Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut],
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.5.1 dated 2024-01-09 and 0.6.0 dated 2024-04-16
DESCRIPTION | 8 MD5 | 72 - NEWS.md | 292 ++-- R/cov_betahat_adjust.R | 2 R/cov_estimate_gloglik.R | 6 R/cov_estimate_sv.R | 98 - R/cov_initial_search.R | 2258 +++++++++++++++++----------------- R/cov_initial_search_glm.R | 2105 +++++++++++++++---------------- R/get_data_object.R | 28 R/get_data_object_glm.R | 28 R/get_fitted.R | 20 R/get_fitted_glm.R | 19 R/get_local_list.R | 7 R/get_loocv.R | 96 - R/get_model_stats.R | 103 + R/get_model_stats_glm.R | 1 R/get_randcov_list.R | 79 - R/laploglik_products.R | 3 R/partition_matrix.R | 52 R/predict.R | 4 R/predict_glm.R | 4 R/spautor.R | 7 R/spgautor.R | 740 +++++------ R/spglm.R | 946 +++++++------- R/splm.R | 14 R/sprnorm.R | 2 R/utils.R | 70 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 6 inst/doc/introduction.html | 13 man/spautor.Rd | 4 man/spgautor.Rd | 4 man/splm.Rd | 2 tests/testthat/test-extras-spautor.R | 11 tests/testthat/test-extras-spgautor.R | 11 tests/testthat/test-extras-splm.R | 22 37 files changed, 3701 insertions(+), 3436 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.2.1 dated 2024-02-17 and 0.3.0 dated 2024-04-16
DESCRIPTION | 6 - MD5 | 72 +++++++------- NAMESPACE | 9 + NEWS.md | 19 +++ R/genetrack_ly.R | 92 +++++++++++++----- R/genetracks.R | 69 ++++++++++++- R/genetracks_grob.R | 61 +++++++----- R/gg_genetracks.R | 35 +++++-- R/gg_scatter.R | 108 ++++++++++++++++----- R/link_LD.R | 57 ++++++++--- R/link_recomb.R | 38 ++++++- R/locus.R | 151 +++++++++++++++++------------- R/locus_ggplot.R | 15 ++- R/locus_plot.R | 16 ++- R/locus_plotly.R | 25 +++-- R/quick_peak.R | 27 +---- R/scatter_plot.R | 75 ++++++++++++--- R/scatter_plotly.R | 234 ++++++++++++++++++++++++++++++++++------------- README.md | 12 +- build/vignette.rds |binary inst/doc/locuszoomr.R | 8 + inst/doc/locuszoomr.Rmd | 41 +++++++- inst/doc/locuszoomr.html | 49 +++++++-- man/genetrack_ly.Rd | 31 +++++- man/genetracks.Rd | 25 ++++- man/genetracks_grob.Rd | 18 +++ man/gg_genetracks.Rd | 32 +++++- man/gg_scatter.Rd | 10 +- man/link_LD.Rd | 25 ++++- man/link_recomb.Rd | 26 +++-- man/locus.Rd | 29 ++++- man/locus_ggplot.Rd | 12 ++ man/locus_plot.Rd | 14 ++ man/locus_plotly.Rd | 21 +++- man/scatter_plot.Rd | 30 ++++-- man/scatter_plotly.Rd | 32 ++++-- vignettes/locuszoomr.Rmd | 41 +++++++- 37 files changed, 1150 insertions(+), 415 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.0-2 dated 2024-01-30 and 1.0-3 dated 2024-04-16
DESCRIPTION | 10 ++-- MD5 | 26 +++++----- R/internal.R | 2 R/mmlt.R | 131 +++++++++++++++++++++++++++++++++++++++-------------- R/models.R | 3 - R/tram.R | 11 ++++ build/partial.rdb |binary build/vignette.rds |binary demo/survtram.R | 119 +++++++++++++++++++++++++++++++++--------------- inst/NEWS.Rd | 12 ++++ inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary man/mmlt.Rd | 23 ++++++--- tests/bugfixes.R | 7 ++ 14 files changed, 246 insertions(+), 98 deletions(-)
Title: Analyzing and Visualizing Symptom Checker Performance
Description: Easily analyze and visualize the performance of symptom
checkers. This package can be used to gain comprehensive insights into
the performance of single symptom checkers or the performance of
multiple symptom checkers. It can be used to easily compare these
symptom checkers across several metrics to gain an understanding of
their strengths and weaknesses. The metrics are developed in
Kopka et al. (2023) <doi:10.1177/20552076231194929>.
Author: Marvin Kopka [cre, aut] ,
Malte L. Schmieding [aut] ,
Markus A. Feufel [aut]
Maintainer: Marvin Kopka <marvin.kopka@tu-berlin.de>
Diff between symptomcheckR versions 0.1.1 dated 2024-01-12 and 0.1.3 dated 2024-04-16
DESCRIPTION | 13 +++--- MD5 | 34 +++++++++-------- NAMESPACE | 2 + NEWS.md | 8 +++- R/get_accuracy.R | 51 ++++++++++++++++++++++++- R/get_accuracy_by_triage.R | 66 +++++++++++++++++++++++++++++---- R/get_comprehensiveness.R | 70 +++++++++++++++++++++++++++++++++-- R/get_inclination_to_overtriage.R | 67 ++++++++++++++++++++++++++++++++- R/get_irr.R |only R/get_safety_of_advice.R | 67 ++++++++++++++++++++++++++++++++- R/plot_safety_of_advice.R | 4 +- README.md | 37 +++++++++++++++--- man/get_accuracy.Rd | 7 ++- man/get_accuracy_by_triage.Rd | 7 ++- man/get_comprehensiveness.Rd | 8 +++- man/get_inclination_to_overtriage.Rd | 8 +++- man/get_irr.Rd |only man/get_safety_of_advice.Rd | 10 +++-- man/plot_safety_of_advice.Rd | 4 +- 19 files changed, 397 insertions(+), 66 deletions(-)
Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation,
model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs,
correlation between graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Grover E. Castro Guzman [aut],
Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 0.5.1 dated 2024-01-25 and 1.0.0 dated 2024-04-16
statGraph-0.5.1/statGraph/R/statGraph-package.R |only statGraph-0.5.1/statGraph/R/statGraph.R |only statGraph-0.5.1/statGraph/build |only statGraph-0.5.1/statGraph/man/cerqueira.test.Rd |only statGraph-0.5.1/statGraph/man/fast.eigenvalue.probability.Rd |only statGraph-0.5.1/statGraph/man/fast.graph.param.estimator.Rd |only statGraph-0.5.1/statGraph/man/fast.spectral.density.Rd |only statGraph-0.5.1/statGraph/man/fraiman.test.Rd |only statGraph-0.5.1/statGraph/man/ghoshdastidar.test.Rd |only statGraph-0.5.1/statGraph/man/statGraph-package.Rd |only statGraph-0.5.1/statGraph/man/takahashi.test.Rd |only statGraph-0.5.1/statGraph/man/tang.test.Rd |only statGraph-1.0.0/statGraph/DESCRIPTION | 23 +- statGraph-1.0.0/statGraph/MD5 | 63 ++++--- statGraph-1.0.0/statGraph/NAMESPACE | 14 - statGraph-1.0.0/statGraph/R/GIC.R |only statGraph-1.0.0/statGraph/R/anogva.R |only statGraph-1.0.0/statGraph/R/graph.acf.R |only statGraph-1.0.0/statGraph/R/graph.cem.R |only statGraph-1.0.0/statGraph/R/graph.cor.test.R |only statGraph-1.0.0/statGraph/R/graph.dist.R |only statGraph-1.0.0/statGraph/R/graph.entropy.R |only statGraph-1.0.0/statGraph/R/graph.hclust.R |only statGraph-1.0.0/statGraph/R/graph.kmeans.R |only statGraph-1.0.0/statGraph/R/graph.model.selection.R |only statGraph-1.0.0/statGraph/R/graph.models.R |only statGraph-1.0.0/statGraph/R/graph.mult.scaling.R |only statGraph-1.0.0/statGraph/R/graph.param.estimator.R |only statGraph-1.0.0/statGraph/R/graph.spectral.density.R |only statGraph-1.0.0/statGraph/R/graph.takahashi.test.R |only statGraph-1.0.0/statGraph/R/graph.tang.test.R |only statGraph-1.0.0/statGraph/R/showResults.R |only statGraph-1.0.0/statGraph/R/sp.anogva.R |only statGraph-1.0.0/statGraph/R/utils.R |only statGraph-1.0.0/statGraph/man/GIC.Rd | 75 +++----- statGraph-1.0.0/statGraph/man/anogva.Rd | 35 ++- statGraph-1.0.0/statGraph/man/graph.acf.Rd | 14 - statGraph-1.0.0/statGraph/man/graph.cem.Rd | 40 ++-- statGraph-1.0.0/statGraph/man/graph.cor.test.Rd | 29 +-- statGraph-1.0.0/statGraph/man/graph.dist.Rd |only statGraph-1.0.0/statGraph/man/graph.entropy.Rd | 43 +--- statGraph-1.0.0/statGraph/man/graph.hclust.Rd | 28 +-- statGraph-1.0.0/statGraph/man/graph.kmeans.Rd | 25 ++ statGraph-1.0.0/statGraph/man/graph.model.selection.Rd | 99 +++-------- statGraph-1.0.0/statGraph/man/graph.mult.scaling.Rd | 42 ++-- statGraph-1.0.0/statGraph/man/graph.param.estimator.Rd | 95 ++++------ statGraph-1.0.0/statGraph/man/graph.spectral.density.Rd |only statGraph-1.0.0/statGraph/man/graph.takahashi.test.Rd |only statGraph-1.0.0/statGraph/man/graph.tang.test.Rd |only statGraph-1.0.0/statGraph/man/sp.anogva.Rd | 63 ++----- 50 files changed, 293 insertions(+), 395 deletions(-)
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
Author: Richard Hanna [aut, cre] ,
Stephan Kadauke [aut] ,
Ezra Porter [aut]
Maintainer: Richard Hanna <richardshanna91@gmail.com>
Diff between REDCapTidieR versions 1.1.0 dated 2024-03-28 and 1.1.1 dated 2024-04-16
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 12 ++++++++++-- R/checks.R | 6 +++--- R/utils.R | 26 ++++++++++++-------------- build/vignette.rds |binary tests/testthat/test-read_redcap.R | 1 - tests/testthat/test-utils.R | 6 ++---- 8 files changed, 37 insertions(+), 34 deletions(-)
More information about Paris2024Colours at CRAN
Permanent link
More information about CohortCharacteristics at CRAN
Permanent link
Title: Graphical Elements of the University of Konstanz's Corporate
Design
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for finding, changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text decoration functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other purposes or institutions.
