Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
NPX Manager or MyData. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Kristian Hoden [ctb] ,
Per Eriksson [ctb] ,
Klev Diamant [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 3.1.0 dated 2022-06-10 and 3.2.0 dated 2022-10-31
DESCRIPTION | 14 MD5 | 172 +- NAMESPACE | 6 NEWS.md | 21 R/Olink_anova.R | 74 - R/Olink_boxplot.R | 8 R/Olink_bridgeselector.R | 4 R/Olink_heatmap.R | 12 R/Olink_one_non_parametric.R | 312 ++-- R/Olink_ordinalRegression.R | 214 +-- R/Olink_ttest.R | 38 R/Olink_wilcox.R | 72 - R/Read_NPX_data.R | 482 ++++--- R/dist_plot.R | 6 R/globals.R | 2 R/linear_mixed_model.R | 73 - R/npxProcessing.R | 59 R/olink_Pathway_Enrichment.R | 111 + R/olink_Pathway_Heatmap.R | 61 R/olink_Pathway_Visualization.R | 114 - R/olink_qc_plot.R | 4 R/pca_plot.R | 155 +- R/print_and_capture.R |only R/umap_plot.R |only build/vignette.rds |binary inst/doc/Vignett.R | 51 inst/doc/Vignett.Rmd | 162 +- inst/doc/Vignett.html | 600 +++++---- inst/extdata/Example_NPX_Data_3K.zip |only man/check_data_completeness.Rd |only man/olink_anova.Rd | 4 man/olink_anova_posthoc.Rd | 6 man/olink_dist_plot.Rd | 2 man/olink_lmer.Rd | 4 man/olink_lmer_posthoc.Rd | 10 man/olink_one_non_parametric.Rd | 54 man/olink_one_non_parametric_posthoc.Rd | 59 man/olink_ordinalRegression.Rd | 19 man/olink_ordinalRegression_posthoc.Rd | 53 man/olink_pathway_enrichment.Rd | 8 man/olink_pathway_heatmap.Rd | 4 man/olink_pathway_visualization.Rd | 4 man/olink_pca_plot.Rd | 3 man/olink_ttest.Rd | 4 man/olink_umap_plot.Rd |only man/olink_wilcox.Rd | 18 man/print_and_capture.Rd |only tests/data/npx_data_format221010.RData |only tests/data/refResults.R | 93 + tests/data/refResults.RData |binary tests/testthat.R | 5 tests/testthat/_snaps/Read_NPX_data.md | 15 tests/testthat/_snaps/Volcano_plot/volcano-plot-with-coloroption.svg | 30 tests/testthat/_snaps/Volcano_plot/volcano-plot.svg | 30 tests/testthat/_snaps/olink_Pathway_Heatmap/gsea-heatmap.svg | 648 +++++----- tests/testthat/_snaps/olink_Pathway_Heatmap/ora-heatmap-with-keyword.svg | 82 - tests/testthat/_snaps/olink_Pathway_Visualization/gsea-vis-with-keyword.svg | 108 - tests/testthat/_snaps/olink_Pathway_Visualization/gsea-visualization.svg | 138 -- tests/testthat/_snaps/olink_Pathway_Visualization/ora-vis-with-keyword.svg | 62 tests/testthat/_snaps/olink_Pathway_Visualization/ora-vis-with-terms.svg | 149 -- tests/testthat/_snaps/olink_qc_plot/qc-plot-with-coloroption.svg | 3 tests/testthat/_snaps/olink_qc_plot/qc-plot.svg | 3 tests/testthat/_snaps/pca_plot.md |only tests/testthat/_snaps/pca_plot/pca-basic-plotting.svg |only tests/testthat/_snaps/pca_plot/pca-plot-color-by-treatment.svg | 328 ++--- tests/testthat/_snaps/pca_plot/pca-plot-internal-2.svg |only tests/testthat/_snaps/pca_plot/pca-plot-internal-3.svg |only tests/testthat/_snaps/pca_plot/pca-plot-internal-4.svg |only tests/testthat/_snaps/pca_plot/pca-plot-internal.svg |only tests/testthat/_snaps/pca_plot/pca-plot-label-outliers.svg |only tests/testthat/_snaps/pca_plot/pca-plot-not-label-outliers.svg |only tests/testthat/_snaps/pca_plot/pca-plot-panel-1.svg | 28 tests/testthat/_snaps/pca_plot/pca-plot-panel-2.svg | 356 ++--- tests/testthat/_snaps/pca_plot/pca-plot-with-loadings.svg | 378 ++--- tests/testthat/_snaps/pca_plot/pca-plot.svg | 360 ++--- tests/testthat/test-Olink_anova.R | 7 tests/testthat/test-Olink_boxplot.R | 12 tests/testthat/test-Olink_bridgeselector.R | 4 tests/testthat/test-Olink_heatmap.R |only tests/testthat/test-Olink_normalization.R | 61 tests/testthat/test-Olink_one_non_parametric.R |only tests/testthat/test-Olink_ordinalRegression.R |only tests/testthat/test-Olink_ttest.R | 5 tests/testthat/test-Read_NPX_data.R | 39 tests/testthat/test-Volcano_plot.R | 12 tests/testthat/test-dist_plot.R | 5 tests/testthat/test-linear_mixed_model.R | 24 tests/testthat/test-npxProcessing.R | 16 tests/testthat/test-olink_Pathway_Enrichment.R | 9 tests/testthat/test-olink_Pathway_Heatmap.R | 31 tests/testthat/test-olink_Pathway_Visualization.R | 52 tests/testthat/test-olink_qc_plot.R | 10 tests/testthat/test-pca_plot.R | 199 +++ tests/testthat/test-print_and_capture.R |only tests/testthat/test-umap_plot.R |only tests/testthat/test_Olink_wilcox.R |only vignettes/Vignett.Rmd | 162 +- vignettes/bridging_introduction.html |only 98 files changed, 3710 insertions(+), 2833 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing some larger and/or
higher-resolution databases. NOTE: this is a legacy package. The world map is out-dated.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapdata versions 2.3.0 dated 2018-03-30 and 2.3.1 dated 2022-10-31
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- man/china.Rd | 4 ++-- man/japan.Rd | 4 ++-- man/nzHires.Rd | 4 ++-- man/rivers.Rd | 4 ++-- man/world2Hires.Rd | 8 ++++---- man/worldHires.Rd | 6 +++--- src/Gmake.c | 49 +++++++++++++++---------------------------------- src/Lmake.c | 44 ++++++++++++-------------------------------- 10 files changed, 57 insertions(+), 96 deletions(-)
Title: Climate Crop Zoning Based in Air Temperature for Brazil
Description: Climate crop zoning based in minimum and maximum air temperature. The data used in the package are from 'TerraClimate' dataset (<https://www.climatologylab.org/terraclimate.html>), but, it have been calibrated with automatic weather stations of National Meteorological Institute of Brazil. The climate crop zoning of this package can be run for all the Brazilian territory.
Author: Roberto Filgueiras [aut, cre] ,
Luan P. Venancio [aut] ,
Catariny C. Aleman [aut] ,
Fernando F. da Cunha [aut]
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Diff between cropZoning versions 1.0.1 dated 2021-03-20 and 1.0.2 dated 2022-10-31
DESCRIPTION | 10 ++++----- MD5 | 43 ++++++++++++++++++++++-------------------- NEWS.md | 24 +++++++++++++++++++++++ R/calibration_tmax_and_tmin.R | 3 -- R/ccrop_zoning.R | 1 R/download_terraclimate.R | 3 -- R/loadROI.R | 1 R/plot_ccrop_zoning.R | 1 R/see_brazil_biomes.R | 1 R/see_brazil_states.R | 3 -- R/tmean.R | 2 - R/tmean_monthly_stack.R | 1 inst/desktop.ini |only inst/extdata/desktop.ini |only man/ccrop_zoning.Rd | 3 -- man/download_terraclimate.Rd | 3 -- man/figures/desktop.ini |only man/loadROI.Rd | 3 -- man/plot_ccrop_zoning.Rd | 3 -- man/see_brazil_biomes.Rd | 3 -- man/see_brazil_states.Rd | 3 -- man/tmax_calibration.Rd | 3 -- man/tmean.Rd | 3 -- man/tmean_monthly_stack.Rd | 3 -- 24 files changed, 65 insertions(+), 55 deletions(-)
Title: An R Interface to the Onigmo Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Onigmo library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.7.1.1 dated 2021-11-02 and 1.7.2.1 dated 2022-10-31
DESCRIPTION | 8 MD5 | 20 NEWS | 16 README.md | 10 src/onig/enc/jis/props.h | 8 src/onig/enc/unicode/name2ctype.h | 8 src/onig/regparse.c | 6 src/onig/st.c | 1261 +++++++++++++++++++++++--------------- src/onig/st.h | 19 src/zzz.c | 4 src/zzz.h | 4 11 files changed, 826 insertions(+), 538 deletions(-)
Title: Logic Regression
Description: Routines for fitting Logic Regression models. Logic Regression is described
in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte
Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005)
<DOI:10.1002/gepi.20042>.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between LogicReg versions 1.6.4 dated 2021-07-06 and 1.6.5 dated 2022-10-31
