Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies. Implements stopping rule methods described in Goldman (1987) <doi:10.1016/0197-2456(87)90153-X>; Geller et al. (2003, ISBN:9781135524388); Ivanova, Qaqish, and Schell (2005) <doi:10.1111/j.1541-0420.2005.00311.x>; Chen and Chaloner (2006) <doi:10.1002/sim.2429>; and Kulldorff et al. (2011) <doi:10.1080/07474946.2011.539924>.
Author: Michael J. Martens [aut, cre],
Qinghua Lian [aut],
Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>
Diff between stoppingrule versions 0.5.0 dated 2024-09-14 and 0.5.1 dated 2024-12-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/OC.rule.bin.R | 4 ++-- R/OC.rule.surv.R | 6 +++--- R/simtrials.surv.R | 2 +- man/OC.rule.bin.Rd | 2 +- man/OC.rule.surv.Rd | 4 ++-- 7 files changed, 19 insertions(+), 19 deletions(-)
Title: Amyloid Propensity Prediction Neural Network
Description: Amyloid propensity prediction neural network (APPNN) is an amyloidogenicity propensity predictor based on a machine learning approach through recursive feature selection and feed-forward neural networks, taking advantage of newly published sequences with experimental, in vitro, evidence of amyloid formation.
Author: Carlos Familia [aut, cre],
Sarah R. Dennison [aut],
Alexandre Quintas [aut],
David A. Phoenix [aut]
Maintainer: Carlos Familia <carlosfamilia@gmail.com>
Diff between appnn versions 1.0-0 dated 2015-07-12 and 1.0-1 dated 2024-12-05
DESCRIPTION | 27 +++++++++++++++++++++------ MD5 | 11 ++++++----- inst |only man/appnn-package.Rd | 7 ++++--- man/appnn.Rd | 2 -- man/plot.Rd | 2 -- man/print.Rd | 2 -- 7 files changed, 31 insertions(+), 20 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 2.1.2 dated 2024-02-28 and 3.0.0 dated 2024-12-05
scCustomize-2.1.2/scCustomize/R/Nebulosa_Plotting.R |only scCustomize-2.1.2/scCustomize/R/QC_Plotting_Seq_10X.R |only scCustomize-2.1.2/scCustomize/R/QC_Plotting_Seurat.R |only scCustomize-2.1.2/scCustomize/R/Seurat_Iterative_Plotting.R |only scCustomize-2.1.2/scCustomize/R/Seurat_Plotting.R |only scCustomize-2.1.2/scCustomize/R/Statistics_Plotting.R |only scCustomize-2.1.2/scCustomize/man/Add_Top_Gene_Pct_Seurat.Rd |only scCustomize-2.1.2/scCustomize/man/Gene_Present.Rd |only scCustomize-2.1.2/scCustomize/man/LIGER_Features.Rd |only scCustomize-3.0.0/scCustomize/DESCRIPTION | 10 scCustomize-3.0.0/scCustomize/MD5 | 255 - scCustomize-3.0.0/scCustomize/NAMESPACE | 45 scCustomize-3.0.0/scCustomize/NEWS.md | 112 scCustomize-3.0.0/scCustomize/R/Color_Palettes.R | 13 scCustomize-3.0.0/scCustomize/R/Data.R | 100 scCustomize-3.0.0/scCustomize/R/Deprecated.R | 35 scCustomize-3.0.0/scCustomize/R/Generics.R | 99 scCustomize-3.0.0/scCustomize/R/Internal_Utilities.R | 1596 ++++++- scCustomize-3.0.0/scCustomize/R/LIGER_Internal_Utilities.R |only scCustomize-3.0.0/scCustomize/R/LIGER_Plotting.R | 618 +-- scCustomize-3.0.0/scCustomize/R/LIGER_Utilities.R | 2004 ++++++---- scCustomize-3.0.0/scCustomize/R/Object_Conversion.R | 93 scCustomize-3.0.0/scCustomize/R/Object_Utilities.R | 947 ---- scCustomize-3.0.0/scCustomize/R/Plotting_Nebulosa.R |only scCustomize-3.0.0/scCustomize/R/Plotting_QC_Seq_10X.R |only scCustomize-3.0.0/scCustomize/R/Plotting_QC_Seurat.R |only scCustomize-3.0.0/scCustomize/R/Plotting_Seurat.R |only scCustomize-3.0.0/scCustomize/R/Plotting_Seurat_Iterative.R |only scCustomize-3.0.0/scCustomize/R/Plotting_Statistics.R |only scCustomize-3.0.0/scCustomize/R/Plotting_Utilities.R | 606 ++- scCustomize-3.0.0/scCustomize/R/QC_Utilities_Seurat.R |only scCustomize-3.0.0/scCustomize/R/Read_&_Write_Data.R | 157 scCustomize-3.0.0/scCustomize/R/Reexports.R | 42 scCustomize-3.0.0/scCustomize/R/Statistics.R | 108 scCustomize-3.0.0/scCustomize/R/Utilities.R | 572 +- scCustomize-3.0.0/scCustomize/R/sysdata.rda |binary scCustomize-3.0.0/scCustomize/build/partial.rdb |binary scCustomize-3.0.0/scCustomize/data/ensembl_hemo_id.rda |only scCustomize-3.0.0/scCustomize/data/ensembl_ieg_list.rda |only scCustomize-3.0.0/scCustomize/data/ensembl_mito_id.rda |binary scCustomize-3.0.0/scCustomize/data/ensembl_ribo_id.rda |binary scCustomize-3.0.0/scCustomize/data/msigdb_qc_ensembl_list.rda |only scCustomize-3.0.0/scCustomize/data/msigdb_qc_gene_list.rda |binary scCustomize-3.0.0/scCustomize/man/Add_Alt_Feature_ID.Rd | 13 scCustomize-3.0.0/scCustomize/man/Add_CellBender_Diff.Rd | 2 scCustomize-3.0.0/scCustomize/man/Add_Cell_Complexity.Rd | 2 scCustomize-3.0.0/scCustomize/man/Add_Cell_QC_Metrics.Rd | 93 scCustomize-3.0.0/scCustomize/man/Add_Hemo.Rd |only scCustomize-3.0.0/scCustomize/man/Add_Mito_Ribo.Rd | 18 scCustomize-3.0.0/scCustomize/man/Add_Top_Gene_Pct.Rd |only scCustomize-3.0.0/scCustomize/man/Barcode_Plot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Case_Check.Rd | 4 scCustomize-3.0.0/scCustomize/man/CellBender_Diff_Plot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Cell_Highlight_Plot.Rd | 5 scCustomize-3.0.0/scCustomize/man/Cells.Rd |only scCustomize-3.0.0/scCustomize/man/Cells_by_Identities_LIGER.Rd |only scCustomize-3.0.0/scCustomize/man/Cells_per_Sample.Rd |only scCustomize-3.0.0/scCustomize/man/Cluster_Highlight_Plot.Rd | 11 scCustomize-3.0.0/scCustomize/man/Cluster_Stats_All_Samples.Rd | 4 scCustomize-3.0.0/scCustomize/man/Clustered_DotPlot.Rd | 29 scCustomize-3.0.0/scCustomize/man/DimPlot_All_Samples.Rd | 2 scCustomize-3.0.0/scCustomize/man/DimPlot_LIGER.Rd | 7 scCustomize-3.0.0/scCustomize/man/DimPlot_scCustom.Rd | 17 scCustomize-3.0.0/scCustomize/man/DotPlot_scCustom.Rd | 4 scCustomize-3.0.0/scCustomize/man/Embeddings.Rd |only scCustomize-3.0.0/scCustomize/man/Factor_Cor_Plot.Rd |only scCustomize-3.0.0/scCustomize/man/FeaturePlot_DualAssay.Rd | 8 scCustomize-3.0.0/scCustomize/man/FeaturePlot_scCustom.Rd | 5 scCustomize-3.0.0/scCustomize/man/FeatureScatter_scCustom.Rd | 5 scCustomize-3.0.0/scCustomize/man/Features.Rd |only scCustomize-3.0.0/scCustomize/man/Fetch_Meta.Rd | 13 scCustomize-3.0.0/scCustomize/man/Find_Factor_Cor.Rd |only scCustomize-3.0.0/scCustomize/man/Idents.Rd |only scCustomize-3.0.0/scCustomize/man/Iterate_Barcode_Rank_Plot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_Cluster_Highlight_Plot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_DimPlot_bySample.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_FeaturePlot_scCustom.Rd | 7 scCustomize-3.0.0/scCustomize/man/Iterate_Meta_Highlight_Plot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_PC_Loading_Plots.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_Plot_Density_Custom.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_Plot_Density_Joint.Rd | 2 scCustomize-3.0.0/scCustomize/man/Iterate_VlnPlot_scCustom.Rd | 7 scCustomize-3.0.0/scCustomize/man/Merge_Sparse_Data_All.Rd | 4 scCustomize-3.0.0/scCustomize/man/Meta_Highlight_Plot.Rd | 5 scCustomize-3.0.0/scCustomize/man/Meta_Present.Rd | 3 scCustomize-3.0.0/scCustomize/man/Percent_Expressing.Rd | 3 scCustomize-3.0.0/scCustomize/man/Plot_Cells_per_Sample.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Density_Custom.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Density_Joint_Only.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Median_Genes.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Median_Mito.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Median_Other.Rd | 2 scCustomize-3.0.0/scCustomize/man/Plot_Median_UMIs.Rd | 2 scCustomize-3.0.0/scCustomize/man/Proportion_Plot.Rd |only scCustomize-3.0.0/scCustomize/man/QC_Histogram.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plot_GenevsFeature.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plot_UMIvsFeature.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plot_UMIvsGene.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plots_Combined_Vln.Rd | 7 scCustomize-3.0.0/scCustomize/man/QC_Plots_Complexity.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plots_Feature.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plots_Genes.Rd | 5 scCustomize-3.0.0/scCustomize/man/QC_Plots_Mito.Rd | 7 scCustomize-3.0.0/scCustomize/man/QC_Plots_UMIs.Rd | 5 scCustomize-3.0.0/scCustomize/man/Random_Cells_Downsample.Rd |only scCustomize-3.0.0/scCustomize/man/Read10X_h5_Multi_Directory.Rd | 4 scCustomize-3.0.0/scCustomize/man/Read_CellBender_h5_Multi_Directory.Rd | 3 scCustomize-3.0.0/scCustomize/man/Read_Metrics_10X.Rd | 5 scCustomize-3.0.0/scCustomize/man/Read_Metrics_CellBender.Rd |only scCustomize-3.0.0/scCustomize/man/Reduction_Loading_Present.Rd | 2 scCustomize-3.0.0/scCustomize/man/Rename_Clusters.Rd | 58 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Alignment_Combined.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Antisense.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Basic_Combined.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Exonic.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Genes.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Genome.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Intergenic.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Intronic.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Number_Cells.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Reads_in_Cells.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Reads_per_Cell.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Saturation.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Total_Genes.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_Transcriptome.Rd | 2 scCustomize-3.0.0/scCustomize/man/Seq_QC_Plot_UMIs.Rd | 2 scCustomize-3.0.0/scCustomize/man/SpatialDimPlot_scCustom.Rd |only scCustomize-3.0.0/scCustomize/man/Split_Vector.Rd | 8 scCustomize-3.0.0/scCustomize/man/Stacked_VlnPlot.Rd | 2 scCustomize-3.0.0/scCustomize/man/Store_Misc_Info_Seurat.Rd | 5 scCustomize-3.0.0/scCustomize/man/Store_Palette_Seurat.Rd | 5 scCustomize-3.0.0/scCustomize/man/Subset_LIGER.Rd |only scCustomize-3.0.0/scCustomize/man/Updated_MGI_Symbols.Rd |only scCustomize-3.0.0/scCustomize/man/VariableFeaturePlot_scCustom.Rd | 2 scCustomize-3.0.0/scCustomize/man/Variable_Features_ALL_LIGER.Rd | 5 scCustomize-3.0.0/scCustomize/man/VlnPlot_scCustom.Rd | 2 scCustomize-3.0.0/scCustomize/man/WhichCells.Rd |only scCustomize-3.0.0/scCustomize/man/as.anndata.Rd | 4 scCustomize-3.0.0/scCustomize/man/deprecated.Rd | 10 scCustomize-3.0.0/scCustomize/man/ensembl_hemo_id.Rd |only scCustomize-3.0.0/scCustomize/man/ensembl_ieg_list.Rd |only scCustomize-3.0.0/scCustomize/man/ensembl_mito_id.Rd | 7 scCustomize-3.0.0/scCustomize/man/ensembl_ribo_id.Rd | 9 scCustomize-3.0.0/scCustomize/man/ieg_gene_list.Rd | 2 scCustomize-3.0.0/scCustomize/man/msigdb_qc_ensembl_list.Rd |only scCustomize-3.0.0/scCustomize/man/msigdb_qc_gene_list.Rd | 8 scCustomize-3.0.0/scCustomize/man/plotFactors_scCustom.Rd | 9 scCustomize-3.0.0/scCustomize/man/reexports.Rd | 20 scCustomize-3.0.0/scCustomize/man/seq_zeros.Rd |only 149 files changed, 5317 insertions(+), 2652 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut],
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.5 dated 2023-09-12 and 0.1.6 dated 2024-12-05
DESCRIPTION | 15 MD5 | 72 - NAMESPACE | 31 NEWS.md | 7 R/as_draws.R |only R/create_model_frame.R | 78 - R/extract_param.R | 31 R/posterior_predict.R | 283 +++- R/rstanemax-package.R | 5 R/set_prior.R | 62 R/stan_emax.R | 170 +- R/stanemax-methods.R | 123 + R/stanmodels.R | 3 R/utils.R | 1 R/yyy.R | 34 build/vignette.rds |binary data/exposure.response.sample.binary.rda |only inst/doc/emaxmodel.R | 91 - inst/doc/emaxmodel.Rmd | 85 - inst/doc/emaxmodel.html | 402 +++--- inst/stan/emax_binary.stan |only man/as_draws.Rd |only man/exposure.response.sample.binary.Rd |only man/posterior_predict.Rd | 34 man/rstanemax-package.Rd | 23 man/stan_emax.Rd | 32 man/stan_emax_binary.Rd |only man/stanemax-methods.Rd | 8 src/RcppExports.cpp | 2 src/stanExports_emax.h | 1976 ++++++++++++++----------------- src/stanExports_emax_binary.cc |only src/stanExports_emax_binary.h |only tests/spelling.R | 9 tests/testthat.R | 1 tests/testthat/test-as_draws.R |only tests/testthat/test-create_model_frame.R | 16 tests/testthat/test-extract_param.R | 30 tests/testthat/test-posterior_predict.R | 66 - tests/testthat/test-set_prior.R | 78 - tests/testthat/test-stan_emax.R | 82 - tests/testthat/test-stan_emax_binary.R |only vignettes/emaxmodel.Rmd | 85 - 42 files changed, 2130 insertions(+), 1805 deletions(-)
Title: Robust Expectation-Maximization Estimation for Latent Variable
Models
Description: Traditional latent variable models assume that the population
is homogeneous, meaning that all individuals in the population are
assumed to have the same latent structure. However, this assumption is
often violated in practice given that individuals may differ in their
age, gender, socioeconomic status, and other factors that can affect
their latent structure. The robust expectation maximization (REM)
algorithm is a statistical method for estimating the parameters of a
latent variable model in the presence of population heterogeneity as recommended by
Nieser & Cochran (2023) <doi:10.1037/met0000413>. The REM algorithm is based on the
expectation-maximization (EM) algorithm, but it allows for the case
when all the data are generated by the assumed data generating model.
Author: Bryan Ortiz-Torres [aut, cre],
Kenneth Nieser [aut]
Maintainer: Bryan Ortiz-Torres <bortiztorres@wisc.edu>
Diff between REMLA versions 1.1 dated 2024-05-11 and 1.2.0 dated 2024-12-05
REMLA-1.1/REMLA/tests/testthat/test-tests.R |only REMLA-1.2.0/REMLA/DESCRIPTION | 10 - REMLA-1.2.0/REMLA/MD5 | 50 +++--- REMLA-1.2.0/REMLA/NAMESPACE | 1 REMLA-1.2.0/REMLA/R/EMAlg.R | 13 + REMLA-1.2.0/REMLA/R/REM_CFA.R | 29 +-- REMLA-1.2.0/REMLA/R/REM_EFA.R | 33 ++-- REMLA-1.2.0/REMLA/R/REM_estimates.R | 4 REMLA-1.2.0/REMLA/R/RobustEMAlg.R | 6 REMLA-1.2.0/REMLA/R/calcSE.R | 4 REMLA-1.2.0/REMLA/R/checkEpsFA.R | 4 REMLA-1.2.0/REMLA/R/constraints.R | 16 -- REMLA-1.2.0/REMLA/R/controlREM.R | 10 + REMLA-1.2.0/REMLA/R/epsilon_search.R | 4 REMLA-1.2.0/REMLA/R/summary.REMLA.R | 6 REMLA-1.2.0/REMLA/build/vignette.rds |binary REMLA-1.2.0/REMLA/inst/doc/REMLA_tutorial.R | 9 - REMLA-1.2.0/REMLA/inst/doc/REMLA_tutorial.Rmd | 77 ++++------ REMLA-1.2.0/REMLA/inst/doc/REMLA_tutorial.html | 161 ++++++++++----------- REMLA-1.2.0/REMLA/man/REM_CFA.Rd | 14 - REMLA-1.2.0/REMLA/man/REM_EFA.Rd | 11 - REMLA-1.2.0/REMLA/man/controlREM.Rd | 2 REMLA-1.2.0/REMLA/man/summary.REMLA.Rd | 6 REMLA-1.2.0/REMLA/tests/testthat/test-REM_CFA.R | 29 +++ REMLA-1.2.0/REMLA/tests/testthat/test-REM_EFA.R | 28 +++ REMLA-1.2.0/REMLA/tests/testthat/test-controlREM.R |only REMLA-1.2.0/REMLA/vignettes/REMLA_tutorial.Rmd | 77 ++++------ 27 files changed, 323 insertions(+), 281 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph] ,
David Barnett [ctb],
Michael Brusco [ctb, cph],
Michael Friendly [ctb],
Hans-Friedrich Koehn [ctb, cph],
Fionn Murtagh [ctb, cph],
Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.5.6 dated 2024-08-19 and 1.5.7 dated 2024-12-05
