Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] ,
Barret Schloerke [aut] ,
Carson Sievert [aut, cre] ,
Christophe Dervieux [ctb] ,
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] ,
Greter Marcel [ctb, cph] ,
Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.4.5 dated 2023-01-23 and 0.4.6 dated 2023-05-03
sass-0.4.5/sass/src/libsass/docs/allocator.md |only sass-0.4.5/sass/src/libsass/docs/developing.md |only sass-0.4.6/sass/DESCRIPTION | 6 sass-0.4.6/sass/MD5 | 10 sass-0.4.6/sass/NEWS.md | 4 sass-0.4.6/sass/inst/doc/sass.html | 344 +++++++++--------- sass-0.4.6/sass/src/libsass/src/memory/shared_ptr.hpp | 8 7 files changed, 191 insertions(+), 181 deletions(-)
Title: Scatterplots with More Points
Description: C-based conversion of large scatterplot data to rasters plus other
operations such as data blurring or data alpha blending. Speeds up
plotting of data with millions of points.
Author: Tereza Kulichova [aut],
Mirek Kratochvil [aut, cre]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between scattermore versions 0.8 dated 2022-02-14 and 1.0 dated 2023-05-03
DESCRIPTION | 23 ++- MD5 | 91 ++++++++++++- NAMESPACE | 58 +++++--- R/apply_kernel_histogram.R |only R/apply_kernel_rgbwt.R |only R/blend_rgba_float.R |only R/globals.R |only R/histogram_to_rgbwt.R |only R/merge_rgbwt.R |only R/rgba_float_to_rgba_int.R |only R/rgba_int_to_raster.R |only R/rgbwt_to_rgba_float.R |only R/rgbwt_to_rgba_int.R |only R/scatter_lines_histogram.R |only R/scatter_lines_rgbwt.R |only R/scatter_points_histogram.R |only R/scatter_points_rgbwt.R |only R/scattermore.R | 250 ++++++++++++++++++-------------------- build |only inst |only man/GeomScattermore.Rd |only man/GeomScattermost.Rd |only man/apply_kernel_histogram.Rd |only man/apply_kernel_rgbwt.Rd |only man/blend_rgba_float.Rd |only man/geom_scattermore.Rd | 13 + man/geom_scattermost.Rd | 15 +- man/histogram_to_rgbwt.Rd |only man/merge_rgbwt.Rd |only man/rgba_float_to_rgba_int.Rd |only man/rgba_int_to_raster.Rd |only man/rgbwt_to_rgba_float.Rd |only man/rgbwt_to_rgba_int.Rd |only man/scatter_lines_histogram.Rd |only man/scatter_lines_rgbwt.Rd |only man/scatter_points_histogram.Rd |only man/scatter_points_rgbwt.Rd |only man/scattermore.Rd | 2 man/scattermoreplot.Rd | 11 - src/histogram_to_rgbwt.cpp |only src/kernel_histogram.cpp |only src/kernel_rgbwt.cpp |only src/kernels.h |only src/macros.h |only src/scatter_histogram.cpp |only src/scatter_indexed_rgbwt.cpp |only src/scatter_lines_histogram.cpp |only src/scatter_lines_impl.h |only src/scatter_lines_rgbwt.cpp |only src/scatter_multicolor_rgbwt.cpp |only src/scatter_singlecolor_rgbwt.cpp |only src/scattermore.c | 154 +++-------------------- src/scatters.h |only src/scatters_lines.h |only src/thread_blocks.h |only tests |only vignettes |only 57 files changed, 296 insertions(+), 321 deletions(-)
Title: An Implementation of Ordinal Pattern Analysis
Description: Quantifies hypothesis to data fit for repeated measures
and longitudinal data, as described by Thorngate (1987)
<doi:10.1016/S0166-4115(08)60083-7> and Grice et al., (2015)
<doi:10.1177/2158244015604192>. Hypothesis and data are encoded as
pairwise relative orderings which are then compared to determine the
percentage of orderings in the data that are matched by the hypothesis.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>
Diff between opa versions 0.7.4 dated 2023-02-17 and 0.8.1 dated 2023-05-03
opa-0.7.4/opa/man/figures/README-unnamed-chunk-4-1.png |only opa-0.8.1/opa/DESCRIPTION | 8 opa-0.8.1/opa/MD5 | 31 - opa-0.8.1/opa/NAMESPACE | 1 opa-0.8.1/opa/R/condition_comparison.R | 45 - opa-0.8.1/opa/R/fitopa.R | 7 opa-0.8.1/opa/R/utility.R | 47 + opa-0.8.1/opa/README.md | 92 +-- opa-0.8.1/opa/inst/tinytest/test_opa.R | 106 ++-- opa-0.8.1/opa/man/compare_conditions.Rd | 18 opa-0.8.1/opa/man/figures/README-plot_opamod1-1.png |binary opa-0.8.1/opa/man/figures/README-plot_opamod2-1.png |binary opa-0.8.1/opa/man/figures/README-threshold_plots-2.png |binary opa-0.8.1/opa/man/opa.Rd | 4 opa-0.8.1/opa/man/print.opafit.Rd |only opa-0.8.1/opa/man/print.pairwiseopafit.Rd |only opa-0.8.1/opa/src/RcppExports.cpp | 39 - opa-0.8.1/opa/src/cpp_functions.cpp | 402 ++++++++--------- 18 files changed, 423 insertions(+), 377 deletions(-)
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke
and Pearl and Extensions
Description: Implementation of the nonparametric bounds for the average
causal effect under an instrumental variable model by Balke and Pearl
(Bounds on Treatment Effects from Studies with Imperfect Compliance,
JASA, 1997, 92, 439, 1171-1176). The package can calculate bounds for
a binary outcome, a binary treatment/phenotype, and an instrument with
either 2 or 3 categories. The package implements bounds for situations
where these 3 variables are measured in the same dataset (trivariate
data) or where the outcome and instrument are measured in one study
and the treatment/phenotype and instrument are measured in another
study (bivariate data).