LogicReg-1.6.4/LogicReg/src/My_own_scoring.f |only LogicReg-1.6.5/LogicReg/DESCRIPTION | 8 ++-- LogicReg-1.6.5/LogicReg/MD5 | 35 +++++++++---------- LogicReg-1.6.5/LogicReg/R/LogicReg.R | 2 - LogicReg-1.6.5/LogicReg/inst/condlogic.ff | 12 +++--- LogicReg-1.6.5/LogicReg/man/logreg.Rd | 5 +- LogicReg-1.6.5/LogicReg/man/logreg.anneal.control.Rd | 4 +- LogicReg-1.6.5/LogicReg/man/logreg.myown.Rd | 27 +++++++------- LogicReg-1.6.5/LogicReg/man/logreg.tree.control.Rd | 5 +- LogicReg-1.6.5/LogicReg/man/logregmodel.Rd | 5 +- LogicReg-1.6.5/LogicReg/man/logregtree.Rd | 5 +- LogicReg-1.6.5/LogicReg/man/plot.logreg.Rd | 5 +- LogicReg-1.6.5/LogicReg/man/plot.logregmodel.Rd | 4 +- LogicReg-1.6.5/LogicReg/man/plot.logregtree.Rd | 5 +- LogicReg-1.6.5/LogicReg/src/Myownscoring.f |only LogicReg-1.6.5/LogicReg/src/clogic.c | 25 +++++-------- LogicReg-1.6.5/LogicReg/src/clogic.h |only LogicReg-1.6.5/LogicReg/src/registerDynamicSymbol.c | 3 + LogicReg-1.6.5/LogicReg/src/slogic.f | 6 +-- LogicReg-1.6.5/LogicReg/src/swrite.c | 6 +-- 20 files changed, 78 insertions(+), 84 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 1.1-30 dated 2022-07-08 and 1.1-31 dated 2022-10-31
lme4-1.1-30/lme4/inst/doc/Doxyfile |only lme4-1.1-30/lme4/inst/doc/lme4-extras.pdf |only lme4-1.1-30/lme4/inst/doc/profiling.txt |only lme4-1.1-31/lme4/DESCRIPTION | 8 +-- lme4-1.1-31/lme4/MD5 | 61 +++++++++++-------------- lme4-1.1-31/lme4/R/GHrule.R | 39 +++------------ lme4-1.1-31/lme4/R/hooks.R | 2 lme4-1.1-31/lme4/R/lmer.R | 58 +++++++++++++++++------ lme4-1.1-31/lme4/R/predict.R | 4 - lme4-1.1-31/lme4/R/profile.R | 3 + lme4-1.1-31/lme4/build/partial.rdb |binary lme4-1.1-31/lme4/build/vignette.rds |binary lme4-1.1-31/lme4/inst/NEWS.Rd | 20 ++++++-- lme4-1.1-31/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-31/lme4/inst/doc/Theory.pdf |binary lme4-1.1-31/lme4/inst/doc/lmer.pdf |binary lme4-1.1-31/lme4/inst/doc/lmerperf.html | 17 ++---- lme4-1.1-31/lme4/man/GHrule.Rd | 36 ++++++++++++-- lme4-1.1-31/lme4/man/VerbAgg.Rd | 4 - lme4-1.1-31/lme4/man/convergence.Rd | 4 + lme4-1.1-31/lme4/tests/boundary.R | 5 -- lme4-1.1-31/lme4/tests/confint.R | 12 +++- lme4-1.1-31/lme4/tests/elston.R | 21 ++++---- lme4-1.1-31/lme4/tests/hatvalues.R | 5 +- lme4-1.1-31/lme4/tests/lmer-1.R | 6 ++ lme4-1.1-31/lme4/tests/testthat/test-allFit.R | 4 - lme4-1.1-31/lme4/tests/testthat/test-glmer.R | 4 - lme4-1.1-31/lme4/tests/testthat/test-glmernb.R | 4 - lme4-1.1-31/lme4/tests/testthat/test-lmer.R | 2 lme4-1.1-31/lme4/tests/testthat/test-methods.R | 11 +++- lme4-1.1-31/lme4/tests/testthat/test-predict.R | 11 ++++ lme4-1.1-31/lme4/tests/testthat/test-start.R | 4 - lme4-1.1-31/lme4/tests/testthat/test-summary.R | 23 +++++++-- 33 files changed, 224 insertions(+), 144 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms, see
Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre],
Isaac Gravestock [aut],
Robert Davies [cph],
Stephen Moshier [cph],
Gareth Ambler [cph],
Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Diff between bfp versions 0.0-45 dated 2022-04-02 and 0.0-46 dated 2022-10-31
ChangeLog | 5 ++ DESCRIPTION | 13 ++----- MD5 | 12 +++--- data/ozone.RData |binary man/scrHpd.Rd | 102 +++++++++++++++++++++++++++---------------------------- src/hyp2f1.c | 11 +---- src/mtherr.c | 4 -- 7 files changed, 71 insertions(+), 76 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis' (included as a fallback) with
'MsgPack' encoding provided via 'RcppMsgPack' headers. It now also
includes the pub/sub functions from the 'rredis' package.
Author: Dirk Eddelbuettel and Bryan W. Lewis
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.2.1 dated 2022-04-09 and 0.2.2 dated 2022-10-31
ChangeLog | 15 DESCRIPTION | 12 MD5 | 20 build/vignette.rds |binary configure | 2142 ++++++++++++++++--------------- configure.ac | 2 inst/NEWS.Rd | 22 inst/doc/market-monitoring.pdf |binary inst/doc/redis-introduction.pdf |binary inst/pubsub/intraday-GLOBEX-from-Redis.r | 10 src/init.c | 4 11 files changed, 1195 insertions(+), 1032 deletions(-)
Title: Functional Data Analysis and Partial Differential Equations
(PDE); Statistical Analysis of Functional and Spatial Data,
Based on Regression with PDE Regularization
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021). Spatial Regression With Partial Differential Equation Regularisation. International Statistical Review, 89(3), 505-531. for an overview. The release 1.1-9 requires R (>= 4.2.0) to be installed on windows machines.
Author: Eleonora Arnone [aut, cre],
Laura M. Sangalli [aut],
Eardi Lila [aut],
Jim Ramsay [aut],
Luca Formaggia [aut],
Giovanni Ardenghi [ctb],
Michele Cavazzutti [ctb],
Aldo Clemente [ctb],
Alessandra Colli [ctb],
Alberto Colombo [ctb],
Luca Colombo [ctb],
[...truncated...]
Maintainer: Eleonora Arnone <eleonora.arnone@polimi.it>
Diff between fdaPDE versions 1.1-8 dated 2022-06-17 and 1.1-10 dated 2022-10-31
DESCRIPTION | 20 MD5 | 73 NAMESPACE | 7 NEWS.md | 8 R/InferenceDataObject.R |only R/checkInferenceParameters.R |only R/smoothing.R | 238 ++ R/smoothing_CPP.R | 144 + R/smoothing_CPP_time.R | 294 +++ R/smoothing_graph_CPP.R | 46 R/smoothing_graph_CPP_time.R | 95 + R/smoothing_manifold_CPP.R | 47 R/smoothing_manifold_CPP_time.R | 99 + R/smoothing_time.R | 196 ++ R/smoothing_volume_CPP.R | 142 + R/smoothing_volume_CPP_time.R | 285 +++ README.md | 5 man/inferenceDataObject-class.Rd |only man/inferenceDataObjectBuilder.Rd |only man/smooth.FEM.Rd | 35 man/smooth.FEM.time.Rd | 21 src/C_Libraries/triangle.c | 1001 ------------ src/C_Libraries/triangle.h | 7 src/FdaPDE_init.c | 24 src/Inference |only src/Lambda_Optimization/Include/Solution_Builders.h | 10 src/Lambda_Optimization/Include/Solution_Builders_imp.h | 521 ++++-- src/Regression/Include/Mixed_FE_Regression.h | 71 src/Regression/Source/Rfun_Regression_Laplace.cpp | 581 +++--- src/Regression/Source/Rfun_Regression_PDE.cpp | 695 ++++---- src/Regression/Source/Rfun_Regression_PDE_Space_Varying.cpp | 685 ++++---- src/Skeletons/Include/Regression_Skeleton.h | 673 +++++--- src/Skeletons/Include/Regression_Skeleton_Time.h | 109 + 33 files changed, 3651 insertions(+), 2481 deletions(-)
Title: Additional Operators for Image Models
Description: Implements additional operators for computer vision models, including
operators necessary for image segmentation and object detection deep learning
models.
Author: Daniel Falbel [aut, cre],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvisionlib versions 0.2.0 dated 2022-06-14 and 0.3.0 dated 2022-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ R/package.R | 20 ++++++++++++++++++-- 4 files changed, 30 insertions(+), 9 deletions(-)
More information about torchvisionlib at CRAN
Permanent link
Title: Heart Rate Variability Analysis of ECG Data
Description: Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis. See Garcia et al. (2017) <DOI:10.1007/978-3-319-65355-6>.
Author: Leandro Rodriguez-Linares [aut, cre],
Xose Vila [aut],
Maria Jose Lado [aut],
Arturo Mendez [aut],
Abraham Otero [aut],
Constantino Antonio Garcia [aut],
Matti Lassila [ctb]
Maintainer: Leandro Rodriguez-Linares <leandro@uvigo.es>
Diff between RHRV versions 4.2.6 dated 2020-12-14 and 4.2.7 dated 2022-10-31
DESCRIPTION | 13 +++++-------- MD5 | 10 +++++----- R/CalculateNonLinearParameters.R | 4 ++-- build/vignette.rds |binary inst/doc/RHRV-quickstart.html | 6 +++--- src/filterhr.c | 2 +- 6 files changed, 16 insertions(+), 19 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 1.4-2 dated 2022-06-30 and 1.4-3 dated 2022-10-31
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/dpq_etc.R | 8 ++++++-- R/mlt.R | 2 +- R/plot.R | 22 ++++++++++++++++------ R/predict.R | 17 ++++++++++++----- inst/NEWS.Rd | 15 ++++++++++++++- man/predict.Rd | 22 ++++++++++++++++------ tests/predict-Ex.R | 11 +++++++++++ tests/predict-Ex.Rout.save | 17 ++++++++++++++--- 10 files changed, 103 insertions(+), 37 deletions(-)
Title: Downloads and Organizes Financial Data from Yahoo Finance
Description: Facilitates download of financial data from Yahoo Finance <https://finance.yahoo.com/>,
a vast repository of stock price data across multiple financial exchanges. The package offers a local caching system
and support for parallel computation.