seriation-1.5.6/seriation/man/registry_for_seriaiton_methods.Rd |only seriation-1.5.7/seriation/DESCRIPTION | 23 +-- seriation-1.5.7/seriation/MD5 | 69 ++++----- seriation-1.5.7/seriation/NEWS.md | 12 + seriation-1.5.7/seriation/R/AAA_registry_seriate.R | 10 - seriation-1.5.7/seriation/R/hmap.R | 18 -- seriation-1.5.7/seriation/R/register_tsne.R | 2 seriation-1.5.7/seriation/R/ser_permutation_vector.R | 5 seriation-1.5.7/seriation/R/seriate.R | 14 + seriation-1.5.7/seriation/R/seriate.array.R | 5 seriation-1.5.7/seriation/R/seriate.dist.R | 17 +- seriation-1.5.7/seriation/R/seriate_ARSA_Branch-Bound.R | 44 ++++-- seriation-1.5.7/seriation/R/seriate_BEA.R | 25 ++- seriation-1.5.7/seriation/R/seriate_BK.R |only seriation-1.5.7/seriation/R/seriate_PCA.R | 26 +-- seriation-1.5.7/seriation/R/seriate_best.R | 3 seriation-1.5.7/seriation/README.md | 9 - seriation-1.5.7/seriation/build/partial.rdb |binary seriation-1.5.7/seriation/build/vignette.rds |binary seriation-1.5.7/seriation/inst/README_files/configuration-1.png |binary seriation-1.5.7/seriation/inst/README_files/seriation-1.png |binary seriation-1.5.7/seriation/inst/README_files/seriation-2.png |binary seriation-1.5.7/seriation/inst/doc/seriation.Rnw | 12 - seriation-1.5.7/seriation/inst/doc/seriation.pdf |binary seriation-1.5.7/seriation/man/hmap.Rd | 18 -- seriation-1.5.7/seriation/man/register_DendSer.Rd | 2 seriation-1.5.7/seriation/man/register_GA.Rd | 2 seriation-1.5.7/seriation/man/register_optics.Rd | 2 seriation-1.5.7/seriation/man/register_smacof.Rd | 2 seriation-1.5.7/seriation/man/register_tsne.Rd | 4 seriation-1.5.7/seriation/man/register_umap.Rd | 2 seriation-1.5.7/seriation/man/registry_for_seriation_methods.Rd |only seriation-1.5.7/seriation/man/seriate.Rd | 15 +- seriation-1.5.7/seriation/man/seriate_best.Rd | 4 seriation-1.5.7/seriation/src/stress.c | 4 seriation-1.5.7/seriation/tests/testthat/test-seriate.R | 73 ++++++++-- seriation-1.5.7/seriation/vignettes/seriation.Rnw | 12 - 37 files changed, 264 insertions(+), 170 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.4.0 dated 2024-11-22 and 0.4.1 dated 2024-12-05
DESCRIPTION | 6 MD5 | 20 R/classAchillesTable.R | 4 R/classSummarisedResult.R | 12 R/columns.R | 11 R/filter.R | 4 R/pivot.R | 21 R/split.R | 7 R/utilities.R | 3 inst/doc/summarised_result.html | 880 ++++++++++++++++++++-------------------- tests/testthat/test-utilities.R | 14 11 files changed, 506 insertions(+), 476 deletions(-)
Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2023)
<doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.5.0 dated 2024-10-05 and 4.5.1 dated 2024-12-05
mlpack-4.5.0/mlpack/inst/include/mlpack/methods/decision_tree/split_functions |only mlpack-4.5.1/mlpack/DESCRIPTION | 18 mlpack-4.5.1/mlpack/MD5 | 706 +++++----- mlpack-4.5.1/mlpack/inst/include/mlpack/core/cereal/is_loading.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cereal/is_saving.hpp | 16 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cv/cv_base.hpp | 18 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cv/cv_base_impl.hpp | 37 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cv/k_fold_cv.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cv/meta_info_extractor.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/core/cv/simple_cv.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/check_categorical_param.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/dataset_mapper.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/dataset_mapper_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/has_serialize.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/load_arff_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/load_numeric_csv.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/map_policies/increment_policy.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/map_policies/missing_policy.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/split_data.hpp | 130 + mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/string_encoding.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/string_encoding_impl.hpp | 22 mlpack-4.5.1/mlpack/inst/include/mlpack/core/data/string_encoding_policies/tf_idf_encoding_policy.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distances/iou_distance.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distances/lmetric.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distances/mahalanobis_distance.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/diagonal_gaussian_distribution.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/discrete_distribution.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/discrete_distribution_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/gamma_distribution.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/gaussian_distribution.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/laplace_distribution.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/distributions/regression_distribution.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/hpt/cv_function.hpp | 16 mlpack-4.5.1/mlpack/inst/include/mlpack/core/hpt/deduce_hp_types.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/hpt/fixed.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/hpt/hpt.hpp | 11 mlpack-4.5.1/mlpack/inst/include/mlpack/core/hpt/hpt_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/kernels/cosine_similarity.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/ccov_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/digamma.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/log_add_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/rand_vector.hpp | 3 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/range.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/math/trigamma.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/metrics/bleu_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/metrics/iou_metric_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/metrics/non_maximal_suppression_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/address.hpp | 28 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/ballbound.hpp | 7 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/binary_space_tree.hpp | 25 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/binary_space_tree_impl.hpp | 48 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/breadth_first_dual_tree_traverser.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/mean_split_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/midpoint_split.hpp | 1 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/rp_tree_max_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/rp_tree_mean_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/rp_tree_mean_split_impl.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/typedef.hpp | 33 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/ub_tree_split.hpp | 5 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/vantage_point_split.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/binary_space_tree/vantage_point_split_impl.hpp | 1 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/build_tree.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cellbound.hpp | 5 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cellbound_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cosine_tree/cosine_tree.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cover_tree/cover_tree.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cover_tree/cover_tree_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cover_tree/dual_tree_traverser_impl.hpp | 1 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/cover_tree/single_tree_traverser_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/hollow_ball_bound.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/hollow_ball_bound_impl.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/hrectbound.hpp | 3 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/hrectbound_impl.hpp | 15 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/octree/octree.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/perform_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/discrete_hilbert_value.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/discrete_hilbert_value_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/hilbert_r_tree_auxiliary_information.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/minimal_coverage_sweep.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/minimal_coverage_sweep_impl.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/minimal_splits_number_sweep.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/minimal_splits_number_sweep_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_plus_tree_auxiliary_information.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_plus_tree_auxiliary_information_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_descent_heuristic_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_split_impl.hpp | 9 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_star_tree_descent_heuristic_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_star_tree_split_impl.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_tree_descent_heuristic_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_tree_split_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/rectangle_tree.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/x_tree_auxiliary_information.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/rectangle_tree/x_tree_split_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/space_split/hyperplane.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/tree/spill_tree/spill_tree.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/arma_traits.hpp | 34 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/ens_traits.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/first_element_is_arma.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/gitversion.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/io.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/params.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/prefixedoutstream.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/prefixedoutstream_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/sfinae_utility.hpp | 36 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/size_checks.hpp | 9 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/timers.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/timers_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/using.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/core/util/version.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/adaboost/adaboost.hpp | 11 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/adaboost/adaboost_impl.hpp | 15 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/amf/amf.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/amf/update_rules/incremental_iterators.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/amf/update_rules/svd_incomplete_incremental_learning.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/activation_functions/bipolar_sigmoid_function.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/convolution_rules/fft_convolution.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/convolution_rules/naive_convolution.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/convolution_rules/svd_convolution.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/ffn.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/ffn_impl.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/init_rules/kathirvalavakumar_subavathi_init.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/init_rules/orthogonal_init.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/adaptive_max_pooling.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/adaptive_mean_pooling.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/add.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/add_merge.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/alpha_dropout.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/base_layer.hpp | 34 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/batch_norm.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/c_relu.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/celu.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/concat.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/concatenate.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/convolution.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/dropconnect.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/dropout.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/elu.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/flexible_relu.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/ftswish.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/grouped_convolution.hpp | 7 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/hard_tanh.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/identity.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/layer_norm.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/leaky_relu.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/linear.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/linear3d.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/linear3d_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/linear_no_bias.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/log_softmax.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/lstm.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/lstm_impl.hpp | 20 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/max_pooling.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/mean_pooling.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/multi_layer_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/multihead_attention.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/multihead_attention_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/nearest_interpolation.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/noisylinear.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/bicubic_interpolation.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/bilinear_interpolation.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/constant.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/fast_lstm.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/glimpse.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/hardshrink.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/highway.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/join.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/lookup.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/lookup_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/multiply_constant.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/multiply_merge.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/positional_encoding.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/reinforce_normal.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/reparametrization.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/select.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/sequential.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/softshrink.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/spatial_dropout.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/spatial_dropout_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/subview.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/transposed_convolution.hpp | 13 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/transposed_convolution_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/virtual_batch_norm.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/virtual_batch_norm_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/weight_norm.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/padding.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/parametric_relu.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/radial_basis_function.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/relu6.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/repeat.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/softmax.