm_stubhead.Rd |only gt-0.8.0/gt/man/row_group_order.Rd | 9 gt-0.8.0/gt/man/stub.Rd |only gt-0.8.0/gt/man/sub_large_vals.Rd | 15 gt-0.8.0/gt/man/sub_missing.Rd | 4 gt-0.8.0/gt/man/sub_small_vals.Rd | 4 gt-0.8.0/gt/man/sub_values.Rd |only gt-0.8.0/gt/man/sub_zero.Rd | 4 gt-0.8.0/gt/man/summary_rows.Rd | 9 gt-0.8.0/gt/man/tab_caption.Rd |only gt-0.8.0/gt/man/tab_footnote.Rd | 3 gt-0.8.0/gt/man/tab_header.Rd | 3 gt-0.8.0/gt/man/tab_info.Rd |only gt-0.8.0/gt/man/tab_options.Rd | 18 gt-0.8.0/gt/man/tab_row_group.Rd | 3 gt-0.8.0/gt/man/tab_source_note.Rd | 5 gt-0.8.0/gt/man/tab_spanner.Rd | 5 gt-0.8.0/gt/man/tab_spanner_delim.Rd | 3 gt-0.8.0/gt/man/tab_stub_indent.Rd | 3 gt-0.8.0/gt/man/tab_stubhead.Rd | 3 gt-0.8.0/gt/man/tab_style.Rd | 7 gt-0.8.0/gt/man/tab_style_body.Rd |only gt-0.8.0/gt/man/text_transform.Rd | 4 gt-0.8.0/gt/man/vec_fmt_bytes.Rd | 13 gt-0.8.0/gt/man/vec_fmt_currency.Rd | 28 gt-0.8.0/gt/man/vec_fmt_date.Rd | 134 + gt-0.8.0/gt/man/vec_fmt_datetime.Rd | 836 +++++++-- gt-0.8.0/gt/man/vec_fmt_duration.Rd | 13 gt-0.8.0/gt/man/vec_fmt_engineering.Rd | 11 gt-0.8.0/gt/man/vec_fmt_fraction.Rd | 11 gt-0.8.0/gt/man/vec_fmt_integer.Rd | 11 gt-0.8.0/gt/man/vec_fmt_markdown.Rd | 3 gt-0.8.0/gt/man/vec_fmt_number.Rd | 11 gt-0.8.0/gt/man/vec_fmt_partsper.Rd | 20 gt-0.8.0/gt/man/vec_fmt_percent.Rd | 11 gt-0.8.0/gt/man/vec_fmt_roman.Rd |only gt-0.8.0/gt/man/vec_fmt_scientific.Rd | 11 gt-0.8.0/gt/man/vec_fmt_time.Rd | 122 - gt-0.8.0/gt/tests/testthat/helper-gt_attr_expectations.R | 42 gt-0.8.0/gt/tests/testthat/test-color_handling.R | 7 gt-0.8.0/gt/tests/testthat/test-cols_align.R | 96 + gt-0.8.0/gt/tests/testthat/test-fmt_date_time.R | 290 ++- gt-0.8.0/gt/tests/testthat/test-gt_object.R | 70 gt-0.8.0/gt/tests/testthat/test-info_tables.R | 4 gt-0.8.0/gt/tests/testthat/test-input_data_validation.R | 37 gt-0.8.0/gt/tests/testthat/test-l_fmt_date_time.R | 201 +- gt-0.8.0/gt/tests/testthat/test-r_table_parts.R | 12 gt-0.8.0/gt/tests/testthat/test-tab_caption.R |only gt-0.8.0/gt/tests/testthat/test-tab_style.R | 47 gt-0.8.0/gt/tests/testthat/test-text_transform.R | 9 gt-0.8.0/gt/tests/testthat/test-util_functions.R | 196 -- gt-0.8.0/gt/tests/testthat/test-utils_render_html.R | 5 188 files changed, 7662 insertions(+), 2503 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut],
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
D [...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.4 dated 2022-07-12 and 1.1.5 dated 2022-11-16
glmmTMB-1.1.4/glmmTMB/inst/doc/parallel.Rmd |only glmmTMB-1.1.4/glmmTMB/vignettes/parallel.Rmd |only glmmTMB-1.1.5/glmmTMB/DESCRIPTION | 17 - glmmTMB-1.1.5/glmmTMB/MD5 | 97 +++-- glmmTMB-1.1.5/glmmTMB/NAMESPACE | 8 glmmTMB-1.1.5/glmmTMB/R/VarCorr.R | 8 glmmTMB-1.1.5/glmmTMB/R/enum.R | 1 glmmTMB-1.1.5/glmmTMB/R/family.R | 34 +- glmmTMB-1.1.5/glmmTMB/R/glmmTMB.R | 146 +++++++- glmmTMB-1.1.5/glmmTMB/R/methods.R | 76 +++- glmmTMB-1.1.5/glmmTMB/R/predict.R | 30 + glmmTMB-1.1.5/glmmTMB/R/utils.R | 109 +++--- glmmTMB-1.1.5/glmmTMB/build/partial.rdb |binary glmmTMB-1.1.5/glmmTMB/build/vignette.rds |binary glmmTMB-1.1.5/glmmTMB/inst/CITATION | 9 glmmTMB-1.1.5/glmmTMB/inst/Matrix-version | 2 glmmTMB-1.1.5/glmmTMB/inst/NEWS.Rd | 62 +++ glmmTMB-1.1.5/glmmTMB/inst/TMB-version | 2 glmmTMB-1.1.5/glmmTMB/inst/doc/covstruct.html | 8 glmmTMB-1.1.5/glmmTMB/inst/doc/glmmTMB.Rnw | 6 glmmTMB-1.1.5/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.1.5/glmmTMB/inst/doc/hacking.R |only glmmTMB-1.1.5/glmmTMB/inst/doc/hacking.html |only glmmTMB-1.1.5/glmmTMB/inst/doc/hacking.rmd |only glmmTMB-1.1.5/glmmTMB/inst/doc/mcmc.html | 4 glmmTMB-1.1.5/glmmTMB/inst/doc/miscEx.html | 4 glmmTMB-1.1.5/glmmTMB/inst/doc/model_evaluation.pdf |binary glmmTMB-1.1.5/glmmTMB/inst/doc/parallel.html | 4 glmmTMB-1.1.5/glmmTMB/inst/doc/parallel.rmd |only glmmTMB-1.1.5/glmmTMB/inst/doc/sim.html | 6 glmmTMB-1.1.5/glmmTMB/inst/doc/troubleshooting.html | 6 glmmTMB-1.1.5/glmmTMB/inst/test_data/agridat_john.alpha.rds |only glmmTMB-1.1.5/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.1.5/glmmTMB/man/bootmer_methods.Rd | 9 glmmTMB-1.1.5/glmmTMB/man/dot-adjustX.Rd |only glmmTMB-1.1.5/glmmTMB/man/dot-checkRankX.Rd |only glmmTMB-1.1.5/glmmTMB/man/family_params.Rd |only glmmTMB-1.1.5/glmmTMB/man/glmmTMB.Rd | 5 glmmTMB-1.1.5/glmmTMB/man/glmmTMBControl.Rd | 8 glmmTMB-1.1.5/glmmTMB/man/mkTMBStruc.Rd | 2 glmmTMB-1.1.5/glmmTMB/man/nbinom2.Rd | 15 glmmTMB-1.1.5/glmmTMB/man/sigma.glmmTMB.Rd | 4 glmmTMB-1.1.5/glmmTMB/man/startParams.Rd | 2 glmmTMB-1.1.5/glmmTMB/src/Makevars | 1 glmmTMB-1.1.5/glmmTMB/src/glmmTMB.cpp | 169 +++++++--- glmmTMB-1.1.5/glmmTMB/tests/testthat/test-basics.R | 1 glmmTMB-1.1.5/glmmTMB/tests/testthat/test-checkRank.R |only glmmTMB-1.1.5/glmmTMB/tests/testthat/test-families.R | 18 + glmmTMB-1.1.5/glmmTMB/tests/testthat/test-methods.R | 6 glmmTMB-1.1.5/glmmTMB/tests/testthat/test-predict.R | 148 ++++++++ glmmTMB-1.1.5/glmmTMB/tests/testthat/test-reml.R | 11 glmmTMB-1.1.5/glmmTMB/tests/testthat/test-varstruc.R | 9 glmmTMB-1.1.5/glmmTMB/vignettes/glmmTMB.Rnw | 6 glmmTMB-1.1.5/glmmTMB/vignettes/glmmTMB.bib | 10 glmmTMB-1.1.5/glmmTMB/vignettes/hacking.rmd |only glmmTMB-1.1.5/glmmTMB/vignettes/parallel.rmd |only 56 files changed, 831 insertions(+), 232 deletions(-)
Title: Fast Extraction from Raster Datasets using Polygons
Description: Provides a replacement for the 'extract' function from the 'raster' package
that is suitable for extracting raster values using 'sf' polygons.
Author: Daniel Baston [aut, cre],
ISciences, LLC [cph]
Maintainer: Daniel Baston <dbaston@isciences.com>
Diff between exactextractr versions 0.9.0 dated 2022-08-23 and 0.9.1 dated 2022-11-16
DESCRIPTION | 6 MD5 | 12 NEWS.md | 6 R/exact_extract.R | 2 README.md | 1 configure | 820 ++++++++++++++++++------------------ tests/testthat/test_exact_extract.R | 12 7 files changed, 454 insertions(+), 405 deletions(-)
Title: Causal Discovery under a Confounder Blanket
Description: Methods for learning causal relationships among a set of
foreground variables X based on signals from a (potentially much
larger) set of background variables Z, which are known non-descendants
of X. The confounder blanket learner (CBL) uses sparse regression
techniques to simultaneously perform many conditional independence
tests, with complementary pairs stability selection to guarantee
finite sample error control. CBL is sound and complete with respect to
a so-called "lazy oracle", and works with both linear and nonlinear
systems. For details, see Watson & Silva (2022) <arXiv:2205.05715>.
Author: David Watson [aut, cre]
Maintainer: David Watson <david.s.watson11@gmail.com>
Diff between cbl versions 0.1.1 dated 2022-06-17 and 0.1.2 dated 2022-11-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS.md | 6 +++++- R/cbl.R | 3 ++- 5 files changed, 17 insertions(+), 11 deletions(-)
Title: Statistics: Data Analysis and Modelling
Description: Data sets and functions to support the books "Statistics: Data
analysis and modelling" by Speekenbrink, M. (2021)
<https://mspeekenbrink.github.io/sdam-book/> and "An R companion to
Statistics: data analysis and modelling" by Speekenbrink, M. (2021)
<https://mspeekenbrink.github.io/sdam-r-companion/>. All datasets
analysed in these books are provided in this package. In addition, the
package provides functions to compute sample statistics (variance,
standard deviation, mode), create raincloud and enhanced Q-Q plots, and
expand Anova results into omnibus tests and tests of individual
contrasts.
Author: Maarten Speekenbrink [aut, cre]
Maintainer: Maarten Speekenbrink <m.speekenbrink@ucl.ac.uk>
Diff between sdamr versions 0.1.0 dated 2021-09-29 and 0.2.0 dated 2022-11-16
DESCRIPTION | 8 ++--- MD5 | 22 ++++++++++---- NEWS.md | 4 ++ R/data.R | 72 ++++++++++++++++++++++++++++++++++++++++++++++--- R/plot_raincloud.R | 2 - build/partial.rdb |binary data/gestures.rda |only data/metacognition.rda |only data/papervotes.rda |only data/rps.rda |only man/anchoring.Rd | 2 - man/gestures.Rd |only man/metacognition.Rd |only man/papervotes.Rd |only man/rps.Rd |only man/trump2016.Rd | 2 - 16 files changed, 95 insertions(+), 17 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ts versions 0.2.4 dated 2022-11-10 and 0.2.5 dated 2022-11-16
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 15 + R/ts-lag-correlation.R | 3 README.md | 16 +- inst/doc/getting-started.html | 141 ++++++++---------- inst/doc/using-tidy-fft.html | 127 ++++++++-------- man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary 9 files changed, 168 insertions(+), 158 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb [...truncated...]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.14.4 dated 2022-10-17 and 1.14.6 dated 2022-11-16
DESCRIPTION | 6 MD5 | 46 ++-- NEWS.md | 17 + R/onAttach.R | 4 R/test.data.table.R | 117 +++++------- R/utils.R | 10 + build/vignette.rds |binary inst/cc | 2 inst/doc/datatable-benchmarking.html | 4 inst/doc/datatable-faq.html | 4 inst/doc/datatable-importing.html | 4 inst/doc/datatable-intro.html | 4 inst/doc/datatable-keys-fast-subset.html | 10 - inst/doc/datatable-reference-semantics.html | 4 inst/doc/datatable-reshape.html | 4 inst/doc/datatable-sd-usage.html | 4 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 10 - inst/tests/benchmark.Rraw.bz2 |binary inst/tests/tests.Rraw.bz2 |binary man/test.data.table.Rd | 4 src/data.table.h | 4 src/fread.c | 3 src/freadR.c | 8 src/init.c | 13 + 24 files changed, 157 insertions(+), 125 deletions(-)
Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms
using adequate sample sizes for power and accuracy. Implements the
methodology originally presented in Campelo and Takahashi (2019)
<doi:10.1007/s10732-018-9396-7>
for the comparison of two algorithms, and later generalised in
Campelo and Wanner (Submitted, 2019) <arxiv:1908.01720>.
Author: Felipe Campelo [aut, cre],
Fernanda Takahashi [ctb],
Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <fcampelo@gmail.com>
Diff between CAISEr versions 1.0.16 dated 2020-02-04 and 1.0.17 dated 2022-11-16
DESCRIPTION | 15 MD5 | 14 NEWS.md | 4 build/vignette.rds |binary inst/doc/Adapting_Algorithm_for_CAISEr.R | 183 ++++---- inst/doc/Adapting_Algorithm_for_CAISEr.Rmd | 20 inst/doc/Adapting_Algorithm_for_CAISEr.html | 625 +++++++++++++++++----------- vignettes/Adapting_Algorithm_for_CAISEr.Rmd | 20 8 files changed, 526 insertions(+), 355 deletions(-)
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics,
prior and posterior predictive checks, and other visualizations
to support the applied Bayesian workflow advocated in
Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
The package is designed not only to provide convenient functionality
for users, but also a common set of functions that can be easily used by
developers working on a variety of R packages for Bayesian modeling,
particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut],
Paul-Christian Buerkner [ctb],
Martin Modrak [ctb],
Malcolm Barrett [ctb],
Frank Weber [ctb],
Eduardo Coronado Sroka [ctb],
Teemu Sailynoja [ctb],
Aki Vehtari [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between bayesplot versions 1.9.0 dated 2022-03-10 and 1.10.0 dated 2022-11-16
DESCRIPTION | 12 MD5 | 147 +-- NAMESPACE | 6 NEWS.md | 20 R/bayesplot-colors.R | 4 R/bayesplot-ggplot-themes.R | 4 R/bayesplot-helpers.R | 47 - R/bayesplot-package.R | 10 R/example-data.R | 42 - R/helpers-gg.R | 37 R/helpers-ppc.R | 323 ++++++++ R/mcmc-diagnostics-nuts.R | 107 +- R/mcmc-diagnostics.R | 72 - R/mcmc-distributions.R | 36 R/mcmc-intervals.R | 99 +- R/mcmc-parcoord.R | 10 R/mcmc-recover.R | 26 R/mcmc-scatterplots.R | 12 R/mcmc-traces.R | 151 +++- R/ppc-censoring.R | 18 R/ppc-discrete.R | 47 - R/ppc-distributions.R | 340 ++++++--- R/ppc-errors.R | 14 R/ppc-intervals.R | 47 - R/ppc-loo.R | 56 - R/ppc-scatterplots.R | 2 R/ppc-test-statistics.R | 40 - R/ppd-distributions.R | 32 R/ppd-intervals.R | 54 - R/ppd-test-statistics.R | 14 R/sysdata.rda |binary R/zzz.R | 4 build/vignette.rds |binary inst/doc/graphical-ppcs.html | 618 +++++++++++++--- inst/doc/plotting-mcmc-draws.Rmd | 8 inst/doc/plotting-mcmc-draws.html | 532 +++++++++++--- inst/doc/visual-mcmc-diagnostics.R | 1 inst/doc/visual-mcmc-diagnostics.Rmd | 5 inst/doc/visual-mcmc-diagnostics.html | 895 ++++++++++++++++++------ man/MCMC-diagnostics.Rd | 4 man/MCMC-intervals.Rd | 3 man/MCMC-traces.Rd | 51 + man/PPC-discrete.Rd | 9 man/PPC-distributions.Rd | 92 ++ man/PPC-intervals.Rd | 19 man/PPC-loo.Rd | 7 man/PPD-distributions.Rd | 19 man/PPD-intervals.Rd | 49 - man/PPD-test-statistics.Rd | 5 man/bayesplot-helpers.Rd | 26 man/figures/logo.svg |only man/tidy-params.Rd | 12 tests/testthat/data-for-mcmc-tests.R | 29 tests/testthat/data-for-ordinal.rda |binary tests/testthat/data-for-ppc-tests.R | 5 tests/testthat/test-aesthetics.R | 10 tests/testthat/test-bayesplot_grid.R | 3 tests/testthat/test-convenience-functions.R | 78 -- tests/testthat/test-extractors.R | 3 tests/testthat/test-helpers-ppc.R | 63 + tests/testthat/test-mcmc-diagnostics.R | 34 tests/testthat/test-mcmc-distributions.R | 72 + tests/testthat/test-mcmc-intervals.R | 16 tests/testthat/test-mcmc-nuts.R | 62 + tests/testthat/test-mcmc-recover.R | 67 + tests/testthat/test-mcmc-scatter-and-parcoord.R | 89 ++ tests/testthat/test-mcmc-traces.R | 45 + tests/testthat/test-ppc-discrete.R | 2 tests/testthat/test-ppc-distributions.R | 41 - tests/testthat/test-ppc-errors.R | 8 tests/testthat/test-ppc-input-validation.R | 13 tests/testthat/test-ppc-loo.R | 104 ++ tests/testthat/test-ppc-test-statistics.R | 62 - vignettes/plotting-mcmc-draws.Rmd | 8 vignettes/visual-mcmc-diagnostics.Rmd | 5 75 files changed, 3712 insertions(+), 1295 deletions(-)
Title: Optimally Robust Estimation
Description: Optimally robust estimation in general smoothly parameterized models using S4
classes and methods.
Author: Matthias Kohl [cre, cph],
Mykhailo Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between ROptEst versions 1.2.1 dated 2019-04-25 and 1.3.1 dated 2022-11-16
DESCRIPTION | 16 MD5 | 41 +- R/CheckMakeContIC.R | 10 R/L1L2normL2deriv.R | 9 R/LowerCaseMultivariate.R | 19 - R/getInfCent.R | 5 R/getInfGamma.R | 14 R/getInfStand.R | 7 R/getInfV.R | 5 R/roptest.new.R | 13 R/updateNorm.R | 9 build |only inst/NEWS | 18 + man/0ROptEst-package.Rd | 154 ++++---- man/RMXEOMSEMBREOBRE.Rd | 644 ++++++++++++++++++------------------ man/getIneffDiff.Rd | 190 +++++----- man/getMaxIneff.Rd | 146 ++++---- man/internal-interpolate.Rd | 3 man/leastFavorableRadius.Rd | 160 ++++----- man/optIC.Rd | 280 +++++++-------- man/radiusMinimaxIC.Rd | 206 +++++------ man/roptest.Rd | 774 ++++++++++++++++++++++---------------------- 22 files changed, 1376 insertions(+), 1347 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Steve Broll [aut],
David Buchanan [aut],
Elizabeth Chun [aut],
John Muschelli [aut] ,
Nathaniel Fernandes [aut],
Jung Hoon Seo [aut],
Johnathan Shih [aut],
Jacek Urbanek [aut],
John Schwenck [aut],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Pat [...truncated...]
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between iglu versions 3.3.2 dated 2022-10-19 and 3.4.2 dated 2022-11-16
DESCRIPTION | 6 MD5 | 32 - R/mag.R | 2 R/mage_ma_single.R | 11 R/meal_metrics.R | 2 R/utils.R | 21 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/AGP_and_Episodes.html | 113 +++--- inst/doc/MAGE.html | 115 +++--- inst/doc/iglu.html | 115 +++--- inst/doc/lasagna_plots.Rmd | 2 inst/doc/lasagna_plots.html | 167 +++++----- inst/doc/metrics_list.html | 14 vignettes/lasagna_plots.Rmd | 2 vignettes/lasagna_plots_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-12-1.png |binary 17 files changed, 313 insertions(+), 289 deletions(-)
Title: Genealogical Data Analysis
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) <doi:10.1186/s12859-015-0581-5>.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Jarno van der Kolk [ctb],
Mohan Rakesh [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
Diff between GENLIB versions 1.1.6 dated 2022-08-11 and 1.1.7 dated 2022-11-16
DESCRIPTION | 8 - MD5 | 64 ++++++------ src/apparentement.cpp | 104 ++++++++++---------- src/apparentement.h | 8 - src/base.h | 22 ++-- src/basemt.h | 18 +-- src/cbignum.h | 4 src/congen.cpp | 68 ++++++------- src/congen.h | 6 - src/consanguinite.cpp | 50 ++++----- src/consanguinite.h | 6 - src/exception.cpp | 4 src/exception.h | 26 ++--- src/fondateur.cpp | 256 +++++++++++++++++++++++++------------------------- src/fondateur.h | 4 src/genphi.cpp | 30 ++--- src/hal.cpp | 4 src/hal.h | 4 src/hashtable.h | 34 +++--- src/interface.cpp | 16 +-- src/md5.cpp | 2 src/mpajout.c | 6 - src/mpi.c | 6 - src/outilanal.cpp | 22 ++-- src/outilanal.h | 12 +- src/outils.cpp | 248 ++++++++++++++++++++++++------------------------ src/outils.h | 12 +- src/outilsalloc.h | 12 +- src/probsimul.cpp | 110 ++++++++++----------- src/probsimul.h | 4 src/statanal.cpp | 28 ++--- src/userInterface.cpp | 28 ++--- src/userInterface.h | 2 33 files changed, 614 insertions(+), 614 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] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.34 dated 2022-10-18 and 0.35 dated 2022-11-16
xfun-0.34/xfun/man/stringsAsStrings.Rd |only xfun-0.35/xfun/DESCRIPTION | 6 ++--- xfun-0.35/xfun/MD5 | 21 +++++++++----------- xfun-0.35/xfun/NAMESPACE | 1 xfun-0.35/xfun/NEWS.md | 8 +++++++ xfun-0.35/xfun/R/base64.R | 25 +++++++++++++++++++++++- xfun-0.35/xfun/R/markdown.R | 26 ++++++++++++++----------- xfun-0.35/xfun/R/utils.R | 16 --------------- xfun-0.35/xfun/build/vignette.rds |binary xfun-0.35/xfun/inst/doc/xfun.html | 8 +++---- xfun-0.35/xfun/man/protect_math.Rd | 7 +++++- xfun-0.35/xfun/tests/test-cran/test-markdown.R | 1 12 files changed, 71 insertions(+), 48 deletions(-)
Title: Satellite Image Time Series Analysis for Earth Observation Data
Cubes
Description: An end-to-end toolkit for land use and land cover classification
using big Earth observation data, based on machine learning methods
applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>.
