Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame
and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsindf versions 0.3.11 dated 2022-05-19 and 0.3.12 dated 2023-01-24
DESCRIPTION | 13 LICENSE | 2 MD5 | 44 +- NAMESPACE | 1 NEWS.md | 34 + R/data.R | 14 R/expand.R | 59 +-- R/matsindf_apply.R | 16 R/utilities.R | 66 +++ build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/doc/iris_pca.html | 128 +++--- inst/doc/matsindf.html | 152 ++++---- inst/doc/midf_apply_primer.R | 33 + inst/doc/midf_apply_primer.Rmd | 102 +++-- inst/doc/midf_apply_primer.html | 648 ++++++++++++++++++++--------------- man/UKEnergy2000.Rd | 14 man/expand_to_tidy.Rd | 45 +- man/matrix_cols.Rd |only man/matsindf_apply.Rd | 4 tests/testthat/test-matsindf_apply.R | 17 tests/testthat/test-utilities.R | 75 +++- vignettes/midf_apply_primer.Rmd | 102 +++-- 24 files changed, 985 insertions(+), 592 deletions(-)
Title: Rank Intraclass Correlation for Clustered Data
Description: Estimates the rank intraclass correlation coefficient (ICC) for clustered continuous, ordinal, binary, and count data <https://github.com/shengxintu/rankICC>.
Author: Shengxin Tu [aut, cre],
Chun Li [aut],
Donglin Zeng [aut],
Bryan Shepherd [aut]
Maintainer: Shengxin Tu <shengxin.tu@vanderbilt.edu>
Diff between rankICC versions 0.1.0 dated 2022-09-21 and 1.0.1 dated 2023-01-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/rankICC.R | 2 +- R/rankICC3levels.R | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
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
Software. 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] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Kristian Hoden [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 3.2.2 dated 2022-11-15 and 3.3.0 dated 2023-01-24
DESCRIPTION | 29 MD5 | 61 NEWS.md | 10 R/Olink_normalization.R | 62 R/Olink_one_non_parametric.R | 6 R/Olink_theme.R | 25 R/Read_NPX_data.R | 536 ++++-- R/globals.R | 2 R/npxProcessing.R | 18 build/vignette.rds |binary inst/doc/Vignett.Rmd | 2 inst/doc/Vignett.html | 125 - inst/extdata/Example_NPX_Data2_1.csv |only man/olink_one_non_parametric.Rd | 2 man/olink_one_non_parametric_posthoc.Rd | 4 man/read_NPX.Rd | 6 tests/data/npx_data_format221121.RData |only tests/data/refResults.RData |binary tests/testthat/_snaps/pca_plot/pca-plot-minimal-no-index-removing-index-dependence.svg |only tests/testthat/_snaps/pca_plot/pca-plot-minimal-no-index.svg |only tests/testthat/_snaps/pca_plot/pca-plot-removing-index-dependence.svg |only tests/testthat/refs |only tests/testthat/test-Olink_boxplot.R | 3 tests/testthat/test-Olink_normalization.R | 187 ++ tests/testthat/test-Read_NPX_data.R | 30 tests/testthat/test-dist_plot.R | 5 tests/testthat/test-linear_mixed_model.R | 1 tests/testthat/test-npxProcessing.R | 16 tests/testthat/test-olink_Pathway_Heatmap.R | 1 tests/testthat/test-olink_Pathway_Visualization.R | 1 tests/testthat/test-olink_qc_plot.R | 4 tests/testthat/test-pca_plot.R | 28 vignettes/Vignett.Rmd | 2 vignettes/bridging_introduction.html | 783 +++++++--- 34 files changed, 1409 insertions(+), 540 deletions(-)
Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin [aut, cre] ,
Andrew Clausen [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 2.1-7.1 dated 2021-11-02 and 2.1-8 dated 2023-01-24
gsl-2.1-7.1/gsl/inst/doc/gslpaper.R |only gsl-2.1-7.1/gsl/inst/doc/gslpaper.Rnw |only gsl-2.1-7.1/gsl/inst/doc/gslpaper.pdf |only gsl-2.1-7.1/gsl/inst/gsl_stickermaker.R |only gsl-2.1-7.1/gsl/vignettes/gslpaper.Rnw |only gsl-2.1-8/gsl/DESCRIPTION | 10 +- gsl-2.1-8/gsl/INSTALL | 8 + gsl-2.1-8/gsl/MD5 | 34 +++---- gsl-2.1-8/gsl/NEWS.md |only gsl-2.1-8/gsl/README.md | 13 ++ gsl-2.1-8/gsl/build/partial.rdb |binary gsl-2.1-8/gsl/build/vignette.rds |binary gsl-2.1-8/gsl/cleanup | 5 - gsl-2.1-8/gsl/configure | 150 +++++++++++++++++--------------- gsl-2.1-8/gsl/configure.ac | 15 ++- gsl-2.1-8/gsl/inst/doc/gsl.R |only gsl-2.1-8/gsl/inst/doc/gsl.Rnw |only gsl-2.1-8/gsl/inst/doc/gsl.pdf |only gsl-2.1-8/gsl/man/figures/gsl.png |binary gsl-2.1-8/gsl/man/gsl-deprecated.Rd | 2 gsl-2.1-8/gsl/man/gsl-package.Rd | 2 gsl-2.1-8/gsl/vignettes/gsl.Rnw |only gsl-2.1-8/gsl/vignettes/gsl.bib | 2 23 files changed, 137 insertions(+), 104 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tibbletime versions 0.1.7 dated 2022-10-29 and 0.1.8 dated 2023-01-24
DESCRIPTION | 12 +- MD5 | 62 +++++++------- NEWS.md | 8 + R/as_period.R | 17 +--- R/collapse_index.R | 12 +- R/create_series.R | 4 R/partition_index.R | 4 R/time_join.R | 4 build/vignette.rds |binary inst/doc/TT-01-time-based-filtering.html | 4 inst/doc/TT-02-changing-time-periods.R | 2 inst/doc/TT-02-changing-time-periods.Rmd | 6 - inst/doc/TT-02-changing-time-periods.html | 18 ++-- inst/doc/TT-03-rollify-for-rolling-analysis.html | 8 - inst/doc/TT-04-use-with-dplyr.R | 8 - inst/doc/TT-04-use-with-dplyr.Rmd | 8 - inst/doc/TT-04-use-with-dplyr.html | 96 +++++++++++------------ man/as_period.Rd | 15 +-- man/ceiling_index.Rd | 19 +++- man/collapse_by.Rd | 8 - man/collapse_index.Rd | 8 - man/create_series.Rd | 6 - man/floor_index.Rd | 19 +++- man/parse_period.Rd | 2 man/partition_index.Rd | 4 man/rollify.Rd | 26 +----- tests/testthat/test_as_period.R | 18 ++-- tests/testthat/test_ceiling_index.R | 4 tests/testthat/test_collapse_index.R | 10 +- tests/testthat/test_floor_index.R | 4 vignettes/TT-02-changing-time-periods.Rmd | 6 - vignettes/TT-04-use-with-dplyr.Rmd | 8 - 32 files changed, 217 insertions(+), 213 deletions(-)
Title: Multivariate Meta-Analysis
Description: Multiple 2 by 2 tables often arise in meta-analysis which combines statistical evidence from multiple studies. Two risks within the same study are possibly correlated because they share some common factors such as environment and population structure. This package implements a set of novel Bayesian approaches for multivariate meta analysis when the risks within the same study are independent or correlated. The exact posterior inference of odds ratio, relative risk, and risk difference given either a single 2 by 2 table or multiple 2 by 2 tables is provided. Luo, Chen, Su, Chu, (2014) <doi:10.18637/jss.v056.i11>, Chen, Luo, (2011) <doi:10.1002/sim.4248>, Chen, Chu, Luo, Nie, Chen, (2015) <doi:10.1177/0962280211430889>, Chen, Luo, Chu, Su, Nie, (2014) <doi:10.1080/03610926.2012.700379>, Chen, Luo, Chu, Wei, (2013) <doi:10.1080/19466315.2013.791483>.
