Title: A Library for using 'Pathling'
Description: R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.
Author: Australian e-Health Research Centre, CSIRO [cph, cre],
Piotr Szul [aut],
John Grimes [aut]
Maintainer: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>
Diff between pathling versions 9.7.1 dated 2026-06-03 and 9.9.0 dated 2026-09-02
DESCRIPTION | 8 +- MD5 | 17 +++--- NAMESPACE | 23 ++++---- R/context.R | 88 +++++++++++++++++++++++++++++++- R/encoding.R | 2 R/terminology_import.R |only R/utils.R | 9 +++ man/conditions.Rd | 2 man/pathling_connect.Rd | 25 ++++++++- man/pathling_import_fhir_terminology.Rd |only man/pathling_import_snomed.Rd |only 11 files changed, 147 insertions(+), 27 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and
'SubCortexMesh' subcortical outputs for a given sample by
restructuring the data values into a single file. The single file can
then be used by the package for analyses independently from its base
dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.5.2 dated 2026-06-25 and 1.5.3 dated 2026-09-02
VertexWiseR-1.5.2/VertexWiseR/R/miniconda_installer_url_py39.r |only VertexWiseR-1.5.3/VertexWiseR/DESCRIPTION | 10 VertexWiseR-1.5.3/VertexWiseR/MD5 | 30 - VertexWiseR-1.5.3/VertexWiseR/NEWS.md | 10 VertexWiseR-1.5.3/VertexWiseR/R/RFT_vertex_analysis.R | 13 VertexWiseR-1.5.3/VertexWiseR/R/TFCE_vertex_analysis.R | 10 VertexWiseR-1.5.3/VertexWiseR/R/VWRfirstrun.R | 40 + VertexWiseR-1.5.3/VertexWiseR/R/miniconda_installer_url_py310.r |only VertexWiseR-1.5.3/VertexWiseR/R/other_functions_scm.R | 2 VertexWiseR-1.5.3/VertexWiseR/R/plot_surf3d.R | 11 VertexWiseR-1.5.3/VertexWiseR/inst/doc/Python_troubleshooting.html | 38 - VertexWiseR-1.5.3/VertexWiseR/inst/doc/VertexWiseR_Example_3.html | 257 +++++----- VertexWiseR-1.5.3/VertexWiseR/man/RFT_vertex_analysis.Rd | 2 VertexWiseR-1.5.3/VertexWiseR/man/TFCE_threshold.Rd | 2 VertexWiseR-1.5.3/VertexWiseR/man/plot_surf3d.Rd | 2 VertexWiseR-1.5.3/VertexWiseR/vignettes/Python_troubleshooting.Rmd | 8 VertexWiseR-1.5.3/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd | 21 17 files changed, 288 insertions(+), 168 deletions(-)
Title: Plotting Mutational Signatures and Mutational Spectra
Description: Plotting functions for mutational signatures and mutational
spectra, including single base substitutions (SBS), doublet base
substitutions (DBS), and small insertions and deletions (indels).
Generates plots similar to those used previously in
Alexandrov et al. (2020)<doi:10.1038/s41586-020-1943-3> and
Rozen et al. (2026)<doi:10.5281/zenodo.18451842>.
Author: Steven Rozen [aut, cre]
Maintainer: Steven Rozen <steverozen@pm.me>
Diff between mSigPlot versions 2.0.41 dated 2026-07-15 and 2.0.42 dated 2026-09-02
mSigPlot-2.0.41/mSigPlot/tests/testthat/tests |only mSigPlot-2.0.42/mSigPlot/DESCRIPTION | 8 +- mSigPlot-2.0.42/mSigPlot/MD5 | 24 ++---- mSigPlot-2.0.42/mSigPlot/NAMESPACE | 30 ++++---- mSigPlot-2.0.42/mSigPlot/NEWS.md | 16 ++++ mSigPlot-2.0.42/mSigPlot/R/plot_DBS144.R | 2 mSigPlot-2.0.42/mSigPlot/R/plot_DBS78_pdf.R | 11 ++ mSigPlot-2.0.42/mSigPlot/R/plot_ID166.R | 2 mSigPlot-2.0.42/mSigPlot/R/plot_ID89.R | 2 mSigPlot-2.0.42/mSigPlot/inst/doc/mSigPlot.html | 37 ++++------ mSigPlot-2.0.42/mSigPlot/man/bar_plots.Rd | 4 + mSigPlot-2.0.42/mSigPlot/tests/testthat/fixtures/reference_hashes/plot_ID89.hash | 2 mSigPlot-2.0.42/mSigPlot/tests/testthat/fixtures/reference_hashes/plot_ID89_peaks.hash | 2 13 files changed, 87 insertions(+), 53 deletions(-)
Title: Consensus Clustering Methods for Multiple Imputed Data
Description: Provides tools for performing consensus clustering on multiple
imputed datasets. The package supports a range of clustering algorithms
across imputations, including hierarchical methods (e.g., Ward, single,
complete, average) and partition-based approaches such as k-means,
k-medoids (PAM), fuzzy clustering, model-based clustering ('mclust'),
and methods for mixed or categorical data (k-modes and k-prototypes).
A co-assignment matrix is constructed to quantify agreement between
partitions, and consensus solutions are derived via hierarchical
clustering applied to the resulting dissimilarity matrix. Additional
functions are provided for validation and visualization of clustering
results, facilitating robust analysis in the presence of missing data.
Consensus clustering framework is based on Monti et al. (2003)
<doi:10.1023/A:1023949509487>, rank aggregation methods follow
Pihur et al. (2007) <doi:10.1093/bioinformatics/btm158>, and the
PAC (Proportion of Ambiguous Clustering) [...truncated...]
Author: Anhuar Duran Mendoza [aut],
Andres Montenegro Lemus [aut, cre],
Mario Pacheco Lopez [aut]
Maintainer: Andres Montenegro Lemus <andresfemole@gmail.com>
Diff between cclustr versions 0.1.1 dated 2026-05-18 and 0.1.2 dated 2026-09-02
DESCRIPTION | 10 MD5 | 48 - NEWS.md | 10 R/Cluster.R | 1262 ++++++++++++++++++------------------- R/Coassignment.R | 642 +++++++++--------- R/Complete_Sequence.R | 662 +++++++++---------- R/Dendrogram.R | 356 +++++----- R/Heatmap.R | 348 +++++----- R/Imputation.R | 532 +++++++-------- R/Selection.R | 670 +++++++++---------- R/Validation.R | 692 ++++++++++---------- R/ValidationK.R | 370 +++++----- R/cclustr-package.R | 208 +++--- R/globals.R | 6 inst/WORDLIST | 2 inst/doc/cclustr-introduction.R | 35 - inst/doc/cclustr-introduction.Rmd | 49 - inst/doc/cclustr-introduction.html | 147 ++-- man/cclustr-package.Rd | 222 +++--- man/run_mi_clustering.Rd | 522 +++++++-------- tests/testthat.R | 24 tests/testthat/test-cluster.R | 720 ++++++++++----------- tests/testthat/test-consensus.R | 666 +++++++++---------- tests/testthat/test-imputation.R | 324 ++++----- vignettes/cclustr-introduction.Rmd | 49 - 25 files changed, 4296 insertions(+), 4280 deletions(-)
Title: Fast and Efficient Graph Data Structures
Description: Seamlessly build and manipulate graph structures, leveraging
its high-performance methods for filtering, joining, and mutating
data. Ensures that mutations and changes to the graph are performed in
place, streamlining your workflow for optimal productivity.
Author: ixpantia, SRL [cph],
Andres Quintero [aut, cre],
The authors of the dependency Rust crates [ctb]
Maintainer: Andres Quintero <andres@ixpantia.com>
Diff between orbweaver versions 0.18.2 dated 2025-04-28 and 0.18.3 dated 2026-09-02
DESCRIPTION | 6 +-- MD5 | 14 ++++---- src/rust/Cargo.lock | 69 ++++++++++++++++++++++++++--------------- src/rust/Cargo.toml | 2 - src/rust/src/from_dataframe.rs | 2 - src/rust/src/lib.rs | 48 ++++++++++++++-------------- src/rust/src/macros.rs | 42 ++++++++++++------------ src/rust/vendor.tar.xz |binary 8 files changed, 102 insertions(+), 81 deletions(-)
Title: Transmutation of Languages
Description: Tools for transforming 'R' expressions. Provides functions for
finding, extracting, and replacing patterns in 'R' language objects, similarly
to how regular expressions can be used to find, extract, and replace patterns
in text. Also provides functions for generating code using specially-formatted
template files and for translating 'R' expressions into similar expressions in
other programming languages. The package may be helpful for advanced uses of
'R' expressions, such as developing domain-specific languages.
Author: Nicholas Davies [cre, aut, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between elixir versions 0.1.1 dated 2025-12-02 and 0.1.2 dated 2026-09-02
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 34 ++++++------ NAMESPACE | 6 +- NEWS.md | 7 ++ R/match.R | 93 ++++++++++++++++++++++++++++------ R/reindent.R | 2 R/replace.R | 113 +++++++++++++++++++++++++++++++++++------- R/rules.R | 3 + README.md | 20 ++++++- build/vignette.rds |binary man/elixir-expression.Rd | 2 man/elixir.Rd | 2 man/expr_match.Rd | 51 +++++++++++++++++- man/expr_replace.Rd | 43 ++++++++++++++- man/reindent.Rd | 2 man/translate.Rd | 2 tests/testthat/test-replace.R | 45 ++++++++++++++++ 18 files changed, 360 insertions(+), 75 deletions(-)
Title: Reconstruct and Visualize Transit Vehicle Trajectories
Description: Today's public transit vehicles produce a large amount of automatic
vehicle location (AVL) data. This data is very useful for planning and
performance studies, but can be noisy, error-prone, and sparse. This package
provides tools for cleaning AVL point data and turning it into continuous,
differentiable, monotonic, and invertible vehicle trajectory functions,
based on the work of Robbennolt et al. (2025)
<doi:10.48550/arXiv.2509.00119> and
Huang et al. (2023) <doi:10.1109/ITSC57777.2023.10422524>.
Author: Benjamin O'Brien [aut, cre, cph],
Lewis Lehe [aut]
Maintainer: Benjamin O'Brien <obrienbenjaminj@gmail.com>
Diff between transittraj versions 1.0.0 dated 2026-08-31 and 1.1.0 dated 2026-09-02
transittraj-1.0.0/transittraj/inst/doc/data-workflow.R |only transittraj-1.0.0/transittraj/inst/doc/data-workflow.Rmd |only transittraj-1.0.0/transittraj/inst/doc/data-workflow.html |only transittraj-1.0.0/transittraj/vignettes/data-workflow.Rmd |only transittraj-1.1.0/transittraj/DESCRIPTION | 12 - transittraj-1.1.0/transittraj/MD5 | 37 ++--- transittraj-1.1.0/transittraj/NEWS.md | 21 ++ transittraj-1.1.0/transittraj/R/avl_cleaning.R | 72 +++++----- transittraj-1.1.0/transittraj/R/gtfs_helpers.R | 17 +- transittraj-1.1.0/transittraj/R/trajectory_visualization.R | 4 transittraj-1.1.0/transittraj/R/utils.R | 1 transittraj-1.1.0/transittraj/README.md | 21 +- transittraj-1.1.0/transittraj/build/vignette.rds |binary transittraj-1.1.0/transittraj/inst/CITATION |only transittraj-1.1.0/transittraj/inst/doc/avl-data-workflow.R |only transittraj-1.1.0/transittraj/inst/doc/avl-data-workflow.Rmd |only transittraj-1.1.0/transittraj/inst/doc/avl-data-workflow.html |only transittraj-1.1.0/transittraj/inst/doc/intro-trajectories.Rmd | 2 transittraj-1.1.0/transittraj/inst/doc/intro-trajectories.html | 13 - transittraj-1.1.0/transittraj/man/get_linear_distances.Rd | 14 + transittraj-1.1.0/transittraj/man/plot_animated_line.Rd | 4 transittraj-1.1.0/transittraj/tests/testthat/test-gtfs_helpers.R | 43 ++--- transittraj-1.1.0/transittraj/vignettes/avl-data-workflow.Rmd |only transittraj-1.1.0/transittraj/vignettes/intro-trajectories.Rmd | 2 24 files changed, 154 insertions(+), 109 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Generate stimuli and analyze data of reverse correlation image
classification experiments (psychophysical tasks aimed at visualizing
cognitive mental representations of faces). For the method see Dotsch and
Todorov (2012) <doi:10.1177/1948550611430272>; for a practical primer see
Brinkman, Todorov and Dotsch (2017) <doi:10.1080/10463283.2017.1381469>.
Author: Ron Dotsch [aut, cre]
Maintainer: Ron Dotsch <rdotsch@gmail.com>
This is a re-admission after prior archival of version 0.3.4.1 dated 2016-07-13
Diff between rcicr versions 0.3.4.1 dated 2016-07-13 and 1.3.0 dated 2026-09-02
rcicr-0.3.4.1/rcicr/R/rcicr.R |only rcicr-0.3.4.1/rcicr/R/rcicr_2IFC.R |only rcicr-0.3.4.1/rcicr/R/rcicr_simulations.R |only rcicr-1.3.0/rcicr/ChangeLog | 95 ++++++++- rcicr-1.3.0/rcicr/DESCRIPTION | 36 ++- rcicr-1.3.0/rcicr/MD5 | 126 ++++++++++-- rcicr-1.3.0/rcicr/NAMESPACE | 39 +++ rcicr-1.3.0/rcicr/NEWS.md |only rcicr-1.3.0/rcicr/R/autoscale.R |only rcicr-1.3.0/rcicr/R/batchGenerateCI.R |only rcicr-1.3.0/rcicr/R/batchGenerateCI2IFC.R |only rcicr-1.3.0/rcicr/R/ci-compute.R |only rcicr-1.3.0/rcicr/R/ci-inputs.R |only rcicr-1.3.0/rcicr/R/computeCumulativeCICorrelation.R |only rcicr-1.3.0/rcicr/R/computeInfoVal2IFC.R |only rcicr-1.3.0/rcicr/R/deg2rad.R |only rcicr-1.3.0/rcicr/R/generateCI.R |only rcicr-1.3.0/rcicr/R/generateCI2IFC.R |only rcicr-1.3.0/rcicr/R/generateCINoise.R |only rcicr-1.3.0/rcicr/R/generateGabor.R |only rcicr-1.3.0/rcicr/R/generateNoiseImage.R |only rcicr-1.3.0/rcicr/R/generateNoisePattern.R |only rcicr-1.3.0/rcicr/R/generateReferenceDistribution.R |only rcicr-1.3.0/rcicr/R/generateSinusoid.R |only rcicr-1.3.0/rcicr/R/generateStimuli2IFC.R |only rcicr-1.3.0/rcicr/R/parallel.R |only rcicr-1.3.0/rcicr/R/plotZmap.R |only rcicr-1.3.0/rcicr/R/rcicr-package.R |only rcicr-1.3.0/rcicr/R/rdata.R |only rcicr-1.3.0/rcicr/R/simulateNoiseIntensities.R |only rcicr-1.3.0/rcicr/R/zmap-compute.R |only rcicr-1.3.0/rcicr/R/zzz.R |only rcicr-1.3.0/rcicr/README.md |only rcicr-1.3.0/rcicr/build |only rcicr-1.3.0/rcicr/inst/CITATION | 36 ++- rcicr-1.3.0/rcicr/inst/doc |only rcicr-1.3.0/rcicr/man/autoscale.Rd | 40 ++- rcicr-1.3.0/rcicr/man/batchGenerateCI.Rd | 72 +++++- rcicr-1.3.0/rcicr/man/batchGenerateCI2IFC.Rd | 72 +++++- rcicr-1.3.0/rcicr/man/computeCumulativeCICorrelation.Rd | 81 +++++++ rcicr-1.3.0/rcicr/man/computeInfoVal2IFC.Rd |only rcicr-1.3.0/rcicr/man/deg2rad.Rd |only rcicr-1.3.0/rcicr/man/figures |only rcicr-1.3.0/rcicr/man/generateCI.Rd | 135 +++++++++++-- rcicr-1.3.0/rcicr/man/generateCI2IFC.Rd | 76 +++++-- rcicr-1.3.0/rcicr/man/generateCINoise.Rd | 23 +- rcicr-1.3.0/rcicr/man/generateGabor.Rd | 22 +- rcicr-1.3.0/rcicr/man/generateNoiseImage.Rd | 20 + rcicr-1.3.0/rcicr/man/generateNoisePattern.Rd | 20 + rcicr-1.3.0/rcicr/man/generateReferenceDistribution2IFC.Rd |only rcicr-1.3.0/rcicr/man/generateSinusoid.Rd | 15 - rcicr-1.3.0/rcicr/man/generateStimuli2IFC.Rd | 74 +++++-- rcicr-1.3.0/rcicr/man/plotZmap.Rd |only rcicr-1.3.0/rcicr/man/rcicr-package.Rd | 97 +++------ rcicr-1.3.0/rcicr/man/simulateNoiseIntensities.Rd | 10 rcicr-1.3.0/rcicr/tests |only rcicr-1.3.0/rcicr/vignettes |only 57 files changed, 819 insertions(+), 270 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Circumplex models, which organize constructs in a circle around two
underlying dimensions, are popular for studying interpersonal functioning,
mood/affect, and vocational preferences/environments. This package provides
tools for analyzing and visualizing circular data, including scoring
functions for relevant instruments and a generalization of the bootstrapped
structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results.