Author: Marcelo Perlin [aut, cre],
Nic Crane [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>),
Alexander Fischer [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>)
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between yfR versions 1.0.2 dated 2022-08-27 and 1.0.3 dated 2022-10-31
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 4 R/yf_get.R | 2 inst/doc/diff-batchgetsymbols.html | 18 +-- inst/doc/getting-started.html | 171 ++++++++++++++++++------------------- inst/doc/using-collections.html | 115 ++++++++++++------------ 7 files changed, 165 insertions(+), 163 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] ,
EDJNet [fnd]
Maintainer: Giorgio Comai <giorgio.comai@cci.tn.it>
Diff between tidywikidatar versions 0.5.4 dated 2022-08-06 and 0.5.5 dated 2022-10-31
DESCRIPTION | 8 MD5 | 38 +-- NEWS.md | 5 R/tw_check_qid.R | 2 R/tw_extract.R | 32 +-- R/tw_get.R | 3 R/tw_get_cached_search.R | 6 R/tw_get_field.R | 4 R/tw_get_image.R | 4 R/tw_get_others.R | 4 R/tw_get_p_wide.R | 36 +-- R/tw_get_property.R | 6 R/tw_get_property_label_description.R | 6 R/tw_get_property_with_details.R | 2 R/tw_get_wikipedia_page_links.R | 8 R/tw_get_wikipedia_page_section_links.R | 4 R/tw_search.R | 19 - README.md | 12 - inst/doc/caching.html | 272 ++++++++++++++++++++++++-- inst/doc/wikipedia_start.html | 333 +++++++++++++++++++++++++++++--- 20 files changed, 664 insertions(+), 140 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative workflows for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible workflows concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between tarchetypes versions 0.7.1 dated 2022-09-07 and 0.7.2 dated 2022-10-31
DESCRIPTION | 6 - MD5 | 114 ++++++++++---------- NAMESPACE | 6 - NEWS.md | 5 R/tar_force.R | 3 R/tar_map2.R | 1 R/tar_map2_count.R | 1 R/tar_map2_count_raw.R | 1 R/tar_map2_raw.R | 32 ++++- R/tar_map2_size.R | 1 R/tar_map2_size_raw.R | 1 R/tar_map_rep.R | 1 R/tar_map_rep_raw.R | 12 +- R/tar_package.R | 12 +- R/tar_quarto_rep_raw.R | 24 +++- R/tar_render_rep_raw.R | 21 +++ R/tar_rep.R | 35 +++++- R/tar_rep2.R | 1 R/tar_rep2_raw.R | 24 +++- R/tar_rep_raw.R | 56 ++++++++-- man/tar_age.Rd | 7 - man/tar_change.Rd | 7 - man/tar_combine.Rd | 7 - man/tar_combine_raw.Rd | 7 - man/tar_download.Rd | 7 - man/tar_file_read.Rd | 7 - man/tar_files.Rd | 7 - man/tar_files_raw.Rd | 7 - man/tar_force.Rd | 7 - man/tar_formats.Rd | 7 - man/tar_group_by.Rd | 7 - man/tar_group_count.Rd | 7 - man/tar_group_select.Rd | 7 - man/tar_group_size.Rd | 7 - man/tar_map2.Rd | 38 +++++- man/tar_map2_count.Rd | 38 +++++- man/tar_map2_count_raw.Rd | 38 +++++- man/tar_map2_raw.Rd | 38 +++++- man/tar_map2_size.Rd | 38 +++++- man/tar_map2_size_raw.Rd | 38 +++++- man/tar_map_rep.Rd | 38 +++++- man/tar_map_rep_raw.Rd | 38 +++++- man/tar_rep.Rd | 43 ++++++- man/tar_rep2.Rd | 38 +++++- man/tar_rep2_raw.Rd | 38 +++++- man/tar_rep_map.Rd | 7 - man/tar_rep_map_raw.Rd | 7 - man/tar_rep_raw.Rd | 38 +++++- man/tar_rep_run.Rd | 4 man/tar_skip.Rd | 7 - tests/testthat/test-tar_map2.R | 192 +++++++++++++++++++++++++++++++++-- tests/testthat/test-tar_map2_count.R | 2 tests/testthat/test-tar_map2_size.R | 2 tests/testthat/test-tar_map_rep.R | 142 +++++++++++++++++++++++++ tests/testthat/test-tar_render_rep.R | 56 ++++++++++ tests/testthat/test-tar_rep.R | 102 +++++++++++++++++- tests/testthat/test-tar_rep2.R | 178 ++++++++++++++++++++++++++++++++ tests/testthat/test-tar_skip.R | 3 58 files changed, 1320 insertions(+), 298 deletions(-)
Title: Fast n-Gram 'Tokenization'
Description: An n-gram is a sequence of n "words" taken, in order, from a
body of text. This is a collection of utilities for creating,
displaying, summarizing, and "babbling" n-grams. The
'tokenization' and "babbling" are handled by very efficient C
code, which can even be built as its own standalone library.
The babbler is a simple Markov chain. The package also offers
a vignette with complete example 'workflows' and information about
the utilities offered in the package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [aut]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between ngram versions 3.2.1 dated 2022-03-13 and 3.2.2 dated 2022-10-31
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ README.md | 2 +- src/getseed.c | 9 ++++----- src/ngram/src/rand/utils.c | 4 +--- src/ngram_native.c | 2 +- 7 files changed, 19 insertions(+), 19 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Jakub Nowosad [aut] ,
Sebastian Hanss [aut] ,
Laura J. Graham [ctb] ,
Jeffrey Hollister [ctb] ,
Kimberly A. With [ctb] ,
Florian Prive [ctb] function),
Project Nayuki [ctb] ,
Matt Strima [...truncated...]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between landscapemetrics versions 1.5.4 dated 2021-09-02 and 1.5.5 dated 2022-10-31
landscapemetrics-1.5.4/landscapemetrics/inst/doc/getstarted.R |only landscapemetrics-1.5.4/landscapemetrics/inst/doc/getstarted.Rmd |only landscapemetrics-1.5.4/landscapemetrics/inst/doc/getstarted.html |only landscapemetrics-1.5.4/landscapemetrics/man/figures/README-unnamed-chunk-1-1.png |only landscapemetrics-1.5.4/landscapemetrics/vignettes/getstarted.Rmd |only landscapemetrics-1.5.5/landscapemetrics/DESCRIPTION | 16 landscapemetrics-1.5.5/landscapemetrics/MD5 | 561 ++++------ landscapemetrics-1.5.5/landscapemetrics/NEWS.md | 7 landscapemetrics-1.5.5/landscapemetrics/R/calculate_lsm.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/extract_lsm.R | 16 landscapemetrics-1.5.5/landscapemetrics/R/get_centroids.R | 6 landscapemetrics-1.5.5/landscapemetrics/R/get_patches.R | 147 +- landscapemetrics-1.5.5/landscapemetrics/R/get_unique_values.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/landscapemetrics-package.R | 4 landscapemetrics-1.5.5/landscapemetrics/R/list_lsm.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_ai.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_area_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_area_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_area_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_ca.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_cai_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_cai_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_cai_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_circle_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_circle_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_circle_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_clumpy.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_cohesion.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_contig_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_contig_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_contig_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_core_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_core_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_core_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_cpland.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_dcad.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_dcore_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_dcore_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_dcore_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_division.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_ed.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_enn_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_enn_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_enn_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_frac_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_frac_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_frac_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_gyrate_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_gyrate_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_gyrate_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_iji.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_lpi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_lsi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_mesh.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_ndca.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_nlsi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_np.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_pafrac.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_para_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_para_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_para_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_pd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_pladj.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_pland.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_shape_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_shape_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_shape_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_split.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_tca.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_c_te.R | 4 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_ai.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_area_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_area_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_area_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_cai_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_cai_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_cai_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_circle_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_circle_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_circle_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_cohesion.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_contag.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_contig_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_contig_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_contig_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_core_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_core_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_core_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_dcad.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_dcore_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_dcore_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_dcore_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_division.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_ed.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_enn_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_enn_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_enn_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_frac_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_frac_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_frac_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_gyrate_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_gyrate_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_gyrate_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_iji.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_lpi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_lsi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_mesh.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_msidi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_msiei.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_ndca.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_np.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_pafrac.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_para_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_para_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_para_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_pd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_pladj.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_pr.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_prd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_rpr.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_shape_cv.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_shape_mn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_shape_sd.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_shdi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_shei.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_sidi.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_siei.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_split.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_ta.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_tca.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_l_te.R | 4 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_area.R | 3 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_cai.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_circle.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_contig.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_core.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_enn.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_frac.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_gyrate.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_ncore.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_para.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_perim.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/lsm_p_shape.R | 2 landscapemetrics-1.5.5/landscapemetrics/R/show_cores.R | 10 landscapemetrics-1.5.5/landscapemetrics/R/show_lsm.R | 7 landscapemetrics-1.5.5/landscapemetrics/R/show_patches.R | 7 landscapemetrics-1.5.5/landscapemetrics/R/spatialize_lsm.R | 34 landscapemetrics-1.5.5/landscapemetrics/R/window_lsm.R | 17 landscapemetrics-1.5.5/landscapemetrics/build/vignette.rds |binary landscapemetrics-1.5.5/landscapemetrics/inst/doc/get_started.R |only landscapemetrics-1.5.5/landscapemetrics/inst/doc/get_started.Rmd |only landscapemetrics-1.5.5/landscapemetrics/inst/doc/get_started.html |only landscapemetrics-1.5.5/landscapemetrics/man/calculate_lsm.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/figures/README-unnamed-chunk-2-1.png |binary landscapemetrics-1.5.5/landscapemetrics/man/landscapemetrics.Rd | 3 landscapemetrics-1.5.5/landscapemetrics/man/list_lsm.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_ai.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_area_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_area_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_area_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_ca.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_cai_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_cai_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_cai_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_circle_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_circle_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_circle_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_clumpy.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_cohesion.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_contig_cv.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_contig_mn.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_contig_sd.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_core_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_core_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_core_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_cpland.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_dcad.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_dcore_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_dcore_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_dcore_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_division.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_ed.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_enn_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_enn_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_enn_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_frac_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_frac_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_frac_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_gyrate_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_gyrate_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_gyrate_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_iji.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_lpi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_lsi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_mesh.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_ndca.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_nlsi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_np.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_pafrac.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_para_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_para_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_para_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_pd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_pladj.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_pland.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_shape_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_shape_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_shape_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_split.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_tca.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_c_te.Rd | 4 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_ai.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_area_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_area_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_area_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_cai_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_cai_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_cai_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_circle_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_circle_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_circle_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_cohesion.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_contag.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_contig_cv.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_contig_mn.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_contig_sd.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_core_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_core_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_core_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_dcad.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_dcore_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_dcore_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_dcore_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_division.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_ed.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_enn_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_enn_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_enn_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_frac_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_frac_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_frac_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_gyrate_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_gyrate_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_gyrate_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_iji.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_lpi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_lsi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_mesh.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_msidi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_msiei.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_ndca.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_np.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_pafrac.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_para_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_para_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_para_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_pd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_pladj.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_pr.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_prd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_rpr.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_shape_cv.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_shape_mn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_shape_sd.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_shdi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_shei.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_sidi.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_siei.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_split.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_ta.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_tca.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_l_te.Rd | 4 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_area.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_cai.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_circle.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_contig.Rd | 8 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_core.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_enn.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_frac.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_gyrate.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_ncore.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_para.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_perim.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/lsm_p_shape.Rd | 2 landscapemetrics-1.5.5/landscapemetrics/man/window_lsm.Rd | 5 landscapemetrics-1.5.5/landscapemetrics/vignettes/get_started.Rmd |only 286 files changed, 688 insertions(+), 725 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
Description: Maximum likelihood estimation of the parameters of a fractionally
differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
including inference and basic methods. Some alternative algorithms to estimate "H".
Author: Martin Maechler [aut, cre] ,
Chris Fraley [ctb, cph] ,
Friedrich Leisch [ctb] ,
Valderio Reisen [ctb] & fdSperio),
Artur Lemonte [ctb] & fdSperio),
Rob Hyndman [ctb] & fitted,
<https://orcid.org/0000-0002-2140-5352>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between fracdiff versions 1.5-1 dated 2020-01-24 and 1.5-2 dated 2022-10-31
ChangeLog | 5 +++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- build/partial.rdb |binary man/fracdiff.Rd | 2 +- src/fdcore.c | 8 +++----- src/fracdiff.h | 2 +- src/init.c | 12 ++++++------ 8 files changed, 28 insertions(+), 25 deletions(-)
Title: Spatial Crop Water Demand for Brazil
Description: Estimation of crop water demand can be processed via this package. As example, the data from 'TerraClimate' dataset (<https://www.climatologylab.org/terraclimate.html>) calibrated with automatic weather stations of National Meteorological Institute of Brazil is available in a coarse spatial resolution to do the crop water demand. However, the user have also the option to download the variables directly from 'TerraClimate' repository with the download.terraclimate function and access the original 'TerraClimate' products. If the user believes that is necessary calibrate the variables, there is another function to do it. Lastly, the estimation of the crop water demand present in this package can be run for all the Brazilian territory with 'TerraClimate' dataset.