Builds regular data cubes from collections in AWS, Microsoft Planetary Computer,
Brazil Data Cube, and Digital Earth Africa using the STAC protocol <https://stacspec.org/>
and the 'gdalcubes' R package <doi:10.3390/data4030092>.
Supports visualization methods for images and time series and
smoothing filters for dealing with noisy time series.
Includes functions for quality assessment of training samples using self-organized maps
as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>.
Provides machine learning methods including support vector machines,
random forests, extreme gradient boosting, multi-layer perceptrons,
temporal convolutional neural networks <doi:10.3390/rs11050523>,
residual networks <arxi [...truncated...]
Author: Rolf Simoes [aut],
Gilberto Camara [aut, cre],
Felipe Souza [aut],
Lorena Santos [aut],
Pedro Andrade [aut],
Karine Ferreira [aut],
Alber Sanchez [aut],
Gilberto Queiroz [aut]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between sits versions 1.1.0 dated 2022-07-07 and 1.2.0 dated 2022-11-16
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sits-1.1.0/sits/man/dot-cube_band_scale_factor.Rd |only sits-1.1.0/sits/man/dot-cube_bands.Rd |only sits-1.1.0/sits/man/dot-cube_check.Rd |only sits-1.1.0/sits/man/dot-cube_collection.Rd |only sits-1.1.0/sits/man/dot-cube_create.Rd |only sits-1.1.0/sits/man/dot-cube_crs.Rd |only sits-1.1.0/sits/man/dot-cube_derived_create.Rd |only sits-1.1.0/sits/man/dot-cube_extract.Rd |only sits-1.1.0/sits/man/dot-cube_is_equal.Rd |only sits-1.1.0/sits/man/dot-cube_is_regular.Rd |only sits-1.1.0/sits/man/dot-cube_labels.Rd |only sits-1.1.0/sits/man/dot-cube_params_block.Rd |only sits-1.1.0/sits/man/dot-cube_resolution.Rd |only sits-1.1.0/sits/man/dot-cube_s3class.Rd |only sits-1.1.0/sits/man/dot-cube_size.Rd |only sits-1.1.0/sits/man/dot-cube_source.Rd |only sits-1.1.0/sits/man/dot-cube_tile_bbox.Rd |only sits-1.1.0/sits/man/dot-cube_tiles.Rd |only sits-1.1.0/sits/man/dot-cube_token_generator.Rd |only sits-1.1.0/sits/man/dot-cube_unique_bands.Rd |only sits-1.1.0/sits/man/dot-cube_unique_bbox.Rd |only sits-1.1.0/sits/man/dot-cube_unique_tile_size.Rd |only sits-1.1.0/sits/man/dot-cube_unique_timeline.Rd |only sits-1.1.0/sits/man/dot-cube_xres.Rd |only sits-1.1.0/sits/man/dot-cube_yres.Rd |only sits-1.1.0/sits/man/dot-find_closest.Rd |only sits-1.1.0/sits/man/dot-gc_arrange_images.Rd |only sits-1.1.0/sits/man/dot-gc_create_cloud_mask.Rd |only sits-1.1.0/sits/man/dot-gc_create_cube_view.Rd |only sits-1.1.0/sits/man/dot-gc_create_database_stac.Rd |only sits-1.1.0/sits/man/dot-gc_create_pack.Rd |only sits-1.1.0/sits/man/dot-gc_create_raster_cube.Rd |only sits-1.1.0/sits/man/dot-gc_get_valid_timeline.Rd |only sits-1.1.0/sits/man/dot-gc_missing_tiles.Rd |only sits-1.1.0/sits/man/dot-gc_regularize.Rd |only sits-1.1.0/sits/man/dot-gc_save_raster_cube.Rd |only sits-1.1.0/sits/man/dot-mesma_raster_blocks.Rd |only sits-1.1.0/sits/man/dot-mesma_raster_blocks_estimate.Rd |only sits-1.1.0/sits/man/dot-mesma_scale_endmembers.Rd |only sits-1.1.0/sits/man/dot-raster_check_bbox.Rd |only sits-1.1.0/sits/man/dot-raster_check_block.Rd |only sits-1.1.0/sits/man/dot-raster_check_package.Rd |only sits-1.1.0/sits/man/dot-raster_colrow.Rd |only sits-1.1.0/sits/man/dot-raster_crop.Rd |only sits-1.1.0/sits/man/dot-raster_crop_metadata.Rd |only sits-1.1.0/sits/man/dot-raster_data_type.Rd |only sits-1.1.0/sits/man/dot-raster_extract.Rd |only sits-1.1.0/sits/man/dot-raster_freq.Rd |only sits-1.1.0/sits/man/dot-raster_gdal_datatype.Rd |only sits-1.1.0/sits/man/dot-raster_gdal_datatypes.Rd |only sits-1.1.0/sits/man/dot-raster_get_values.Rd |only sits-1.1.0/sits/man/dot-raster_merge.Rd |only sits-1.1.0/sits/man/dot-raster_new_rast.Rd |only sits-1.1.0/sits/man/dot-raster_open_rast.Rd |only sits-1.1.0/sits/man/dot-raster_open_stack.Rd |only sits-1.1.0/sits/man/dot-raster_params_file.Rd |only sits-1.1.0/sits/man/dot-raster_properties.Rd |only sits-1.1.0/sits/man/dot-raster_rast.Rd |only sits-1.1.0/sits/man/dot-raster_read_stack.Rd |only sits-1.1.0/sits/man/dot-raster_resampling.Rd |only sits-1.1.0/sits/man/dot-raster_set_values.Rd |only sits-1.1.0/sits/man/dot-raster_supported_packages.Rd |only sits-1.1.0/sits/man/dot-raster_write_rast.Rd |only sits-1.1.0/sits/man/dot-sits_accuracy_area_assess.Rd |only sits-1.1.0/sits/man/dot-sits_accuracy_pred_ref.Rd |only sits-1.1.0/sits/man/dot-sits_avg_polygon.Rd |only sits-1.1.0/sits/man/dot-sits_bbox_intersect.Rd |only sits-1.1.0/sits/man/dot-sits_bbox_to_sf.Rd |only sits-1.1.0/sits/man/dot-sits_classify_check_params.Rd |only sits-1.1.0/sits/man/dot-sits_classify_multicores.Rd |only sits-1.1.0/sits/man/dot-sits_cluster_dendro_bestcut.Rd |only sits-1.1.0/sits/man/dot-sits_cluster_dendrogram.Rd |only sits-1.1.0/sits/man/dot-sits_cluster_validity.Rd |only sits-1.1.0/sits/man/dot-sits_coords_to_bbox_wgs84.Rd |only sits-1.1.0/sits/man/dot-sits_create_folds.Rd |only sits-1.1.0/sits/man/dot-sits_csv_check.Rd |only sits-1.1.0/sits/man/dot-sits_distances.Rd |only sits-1.1.0/sits/man/dot-sits_distances_classify.Rd |only sits-1.1.0/sits/man/dot-sits_distances_sample.Rd |only sits-1.1.0/sits/man/dot-sits_fast_apply.Rd |only sits-1.1.0/sits/man/dot-sits_filter_intersecting_tiles.Rd |only sits-1.1.0/sits/man/dot-sits_function_factory.Rd |only sits-1.1.0/sits/man/dot-sits_get_data_check.Rd |only sits-1.1.0/sits/man/dot-sits_get_samples_from_csv.Rd |only sits-1.1.0/sits/man/dot-sits_get_samples_from_sf.Rd |only sits-1.1.0/sits/man/dot-sits_get_samples_from_shp.Rd |only sits-1.1.0/sits/man/dot-sits_get_top_values.Rd |only sits-1.1.0/sits/man/dot-sits_get_ts.Rd |only sits-1.1.0/sits/man/dot-sits_mass_ginv.Rd |only sits-1.1.0/sits/man/dot-sits_ml_model_samples.Rd |only sits-1.1.0/sits/man/dot-sits_ml_normalization_param.Rd |only sits-1.1.0/sits/man/dot-sits_ml_normalize_data.Rd |only sits-1.1.0/sits/man/dot-sits_ml_normalize_matrix.Rd |only sits-1.1.0/sits/man/dot-sits_oversample_smote.Rd |only sits-1.1.0/sits/man/dot-sits_parallel_is_open.Rd |only sits-1.1.0/sits/man/dot-sits_parallel_map.Rd |only sits-1.1.0/sits/man/dot-sits_parallel_reset_node.Rd |only sits-1.1.0/sits/man/dot-sits_parallel_start.Rd |only sits-1.1.0/sits/man/dot-sits_parallel_stop.Rd |only sits-1.1.0/sits/man/dot-sits_parse_roi_cube.Rd |only sits-1.1.0/sits/man/dot-sits_parse_roi_cube.ll.Rd |only sits-1.1.0/sits/man/dot-sits_parse_roi_cube.sf.Rd |only sits-1.1.0/sits/man/dot-sits_parse_roi_cube.xy.Rd |only sits-1.1.0/sits/man/dot-sits_plot_allyears.Rd |only sits-1.1.0/sits/man/dot-sits_plot_dendrogram.Rd |only sits-1.1.0/sits/man/dot-sits_plot_ggplot_series.Rd |only sits-1.1.0/sits/man/dot-sits_plot_ggplot_series_na.Rd |only sits-1.1.0/sits/man/dot-sits_plot_ggplot_series_no_na.Rd |only sits-1.1.0/sits/man/dot-sits_plot_ggplot_together.Rd |only sits-1.1.0/sits/man/dot-sits_plot_resample_class.Rd |only sits-1.1.0/sits/man/dot-sits_plot_title.Rd |only sits-1.1.0/sits/man/dot-sits_plot_together.Rd |only sits-1.1.0/sits/man/dot-sits_plot_twdtw_alignments.Rd |only sits-1.1.0/sits/man/dot-sits_plot_twdtw_class.Rd |only sits-1.1.0/sits/man/dot-sits_proj_format_crs.Rd |only sits-1.1.0/sits/man/dot-sits_proj_from_latlong.Rd |only sits-1.1.0/sits/man/dot-sits_proj_to_latlong.Rd |only sits-1.1.0/sits/man/dot-sits_raster_block_list.Rd |only sits-1.1.0/sits/man/dot-sits_raster_blocks.Rd |only sits-1.1.0/sits/man/dot-sits_raster_blocks_estimate.Rd |only sits-1.1.0/sits/man/dot-sits_raster_data_get_ts.Rd |only sits-1.1.0/sits/man/dot-sits_raster_data_preprocess.Rd |only sits-1.1.0/sits/man/dot-sits_raster_data_read.Rd |only sits-1.1.0/sits/man/dot-sits_raster_sub_image.Rd |only sits-1.1.0/sits/man/dot-sits_raster_sub_image_default.Rd |only sits-1.1.0/sits/man/dot-sits_raster_sub_image_from_bbox.Rd |only sits-1.1.0/sits/man/dot-sits_raster_sub_image_from_block.Rd |only sits-1.1.0/sits/man/dot-sits_raster_sub_image_intersects.Rd |only sits-1.1.0/sits/man/dot-sits_roi_bbox.Rd |only sits-1.1.0/sits/man/dot-sits_roi_bbox.ll.Rd |only sits-1.1.0/sits/man/dot-sits_roi_bbox.sf.Rd |only sits-1.1.0/sits/man/dot-sits_roi_bbox.xy.Rd |only sits-1.1.0/sits/man/dot-sits_roi_sf_to_geojson.Rd |only sits-1.1.0/sits/man/dot-sits_samples_split.Rd |only sits-1.1.0/sits/man/dot-sits_sf_point_to_tibble.Rd |only sits-1.1.0/sits/man/dot-sits_sf_polygon_to_tibble.Rd |only sits-1.1.0/sits/man/dot-sits_sf_to_tibble.Rd |only sits-1.1.0/sits/man/dot-sits_sgolay_coef.Rd |only sits-1.1.0/sits/man/dot-sits_shp_check_validity.Rd |only sits-1.1.0/sits/man/dot-sits_smote.Rd |only sits-1.1.0/sits/man/dot-sits_som_bayes_estimate.Rd |only sits-1.1.0/sits/man/dot-sits_som_label_neurons.Rd |only sits-1.1.0/sits/man/dot-sits_som_paint_neurons.Rd |only sits-1.1.0/sits/man/dot-sits_tibble.Rd |only sits-1.1.0/sits/man/dot-sits_tibble_align_dates.Rd |only sits-1.1.0/sits/man/dot-sits_tibble_bands_check.Rd |only sits-1.1.0/sits/man/dot-sits_tibble_prediction.Rd |only sits-1.1.0/sits/man/dot-sits_tibble_prune.Rd |only sits-1.1.0/sits/man/dot-sits_tibble_test.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_check.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_check_cube.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_class_info.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_dist_indexes.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_during.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_format.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_idx_from_dates.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_match.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_match_indexes.Rd |only sits-1.1.0/sits/man/dot-sits_timeline_valid_date.Rd |only sits-1.1.0/sits/man/dot-sits_transform_samples.Rd |only sits-1.1.0/sits/man/dot-sits_twdtw_breaks.Rd |only sits-1.1.0/sits/man/dot-sits_twdtw_from_tibble.Rd |only sits-1.1.0/sits/man/dot-sits_twdtw_matches_to_prediction.Rd |only sits-1.1.0/sits/man/dot-smth_block_filename.Rd |only sits-1.1.0/sits/man/dot-smth_estimate_block_size.Rd |only sits-1.1.0/sits/man/dot-stac_add_gdal_vsi.Rd |only sits-1.1.0/sits/man/dot-stac_format_datetime.Rd |only sits-1.1.0/sits/man/dot-stac_format_platform.Rd |only sits-1.1.0/sits/man/dot-stac_items_query.Rd |only sits-1.1.0/sits/man/dot-stac_select_bands.Rd |only sits-1.1.0/sits/man/dot-torch_batch_conv1D_batch_norm_relu.Rd |only sits-1.1.0/sits/man/dot-torch_conv1D_batch_norm.Rd |only sits-1.1.0/sits/man/dot-torch_conv1D_batch_norm_relu.Rd |only sits-1.1.0/sits/man/dot-torch_conv1D_batch_norm_relu_dropout.Rd |only sits-1.1.0/sits/man/dot-torch_light_temporal_attention_encoder.Rd |only sits-1.1.0/sits/man/dot-torch_linear_batch_norm_relu.Rd |only sits-1.1.0/sits/man/dot-torch_linear_batch_norm_relu_dropout.Rd |only sits-1.1.0/sits/man/dot-torch_linear_relu_dropout.Rd |only sits-1.1.0/sits/man/dot-torch_multi_head_attention.Rd |only sits-1.1.0/sits/man/dot-torch_multi_linear_batch_norm_relu.Rd |only sits-1.1.0/sits/man/dot-torch_pixel_spatial_encoder.Rd |only sits-1.1.0/sits/man/dot-torch_positional_encoder.Rd |only sits-1.1.0/sits/man/dot-torch_scaled_dot_product_attention.Rd |only sits-1.1.0/sits/man/dot-torch_temporal_attention_encoder.Rd |only sits-1.1.0/sits/man/dot-tuning_params_as_tibble.Rd |only sits-1.1.0/sits/man/dot-tuning_pick_random.Rd |only sits-1.1.0/sits/man/dot-usgs_format_tiles.Rd |only sits-1.1.0/sits/man/dot-view_get_colors.Rd |only sits-1.1.0/sits/man/dot-view_resample_size.Rd |only sits-1.1.0/sits/man/file_info_functions.Rd |only sits-1.1.0/sits/man/plot.classified_image.Rd |only sits-1.1.0/sits/man/print.sits_area_assessment.Rd |only sits-1.1.0/sits/man/print.sits_assessment.Rd |only sits-1.1.0/sits/man/samples_modis_4bands.Rd |only sits-1.1.0/sits/man/sits_debug_log.Rd |only sits-1.1.0/sits/man/sits_parallel_fault_tolerant.Rd |only sits-1.1.0/sits/man/sits_time_series.Rd |only sits-1.1.0/sits/man/sits_twdtw_classify.Rd |only sits-1.1.0/sits/man/source_bands.Rd |only sits-1.1.0/sits/man/source_collection.Rd |only sits-1.1.0/sits/man/source_cube.Rd |only sits-1.1.0/sits/man/source_functions.Rd |only sits-1.1.0/sits/src/bayesian_smoothing.cpp |only sits-1.1.0/sits/src/entropy_probs.cpp |only sits-1.1.0/sits/src/kernel_functions.cpp |only sits-1.1.0/sits/src/least_probs.cpp |only sits-1.1.0/sits/src/margin_probs.cpp |only sits-1.1.0/sits/src/ratio_probs.cpp |only sits-1.2.0/sits/DESCRIPTION | 74 sits-1.2.0/sits/MD5 | 703 +--- sits-1.2.0/sits/NAMESPACE | 118 sits-1.2.0/sits/NEWS.md | 40 sits-1.2.0/sits/R/RcppExports.R | 92 sits-1.2.0/sits/R/data.R | 6 sits-1.2.0/sits/R/sits_accuracy.R | 179 - sits-1.2.0/sits/R/sits_active_learning.R | 163 sits-1.2.0/sits/R/sits_apply.R | 760 +--- sits-1.2.0/sits/R/sits_bands.R | 136 sits-1.2.0/sits/R/sits_bbox.R | 407 +- sits-1.2.0/sits/R/sits_block.R |only sits-1.2.0/sits/R/sits_check.R | 1129 ++++++ sits-1.2.0/sits/R/sits_chunks.R |only sits-1.2.0/sits/R/sits_classification.R | 296 - sits-1.2.0/sits/R/sits_classify_cube.R | 525 +-- sits-1.2.0/sits/R/sits_classify_ts.R | 167 sits-1.2.0/sits/R/sits_cluster.R | 32 sits-1.2.0/sits/R/sits_colors.R |only sits-1.2.0/sits/R/sits_combine_predictions.R |only sits-1.2.0/sits/R/sits_compare.R | 79 sits-1.2.0/sits/R/sits_config.R | 527 +-- sits-1.2.0/sits/R/sits_csv.R | 42 sits-1.2.0/sits/R/sits_cube.R | 41 sits-1.2.0/sits/R/sits_cube_aux_functions.R | 1304 ++----- sits-1.2.0/sits/R/sits_cube_copy.R |only sits-1.2.0/sits/R/sits_debug.R | 169 sits-1.2.0/sits/R/sits_distances.R | 116 sits-1.2.0/sits/R/sits_factory.R | 1 sits-1.2.0/sits/R/sits_file.R |only sits-1.2.0/sits/R/sits_file_info.R | 397 +- sits-1.2.0/sits/R/sits_filters.R | 8 sits-1.2.0/sits/R/sits_gdalcubes.R | 202 - sits-1.2.0/sits/R/sits_geo_dist.R | 39 sits-1.2.0/sits/R/sits_get_data.R | 299 + sits-1.2.0/sits/R/sits_imputation.R | 2 sits-1.2.0/sits/R/sits_internals.R |only sits-1.2.0/sits/R/sits_jobs.R |only sits-1.2.0/sits/R/sits_label_classification.R | 365 -- sits-1.2.0/sits/R/sits_labels.R | 74 sits-1.2.0/sits/R/sits_lighttae.R | 304 - sits-1.2.0/sits/R/sits_machine_learning.R | 462 +- sits-1.2.0/sits/R/sits_merge.R | 28 sits-1.2.0/sits/R/sits_mixture_model.R | 817 ++-- sits-1.2.0/sits/R/sits_mlp.R | 319 - sits-1.2.0/sits/R/sits_model_export.R |only sits-1.2.0/sits/R/sits_mosaic.R |only sits-1.2.0/sits/R/sits_parallel.R | 29 sits-1.2.0/sits/R/sits_patterns.R | 13 sits-1.2.0/sits/R/sits_period.R |only sits-1.2.0/sits/R/sits_plot.R | 1709 +++++----- sits-1.2.0/sits/R/sits_raster_api.R | 578 ++- sits-1.2.0/sits/R/sits_raster_api_terra.R | 203 - sits-1.2.0/sits/R/sits_raster_data.R | 297 - sits-1.2.0/sits/R/sits_raster_sub_image.R | 198 - sits-1.2.0/sits/R/sits_reclassify.R |only sits-1.2.0/sits/R/sits_regularize.R | 35 sits-1.2.0/sits/R/sits_resnet.R | 346 -- sits-1.2.0/sits/R/sits_roi.R | 242 - sits-1.2.0/sits/R/sits_sample_functions.R | 39 sits-1.2.0/sits/R/sits_select.R | 65 sits-1.2.0/sits/R/sits_sf.R | 196 - sits-1.2.0/sits/R/sits_shp.R | 42 sits-1.2.0/sits/R/sits_smooth.R | 932 +---- sits-1.2.0/sits/R/sits_som.R | 121 sits-1.2.0/sits/R/sits_source_api.R | 341 - sits-1.2.0/sits/R/sits_source_api_aws.R | 9 sits-1.2.0/sits/R/sits_source_api_bdc.R | 5 sits-1.2.0/sits/R/sits_source_api_deafrica.R | 5 sits-1.2.0/sits/R/sits_source_api_local.R | 155 sits-1.2.0/sits/R/sits_source_api_mpc.R | 41 sits-1.2.0/sits/R/sits_source_api_sdc.R | 8 sits-1.2.0/sits/R/sits_source_api_stac.R | 60 sits-1.2.0/sits/R/sits_source_api_usgs.R | 61 sits-1.2.0/sits/R/sits_space_time_operations.R | 96 sits-1.2.0/sits/R/sits_stac.R | 23 sits-1.2.0/sits/R/sits_tae.R | 299 - sits-1.2.0/sits/R/sits_tempcnn.R | 349 -- sits-1.2.0/sits/R/sits_tibble.R | 263 - sits-1.2.0/sits/R/sits_tile_api.R |only sits-1.2.0/sits/R/sits_timeline.R | 249 - sits-1.2.0/sits/R/sits_torch_conv1d.R | 4 sits-1.2.0/sits/R/sits_torch_linear.R | 4 sits-1.2.0/sits/R/sits_torch_spatial_encoder.R | 20 sits-1.2.0/sits/R/sits_torch_temporal_attention_encoder.R | 77 sits-1.2.0/sits/R/sits_train.R | 19 sits-1.2.0/sits/R/sits_tuning.R | 57 sits-1.2.0/sits/R/sits_uncertainty.R | 1457 +------- sits-1.2.0/sits/R/sits_utils.R | 162 sits-1.2.0/sits/R/sits_validate.R | 159 sits-1.2.0/sits/R/sits_values.R | 47 sits-1.2.0/sits/R/sits_view.R | 100 sits-1.2.0/sits/R/sits_xlsx.R | 9 sits-1.2.0/sits/R/zzz.R | 1 sits-1.2.0/sits/data/samples_modis_ndvi.rda |only sits-1.2.0/sits/demo/00Index | 1 sits-1.2.0/sits/demo/classify_deeplearning.R | 2 sits-1.2.0/sits/demo/classify_raster_rfor.R | 2 sits-1.2.0/sits/demo/classify_ts.R | 6 sits-1.2.0/sits/inst/extdata/config.yml | 208 + sits-1.2.0/sits/inst/extdata/config_colors.yml | 10 sits-1.2.0/sits/inst/extdata/config_internals.yml | 100 sits-1.2.0/sits/inst/extdata/raster/classif |only sits-1.2.0/sits/inst/extdata/raster/gdal |only sits-1.2.0/sits/inst/extdata/raster/mod13q1/TERRA-MODIS_h12v10_NDVI_2013-09-14.jp2 |only sits-1.2.0/sits/inst/extdata/raster/mod13q1/TERRA-MODIS_h12v10_NDVI_2013-09-30.jp2 |only sits-1.2.0/sits/inst/extdata/raster/mod13q1/TERRA-MODIS_h12v10_NDVI_2013-10-16.jp2 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sits-1.2.0/sits/man/sits_mosaic.Rd |only sits-1.2.0/sits/man/sits_reclassify.Rd |only sits-1.2.0/sits/man/sits_reduce_imbalance.Rd | 4 sits-1.2.0/sits/man/sits_regularize.Rd | 10 sits-1.2.0/sits/man/sits_resnet.Rd | 6 sits-1.2.0/sits/man/sits_rfor.Rd | 9 sits-1.2.0/sits/man/sits_run_examples.Rd | 2 sits-1.2.0/sits/man/sits_select.Rd | 15 sits-1.2.0/sits/man/sits_show_prediction.Rd | 7 sits-1.2.0/sits/man/sits_smooth.Rd | 61 sits-1.2.0/sits/man/sits_som.Rd | 33 sits-1.2.0/sits/man/sits_som_clean_samples.Rd |only sits-1.2.0/sits/man/sits_som_evaluate_cluster.Rd |only sits-1.2.0/sits/man/sits_svm.Rd | 9 sits-1.2.0/sits/man/sits_tae.Rd | 6 sits-1.2.0/sits/man/sits_tempcnn.Rd | 6 sits-1.2.0/sits/man/sits_timeline.Rd | 2 sits-1.2.0/sits/man/sits_to_xlsx.Rd | 2 sits-1.2.0/sits/man/sits_train.Rd | 5 sits-1.2.0/sits/man/sits_tuning.Rd | 6 sits-1.2.0/sits/man/sits_tuning_hparams.Rd | 2 sits-1.2.0/sits/man/sits_uncertainty.Rd | 73 sits-1.2.0/sits/man/sits_uncertainty_sampling.Rd | 5 sits-1.2.0/sits/man/sits_view.Rd | 13 sits-1.2.0/sits/man/sits_xgboost.Rd | 9 sits-1.2.0/sits/man/tick-sits_labels-set-tick.Rd | 5 sits-1.2.0/sits/src/Makevars | 7 sits-1.2.0/sits/src/RcppExports.cpp | 369 +- sits-1.2.0/sits/src/combine_data.cpp |only sits-1.2.0/sits/src/kernel.cpp |only sits-1.2.0/sits/src/label_class.cpp |only sits-1.2.0/sits/src/linear_interp.cpp | 102 sits-1.2.0/sits/src/nnls_solver.cpp | 145 sits-1.2.0/sits/src/normalize_data.cpp | 38 sits-1.2.0/sits/src/normalize_data_0.cpp |only sits-1.2.0/sits/src/smooth.cpp |only sits-1.2.0/sits/src/smooth_sgp.cpp | 7 sits-1.2.0/sits/src/uncertainty.cpp |only sits-1.2.0/sits/tests/testthat/Rplots.pdf |only sits-1.2.0/sits/tests/testthat/test-accuracy.R | 32 sits-1.2.0/sits/tests/testthat/test-active_learning.R | 16 sits-1.2.0/sits/tests/testthat/test-apply.R | 30 sits-1.2.0/sits/tests/testthat/test-check.R | 4 sits-1.2.0/sits/tests/testthat/test-classification.R | 47 sits-1.2.0/sits/tests/testthat/test-color.R |only 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| 6 sits-1.2.0/sits/tests/testthat/test-tibble.R | 33 sits-1.2.0/sits/tests/testthat/test-tuning.R | 6 sits-1.2.0/sits/tests/testthat/test-uncertainty.R | 32 sits-1.2.0/sits/tests/testthat/test-view.R | 28 sits-1.2.0/sits/tests/testthat/test-vignette.R | 8 526 files changed, 11023 insertions(+), 12423 deletions(-)
Title: Inferential Statistics
Description: Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test. Graphical visualization by volcano plots.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKinfer versions 0.8 dated 2022-11-06 and 0.9 dated 2022-11-16
DESCRIPTION | 8 - MD5 | 12 +- NEWS | 6 + R/pairwise.ext.t.test.R | 4 R/pairwise.wilcox.exact.R | 18 +-- inst/doc/MKinfer.html | 246 +++++++++++++++++++++++----------------------- man/0MKinfer-package.Rd | 8 - 7 files changed, 154 insertions(+), 148 deletions(-)
Title: Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
Description: Provides an optimization method based on sequential
quadratic programming (SQP) for maximum likelihood estimation of
the mixture proportions in a finite mixture model where the
component densities are known. The algorithm is expected to obtain
solutions that are at least as accurate as the state-of-the-art
MOSEK interior-point solver (called by function "KWDual" in the
'REBayes' package), and they are expected to arrive at solutions
more quickly when the number of samples is large and the number of
mixture components is not too large. This implements the "mix-SQP"
algorithm, with some improvements, described in Y. Kim,
P. Carbonetto, M. Stephens & M. Anitescu (2020)
<DOI:10.1080/10618600.2019.1689985>.