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/layer/softmin.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/binary_cross_entropy_loss.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/binary_cross_entropy_loss_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/cosine_embedding_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/cosine_embedding_loss_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/dice_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/earth_mover_distance.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/empty_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/hinge_embedding_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/hinge_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/huber_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/huber_loss_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/kl_divergence.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/l1_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/log_cosh_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/log_cosh_loss_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/margin_ranking_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_absolute_percentage_error.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_bias_error.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_squared_error.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_squared_logarithmic_error.hpp | 3 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/multilabel_softmargin_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/negative_log_likelihood.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/negative_log_likelihood_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/poisson_nll_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/poisson_nll_loss_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/reconstruction_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/sigmoid_cross_entropy_error.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/sigmoid_cross_entropy_error_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/soft_margin_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/triplet_margin_loss.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/vr_class_reward.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/loss_functions/vr_class_reward_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/brnn.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/brnn_impl.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/gan/gan.hpp | 29 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/gan/gan_impl.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/gan/wgan_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/gan/wgangp_impl.hpp | 9 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/rbm/rbm.hpp | 39 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/rbm/rbm_impl.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/not_adapted/rbm/spike_slab_rbm_impl.hpp | 22 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/ann/regularizer/lregularizer.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/approx_kfn/drusilla_select_impl.hpp | 5 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/bayesian_linear_regression/bayesian_linear_regression.hpp | 36 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/bayesian_linear_regression/bayesian_linear_regression_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/cf/cf.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/cf/cf_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/cf/cf_model.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/cf/svd_wrapper.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/dbscan/dbscan.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/decision_tree.hpp | 41 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/decision_tree_impl.hpp | 72 - mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/decision_tree_main.cpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/decision_tree_regressor.hpp | 31 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/decision_tree_regressor_impl.hpp | 94 - mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/fitness_functions/mse_gain.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/splits |only mlpack-4.5.1/mlpack/inst/include/mlpack/methods/decision_tree/utils.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/det/dt_utils.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/det/dtree.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/det/dtree_impl.hpp | 11 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/emst/dtb.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/emst/dtb_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/emst/dtb_rules.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/emst/dtb_rules_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/emst/edge_pair.hpp | 1 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/fastmks/fastmks.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/fastmks/fastmks_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/fastmks/fastmks_rules.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/fastmks/fastmks_rules_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/gmm/em_fit_impl.hpp | 20 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/gmm/gmm_train_main.cpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/gmm/positive_definite_constraint.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hmm/hmm_impl.hpp | 5 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/binary_numeric_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/binary_numeric_split_impl.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_categorical_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_categorical_split_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_numeric_split.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_numeric_split_impl.hpp | 9 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_tree.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_tree_main.cpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/hoeffding_tree_model.hpp | 16 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/hoeffding_trees/typedef.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kde/kde.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kde/kde_impl.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kde/kde_model.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kde/kde_rules.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/dual_tree_kmeans.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/dual_tree_kmeans_impl.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/dual_tree_kmeans_rules.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/max_variance_new_cluster_impl.hpp | 3 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/naive_kmeans_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/pelleg_moore_kmeans.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/kmeans/pelleg_moore_kmeans_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lars/lars.hpp | 86 - mlpack-4.5.1/mlpack/inst/include/mlpack/methods/linear_regression/linear_regression.hpp | 40 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/linear_regression/linear_regression_impl.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/linear_svm/linear_svm.hpp | 50 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/linear_svm/linear_svm_function.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lmnn/constraints.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lmnn/constraints_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lmnn/lmnn.hpp | 21 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lmnn/lmnn_function.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/local_coordinate_coding/lcc.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/local_coordinate_coding/lcc_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/logistic_regression/logistic_regression.hpp | 54 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/logistic_regression/logistic_regression_function_impl.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lsh/lsh_search.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/lsh/lsh_search_impl.hpp | 5 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/mean_shift/mean_shift.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/mean_shift/mean_shift_impl.hpp | 14 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/naive_bayes/naive_bayes_classifier.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/naive_bayes/naive_bayes_classifier_impl.hpp | 36 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/nca/nca.hpp | 23 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/nca/nca_softmax_error_function.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/kfn_main.cpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/knn_main.cpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/neighbor_search.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/neighbor_search_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/neighbor_search_rules.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/ns_model.hpp | 12 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/neighbor_search/typedef.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/pca/pca_impl.hpp | 22 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/perceptron/perceptron.hpp | 10 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/perceptron/perceptron_impl.hpp | 15 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/preprocess/preprocess_split_main.cpp | 43 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/radical/radical_impl.hpp | 13 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/random_forest/random_forest.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/random_forest/random_forest_impl.hpp | 3 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/range_search/range_search.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/range_search/range_search_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/range_search/range_search_rules.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/range_search/rs_model.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_model.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_search.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_search_impl.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_search_rules.hpp | 8 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_typedef.hpp | 4 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/rann/ra_util_impl.hpp | 2 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/softmax_regression/softmax_regression.hpp | 57 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/softmax_regression/softmax_regression_function.hpp | 6 mlpack-4.5.1/mlpack/inst/include/mlpack/methods/sparse_coding/sparse_coding.hpp | 4 mlpack-4.5.1/mlpack/man/mlpack.Rd | 4 mlpack-4.5.1/mlpack/src/Makevars | 1 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/get_printable_param.hpp | 24 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/get_r_type.hpp | 81 - mlpack-4.5.1/mlpack/src/mlpack/bindings/R/get_type.hpp | 89 - mlpack-4.5.1/mlpack/src/mlpack/bindings/R/print_doc.hpp | 2 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/print_input_param.hpp | 2 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/print_input_processing.hpp | 20 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/print_output_processing.hpp | 24 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/print_serialize_util.hpp | 12 mlpack-4.5.1/mlpack/src/mlpack/bindings/R/tests/test_r_binding_main.cpp | 2 mlpack-4.5.1/mlpack/tests/testthat/test-R_binding.R | 14 347 files changed, 1844 insertions(+), 1766 deletions(-)
More information about BayesianFitForecast at CRAN
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Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.1 dated 2024-11-01 and 0.1.2 dated 2024-12-05
DESCRIPTION | 11 - MD5 | 63 ++++--- NEWS.md | 5 R/RcppExports.R | 4 R/logisregr.R | 26 ++- R/print.logisregr.R | 10 - inst/doc/ipcw.R | 26 +++ inst/doc/ipcw.Rmd | 4 inst/doc/ipcw.html | 202 ++++++++++++------------ inst/doc/ipe.R | 12 + inst/doc/ipe.Rmd | 4 inst/doc/ipe.html | 22 +- inst/doc/rpsftm.R | 22 ++ inst/doc/rpsftm.Rmd | 4 inst/doc/rpsftm.html | 42 ++--- inst/doc/tsegest.R | 11 + inst/doc/tsegest.Rmd | 2 inst/doc/tsegest.html | 21 +- man/logisregr.Rd | 7 src/RcppExports.cpp | 9 - src/ipcw.cpp | 8 src/logistic_regression.cpp | 277 ++++++++++++++++++++++++--------- src/logistic_regression.h | 2 src/tsegest.cpp | 4 tests/testthat/test-kmest.R |only tests/testthat/test-liferegr.R |only tests/testthat/test-logisregr.R |only tests/testthat/test-lrtest.R |only tests/testthat/test-phregr.R |only tests/testthat/test-residuals_phregr.R |only tests/testthat/test-rmdiff.R |only tests/testthat/test-rmest.R |only tests/testthat/test-survfit_phregr.R |only vignettes/ipcw.Rmd | 4 vignettes/ipe.Rmd | 4 vignettes/rpsftm.Rmd | 4 vignettes/tsegest.Rmd | 2 37 files changed, 512 insertions(+), 300 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 2.4.2 dated 2024-04-30 and 2.4.3 dated 2024-12-05
DESCRIPTION | 10 ++--- MD5 | 16 ++++----- NEWS.md | 9 +++++ R/readTableNEON.R | 2 - R/stackDataFilesParallel.R | 78 ++++++++++++++++++++++++++++++++++++++------- R/sysdata.rda |binary R/zipsByProduct.R | 11 ++++++ README.md | 6 ++- data/table_types.rda |binary 9 files changed, 105 insertions(+), 27 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.12 dated 2024-11-18 and 2.2.13 dated 2024-12-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/RcppExports.R | 8 ++++---- man/bWGR.Rd | 4 ++-- src/RcppEigen20230423.cpp | 38 ++++++++++++++++++++++++++------------ src/RcppExports.cpp | 18 ++++++++++-------- 6 files changed, 51 insertions(+), 35 deletions(-)
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 1.2.3 dated 2024-05-05 and 1.2.4 dated 2024-12-05
DESCRIPTION | 20 MD5 | 43 - NEWS.md | 9 R/DynaMaze.R |only R/RussianTiger.R | 2 R/gridworld.R | 16 R/policy_graph.R | 2 R/simulate_POMDP.R | 2 R/solve_POMDP.R | 29 - README.md | 4 build/partial.rdb |binary build/vignette.rds |binary data/DynaMaze.rda |only inst/doc/gridworlds.html | 579 ++++++++++++---------- inst/doc/pomdp.html | 1191 +++++++++++++++++++++++++++-------------------- man/Cliff_walking.Rd | 2 man/DynaMaze.Rd |only man/MDP.Rd | 1 man/Maze.Rd | 2 man/RussianTiger.Rd | 2 man/Windy_gridworld.Rd | 2 man/gridworld.Rd | 15 man/simulate_POMDP.Rd | 2 man/solve_POMDP.Rd | 29 - 24 files changed, 1122 insertions(+), 830 deletions(-)
Title: Just a Rather Bayesian Evidence Synthesis
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between jarbes versions 2.2.2 dated 2024-10-07 and 2.2.3 dated 2024-12-05
ChangeLog | 21 DESCRIPTION | 8 MD5 | 62 - R/b3lmeta.R | 46 R/bcdpmeta.R | 20 R/bcmeta.R | 41 R/bcmixmeta.R | 18 R/bmeta.R | 3 R/data-documentation.R | 9 R/dpmeta.R | 17 R/dpmetareg.R | 17 R/dpmmeta.R | 15 R/hmr.R | 2469 ++++++++++++++++++++++++------------------------- R/jarbes-package.R | 4 R/metarisk.R | 43 R/summary.bmeta.R | 4 data/stemcells.rda |binary man/b3lmeta.Rd | 8 man/bcdpmeta.Rd | 5 man/bcmeta.Rd | 8 man/bcmixmeta.Rd | 5 man/dpmeta.Rd | 5 man/dpmetareg.Rd | 7 man/dpmmeta.Rd | 5 man/hmr.Rd | 10 man/metarisk.Rd | 8 man/plot.b3lmeta.Rd | 4 man/print.b3lmeta.Rd | 6 man/print.bcdpmeta.Rd | 2 man/print.bcmixmeta.Rd | 6 man/print.dpmeta.Rd | 2 man/stemcells.Rd | 9 32 files changed, 1361 insertions(+), 1526 deletions(-)
Title: Messages, Warnings, Strings with Ascii Animals
Description: Allows printing of character strings as messages/warnings/etc.