Author: Roberto Filgueiras [aut, cre] ,
Luan P. Venancio [aut] ,
Catariny C. Aleman [aut] ,
Fernando F. da Cunha [aut]
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Diff between cropDemand versions 1.0.1 dated 2021-01-26 and 1.0.2 dated 2022-10-31
cropDemand-1.0.1/cropDemand/inst/desktop.ini |only cropDemand-1.0.1/cropDemand/inst/extdata/desktop.ini |only cropDemand-1.0.1/cropDemand/man/figures/desktop.ini |only cropDemand-1.0.2/cropDemand/DESCRIPTION | 10 +-- cropDemand-1.0.2/cropDemand/MD5 | 41 ++++++--------- cropDemand-1.0.2/cropDemand/NEWS.md | 25 +++++++++ cropDemand-1.0.2/cropDemand/R/LoadROI.R | 1 cropDemand-1.0.2/cropDemand/R/WaterDemand.R | 1 cropDemand-1.0.2/cropDemand/R/calibration_ppt_etp.R | 2 cropDemand-1.0.2/cropDemand/R/download_terraclimate.R | 1 cropDemand-1.0.2/cropDemand/R/monthly_stack.R | 1 cropDemand-1.0.2/cropDemand/R/plot_AWC.R | 1 cropDemand-1.0.2/cropDemand/R/see_brazil_biomes.R | 1 cropDemand-1.0.2/cropDemand/R/see_brazil_states.R | 1 cropDemand-1.0.2/cropDemand/man/download_terraclimate.Rd | 3 - cropDemand-1.0.2/cropDemand/man/eto_calibration.Rd | 3 - cropDemand-1.0.2/cropDemand/man/loadROI.Rd | 3 - cropDemand-1.0.2/cropDemand/man/monthly_stack.Rd | 3 - cropDemand-1.0.2/cropDemand/man/plot_AWC.Rd | 3 - cropDemand-1.0.2/cropDemand/man/ppt_calibration.Rd | 3 - cropDemand-1.0.2/cropDemand/man/see_brazil_biomes.Rd | 3 - cropDemand-1.0.2/cropDemand/man/see_brazil_states.Rd | 3 - cropDemand-1.0.2/cropDemand/man/waterDemand.Rd | 3 - 23 files changed, 58 insertions(+), 54 deletions(-)
Title: Download Data from Kenneth French's Website
Description: Downloads all the datasets (you can exclude the daily ones or specify a list of those you are targeting specifically) from Kenneth French's Website at <https://mba.tuck.dartmouth.edu/pages/faculty/ken.french/data_library.html>, process them and convert them to list of 'xts' (time series).
Author: Sebastian Stoeckl [aut, cre] ,
Annar Massimov [ctb]
Maintainer: Sebastian Stoeckl <sebastian.stoeckl@uni.li>
Diff between FFdownload versions 1.0.6 dated 2021-05-27 and 1.1.0 dated 2022-10-31
DESCRIPTION | 18 ++++++--- MD5 | 25 +++++++++--- NAMESPACE | 1 NEWS.md | 5 ++ R/FFdownload.R | 15 ++++++- R/converter.R | 85 ++++++++++++++++++++++++++++++++++++++++++- README.md | 100 ++++++++++++++++++++++++++++++++++----------------- build |only inst |only man/FFdownload.Rd | 11 ++++- man/converter_tbl.Rd |only vignettes |only 12 files changed, 208 insertions(+), 52 deletions(-)
Title: Starter Kit for New Projects
Description: Get started with new projects by dropping a skeleton of a new
project into a new or existing directory, initialise git repositories,
and create reproducible environments with the 'renv' package. The
package allows for dynamically named files, folders, file content, as
well as the functionality to drop individual template files into
existing projects.
Author: Daniel D. Sjoberg [aut, cre] ,
Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between starter versions 0.1.11 dated 2022-10-27 and 0.1.12 dated 2022-10-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/create_project.R | 1 - inst/doc/create_project.html | 8 ++++---- 5 files changed, 15 insertions(+), 12 deletions(-)
Title: Metrics (with Uncertainty) for Simulation Studies that Evaluate
Statistical Methods
Description: Allows users to quickly apply individual or multiple metrics to evaluate Monte Carlo simulation studies.
Author: Rex Parsons [aut, cre]
Maintainer: Rex Parsons <Rex.Parsons94@gmail.com>
Diff between simMetric versions 0.1.0 dated 2022-01-04 and 0.1.1 dated 2022-10-31
DESCRIPTION | 8 - MD5 | 43 +++---- NEWS.md | 28 ++-- R/bias.R | 10 - R/biasEliminatedCoverage.R | 10 - R/coverage.R | 10 - R/empSE.R | 12 +- R/modSE.R | 14 +- R/mse.R | 12 +- R/rejection.R | 10 - R/relativeErrorModSE.R | 16 +- R/relativePrecision.R | 16 +- R/utils.R | 104 +++++++++--------- README.md | 172 ++++++++++++++++-------------- inst |only man/figures/README-unnamed-chunk-10-1.png |binary tests/testthat/test-bias.R | 12 +- tests/testthat/test-coverage.R | 27 ++-- tests/testthat/test-empSE.R | 12 +- tests/testthat/test-join_metrics.R | 57 ++++----- tests/testthat/test-modSE.R | 14 +- tests/testthat/test-mse.R | 16 +- tests/testthat/test-rejection.R | 12 +- 23 files changed, 321 insertions(+), 294 deletions(-)
Title: Targets for JAGS Workflows
Description: Bayesian data analysis usually incurs long runtimes
and cumbersome custom code.
A pipeline toolkit tailored to Bayesian statisticians,
the 'jagstargets' R package is leverages
'targets' and 'R2jags' to ease this burden.
'jagstargets' makes it super easy to set up scalable
JAGS pipelines that automatically parallelize the computation
and skip expensive steps when the results are already up to date.
Minimal custom code is required, and there is no need to manually
configure branching, so usage is much easier than 'targets' alone.
For the underlying methodology, please refer
to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS'
(Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
Author: William Michael Landau [aut, cre]
,
David Lawrence Miller [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between jagstargets versions 1.0.3 dated 2022-06-24 and 1.0.4 dated 2022-10-31
DESCRIPTION | 8 +- MD5 | 50 +++++++------- NAMESPACE | 6 + NEWS.md | 5 + R/tar_jags.R | 1 R/tar_jags_package.R | 9 +- R/tar_jags_rep.R | 58 +++++++++++++---- R/tar_jags_rep_dic.R | 3 R/tar_jags_rep_draws.R | 3 R/tar_jags_rep_summary.R | 3 R/utils_data.R | 13 +++ R/utils_deprecate.R |only build/vignette.rds |binary inst/doc/introduction.html | 97 +++++++++++++++-------------- inst/doc/simulation.html | 93 ++++++++++++++------------- man/tar_jags.Rd | 30 +++----- man/tar_jags_rep.Rd | 49 ++++++++------ man/tar_jags_rep_data_batch.Rd | 6 + man/tar_jags_rep_dic.Rd | 49 ++++++++------ man/tar_jags_rep_draws.Rd | 49 ++++++++------ man/tar_jags_rep_run.Rd | 6 - man/tar_jags_rep_summary.Rd | 49 ++++++++------ tests/testthat/test-tar_jags_rep_dic.R | 2 tests/testthat/test-tar_jags_rep_draws.R | 2 tests/testthat/test-tar_jags_rep_summary.R | 76 ++++++++++++++++++++++ tests/testthat/test-utils_data.R | 12 +++ tests/testthat/test-utils_deprecate.R |only 27 files changed, 426 insertions(+), 253 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Tools for computing various vector summaries of persistence diagrams
studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' package.
Author: Umar Islambekov [aut],
Alexey Luchinsky [aut, cre],
Hasani Pathirana [ctb]
Maintainer: Alexey Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.2 dated 2022-10-17 and 0.1.3 dated 2022-10-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/TDAvec_vignette.html | 2 +- man/computeVPB.Rd | 2 +- src/VPB.cpp | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Ready to Use Extra Datasets for Torch
Description: Provides datasets in a format that can be easily consumed by torch 'dataloaders'.
Handles data downloading from multiple sources, caching and pre-processing so
users can focus only on their model implementations.
Author: Daniel Falbel [aut, cre],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchdatasets versions 0.1.0 dated 2021-10-07 and 0.2.0 dated 2022-10-31
DESCRIPTION | 11 ++- MD5 | 28 ++++----- NAMESPACE | 1 NEWS.md | 5 + R/bank-marketing.R | 2 R/bird-species.R | 40 +++++++------ R/dogs-vs-cats.R | 82 +++++++++++++++++++--------- R/guess-the-correlation.R | 6 +- R/utils.R | 9 +++ README.md | 21 ++++--- man/bird_species_dataset.Rd | 20 +----- man/dogs_vs_cats_dataset.Rd | 21 +++++-- tests/testthat/test-bird-species.R | 3 - tests/testthat/test-dogs-vs-cats.R | 10 --- tests/testthat/test-guess-the-correlation.R | 3 - 15 files changed, 153 insertions(+), 109 deletions(-)
Title: Easy Linear, Quadratic and Cubic Regression Models
Description: Focused on linear, quadratic and cubic regression models, it has a function for calculating the models, obtaining a list with their parameters, and a function for making the graphs for the respective models.