Author: Sheng Luo [aut],
Yong Chen [aut],
Xiao Su [aut],
Haitao Chu [aut],
Jiajie Chen [cre],
Wally Gilks [ctb],
Giovanni Petris [ctb],
Luca Tardella [ctb]
Maintainer: Jiajie Chen <jiajie.chen@pennmedicine.upenn.edu>
Diff between mmeta versions 2.4 dated 2022-12-13 and 3.0.0 dated 2023-01-24
mmeta-2.4/mmeta/R/MLE.r |only mmeta-2.4/mmeta/R/arms.R |only mmeta-2.4/mmeta/R/computation.r |only mmeta-2.4/mmeta/R/densityfunction.r |only mmeta-2.4/mmeta/R/multiple.r |only mmeta-2.4/mmeta/R/multipleplot.r |only mmeta-2.4/mmeta/R/overall.r |only mmeta-2.4/mmeta/R/sampling.r |only mmeta-2.4/mmeta/R/single.r |only mmeta-2.4/mmeta/R/singleplot.r |only mmeta-2.4/mmeta/R/summary.r |only mmeta-2.4/mmeta/man/multipletables.rd |only mmeta-2.4/mmeta/man/plot.multipletables.rd |only mmeta-2.4/mmeta/man/plot.singletable.rd |only mmeta-2.4/mmeta/man/singletable.Rd |only mmeta-2.4/mmeta/man/summary.multipletables.rd |only mmeta-2.4/mmeta/man/summary.singletable.rd |only mmeta-2.4/mmeta/tests |only mmeta-3.0.0/mmeta/DESCRIPTION | 17 +- mmeta-3.0.0/mmeta/MD5 | 57 +++++---- mmeta-3.0.0/mmeta/NAMESPACE | 23 +-- mmeta-3.0.0/mmeta/NEWS.md |only mmeta-3.0.0/mmeta/R/MultipleTables-method-exported.R |only mmeta-3.0.0/mmeta/R/MultipleTables-method-internal.R |only mmeta-3.0.0/mmeta/R/SingleTable-methods-exported.R |only mmeta-3.0.0/mmeta/R/SingleTable-methods-internal.R |only mmeta-3.0.0/mmeta/R/computation-armsSampler.R |only mmeta-3.0.0/mmeta/R/computation-exactDensity.R |only mmeta-3.0.0/mmeta/R/computation-exactMoment.R |only mmeta-3.0.0/mmeta/R/computation-loglikelihood.R |only mmeta-3.0.0/mmeta/R/computation-mathFun.R |only mmeta-3.0.0/mmeta/R/computation-overallMeasure.R |only mmeta-3.0.0/mmeta/R/computation-samplePosterior.R |only mmeta-3.0.0/mmeta/R/computation-summary.R |only mmeta-3.0.0/mmeta/R/config-globalConstant.R |only mmeta-3.0.0/mmeta/R/plot-density.R |only mmeta-3.0.0/mmeta/R/plot-forest.R |only mmeta-3.0.0/mmeta/R/utility-checkArgument.R |only mmeta-3.0.0/mmeta/R/utility-others.R |only mmeta-3.0.0/mmeta/R/utility-parmsTransform.R |only mmeta-3.0.0/mmeta/man/MultipleTables.create.Rd |only mmeta-3.0.0/mmeta/man/MultipleTables.modelFit.Rd |only mmeta-3.0.0/mmeta/man/MultipleTables.plot.Rd |only mmeta-3.0.0/mmeta/man/MultipleTables.summary.Rd |only mmeta-3.0.0/mmeta/man/SingleTable.create.Rd |only mmeta-3.0.0/mmeta/man/SingleTable.modelFit.Rd |only mmeta-3.0.0/mmeta/man/SingleTable.plot.Rd |only mmeta-3.0.0/mmeta/man/SingleTable.summary.Rd |only mmeta-3.0.0/mmeta/man/colorectal.Rd | 120 ++++++++----------- mmeta-3.0.0/mmeta/man/diabetes.Rd | 119 ++++++++---------- mmeta-3.0.0/mmeta/man/withdrawal.Rd | 104 +++++++--------- mmeta-3.0.0/mmeta/src/arms-R.c | 34 ----- 52 files changed, 213 insertions(+), 261 deletions(-)
Title: Routines for Common fMRI Processing Tasks
Description: Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Mark Fiecas [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRItools versions 0.1.3 dated 2022-11-10 and 0.2.2 dated 2023-01-24
fMRItools-0.1.3/fMRItools/man/erode_vol.Rd |only fMRItools-0.1.3/fMRItools/man/neighbor_counts.Rd |only fMRItools-0.1.3/fMRItools/man/unmask_subcortex.Rd |only fMRItools-0.1.3/fMRItools/man/validate_design_matrix.Rd |only fMRItools-0.1.3/fMRItools/man/vec2image.Rd |only fMRItools-0.2.2/fMRItools/DESCRIPTION | 24 + fMRItools-0.2.2/fMRItools/MD5 | 134 +++++---- fMRItools-0.2.2/fMRItools/NAMESPACE | 40 ++ fMRItools-0.2.2/fMRItools/NEWS.md |only fMRItools-0.2.2/fMRItools/R/CompCor.R | 14 fMRItools-0.2.2/fMRItools/R/CompCor_HCP.R | 4 fMRItools-0.2.2/fMRItools/R/DCT_FFT_detrending.R | 9 fMRItools-0.2.2/fMRItools/R/PCA.R | 20 - fMRItools-0.2.2/fMRItools/R/as.matrix_ifti.R | 18 - fMRItools-0.2.2/fMRItools/R/bandstop_filter.R | 21 - fMRItools-0.2.2/fMRItools/R/carpetplot.R |only fMRItools-0.2.2/fMRItools/R/despike_3D.R |only fMRItools-0.2.2/fMRItools/R/dim_reduce.R | 9 fMRItools-0.2.2/fMRItools/R/format_data.R | 8 fMRItools-0.2.2/fMRItools/R/fsl_bptf.R | 6 fMRItools-0.2.2/fMRItools/R/hat_matrix.R | 4 fMRItools-0.2.2/fMRItools/R/infer_format_ifti.R | 62 +++- fMRItools-0.2.2/fMRItools/R/nuisance_regression.R | 9 fMRItools-0.2.2/fMRItools/R/read_nifti.R | 7 fMRItools-0.2.2/fMRItools/R/rox_args_docs.R | 6 fMRItools-0.2.2/fMRItools/R/scale_matrix.R | 90 ++---- fMRItools-0.2.2/fMRItools/R/utils_checkValue.R | 52 +-- fMRItools-0.2.2/fMRItools/R/utils_files.R | 1 fMRItools-0.2.2/fMRItools/R/utils_mat.R |only fMRItools-0.2.2/fMRItools/R/utils_misc.R | 78 +---- fMRItools-0.2.2/fMRItools/R/utils_volume.R | 227 +++++++++------- fMRItools-0.2.2/fMRItools/R/validate_design_matrix.R | 6 fMRItools-0.2.2/fMRItools/R/var_decomp.R |only fMRItools-0.2.2/fMRItools/README.md | 6 fMRItools-0.2.2/fMRItools/man/CompCor.Rd | 6 fMRItools-0.2.2/fMRItools/man/Mode.Rd |only fMRItools-0.2.2/fMRItools/man/PCA.Rd | 8 fMRItools-0.2.2/fMRItools/man/Q2_max_check.Rd | 5 fMRItools-0.2.2/fMRItools/man/all_integers.Rd | 1 fMRItools-0.2.2/fMRItools/man/as.matrix_ifti.Rd | 8 fMRItools-0.2.2/fMRItools/man/bandstop_filter.Rd | 15 - fMRItools-0.2.2/fMRItools/man/carpetplot.Rd |only fMRItools-0.2.2/fMRItools/man/carpetplot_stack.Rd |only fMRItools-0.2.2/fMRItools/man/colCenter.Rd | 9 fMRItools-0.2.2/fMRItools/man/coordlist_to_vol.Rd | 15 - fMRItools-0.2.2/fMRItools/man/crop_vol.Rd | 8 fMRItools-0.2.2/fMRItools/man/data_CompCor_Params.Rd | 6 fMRItools-0.2.2/fMRItools/man/despike_3D.Rd |only fMRItools-0.2.2/fMRItools/man/despike_3D.interpolate.Rd |only fMRItools-0.2.2/fMRItools/man/despike_3D.qreg.Rd |only fMRItools-0.2.2/fMRItools/man/detrend.Rd | 9 fMRItools-0.2.2/fMRItools/man/dim_reduce.Rd | 4 fMRItools-0.2.2/fMRItools/man/erode_mask_vol.Rd |only fMRItools-0.2.2/fMRItools/man/fsl_bptf.Rd | 6 fMRItools-0.2.2/fMRItools/man/hat_matrix.Rd | 5 fMRItools-0.2.2/fMRItools/man/infer_format_ifti.Rd | 8 fMRItools-0.2.2/fMRItools/man/infer_format_ifti_vec.Rd |only fMRItools-0.2.2/fMRItools/man/is_1.Rd | 1 fMRItools-0.2.2/fMRItools/man/is_constant.Rd | 1 fMRItools-0.2.2/fMRItools/man/is_integer.Rd | 1 fMRItools-0.2.2/fMRItools/man/is_posNum.Rd | 12 fMRItools-0.2.2/fMRItools/man/match_exactly.Rd | 1 fMRItools-0.2.2/fMRItools/man/match_input.Rd | 1 fMRItools-0.2.2/fMRItools/man/mean_squares.Rd |only fMRItools-0.2.2/fMRItools/man/nuisance_regression.Rd | 8 fMRItools-0.2.2/fMRItools/man/pad_vol.Rd | 25 + fMRItools-0.2.2/fMRItools/man/pct_sig.Rd |only fMRItools-0.2.2/fMRItools/man/read_nifti.Rd | 7 fMRItools-0.2.2/fMRItools/man/rowMedians2.Rd |only fMRItools-0.2.2/fMRItools/man/scale_design_mat.Rd | 19 - fMRItools-0.2.2/fMRItools/man/scale_med.Rd | 17 - fMRItools-0.2.2/fMRItools/man/sign_flip.Rd | 3 fMRItools-0.2.2/fMRItools/man/skew_pos.Rd | 8 fMRItools-0.2.2/fMRItools/man/sum_neighbors_vol.Rd |only fMRItools-0.2.2/fMRItools/man/unmask_mat.Rd | 22 + fMRItools-0.2.2/fMRItools/man/unvec_mat.Rd |only fMRItools-0.2.2/fMRItools/man/unvec_vol.Rd |only fMRItools-0.2.2/fMRItools/man/validate_design_mat.Rd |only fMRItools-0.2.2/fMRItools/man/var_decomp.Rd |only fMRItools-0.2.2/fMRItools/man/vox_locations.Rd | 17 - fMRItools-0.2.2/fMRItools/tests/testthat/test-misc.R | 13 81 files changed, 658 insertions(+), 466 deletions(-)
Title: High Dimensional Bayesian Mediation Analysis
Description: Perform mediation analysis in the presence of high-dimensional
mediators based on the potential outcome framework. Bayesian Mediation
Analysis (BAMA), developed by Song et al (2019) <doi:10.1111/biom.13189> and
Song et al (2020) <arXiv:2009.11409>,
relies on two Bayesian sparse linear mixed models to simultaneously analyze
a relatively large number of mediators for a continuous exposure and outcome
assuming a small number of mediators are truly active. This sparsity
assumption also allows the extension of univariate mediator analysis by
casting the identification of active mediators as a variable selection
problem and applying Bayesian methods with continuous shrinkage priors on
the effects.