Author: Tom Palmer [aut, cre] ,
Roland Ramsahai [aut] ,
Vanessa Didelez [aut] ,
Nuala Sheehan [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between bpbounds versions 0.1.4 dated 2020-01-21 and 0.1.5 dated 2023-05-03
DESCRIPTION | 60 - MD5 | 54 - NAMESPACE | 13 NEWS.md | 50 - R/bpbounds-package.r | 36 - R/bpbounds.R | 676 +++++++++---------- R/bpbounds_biv_x2y2z2.R | 174 ++--- R/bpbounds_biv_x2y2z3.R | 200 ++--- R/bpbounds_calc_biv_z2.R | 240 +++---- R/bpbounds_calc_biv_z3.R | 388 +++++------ R/bpbounds_calc_tri_z2.R | 188 ++--- R/bpbounds_calc_tri_z3.R | 378 +++++------ R/bpbounds_tri_x2y2z2.R | 156 ++-- R/bpbounds_tri_x2y2z3.R | 764 +++++++++++----------- R/runExample.R | 39 - README.md | 86 +- build/vignette.rds |binary inst/CITATION | 34 inst/doc/bpbounds.R | 218 +++--- inst/doc/bpbounds.Rmd | 384 +++++------ inst/doc/bpbounds.html | 1369 +++++++++++++++++++++------------------- inst/shiny-examples/myapp/app.R | 486 +++++++------- man/bpbounds.Rd | 6 man/runExample.Rd | 6 tests/testthat.R | 8 tests/testthat/test-bpbounds.R | 653 +++++++++---------- vignettes/bibliography.bib | 142 ++-- vignettes/bpbounds.Rmd | 384 +++++------ 28 files changed, 3696 insertions(+), 3496 deletions(-)
More information about switchSelection at CRAN
Permanent link
More information about ROI.plugin.clarabel at CRAN
Permanent link
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee
(2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert
and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>. For
models with up to eight features, the results are exact regarding the
selected background data. Otherwise, an almost exact hybrid algorithm
involving iterative sampling is used. The package plays well together
with meta-learning packages like 'tidymodels', 'caret' or 'mlr3'.
Visualizations can be done using the R package 'shapviz'.
Author: Michael Mayer [aut, cre],
David Watson [aut],
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.3.5 dated 2023-03-31 and 0.3.6 dated 2023-05-03
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 6 + R/kernelshap.R | 222 +++++++++++++++++++++++----------------------- R/methods.R | 19 ++- README.md | 2 man/is.kernelshap.Rd | 6 - man/kernelshap.Rd | 151 ++++++++++++++++--------------- man/print.kernelshap.Rd | 2 man/summary.kernelshap.Rd | 5 - 10 files changed, 233 insertions(+), 204 deletions(-)
More information about CooccurrenceAffinity at CRAN
Permanent link
More information about BayesRepDesign at CRAN
Permanent link
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Cleve Moler [ctb] ,
Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between KernSmooth versions 2.23-20 dated 2021-05-03 and 2.23-21 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- PORTING | 1 + R/all.R | 40 ++++++++++++++++++++-------------------- 4 files changed, 28 insertions(+), 27 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.9-5 dated 2022-02-09 and 0.9-6 dated 2023-05-03
DESCRIPTION | 10 - MD5 | 24 ++-- build/vignette.rds |binary inst/NEWS.Rd | 6 + inst/doc/introduction.html | 263 ++++++++++++++++++++++++++++++--------------- src/cairodev.c | 2 src/cairodev.h | 2 src/outline.c | 2 src/outline.h | 2 src/register_routines.c | 2 src/showtext.c | 2 src/util.c | 4 src/util.h | 4 13 files changed, 212 insertions(+), 111 deletions(-)
Title: Variance Components Testing for Linear and Nonlinear Mixed
Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that,
in a (non)linear mixed effects model, the variances of a subset of the random
effects are equal to zero. There is no restriction on the subset of variances
that can be tested: for example, it is possible to test that all the variances
are equal to zero. Note that the implemented test is asymptotic.
This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'.
Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] ,
Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>
Diff between varTestnlme versions 1.3.1 dated 2022-03-08 and 1.3.2 dated 2023-05-03
DESCRIPTION | 12 +- MD5 | 16 +-- NAMESPACE | 4 NEWS.md | 4 R/generics.R | 2 R/lme_utilities.R | 84 ++++++++++------- build/vignette.rds |binary inst/doc/varTestnlme.html | 217 +++++++++++++++++++++++++++++----------------- man/objFunction.Rd | 16 +-- 9 files changed, 220 insertions(+), 135 deletions(-)
Title: One Sample Mendelian Randomization and Instrumental Variable
Analyses
Description: Useful functions for one-sample (individual level data)
Mendelian randomization and instrumental variable analyses. The
package includes implementations of; the Sanderson and Windmeijer
(2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic,
the multiplicative structural mean model Hernán and Robins (2006)
<doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor
substitution and two-stage residual inclusion estimators explained by
Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] ,
Wes Spiller [aut] ,
Eleanor Sanderson [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between OneSampleMR versions 0.1.2 dated 2022-05-11 and 0.1.3 dated 2023-05-03
DESCRIPTION | 8 MD5 | 40 +- NAMESPACE | 21 - NEWS.md | 5 R/asmm.R | 2 R/fsw.R | 38 +- R/msmm.R | 41 +- R/tsps.R | 61 +--- R/tsri.R | 61 +--- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/compare-smm-fits.Rmd | 2 inst/doc/compare-smm-fits.html | 512 +++++++++++++++++------------------ inst/doc/f-statistic-comparison.html | 314 ++++++++++----------- man/fsw.Rd | 2 man/msmm.Rd | 2 man/tsps.Rd | 13 man/tsri.Rd | 13 tests/testthat/test-msmm.R | 4 vignettes/compare-smm-fits.Rmd | 2 21 files changed, 557 insertions(+), 585 deletions(-)
Title: Miscellaneous Tools and Utilities
Description: Miscellaneous small tools and utilities.