Author: Jeffrey Girard [aut, cre] ,
Johannes Zimmermann [aut] ,
Aidan Wright [aut]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 1.2.0 dated 2026-07-02 and 2.0.0 dated 2026-09-02
circumplex-1.2.0/circumplex/inst/doc/intermediate-ssm-analysis.R |only circumplex-1.2.0/circumplex/inst/doc/introduction-to-ssm-analysis.R |only circumplex-1.2.0/circumplex/tests/testthat/test-RcppExport.R.R |only circumplex-2.0.0/circumplex/DESCRIPTION | 21 circumplex-2.0.0/circumplex/MD5 | 372 ++- circumplex-2.0.0/circumplex/NAMESPACE | 43 circumplex-2.0.0/circumplex/NEWS.md | 1008 +++++++++ circumplex-2.0.0/circumplex/R/axes_certificate.R |only circumplex-2.0.0/circumplex/R/axes_corrected_se.R |only circumplex-2.0.0/circumplex/R/axes_fiml.R |only circumplex-2.0.0/circumplex/R/axes_reliability.R |only circumplex-2.0.0/circumplex/R/axes_reliability_oop.R |only circumplex-2.0.0/circumplex/R/axes_scaled_fit.R |only circumplex-2.0.0/circumplex/R/convenience_functions.R | 54 circumplex-2.0.0/circumplex/R/coord_circumplex.R |only circumplex-2.0.0/circumplex/R/cpm_fit.R |only circumplex-2.0.0/circumplex/R/cpm_oop.R |only circumplex-2.0.0/circumplex/R/example_data.R | 22 circumplex-2.0.0/circumplex/R/fit_structure.R |only circumplex-2.0.0/circumplex/R/fit_structure_oop.R |only circumplex-2.0.0/circumplex/R/geom_ssm.R |only circumplex-2.0.0/circumplex/R/instrument_data.R | 515 ++-- circumplex-2.0.0/circumplex/R/instrument_oop.R | 90 circumplex-2.0.0/circumplex/R/scale_circumplex.R |only circumplex-2.0.0/circumplex/R/ssm_analysis.R | 1048 ++++++++-- circumplex-2.0.0/circumplex/R/ssm_analyze_long.R |only circumplex-2.0.0/circumplex/R/ssm_bootstrap.R | 140 + circumplex-2.0.0/circumplex/R/ssm_ci_accuracy.R |only circumplex-2.0.0/circumplex/R/ssm_ci_oop.R |only circumplex-2.0.0/circumplex/R/ssm_draws.R |only circumplex-2.0.0/circumplex/R/ssm_montecarlo.R |only circumplex-2.0.0/circumplex/R/ssm_oop.R | 61 circumplex-2.0.0/circumplex/R/ssm_parameters_id.R |only circumplex-2.0.0/circumplex/R/ssm_plot.R | 419 ++- circumplex-2.0.0/circumplex/R/ssm_sem.R |only circumplex-2.0.0/circumplex/R/ssm_sem_syntax.R |only circumplex-2.0.0/circumplex/R/ssm_table.R | 9 circumplex-2.0.0/circumplex/R/ssm_trajectory.R |only circumplex-2.0.0/circumplex/R/tidying_functions.R | 178 + circumplex-2.0.0/circumplex/R/utils.R | 86 circumplex-2.0.0/circumplex/build/vignette.rds |binary circumplex-2.0.0/circumplex/data/cais.rda |binary circumplex-2.0.0/circumplex/data/csie.rda |binary circumplex-2.0.0/circumplex/data/csig.rda |binary circumplex-2.0.0/circumplex/data/csip.rda |binary circumplex-2.0.0/circumplex/data/csiv.rda |binary circumplex-2.0.0/circumplex/data/iei.rda |binary circumplex-2.0.0/circumplex/data/igicr.rda |binary circumplex-2.0.0/circumplex/data/iip32.rda |binary circumplex-2.0.0/circumplex/data/iip64.rda |binary circumplex-2.0.0/circumplex/data/iipsc.rda |binary circumplex-2.0.0/circumplex/data/iis32.rda |binary circumplex-2.0.0/circumplex/data/iis64.rda |binary circumplex-2.0.0/circumplex/data/iitc.rda |binary circumplex-2.0.0/circumplex/data/ipipipc.rda |binary circumplex-2.0.0/circumplex/data/isc.rda |binary circumplex-2.0.0/circumplex/data/simulated_items.rda |only circumplex-2.0.0/circumplex/inst/doc/advanced-visualization.Rmd |only circumplex-2.0.0/circumplex/inst/doc/advanced-visualization.html |only circumplex-2.0.0/circumplex/inst/doc/axes-reliability.Rmd |only circumplex-2.0.0/circumplex/inst/doc/axes-reliability.html |only circumplex-2.0.0/circumplex/inst/doc/bayesian-ssm-analysis.R |only circumplex-2.0.0/circumplex/inst/doc/bayesian-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/inst/doc/bayesian-ssm-analysis.html |only circumplex-2.0.0/circumplex/inst/doc/evaluating-circumplex-structure.Rmd |only circumplex-2.0.0/circumplex/inst/doc/evaluating-circumplex-structure.html |only circumplex-2.0.0/circumplex/inst/doc/growth-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/inst/doc/growth-ssm-analysis.html |only circumplex-2.0.0/circumplex/inst/doc/intermediate-ssm-analysis.Rmd | 727 ++++++ circumplex-2.0.0/circumplex/inst/doc/intermediate-ssm-analysis.html | 278 -- circumplex-2.0.0/circumplex/inst/doc/introduction-to-ssm-analysis.Rmd | 458 +--- circumplex-2.0.0/circumplex/inst/doc/introduction-to-ssm-analysis.html | 263 -- circumplex-2.0.0/circumplex/inst/doc/sem-based-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/inst/doc/sem-based-ssm-analysis.html |only circumplex-2.0.0/circumplex/inst/doc/using-instruments.R | 18 circumplex-2.0.0/circumplex/inst/doc/using-instruments.Rmd | 31 circumplex-2.0.0/circumplex/inst/doc/using-instruments.html | 181 + circumplex-2.0.0/circumplex/man/angle_unwrap.Rd |only circumplex-2.0.0/circumplex/man/axes_reliability.Rd |only circumplex-2.0.0/circumplex/man/cais.Rd | 16 circumplex-2.0.0/circumplex/man/circumplex-ggproto.Rd |only circumplex-2.0.0/circumplex/man/coord_circumplex.Rd |only circumplex-2.0.0/circumplex/man/cpm_fit.Rd |only circumplex-2.0.0/circumplex/man/cpm_simulate.Rd |only circumplex-2.0.0/circumplex/man/csie.Rd | 5 circumplex-2.0.0/circumplex/man/csiv.Rd | 7 circumplex-2.0.0/circumplex/man/figures/README-plot-1.png |binary circumplex-2.0.0/circumplex/man/fit_structure.Rd |only circumplex-2.0.0/circumplex/man/geom_ssm_arc.Rd |only circumplex-2.0.0/circumplex/man/geom_ssm_path.Rd |only circumplex-2.0.0/circumplex/man/geom_ssm_point.Rd |only circumplex-2.0.0/circumplex/man/ggcircumplex.Rd |only circumplex-2.0.0/circumplex/man/iei.Rd | 8 circumplex-2.0.0/circumplex/man/iip32.Rd | 23 circumplex-2.0.0/circumplex/man/iip64.Rd | 23 circumplex-2.0.0/circumplex/man/iipsc.Rd | 9 circumplex-2.0.0/circumplex/man/iis32.Rd | 9 circumplex-2.0.0/circumplex/man/iitc.Rd | 7 circumplex-2.0.0/circumplex/man/ipipipc.Rd | 12 circumplex-2.0.0/circumplex/man/norm_standardize.Rd | 44 circumplex-2.0.0/circumplex/man/norms.Rd | 30 circumplex-2.0.0/circumplex/man/plot.circumplex_ci_accuracy.Rd |only circumplex-2.0.0/circumplex/man/plot.circumplex_cpm.Rd |only circumplex-2.0.0/circumplex/man/plot.circumplex_structure.Rd |only circumplex-2.0.0/circumplex/man/print.circumplex_axes_reliability.Rd |only circumplex-2.0.0/circumplex/man/print.circumplex_cpm.Rd |only circumplex-2.0.0/circumplex/man/print.circumplex_structure.Rd |only circumplex-2.0.0/circumplex/man/scale_x_circumplex.Rd |only circumplex-2.0.0/circumplex/man/score.Rd | 5 circumplex-2.0.0/circumplex/man/simulated_items.Rd |only circumplex-2.0.0/circumplex/man/ssm_analyze.Rd | 235 +- circumplex-2.0.0/circumplex/man/ssm_analyze_long.Rd |only circumplex-2.0.0/circumplex/man/ssm_ci_accuracy.Rd |only circumplex-2.0.0/circumplex/man/ssm_draws.Rd |only circumplex-2.0.0/circumplex/man/ssm_parameters.Rd | 35 circumplex-2.0.0/circumplex/man/ssm_parameters_id.Rd |only circumplex-2.0.0/circumplex/man/ssm_plot_circle.Rd | 32 circumplex-2.0.0/circumplex/man/ssm_plot_contrast.Rd | 14 circumplex-2.0.0/circumplex/man/ssm_plot_curve.Rd | 14 circumplex-2.0.0/circumplex/man/ssm_plot_trajectory.Rd |only circumplex-2.0.0/circumplex/man/ssm_score.Rd | 37 circumplex-2.0.0/circumplex/man/ssm_sem.Rd |only circumplex-2.0.0/circumplex/man/ssm_sem_parameters.Rd |only circumplex-2.0.0/circumplex/man/ssm_sem_syntax.Rd |only circumplex-2.0.0/circumplex/man/ssm_table.Rd | 19 circumplex-2.0.0/circumplex/man/summary.circumplex_axes_reliability.Rd |only circumplex-2.0.0/circumplex/man/summary.circumplex_ci_accuracy.Rd |only circumplex-2.0.0/circumplex/man/summary.circumplex_cpm.Rd |only circumplex-2.0.0/circumplex/man/summary.circumplex_ssm_id.Rd |only circumplex-2.0.0/circumplex/man/summary.circumplex_structure.Rd |only circumplex-2.0.0/circumplex/man/theme_circumplex.Rd |only circumplex-2.0.0/circumplex/src/circular.cpp | 8 circumplex-2.0.0/circumplex/src/parameters.cpp | 9 circumplex-2.0.0/circumplex/tests/testthat/Rplots.pdf |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/ci_accuracy |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/ci_accuracy.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/coord_circumplex |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/cpm_api.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/cpm_plot |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/cpm_summary_markers.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/fit_structure_api |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/fit_structure_api.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/geom_ssm |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/geom_ssm_path |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/instrument_oop.md | 5 circumplex-2.0.0/circumplex/tests/testthat/_snaps/ssm_draws.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/ssm_occasions.md |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/ssm_plot/cross-zero-circle.svg | 81 circumplex-2.0.0/circumplex/tests/testthat/_snaps/ssm_plot/ggcircumplex-instrument-canvas.svg |only circumplex-2.0.0/circumplex/tests/testthat/_snaps/ssm_plot/ggcircumplex-octant-canvas.svg |only 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circumplex-2.0.0/circumplex/tests/testthat/helper-m68-cells.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-norms-audit-manifest.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-norms-audit-script.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-norms.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-ssm-legend.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-ssm-sem.R |only circumplex-2.0.0/circumplex/tests/testthat/helper-vignette.R |only circumplex-2.0.0/circumplex/tests/testthat/test-RcppExports.R |only circumplex-2.0.0/circumplex/tests/testthat/test-angle_unwrap.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-certificate-refusal.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-certificate.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-corrected-se.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-fiml.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-reliability.R |only circumplex-2.0.0/circumplex/tests/testthat/test-axes-scaled-fit.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ci_accuracy.R |only circumplex-2.0.0/circumplex/tests/testthat/test-coord_circumplex.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_angle_ci.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_api.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_boundary.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_boundary_vignette.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_fit.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_nesting.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_oracles.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_plot.R |only circumplex-2.0.0/circumplex/tests/testthat/test-cpm_summary_markers.R |only circumplex-2.0.0/circumplex/tests/testthat/test-fit_structure.R |only circumplex-2.0.0/circumplex/tests/testthat/test-fit_structure_api.R |only circumplex-2.0.0/circumplex/tests/testthat/test-geom_ssm.R |only circumplex-2.0.0/circumplex/tests/testthat/test-geom_ssm_path.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ggproto-classes.R |only circumplex-2.0.0/circumplex/tests/testthat/test-growth_invariants.R |only circumplex-2.0.0/circumplex/tests/testthat/test-instrument_oop.R | 35 circumplex-2.0.0/circumplex/tests/testthat/test-lavaan-cfi-helper.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-anchor-range.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-batch.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-compare.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-coverage.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-manifest.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-markers.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-roster.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-sample-key.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-audit-walk.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-disclosure.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-kind.R |only circumplex-2.0.0/circumplex/tests/testthat/test-norms-provenance.R |only circumplex-2.0.0/circumplex/tests/testthat/test-plot-cran-guards.R |only circumplex-2.0.0/circumplex/tests/testthat/test-pole-values.R |only circumplex-2.0.0/circumplex/tests/testthat/test-rd-latex-safe.R |only circumplex-2.0.0/circumplex/tests/testthat/test-scale_circumplex.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_analysis.R | 267 ++ circumplex-2.0.0/circumplex/tests/testthat/test-ssm_analyze_long.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_bootstrap.R | 183 + circumplex-2.0.0/circumplex/tests/testthat/test-ssm_draws.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_montecarlo.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_occasions.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_oop.R | 120 + circumplex-2.0.0/circumplex/tests/testthat/test-ssm_parameters_id.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_plot.R | 166 + circumplex-2.0.0/circumplex/tests/testthat/test-ssm_sem.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_sem_groups.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_sem_syntax.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_table.R | 1 circumplex-2.0.0/circumplex/tests/testthat/test-ssm_trajectory.R |only circumplex-2.0.0/circumplex/tests/testthat/test-ssm_trajectory_table.R |only circumplex-2.0.0/circumplex/tests/testthat/test-suff_stats.R |only circumplex-2.0.0/circumplex/tests/testthat/test-tidying_functions.R | 96 circumplex-2.0.0/circumplex/tests/testthat/test-utils.R | 84 circumplex-2.0.0/circumplex/vignettes/advanced-visualization.Rmd |only circumplex-2.0.0/circumplex/vignettes/axes-reliability.Rmd |only circumplex-2.0.0/circumplex/vignettes/bayesian-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/vignettes/bayesian_ssm_draws.rds |only circumplex-2.0.0/circumplex/vignettes/evaluating-circumplex-structure.Rmd |only circumplex-2.0.0/circumplex/vignettes/figures |only circumplex-2.0.0/circumplex/vignettes/growth-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/vignettes/intermediate-ssm-analysis.Rmd | 727 ++++++ circumplex-2.0.0/circumplex/vignettes/introduction-to-ssm-analysis.Rmd | 458 +--- circumplex-2.0.0/circumplex/vignettes/sem-based-ssm-analysis.Rmd |only circumplex-2.0.0/circumplex/vignettes/using-instruments.Rmd | 31 241 files changed, 7072 insertions(+), 2379 deletions(-)
Title: Tools for Processing and Analyzing Files from the Hydrological
Catchment Model HYPE
Description: Work with model files (setup, input, output) from
the hydrological catchment model HYPE: Streamlined file import and export, standard
evaluation plot routines, diverse post-processing and aggregation routines
for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955>
and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
Author: Rene Capell [aut, cre] ,
Conrad Brendel [aut] ,
Jafet Andersson [ctb],
David Gustafsson [ctb],
Jude Musuuza [ctb],
Jude Lubega [ctb]
Maintainer: Rene Capell <hypetools.rene@smhi.se>
Diff between HYPEtools versions 1.6.7 dated 2026-04-08 and 1.6.8 dated 2026-09-02
DESCRIPTION | 8 MD5 | 77 ++-- NAMESPACE | 16 NEWS.md | 16 R/function_CalculateRiverDistance.R |only R/function_LakeDataOutlets.R |only R/function_MapRegionalSources.R | 5 R/function_OutletNearObs.R | 232 +++++++------ R/function_PlotMapOutput.R | 130 +++++-- R/function_PlotMapPoints.R | 13 R/function_PlotParValues.R | 97 +++++ R/function_PlotPerformanceByAttribute.R | 192 +++++------ R/function_PlotSubbasinRouting.R | 48 ++ R/function_SimToPar.R | 7 R/functioncollection_import.R | 16 R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/demo_model/ClassData.txt | 4 inst/demo_model/GeoData.txt | 50 +- inst/demo_model/LakeData.txt |only inst/demo_model/PointSourceData.txt | 24 - inst/demo_model/par.txt | 88 ++++- inst/doc/basin_network.html | 2 inst/doc/import_files.html | 173 ++++++--- inst/doc/modify_par.html | 540 +++++++++++++++++++------------ inst/doc/plot_map_statistics.html | 8 man/CalculateRiverDistance.Rd |only man/CompareFiles.Rd | 4 man/HYPEtools-package.Rd | 79 ++-- man/HypeDataImport.Rd | 12 man/LakeDataOutlets.Rd |only man/MapRegionalSources.Rd | 16 man/OutletNearObs.Rd | 28 + man/PlotMapOutput.Rd | 14 man/PlotMapPoints.Rd | 26 - man/PlotParValues.Rd | 9 man/PlotPerformanceByAttribute.Rd | 30 - man/PlotSubbasinRouting.Rd | 53 ++- man/WriteHarmonizedData.Rd | 110 +++--- man/WriteHarmonizedSpatialDescription.Rd | 122 +++---- man/distinctColorPalette.Rd | 56 +-- 42 files changed, 1416 insertions(+), 889 deletions(-)
Title: Graph Signal Processing
Description: Provides the standard operations for signal processing on graphs:
graph Fourier transform, spectral graph wavelet transform,
visualization tools. It also implements a data driven method
for graph signal denoising/regression, for details see
De Loynes, Navarro, Olivier (2021) <doi:10.1016/j.cam.2020.113319>.
The package also provides an interface to the SuiteSparse Matrix Collection,
<https://sparse.tamu.edu/>, a large and widely used set of sparse matrix
benchmarks collected from a wide range of applications.
Author: Basile de Loynes [aut] ,
Fabien Navarro [aut, cre] ,
Baptiste Olivier [aut]
Maintainer: Fabien Navarro <fabien.navarro@math.cnrs.fr>
Diff between gasper versions 1.1.6 dated 2024-02-28 and 1.1.7 dated 2026-09-02
DESCRIPTION | 17 ++- MD5 | 26 +++--- NEWS.md | 173 ++++++++++++++++++++-------------------- R/GVN.R | 7 - R/zetav.R | 2 build/vignette.rds |binary inst/doc/gasper_vignette.R | 88 ++++++++++---------- inst/doc/gasper_vignette.pdf |binary inst/doc/gasper_vignette.rmd | 2 man/GVN.Rd | 5 - vignettes/gasper_vignette.rmd | 2 vignettes/gasper_vignette_files |only 12 files changed, 165 insertions(+), 157 deletions(-)
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 1.1.1 dated 2026-07-13 and 1.2.0 dated 2026-09-02
DESCRIPTION | 6 - MD5 | 77 ++++++++----- NAMESPACE | 13 ++ NEWS.md | 14 ++ R/0_utils.R | 17 ++- R/aaa.R | 6 - R/augment.R |only R/autoint-predict.R | 3 R/checks.R | 42 +++++++ R/chronos2-predict.R | 43 +++++-- R/coef.R | 14 -- R/linear_reg-predict.R | 3 R/logistic_reg-predict.R | 3 R/mlp-predict.R | 21 ++- R/multinomial_reg-predict.R | 3 R/resnet-predict.R | 3 R/rln-predict.R | 6 - R/saint-predict.R | 3 R/tabicl-ensemble.R | 115 ++++++++++++++++++-- R/tabicl-fit.R | 6 - R/tabicl-predict.R | 154 +++++++++++++++++++++++---- inst/WORDLIST | 6 - man/brulee-augment.Rd |only man/brulee_tab_icl.Rd | 6 - man/predict.brulee_tab_icl.Rd | 115 +++++++++++++++++--- man/reexports.Rd | 3 tests/testthat/_snaps/0_utils.md |only tests/testthat/_snaps/augment.md |only tests/testthat/_snaps/check-type.md |only tests/testthat/_snaps/chronos2-predict.md | 35 ++++++ tests/testthat/_snaps/mlp-regression.md | 8 + tests/testthat/_snaps/predict-epoch.md |only tests/testthat/_snaps/rln-regression.md |only tests/testthat/_snaps/tabicl-ensemble.md |only tests/testthat/_snaps/tabicl-predict.md |only tests/testthat/helper-tabicl.R | 38 ++++++ tests/testthat/test-0_utils.R | 41 +++++++ tests/testthat/test-augment.R |only tests/testthat/test-autoint.R | 2 tests/testthat/test-check-type.R |only tests/testthat/test-chronos2-predict.R | 74 +++++++++++++ tests/testthat/test-mlp-regression.R | 5 tests/testthat/test-predict-epoch.R |only tests/testthat/test-rln-regression.R | 7 - tests/testthat/test-tabicl-ensemble.R | 168 ++++++++++++++++++++++++++++++ tests/testthat/test-tabicl-predict.R |only 46 files changed, 917 insertions(+), 143 deletions(-)
Title: Plot a Correlogram
Description: Calculates correlation of variables and displays the results
graphically. Included panel functions can display points, shading,
ellipses, and correlation values with confidence intervals. See
Friendly (2002) <doi:10.1198/000313002533>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between corrgram versions 1.15 dated 2026-05-18 and 1.16 dated 2026-09-02
corrgram-1.15/corrgram/data/auto.R |only corrgram-1.15/corrgram/data/baseball.R |only corrgram-1.15/corrgram/data/vote.r |only corrgram-1.16/corrgram/DESCRIPTION | 10 +-- corrgram-1.16/corrgram/MD5 | 38 ++++++------- corrgram-1.16/corrgram/NAMESPACE | 20 ++++--- corrgram-1.16/corrgram/NEWS.md | 7 ++ corrgram-1.16/corrgram/R/corrgram_base.R | 2 corrgram-1.16/corrgram/R/corrgram_grid.R | 2 corrgram-1.16/corrgram/R/data.R | 49 +++++++++--------- corrgram-1.16/corrgram/build/partial.rdb |binary corrgram-1.16/corrgram/build/vignette.rds |binary corrgram-1.16/corrgram/data/auto.rda |only corrgram-1.16/corrgram/data/baseball.rda |only corrgram-1.16/corrgram/data/vote.rda |only corrgram-1.16/corrgram/inst/doc/corrgram_base.html | 6 +- corrgram-1.16/corrgram/inst/doc/corrgram_cov2cor.html | 4 - corrgram-1.16/corrgram/inst/doc/corrgram_lattice.html | 4 - corrgram-1.16/corrgram/man/auto.Rd | 28 +++++----- corrgram-1.16/corrgram/man/baseball.Rd | 5 + corrgram-1.16/corrgram/man/vote.Rd | 7 +- corrgram-1.16/corrgram/tests/testthat/test_bounds.R | 4 - corrgram-1.16/corrgram/tests/testthat/test_order.R | 8 +- 23 files changed, 102 insertions(+), 92 deletions(-)
Title: Large Language Model Evaluation
Description: A port of 'Inspect', a widely adopted 'Python' framework for
large language model evaluation. Specifically aimed at 'ellmer' users
who want to measure the effectiveness of their large language model-based
products, the package supports prompt engineering, tool usage,
multi-turn dialog, and model graded evaluations.