Author: Alexander Rix [aut],
Mike Kleinsasser [aut, cre],
Yanyi Song [aut]
Maintainer: Mike Kleinsasser <mkleinsa@umich.edu>
Diff between bama versions 1.2.5 dated 2022-10-20 and 1.3.0 dated 2023-01-24
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/RcppExports.R | 4 ++-- R/bama.R | 17 +++++++++++++---- R/fdr.bama.R | 16 +++++++++------- build/partial.rdb |binary build/vignette.rds |binary man/bama.Rd | 12 +++++++----- man/fdr.bama.Rd | 6 +++++- src/RcppExports.cpp | 9 +++++---- src/bama.cpp | 12 +++++++----- src/ptg.cpp | 43 +++++++++++++++++-------------------------- 12 files changed, 79 insertions(+), 68 deletions(-)
Title: Compute Power or Sample Size for GWAS with Covariate Effect
Description: Fast computation of the required sample size or the
achieved power, for GWAS studies with different types of covariate
effects and different types of covariate-gene dependency structure.
For the detailed description of the methodology, see Zhang (2022)
"Power and Sample Size Computation for Genetic Association Studies
of Binary Traits: Accounting for Covariate Effects" <arXiv:2203.15641>.
Author: Ziang Zhang, Lei Sun
Maintainer: Ziang Zhang <aguero.zhang@mail.utoronto.ca>
Diff between SPCompute versions 1.0.2 dated 2022-09-05 and 1.0.3 dated 2023-01-24
SPCompute-1.0.2/SPCompute/R/04_wrapper.R |only SPCompute-1.0.3/SPCompute/DESCRIPTION | 8 SPCompute-1.0.3/SPCompute/MD5 | 26 SPCompute-1.0.3/SPCompute/NEWS.md | 4 SPCompute-1.0.3/SPCompute/R/02_multiple_E_binary_trait.R | 4 SPCompute-1.0.3/SPCompute/R/04_multiple_E_binary_trait_dep.R |only SPCompute-1.0.3/SPCompute/R/05_multiple_E_continuous_trait_dep.R |only SPCompute-1.0.3/SPCompute/R/06_wrapper.R |only SPCompute-1.0.3/SPCompute/build/vignette.rds |binary SPCompute-1.0.3/SPCompute/inst/doc/SPCompute-vignette.R | 7 SPCompute-1.0.3/SPCompute/inst/doc/SPCompute-vignette.Rmd | 41 SPCompute-1.0.3/SPCompute/inst/doc/SPCompute-vignette.html | 469 ++++++++-- SPCompute-1.0.3/SPCompute/man/Compute_Power_multi.Rd | 5 SPCompute-1.0.3/SPCompute/man/Compute_Size_multi.Rd | 2 SPCompute-1.0.3/SPCompute/man/convert_preva_to_intercept.Rd | 2 SPCompute-1.0.3/SPCompute/vignettes/SPCompute-vignette.Rmd | 41 16 files changed, 495 insertions(+), 114 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, and implicitly supports parallel processing.
For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.9.1 dated 2022-08-30 and 2.10 dated 2023-01-24
DESCRIPTION | 14 MD5 | 30 NAMESPACE | 3 NEWS.md | 10 R/SimDesign.R | 2 R/analysis.R | 24 R/functions.R | 4 R/runSimulation.R | 58 + inst/doc/Catch_errors.html | 1311 -------------------------------------- inst/doc/Fixed_obj_fun.html | 1303 -------------------------------------- inst/doc/MultipleAnalyses.html | 1302 -------------------------------------- inst/doc/Parallel-computing.html | 1297 -------------------------------------- inst/doc/Saving-results.html | 1323 -------------------------------------- inst/doc/SimDesign-intro.html | 1324 --------------------------------------- man/runSimulation.Rd | 70 +- tests/tests/test-SimDesign.R | 7 16 files changed, 308 insertions(+), 7774 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single
value. 'tidyr' contains tools for changing the shape (pivoting) and
hierarchy (nesting and 'unnesting') of a dataset, turning deeply
nested lists into rectangular data frames ('rectangling'), and
extracting values out of string columns. It also includes tools for
working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Davis Vaughan [aut],
Maximilian Girlich [aut],
Kevin Ushey [ctb],
Posit, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between tidyr versions 1.2.1 dated 2022-09-08 and 1.3.0 dated 2023-01-24
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Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.21 dated 2023-01-09 and 2.3.22 dated 2023-01-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/matrix_tapply.cpp | 10 ++++++++++ 4 files changed, 20 insertions(+), 6 deletions(-)
Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications. For more information regarding the methodology see Meier, Mata & Wulff (2022) <arXiv:2110.05856>.