Many of them facilitate the work with matrices,
e.g. inserting rows or columns, creating symmetric matrices,
or checking for semidefiniteness.
Other tools facilitate the work with regression models,
e.g. extracting the standard errors,
obtaining the number of (estimated) parameters,
or calculating R-squared values.
Author: Arne Henningsen, Ott Toomet
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between miscTools versions 0.6-26 dated 2019-12-08 and 0.6-28 dated 2023-05-03
DESCRIPTION | 11 ++++++----- MD5 | 10 ++++++---- NAMESPACE | 4 ++++ NEWS | 9 +++++++-- R/histDens.R |only man/histDens.Rd |only man/nObs.Rd | 2 +- 7 files changed, 24 insertions(+), 12 deletions(-)
Title: Manipulate and Analyze Growth Curve Data
Description: Easy import, manipulation, and model-free analysis of
microbial growth curve data, as commonly output by plate readers.
Tools for reshaping common plate reader outputs into 'tidy' formats and
merging them with design information, making data easy to work with using
'gcplyr' and other packages. Also streamlines common growth curve
processing steps, like smoothing and calculating derivatives, and
facilitates model-free characterization and analysis of growth data.
See methods at <https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Diff between gcplyr versions 1.5.1 dated 2023-04-14 and 1.5.2 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 4 ++++ R/utility_functions.R | 7 +++---- README.md | 6 +++--- inst/CITATION | 14 ++++++++------ inst/doc/analyze.pdf |binary inst/doc/conclusion.pdf |binary inst/doc/gcplyr.pdf |binary inst/doc/import_transform.Rmd | 1 + inst/doc/import_transform.pdf |binary inst/doc/incorporate_designs.pdf |binary inst/doc/noise.pdf |binary inst/doc/preprocess_plot.pdf |binary inst/doc/process.pdf |binary vignettes/analyze.html | 6 +++--- vignettes/conclusion.html | 4 ++-- vignettes/import_transform.Rmd | 1 + vignettes/import_transform.html | 25 ++++++++++++++----------- 19 files changed, 61 insertions(+), 51 deletions(-)
Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.5.2 dated 2023-04-13 and 3.5.3 dated 2023-05-03
DESCRIPTION | 10 MD5 | 52 +- R/DBgetPlots.R | 17 R/DBgetXY.R | 33 - R/check.popdataCHNG.R | 300 +++++++----- R/check.popdataPLT.R | 16 R/check.popdataVOL.R | 29 - R/datSumCond.R | 90 ++- R/datSumTree.R | 8 R/modGBarea.R | 2 R/modGBchng.R | 9 R/modGBpop.R | 74 ++- R/spGetPlots.R | 21 R/spGetSAdoms.R | 15 R/spZonalRast.R | 2 build/vignette.rds |binary inst/doc/FIESTA_manual_mod_est.html | 14 inst/doc/FIESTA_manual_mod_pop.html | 14 inst/doc/FIESTA_tutorial_DB.html | 14 inst/doc/FIESTA_tutorial_GB.html | 867 ++++++++++++++++-------------------- inst/doc/FIESTA_tutorial_MA.html | 669 +++++++++++++-------------- inst/doc/FIESTA_tutorial_PB.html | 123 ++--- inst/doc/FIESTA_tutorial_SA.html | 203 ++++---- inst/doc/FIESTA_tutorial_dat.html | 127 ++--- inst/doc/FIESTA_tutorial_sp.html | 111 ++-- man/modGBpop.Rd | 9 man/spZonalRast.Rd | 2 27 files changed, 1446 insertions(+), 1385 deletions(-)
Title: Development Utilities for R Packages
Description: Provides some low-level utilities to use for package
development. It currently provides managers for multiple package specific
options and registries, vignette, unit test and bibtex related utilities.
It serves as a base package for packages like 'NMF', 'RcppOctave', 'doRNG', and
as an incubator package for other general purposes utilities, that will
eventually be packaged separately.
It is still under heavy development and changes in the interface(s) are
more than likely to happen.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between pkgmaker versions 0.32.8 dated 2023-02-14 and 0.32.10 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/devutils.R | 39 +-------------------------------------- R/graphics.R | 2 +- R/knitr.R | 2 +- man/knit_ex.Rd | 2 +- 6 files changed, 13 insertions(+), 50 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between nnet versions 7.3-18 dated 2022-09-28 and 7.3-19 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/multinom.R | 4 ++-- R/nnet.R | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated. A first approach was described in Rousset et al. (2017 <doi:10.1111/1755-0998.12627>) but the package implements more advanced methods.