Author: Hansjoerg Neth [aut, cre] ,
Nico Gradwohl [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between unikn versions 0.9.0 dated 2023-08-10 and 1.0.0 dated 2024-04-16
unikn-0.9.0/unikn/inst/doc/color_inst.R |only unikn-0.9.0/unikn/inst/doc/color_inst.Rmd |only unikn-0.9.0/unikn/inst/doc/color_inst.html |only unikn-0.9.0/unikn/inst/doc/colors.R |only unikn-0.9.0/unikn/inst/doc/colors.Rmd |only unikn-0.9.0/unikn/inst/doc/colors.html |only unikn-0.9.0/unikn/inst/doc/text.R |only unikn-0.9.0/unikn/inst/doc/text.Rmd |only unikn-0.9.0/unikn/inst/doc/text.html |only unikn-0.9.0/unikn/inst/pix/README-others-txt-demo-1.png |only unikn-0.9.0/unikn/inst/pix/README-seecol-add-pals-1.png |only unikn-0.9.0/unikn/inst/pix/logo.png |only unikn-0.9.0/unikn/inst/pix/logo_freiburg_2023.png |only unikn-0.9.0/unikn/vignettes/color_inst.Rmd |only unikn-0.9.0/unikn/vignettes/colors.Rmd |only unikn-0.9.0/unikn/vignettes/text.Rmd |only unikn-1.0.0/unikn/DESCRIPTION | 12 unikn-1.0.0/unikn/MD5 | 122 ++++----- unikn-1.0.0/unikn/NEWS.md | 81 +++--- unikn-1.0.0/unikn/R/color_fun_1.R | 193 +++++++-------- unikn-1.0.0/unikn/R/color_fun_2.R | 77 ++++- unikn-1.0.0/unikn/R/plot_demo.R | 65 ++++- unikn-1.0.0/unikn/R/plot_kn.R | 28 +- unikn-1.0.0/unikn/R/plot_text_calls.R | 11 unikn-1.0.0/unikn/R/util.R | 15 - unikn-1.0.0/unikn/R/util_color.R | 20 - unikn-1.0.0/unikn/R/util_plot.R | 15 - unikn-1.0.0/unikn/README.md | 170 +++++++------ unikn-1.0.0/unikn/build/vignette.rds |binary unikn-1.0.0/unikn/inst/CITATION | 10 unikn-1.0.0/unikn/inst/doc/color_functions.R |only unikn-1.0.0/unikn/inst/doc/color_functions.Rmd |only unikn-1.0.0/unikn/inst/doc/color_functions.html |only unikn-1.0.0/unikn/inst/doc/color_recipes.R | 13 + unikn-1.0.0/unikn/inst/doc/color_recipes.Rmd | 39 ++- unikn-1.0.0/unikn/inst/doc/color_recipes.html | 42 +-- unikn-1.0.0/unikn/inst/doc/inst_colors.R |only unikn-1.0.0/unikn/inst/doc/inst_colors.Rmd |only unikn-1.0.0/unikn/inst/doc/inst_colors.html |only unikn-1.0.0/unikn/inst/doc/text_decorations.R |only unikn-1.0.0/unikn/inst/doc/text_decorations.Rmd |only unikn-1.0.0/unikn/inst/doc/text_decorations.html |only unikn-1.0.0/unikn/inst/pix/README-grepal-example-1-1.png |binary unikn-1.0.0/unikn/inst/pix/README-newpal-google-1.png |binary unikn-1.0.0/unikn/inst/pix/README-pal-all-1.png |binary unikn-1.0.0/unikn/inst/pix/README-pal-unikn-1.png |binary unikn-1.0.0/unikn/inst/pix/README-pal-unikn-pref-1.png |binary unikn-1.0.0/unikn/inst/pix/README-seecol-pref-1.png |binary unikn-1.0.0/unikn/inst/pix/README-simcol-example-1.png |binary unikn-1.0.0/unikn/inst/pix/logo_unicol.png |only unikn-1.0.0/unikn/inst/pix/unikn.png |binary unikn-1.0.0/unikn/inst/pix/unikn_box.png |only unikn-1.0.0/unikn/man/mark.Rd | 3 unikn-1.0.0/unikn/man/newpal.Rd | 39 ++- unikn-1.0.0/unikn/man/pal_bordeaux.Rd | 4 unikn-1.0.0/unikn/man/pal_grau.Rd | 4 unikn-1.0.0/unikn/man/pal_karpfenblau.Rd | 4 unikn-1.0.0/unikn/man/pal_peach.Rd | 4 unikn-1.0.0/unikn/man/pal_petrol.Rd | 4 unikn-1.0.0/unikn/man/pal_pinky.Rd | 4 unikn-1.0.0/unikn/man/pal_seeblau.Rd | 4 unikn-1.0.0/unikn/man/pal_seegruen.Rd | 4 unikn-1.0.0/unikn/man/pal_signal.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_dark.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_light.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_pair.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_ppt.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_pref.Rd | 4 unikn-1.0.0/unikn/man/pal_unikn_web.Rd | 4 unikn-1.0.0/unikn/man/post.Rd | 2 unikn-1.0.0/unikn/man/seecol.Rd | 13 - unikn-1.0.0/unikn/man/uline.Rd | 4 unikn-1.0.0/unikn/man/url_unikn.Rd | 4 unikn-1.0.0/unikn/vignettes/color_functions.Rmd |only unikn-1.0.0/unikn/vignettes/color_recipes.Rmd | 39 ++- unikn-1.0.0/unikn/vignettes/inst_colors.Rmd |only unikn-1.0.0/unikn/vignettes/text_decorations.Rmd |only 77 files changed, 631 insertions(+), 446 deletions(-)
Title: Makes 'R' Easier for Everyone
Description: A meta-package that aims to make 'R' easier for everyone,
especially programmers who have a background in 'SAS®' software.
This set of packages brings many useful concepts to 'R', including
data libraries, data dictionaries, formats
and format catalogs, a data step, and a traceable log. The 'flagship'
package is a reporting package that can output in text, rich text, 'PDF',
'HTML', and 'DOCX' file formats.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between sassy versions 1.2.3 dated 2024-02-07 and 1.2.4 dated 2024-04-16
sassy-1.2.3/sassy/tests/testthat/IQ/log |only sassy-1.2.3/sassy/tests/testthat/IQ/output |only sassy-1.2.3/sassy/tests/testthat/IQ/sassyIQ-2023-09-06.pdf |only sassy-1.2.3/sassy/tests/testthat/OQ/log |only sassy-1.2.3/sassy/tests/testthat/OQ/output |only sassy-1.2.4/sassy/DESCRIPTION | 12 ++-- sassy-1.2.4/sassy/MD5 | 36 ++----------- sassy-1.2.4/sassy/NEWS.md | 6 ++ sassy-1.2.4/sassy/R/oq.R | 18 ++++++ sassy-1.2.4/sassy/inst/doc/sassy.Rmd | 3 - sassy-1.2.4/sassy/inst/doc/sassy.html | 3 - sassy-1.2.4/sassy/man/sassy.Rd | 1 sassy-1.2.4/sassy/tests/testthat/test-oq.R | 2 sassy-1.2.4/sassy/vignettes/sassy.Rmd | 3 - 14 files changed, 46 insertions(+), 38 deletions(-)
Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Steve Lianoglou [ctb],
Jim Nikelski [ctb],
Kirill Mueller [ctb],
Peter Humburg [ctb],
Rich FitzJohn [ctb],
Gyu Jin Choi [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between optparse versions 1.7.4 dated 2024-01-16 and 1.7.5 dated 2024-04-16
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/optparse-package.R | 5 ++--- R/optparse.R | 9 +++++++-- build/vignette.rds |binary inst/COPYRIGHTS | 4 ++-- inst/doc/optparse.html | 38 +++++++++++++++++++------------------- man/optparse-package.Rd | 2 +- tests/testthat/test-optparse.R | 20 ++++++++++++-------- 10 files changed, 66 insertions(+), 51 deletions(-)
Title: Forecast the Diffusion of New Products
Description: Various diffusion models to forecast new product growth. Currently
the package contains Bass, Gompertz, Gamma/Shifted Gompertz and Weibull curves. See
Meade and Islam (2006) <doi:10.1016/j.ijforecast.2006.01.005>.
Author: Oliver Schaer [aut, cre] ,
Nikolaos Kourentzes [aut] ,
Ivan Svetunkov [aut]
Maintainer: Oliver Schaer <info@oliverschaer.ch>
Diff between diffusion versions 0.2.7 dated 2018-01-05 and 0.4.0 dated 2024-04-16
diffusion-0.2.7/diffusion/data/tsbroadband.RData |only diffusion-0.2.7/diffusion/man/tsBroadband.Rd |only diffusion-0.4.0/diffusion/DESCRIPTION | 32 diffusion-0.4.0/diffusion/MD5 | 66 - diffusion-0.4.0/diffusion/NAMESPACE | 23 diffusion-0.4.0/diffusion/NEWS.md |only diffusion-0.4.0/diffusion/R/auxiliary.R | 486 +++++++++- diffusion-0.4.0/diffusion/R/bass.R | 83 - diffusion-0.4.0/diffusion/R/datasets.R | 58 - diffusion-0.4.0/diffusion/R/diffusion.R | 763 +++++++++------- diffusion-0.4.0/diffusion/R/gompertz.R | 106 -- diffusion-0.4.0/diffusion/R/gsgompertz.R | 85 - diffusion-0.4.0/diffusion/R/isFunctions.R |only diffusion-0.4.0/diffusion/R/nortonbass.R | 36 diffusion-0.4.0/diffusion/R/seqdiffusion.R | 242 +++-- diffusion-0.4.0/diffusion/R/weibull.R |only diffusion-0.4.0/diffusion/README.md | 25 diffusion-0.4.0/diffusion/data/tsCovid.RData |only diffusion-0.4.0/diffusion/data/tsmetal.RData |only diffusion-0.4.0/diffusion/man/Nortonbass.Rd | 225 ++-- diffusion-0.4.0/diffusion/man/Nortonbass_error.Rd | 62 - diffusion-0.4.0/diffusion/man/Nortonbass_startvalgen.Rd | 6 diffusion-0.4.0/diffusion/man/difcurve.Rd | 23 diffusion-0.4.0/diffusion/man/diffusion.Rd | 129 +- diffusion-0.4.0/diffusion/man/isFunctions.Rd |only diffusion-0.4.0/diffusion/man/plot.diffusion.Rd | 68 - diffusion-0.4.0/diffusion/man/plot.seqdiffusion.Rd | 70 - diffusion-0.4.0/diffusion/man/predict.diffusion.Rd | 4 diffusion-0.4.0/diffusion/man/print.diffusion.Rd | 64 - diffusion-0.4.0/diffusion/man/print.seqdiffusion.Rd | 66 - diffusion-0.4.0/diffusion/man/seqdiffusion.Rd | 109 +- diffusion-0.4.0/diffusion/man/tsAc.Rd | 6 diffusion-0.4.0/diffusion/man/tsCarstock.Rd | 6 diffusion-0.4.0/diffusion/man/tsChicken.Rd | 6 diffusion-0.4.0/diffusion/man/tsCovid.Rd |only diffusion-0.4.0/diffusion/man/tsIbm.Rd | 8 diffusion-0.4.0/diffusion/man/tsMetal.Rd |only diffusion-0.4.0/diffusion/man/tsSafari.Rd | 10 diffusion-0.4.0/diffusion/man/tsWindows.Rd | 6 39 files changed, 1772 insertions(+), 1101 deletions(-)
Title: Provides a 'PySpark' Back-End for the 'sparklyr' Package
Description: It enables 'sparklyr' to integrate with 'Spark Connect', and
'Databricks Connect' by providing a wrapper over the 'PySpark' 'python'
library.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between pysparklyr versions 0.1.3 dated 2024-01-12 and 0.1.4 dated 2024-04-16
pysparklyr-0.1.3/pysparklyr/tests/testthat/requirements.txt |only pysparklyr-0.1.4/pysparklyr/DESCRIPTION | 10 - pysparklyr-0.1.4/pysparklyr/MD5 | 75 +++++----- pysparklyr-0.1.4/pysparklyr/NAMESPACE | 9 + pysparklyr-0.1.4/pysparklyr/NEWS.md | 23 ++- pysparklyr-0.1.4/pysparklyr/R/databricks-utils.R | 34 ++-- pysparklyr-0.1.4/pysparklyr/R/deploy.R | 9 - pysparklyr-0.1.4/pysparklyr/R/dplyr.R | 7 pysparklyr-0.1.4/pysparklyr/R/ide-snippet.R | 4 pysparklyr-0.1.4/pysparklyr/R/ml-connect-model.R | 1 pysparklyr-0.1.4/pysparklyr/R/ml-utils.R | 30 ---- pysparklyr-0.1.4/pysparklyr/R/package.R | 2 pysparklyr-0.1.4/pysparklyr/R/python-import-check.R | 6 pysparklyr-0.1.4/pysparklyr/R/python-install.R | 19 +- pysparklyr-0.1.4/pysparklyr/R/python-use-envname.R | 14 - pysparklyr-0.1.4/pysparklyr/R/sparklyr-sdf.R | 4 pysparklyr-0.1.4/pysparklyr/R/sparklyr-spark-apply.R |only pysparklyr-0.1.4/pysparklyr/R/sparklyr-spark-connect.R | 22 ++ pysparklyr-0.1.4/pysparklyr/R/utils.R | 29 +++ pysparklyr-0.1.4/pysparklyr/README.md | 2 pysparklyr-0.1.4/pysparklyr/inst/udf |only pysparklyr-0.1.4/pysparklyr/tests/testthat/_snaps/data-write.md | 18 +- pysparklyr-0.1.4/pysparklyr/tests/testthat/_snaps/dplyr.md | 14 + pysparklyr-0.1.4/pysparklyr/tests/testthat/_snaps/pivot-longer.md | 5 pysparklyr-0.1.4/pysparklyr/tests/testthat/_snaps/python-install.md | 11 - pysparklyr-0.1.4/pysparklyr/tests/testthat/test-connections-pane.R | 3 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-data-write.R | 2 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-databricks-utils.R | 13 + pysparklyr-0.1.4/pysparklyr/tests/testthat/test-deploy.R | 12 - pysparklyr-0.1.4/pysparklyr/tests/testthat/test-dplyr.R | 4 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-ide-snippet.R | 2 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-ml-utils.R | 20 +- pysparklyr-0.1.4/pysparklyr/tests/testthat/test-pivot-longer.R | 3 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-python-requirements.R | 3 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-sparklyr-sdf.R | 1 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-sparklyr-spark-apply.R |only pysparklyr-0.1.4/pysparklyr/tests/testthat/test-sparklyr-spark-connect.R | 4 pysparklyr-0.1.4/pysparklyr/tests/testthat/test-utils.R | 10 - pysparklyr-0.1.4/pysparklyr/tests/testthat/test-zzz-spark-connect.R | 2 39 files changed, 249 insertions(+), 178 deletions(-)
Title: Interacting with BibTeX Databases
Description: Reading and writing BibTeX files using data frames in R sessions.