Author: Wagner Martins dos Santos [aut, cre]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
Diff between regr.easy versions 1.0.1 dated 2022-09-13 and 1.0.2 dated 2022-10-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/regr_easy_calc.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <h.charvat.ef@juntendo.ac.jp>
Diff between mexhaz versions 2.3 dated 2022-05-03 and 2.4 dated 2022-10-31
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS | 127 ++--------------------------------------------------- R/adjsurv.R | 2 R/mexhaz.R | 4 - R/mexhazEgh.R | 85 ++++++++++++++++++----------------- R/predict.mexhaz.R | 3 - R/riskfunc.R | 2 man/mexhaz.Rd | 26 ++++++++-- src/SplineFunc.c | 6 +- src/SplineFunc.h | 6 +- 11 files changed, 97 insertions(+), 192 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <http://vcg.isti.cnr.it>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb],
Tim Schaefer [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.21 dated 2022-03-18 and 0.22 dated 2022-10-31
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/Rvcg-package.R | 4 ++-- R/vcgCurve.r | 4 ++-- R/vcgDijkstra.r | 6 ------ inst/NEWS.Rd | 8 ++++++++ man/Rvcg-package.Rd | 4 ++-- man/vcgCurve.Rd | 4 ++-- man/vcgDijkstra.Rd | 2 -- man/vcgGeodesicPath.Rd | 2 -- man/vcgGeodist.Rd | 2 -- src/Rcurvature.cpp | 26 +++++++++++++------------- src/Rexport.cpp | 1 + src/vcglib/wrap/io_trimesh/export_off.h | 4 ++-- 14 files changed, 50 insertions(+), 53 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.4.1 dated 2022-07-01 and 1.4.2 dated 2022-10-31
RNifti-1.4.1/RNifti/inst/doxygen |only RNifti-1.4.2/RNifti/DESCRIPTION | 8 - RNifti-1.4.2/RNifti/MD5 | 202 --------------------------- RNifti-1.4.2/RNifti/NEWS | 15 +- RNifti-1.4.2/RNifti/inst/include/RNifti.h | 2 RNifti-1.4.2/RNifti/inst/include/RNiftiAPI.h | 20 +- 6 files changed, 31 insertions(+), 216 deletions(-)
Title: R Interface to PXWEB APIs
Description: Generic interface for the PX-Web/PC-Axis API. The
PX-Web/PC-Axis API is used by organizations such as Statistics Sweden
and Statistics Finland to disseminate data. The R package can interact
with all PX-Web/PC-Axis APIs to fetch information about the data
hierarchy, extract metadata and extract and parse statistics to R
data.frame format. PX-Web is a solution to disseminate PC-Axis data
files in dynamic tables on the web. Since 2013 PX-Web contains an API
to disseminate PC-Axis files.
Author: Mans Magnusson [aut, cre] ,
Markus Kainu [aut],
Janne Huovari [aut],
Leo Lahti [aut] ,
Love Hansson [ctb],
Eydun Nielsen [ctb],
Bo Werth [ctb],
Thomas Runarsson [ctb],
Torbjoern Lindquist [ctb],
Palmar Thorsteinsson [ctb],
Pyry Kantanen [ctb],
Sebasti [...truncated...]
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between pxweb versions 0.16.1 dated 2022-08-24 and 0.16.2 dated 2022-10-31
pxweb-0.16.1/pxweb/tests/testthat/log_pxweb_api_http_calls.txt |only pxweb-0.16.2/pxweb/DESCRIPTION | 8 - pxweb-0.16.2/pxweb/MD5 | 63 ++++---- pxweb-0.16.2/pxweb/NAMESPACE | 1 pxweb-0.16.2/pxweb/NEWS.md | 11 + pxweb-0.16.2/pxweb/R/pxweb.R | 4 pxweb-0.16.2/pxweb/R/pxweb_as_data_frame.R | 11 + pxweb-0.16.2/pxweb/R/pxweb_data_comments.R | 2 pxweb-0.16.2/pxweb/R/pxweb_get.R | 10 - pxweb-0.16.2/pxweb/R/pxweb_interactive.R | 8 - pxweb-0.16.2/pxweb/R/pxweb_query.R | 2 pxweb-0.16.2/pxweb/inst/doc/pxweb.R | 14 - pxweb-0.16.2/pxweb/inst/doc/pxweb.Rmd | 14 - pxweb-0.16.2/pxweb/inst/doc/pxweb.html | 71 +++++----- pxweb-0.16.2/pxweb/inst/extdata/api.json | 4 pxweb-0.16.2/pxweb/man/pxweb.Rd | 4 pxweb-0.16.2/pxweb/man/pxweb_as_data_frame.Rd | 9 + pxweb-0.16.2/pxweb/man/pxweb_data_comments.Rd | 2 pxweb-0.16.2/pxweb/man/pxweb_explorer.Rd | 4 pxweb-0.16.2/pxweb/man/pxweb_get.Rd | 8 - pxweb-0.16.2/pxweb/man/pxweb_get_data.Rd | 2 pxweb-0.16.2/pxweb/man/pxweb_interactive.Rd | 4 pxweb-0.16.2/pxweb/man/pxweb_validate_query_with_metadata.Rd | 2 pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_api_catalogue.R | 4 pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_api_paths.R | 2 pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_as_dataframe.R | 5 pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_constructor.R | 26 +-- pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_data_comments.R | 4 pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_get.R | 40 ++--- pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_interactive.R | 10 - pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_query.R | 8 - pxweb-0.16.2/pxweb/tests/testthat/test-pxweb_test_api.R | 6 pxweb-0.16.2/pxweb/vignettes/pxweb.Rmd | 14 - 33 files changed, 207 insertions(+), 170 deletions(-)
Title: Datasets for Teaching Archaeology and Paleontology
Description: Datasets for teaching quantitative approaches and
modeling in archaeology and paleontology. This package provides
several types of data related to broad topics (cultural evolution,
radiocarbon dating, paleoenvironments, etc.), which can be used to
illustrate statistical methods in the classroom (multivariate data
analysis, compositional data analysis, diversity measurement, etc.).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb]
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between folio versions 1.2.0 dated 2022-08-15 and 1.3.0 dated 2022-10-31
DESCRIPTION | 6 +++--- MD5 | 30 ++++++++++++++++-------------- NEWS.md | 4 ++++ R/counts.R | 24 ++++++++++++++++++++++++ R/folio-package.R | 2 +- README.md | 1 + data/loire.rda |only inst/CITATION | 4 ++-- man/birds.Rd | 1 + man/boves.Rd | 1 + man/chevelon.Rd | 1 + man/compiegne.Rd | 1 + man/folio-package.Rd | 2 +- man/loire.Rd |only man/merzbach.Rd | 1 + man/mississippi.Rd | 1 + man/zuni.Rd | 1 + 17 files changed, 59 insertions(+), 21 deletions(-)
Title: Auto-Generate Changelog using Conventional Commits
Description: Automatically generate a changelog file (NEWS.md /
CHANGELOG.md) from the git history using conventional commit messages
(<https://www.conventionalcommits.org/en/v1.0.0/>).
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between autonewsmd versions 0.0.3 dated 2022-09-03 and 0.0.4 dated 2022-10-31
autonewsmd-0.0.3/autonewsmd/R/get_git_log.R |only autonewsmd-0.0.3/autonewsmd/R/markdown_render.R |only autonewsmd-0.0.4/autonewsmd/DESCRIPTION | 6 autonewsmd-0.0.4/autonewsmd/MD5 | 23 +- autonewsmd-0.0.4/autonewsmd/R/autonewsmd.R | 115 ++-------- autonewsmd-0.0.4/autonewsmd/R/generate_autonewsmd.R |only autonewsmd-0.0.4/autonewsmd/R/init_autonewsmd.R |only autonewsmd-0.0.4/autonewsmd/R/mdtemplate_tags_decreasing.R |only autonewsmd-0.0.4/autonewsmd/R/write_autonewsmd.R |only autonewsmd-0.0.4/autonewsmd/R/zzz.R |only autonewsmd-0.0.4/autonewsmd/inst/doc/autonewsmd.Rmd | 26 ++ autonewsmd-0.0.4/autonewsmd/inst/doc/autonewsmd.html | 81 ++++++- autonewsmd-0.0.4/autonewsmd/inst/templates/news-md-template.Rmd | 30 -- autonewsmd-0.0.4/autonewsmd/man/autonewsmd.Rd | 6 autonewsmd-0.0.4/autonewsmd/tests/testthat/test-autonewsmd.R | 49 ++++ autonewsmd-0.0.4/autonewsmd/vignettes/autonewsmd.Rmd | 26 ++ 16 files changed, 227 insertions(+), 135 deletions(-)
Title: Analysis of Quaternary Science Data
Description: Constrained clustering, transfer functions, and other methods for analysing Quaternary science data.
Author: Steve Juggins
Maintainer: Steve Juggins <Stephen.Juggins@ncl.ac.uk>
Diff between rioja versions 1.0-2 dated 2022-10-25 and 1.0-5 dated 2022-10-31
rioja-1.0-2/rioja/R/riojaPlot.R |only rioja-1.0-2/rioja/build/vignette.rds |only rioja-1.0-2/rioja/inst/doc |only rioja-1.0-2/rioja/inst/extdata |only rioja-1.0-2/rioja/man/riojaPlot.Rd |only rioja-1.0-2/rioja/vignettes |only rioja-1.0-5/rioja/.aspell |only rioja-1.0-5/rioja/DESCRIPTION | 18 ++++++++---------- rioja-1.0-5/rioja/MD5 | 22 ++++------------------ rioja-1.0-5/rioja/NAMESPACE | 16 ++++------------ rioja-1.0-5/rioja/R/zzz.r | 3 +-- rioja-1.0-5/rioja/build/partial.rdb |binary 12 files changed, 17 insertions(+), 42 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.8.1 dated 2022-07-01 and 0.9.0 dated 2022-10-31
DESCRIPTION | 21 +- MD5 | 45 +++-- NAMESPACE | 9 + NEWS.md | 12 + R/create.R | 222 +++++++++++++++++++++++++---- R/delete.R | 69 ++------- R/exists.R | 6 R/get.R | 58 +++---- R/list.R | 8 - R/nodbi-package.R | 3 R/query.R | 326 +++++++++++++++++++++++++++++++++++++++---- R/src_duckdb.R |only R/update.R | 75 ++++----- man/docdb_create.Rd | 3 man/docdb_delete.Rd | 1 man/docdb_exists.Rd | 1 man/docdb_get.Rd | 7 man/docdb_list.Rd | 1 man/docdb_query.Rd | 8 - man/docdb_update.Rd | 1 man/nodbi-package.Rd | 2 man/src_duckdb.Rd |only tests/testthat/core-nodbi.R | 87 +++++++---- tests/testthat/helper.R | 30 +++ tests/testthat/test-duckdb.R |only 25 files changed, 738 insertions(+), 257 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.4.10 dated 2022-05-20 and 6.0.0 dated 2022-10-31
mclust-5.4.10/mclust/data/Baudry_etal_2010_JCGS_examples.rda |only mclust-5.4.10/mclust/data/EuroUnemployment.rda |only mclust-5.4.10/mclust/data/GvHD.rda |only mclust-5.4.10/mclust/data/acidity.rda |only mclust-5.4.10/mclust/data/banknote.txt.gz |only mclust-5.4.10/mclust/data/chevron.rda |only mclust-5.4.10/mclust/data/cross.rda |only mclust-5.4.10/mclust/data/diabetes.rda |only mclust-5.4.10/mclust/data/thyroid.rda |only mclust-5.4.10/mclust/data/wdbc.txt.gz |only mclust-5.4.10/mclust/data/wreath.rda |only mclust-6.0.0/mclust/DESCRIPTION | 8 mclust-6.0.0/mclust/MD5 | 40 +- mclust-6.0.0/mclust/NAMESPACE | 5 mclust-6.0.0/mclust/NEWS.md | 9 mclust-6.0.0/mclust/R/graphics.R | 38 ++ mclust-6.0.0/mclust/R/mbahc.R | 2 mclust-6.0.0/mclust/build/vignette.rds |binary mclust-6.0.0/mclust/data/Baudry_etal_2010_JCGS_examples.R |only mclust-6.0.0/mclust/data/EuroUnemployment.R |only mclust-6.0.0/mclust/data/GvHD.R |only mclust-6.0.0/mclust/data/acidity.R |only mclust-6.0.0/mclust/data/banknote.txt |only mclust-6.0.0/mclust/data/chevron.R |only mclust-6.0.0/mclust/data/cross.R |only mclust-6.0.0/mclust/data/diabetes.R |only mclust-6.0.0/mclust/data/thyroid.R |only mclust-6.0.0/mclust/data/wdbc.txt |only mclust-6.0.0/mclust/data/wreath.R |only mclust-6.0.0/mclust/inst/doc/mclust.html | 151 +++++------ mclust-6.0.0/mclust/man/acidity.Rd | 2 mclust-6.0.0/mclust/man/crimcoords.Rd | 27 + 32 files changed, 167 insertions(+), 115 deletions(-)
Title: Systematical Metabolic Reconstruction
Description: The tool that quantitatively and qualitatively specifies each reconstruction steps
and can generate a template list of reconstruction steps dynamically selected from a reconstruction step reservoir,
constructed based on all available published GSM papers.