Author: Dirk U. Wulff [aut] ,
Dominik S. Meier [aut, cre] ,
Rui Mata [ctb]
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>
Diff between text2sdg versions 0.1.6 dated 2022-09-08 and 1.0.0 dated 2023-01-24
text2sdg-0.1.6/text2sdg/R/detect.R |only text2sdg-0.1.6/text2sdg/data/osdg_queries.RData |only text2sdg-0.1.6/text2sdg/data/sdsn_queries.RData |only text2sdg-0.1.6/text2sdg/man/osdg_queries.Rd |only text2sdg-1.0.0/text2sdg/DESCRIPTION | 13 text2sdg-1.0.0/text2sdg/MD5 | 59 +-- text2sdg-1.0.0/text2sdg/NAMESPACE | 2 text2sdg-1.0.0/text2sdg/NEWS.md | 4 text2sdg-1.0.0/text2sdg/R/auckland.R |only text2sdg-1.0.0/text2sdg/R/crosstab.R | 6 text2sdg-1.0.0/text2sdg/R/datasets.R | 30 + text2sdg-1.0.0/text2sdg/R/detect_any.R | 2 text2sdg-1.0.0/text2sdg/R/elsevier.R | 9 text2sdg-1.0.0/text2sdg/R/ensemble.R |only text2sdg-1.0.0/text2sdg/R/globals.R | 2 text2sdg-1.0.0/text2sdg/R/osdg.R | 12 text2sdg-1.0.0/text2sdg/R/plot.R | 6 text2sdg-1.0.0/text2sdg/R/systems.R |only text2sdg-1.0.0/text2sdg/R/text2sdg.R | 10 text2sdg-1.0.0/text2sdg/README.md | 6 text2sdg-1.0.0/text2sdg/data/auckland_queries.RData |only text2sdg-1.0.0/text2sdg/data/ensembles.rda |only text2sdg-1.0.0/text2sdg/data/sdgo_queries.RData |only text2sdg-1.0.0/text2sdg/data/sdsn_queries.rda |only text2sdg-1.0.0/text2sdg/inst/doc/text2sdg.R | 22 - text2sdg-1.0.0/text2sdg/inst/doc/text2sdg.Rmd | 63 ++- text2sdg-1.0.0/text2sdg/inst/doc/text2sdg.html | 334 ++++++++++---------- text2sdg-1.0.0/text2sdg/man/auckland_queries.Rd |only text2sdg-1.0.0/text2sdg/man/crosstab_sdg.Rd | 6 text2sdg-1.0.0/text2sdg/man/detect_any.Rd | 2 text2sdg-1.0.0/text2sdg/man/detect_sdg.Rd | 35 +- text2sdg-1.0.0/text2sdg/man/detect_sdg_systems.Rd |only text2sdg-1.0.0/text2sdg/man/ensembles.Rd |only text2sdg-1.0.0/text2sdg/man/plot_sdg.Rd | 6 text2sdg-1.0.0/text2sdg/man/projects.Rd | 2 text2sdg-1.0.0/text2sdg/man/sdgo_queries.Rd |only text2sdg-1.0.0/text2sdg/man/text2sdg.Rd | 10 text2sdg-1.0.0/text2sdg/vignettes/text2sdg.Rmd | 63 ++- 38 files changed, 408 insertions(+), 296 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre] ,
Skye Bender-deMoll [ctb],
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between statnet.common versions 4.7.0 dated 2022-09-08 and 4.8.0 dated 2023-01-24
DESCRIPTION | 12 +++++------ LICENSE | 2 - MD5 | 47 ++++++++++++++++++++++----------------------- NAMESPACE | 1 NEWS | 9 ++++++++ NEWS.md | 6 +++++ R/Welford.R | 2 - R/cite.utilities.R | 2 - R/control.utilities.R | 2 - R/deprecation_utils.R | 2 - R/formula.utilities.R | 2 - R/locator.R | 2 - R/logspace.utils.R | 2 - R/mcmc-utils.R | 2 - R/misc.utilities.R | 44 +++++++++++++++++++++++++++++++++++++++++- R/startup.utilities.R | 2 - R/string.utilities.R | 2 - R/wmatrix.R | 2 - R/zzz.R | 2 - build/statnet.common.pdf |binary inst/CITATION | 12 +++++------ inst/templates/snctrl.R | 2 - man/unused_dots_warning.Rd |only src/init.c | 2 - src/logspace_utils.c | 2 - 25 files changed, 111 insertions(+), 52 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre]
,
Hossein Kamalzadeh [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.0.3 dated 2022-05-19 and 1.1.0 dated 2023-01-24
pomdp-1.0.3/pomdp/R/AAA_imports.R |only pomdp-1.0.3/pomdp/R/transition_matrix.R |only pomdp-1.0.3/pomdp/R/visNetwork.R |only pomdp-1.0.3/pomdp/man/policy_graph.Rd |only pomdp-1.0.3/pomdp/man/transition_matrix.Rd |only pomdp-1.0.3/pomdp/tests/testthat/test-matrix_extractors.R |only pomdp-1.1.0/pomdp/DESCRIPTION | 42 pomdp-1.1.0/pomdp/MD5 | 124 +- pomdp-1.1.0/pomdp/NAMESPACE | 41 pomdp-1.1.0/pomdp/NEWS.md | 19 pomdp-1.1.0/pomdp/R/AAA_pomdp-package.R | 14 pomdp-1.1.0/pomdp/R/MDP.R | 13 pomdp-1.1.0/pomdp/R/POMDP.R | 594 +++++++++---- pomdp-1.1.0/pomdp/R/POMDP_accessors.R |only pomdp-1.1.0/pomdp/R/RcppExports.R |only pomdp-1.1.0/pomdp/R/estimate_belief_for_nodes.R |only pomdp-1.1.0/pomdp/R/foreach_helper.R |only pomdp-1.1.0/pomdp/R/plot_belief_space.R | 164 +-- pomdp-1.1.0/pomdp/R/plot_policy_graph.R | 393 ++------ pomdp-1.1.0/pomdp/R/plot_value_function.R | 63 - pomdp-1.1.0/pomdp/R/policy.R | 21 pomdp-1.1.0/pomdp/R/policy_graph.R |only pomdp-1.1.0/pomdp/R/projection.R |only pomdp-1.1.0/pomdp/R/queue.R |only pomdp-1.1.0/pomdp/R/read_write_POMDP.R | 627 ++++++++++++-- pomdp-1.1.0/pomdp/R/reward.R | 27 pomdp-1.1.0/pomdp/R/round_stochchastic.R | 50 - pomdp-1.1.0/pomdp/R/sample_belief_space.R | 191 ++-- pomdp-1.1.0/pomdp/R/simulate_MDP.R | 226 +++-- pomdp-1.1.0/pomdp/R/simulate_POMDP.R | 315 +++++-- pomdp-1.1.0/pomdp/R/solve_MDP.R | 120 +- pomdp-1.1.0/pomdp/R/solve_POMDP.R | 159 +-- pomdp-1.1.0/pomdp/R/solve_SARSOP.R | 20 pomdp-1.1.0/pomdp/R/update_belief.R | 10 pomdp-1.1.0/pomdp/README.md | 29 pomdp-1.1.0/pomdp/build/vignette.rds |binary pomdp-1.1.0/pomdp/data/Maze.rda |binary pomdp-1.1.0/pomdp/data/Three_doors.rda |binary pomdp-1.1.0/pomdp/data/Tiger.rda |binary pomdp-1.1.0/pomdp/inst/README_files/policy_graph-1.png |binary pomdp-1.1.0/pomdp/inst/doc/POMDP.html | 202 ++++ pomdp-1.1.0/pomdp/inst/examples |only pomdp-1.1.0/pomdp/man/MDP.Rd | 6 pomdp-1.1.0/pomdp/man/POMDP.Rd | 57 + pomdp-1.1.0/pomdp/man/POMDP_accessors.Rd |only pomdp-1.1.0/pomdp/man/estimate_belief_for_nodes.Rd |only pomdp-1.1.0/pomdp/man/figures |only pomdp-1.1.0/pomdp/man/optimal_action.Rd | 5 pomdp-1.1.0/pomdp/man/plot_belief_space.Rd | 66 + pomdp-1.1.0/pomdp/man/plot_policy_graph.Rd |only pomdp-1.1.0/pomdp/man/plot_value_function.Rd | 36 pomdp-1.1.0/pomdp/man/policy.Rd | 5 pomdp-1.1.0/pomdp/man/projection.Rd |only pomdp-1.1.0/pomdp/man/reward.Rd | 5 pomdp-1.1.0/pomdp/man/round_stochastic.Rd | 16 pomdp-1.1.0/pomdp/man/sample_belief_space.Rd | 36 pomdp-1.1.0/pomdp/man/simulate_MDP.Rd | 63 + pomdp-1.1.0/pomdp/man/simulate_POMDP.Rd | 88 + pomdp-1.1.0/pomdp/man/solve_MDP.Rd | 5 pomdp-1.1.0/pomdp/man/solve_POMDP.Rd | 93 +- pomdp-1.1.0/pomdp/man/solve_SARSOP.Rd | 15 pomdp-1.1.0/pomdp/man/update_belief.Rd | 4 pomdp-1.1.0/pomdp/man/write_POMDP.Rd | 24 pomdp-1.1.0/pomdp/src |only pomdp-1.1.0/pomdp/tests/testthat/test-POMDP_accessors.R |only pomdp-1.1.0/pomdp/tests/testthat/test-cpp.R |only pomdp-1.1.0/pomdp/tests/testthat/test-read_write_POMDP.R | 21 pomdp-1.1.0/pomdp/tests/testthat/test-simulate.R |only pomdp-1.1.0/pomdp/tests/testthat/test-solve_POMDP.R | 22 pomdp-1.1.0/pomdp/tests/testthat/test-solve_SARSOP.R | 2 70 files changed, 2721 insertions(+), 1312 deletions(-)
Title: Calculating Topological Properties of Phylogenies
Description: Tools for calculating and viewing topological properties of phylogenetic trees.