Author: Francois Rousset [aut, cre, cph]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between Infusion versions 2.0.0 dated 2022-09-28 and 2.1.0 dated 2023-05-03
Infusion-2.0.0/Infusion/R/smoothopt.R |only Infusion-2.1.0/Infusion/DESCRIPTION | 15 Infusion-2.1.0/Infusion/MD5 | 75 - Infusion-2.1.0/Infusion/NAMESPACE | 9 Infusion-2.1.0/Infusion/R/MSL.R | 57 - Infusion-2.1.0/Infusion/R/Rmixmod.R | 44 Infusion-2.1.0/Infusion/R/SLik.R | 8 Infusion-2.1.0/Infusion/R/SLikSQuant.R | 66 + Infusion-2.1.0/Infusion/R/add_simulation.R | 555 ++++++------ Infusion-2.1.0/Infusion/R/bootLRT.R | 14 Infusion-2.1.0/Infusion/R/confintLR.SLik.R | 30 Infusion-2.1.0/Infusion/R/coresWrapper.R | 1 Infusion-2.1.0/Infusion/R/gllim.R |only Infusion-2.1.0/Infusion/R/goodness.R | 10 Infusion-2.1.0/Infusion/R/infer_logLs.R | 9 Infusion-2.1.0/Infusion/R/infer_surface.R | 4 Infusion-2.1.0/Infusion/R/jointDens.R | 234 +++-- Infusion-2.1.0/Infusion/R/mclust.R | 4 Infusion-2.1.0/Infusion/R/plotProfiles.R | 170 ++- Infusion-2.1.0/Infusion/R/profile.R | 7 Infusion-2.1.0/Infusion/R/project.R | 57 - Infusion-2.1.0/Infusion/R/quantiles.R | 4 Infusion-2.1.0/Infusion/R/write_workflow.R |only Infusion-2.1.0/Infusion/inst/CITATION | 28 Infusion-2.1.0/Infusion/inst/NEWS.Rd | 33 Infusion-2.1.0/Infusion/man/add.reftable.Rd |only Infusion-2.1.0/Infusion/man/add.simulation.Rd | 54 - Infusion-2.1.0/Infusion/man/example_raw.Rd | 2 Infusion-2.1.0/Infusion/man/example_raw_proj.Rd | 2 Infusion-2.1.0/Infusion/man/example_reftable.Rd | 8 Infusion-2.1.0/Infusion/man/get_nbCluster_range.Rd | 5 Infusion-2.1.0/Infusion/man/infer_jointDens.Rd | 3 Infusion-2.1.0/Infusion/man/init_grid.Rd | 22 Infusion-2.1.0/Infusion/man/plot1Dprof.Rd | 65 + Infusion-2.1.0/Infusion/man/predict.SLik_j.Rd | 2 Infusion-2.1.0/Infusion/man/project.Rd | 15 Infusion-2.1.0/Infusion/man/refine.SLik.Rd | 34 Infusion-2.1.0/Infusion/man/write_workflow.Rd |only Infusion-2.1.0/Infusion/tests/testthat/test-3par.R | 2 Infusion-2.1.0/Infusion/tests/testthat/test-reftable.R | 10 Infusion-2.1.0/Infusion/tests/testthat/test-reftable_3par.R | 8 41 files changed, 1025 insertions(+), 641 deletions(-)
Title: Multi-Trait Dissimilarity with more Uniform Contributions
Description: R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
Author: Francesco de Bello [aut],
Zoltan Botta-Dukat [aut],
Jan Leps [aut],
Pavel Fibich [aut, cre]
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between gawdis versions 0.1.4 dated 2023-04-13 and 0.1.5 dated 2023-05-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/gawdis.R | 4 ++-- inst/doc/gawdis.html | 14 +++++++------- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-21 dated 2023-01-23 and 7.3-22 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SOM.R | 4 ++-- man/SOM.Rd | 4 ++-- man/batchSOM.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Basic Sequence Processing Tool for Biological Data
Description: Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
Author: Ambu Vijayan [aut, cre] ,
J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>
Diff between baseq versions 0.1.2 dated 2023-04-28 and 0.1.4 dated 2023-05-03
DESCRIPTION | 7 +-- MD5 | 52 +++++++++++----------- NEWS.md | 4 + R/clean_DNA.R | 10 ++-- R/clean_RNA.R | 10 ++-- R/fastq_to_fasta.R | 10 ++-- R/gc_content_file.R | 81 +++++++++++++++++------------------ R/read_fasta_df.R | 100 ++++++++++++++++++++++--------------------- R/read_fasta_list.R | 97 +++++++++++++++++++++--------------------- R/read_fastq_df.R | 105 +++++++++++++++++++++++----------------------- R/read_fastq_list.R | 94 ++++++++++++++++++++--------------------- R/write_df_to_fasta.R | 12 ++--- R/write_df_to_fastq.R | 12 ++--- R/write_dna_to_rna.R | 10 ++-- R/write_rna_to_dna.R | 10 ++-- man/clean_DNA_file.Rd | 10 ++-- man/clean_RNA_file.Rd | 10 ++-- man/fastq_to_fasta.Rd | 10 ++-- man/gc_content_file.Rd | 5 -- man/read.fasta_to_df.Rd | 4 + man/read.fasta_to_list.Rd | 7 +-- man/read.fastq_to_df.Rd | 7 ++- man/read.fastq_to_list.Rd | 2 man/write.df_to_fasta.Rd | 12 ++--- man/write.df_to_fastq.Rd | 12 ++--- man/write.dna_to_rna.Rd | 10 ++-- man/write.rna_to_dna.Rd | 10 ++-- 27 files changed, 362 insertions(+), 351 deletions(-)
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.4.0 dated 2023-02-27 and 0.4.1 dated 2023-05-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/DataBackendRaster.R | 2 +- R/zzz.R | 5 +++++ build/vignette.rds |binary tests/testthat/test_DataBackendRaster.R | 4 ++-- 7 files changed, 22 insertions(+), 13 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-16 dated 2021-06-11 and 0.9-18 dated 2023-05-03