with ASCII animals, including cats, cows, frogs, chickens, ghosts,
and more.
Author: Scott Chamberlain [aut, cre],
Amanda Dobbyn [aut],
Tyler Rinker [ctb],
Thomas Leeper [ctb],
Noam Ross [ctb],
Rich FitzJohn [ctb],
Carson Sievert [ctb],
Kiyoko Gotanda [ctb],
Andy Teucher [ctb],
Karl Broman [ctb],
Franz-Sebastian Krah [ctb],
Lucy D'Ag [...truncated...]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between cowsay versions 0.9.0 dated 2023-11-02 and 1.0.0 dated 2024-12-05
cowsay-0.9.0/cowsay/R/animals.r |only cowsay-0.9.0/cowsay/R/cowsay-package.r |only cowsay-0.9.0/cowsay/R/rms.r |only cowsay-0.9.0/cowsay/R/say.r |only cowsay-0.9.0/cowsay/R/utils.R |only cowsay-0.9.0/cowsay/man/img |only cowsay-1.0.0/cowsay/DESCRIPTION | 24 cowsay-1.0.0/cowsay/MD5 | 56 - cowsay-1.0.0/cowsay/NAMESPACE | 15 cowsay-1.0.0/cowsay/NEWS.md | 25 cowsay-1.0.0/cowsay/R/animals.R |only cowsay-1.0.0/cowsay/R/bubble.R |only cowsay-1.0.0/cowsay/R/constants.R |only cowsay-1.0.0/cowsay/R/cowsay-package.R |only cowsay-1.0.0/cowsay/R/endless_horse.R | 63 - cowsay-1.0.0/cowsay/R/get_who.R | 57 - cowsay-1.0.0/cowsay/R/init.R |only cowsay-1.0.0/cowsay/R/rms.R |only cowsay-1.0.0/cowsay/R/say.R |only cowsay-1.0.0/cowsay/R/zzz.R | 50 cowsay-1.0.0/cowsay/README.md | 1332 +++++++++++++------------- cowsay-1.0.0/cowsay/build/vignette.rds |binary cowsay-1.0.0/cowsay/inst/doc/cowsay.R | 8 cowsay-1.0.0/cowsay/inst/doc/cowsay.Rmd | 9 cowsay-1.0.0/cowsay/inst/doc/cowsay.html | 163 +-- cowsay-1.0.0/cowsay/man/animals.Rd | 14 cowsay-1.0.0/cowsay/man/bubble_say.Rd |only cowsay-1.0.0/cowsay/man/bubble_tail.Rd |only cowsay-1.0.0/cowsay/man/cowsay-package.Rd | 4 cowsay-1.0.0/cowsay/man/figures |only cowsay-1.0.0/cowsay/man/say.Rd | 114 +- cowsay-1.0.0/cowsay/man/say_think.Rd |only cowsay-1.0.0/cowsay/tests/testthat/test-say.R | 94 - cowsay-1.0.0/cowsay/vignettes/cowsay.Rmd | 9 34 files changed, 1110 insertions(+), 927 deletions(-)
Title: R-Squared with Multiply Imputed Data
Description: Provides R-squared values and standardized regression coefficients for linear models applied to multiply imputed datasets as obtained by 'mice'. Confidence intervals, zero-order correlations, and alternative adjusted R-squared estimates are also available. The methods are described in Van Ginkel and Karch (2024) <doi:10.1111/bmsp.12344> and in Van Ginkel (2020) <doi:10.1007/s11336-020-09696-4>.
Author: Julian D. Karch [aut, cph, cre]
,
Joost van Ginkel [aut, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between RSquaredMI versions 0.1.1 dated 2024-09-19 and 0.2.0 dated 2024-12-05
DESCRIPTION | 17 +++++++++-------- MD5 | 5 +++-- NEWS.md |only R/RsquareMI.R | 31 +++++++++++++++++-------------- 4 files changed, 29 insertions(+), 24 deletions(-)
Title: Hierarchical Partitioning of R2 for Phylogenetic Linear
Regression
Description: Conducts hierarchical partitioning to calculate individual contributions of phylogenetic tree and predictors (groups) towards total R2 for phylogenetic linear regression models.
Author: Jiangshan Lai [aut, cre] ,
Gang Wang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between phylolm.hp versions 0.0-2 dated 2024-11-23 and 0.0-3 dated 2024-12-05
DESCRIPTION | 8 ++++---- MD5 | 4 +++- R/phylolmhp.r |only man/phylolm.hp.Rd |only 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Graphical User Interface with Integrated 'Diagrammer' for
'Lavaan'
Description: Provides a graphical user interface with an
integrated diagrammer for latent variables from the 'lavaan' package.
It offers two core functions: first, lavaangui() launches a web application
that allows users to specify models by drawing path diagrams, fitting them,
assessing model fit, and more; second, plot_lavaan() creates
interactive path diagrams from models specified in 'lavaan'.
Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between lavaangui versions 0.2.0 dated 2024-10-16 and 0.2.1 dated 2024-12-05
lavaangui-0.2.0/lavaangui/inst/www/assets/index-45d83e26.js |only lavaangui-0.2.1/lavaangui/DESCRIPTION | 8 - lavaangui-0.2.1/lavaangui/MD5 | 12 +- lavaangui-0.2.1/lavaangui/NEWS.md | 11 ++ lavaangui-0.2.1/lavaangui/R/serverLavaanRun.R | 63 ++++-------- lavaangui-0.2.1/lavaangui/R/start_app.R | 2 lavaangui-0.2.1/lavaangui/inst/www/assets/index-43dbfde1.js |only lavaangui-0.2.1/lavaangui/inst/www/index.html | 2 8 files changed, 49 insertions(+), 49 deletions(-)
Title: Tools for Data Analysis in Experimental Agriculture
Description: Methods to analyse experimental agriculture data,
from data synthesis to model selection and visualisation.
The package is named after W.S. Gosset aka ‘Student’, a pioneer
of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
David Brown [aut] ,
Jonathan Steinke [aut] ,
Joost van Heerwaarden [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between gosset versions 1.3 dated 2024-05-27 and 1.4 dated 2024-12-05
gosset-1.3/gosset/inst/paper/paper.docx |only gosset-1.3/gosset/vignettes/example_01.R |only gosset-1.4/gosset/DESCRIPTION | 10 gosset-1.4/gosset/MD5 | 44 gosset-1.4/gosset/NAMESPACE | 5 gosset-1.4/gosset/NEWS.md | 15 gosset-1.4/gosset/R/cassava.R |only gosset-1.4/gosset/R/kendallTau.R | 46 gosset-1.4/gosset/R/kendall_permute.R |only gosset-1.4/gosset/R/nodeinfo.R | 518 +++++----- gosset-1.4/gosset/R/regret.R | 83 - gosset-1.4/gosset/R/resample.R | 86 + gosset-1.4/gosset/R/worth_map.R | 76 + gosset-1.4/gosset/build/vignette.rds |binary gosset-1.4/gosset/data/cassava.rda |only gosset-1.4/gosset/inst/doc/vignette-1-trait-prioritization-and-crop-performance.Rmd | 105 +- gosset-1.4/gosset/inst/doc/vignette-1-trait-prioritization-and-crop-performance.html | 467 ++++----- gosset-1.4/gosset/inst/doc/vignette-2-gari-eba-consumer-testing.Rmd |only gosset-1.4/gosset/inst/doc/vignette-2-gari-eba-consumer-testing.html |only gosset-1.4/gosset/man/cassava.Rd |only gosset-1.4/gosset/man/figures |only gosset-1.4/gosset/man/gosset.Rd | 2 gosset-1.4/gosset/man/kendallTau.Rd | 57 + gosset-1.4/gosset/man/node_labels.Rd | 59 - gosset-1.4/gosset/man/worth_map.Rd | 6 gosset-1.4/gosset/vignettes/vignette-1-trait-prioritization-and-crop-performance.Rmd | 105 +- gosset-1.4/gosset/vignettes/vignette-2-gari-eba-consumer-testing.Rmd |only gosset-1.4/gosset/vignettes/vignette.bib | 104 +- 28 files changed, 1095 insertions(+), 693 deletions(-)
Title: Working with netCDF for Essential Biodiversity Variables
Description: The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>)
comes with a data structure based on the Network Common Data Form (netCDF).