Author: Youngseok Kim [aut],
Peter Carbonetto [aut, cre],
Mihai Anitescu [aut],
Matthew Stephens [aut],
Jason Willwerscheid [ctb],
Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between mixsqp versions 0.3-43 dated 2020-05-14 and 0.3-48 dated 2022-11-16
mixsqp-0.3-43/mixsqp/README.md |only mixsqp-0.3-48/mixsqp/DESCRIPTION | 10 mixsqp-0.3-48/mixsqp/LICENSE | 4 mixsqp-0.3-48/mixsqp/MD5 | 26 - mixsqp-0.3-48/mixsqp/R/mixsqp.R | 9 mixsqp-0.3-48/mixsqp/build/partial.rdb |only mixsqp-0.3-48/mixsqp/inst/CITATION | 7 mixsqp-0.3-48/mixsqp/inst/doc/mixsqp-intro.R | 2 mixsqp-0.3-48/mixsqp/inst/doc/mixsqp-intro.Rmd | 2 mixsqp-0.3-48/mixsqp/inst/doc/mixsqp-intro.html | 384 ++++++++++++++---------- mixsqp-0.3-48/mixsqp/man/mixsqp.Rd | 7 mixsqp-0.3-48/mixsqp/src/Makevars | 3 mixsqp-0.3-48/mixsqp/src/Makevars.win | 3 mixsqp-0.3-48/mixsqp/src/RcppExports.cpp | 5 mixsqp-0.3-48/mixsqp/vignettes/mixsqp-intro.Rmd | 2 15 files changed, 275 insertions(+), 189 deletions(-)
Title: Fuzzy and Non-Fuzzy Classifiers
Description: It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' (<http://www.de.ufpb.br/~labteve/>) and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' (<http://www.de.ufpb.br/~leapig/>) at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
Author: Jodavid Ferreira [aut, cre] ,
Ronei Moraes [ctb] ,
Arthur Ricardo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Diff between FuzzyClass versions 0.1.2 dated 2022-08-25 and 0.1.3 dated 2022-11-16
DESCRIPTION | 8 - MD5 | 50 +++--- NAMESPACE | 4 NEWS.md | 7 R/ExpNBFuzzyParam.R | 58 +++---- R/FuzzyBetaNaiveBayes.R | 96 +++++-------- R/FuzzyBinomialNaiveBayes.R | 125 ++++++++--------- R/FuzzyExponentialNaiveBayes.R | 105 ++++++-------- R/FuzzyGammaNaiveBayes.R | 103 ++++++-------- R/FuzzyGaussianNaiveBayes.R | 5 R/FuzzyGeoNaiveBayes.R |only R/FuzzyNaiveBayes.R | 5 R/FuzzyPoissonNaiveBayes.R | 99 ++++++------- R/FuzzyTrapeNaiveBayes.R | 5 R/FuzzyTriangNaiveBayes.R | 119 ++++++---------- R/GauNBFuzzyParam.R | 50 +++--- R/PoiNBFuzzyParam.R | 54 +++---- R/functions.R | 129 ++++++++++++++++- R/globals.R | 2 README.md | 300 ++++++++++++++++++++--------------------- build/partial.rdb |binary inst/WORDLIST | 2 man/ExpNBFuzzyParam.Rd | 2 man/FuzzyClass-package.Rd | 2 man/FuzzyGeoNaiveBayes.Rd |only man/GauNBFuzzyParam.Rd | 6 man/PoiNBFuzzyParam.Rd | 2 27 files changed, 695 insertions(+), 643 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2 [...truncated...]
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut],
Marc Kery [ctb]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.4.0 dated 2022-07-13 and 0.5.0 dated 2022-11-16
DESCRIPTION | 6 MD5 | 134 +++- NAMESPACE | 27 NEWS.md | 13 R/PGOcc.R | 285 +++++----- R/generics.R | 1173 ++++++++++++++++++++++++++----------------- R/getSVCSamples.R |only R/intPGOcc.R | 110 ++-- R/lfJSDM.R | 264 ++++----- R/lfMsPGOcc.R | 468 ++++++++--------- R/msPGOcc.R | 430 +++++++-------- R/ppcOcc.R | 13 R/sfJSDM.R | 582 ++++++++++++++------- R/sfMsPGOcc.R | 585 ++++++++++----------- R/simBinom.R |only R/simOcc.R | 69 +- R/simTBinom.R |only R/simTOcc.R | 74 ++ R/spIntPGOcc.R | 182 +++--- R/spMsPGOcc.R | 589 +++++++++------------ R/spPGOcc.R | 493 ++++++++---------- R/stPGOcc.R | 110 +--- R/svcPGBinom.R |only R/svcPGOcc.R |only R/svcTPGBinom.R |only R/svcTPGOcc.R |only R/tPGOcc.R | 67 -- R/updateMCMC.R |only R/waicOcc.R | 9 README.md | 78 +- man/PGOcc.Rd | 6 man/fitted.svcPGBinom.Rd |only man/fitted.svcPGOcc.Rd |only man/fitted.svcTPGBinom.Rd |only man/fitted.svcTPGOcc.Rd |only man/getSVCSamples.Rd |only man/intPGOcc.Rd | 7 man/lfJSDM.Rd | 6 man/lfMsPGOcc.Rd | 12 man/msPGOcc.Rd | 6 man/ppcOcc.Rd | 10 man/predict.svcPGBinom.Rd |only man/predict.svcPGOcc.Rd |only man/predict.svcTPGBinom.Rd |only man/predict.svcTPGOcc.Rd |only man/sfJSDM.Rd | 138 +++-- man/sfMsPGOcc.Rd | 7 man/simBinom.Rd |only man/simOcc.Rd | 12 man/simTBinom.Rd |only man/simTOcc.Rd | 11 man/spIntPGOcc.Rd | 6 man/spMsPGOcc.Rd | 7 man/spOccupancy-package.Rd |only man/spPGOcc.Rd | 6 man/stPGOcc.Rd | 4 man/summary.svcPGBinom.Rd |only man/summary.svcPGOcc.Rd |only man/summary.svcTPGBinom.Rd |only man/summary.svcTPGOcc.Rd |only man/svcPGBinom.Rd |only man/svcPGOcc.Rd |only man/svcTPGBinom.Rd |only man/svcTPGOcc.Rd |only man/waicOcc.Rd | 6 src/PGOcc.cpp | 33 - src/init.cpp | 8 src/lfJSDM.cpp | 24 src/lfMsPGOcc.cpp | 41 - src/msPGOcc.cpp | 42 + src/sfJSDMNNGP.cpp | 251 ++++++--- src/sfMsPGOccNNGP.cpp | 40 - src/spMsPGOcc.cpp | 42 + src/spMsPGOccNNGP.cpp | 42 + src/spOccupancy.h | 142 ++++- src/spPGOcc.cpp | 30 - src/spPGOccNNGP.cpp | 30 - src/stPGOccNNGP.cpp | 91 ++- src/svcPGBinomNNGP.cpp |only src/svcPGOccNNGP.cpp |only src/svcPGOccNNGPPredict.cpp |only src/svcTPGBinomNNGP.cpp |only src/svcTPGOccNNGP.cpp |only src/svcTPGOccNNGPPredict.cpp |only src/tPGOcc.cpp | 30 - 85 files changed, 3912 insertions(+), 2939 deletions(-)
Title: 'RBi' Helper Functions
Description: Contains a collection of helper functions to use with 'RBi', the R interface to 'LibBi', described in Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to adapt the proposal distribution and number of particles in particle Markov-Chain Monte Carlo, as well as calculating the Deviance Information Criterion (DIC) and converting between times in 'LibBi' results and R time/dates.
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi.helpers versions 0.3.2 dated 2020-06-18 and 0.3.3 dated 2022-11-16
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS.md | 4 README.md | 2 build/vignette.rds |binary inst/doc/introduction.Rmd.rsp | 6 - inst/doc/introduction.html | 174 ++++++++++------------------------------- vignettes/introduction.Rmd.rsp | 6 - 8 files changed, 67 insertions(+), 149 deletions(-)
Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the
'bbotk' package. 'miesmuschel' offers both ready-to-use optimization
algorithms, as well as their fundamental building blocks that can be used to
manually construct specialized optimization loops. The Mixed Integer Evolution
Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be
implemented, as well as the multi-objective optimization algorithms NSGA-II
by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre],
Lennart Schneider [ctb] ,
Susanne Dandl [ctb] ,
Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between miesmuschel versions 0.0.1 dated 2022-11-09 and 0.0.2 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/RecombinatorSimulatedBinaryCrossover.R | 23 +++++++++++++++++++++-- man/dict_recombinators_sbx.Rd | 2 +- 5 files changed, 34 insertions(+), 11 deletions(-)
Title: Dynamic Mixed-Membership Network Regression Model
Description: Stochastic collapsed variational inference on mixed-membership stochastic blockmodel for networks,
incorporating node-level predictors of mixed-membership vectors, as well as
dyad-level predictors. For networks observed over time, the model defines a hidden
Markov process that allows the effects of node-level predictors to evolve in discrete,
historical periods. In addition, the package offers a variety of utilities for
exploring results of estimation, including tools for conducting posterior
predictive checks of goodness-of-fit and several plotting functions. The package
implements methods described in Olivella, Pratt and Imai (2019) 'Dynamic Stochastic
Blockmodel Regression for Social Networks: Application to International Conflicts',
available at <https://www.santiagoolivella.info/pdfs/socnet.pdf>.
Author: Santiago Olivella [aut, cre],
Adeline Lo [aut, cre],
Tyler Pratt [aut, cre],
Kosuke Imai [aut, cre]
Maintainer: Santiago Olivella <olivella@unc.edu>
Diff between NetMix versions 0.2.0 dated 2021-03-01 and 0.2.0.1 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- data/lazega_dyadic.RData |binary data/lazega_monadic.RData |binary src/MMModelClass.cpp | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 2.1.4 dated 2022-04-14 and 2.2.0 dated 2022-11-16
DESCRIPTION | 10 ++--- MD5 | 46 +++++++++++++------------- R/byFileAOP.R | 10 ++++- R/byTileAOP.R | 10 ++++- R/findTablesByFormat.R | 2 - R/footRaster.R | 20 ++++++++--- R/getAPI.R | 8 ++-- R/getAPIHeaders.R | 4 +- R/getFileUrls.R | 26 +++++++++------ R/getReadmePublicationDate.R | 2 - R/getTaxonTable.R | 61 ----------------------------------- R/getTileUrls.R | 28 ++++++++++------ R/loadByProduct.R | 5 ++ R/stackByTable.R | 2 - R/stackDataFilesParallel.R | 74 ++++++++++++++++++++++++++++++++++++++++++- R/sysdata.rda |binary R/zipsByProduct.R | 13 ++++++- README.md | 14 ++++++++ data/chem_bundles.rda |binary data/other_bundles.rda |binary data/shared_aquatic.rda |binary data/shared_flights.rda |binary data/table_types.rda |binary man/getTaxonTable.Rd | 11 ------ 24 files changed, 205 insertions(+), 141 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro, Alessio Serafini
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 2.1.1 dated 2019-09-17 and 2.1.1.1 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- data/Mc.rda |binary data/NBA.rda |binary data/butterfly.rda |binary data/houseVotes.rda |binary data/synt.data.rda |binary data/synt.data2.rda |binary data/unemployment.rda |binary src/func.cpp | 2 +- 10 files changed, 13 insertions(+), 13 deletions(-)
Title: Wavelets Statistics and Transforms
Description: Performs 1, 2 and 3D real and complex-valued wavelet transforms,
nondecimated transforms, wavelet packet transforms, nondecimated
wavelet packet transforms, multiple wavelet transforms,
complex-valued wavelet transforms, wavelet shrinkage for
various kinds of data, locally stationary wavelet time series,
nonstationary multiscale transfer function modeling, density
estimation.
Author: Guy Nason [aut, cre],
Stuart Barber [ctb],
Tim Downie [ctb],
Piotr Frylewicz [ctb],
Arne Kovac [ctb],
Todd Ogden [ctb],
Bernard Silverman [ctb]
Maintainer: Guy Nason <g.nason@imperial.ac.uk>
Diff between wavethresh versions 4.7.1 dated 2022-11-09 and 4.7.2 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/function.r | 2 +- build/partial.rdb |binary inst/CHANGES | 3 +++ src/wavethresh_init.c | 2 +- 6 files changed, 14 insertions(+), 11 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.2.3 dated 2022-10-04 and 1.2.4 dated 2022-11-16
TidyDensity-1.2.3/TidyDensity/R/autoplot-density.R |only TidyDensity-1.2.4/TidyDensity/DESCRIPTION | 10 TidyDensity-1.2.4/TidyDensity/MD5 | 310 ++-- TidyDensity-1.2.4/TidyDensity/NAMESPACE | 4 TidyDensity-1.2.4/TidyDensity/NEWS.md | 25 TidyDensity-1.2.4/TidyDensity/R/00_global_variables.R | 24 TidyDensity-1.2.4/TidyDensity/R/augment-bootstrap-density.R | 178 +- TidyDensity-1.2.4/TidyDensity/R/augment-bootstrap-p.R | 143 - TidyDensity-1.2.4/TidyDensity/R/augment-bootstrap-q.R | 145 - TidyDensity-1.2.4/TidyDensity/R/autoplot-combined-dist.R | 415 ++--- TidyDensity-1.2.4/TidyDensity/R/autoplot-four-graphs.R | 71 TidyDensity-1.2.4/TidyDensity/R/autoplot-multi-dist.R | 730 ++++----- TidyDensity-1.2.4/TidyDensity/R/autoplot-randomwalk.R | 383 ++--- TidyDensity-1.2.4/TidyDensity/R/autoplot.R |only TidyDensity-1.2.4/TidyDensity/R/bootstrap-unnest-tbl.R | 45 TidyDensity-1.2.4/TidyDensity/R/combine-multi-single-dist-tbl.R | 239 +-- TidyDensity-1.2.4/TidyDensity/R/combine-tidy-distributions-tbl.R | 47 TidyDensity-1.2.4/TidyDensity/R/empirical-tidy-bootstrap.R | 188 +- TidyDensity-1.2.4/TidyDensity/R/empirical-tidy.R | 112 - TidyDensity-1.2.4/TidyDensity/R/est-param-bernoulli.R |only TidyDensity-1.2.4/TidyDensity/R/est-param-beta.R | 204 +- TidyDensity-1.2.4/TidyDensity/R/est-param-binomial.R | 229 +-- TidyDensity-1.2.4/TidyDensity/R/est-param-cauchy.R | 103 - TidyDensity-1.2.4/TidyDensity/R/est-param-exponential.R | 117 - TidyDensity-1.2.4/TidyDensity/R/est-param-gamma.R | 163 +- TidyDensity-1.2.4/TidyDensity/R/est-param-geometric.R | 143 - TidyDensity-1.2.4/TidyDensity/R/est-param-hypergeometric.R | 315 ++-- TidyDensity-1.2.4/TidyDensity/R/est-param-logistic.R | 170 +- TidyDensity-1.2.4/TidyDensity/R/est-param-lognormal.R | 123 - TidyDensity-1.2.4/TidyDensity/R/est-param-negative-binomial.R | 191 +- TidyDensity-1.2.4/TidyDensity/R/est-param-normal.R | 123 - TidyDensity-1.2.4/TidyDensity/R/est-param-pareto.R | 135 - TidyDensity-1.2.4/TidyDensity/R/est-param-poisson.R | 117 - TidyDensity-1.2.4/TidyDensity/R/est-param-uniform.R | 129 - TidyDensity-1.2.4/TidyDensity/R/est-param-weibull.R | 111 - TidyDensity-1.2.4/TidyDensity/R/helper-dist-type-extract.R |only TidyDensity-1.2.4/TidyDensity/R/palette-color-blind.R | 30 TidyDensity-1.2.4/TidyDensity/R/plot-bootstrap-stat.R | 506 +++--- TidyDensity-1.2.4/TidyDensity/R/random-tidy-bernoulli.R |only TidyDensity-1.2.4/TidyDensity/R/random-tidy-beta.R | 252 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-binomial.R | 256 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-burr-inverse.R | 174 +- TidyDensity-1.2.4/TidyDensity/R/random-tidy-burr.R | 174 +- TidyDensity-1.2.4/TidyDensity/R/random-tidy-cauchy.R | 248 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-chisquare.R | 248 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-exponential-inverse.R | 148 - TidyDensity-1.2.4/TidyDensity/R/random-tidy-exponential.R | 234 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-f.R | 252 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-gamma-inverse.R | 164 +- TidyDensity-1.2.4/TidyDensity/R/random-tidy-gamma.R | 258 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-general-beta.R | 182 +- TidyDensity-1.2.4/TidyDensity/R/random-tidy-general-pareto.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-geom.R | 236 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-hypergeometric.R | 254 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-logistic.R | 240 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-lognormal.R | 248 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-mixture.R | 298 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-negative-binomial.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-normal-inverse.R | 272 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-normal.R | 256 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-paralogistic.R | 274 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-pareto-inverse.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-pareto-single-param.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-pareto.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-poisson.R | 240 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-t.R | 250 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-uniform.R | 242 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-weibull-inverse.R | 162 +- TidyDensity-1.2.4/TidyDensity/R/random-tidy-weibull.R | 248 +-- TidyDensity-1.2.4/TidyDensity/R/random-tidy-zero-truc-poisson.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-zero-trunc-geometric.R | 4 TidyDensity-1.2.4/TidyDensity/R/random-tidy-zero-truncated-binomial.R | 10 TidyDensity-1.2.4/TidyDensity/R/random-zero-trunc-negative-binomial.R | 7 TidyDensity-1.2.4/TidyDensity/R/stats-bernoulli-tbl.R |only TidyDensity-1.2.4/TidyDensity/R/stats-beta-tbl.R | 167 +- TidyDensity-1.2.4/TidyDensity/R/stats-binomial-tbl.R | 171 +- TidyDensity-1.2.4/TidyDensity/R/stats-cauchy-tbl.R | 167 +- TidyDensity-1.2.4/TidyDensity/R/stats-chisquare-tbl.R | 177 +- TidyDensity-1.2.4/TidyDensity/R/stats-confidence-intervals.R | 22 TidyDensity-1.2.4/TidyDensity/R/stats-exponential-tbl.R | 169 +- TidyDensity-1.2.4/TidyDensity/R/stats-f-tbl.R | 205 +- TidyDensity-1.2.4/TidyDensity/R/stats-gamma-tbl.R | 165 +- TidyDensity-1.2.4/TidyDensity/R/stats-geometric-tbl.R | 173 +- TidyDensity-1.2.4/TidyDensity/R/stats-hypergeometric-tbl.R | 193 +- TidyDensity-1.2.4/TidyDensity/R/stats-logistic-tbl.R | 169 +- TidyDensity-1.2.4/TidyDensity/R/stats-lognormal-tbl.R | 171 +- TidyDensity-1.2.4/TidyDensity/R/stats-negative-binomial-tbl.R | 171 +- TidyDensity-1.2.4/TidyDensity/R/stats-normal-tbl.R | 167 +- TidyDensity-1.2.4/TidyDensity/R/stats-pareto-tbl.R | 169 +- TidyDensity-1.2.4/TidyDensity/R/stats-poisson-tbl.R | 167 +- TidyDensity-1.2.4/TidyDensity/R/stats-t-tbl.R | 167 +- TidyDensity-1.2.4/TidyDensity/R/stats-tidy-stat-func-tbl.R | 312 ++-- TidyDensity-1.2.4/TidyDensity/R/stats-uniform-tbl.R | 173 +- TidyDensity-1.2.4/TidyDensity/R/stats-weibull-tbl.R | 195 +- TidyDensity-1.2.4/TidyDensity/R/tidy-random-walk.R | 12 TidyDensity-1.2.4/TidyDensity/R/util-distribution-comparison.R | 751 +++++----- TidyDensity-1.2.4/TidyDensity/R/vec-bootstrap-p.R | 95 - TidyDensity-1.2.4/TidyDensity/R/vec-bootstrap-q.R | 89 - TidyDensity-1.2.4/TidyDensity/R/vec-cumulative-functions.R | 482 +++--- TidyDensity-1.2.4/TidyDensity/R/vec-kurtosis.R | 40 TidyDensity-1.2.4/TidyDensity/R/vec-range.R | 17 TidyDensity-1.2.4/TidyDensity/R/vec-scale-zero-one.R | 29 TidyDensity-1.2.4/TidyDensity/R/vec-skewness.R | 40 TidyDensity-1.2.4/TidyDensity/README.md | 32 TidyDensity-1.2.4/TidyDensity/inst/doc/getting-started.html | 147 - TidyDensity-1.2.4/TidyDensity/man/bootstrap_stat_plot.Rd | 6 TidyDensity-1.2.4/TidyDensity/man/dist_type_extractor.Rd |only TidyDensity-1.2.4/TidyDensity/man/figures/README-more_than_nine_simulations-1.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-more_than_nine_simulations-2.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-more_than_nine_simulations-3.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-more_than_nine_simulations-4.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-plot_density-1.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-plot_density-2.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-plot_density-3.png |binary TidyDensity-1.2.4/TidyDensity/man/figures/README-plot_density-4.png |binary TidyDensity-1.2.4/TidyDensity/man/tidy_autoplot.Rd | 2 TidyDensity-1.2.4/TidyDensity/man/tidy_bernoulli.Rd |only TidyDensity-1.2.4/TidyDensity/man/tidy_binomial.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/tidy_hypergeometric.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/tidy_negative_binomial.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/tidy_poisson.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/tidy_scale_zero_one_vec.Rd | 6 TidyDensity-1.2.4/TidyDensity/man/tidy_stat_tbl.Rd | 5 TidyDensity-1.2.4/TidyDensity/man/tidy_zero_truncated_binomial.Rd | 3 TidyDensity-1.2.4/TidyDensity/man/tidy_zero_truncated_negative_binomial.Rd | 3 TidyDensity-1.2.4/TidyDensity/man/tidy_zero_truncated_poisson.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_bernoulli_param_estimate.Rd |only TidyDensity-1.2.4/TidyDensity/man/util_bernoulli_stats_tbl.Rd |only TidyDensity-1.2.4/TidyDensity/man/util_beta_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_beta_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_binomial_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_binomial_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_cauchy_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_cauchy_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_chisquare_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_exponential_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_exponential_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_f_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_gamma_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_gamma_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_geometric_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_geometric_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_hypergeometric_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_hypergeometric_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_logistic_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_logistic_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_lognormal_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_lognormal_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_negative_binomial_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_negative_binomial_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_normal_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_normal_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_pareto_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_pareto_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_poisson_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_poisson_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_t_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_uniform_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_uniform_stats_tbl.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_weibull_param_estimate.Rd | 1 TidyDensity-1.2.4/TidyDensity/man/util_weibull_stats_tbl.Rd | 1 161 files changed, 8621 insertions(+), 8479 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 2.0.1 dated 2022-11-01 and 2.0.2 dated 2022-11-16
DESCRIPTION | 16 ++++++++-------- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ R/calculate_energy.R | 18 +++++++++--------- R/estimate_pcf_fast.R | 4 ++-- R/fit_point_process.R | 14 +++++++------- R/plot.rd_mar.R | 4 ++-- R/plot.rd_pat.R | 8 ++++---- R/reconstruct_pattern_cluster.R | 34 +++++++++++++++++----------------- R/reconstruct_pattern_hetero.R | 22 +++++++++++----------- R/reconstruct_pattern_homo.R | 20 ++++++++++---------- R/reconstruct_pattern_marks.R | 8 ++++---- build/vignette.rds |binary inst/doc/get_started.html | 10 +++++----- tests/testthat.R | 3 ++- tests/testthat/Rplots.pdf |binary 16 files changed, 100 insertions(+), 95 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
RStudio [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between pkgload versions 1.3.1 dated 2022-10-28 and 1.3.2 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ tests/testthat/test-help.R | 12 +++++------- 4 files changed, 16 insertions(+), 13 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library providing high-performance scalability protocols,
implementing a cross-platform standard for messaging and communications.