Author: Michelle Kendall [aut, cre] ,
Michael Boyd [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <michelle.kendall@warwick.ac.uk>
Diff between phyloTop versions 2.1.1 dated 2018-02-21 and 2.1.2 dated 2023-01-24
phyloTop-2.1.1/phyloTop/inst |only phyloTop-2.1.2/phyloTop/DESCRIPTION | 19 - phyloTop-2.1.2/phyloTop/MD5 | 125 +++---- phyloTop-2.1.2/phyloTop/NAMESPACE | 77 ++-- phyloTop-2.1.2/phyloTop/NEWS.md | 60 ++- phyloTop-2.1.2/phyloTop/R/ILnumber.R | 64 +-- phyloTop-2.1.2/phyloTop/R/avgLadder.R | 64 +-- phyloTop-2.1.2/phyloTop/R/cherries.R | 74 ++-- phyloTop-2.1.2/phyloTop/R/colless.R | 78 ++-- phyloTop-2.1.2/phyloTop/R/configShow.R | 94 ++--- phyloTop-2.1.2/phyloTop/R/deprecated.R | 240 +++++++------- phyloTop-2.1.2/phyloTop/R/getDepths.R | 92 ++--- phyloTop-2.1.2/phyloTop/R/getLabGenealogy.R | 298 +++++++++--------- phyloTop-2.1.2/phyloTop/R/ladderShow.R | 94 ++--- phyloTop-2.1.2/phyloTop/R/ladderSizes.R | 160 ++++----- phyloTop-2.1.2/phyloTop/R/makeEpiRecord.R | 92 ++--- phyloTop-2.1.2/phyloTop/R/makePhyloTree.R | 84 ++--- phyloTop-2.1.2/phyloTop/R/maxHeight.R | 56 +-- phyloTop-2.1.2/phyloTop/R/nConfig.R | 96 ++--- phyloTop-2.1.2/phyloTop/R/nodeDepth.R | 60 +-- phyloTop-2.1.2/phyloTop/R/nodeDepthFrac.R | 68 ++-- phyloTop-2.1.2/phyloTop/R/nodeImb.R | 56 +-- phyloTop-2.1.2/phyloTop/R/nodeImbFrac.R | 70 ++-- phyloTop-2.1.2/phyloTop/R/phyloCheck.R | 63 +-- phyloTop-2.1.2/phyloTop/R/phyloTop.R | 324 ++++++++++---------- phyloTop-2.1.2/phyloTop/R/pitchforks.R | 74 ++-- phyloTop-2.1.2/phyloTop/R/rtree4.R | 48 +- phyloTop-2.1.2/phyloTop/R/sackin.R | 72 ++-- phyloTop-2.1.2/phyloTop/R/splitTop.R | 78 ++-- phyloTop-2.1.2/phyloTop/R/stairs.R | 72 ++-- phyloTop-2.1.2/phyloTop/R/subtreeShow.R | 114 +++---- phyloTop-2.1.2/phyloTop/R/treeImb.R | 98 +++--- phyloTop-2.1.2/phyloTop/R/widths.R | 52 +-- phyloTop-2.1.2/phyloTop/README.md | 283 +++++++++-------- phyloTop-2.1.2/phyloTop/build/partial.rdb |binary phyloTop-2.1.2/phyloTop/man/ILnumber.Rd | 66 ++-- phyloTop-2.1.2/phyloTop/man/avgLadder.Rd | 70 ++-- phyloTop-2.1.2/phyloTop/man/cherries.Rd | 76 ++-- phyloTop-2.1.2/phyloTop/man/colless.phylo.Rd | 68 ++-- phyloTop-2.1.2/phyloTop/man/configShow.Rd | 70 ++-- phyloTop-2.1.2/phyloTop/man/getDepths.Rd | 76 ++-- phyloTop-2.1.2/phyloTop/man/getLabGenealogy.Rd | 70 ++-- phyloTop-2.1.2/phyloTop/man/ladderShow.Rd | 91 ++--- phyloTop-2.1.2/phyloTop/man/ladderSizes.Rd | 86 ++--- phyloTop-2.1.2/phyloTop/man/makeEpiRecord.Rd | 68 ++-- phyloTop-2.1.2/phyloTop/man/makePhyloTree.Rd | 54 +-- phyloTop-2.1.2/phyloTop/man/maxHeight.Rd | 64 +-- phyloTop-2.1.2/phyloTop/man/nConfig.Rd | 72 ++-- phyloTop-2.1.2/phyloTop/man/nodeDepth.Rd | 64 +-- phyloTop-2.1.2/phyloTop/man/nodeDepthFrac.Rd | 66 ++-- phyloTop-2.1.2/phyloTop/man/nodeImb.Rd | 68 ++-- phyloTop-2.1.2/phyloTop/man/nodeImbFrac.Rd | 66 ++-- phyloTop-2.1.2/phyloTop/man/phyloCheck.Rd | 48 +- phyloTop-2.1.2/phyloTop/man/phyloTop.Rd | 90 ++--- phyloTop-2.1.2/phyloTop/man/pitchforks.Rd | 76 ++-- phyloTop-2.1.2/phyloTop/man/rtree4.Rd | 60 +-- phyloTop-2.1.2/phyloTop/man/sackin.phylo.Rd | 70 ++-- phyloTop-2.1.2/phyloTop/man/splitTop.Rd | 66 ++-- phyloTop-2.1.2/phyloTop/man/stairs.Rd | 60 +-- phyloTop-2.1.2/phyloTop/man/subtreeShow.Rd | 95 +++-- phyloTop-2.1.2/phyloTop/man/treeImb.Rd | 64 +-- phyloTop-2.1.2/phyloTop/man/widths.Rd | 60 +-- phyloTop-2.1.2/phyloTop/tests/testthat.R | 8 phyloTop-2.1.2/phyloTop/tests/testthat/testbasics.R | 172 +++++----- 64 files changed, 2753 insertions(+), 2710 deletions(-)
Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix?
How much ram is your current R session using? How much ram do you even have?
Learn the scintillating answer to these and many more such questions with
the 'memuse' package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [ctb] ,
Wei-Chen Chen [ctb] ,
Dan Burgess [ctb]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between memuse versions 4.2-2 dated 2022-11-01 and 4.2-3 dated 2023-01-24
ChangeLog | 3 DESCRIPTION | 6 MD5 | 10 README.md | 2 configure | 2341 +++++++++++++++++++++++++++++------------------------------ configure.ac | 14 6 files changed, 1210 insertions(+), 1166 deletions(-)
Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between huito versions 0.2.1 dated 2022-08-11 and 0.2.2 dated 2023-01-24
DESCRIPTION | 10 MD5 | 46 +- NAMESPACE | 42 +- NEWS.md | 4 build/vignette.rds |binary inst/doc/germinar.html | 126 +++---- inst/doc/huito.html | 14 inst/doc/labels.R | 6 inst/doc/labels.Rmd | 6 inst/doc/labels.html | 738 ++++++++++++++++++++--------------------- inst/doc/stickers.html | 126 +++---- man/barcode_qr.Rd | 64 +-- man/fieldbook.Rd | 54 +-- man/huito_fonts.Rd | 40 +- man/image_import.Rd | 38 +- man/include_barcode.Rd | 74 ++-- man/include_image.Rd | 74 ++-- man/include_shape.Rd | 136 +++---- man/include_text.Rd | 86 ++-- man/label_print.Rd | 174 ++++----- man/reexports.Rd | 32 - man/shape_hexagon.Rd | 94 ++--- vignettes/huito/huito-intro.md | 28 - vignettes/labels.Rmd | 6 24 files changed, 1021 insertions(+), 997 deletions(-)
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, [...truncated...]
Author: Marie-Laure Delignette-Muller [aut]
,
Elise Billoir [aut] ,
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.4-0 dated 2022-01-06 and 2.5-0 dated 2023-01-24
DESCRIPTION | 25 MD5 | 132 - NAMESPACE | 4 NEWS.md |only R/PCAdataplot.R |only R/RNAseqdata.R | 20 R/bmdplot.R | 8 R/bmdplotwithgradient.R | 61 R/continuousanchoringdata.R | 1 R/curvesplot.R | 46 R/drcfit.R | 65 R/ecdfquantileplot.R | 5 R/formatdata4DRomics.R |only R/metabolomicdata.R | 5 R/microarraydata.R | 9 R/selectgroups.R |only R/sensitivityplot.R | 71 R/targetplot.R | 2 R/trendplot.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/zebraf.rda |only inst/DRomics-shiny/apt.txt |only inst/DRomics-shiny/install.R |only inst/DRomics-shiny/rinstall.txt | 5 inst/DRomics-shiny/server.R | 9 inst/DRomics-shiny/ui.R | 96 inst/DRomics-shiny/www/LogoHelmholtz.jpg |binary inst/DRomics-shiny/www/LogoUniversiteLorraine.png |binary inst/DRomics-shiny/www/flag_yellow_high.jpg |binary inst/DRomics-shiny/www/informations_bmdcalc_results.txt | 4 inst/DRomics-shiny/www/intro.txt | 3 inst/DRomics-shiny/www/logoLiec.png |binary inst/DRomics-shiny/www/logoLyon1.png |binary inst/DRomics-shiny/www/logodromics-dr.png |binary inst/DRomics-shiny/www/logodromics.png |binary inst/DRomicsInterpreter-shiny |only inst/NEWS | 35 inst/doc/DRomics_vignette.R | 374 ++- inst/doc/DRomics_vignette.Rmd | 1311 ++++++++---- inst/doc/DRomics_vignette.html | 1740 +++++++++------- inst/extdata/insitu_RNAseq_sample.txt | 2 inst/extdata/triclosanSVcontigannot.txt | 94 inst/extdata/triclosanSVcontigres.txt | 892 ++++---- inst/extdata/triclosanSVmetabres.txt | 64 inst/hexsticker |only man/PCAdataplot.Rd |only man/RNAseqdata.Rd | 15 man/bmdboot.Rd | 6 man/bmdcalc.Rd | 6 man/bmdplotwithgradient.Rd | 22 man/curvesplot.Rd | 44 man/drcfit.Rd | 7 man/figures |only man/formatdata4DRomics.Rd |only man/metabolomicdata.Rd | 10 man/microarraydata.Rd | 10 man/selectgroups.Rd |only man/sensitivityplot.Rd | 1 man/zebraf.Rd |only tests/examplewithRNAseq.R | 9 tests/examplewithanchoringdata.R | 2 tests/test_selectgroups.R |only tests/testbmdplotwithgradient.R |only tests/testscaling.R |only tests/testsensitivityplot.R |only tests/testthat/test_bmdcalc.R | 1 tests/testthat/test_drcfit.R | 1 tests/testthat/test_itemselect.R | 1 vignettes/DRomics_vignette.Rmd | 1311 ++++++++---- 70 files changed, 4220 insertions(+), 2311 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Also used to display, in tables and graphs, predictions
obtained using any model fitting function and to explore differences between predictions.