Author: Simon Couch [aut, cre] ,
Max Kuhn [ctb],
Hadley Wickham [ctb] ,
Mine Cetinkaya-Rundel [ctb] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between vitals versions 0.3.0 dated 2026-05-15 and 0.4.0 dated 2026-09-02
DESCRIPTION | 16 MD5 | 59 +- NAMESPACE | 3 NEWS.md | 56 ++ R/bundle.R | 2 R/log-dir.R | 42 + R/log-read.R |only R/scorer-detect.R | 8 R/solver-agent.R |only R/task.R | 23 - R/translate-events.R | 705 +++++++------------------------ R/translate-messages.R | 64 +- R/translate-utils.R | 202 +++++++- R/translate.R | 74 +++ R/view.R | 13 inst/README.md | 11 inst/dist/assets/index.js | 16 inst/python |only inst/test/inspect/logs |only man/Task.Rd | 451 ++++++++++--------- man/agent_solvers.Rd |only man/generate.Rd | 2 man/generate_structured.Rd | 10 man/scorer_model.Rd | 2 man/vitals-package.Rd | 5 man/vitals_log_read.Rd |only tests/testthat/_snaps/log-read.md |only tests/testthat/_snaps/solver-agent.md |only tests/testthat/helper-.R | 83 +++ tests/testthat/test-log-read.R |only tests/testthat/test-scorer-detect.R | 1 tests/testthat/test-solver-agent.R |only tests/testthat/test-translate-messages.R | 9 tests/testthat/test-translate-utils.R | 31 + tests/testthat/test-translate.R | 180 +++++++ 35 files changed, 1196 insertions(+), 872 deletions(-)
Title: Model Based Clustering for Spherical Data Using Elliptically
Symmetric Distributions
Description: Model based clustering with spherical data using mixtures of elliptically symmetric distributions, namely mixtures of spherical elliptically symmetric projected Cauchy (SESPC) or mixtures of elliptically symmetric angular Gaussian (ESAG) distributions. The relevant paper is: Perdikis T., Alharbi N. and Tsagris M. (2026). <doi:10.48550/arXiv.2605.27496>.
Author: Michail Tsagris [aut, cre],
Theodoros Perdikis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between sphereclust versions 1.0 dated 2026-06-01 and 1.1 dated 2026-09-02
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++++------- R/bic.mixkent.R |only R/dmixkent.R |only R/mixkent.contour.R |only R/mixkent.mle.R |only R/rmixkent.R |only man/bic.mixsespc.Rd | 9 +++++++-- man/dmixsespc.Rd | 9 +++++++++ man/mixsespc.contour.Rd | 10 ++++++++++ man/mixsespc.mle.Rd | 14 ++++++++++++-- man/rmixsespc.Rd | 12 ++++++++++-- man/sphereclust-package.Rd | 4 ++-- 13 files changed, 66 insertions(+), 19 deletions(-)
Title: A 'Shiny' Application for Inspecting Structural Topic Models
Description: This app enables interactive validation, interpretation and visualization of structural topic models from the 'stm' package by Roberts and others (2014) . It also includes helper functions for model diagnostics and extracting data from effect estimates.
Author: Carsten Schwemmer [aut, cre] ,
Jonne Guyt [ctb]
Maintainer: Carsten Schwemmer <c.schwem2er@gmail.com>
This is a re-admission after prior archival of version 0.4.3 dated 2024-06-21
Diff between stminsights versions 0.4.3 dated 2024-06-21 and 0.4.4 dated 2026-09-02
DESCRIPTION | 20 ++++++------ MD5 | 21 ++++++------ NAMESPACE | 2 - NEWS.md | 12 ++++++- R/stm_diag.R | 2 - R/stm_network.R | 8 ++++ README.md | 8 ++-- build/vignette.rds |binary inst/doc/intro.R | 68 +++++++++++++++++++++--------------------- inst/doc/intro.html | 5 +-- man/get_network.Rd | 9 ++++- vignettes/fileb405752e81.html |only 12 files changed, 91 insertions(+), 64 deletions(-)
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Qian Xu [aut, ctb],
Yongjian Yang [aut, ctb],
Yanan Tian [aut, ctb],
Robert Chapkin [aut, ctb],
Jianhua Huang [aut, ctb],
James J. Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldKnk versions 1.0.3 dated 2026-01-25 and 1.1 dated 2026-09-02
scTenifoldKnk-1.0.3/scTenifoldKnk/README.md |only scTenifoldKnk-1.1/scTenifoldKnk/DESCRIPTION | 16 - scTenifoldKnk-1.1/scTenifoldKnk/MD5 | 19 - scTenifoldKnk-1.1/scTenifoldKnk/NAMESPACE | 18 - scTenifoldKnk-1.1/scTenifoldKnk/R/dRegulation.R | 175 ++++++++++-- scTenifoldKnk-1.1/scTenifoldKnk/R/plotKO.R | 55 ++- scTenifoldKnk-1.1/scTenifoldKnk/R/scQC.R | 128 +++++++-- scTenifoldKnk-1.1/scTenifoldKnk/R/scTenifoldKnk.R | 262 ++++++++++++++----- scTenifoldKnk-1.1/scTenifoldKnk/man/dRegulation.Rd |only scTenifoldKnk-1.1/scTenifoldKnk/man/plotKO.Rd | 51 ++- scTenifoldKnk-1.1/scTenifoldKnk/man/scQC.Rd |only scTenifoldKnk-1.1/scTenifoldKnk/man/scTenifoldKnk.Rd | 104 ++++++- 12 files changed, 626 insertions(+), 202 deletions(-)
Title: Examples using 'RcppClassic' to Interface R and C++
Description: The 'Rcpp' package contains a C++ library that facilitates the
integration of R and C++ in various ways via a rich API. This API was
preceded by an earlier version which has been deprecated since 2010 (but is
still supported to provide backwards compatibility in the package
'RcppClassic'). This package 'RcppClassicExamples' provides usage examples for
the older, deprecated API. There is also a corresponding package
'RcppExamples' with examples for the newer, current API which we
strongly recommend as the basis for all new development.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Dominick Samperi [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppClassicExamples versions 0.1.4 dated 2026-03-16 and 0.1.5 dated 2026-09-02
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/NEWS.Rd | 6 ++++++ man/RcppDate.Rd | 17 +++++++++++++---- man/RcppParams.Rd | 3 +++ man/RcppVector.Rd | 15 +++++++++++++++ 7 files changed, 55 insertions(+), 14 deletions(-)
More information about RcppClassicExamples at CRAN
Permanent link
Title: Location and Scale Invariant Power Transformations
Description: Location- and scale-invariant Box-Cox and Yeo-Johnson power transformations
allow for transforming variables with distributions distant from 0 to
normality. Transformers are implemented as S4 objects. These allow for
transforming new instances to normality after optimising fitting parameters
on other data. A test for central normality allows for rejecting
transformations that fail to produce a suitably normal distribution,
independent of sample number.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alex.zwanenburg@outlook.com>
Diff between power.transform versions 1.0.4 dated 2026-03-02 and 1.0.5 dated 2026-09-02
DESCRIPTION | 12 MD5 | 48 - NEWS.md | 92 + R/AccessorsMutatorsScale.R | 244 ++--- R/AccessorsTransformationMethod.R | 52 - R/Checks.R | 432 ++++----- R/FindParameters.R | 667 +++++++------- R/GoodnessOfFit.R | 1045 +++++++++++----------- R/ParameterEstimatorEDF.R | 582 ++++++------ R/ParameterEstimatorMLE.R | 226 ++-- R/PlotQQPlot.R | 299 +++--- R/PlotResidualPlot.R | 379 ++++---- R/TransformationBoxCox.R | 1466 +++++++++++++++---------------- R/TransformationObjects.R | 1026 ++++++++++----------- R/TransformationSkeleton.R | 96 +- R/TransformationYeoJohnson.R | 1416 ++++++++++++++--------------- R/WeightingFunctionParameters.R | 540 +++++------ R/WeightingFunctions.R | 804 ++++++++--------- R/power.transform-package.R | 34 inst/CITATION | 22 man/power.transform.Rd | 3 man/power_transform.Rd | 2 tests/testthat.R | 19 tests/testthat/test-accessors-mutators.R | 300 +++--- tests/testthat/test-estimators.R | 442 ++++----- 25 files changed, 5134 insertions(+), 5114 deletions(-)
More information about power.transform at CRAN
Permanent link
Title: LUCID with Multiple Omics Data
Description: Implements Latent Unknown Clusters By Integrating Multi-omics Data
(LUCID; Peng (2019) <doi:10.1093/bioinformatics/btz667>) for integrative
clustering with exposures, multi-omics data, and health outcomes.
Supports three integration strategies: early, parallel, and serial.
Provides model fitting and tuning, lasso-type regularization for exposure
and omics feature selection, handling of missing data, including both
sporadic and complete-case patterns, prediction, and g-computation for
estimating causal effects of exposures, bootstrap inference for
uncertainty estimation, and S3 summary and plot methods. For the
multi-omics integration framework, see Jia (2024)
<https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf>.
For the missing-data imputation mechanism, see Jia (2024)
<doi:10.1093/bioadv/vbae123>.
Author: Qiran Jia [aut, cre] ,
Yinqi Zhao [aut] ,
David Conti [ths] ,
Jesse Goodrich [ctb]
Maintainer: Qiran Jia <qiranjia@usc.edu>
Diff between LUCIDus versions 3.2.0 dated 2026-09-01 and 3.2.1 dated 2026-09-02
DESCRIPTION | 6 MD5 | 41 NEWS.md | 42 R/boot_lucid.R | 209 ++ R/estimate_lucid.R | 18 R/outcome_utils.R | 69 R/summary.R | 106 - inst/doc/lucid_3models_binary_outcome.R | 8 inst/doc/lucid_3models_binary_outcome.Rmd | 16 inst/doc/lucid_3models_binary_outcome.html | 930 +++++----- inst/doc/lucid_3models_normal_outcome.R | 8 inst/doc/lucid_3models_normal_outcome.Rmd | 25 inst/doc/lucid_3models_normal_outcome.html | 909 +++++---- inst/doc/lucid_early_sankey_top_omics_tutorial.html | 8 inst/doc/lucidus_full_functionality_guide.html | 225 +- inst/doc/serial_6stage_parallel_monotone_missing_tutorial.html | 214 +- tests/testthat/test-boot-lucid-early.R | 10 tests/testthat/test-boot-lucid-parallel.R | 6 tests/testthat/test-correctness-boot-align.R |only tests/testthat/test-workhorse-p0-p1-regressions.R | 9 vignettes/lucid_3models_binary_outcome.Rmd | 16 vignettes/lucid_3models_normal_outcome.Rmd | 25 22 files changed, 1829 insertions(+), 1071 deletions(-)
Title: Fast, Accurate and Automatic Tuning Parameter Selection for
Lasso
Description: Fits Lasso paths for high-dimensional regression using coordinate descent with automatic, data-driven tuning of the regularization parameter. The implementation is 10 to 200 times faster than the standard 'glmnet' implementation of Lasso tuned via Cross Validation and over 100 times faster than scaled Lasso. It also provides a reliable estimate of the regression noise level and a new diagnostic for sparsity.
For details of the method, see Sadhukhan, Wilms, Smeekes and Basu (2025)
"Autotune: fast, accurate, and automatic tuning parameter selection for Lasso"
<doi:10.48550/arXiv.2512.11139>.
Author: Tathagata Sadhukhan [aut, cre],
Ines Wilms [aut],
Stephan Smeekes [aut],
Sumanta Basu [aut]
Maintainer: Tathagata Sadhukhan <ts767@cornell.edu>
Diff between autotune versions 0.1.0 dated 2026-08-21 and 0.1.1 dated 2026-09-02
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/autotune-package.R | 10 ++++------ README.md | 2 +- inst/doc/autotune-lasso-vignette.html | 9 +++++---- man/autotune-package.Rd | 10 ++++------ 6 files changed, 25 insertions(+), 28 deletions(-)
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel de Siqueira Gesteira [aut],
Jeekin Lau [aut],
Olivia Angelin-Bonnet [aut],
Susan Thomson [ctb],
Guilherme da Silva Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Moll [...truncated...]
Maintainer: Cristiane Taniguti <ctaniguti@ufl.edu>
Diff between viewpoly versions 1.0.2 dated 2026-07-10 and 1.0.3 dated 2026-09-02
viewpoly-1.0.2/viewpoly/tests/testthat/_snaps |only viewpoly-1.0.3/viewpoly/DESCRIPTION | 11 +-- viewpoly-1.0.3/viewpoly/MD5 | 35 ++++------ viewpoly-1.0.3/viewpoly/NAMESPACE | 1 viewpoly-1.0.3/viewpoly/NEWS.md | 7 ++ viewpoly-1.0.3/viewpoly/R/mod_genes_view.R | 8 +- viewpoly-1.0.3/viewpoly/R/mod_help.R | 32 ++++----- viewpoly-1.0.3/viewpoly/R/mod_hidecan.R | 4 - viewpoly-1.0.3/viewpoly/R/mod_home.R | 9 +- viewpoly-1.0.3/viewpoly/R/mod_map_view.R | 10 +- viewpoly-1.0.3/viewpoly/R/mod_qtl_view.R | 4 - viewpoly-1.0.3/viewpoly/R/mod_upload.R | 4 - viewpoly-1.0.3/viewpoly/R/utils_helpers.R | 5 + viewpoly-1.0.3/viewpoly/inst/app/www/custom.js | 11 +++ viewpoly-1.0.3/viewpoly/inst/help_files/Inputs_par.Rmd | 5 + viewpoly-1.0.3/viewpoly/tests/testthat/test-golem-recommended.R | 3 16 files changed, 86 insertions(+), 63 deletions(-)
Title: Functions and Utilities for Tidy Time Series Forecasting and
Time Series Cross-Validation
Description: Functions and tools for tidy time series analysis and
forecasting as well as time series cross-validation. This is mainly a set
of wrapper and helper functions as well as some extensions for the packages
'tsibble', 'fable', and 'fabletools'.
Author: Alexander Haeusser [aut, cre, cph]
Maintainer: Alexander Haeusser <alexander-haeusser@gmx.de>
Diff between tscv versions 1.0.0 dated 2026-05-13 and 1.0.1 dated 2026-09-02
DESCRIPTION | 8 MD5 | 59 +- NAMESPACE | 9 NEWS.md | 7 R/analyze_data.R | 56 ++ R/data.R | 4 R/methods-base.R |only R/methods-fable.R | 345 ++++++++++++ R/tscv-package.R | 2 README.md | 49 + inst/doc/vignette_01_monthly_expanding.Rmd | 10 inst/doc/vignette_01_monthly_expanding.html | 681 ++++++++++++------------- inst/doc/vignette_02_hourly_fixed.R | 1 inst/doc/vignette_02_hourly_fixed.Rmd | 9 inst/doc/vignette_02_hourly_fixed.html | 616 +++++++++++----------- inst/doc/vignette_03_data_visualization.R | 1 inst/doc/vignette_03_data_visualization.Rmd | 11 inst/doc/vignette_03_data_visualization.html | 342 ++++++------ man/NAIVE2.Rd |only man/elec_load.Rd | 2 man/elec_price.Rd | 2 man/figures/README-expanding-window-plot-1.svg | 58 +- man/figures/README-fixed-window-plot-1.svg | 114 ++-- man/fitted.NAIVE2.Rd |only man/forecast.NAIVE2.Rd |only man/forecast_naive2.Rd |only man/model_sum.NAIVE2.Rd |only man/residuals.NAIVE2.Rd |only man/test_seasonality.Rd |only tests/testthat/test-analyze_data.R | 29 + tests/testthat/test-methods-base.R |only tests/testthat/test-methods-fable.R | 129 ++++ vignettes/vignette_01_monthly_expanding.Rmd | 10 vignettes/vignette_02_hourly_fixed.Rmd | 9 vignettes/vignette_03_data_visualization.Rmd | 11 35 files changed, 1618 insertions(+), 956 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.6.1 dated 2026-07-25 and 1.7.0 dated 2026-09-02
DESCRIPTION | 14 ++++---- MD5 | 44 ++++++++++++------------- NAMESPACE | 22 ++++++++---- NEWS.md | 6 +++ R/CallbackAsyncTuning.R | 17 +++++++-- R/CallbackBatchTuning.R | 16 ++++++--- R/ObjectiveTuningAsync.R | 8 ++-- R/ObjectiveTuningBatch.R | 8 ++-- R/TunerBatchCmaes.R | 19 ++-------- R/TuningInstanceAsyncMulticrit.R | 2 - R/TuningInstanceAsyncSingleCrit.R | 2 - R/TuningInstanceBatchMulticrit.R | 2 - R/TuningInstanceBatchSingleCrit.R | 2 - R/helper.R | 12 ++++++ man/assert_async_tuning_callback.Rd | 7 ++-- man/assert_batch_tuning_callback.Rd | 7 ++-- man/callback_async_tuning.Rd | 8 ++++ man/callback_batch_tuning.Rd | 7 ++++ man/mlr_tuners_cmaes.Rd | 52 ++++++++++++++++++++---------- tests/testthat/test_CallbackAsyncTuning.R | 31 ++++++++++++++++- tests/testthat/test_CallbackBatchTuning.R | 20 ++++++++++- tests/testthat/test_TunerBatchCmaes.R | 27 ++++++++++++++- tests/testthat/test_mlr_tuners.R | 4 +- 23 files changed, 236 insertions(+), 101 deletions(-)
Title: Immunity: Geographic and Age-Based Projection
Description: Fits Bayesian hierarchical models of vaccine
coverage by location, birth cohort, and age. Observations
of vaccination status (which may span cohorts, ages, and doses) are
used to fit a latent survival-style process model that decomposes
coverage into a lifetime propensity to vaccinate and a
time-varying force of vaccination. Hierarchical spatial structure
(e.g., state, county, school) supports partial pooling via random
effects. Models are implemented in 'Stan' and fit via 'rstan'.
Provides helpers to validate user-supplied input data, and to predict
coverage from fitted models.