Serves as a concurrency framework for building distributed applications,
utilising 'aio' objects which resolve automatically upon completion of
asynchronous operations.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 0.7.0 dated 2022-11-07 and 0.7.1 dated 2022-11-16
DESCRIPTION | 10 - MD5 | 63 +++---- NAMESPACE | 1 NEWS.md | 21 +- R/aio.R | 23 +- R/context.R | 4 R/docs.R | 3 R/nano.R | 41 ++-- R/nanonext-package.R | 2 R/ncurl.R | 14 - R/opts.R | 70 +++++-- R/utils.R | 19 +- README.md | 23 +- man/call_aio.Rd | 6 man/device.Rd | 3 man/getopt.Rd |only man/is_nano.Rd | 2 man/mclock.Rd | 6 man/msleep.Rd | 3 man/nano.Rd | 2 man/nano_init.Rd | 3 man/nanonext-package.Rd | 2 man/ncurl.Rd | 14 - man/opts.Rd | 3 man/setopt.Rd | 28 +-- man/stop_aio.Rd | 6 man/unresolved.Rd | 9 - src/aio.c | 116 +++++++------ src/core.c | 425 +++++++++++++++++++++++++++++++----------------- src/init.c | 27 +-- src/nanonext.h | 5 src/utils.c | 50 +++-- tests/tests.R | 84 +++++---- 33 files changed, 671 insertions(+), 417 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.2.7 dated 2022-08-20 and 2.2.8 dated 2022-11-16
DESCRIPTION | 6 MD5 | 364 ++--- NAMESPACE | 244 +-- NEWS | 897 +++++++------- R/AIC.R | 70 - R/DeltaMethod.R | 98 - R/add.df.covar.line.R | 560 ++++---- R/check.bounds.R | 118 - R/check.mono.R | 474 +++---- R/coef.ds.R | 206 +-- R/create.bins.R | 72 - R/ddf.R | 676 +++++----- R/ddf.ds.R | 586 ++++----- R/ddf.gof.R | 178 +- R/ddf.io.R | 248 +-- R/ddf.io.fi.R | 634 ++++----- R/ddf.rem.fi.R | 534 ++++---- R/ddf.trial.fi.R | 402 +++--- R/detfct.R | 6 R/detfct.fit.R | 420 +++--- R/detfct.fit.mono.R | 10 R/detfct.fit.opt.R | 1071 ++++++++-------- R/dht.R | 1259 +++++++++---------- R/dht.se.R | 750 +++++------ R/fixform.R | 26 R/flpt.lnl.r | 14 R/gof.pvalues.R | 140 +- R/keyfct.hn.R | 30 R/keyfct.hz.R | 28 R/keyfct.tpn.R | 148 +- R/logLik.R | 50 R/mcds.R | 156 +- R/model.description.R | 58 R/mrds-package.R | 2362 ++++++++++++++++++------------------- R/nlminb_wrapper.R | 250 +-- R/optimx.setup.R | 446 +++--- R/p.dist.table.R | 200 +-- R/parse.optimx.R | 48 R/pcramer.R | 30 R/pdot.dsr.integrate.logistic.R | 310 ++-- R/plot.ds.R | 799 ++++++------ R/plot.rem.R | 2 R/plot.rem.fi.R | 4 R/plot_cond.R | 192 +-- R/plot_uncond.R | 222 +-- R/print.ddf.R | 36 R/print.ddf.gof.R | 218 +-- R/print.dht.R | 16 R/qqplot.ddf.R | 354 ++--- R/rescale_pars.R | 100 - R/sample_ddf.R | 404 +++--- R/scalecheck.R | 86 - R/setinitial.ds.R | 210 +-- R/sim.mix.R | 92 - R/varn.R | 418 +++--- README.md | 88 - build/partial.rdb |binary man/AIC.ddf.Rd | 58 man/DeltaMethod.Rd | 106 - man/NCovered.Rd | 70 - man/add.df.covar.line.Rd | 168 +- man/adj.check.order.Rd | 84 - man/apex.gamma.Rd | 40 man/assign.default.values.Rd | 52 man/assign.par.Rd | 76 - man/average.line.Rd | 76 - man/average.line.cond.Rd | 72 - man/book.tee.data.Rd | 62 man/calc.se.Np.Rd | 46 man/cdf.ds.Rd | 76 - man/cds.Rd | 102 - man/check.bounds.Rd | 66 - man/check.mono.Rd | 126 - man/coef.ds.Rd | 96 - man/compute.Nht.Rd | 60 man/covered.region.dht.Rd | 58 man/create.bins.Rd | 46 man/create.ddfobj.Rd | 96 - man/create.model.frame.Rd | 84 - man/create.varstructure.Rd | 98 - man/ddf.Rd | 622 ++++----- man/ddf.ds.Rd | 182 +- man/ddf.gof.Rd | 174 +- man/ddf.io.Rd | 140 +- man/ddf.io.fi.Rd | 140 +- man/ddf.rem.Rd | 136 +- man/ddf.rem.fi.Rd | 140 +- man/ddf.trial.Rd | 132 +- man/ddf.trial.fi.Rd | 136 +- man/det.tables.Rd | 92 - man/detfct.fit.Rd | 114 - man/detfct.fit.opt.Rd | 116 - man/dht.Rd | 510 +++---- man/dht.deriv.Rd | 80 - man/dht.se.Rd | 242 +-- man/distpdf.Rd | 272 ++-- man/ds.function.Rd | 92 - man/flnl.Rd | 130 +- man/flt.var.Rd | 78 - man/g0.Rd | 44 man/getpar.Rd | 82 - man/gof.ds.Rd | 54 man/gstdint.Rd | 116 - man/histline.Rd | 106 - man/integratedetfct.logistic.Rd | 66 - man/integratelogistic.analytic.Rd | 50 man/integratepdf.Rd | 96 - man/io.glm.Rd | 132 +- man/is.linear.logistic.Rd | 78 - man/is.logistic.constant.Rd | 50 man/keyfct.th1.Rd | 42 man/keyfct.th2.Rd | 42 man/keyfct.tpn.Rd | 92 - man/lfbcvi.Rd | 666 +++++----- man/lfgcwa.Rd | 778 ++++++------ man/logLik.ddf.Rd | 62 man/logisticbyx.Rd | 60 man/logisticbyz.Rd | 54 man/logisticdetfct.Rd | 48 man/logisticdupbyx.Rd | 64 - man/logisticdupbyx_fast.Rd | 60 man/logit.Rd | 42 man/mcds.Rd | 100 - man/mrds-opt.Rd | 172 +- man/mrds-package.Rd | 74 - man/nlminb_wrapper.Rd | 102 - man/p.det.Rd | 54 man/p.dist.table.Rd | 130 +- man/parse.optimx.Rd | 42 man/pdot.dsr.integrate.logistic.Rd | 120 - man/plot.det.tables.Rd | 144 +- man/plot.ds.Rd | 236 +-- man/plot.io.Rd | 242 +-- man/plot.io.fi.Rd | 242 +-- man/plot.layout.Rd | 48 man/plot.rem.Rd | 194 +-- man/plot.rem.fi.Rd | 194 +-- man/plot.trial.Rd | 192 +-- man/plot.trial.fi.Rd | 192 +-- man/plot_cond.Rd | 162 +- man/plot_uncond.Rd | 174 +- man/predict.ds.Rd | 252 +-- man/print.ddf.Rd | 40 man/print.ddf.gof.Rd | 58 man/print.det.tables.Rd | 52 man/print.dht.Rd | 66 - man/print.p_dist_table.Rd | 48 man/print.summary.ds.Rd | 52 man/print.summary.io.Rd | 52 man/print.summary.io.fi.Rd | 52 man/print.summary.rem.Rd | 52 man/print.summary.rem.fi.Rd | 52 man/print.summary.trial.Rd | 52 man/print.summary.trial.fi.Rd | 52 man/prob.deriv.Rd | 78 - man/prob.se.Rd | 84 - man/process.data.Rd | 128 +- man/pronghorn.Rd | 86 - man/ptdata.distance.Rd | 68 - man/ptdata.dual.Rd | 60 man/ptdata.removal.Rd | 62 man/ptdata.single.Rd | 52 man/qqplot.ddf.Rd | 144 +- man/rem.glm.Rd | 148 +- man/rescale_pars.Rd | 54 man/sample_ddf.Rd | 46 man/setbounds.Rd | 66 - man/setcov.Rd | 66 - man/setinitial.ds.Rd | 76 - man/sim.mix.Rd | 72 - man/solvecov.Rd | 70 - man/stake77.Rd | 190 +- man/stake78.Rd | 220 +-- man/summary.ds.Rd | 88 - man/summary.io.Rd | 84 - man/summary.io.fi.Rd | 98 - man/summary.rem.Rd | 84 - man/summary.rem.fi.Rd | 94 - man/summary.trial.Rd | 84 - man/summary.trial.fi.Rd | 94 - man/survey.region.dht.Rd | 72 - man/test.breaks.Rd | 52 man/varn.Rd | 160 +- 183 files changed, 16043 insertions(+), 15981 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method. See Gasparyan SB et al (2022) <doi:10.1007/s43441-022-00420-1>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.0.2 dated 2022-09-26 and 0.0.8 dated 2022-11-16
DESCRIPTION | 11 +++-- MD5 | 88 +++++++++++++++++++++++++------------------- NAMESPACE | 3 + R/calcWO.R | 2 - R/calcWO_data_frame.R | 17 +++++--- R/calcWO_formula.R | 6 +++ R/calcWO_hce.R | 20 ++++++---- R/data.R | 24 ++++++------ R/hce.R | 37 ++++++++++++------ R/minWO.R | 2 - R/new_hce.R | 7 ++- R/plot_results.R | 2 - R/powerWO.R | 2 - R/print_results.R | 2 - R/simHCE.R | 55 ++++++++++++++++++--------- R/sizeWO.R | 2 - R/summaryWO.R |only R/summaryWO_data_frame.R |only R/summaryWO_hce.R |only R/valicate_hce.R | 8 ++-- README.md |only build |only data/HCE1.rda |binary data/HCE2.rda |binary data/HCE3.rda |binary data/HCE4.rda |binary inst |only man/HCE1.Rd | 6 +-- man/HCE2.Rd | 6 +-- man/HCE3.Rd | 6 +-- man/HCE4.Rd | 6 +-- man/calcWO.Rd | 2 - man/calcWO.data.frame.Rd | 6 ++- man/calcWO.formula.Rd | 6 +++ man/calcWO.hce.Rd | 17 +++++--- man/hce.Rd | 27 +++++++++---- man/minWO.Rd | 2 - man/new_hce.Rd | 8 ++-- man/plot.hce_results.Rd | 4 +- man/powerWO.Rd | 2 - man/print.hce_results.Rd | 4 +- man/simHCE.Rd | 26 +++++++++---- man/sizeWO.Rd | 2 - man/summaryWO.Rd |only man/summaryWO.data.frame.Rd |only man/summaryWO.hce.Rd |only man/validate_hce.Rd | 10 ++--- vignettes |only 48 files changed, 261 insertions(+), 167 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2020) <arXiv:1911.06583>,
Myl [...truncated...]
Author: Mari Myllymaeki [aut, cre],
Tomas Mrkvička [aut],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Mikko Kuronen [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 0.3-1 dated 2022-08-17 and 0.3-2 dated 2022-11-16
DESCRIPTION | 15 - MD5 | 159 ++++++++-------- R/adjusted_envelopes.r | 10 - R/adult_trees.r | 2 R/appl_indeptest.r | 2 R/appl_localcor.r | 7 R/appl_spatialF.r | 12 - R/combined_envelope_tests.R | 2 R/curve-set.r | 17 + R/deviation_test.r | 2 R/envelopes.r | 18 - R/fallen_trees.r | 2 R/fboxplot.r | 7 R/fclustering.r | 14 - R/fdr.r | 2 R/forder.r | 13 - R/glm.R | 6 R/graphfanova.r | 23 +- R/plot_envelope_helper.R | 7 R/saplings.r | 4 build/vignette.rds |binary data/GDPtax.RData |binary data/abide_9002_23.RData |binary data/adult_trees.RData |binary data/cgec.RData |binary data/fallen_trees.RData |binary data/imageset3.RData |binary data/popgrowthmillion.RData |binary data/rimov.RData |binary data/saplings.RData |binary inst/doc/GET.pdf |binary inst/doc/GET.tex.rsp | 6 inst/doc/pointpatterns.pdf |binary inst/doc/pointpatterns.tex.rsp | 4 man/GET.composite.Rd | 6 man/GET.spatialF.Rd | 4 man/adult_trees.Rd | 2 man/combined_scaled_MAD_envelope_test.Rd | 2 man/deviation_test.Rd | 2 man/fallen_trees.Rd | 2 man/global_envelope_test.Rd | 2 man/plot.global_envelope.Rd | 2 man/qdir_envelope.Rd | 2 man/rank_envelope.Rd | 2 man/saplings.Rd | 4 tests/testthat/test-contrank.R |only vignettes/GET-NOx_data.pdf |binary vignettes/GET-abide_9002_23_subj1and27.pdf |binary vignettes/GET-adulttrees.pdf |binary vignettes/GET-adulttrees_CSR_plot.pdf |binary vignettes/GET-flm_frank_abide.pdf |binary vignettes/GET-flm_graph_abide.pdf |binary vignettes/GET-girls_curves_fig.pdf |binary vignettes/GET-girls_fboxplot_plot.pdf |binary vignettes/GET-graphfanova_logNOx.pdf |binary vignettes/GET-necdfs.pdf |binary vignettes/GET-necdfs_means_GET.pdf |binary vignettes/GET-normalitytest.pdf |binary vignettes/GET-polynomial.pdf |binary vignettes/GET.Rnw.orig | 6 vignettes/GET.tex.rsp | 6 vignettes/pointpatterns-HC_goodness-of-fit_test.pdf |binary vignettes/pointpatterns-combined_test.pdf |binary vignettes/pointpatterns-saplings.pdf |binary vignettes/pointpatterns-saplings_adjusted_test.pdf |binary vignettes/pointpatterns-saplings_csr_L3.pdf |binary vignettes/pointpatterns-saplings_matclust4.pdf |binary vignettes/pointpatterns-saplings_matclust_J_plot.pdf |binary vignettes/pointpatterns-saplings_matclust_L_plot.pdf |binary vignettes/pointpatterns-spatialF_bei_F.pdf |binary vignettes/pointpatterns-spatialF_bei_S.pdf |binary vignettes/pointpatterns-spatialF_forestfires_F.pdf |binary vignettes/pointpatterns-spatialF_forestfires_S.pdf |binary vignettes/pointpatterns-spruces.pdf |binary vignettes/pointpatterns-spruces_csr.pdf |binary vignettes/pointpatterns-spruces_csr_crop.pdf |binary vignettes/pointpatterns-spruces_mpp.pdf |binary vignettes/pointpatterns-spruces_randomlabeling_test.pdf |binary vignettes/pointpatterns-workflow_res.pdf |binary vignettes/pointpatterns.Rnw.orig | 4 vignettes/pointpatterns.tex.rsp | 4 81 files changed, 203 insertions(+), 181 deletions(-)
Title: Event History Analysis
Description: Parametric proportional hazards fitting with left truncation and
right censoring for common families of distributions, piecewise constant
hazards, and discrete models. Parametric accelerated failure time models
for left truncated and right censored data. Proportional hazards
models for tabular and register data. Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Broström (2012) <doi:10.1201/9781315373942>.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between eha versions 2.10.0 dated 2022-04-17 and 2.10.1 dated 2022-11-16
eha-2.10.0/eha/src/GB_zeroin.c |only eha-2.10.0/eha/src/GB_zeroin.h |only eha-2.10.1/eha/ChangeLog | 26 +++ eha-2.10.1/eha/DESCRIPTION | 10 - eha-2.10.1/eha/MD5 | 49 ++---- eha-2.10.1/eha/NAMESPACE | 1 eha-2.10.1/eha/NEWS.md | 14 + eha-2.10.1/eha/R/aftreg.R | 5 eha-2.10.1/eha/R/coxreg2.R | 9 - eha-2.10.1/eha/R/ltx2.R | 261 +++++++++++++++++++++++++++----- eha-2.10.1/eha/R/print.logrank.R | 3 eha-2.10.1/eha/R/print.risksets.R | 3 eha-2.10.1/eha/build/partial.rdb |only eha-2.10.1/eha/build/vignette.rds |binary eha-2.10.1/eha/inst/doc/eha.html | 17 +- eha-2.10.1/eha/inst/doc/gompertz.html | 21 -- eha-2.10.1/eha/inst/doc/parametric.html | 25 +-- eha-2.10.1/eha/inst/doc/parametric1.pdf |binary eha-2.10.1/eha/inst/doc/tpchreg.html | 29 +-- eha-2.10.1/eha/man/aftreg.Rd | 2 eha-2.10.1/eha/man/eha-package.Rd | 2 eha-2.10.1/eha/man/ltx.Rd | 5 eha-2.10.1/eha/man/ltx2.Rd | 13 - eha-2.10.1/eha/src/eha_zeroin.c | 2 eha-2.10.1/eha/src/expreg.c | 2 eha-2.10.1/eha/src/phexpreg.c | 2 eha-2.10.1/eha/src/phreg.c | 2 27 files changed, 360 insertions(+), 143 deletions(-)
Title: An R Shiny Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological Dosimetry Laboratories.