The 'ebvcube' 'R' package provides functionality to easily create, access and
visualise this data. The EBV netCDFs can be downloaded from the EBV Data
Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
Author: Luise Quoss [aut, cre] ,
Nestor Fernandez [aut] ,
Christian Langer [aut] ,
Jose Valdez [aut] ,
Henrique Miguel Pereira [aut]
Maintainer: Luise Quoss <luise.quoss@idiv.de>
Diff between ebvcube versions 0.2.3 dated 2024-07-10 and 0.3.1 dated 2024-12-05
DESCRIPTION | 16 +-- MD5 | 63 +++++++------- NAMESPACE | 49 +++++------ NEWS.md | 133 ++++++++++++++++++++---------- R/ebv_add_data.R | 19 +++- R/ebv_analyse.R | 2 R/ebv_attribute.R | 3 R/ebv_create.R | 18 ++-- R/ebv_create_taxonomy.R | 57 +++++++++--- R/ebv_download.R | 2 R/ebv_map.R | 26 ++++- R/ebv_metadata.R |only R/ebv_properties.R | 35 ++++--- R/ebv_read.R | 5 - R/ebv_utils.R | 94 ++++++++++++++++++++- R/ebv_write.R | 38 ++++---- R/ebvcube-package.R | 3 README.md | 99 +++++++++++++--------- inst/CITATION | 34 +++---- inst/docs/ebvcube_0.3.1.pdf |only inst/extdata/test.nc |binary man/EBV-netCDF-properties-class.Rd | 17 ++- man/ebv_add_data.Rd | 5 + man/ebv_create.Rd | 6 - man/ebv_create_taxonomy.Rd | 18 ++-- man/ebv_metadata.Rd |only man/ebv_properties.Rd | 6 - man/ebvcube.Rd | 21 ++++ tests/testthat/test-download.R | 17 +++ tests/testthat/test-ebv_create_taxonomy.R | 14 +++ tests/testthat/test-ebv_metadata.R |only tests/testthat/test-ebv_properties.R | 6 + tests/testthat/test-ebv_utils.R | 24 +++++ tests/testthat/test-lintr.R |only tests/testthat/test-write.R | 16 +-- 35 files changed, 580 insertions(+), 266 deletions(-)
Title: Semi-Automatic Preprocessing of Messy Data with Change Tracking
for Dataset Cleaning
Description: Tools for assessing data quality, performing exploratory analysis, and
semi-automatic preprocessing of messy data with change tracking for integral dataset cleaning.
Author: David Hervas Marin [aut, cre]
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.9.43 dated 2024-09-17 and 0.9.45 dated 2024-12-05
DESCRIPTION | 8 +-- MD5 | 11 ++--- NAMESPACE | 2 NEWS | 117 +----------------------------------------------------- R/check_quality.R | 38 +++++++++++++++++ R/descriptive.R | 8 ++- man/xscores.Rd |only 7 files changed, 58 insertions(+), 126 deletions(-)
Title: Analysis of Elliptical Tubes Under the Relative Curvature
Condition
Description: Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition (RCC), computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube. The intrinsic approach relies on the interior path of the original non-convex space, incorporating the RCC, while the non-intrinsic approach uses a basic robotic arm transformation that disregards the RCC.
Author: Mohsen Taheri Shalmani [aut, cre]
,
Joern Schulz [aut],
Stephen M. Pizer [aut]
Maintainer: Mohsen Taheri Shalmani <MohsenTaheriShalmani@gmail.com>
Diff between ETRep versions 0.1.0 dated 2024-11-04 and 1.1.0 dated 2024-12-05
DESCRIPTION | 28 ++++- MD5 | 25 ++--- NEWS |only R/ETRep_Functions.R | 98 +++++++++++++++++--- build |only man/check_Tube_Legality.Rd | 7 + man/create_Elliptical_Tube.Rd | 7 + man/elliptical_Tube_Euclideanization.Rd |only man/intrinsic_Distance_Between2tubes.Rd | 7 + man/intrinsic_Transformation_Elliptical_Tubes.Rd | 9 + man/intrinsic_mean_tube.Rd | 9 + man/nonIntrinsic_Distance_Between2tubes.Rd | 7 + man/nonIntrinsic_Transformation_Elliptical_Tubes.Rd | 11 +- man/nonIntrinsic_mean_tube.Rd | 4 man/simulate_etube.Rd | 7 + 15 files changed, 185 insertions(+), 34 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-04 0.1.3
Title: Spatial Simulation and Scale-Dependent Analysis of Biodiversity
Changes
Description: Simulation, analysis and sampling of spatial
biodiversity data (May, Gerstner, McGlinn, Xiao & Chase 2017)
<doi:10.1111/2041-210x.12986>.
In the simulation tools user define the numbers of
species and individuals, the species abundance distribution and species
aggregation. Functions for analysis include species rarefaction
and accumulation curves, species-area relationships and the distance
decay of similarity.
Author: Felix May [aut, cre, cph] ,
Alban Sagouis [aut]
Maintainer: Felix May <felix.may@fu-berlin.de>
Diff between mobsim versions 0.3.1 dated 2024-03-22 and 0.3.2 dated 2024-12-05
DESCRIPTION | 12 ++-- MD5 | 36 ++++++------- NEWS.md | 6 ++ R/Diversity_Area_Relationships.R | 2 R/SAC_spatial.R | 4 - R/Sample_quadrats.R | 2 R/Sim_Community.R | 12 ++-- build/vignette.rds |binary inst/doc/Biodiversity_Changes.html | 18 +++--- inst/doc/Biodiversity_Patterns.html | 92 +++++++++++++++++------------------ inst/doc/Introduction_mobsim.html | 92 +++++++++++++++++------------------ inst/doc/Sampling_communities.html | 70 +++++++++++++------------- inst/doc/Simulating_communities.html | 62 +++++++++++------------ man/plot.dist_decay.Rd | 2 man/plot.sad.Rd | 2 man/rare_curve.Rd | 2 man/sample_quadrats.Rd | 2 man/sim_sad.Rd | 10 +-- man/spec_sample.Rd | 2 19 files changed, 217 insertions(+), 211 deletions(-)
Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov Random Field model for a network of binary and/or ordinal variables. Details of the implemented methods can be found in: Marsman, van den Bergh, and Haslbeck (in press) <doi:10.31234/osf.io/ukwrf>.
Author: Maarten Marsman [aut, cre] ,
Karoline Huth [ctb] ,
Nikola Sekulovski [ctb] ,
Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.4.1 dated 2024-11-12 and 0.1.4.2 dated 2024-12-05
DESCRIPTION | 8 +-- MD5 | 24 ++++----- NEWS.md | 8 ++- R/bgm.R | 15 +++-- R/bgmCompare.R | 8 ++- R/utility_functions.R | 17 +----- build/partial.rdb |binary build/vignette.rds |binary man/bgm.Rd | 15 +++-- man/bgmCompare.Rd | 10 +++ src/gibbs_functions.cpp | 70 +++++++++++++++++++-------- src/gibbs_functions_compare.cpp | 93 +++++++++++++++---------------------- src/gibbs_functions_edge_prior.cpp | 2 13 files changed, 150 insertions(+), 120 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@studenti.unipd.it>
Diff between XDNUTS versions 1.5.3 dated 2024-11-29 and 1.5.4 dated 2024-12-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/interface.R | 2 +- build/partial.rdb |binary src/epsilon_adapt.cpp | 8 ++++---- src/epsilon_init.cpp | 6 +++--- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.2.3 dated 2024-07-29 and 1.3.0 dated 2024-12-05
text-1.2.3/text/R/2_4_textPredict.R |only text-1.2.3/text/R/2_5_textTrainN.R |only text-1.2.3/text/R/4_4_textPlotWordPrediction.R |only text-1.2.3/text/R/5_1_textClassify.R |only text-1.2.3/text/inst/doc/pre_trained_models.R |only text-1.2.3/text/inst/doc/pre_trained_models.Rmd |only text-1.2.3/text/inst/doc/pre_trained_models.html |only text-1.2.3/text/inst/extdata/test_save.csv |only text-1.2.3/text/inst/extdata/text_models_info.csv |only text-1.2.3/text/man/find_textrpp.Rd |only text-1.2.3/text/man/textClassify.Rd |only text-1.2.3/text/man/textWordPrediction.Rd |only text-1.2.3/text/vignettes/pre_trained_models.Rmd |only text-1.3.0/text/DESCRIPTION | 18 text-1.3.0/text/MD5 | 217 +- text-1.3.0/text/NAMESPACE | 23 text-1.3.0/text/NEWS.md | 41 text-1.3.0/text/R/0_0_1_text_initialize.R | 134 - text-1.3.0/text/R/0_0_text_install.R | 18 text-1.3.0/text/R/0_1_globals.R | 12 text-1.3.0/text/R/0_2_privateFunctions.R | 846 +------- text-1.3.0/text/R/0_3_textModels.R | 15 text-1.3.0/text/R/1_0_textDescriptives.R | 71 text-1.3.0/text/R/1_1_textEmbed.R | 168 + text-1.3.0/text/R/1_2_textEmbedStatic.R | 4 text-1.3.0/text/R/2_1_1_textTrainN.R |only text-1.3.0/text/R/2_1_textTrain.R | 7 text-1.3.0/text/R/2_2_textTrainRegression.R | 108 + text-1.3.0/text/R/2_3_textTrainRandomForest.R | 5 text-1.3.0/text/R/2_4_0_textPredict_Assess_Classify.R |only text-1.3.0/text/R/2_4_1_textPredictTextTrained.R |only text-1.3.0/text/R/2_4_2_textPredictImplicitMotives.R |only text-1.3.0/text/R/2_5_textDomainCompare.R |only text-1.3.0/text/R/3_1_textSimilarity.R | 31 text-1.3.0/text/R/4_0_textPlot.R | 4 text-1.3.0/text/R/4_1_textPlotCentrality.R | 38 text-1.3.0/text/R/4_2_textPlotPCA.R | 8 text-1.3.0/text/R/4_3_textPlotProjection.R | 10 text-1.3.0/text/R/5_1_textClassifyPipe.R |only text-1.3.0/text/R/5_2_textGeneration.R | 29 text-1.3.0/text/R/5_3_textNER.R | 8 text-1.3.0/text/R/5_4_textSum.R | 8 text-1.3.0/text/R/5_5_textQA.R | 12 text-1.3.0/text/R/5_6_textTranslate.R | 8 text-1.3.0/text/R/5_7_textZeroShot.R | 6 text-1.3.0/text/R/6_1_textFineTune.R | 8 text-1.3.0/text/R/6_2_textFineTuneDomain.R | 8 text-1.3.0/text/R/7_1_textTopics.R | 10 text-1.3.0/text/R/7_2_textTopicsAnalysis.R | 809 +------- text-1.3.0/text/R/zzz.R | 5 text-1.3.0/text/README.md | 2 text-1.3.0/text/build/vignette.rds |binary text-1.3.0/text/inst/doc/LBAM.R |only text-1.3.0/text/inst/doc/LBAM.Rmd |only text-1.3.0/text/inst/doc/LBAM.html |only text-1.3.0/text/inst/doc/huggingface_in_r_extended_installation_guide.Rmd | 486 ++-- text-1.3.0/text/inst/doc/huggingface_in_r_extended_installation_guide.html | 112 - text-1.3.0/text/inst/doc/implicit_motives_tutorial.R |only text-1.3.0/text/inst/doc/implicit_motives_tutorial.Rmd |only text-1.3.0/text/inst/doc/implicit_motives_tutorial.html |only text-1.3.0/text/inst/doc/lbam_tutorial.R |only text-1.3.0/text/inst/doc/lbam_tutorial.Rmd |only text-1.3.0/text/inst/doc/lbam_tutorial.html |only text-1.3.0/text/inst/doc/text.Rmd | 2 text-1.3.0/text/inst/doc/text.html | 2 text-1.3.0/text/inst/extdata/The_L-BAM_Library.csv |only text-1.3.0/text/inst/python/huggingface_Interface3.py | 132 - text-1.3.0/text/inst/python/text_cleaner.py |only text-1.3.0/text/man/find_textrpp_env.Rd | 2 text-1.3.0/text/man/textCentrality.Rd | 5 text-1.3.0/text/man/textCentralityPlot.Rd | 4 text-1.3.0/text/man/textClean.Rd |only text-1.3.0/text/man/textCleanNonASCII.Rd |only text-1.3.0/text/man/textDimName.Rd | 4 text-1.3.0/text/man/textDistance.Rd | 8 text-1.3.0/text/man/textDistanceMatrix.Rd | 6 text-1.3.0/text/man/textDistanceNorm.Rd | 7 text-1.3.0/text/man/textDomainCompare.Rd |only text-1.3.0/text/man/textEmbed.Rd | 7 text-1.3.0/text/man/textEmbedLayerAggregation.Rd | 4 text-1.3.0/text/man/textEmbedRawLayers.Rd | 8 text-1.3.0/text/man/textEmbedStatic.Rd | 5 text-1.3.0/text/man/textFindNonASCII.Rd |only text-1.3.0/text/man/textGeneration.Rd | 8 text-1.3.0/text/man/textLBAM.Rd |only text-1.3.0/text/man/textModelLayers.Rd | 9 text-1.3.0/text/man/textModelsRemove.Rd | 4 text-1.3.0/text/man/textNER.Rd | 4 text-1.3.0/text/man/textPCA.Rd | 4 text-1.3.0/text/man/textPCAPlot.Rd | 4 text-1.3.0/text/man/textPlot.Rd | 4 text-1.3.0/text/man/textPredict.Rd | 171 + text-1.3.0/text/man/textPredictAll.Rd | 2 text-1.3.0/text/man/textPredictTest.Rd | 2 text-1.3.0/text/man/textProjection.Rd | 4 text-1.3.0/text/man/textProjectionPlot.Rd | 4 text-1.3.0/text/man/textQA.Rd | 4 text-1.3.0/text/man/textSimilarity.Rd | 8 text-1.3.0/text/man/textSimilarityMatrix.Rd | 6 text-1.3.0/text/man/textSimilarityNorm.Rd | 7 text-1.3.0/text/man/textSum.Rd | 4 text-1.3.0/text/man/textTokenize.Rd | 16 text-1.3.0/text/man/textTokenizeAndCount.Rd |only text-1.3.0/text/man/textTopics.Rd | 7 text-1.3.0/text/man/textTopicsReduce.Rd | 2 text-1.3.0/text/man/textTopicsTest.Rd | 34 text-1.3.0/text/man/textTopicsWordcloud.Rd | 39 text-1.3.0/text/man/textTrain.Rd | 4 text-1.3.0/text/man/textTrainLists.Rd | 4 text-1.3.0/text/man/textTrainN.Rd | 7 text-1.3.0/text/man/textTrainNPlot.Rd | 12 text-1.3.0/text/man/textTrainRandomForest.Rd | 4 text-1.3.0/text/man/textTrainRegression.Rd | 17 text-1.3.0/text/man/textTranslate.Rd | 4 text-1.3.0/text/man/textZeroShot.Rd | 4 text-1.3.0/text/man/textrpp_install.Rd | 2 text-1.3.0/text/tests/testthat/test_1_0_Describe_Clean.R |only text-1.3.0/text/tests/testthat/test_1_1_Analyses_flow.R | 57 text-1.3.0/text/tests/testthat/test_1_2_textEmbed.R | 2 text-1.3.0/text/tests/testthat/test_2_1_textTrainRegression.R | 980 +++++----- text-1.3.0/text/tests/testthat/test_2_5_textPredict.R | 188 - text-1.3.0/text/tests/testthat/test_2_6_textPredict_implicitmotives.R |only text-1.3.0/text/tests/testthat/test_2_8_textDomainCompare.R |only text-1.3.0/text/tests/testthat/test_5_Tasks.R | 37 text-1.3.0/text/tests/testthat/test_7_textTopics.R | 63 text-1.3.0/text/tests/testthat/test_Assess_tutorial.R |only text-1.3.0/text/vignettes/LBAM.Rmd |only text-1.3.0/text/vignettes/huggingface_in_r_extended_installation_guide.Rmd | 486 ++-- text-1.3.0/text/vignettes/implicit_motives_tutorial.Rmd |only text-1.3.0/text/vignettes/lbam_tutorial.Rmd |only text-1.3.0/text/vignettes/text.Rmd | 2 131 files changed, 2602 insertions(+), 3103 deletions(-)