Author: Carl Pearson [aut, cre] ,
Claire Perrin Smith [aut] ,
Kelly Zhen [ctb],
Weston Voglesonger [ctb],
Joshua Chen [ctb],
Minjae Kung [ctb]
Maintainer: Carl Pearson <carl.ab.pearson@gmail.com>
Diff between imuGAP versions 0.1.0 dated 2026-06-22 and 0.2.0 dated 2026-09-02
imuGAP-0.1.0/imuGAP/inst/stan/data/shared_stateonly.stan |only imuGAP-0.1.0/imuGAP/inst/stan/generated_quantities |only imuGAP-0.1.0/imuGAP/inst/stan/include |only imuGAP-0.1.0/imuGAP/inst/stan/model/cnty_sch.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/cnty_sch_calc.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/cnty_sch_linear.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/cnty_sch_linear_calc.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/constant_phi.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/p_obs_calc.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/shared.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/stateonly_calc.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/stateonly_shared.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/static_lambda_calc.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model/v6_shared.stan |only imuGAP-0.1.0/imuGAP/inst/stan/model_scripts |only imuGAP-0.1.0/imuGAP/inst/stan/parameters/cnty_sch.stan |only imuGAP-0.1.0/imuGAP/inst/stan/parameters/cnty_sch_linear.stan |only imuGAP-0.1.0/imuGAP/inst/stan/parameters/constant_phi.stan |only imuGAP-0.1.0/imuGAP/inst/stan/transformed_data/cnty_schl.stan |only imuGAP-0.1.0/imuGAP/inst/stan/transformed_data/fixed_logit_phi.stan |only imuGAP-0.1.0/imuGAP/inst/stan/transformed_data/fixed_raw_lambda.stan |only imuGAP-0.1.0/imuGAP/inst/stan/transformed_data/stateonly.stan |only imuGAP-0.1.0/imuGAP/inst/stan/transformed_parameters |only imuGAP-0.1.0/imuGAP/man/stan_options.Rd |only imuGAP-0.1.0/imuGAP/tests/testthat/test-stan-options.R |only imuGAP-0.2.0/imuGAP/DESCRIPTION | 23 imuGAP-0.2.0/imuGAP/MD5 | 182 - imuGAP-0.2.0/imuGAP/NAMESPACE | 44 imuGAP-0.2.0/imuGAP/NEWS.md | 30 imuGAP-0.2.0/imuGAP/R/canonicalize.R | 419 ++- imuGAP-0.2.0/imuGAP/R/checkers.R | 279 +- imuGAP-0.2.0/imuGAP/R/flexstanr.R |only imuGAP-0.2.0/imuGAP/R/globals.R | 25 imuGAP-0.2.0/imuGAP/R/helpers.R |only imuGAP-0.2.0/imuGAP/R/imuGAP-package.R | 96 imuGAP-0.2.0/imuGAP/R/imuGAP.R | 520 --- imuGAP-0.2.0/imuGAP/R/methods.R | 185 - imuGAP-0.2.0/imuGAP/R/options.R | 99 imuGAP-0.2.0/imuGAP/R/stanmodels.R | 3 imuGAP-0.2.0/imuGAP/README.md | 10 imuGAP-0.2.0/imuGAP/build/vignette.rds |binary imuGAP-0.2.0/imuGAP/data/fit_sim.rda |binary imuGAP-0.2.0/imuGAP/data/fit_sim_1layer.rda |only imuGAP-0.2.0/imuGAP/data/fit_sim_2layer.rda |only imuGAP-0.2.0/imuGAP/data/latent_params_sim.rda |binary imuGAP-0.2.0/imuGAP/data/locations_sim.rda |binary imuGAP-0.2.0/imuGAP/data/observations_sim.rda |binary imuGAP-0.2.0/imuGAP/data/populations_sim.rda |binary imuGAP-0.2.0/imuGAP/data/predict_sim.rda |binary imuGAP-0.2.0/imuGAP/data/predict_sim_1layer.rda |only imuGAP-0.2.0/imuGAP/data/predict_sim_2layer.rda |only imuGAP-0.2.0/imuGAP/data/target_sim.rda |binary imuGAP-0.2.0/imuGAP/data/target_sim_1layer.rda |only imuGAP-0.2.0/imuGAP/data/target_sim_2layer.rda |only imuGAP-0.2.0/imuGAP/inst/WORDLIST | 28 imuGAP-0.2.0/imuGAP/inst/doc/imuGAP.R | 614 ++++ imuGAP-0.2.0/imuGAP/inst/doc/imuGAP.Rmd | 655 ++++ imuGAP-0.2.0/imuGAP/inst/doc/imuGAP.html | 1023 ++++++- imuGAP-0.2.0/imuGAP/inst/doc/user_specified_layers.R |only imuGAP-0.2.0/imuGAP/inst/doc/user_specified_layers.Rmd |only imuGAP-0.2.0/imuGAP/inst/doc/user_specified_layers.html |only imuGAP-0.2.0/imuGAP/inst/stan/data/censoring.stan | 8 imuGAP-0.2.0/imuGAP/inst/stan/data/shared.stan | 32 imuGAP-0.2.0/imuGAP/inst/stan/data/shared_single.stan |only imuGAP-0.2.0/imuGAP/inst/stan/impute_school_coverage_process_v6.stan | 100 imuGAP-0.2.0/imuGAP/inst/stan/impute_school_coverage_process_v6_single_layer.stan |only imuGAP-0.2.0/imuGAP/inst/stan/model/censored.stan | 12 imuGAP-0.2.0/imuGAP/inst/stan/model/hierarchical_phi.stan |only imuGAP-0.2.0/imuGAP/inst/stan/model/layer_offsets.stan |only imuGAP-0.2.0/imuGAP/inst/stan/model/single_phi.stan |only imuGAP-0.2.0/imuGAP/inst/stan/parameters/layer_offsets.stan |only imuGAP-0.2.0/imuGAP/inst/stan/transformed_data/censoring.stan | 2 imuGAP-0.2.0/imuGAP/inst/stan/transformed_data/layer_indices.stan |only imuGAP-0.2.0/imuGAP/inst/stan/transformed_data/single_indices.stan |only imuGAP-0.2.0/imuGAP/man/assemble_layer_data.Rd |only imuGAP-0.2.0/imuGAP/man/canonicalize.Rd | 20 imuGAP-0.2.0/imuGAP/man/canonicalize_target.Rd |only imuGAP-0.2.0/imuGAP/man/create_observation_populations.Rd |only imuGAP-0.2.0/imuGAP/man/create_target.Rd | 136 - imuGAP-0.2.0/imuGAP/man/fit_sim.Rd | 11 imuGAP-0.2.0/imuGAP/man/fit_sim_1layer.Rd |only imuGAP-0.2.0/imuGAP/man/fit_sim_2layer.Rd |only imuGAP-0.2.0/imuGAP/man/imugap_options.Rd | 15 imuGAP-0.2.0/imuGAP/man/is_canonical.Rd |only imuGAP-0.2.0/imuGAP/man/latent_params_sim.Rd | 7 imuGAP-0.2.0/imuGAP/man/locations_sim.Rd | 3 imuGAP-0.2.0/imuGAP/man/observations_sim.Rd | 3 imuGAP-0.2.0/imuGAP/man/populations_sim.Rd | 3 imuGAP-0.2.0/imuGAP/man/predict.imugap_fit.Rd | 3 imuGAP-0.2.0/imuGAP/man/predict_sim.Rd | 3 imuGAP-0.2.0/imuGAP/man/predict_sim_1layer.Rd |only imuGAP-0.2.0/imuGAP/man/predict_sim_2layer.Rd |only imuGAP-0.2.0/imuGAP/man/reexports.Rd |only imuGAP-0.2.0/imuGAP/man/sampling.Rd | 40 imuGAP-0.2.0/imuGAP/man/stop_fmt_if.Rd |only imuGAP-0.2.0/imuGAP/man/target_sim.Rd | 8 imuGAP-0.2.0/imuGAP/man/target_sim_1layer.Rd |only imuGAP-0.2.0/imuGAP/man/target_sim_2layer.Rd |only imuGAP-0.2.0/imuGAP/man/warn_fmt_if.Rd |only imuGAP-0.2.0/imuGAP/src/RcppExports.cpp | 2 imuGAP-0.2.0/imuGAP/src/stanExports_impute_school_coverage_process_v6.h | 1359 +++++----- imuGAP-0.2.0/imuGAP/src/stanExports_impute_school_coverage_process_v6_single_layer.cc |only imuGAP-0.2.0/imuGAP/src/stanExports_impute_school_coverage_process_v6_single_layer.h |only imuGAP-0.2.0/imuGAP/tests/testthat/helper-fixtures.R | 10 imuGAP-0.2.0/imuGAP/tests/testthat/test-assemble_layer_data.R |only imuGAP-0.2.0/imuGAP/tests/testthat/test-assert-positive-int.R |only imuGAP-0.2.0/imuGAP/tests/testthat/test-canonicalize_locations.R | 177 + imuGAP-0.2.0/imuGAP/tests/testthat/test-canonicalize_populations.R | 143 + imuGAP-0.2.0/imuGAP/tests/testthat/test-checkers.R | 210 + imuGAP-0.2.0/imuGAP/tests/testthat/test-cmdstanr-smoke.R |only imuGAP-0.2.0/imuGAP/tests/testthat/test-create-target.R | 226 - imuGAP-0.2.0/imuGAP/tests/testthat/test-create_observation_populations.R |only imuGAP-0.2.0/imuGAP/tests/testthat/test-extract-imugap.R | 11 imuGAP-0.2.0/imuGAP/tests/testthat/test-imugap-options.R | 68 imuGAP-0.2.0/imuGAP/tests/testthat/test-predict.R | 51 imuGAP-0.2.0/imuGAP/tests/testthat/test-sampling-smoke.R | 57 imuGAP-0.2.0/imuGAP/tests/testthat/test-sampling.R | 127 imuGAP-0.2.0/imuGAP/tests/testthat/test-summary.R | 41 imuGAP-0.2.0/imuGAP/vignettes/imuGAP.Rmd | 655 ++++ imuGAP-0.2.0/imuGAP/vignettes/user_specified_layers.Rmd |only 120 files changed, 5464 insertions(+), 2314 deletions(-)
Title: Rearrangement Distances Between Phylogenetic Trees
Description: Fast calculation of tree rearrangement distances.
For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and
Reconnection (TBR), and Replug distances, using the algorithms of Whidden
and Matsen (2017) <doi:10.48550/arXiv.1511.07529>.
For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter
algorithms of Whidden, Beiko, and Zeh (2013) <doi:10.1137/110845045>.
Author: Martin R. Smith [aut, cre, cph] ,
Chris Whidden [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TBRDist versions 2.0.1 dated 2026-07-21 and 2.0.2 dated 2026-09-02
DESCRIPTION | 8 +-- MD5 | 18 +++---- NEWS.md | 86 +++++++++++++++++---------------- R/RcppExports.R | 64 ++++++++++++------------- inst/doc/TBRDist.html | 4 - src/rspr/ClusterForest.h | 3 - src/rspr/Forest.h | 3 - src/rspr/Node.h | 2 src/rspr/rspr.h | 115 +++++++++++++++++++++++++++++++++++---------- tests/testthat/test-rspr.R | 14 +++++ 10 files changed, 202 insertions(+), 115 deletions(-)
Title: Single Cell Oriented Reconstruction of PANDA Individually
Optimized Networks
Description: Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data. The method implements the SCORPION algorithm, which first aggregates individual cells into super-cells and then applies PANDA (Passing Attributes between Networks for Data Assimilation) to infer transcription factor-target regulatory relationships. It also provides statistical methods for differential edge analysis.
Author: Daniel Osorio [aut, cre] ,
Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between SCORPION versions 1.3.2 dated 2026-03-10 and 1.3.3 dated 2026-09-02
SCORPION-1.3.2/SCORPION/man/dot-computeGlobalS0.Rd |only SCORPION-1.3.3/SCORPION/DESCRIPTION | 10 SCORPION-1.3.3/SCORPION/MD5 | 51 SCORPION-1.3.3/SCORPION/NAMESPACE | 13 SCORPION-1.3.3/SCORPION/R/circosEdges.R |only SCORPION-1.3.3/SCORPION/R/data-scorpionTest.R | 45 SCORPION-1.3.3/SCORPION/R/enrichEdges.R |only SCORPION-1.3.3/SCORPION/R/fastCorrelation.R | 8 SCORPION-1.3.3/SCORPION/R/maEdges.R |only SCORPION-1.3.3/SCORPION/R/makeSuperCells.R | 3 SCORPION-1.3.3/SCORPION/R/normalizeNetwork.R | 50 SCORPION-1.3.3/SCORPION/R/pcNet.R | 5 SCORPION-1.3.3/SCORPION/R/prepResult.R | 5 SCORPION-1.3.3/SCORPION/R/regressEdges.R |only SCORPION-1.3.3/SCORPION/R/removeBatch.R | 30 SCORPION-1.3.3/SCORPION/R/runPANDA.R | 52 SCORPION-1.3.3/SCORPION/R/runSCORPION.R | 207 ++- SCORPION-1.3.3/SCORPION/R/scorpion.R | 15 SCORPION-1.3.3/SCORPION/R/tanimotoSimilarity.R | 17 SCORPION-1.3.3/SCORPION/R/testEdges.R | 1024 ++++++++++-------- SCORPION-1.3.3/SCORPION/data/scorpionTest.RData |binary SCORPION-1.3.3/SCORPION/man/circosEdges.Rd |only SCORPION-1.3.3/SCORPION/man/dot-drawCircosLegends.Rd |only SCORPION-1.3.3/SCORPION/man/dot-fetchGeneCoords.Rd |only SCORPION-1.3.3/SCORPION/man/dot-orderChr.Rd |only SCORPION-1.3.3/SCORPION/man/dot-parseGMT.Rd |only SCORPION-1.3.3/SCORPION/man/dot-validateGeneCoords.Rd |only SCORPION-1.3.3/SCORPION/man/enrichEdges.Rd |only SCORPION-1.3.3/SCORPION/man/maEdges.Rd |only SCORPION-1.3.3/SCORPION/man/regressEdges.Rd | 14 SCORPION-1.3.3/SCORPION/man/runSCORPION.Rd | 10 SCORPION-1.3.3/SCORPION/man/scorpionTest.Rd | 44 SCORPION-1.3.3/SCORPION/man/testEdges.Rd | 33 33 files changed, 984 insertions(+), 652 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between parameters versions 0.29.2 dated 2026-06-28 and 0.29.3 dated 2026-09-02
DESCRIPTION | 22 - MD5 | 54 +- NAMESPACE | 1 NEWS.md | 18 R/1_model_parameters.R | 1 R/format_parameters.R | 13 R/methods_brms.R | 1 R/methods_coxme.R | 1 R/methods_glmmTMB.R | 1 R/methods_loo.R | 3 R/methods_rstan.R | 1 R/methods_rstanarm.R | 1 R/parameters_type.R | 16 R/print.parameters_model.R | 9 R/tinyplot.R |only R/utils_cleaners.R | 17 R/utils_format.R | 8 R/utils_model_parameters.R | 8 inst/WORDLIST | 1 man/parameters-package.Rd | 1 man/tinyplot.parameters_model.Rd |only tests/testthat/test-factor_analysis.R | 2 tests/testthat/test-format_model_parameters.R | 435 ++++++++++++--------- tests/testthat/test-model_parameters_random_pars.R | 238 ++++++++--- tests/testthat/test-parameters_table.R | 14 tests/testthat/test-parameters_type.R | 39 + tests/testthat/test-print-grouplevel.R |only tests/testthat/test-random_effects_ci.R | 139 +----- tests/testthat/test-standardize_parameters.R | 7 tests/testthat/test-tinyplot.R |only 30 files changed, 642 insertions(+), 409 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Caceres [aut, cre] ,
Victor Granda [aut] ,
Nicolas Martin [aut] ,
Antoine Cabon [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between meteoland versions 2.2.7 dated 2026-05-08 and 2.2.8 dated 2026-09-02
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- NEWS.md | 5 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/reshaping-meteo.html | 62 ++++++++++++++++----------------- inst/include/meteoland/pet_c.hpp | 1 inst/include/meteoland/radiation_c.hpp | 1 inst/include/meteoland/utils_c.hpp | 1 9 files changed, 50 insertions(+), 44 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre] ,
Ana Carolina Sa [aut],
Antonio Castro [aut],
Caio Santos [aut],
Diego Carvalho [ctb],
Diego Salles [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Janio Lima [aut],
Lucas Tavares [aut],
Rafae [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.3.777 dated 2026-08-24 and 1.3.787 dated 2026-09-02
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- R/pat_dara.R | 59 ++++++++++++++++++++++++++++++++------------ R/pat_rule_filter.R | 13 ++++++--- README.md | 4 +- man/pat_dara.Rd | 18 +++++++------ man/pat_rule_filter_dara.Rd | 6 ++-- 7 files changed, 77 insertions(+), 41 deletions(-)
Title: Bayesian Analysis to Compare Models using Resampling Statistics
Description: Bayesian analysis used here to answer the question: "when
looking at resampling results, are the differences between models
'real'?" To answer this, a model can be created were the performance
statistic is the resampling statistics (e.g. accuracy or RMSE). These
values are explained by the model types. In doing this, we can get
parameter estimates for each model's affect on performance and make
statistical (and practical) comparisons between models. The methods
included here are similar to Benavoli et al (2017)
<https://jmlr.org/papers/v18/16-305.html>.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tidyposterior versions 1.0.2 dated 2025-07-31 and 1.1.0 dated 2026-09-02
DESCRIPTION | 20 +-- MD5 | 48 ++++++--- NAMESPACE | 18 +++ NEWS.md | 14 ++ R/compare_to_leader.R |only R/initialization.R |only R/perf_mod.R | 103 ++++++++++++++++---- R/tidyposterior-package.R | 57 +++++++++++ R/zzz.R | 1 build/vignette.rds |binary inst/generate_lme4_layouts.R |only inst/stan_glmer_inits.md |only man/autoplot.compare_to_leader.Rd |only man/compare_to_leader.Rd |only man/initialize_keys.Rd |only man/perf_mod.Rd | 33 +++++- man/reexports.Rd | 4 man/stan_glmer_inits.Rd |only man/tidyposterior-package.Rd | 7 + man/transformations.Rd | 13 -- tests/testthat/_snaps/compare_to_leader.md |only tests/testthat/_snaps/initialization.md |only tests/testthat/_snaps/perf_mod.md | 27 +++++ tests/testthat/fixtures |only tests/testthat/helper-initialization.R |only tests/testthat/test_compare_to_leader.R |only tests/testthat/test_contrast.R | 11 +- tests/testthat/test_dplyr_new.R | 2 tests/testthat/test_initialization.R |only tests/testthat/test_perf_mod.R | 149 ++++++++++++++++++++++++++--- tests/testthat/test_tidy.R | 11 +- vignettes/articles/Getting_Started.Rmd | 16 +-- 32 files changed, 446 insertions(+), 88 deletions(-)
Title: Bayesian Tree Ensembles for Survival Analysis and Causal
Inference
Description: Bayesian regression tree ensembles for survival analysis
and causal inference. Implements BART, DART, Bayesian Causal
Forests (BCF), and Horseshoe Forest models. Supports
right-censored and interval-censored survival outcomes via
accelerated failure time (AFT) formulations. Designed for
high-dimensional prediction and heterogeneous treatment effect
estimation.
Author: Tijn Jacobs [aut, cre]
Maintainer: Tijn Jacobs <t.jacobs@vu.nl>
Diff between ShrinkageTrees versions 2.0.2 dated 2026-04-21 and 2.1.0 dated 2026-09-02
DESCRIPTION | 14 MD5 | 68 NAMESPACE | 6 NEWS.md | 126 + R/CausalHorseForest.R | 46 R/CausalShrinkageForest.R | 99 - R/HorseTrees.R | 52 R/ShrinkageTrees.R | 73 R/constructors.R | 4 R/data-documentation.R | 94 - R/helpers.R | 34 R/methods.R | 29 R/plots.R | 3 R/posterior-projection.R |only README.md | 43 data/ovarian.rda |binary data/ovarian_truth.rda |binary demo/pdac_analysis.R | 10 inst/CITATION | 31 inst/doc/ShrinkageTrees.R | 116 + inst/doc/ShrinkageTrees.Rmd | 340 ++++ inst/doc/ShrinkageTrees.html | 2174 +++++++++++++++++------------ man/CausalHorseForest.Rd | 34 man/CausalShrinkageForest.Rd | 59 man/HorseTrees.Rd | 34 man/ShrinkageTrees.Rd | 38 man/ovarian.Rd | 33 man/ovarian_truth.Rd | 57 man/plot.PosteriorProjection.Rd |only man/posterior_projection.Rd |only man/print.PosteriorProjection.Rd |only src/CausalHorseForest.cpp | 2 src/HorseTrees.cpp | 2 src/ScaleMixture.cpp | 31 tests/testthat/test-horseshoe-defaults.R |only tests/testthat/test-interval-censored.R | 75 + tests/testthat/test-posterior-projection.R |only vignettes/ShrinkageTrees.Rmd | 340 ++++ 38 files changed, 2841 insertions(+), 1226 deletions(-)
More information about ShrinkageTrees at CRAN
Permanent link
Title: 'Alphavantage Financial Data' API R Wrapper and Shiny Interface
Description: Download, manage, and visualize via Shiny App 'Alphavantage financial data' <https://www.alphavantage.co/documentation/>. Data is downloaded into `data.table`s using one parameterized function. Results can be piped to optional helper functions to extract and simplify more complex data. A Shiny interface is also provided to download, manage, analyze and visualize market data.
Author: Derek Holmes [aut, cre, cph]
Maintainer: Derek Holmes <derek@derekholmes.com>
Diff between alphavantagepf versions 0.8.1 dated 2026-06-24 and 0.9.0 dated 2026-09-02
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More information about alphavantagepf at CRAN
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Title: Convert, Validate, Format and Print Geographic Coordinates and
Waypoints
Description: Convert, validate, format and elegantly print geographic coordinates and waypoints
(paired latitude and longitude values) in decimal degrees, degrees and minutes, and degrees,
minutes and seconds using high performance C++ code to enable rapid conversion and formatting
of large coordinate and waypoint datasets.