Author: Alfredo Hernandez [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Alfredo Hernandez <aldomann.designs@gmail.com>
Diff between biodosetools versions 3.6.0 dated 2022-01-27 and 3.6.1 dated 2022-11-16
biodosetools-3.6.0/biodosetools/R/calcs_decision_threshold.R |only biodosetools-3.6.0/biodosetools/R/golem_utils_server.R |only biodosetools-3.6.0/biodosetools/data/gardner_confidence_table.rda |only biodosetools-3.6.0/biodosetools/inst/app/help/fitting/fitting_options_decision_thresholds.md |only biodosetools-3.6.0/biodosetools/inst/app/help/trans/fitting_options_decision_thresholds.md |only biodosetools-3.6.0/biodosetools/inst/app/translations |only biodosetools-3.6.0/biodosetools/man/calculate_decision_threshold.Rd |only biodosetools-3.6.0/biodosetools/man/gardner_confidence_table.Rd |only biodosetools-3.6.0/biodosetools/tests/testthat/test-decision-threshold.R |only biodosetools-3.6.0/biodosetools/tests/testthat/test-golem-additional.R |only biodosetools-3.6.1/biodosetools/DESCRIPTION | 12 biodosetools-3.6.1/biodosetools/MD5 | 144 biodosetools-3.6.1/biodosetools/NAMESPACE | 9 biodosetools-3.6.1/biodosetools/NEWS.md | 49 biodosetools-3.6.1/biodosetools/R/app_config.R | 20 biodosetools-3.6.1/biodosetools/R/app_server.R | 140 biodosetools-3.6.1/biodosetools/R/calcs_aberrations.R | 51 biodosetools-3.6.1/biodosetools/R/calcs_estimation.R | 52 biodosetools-3.6.1/biodosetools/R/calcs_fitting.R | 95 biodosetools-3.6.1/biodosetools/R/calcs_translocations.R | 4 biodosetools-3.6.1/biodosetools/R/data.R | 13 biodosetools-3.6.1/biodosetools/R/golem_utils_ui.R | 47 biodosetools-3.6.1/biodosetools/R/mod_estimation_dicent_ui.R | 2 biodosetools-3.6.1/biodosetools/R/mod_estimation_micro_ui.R | 11 biodosetools-3.6.1/biodosetools/R/mod_estimation_server.R | 2467 +++++----- biodosetools-3.6.1/biodosetools/R/mod_estimation_trans_ui.R | 10 biodosetools-3.6.1/biodosetools/R/mod_fitting_dicent_ui.R | 30 biodosetools-3.6.1/biodosetools/R/mod_fitting_micro_ui.R | 29 biodosetools-3.6.1/biodosetools/R/mod_fitting_server.R | 919 +-- biodosetools-3.6.1/biodosetools/R/mod_fitting_trans_ui.R | 33 biodosetools-3.6.1/biodosetools/R/mod_help_server.R | 54 biodosetools-3.6.1/biodosetools/R/mod_trans_server.R | 204 biodosetools-3.6.1/biodosetools/R/utils.R | 42 biodosetools-3.6.1/biodosetools/R/utils_estimation.R | 4 biodosetools-3.6.1/biodosetools/R/utils_fitting.R | 2 biodosetools-3.6.1/biodosetools/README.md | 39 biodosetools-3.6.1/biodosetools/build/partial.rdb |binary biodosetools-3.6.1/biodosetools/build/vignette.rds |binary biodosetools-3.6.1/biodosetools/inst/CITATION | 6 biodosetools-3.6.1/biodosetools/inst/app/help/estimation/dose_error.md | 2 biodosetools-3.6.1/biodosetools/inst/app/help/estimation/dose_exposure.md | 6 biodosetools-3.6.1/biodosetools/inst/app/help/fitting/fitting_options_formula.md | 4 biodosetools-3.6.1/biodosetools/inst/app/www/about_body.md | 6 biodosetools-3.6.1/biodosetools/inst/app/www/contributors_app.md | 36 biodosetools-3.6.1/biodosetools/inst/doc/dicent-estimation.R | 20 biodosetools-3.6.1/biodosetools/inst/doc/dicent-estimation.Rmd | 30 biodosetools-3.6.1/biodosetools/inst/doc/dicent-estimation.html | 432 + biodosetools-3.6.1/biodosetools/inst/doc/dicent-fitting.R | 2 biodosetools-3.6.1/biodosetools/inst/doc/dicent-fitting.Rmd | 6 biodosetools-3.6.1/biodosetools/inst/doc/dicent-fitting.html | 385 + biodosetools-3.6.1/biodosetools/inst/doc/trans-estimation.R | 19 biodosetools-3.6.1/biodosetools/inst/doc/trans-estimation.Rmd | 32 biodosetools-3.6.1/biodosetools/inst/doc/trans-estimation.html | 448 + biodosetools-3.6.1/biodosetools/inst/doc/trans-fitting.R | 16 biodosetools-3.6.1/biodosetools/inst/doc/trans-fitting.Rmd | 22 biodosetools-3.6.1/biodosetools/inst/doc/trans-fitting.html | 447 + biodosetools-3.6.1/biodosetools/man/calculate_aberr.Rd | 6 biodosetools-3.6.1/biodosetools/man/calculate_aberr_table.Rd | 9 biodosetools-3.6.1/biodosetools/man/estimate_hetero_mixed_poisson.Rd | 6 biodosetools-3.6.1/biodosetools/man/estimate_partial_body_dolphin.Rd | 7 biodosetools-3.6.1/biodosetools/man/estimate_whole_body_delta.Rd | 4 biodosetools-3.6.1/biodosetools/man/estimate_whole_body_merkle.Rd | 4 biodosetools-3.6.1/biodosetools/man/fit.Rd | 2 biodosetools-3.6.1/biodosetools/man/fit_glm_method.Rd | 2 biodosetools-3.6.1/biodosetools/man/fit_maxlik_method.Rd | 2 biodosetools-3.6.1/biodosetools/man/prepare_maxlik_count_data.Rd | 6 biodosetools-3.6.1/biodosetools/tests/testthat/test-dicentrics.R | 14 biodosetools-3.6.1/biodosetools/tests/testthat/test-golem-recommended.R | 84 biodosetools-3.6.1/biodosetools/tests/testthat/test-golem_utils_ui.R |only biodosetools-3.6.1/biodosetools/tests/testthat/test-mod_estimation_server.R |only biodosetools-3.6.1/biodosetools/tests/testthat/test-mod_fitting_server.R |only biodosetools-3.6.1/biodosetools/tests/testthat/test-mod_help_server.R |only biodosetools-3.6.1/biodosetools/tests/testthat/test-translocations.R | 7 biodosetools-3.6.1/biodosetools/tests/testthat/test-utils.R | 56 biodosetools-3.6.1/biodosetools/vignettes/dicent-estimation.Rmd | 30 biodosetools-3.6.1/biodosetools/vignettes/dicent-fitting.Rmd | 6 biodosetools-3.6.1/biodosetools/vignettes/figures/screenshot-dicentrics-estimate-01b.png |only biodosetools-3.6.1/biodosetools/vignettes/figures/screenshot-translocations-estimate-01b.png |only biodosetools-3.6.1/biodosetools/vignettes/trans-estimation.Rmd | 32 biodosetools-3.6.1/biodosetools/vignettes/trans-fitting.Rmd | 22 80 files changed, 3834 insertions(+), 2866 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.9.0 dated 2022-11-07 and 0.9.2 dated 2022-11-16
vapour-0.9.0/vapour/man/vapour_read_names.Rd |only vapour-0.9.2/vapour/DESCRIPTION | 11 vapour-0.9.2/vapour/MD5 | 65 vapour-0.9.2/vapour/NAMESPACE | 1 vapour-0.9.2/vapour/NEWS.md | 15 vapour-0.9.2/vapour/R/RcppExports.R | 374 +-- vapour-0.9.2/vapour/R/vapour-package.R | 96 vapour-0.9.2/vapour/R/vapour_input_attributes.R | 15 vapour-0.9.2/vapour/R/vapour_input_geometry.R | 27 vapour-0.9.2/vapour/R/zzz.R | 6 vapour-0.9.2/vapour/configure | 18 vapour-0.9.2/vapour/configure.ac | 17 vapour-0.9.2/vapour/inst/WORDLIST | 7 vapour-0.9.2/vapour/inst/doc/feature-access.Rmd | 4 vapour-0.9.2/vapour/inst/doc/feature-access.html | 5 vapour-0.9.2/vapour/inst/doc/vapour.R | 23 vapour-0.9.2/vapour/inst/doc/vapour.Rmd | 43 vapour-0.9.2/vapour/inst/doc/vapour.html | 125 - vapour-0.9.2/vapour/inst/extdata/index_point.csv |only vapour-0.9.2/vapour/inst/include/gdalgeometry/gdalgeometry.h | 968 +++++----- vapour-0.9.2/vapour/inst/include/gdallibrary/gdallibrary.h | 158 - vapour-0.9.2/vapour/inst/include/gdalmiscutils/gdalmiscutils.h | 41 vapour-0.9.2/vapour/inst/include/gdalraster/gdalraster.h | 12 vapour-0.9.2/vapour/man/vapour-package.Rd | 88 vapour-0.9.2/vapour/man/vapour_layer_info.Rd | 16 vapour-0.9.2/vapour/man/vapour_read_fids.Rd |only vapour-0.9.2/vapour/man/vapour_read_geometry.Rd | 2 vapour-0.9.2/vapour/src/00_geometry.cpp | 190 - vapour-0.9.2/vapour/src/RcppExports.cpp | 191 - vapour-0.9.2/vapour/tests/testthat.R | 2 vapour-0.9.2/vapour/tests/testthat/test-crs-less-warp.R | 10 vapour-0.9.2/vapour/tests/testthat/test-features.R | 6 vapour-0.9.2/vapour/tests/testthat/test-limit_skip_n.R | 23 vapour-0.9.2/vapour/vignettes/feature-access.Rmd | 4 vapour-0.9.2/vapour/vignettes/vapour.Rmd | 43 35 files changed, 1375 insertions(+), 1231 deletions(-)
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization. SWU.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sevin.ru>
Diff between ursa versions 3.9.7 dated 2022-09-11 and 3.9.8 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++--------------- NAMESPACE | 1 + NEWS.md | 15 ++++++++++++++- R/classRaster_sort.R |only R/colorize.R | 1 + R/compose_panel.R | 14 +++++++++----- R/conn.write_gdal.R | 2 +- R/session.R | 43 +++++++++++++++++++++++-------------------- R/spatial_engine.R | 11 +++++------ R/xxx.geocode.R | 2 +- R/xxx.panel_cluster.R | 6 ++++-- R/xxx.panel_legend.R | 5 ++++- R/xxx.polarmap.R | 2 +- R/yyy.util.R | 3 ++- inst/requisite/coast-l.rds |binary man/classRaster_sort.Rd |only src/ursa.c | 3 +-- 18 files changed, 87 insertions(+), 59 deletions(-)
Title: Small N Sequential Multiple Assignment Randomized Trial Methods
Description: Consolidated data simulation, sample size calculation and
analysis functions for several snSMART (small sample sequential,
multiple assignment, randomized trial) designs under one library. See
Wei, B., Braun, T.M., Tamura, R.N. and Kidwell, K.M. "A Bayesian
analysis of small n sequential multiple assignment randomized trials
(snSMARTs)." (2018) Statistics in medicine, 37(26), pp.3723-3732
<doi:10.1002/sim.7900>.
Author: Sidi Wang [aut],
Kelley Kidwell [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between snSMART versions 0.2.1 dated 2022-10-06 and 0.2.2 dated 2022-11-16
DESCRIPTION | 42 +++--- MD5 | 40 +++--- R/BJSM_binary.R | 98 +++++++-------- R/BJSM_c.R | 46 +++---- R/JSRM_binary.R | 22 +-- R/bug_files.R | 68 +++------- R/data.R | 48 ++++--- R/globalVariables.R | 14 +- R/group_seq.R | 74 +++++------ R/sample_size.R | 39 +++--- README.md | 299 +++++++++++++++++++++++++++++++++++++++++++--- man/BJSM_binary.Rd | 33 ++--- man/BJSM_c.Rd | 11 - man/LPJSM_binary.Rd | 8 - man/data_binary.Rd | 4 man/data_dose.Rd | 10 - man/group_seq.Rd | 18 +- man/groupseqDATA_full.Rd | 11 + man/groupseqDATA_look1.Rd | 12 - man/sample_size.Rd | 34 ++--- man/trialDataMF.Rd | 10 - 21 files changed, 591 insertions(+), 350 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.0.2 dated 2022-10-12 and 1.0.3 dated 2022-11-16
DESCRIPTION | 8 MD5 | 8 NEWS.md | 5 R/RoundViaDummy.R | 3 inst/doc/Introduction_to_SmallCountRounding.html | 656 +++++++++++++++++++---- 5 files changed, 583 insertions(+), 97 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: Read from/Write to Disk Matrices with any Data Type in a Binary
Format
Description: A mainly instrumental package meant to allow other packages whose core is written in 'C++' to read, write
and manipulate matrices in a binary format so that the memory used for them is no more than strictly needed. Its functionality
is already inside 'parallelpam' and 'scellpam', so if you have installed any of these, you do not need to install 'jmatrix'.
Using just the needed memory is not always true with 'R' matrices or vectors, since by default they are of double type. Trials
like the 'float' package have been done, but to use them you have to coerce a matrix already loaded in 'R' memory to a float matrix,
and then you can delete it. The problem comes when your computer has not memory enough to hold the matrix in the first place, so
you are forced to load it by chunks. This is the problem this package tries to address (with partial success, but this is a
difficult problem since 'R' is not a strictly typed language, which is anyway quite hard to get in an interpreted language).
This [...truncated...]
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Diff between jmatrix versions 1.0 dated 2022-11-01 and 1.1 dated 2022-11-16
DESCRIPTION | 6 +- MD5 | 14 ++--- inst/doc/jmatrix.html | 135 +++++++++++++++++++++++-------------------------- inst/include/jmatrix.h | 20 +++++++ src/jmatrix.cpp | 54 ++++++++++++++++--- src/jmatrixaux.cpp | 38 +++++++++++++ src/matinfo.cpp | 20 +++---- src/matmetadata.cpp | 14 ++--- 8 files changed, 194 insertions(+), 107 deletions(-)
Title: Distributions Hermite Polynomial Approximation
Description: Multivariate conditional and marginal densities, moments, cumulative distribution functions as well as binary choice and sample selection models based on Hermite polynomial approximation which was proposed and described by A. Gallant and D. W. Nychka (1987) <doi:10.2307/1913241>.
Author: Potanin Bogdan
Maintainer: Potanin Bogdan <bogdanpotanin@gmail.com>
Diff between hpa versions 1.2.1 dated 2021-07-04 and 1.3.0 dated 2022-11-16
DESCRIPTION | 10 MD5 | 31 - NAMESPACE | 2 R/RcppExports.R | 77 ++ inst |only man/hpaDist0.Rd |only src/ParallelFunctions.cpp | 6 src/RcppExports.cpp | 1420 +++++++++++++++++++++++++++++++++++++++++----- src/hpa0.cpp |only src/hpa0.h |only src/hpaBinary.cpp | 27 src/hpaML.cpp | 49 - src/hpaMain.cpp | 267 +++++--- src/hpaSelection.cpp | 31 - src/hpaValidation.cpp | 3 src/normalMoments.cpp | 21 src/polynomialIndex.cpp | 1 src/spline.cpp | 20 18 files changed, 1644 insertions(+), 321 deletions(-)
Title: Extreme Value Statistics and Quantile Estimation
Description: Fit, plot and compare several (extreme value) distribution functions.
Compute (truncated) distribution quantile estimates and plot return periods on a linear scale.
On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...] ISBN 1463508417.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between extremeStat versions 1.5.2 dated 2022-08-23 and 1.5.3 dated 2022-11-16
DESCRIPTION | 8 ++-- MD5 | 6 +-- inst/doc/extremeStat.html | 70 +++++++++++++++++++++-------------------- tests/testthat/test-quantile.R | 4 +- 4 files changed, 46 insertions(+), 42 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.ship-med.uni-greifswald.de/Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
European Union’s Horizon 2020 programme [fnd]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 1.0.12 dated 2022-11-11 and 1.0.13 dated 2022-11-16
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 4 ++ R/acc_margins.R | 2 - inst/doc/DQ-report-example.html | 58 ++++++++++++++++++++-------------------- 5 files changed, 41 insertions(+), 37 deletions(-)
More information about custom.gauss.quad at CRAN
Permanent link
Title: Barycenter Methods for Spatial Point Patterns
Description: Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2020) <doi:10.1007/s11222-020-09932-y>.
Author: Raoul Mueller [aut],
Dominic Schuhmacher [aut, cre]
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between ttbary versions 0.3-0 dated 2022-08-15 and 0.3-1 dated 2022-11-16
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS | 13 ++++++++++++- R/kmeansbary.R | 1 + build/partial.rdb |binary 6 files changed, 27 insertions(+), 14 deletions(-)
Title: Translation Layer from MATLAB to R
Description: Allows users familiar with MATLAB to use MATLAB-named functions in
R. Several basic MATLAB functions are written in this package to mimic the
behavior of their original counterparts, with more to come as this package
grows.
Author: Waldir Leoncio [aut, cre]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between matlab2r versions 1.2.0 dated 2022-08-17 and 1.3.0 dated 2022-11-16
DESCRIPTION | 10 ++++++---- MD5 | 14 ++++++++++---- NAMESPACE | 2 ++ NEWS.md | 9 ++++++++- R/assert.R |only R/linspace.R |only R/matlab2r.R | 14 +++++++++++++- man/assert.Rd |only man/linspace.Rd |only tests/testthat/test-assert.R |only tests/testthat/test-linspace.R |only 11 files changed, 39 insertions(+), 10 deletions(-)
Title: Directional Highest Density Regions
Description: We provide an R tool for computation and nonparametric plug-in estimation of Highest Density Regions (HDRs) and general level sets in the directional setting. Concretely, circular and spherical HDRs can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2021) <doi:10.1007/s11634-021-00457-4>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.
Author: Paula Saavedra-Nieves [aut, cre],
Rosa M Crujeiras [aut],
Andres Prieto [ctb],
Felicita Scapini [dtc]
Maintainer: Paula Saavedra-Nieves <paula.saavedra@usc.es>
Diff between HDiR versions 1.1.2 dated 2022-08-06 and 1.1.3 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/circ.plugin.hdr.R | 4 ++-- R/circ.scatterplot.R | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <https://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Mike Malecki [aut],
Neal Richardson [aut],
Gordon Shotwell [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunch versions 1.30.0 dated 2022-05-02 and 1.30.1 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + R/expressions.R | 2 +- inst/mocks.tgz |binary man/ContextManager.Rd | 6 ++++-- man/crunch-api-key.Rd | 6 ++++-- man/expressions-internal.Rd | 2 +- man/expressions.Rd | 6 ++++-- tests/testthat/test-api.R | 1 + tests/testthat/test-as-data-frame.R | 4 ++-- 11 files changed, 32 insertions(+), 24 deletions(-)
Title: Linear and Nonlinear Autoregressive Distributed Lag Models
Description: Estimate the linear and nonlinear autoregressive distributed lag (ARDL & NARDL) models and the corresponding error correction models, and test for longrun and short-run asymmetric. The Pesaran, Shin & Smith (2001) (<doi:10.1002/jae.616>) bounds test for level relationships is also provided. The 'ardl.nardl' package also performs short-run and longrun symmetric restrictions available at Shin et al. (2014) <doi:10.1007/978-1-4899-8008-3_9> and their corresponding tests.
Author: Eric I. Otoakhia [aut, cre]
Maintainer: Eric I. Otoakhia <otoakhiai@gmail.com>
Diff between ardl.nardl versions 1.0.1 dated 2022-11-04 and 1.0.2 dated 2022-11-16
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS | 9 +++++- R/ARDLM_.R | 31 +++++------------------ R/NARDLM_.R | 62 +++++++--------------------------------------- R/NARDLM_sym.R | 37 +++------------------------ man/ardl.nardl-package.Rd | 3 -- man/ardl_uecm.Rd | 8 ++--- man/nardl_uecm.Rd | 6 ++-- man/nardl_uecm_sym.Rd | 14 +++++----- 10 files changed, 56 insertions(+), 138 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-09 0.4.0
2021-01-29 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-21 0.4.3
2018-04-18 0.4.2
2016-09-14 0.4.1
Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The
goal of 'workflows' is to streamline this process by bundling the
model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between workflows versions 1.1.0 dated 2022-09-26 and 1.1.2 dated 2022-11-16
DESCRIPTION | 11 +++++----- MD5 | 24 +++++++++++------------ NEWS.md | 9 ++++++++ R/fit-action-model.R | 8 +++++++ R/fit.R | 6 ++++- R/utils.R | 4 +-- build/vignette.rds |binary inst/doc/stages.html | 14 ++++++------- tests/testthat/_snaps/fit-action-model.md | 20 +++++++++++++++++++ tests/testthat/_snaps/pre-action-case-weights.md | 2 - tests/testthat/_snaps/pull.md | 10 ++++----- tests/testthat/test-fit-action-model.R | 10 +++++++++ vignettes/extras/getting-started.Rmd | 2 - 13 files changed, 86 insertions(+), 34 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.5 dated 2022-09-08 and 1.0.6 dated 2022-11-16
DESCRIPTION | 14 - MD5 | 28 +- NEWS.md | 10 R/tq_portfolio.R | 5 inst/doc/TQ00-introduction-to-tidyquant.html | 18 - inst/doc/TQ01-core-functions-in-tidyquant.html | 135 ++++------ inst/doc/TQ02-quant-integrations-in-tidyquant.html | 127 ++++----- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 2 inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 229 ++++++++--------- inst/doc/TQ04-charting-with-tidyquant.html | 115 ++++---- inst/doc/TQ05-performance-analysis-with-tidyquant.html | 141 +++++----- inst/doc/TQ06-excel-in-r.html | 14 - tests/testthat/test-tq_performance.R | 4 tests/testthat/test-tq_transmute.R | 42 +-- vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 2 15 files changed, 446 insertions(+), 440 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available mon [...truncated...]
Author: Michael Hoehle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Sabanes B [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.20.1 dated 2022-07-19 and 1.20.3 dated 2022-11-16
DESCRIPTION | 62 - MD5 | 152 ++-- NEWS.md | 33 R/algo_twins.R | 17 R/boda.R | 4 R/bodaDelay.R | 6 R/farringtonFlexible.R | 17 R/hhh4.R | 9 R/hhh4_plot.R | 11 R/magic.dim.R | 28 R/spatial_tools.R | 59 + R/twinstim_intensity.R | 46 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.Rnw | 50 - inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.R | 659 ++---------------- inst/doc/monitoringCounts.Rnw | 364 ++++------ inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.Rnw | 31 inst/doc/twinSIR.pdf |binary inst/doc/twinstim.Rnw | 62 - inst/doc/twinstim.pdf |binary man/addSeason2formula.Rd | 34 man/algo.cdc.Rd | 2 man/algo.farrington.Rd | 8 man/algo.glrnb.Rd | 2 man/algo.hmm.Rd | 6 man/algo.quality.Rd | 2 man/algo.rogerson.Rd | 19 man/algo.twins.Rd | 24 man/epidata.Rd | 13 man/epidataCS.Rd | 6 man/epidataCS_animate.Rd | 2 man/farringtonFlexible.Rd | 42 - man/fluBYBW.Rd | 2 man/ha.Rd | 11 man/hagelloch.Rd | 2 man/hhh4_internals.Rd | 3 man/hhh4_plot.Rd | 9 man/hhh4_predict.Rd | 35 man/hhh4_validation.Rd | 1 man/isoWeekYear.Rd | 10 man/measles.weser.Rd | 8 man/plot.atwins.Rd | 32 man/polyAtBorder.Rd | 6 man/sts_animate.Rd | 2 man/sts_ggplot.Rd | 4 man/stsplot_spacetime.Rd | 11 man/surveillance-package.Rd | 9 man/twinSIR_intensityplot.Rd | 2 man/twinstim_epitest.Rd | 2 man/twinstim_intensity.Rd | 11 man/twinstim_simEndemicEvents.Rd | 11 man/twinstim_simulation.Rd | 8 src/gsl_wrappers.h | 2 src/stcd-assuncaocorrea.cc | 2 src/stcd-assuncaocorrea.h | 2 src/surveillance.c | 2 src/twins.cc | 718 -------------------- tests/testthat/test-algo.glrnb.R | 2 tests/testthat/test-bodaDelay.R | 45 - tests/testthat/test-earsC.R | 4 tests/testthat/test-farringtonFlexible.R | 12 tests/tinytest.R | 5 vignettes/hhh4_spacetime.Rnw | 50 - vignettes/monitoringCounts-cache/boda.RData |binary vignettes/monitoringCounts-cache/boda.covars.RData |binary vignettes/monitoringCounts-cache/pMC.RData |binary vignettes/monitoringCounts-cache/pMarkovChain.RData |binary vignettes/monitoringCounts.Rnw | 364 ++++------ vignettes/references.bib | 11 vignettes/twinSIR.Rnw | 31 vignettes/twinstim.Rnw | 62 - 77 files changed, 1093 insertions(+), 2168 deletions(-)
Title: Blind Source Separation for Multivariate Spatial Data
Description: Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of (robust) local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.