Author: Shilin Ouyang [aut, cre],
Zihao Li [aut],
Jiamin Hu [aut],
Miyuan Cao [aut],
Feng Yu [aut],
Longfei Mao [aut],
RStudio [cph, fnd]
Maintainer: Shilin Ouyang <ouyangshilin@hnu.edu.cn>
Diff between Sysrecon versions 0.1.0 dated 2022-10-18 and 0.1.1 dated 2022-10-31
DESCRIPTION | 11 ++++++----- MD5 | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-)
Title: Revealing Splicing Dynamics at Single-Cell Resolution
Description: Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of software to investigate splicing dynamics at single-cell resolution. 'MARVEL' enables splicing analysis of single-cell RNA-sequencing data generated from plate- and droplet-based library preparation methods.
Author: Sean Wen [aut, cre]
Maintainer: Sean Wen <sean.wenwx@gmail.com>
Diff between MARVEL versions 1.3.0 dated 2022-10-29 and 1.4.0 dated 2022-10-31
DESCRIPTION | 23 - MD5 | 185 ++++++---- NAMESPACE | 43 ++ R/Script_DROPLET_01_CREATE_MARVEL_OBJECT.R |only R/Script_DROPLET_02_PREPROCESS_1_AnnotateGenes.R |only R/Script_DROPLET_02_PREPROCESS_2_AnnotateSJ.R |only R/Script_DROPLET_02_PREPROCESS_3_ValidateSJ.R |only R/Script_DROPLET_02_PREPROCESS_4_FilterGenes.R |only R/Script_DROPLET_02_PREPROCESS_5_CheckAlignment.R |only R/Script_DROPLET_03_EXPLORE_EXPRESSION_1_Gene.R |only R/Script_DROPLET_03_EXPLORE_EXPRESSION_2_SJ.R |only R/Script_DROPLET_04_DE_1_SJ.R |only R/Script_DROPLET_04_DE_2_Gene.R |only R/Script_DROPLET_04_DE_3_VolcanoPlot_SJ.R |only R/Script_DROPLET_04_DE_4_VolcanoPlot_Gene.R |only R/Script_DROPLET_05_DE_5_IsoSwitch.R |only R/Script_DROPLET_05_DE_6_1_GO.R |only R/Script_DROPLET_05_DE_6_2_GO_Plot.R |only R/Script_DROPLET_07_ADHOC_PLOT_PCA_1_PlotFeatures.R |only R/Script_DROPLET_07_ADHOC_PLOT_PCA_2_PlotValues_PSI.R |only R/Script_DROPLET_07_ADHOC_PLOT_PCA_3_PlotValues_Gene.R |only R/Script_DROPLET_09_ADHOC_GENE_1_TabulateExpression_Gene.R |only R/Script_DROPLET_09_ADHOC_GENE_2_TabulateExpression_PSI.R |only R/Script_DROPLET_09_ADHOC_GENE_3_DE_Gene.R |only R/Script_DROPLET_09_ADHOC_GENE_4_DE_PSI.R |only R/Script_DROPLET_09_ADHOC_GENE_5_PlotDEValues.R |only R/Script_DROPLET_09_ADHOC_GENE_6_PlotSJPositions.R |only R/Script_PLATE_01_CREATE_MARVEL_OBJECT.R | 1 R/Script_PLATE_02_DETECT_EVENTS_0.R | 1 R/Script_PLATE_02_DETECT_EVENTS_1_0_ALE.R | 1 R/Script_PLATE_02_DETECT_EVENTS_1_1_ALE_PosStrand.R | 7 R/Script_PLATE_02_DETECT_EVENTS_1_2_ALE_NegStrand.R | 7 R/Script_PLATE_02_DETECT_EVENTS_2_0_AFE.R | 1 R/Script_PLATE_02_DETECT_EVENTS_2_1_AFE_PosStrand.R | 7 R/Script_PLATE_02_DETECT_EVENTS_2_2_AFE_NegStrand.R | 7 R/Script_PLATE_03_COMPUTE_PSI_0_Compute.R | 1 R/Script_PLATE_03_COMPUTE_PSI_1_Compute_SE.R | 1 R/Script_PLATE_03_COMPUTE_PSI_2_Compute_MXE.R | 1 R/Script_PLATE_03_COMPUTE_PSI_3_Compute_A5SS.R | 1 R/Script_PLATE_03_COMPUTE_PSI_4_Compute_A3SS.R | 1 R/Script_PLATE_03_COMPUTE_PSI_5_Compute_RI.R | 4 R/Script_PLATE_03_COMPUTE_PSI_6_Compute_ALE.R | 1 R/Script_PLATE_03_COMPUTE_PSI_7_Compute_AFE.R | 1 R/Script_PLATE_04_PREPROCESS_2_SubsetSamples.R | 1 R/Script_PLATE_04_PREPROCESS_3_0_CheckAlignment.R | 1 R/Script_PLATE_04_PREPROCESS_3_1_CheckAlignment_PSI.R | 1 R/Script_PLATE_04_PREPROCESS_3_2_CheckAlignment_Gene.R | 1 R/Script_PLATE_04_PREPROCESS_3_3_CheckAlignment_PSI_Gene.R | 1 R/Script_PLATE_04_PREPROCESS_3_4_CheckAlignment_SJ.R | 1 R/Script_PLATE_04_PREPROCESS_4_TransformGeneValues.R | 1 R/Script_PLATE_05_EVENTS_EXPRESSED.R | 1 R/Script_PLATE_06_MODALITY_ANALYSIS_1_AssignModality.R | 2 R/Script_PLATE_06_MODALITY_ANALYSIS_2_0_PropModality.R | 3 R/Script_PLATE_06_MODALITY_ANALYSIS_2_1_PropModality_Doughnut.R | 1 R/Script_PLATE_06_MODALITY_ANALYSIS_2_2_PropModality_Bar.R | 4 R/Script_PLATE_07_PCA_0_RunPCA.R | 2 R/Script_PLATE_07_PCA_1_RunPCA_PSI.R | 3 R/Script_PLATE_07_PCA_2_RunPCA_Gene.R | 2 R/Script_PLATE_08_DE_1_0_CompareValues.R | 2 R/Script_PLATE_08_DE_1_2_CompareValues_PSI.R | 19 - R/Script_PLATE_08_DE_1_3_CompareValues_Gene.R | 13 R/Script_PLATE_08_DE_1_4_CompareValues_SplicedGene.R | 4 R/Script_PLATE_08_DE_1_5_SubsetCrypticA3SS.R | 7 R/Script_PLATE_08_DE_2_0_PlotDEValues.R | 2 R/Script_PLATE_08_DE_2_1_PlotDEValues_PSI_Distance.R | 2 R/Script_PLATE_08_DE_2_2_PlotDEValues_PSI_Mean.R | 2 R/Script_PLATE_08_DE_2_3_PlotDEValues_PSI_Mean_Group1vs2.R | 2 R/Script_PLATE_08_DE_2_4_PlotDEValues_Gene_Mean_Global.R | 2 R/Script_PLATE_08_DE_2_5_PlotDEValues_Gene_Mean_Spliced.R | 4 R/Script_PLATE_08_DE_3_PctASE.R | 6 R/Script_PLATE_08_DE_4_ModalityChange.R | 5 R/Script_PLATE_08_DE_5_1_IsoSwitch.R | 4 R/Script_PLATE_08_DE_5_2_IsoSwitch_PlotExpr.R | 2 R/Script_PLATE_08_DE_6_1_GO.R | 3 R/Script_PLATE_08_DE_6_2_GO_Plot.R | 2 R/Script_PLATE_09_PREDICT_NMD_1_ParseGTF.R | 2 R/Script_PLATE_09_PREDICT_NMD_2_0_FindPTC.R | 2 R/Script_PLATE_09_PREDICT_NMD_2_1_FindPTC_SE_PosStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_2_2_FindPTC_SE_NegStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_3_1_FindPTC_RI_PosStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_3_2_FindPTC_RI_NegStrand.R | 3 R/Script_PLATE_09_PREDICT_NMD_4_1_FindPTC_A5SS_PosStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_4_2_FindPTC_A5SS_NegStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_5_1_FindPTC_A3SS_PosStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_5_2_FindPTC_A3SS_NegStrand.R | 2 R/Script_PLATE_09_PREDICT_NMD_6_PropPTC.R | 2 R/Script_PLATE_09_PREDICT_NMD_7_CompareExpr.R | 5 R/Script_PLATE_09_PREDICT_NMD_8_AnnoVolcanoPlot.R | 3 R/Script_PLATE_10_ADHOC_PLOT_0_PlotValues.R | 2 R/Script_PLATE_10_ADHOC_PLOT_1_PlotValues_PSI.R | 4 R/Script_PLATE_10_ADHOC_PLOT_2_PlotValues_Gene.R | 6 inst/doc/MARVEL.html | 2 inst/extdata/data/marvel.demo.10x.raw.rds |only inst/extdata/data/marvel.demo.10x.rds |only inst/extdata/figures/Cover_Figure.png |only man/AnnotateGenes.10x.Rd |only man/AnnotateSJ.10x.Rd |only man/BioPathways.10x.Rd |only man/BioPathways.Plot.10x.Rd |only man/CheckAlignment.10x.Rd |only man/CompareValues.Genes.10x.Rd |only man/CompareValues.SJ.10x.Rd |only man/CreateMarvelObject.10x.Rd |only man/FilterGenes.10x.Rd |only man/IsoSwitch.10x.Rd |only man/PlotDEValues.Genes.10x.Rd |only man/PlotDEValues.SJ.10x.Rd |only man/PlotPctExprCells.Genes.10x.Rd |only man/PlotPctExprCells.SJ.10x.Rd |only man/PlotValues.PCA.CellGroup.10x.Rd |only man/PlotValues.PCA.Gene.10x.Rd |only man/PlotValues.PCA.PSI.10x.Rd |only man/ValidateSJ.10x.Rd |only man/adhocGene.DE.Gene.10x.Rd |only man/adhocGene.DE.PSI.10x.Rd |only man/adhocGene.PlotDEValues.10x.Rd |only man/adhocGene.PlotSJPosition.10x.Rd |only man/adhocGene.TabulateExpression.Gene.10x.Rd |only man/adhocGene.TabulateExpression.PSI.10x.Rd |only 119 files changed, 299 insertions(+), 146 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre]