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark.eisler@bristol.ac.uk>
Diff between Waypoint versions 2.0.0 dated 2026-07-16 and 2.0.1 dated 2026-09-02
DESCRIPTION | 10 ++--- MD5 | 22 ++++++------ NEWS.md | 21 +++++++++++ R/RcppExports.R | 10 ++--- build/partial.rdb |binary man/convert.Rd | 2 - man/coords.Rd | 4 +- man/review.Rd | 4 +- man/validate.Rd | 4 +- man/waypoints.Rd | 4 +- src/CoordBase.cpp | 98 +++++++++++++++++++++++++++--------------------------- src/CoordBase.h | 29 +++++++-------- 12 files changed, 114 insertions(+), 94 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.32.10 dated 2024-07-15 and 2.39.1 dated 2026-09-02
StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/fwd/fun/grad_inc_beta.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/fwd/fun/unit_vector_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/prim/lb_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/prim/lub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/prim/offset_multiplier_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/prim/ub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/prim/unit_vector_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/rev/lb_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/rev/lub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/rev/offset_multiplier_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/rev/ub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/opencl/rev/unit_vector_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cholesky_corr_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cholesky_corr_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cholesky_factor_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cholesky_factor_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/corr_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/corr_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/corr_matrix_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/corr_matrix_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cov_matrix_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cov_matrix_constrain_lkj.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cov_matrix_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/cov_matrix_free_lkj.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/grad_inc_beta.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/identity_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/identity_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/lb_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/lb_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/lub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/lub_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/offset_multiplier_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/offset_multiplier_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/ordered_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/ordered_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/positive_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/positive_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/positive_ordered_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/positive_ordered_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/prob_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/prob_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/simplex_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/simplex_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/ub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/ub_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/unit_vector_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/fun/unit_vector_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/meta/child_type.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/meta/contains_fvar.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/meta/scalar_type_pre.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_logit_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/beta_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/binomial_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/binomial_logit_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/categorical_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/categorical_logit_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/cauchy_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/chi_square_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/dirichlet_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/dirichlet_lpmf.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/exponential_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/frechet_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/gamma_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/gaussian_dlm_obs_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/gumbel_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/hypergeometric_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/inv_wishart_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_cholesky_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/lkj_cov_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/logistic_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/loglogistic_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/lognormal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/matrix_normal_prec_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_gp_cholesky_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_gp_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_cholesky_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_prec_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multi_student_t_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multinomial_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/multinomial_logit_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log_glm_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/normal_id_glm_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/normal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/normal_sufficient_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/ordered_logistic_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/ordered_probit_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/pareto_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/poisson_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/poisson_log_glm_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/poisson_log_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/std_normal_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/student_t_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/uniform_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/von_mises_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/weibull_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/wiener_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/prim/prob/wishart_log.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/cholesky_corr_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/cholesky_factor_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/corr_matrix_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/cov_matrix_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/cov_matrix_constrain_lkj.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/grad_inc_beta.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/identity_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/identity_free.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/lb_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/lub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/ordered_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/positive_ordered_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/simplex_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/ub_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/inst/include/stan/math/rev/fun/unit_vector_constrain.hpp |only StanHeaders-2.32.10/StanHeaders/tests |only StanHeaders-2.39.1/StanHeaders/DESCRIPTION | 14 StanHeaders-2.39.1/StanHeaders/MD5 | 2804 StanHeaders-2.39.1/StanHeaders/R/Flags.R | 21 StanHeaders-2.39.1/StanHeaders/R/stanFunction.R | 11 StanHeaders-2.39.1/StanHeaders/build/vignette.rds |binary StanHeaders-2.39.1/StanHeaders/inst/doc/stanmath.html | 2039 StanHeaders-2.39.1/StanHeaders/inst/include/overrides |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/check_chains.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_effective_sample_size.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/ess.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/mcse.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/rank_normalization.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/rhat.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/split_chains.hpp | 58 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/split_rank_normalized_ess.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/analyze/mcmc/split_rank_normalized_rhat.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/concurrent_writer.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/json_writer.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/stream_writer.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/structured_writer.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/tee_writer.hpp | 97 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/unique_stream_writer.hpp | 100 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/callbacks/writer.hpp | 38 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/deserializer.hpp | 430 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/dump.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/json/json_data.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/json/json_data_handler.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/json/json_handler.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/serializer.hpp | 78 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 135 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/io/validate_zero_buf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/base_adapter.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/chains.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/chainset.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/base_hmc.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/ps_point.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_point.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_point.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_dense_e_nuts.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_softabs_nuts.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_unit_e_nuts.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_dense_e_nuts_classic.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_diag_e_nuts_classic.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_unit_e_nuts_classic.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_diag_e_static_hmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_softabs_static_hmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_unit_e_static_hmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_dense_e_static_uniform.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_diag_e_static_uniform.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_softabs_static_uniform.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_unit_e_static_uniform.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_dense_e_xhmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_diag_e_xhmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_softabs_xhmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_unit_e_xhmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/base_xhmc.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/mcmc/stepsize_adaptation.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/access_helpers.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/assign.hpp | 40 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/assign_cl.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/assign_varmat.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/rvalue.hpp | 277 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/indexing/rvalue_cl.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/model_base.hpp | 31 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/model_base_crtp.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/model_header.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/model/prob_grad.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 146 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 35 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/optimization/newton.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/diagnose/diagnose.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/experimental/advi/fullrank.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/experimental/advi/meanfield.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/optimize/bfgs.hpp | 174 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/optimize/laplace_sample.hpp | 112 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/optimize/lbfgs.hpp | 159 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/optimize/newton.hpp | 40 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/pathfinder |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/fixed_param.hpp | 128 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e.hpp | 211 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e_adapt.hpp | 437 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e.hpp | 205 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e_adapt.hpp | 444 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e.hpp | 126 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e_adapt.hpp | 268 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e_adapt.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e_adapt.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e_adapt.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp | 145 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/create_rng.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/create_unit_e_dense_inv_metric.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/create_unit_e_diag_inv_metric.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/duration_diff.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/generate_transitions.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/gq_writer.hpp | 79 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/initialize.hpp | 83 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/mcmc_writer.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/run_adaptive_sampler.hpp | 60 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/run_sampler.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/services/util/validate_dense_inv_metric.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/variational/advi.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/src/stan/version.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/constraint |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/constraint.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/Phi.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/Phi_approx.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/abs.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/accumulator.hpp | 90 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/acos.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/acosh.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/asin.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/asinh.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/atan.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/atan2.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/atanh.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/beta.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/cbrt.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/ceil.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/conj.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/cos.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/cosh.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/determinant.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/digamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/erf.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/erfc.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/exp.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/exp2.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/expm1.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/fabs.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/falling_factorial.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/floor.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/fmax.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/fmin.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/fmod.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/gamma_p.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/gamma_q.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/hypergeometric_1F0.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/hypergeometric_2F1.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/hypergeometric_pFq.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/hypot.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inc_beta.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_Phi.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_cloglog.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_erfc.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_inc_beta.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_logit.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_sqrt.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inv_square.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/inverse.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/lambert_w.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/lbeta.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/lgamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/lmgamma.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/lmultiply.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log10.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log1m_exp.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log1m_inv_logit.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log1p_exp.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_determinant.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_diff_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_falling_factorial.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_inv_logit.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_inv_logit_diff.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_mix.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_rising_factorial.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_softmax.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/log_sum_exp.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/logit.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/mdivide_left.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/mdivide_left_ldlt.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/mdivide_left_tri_low.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/mdivide_right.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/mdivide_right_tri_low.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/multiply.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/multiply_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/multiply_lower_tri_self_transpose.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/norm.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/norm1.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/norm2.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/owens_t.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/polar.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/pow.hpp | 264 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/proj.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/read_fvar.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/rising_factorial.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/round.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/sin.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/sinh.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/softmax.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/sqrt.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/sum.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/tan.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/tanh.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/tcrossprod.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/tgamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/to_fvar.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/trace_dot.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/trace_quad_form.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/trigamma.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/value_of.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/fun/value_of_rec.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/apply_scalar_unary.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/finite_diff.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/gradient.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/hessian.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/integrate_1d.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/functor/jacobian.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/prob.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/prob/std_normal_log_qf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/fwd/prob/student_t_qf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/fun/typedefs.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/barzilai_borwein_step_size.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/conditional_copy_and_promote.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/derivative.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/finite_diff_grad_hessian.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/finite_diff_grad_hessian_auto.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/grad_hessian.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/grad_tr_mat_times_hessian.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/gradient_dot_vector.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/hessian.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/hessian_block_diag.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/hessian_times_vector.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/laplace_base_rng.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/laplace_likelihood.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/laplace_marginal_density.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/laplace_marginal_density_estimator.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/partial_derivative.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/functor/wolfe_line_search.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/meta.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/prob |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/mix/prob.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/copy.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/double_d.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/indexing_rev.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_cl.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/append.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/as_column_vector_or_scalar.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/as_operation_cl.hpp | 38 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/assignment_ops.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/block_zero_based.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/broadcast.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/calc_if.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/check_cl.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/colwise_reduction.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/constant.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/elt_function_cl.hpp | 65 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/evaluate_into.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/holder_cl.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/indexing.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/load.hpp | 43 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/matrix_cl_conversion.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/multi_result_kernel.hpp | 161 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/opencl_code.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/operation_cl.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/operation_cl_lhs.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/optional_broadcast.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/reduction_2d.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/rowwise_reduction.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernel_generator/scalar.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/add.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/batch_identity.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/categorical_logit_glm_lpmf.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/check_symmetric.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/cholesky_decompose.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/cumulative_sum.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/Phi.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/Phi_approx.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/atomic_add_double.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/beta.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/binomial_coefficient_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/digamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_Phi.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_logit.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_square.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lbeta.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lgamma_stirling.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lgamma_stirling_diff.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lmultiply.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m_inv_logit.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1p_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_diff_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_inv_logit.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_inv_logit_diff.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/logit.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/multiply_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/std_normal_lcdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/trigamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/diag_inv.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/divide_columns.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/fill_strict_tri.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/gp_exp_quad_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/gp_exponential_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/gp_matern32_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/gp_matern52_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/indexing_rev.hpp | 103 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/inv_lower_tri_multiply.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/matrix_multiply.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/mergesort.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/mrrr.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/multiply_transpose.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/neg_binomial_2_log_glm_lpmf.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/neg_rect_lower_tri_multiply.hpp | 200 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/ordered_logistic_glm_lpmf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/ordered_logistic_lpmf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/pack.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/rep_matrix.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/tridiagonalization.hpp | 550 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/kernels/unpack.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/matrix_cl.hpp | 61 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/matrix_cl_view.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/mrrr.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/opencl_context.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/add_diag.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_cdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_lccdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_lcdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_logit_glm_lpmf.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_logit_lpmf.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_lpmf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/beta_binomial_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/beta_lpdf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/beta_proportion_lpdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/binomial_logit_glm_lpmf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/binomial_logit_lpmf.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/binomial_lpmf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/categorical_logit_glm_lpmf.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cauchy_cdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cauchy_lccdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cauchy_lcdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cauchy_lpdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/chi_square_lpdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cols.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/columns_dot_product.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/constraint |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/cumulative_sum.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/dirichlet_lpdf.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/double_exponential_cdf.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/double_exponential_lccdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/double_exponential_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/double_exponential_lpdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exp_mod_normal_cdf.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exp_mod_normal_lccdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exp_mod_normal_lcdf.hpp | 94 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exp_mod_normal_lpdf.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exponential_cdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exponential_lccdf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exponential_lcdf.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/exponential_lpdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/frechet_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/frechet_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/frechet_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/frechet_lpdf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/gamma_lpdf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_cdf.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_lpdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/inv_chi_square_lpdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/inv_gamma_lpdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/log_mix.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/log_softmax.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/log_sum_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/logistic_cdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/logistic_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/logistic_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/logistic_lpdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/lognormal_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/lognormal_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/lognormal_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/lognormal_lpdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/multi_normal_cholesky_lpdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_log_glm_lpmf.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_log_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/normal_cdf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/normal_id_glm_lpdf.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/normal_lccdf.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/normal_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/normal_lpdf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/num_elements.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/ordered_logistic_glm_lpmf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/ordered_logistic_lpmf.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_cdf.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_lpdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_type_2_cdf.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_type_2_lccdf.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_type_2_lcdf.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/pareto_type_2_lpdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/poisson_log_glm_lpmf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/poisson_log_lpmf.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/poisson_lpmf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/prod.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rayleigh_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rayleigh_lccdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rayleigh_lcdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rayleigh_lpdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rep_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rep_row_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rep_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rows.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/rows_dot_product.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/scaled_inv_chi_square_lpdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/sign.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/size.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/skew_double_exponential_cdf.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/skew_double_exponential_lccdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/skew_double_exponential_lcdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/skew_double_exponential_lpdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/skew_normal_lpdf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/softmax.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/std_normal_cdf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/std_normal_lccdf.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/std_normal_lcdf.hpp | 177 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/std_normal_lpdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/student_t_lpdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/sum.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/symmetrize_from_lower_tri.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/symmetrize_from_upper_tri.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/trace.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/uniform_cdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/uniform_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/uniform_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/uniform_lpdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/variance.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/weibull_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/weibull_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/weibull_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim/weibull_lpdf.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/prim_constraint.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/qr_decomposition.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/add_diag.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/adjoint_results.hpp | 31 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/append_col.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/append_row.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/arena_matrix_cl.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/columns_dot_product.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/constraint |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/copy.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/diag_post_multiply.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/diag_pre_multiply.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/grad.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/mdivide_left_tri_low.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/mdivide_right_tri_low.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/multiply.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/rows_dot_product.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/to_arena.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev/vari.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/rev_constraint.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/symmetric_eigensolver.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/tri_inverse.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/tridiagonalization.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/value_type.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/opencl/zeros_strict_tri.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/constraint |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/constraint.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/core/operator_equal_equal.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/core/operator_minus.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/core/operator_not_equal.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/core/operator_plus.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/eigen_plugins.h | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_cholesky_factor.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_cholesky_factor_corr.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_consistent_sizes.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_consistent_sizes_mvt.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_corr_matrix.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_cov_matrix.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_flag_sundials.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_matching_dims.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_ordered.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_positive_ordered.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_simplex.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_sorted.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_stochastic_column.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_stochastic_row.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_sum_to_zero.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_symmetric.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/check_unit_vector.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/elementwise_check.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/hmm_check.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/throw_domain_error_mat.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/err/validate_positive_index.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/Eigen.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/Phi.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/Phi_approx.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/abs.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/acos.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/acosh.hpp | 53 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/add_diag.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/all.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/any.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/arg.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/as_array_or_scalar.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/as_column_vector_or_scalar.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/asin.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/asinh.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/atan.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/atan2.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/atanh.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/autocorrelation.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/autocovariance.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/bessel_first_kind.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/bessel_second_kind.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/beta.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/binary_log_loss.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/binomial_coefficient_log.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/cbrt.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/ceil.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/chol2inv.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/cholesky_decompose.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/choose.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/cols.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/columns_dot_product.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/conj.hpp | 50 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/constants.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/copysign.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/cos.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/cosh.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/diag_matrix.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/diag_post_multiply.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/diag_pre_multiply.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/digamma.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/divide.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/divide_columns.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/dot_self.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/eigen_comparisons.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/eigenvalues_sym.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/eigenvectors_sym.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/elt_divide.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/elt_multiply.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/erf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/erfc.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/exp.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/exp2.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/expm1.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fabs.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/factor_U.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/factor_cov_matrix.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/falling_factorial.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fdim.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fft.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/floor.hpp | 31 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fma.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fmax.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fmin.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/fmod.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gamma_p.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gamma_q.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/generalized_inverse.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/generate_laplace_options.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/get_base1.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/get_base1_lhs.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gp_dot_prod_cov.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gp_exp_quad_cov.hpp | 42 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gp_matern32_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/gp_periodic_cov.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_2F1.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_F32.hpp | 135 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_pFq.hpp | 454 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_reg_inc_beta.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_reg_inc_gamma.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/grad_reg_lower_inc_gamma.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypergeometric_1F0.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypergeometric_2F1.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypergeometric_2F2.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypergeometric_3F2.hpp | 62 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypergeometric_pFq.hpp | 62 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/hypot.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/i_times.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/imag.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inc_beta.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inc_beta_dda.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inc_beta_ddb.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inc_beta_ddz.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_Phi.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_cloglog.hpp | 44 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_erfc.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_inc_beta.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_logit.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_sqrt.hpp | 40 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inv_square.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/inverse_softmax.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/isfinite.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/isinf.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/isnan.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/isnormal.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lambert_w.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lbeta.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/ldexp.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lgamma.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lgamma_stirling.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lgamma_stirling_diff.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/linspaced_array.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/linspaced_int_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/linspaced_row_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/linspaced_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lmgamma.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/lmultiply.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log10.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log1m.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log1m_exp.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log1m_inv_logit.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log1p.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log1p_exp.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log2.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_diff_exp.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_falling_factorial.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_gamma_q_dgamma.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_inv_logit.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_inv_logit_diff.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_mix.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_modified_bessel_first_kind.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_rising_factorial.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_softmax.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/log_sum_exp.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/logb.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/logit.hpp | 38 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/make_nu.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/matrix_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/matrix_exp_2x2.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/matrix_exp_pade.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/max.