Author: Christoph Muehlmann [aut, cre]
,
Mika Sipil<e4> [aut] ,
Klaus Nordhausen [aut] ,
Sara Taskinen [aut] ,
Joni Virta [aut]
Maintainer: Christoph Muehlmann <christoph.muehlmann@tuwien.ac.at>
Diff between SpatialBSS versions 0.12-0 dated 2021-10-07 and 0.13-0 dated 2022-11-16
DESCRIPTION | 27 +++++++++++---- MD5 | 55 +++++++++++++++++------------- NAMESPACE | 8 +++- R/lcov.R |only R/outl_gen.R |only R/robsbss.R |only R/sbss.R | 12 +++++- R/sbss_methods.R | 2 - R/snss.R | 2 - R/utils.R | 65 +++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary inst/ChangeLog.txt | 7 +++ inst/doc/SBSS.R | 26 ++++++++------ inst/doc/SBSS.Rmd | 26 ++++++++------ inst/doc/SBSS.pdf |binary man/SpatialBSS-package.Rd | 18 ++++++---- man/gen_glob_outl.Rd |only man/gen_loc_outl.Rd |only man/local_covariance_matrix.Rd | 27 ++++++++------- man/local_gss_covariance_matrix.Rd |only man/plot.sbss.Rd | 27 ++++++++------- man/predict.sbss.Rd | 27 ++++++++------- man/robsbss.Rd |only man/sbss.Rd | 42 ++++++++++++++--------- man/sbss_asymp.Rd | 25 +++++++------- man/sbss_boot.Rd | 25 +++++++------- man/snss_jd.Rd | 2 - man/snss_sd.Rd | 4 +- man/snss_sjd.Rd | 2 - man/white_data.Rd | 66 ++++++++++++++++++++++--------------- vignettes/SBSS.Rmd | 26 ++++++++------ 32 files changed, 309 insertions(+), 212 deletions(-)
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to fourth-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of the package can be found in Puy et al. (2022) <doi:10.18637/jss.v102.i05>.
Author: Arnald Puy [aut, cre] ,
Bertrand Ioos [ctb] ,
Gilles Pujol [ctb] ,
RStudio [cph]
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 1.1.1 dated 2022-04-26 and 1.1.2 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/sobol_convergence.R | 1 + R/sobol_indices.R | 6 +++--- R/sobol_matrices.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 8 ++++---- inst/doc/sensobol.pdf |binary 10 files changed, 29 insertions(+), 22 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.4.0 dated 2022-06-07 and 1.4.1 dated 2022-11-16
SAMtool-1.4.0/SAMtool/R/assess_SCA_CAL.R |only SAMtool-1.4.0/SAMtool/R/assess_SCA_DDM.R |only SAMtool-1.4.0/SAMtool/R/assess_SCA_RWM.R |only SAMtool-1.4.1/SAMtool/DESCRIPTION | 12 +++---- SAMtool-1.4.1/SAMtool/MD5 | 34 ++++++++++------------ SAMtool-1.4.1/SAMtool/NEWS.md | 4 ++ SAMtool-1.4.1/SAMtool/R/Misc_fun.R | 8 +++++ SAMtool-1.4.1/SAMtool/R/assess_DD.R | 3 + SAMtool-1.4.1/SAMtool/R/assess_SCA.R | 6 +++ SAMtool-1.4.1/SAMtool/R/assess_SCA_ext.R |only SAMtool-1.4.1/SAMtool/R/assess_SP.R | 7 ++-- SAMtool-1.4.1/SAMtool/R/assess_VPA.R | 1 SAMtool-1.4.1/SAMtool/R/assess_cDD.R | 4 +- SAMtool-1.4.1/SAMtool/R/assess_shortcut.R | 4 +- SAMtool-1.4.1/SAMtool/R/define_S4_class_RCModel.R | 2 - SAMtool-1.4.1/SAMtool/R/define_S4_generic_RCM.R | 2 - SAMtool-1.4.1/SAMtool/R/retrospective_AM.R | 4 +- SAMtool-1.4.1/SAMtool/build/partial.rdb |binary SAMtool-1.4.1/SAMtool/man/HCR_ramp.Rd | 10 +++--- SAMtool-1.4.1/SAMtool/man/Model-based-MP.Rd | 26 ++++++++-------- 20 files changed, 74 insertions(+), 53 deletions(-)
Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalized ratio-of-uniforms (RU) method to simulate
from univariate and (low-dimensional) multivariate continuous distributions.
The user specifies the log-density, up to an additive constant. The RU
algorithm is applied after relocation of mode of the density to zero, and
the user can choose a tuning parameter r. For details see Wakefield, Gelfand
and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random
variates via the ratio-of-uniforms method, Statistics and Computing (1991)
1, 129-133. A Box-Cox variable transformation can be used to make the input
density suitable for the RU method and to improve efficiency. In the
multivariate case rotation of axes can also be used to improve efficiency.
From version 1.2.0 the 'Rcpp' package
<https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between rust versions 1.3.13 dated 2021-10-31 and 1.4.0 dated 2022-11-16
rust-1.3.13/rust/R/rust.R |only rust-1.3.13/rust/man/print.summary.ru.Rd |only rust-1.3.13/rust/man/rust.Rd |only rust-1.3.13/rust/src/init.c |only rust-1.4.0/rust/DESCRIPTION | 11 rust-1.4.0/rust/MD5 | 97 - rust-1.4.0/rust/NEWS.md | 24 rust-1.4.0/rust/R/RcppExports.R | 41 rust-1.4.0/rust/R/box_cox_functions.R | 135 +- rust-1.4.0/rust/R/box_cox_functions_rcpp.R | 116 +- rust-1.4.0/rust/R/gp_example.R | 86 - rust-1.4.0/rust/R/ru_sampling.R | 206 ++- rust-1.4.0/rust/R/ru_sampling_rcpp.R | 182 ++- rust-1.4.0/rust/R/rust-internal.R | 86 + rust-1.4.0/rust/R/rust-package.R |only rust-1.4.0/rust/R/sample_diagnostics.R | 129 -- rust-1.4.0/rust/README.md | 5 rust-1.4.0/rust/build/partial.rdb |binary rust-1.4.0/rust/build/vignette.rds |binary rust-1.4.0/rust/inst/doc/rust-a-vignette.R | 8 rust-1.4.0/rust/inst/doc/rust-a-vignette.Rmd | 20 rust-1.4.0/rust/inst/doc/rust-a-vignette.html | 770 +++++++++++--- rust-1.4.0/rust/inst/doc/rust-b-when-to-use-vignette.html | 541 +++++++-- rust-1.4.0/rust/inst/doc/rust-c-using-rcpp-vignette.html | 545 +++++++-- rust-1.4.0/rust/inst/include/rust_RcppExports.h | 105 + rust-1.4.0/rust/man/create_log_j_xptr.Rd | 13 rust-1.4.0/rust/man/create_phi_to_theta_xptr.Rd | 13 rust-1.4.0/rust/man/create_xptr.Rd | 13 rust-1.4.0/rust/man/find_lambda.Rd | 63 - rust-1.4.0/rust/man/find_lambda_one_d.Rd | 76 - rust-1.4.0/rust/man/find_lambda_one_d_rcpp.Rd | 66 - rust-1.4.0/rust/man/find_lambda_rcpp.Rd | 54 rust-1.4.0/rust/man/gpd_init.Rd | 72 - rust-1.4.0/rust/man/gpd_logpost.Rd | 6 rust-1.4.0/rust/man/gpd_sum_stats.Rd | 2 rust-1.4.0/rust/man/plot.ru.Rd | 41 rust-1.4.0/rust/man/print.ru.Rd | 3 rust-1.4.0/rust/man/rgpd.Rd | 6 rust-1.4.0/rust/man/ru.Rd | 148 +- rust-1.4.0/rust/man/ru_rcpp.Rd | 143 +- rust-1.4.0/rust/man/rust-internal.Rd | 5 rust-1.4.0/rust/man/rust-package.Rd |only rust-1.4.0/rust/man/summary.ru.Rd | 28 rust-1.4.0/rust/src/RcppExports.cpp | 267 ++++ rust-1.4.0/rust/src/built_in_fns.cpp | 130 ++ rust-1.4.0/rust/src/user_fns.cpp | 23 rust-1.4.0/rust/tests/testthat/test-find_lambda.R | 138 +- rust-1.4.0/rust/tests/testthat/test-find_lambda_one_d.R | 52 rust-1.4.0/rust/tests/testthat/test-mode.R |only rust-1.4.0/rust/tests/testthat/test-ru.R | 658 ++++++----- rust-1.4.0/rust/tests/testthat/test-ru_equal_ru_rcpp.R | 342 +++--- rust-1.4.0/rust/tests/testthat/test-ru_rcpp.R | 657 ++++++----- rust-1.4.0/rust/vignettes/rust-a-vignette.Rmd | 20 53 files changed, 4218 insertions(+), 1928 deletions(-)
Title: Collection of Tools for PD Rating Model Development and
Validation
Description: The goal of this package is to cover the most common steps in probability of default (PD) rating model development and validation.
The main procedures available are those that refer to univariate, bivariate, multivariate analysis, calibration and validation.
Along with accompanied 'monobin' and 'monobinShiny' packages, 'PDtoolkit' provides functions which are suitable for different
data transformation and modeling tasks such as:
imputations, monotonic binning of numeric risk factors, binning of categorical risk factors, weights of evidence (WoE) and
information value (IV) calculations, WoE coding (replacement of risk factors modalities with WoE values), risk factor clustering,
area under curve (AUC) calculation and others. Additionally, package provides set of validation functions for testing homogeneity,
heterogeneity, discriminatory and predictive power of the model.
Author: Andrija Djurovic [aut, cre]
Maintainer: Andrija Djurovic <djandrija@gmail.com>
Diff between PDtoolkit versions 0.4.0 dated 2022-06-06 and 1.0.0 dated 2022-11-16
DESCRIPTION | 6 +-- MD5 | 69 ++++++++++++++++++++++++++------------ NAMESPACE | 20 +++++++++++ NEWS.md | 25 +++++++++++++ R/00_GLOBALS.R | 3 + R/01_UNIVARIATE_ANALYSIS.R | 16 ++++---- R/03_CAT_RF_BINNING.R | 15 +++----- R/07_SEGMENT_VLD.R | 11 ++++-- R/11_HOMOGENEITY.R | 12 +++--- R/15_PSI.R | 4 +- R/18_INTERACTION_TRANSFORMER.R | 2 - R/19_STEP_FWD.R | 6 ++- R/21_STAGED_BLOCKS.R | 3 + R/22_EMBEDDED_BLOCKS.R | 1 R/23_ENSEMBLE_BLOCKS.R | 1 R/24_NZV.R |only R/25_SMOTE.R |only R/26_CONSTRAINED_LOGIT.R |only R/27_RF_INTERACTION_TRANSFORMER.R |only R/28_HHI.R |only R/29_NORMAL_TEST.R |only R/30_CONFUSION_MATRIX.R |only R/31_U_SHAPE.R |only R/32_KFOLD_INDICES.R |only R/33_FAIRNESS_VLD.R |only R/34_DECISION_TREE.R |only R/55_HELPERS_.R |only README.md | 2 - build/partial.rdb |binary man/cat.slice.Rd |only man/confusion.matrix.Rd |only man/constrained.logit.Rd |only man/cutoff.palette.Rd |only man/decision.tree.Rd |only man/encode.woe.Rd |only man/fairness.vld.Rd |only man/hhi.Rd |only man/imp.outliers.Rd | 2 - man/imp.sc.Rd | 4 +- man/kfold.idx.Rd |only man/normal.test.Rd |only man/num.slice.Rd |only man/nzv.Rd |only man/predict.cdt.Rd |only man/rf.interaction.transformer.Rd |only man/segment.vld.Rd | 5 ++ man/smote.Rd |only man/univariate.Rd | 2 - man/ush.bin.Rd |only man/ush.test.Rd |only 50 files changed, 149 insertions(+), 60 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.facebook.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 1.2.3 dated 2022-10-18 and 1.2.4 dated 2022-11-16
DESCRIPTION | 6 MD5 | 8 NEWS.md | 4 inst/doc/getting-started-with-modeltime.html | 864 ++++++++++++--------------- tests/testthat/test-developer-tools-xregs.R | 40 - 5 files changed, 441 insertions(+), 481 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class
'AutoFSelector' provides a convenient way to perform nested resampling
in combination with 'mlr3'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.7.2 dated 2022-08-25 and 0.8.0 dated 2022-11-16
mlr3fselect-0.7.2/mlr3fselect/tests/testthat/extract_inner_fselect_archives.R |only mlr3fselect-0.8.0/mlr3fselect/DESCRIPTION | 26 mlr3fselect-0.8.0/mlr3fselect/MD5 | 106 +-- mlr3fselect-0.8.0/mlr3fselect/NAMESPACE | 1 mlr3fselect-0.8.0/mlr3fselect/NEWS.md | 9 mlr3fselect-0.8.0/mlr3fselect/R/ArchiveFSelect.R | 98 +-- mlr3fselect-0.8.0/mlr3fselect/R/AutoFSelector.R | 321 ++++++---- mlr3fselect-0.8.0/mlr3fselect/R/FSelectInstanceMultiCrit.R | 104 +-- mlr3fselect-0.8.0/mlr3fselect/R/FSelectInstanceSingleCrit.R | 116 +-- mlr3fselect-0.8.0/mlr3fselect/R/FSelector.R | 96 +- mlr3fselect-0.8.0/mlr3fselect/R/FSelectorDesignPoints.R | 31 mlr3fselect-0.8.0/mlr3fselect/R/FSelectorExhaustiveSearch.R | 13 mlr3fselect-0.8.0/mlr3fselect/R/FSelectorGeneticSearch.R | 19 mlr3fselect-0.8.0/mlr3fselect/R/FSelectorRFE.R | 33 - mlr3fselect-0.8.0/mlr3fselect/R/FSelectorRandomSearch.R | 29 mlr3fselect-0.8.0/mlr3fselect/R/FSelectorSequential.R | 15 mlr3fselect-0.8.0/mlr3fselect/R/FSelectorShadowVariableSearch.R | 18 mlr3fselect-0.8.0/mlr3fselect/R/ObjectiveFSelect.R | 97 +-- mlr3fselect-0.8.0/mlr3fselect/R/auto_fselector.R | 31 mlr3fselect-0.8.0/mlr3fselect/R/extract_inner_fselect_archives.R | 35 - mlr3fselect-0.8.0/mlr3fselect/R/extract_inner_fselect_results.R | 36 - mlr3fselect-0.8.0/mlr3fselect/R/fselect.R | 54 + mlr3fselect-0.8.0/mlr3fselect/R/fselect_nested.R | 9 mlr3fselect-0.8.0/mlr3fselect/R/helper.R | 10 mlr3fselect-0.8.0/mlr3fselect/R/sugar.R | 44 + mlr3fselect-0.8.0/mlr3fselect/README.md | 107 +-- mlr3fselect-0.8.0/mlr3fselect/build/partial.rdb |binary mlr3fselect-0.8.0/mlr3fselect/inst/WORDLIST | 7 mlr3fselect-0.8.0/mlr3fselect/man/ArchiveFSelect.Rd | 96 +- mlr3fselect-0.8.0/mlr3fselect/man/AutoFSelector.Rd | 227 +++++-- mlr3fselect-0.8.0/mlr3fselect/man/FSelectInstanceMultiCrit.Rd | 110 +-- mlr3fselect-0.8.0/mlr3fselect/man/FSelectInstanceSingleCrit.Rd | 120 ++- mlr3fselect-0.8.0/mlr3fselect/man/FSelector.Rd | 75 -- mlr3fselect-0.8.0/mlr3fselect/man/ObjectiveFSelect.Rd | 33 - mlr3fselect-0.8.0/mlr3fselect/man/auto_fselector.Rd | 119 +++ mlr3fselect-0.8.0/mlr3fselect/man/extract_inner_fselect_archives.Rd | 24 mlr3fselect-0.8.0/mlr3fselect/man/extract_inner_fselect_results.Rd | 27 mlr3fselect-0.8.0/mlr3fselect/man/fs.Rd | 18 mlr3fselect-0.8.0/mlr3fselect/man/fselect.Rd | 80 ++ mlr3fselect-0.8.0/mlr3fselect/man/fselect_nested.Rd | 12 mlr3fselect-0.8.0/mlr3fselect/man/fsi.Rd |only mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors.Rd | 9 mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_design_points.Rd | 48 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_exhaustive_search.Rd | 44 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_genetic_search.Rd | 48 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_random_search.Rd | 46 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_rfe.Rd | 46 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_sequential.Rd | 40 - mlr3fselect-0.8.0/mlr3fselect/man/mlr_fselectors_shadow_variable_search.Rd | 35 - mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_ArchiveFSelect.R | 32 mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_AutoFSelector.R | 66 +- mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_FSelectorRFE.R | 14 mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_ObjectiveFSelect.R | 16 mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_extract_inner_fselect_archives.R |only mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_extract_inner_fselect_result.R | 100 +-- mlr3fselect-0.8.0/mlr3fselect/tests/testthat/test_fsi.R |only 56 files changed, 1792 insertions(+), 1158 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] ,
Kosuke Imai [aut] ,
Gary King [aut] ,
Elizabeth Stuart [aut] ,
Alex Whitworth [ctb],
Noah Greifer [cre, aut]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.4.0 dated 2022-05-18 and 4.5.0 dated 2022-11-16
MatchIt-4.4.0/MatchIt/R/cardinality_matchit.R |only MatchIt-4.4.0/MatchIt/R/cem_matchit.R |only MatchIt-4.4.0/MatchIt/R/class_functions.R |only MatchIt-4.4.0/MatchIt/R/hist.pscore.R |only MatchIt-4.4.0/MatchIt/R/jitter.pscore.R |only MatchIt-4.4.0/MatchIt/R/matchit2_methods.R |only MatchIt-4.4.0/MatchIt/R/plots.R |only MatchIt-4.4.0/MatchIt/man/euclidean_dist.Rd |only MatchIt-4.5.0/MatchIt/DESCRIPTION | 24 MatchIt-4.5.0/MatchIt/MD5 | 132 MatchIt-4.5.0/MatchIt/NAMESPACE | 52 MatchIt-4.5.0/MatchIt/NEWS.md | 36 MatchIt-4.5.0/MatchIt/R/MatchIt-package.R |only MatchIt-4.5.0/MatchIt/R/add_s.weights.R | 63 MatchIt-4.5.0/MatchIt/R/aux_functions.R | 571 --- MatchIt-4.5.0/MatchIt/R/dist_functions.R | 202 + MatchIt-4.5.0/MatchIt/R/distance2_methods.R | 294 + MatchIt-4.5.0/MatchIt/R/input_processing.R |only MatchIt-4.5.0/MatchIt/R/lalonde.R |only MatchIt-4.5.0/MatchIt/R/match.data.R | 258 + MatchIt-4.5.0/MatchIt/R/match.qoi.R | 150 MatchIt-4.5.0/MatchIt/R/matchit.R | 532 +++ MatchIt-4.5.0/MatchIt/R/matchit2cardinality.R |only MatchIt-4.5.0/MatchIt/R/matchit2cem.R |only MatchIt-4.5.0/MatchIt/R/matchit2exact.R |only MatchIt-4.5.0/MatchIt/R/matchit2full.R |only MatchIt-4.5.0/MatchIt/R/matchit2genetic.R |only MatchIt-4.5.0/MatchIt/R/matchit2nearest.R |only MatchIt-4.5.0/MatchIt/R/matchit2optimal.R |only MatchIt-4.5.0/MatchIt/R/matchit2quick.R |only MatchIt-4.5.0/MatchIt/R/matchit2subclass.R |only MatchIt-4.5.0/MatchIt/R/plot.matchit.R |only MatchIt-4.5.0/MatchIt/R/plot.summary.matchit.R |only MatchIt-4.5.0/MatchIt/R/rbind.matchdata.R |only MatchIt-4.5.0/MatchIt/R/summary.matchit.R |only MatchIt-4.5.0/MatchIt/R/weights.subclass.R | 58 MatchIt-4.5.0/MatchIt/R/zzz.R |only MatchIt-4.5.0/MatchIt/build/MatchIt.pdf |binary MatchIt-4.5.0/MatchIt/build/vignette.rds |binary MatchIt-4.5.0/MatchIt/inst/doc/MatchIt.R | 83 MatchIt-4.5.0/MatchIt/inst/doc/MatchIt.Rmd | 119 MatchIt-4.5.0/MatchIt/inst/doc/MatchIt.html | 409 +- MatchIt-4.5.0/MatchIt/inst/doc/assessing-balance.R | 29 MatchIt-4.5.0/MatchIt/inst/doc/assessing-balance.Rmd | 48 MatchIt-4.5.0/MatchIt/inst/doc/assessing-balance.html | 338 -- MatchIt-4.5.0/MatchIt/inst/doc/estimating-effects.R | 659 +-- MatchIt-4.5.0/MatchIt/inst/doc/estimating-effects.Rmd | 954 +---- MatchIt-4.5.0/MatchIt/inst/doc/estimating-effects.html | 2861 ++++++----------- MatchIt-4.5.0/MatchIt/inst/doc/matching-methods.Rmd | 22 MatchIt-4.5.0/MatchIt/inst/doc/matching-methods.html | 228 - MatchIt-4.5.0/MatchIt/inst/doc/sampling-weights.R | 33 MatchIt-4.5.0/MatchIt/inst/doc/sampling-weights.Rmd | 39 MatchIt-4.5.0/MatchIt/inst/doc/sampling-weights.html | 297 - MatchIt-4.5.0/MatchIt/man/MatchIt-package.Rd |only MatchIt-4.5.0/MatchIt/man/add_s.weights.Rd | 58 MatchIt-4.5.0/MatchIt/man/distance.Rd | 285 + MatchIt-4.5.0/MatchIt/man/lalonde.Rd | 64 MatchIt-4.5.0/MatchIt/man/mahalanobis_dist.Rd |only MatchIt-4.5.0/MatchIt/man/match.data.Rd | 256 + MatchIt-4.5.0/MatchIt/man/matchit.Rd | 540 ++- MatchIt-4.5.0/MatchIt/man/method_cardinality.Rd | 291 + MatchIt-4.5.0/MatchIt/man/method_cem.Rd | 296 + MatchIt-4.5.0/MatchIt/man/method_exact.Rd | 107 MatchIt-4.5.0/MatchIt/man/method_full.Rd | 278 + MatchIt-4.5.0/MatchIt/man/method_genetic.Rd | 294 + MatchIt-4.5.0/MatchIt/man/method_nearest.Rd | 310 + MatchIt-4.5.0/MatchIt/man/method_optimal.Rd | 296 + MatchIt-4.5.0/MatchIt/man/method_quick.Rd |only MatchIt-4.5.0/MatchIt/man/method_subclass.Rd | 204 - MatchIt-4.5.0/MatchIt/man/plot.matchit.Rd | 179 - MatchIt-4.5.0/MatchIt/man/plot.summary.matchit.Rd | 111 MatchIt-4.5.0/MatchIt/man/rbind.matchdata.Rd | 77 MatchIt-4.5.0/MatchIt/man/summary.matchit.Rd | 302 + MatchIt-4.5.0/MatchIt/src/nn_matchC.cpp | 7 MatchIt-4.5.0/MatchIt/src/pairdistC.cpp | 32 MatchIt-4.5.0/MatchIt/vignettes/MatchIt.Rmd | 119 MatchIt-4.5.0/MatchIt/vignettes/assessing-balance.Rmd | 48 MatchIt-4.5.0/MatchIt/vignettes/estimating-effects.Rmd | 954 +---- MatchIt-4.5.0/MatchIt/vignettes/matching-methods.Rmd | 22 MatchIt-4.5.0/MatchIt/vignettes/references.bib | 121 MatchIt-4.5.0/MatchIt/vignettes/sampling-weights.Rmd | 39 81 files changed, 7213 insertions(+), 6568 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.7 dated 2022-11-12 and 1.0.8 dated 2022-11-16
marmap-1.0.7/marmap/inst/CITATION |only marmap-1.0.8/marmap/DESCRIPTION | 8 ++++---- marmap-1.0.8/marmap/MD5 | 11 +++++------ marmap-1.0.8/marmap/R/getNOAA.bathy.R | 2 +- marmap-1.0.8/marmap/inst/doc/marmap-DataAnalysis.pdf |binary marmap-1.0.8/marmap/inst/doc/marmap.pdf |binary marmap-1.0.8/marmap/man/marmap.Rd | 4 ++-- 7 files changed, 12 insertions(+), 13 deletions(-)
Title: Render Markdown with 'commonmark'
Description: Render Markdown to full HTML documents with the 'commonmark'
package. Markdown is a plain-text formatting
syntax that can be converted to 'XHTML' or other formats. See
<https://en.wikipedia.org/wiki/Markdown> for more information about Markdown.