Author: Miguel Alvarez [aut, cre]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between biblio versions 0.0.8 dated 2023-03-11 and 0.0.9 dated 2024-04-16
DESCRIPTION | 10 ++-- MD5 | 30 +++++++----- NAMESPACE | 6 ++ NEWS.md | 21 +++++++- R/bib2bibentry.R |only R/coerce-methods.R |only R/detect_keys.R | 7 -- R/imports.R | 6 +- R/print.R | 23 +++++---- R/read_bib.R | 119 ++++++++++++++++++++++++-------------------------- R/sysdata.rda |binary build/partial.rdb |binary data/synopsis.rda |binary man/bib2bibentry.Rd |only man/coerce-methods.Rd |only man/detect_keys.Rd | 9 +-- man/print.Rd | 14 ++++- man/read_bib.Rd | 4 + 18 files changed, 140 insertions(+), 109 deletions(-)
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.8.1 dated 2024-03-21 and 0.8.2 dated 2024-04-16
TOSTER-0.8.1/TOSTER/tests/testthat/Rplots.pdf |only TOSTER-0.8.2/TOSTER/DESCRIPTION | 6 TOSTER-0.8.2/TOSTER/MD5 | 359 - TOSTER-0.8.2/TOSTER/NAMESPACE | 260 TOSTER-0.8.2/TOSTER/NEWS.md | 286 TOSTER-0.8.2/TOSTER/R/00jmv.R | 36 TOSTER-0.8.2/TOSTER/R/TOSTER-package.R | 14 TOSTER-0.8.2/TOSTER/R/TOSTmeta.R | 242 TOSTER-0.8.2/TOSTER/R/TOSTone.R | 474 - TOSTER-0.8.2/TOSTER/R/TOSTpaired.R | 938 +-- TOSTER-0.8.2/TOSTER/R/TOSTr.R | 238 TOSTER-0.8.2/TOSTER/R/TOSTtwo.R | 1070 +-- TOSTER-0.8.2/TOSTER/R/TOSTtwo.prop.R | 320 - TOSTER-0.8.2/TOSTER/R/anova_summary.R | 470 - TOSTER-0.8.2/TOSTER/R/boot_compare_cor.R | 434 - TOSTER-0.8.2/TOSTER/R/boot_compare_smd.R | 536 - TOSTER-0.8.2/TOSTER/R/boot_cor_test.R | 416 - TOSTER-0.8.2/TOSTER/R/boot_log_TOST.R | 936 +-- TOSTER-0.8.2/TOSTER/R/boot_ses_calc.R | 442 - TOSTER-0.8.2/TOSTER/R/boot_smd_calc.R | 436 - TOSTER-0.8.2/TOSTER/R/boot_t_TOST.R | 1146 +-- TOSTER-0.8.2/TOSTER/R/boot_t_test.R | 766 +- TOSTER-0.8.2/TOSTER/R/brunner_munzel.R | 898 +- TOSTER-0.8.2/TOSTER/R/cohend_calcs.R | 1488 ++-- TOSTER-0.8.2/TOSTER/R/compare_cor.R | 342 - TOSTER-0.8.2/TOSTER/R/compare_smd.R | 378 - TOSTER-0.8.2/TOSTER/R/compare_smd_functions.R | 76 TOSTER-0.8.2/TOSTER/R/cor_test.R | 372 - TOSTER-0.8.2/TOSTER/R/corr_calcs.R | 434 - TOSTER-0.8.2/TOSTER/R/corsum_test.R | 342 - TOSTER-0.8.2/TOSTER/R/data.R | 14 TOSTER-0.8.2/TOSTER/R/datatostone.b.R | 374 - TOSTER-0.8.2/TOSTER/R/datatostone.h.R | 992 +-- TOSTER-0.8.2/TOSTER/R/datatostpaired.b.R | 808 +- TOSTER-0.8.2/TOSTER/R/datatostpaired.h.R | 972 +-- TOSTER-0.8.2/TOSTER/R/datatostr.b.R | 382 - TOSTER-0.8.2/TOSTER/R/datatostr.h.R | 656 +- TOSTER-0.8.2/TOSTER/R/datatosttwo.b.R | 616 +- TOSTER-0.8.2/TOSTER/R/datatosttwo.h.R | 1152 +-- TOSTER-0.8.2/TOSTER/R/datatosttwoprop.b.R | 248 TOSTER-0.8.2/TOSTER/R/datatosttwoprop.h.R | 714 +- TOSTER-0.8.2/TOSTER/R/equ_anova.R | 188 TOSTER-0.8.2/TOSTER/R/equ_ftest.R | 206 TOSTER-0.8.2/TOSTER/R/extract_r_paired.R | 78 TOSTER-0.8.2/TOSTER/R/gg_curv_t.R | 390 - TOSTER-0.8.2/TOSTER/R/globals.R | 10 TOSTER-0.8.2/TOSTER/R/htest.R | 257 TOSTER-0.8.2/TOSTER/R/htest_helpers.R | 750 +- TOSTER-0.8.2/TOSTER/R/jamovi_functions.R | 928 +-- TOSTER-0.8.2/TOSTER/R/log_TOST.R | 798 +- TOSTER-0.8.2/TOSTER/R/log_pair.R | 462 - TOSTER-0.8.2/TOSTER/R/methods.TOSTnp.R | 186 TOSTER-0.8.2/TOSTER/R/methods.TOSTt.R | 1650 ++--- TOSTER-0.8.2/TOSTER/R/others.R | 276 TOSTER-0.8.2/TOSTER/R/pes_calc.R | 440 - TOSTER-0.8.2/TOSTER/R/plot.R | 28 TOSTER-0.8.2/TOSTER/R/plot_corr.R | 90 TOSTER-0.8.2/TOSTER/R/plot_pes.R | 98 TOSTER-0.8.2/TOSTER/R/plot_scripts.R | 214 TOSTER-0.8.2/TOSTER/R/plot_smd.R | 132 TOSTER-0.8.2/TOSTER/R/powerTOSTanova.R | 120 TOSTER-0.8.2/TOSTER/R/powerTOSTone.R | 240 TOSTER-0.8.2/TOSTER/R/powerTOSTpaired.R | 246 TOSTER-0.8.2/TOSTER/R/powerTOSTtwo.R | 230 TOSTER-0.8.2/TOSTER/R/power_TOST_functions.R | 596 - TOSTER-0.8.2/TOSTER/R/power_correlations.R | 518 - TOSTER-0.8.2/TOSTER/R/power_t_TOST.R | 228 TOSTER-0.8.2/TOSTER/R/power_two_proportions.R | 522 - TOSTER-0.8.2/TOSTER/R/rbs.R | 388 - TOSTER-0.8.2/TOSTER/R/rbs_calcs.R | 230 TOSTER-0.8.2/TOSTER/R/ses_calc.R | 256 TOSTER-0.8.2/TOSTER/R/simple_htest.R | 674 +- TOSTER-0.8.2/TOSTER/R/smd_calc.R | 444 - TOSTER-0.8.2/TOSTER/R/t_TOST.R | 936 +-- TOSTER-0.8.2/TOSTER/R/tsum_TOST.R | 748 +- TOSTER-0.8.2/TOSTER/R/tsum_funcs.R | 240 TOSTER-0.8.2/TOSTER/R/two_proportions.R | 1010 +-- TOSTER-0.8.2/TOSTER/R/wilcox_TOST.R | 682 +- TOSTER-0.8.2/TOSTER/README.md | 104 TOSTER-0.8.2/TOSTER/build/partial.rdb |binary TOSTER-0.8.2/TOSTER/build/vignette.rds |binary TOSTER-0.8.2/TOSTER/inst/CITATION | 40 TOSTER-0.8.2/TOSTER/inst/doc/IntroTOSTt.R | 542 - TOSTER-0.8.2/TOSTER/inst/doc/IntroTOSTt.Rmd | 770 +- TOSTER-0.8.2/TOSTER/inst/doc/IntroTOSTt.html | 1823 +++--- TOSTER-0.8.2/TOSTER/inst/doc/IntroductionToTOSTER.R | 112 TOSTER-0.8.2/TOSTER/inst/doc/IntroductionToTOSTER.Rmd | 390 - TOSTER-0.8.2/TOSTER/inst/doc/IntroductionToTOSTER.html | 1976 +++--- TOSTER-0.8.2/TOSTER/inst/doc/SMD_calcs.R | 154 TOSTER-0.8.2/TOSTER/inst/doc/SMD_calcs.Rmd | 1414 ++-- TOSTER-0.8.2/TOSTER/inst/doc/SMD_calcs.html | 2396 +++---- TOSTER-0.8.2/TOSTER/inst/doc/correlations.R | 202 TOSTER-0.8.2/TOSTER/inst/doc/correlations.Rmd | 346 - TOSTER-0.8.2/TOSTER/inst/doc/correlations.html | 1512 ++--- TOSTER-0.8.2/TOSTER/inst/doc/robustTOST.R | 202 TOSTER-0.8.2/TOSTER/inst/doc/robustTOST.Rmd | 660 +- TOSTER-0.8.2/TOSTER/inst/doc/robustTOST.html | 2006 +++--- TOSTER-0.8.2/TOSTER/inst/doc/the_ftestTOSTER.R | 66 TOSTER-0.8.2/TOSTER/inst/doc/the_ftestTOSTER.Rmd | 230 TOSTER-0.8.2/TOSTER/inst/doc/the_ftestTOSTER.html | 1172 +-- TOSTER-0.8.2/TOSTER/man/TOSTER-package.Rd | 54 TOSTER-0.8.2/TOSTER/man/TOSTmeta.Rd | 110 TOSTER-0.8.2/TOSTER/man/TOSTnp-methods.Rd | 82 TOSTER-0.8.2/TOSTER/man/TOSTone.Rd | 138 TOSTER-0.8.2/TOSTER/man/TOSTpaired.Rd | 166 TOSTER-0.8.2/TOSTER/man/TOSTr.Rd | 82 TOSTER-0.8.2/TOSTER/man/TOSTt-methods.Rd | 142 TOSTER-0.8.2/TOSTER/man/TOSTtwo.Rd | 202 TOSTER-0.8.2/TOSTER/man/TOSTtwo.prop.Rd | 126 TOSTER-0.8.2/TOSTER/man/as_htest.Rd | 76 TOSTER-0.8.2/TOSTER/man/boot_compare_cor.Rd | 128 TOSTER-0.8.2/TOSTER/man/boot_compare_smd.Rd | 136 TOSTER-0.8.2/TOSTER/man/boot_cor_test.Rd | 162 TOSTER-0.8.2/TOSTER/man/boot_log_TOST.Rd | 236 TOSTER-0.8.2/TOSTER/man/boot_ses_calc.Rd | 164 TOSTER-0.8.2/TOSTER/man/boot_smd_calc.Rd | 188 TOSTER-0.8.2/TOSTER/man/boot_t_TOST.Rd | 266 TOSTER-0.8.2/TOSTER/man/boot_t_test.Rd | 208 TOSTER-0.8.2/TOSTER/man/brunner_munzel.Rd | 232 TOSTER-0.8.2/TOSTER/man/compare_cor.Rd | 126 TOSTER-0.8.2/TOSTER/man/compare_smd.Rd | 128 TOSTER-0.8.2/TOSTER/man/corsum_test.Rd | 124 TOSTER-0.8.2/TOSTER/man/dataTOSTone.Rd | 166 TOSTER-0.8.2/TOSTER/man/dataTOSTpaired.Rd | 196 TOSTER-0.8.2/TOSTER/man/dataTOSTr.Rd | 126 TOSTER-0.8.2/TOSTER/man/dataTOSTtwo.Rd | 212 TOSTER-0.8.2/TOSTER/man/datatosttwoprop.Rd | 122 TOSTER-0.8.2/TOSTER/man/equ_anova.Rd | 104 TOSTER-0.8.2/TOSTER/man/equ_ftest.Rd | 108 TOSTER-0.8.2/TOSTER/man/extract_r_paired.Rd | 70 TOSTER-0.8.2/TOSTER/man/hawthorne.Rd | 38 TOSTER-0.8.2/TOSTER/man/htest-helpers.Rd | 90 TOSTER-0.8.2/TOSTER/man/log_TOST.Rd | 222 TOSTER-0.8.2/TOSTER/man/plot_cor.Rd | 100 TOSTER-0.8.2/TOSTER/man/plot_pes.Rd | 86 TOSTER-0.8.2/TOSTER/man/plot_smd.Rd | 108 TOSTER-0.8.2/TOSTER/man/powerTOSTone.Rd | 144 TOSTER-0.8.2/TOSTER/man/powerTOSTpaired.Rd | 148 TOSTER-0.8.2/TOSTER/man/powerTOSTtwo.Rd | 156 TOSTER-0.8.2/TOSTER/man/power_eq_f.Rd | 84 TOSTER-0.8.2/TOSTER/man/power_t_TOST.Rd | 120 TOSTER-0.8.2/TOSTER/man/power_twoprop.Rd | 216 TOSTER-0.8.2/TOSTER/man/power_z_cor.Rd | 158 TOSTER-0.8.2/TOSTER/man/rbs.Rd | 176 TOSTER-0.8.2/TOSTER/man/ses_calc.Rd | 146 TOSTER-0.8.2/TOSTER/man/simple_htest.Rd | 210 TOSTER-0.8.2/TOSTER/man/smd_calc.Rd | 180 TOSTER-0.8.2/TOSTER/man/t_TOST.Rd | 264 TOSTER-0.8.2/TOSTER/man/tsum_TOST.Rd | 230 TOSTER-0.8.2/TOSTER/man/twoprop_test.Rd | 222 TOSTER-0.8.2/TOSTER/man/wilcox_TOST.Rd | 266 TOSTER-0.8.2/TOSTER/man/z_cor_test.Rd | 140 TOSTER-0.8.2/TOSTER/tests/spelling.R | 6 TOSTER-0.8.2/TOSTER/tests/testthat.R | 8 TOSTER-0.8.2/TOSTER/tests/testthat/test-NCSS1.R | 162 TOSTER-0.8.2/TOSTER/tests/testthat/test-bootTOST.R | 602 +- TOSTER-0.8.2/TOSTER/tests/testthat/test-compare_smds.R | 388 - TOSTER-0.8.2/TOSTER/tests/testthat/test-corr.R | 1282 ++-- TOSTER-0.8.2/TOSTER/tests/testthat/test-data_summary_equivalent.R | 190 TOSTER-0.8.2/TOSTER/tests/testthat/test-ftests.R | 224 TOSTER-0.8.2/TOSTER/tests/testthat/test-htest.R | 1010 +-- TOSTER-0.8.2/TOSTER/tests/testthat/test-jamovi.R | 1286 ++-- TOSTER-0.8.2/TOSTER/tests/testthat/test-known_results.R | 570 - TOSTER-0.8.2/TOSTER/tests/testthat/test-log.R | 456 - TOSTER-0.8.2/TOSTER/tests/testthat/test-old_errors.R | 518 - TOSTER-0.8.2/TOSTER/tests/testthat/test-power_consistent.R | 308 - TOSTER-0.8.2/TOSTER/tests/testthat/test-power_correlation.R | 282 TOSTER-0.8.2/TOSTER/tests/testthat/test-power_t_TOST.R | 732 +- TOSTER-0.8.2/TOSTER/tests/testthat/test-powerraw.R | 102 TOSTER-0.8.2/TOSTER/tests/testthat/test-tTOST.R | 3000 +++++----- TOSTER-0.8.2/TOSTER/tests/testthat/test-twoprop.R | 752 +- TOSTER-0.8.2/TOSTER/tests/testthat/test-wilcox.R | 444 - TOSTER-0.8.2/TOSTER/vignettes/IntroTOSTt.Rmd | 770 +- TOSTER-0.8.2/TOSTER/vignettes/IntroductionToTOSTER.Rmd | 390 - TOSTER-0.8.2/TOSTER/vignettes/SMD_calcs.Rmd | 1414 ++-- TOSTER-0.8.2/TOSTER/vignettes/anovaTOSTER.R | 56 TOSTER-0.8.2/TOSTER/vignettes/anovaTOSTER.html | 976 +-- TOSTER-0.8.2/TOSTER/vignettes/correlations.Rmd | 346 - TOSTER-0.8.2/TOSTER/vignettes/references.bib | 586 - TOSTER-0.8.2/TOSTER/vignettes/robustTOST.Rmd | 660 +- TOSTER-0.8.2/TOSTER/vignettes/the_ftestTOSTER.Rmd | 230 181 files changed, 39164 insertions(+), 39159 deletions(-)