The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions (for further
details see 'asremlPlus-package' in help). A history of
the fitting of a sequence of models is kept in a data frame. Procedures are available for
choosing models that conform to the hierarchy or marginality principle and for displaying
predictions for significant terms in tables and graphs. The 'asreml' package provides a
computationally efficient algorithm for fitting mixed models using Resi [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.3.40 dated 2022-11-16 and 4.3.45 dated 2023-01-24
asremlPlus-4.3.40/asremlPlus/vignettes/asremlPlus_4.3.39.pdf |only asremlPlus-4.3.40/asremlPlus/vignettes/dae-manual.pdf |only asremlPlus-4.3.45/asremlPlus/DESCRIPTION | 8 asremlPlus-4.3.45/asremlPlus/MD5 | 64 +++--- asremlPlus-4.3.45/asremlPlus/NAMESPACE | 14 + asremlPlus-4.3.45/asremlPlus/R/REMLRTIC.v3.r | 2 asremlPlus-4.3.45/asremlPlus/R/S3methodsDeprecations.r | 4 asremlPlus-4.3.45/asremlPlus/R/asremlPlusUtilities.r | 40 +++- asremlPlus-4.3.45/asremlPlus/R/bbasis.R |only asremlPlus-4.3.45/asremlPlus/R/choose.r | 96 +++++----- asremlPlus-4.3.45/asremlPlus/R/reml4.v8.r | 4 asremlPlus-4.3.45/asremlPlus/R/spatial.funcs.r |only asremlPlus-4.3.45/asremlPlus/R/tpsmmb.r |only asremlPlus-4.3.45/asremlPlus/build/partial.rdb |binary asremlPlus-4.3.45/asremlPlus/inst/NEWS.Rd | 30 +++ asremlPlus-4.3.45/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.3.45/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.3.45/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.3.45/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.3.45/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.3.45/asremlPlus/man/addSpatialModel.asrtests.Rd |only asremlPlus-4.3.45/asremlPlus/man/addSpatialModelOnIC.asrtests.Rd |only asremlPlus-4.3.45/asremlPlus/man/asremlPlus-package.Rd | 14 + asremlPlus-4.3.45/asremlPlus/man/changeModelOnIC.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/changeTerms.asrtests.Rd | 4 asremlPlus-4.3.45/asremlPlus/man/chooseSpatialModelOnIC.asrtests.Rd |only asremlPlus-4.3.45/asremlPlus/man/getTestEntry.asrtests.Rd | 4 asremlPlus-4.3.45/asremlPlus/man/getTestPvalue.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/iterate.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/makeTPSPlineXZMats.data.frame.Rd |only asremlPlus-4.3.45/asremlPlus/man/recalcWaldTab.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/reparamSigDevn.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/rmboundary.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/man/testranfix.asrtests.Rd | 2 asremlPlus-4.3.45/asremlPlus/tests/testthat/test4EstimateV.r | 8 asremlPlus-4.3.45/asremlPlus/tests/testthat/test4Selection.r | 10 - asremlPlus-4.3.45/asremlPlus/tests/testthat/test4SpatialModels.r |only asremlPlus-4.3.45/asremlPlus/tests/testthat/test4alldiffslme.r | 4 38 files changed, 212 insertions(+), 108 deletions(-)
Title: Code-Logics to Handle Ontologies
Description: Provides tools to build and work with an ontology of linked (open)
data in a tidy workflow. It is inspired by the Food and Agrilculture
Organizations (FAO) caliper platform
<https://www.fao.org/statistics/caliper/web/> and
makes use of the Simple Knowledge Organisation System (SKOS).
Author: Steffen Ehrmann [aut, cre] ,
Arne Ruemmler [aut, ctb]
Maintainer: Steffen Ehrmann <steffen.ehrmann@posteo.de>
Diff between ontologics versions 0.5.2 dated 2022-10-19 and 0.6.4 dated 2023-01-24
DESCRIPTION | 11 MD5 | 98 - NAMESPACE | 10 NEWS.md | 39 R/1onto.R | 503 +++---- R/edit_matches.R | 556 +++++--- R/export_as_rdf.R | 902 ++++++------- R/get_class.R |only R/get_concept.R | 485 +++---- R/get_source.R |only R/imports.R | 30 R/load_ontology.R | 70 - R/makeTreeMap.R | 132 - R/make_tree.R | 76 - R/new_class.R | 184 +- R/new_concept.R | 522 +++---- R/new_mapping.R | 555 ++++---- R/new_source.R | 246 +-- R/start_ontology.R | 179 +- R/zzz.R | 6 README.md | 130 - build/vignette.rds |binary inst/doc/conversion_to_rdf.R | 36 inst/doc/conversion_to_rdf.Rmd | 2 inst/doc/conversion_to_rdf.html | 1268 +++++++++--------- inst/doc/create_an_ontology.R | 184 +- inst/doc/create_an_ontology.Rmd | 270 +-- inst/doc/create_an_ontology.html | 1940 ++++++++++++++-------------- inst/doc/map_new_concepts.R | 177 +- inst/doc/map_new_concepts.Rmd | 249 +-- inst/doc/map_new_concepts.html | 1571 +++++++++++----------- inst/doc/ontology_database_description.Rmd | 220 +-- inst/doc/ontology_database_description.html | 1006 +++++++------- man/edit_matches.Rd | 124 - man/export_as_rdf.Rd | 66 man/figures/logo.svg | 744 +++++----- man/get_class.Rd |only man/get_concept.Rd | 130 - man/get_source.Rd |only man/make_tree.Rd | 35 man/new_class.Rd | 68 man/new_concept.Rd | 6 man/new_mapping.Rd | 185 +- man/new_source.Rd | 162 +- man/onto-class.Rd | 40 man/pipe.Rd | 40 man/show-onto-method.Rd | 28 vignettes/conversion_to_rdf.Rmd | 2 vignettes/create_an_ontology.Rmd | 270 +-- vignettes/map_new_concepts.Rmd | 249 +-- vignettes/ontology_database_description.Rmd | 220 +-- vignettes/skos.rdf | 936 ++++++------- 52 files changed, 7717 insertions(+), 7245 deletions(-)
Title: Load Data for Analysis System
Description: Provides a framework to load text and excel files through a 'shiny' graphical interface. It allows renaming, transforming, ordering and removing variables. It includes basic exploratory methods such as the mean, median, mode, normality test, histogram and correlation.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [aut],
Joseline Quiros [aut]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between loadeR versions 1.1.1 dated 2023-01-12 and 1.1.3 dated 2023-01-24
DESCRIPTION | 6 ++--- MD5 | 32 ++++++++++++++-------------- NEWS.md | 10 ++++++++ R/golem_utils_server.R | 14 ------------ R/golem_utils_ui.R | 2 - R/loadeR.R | 4 +-- R/mod_acercade.R | 2 - R/mod_carga_datos.R | 38 +++++++++++++++++++++++++++++----- R/mod_carga_datos_fct.R | 4 +-- R/mod_carga_datos_utils.R | 8 +++++-- R/mod_distribuciones.R | 2 - inst/app/lang/diccionario.csv | 2 + inst/app/lang/translation_loadeR.bin |binary inst/assets/cargaDatos/cargaDatos.css | 5 ++-- inst/golem-config.yml | 2 - man/loadeR.Rd | 4 +-- man/tabsOptions.Rd | 2 - 17 files changed, 85 insertions(+), 52 deletions(-)
Title: Implementation of the 3D Alpha-Shape for the Reconstruction of
3D Sets from a Point Cloud
Description: Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.