Title: Stepwise Regression Analysis
Description: The stepwise regression analysis is a statistical technique used to identify a subset of predictor variables essential for constructing predictive models. This package performs stepwise regression analysis across various regression models such as linear, logistic, Cox proportional hazards, Poisson, Gamma, and negative binomial regression. It incorporates diverse stepwise regression algorithms like forward selection, backward elimination, and bidirectional elimination alongside the best subset method. Additionally, it offers a wide range of selection criteria, including Akaike Information Criterion (AIC), Sawa Bayesian Information Criterion (BIC), and Significance Levels (SL). We validated the output accuracy of StepReg using public datasets within the SAS software environment. To facilitate efficient model comparison and selection, StepReg allows for multiple strategies and selection metrics to be executed in a single function call. Moreover, StepReg integrates a Shiny application for [...truncated...]
Author: Junhui Li [cre] ,
Junhui Li [aut],
Kai Hu [aut],
Xiaohuan Lu [aut],
Kun Cheng [ctb],
Sushmita N Nayak [ctb],
Cesar Bautista Sotelo [ctb],
Michael A Lodato [ctb],
Robert H Brown [ctb],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.5.5 dated 2024-11-04 and 1.5.6 dated 2024-12-05
DESCRIPTION | 14 MD5 | 42 NAMESPACE | 5 R/plot.StepReg.R | 152 +- R/print.StepReg.R | 50 R/report.R | 38 R/stepwise.R | 42 R/stepwiseUtils.R | 162 -- R/vote.R | 2 inst/doc/StepReg.R | 130 + inst/doc/StepReg.Rmd | 135 +- inst/doc/StepReg.html | 994 ++++----------- inst/shiny/report.Rmd | 10 inst/shiny/rsconnect/shinyapps.io/junhuili1017/shiny.dcf | 2 inst/shiny/server.R | 32 inst/shiny/ui.R | 3 inst/shiny/utils.R | 1 man/plot.StepReg.Rd | 15 man/print.StepReg.Rd | 2 man/report.Rd | 2 man/stepwise.Rd | 14 vignettes/StepReg.Rmd | 135 +- 22 files changed, 884 insertions(+), 1098 deletions(-)
Title: Fast Spatial and Spatio-Temporal Regression using Moran
Eigenvectors
Description: A collection of functions for estimating spatial and spatio-temporal regression models. Moran eigenvectors are used as spatial basis functions to efficiently approximate spatially dependent Gaussian processes (i.e., random effects eigenvector spatial filtering; see Murakami and Griffith 2015 <doi: 10.1007/s10109-015-0213-7>). The implemented models include linear regression with residual spatial dependence, spatially/spatio-temporally varying coefficient models (Murakami et al., 2017, 2024; <doi:10.1016/j.spasta.2016.12.001>,<doi:10.48550/arXiv.2410.07229>), spatially filtered unconditional quantile regression (Murakami and Seya, 2019 <doi:10.1002/env.2556>), Gaussian and non-Gaussian spatial mixed models through compositionally-warping (Murakami et al. 2021, <doi:10.1016/j.spasta.2021.100520>).
Author: Daisuke Murakami [aut, cre]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.3.2 dated 2024-12-03 and 0.3.3 dated 2024-12-05
DESCRIPTION | 8 MD5 | 4 R/resf_vc.R | 7610 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 3811 insertions(+), 3811 deletions(-)
Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials.
Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the
probability that a jury will find a defendant guilty given jurors' preferences for a guilty
verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical
trial conditions to conduct harmful error analysis. The relationship between individual jurors'
verdict preferences and the probability that a jury returns a guilty verdict has been studied
by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>,
and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>
Diff between sate versions 2.2.0 dated 2024-09-11 and 2.2.1 dated 2024-12-05
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Data and Functions for R Companion to Political Analysis 3rd Ed
Description: Bundles the datasets and functions featured in Philip H.
Pollock and Barry C. Edwards<https://edge.sagepub.com/pollock>, "An R Companion to Political Analysis, 3rd Edition," Thousand Oaks, CA: Sage Publications.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>
Diff between RCPA3 versions 1.2.1 dated 2024-01-15 and 1.3.1 dated 2024-12-05
DESCRIPTION | 16 ++++++------- MD5 | 62 +++++++++++++++++++++++++++--------------------------- NEWS.md | 9 +++++++ R/CImean.r | 2 - R/CIprop.r | 2 - R/compmeansC.r | 7 +++--- R/correlateC.r | 2 - R/crosstabC.r | 5 +--- R/describeC.r | 2 - R/logregC.r | 2 - R/pchisqC.r | 2 - R/printC.r | 2 - R/regC.r | 2 - R/sampdistC.r | 5 ++-- R/sortC.r | 2 + R/testmeansC.r | 2 - R/testpropsC.r | 2 - R/transformC.r | 5 +--- man/CImean.Rd | 2 - man/CIprop.Rd | 2 - man/compmeansC.Rd | 7 +++--- man/correlateC.Rd | 2 - man/crosstabC.Rd | 5 +--- man/describeC.Rd | 2 - man/logregC.Rd | 2 - man/pchisqC.Rd | 2 - man/printC.Rd | 2 - man/regC.Rd | 2 - man/sampdistC.Rd | 5 ++-- man/sortC.Rd | 2 + man/testmeansC.Rd | 2 - man/testpropsC.Rd | 2 - 32 files changed, 91 insertions(+), 79 deletions(-)
Title: Lightweight, General-Purpose Data Analysis Pipelines
Description: A lightweight yet powerful framework for building robust
data analysis pipelines. With 'pipeflow', you initialize a pipeline
with your dataset and construct your workflow step by step by seamlessly
adding R functions. Modify, remove, or insert steps at any stage while
'pipeflow' ensures the integrity and correctness of your pipeline.
Designed to help you focus on the 'what' rather than the 'how', this
package simplifies the implementation of complex workflows, making
even large-scale data analysis projects manageable, adaptable, and
reusable with ease.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between pipeflow versions 0.1.1 dated 2024-12-02 and 0.2.1 dated 2024-12-05
pipeflow-0.1.1/pipeflow/inst/doc/collect-output.R |only pipeflow-0.1.1/pipeflow/inst/doc/collect-output.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/collect-output.html |only pipeflow-0.1.1/pipeflow/inst/doc/combine-pipelines.R |only pipeflow-0.1.1/pipeflow/inst/doc/combine-pipelines.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/combine-pipelines.html |only pipeflow-0.1.1/pipeflow/inst/doc/get-started.R |only pipeflow-0.1.1/pipeflow/inst/doc/get-started.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/get-started.html |only pipeflow-0.1.1/pipeflow/inst/doc/modify-pipeline.R |only pipeflow-0.1.1/pipeflow/inst/doc/modify-pipeline.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/modify-pipeline.html |only pipeflow-0.1.1/pipeflow/inst/doc/self-modify-pipeline.R |only pipeflow-0.1.1/pipeflow/inst/doc/self-modify-pipeline.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/self-modify-pipeline.html |only pipeflow-0.1.1/pipeflow/inst/doc/split-and-combine.R |only pipeflow-0.1.1/pipeflow/inst/doc/split-and-combine.Rmd |only pipeflow-0.1.1/pipeflow/inst/doc/split-and-combine.html |only pipeflow-0.1.1/pipeflow/vignettes/collect-output.Rmd |only pipeflow-0.1.1/pipeflow/vignettes/combine-pipelines.Rmd |only pipeflow-0.1.1/pipeflow/vignettes/get-started.Rmd |only pipeflow-0.1.1/pipeflow/vignettes/modify-pipeline.Rmd |only pipeflow-0.1.1/pipeflow/vignettes/self-modify-pipeline.Rmd |only pipeflow-0.1.1/pipeflow/vignettes/split-and-combine.Rmd |only pipeflow-0.2.1/pipeflow/DESCRIPTION | 26 +++-- pipeflow-0.2.1/pipeflow/MD5 | 52 +++++----- pipeflow-0.2.1/pipeflow/build/vignette.rds |binary pipeflow-0.2.1/pipeflow/inst/doc/v01-get-started.R |only pipeflow-0.2.1/pipeflow/inst/doc/v01-get-started.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v01-get-started.html |only pipeflow-0.2.1/pipeflow/inst/doc/v02-modify-pipeline.R |only pipeflow-0.2.1/pipeflow/inst/doc/v02-modify-pipeline.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v02-modify-pipeline.html |only pipeflow-0.2.1/pipeflow/inst/doc/v03-combine-pipelines.R |only pipeflow-0.2.1/pipeflow/inst/doc/v03-combine-pipelines.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v03-combine-pipelines.html |only pipeflow-0.2.1/pipeflow/inst/doc/v04-collect-output.R |only pipeflow-0.2.1/pipeflow/inst/doc/v04-collect-output.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v04-collect-output.html |only pipeflow-0.2.1/pipeflow/inst/doc/v05-split-and-combine.R |only pipeflow-0.2.1/pipeflow/inst/doc/v05-split-and-combine.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v05-split-and-combine.html |only pipeflow-0.2.1/pipeflow/inst/doc/v06-self-modify-pipeline.R |only pipeflow-0.2.1/pipeflow/inst/doc/v06-self-modify-pipeline.Rmd |only pipeflow-0.2.1/pipeflow/inst/doc/v06-self-modify-pipeline.html |only pipeflow-0.2.1/pipeflow/vignettes/v01-get-started.Rmd |only pipeflow-0.2.1/pipeflow/vignettes/v02-modify-pipeline.Rmd |only pipeflow-0.2.1/pipeflow/vignettes/v03-combine-pipelines.Rmd |only pipeflow-0.2.1/pipeflow/vignettes/v04-collect-output.Rmd |only pipeflow-0.2.1/pipeflow/vignettes/v05-split-and-combine.Rmd |only pipeflow-0.2.1/pipeflow/vignettes/v06-self-modify-pipeline.Rmd |only 51 files changed, 42 insertions(+), 36 deletions(-)
Title: Model II Regression
Description: Computes model II simple linear regression using ordinary
least squares (OLS), major axis (MA), standard major axis (SMA), and
ranged major axis (RMA).