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/max_size.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/max_size_mvt.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/mdivide_left_spd.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/mdivide_right_spd.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/mdivide_right_tri.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/mean.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/min.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/minus.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/modified_bessel_first_kind.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/modified_bessel_second_kind.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/multiply_log.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/multiply_lower_tri_self_transpose.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/norm.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/norm1.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/norm2.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/num_elements.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/one_hot_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/one_hot_int_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/one_hot_row_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/one_hot_vector.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/owens_t.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/plus.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/poisson_binomial_log_probs.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/polar.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/pow.hpp | 83 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/prod.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/proj.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/promote_scalar.hpp | 133 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/pseudo_eigenvalues.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/pseudo_eigenvectors.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr_Q.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr_R.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr_thin.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr_thin_Q.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/qr_thin_R.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/quad_form.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/quad_form_diag.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/quad_form_sym.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rank.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/read_corr_L.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/read_corr_matrix.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/read_cov_L.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/read_cov_matrix.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/real.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rep_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rep_matrix.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/resize.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rising_factorial.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/round.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rows.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/rows_dot_product.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/scalar_seq_view.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/scalbn.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/scale_matrix_exp_multiply.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sd.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/select.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/serializer.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sign.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/signbit.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sin.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/singular_values.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sinh.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/size.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/size_mvt.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sqrt.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/square.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/stan_print.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/step.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/sum.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/svd_U.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/svd_V.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/tan.hpp | 46 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/tanh.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/tgamma.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/to_complex.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/to_int.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/to_matrix.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/to_ref.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/trace.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/trace_dot.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/transpose.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/trigamma.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/trunc.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/unitspaced_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/value_of.hpp | 54 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/value_of_rec.hpp | 96 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/vec_concat.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/fun/vector_seq_view.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/apply.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/apply_scalar_binary.hpp | 202 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/apply_scalar_ternary.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/apply_scalar_unary.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/apply_vector_unary.hpp | 60 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/coupled_ode_system.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/filter_map.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/finite_diff_gradient.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/finite_diff_gradient_auto.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/for_each.hpp | 44 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/hcubature.hpp | 683 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/integrate_1d.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/iter_tuple_nested.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/make_holder_tuple.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/map_if.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/map_rect.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/map_rect_combine.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/map_rect_concurrent.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/map_rect_mpi.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/mpi_parallel_call.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/ode_ckrk.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/ode_rk45.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/ode_store_sensitivities.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/operands_and_partials.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/reduce_sum_static.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/functor/tuple_concat.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/VectorBuilderHelper.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/base_type.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/common_container_type.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/compiler_attributes.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/contains_tuple.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/forward_as.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/holder.hpp | 144 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_all_arithmetic.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_arena_matrix.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_autodiff.hpp | 134 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_complex.hpp | 119 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_constant.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_container.hpp | 83 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_container_or_var_matrix.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_dense_dynamic.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_double_or_int.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen.hpp | 263 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen_dense_base.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen_dense_dynamic.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen_matrix.hpp | 43 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen_matrix_base.hpp | 35 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_eigen_sparse_base.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_floating_point.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_fvar.hpp | 95 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_integral.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_kernel_expression.hpp | 96 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_matrix.hpp | 68 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_matrix_cl.hpp | 116 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_plain_type.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_real.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_rev_matrix.hpp | 70 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_stan_scalar.hpp | 77 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_stan_scalar_or_eigen.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_string_convertible.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_tuple.hpp | 64 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var.hpp | 192 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var_and_matrix_types.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var_dense_dynamic.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var_eigen.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var_matrix.hpp | 91 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_var_or_arithmetic.hpp | 58 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_vari.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_vector.hpp | 590 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/is_vector_like.hpp | 59 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/modify_eigen_options.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/plain_type.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/possibly_sum.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/promote_scalar_type.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/ref_type.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/require_generics.hpp | 439 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/require_helpers.hpp | 336 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/return_type.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/scalar_type.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/static_select.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/tuple_element.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/meta/tuple_size.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob.hpp | 88 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_ccdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_cdf.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_cdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_lccdf.hpp | 50 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_lcdf.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_logit_glm_rng.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_logit_lpmf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/bernoulli_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_ccdf_log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_cdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_cdf_log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_lccdf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_lcdf.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_lpmf.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_binomial_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_cdf.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_lccdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_lcdf.hpp | 88 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_lpdf.hpp | 41 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_neg_binomial_cdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_neg_binomial_lccdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_neg_binomial_lcdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_neg_binomial_lpmf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_neg_binomial_rng.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_lccdf.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_lcdf.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_lpdf.hpp | 42 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_proportion_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/beta_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_cdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_lccdf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_lcdf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_logit_glm_lpmf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_logit_lpmf.hpp | 50 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_lpmf.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/binomial_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/categorical_logit_glm_lpmf.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/categorical_logit_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/categorical_logit_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/categorical_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/categorical_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_cdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_lccdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_lpdf.hpp | 43 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/cauchy_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_ccdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_cdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_lccdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_lpdf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/chi_square_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/dirichlet_lpdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/dirichlet_multinomial_lpmf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/dirichlet_multinomial_rng.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_cdf.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_lccdf.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_lcdf.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_lpmf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/discrete_range_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_cdf.hpp | 51 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_lccdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_lcdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_lpdf.hpp | 35 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/double_exponential_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_cdf.hpp | 68 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_lccdf.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_lcdf.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_lpdf.hpp | 53 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exp_mod_normal_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_cdf.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_lccdf.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_lcdf.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_lpdf.hpp | 35 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/exponential_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_cdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_lccdf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_lcdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_lpdf.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/frechet_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_cdf.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_lccdf.hpp | 190 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_lpdf.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gamma_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gaussian_dlm_obs_lpdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gaussian_dlm_obs_rng.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_ccdf_log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_cdf.hpp | 49 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_lccdf.hpp | 42 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_lcdf.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_lpdf.hpp | 38 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/gumbel_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/hmm_marginal.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/hypergeometric_lpmf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/hypergeometric_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_cdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_lccdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_lpdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_chi_square_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_cdf.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_lccdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_lcdf.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_lpdf.hpp | 35 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_gamma_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_wishart_cholesky_lpdf.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_wishart_cholesky_rng.hpp | 23 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_wishart_lpdf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/inv_wishart_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_cholesky_lpdf.hpp | 31 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_cholesky_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_lpdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lkj_corr_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lkj_cov_lpdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_cdf.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_lccdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_lcdf.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_lpdf.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/logistic_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/loglogistic_cdf.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/loglogistic_lpdf.hpp | 59 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/loglogistic_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_cdf.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_lccdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_lcdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_lpdf.hpp | 42 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/lognormal_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/matrix_normal_prec_lpdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/matrix_normal_prec_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_gp_cholesky_lpdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_gp_lpdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_cholesky_lpdf.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_cholesky_rng.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_lpdf.hpp | 239 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_prec_lpdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_prec_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_normal_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_student_t_cholesky_lpdf.hpp | 322 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_student_t_cholesky_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_student_t_lpdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multi_student_t_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multinomial_logit_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multinomial_logit_rng.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multinomial_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/multinomial_rng.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_cdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_lccdf.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_lcdf.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log_glm_lpmf.hpp | 83 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log_lpmf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_log_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_2_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_cdf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_lccdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_lcdf.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_lpmf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/neg_binomial_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_cdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_id_glm_lpdf.hpp | 70 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_lccdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_lcdf.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_lpdf.hpp | 57 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/normal_sufficient_lpdf.hpp | 56 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/ordered_logistic_glm_lpmf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/ordered_logistic_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/ordered_probit_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/ordered_probit_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_cdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_lccdf.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_lcdf.hpp | 49 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_lpdf.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_cdf.hpp | 47 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_lccdf.hpp | 48 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_lcdf.hpp | 43 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_lpdf.hpp | 49 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/pareto_type_2_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_cdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_lccdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_lcdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_lpmf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_binomial_rng.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_ccdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_cdf.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_cdf_log.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_lccdf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_lcdf.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp | 53 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_log_lpmf.hpp | 22 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_log_rng.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_lpmf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/poisson_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_ccdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_cdf.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_cdf_log.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_lccdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_lcdf.hpp | 25 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_lpdf.hpp | 31 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/rayleigh_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_cdf.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_lccdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_lcdf.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_lpdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/scaled_inv_chi_square_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_cdf.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_lccdf.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_lcdf.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_lpdf.hpp | 52 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_double_exponential_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_cdf.hpp | 75 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_lccdf.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_lcdf.hpp | 40 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_lpdf.hpp | 53 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/skew_normal_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/std_normal_cdf.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/std_normal_lccdf.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/std_normal_lcdf.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/std_normal_log_qf.hpp | 146 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/std_normal_lpdf.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_ccdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_cdf.hpp | 44 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_cdf_log.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_lccdf.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_lcdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_lpdf.hpp | 56 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_qf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/student_t_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_ccdf_log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_cdf.hpp | 41 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_cdf_log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_lccdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_lcdf.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_lpdf.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/uniform_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/von_mises_cdf.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/von_mises_lpdf.hpp | 36 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/von_mises_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_ccdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_cdf.hpp | 55 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_cdf_log.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_lccdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_lcdf.hpp | 60 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_lpdf.hpp | 33 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/weibull_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener4_lccdf_unnorm.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener4_lcdf_unnorm.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener5_lpdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener_full_lccdf_unnorm.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener_full_lcdf_unnorm.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener_full_lpdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wiener_lpdf.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wishart_cholesky_lpdf.hpp | 37 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wishart_cholesky_rng.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wishart_lpdf.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/wishart_rng.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/yule_simon_cdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/yule_simon_lccdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/yule_simon_lcdf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/yule_simon_lpmf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/prim/prob/yule_simon_rng.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/constraint |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/constraint.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/arena_matrix.hpp | 127 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/build_vari_array.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/callback_vari.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/chainable_object.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/collect_adjoints.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/count_vars.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/filter_var_scalar_types.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/init_chainablestack.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/make_zeroed_arena.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp | 44 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/profiling.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/var.hpp | 115 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/vari.hpp | 28 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/core/zero_adjoints.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/Phi_approx.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/abs.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/accumulator.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/acos.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/acosh.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/adjoint_of.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/append_col.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/append_row.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/asin.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/asinh.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/atan.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/atan2.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/atanh.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/bessel_second_kind.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/beta.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/binary_log_loss.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/ceil.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/cholesky_decompose.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/columns_dot_product.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/columns_dot_self.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/conj.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/cos.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/cosh.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/cov_exp_quad.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/csr_matrix_times_vector.hpp | 90 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/determinant.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/diag_post_multiply.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/diag_pre_multiply.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/digamma.hpp | 26 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/dims.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/dot_product.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/dot_self.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/eigendecompose_sym.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/eigenvalues_sym.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/eigenvectors_sym.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/elt_divide.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/elt_multiply.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/exp.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/exp2.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fabs.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/falling_factorial.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fdim.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fft.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fill.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/floor.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fma.hpp | 141 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fmax.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fmin.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/fmod.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/from_var_value.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/gamma_p.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/gamma_q.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/generalized_inverse.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/gp_exp_quad_cov.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/gp_periodic_cov.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/hypergeometric_1F0.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/hypergeometric_2F1.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/hypergeometric_pFq.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inc_beta.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/initialize_fill.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_Phi.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_cloglog.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_erfc.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_inc_beta.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_logit.hpp | 29 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_sqrt.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inv_square.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/inverse.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/lambert_w.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/lbeta.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/ldexp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/lgamma.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/lmgamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/lmultiply.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log10.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log1m.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log1m_exp.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log1m_inv_logit.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log1p.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log1p_exp.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log2.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_determinant.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_determinant_ldlt.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_determinant_spd.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_diff_exp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_falling_factorial.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_inv_logit.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_inv_logit_diff.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_mix.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_rising_factorial.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_softmax.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/log_sum_exp.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/logit.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/matrix_exp_multiply.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/matrix_power.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/mdivide_left.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/mdivide_left_ldlt.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/mdivide_left_spd.hpp | 13 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/mdivide_left_tri.hpp | 21 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/multiply.hpp | 80 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/multiply_log.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/multiply_lower_tri_self_transpose.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/norm.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/norm1.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/norm2.hpp | 39 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/owens_t.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/polar.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/pow.hpp | 285 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/proj.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/quad_form.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/quad_form_sym.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/read_corr_L.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/read_corr_matrix.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/read_cov_L.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/read_cov_matrix.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rep_matrix.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rep_row_vector.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rep_vector.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rising_factorial.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rows_dot_product.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/rows_dot_self.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/sd.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/sin.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/singular_values.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/sinh.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/softmax.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/sqrt.hpp | 11 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/square.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/squared_distance.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/step.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/sum.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/svd.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/svd_U.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/svd_V.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/tan.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/tanh.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/tcrossprod.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/tgamma.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/to_arena.hpp | 19 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/to_var_value.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace_dot.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace_gen_inv_quad_form_ldlt.hpp | 45 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace_gen_quad_form.hpp | 24 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace_inv_quad_form_ldlt.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/trace_quad_form.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/fun/variance.hpp | 3 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/algebra_solver_fp.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/algebra_system.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/apply_scalar_binary.hpp | 44 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/apply_scalar_unary.hpp | 15 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/apply_vector_unary.hpp | 18 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/coupled_ode_system.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/cvodes_integrator_adjoint.hpp | 27 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/dae.hpp | 9 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/finite_diff_hessian_auto.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/finite_diff_hessian_times_vector_auto.hpp | 8 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/gradient.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/idas_integrator.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/idas_service.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/integrate_1d.hpp | 32 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/jacobian.hpp | 7 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/kinsol_solve.hpp | 17 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/map_rect_concurrent.hpp | 5 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/ode_adams.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/ode_adjoint.hpp | 6 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/ode_bdf.hpp | 12 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/ode_store_sensitivities.hpp | 14 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/operands_and_partials.hpp | 16 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/partials_propagator.hpp | 10 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/reduce_sum.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/solve_newton.hpp | 34 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/functor/solve_powell.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/meta.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/meta/arena_type.hpp | 2 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/meta/is_rev_matrix.hpp | 20 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/meta/modify_eigen_options.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/prob.hpp | 1 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/prob/std_normal_log_qf.hpp | 30 StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/rev/prob/student_t_qf.hpp |only StanHeaders-2.39.1/StanHeaders/inst/include/stan/math/version.hpp | 4 StanHeaders-2.39.1/StanHeaders/inst/stanc.js |41674 ++++------ StanHeaders-2.39.1/StanHeaders/man/CxxFlags.Rd | 5 StanHeaders-2.39.1/StanHeaders/src/sundials/sundials_hashmap.h | 7 1477 files changed, 37078 insertions(+), 37808 deletions(-)
Title: Expander Functions for Generating Full Gradient and Hessian from
Single-Slot and Multi-Slot Base Distributions
Description: The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansio [...truncated...]
Author: Alireza S. Mahani [aut, cre],
Mansour T.A. Sharabiani [aut]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between RegressionFactory versions 0.7.4 dated 2020-10-26 and 0.7.5 dated 2026-09-02
ChangeLog | 43 - DESCRIPTION | 18 MD5 | 48 - NAMESPACE | 12 R/aaa.R | 14 R/expanders.R | 108 +-- R/fbase.1par.R | 164 ++--- R/fbase.2par.R | 92 +- R/utils.R | 14 build/vignette.rds |binary inst/doc/RegressionFactory.R | 459 +++++++------- inst/doc/RegressionFactory.Rnw | 1032 ++++++++++++++++----------------- inst/doc/RegressionFactory.pdf |binary man/fbase1.binomial.Rd | 214 +++--- man/fbase1.exponential.Rd | 188 +++--- man/fbase1.geometric.Rd | 188 +++--- man/fbase1.poisson.Rd | 198 +++--- man/fbase2.gamma.log.log.Rd | 170 ++--- man/fbase2.gaussian.identity.log.Rd | 206 +++--- man/fbase2.inverse.gaussian.log.log.Rd | 162 ++--- man/regfac.expand.1par.Rd | 122 +-- man/regfac.expand.2par.Rd | 166 ++--- man/regfac.merge.Rd | 100 +-- vignettes/RegressionFactory.Rnw | 1032 ++++++++++++++++----------------- vignettes/RegressionFactory.bib | 266 ++++---- 25 files changed, 2513 insertions(+), 2503 deletions(-)
More information about RegressionFactory at CRAN
Permanent link
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Hugues Pecout [ctb] ,
Ronan Ysebaert [ctb] ,
Elina Marveaux [ctb] ,
Ian Fellows [cph] ,
Danielle Navarro [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 1.2.1 dated 2026-05-29 and 1.2.2 dated 2026-09-02
mapsf-1.2.1/mapsf/R/mf_map_help.R |only mapsf-1.2.1/mapsf/man/mf_map_base.Rd |only mapsf-1.2.1/mapsf/man/mf_map_choro.Rd |only mapsf-1.2.1/mapsf/man/mf_map_grad.Rd |only mapsf-1.2.1/mapsf/man/mf_map_prop.Rd |only mapsf-1.2.1/mapsf/man/mf_map_prop_choro.Rd |only mapsf-1.2.1/mapsf/man/mf_map_prop_typo.Rd |only mapsf-1.2.1/mapsf/man/mf_map_symb.Rd |only mapsf-1.2.1/mapsf/man/mf_map_symb_choro.Rd |only mapsf-1.2.1/mapsf/man/mf_map_typo.Rd |only mapsf-1.2.2/mapsf/DESCRIPTION | 14 mapsf-1.2.2/mapsf/MD5 | 88 +--- mapsf-1.2.2/mapsf/NAMESPACE | 188 +++++---- mapsf-1.2.2/mapsf/NEWS.md | 16 mapsf-1.2.2/mapsf/R/deprecated.R | 18 mapsf-1.2.2/mapsf/R/mf_arrow.R | 5 mapsf-1.2.2/mapsf/R/mf_distr.R | 12 mapsf-1.2.2/mapsf/R/mf_get_pal.R | 5 mapsf-1.2.2/mapsf/R/mf_get_ratio.R | 4 mapsf-1.2.2/mapsf/R/mf_graticule.R | 4 mapsf-1.2.2/mapsf/R/mf_label.R | 4 mapsf-1.2.2/mapsf/R/mf_map.R | 541 ++++++++++++++++++++++++--- mapsf-1.2.2/mapsf/R/mf_map_utils.R | 3 mapsf-1.2.2/mapsf/R/mf_png.R | 4 mapsf-1.2.2/mapsf/R/mf_prop_choro.R | 2 mapsf-1.2.2/mapsf/R/mf_raster.R | 17 mapsf-1.2.2/mapsf/R/mf_shadow.R | 4 mapsf-1.2.2/mapsf/R/mf_svg.R | 4 mapsf-1.2.2/mapsf/R/mf_symb.R | 2 mapsf-1.2.2/mapsf/R/mf_symb_choro.R | 2 mapsf-1.2.2/mapsf/R/mf_text.R | 10 mapsf-1.2.2/mapsf/R/mf_theme.R | 3 mapsf-1.2.2/mapsf/R/mf_typo.R | 6 mapsf-1.2.2/mapsf/build/vignette.rds |binary mapsf-1.2.2/mapsf/inst/doc/mapsf.Rmd | 29 - mapsf-1.2.2/mapsf/inst/doc/mapsf.html | 91 +--- mapsf-1.2.2/mapsf/inst/tinytest/test_logo.R | 12 mapsf-1.2.2/mapsf/man/mapsf-deprecated.Rd | 18 mapsf-1.2.2/mapsf/man/mapsf.Rd | 1 mapsf-1.2.2/mapsf/man/mf_distr.Rd | 8 mapsf-1.2.2/mapsf/man/mf_get_pal.Rd | 5 mapsf-1.2.2/mapsf/man/mf_get_ratio.Rd | 4 mapsf-1.2.2/mapsf/man/mf_graticule.Rd | 4 mapsf-1.2.2/mapsf/man/mf_label.Rd | 4 mapsf-1.2.2/mapsf/man/mf_map.Rd | 558 +++++++++++++++++++++++++--- mapsf-1.2.2/mapsf/man/mf_png.Rd | 4 mapsf-1.2.2/mapsf/man/mf_raster.Rd | 8 mapsf-1.2.2/mapsf/man/mf_shadow.Rd | 4 mapsf-1.2.2/mapsf/man/mf_svg.Rd | 4 mapsf-1.2.2/mapsf/vignettes/mapsf.Rmd | 29 - 50 files changed, 1298 insertions(+), 441 deletions(-)
Title: Classes and Methods for 'IP' Addresses
Description: Provides S4 classes for Internet Protocol (IP) versions 4 and 6 addresses and efficient methods for 'IP' addresses comparison, arithmetic, bit manipulation and lookup. Both 'IPv4' and 'IPv6' arbitrary ranges are also supported as well as internationalized ('IDN') domain lookup with and 'whois' query.
Author: Thomas Soubiran [aut],
Rucknium [cre]
Maintainer: Rucknium <Rucknium@protonmail.com>
This is a re-admission after prior archival of version 0.1.6-1 dated 2026-04-15
Diff between IP versions 0.1.6-1 dated 2026-04-15 and 0.1.7 dated 2026-09-02
DESCRIPTION | 8 +++--- MD5 |only build/vignette.rds |binary inst/doc/ip-host.html | 2 - inst/doc/ip-intro.html | 20 +++++++++------- man/Bitwise-methods.Rd | 56 ++++++++++++++++++++++++++-------------------- man/Compare-methods.Rd | 7 +++-- man/Conversion-methods.Rd | 17 ++++++++----- man/hostinfo.Rd | 2 - src/Rip-IP-macros.h | 18 +++++++------- src/Rip-match.c | 10 ++++---- src/Rip.h | 1 12 files changed, 78 insertions(+), 63 deletions(-)
More information about ExperimentalDesignGeneratorandRandomiser at CRAN
Permanent link
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 7.7 dated 2026-07-20 and 7.8 dated 2026-09-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/kent.logcon.R | 2 +- R/kent.mle.R | 39 +++++++++++++++++---------------------- man/Directional-package.Rd | 13 +++---------- 5 files changed, 29 insertions(+), 41 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.1.6 dated 2026-08-25 and 0.2.0 dated 2026-09-02
DESCRIPTION | 18 MD5 | 68 NAMESPACE | 12 NEWS.md | 53 R/fit.R |only R/paper.R | 709 +++---- R/plotting.R | 1829 ++++++++++--------- R/questionnaire-defs.R |only R/questionnaires.R |only R/reporting.R | 3337 +++++++++++++++++------------------ R/setup.R | 29 R/study-project.R |only R/utils.R | 2560 ++++++++++++++------------ README.md | 124 + build/vignette.rds |binary inst/WORDLIST | 243 +- inst/doc/analyzing-a-user-study.html | 10 inst/doc/overleaf.html | 12 inst/doc/scoring-questionnaires.R |only inst/doc/scoring-questionnaires.Rmd |only inst/doc/scoring-questionnaires.html |only inst/templates |only man/add_pareto_emoa_column.Rd | 21 man/add_pareto_moocore_column.Rd | 28 man/animate_mobo2.Rd |only man/check_questionnaire.Rd |only man/define_questionnaire.Rd |only man/fit_recommended.Rd |only man/list_questionnaires.Rd |only man/questionnaire_items.Rd |only man/reverse_code.Rd |only man/score_questionnaire.Rd |only man/score_reliability.Rd |only man/summarize_sickness.Rd |only man/use_study_project.Rd |only tests/testthat/test-fit.R |only tests/testthat/test-paper.R | 681 +++---- tests/testthat/test-plotting.R | 500 ++--- tests/testthat/test-questionnaires.R |only tests/testthat/test-reporting.R | 1095 ++++++----- tests/testthat/test-study-project.R |only tests/testthat/test-utils.R | 110 + vignettes/scoring-questionnaires.Rmd |only 43 files changed, 6201 insertions(+), 5238 deletions(-)
Title: Automated Statistical Analysis and Tools for Agricultural
Research
Description: A comprehensive suite of statistical tools tailored for agricultural
and plant breeding research. Provides automated pipelines for analysis of
variance and covariance under randomized complete block designs and completely
randomized designs, descriptive summary statistics, and post-hoc multiple
range tests including Least Significant Difference, Tukey, and Scheffe based on
Steel et al. (1997) <isbn:978-0070610286>. Quantitative genetic parameters including
genotypic, phenotypic, and environmental variance components and broad-sense
heritability follow Burton and Devane (1953) <doi:10.2134/agronj1953.00021962004500100005x>.
Genetic advance and genetic advance as percentage of mean estimation follow
Johnson et al. (1955) <doi:10.2134/agronj1955.00021962004700070009x>. Genotypic, phenotypic,
and environmental correlations follow Miller et al. (1958)
<doi:10.2134/agronj1958.00021962005000100020x>. Genotypic and phenotypic path coefficient
analysis direct and indirec [...truncated...]