Author: Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>
Diff between alphashape3d versions 1.3.1 dated 2020-12-09 and 1.3.2 dated 2023-01-24
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + R/ashape3d.R | 10 +++++++--- R/components_ashape3d.R | 4 ++-- R/inashape3d.R | 4 ++-- R/plot.ashape3d.R | 28 ++++++++++++++-------------- R/rtorus.R | 6 +++--- R/surfaceNormals.R | 6 +++--- R/volume_ashape3d.R | 4 ++-- man/inashape3d.Rd | 2 +- man/plot.ashape3d.Rd | 2 +- man/rtorus.Rd | 7 ++++--- man/surfaceNormals.Rd | 2 +- 14 files changed, 59 insertions(+), 52 deletions(-)
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] ,
Graph Builder [ctb, cph] ,
Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 1.0.6 dated 2022-10-21 and 1.0.7 dated 2023-01-24
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++------- NEWS | 3 +++ R/onLoad.R | 4 ++-- README.md | 2 +- build/vignette.rds |binary inst/doc/XLConnect.pdf |binary inst/doc/XLConnectImpatient.pdf |binary inst/unitTests/resources/testBug181.xlsx |only inst/unitTests/runit.workbook.testBug181.R |only 10 files changed, 18 insertions(+), 13 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include standard operations such as intersect and buffer. Raster methods include global, local, zonal, and focal computations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is a replacement for the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.6-53 dated 2023-01-17 and 1.7-3 dated 2023-01-24
DESCRIPTION | 8 - MD5 | 54 +++---- NAMESPACE | 2 NEWS.md | 82 +++++----- R/Agenerics.R | 1 R/generics.R | 7 R/geom.R | 2 R/rast.R | 11 + R/sample.R | 15 + R/vect.R | 12 + R/write.R | 23 ++- R/zonal.R | 41 ++++- inst/tinytest/test_arith.R |only man/clamp_ts.Rd |only man/terra-package.Rd | 9 - man/writeRaster.Rd | 2 man/zonal.Rd | 48 ++++-- src/RcppModule.cpp | 6 src/arith.cpp | 10 - src/concaveman.cpp |only src/concaveman.h |only src/raster_methods.cpp | 78 ++++++++++ src/raster_stats.cpp | 344 ++++++++++++++++++++++++++++++++++++++++++++- src/rasterize.cpp | 9 + src/read_gdal.cpp | 64 ++++---- src/spatRaster.cpp | 2 src/spatRaster.h | 6 src/vecmathse.cpp | 109 +++++++------- src/vecmathse.h | 88 +++++------ src/write_gdal.cpp | 5 30 files changed, 797 insertions(+), 241 deletions(-)
Title: Flexible Segment Geoms with Arrows for 'ggplot2'
Description: Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.
Author: Matthew Hall [aut, cre]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Diff between ggarchery versions 0.4.1 dated 2022-08-05 and 0.4.2 dated 2023-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/geom-arrowsegment.R | 12 ++++++------ R/position-attractsegment.R | 8 ++++---- README.md | 42 ++++++++++++++++++++++++++---------------- man/geom_arrowsegment.Rd | 8 ++++---- 6 files changed, 48 insertions(+), 38 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and time-spans: fast and
user friendly parsing of date-time data, extraction and updating of
components of a date-time (years, months, days, hours, minutes, and
seconds), algebraic manipulation on date-time and time-span objects.
The 'lubridate' package has a consistent and memorable syntax that
makes working with dates easy and fun.
Author: Vitalie Spinu [aut, cre],
Garrett Grolemund [aut],
Hadley Wickham [aut],
Davis Vaughan [ctb],
Ian Lyttle [ctb],
Imanuel Costigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.9.0 dated 2022-11-06 and 1.9.1 dated 2023-01-24
DESCRIPTION | 10 +++---- MD5 | 38 +++++++++++++-------------- NEWS.md | 15 ++++++++++ R/accessors-day.r | 50 ++++++++++++++++++++---------------- R/coercion.r | 4 +- R/guess.r | 16 ++++++----- R/instants.r | 3 +- R/parse.r | 9 ++++-- R/periods.r | 7 ++--- R/util.r | 13 +++++++++ inst/doc/lubridate.html | 23 +++++++--------- man/DateTimeUpdate.Rd | 19 +++++++++++-- man/day.Rd | 54 ++++++++++++++++++++++----------------- man/force_tz.Rd | 19 +++++++++++-- tests/testthat/test-Dates.R | 11 +++++++ tests/testthat/test-instants.R | 8 +++++ tests/testthat/test-parsers.R | 12 ++++++++ tests/testthat/test-periods.R | 5 +++ tests/testthat/test-round.R | 8 +++++ tests/testthat/test-time-zones.R | 10 +++++++ 20 files changed, 232 insertions(+), 102 deletions(-)
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.36 dated 2023-01-06 and 0.0.37 dated 2023-01-24
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 1 + R/globals.R | 2 +- R/winProbDL.R |only R/winProbLR.R | 23 ++++++++++++++++------- man/winProbabilityDL.Rd |only 7 files changed, 28 insertions(+), 16 deletions(-)
Title: Build Tables for Publication
Description: Functions for building customized ready-to-export tables for publication.
Author: Eric Finnesgard [aut, cre],
Jennifer Grauberger [aut]
Maintainer: Eric Finnesgard <efinite@outlook.com>
Diff between utile.tables versions 0.2.2 dated 2022-11-20 and 0.3.0 dated 2023-01-24
utile.tables-0.2.2/utile.tables/man/build_row.data.frame.Rd |only utile.tables-0.2.2/utile.tables/man/build_row.factor.Rd |only utile.tables-0.2.2/utile.tables/man/build_row.logical.Rd |only utile.tables-0.2.2/utile.tables/man/build_row.numeric.Rd |only utile.tables-0.3.0/utile.tables/DESCRIPTION | 15 utile.tables-0.3.0/utile.tables/MD5 | 28 utile.tables-0.3.0/utile.tables/NEWS.md | 131 +- utile.tables-0.3.0/utile.tables/R/build_model.R | 302 ++--- utile.tables-0.3.0/utile.tables/R/build_row.R | 595 ++++------ utile.tables-0.3.0/utile.tables/R/build_table.R | 166 +- utile.tables-0.3.0/utile.tables/R/utils.R | 92 - utile.tables-0.3.0/utile.tables/README.md | 22 utile.tables-0.3.0/utile.tables/man/build_model.coxph.Rd | 14 utile.tables-0.3.0/utile.tables/man/build_row.Rd | 128 ++ utile.tables-0.3.0/utile.tables/man/build_table.coxph.Rd | 17 utile.tables-0.3.0/utile.tables/man/build_table.data.frame.Rd | 57 utile.tables-0.3.0/utile.tables/man/build_table.lm.Rd | 17 17 files changed, 852 insertions(+), 732 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-25 0.7.0
2022-02-24 0.6.1
2022-02-23 0.6.0
2021-12-07 0.5.0
2021-09-16 0.4.0
2021-03-09 0.3.0
2020-09-29 0.2.0
2020-07-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-10 1.0.2
2021-10-27 1.0.1
2021-03-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-06 1.0.7
2019-03-15 1.0.6
2018-07-16 1.0.5
2018-06-12 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-25 1.1.1
2022-03-28 1.1.0
2021-11-29 1.0.1
2021-11-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-20 1.0.3
2016-11-30 1.0.2
2016-11-15 1.0.1
2016-11-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-09 1.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-02 1.3.0
2021-09-20 1.2.1
2021-09-18 1.2.0
2021-04-02 1.1.1
2021-04-01 1.1.0
2021-01-21 1.0.1
2021-01-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-05 1.0.4.3
2020-11-12 1.0.4.2
2020-02-02 1.0.4.1
2019-12-02 1.0.4
2018-06-29 1.0.3
2018-06-22 1.0.2
2018-05-15 1.0.1
2018-05-11 1.0.0
Title: Summarize Data for Publication
Description: Tools for formatting and summarizing data for outcomes research.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <efinite@outlook.com>
Diff between utile.tools versions 0.2.8 dated 2022-11-20 and 0.3.0 dated 2023-01-24
utile.tools-0.2.8/utile.tools/man/calc_cumsum.Rd |only utile.tools-0.3.0/utile.tools/DESCRIPTION | 14 utile.tools-0.3.0/utile.tools/MD5 | 37 + utile.tools-0.3.0/utile.tools/NAMESPACE | 6 utile.tools-0.3.0/utile.tools/NEWS.md | 204 ++++++--- utile.tools-0.3.0/utile.tools/R/calc.R | 227 +++++------ utile.tools-0.3.0/utile.tools/R/chunk.R | 70 +-- utile.tools-0.3.0/utile.tools/R/cusum.R |only utile.tools-0.3.0/utile.tools/R/paste.R | 389 +++++++++---------- utile.tools-0.3.0/utile.tools/R/test.R | 284 +++++++++---- utile.tools-0.3.0/utile.tools/R/utils.R | 16 utile.tools-0.3.0/utile.tools/README.md | 42 -- utile.tools-0.3.0/utile.tools/man/cusum_failure.Rd |only utile.tools-0.3.0/utile.tools/man/cusum_loglike.Rd |only utile.tools-0.3.0/utile.tools/man/cusum_ome.Rd |only utile.tools-0.3.0/utile.tools/man/cusum_sprt.Rd |only utile.tools-0.3.0/utile.tools/man/paste.Rd | 18 utile.tools-0.3.0/utile.tools/man/paste_efs.Rd | 4 utile.tools-0.3.0/utile.tools/man/paste_freq.Rd | 2 utile.tools-0.3.0/utile.tools/man/paste_mean.Rd | 3 utile.tools-0.3.0/utile.tools/man/paste_median.Rd | 2 utile.tools-0.3.0/utile.tools/man/paste_pval.Rd |only utile.tools-0.3.0/utile.tools/man/test_hypothesis.Rd | 101 +++- 23 files changed, 825 insertions(+), 594 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
Kasper Klitgaard Berthelsen [ctb],
Ya-Mei Chang [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.0-1 dated 2022-11-03 and 3.1-2 dated 2023-01-24
DESCRIPTION | 34 +-- MD5 | 61 +++-- NAMESPACE | 15 + NEWS | 80 +++++++ R/clusterfunctions.R | 2 R/clusterinfo.R | 127 ++++++++++-- R/clustersiminfo.R |only R/pakes.R |only R/random.R | 188 +++++++++++++----- R/randomNS.R | 414 ++++++++++------------------------------ R/rcauchy.R |only R/rclusterBKBC.R |only R/reach.R | 2 R/rmatclust.R |only R/rthomas.R |only R/rvargamma.R |only R/truncpois.R |only inst/CITATION | 6 inst/doc/packagesizes.txt | 2 man/dpakes.Rd |only man/macros/defns.Rd | 2 man/rCauchy.Rd | 202 ++++++++++++++----- man/rMatClust.Rd | 165 +++++++++++---- man/rNeymanScott.Rd | 19 + man/rPoissonCluster.Rd | 10 man/rThomas.Rd | 192 ++++++++++++++---- man/rVarGamma.Rd | 218 +++++++++++++++------ man/rclusterBKBC.Rd |only man/spatstat.random-internal.Rd | 22 ++ man/spatstat.random-package.Rd | 42 ++-- src/init.c | 10 src/proto.h | 9 src/rcauchy.c |only src/rcauchy.h |only src/rmatclus.c |only src/rmatclus.h |only src/rthomas.c |only src/rthomas.h |only src/rtruncpois.c |only tests/Random.R | 6 40 files changed, 1179 insertions(+), 649 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Tools for Social Network Analysis
Description: A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.