Author: Pierre Legendre [aut],
Jari Oksanen [cre]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between lmodel2 versions 1.7-3 dated 2018-02-05 and 1.7-4 dated 2024-12-05
DESCRIPTION | 23 +- MD5 | 14 - build/vignette.rds |binary inst/doc/mod2user.R | 1 inst/doc/mod2user.Rnw | 2 inst/doc/mod2user.pdf |binary man/lmodel2.Rd | 380 ++++++++++++++++++++++++------------------------- vignettes/mod2user.Rnw | 2 8 files changed, 214 insertions(+), 208 deletions(-)
Title: Individual Dynamic Latent Factor Model
Description: A personalized dynamic latent factor model (Zhang et al. (2024) <doi:10.1093/biomet/asae015>) for irregular multi-resolution time series data, to interpolate unsampled measurements from low-resolution time series.
Author: Siyang Liu [aut, cre],
Jiuchen Zhang [aut],
Annie Qu [aut]
Maintainer: Siyang Liu <liusiyang.lucia@gmail.com>
Diff between IDLFM versions 0.0.1 dated 2024-12-02 and 0.0.2 dated 2024-12-05
DESCRIPTION | 15 ++++++++++----- LICENSE | 2 +- MD5 | 4 ++-- 3 files changed, 13 insertions(+), 8 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 6.9 dated 2024-10-29 and 7.0 dated 2024-12-05
DESCRIPTION | 29 ++++++---------- MD5 | 81 ++++++++++++++++++++++++--------------------- NAMESPACE | 4 +- R/esag.reg.R | 2 - R/hspher.reg.R |only R/mixpkbd.mle.R | 4 +- R/mixspcauchy.mle.R | 4 +- R/pk2.R | 41 +++++++++++----------- R/pkbd.reg.R | 3 + R/pkbd.reg2.R | 14 +++---- R/pkbd2test.R | 4 +- R/score.cipc.R |only R/score.spml.R |only R/sp2.R | 40 +++++++++++----------- R/spcauchy.reg.R | 2 - R/spcauchy2test.R | 4 +- R/spher.reg.R | 8 ++-- R/vmf.reg.R | 1 R/vmf2.R |only R/vmf2test.R |only R/vmfreg.R | 2 - man/Directional-package.Rd | 4 +- man/bic.mixvmf.Rd | 2 - man/dirda.Rd | 2 - man/dirda.cv.Rd | 4 +- man/dmixvmf.Rd | 2 - man/dsespc.Rd | 4 -- man/dvmf.Rd | 2 - man/hspher.reg.Rd |only man/mixvmf.mle.Rd | 2 - man/rmixvmf.Rd | 2 - man/rsespc.Rd | 4 +- man/score.cipc.Rd |only man/sespc.mle.Rd | 8 +--- man/sespc.reg.Rd | 4 -- man/spcauchy2test.Rd | 24 ++++++++++--- man/spher.reg.Rd | 17 +++++---- man/spher.sespc.contour.Rd | 4 -- man/spher.vmf.contour.Rd | 2 - man/spml.mle.Rd | 12 ++---- man/spml.reg.Rd | 5 +- man/spml.regs.Rd | 4 +- man/vmf.contour.Rd | 2 - man/vmf.mle.Rd | 2 - man/vmfreg.Rd | 2 - 45 files changed, 184 insertions(+), 173 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from raw data obtained using volumetric, manometric, gravimetric, or gas density methods for any number of bottles. With cumulative methane production data and data on bottle contents, biochemical methane potential (BMP) or specific methane production (SMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways [...truncated...]
Author: Sasha D. Hafner [aut, cre] ,
Charlotte Rennuit [aut],
Camilla Justesen [aut],
Nanna Lojborg [aut],
Jacob Mortensen [aut],
Jonas Ohlsson [aut],
Sergi Astals [ctb],
Konrad Koch [ctb],
Soeren Weinrich [ctb],
Jin Mi Triolo [ctb],
Ali Heidarzadeh Vazifehk [...truncated...]
Maintainer: Sasha D. Hafner <sasha.hafner@bce.au.dk>
Diff between biogas versions 1.23.2 dated 2020-01-08 and 1.61 dated 2024-12-05
biogas-1.23.2/biogas/NEWS |only biogas-1.23.2/biogas/tests/testthat |only biogas-1.23.2/biogas/tests/testthat.R |only biogas-1.61/biogas/ChangeLog | 14 +++ biogas-1.61/biogas/DESCRIPTION | 36 +++++--- biogas-1.61/biogas/MD5 | 82 ++++++++++-------- biogas-1.61/biogas/NAMESPACE | 5 - biogas-1.61/biogas/NEWS.md |only biogas-1.61/biogas/R/FOM.R |only biogas-1.61/biogas/R/airDens.R |only biogas-1.61/biogas/R/calcBgGD.R | 13 ++ biogas-1.61/biogas/R/calcBgGrav.R |only biogas-1.61/biogas/R/calcBgVol.R | 16 +-- biogas-1.61/biogas/R/constants.R | 13 ++ biogas-1.61/biogas/R/convertBPC.R |only biogas-1.61/biogas/R/cumBg.R | 18 ++-- biogas-1.61/biogas/R/cumBgDataPrep.R | 10 +- biogas-1.61/biogas/R/gasDens.R | 50 ++++++++--- biogas-1.61/biogas/R/logistic.R |only biogas-1.61/biogas/R/mass2vol.R | 44 +++++++--- biogas-1.61/biogas/R/model_stats.R |only biogas-1.61/biogas/R/molMass.R | 2 biogas-1.61/biogas/R/planBMP.R | 66 +++++++++++++-- biogas-1.61/biogas/R/readFormula.R | 11 -- biogas-1.61/biogas/R/summBg.R | 87 +++++++++++++------- biogas-1.61/biogas/README.md | 81 ++++++++++++++++-- biogas-1.61/biogas/build/partial.rdb |only biogas-1.61/biogas/build/vignette.rds |binary biogas-1.61/biogas/data/UQGravBiogas.rda |only biogas-1.61/biogas/data/UQGravSetup.rda |only biogas-1.61/biogas/data/feedSetup.rda |binary biogas-1.61/biogas/inst/doc/biogas_quick_start.Rnw | 14 +-- biogas-1.61/biogas/inst/doc/biogas_quick_start.pdf |binary biogas-1.61/biogas/inst/doc/calcBgMan_function.pdf |binary biogas-1.61/biogas/inst/doc/calcBgVol_function.pdf |binary biogas-1.61/biogas/inst/doc/predBg_function.Rnw | 2 biogas-1.61/biogas/inst/doc/predBg_function.pdf |binary biogas-1.61/biogas/inst/tinytest |only biogas-1.61/biogas/man/UQGDSetup.Rd | 2 biogas-1.61/biogas/man/UQGravBiogas.Rd |only biogas-1.61/biogas/man/UQGravSetup.Rd |only biogas-1.61/biogas/man/calcBgGrav.Rd |only biogas-1.61/biogas/man/calcBgVol.Rd | 2 biogas-1.61/biogas/man/feedSetup.Rd | 1 biogas-1.61/biogas/man/fitFOM.Rd |only biogas-1.61/biogas/man/mass2vol.Rd | 10 +- biogas-1.61/biogas/man/planBMP.Rd | 24 ++--- biogas-1.61/biogas/tests/tinytest.R |only biogas-1.61/biogas/vignettes/biogas_quick_start.Rnw | 14 +-- biogas-1.61/biogas/vignettes/predBg_function.Rnw | 2 50 files changed, 431 insertions(+), 188 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 17.0.0.1 dated 2024-08-21 and 18.1.0 dated 2024-12-05
arrow-17.0.0.1/arrow/tools/checksums/darwin-arm64-openssl-1.1/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/darwin-arm64-openssl-3.0/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/darwin-x86_64-openssl-1.1/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/darwin-x86_64-openssl-3.0/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/linux-openssl-1.0/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/linux-openssl-1.1/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/linux-openssl-3.0/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/checksums/windows/arrow-17.0.0.zip.sha512 |only arrow-17.0.0.1/arrow/tools/cpp/src/arrow/acero/unmaterialized_table.h |only arrow-17.0.0.1/arrow/tools/cpp/src/arrow/compute/kernels/row_encoder.cc |only arrow-17.0.0.1/arrow/tools/cpp/src/arrow/compute/kernels/row_encoder_internal.h |only arrow-17.0.0.1/arrow/tools/cpp/src/arrow/util/bit_stream_utils.h |only arrow-17.0.0.1/arrow/tools/cpp/src/arrow/util/rle_encoding.h |only arrow-17.0.0.1/arrow/tools/cpp/src/parquet/encoding.cc |only arrow-18.1.0/arrow/DESCRIPTION | 8 arrow-18.1.0/arrow/MD5 | 802 +++---- arrow-18.1.0/arrow/NEWS.md | 27 arrow-18.1.0/arrow/R/arrow-package.R | 2 arrow-18.1.0/arrow/R/arrow-tabular.R | 8 arrow-18.1.0/arrow/R/compute.R | 1 arrow-18.1.0/arrow/R/dplyr-datetime-helpers.R | 4 arrow-18.1.0/arrow/R/dplyr-funcs-conditional.R | 11 arrow-18.1.0/arrow/R/dplyr-funcs-datetime.R | 2 arrow-18.1.0/arrow/R/dplyr-funcs-doc.R | 2 arrow-18.1.0/arrow/R/dplyr-funcs-string.R | 10 arrow-18.1.0/arrow/R/dplyr-slice.R | 2 arrow-18.1.0/arrow/R/dplyr-summarize.R | 2 arrow-18.1.0/arrow/R/duckdb.R | 8 arrow-18.1.0/arrow/R/metadata.R | 21 arrow-18.1.0/arrow/R/parquet.R | 7 arrow-18.1.0/arrow/README.md | 15 arrow-18.1.0/arrow/man/ParquetFileWriter.Rd | 1 arrow-18.1.0/arrow/man/acero.Rd | 2 arrow-18.1.0/arrow/man/list_compute_functions.Rd | 3 arrow-18.1.0/arrow/man/to_arrow.Rd | 9 arrow-18.1.0/arrow/src/altrep.cpp | 14 arrow-18.1.0/arrow/src/r_to_arrow.cpp | 9 arrow-18.1.0/arrow/tests/testthat/helper-data.R | 2 arrow-18.1.0/arrow/tests/testthat/test-Array.R | 10 arrow-18.1.0/arrow/tests/testthat/test-RecordBatch.R | 6 arrow-18.1.0/arrow/tests/testthat/test-Table.R | 6 arrow-18.1.0/arrow/tests/testthat/test-compute-aggregate.R | 2 arrow-18.1.0/arrow/tests/testthat/test-compute-arith.R | 8 arrow-18.1.0/arrow/tests/testthat/test-csv.R | 4 arrow-18.1.0/arrow/tests/testthat/test-dataset-csv.R | 16 arrow-18.1.0/arrow/tests/testthat/test-dataset-json.R | 2 arrow-18.1.0/arrow/tests/testthat/test-dataset.R | 20 arrow-18.1.0/arrow/tests/testthat/test-dplyr-filter.R | 6 arrow-18.1.0/arrow/tests/testthat/test-dplyr-funcs-conditional.R | 10 arrow-18.1.0/arrow/tests/testthat/test-dplyr-funcs-datetime.R | 2 arrow-18.1.0/arrow/tests/testthat/test-dplyr-funcs-string.R | 9 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arrow-18.1.0/arrow/tools/cpp/src/parquet/arrow/schema_internal.h | 8 arrow-18.1.0/arrow/tools/cpp/src/parquet/arrow/test_util.h | 20 arrow-18.1.0/arrow/tools/cpp/src/parquet/arrow/writer.cc | 20 arrow-18.1.0/arrow/tools/cpp/src/parquet/arrow/writer.h | 12 arrow-18.1.0/arrow/tools/cpp/src/parquet/bloom_filter.h | 4 arrow-18.1.0/arrow/tools/cpp/src/parquet/column_reader.cc | 146 - arrow-18.1.0/arrow/tools/cpp/src/parquet/column_reader.h | 51 arrow-18.1.0/arrow/tools/cpp/src/parquet/column_writer.cc | 66 arrow-18.1.0/arrow/tools/cpp/src/parquet/column_writer.h | 27 arrow-18.1.0/arrow/tools/cpp/src/parquet/decoder.cc |only arrow-18.1.0/arrow/tools/cpp/src/parquet/encoder.cc |only arrow-18.1.0/arrow/tools/cpp/src/parquet/encoding.h | 36 arrow-18.1.0/arrow/tools/cpp/src/parquet/encryption/crypto_factory.cc | 6 arrow-18.1.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal.cc | 432 ++- arrow-18.1.0/arrow/tools/cpp/src/parquet/encryption/encryption_internal.h | 51 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Title: Variational Bayes for Fast and Accurate Empirical Likelihood
Inference
Description: Computes the Gaussian variational approximation of the Bayesian
empirical likelihood posterior. This is an implementation of the function
found in Yu, W., & Bondell, H. D. (2023) <doi:10.1080/01621459.2023.2169701>.