Author: JJ Allaire [aut],
Jeffrey Horner [aut],
Yihui Xie [aut, cre] ,
Henrik Bengtsson [ctb],
Jim Hester [ctb],
Yixuan Qiu [ctb],
Kohske Takahashi [ctb],
Adam November [ctb],
Nacho Caballero [ctb],
Jeroen Ooms [ctb],
Thomas Leeper [ctb],
Joe Cheng [ctb],
An [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between markdown versions 1.3 dated 2022-10-29 and 1.4 dated 2022-11-16
markdown-1.3/markdown/inst/resources/r_highlight.html |only markdown-1.3/markdown/man/markdownExtensions.Rd |only markdown-1.4/markdown/DESCRIPTION | 8 markdown-1.4/markdown/MD5 | 48 +-- markdown-1.4/markdown/NAMESPACE | 1 markdown-1.4/markdown/NEWS.md | 10 markdown-1.4/markdown/R/render.R | 49 +-- markdown-1.4/markdown/R/rmarkdown.R | 4 markdown-1.4/markdown/R/utils.R | 76 +++-- markdown-1.4/markdown/build/vignette.rds |binary markdown-1.4/markdown/inst/doc/markdown-examples.R | 11 markdown-1.4/markdown/inst/doc/markdown-examples.Rmd | 4 markdown-1.4/markdown/inst/doc/markdown-examples.html | 242 +++-------------- markdown-1.4/markdown/inst/doc/markdown-output.R | 23 - markdown-1.4/markdown/inst/doc/markdown-output.Rmd | 17 - markdown-1.4/markdown/inst/doc/markdown-output.html | 245 ++++-------------- markdown-1.4/markdown/inst/examples/render-options.R | 11 markdown-1.4/markdown/inst/resources/highlight.html |only markdown-1.4/markdown/inst/resources/markdown.css | 160 +++-------- markdown-1.4/markdown/inst/resources/markdown.html | 26 - markdown-1.4/markdown/inst/resources/markdown.latex | 1 markdown-1.4/markdown/man/mark.Rd | 28 -- markdown-1.4/markdown/man/markdown_options.Rd | 11 markdown-1.4/markdown/tests/smartypants.R |only markdown-1.4/markdown/tests/tests.Rout.save | 20 - markdown-1.4/markdown/vignettes/markdown-examples.Rmd | 4 markdown-1.4/markdown/vignettes/markdown-output.Rmd | 17 - 27 files changed, 327 insertions(+), 689 deletions(-)
Title: Regression Methods for IBD Linkage with Covariates
Description: Method to test genetic linkage with covariates by
regression methods with response IBD sharing for relative
pairs. Account for correlations of IBD statistics and
covariates for relative pairs within the same pedigree.
Author: Jason P. Sinnwell and Daniel J. Schaid
Maintainer: Jason P. Sinnwell <Sinnwell.Jason@mayo.edu>
Diff between ibdreg versions 0.3.6 dated 2021-09-05 and 0.3.8 dated 2022-11-16
DESCRIPTION | 8 +-- MD5 | 22 +++++----- build/vignette.rds |binary inst/doc/ibdreg.pdf |binary man/exact.ibd.var.Rd | 21 ++------- man/ibd.df.merlin.Rd | 17 ++----- man/ibdreg.Rd | 2 man/sim.ibd.var.Rd | 16 ++----- man/sim.mark.prop.Rd | 85 ++++++++++++--------------------------- src/ibdreg_init.c | 2 src/mcmemory.h | 110 +-------------------------------------------------- src/sim.mark.prop.c | 27 +++++------- 12 files changed, 75 insertions(+), 235 deletions(-)
Title: The Machine Learning and AI Modeling Companion to 'healthyR'
Description: Hospital machine learning and ai data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative
hospital data. Some of these include predicting length of stay, and readmits.
The aim is to provide a simple and consistent verb framework that takes the
guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ai versions 0.0.9 dated 2022-10-04 and 0.0.10 dated 2022-11-16
DESCRIPTION | 8 MD5 | 62 ++-- NAMESPACE | 5 NEWS.md | 11 R/hai-data-impute-missing.R | 467 ++++++++++++++++++------------------- R/hai-data-poly.R | 173 ++++++------- R/hai-data-scale.R | 323 ++++++++++++------------- R/hai-data-transform.R | 405 ++++++++++++++++---------------- R/hai-data-trig.R | 229 +++++++++--------- R/pca-data.R | 491 +++++++++++++++++++-------------------- R/step-hai-fourier-discrete.R | 423 ++++++++++++++++----------------- R/step-hai-fourier.R | 423 ++++++++++++++++----------------- R/step-hai-hyperbolic.R | 393 +++++++++++++++---------------- R/step-hai-scale-zero-one.R | 353 ++++++++++++++-------------- R/step-hai-scale-zscore.R | 361 ++++++++++++++-------------- R/step-hai-winsorized-move.R | 383 +++++++++++++++--------------- R/step-hai-winsorized-truncate.R | 382 +++++++++++++++--------------- README.md | 1 inst/doc/auto-kmeans.html | 115 ++++----- inst/doc/getting-started.R | 21 - inst/doc/getting-started.Rmd | 387 +++++++++++++++--------------- inst/doc/getting-started.html | 337 +++++++++++++------------- inst/doc/kmeans-umap.html | 165 ++++++------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/hai_data_impute.Rd | 5 man/hai_data_poly.Rd | 5 man/hai_data_scale.Rd | 5 man/hai_data_transform.Rd | 5 man/hai_data_trig.Rd | 5 man/pca_your_recipe.Rd | 3 vignettes/getting-started.Rmd | 387 +++++++++++++++--------------- 32 files changed, 3181 insertions(+), 3152 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.4.0 dated 2020-06-27 and 0.5.0 dated 2022-11-16
DESCRIPTION | 56 +++--- MD5 | 127 ++++++++------ NAMESPACE | 13 + NEWS.md | 42 ++++ R/as_npc.R |only R/compare_means.R | 2 R/create_aes.R | 37 +++- R/geom_pwc.R |only R/get_coord.R |only R/ggdensity.R | 8 R/gghistogram.R | 9 R/ggpubr-package.R |only R/ggpubr_options.R |only R/ggsummarystats.R | 10 - R/npc_to_data_coord.R |only R/stat_anova_test.R |only R/stat_compare_means.R | 51 ++++- R/stat_conf_ellipse.R | 2 R/stat_friedman_test.R |only R/stat_kruskal_test.R |only R/stat_pvalue_manual.R | 16 + R/stat_welch_anova_test.R |only R/utilities.R | 7 R/utils-aes.R |only R/utils_stat_test_label.R |only README.md | 63 ++++-- man/as_npc.Rd |only man/compare_means.Rd | 2 man/create_aes.Rd | 2 man/geom_bracket.Rd | 18 + man/geom_pwc.Rd |only man/get_coord.Rd |only man/ggbarplot.Rd | 6 man/ggdensity.Rd | 4 man/ggerrorplot.Rd | 6 man/gghistogram.Rd | 4 man/ggline.Rd | 6 man/ggpubr-package.Rd |only man/ggpubr_options.Rd |only man/ggsummarystats.Rd | 4 man/ggviolin.Rd | 6 man/npc_to_data_coord.Rd |only man/stat_anova_test.Rd |only man/stat_central_tendency.Rd | 20 +- man/stat_chull.Rd | 20 +- man/stat_compare_means.Rd | 26 +- man/stat_conf_ellipse.Rd | 20 +- man/stat_cor.Rd | 20 +- man/stat_friedman_test.Rd |only man/stat_kruskal_test.Rd |only man/stat_mean.Rd | 20 +- man/stat_overlay_normal_density.Rd | 20 +- man/stat_pvalue_manual.Rd | 10 - man/stat_regline_equation.Rd | 20 +- man/stat_stars.Rd | 20 +- man/stat_welch_anova_test.Rd |only tests |only tools/README-cleveland-dot-plots-1.png |binary tools/README-deviation-graphs-1.png |binary tools/README-deviation-graphs-horizontal-1.png |binary tools/README-ggpubr-1.png |binary tools/README-ggpubr-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-1.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-3.png |binary tools/README-lollipop-chart-1.png |binary tools/README-lollipop-chart-deviation-1.png |binary tools/README-lollipop-chart-rotate-1.png |binary tools/README-ordered-bar-plots-1.png |binary tools/README-ordered-bar-plots-by-groups-1.png |binary 70 files changed, 475 insertions(+), 222 deletions(-)
Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] ,
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distr versions 2.9.0 dated 2022-11-12 and 2.9.1 dated 2022-11-16
DESCRIPTION | 14 - MD5 | 22 +- inst/NEWS | 5 inst/doc/newDistributions-knitr.pdf |binary man/0distr-package.Rd | 9 - man/MinMaximum-methods.Rd | 6 man/RtoDPQ.Rd | 3 man/RtoDPQ.d.Rd | 4 man/qqbounds.Rd | 7 man/qqplot.Rd | 6 man/simplifyr-methods.Rd | 8 - tests/Examples/distr-Ex.Rout.save | 285 ++++++++++++++++-------------------- 12 files changed, 187 insertions(+), 182 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: A suite of machine learning algorithms written in C++ with the R
interface contains several learning techniques for classification and regression.
Predictive models include e.g., classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with the 'ExplainPrediction' package.
This package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for feature selection
or discretization of numeric attributes.
The OrdEval algorithm and its visualization is used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded executi [...truncated...]
Author: Marko Robnik-Sikonja and Petr Savicky
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 1.57.1 dated 2022-11-06 and 1.57.2 dated 2022-11-16
ChangeLog | 4 +++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/c45read.cpp | 8 +++----- src/expr.cpp | 8 ++++---- src/exprReg.cpp | 4 ++-- src/frontend.cpp | 2 +- src/trutil.cpp | 6 +++--- 8 files changed, 27 insertions(+), 27 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>
Diff between cgam versions 1.19 dated 2022-10-04 and 1.20 dated 2022-11-16
ChangeLog | 5 DESCRIPTION | 8 MD5 | 10 R/cgam.R | 1648 +++++++++++++++++++++++++++++--------------------------- R/cgamm.R | 582 ++++++++++--------- man/COforest.Rd | 2 6 files changed, 1170 insertions(+), 1085 deletions(-)
Title: Learning Discrete Bayesian Network Classifiers from Data
Description: State-of-the art algorithms for learning discrete Bayesian network classifiers from data, including a number of those described in Bielza & Larranaga (2014) <doi:10.1145/2576868>, with functions for prediction, model evaluation and inspection.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut],
Wickham Hadley [ctb]
Maintainer: Mihaljevic Bojan <boki.mihaljevic@gmail.com>
Diff between bnclassify versions 0.4.6 dated 2021-10-29 and 0.4.7 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 3 +++ README.md | 18 +++++++----------- build/vignette.rds |binary data/car.RData |binary data/voting.RData |binary inst/doc/methods.pdf |binary inst/doc/overview.pdf |binary inst/doc/usage.pdf |binary man/figures/README-unnamed-chunk-2-1.png |binary src/RcppExports.cpp | 5 +++++ src/basic-misc.cpp | 2 +- 13 files changed, 31 insertions(+), 27 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Also used to display, in tables and graphs, predictions
obtained using any model fitting function and to explore differences between predictions.
The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions (for further
details see 'asremlPlus-package' in help). A history of
the fitting of a sequence of models is kept in a data frame. Procedures are available for
choosing models that conform to the hierarchy or marginality principle and for displaying
predictions for significant terms in tables and graphs. The 'asreml' package provides a
computationally efficient algorithm for fitting mixed models using Resi [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.3.36 dated 2022-08-17 and 4.3.40 dated 2022-11-16
asremlPlus-4.3.36/asremlPlus/tests/testthat/testthat-problems.rds |only asremlPlus-4.3.40/asremlPlus/DESCRIPTION | 8 asremlPlus-4.3.40/asremlPlus/MD5 | 107 ++-- asremlPlus-4.3.40/asremlPlus/NAMESPACE | 7 asremlPlus-4.3.40/asremlPlus/R/S3methodsDeprecations.r | 1 asremlPlus-4.3.40/asremlPlus/R/alldiffs.v2.r | 35 + asremlPlus-4.3.40/asremlPlus/R/asremlPlusUtilities.r | 45 +- asremlPlus-4.3.40/asremlPlus/R/choose.r | 1 asremlPlus-4.3.40/asremlPlus/R/reml4.v8.r | 171 +++++-- asremlPlus-4.3.40/asremlPlus/build/partial.rdb |binary asremlPlus-4.3.40/asremlPlus/build/vignette.rds |binary asremlPlus-4.3.40/asremlPlus/data/ChickpeaEnd.dat.rda |binary asremlPlus-4.3.40/asremlPlus/data/Ladybird.dat.rda |binary asremlPlus-4.3.40/asremlPlus/data/Oats.dat.rda |binary asremlPlus-4.3.40/asremlPlus/data/WaterRunoff.dat.rda |binary asremlPlus-4.3.40/asremlPlus/data/Wheat.dat.rda |binary asremlPlus-4.3.40/asremlPlus/inst/NEWS.Rd | 19 asremlPlus-4.3.40/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.3.40/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.3.40/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.3.40/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.3.40/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.3.40/asremlPlus/inst/extdata/testDiffs.rda |binary asremlPlus-4.3.40/asremlPlus/man/LSD.frame.Rd | 61 +- asremlPlus-4.3.40/asremlPlus/man/addto.test.summary.Rd |only asremlPlus-4.3.40/asremlPlus/man/allDifferences.data.frame.Rd | 67 +-- asremlPlus-4.3.40/asremlPlus/man/asremlPlus-package.Rd | 5 asremlPlus-4.3.40/asremlPlus/man/asrtests.object.Rd | 9 asremlPlus-4.3.40/asremlPlus/man/changeModelOnIC.asrtests.Rd | 16 asremlPlus-4.3.40/asremlPlus/man/changeTerms.asrtests.Rd | 18 asremlPlus-4.3.40/asremlPlus/man/chooseModel.asrtests.Rd | 6 asremlPlus-4.3.40/asremlPlus/man/exploreLSDs.alldiffs.Rd | 15 asremlPlus-4.3.40/asremlPlus/man/linTransform.alldiffs.Rd | 66 +- asremlPlus-4.3.40/asremlPlus/man/pairdiffsTransform.alldiffs.Rd | 64 +- asremlPlus-4.3.40/asremlPlus/man/pickLSDstatistics.alldiffs.Rd |only asremlPlus-4.3.40/asremlPlus/man/predictPlus.asreml.Rd | 68 +-- asremlPlus-4.3.40/asremlPlus/man/predictPresent.asreml.Rd | 66 +- asremlPlus-4.3.40/asremlPlus/man/recalcLSD.alldiffs.Rd | 68 +-- asremlPlus-4.3.40/asremlPlus/man/redoErrorIntervals.alldiffs.Rd | 70 +-- asremlPlus-4.3.40/asremlPlus/man/testranfix.asrtests.Rd | 18 asremlPlus-4.3.40/asremlPlus/man/testswapran.asrtests.Rd | 8 asremlPlus-4.3.40/asremlPlus/tests/testthat/data/Exp355.Control.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/MET.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/PSA.27.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/Ricecart.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/Smarthouse.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/cart.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/chkpeadat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/gw.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/local851.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/longit.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/orange.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/data/sPSA.DASTs.dat.rda |only asremlPlus-4.3.40/asremlPlus/tests/testthat/data/wheat94.dat.rda |binary asremlPlus-4.3.40/asremlPlus/tests/testthat/test4Selection.r | 221 +++++++++- asremlPlus-4.3.40/asremlPlus/tests/testthat/test4Wheat.r | 68 +++ asremlPlus-4.3.40/asremlPlus/vignettes/asremlPlus_4.3.39.pdf |only 57 files changed, 902 insertions(+), 406 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.4.1 dated 2022-07-08 and 1.0.4.2 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS.Rd | 6 ++++++ src/getLL.c | 4 ++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Schloss Lab Tools for Reproducible Microbiome Research
Description: A collection of useful functions and example code created and
used by the Schloss Lab for reproducible microbiome research. Perform
common tasks like read files created by mothur <https://mothur.org/>,
tidy up your microbiome data, and format R Markdown documents for
publication. See the website <http://www.schlosslab.org/schtools/>
for more information, documentation, and examples.
Author: Kelly Sovacool [aut, cre] ,
Nick Lesniak [aut] ,
Patrick Schloss [aut],
Sarah Lucas [ctb] ,
Courtney Armour [ctb] ,
Jacqueline Moltzau [ctb] ,
Andrew Hannah [ctb],
Nielson Baxter [ctb],
Alyxandria Schubert [ctb],
Kathryn Iverson [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between schtools versions 0.3.0 dated 2022-10-05 and 0.3.1 dated 2022-11-16
DESCRIPTION | 8 MD5 | 36 - NEWS.md | 6 R/plot.R | 2 R/read_dist.R | 5 R/read_tax.R | 54 +- R/shared.R | 34 + README.md | 20 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 60 +-- inst/doc/introduction.Rmd | 60 +-- inst/doc/introduction.html | 115 ++--- man/pool_taxon_counts.Rd | 11 tests/testthat/test-plot.R | 789 +--------------------------------------- tests/testthat/test-read_dist.R | 34 - tests/testthat/test-read_tax.R | 19 tests/testthat/test-shared.R | 13 vignettes/introduction.Rmd | 60 +-- 19 files changed, 326 insertions(+), 1000 deletions(-)
Title: Print a Daily Bible Proverb to Console
Description: A simple package to grab a Bible proverb corresponding to the
day of the month.