,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Jessica Burnett [rev] ,
Johannes Karreth [rev]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 0.8.1 dated 2022-10-18 and 0.8.2 dated 2022-10-31
DESCRIPTION | 6 +-- MD5 | 32 ++++++++-------- NEWS.md | 7 +++ R/convert_stat_to_anova.R | 9 +--- R/effectsize.R | 46 ++++++++++++------------ R/eta_squared-main.R | 12 ++++-- R/rank_ANOVA.R | 2 - inst/doc/effectsize_API.html | 4 +- inst/doc/from_test_statistics.R | 4 +- inst/doc/from_test_statistics.Rmd | 4 +- inst/doc/from_test_statistics.html | 10 ++--- man/F_to_eta2.Rd | 5 -- man/effectsize.Rd | 46 ++++++++++++------------ man/eta_squared.Rd | 4 -- tests/testthat/test-eta_squared.R | 18 ++++----- tests/testthat/test-utils_validate_input_data.R | 26 +++++++------ vignettes/from_test_statistics.Rmd | 4 +- 17 files changed, 121 insertions(+), 118 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 0.3 dated 2022-09-30 and 0.3.1 dated 2022-10-31
openxlsx2-0.3.1/openxlsx2/DESCRIPTION | 6 openxlsx2-0.3.1/openxlsx2/MD5 | 144 +- openxlsx2-0.3.1/openxlsx2/NAMESPACE | 2 openxlsx2-0.3.1/openxlsx2/NEWS.md | 42 openxlsx2-0.3.1/openxlsx2/R/RcppExports.R | 36 openxlsx2-0.3.1/openxlsx2/R/all-equal.R | 4 openxlsx2-0.3.1/openxlsx2/R/baseXML.R | 144 -- openxlsx2-0.3.1/openxlsx2/R/class-comment.R | 2 openxlsx2-0.3.1/openxlsx2/R/class-style_mgr.R | 4 openxlsx2-0.3.1/openxlsx2/R/class-workbook-utils.R | 4 openxlsx2-0.3.1/openxlsx2/R/class-workbook-wrappers.R | 32 openxlsx2-0.3.1/openxlsx2/R/class-workbook.R | 323 ++---- openxlsx2-0.3.1/openxlsx2/R/class-worksheet.R | 53 - openxlsx2-0.3.1/openxlsx2/R/converters.R | 37 openxlsx2-0.3.1/openxlsx2/R/dates.R | 6 openxlsx2-0.3.1/openxlsx2/R/get-named-regions.R | 8 openxlsx2-0.3.1/openxlsx2/R/helperFunctions.R | 2 openxlsx2-0.3.1/openxlsx2/R/openxlsx2.R | 16 openxlsx2-0.3.1/openxlsx2/R/pugixml.R | 2 openxlsx2-0.3.1/openxlsx2/R/utils.R | 60 - openxlsx2-0.3.1/openxlsx2/R/wb_functions.R | 95 + openxlsx2-0.3.1/openxlsx2/R/wb_load.R | 115 +- openxlsx2-0.3.1/openxlsx2/R/wb_styles.R | 73 - openxlsx2-0.3.1/openxlsx2/R/write.R | 526 +++++----- openxlsx2-0.3.1/openxlsx2/R/write_xlsx.R | 4 openxlsx2-0.3.1/openxlsx2/README.md | 2 openxlsx2-0.3.1/openxlsx2/inst/WORDLIST | 2 openxlsx2-0.3.1/openxlsx2/inst/doc/Update-from-openxlsx.R | 4 openxlsx2-0.3.1/openxlsx2/inst/doc/Update-from-openxlsx.Rmd | 4 openxlsx2-0.3.1/openxlsx2/inst/doc/Update-from-openxlsx.html | 4 openxlsx2-0.3.1/openxlsx2/inst/doc/conditional-formatting.R | 50 openxlsx2-0.3.1/openxlsx2/inst/doc/conditional-formatting.Rmd | 50 openxlsx2-0.3.1/openxlsx2/inst/doc/conditional-formatting.html | 50 openxlsx2-0.3.1/openxlsx2/inst/doc/openxlsx2_basic_manual.html | 22 openxlsx2-0.3.1/openxlsx2/inst/doc/openxlsx2_style_manual.R | 134 +- openxlsx2-0.3.1/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 138 +- openxlsx2-0.3.1/openxlsx2/inst/doc/openxlsx2_style_manual.html | 323 +++--- openxlsx2-0.3.1/openxlsx2/inst/include/pugixml/pugixml.cpp | 291 +++-- openxlsx2-0.3.1/openxlsx2/inst/include/pugixml/pugixml.hpp | 5 openxlsx2-0.3.1/openxlsx2/man/create_dxfs_style.Rd | 32 openxlsx2-0.3.1/openxlsx2/man/wbWorkbook.Rd | 21 openxlsx2-0.3.1/openxlsx2/man/wb_add_data_table.Rd | 6 openxlsx2-0.3.1/openxlsx2/man/wb_add_formula.Rd | 8 openxlsx2-0.3.1/openxlsx2/man/wb_modify_basefont.Rd | 7 openxlsx2-0.3.1/openxlsx2/man/write_data.Rd | 4 openxlsx2-0.3.1/openxlsx2/man/write_data2.Rd | 8 openxlsx2-0.3.1/openxlsx2/man/write_datatable.Rd | 6 openxlsx2-0.3.1/openxlsx2/man/write_formula.Rd | 8 openxlsx2-0.3.1/openxlsx2/man/write_xlsx.Rd | 3 openxlsx2-0.3.1/openxlsx2/src/RcppExports.cpp | 33 openxlsx2-0.3.1/openxlsx2/src/helper_functions.cpp | 203 --- openxlsx2-0.3.1/openxlsx2/src/write_file.cpp | 3 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-asserts.R | 2 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-base_font.R | 4 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-class-hyperlink.R | 39 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-class-workbook.R | 46 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-class-worksheet.R | 34 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-conditional_formatting.R | 33 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-fill_merged_cells.R | 14 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-loading_workbook.R | 37 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-names.R | 6 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-pugi_cpp.R | 12 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-pugixml.R | 8 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-read_from_created_wb.R | 2 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-read_sources.R | 2 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-save.R | 4 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-wb_functions.R | 34 openxlsx2-0.3.1/openxlsx2/tests/testthat/test-wb_styles.R | 155 ++ openxlsx2-0.3.1/openxlsx2/tests/testthat/test-write.R | 107 +- openxlsx2-0.3.1/openxlsx2/vignettes/Update-from-openxlsx.Rmd | 4 openxlsx2-0.3.1/openxlsx2/vignettes/conditional-formatting.Rmd | 50 openxlsx2-0.3.1/openxlsx2/vignettes/openxlsx2_style_manual.Rmd | 138 +- openxlsx2-0.3/openxlsx2/R/names.R |only openxlsx2-0.3/openxlsx2/man/names.wbWorkbook.Rd |only 74 files changed, 2153 insertions(+), 1739 deletions(-)
Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package will be described in Šlenker et al. (in prep).
Author: Marek Šlenker [aut, cre]
Petr Koutecky [ctb]
Karol Marhold [ctb]
Maintainer: Marek Šlenker <marek.slenker@savba.sk>
Diff between MorphoTools2 versions 1.0.0.0 dated 2022-05-26 and 1.0.1.0 dated 2022-10-31
DESCRIPTION | 8 +-- MD5 | 25 ++++++----- NEWS.md |only R/classif.lda.R | 77 +++++++++++++++++++++++++++++++++++- R/classif.qda.R | 2 R/newObject.R | 1 R/print.R | 8 +++ R/summary.R | 18 ++++---- inst/doc/MorphoTools2_tutorial.R | 22 +++++++--- inst/doc/MorphoTools2_tutorial.Rmd | 71 ++++++++++++++++++++++++--------- inst/doc/MorphoTools2_tutorial.pdf |binary man/classif.lda.Rd | 5 ++ man/classifdata.Rd | 4 - vignettes/MorphoTools2_tutorial.Rmd | 71 ++++++++++++++++++++++++--------- 14 files changed, 242 insertions(+), 70 deletions(-)
Title: An Interface to the 'fastText' Library
Description: An interface to the 'fastText' library
<https://github.com/facebookresearch/fastText>. The package
can be used for text classification and to learn word vectors.
An example how to use 'fastTextR' can be found in the 'README' file.