Author: Faheem Khan [aut, cre]
Maintainer: Faheem Khan <2022ag94@uaf.edu.pk>
Diff between AgriDataTools versions 0.1.2 dated 2026-08-08 and 0.2.1 dated 2026-09-02
AgriDataTools-0.1.2/AgriDataTools/tests/testthat/testthat.R |only AgriDataTools-0.2.1/AgriDataTools/DESCRIPTION | 12 AgriDataTools-0.2.1/AgriDataTools/MD5 | 83 - AgriDataTools-0.2.1/AgriDataTools/NAMESPACE | 10 AgriDataTools-0.2.1/AgriDataTools/NEWS.md | 18 AgriDataTools-0.2.1/AgriDataTools/R/AgriDataTools-package.R | 8 AgriDataTools-0.2.1/AgriDataTools/R/cluster_analysis.R | 64 - AgriDataTools-0.2.1/AgriDataTools/R/compute_ancova.R | 272 +++--- AgriDataTools-0.2.1/AgriDataTools/R/correlation_analysis.R | 124 +- AgriDataTools-0.2.1/AgriDataTools/R/crd_anova.R | 157 +-- AgriDataTools-0.2.1/AgriDataTools/R/data.R | 10 AgriDataTools-0.2.1/AgriDataTools/R/lsd_test.R | 183 +++- AgriDataTools-0.2.1/AgriDataTools/R/path_analysis.R | 124 +- AgriDataTools-0.2.1/AgriDataTools/R/pca_analysis.R | 130 +- AgriDataTools-0.2.1/AgriDataTools/R/plotting.R | 445 ++++++---- AgriDataTools-0.2.1/AgriDataTools/R/rcbd_anova.R | 175 ++- AgriDataTools-0.2.1/AgriDataTools/R/scheffe_test.R | 200 +++- AgriDataTools-0.2.1/AgriDataTools/R/summary_statistics.R | 67 - AgriDataTools-0.2.1/AgriDataTools/R/tukey_test.R | 203 +++- AgriDataTools-0.2.1/AgriDataTools/R/validation.R | 287 ++---- AgriDataTools-0.2.1/AgriDataTools/R/variability_analysis.R | 124 +- AgriDataTools-0.2.1/AgriDataTools/build/vignette.rds |binary AgriDataTools-0.2.1/AgriDataTools/inst/CITATION |only AgriDataTools-0.2.1/AgriDataTools/inst/doc/AgriDataTools.Rmd | 221 ++-- AgriDataTools-0.2.1/AgriDataTools/inst/doc/AgriDataTools.html | 248 +++-- AgriDataTools-0.2.1/AgriDataTools/man/AgriDataTools-package.Rd | 16 AgriDataTools-0.2.1/AgriDataTools/man/analyze_clustering.Rd | 16 AgriDataTools-0.2.1/AgriDataTools/man/analyze_pca.Rd | 33 AgriDataTools-0.2.1/AgriDataTools/man/anova_crd.Rd | 34 AgriDataTools-0.2.1/AgriDataTools/man/anova_rcbd.Rd | 40 AgriDataTools-0.2.1/AgriDataTools/man/compute_ancova.Rd | 73 - AgriDataTools-0.2.1/AgriDataTools/man/compute_correlation.Rd | 40 AgriDataTools-0.2.1/AgriDataTools/man/compute_lsd.Rd | 31 AgriDataTools-0.2.1/AgriDataTools/man/compute_path_analysis.Rd | 28 AgriDataTools-0.2.1/AgriDataTools/man/compute_scheffe.Rd | 36 AgriDataTools-0.2.1/AgriDataTools/man/compute_summary_stats.Rd | 14 AgriDataTools-0.2.1/AgriDataTools/man/compute_tukey.Rd | 36 AgriDataTools-0.2.1/AgriDataTools/man/estimate_variability.Rd | 18 AgriDataTools-0.2.1/AgriDataTools/man/gv_data.Rd | 10 AgriDataTools-0.2.1/AgriDataTools/man/plot_agri_graphics.Rd | 122 +- AgriDataTools-0.2.1/AgriDataTools/man/validate_agri_data.Rd | 54 - AgriDataTools-0.2.1/AgriDataTools/tests/test.R |only AgriDataTools-0.2.1/AgriDataTools/tests/testthat/test-statistical-engines.R | 130 ++ AgriDataTools-0.2.1/AgriDataTools/vignettes/AgriDataTools.Rmd | 221 ++-- 44 files changed, 2443 insertions(+), 1674 deletions(-)
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH)
Data
Description: A toolkit to set up an R data package in a consistent
structure. Automates tasks like tidy data export, data dictionary
documentation, README and website creation, and citation management.
Author: Mian Zhong [aut] ,
Margaux Goetschmann [aut] ,
Colin Walder [aut] ,
Lars Schoebitz [aut, cre] ,
Global Health Engineering, ETH Zurich [cph]
Maintainer: Lars Schoebitz <lschoebitz@ethz.ch>
Diff between washr versions 1.0.2 dated 2026-07-26 and 1.1.0 dated 2026-09-02
DESCRIPTION | 29 +++-- MD5 | 84 +++++++++------- NAMESPACE | 6 - NEWS.md | 134 ++++++++++++++++++++++++++ R/generate_jsonld.R |only R/setup_ci.R |only R/setup_dictionary.R | 8 + R/setup_rawdata.R | 4 R/setup_readme.R | 31 ++++-- R/setup_roxygen.R | 57 ++++++----- R/setup_website.R | 110 ++++++++++++++------- R/update_citation.R | 54 +++++++++- R/update_description.R | 4 R/update_metadata.R |only R/use_brand.R |only R/utils.R | 17 ++- R/washr-package.R |only README.md | 66 +++++++++--- inst/doc/washr.R | 41 +++++++ inst/doc/washr.Rmd | 132 ++++++++++++++++++++++++- inst/doc/washr.html | 170 ++++++++++++++++++++++++++++++--- inst/templates/R-CMD-check.yaml |only inst/templates/README.Rmd | 17 ++- inst/templates/_pkgdown.yml | 20 +++ man/figures |only man/fill_dictionary.Rd | 1 man/generate_roxygen_docs.Rd | 1 man/setup_ci.Rd |only man/setup_dictionary.Rd | 9 + man/setup_rawdata.Rd | 9 + man/setup_readme.Rd | 21 +++- man/setup_roxygen.Rd | 9 + man/setup_website.Rd | 31 +++++- man/update_citation.Rd | 18 +++ man/update_description.Rd | 8 + man/update_metadata.Rd |only man/use_brand.Rd |only man/washr-package.Rd |only tests/testthat/test_idempotency.R |only tests/testthat/test_setup_ci.R |only tests/testthat/test_setup_dictionary.R | 30 +++++ tests/testthat/test_setup_rawdata.R | 28 ++++- tests/testthat/test_setup_readme.R | 46 ++++++++ tests/testthat/test_setup_roxygen.R | 50 +++++++++ tests/testthat/test_setup_website.R | 69 +++++++++++++ tests/testthat/test_update_citation.R | 49 +++++++++ tests/testthat/test_update_metadata.R |only tests/testthat/test_use_brand.R |only vignettes/washr.Rmd | 132 ++++++++++++++++++++++++- 49 files changed, 1307 insertions(+), 188 deletions(-)
More information about rhythm.metrics at CRAN
Permanent link
Title: Result Stability Checks for Empirical R Projects
Description: Lightweight helpers for checking whether empirical results remain
substantively unchanged across code revisions, platform differences,
and package updates. The package supports regression-style testing of
derived datasets, statistical model outputs, tables, and plots, helping
researchers detect unintended result drift early and distinguish material
from non-material changes in empirical workflows.
Author: Dianyi Yang [aut, cre, ctb]
Maintainer: Dianyi Yang <dianyi.yang@politics.ox.ac.uk>
Diff between resultcheck versions 0.2.1 dated 2026-05-08 and 0.3.0 dated 2026-09-02
DESCRIPTION | 8 MD5 | 35 NAMESPACE | 12 NEWS.md | 5 R/snapshot.R | 82 +- build/vignette.rds |binary inst/doc/faq.R | 12 inst/doc/faq.html | 1174 +++++++++++++++---------------- inst/doc/renv-github-actions.R | 12 inst/doc/renv-github-actions.html | 1350 ++++++++++++++++++------------------ inst/doc/resultcheck.R | 12 inst/doc/resultcheck.html | 1402 +++++++++++++++++++------------------- inst/doc/snapshot-tolerance.R | 18 inst/doc/snapshot-tolerance.html | 1064 ++++++++++++++-------------- man/detect_script_name.Rd | 6 man/get_snapshot_path.Rd | 5 man/is_quarto_render.Rd |only man/snapshot.Rd | 15 tests/testthat/test-snapshot.R | 94 ++ 19 files changed, 2739 insertions(+), 2567 deletions(-)
Title: Adsorption Isotherm Models
Description: Model adsorption behavior using classical isotherms, including Langmuir,
Freundlich, Brunauer–Emmett–Teller (BET), and Temkin models. The package supports
parameter estimation through both linearized and non-linear fitting techniques and
generates high-quality plots for model diagnostics. It is intended for environmental
scientists, chemists, and researchers working on adsorption phenomena in soils,
water treatment, and material sciences. Functions are compatible with base 'R' and
'ggplot2' for visualization.
Author: Jajati Mandal [cre],
Sandipan Samanta [aut]
Maintainer: Jajati Mandal <J.Mandal2@salford.ac.uk>
Diff between AdsorpR versions 0.1.0 dated 2025-04-09 and 0.1.1 dated 2026-09-02
AdsorpR-0.1.0/AdsorpR/build/partial.rdb |only AdsorpR-0.1.1/AdsorpR/DESCRIPTION | 8 +- AdsorpR-0.1.1/AdsorpR/MD5 | 28 +++++----- AdsorpR-0.1.1/AdsorpR/NAMESPACE | 34 ++++++------ AdsorpR-0.1.1/AdsorpR/NEWS.md |only AdsorpR-0.1.1/AdsorpR/R/Isotherms.R | 52 +++++++++++++++++-- AdsorpR-0.1.1/AdsorpR/build/vignette.rds |binary AdsorpR-0.1.1/AdsorpR/inst/doc/AdsorpR-vignette.html | 20 +++---- AdsorpR-0.1.1/AdsorpR/man/bet_model.Rd | 27 ++++----- AdsorpR-0.1.1/AdsorpR/man/freundlich_model.Rd | 25 ++++----- AdsorpR-0.1.1/AdsorpR/man/langmuir_model.Rd | 32 ++++++----- AdsorpR-0.1.1/AdsorpR/man/nonlinear_bet.Rd | 26 +++------ AdsorpR-0.1.1/AdsorpR/man/nonlinear_freundlich.Rd | 25 ++------- AdsorpR-0.1.1/AdsorpR/man/nonlinear_langmuir.Rd | 24 ++------ AdsorpR-0.1.1/AdsorpR/man/nonlinear_temkin.Rd | 29 +++------- AdsorpR-0.1.1/AdsorpR/man/temkin_model.Rd | 29 ++++------ 16 files changed, 187 insertions(+), 172 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: Provides methods for imputation and visualization of
missing values. It includes graphical tools to explore the amount, structure
and patterns of missing and/or imputed values, supporting exploratory
data analysis and helping to investigate potential missingness mechanisms
(details in Alfons, Templ and Filzmoser, <doi:10.1007/s11634-011-0102-y>).
The quality of imputations can be assessed visually using a wide range of
univariate, bivariate and multivariate plots.
The package further provides several imputation methods,
including efficient implementations of k-nearest neighbour and hot-deck
imputation (Kowarik and Templ 2013, <doi:10.18637/jss.v074.i07>),
iterative robust model-based multiple
imputation (Templ 2011, <doi:10.1016/j.csda.2011.04.012>;
Templ 2023, <doi:10.3390/math11122729>), and machine learning–based
approaches such as robust GAM-based multiple imputation
(Templ 2024, <doi:10.1007/s11222-024-10429-1>) as well as random forest
and gradient b [...truncated...]
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] ,
Andreas Alfons [aut],
Johannes Gussenbauer [aut],
Nina Niederhametner [aut],
Eileen Vattheuer [aut],
Gregor de Cillia [aut],
Bernd Prantner [ctb],
Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 7.0.0 dated 2026-01-10 and 7.3.0 dated 2026-09-02
DESCRIPTION | 58 MD5 | 364 +- NAMESPACE | 56 NEWS.md | 82 R/RcppExports.R | 8 R/VIM-package.R | 182 - R/aggr.R | 2 R/barMiss.R | 2 R/bgmap.R | 4 R/cellwise_utils.R |only R/colormapMiss.R | 2 R/evaluation.R | 44 R/gowerD.R | 49 R/growdotMiss.R | 2 R/helper_vimpute.R | 3523 ++++++++++++++++++++++-- R/histMiss.R | 2 R/imputeCellEM.R |only R/imputeCellMM.R |only R/imputeCellReg.R |only R/imputeCellwise.R |only R/imputeRobust.R | 71 R/imputeRobustChain.R | 178 - R/irmi.R | 25 R/kNN.R | 38 R/makeMissing.R |only R/mapMiss.R | 2 R/marginmatrix.R | 2 R/marginplot.R | 2 R/matrixplot.R | 2 R/mosaicMiss.R | 2 R/overimpute.R |only R/pairsVIM.R | 2 R/parcoordMiss.R | 2 R/pbox.R | 2 R/prepare.R | 33 R/rangerImpute.R | 121 R/regressionImp.R | 376 +- R/restricted_helpers.R |only R/scattJitt.R | 2 R/scattMiss.R | 2 R/scattmatrixMiss.R | 2 R/spineMiss.R | 2 R/threads.R |only R/vimmi.R |only R/vimpute.R | 2842 +++++++++++++------ R/vimpute_registry.R |only R/vimpute_spec.R |only R/vimpute_tune_control.R |only R/xgboostImpute.R | 144 R/zzz.R | 5 build/vignette.rds |binary data/Animals_na.rda |binary data/SBS5242.rda |binary data/bcancer.rda |binary data/brittleness.rda |binary data/chorizonDL.rda |binary data/colic.rda |binary data/collisions.rda |binary data/diabetes.rda |binary data/food.rda |binary data/kola.background.rda |binary data/lse_synthetic.rda |only data/lse_synthetic_rules.rda |only data/pulplignin.rda |binary data/sleep.rda |binary data/tao.rda |binary data/testdata.RData |binary data/toydataMiss.rda |binary data/wine.rda |binary inst/doc/VIM.Rmd | 4 inst/doc/VIM.html | 152 - inst/doc/VisualImp.Rmd | 3 inst/doc/VisualImp.html | 427 +- inst/doc/donorImp.Rmd | 4 inst/doc/donorImp.html | 216 - inst/doc/impPCA.Rmd | 5 inst/doc/impPCA.html | 208 - inst/doc/irmi.Rmd | 15 inst/doc/irmi.html | 231 - inst/doc/modelImp.Rmd | 5 inst/doc/modelImp.html | 233 - inst/doc/vimpute-benchmark.Rmd |only inst/doc/vimpute-benchmark.html |only inst/doc/vimpute-coverage.Rmd |only inst/doc/vimpute-coverage.html |only inst/doc/vimpute-mi.R |only inst/doc/vimpute-mi.Rmd |only inst/doc/vimpute-mi.html |only inst/doc/vimpute-restricted.R |only inst/doc/vimpute-restricted.Rmd |only inst/doc/vimpute-restricted.html |only inst/doc/vimpute.R | 159 - inst/doc/vimpute.Rmd | 332 +- inst/doc/vimpute.html | 589 +++- inst/doc/xgboostImpute.Rmd | 4 inst/doc/xgboostImpute.html | 214 - inst/tinytest/test_cellwise.R |only inst/tinytest/test_cellwise_df_interface.R |only inst/tinytest/test_cellwise_irmi_quality.R |only inst/tinytest/test_diabetes_synthetic.R |only inst/tinytest/test_evaluation.R |only inst/tinytest/test_evaluation_where.R |only inst/tinytest/test_gowerD_cpp.R |only inst/tinytest/test_gowerD_mixed_scaling.R |only inst/tinytest/test_imputeCellReg_weights.R |only inst/tinytest/test_imputeRobust.R |only inst/tinytest/test_imputeRobustChain.R |only inst/tinytest/test_irmi_mi.R |only inst/tinytest/test_kNN_weightdist.R |only inst/tinytest/test_lse_synthetic_rules_plain.R |only inst/tinytest/test_makeMissing.R |only inst/tinytest/test_overimpute.R |only inst/tinytest/test_prepare_boxcox.R |only inst/tinytest/test_rangerImpute.R | 49 inst/tinytest/test_regressionImp.R | 12 inst/tinytest/test_regressionImp_lm.R |only inst/tinytest/test_threads.R |only inst/tinytest/test_vimmi.R |only inst/tinytest/test_vimmi_bridge.R |only inst/tinytest/test_vimmi_complete_masking.R |only inst/tinytest/test_vimpute.R | 332 +- inst/tinytest/test_vimpute_boot_default.R |only inst/tinytest/test_vimpute_considered_columns.R |only inst/tinytest/test_vimpute_convergence.R |only inst/tinytest/test_vimpute_fallback.R |only inst/tinytest/test_vimpute_glm_rob_direction.R |only inst/tinytest/test_vimpute_issue_98.R |only inst/tinytest/test_vimpute_method_list.R |only inst/tinytest/test_vimpute_method_unnamed.R |only inst/tinytest/test_vimpute_mi_properness.R |only inst/tinytest/test_vimpute_model_error.R |only inst/tinytest/test_vimpute_oob_scale.R |only inst/tinytest/test_vimpute_ordered_factor.R |only inst/tinytest/test_vimpute_predictors.R |only inst/tinytest/test_vimpute_registry.R |only inst/tinytest/test_vimpute_restricted.R |only inst/tinytest/test_vimpute_restricted_lse.R |only inst/tinytest/test_vimpute_restricted_uncert.R |only inst/tinytest/test_vimpute_return_type.R |only inst/tinytest/test_vimpute_seed.R |only inst/tinytest/test_vimpute_spec.R |only inst/tinytest/test_vimpute_true_pmm.R |only inst/tinytest/test_vimpute_tune.R |only inst/tinytest/test_vimpute_tune_control.R |only inst/tinytest/test_vimpute_tune_once.R |only inst/tinytest/test_vimpute_uncert_default.R |only inst/tinytest/test_wrapper_hyperparams.R |only inst/tinytest/test_xgboostImpute.R | 16 man/VIM-package.Rd | 7 man/aggr.Rd | 2 man/barMiss.Rd | 2 man/bgmap.Rd | 4 man/bootstrap_resample.Rd |only man/build_gam_formula.Rd |only man/cellIRWLS.Rd |only man/cellWeights.Rd |only man/cellWeightsFromResiduals.Rd |only man/cellWeightsMCD.Rd |only man/colormapMiss.Rd | 2 man/complete_model_info.Rd |only man/diabetes.Rd | 89 man/dot-apply_weight_fun.Rd |only man/dot-robust_scale.Rd |only man/dot-weighted_qr_solve.Rd |only man/evaluation.Rd | 19 man/extract_model_info.Rd |only man/gowerD.Rd | 20 man/growdotMiss.Rd | 2 man/histMiss.Rd | 2 man/hotdeck.Rd | 8 man/huber_weight.Rd |only man/impPCA.Rd | 8 man/imputeCellEM.Rd |only man/imputeCellIRMI.Rd |only man/imputeCellM.Rd |only man/imputeCellMCD.Rd |only man/imputeCellMM.Rd |only man/imputeCellReg.Rd |only man/imputeCellwise.Rd |only man/imputeRobust.Rd | 21 man/imputeRobustChain.Rd | 21 man/inject_uncertainty.Rd |only man/irmi.Rd | 17 man/kNN.Rd | 47 man/lse_synthetic.Rd |only man/lse_synthetic_rules.Rd |only man/makeMissing.Rd |only man/mapMiss.Rd | 2 man/marginmatrix.Rd | 2 man/marginplot.Rd | 2 man/matchImpute.Rd | 8 man/matrixplot.Rd | 2 man/medianSamp.Rd | 8 man/midastouch_donors.Rd |only man/mosaicMiss.Rd | 2 man/new_vimmi.Rd |only man/oob_predictions.Rd |only man/overimpute.Rd |only man/pairsVIM.Rd | 2 man/parcoordMiss.Rd | 2 man/pbox.Rd | 2 man/plot.vimmi.Rd |only man/pmm_donor_selection.Rd |only man/pmm_observed_scores.Rd |only man/rangerImpute.Rd | 20 man/register_gam_learners.Rd |only man/register_vimpute_method.Rd |only man/regressionImp.Rd | 56 man/sampleCat.Rd | 8 man/scattJitt.Rd | 2 man/scattMiss.Rd | 2 man/scattmatrixMiss.Rd | 2 man/spineMiss.Rd | 2 man/tukey_weight.Rd |only man/unregister_vimpute_method.Rd |only man/unwrap_raw_model.Rd |only man/vim_as_mids.Rd |only man/vim_complete.Rd |only man/vimmi.Rd |only man/vimpute.Rd | 351 ++ man/vimpute_methods.Rd |only man/vimpute_search_space.Rd |only man/vimpute_spec.Rd |only man/vimpute_tune_control.Rd |only man/with.vimmi.Rd |only man/xgboostImpute.Rd | 17 src/Makevars |only src/RcppExports.cpp | 14 src/gowerD.cpp | 107 tests/test_vimpute_new_features.R |only tests/test_vimpute_smoke.R |only tests/tinytest.R | 9 vignettes/VIM.Rmd | 4 vignettes/VisualImp.Rmd | 3 vignettes/donorImp.Rmd | 4 vignettes/figures |only vignettes/impPCA.Rmd | 5 vignettes/irmi.Rmd | 15 vignettes/modelImp.Rmd | 5 vignettes/vimpute-benchmark.Rmd |only vignettes/vimpute-coverage.Rmd |only vignettes/vimpute-mi.Rmd |only vignettes/vimpute-restricted.Rmd |only vignettes/vimpute.Rmd | 332 +- vignettes/xgboostImpute.Rmd | 4 245 files changed, 9406 insertions(+), 3306 deletions(-)
Title: Clustering via Quadratic Scoring
Description: Performs tuning of clustering models, methods and algorithms including the problem of determining an appropriate number of clusters. Validation of cluster analysis results is performed via quadratic scoring using resampling methods, as in Coraggio, L. and Coretto, P. (2023) <doi:10.1016/j.jmva.2023.105181>.