Author: Brad Lindblad [aut, cre, cph]
Maintainer: Brad Lindblad <me@bradlindblad.com>
Diff between proverbs versions 0.1.0 dated 2022-02-01 and 0.2.0 dated 2022-11-16
DESCRIPTION | 9 ++++---- MD5 | 16 ++++++++++----- NEWS.md |only R/get_proverbs.R | 44 +++++++++++++++++++++++++++++++++++++----- README.md | 9 +++++++- build |only inst |only man/proverb.Rd | 9 +++++++- tests/testthat/test-proverb.R | 14 +++++++++++++ vignettes |only 10 files changed, 85 insertions(+), 16 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Helps with trivial but tedious tasks and tries to identify errors to save time on debugging. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.0.13 dated 2022-09-07 and 0.0.14 dated 2022-11-16
NMdata-0.0.13/NMdata/tests/testthat/testReference/NMgetSection.rds |only NMdata-0.0.13/NMdata/tests/testthat/testReference/NMreadSection_1.rds |only NMdata-0.0.13/NMdata/tests/testthat/test_addTAD.R |only NMdata-0.0.14/NMdata/DESCRIPTION | 10 NMdata-0.0.14/NMdata/MD5 | 275 - NMdata-0.0.14/NMdata/NAMESPACE | 1 NMdata-0.0.14/NMdata/NEWS.md | 66 NMdata-0.0.14/NMdata/R/NMapplyFilters.R | 4 NMdata-0.0.14/NMdata/R/NMcheckData.R | 2 NMdata-0.0.14/NMdata/R/NMcheckDataFile.R | 7 NMdata-0.0.14/NMdata/R/NMexpandDoses.R | 76 NMdata-0.0.14/NMdata/R/NMgenText.R | 28 NMdata-0.0.14/NMdata/R/NMisNumeric.R | 5 NMdata-0.0.14/NMdata/R/NMorderColumns.R | 4 NMdata-0.0.14/NMdata/R/NMreadCsv.R | 4 NMdata-0.0.14/NMdata/R/NMreadTab.R | 33 NMdata-0.0.14/NMdata/R/NMscanData.R | 489 +- NMdata-0.0.14/NMdata/R/NMscanInput.R | 19 NMdata-0.0.14/NMdata/R/NMscanTables.R | 29 NMdata-0.0.14/NMdata/R/NMstamp.R | 2 NMdata-0.0.14/NMdata/R/NMwriteData.R | 93 NMdata-0.0.14/NMdata/R/NMwriteSection.R | 33 NMdata-0.0.14/NMdata/R/addTAPD.R | 90 NMdata-0.0.14/NMdata/R/cc.R | 1 NMdata-0.0.14/NMdata/R/cl.R | 1 NMdata-0.0.14/NMdata/R/egdt.R | 4 NMdata-0.0.14/NMdata/R/flagsAssign.R | 29 NMdata-0.0.14/NMdata/R/fnAppend.R | 1 NMdata-0.0.14/NMdata/R/fnExtension.R | 22 NMdata-0.0.14/NMdata/R/listMissings.R | 20 NMdata-0.0.14/NMdata/R/lstExtractTime.R | 8 NMdata-0.0.14/NMdata/R/reduceTables.R |only NMdata-0.0.14/NMdata/R/searchColRow.R |only NMdata-0.0.14/NMdata/R/summary_NMdata.R | 2 NMdata-0.0.14/NMdata/R/zzz.R | 3 NMdata-0.0.14/NMdata/man/NMapplyFilters.Rd | 1 NMdata-0.0.14/NMdata/man/NMcheckData.Rd | 3 NMdata-0.0.14/NMdata/man/NMcheckDataFile.Rd | 7 NMdata-0.0.14/NMdata/man/NMexpandDoses.Rd | 10 NMdata-0.0.14/NMdata/man/NMextractText.Rd | 1 NMdata-0.0.14/NMdata/man/NMgenText.Rd | 10 NMdata-0.0.14/NMdata/man/NMorderColumns.Rd | 3 NMdata-0.0.14/NMdata/man/NMreadCsv.Rd | 4 NMdata-0.0.14/NMdata/man/NMreadSection.Rd | 5 NMdata-0.0.14/NMdata/man/NMreadTab.Rd | 23 NMdata-0.0.14/NMdata/man/NMscanData.Rd | 23 NMdata-0.0.14/NMdata/man/NMscanInput.Rd | 10 NMdata-0.0.14/NMdata/man/NMscanTables.Rd | 23 NMdata-0.0.14/NMdata/man/NMstamp.Rd | 1 NMdata-0.0.14/NMdata/man/NMwriteData.Rd | 43 NMdata-0.0.14/NMdata/man/NMwriteSection.Rd | 19 NMdata-0.0.14/NMdata/man/addTAPD.Rd | 25 NMdata-0.0.14/NMdata/man/cc.Rd | 3 NMdata-0.0.14/NMdata/man/cl.Rd | 3 NMdata-0.0.14/NMdata/man/findCovs.Rd | 1 NMdata-0.0.14/NMdata/man/findVars.Rd | 1 NMdata-0.0.14/NMdata/man/flagsAssign.Rd | 1 NMdata-0.0.14/NMdata/man/flagsCount.Rd | 1 NMdata-0.0.14/NMdata/man/fnAppend.Rd | 3 NMdata-0.0.14/NMdata/man/fnExtension.Rd | 15 NMdata-0.0.14/NMdata/man/mergeCheck.Rd | 1 NMdata-0.0.14/NMdata/man/print.summary_NMdata.Rd | 3 NMdata-0.0.14/NMdata/man/reduceTables.Rd |only NMdata-0.0.14/NMdata/man/searchColRow.Rd |only NMdata-0.0.14/NMdata/man/tmpcol.Rd | 1 NMdata-0.0.14/NMdata/tests/testthat/testData/data/xgxr2_flag0_nocolnames.csv |only NMdata-0.0.14/NMdata/tests/testthat/testData/data/xgxr2_flag0_nocolnames.rds |only NMdata-0.0.14/NMdata/tests/testthat/testData/data/xgxr2_flag0_nocolnames_meta.txt |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr001.lst | 2 NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr001_res.txt | 1810 +++++----- NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr013.lst | 1 NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr013_fo1.txt | 180 NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr013_res1.txt | 1460 ++++---- NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr014.lst | 1 NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr023.lst | 2 NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr023_res_fo.txt | 300 - NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr027.lst |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr027.mod |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr027_res1.txt |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr028.lst |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr028.mod |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr028_res.txt |only NMdata-0.0.14/NMdata/tests/testthat/testData/nonmem/xgxr029.mod |only NMdata-0.0.14/NMdata/tests/testthat/testData/simulations |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/NMwriteData10.csv |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/NMwriteData10.rds |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/NMwriteData11.csv |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/NMwriteData11.rds |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/pk.RData |binary NMdata-0.0.14/NMdata/tests/testthat/testOutput/pk.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testOutput/stampedData_9.csv |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/stampedData_9_meta.txt |only NMdata-0.0.14/NMdata/tests/testthat/testOutput/xgxr011_update1b.mod |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMexpandDoses_02.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMgenText_1.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMgenText_3.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMgenText_4.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMgenText_5.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMgenText_6.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMisNumeric_4.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMreadSection_01.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMreadSection_02.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData1.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData11.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData13.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData14.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData15b.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData16.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData17.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData18.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData1_bu.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData20.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData22.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData22b.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData23.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData24.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData25.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData27.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMscanData28.rds |binary 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NMdata-0.0.14/NMdata/tests/testthat/testReference/NMwriteData_11.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMwriteData_4.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMwriteData_5.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/NMwriteData_9.rds |only NMdata-0.0.14/NMdata/tests/testthat/testReference/NMwriteSection_5.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/addTAPD_01.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/addTAPD_02.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/fnExtension_1.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/lstExtractTime1.rds |binary NMdata-0.0.14/NMdata/tests/testthat/testReference/lstExtractTime2.rds |binary NMdata-0.0.14/NMdata/tests/testthat/test_NMexpandDoses.R | 9 NMdata-0.0.14/NMdata/tests/testthat/test_NMgenText.R | 13 NMdata-0.0.14/NMdata/tests/testthat/test_NMgetSection.R | 13 NMdata-0.0.14/NMdata/tests/testthat/test_NMisNumeric.R | 18 NMdata-0.0.14/NMdata/tests/testthat/test_NMreadSection.R |only NMdata-0.0.14/NMdata/tests/testthat/test_NMscanData.R | 135 NMdata-0.0.14/NMdata/tests/testthat/test_NMscanInput.R | 28 NMdata-0.0.14/NMdata/tests/testthat/test_NMscanTables.R | 32 NMdata-0.0.14/NMdata/tests/testthat/test_NMwriteData.R | 105 NMdata-0.0.14/NMdata/tests/testthat/test_NMwriteSection.R | 37 NMdata-0.0.14/NMdata/tests/testthat/test_addTAPD.R |only NMdata-0.0.14/NMdata/tests/testthat/test_flagsAssign.R |only NMdata-0.0.14/NMdata/tests/testthat/test_fnExtension.R | 13 NMdata-0.0.14/NMdata/tests/testthat/test_listMissings.R | 1 NMdata-0.0.14/NMdata/tests/testthat/test_lstExtractTime.R | 3 157 files changed, 3223 insertions(+), 2545 deletions(-)
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.3.0 dated 2022-10-07 and 0.3.1 dated 2022-11-16
DESCRIPTION | 10 +- MD5 | 38 +++---- NAMESPACE | 3 NEWS.md | 170 ++++++++++++++++++----------------- R/bde_check_access.R | 1 R/catalogs.R | 2 R/series.R | 84 ++++++++++++----- R/theme_tidybde.R | 68 ++++++++------ README.md | 27 +++-- build/vignette.rds |binary inst/WORDLIST | 13 -- inst/doc/tidyBdE.html | 115 +++++++++++------------ man/bde_indicators.Rd | 3 man/bde_series_load.Rd | 46 ++++++++- man/figures/README-chart-1.png |binary man/figures/README-macroseries-1.png |binary man/theme_tidybde.Rd | 18 ++- tests/testthat/test-series.R | 28 +++++ vignettes/chart-1.png |binary vignettes/macroseries-1.png |binary 20 files changed, 382 insertions(+), 244 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.5.7 dated 2022-08-09 and 0.5.8 dated 2022-11-16
DESCRIPTION | 10 MD5 | 46 +- NAMESPACE | 2 NEWS.md | 17 R/figure2qmd.R | 2 R/figure2rmd.R |only R/gdoc2qmd.R | 21 R/table2qmd.R | 2 R/table2rmd.R |only R/yupana_reshape.R | 2 inst/doc/apps.html | 16 inst/doc/heritability.html | 142 +++--- inst/doc/policy.html | 14 inst/doc/rticles.Rmd | 2 inst/doc/rticles.html | 128 +++-- inst/doc/tarpuy.html | 14 inst/doc/yupana.html | 14 inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 6 inst/yupana/server.R | 367 ++++++++++------- man/figure2qmd.Rd | 2 man/figure2rmd.Rd |only man/gdoc2qmd.Rd | 6 man/table2qmd.Rd | 2 man/table2rmd.Rd |only vignettes/rticles.Rmd | 2 26 files changed, 470 insertions(+), 353 deletions(-)
Title: R API to Interactive Brokers Trader Workstation
Description: Provides native R access to Interactive Brokers Trader Workstation API.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
J.W. de Roode [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between IBrokers versions 0.10-1 dated 2022-04-10 and 0.10-2 dated 2022-11-16
DESCRIPTION | 18 +++++++++----- MD5 | 33 ++++++++++++++------------ NAMESPACE | 10 +++++-- R/eWrapper.R | 6 +++- R/processMsg.R | 53 ++++++++++++++++++++++++++++++++++++++---- R/reqAccountUpdates.R | 16 ++++++------ R/reqManagedAccts.R | 45 +++++++++++++++++++++++++++-------- R/reqMatchingSymbols.R |only R/twsIDs.R | 6 +++- build/vignette.rds |binary inst/doc/IBrokers.pdf |binary inst/doc/IBrokersREFCARD.Rnw | 23 ++---------------- inst/doc/IBrokersREFCARD.pdf |binary inst/doc/RealTime.pdf |binary man/internal.Rd | 1 man/placeOrder.Rd | 2 - man/reqManagedAccts.Rd |only man/reqMatchingSymbols.Rd |only vignettes/IBrokersREFCARD.Rnw | 23 ++---------------- 19 files changed, 145 insertions(+), 91 deletions(-)
Title: Regression Helper Functions
Description: Methods for manipulating regression models and for describing these in a style adapted for medical journals.
Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model
estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots.
In addition to the descriptive methods, there are functions for the robust covariance matrix provided by the 'sandwich'
package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for
time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Author: Max Gordon [aut, cre],
Reinhard Seifert [aut]
Maintainer: Max Gordon <max@gforge.se>
Diff between Greg versions 2.0.0 dated 2022-10-13 and 2.0.1 dated 2022-11-16
DESCRIPTION | 6 - MD5 | 30 +++--- NAMESPACE | 2 NEWS.md | 4 R/forestplotRegrObj_prForestplotPrep.R | 32 ++++-- R/plotHR.R | 2 build/vignette.rds |binary inst/doc/printCrudeAndAdjustedModel.html | 115 +++++++++++------------ inst/doc/timeSplitter.html | 115 +++++++++++------------ inst/examples/forestplotCombineRegrObj_example.R | 4 inst/examples/forestplotRegrObj_example.R | 11 +- man/forestplotCombineRegrObj.Rd | 4 man/forestplotRegrObj.Rd | 11 +- man/getModelData4Forestplot.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-forestplotRegrObj.R | 8 - 16 files changed, 191 insertions(+), 157 deletions(-)
Title: Canadian Hydrological Analyses
Description: A collection of user-submitted functions to aid in the analysis of hydrological data, particularly for users in Canada. The functions focus on the use of Canadian data sets, and are suited to Canadian hydrology, such as the important cold region hydrological processes and will work with Canadian hydrological models. The functions are grouped into several themes, currently including Statistical hydrology, Basic data manipulations, Visualization, and Spatial hydrology. Functions developed by the Floodnet project are also included. CSHShydRology has been developed with the assistance of the Canadian Society for Hydrological Sciences (CSHS) which is an affiliated society of the Canadian Water Resources Association (CWRA). As of version 1.2.6, functions now fail gracefully when attempting to download data from a url which is unavailable.
Author: Kevin Shook [cre, aut],
Paul Whitfield [aut],
Robert Chlumsky [aut],
Daniel Moore [aut],
Martin Durocher [aut],
Matthew Lemieux [ctb],
Jason Chiang [ctb],
Joel Trubilowicz [ctb],
SJ Kim [ctb]
Maintainer: Kevin Shook <kevin.shook@usask.ca>
Diff between CSHShydRology versions 1.2.10 dated 2022-10-18 and 1.3.0 dated 2022-11-16
DESCRIPTION | 11 ++- MD5 | 21 +++++-- NAMESPACE | 5 + R/ch_circ_mean_reg.R |only R/ch_col_gradient.R |only R/ch_col_transparent.R |only R/ch_polar_plot_peaks.R |only R/ch_sh_get_amax.R |only R/utils.R | 46 --------------- build/vignette.rds |binary inst/doc/hydrograph_plot.html | 125 ++++++++++++++++++++---------------------- man/ch_circ_mean_reg.Rd |only man/ch_col_gradient.Rd |only man/ch_col_transparent.Rd | 37 ++++++++---- man/ch_polar_plot_peaks.Rd |only man/ch_sh_get_amax.Rd |only 16 files changed, 113 insertions(+), 132 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] and
their contribution to R's order),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.5.0 dated 2022-10-21 and 0.5.1 dated 2022-11-16
DESCRIPTION | 6 ++--- MD5 | 16 +++++++-------- NEWS.md | 5 ++++ R/type2.R | 4 +-- build/vignette.rds |binary inst/doc/stability.html | 6 ++--- src/version.c | 2 - tests/testthat/test-slice-assign.R | 38 ++++++++++++++++++++++++++----------- tests/testthat/test-type-dplyr.R | 2 - 9 files changed, 50 insertions(+), 29 deletions(-)
Title: Implementation of the Hydrological Model TOPMODEL in R
Description: Set of hydrological functions including an R
implementation of the hydrological model TOPMODEL, which is
based on the 1995 FORTRAN version by Keith Beven. From version
0.7.0, the package is put into maintenance mode.
Author: Wouter Buytaert
Maintainer: Wouter Buytaert <w.buytaert@imperial.ac.uk>
Diff between topmodel versions 0.7.4 dated 2022-05-05 and 0.7.5 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/c_topidx.c | 10 +++++----- src/topmodel.h | 23 +++++++++++------------ 4 files changed, 23 insertions(+), 24 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] ,
Layik Hama [aut] ,
Nathanael Sheehan [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.9.3 dated 2021-11-02 and 0.9.5 dated 2022-11-16
DESCRIPTION | 8 MD5 | 64 NEWS.md | 8 R/desire_lines.R | 2 R/get_pct.R | 20 R/uptake.R | 2 README.md | 19 build/vignette.rds |binary inst/doc/cycling-potential-uk.html | 427 ++ inst/doc/getting.R | 49 inst/doc/getting.Rmd | 62 inst/doc/getting.html | 469 ++ inst/doc/km-cycled.html | 442 ++ inst/doc/pct-international.html | 4471 +++++++++++++++++++++++++++ inst/doc/pct.Rmd | 2 inst/doc/pct.html | 4656 ++++++++++++++++++++++++++++ inst/doc/pct_training.Rmd | 17 inst/doc/pct_training.html | 339 +- inst/doc/uk-cities.html | 5630 ++++++++++++++++++++++++++++++++++- man/figures/README-rnetgove-1.png |binary man/figures/README-routes_fast-1.png |binary man/get_od.Rd | 2 man/get_pct.Rd | 2 man/get_pct_centroids.Rd | 2 man/get_pct_lines.Rd | 4 man/get_pct_rnet.Rd | 6 man/get_pct_routes_fast.Rd | 2 man/get_pct_routes_quiet.Rd | 2 man/get_pct_zones.Rd | 2 man/uptake_pct_govtarget.Rd | 8 vignettes/getting.Rmd | 62 vignettes/pct.Rmd | 2 vignettes/pct_training.Rmd | 17 33 files changed, 16003 insertions(+), 795 deletions(-)
Title: Parallel Digital Soil Mapping using Machine Learning
Description: Parallel computing, multi-core CPU is used to efficiently compute
and process multi-dimensional soil data.This package includes the
parallelized 'Quantile Regression Forests' algorithm for Digital Soil Mapping
and is mainly dependent on the package 'quantregForest' and 'snowfall'.
Detailed references to the R package and the web site are described in the
methods, as detailed in the method documentation.
Author: Xiaodong Song [aut],
Peicong Tang [aut, cre],
Wentao Zhu [aut],
Gaoqiang Ge [aut],
Jun Zhu [aut],
Ganlin Zhang [aut]
Maintainer: Peicong Tang <peicongtang0409@163.com>
Diff between ParallelDSM versions 0.3.6 dated 2022-11-02 and 0.3.7 dated 2022-11-16
DESCRIPTION | 6 MD5 | 21 +-- NAMESPACE | 9 - R/InsepectionVariable.R | 291 ++++++++++++++++++++++++++------------------- R/MergingTiles.R | 24 ++- R/ParallelInit.R | 200 +++++++++++++++--------------- man/Insepect_MLR.Rd |only man/Insepect_QRF.Rd |only man/Insepect_RF.Rd |only man/InsepectionVariable.Rd | 2 man/ParallelComputing.Rd | 8 - man/ParallelInit.Rd | 2 man/ParallelInit_Test.Rd | 2 13 files changed, 316 insertions(+), 249 deletions(-)
Title: Phylogenetic Comparative Methods with Uncertainty Estimates
Description: A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
Author: Hao Chi Kiang [cre, aut]
Maintainer: Hao Chi Kiang <hello@hckiang.com>
Diff between glinvci versions 1.1.18 dated 2022-03-16 and 1.1.20 dated 2022-11-16
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ R/glinvci.R | 22 ++++++++++++++++------ R/missingness.R | 4 ++-- R/ou.R | 12 ++++++------ R/utils.R | 8 ++++++-- build/vignette.rds |binary configure.ac | 2 +- inst/doc/Getting_Started.pdf |binary man/glinv.Rd | 2 ++ src/Makevars.in | 2 +- src/phytr.c | 34 +++++++++++++++++++--------------- 13 files changed, 71 insertions(+), 49 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2021) <arXiv:2104.02705>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 0.2 dated 2022-09-21 and 0.3 dated 2022-11-16
deepregression-0.2/deepregression/inst/python/misc |only deepregression-0.3/deepregression/DESCRIPTION | 6 deepregression-0.3/deepregression/MD5 | 40 +++--- deepregression-0.3/deepregression/NAMESPACE | 2 deepregression-0.3/deepregression/R/controls.R | 12 + deepregression-0.3/deepregression/R/deepregression.R | 5 deepregression-0.3/deepregression/R/generator.R | 13 ++ deepregression-0.3/deepregression/R/helperfuns.R | 7 + deepregression-0.3/deepregression/R/methods.R | 8 - deepregression-0.3/deepregression/R/orthogonalization.R | 63 +++++++++- deepregression-0.3/deepregression/R/psplinelayer.R | 3 deepregression-0.3/deepregression/R/tf_helpers.R | 4 deepregression-0.3/deepregression/R/zzz.R | 50 +++++++ deepregression-0.3/deepregression/inst/python/layers/__pycache__/lasso.cpython-310.pyc |binary deepregression-0.3/deepregression/inst/python/layers/lasso.py | 2 deepregression-0.3/deepregression/inst/python/tffuns |only deepregression-0.3/deepregression/man/get_names_pfc.Rd |only deepregression-0.3/deepregression/man/orthog_control.Rd | 6 deepregression-0.3/deepregression/man/orthog_post_fitting.Rd |only deepregression-0.3/deepregression/man/predict_gen.Rd |only deepregression-0.3/deepregression/man/update_miniconda_deepregression.Rd |only 21 files changed, 181 insertions(+), 40 deletions(-)
More information about deepregression at CRAN
Permanent link
Title: Modeling Count Data with Peer Effects
Description: Likelihood-based estimation and data generation from a class of models used to estimate peer effects on count data by controlling for the network endogeneity. This class includes count data models with social interactions (Houndetoungan 2022; <doi:10.2139/ssrn.3721250>), spatial tobit models (Xu and Lee 2015; <doi:10.1016/j.jeconom.2015.05.004>), and spatial linear-in-means models (Lee 2004; <doi:10.1111/j.1468-0262.2004.00558.x>).
Author: Elysee Aristide Houndetoungan [cre, aut]
Maintainer: Elysee Aristide Houndetoungan <ariel92and@gmail.com>
Diff between CDatanet versions 2.0.2 dated 2022-11-14 and 2.0.3 dated 2022-11-16
DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NEWS.md | 2 +- R/CDatanet.R | 4 ++-- R/SARestim.R | 2 +- R/SARsim.R | 2 +- R/homophily.fixed.R | 2 +- build/partial.rdb |binary man/CDatanet-package.Rd | 6 +++--- man/homophily.FE.Rd | 2 +- man/sar.Rd | 2 +- man/simsar.Rd | 2 +- 12 files changed, 30 insertions(+), 30 deletions(-)
Title: Taxa Waterbeheer Nederland voor R
Description: The TWN-list (Taxa Waterbeheer Nederland) is the Dutch standard for naming
taxons in Dutch Watermanagement. This package makes it easier to use the
TWN-list for ecological analyses. It consists of two parts. First it makes the
TWN-list itself available in R. Second, it has a few functions that make it
easy to perform some basic and often recurring tasks for checking and consulting
taxonomic data from the TWN-list.
Author: Johan van Tent [aut, cre]
Maintainer: Johan van Tent <tentvanjohan@hotmail.com>
Diff between twn versions 0.2.2 dated 2022-04-28 and 0.2.3 dated 2022-11-16
DESCRIPTION | 8 - MD5 | 21 +-- NEWS.md | 4 R/sysdata.rda |binary README.md | 24 ++- build/vignette.rds |binary data/twn_lijst.rda |binary data/twn_literatuur.rda |binary data/twn_statuscodes.rda |binary data/twn_taxonlevels.rda |binary inst/doc/krw_beoordeling.html | 265 +++++++++++++++++++++--------------------- inst/extdata/twn_hex.png |only 12 files changed, 169 insertions(+), 153 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Gruen <dominic.gruen@gmail.com>
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.7 dated 2022-11-01 and 0.2.8 dated 2022-11-16
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 + R/VarID_functions.R | 13 +++++++------ inst/doc/RaceID.html | 4 ++-- man/pruneKnn.Rd | 2 +- 6 files changed, 22 insertions(+), 20 deletions(-)
Title: Pie, Donut and Rose Pie Plots
Description: Create pie, donut and rose pie plot with 'ggplot2'.
Author: Yabing Song [aut, cre]
Maintainer: Yabing Song <songyb0519@gmail.com>
Diff between ggpie versions 0.2.4 dated 2022-10-21 and 0.2.5 dated 2022-11-16
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/ggpie.html | 28 ++++++++++++++-------------- 3 files changed, 21 insertions(+), 21 deletions(-)
Title: Analysis of Graph-Structured Data with a Focus on
Protein-Protein Interaction Networks
Description: Provides a general framework for the identification of nodes that are functionally related to a set of seeds in graph structured data. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Nibbe et al. (2010) <doi:10.1371/journal.pcbi.1000639>.
Author: Davis Weaver [aut, cre]
Maintainer: Davis Weaver <davis.weaver@case.edu>
Diff between crosstalkr versions 0.8.0 dated 2022-09-16 and 0.9.0 dated 2022-11-16
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/RandomWalkRepeats.R | 6 +++--- R/compute_crosstalk.R | 16 +++++++++++----- R/create_null.R | 4 ++-- R/ppi_ingest.R | 28 +++++++++++++++------------- R/utils.R | 2 +- README.md | 14 +++++++++++--- man/bootstrap_null.Rd | 4 ++-- man/compute_crosstalk.Rd | 12 +++++++++--- man/ppi_intersection.Rd | 4 +++- man/ppi_union.Rd | 4 +++- man/sparseRWR.Rd | 6 +++--- 13 files changed, 78 insertions(+), 52 deletions(-)