Title: Prepare and Explore Data for Palaeobiological Analyses
Description: Provides functionality to support data preparation and exploration for
palaeobiological analyses, improving code reproducibility and accessibility. The
wider aim of 'palaeoverse' is to bring the palaeobiological community together
to establish agreed standards. The package currently includes functionality for
data cleaning, binning (time and space), exploration, summarisation and
visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>)
and auxiliary functions are also provided. Details can be found in:
Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.
Author: Lewis A. Jones [aut, cre] ,
William Gearty [aut] ,
Bethany J. Allen [aut] ,
Kilian Eichenseer [aut] ,
Christopher D. Dean [aut] ,
Sofia Galvan [ctb] ,
Miranta Kouvari [ctb] ,
Pedro L. Godoy [ctb] ,
Cecily Nicholl [ctb] ,
Lucas Buffan [ctb] ,
Erin M. [...truncated...]
Maintainer: Lewis A. Jones <LewisAlan.Jones@uvigo.es>
Diff between palaeoverse versions 1.2.1 dated 2023-08-17 and 1.3.0 dated 2024-04-16
DESCRIPTION | 12 - MD5 | 67 +++--- NAMESPACE | 4 NEWS.md | 11 + R/bin_time.R | 110 +++++------ R/data.R | 3 R/palaeorotate.R | 33 +-- R/tax_expand_time.R | 56 ++++- R/tax_range_strat.R |only R/tax_range_time.R | 112 +++++++---- README.md | 8 inst/doc/phanerozoic-reefs.Rmd | 64 ++++-- inst/doc/phanerozoic-reefs.html | 90 +++++---- inst/doc/structure-and-standards.Rmd | 14 - inst/doc/structure-and-standards.html | 33 +-- inst/doc/tetrapod-biodiversity.Rmd | 77 +++++-- inst/doc/tetrapod-biodiversity.html | 328 ++++++++++++++++++---------------- man/bin_time.Rd | 31 ++- man/palaeoverse-package.Rd | 4 man/tax_expand_time.Rd | 20 +- man/tax_range_strat.Rd |only man/tax_range_time.Rd | 58 ++++-- man/tetrapods.Rd | 3 tests/testthat/_snaps/tax_range_strat |only tests/testthat/test-palaeorotate.R | 23 ++ tests/testthat/test-tax_expand_time.R | 15 + tests/testthat/test-tax_range_strat.R |only tests/testthat/test-tax_range_time.R | 3 vignettes/alpha-div-plot-3-1.png |binary vignettes/phanerozoic-reefs.Rmd | 64 ++++-- vignettes/reefs-dist-1.png |binary vignettes/reefs-max-1.png |binary vignettes/reefs-max-multi-1.png |binary vignettes/structure-and-standards.Rmd | 14 - vignettes/tetrapod-biodiversity.Rmd | 77 +++++-- 35 files changed, 818 insertions(+), 516 deletions(-)
Title: Measuring Ecosystem Multi-Functionality and Its Decomposition
Description: Provide simple functions to (i) compute a class of
multi-functionality measures for a single ecosystem for given
function weights, (ii) decompose gamma multi-functionality
for multiple ecosystems into a within-ecosystem component
(alpha multi-functionality) and an among-ecosystem component
(beta multi-functionality). In each case, the correlation
between functions can be corrected for. Based on biodiversity
and ecosystem function data, this software also facilitates
graphics for assessing biodiversity-ecosystem functioning
relationships across scales.
Author: Anne Chao [aut, cre],
Chun-Yu Liu [ctb],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between MF.beta4 versions 1.0.2 dated 2024-03-25 and 1.0.3 dated 2024-04-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 2 ++ R/Mainfun.R | 8 ++------ inst/doc/Introduction.pdf |binary 5 files changed, 11 insertions(+), 13 deletions(-)
Title: Analyzes Real-World Treatment Patterns of a Study Population of
Interest
Description: Computes treatment patterns within a given cohort using the Observational
Medical Outcomes Partnership (OMOP) common data model (CDM). As described
in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] ,
Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between TreatmentPatterns versions 2.6.5 dated 2024-02-19 and 2.6.6 dated 2024-04-16
TreatmentPatterns-2.6.5/TreatmentPatterns/R/Module.R |only TreatmentPatterns-2.6.5/TreatmentPatterns/R/R6-CDMInterface.R |only TreatmentPatterns-2.6.5/TreatmentPatterns/R/R6-PathwayConstructor.R |only TreatmentPatterns-2.6.5/TreatmentPatterns/man/InteractivePlots.Rd |only TreatmentPatterns-2.6.5/TreatmentPatterns/man/Module.Rd |only TreatmentPatterns-2.6.5/TreatmentPatterns/tests/testthat/test-PathwayConstructor.R |only TreatmentPatterns-2.6.6/TreatmentPatterns/DESCRIPTION | 14 TreatmentPatterns-2.6.6/TreatmentPatterns/MD5 | 68 +- TreatmentPatterns-2.6.6/TreatmentPatterns/NAMESPACE | 5 TreatmentPatterns-2.6.6/TreatmentPatterns/NEWS.md | 6 TreatmentPatterns-2.6.6/TreatmentPatterns/R/CDMInterface.R |only TreatmentPatterns-2.6.6/TreatmentPatterns/R/CharacterizationPlots.R | 4 TreatmentPatterns-2.6.6/TreatmentPatterns/R/InputHandler.R | 43 + TreatmentPatterns-2.6.6/TreatmentPatterns/R/InteractivePlots.R | 201 ++----- TreatmentPatterns-2.6.6/TreatmentPatterns/R/SankeyDiagram.R |only TreatmentPatterns-2.6.6/TreatmentPatterns/R/ShinyApp.R | 25 TreatmentPatterns-2.6.6/TreatmentPatterns/R/ShinyModule.R |only TreatmentPatterns-2.6.6/TreatmentPatterns/R/SunburstPlot.R |only TreatmentPatterns-2.6.6/TreatmentPatterns/R/computePathways.R | 257 +++++++++- TreatmentPatterns-2.6.6/TreatmentPatterns/R/constructPathways.R | 33 - TreatmentPatterns-2.6.6/TreatmentPatterns/R/createSankeyDiagram.R | 94 ++- TreatmentPatterns-2.6.6/TreatmentPatterns/R/createSunburstPlot.R | 36 + TreatmentPatterns-2.6.6/TreatmentPatterns/R/export.R | 75 ++ TreatmentPatterns-2.6.6/TreatmentPatterns/build/partial.rdb |binary TreatmentPatterns-2.6.6/TreatmentPatterns/build/vignette.rds |binary TreatmentPatterns-2.6.6/TreatmentPatterns/inst/WORDLIST | 8 TreatmentPatterns-2.6.6/TreatmentPatterns/inst/doc/DefiningCohorts.html | 16 TreatmentPatterns-2.6.6/TreatmentPatterns/inst/sql/ageRefTable.sql |only TreatmentPatterns-2.6.6/TreatmentPatterns/man/CharacterizationPlots.Rd | 6 TreatmentPatterns-2.6.6/TreatmentPatterns/man/InputHandler.Rd | 6 TreatmentPatterns-2.6.6/TreatmentPatterns/man/SankeyDiagram.Rd |only TreatmentPatterns-2.6.6/TreatmentPatterns/man/ShinyModule.Rd |only TreatmentPatterns-2.6.6/TreatmentPatterns/man/SunburstPlot.Rd |only TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-CDMInterfaceCDMC.R | 4 TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-CDMInterfaceDBC.R | 13 TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-InputHandler.R | 55 ++ TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-InteracivePlots.R | 42 + TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-ShinyApp.R | 3 TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-computePathways.R | 2 TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-createSankeyDiagram.R | 57 ++ TreatmentPatterns-2.6.6/TreatmentPatterns/tests/testthat/test-export.R | 2 TreatmentPatterns-2.6.6/TreatmentPatterns/vignettes/articles/bestPractices.Rmd |only TreatmentPatterns-2.6.6/TreatmentPatterns/vignettes/articles/bestPractices.html |only 43 files changed, 763 insertions(+), 312 deletions(-)
More information about TreatmentPatterns at CRAN
Permanent link
Title: Spatio-Temporal Point Pattern Methods, Model Fitting,
Diagnostics, Simulation, Local Tests
Description: Toolbox for different kinds of spatio-temporal analyses to be performed on observed point patterns, following the growing stream of literature on point process theory. This R package implements functions to perform different kinds of analyses on point processes, proposed in the papers (Siino, Adelfio, and Mateu 2018<doi:10.1007/s00477-018-1579-0>; Siino et al. 2018<doi:10.1002/env.2463>; Adelfio et al. 2020<doi:10.1007/s00477-019-01748-1>; D’Angelo, Adelfio, and Mateu 2021<doi:10.1016/j.spasta.2021.100534>; D’Angelo, Adelfio, and Mateu 2022<doi:10.1007/s00362-022-01338-4>; D’Angelo, Adelfio, and Mateu 2023<doi:10.1016/j.csda.2022.107679>). The main topics include modeling, statistical inference, and simulation issues on spatio-temporal point processes on Euclidean space and linear networks.