Author: Florian Schwendinger [aut],
Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between fastTextR versions 2.0.0 dated 2020-09-10 and 2.0.1 dated 2022-10-31
DESCRIPTION | 8 - MD5 | 20 +-- build/vignette.rds |binary inst/doc/Cheatsheet.html | 167 ++++++++++++++------------------ inst/doc/Text_classification.R | 2 inst/doc/Text_classification.Rmd | 2 inst/doc/Text_classification.html | 189 +++++++++++++++++-------------------- inst/doc/Word_representations.html | 175 +++++++++++++++------------------- src/RcppExports.cpp | 5 src/clean.cc | 22 ++-- vignettes/Text_classification.Rmd | 2 11 files changed, 279 insertions(+), 313 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.52 dated 2022-09-25 and 2.0.53 dated 2022-10-31
DESCRIPTION | 8 - MD5 | 30 ++--- NEWS | 12 ++ R/epi.insthaz.R | 21 ++- R/rsu.dxtest.R | 170 ++++++++++++++++++++--------- inst/doc/epiR_descriptive.Rmd | 6 - inst/doc/epiR_descriptive.html | 40 +++--- inst/doc/epiR_measures_of_association.html | 52 ++++---- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.Rmd | 4 inst/doc/epiR_surveillance.html | 78 ++++++------- man/epi.insthaz.Rd | 8 - man/epi.sscompb.Rd | 4 man/rsu.dxtest.Rd | 53 +++++++-- vignettes/epiR_descriptive.Rmd | 6 - vignettes/epiR_surveillance.Rmd | 4 16 files changed, 308 insertions(+), 192 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 1.3.2 dated 2022-10-04 and 2.0.0 dated 2022-10-31
BranchGLM-1.3.2/BranchGLM/man/predict.BranchGLMVS.Rd |only BranchGLM-2.0.0/BranchGLM/DESCRIPTION | 12 BranchGLM-2.0.0/BranchGLM/MD5 | 50 BranchGLM-2.0.0/BranchGLM/NAMESPACE | 8 BranchGLM-2.0.0/BranchGLM/R/BranchGLM.R | 10 BranchGLM-2.0.0/BranchGLM/R/RcppExports.R | 12 BranchGLM-2.0.0/BranchGLM/R/VariableSelection.R | 373 ++-- BranchGLM-2.0.0/BranchGLM/R/summaryBranchGLMVS.R |only BranchGLM-2.0.0/BranchGLM/build/vignette.rds |binary BranchGLM-2.0.0/BranchGLM/inst/doc/BranchGLM-Vignette.R | 117 - BranchGLM-2.0.0/BranchGLM/inst/doc/BranchGLM-Vignette.Rmd | 264 +- BranchGLM-2.0.0/BranchGLM/inst/doc/BranchGLM-Vignette.html | 887 ++++------ BranchGLM-2.0.0/BranchGLM/inst/doc/VariableSelection-Vignette.R |only BranchGLM-2.0.0/BranchGLM/inst/doc/VariableSelection-Vignette.Rmd |only BranchGLM-2.0.0/BranchGLM/inst/doc/VariableSelection-Vignette.html |only BranchGLM-2.0.0/BranchGLM/man/BranchGLM.Rd | 4 BranchGLM-2.0.0/BranchGLM/man/VariableSelection.Rd | 123 + BranchGLM-2.0.0/BranchGLM/man/fit.Rd |only BranchGLM-2.0.0/BranchGLM/man/plot.summary.BranchGLMVS.Rd |only BranchGLM-2.0.0/BranchGLM/man/print.BranchGLM.Rd | 2 BranchGLM-2.0.0/BranchGLM/man/print.BranchGLMVS.Rd | 2 BranchGLM-2.0.0/BranchGLM/man/print.summary.BranchGLMVS.Rd |only BranchGLM-2.0.0/BranchGLM/man/summary.BranchGLMVS.Rd |only BranchGLM-2.0.0/BranchGLM/src/BranchAndBound.cpp | 377 ++-- BranchGLM-2.0.0/BranchGLM/src/RcppExports.cpp | 33 BranchGLM-2.0.0/BranchGLM/src/StepwiseMethods.cpp | 33 BranchGLM-2.0.0/BranchGLM/src/VariableSelection.cpp | 42 BranchGLM-2.0.0/BranchGLM/src/VariableSelection.h | 2 BranchGLM-2.0.0/BranchGLM/tests/testthat/test-BranchGLM.R | 62 BranchGLM-2.0.0/BranchGLM/vignettes/BranchGLM-Vignette.Rmd | 264 +- BranchGLM-2.0.0/BranchGLM/vignettes/VariableSelection-Vignette.Rmd |only 31 files changed, 1281 insertions(+), 1396 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.0.2.4 dated 2022-04-21 and 2.0.2.5 dated 2022-10-31
DESCRIPTION | 6 MD5 | 108 ++++---- NEWS.md | 8 R/amend.R | 2 R/bayesnecfit-class.R | 2 R/define_prior.R | 26 - R/extract_simdat.R | 4 R/fit_bayesnec.R | 2 R/helpers.R | 4 R/prebayesnecfit-class.R | 4 R/sample_priors.R | 6 R/sysdata.rda |binary README.md | 4 data/beta_binomial2.rda |binary data/herbicide.rda |binary data/manec_example.rda |binary data/nec_data.rda |binary inst/doc/example1.Rmd | 77 +++-- inst/doc/example1.html | 148 ++++++----- inst/doc/example2.Rmd | 80 +++--- inst/doc/example2.html | 93 ++++--- inst/doc/example2b.Rmd | 196 +++++++++++++++ inst/doc/example2b.html | 169 ++++++++++++ inst/doc/example3.Rmd | 66 +++++ inst/doc/example3.html | 114 +++++++- inst/doc/example4.Rmd | 58 ++-- inst/doc/example4.html | 75 +++-- man/bayesnecfit-class.Rd | 2 man/prebayesnecfit-class.Rd | 2 tests/testthat/test-expand_classes.R | 8 vignettes/example1.Rmd | 77 +++-- vignettes/example2.Rmd | 80 +++--- vignettes/example2b.Rmd | 196 +++++++++++++++ vignettes/example3.Rmd | 66 +++++ vignettes/example4.Rmd | 58 ++-- vignettes/exmp2b_theoretical_curves.R | 6 vignettes/vignette-fig-exmp1-beta-1.png |binary vignettes/vignette-fig-exmp1-binom-1.png |binary vignettes/vignette-fig-exmp1-gammabase-1.png |binary vignettes/vignette-fig-exmp1-negbinbase-1.png |binary vignettes/vignette-fig-exmp1-poisson-1.png |binary vignettes/vignette-fig-exmp2-allmods-1.png |binary vignettes/vignette-fig-exmp2-checkpriors-1.png |binary vignettes/vignette-fig-exmp2-decline-1.png |binary vignettes/vignette-fig-exmp2-ecx4param-1.png |binary vignettes/vignette-fig-exmp2-goodmod-1.png |binary vignettes/vignette-fig-exmp2-pretty-1.png |binary vignettes/vignette-fig-exmp2b-theoretical_ecx_curves.png |binary vignettes/vignette-fig-exmp2b-theoretical_nec_curves.png |binary vignettes/vignette-fig-exmp3-checkpriors-1.png |binary vignettes/vignette-fig-exmp4-differences-1.png |binary vignettes/vignette-fig-exmp4-fitted-1.png |binary vignettes/vignette-fig-exmp4-fitteddiff-1.png |binary vignettes/vignette-fig-exmp4-posterior-1.png |binary vignettes/vignette-fig-exmp4-probplot-1.png |binary 55 files changed, 1331 insertions(+), 416 deletions(-)
Title: Portable Native and Joint Stack Traces
Description: Obtain the native stack trace and fuse it with R's
stack trace for easier debugging of R packages with native code.
Author: Kirill Mueller [aut, cre] ,
R Consortium [fnd],
Ian Lance Taylor [aut] ,
Free Software Foundation [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between winch versions 0.0.10 dated 2022-10-19 and 0.0.11 dated 2022-10-31
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 7 ++ inst/doc/report.html | 114 ++++++++++++++++++++++++------------------------ src/trace_back_unwind.c | 2 5 files changed, 73 insertions(+), 66 deletions(-)
Title: API Client for US Treasury Fiscal Data
Description: Make requests from the US Treasury Fiscal Data API endpoints.
Author: Guillermo Roditi Dominguez [aut, cre]
Maintainer: Guillermo Roditi Dominguez <guillermo@newriverinvestments.com>
Diff between ustfd versions 0.1.1 dated 2022-07-18 and 0.2.0 dated 2022-10-31
DESCRIPTION | 10 +-- MD5 | 12 +-- NEWS.md | 11 +++ R/ustfd.R | 105 +++++++++++++++++---------------- R/ustfd_query.R | 2 R/ustfd_url.R | 8 +- tests/testthat/test-response_payload.R | 25 +++++++ 7 files changed, 109 insertions(+), 64 deletions(-)
Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces.
Playing surfaces are drawn pursuant to rule-book specifications.
This package should be used as a baseline plot for displaying any type of
tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>
Diff between sportyR versions 2.0.1 dated 2022-09-24 and 2.1.0 dated 2022-10-31
DESCRIPTION | 8 MD5 | 87 +++--- NAMESPACE | 1 NEWS.md | 15 + R/features-football.R | 279 ++++++++++++++++++-- R/features-volleyball.R |only R/geom-basketball.R | 37 ++ R/geom-curling.R | 37 ++ R/geom-football.R | 234 +++++++++++----- R/geom-hockey.R | 73 +++-- R/geom-soccer.R | 45 +++ R/geom-tennis.R | 37 ++ R/geom-volleyball.R |only R/plot-helpers.R | 8 R/sysdata.rda |binary R/utils.R | 32 ++ inst/doc/animating-tracking-data.R | 36 +- inst/doc/animating-tracking-data.Rmd | 8 inst/doc/animating-tracking-data.html | 12 inst/doc/customize-plot.html | 4 inst/doc/plotting-tracking-data.html | 6 inst/doc/sportyR.html | 10 man/football_features_set_colors.Rd | 10 man/football_field_apron.Rd | 6 man/football_field_border_outline.Rd | 2 man/football_half_field.Rd | 12 man/football_red_zone_border.Rd |only man/football_red_zone_border_outline.Rd |only man/geom_basketball.Rd | 2 man/geom_curling.Rd | 2 man/geom_football.Rd | 2 man/geom_hockey.Rd | 38 +- man/geom_soccer.Rd | 2 man/geom_tennis.Rd | 2 man/geom_volleyball.Rd |only man/is_hex.Rd |only man/volleyball_attack_line.Rd |only man/volleyball_backcourt.Rd |only man/volleyball_center_line.Rd |only man/volleyball_court_apron.Rd |only man/volleyball_end_line.Rd |only man/volleyball_features_set_colors.Rd |only man/volleyball_free_zone.Rd |only man/volleyball_front_zone.Rd |only man/volleyball_service_zone_mark.Rd |only man/volleyball_sideline.Rd |only man/volleyball_substitution_zone_dash.Rd |only tests/testthat/test-cani-functions.R | 11 tests/testthat/test-is_hex.R |only tests/testthat/test-no-league-error.R | 3 tests/testthat/test-plots-and-features-basketball.R | 7 tests/testthat/test-plots-and-features-volleyball.R |only vignettes/animating-tracking-data.Rmd | 8 vignettes/img |only 54 files changed, 850 insertions(+), 226 deletions(-)
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.1.1 dated 2022-08-10 and 1.2.0 dated 2022-10-31
dcifer-1.1.1/dcifer/man/read.Rd |only dcifer-1.2.0/dcifer/DESCRIPTION | 8 +- dcifer-1.2.0/dcifer/MD5 | 22 +++--- dcifer-1.2.0/dcifer/NAMESPACE | 2 dcifer-1.2.0/dcifer/NEWS.md | 9 ++ dcifer-1.2.0/dcifer/R/prep.R | 74 ++++++++++++++++------- dcifer-1.2.0/dcifer/build/vignette.rds |binary dcifer-1.2.0/dcifer/inst/doc/vignetteDcifer.R | 11 +++ dcifer-1.2.0/dcifer/inst/doc/vignetteDcifer.Rmd | 34 +++++++++- dcifer-1.2.0/dcifer/inst/doc/vignetteDcifer.pdf |binary dcifer-1.2.0/dcifer/man/format.Rd |only dcifer-1.2.0/dcifer/vignettes/dciferpkg.bib | 26 +++++--- dcifer-1.2.0/dcifer/vignettes/vignetteDcifer.Rmd | 34 +++++++++- 13 files changed, 169 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-09 0.5.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-26 1.1.4
2021-08-10 1.1.3
2020-11-23 1.1.2
2020-08-01 1.1.0
2020-08-01 1.1.1
2020-07-05 1.0.1
2020-06-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-01 1.3.1