DESCRIPTION | 6 +- MD5 | 128 ++++++++++++++++++++++----------------------- NAMESPACE | 3 + R/asr-bisse.R | 4 - R/asr-geosse.R | 2 R/asr-mkn.R | 4 - R/asr-musse.R | 2 R/asr-t.R | 8 +- R/asr.R | 10 +-- R/clade-tree.R | 10 +-- R/continuous.R | 8 +- R/diversitree-branches.R | 22 +++---- R/drop.tip.fixed.R | 2 R/history.R | 4 - R/mcmc-norm.R | 4 - R/mle-subplexR.R | 6 +- R/model-bd-nee.R | 5 + R/model-bd-split.R | 6 +- R/model-bd-t.R | 4 - R/model-bd.R | 10 +-- R/model-bisse-split.R | 8 +- R/model-bisse-t.R | 4 - R/model-bisse-td.R | 4 - R/model-bisse.R | 4 - R/model-bisseness.R | 6 +- R/model-bm-contrasts.R | 6 +- R/model-bm-pruning.R | 6 +- R/model-bm-vcv.R | 2 R/model-bm.R | 8 +- R/model-classe.R | 6 +- R/model-eb.R | 16 ++--- R/model-geosse-split.R | 8 +- R/model-geosse-t.R | 4 - R/model-geosse.R | 6 +- R/model-lambda.R | 18 +++--- R/model-mkn-expokit.R | 4 - R/model-mkn-meristic.R | 4 - R/model-mkn-pij.R | 2 R/model-mkn.R | 14 ++-- R/model-musse-multitrait.R | 4 - R/model-musse-split.R | 4 - R/model-musse-t.R | 4 - R/model-musse-td.R | 4 - R/model-musse.R | 6 +- R/model-ou-pruning.R | 6 +- R/model-ou.R | 8 +- R/model-pgls.R | 38 ++++++------- R/model-quasse-split.R | 10 +-- R/model-quasse.R | 12 ++-- R/simulation.R | 2 R/split.R | 10 +-- R/t.R | 4 - R/td.R | 6 +- R/util-tree.R | 2 R/util.R | 2 README.md | 4 + build/partial.rdb |binary configure | 3 + configure.ac | 3 + inst/CITATION | 17 +++-- inst/tests/test-branches.R | 4 - src/rfftw.c | 4 - src/rfftw.h | 2 src/util.c | 2 src/zzz.h | 4 - 65 files changed, 278 insertions(+), 265 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.4.1 dated 2022-04-18 and 1.4.2-1 dated 2023-05-03
DESCRIPTION | 12 +++---- MD5 | 48 ++++++++++++++-------------- NAMESPACE | 4 +- NEWS.md | 79 ++++++++++++++++++++++++++++++++++++++++++----- R/NLR.R | 2 - R/ORD.R | 8 +--- R/ddfMLR.R | 18 +++++----- R/difNLR-package.R | 6 +-- R/difNLR.R | 34 ++++++++++---------- R/difORD.R | 83 +++++++++++++++++++++++++------------------------- R/estimNLR.R | 37 +++++++++++++--------- R/formulaNLR.R | 4 +- R/private.R | 10 +++--- R/startNLR.R | 14 +++++++- README.md | 7 ++-- build/partial.rdb |binary inst/CITATION | 21 +++++------- man/ORD.Rd | 8 +--- man/coef.difORD.Rd | 6 +-- man/difNLR-package.Rd | 6 +-- man/difORD.Rd | 18 ++++++---- man/estimNLR.Rd | 35 ++++++++++++++++----- man/logLik.difORD.Rd | 6 +-- man/plot.difORD.Rd | 14 ++++---- man/predict.difORD.Rd | 25 +++++++-------- 25 files changed, 301 insertions(+), 204 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 4.1-1 dated 2021-07-19 and 4.2-1 dated 2023-05-03
DESCRIPTION | 6 - INDEX | 3 MD5 | 155 +++++++++++++++----------- NAMESPACE | 58 +++++++++- R/DBI.R | 4 R/anova.svyglm.R | 184 ++++++++++++++++++++++++++++++++ R/chisqsum.R | 2 R/confint.R | 24 +++- R/grake.R | 63 +++++++--- R/loglin.R | 16 -- R/logrank.R | 6 - R/margins.R | 2 R/multistage.R | 36 +++++- R/newsvyquantile.R | 23 ++-- R/olr.R | 100 ++++++++++++++--- R/pps.R | 14 +- R/qrule.R | 8 + R/recalibrate.R |only R/regtest.R | 29 +++-- R/score.R |only R/survey.R | 166 ++++++++++++++++------------ R/surveyby.R | 106 ++++++++++-------- R/surveychisq.R | 53 ++++++++- R/surveyrep.R | 8 - R/svyivreg.R | 5 R/svykm.R | 12 +- R/svymi.R | 4 R/svynls.R | 81 ++++++++++++-- R/svyranktest.R | 10 + R/svyttest.R | 2 R/sysdata.rda |binary R/twophase.R | 2 R/xdesign.R |only THANKS | 11 + build/vignette.rds |binary data/api.rda |binary data/crowd.rda |binary data/election.rda |binary data/fpc.rda |binary data/hospital.rda |binary data/mu284.rda |binary data/myco.rda |only data/nhanes.rda |binary data/salamander.rda |only data/scd.rda |binary data/yrbs.rda |binary inst/CITATION | 12 +- inst/NEWS | 105 ++++++++++++++++++ inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/pps.pdf |binary inst/doc/precalibrated.R |only inst/doc/precalibrated.Rnw |only inst/doc/precalibrated.pdf |only inst/doc/qrule.pdf |binary inst/doc/survey.pdf |binary man/anova.svyglm.Rd | 19 ++- man/api.Rd | 2 man/as.svrepdesign.Rd | 4 man/estweights.Rd | 2 man/fpc.Rd | 2 man/myco.Rd |only man/salamander.Rd |only man/surveysummary.Rd | 10 + man/svyby.Rd | 24 ++-- man/svychisq.Rd | 22 +++ man/svycontrast.Rd | 4 man/svycoxph.Rd | 2 man/svydesign.Rd | 22 ++- man/svynls.Rd | 7 + man/svyolr.Rd | 19 ++- man/svyranktest.Rd | 5 man/svyscoretest.Rd |only man/trimWeights.Rd | 6 - man/xdesign.Rd |only man/yrbs.Rd | 2 tests/README | 8 + tests/anova-svycoxph.R |only tests/coxph-termtest.R | 14 ++ tests/mtcars-var.R |only tests/regTermTest-missing.R |only tests/rss_scores.R |only tests/svyby-strings.R |only tests/svyby_bug.R |only tests/svycontrast.R |only tests/svyivreg-var.R |only tests/svyolr-rake-subset.R |only tests/svyolr.R |only tests/testoutput/quantile-new.R |only tests/testoutput/quantile-new.Rout.save |only vignettes/precalibrated.Rnw |only 91 files changed, 1126 insertions(+), 358 deletions(-)
Title: Retrieving Oral Opioid Information
Description: Provides details such as Morphine Equivalent Dose (MED),
brand name and opioid content which are calculated of all oral opioids
authorized for sale by Health Canada based on their Drug Identification Number (DIN).
MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI)
and information obtained from Health Canada's Drug Product Database's monthly data dump.
Please note in no way should output from this package be a substitute for medical advise.
All medications should only be consumed on prescription from a licensed healthcare provider.
Author: Ankona Banerjee [aut, cre] ,
Erik Stricker [aut]
Maintainer: Ankona Banerjee <asb426@mail.usask.ca>
Diff between OralOpioids versions 1.0.1 dated 2023-03-03 and 1.1.0 dated 2023-05-03
OralOpioids-1.0.1/OralOpioids/inst/download/2023-01-03_HealthCanada_Opioid_Table.xlsx |only OralOpioids-1.0.1/OralOpioids/inst/download/2023-02-01_HealthCanada_Opioid_Table.xlsx |only OralOpioids-1.0.1/OralOpioids/inst/extdata/file.csv |only OralOpioids-1.1.0/OralOpioids/DESCRIPTION | 6 - OralOpioids-1.1.0/OralOpioids/MD5 | 13 +- OralOpioids-1.1.0/OralOpioids/NEWS.md | 12 +- OralOpioids-1.1.0/OralOpioids/R/OralOpioids.R | 48 ++++++---- OralOpioids-1.1.0/OralOpioids/inst/doc/OralOpioid.html | 4 OralOpioids-1.1.0/OralOpioids/inst/download/2023-04-03_HealthCanada_Opioid_Table.xlsx |only OralOpioids-1.1.0/OralOpioids/inst/extdata/old_data.csv |only 10 files changed, 48 insertions(+), 35 deletions(-)
Title: HTTP Error Helpers
Description: HTTP error helpers. Methods included for general purpose HTTP
error handling, as well as individual methods for every HTTP status
code, both via status code numbers as well as their descriptive names.
Supports ability to adjust behavior to stop, message or warning.
Includes ability to use custom whisker template to have any configuration
of status code, short description, and verbose message. Currently
supports integration with 'crul', 'curl', and 'httr'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fauxpas versions 0.5.0 dated 2020-04-13 and 0.5.2 dated 2023-05-03
DESCRIPTION | 15 -- MD5 | 28 +-- NEWS.md | 9 + R/errors-children.R | 39 ----- R/errors.R | 72 ---------- R/s3-classes.R | 51 ------- README.md | 18 -- build/vignette.rds |binary inst/doc/fauxpas-vignette.R | 2 inst/doc/fauxpas-vignette.Rmd | 7 inst/doc/fauxpas-vignette.html | 295 ++++++++++++++++++++--------------------- man/Error-Classes.Rd | 39 ----- man/Error.Rd | 72 ---------- man/http.Rd | 51 ------- vignettes/fauxpas-vignette.Rmd | 7 15 files changed, 201 insertions(+), 504 deletions(-)
Title: Several Examined and Concealed States-Dependent Speciation and
Extinction
Description: Simultaneously infers state-dependent diversification across
two or more states of a single or multiple traits while accounting for the
role of a possible concealed trait. See Herrera-Alsina et al. (2019)
<doi:10.1093/sysbio/syy057>.
Author: Leonel Herrera Alsina [aut] ,
Paul van Els [aut] ,
Thijs Janzen [ctb] ,
Hanno Hildenbrandt [ctb] ,
Rampal S. Etienne [cre, aut]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between secsse versions 2.1.7 dated 2021-07-16 and 2.5.0 dated 2023-05-03
secsse-2.1.7/secsse/configure |only secsse-2.1.7/secsse/src/R_init_secsse.c |only secsse-2.1.7/secsse/src/secsse_loglik_rhs_FORTRAN.f95 |only secsse-2.1.7/secsse/tests/testthat/test_secsse.R |only secsse-2.5.0/secsse/DESCRIPTION | 49 secsse-2.5.0/secsse/LICENSE |only secsse-2.5.0/secsse/LICENSE.note |only secsse-2.5.0/secsse/MD5 | 109 - secsse-2.5.0/secsse/NAMESPACE | 14 secsse-2.5.0/secsse/R/RcppExports.R |only secsse-2.5.0/secsse/R/cla_secsse_eval.R |only secsse-2.5.0/secsse/R/cla_secsse_loglik.R | 622 ++----- secsse-2.5.0/secsse/R/cla_secsse_ml.R | 490 ++---- secsse-2.5.0/secsse/R/cla_secsse_ml_func_def_pars.R | 527 +++--- secsse-2.5.0/secsse/R/data.R | 2 secsse-2.5.0/secsse/R/event_times.R | 90 - secsse-2.5.0/secsse/R/plot_state_exact.R |only secsse-2.5.0/secsse/R/plot_state_exact_cla.R |only secsse-2.5.0/secsse/R/secsse-package.R |only secsse-2.5.0/secsse/R/secsse_loglik.R | 1004 +++++------- secsse-2.5.0/secsse/R/secsse_loglik_eval.R |only secsse-2.5.0/secsse/R/secsse_ml.R | 991 ++++++------ secsse-2.5.0/secsse/R/secsse_ml_func_def_pars.R | 491 +++--- secsse-2.5.0/secsse/R/secsse_sim.R |only secsse-2.5.0/secsse/R/secsse_utils.R | 585 +++---- secsse-2.5.0/secsse/build/partial.rdb |only secsse-2.5.0/secsse/build/vignette.rds |binary secsse-2.5.0/secsse/inst/COPYRIGHTS |only secsse-2.5.0/secsse/inst/doc/Using_secsse.R | 230 +- secsse-2.5.0/secsse/inst/doc/Using_secsse.Rmd | 341 ++-- secsse-2.5.0/secsse/inst/doc/Using_secsse.html | 1038 +++++++++---- secsse-2.5.0/secsse/inst/doc/plotting_states.R |only