Author: Nicoletta D'Angelo [aut, cre] ,
Giada Adelfio [aut]
Maintainer: Nicoletta D'Angelo <nicoletta.dangelo@unipa.it>
Diff between stopp versions 0.2.1 dated 2024-04-05 and 0.2.2 dated 2024-04-16
DESCRIPTION | 10 - MD5 | 248 +++++++++++++++++++++++----------------------- NAMESPACE | 12 -- R/globaldiag.R | 107 +++++++------------ R/infl.R | 12 +- R/internals.R | 106 +++++-------------- R/localSTLKinhom.R | 32 +++++ R/localSTLginhom.R | 32 +++++ R/localdiag.R | 69 +++++++----- R/localplot.R | 7 - R/localsummary.R | 10 - R/localtest.R | 24 +++- R/locstppm.R | 36 +++++- R/plot.globaldiag.R |only R/plot.lista.R | 4 R/plot.localdiag.R | 8 - R/plot.localtest.R | 10 - R/plot.locstppm.R | 8 - R/plot.sepstlppm.R | 4 R/plot.sepstppm.R | 4 R/plot.stcov.R | 9 - R/plot.stlgcppm.R | 4 R/plot.stlp.R | 3 R/plot.stlpm.R | 5 R/plot.stp.R | 3 R/plot.stpm.R | 15 +- R/plot.stppm.R | 7 - R/print.globaldiag.R |only R/print.lista.R | 5 R/print.localdiag.R | 8 - R/print.localtest.R | 10 - R/print.locstppm.R | 9 - R/print.sepstlppm.R | 5 R/print.sepstppm.R | 3 R/print.stcov.R | 5 R/print.stlgcppm.R | 5 R/print.stlp.R | 5 R/print.stlpm.R | 5 R/print.stp.R | 5 R/print.stpm.R | 5 R/print.stppm.R | 9 - R/rETASlp.R | 10 - R/rETASp.R | 12 -- R/rstlpp.R | 12 -- R/rstpp.R | 19 +-- R/sepstlppm.R | 2 R/sepstppm.R | 2 R/stcov.R | 44 ++++++-- R/stlgcppm.R | 47 +++++++- R/stp.R | 13 +- R/stpm.R | 12 +- R/stppm.R | 41 ++++++- R/summary.globaldiag.R |only R/summary.lista.R | 5 R/summary.localdiag.R | 8 - R/summary.localtest.R | 10 - R/summary.locstppm.R | 9 - R/summary.sepstlppm.R | 6 - R/summary.sepstppm.R | 5 R/summary.stcov.R | 3 R/summary.stlgcppm.R | 5 R/summary.stlp.R | 5 R/summary.stlpm.R | 6 - R/summary.stp.R | 4 R/summary.stpm.R | 4 R/summary.stppm.R | 9 - man/globaldiag.Rd | 40 +++---- man/infl.Rd | 6 - man/localSTLKinhom.Rd | 2 man/localSTLginhom.Rd | 2 man/localdiag.Rd | 13 +- man/localplot.Rd | 6 - man/localsummary.Rd | 7 - man/localtest.Rd | 8 - man/locstppm.Rd | 9 + man/plot.globaldiag.Rd |only man/plot.lista.Rd | 2 man/plot.localdiag.Rd | 6 - man/plot.localtest.Rd | 7 - man/plot.locstppm.Rd | 6 - man/plot.sepstlppm.Rd | 2 man/plot.sepstppm.Rd | 2 man/plot.stcov.Rd | 2 man/plot.stlgcppm.Rd | 2 man/plot.stlp.Rd | 2 man/plot.stlpm.Rd | 2 man/plot.stp.Rd | 2 man/plot.stpm.Rd | 2 man/plot.stppm.Rd | 5 man/print.globaldiag.Rd |only man/print.lista.Rd | 2 man/print.localdiag.Rd | 5 man/print.localtest.Rd | 7 - man/print.locstppm.Rd | 6 - man/print.sepstlppm.Rd | 2 man/print.sepstppm.Rd | 2 man/print.stcov.Rd | 2 man/print.stlgcppm.Rd | 2 man/print.stlp.Rd | 2 man/print.stlpm.Rd | 2 man/print.stp.Rd | 2 man/print.stpm.Rd | 2 man/print.stppm.Rd | 6 - man/rETASlp.Rd | 10 - man/rETASp.Rd | 11 -- man/rstlpp.Rd | 11 -- man/rstpp.Rd | 18 +-- man/sepstlppm.Rd | 2 man/sepstppm.Rd | 2 man/stcov.Rd | 14 ++ man/stlgcppm.Rd | 6 - man/stp.Rd | 4 man/stpm.Rd | 2 man/stppm.Rd | 14 +- man/summary.globaldiag.Rd |only man/summary.lista.Rd | 2 man/summary.localdiag.Rd | 5 man/summary.localtest.Rd | 7 - man/summary.locstppm.Rd | 6 - man/summary.sepstlppm.Rd | 2 man/summary.sepstppm.Rd | 2 man/summary.stcov.Rd | 2 man/summary.stlgcppm.Rd | 2 man/summary.stlp.Rd | 2 man/summary.stlpm.Rd | 5 man/summary.stp.Rd | 2 man/summary.stpm.Rd | 3 man/summary.stppm.Rd | 6 - 128 files changed, 715 insertions(+), 763 deletions(-)
More information about mlr3resampling at CRAN
Permanent link
Title: Fitting Bayesian Poisson Regression
Description: Posterior sampling and inference for Bayesian Poisson regression models. The model specification makes use of Gaussian (or conditionally Gaussian) prior distributions on the regression coefficients. Details on the algorithm are found in D'Angelo and Canale (2023) <doi:10.1080/10618600.2022.2123337>.
Author: Laura D'Angelo
Maintainer: Laura D'Angelo <laura.dangelo@live.com>
Diff between bpr versions 1.0.7 dated 2024-01-18 and 1.0.8 dated 2024-04-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/commonfunctions.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Optimized Integer Risk Score Models
Description: Implements an optimized approach to learning risk score models, where sparsity and integer constraints are integrated into the model-fitting process.