Author: Carter T. Butts [aut, cre, cph]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between sna versions 2.7 dated 2022-06-01 and 2.7-1 dated 2023-01-24
ChangeLog | 7 +++ DESCRIPTION | 10 ++--- MD5 | 12 +++--- R/visualization.R | 16 ++++---- man/gplot.layout.Rd | 100 +++++++++++++++++++++++++------------------------- man/gplot3d.arrow.Rd | 4 +- man/gplot3d.layout.Rd | 52 +++++++++++++------------- 7 files changed, 104 insertions(+), 97 deletions(-)
Title: Fitting Discrete Distribution Models to Count Data
Description: Provides functions for fitting discrete distribution models to count data.
Included are the Poisson, the negative binomial, the Poisson-inverse gaussian and, most importantly,
a new implementation of the Poisson-beta distribution (density, distribution and quantile
functions, and random number generator) together with a needed new implementation of
Kummer's function (also: confluent hypergeometric function of the first kind). Three
different implementations of the Gillespie algorithm allow data simulation based on the
basic, switching or bursting mRNA generating processes. Moreover, likelihood functions for
four variants of each of the three aforementioned distributions are also available.
The variants include one population and two population mixtures, both with and without
zero-inflation. The package depends on the 'MPFR' libraries (<https://www.mpfr.org/>) which need to be installed separately
(see description at <https://github.com/fuchslab/scModels>).
This package is s [...truncated...]
Author: Lisa Amrhein [aut, cre] ,
Kumar Harsha [aut] ,
Christiane Fuchs [aut] ,
Pavel Holoborodko [ctb]
Maintainer: Lisa Amrhein <amrheinlisa@gmail.com>
Diff between scModels versions 1.0.3 dated 2022-03-29 and 1.0.4 dated 2023-01-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/shared.cpp | 24 +++++++----------------- 4 files changed, 18 insertions(+), 24 deletions(-)
Title: Relational Event Models
Description: Tools to fit and simulate realizations from relational event models.
Author: Carter T. Butts <buttsc@uci.edu>
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between relevent versions 1.2 dated 2022-11-24 and 1.2-1 dated 2023-01-24
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/relevent.c | 10 +++++----- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb],
Pavel N. Krivitsky [ctb] ,
Brendan Knapp [ctb] ,
Michal Bojanowski [ctb] ,
Chad Klumb [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.18.0 dated 2022-10-06 and 1.18.1 dated 2023-01-24
ChangeLog | 4 + DESCRIPTION | 8 +-- MD5 | 18 +++--- NAMESPACE | 1 R/coercion.R | 57 ++++----------------- R/dataframe.R | 113 ++++++++++++++++++++++++------------------- inst/doc/networkVignette.pdf |binary man/as.data.frame.network.Rd | 28 ++++++++-- man/loading.attributes.Rd | 2 src/access.c | 6 +- 10 files changed, 119 insertions(+), 118 deletions(-)
Title: Maximum Likelihood Estimation for Generalized Linear Mixed
Models
Description: Maximum likelihood estimation for generalized linear mixed models via Monte Carlo EM.
For a description of the algorithm see Brian S. Caffo, Wolfgang Jank and Galin L. Jones (2005)
<DOI:10.1111/j.1467-9868.2005.00499.x>.
Author: Felipe Acosta Archila
Maintainer: Felipe Acosta Archila <acosta@umn.edu>
Diff between mcemGLM versions 1.1.1 dated 2020-03-03 and 1.1.2 dated 2023-01-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/mcemGLMMext.R | 2 +- build/vignette.rds |binary inst/doc/mcemGLM-vignette.pdf |binary man/mcemGLM-package.Rd | 4 ++-- man/salamander.Rd | 2 +- src/margloglikelihoodLogit_n.cpp | 2 +- src/margloglikelihoodLogit_t.cpp | 2 +- 9 files changed, 18 insertions(+), 18 deletions(-)
Title: Censored Spatial Models
Description: It fits linear regression models for censored spatial data. It provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. It also offers graphical tools for assessing the fitted model. More details can be found in Ordonez et al. (2018) <doi:10.1016/j.spasta.2017.12.001>.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between CensSpatial versions 3.5 dated 2023-01-17 and 3.6 dated 2023-01-24
DESCRIPTION | 6 +++--- MD5 | 9 ++++++--- R/Seminaiveprin.R | 2 +- R/algnaive12prin.R | 4 ++-- man/figures |only 5 files changed, 12 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-12 2.0.5
2020-03-12 2.0.3
2018-08-24 2.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-27 1.0-4
2017-09-14 1.0-2
2017-07-26 1.0-1
2017-07-11 1.0-0
2016-06-24 0.4-7
2015-08-17 0.4-5
2015-06-26 0.4-4
2015-05-04 0.4-1
2015-04-13 0.4
2015-02-02 0.3-3
2014-10-13 0.3-2
2014-09-30 0.3-1
2014-09-24 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-22 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-24 0.2.3
2020-05-04 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-22 1.2.8
2021-08-25 1.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-08 0.1-20
2021-01-04 0.1-19
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-17 2.2.3
2021-07-06 2.2.2
2021-06-15 2.2.1
2021-06-04 2.2
2021-02-12 2.1.2
2021-02-02 2.1.1
2020-10-03 2.1
2020-09-29 2.0
2020-07-01 1.1
2020-06-09 1.0
Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is currently under peer review but an earlier draft is available in Dahl, Johnson, and Andros (2022+) <doi:10.48550/arXiv.2207.13824>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
Devin J. Johnson [aut] ,
Alex Crichton [cph] ,
Andrii Dmytrenko [cph] ,
Brendan Zabarauskas [cph] ,
David B. Dahl [cph] ,
David Tolnay [cph] ,
DutchGhost [cph] ,
Enthought, Inc. [cph] ,
Gilad Naaman [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between fangs versions 0.2.8 dated 2022-12-19 and 0.2.11 dated 2023-01-24
fangs-0.2.11/fangs/DESCRIPTION | 59 +++++------ fangs-0.2.11/fangs/MD5 | 21 +--- fangs-0.2.11/fangs/NEWS | 3 fangs-0.2.11/fangs/R/fangs.R | 23 ++-- fangs-0.2.11/fangs/inst/cargo.log | 2 fangs-0.2.11/fangs/man/fangs.Rd | 19 +-- fangs-0.2.11/fangs/src/rust/Cargo.lock | 24 ++-- fangs-0.2.11/fangs/src/rust/Cargo.toml | 2 fangs-0.2.11/fangs/src/rust/src/lib.rs | 125 +----------------------- fangs-0.2.11/fangs/src/rust/src/registration.rs | 8 - fangs-0.2.11/fangs/src/rust/vendor.tar.xz |binary fangs-0.2.8/fangs/src/README.md |only 12 files changed, 90 insertions(+), 196 deletions(-)