Author: Weichang Yu [aut] ,
Jeremy Lim [cre, aut]
Maintainer: Jeremy Lim <jeremy.lim@unimelb.edu.au>
Diff between VBel versions 1.0.1 dated 2024-06-04 and 1.1.0 dated 2024-12-05
DESCRIPTION | 14 +- MD5 | 32 +++--- R/RcppExports.R | 8 - R/compute-AEL-functions.R | 119 ++++++++++++------------ R/compute-GVA-functions.R | 183 ++++++++++--------------------------- R/diagnostic-plot.R | 61 ++++++------ README.md | 151 +++++++++++++++++------------- build/partial.rdb |binary man/compute_AEL.Rd | 67 +++++++++---- man/compute_GVA.Rd | 85 +++++++++-------- man/diagnostic_plot.Rd | 61 ++++++------ src/RcppExports.cpp | 34 +----- src/compute-AEL-functions-Rcpp.cpp | 46 ++++----- src/compute-GVA-functions-Rcpp.cpp | 54 +++++----- tests/testthat/test-AEL.R | 12 -- tests/testthat/test-GVA.R | 38 +++---- tests/testthat/test-GVA2.R | 23 +--- 17 files changed, 466 insertions(+), 522 deletions(-)
Title: Prevalence and Regression for Pool-Tested (Group-Tested) Data
Description: An easy-to-use tool for working with presence/absence tests
on 'pooled' or 'grouped' samples. The primary application is for
estimating prevalence of a marker in a population based on the results
of tests on pooled specimens. This sampling method is often employed
in surveillance of rare conditions in humans or animals (e.g.
molecular xenomonitoring). The package was initially conceived as an
R-based alternative to the molecular xenomonitoring software,
'PoolScreen' <https://sites.uab.edu/statgenetics/software/>. However,
it goes further, allowing for estimates of prevalence to be adjusted
for hierarchical sampling frames, and perform flexible mixed-effect
regression analyses (McLure et al. Environmental Modelling and
Software. <DOI:10.1016/j.envsoft.2021.105158>). The package is
currently in early stages, however more features are planned or in the
works: e.g. adjustments for imperfect test specificity/sensitivity,
functions for helping with optimal experimental design, [...truncated...]
Author: Angus McLure [aut, cre] ,
Caitlin Cherryh [ctb]
Maintainer: Angus McLure <angus.mclure@anu.edu.au>
Diff between PoolTestR versions 0.1.3 dated 2022-07-01 and 0.2.0 dated 2024-12-05
PoolTestR-0.1.3/PoolTestR/inst/stan/BayesianPoolScreen.stan |only PoolTestR-0.1.3/PoolTestR/inst/stan/HierBayesianPoolScreen.stan |only PoolTestR-0.1.3/PoolTestR/src/stanExports_BayesianPoolScreen.cc |only PoolTestR-0.1.3/PoolTestR/src/stanExports_BayesianPoolScreen.h |only PoolTestR-0.1.3/PoolTestR/src/stanExports_HierBayesianPoolScreen.cc |only PoolTestR-0.1.3/PoolTestR/src/stanExports_HierBayesianPoolScreen.h |only PoolTestR-0.2.0/PoolTestR/DESCRIPTION | 73 - PoolTestR-0.2.0/PoolTestR/MD5 | 65 - PoolTestR-0.2.0/PoolTestR/NAMESPACE | 8 PoolTestR-0.2.0/PoolTestR/NEWS.md | 88 + PoolTestR-0.2.0/PoolTestR/R/HierPoolPrev.R | 306 +++-- PoolTestR-0.2.0/PoolTestR/R/PoolPrev.R | 402 ++++-- PoolTestR-0.2.0/PoolTestR/R/PoolRegBayes.R | 16 PoolTestR-0.2.0/PoolTestR/R/PoolTestR-package.R | 7 PoolTestR-0.2.0/PoolTestR/R/getPrevalence.R | 587 +++++++--- PoolTestR-0.2.0/PoolTestR/R/stanmodels.R | 9 PoolTestR-0.2.0/PoolTestR/R/utils.R |only PoolTestR-0.2.0/PoolTestR/README.md | 280 ++++ PoolTestR-0.2.0/PoolTestR/build |only PoolTestR-0.2.0/PoolTestR/configure | 2 PoolTestR-0.2.0/PoolTestR/configure.win | 3 PoolTestR-0.2.0/PoolTestR/data/SimpleExampleData.rda |binary PoolTestR-0.2.0/PoolTestR/data/TruePrev.rda |binary PoolTestR-0.2.0/PoolTestR/inst/stan/HierPoolPrevIndividualSD.stan |only PoolTestR-0.2.0/PoolTestR/inst/stan/HierPoolPrevTotalSD.stan |only PoolTestR-0.2.0/PoolTestR/inst/stan/PoolPrev.stan |only PoolTestR-0.2.0/PoolTestR/man/HierPoolPrev.Rd | 132 +- PoolTestR-0.2.0/PoolTestR/man/PoolLink.Rd | 48 PoolTestR-0.2.0/PoolTestR/man/PoolPrev.Rd | 134 +- PoolTestR-0.2.0/PoolTestR/man/PoolReg.Rd | 48 PoolTestR-0.2.0/PoolTestR/man/PoolRegBayes.Rd | 48 PoolTestR-0.2.0/PoolTestR/man/PoolTestR-package.Rd | 22 PoolTestR-0.2.0/PoolTestR/man/getPrevalence.Rd | 130 +- PoolTestR-0.2.0/PoolTestR/src/Makevars | 5 PoolTestR-0.2.0/PoolTestR/src/Makevars.win | 5 PoolTestR-0.2.0/PoolTestR/src/RcppExports.cpp | 10 PoolTestR-0.2.0/PoolTestR/src/stanExports_HierPoolPrevIndividualSD.cc |only PoolTestR-0.2.0/PoolTestR/src/stanExports_HierPoolPrevIndividualSD.h |only PoolTestR-0.2.0/PoolTestR/src/stanExports_HierPoolPrevTotalSD.cc |only PoolTestR-0.2.0/PoolTestR/src/stanExports_HierPoolPrevTotalSD.h |only PoolTestR-0.2.0/PoolTestR/src/stanExports_PoolPrev.cc |only PoolTestR-0.2.0/PoolTestR/src/stanExports_PoolPrev.h |only 42 files changed, 1708 insertions(+), 720 deletions(-)
Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models.
Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and
Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>.
Parametric models from the special exponential family (SEF) are based on
Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and
Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
The parametric location-scale models are based on Dorre et al. (2021) <doi:10.1007/s00180-020-01027-6>.
Author: Takeshi Emura [aut, cre],
Ya-Hsuan Hu [aut],
Chung-Yan Huang [aut]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between double.truncation versions 1.7 dated 2020-09-08 and 1.8 dated 2024-12-05
DESCRIPTION | 26 +++++++++++++++++------- MD5 | 20 ++++++++++-------- NAMESPACE | 2 + R/GoF.R |only R/NPMLE.R | 42 +++++++++++++++++++++------------------ man/GoF.Rd |only man/NPMLE.Rd | 5 +++- man/PMLE.Weibull.Rd | 28 +++++++++++++------------- man/PMLE.loglogistic.Rd | 26 ++++++++++++------------ man/PMLE.lognormal.Rd | 26 ++++++++++++------------ man/double.truncation-package.Rd | 6 ++--- man/simu.Weibull.Rd | 8 +++---- 12 files changed, 106 insertions(+), 83 deletions(-)
More information about double.truncation at CRAN
Permanent link
Title: Access to the List of Birds Species of Peru
Description: Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Author: Paul E. Santos Andrade [aut, cre]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between avesperu versions 0.0.2 dated 2024-03-09 and 0.0.3 dated 2024-12-05
DESCRIPTION | 8 - MD5 | 27 ++-- R/aves_peru_2024_v2.R |only R/avesperu23.R | 94 ++++++++-------- R/avesperu_tab.R | 98 ++++++++--------- R/get_avesperu.R | 158 +++++++++++++++++----------- README.md | 136 +++++++++++++++--------- data/aves_peru_2024_v2.rda |only inst/CITATION | 6 - man/aves_peru_2023.Rd | 112 +++++++++---------- man/aves_peru_2024.Rd | 116 ++++++++++---------- man/aves_peru_2024_v2.Rd |only man/figures/README-unnamed-chunk-2-1.png |binary man/search_avesperu.Rd | 50 ++++++-- tests/testthat/test-test_avesperu_tab.R | 106 +++++++++--------- tests/testthat/test-test_search_avesperu.R | 163 +++++++++++++++++++---------- 16 files changed, 616 insertions(+), 458 deletions(-)