Author: Hannah Eglinton [aut, cre],
Alice Paul [aut, cph],
Oscar Yan [aut],
R Core Team [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Ross Ihaka [ctb, cph] ,
Simon Davies [ctb] ),
Thomas Lumley [ctb] )
Maintainer: Hannah Eglinton <eglintonh@gmail.com>
Diff between riskscores versions 1.0.2 dated 2023-12-14 and 1.1.0 dated 2024-04-16
DESCRIPTION | 6 MD5 | 36 ++-- NAMESPACE | 3 R/cv_risk_mod.R | 55 +++--- R/generic.R | 22 +- R/helpers.R | 327 +++++++++++++++++++++++++++++++++------- R/risk_mod.R | 51 +++++- R/utils.R | 69 ++++++++ README.md | 8 inst/doc/riskscores.R | 17 +- inst/doc/riskscores.Rmd | 31 ++- inst/doc/riskscores.html | 215 ++++++++++++++------------ man/cv_risk_mod.Rd | 13 + man/cv_risk_mod_random_start.Rd |only man/get_metrics.Rd | 24 ++ man/get_metrics_internal.Rd |only man/get_score.Rd |only man/risk_mod.Rd | 11 + man/risk_mod_random_start.Rd |only man/stratify_folds.Rd | 4 vignettes/riskscores.Rmd | 31 ++- 21 files changed, 672 insertions(+), 251 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.5-0 dated 2023-12-14 and 1.5-1 dated 2024-04-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/R.R | 8 +++----- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ tests/bugfixes.R | 8 ++++++++ tests/bugfixes.Rout.save | 15 ++++++++++++--- tests/glm-Ex.Rout.save | 9 +++------ 8 files changed, 45 insertions(+), 25 deletions(-)
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations. Important applications are the use of splines to model spatial or temporal
trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.6 dated 2023-11-27 and 1.0.7 dated 2024-04-16
LMMsolver-1.0.6/LMMsolver/src/NodeList.cpp |only LMMsolver-1.0.6/LMMsolver/src/NodeList.h |only LMMsolver-1.0.7/LMMsolver/DESCRIPTION | 10 LMMsolver-1.0.7/LMMsolver/MD5 | 84 - LMMsolver-1.0.7/LMMsolver/NEWS.md | 10 LMMsolver-1.0.7/LMMsolver/R/LMMsolve-class.R | 9 LMMsolver-1.0.7/LMMsolver/R/LMMsolve.R | 58 - LMMsolver-1.0.7/LMMsolver/R/LMMsolver.R | 4 LMMsolver-1.0.7/LMMsolver/R/RcppExports.R | 36 LMMsolver-1.0.7/LMMsolver/R/constructRinv.R | 5 LMMsolver-1.0.7/LMMsolver/R/obtainSmoothTrend.R | 8 LMMsolver-1.0.7/LMMsolver/R/predictFunctions.R | 119 +- LMMsolver-1.0.7/LMMsolver/R/sparseMixedModels.R | 95 - LMMsolver-1.0.7/LMMsolver/R/spl1D.R | 11 LMMsolver-1.0.7/LMMsolver/R/spl2D.R | 20 LMMsolver-1.0.7/LMMsolver/R/spl3D.R | 20 LMMsolver-1.0.7/LMMsolver/R/utils.R | 38 LMMsolver-1.0.7/LMMsolver/build/partial.rdb |binary LMMsolver-1.0.7/LMMsolver/build/vignette.rds |binary LMMsolver-1.0.7/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.html | 4 LMMsolver-1.0.7/LMMsolver/inst/tinytest/GLMMFull |only LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve0 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve1 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve2 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve3 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve4 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/LMMsolve5 |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/cfFull |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/gam1DFull |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/spl1DFull |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/spl2DFull |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/spl3DFull |binary LMMsolver-1.0.7/LMMsolver/inst/tinytest/test_GLMM.R |only LMMsolver-1.0.7/LMMsolver/inst/tinytest/test_spl1D.R | 5 LMMsolver-1.0.7/LMMsolver/inst/tinytest/test_spl2D.R | 4 LMMsolver-1.0.7/LMMsolver/inst/tinytest/test_spl3D.R | 6 LMMsolver-1.0.7/LMMsolver/man/LMMsolveObject.Rd | 3 LMMsolver-1.0.7/LMMsolver/man/LMMsolver.Rd | 10 LMMsolver-1.0.7/LMMsolver/man/spl1D.Rd | 6 LMMsolver-1.0.7/LMMsolver/src/ADcholesky.cpp | 564 +--------- LMMsolver-1.0.7/LMMsolver/src/AuxFun.cpp | 58 - LMMsolver-1.0.7/LMMsolver/src/AuxFun.h | 17 LMMsolver-1.0.7/LMMsolver/src/RcppExports.cpp | 98 - LMMsolver-1.0.7/LMMsolver/src/SparseMatrix.cpp | 170 --- LMMsolver-1.0.7/LMMsolver/src/cholesky.cpp |only LMMsolver-1.0.7/LMMsolver/src/cholesky.h |only 46 files changed, 543 insertions(+), 929 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges [aut, cre, cph] ,
Sebastian Krey [aut, cph],
Olaf Mersmann [aut, cph],
Sarah Schnackenberg [aut, cph],
Guillaume Guenard [aut, cph] ,
Daniel P. W. Ellis [aut, cph] ,
Underbit Technologies [aut, cph] ,
Andrea Preusser [ctb],
Anita Thieler [ [...truncated...]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.4.6 dated 2023-11-27 and 1.4.7 dated 2024-04-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/plot-Wspec.R | 11 ++++++++--- man/dolpc.Rd | 2 +- man/plot-Wspec.Rd | 2 +- man/plot-WspecMat.Rd | 4 ++-- 6 files changed, 21 insertions(+), 16 deletions(-)
Title: Bayesian Spatial Analysis
Description: For Bayesian inference with spatial data, provides exploratory spatial analysis tools, multiple spatial model specifications, spatial model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health surveillance data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
Author: Connor Donegan [aut, cre] ,
Mitzi Morris [ctb],
Amy Tims [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between geostan versions 0.5.4 dated 2024-03-03 and 0.6.0 dated 2024-04-16
DESCRIPTION | 14 MD5 | 70 NEWS.md | 15 R/convenience-functions.R | 11 R/geostan_fit-methods.R | 4 R/internal-functions.R | 29 R/prep-censored-data.R | 21 R/stan_car.R | 41 R/stan_esf.R | 36 R/stan_glm.R | 52 R/stan_icar.R | 38 R/stan_sar.R | 42 README.md | 209 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/custom-spatial-models.Rmd | 5 inst/doc/custom-spatial-models.html | 4 inst/doc/measuring-sa.html | 18 inst/doc/raster-regression.html | 52 inst/doc/spatial-me-models.html | 16 inst/stan/parts/data.stan | 4 inst/stan/parts/gen_quants_declaration.stan | 2 inst/stan/parts/gen_quants_expression.stan | 10 inst/stan/parts/model.stan | 13 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/print_geostan_fit.Rd | 8 man/stan_car.Rd | 2 man/stan_esf.Rd | 2 man/stan_glm.Rd | 7 man/stan_icar.Rd | 2 man/stan_sar.Rd | 2 src/stanExports_foundation.h | 2057 ++++++++++++++-------------- tests/testthat/test-missing-y.R |only tests/testthat/test-stan-glm.R | 2 vignettes/custom-spatial-models.Rmd | 5 37 files changed, 1501 insertions(+), 1292 deletions(-)
Title: Flexible Odds Ratio Curves
Description: Provides flexible odds ratio curves that enable modeling non-linear relationships between continuous predictors and binary outcomes. This package facilitates a deeper understanding of the impact of each continuous predictor on the outcome by presenting results in terms of odds ratio (OR) curves based on splines. These curves allow for comparison against a specified reference value, aiding in the interpretation of the predictor's effect.
Author: Marta Azevedo [aut, cre] ,
Luis Meira-Machado [aut] ,
Artur Araujo [aut]
Maintainer: Marta Azevedo <marta.vasconcelos4@gmail.com>
Diff between flexOR versions 0.9.6 dated 2024-03-26 and 1.0.0 dated 2024-04-16
DESCRIPTION | 8 - MD5 | 20 ++-- NAMESPACE | 1 R/dfgam.R | 180 ++++++++++++++++++++------------------------ R/plot.OR.R | 20 +++- R/predict.OR.R | 2 inst/doc/main_vignette.html | 12 +- man/dfgam.Rd | 8 + man/flexOR-package.Rd | 2 man/plot.OR.Rd | 5 - man/predict.OR.Rd | 2 11 files changed, 128 insertions(+), 132 deletions(-)
Title: Classification Using Binary Procrustes Rotation
Description: Implements a classification method described by Grice (2011, ISBN:978-0-12-385194-9) using
binary procrustes rotation; a simplified version of procrustes rotation.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>
Diff between clubpro versions 0.6.0 dated 2024-03-12 and 0.6.1 dated 2024-04-16
DESCRIPTION | 6 +-- MD5 | 25 +++++++------ NAMESPACE | 6 +++ NEWS.md | 7 ++- R/classify.R | 2 + R/clubpro-package.R | 5 ++ R/pcc.R | 2 - R/threshold.R |only inst/doc/clubpro.R | 14 +++++-- inst/doc/clubpro.Rmd | 32 ++++++++++++----- inst/doc/clubpro.html | 80 +++++++++++++++++++++++++++---------------- man/plot.clubprothreshold.Rd |only man/threshold.Rd |only src/cpp_functions.cpp | 2 - vignettes/clubpro.Rmd | 32 ++++++++++++----- 15 files changed, 145 insertions(+), 68 deletions(-)
Title: Classification Based on Association Rules
Description: Provides the infrastructure for association rule-based classification including the algorithms
CBA, CMAR, CPAR, C4.5, FOIL, PART, PRM, RCAR, and RIPPER to build associative classifiers.
Hahsler et al (2019) <doi:10.32614/RJ-2019-048>.
Author: Michael Hahsler [aut, cre, cph]
,
Ian Johnson [aut, cph],
Tyler Giallanza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesCBA versions 1.2.5 dated 2022-08-19 and 1.2.6 dated 2024-04-16
DESCRIPTION | 10 +-- MD5 | 72 ++++++++++++------------ NEWS.md | 6 ++ R/AAA_arulesCBA-package.R | 13 ---- R/CBA.R | 3 - R/CBA_helpers.R | 43 +++++++++++--- R/CBA_ruleset.R | 5 + R/FOIL.R | 1 R/LUCS_KDD_CBA.R | 6 +- R/RCAR.R | 108 +++++++++++++++++++++++++++--------- R/RWeka_CBA.R | 7 +- R/discretizeDF.supervised.R | 1 R/formula_helpers.R | 2 R/mineCARs.R | 10 ++- R/predict.R | 2 R/prepareTransactions.R | 56 ++++++++++++++----- R/transactions2DF.R | 4 + README.md | 100 +++++++++++++++++---------------- build/partial.rdb |binary data/Lymphography.rda |binary data/Mushroom.rda |binary inst/CITATION | 4 + man/CBA.Rd | 9 ++- man/CBA_helpers.Rd | 15 ++++- man/CBA_ruleset.Rd | 18 +++++- man/FOIL.Rd | 10 +++ man/LUCS_KDD_CBA.Rd | 13 +++- man/RCAR.Rd | 89 +++++++++++++++++++++++------- man/RWeka_CBA.Rd | 15 ++++- man/arulesCBA-package.Rd | 27 +++++++-- man/discretizeDF.supervised.Rd | 7 ++ man/mineCARs.Rd | 16 ++++- man/predict.CBA.Rd | 1 man/prepareTransactions.Rd | 32 +++++++++- man/transactions2DF.Rd | 10 +++ tests/testthat/test-CBA_helpers.R | 112 +++++++++++++++++++++++++++++++++++--- tests/testthat/test-RCAR.R | 11 ++- 37 files changed, 620 insertions(+), 218 deletions(-)
Title: Extract and Analyze Rivers from Elevation Data
Description: Seamless extraction of river networks from digital
elevation models data. The package allows analysis of digital
elevation models that can be either externally provided or
downloaded from open source repositories (thus interfacing
with the 'elevatr' package). Extraction is performed via the
'D8' flow direction algorithm of TauDEM (Terrain Analysis Using
Digital Elevation Models), thus interfacing with the 'traudem'
package. Resulting river networks are compatible with functions
from the 'OCNet' package. See Carraro (2023)
<doi:10.5194/hess-27-3733-2023> for a presentation of the package.
Author: Luca Carraro [cre, aut],
University of Zurich [cph, fnd]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between rivnet versions 0.4.0 dated 2024-01-09 and 0.4.1 dated 2024-04-16
DESCRIPTION | 7 ++++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/extract_river.R | 10 ++++++---- inst/doc/rivnet.R | 4 ++-- inst/doc/rivnet.html | 41 +++++++++++++++++++++-------------------- man/plot.Rd | 8 +++++--- 7 files changed, 52 insertions(+), 38 deletions(-)
Title: Adverse Events Analysis Using 'metalite'
Description: Analyzes adverse events in clinical trials using the 'metalite'
data structure. The package simplifies the workflow to create
production-ready tables, listings, and figures discussed in the
adverse events analysis chapters of
"R for Clinical Study Reports and Submission"
by Zhang et al. (2022) <https://r4csr.org/>.