secsse-2.5.0/secsse/inst/doc/plotting_states.Rmd |only secsse-2.5.0/secsse/inst/doc/plotting_states.html |only secsse-2.5.0/secsse/man/cla_calThruNodes_cpp.Rd |only secsse-2.5.0/secsse/man/cla_id_paramPos.Rd | 8 secsse-2.5.0/secsse/man/cla_secsse_eval.Rd |only secsse-2.5.0/secsse/man/cla_secsse_loglik.Rd | 107 - secsse-2.5.0/secsse/man/cla_secsse_ml.Rd | 121 - secsse-2.5.0/secsse/man/cla_secsse_ml_func_def_pars.Rd | 159 + secsse-2.5.0/secsse/man/event_times.Rd | 6 secsse-2.5.0/secsse/man/id_paramPos.Rd | 8 secsse-2.5.0/secsse/man/plot_state_exact.Rd |only secsse-2.5.0/secsse/man/plot_state_exact_cla.Rd |only secsse-2.5.0/secsse/man/prepare_full_lambdas.Rd | 9 secsse-2.5.0/secsse/man/q_doubletrans.Rd | 19 secsse-2.5.0/secsse/man/secsse-package.Rd |only secsse-2.5.0/secsse/man/secsse_loglik.Rd | 90 - secsse-2.5.0/secsse/man/secsse_loglik_eval.Rd |only secsse-2.5.0/secsse/man/secsse_ml.Rd | 123 - secsse-2.5.0/secsse/man/secsse_ml_func_def_pars.Rd | 135 + secsse-2.5.0/secsse/man/secsse_sim.Rd |only secsse-2.5.0/secsse/man/sortingtraits.Rd | 53 secsse-2.5.0/secsse/src/Makevars | 9 secsse-2.5.0/secsse/src/Makevars.win |only secsse-2.5.0/secsse/src/RcppExports.cpp |only secsse-2.5.0/secsse/src/cla_loglik.cpp |only secsse-2.5.0/secsse/src/cla_loglik_threaded.cpp |only secsse-2.5.0/secsse/src/cla_secsse_store.cpp |only secsse-2.5.0/secsse/src/config.h |only secsse-2.5.0/secsse/src/odeint.h |only secsse-2.5.0/secsse/src/secsse_loglik.cpp |only secsse-2.5.0/secsse/src/secsse_loglik_store.cpp |only secsse-2.5.0/secsse/src/secsse_loglik_threaded.cpp |only secsse-2.5.0/secsse/src/secsse_sim.cpp |only secsse-2.5.0/secsse/src/secsse_sim.h |only secsse-2.5.0/secsse/src/threaded_ll.h |only secsse-2.5.0/secsse/src/util.cpp |only secsse-2.5.0/secsse/src/util.h |only secsse-2.5.0/secsse/tests/testthat/test_cla_secsse_ml.R |only secsse-2.5.0/secsse/tests/testthat/test_geosse.R |only secsse-2.5.0/secsse/tests/testthat/test_hisse.R |only secsse-2.5.0/secsse/tests/testthat/test_ml_func_def_pars.R |only secsse-2.5.0/secsse/tests/testthat/test_ml_par.R |only secsse-2.5.0/secsse/tests/testthat/test_plotting.R |only secsse-2.5.0/secsse/tests/testthat/test_secsse_cla_ct.R |only secsse-2.5.0/secsse/tests/testthat/test_secsse_ct.R |only secsse-2.5.0/secsse/tests/testthat/test_secsse_sim.R |only secsse-2.5.0/secsse/vignettes/Using_secsse.Rmd | 341 ++-- secsse-2.5.0/secsse/vignettes/output.RDS |only secsse-2.5.0/secsse/vignettes/plotting_states.Rmd |only 81 files changed, 4114 insertions(+), 3657 deletions(-)
Title: Firth's Bias-Reduced Logistic Regression
Description: Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys
prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal
solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) <doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such that ordinary
maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available
in the package as well, see Puhr et al (2017) <doi:10.1002/sim.7273>.
Author: Georg Heinze [aut, cre],
Meinhard Ploner [aut],
Daniela Dunkler [ctb],
Harry Southworth [ctb],
Lena Jiricka [aut],
Gregor Steiner [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between logistf versions 1.24.1 dated 2022-01-18 and 1.25.0 dated 2023-05-03
DESCRIPTION | 19 ++-- MD5 | 27 +++--- NAMESPACE | 220 ++++++++++++++++++++++++------------------------- NEWS.md | 6 + R/emmeans-support.R |only R/flac.R | 13 +- R/flic.R | 14 +-- R/logistf.R | 4 R/terms.logistf.R | 2 R/zzz.R |only README.md | 9 +- man/backward.Rd | 4 man/emmeans-logistf.Rd |only man/flac.Rd | 14 ++- man/flic.Rd | 6 - src/veclib.h | 2 16 files changed, 182 insertions(+), 158 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: Francois Rousset [aut, cre, cph]
,
Raphael Leblois [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.1.32 dated 2020-04-20 and 1.1.43 dated 2023-05-03
DESCRIPTION | 14 +++++----- MD5 | 63 +++++++++++++++++++++++----------------------- NAMESPACE | 10 +++---- R/CKrigcoefs.R | 4 +- R/LowUpFromKnots.R | 11 +++++--- R/RAM_fns.R | 2 - R/blackbox.R | 6 ++-- R/blackbox_internals.R | 37 ++++++++++++++++++++++++--- R/buildPointls.R | 2 - R/calcBounds1D.R | 4 +- R/calcProfileOK.R | 4 +- R/findReplicates.R | 4 +- R/fromFields.R | 2 - R/greedyMAXMINwithFixed.R | 33 +++++++++++++----------- R/init_grid.R | 15 ++++++++-- R/optimWrapper.R | 4 +- R/prepareData.R | 2 - R/profileFn.R | 4 +- R/providefullhull.R | 4 +- R/prune_by_dist.R | 4 +- R/rhull.R | 4 +- R/sampleByResp.R | 2 - R/stripclosestpairs.R | 4 +- R/subHullWrapper.R | 3 +- R/volTriangulation.R | 6 +++- R/zoomProfile.R | 4 +- inst/CITATION |only inst/NEWS.Rd | 15 ++++++++++ man/blackbox.Rd | 4 +- man/init_grid.Rd | 14 ++++++---- man/writeFinalInfo.Rd | 2 - src/RcppExports.cpp | 5 +++ tests/test-all.R | 2 - 33 files changed, 184 insertions(+), 110 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-08 1.4-2