Author: Yilong Zhang [aut],
Yujie Zhao [aut, cre],
Benjamin Wang [aut],
Nan Xiao [aut],
Sarad Nepal [aut],
Madhusudhan Ginnaram [aut],
Venkatesh Burla [ctb],
Ruchitbhai Patel [aut],
Brian Lang [aut],
Xuan Deng [aut],
Hiroaki Fukuda [aut],
Bing Liu [aut],
Mer [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between metalite.ae versions 0.1.1 dated 2023-02-24 and 0.1.2 dated 2024-04-16
metalite.ae-0.1.1/metalite.ae/R/n_subject.R |only metalite.ae-0.1.1/metalite.ae/R/rate_compare_sum.R |only metalite.ae-0.1.1/metalite.ae/R/rtf_output.R |only metalite.ae-0.1.1/metalite.ae/R/to_mock.R |only metalite.ae-0.1.1/metalite.ae/R/to_sentence.R |only metalite.ae-0.1.1/metalite.ae/tests/testthat/Rplots.pdf |only metalite.ae-0.1.2/metalite.ae/DESCRIPTION | 19 metalite.ae-0.1.2/metalite.ae/MD5 | 172 +-- metalite.ae-0.1.2/metalite.ae/NAMESPACE | 15 metalite.ae-0.1.2/metalite.ae/NEWS.md | 37 metalite.ae-0.1.2/metalite.ae/R/avg.R |only metalite.ae-0.1.2/metalite.ae/R/data.R |only metalite.ae-0.1.2/metalite.ae/R/extend_ae_specific.R | 63 - metalite.ae-0.1.2/metalite.ae/R/extend_ae_summary_eaer.R |only metalite.ae-0.1.2/metalite.ae/R/fmt.R | 31 metalite.ae-0.1.2/metalite.ae/R/format_ae_exp_adj.R |only metalite.ae-0.1.2/metalite.ae/R/format_ae_specific.R | 44 metalite.ae-0.1.2/metalite.ae/R/format_ae_specific_subgroup.R |only metalite.ae-0.1.2/metalite.ae/R/meta_ae_example.R | 30 metalite.ae-0.1.2/metalite.ae/R/outdata.R |only metalite.ae-0.1.2/metalite.ae/R/prepare_ae_listing.R | 7 metalite.ae-0.1.2/metalite.ae/R/prepare_ae_specific.R | 78 - metalite.ae-0.1.2/metalite.ae/R/prepare_ae_specific_subgroup.R | 124 -- metalite.ae-0.1.2/metalite.ae/R/prepare_ae_summary.R | 35 metalite.ae-0.1.2/metalite.ae/R/rate_compare.R | 261 ++++ metalite.ae-0.1.2/metalite.ae/R/tlf_ae_exp_adj.R |only metalite.ae-0.1.2/metalite.ae/R/tlf_ae_listing.R | 6 metalite.ae-0.1.2/metalite.ae/R/tlf_ae_specific.R | 19 metalite.ae-0.1.2/metalite.ae/R/tlf_ae_specific_subgroup.R |only metalite.ae-0.1.2/metalite.ae/R/tlf_ae_summary.R | 14 metalite.ae-0.1.2/metalite.ae/R/utility.R |only metalite.ae-0.1.2/metalite.ae/README.md | 93 + metalite.ae-0.1.2/metalite.ae/build/vignette.rds |binary metalite.ae-0.1.2/metalite.ae/data |only metalite.ae-0.1.2/metalite.ae/inst/doc/ae-listing.R | 13 metalite.ae-0.1.2/metalite.ae/inst/doc/ae-listing.Rmd | 44 metalite.ae-0.1.2/metalite.ae/inst/doc/ae-listing.html | 201 +-- metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific-subgroup.R |only metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific-subgroup.Rmd |only metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific-subgroup.html |only metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific.R | 17 metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific.Rmd | 90 - metalite.ae-0.1.2/metalite.ae/inst/doc/ae-specific.html | 550 +++++----- metalite.ae-0.1.2/metalite.ae/inst/doc/ae-summary.R | 15 metalite.ae-0.1.2/metalite.ae/inst/doc/ae-summary.Rmd | 82 - metalite.ae-0.1.2/metalite.ae/inst/doc/ae-summary.html | 441 ++++---- metalite.ae-0.1.2/metalite.ae/inst/doc/exposure-adjusted-event-rate.R |only metalite.ae-0.1.2/metalite.ae/inst/doc/exposure-adjusted-event-rate.Rmd |only metalite.ae-0.1.2/metalite.ae/inst/doc/exposure-adjusted-event-rate.html |only metalite.ae-0.1.2/metalite.ae/inst/doc/metalite-ae.R | 9 metalite.ae-0.1.2/metalite.ae/inst/doc/metalite-ae.Rmd | 69 - metalite.ae-0.1.2/metalite.ae/inst/doc/metalite-ae.html | 94 - metalite.ae-0.1.2/metalite.ae/inst/doc/rate-compare.R | 4 metalite.ae-0.1.2/metalite.ae/inst/doc/rate-compare.html | 48 metalite.ae-0.1.2/metalite.ae/man/extend_ae_specific_duration.Rd | 6 metalite.ae-0.1.2/metalite.ae/man/extend_ae_specific_events.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/extend_ae_specific_inference.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/extend_ae_specific_subgroup.Rd |only metalite.ae-0.1.2/metalite.ae/man/extend_ae_summary_eaer.Rd |only metalite.ae-0.1.2/metalite.ae/man/fmt_est.Rd | 13 metalite.ae-0.1.2/metalite.ae/man/fmt_pval.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/format_ae_exp_adj.Rd |only metalite.ae-0.1.2/metalite.ae/man/format_ae_specific.Rd | 14 metalite.ae-0.1.2/metalite.ae/man/format_ae_specific_subgroup.Rd |only metalite.ae-0.1.2/metalite.ae/man/format_ae_summary.Rd | 14 metalite.ae-0.1.2/metalite.ae/man/meta_ae_example.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/metalite.ae-package.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/metalite_ae_adex.Rd |only metalite.ae-0.1.2/metalite.ae/man/prepare_ae_listing.Rd | 6 metalite.ae-0.1.2/metalite.ae/man/prepare_ae_specific.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/prepare_ae_specific_subgroup.Rd | 27 metalite.ae-0.1.2/metalite.ae/man/prepare_ae_summary.Rd | 6 metalite.ae-0.1.2/metalite.ae/man/rate_compare.Rd | 6 metalite.ae-0.1.2/metalite.ae/man/rate_compare_sum.Rd | 2 metalite.ae-0.1.2/metalite.ae/man/tlf_ae_exp_adj.Rd |only metalite.ae-0.1.2/metalite.ae/man/tlf_ae_listing.Rd | 8 metalite.ae-0.1.2/metalite.ae/man/tlf_ae_specific.Rd | 9 metalite.ae-0.1.2/metalite.ae/man/tlf_ae_specific_subgroup.Rd |only metalite.ae-0.1.2/metalite.ae/man/tlf_ae_summary.Rd | 8 metalite.ae-0.1.2/metalite.ae/tests/testthat.R | 3 metalite.ae-0.1.2/metalite.ae/tests/testthat/helper-extend_ae_summary_eaer.R |only metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-avg_duration.R | 35 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-avg_event.R | 44 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-extend_ae_summary_eaer.R |only metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-fmt_pval.R | 22 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-format_ae-specific-subgroup.R |only metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-meta_ae_dummy.R | 2 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-n_subject.R | 20 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-prepare_ae_listing.R | 18 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-prepare_ae_specificr.R | 187 +-- metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-prepare_ae_summary.R | 528 ++++----- metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-tlf_ae_exp_adj.R |only metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-tlf_ae_specific.R | 157 -- metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-tlf_ae_specific_subgroup.R |only metalite.ae-0.1.2/metalite.ae/tests/testthat/test-independent-testing-tlf_ae_summary.R | 3 metalite.ae-0.1.2/metalite.ae/tests/testthat/test-test-independent-testing-fmt_est.R | 2 metalite.ae-0.1.2/metalite.ae/vignettes/ae-listing.Rmd | 44 metalite.ae-0.1.2/metalite.ae/vignettes/ae-specific-subgroup.Rmd |only metalite.ae-0.1.2/metalite.ae/vignettes/ae-specific.Rmd | 90 - metalite.ae-0.1.2/metalite.ae/vignettes/ae-summary.Rmd | 82 - metalite.ae-0.1.2/metalite.ae/vignettes/exposure-adjusted-event-rate.Rmd |only metalite.ae-0.1.2/metalite.ae/vignettes/metalite-ae.Rmd | 69 - metalite.ae-0.1.2/metalite.ae/vignettes/pdf/ae0specific0sub0gender1.pdf |only metalite.ae-0.1.2/metalite.ae/vignettes/rtf/ae0specific0sub0gender1.rtf |only metalite.ae-0.1.2/metalite.ae/vignettes/rtf/ae0specific1.rtf | 160 +- metalite.ae-0.1.2/metalite.ae/vignettes/rtf/ae0specific2.rtf | 366 +++--- 106 files changed, 2531 insertions(+), 2157 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.3.1 dated 2024-03-07 and 1.3.2 dated 2024-04-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/utilities.R | 2 +- tests/testthat/test-libname.R | 2 +- tests/testthat/test-utilities.R | 12 ++++++++++++ 6 files changed, 25 insertions(+), 10 deletions(-)
Title: Estimating the Age using Auricular Surface by DNE
Description: The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), principal component regression analysis (PCR), and principal component logistic regression analysis (PCLR) methods. The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan.
Author: Jisun Jang [aut, cre]
Maintainer: Jisun Jang <jisun.jang.19@ucl.ac.uk>
Diff between JSDNE versions 4.2.2 dated 2024-02-29 and 4.3.2 dated 2024-04-16
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/PCLR_result.R | 7 ++++--- R/PCQDA_result.R | 5 +++-- R/PCR_result.R | 19 ++++++++----------- R/data_PCR.R | 4 ++-- data/data_PCLR.rda |binary data/data_PCQDA.rda |binary data/data_PCR.rda |binary man/data_PCLR.Rd | 2 +- man/data_PCQDA.Rd | 2 +- man/data_PCR.Rd | 4 ++-- 12 files changed, 35 insertions(+), 36 deletions(-)
Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps.
Author: Guillaume Guenard and Pierre Legendre, Bertrand Pages
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between codep versions 0.9-1 dated 2018-05-16 and 1.2-3 dated 2024-04-16
codep-0.9-1/codep/R/Auxiliary.R |only codep-0.9-1/codep/R/gcd.R |only codep-0.9-1/codep/R/mca.R |only codep-0.9-1/codep/data/Mite.rda |only codep-0.9-1/codep/data/Salmon.rda |only codep-0.9-1/codep/man/Mite.Rd |only codep-0.9-1/codep/man/Salmon.Rd |only codep-0.9-1/codep/man/gcd.Rd |only codep-0.9-1/codep/man/mca.Rd |only codep-0.9-1/codep/src/registerDynamicSymbol.c |only codep-1.2-3/codep/DESCRIPTION | 17 - codep-1.2-3/codep/MD5 | 70 ++-- codep-1.2-3/codep/NAMESPACE | 80 +++- codep-1.2-3/codep/R/Doubs.R |only codep-1.2-3/codep/R/Euclid.R |only codep-1.2-3/codep/R/LGDat.R |only codep-1.2-3/codep/R/LGTransforms.R |only codep-1.2-3/codep/R/MCA.R |only codep-1.2-3/codep/R/cdp-class.R |only codep-1.2-3/codep/R/codep-package.R |only codep-1.2-3/codep/R/cthreshold.R |only codep-1.2-3/codep/R/eigenmap-class.R |only codep-1.2-3/codep/R/eigenmap.R | 418 +++++++++++++++++--------- codep-1.2-3/codep/R/geodesics.R |only codep-1.2-3/codep/R/minpermute.R |only codep-1.2-3/codep/R/mite.R |only codep-1.2-3/codep/R/product-distributions.R |only codep-1.2-3/codep/R/salmon.R |only codep-1.2-3/codep/R/weighting-functions.R |only codep-1.2-3/codep/README.md |only codep-1.2-3/codep/build/partial.rdb |binary codep-1.2-3/codep/data/LGDat.rda |only codep-1.2-3/codep/data/mite.rda |only codep-1.2-3/codep/data/salmon.rda |only codep-1.2-3/codep/man/Doubs.Rd | 94 +++-- codep-1.2-3/codep/man/Euclid.Rd |only codep-1.2-3/codep/man/LGDat.Rd |only codep-1.2-3/codep/man/LGTransforms.Rd |only codep-1.2-3/codep/man/MCA.Rd |only codep-1.2-3/codep/man/cdp-class.Rd | 239 ++++++++------ codep-1.2-3/codep/man/codep-package.Rd | 212 ++++++------- codep-1.2-3/codep/man/cthreshold.Rd | 68 ++-- codep-1.2-3/codep/man/eigenmap-class.Rd | 103 +++--- codep-1.2-3/codep/man/eigenmap.Rd | 390 +++++++++++------------- codep-1.2-3/codep/man/geodesics.Rd |only codep-1.2-3/codep/man/minpermute.Rd | 90 ++--- codep-1.2-3/codep/man/mite.Rd |only codep-1.2-3/codep/man/product-distribution.Rd | 173 +++++----- codep-1.2-3/codep/man/salmon.Rd |only codep-1.2-3/codep/man/weighting-functions.Rd |only codep-1.2-3/codep/src/LGTransforms.c |only codep-1.2-3/codep/src/LGTransforms.h |only codep-1.2-3/codep/src/codep.c | 42 +- codep-1.2-3/codep/src/codep.h | 46 ++ codep-1.2-3/codep/src/geodists.c |only codep-1.2-3/codep/src/geodists.h |only codep-1.2-3/codep/src/init.c |only 57 files changed, 1176 insertions(+), 866 deletions(-)
Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>
Diff between basemaps versions 0.0.6 dated 2024-03-03 and 0.0.7 dated 2024-04-16
basemaps-0.0.6/basemaps/tests/testthat/Rplots.pdf |only basemaps-0.0.7/basemaps/DESCRIPTION | 10 +-- basemaps-0.0.7/basemaps/MD5 | 27 ++++----- basemaps-0.0.7/basemaps/NEWS.md | 13 ++++ basemaps-0.0.7/basemaps/R/basemap.R | 1 basemaps-0.0.7/basemaps/R/get_maptypes.R | 2 basemaps-0.0.7/basemaps/R/internal.R | 3 + basemaps-0.0.7/basemaps/R/plot.R | 20 +++++- basemaps-0.0.7/basemaps/README.md | 2 basemaps-0.0.7/basemaps/man/basemap.Rd | 1 basemaps-0.0.7/basemaps/man/get_maptypes.Rd | 2 basemaps-0.0.7/basemaps/man/plot.Rd | 2 basemaps-0.0.7/basemaps/tests/testthat/helper-vars.R | 9 ++- basemaps-0.0.7/basemaps/tests/testthat/test-basemap.R | 53 ++++++++++++------ basemaps-0.0.7/basemaps/tests/testthat/test-plot.R | 5 + 15 files changed, 103 insertions(+), 47 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 1.2.1 dated 2023-11-23 and 1.2.2 dated 2024-04-16
DESCRIPTION | 7 MD5 | 20 +- NEWS.md | 9 + R/create_OCN.R | 2 R/draw_contour_OCN.R | 15 + R/draw_simple_OCN.R | 11 + inst/doc/OCNet.R | 22 +- inst/doc/OCNet.html | 404 ++++++++++++++++++++++++------------------------ man/draw_contour_OCN.Rd | 6 man/draw_simple_OCN.Rd | 4 man/plot.Rd | 8 11 files changed, 274 insertions(+), 234 deletions(-)
Title: Visualization of Clonal Expansion for Single Cell Immune
Profiles
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Author: Qile Yang [cre, aut, cph]
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Diff between APackOfTheClones versions 1.1.0 dated 2024-04-05 and 1.2.0 dated 2024-04-16
APackOfTheClones-1.1.0/APackOfTheClones/data/mini_clonotype_data.rda |only APackOfTheClones-1.1.0/APackOfTheClones/data/mini_seurat_obj.rda |only APackOfTheClones-1.1.0/APackOfTheClones/man/mini_clonotype_data.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/man/mini_seurat_obj.Rd |only APackOfTheClones-1.1.0/APackOfTheClones/src/exportedMathUtils.cpp |only APackOfTheClones-1.1.0/APackOfTheClones/tests/testthat/testdata/v0/SCIP.R |only APackOfTheClones-1.2.0/APackOfTheClones/DESCRIPTION | 8 APackOfTheClones-1.2.0/APackOfTheClones/MD5 | 128 +- APackOfTheClones-1.2.0/APackOfTheClones/NAMESPACE | 1 APackOfTheClones-1.2.0/APackOfTheClones/R/APOTCPlot.R | 37 APackOfTheClones-1.2.0/APackOfTheClones/R/AdjustAPOTC.R | 87 - APackOfTheClones-1.2.0/APackOfTheClones/R/ApotcClonalNetwork.R | 104 +- APackOfTheClones-1.2.0/APackOfTheClones/R/ApotcData.R | 280 ++++-- APackOfTheClones-1.2.0/APackOfTheClones/R/ApotcIndexing.R | 448 +++++----- APackOfTheClones-1.2.0/APackOfTheClones/R/Main_algo.R | 12 APackOfTheClones-1.2.0/APackOfTheClones/R/RcppExports.R | 8 APackOfTheClones-1.2.0/APackOfTheClones/R/Repulsion.R | 4 APackOfTheClones-1.2.0/APackOfTheClones/R/RunAPOTC.R | 56 - APackOfTheClones-1.2.0/APackOfTheClones/R/cluster_labels.R | 2 APackOfTheClones-1.2.0/APackOfTheClones/R/clusters.R | 60 - APackOfTheClones-1.2.0/APackOfTheClones/R/colors.R | 2 APackOfTheClones-1.2.0/APackOfTheClones/R/data.R | 64 - APackOfTheClones-1.2.0/APackOfTheClones/R/get_clone_sizes.R | 107 +- APackOfTheClones-1.2.0/APackOfTheClones/R/insert_legend.R | 16 APackOfTheClones-1.2.0/APackOfTheClones/R/plot_API.R | 280 +++--- APackOfTheClones-1.2.0/APackOfTheClones/R/showCloneHighlight.R | 15 APackOfTheClones-1.2.0/APackOfTheClones/R/typecheck.R | 61 + APackOfTheClones-1.2.0/APackOfTheClones/R/utils.R | 117 +- APackOfTheClones-1.2.0/APackOfTheClones/R/vizAPOTC.R | 16 APackOfTheClones-1.2.0/APackOfTheClones/inst/WORDLIST | 12 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-install.Rmd | 13 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-install.html | 28 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.R | 2 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.Rmd | 17 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-runs.html | 45 - APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.Rmd | 8 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones-shared.html | 24 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones.R | 6 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones.Rmd | 8 APackOfTheClones-1.2.0/APackOfTheClones/inst/doc/APackOfTheClones.html | 10 APackOfTheClones-1.2.0/APackOfTheClones/man/APOTCPlot.Rd | 21 APackOfTheClones-1.2.0/APackOfTheClones/man/AdjustAPOTC.Rd | 24 APackOfTheClones-1.2.0/APackOfTheClones/man/RunAPOTC.Rd | 30 APackOfTheClones-1.2.0/APackOfTheClones/man/combined_pbmc.Rd | 2 APackOfTheClones-1.2.0/APackOfTheClones/man/countCloneSizes.Rd | 27 APackOfTheClones-1.2.0/APackOfTheClones/man/getSharedClones.Rd | 43 APackOfTheClones-1.2.0/APackOfTheClones/man/overlayLegend.Rd | 4 APackOfTheClones-1.2.0/APackOfTheClones/man/renameApotcRun.Rd |only APackOfTheClones-1.2.0/APackOfTheClones/man/showCloneHighlight.Rd | 5 APackOfTheClones-1.2.0/APackOfTheClones/man/vizAPOTC.Rd | 47 - APackOfTheClones-1.2.0/APackOfTheClones/src/APOTCPlotHelpers.cpp | 4 APackOfTheClones-1.2.0/APackOfTheClones/src/CirclePacker.h | 2 APackOfTheClones-1.2.0/APackOfTheClones/src/CloneLinkHelpers.cpp | 29 APackOfTheClones-1.2.0/APackOfTheClones/src/ClusterList.h | 10 APackOfTheClones-1.2.0/APackOfTheClones/src/RcppExports.cpp | 22 APackOfTheClones-1.2.0/APackOfTheClones/src/exportedUtils.cpp |only APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/helper-testFunctions.R | 10 APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-ApotcClonalNetwork.R | 68 + APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-ApotcData.R | 62 + APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-clusters.R | 7 APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-colors.R | 9 APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-get_clone_sizes.R | 69 + APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-typecheck.R | 16 APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/test-utils.R | 49 + APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/testdata/v0/mini_clonotype_data.rds |only APackOfTheClones-1.2.0/APackOfTheClones/tests/testthat/testdata/v0/mini_seurat_obj.rds |only APackOfTheClones-1.2.0/APackOfTheClones/vignettes/APackOfTheClones-install.Rmd | 13 APackOfTheClones-1.2.0/APackOfTheClones/vignettes/APackOfTheClones-runs.Rmd | 17 APackOfTheClones-1.2.0/APackOfTheClones/vignettes/APackOfTheClones-shared.Rmd | 8 APackOfTheClones-1.2.0/APackOfTheClones/vignettes/APackOfTheClones.Rmd | 8 70 files changed, 1701 insertions(+), 991 deletions(-)
More information about APackOfTheClones at CRAN
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Title: Creation, Reading and Validation of 'mzqc' Files
Description: Reads, writes and validates 'mzQC' files. The 'mzQC' format is a
standardized file format for the exchange, transmission, and archiving of
quality metrics derived from biological mass spectrometry data, as defined
by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative)
Quality Control working group.
See <https://hupo-psi.github.io/mzQC/> for details.
Author: Chris Bielow [aut, cre] ,
David Jimenez-Morales [rev, ctb]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between rmzqc versions 0.5.3 dated 2023-08-25 and 0.5.4 dated 2024-04-16
DESCRIPTION | 10 MD5 | 36 - NEWS.md | 4 R/mzQC.R | 1426 ++++++++++++++++++++-------------------- R/obo.R | 43 - R/validator.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/basic_guide.R | 4 inst/doc/basic_guide.html | 112 +-- inst/doc/using_a_custom_cv.R | 6 inst/doc/using_a_custom_cv.html | 120 +-- inst/doc/validation_guide.R | 6 inst/doc/validation_guide.html | 106 +- man/getCVDictionary.Rd | 5 man/getCVInfo.Rd | 6 man/getLatest_PSICV_URL.Rd | 3 man/validateFromString.Rd | 2 tests/testthat/test_obo.R | 10 19 files changed, 964 insertions(+), 939 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.2 dated 2024-03-28 and 1.1-35.3 dated 2024-04-16
lme4-1.1-35.2/lme4/tests/lmer-1.Rout.save |only lme4-1.1-35.2/lme4/tests/nlmer.Rout.save |only lme4-1.1-35.3/lme4/DESCRIPTION | 13 ++++--- lme4-1.1-35.3/lme4/MD5 | 18 ++++------- lme4-1.1-35.3/lme4/build/partial.rdb |binary lme4-1.1-35.3/lme4/build/vignette.rds |binary lme4-1.1-35.3/lme4/inst/NEWS.Rd | 12 ++++++- lme4-1.1-35.3/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-35.3/lme4/inst/doc/Theory.pdf |binary lme4-1.1-35.3/lme4/inst/doc/lmer.pdf |binary lme4-1.1-35.3/lme4/src/lme4CholmodDecomposition.h | 36 +--------------------- 11 files changed, 30 insertions(+), 49 deletions(-)
Title: Sparse Multiple Canonical Correlation Network Analysis Tool
Description: A canonical correlation based framework (SmCCNet) designed for the construction of phenotype-specific multi-omics networks. This framework adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. It offers a streamlined setup process that can be tailored manually or configured automatically, ensuring a flexible and user-friendly experience.
Author: Weixuan Liu [aut, cre],
Yonghua Zhuang [aut, cre],
W. Jenny Shi [aut, cre],
Thao Vu [aut],
Iain Konigsberg [aut],
Katherine Pratte [aut],
Laura Saba [aut],
Katerina Kechris [aut]
Maintainer: Weixuan Liu <weixuan.liu@cuanschutz.edu>
Diff between SmCCNet versions 2.0.2 dated 2024-01-13 and 2.0.3 dated 2024-04-16
SmCCNet-2.0.2/SmCCNet/README.md |only SmCCNet-2.0.2/SmCCNet/vignettes/figures/example_network_continuous.png |only SmCCNet-2.0.3/SmCCNet/DESCRIPTION | 12 ++--- SmCCNet-2.0.3/SmCCNet/MD5 | 24 +++++----- SmCCNet-2.0.3/SmCCNet/R/AutoSmCCNet.R | 23 +++++++-- SmCCNet-2.0.3/SmCCNet/R/SmCCNet-source.R | 23 ++++++--- SmCCNet-2.0.3/SmCCNet/inst/doc/SmCCNet_Vignette_AutoSmCCNet.pdf |binary SmCCNet-2.0.3/SmCCNet/inst/doc/SmCCNet_Vignette_MultiOmics.Rmd | 2 SmCCNet-2.0.3/SmCCNet/inst/doc/SmCCNet_Vignette_MultiOmics.pdf |binary SmCCNet-2.0.3/SmCCNet/inst/doc/SmCCNet_Vignette_SingleOmics.Rmd | 4 - SmCCNet-2.0.3/SmCCNet/inst/doc/SmCCNet_Vignette_SingleOmics.pdf |binary SmCCNet-2.0.3/SmCCNet/vignettes/SmCCNet_Vignette_MultiOmics.Rmd | 2 SmCCNet-2.0.3/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.Rmd | 4 - SmCCNet-2.0.3/SmCCNet/vignettes/figures/AutoSmCCNet.png |only SmCCNet-2.0.3/SmCCNet/vignettes/figures/example_network_continuous.jpg |only 15 files changed, 58 insertions(+), 36 deletions(-)