2021-06-24 1.4-1
2018-10-10 1.3.1
2018-04-09 1.3.0
2017-09-05 1.2.0
2017-08-29 1.1.0
2017-07-11 1.0.1
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 6.0.0 dated 2023-03-27 and 6.0.5 dated 2023-05-03
DESCRIPTION | 8 MD5 | 106 +- NEWS.md | 58 + R/RcppExports.R | 91 +- R/data.R | 1 R/datamanag.R | 24 R/matrixcreation.R | 4 R/popdyn.R | 167 +-- build/vignette.rds |binary data/anthyllis.rda |binary inst/doc/Chapter1.Rmd | 6 inst/doc/Chapter1.html | 37 inst/doc/Chapter2.Rmd | 70 - inst/doc/Chapter2.html | 123 +- inst/doc/Chapter5.Rmd | 24 inst/doc/Chapter5.html | 61 - inst/doc/Chapter6.Rmd | 2 inst/doc/Chapter6.html | 9 inst/doc/Chapter8.Rmd | 8 inst/doc/Chapter8.html | 30 inst/doc/Chapter9.Rmd | 8 inst/doc/Chapter9.html | 20 inst/include/basic_funcs/main_utils.h | 4 inst/include/basic_funcs/mat_stuff.h | 67 + man/anthyllis.Rd | 1 man/create_lM.Rd | 10 man/ltre3.Rd | 6 man/sf_create.Rd | 61 + man/summary.lefkoLTRE.Rd | 2 src/Makevars | 12 src/Makevars.win | 11 src/MatsNProj.cpp | 489 +++++++--- src/PopChar.cpp | 537 ++++++++--- src/PopDyn2.cpp | 1538 ++-------------------------------- src/RcppExports.cpp | 32 vignettes/Ch2.36-1.png |binary vignettes/Ch5.18-1.png |binary vignettes/Ch5.19-1.png |binary vignettes/Ch5.20-1.png |binary vignettes/Ch5.24-1.png |binary vignettes/Ch5.25-1.png |binary vignettes/Ch5.28-1.png |binary vignettes/Ch8.2-1.png |binary vignettes/Chapter1.Rmd | 6 vignettes/Chapter2.Rmd | 70 - vignettes/Chapter2.Rmd.orig | 24 vignettes/Chapter5.Rmd | 24 vignettes/Chapter5.Rmd.orig | 6 vignettes/Chapter6.Rmd | 2 vignettes/Chapter6.Rmd.orig | 2 vignettes/Chapter8.Rmd | 8 vignettes/Chapter8.Rmd.orig | 8 vignettes/Chapter9.Rmd | 8 vignettes/Chapter9.Rmd.orig | 2 54 files changed, 1539 insertions(+), 2248 deletions(-)
Title: Continuous-Lag Spatial Markov Chains
Description: A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields. More details on the methodology are discussed in Sartore (2013) <doi:10.32614/RJ-2013-022> and Sartore et al. (2016) <doi:10.1016/j.cageo.2016.06.001>.
Author: Luca Sartore [aut, cre]
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between spMC versions 0.3.12 dated 2022-06-11 and 0.3.15 dated 2023-05-03
spMC-0.3.12/spMC/NEWS |only spMC-0.3.12/spMC/cleanup |only spMC-0.3.15/spMC/DESCRIPTION | 8 +-- spMC-0.3.15/spMC/MD5 | 27 +++++----- spMC-0.3.15/spMC/NAMESPACE | 87 +++++++++++++++++++++++------------ spMC-0.3.15/spMC/NEWS.md |only spMC-0.3.15/spMC/R/setCores.R | 8 +-- spMC-0.3.15/spMC/README.md | 4 - spMC-0.3.15/spMC/inst/CITATION | 86 +++++++++++----------------------- spMC-0.3.15/spMC/man/quench.Rd | 2 spMC-0.3.15/spMC/man/sim.Rd | 2 spMC-0.3.15/spMC/man/sim_ck.Rd | 2 spMC-0.3.15/spMC/man/sim_ik.Rd | 2 spMC-0.3.15/spMC/man/spMC-package.Rd | 6 +- spMC-0.3.15/spMC/src/spMC.c | 16 +++--- spMC-0.3.15/spMC/src/spMC.h | 2 16 files changed, 128 insertions(+), 124 deletions(-)
Title: Bivariate Zero-Inflated Count Models Using Copulas
Description: Maximum likelihood estimation of copula-based zero-inflated
(and non-inflated) Poisson and negative binomial count models. Supports Frank
and Gaussian copulas. Allows for mixed margins (e.g., one margin Poisson, the
other zero-inflated negative binomial), and several marginal link functions.
Built-in methods for publication-quality tables using 'texreg', post-estimation
diagnostics using 'DHARMa', and testing for marginal zero-modification
via <doi:10.1177/0962280217749991>. For information on copula regression for count data,
see Genest and Nešlehová (2007) <doi:10.1017/S0515036100014963> as well as
Nikoloulopoulos (2013) <doi:10.1007/978-3-642-35407-6_11>. For information on zero-inflated
count regression generally, see Lambert (1992) <https:www.jstor.org/stable/1269547?origin=crossref>. The author
acknowledges support by NSF DMS-1925119 and DMS-212324.
Author: John Niehaus [aut, cre]
Maintainer: John Niehaus <jniehaus2257@gmail.com>
Diff between bizicount versions 1.3.1 dated 2023-03-16 and 1.3.2 dated 2023-05-03
DESCRIPTION | 7 ++++--- MD5 | 7 +++++-- NEWS.md | 11 +++++++++++ R/data.R |only data |only man/terror.Rd |only 6 files changed, 20 insertions(+), 5 deletions(-)