Author: Luca Coraggio [cre, aut] ,
Pietro Coretto [aut]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
Diff between qcluster versions 2.0.1 dated 2026-06-05 and 3.0.0 dated 2026-09-02
qcluster-2.0.1/qcluster/R/bqs.R |only qcluster-2.0.1/qcluster/R/bqs_implementation_.R |only qcluster-2.0.1/qcluster/R/bqs_rank.R |only qcluster-2.0.1/qcluster/R/bqs_select.R |only qcluster-2.0.1/qcluster/R/d2ellipse_.R |only qcluster-2.0.1/qcluster/R/plot_bqs.R |only qcluster-2.0.1/qcluster/R/plot_mbcfit.R |only qcluster-2.0.1/qcluster/R/predict_mbcfit.R |only qcluster-2.0.1/qcluster/R/print_bqs.R |only qcluster-2.0.1/qcluster/R/print_mbcfit.R |only qcluster-2.0.1/qcluster/man/bqs.Rd |only qcluster-2.0.1/qcluster/man/bqs_rank.Rd |only qcluster-2.0.1/qcluster/man/bqs_select.Rd |only qcluster-2.0.1/qcluster/man/plot.bqs.Rd |only qcluster-2.0.1/qcluster/man/plot.mbcfit.Rd |only qcluster-2.0.1/qcluster/man/predict.mbcfit.Rd |only qcluster-2.0.1/qcluster/man/print.bqs.Rd |only qcluster-2.0.1/qcluster/man/print.mbcfit.Rd |only qcluster-2.0.1/qcluster/tests/testthat/test-bqs-parallel.R |only qcluster-2.0.1/qcluster/tests/testthat/test-bqs-select.R |only qcluster-2.0.1/qcluster/tests/testthat/test-plot-bqs.R |only qcluster-3.0.0/qcluster/DESCRIPTION | 8 qcluster-3.0.0/qcluster/MD5 | 143 ++-- qcluster-3.0.0/qcluster/NAMESPACE | 26 qcluster-3.0.0/qcluster/NEWS | 62 + qcluster-3.0.0/qcluster/R/apply_method.R |only qcluster-3.0.0/qcluster/R/ckclp_.R | 19 qcluster-3.0.0/qcluster/R/ckdat_.R | 5 qcluster-3.0.0/qcluster/R/clust2params.R | 2 qcluster-3.0.0/qcluster/R/dpboundary_.R | 2 qcluster-3.0.0/qcluster/R/dpdt_.R |only qcluster-3.0.0/qcluster/R/gmix.R | 87 +- qcluster-3.0.0/qcluster/R/iso_ellipse_.R |only qcluster-3.0.0/qcluster/R/mbind.R | 15 qcluster-3.0.0/qcluster/R/mset_gmix.R | 76 +- qcluster-3.0.0/qcluster/R/mset_kmeans.R | 43 + qcluster-3.0.0/qcluster/R/mset_names_.R |only qcluster-3.0.0/qcluster/R/mset_pam.R | 54 + qcluster-3.0.0/qcluster/R/mset_screen.R |only qcluster-3.0.0/qcluster/R/mset_screen_.R |only qcluster-3.0.0/qcluster/R/mset_tmix.R |only qcluster-3.0.0/qcluster/R/mset_user.R | 70 +- qcluster-3.0.0/qcluster/R/plot_clustering.R | 133 +++ qcluster-3.0.0/qcluster/R/plot_qcfit.R |only qcluster-3.0.0/qcluster/R/plot_qcluster.R |only qcluster-3.0.0/qcluster/R/predict_qcfit.R |only qcluster-3.0.0/qcluster/R/print_apply_method.R |only qcluster-3.0.0/qcluster/R/print_qcfit.R |only qcluster-3.0.0/qcluster/R/print_qcluster.R |only qcluster-3.0.0/qcluster/R/print_qcmethod.R |only qcluster-3.0.0/qcluster/R/qcluster-package.R | 117 ++- qcluster-3.0.0/qcluster/R/qcluster.R |only qcluster-3.0.0/qcluster/R/qcluster_implementation_.R |only qcluster-3.0.0/qcluster/R/qcluster_provenance_.R |only qcluster-3.0.0/qcluster/R/qcluster_rank.R |only qcluster-3.0.0/qcluster/R/qcluster_select.R |only qcluster-3.0.0/qcluster/R/stop_hint_.R |only qcluster-3.0.0/qcluster/R/tmix.R |only qcluster-3.0.0/qcluster/inst/CITATION | 5 qcluster-3.0.0/qcluster/man/apply_method.Rd |only qcluster-3.0.0/qcluster/man/clust2params.Rd | 2 qcluster-3.0.0/qcluster/man/gmix.Rd | 66 - qcluster-3.0.0/qcluster/man/mbind.Rd | 2 qcluster-3.0.0/qcluster/man/mset_gmix.Rd | 34 qcluster-3.0.0/qcluster/man/mset_kmeans.Rd | 14 qcluster-3.0.0/qcluster/man/mset_pam.Rd | 16 qcluster-3.0.0/qcluster/man/mset_screen.Rd |only qcluster-3.0.0/qcluster/man/mset_tmix.Rd |only qcluster-3.0.0/qcluster/man/mset_user.Rd | 34 qcluster-3.0.0/qcluster/man/plot.gmix.Rd |only qcluster-3.0.0/qcluster/man/plot.qcluster.Rd |only qcluster-3.0.0/qcluster/man/plot_clustering.Rd | 44 + qcluster-3.0.0/qcluster/man/predict.gmix.Rd |only qcluster-3.0.0/qcluster/man/print.apply_method.Rd |only qcluster-3.0.0/qcluster/man/print.mset_screen.Rd |only qcluster-3.0.0/qcluster/man/print.qcfit.Rd |only qcluster-3.0.0/qcluster/man/print.qcluster.Rd |only qcluster-3.0.0/qcluster/man/print.qcmethod.Rd |only qcluster-3.0.0/qcluster/man/qcluster-package.Rd |only qcluster-3.0.0/qcluster/man/qcluster.Rd | 345 ++++++++-- qcluster-3.0.0/qcluster/man/qcluster_rank.Rd |only qcluster-3.0.0/qcluster/man/qcluster_select.Rd |only qcluster-3.0.0/qcluster/man/summary.qcmethod.Rd |only qcluster-3.0.0/qcluster/man/tmix.Rd |only qcluster-3.0.0/qcluster/src/ecm.c | 127 +-- qcluster-3.0.0/qcluster/src/ecm_winit.c | 73 +- qcluster-3.0.0/qcluster/src/helper_ecm.c |only qcluster-3.0.0/qcluster/src/helper_ecm.h |only qcluster-3.0.0/qcluster/src/init.c | 262 +++++++ qcluster-3.0.0/qcluster/src/qclib.h | 27 qcluster-3.0.0/qcluster/src/tecm.c |only qcluster-3.0.0/qcluster/tests/testthat/helper-clustering.R | 16 qcluster-3.0.0/qcluster/tests/testthat/test-ckdat-validation.R | 2 qcluster-3.0.0/qcluster/tests/testthat/test-contour-iso-score.R |only qcluster-3.0.0/qcluster/tests/testthat/test-fit-failure-paths.R |only qcluster-3.0.0/qcluster/tests/testthat/test-gmix-clustering.R | 10 qcluster-3.0.0/qcluster/tests/testthat/test-mset-screen.R |only qcluster-3.0.0/qcluster/tests/testthat/test-mset-tmix.R |only qcluster-3.0.0/qcluster/tests/testthat/test-only-labels.R |only qcluster-3.0.0/qcluster/tests/testthat/test-plot-tmix-boundary.R |only qcluster-3.0.0/qcluster/tests/testthat/test-predict-plot.R | 3 qcluster-3.0.0/qcluster/tests/testthat/test-print-qcfit.R |only qcluster-3.0.0/qcluster/tests/testthat/test-qcluster-regression.R |only qcluster-3.0.0/qcluster/tests/testthat/test-qcluster.R |only qcluster-3.0.0/qcluster/tests/testthat/test-qcmethod-labels.R |only qcluster-3.0.0/qcluster/tests/testthat/test-reference-original-r.R | 4 qcluster-3.0.0/qcluster/tests/testthat/test-tmix-clustering.R |only qcluster-3.0.0/qcluster/tests/testthat/test-tmix-reference.R |only qcluster-3.0.0/qcluster/tests/testthat/test-tmix-scoring.R |only qcluster-3.0.0/qcluster/tests/testthat/test-univariate-and-plot.R |only 110 files changed, 1496 insertions(+), 452 deletions(-)
Title: A Novel Topology-Based Pathway Enrichment Analysis Approach
Description: We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database.
We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
Author: Wei Jiang [aut, cre]
Maintainer: Wei Jiang <jiangwei@hrbmu.edu.cn>
Diff between TPEA versions 3.1.0 dated 2017-06-25 and 3.1.1 dated 2026-09-02
DESCRIPTION | 18 - MD5 | 160 +++++----- NAMESPACE | 18 - R/AUEC.R | 104 +++--- R/DownloadKGML.R | 68 ++-- R/NodeGene.R | 32 +- R/NodeGeneData.R | 84 ++--- R/PathNetwork.R | 36 +- R/TPEA.R | 94 +++--- R/UPDATE.R | 20 - R/ViewLatestTime.R | 12 R/filterNode.R | 40 +- R/getEntry.R | 46 +-- R/getGeneFromEnzyme.R | 8 R/getGeneFromKGene.R | 26 - R/getGeneFromKO.R | 8 R/getGraphics.R | 30 - R/getKGeneFromEnzyme.R | 32 +- R/getKGeneFromKO.R | 26 - R/getNonMetabolicGraph.R | 670 ++++++++++++++++++++++---------------------- R/getOrgAndIdType.R | 12 R/getPathway.R | 158 +++++----- R/getProduct.R | 16 - R/getReaction.R | 76 ++-- R/getRelation.R | 44 +- R/getSimpleGraph.R | 126 ++++---- R/getSubstrate.R | 16 - R/getSubtype.R | 16 - R/getUGraph.R | 24 - R/getUnknowProduct.R | 12 R/getUnknowReaction.R | 12 R/getUnknowRelation.R | 12 R/getUnknowSubstrate.R | 12 R/getUnknowSubtype.R | 12 R/importLatesData.R | 20 - R/mapNode.R | 190 ++++++------ R/simplifyGraph.R | 398 +++++++++++++------------- R/viewpathway.R | 44 +- man/AUEC.Rd | 54 +-- man/DownloadKGML.Rd | 34 +- man/NodeGene.Rd | 40 +- man/NodeGeneData.Rd | 40 +- man/PathNetwork.Rd | 42 +- man/TPEA-package.Rd | 46 +-- man/TPEA.Rd | 100 +++--- man/UPDATE.Rd | 16 - man/ViewLatestTime.Rd | 36 +- man/all_genes.Rd | 12 man/filterNode.Rd | 22 - man/gene2ec.Rd | 20 - man/gene2ko.Rd | 20 - man/getEntry.Rd | 16 - man/getGeneFromEnzyme.Rd | 16 - man/getGeneFromKGene.Rd | 16 - man/getGeneFromKO.Rd | 16 - man/getGraphics.Rd | 16 - man/getKGeneFromEnzyme.Rd | 16 - man/getKGeneFromKO.Rd | 16 - man/getNonMetabolicGraph.Rd | 16 - man/getOrgAndIdType.Rd | 16 - man/getPathway.Rd | 16 - man/getProduct.Rd | 16 - man/getReaction.Rd | 16 - man/getRelation.Rd | 16 - man/getSimpleGraph.Rd | 16 - man/getSubstrate.Rd | 16 - man/getSubtype.Rd | 16 - man/getUGraph.Rd | 50 +-- man/getUnknowProduct.Rd | 16 - man/getUnknowReaction.Rd | 16 - man/getUnknowRelation.Rd | 16 - man/getUnknowSubstrate.Rd | 16 - man/getUnknowSubtype.Rd | 22 - man/importLatesData.Rd | 40 +- man/keggGene2gene.Rd | 20 - man/mapNode.Rd | 16 - man/node_gene.Rd | 12 man/num_node_gene_score.Rd | 12 man/pathway_names.Rd | 12 man/simplifyGraph.Rd | 16 - man/viewpathway.Rd | 72 ++-- 81 files changed, 1905 insertions(+), 1901 deletions(-)
Title: Disclosure Risk and Data Utility Metrics for Synthetic and
Anonymized Data
Description: Provides comprehensive methods to measure disclosure risk and data
utility for anonymized and synthetic data. Implements attribution-based risk
metrics including Correct Attribution Probability (CAP), Targeted CAP (TCAP),
Within Equivalence Class Attribution Probability (WEAP), and RAPID (Risk of
Attribute Prediction-Induced Disclosure). Also provides distance-based privacy
metrics such as Distance to Closest Record (DCR), Nearest Neighbor Distance
Ratio (NNDR), and Identical Match Share (IMS). Utility assessment includes
propensity score analysis, distribution comparisons, and various statistical
tests. Methods are based on Taub et al. (2018) <doi:10.1007/978-3-319-99771-1_9>
and related literature. Designed for integration with 'simPop' S4 classes.
Author: Matthias Templ [aut, cre] ,
Oscar Thees [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between riskutility versions 0.1.0 dated 2026-06-22 and 0.2.0 dated 2026-09-02
DESCRIPTION | 13 MD5 | 40 NAMESPACE | 1 NEWS.md | 60 R/compare_feature_importance.R | 105 R/dcr.R | 15 R/plot_rumap.R | 13 R/propscore.R | 2 R/recordLinkage.R | 10 R/tail_fidelity.R | 2 R/tcap.R | 189 + R/tstr.R | 29 inst/CITATION | 16 inst/doc/riskutility.html | 1707 +++++------ man/compare_feature_importance.Rd | 16 man/recordLinkage.Rd | 10 man/tcap.Rd | 104 tests/testthat/Rplots.pdf |binary tests/testthat/test-compare-feature-importance-permutation.R |only tests/testthat/test-disco-synthpop.R | 3 tests/testthat/test-tcap-dcap-synthpop.R | 94 tests/testthat/test-tcap-kind.R |only 22 files changed, 1433 insertions(+), 996 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb],
Reinhold Kainhofer [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.8.1 dated 2025-10-31 and 4.2.9 dated 2026-09-02
DESCRIPTION | 12 MD5 | 43 - NAMESPACE | 50 + NEWS.md | 9 R/openxlsxCoerce.R | 17 R/readWorkbook.R | 2 R/workbook_read_workbook.R | 2 R/wrappers.R | 1 R/writeData.R | 16 build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/Formatting.html | 4 inst/doc/Introduction.R | 18 inst/doc/Introduction.Rmd | 18 inst/doc/Introduction.html | 576 +++++++++++----------- man/openxlsx_options.Rd | 5 man/writeData.Rd | 5 tests/testthat/test-border_parsing.R | 306 +++++------ tests/testthat/test-date_detection_format_codes.R |only tests/testthat/test-loading_workbook.R | 70 +- tests/testthat/test-read_from_created_wb.R | 4 tests/testthat/test-writeData.R | 32 + vignettes/Introduction.Rmd | 18 23 files changed, 663 insertions(+), 549 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.12.0 dated 2026-07-17 and 1.13.0 dated 2026-09-02
DESCRIPTION | 16 +-- MD5 | 46 ++++---- NAMESPACE | 26 +++- NEWS.md | 7 + R/ArchiveAsync.R | 42 +++++++- R/ArchiveAsyncFrozen.R | 8 + R/OptimInstanceAsync.R | 3 R/OptimizerAsync.R | 61 +++++++++++ R/OptimizerBatchCmaes.R | 110 ++++++++++++++------- R/nds_selection.R | 14 +- R/zzz.R | 2 man/ArchiveAsync.Rd | 32 +++++- man/ArchiveAsyncFrozen.Rd | 8 + man/OptimizerAsync.Rd | 25 ++++ man/mlr_optimizers_cmaes.Rd | 32 ++++-- man/nds_selection.Rd | 4 man/optimize_async_default.Rd | 13 ++ tests/testthat/_snaps/OptimizerBatchCmaes.md | 4 tests/testthat/test_ArchiveAsync.R | 48 +++++++++ tests/testthat/test_ArchiveBatch.R | 2 tests/testthat/test_OptimInstanceAsyncSingleCrit.R | 24 ++++ tests/testthat/test_OptimizerAsync.R | 103 +++++++++++++++++++ tests/testthat/test_OptimizerBatchCmaes.R | 39 +++++++ tests/testthat/test_nds_selection.R | 20 ++- 24 files changed, 572 insertions(+), 117 deletions(-)
Title: Load Data in SQLite from Tabular Files
Description: A lightweight wrapper around the 'RSQLite' package for streamlined loading of
data from tabular files (i,e. text delimited files like Comma Separated Values and
Tab Separated Values, Microsoft Excel, and Arrow Inter-process Communication files)
in 'SQLite' databases. Includes helper functions for inspecting the structure of
the input files, and some functions to simplify activities on the 'SQLite' tables.
Author: Ludovico G. Beretta [aut, cre, cph]
Maintainer: Ludovico G. Beretta <ludovicogiovanni.beretta@gmail.com>
Diff between RSQLite.toolkit versions 0.1.3 dated 2026-06-27 and 0.1.4 dated 2026-09-02
DESCRIPTION | 10 - MD5 | 18 - NAMESPACE | 8 NEWS.md | 6 R/dbTableFromXlsx.R | 3 README.md | 2 inst/doc/dealing_with_DSV_files.R | 56 ++++- inst/doc/dealing_with_DSV_files.Rmd | 65 +++++- inst/doc/dealing_with_DSV_files.html | 337 +++++++++++++++++++---------------- vignettes/dealing_with_DSV_files.Rmd | 65 +++++- 10 files changed, 370 insertions(+), 200 deletions(-)
More information about RSQLite.toolkit at CRAN
Permanent link
Title: Analyzing Revisions in Real-Time Time Series Vintages
Description: Analyzes revisions in real-time time series vintages. The
package converts between wide revision triangles and tidy long
vintages, extracts selected releases, computes revision series,
visualizes vintage paths, and summarizes revision properties such as
bias, dispersion, autocorrelation, and news-noise diagnostics. It
also identifies efficient releases and estimates state-space models
for revision nowcasting. Methods are based on Howrey (1978)
<doi:10.2307/1924972>, Jacobs and Van Norden (2011)
<doi:10.1016/j.jeconom.2010.04.010>, and Kishor and Koenig (2012)
<doi:10.1198/jbes.2010.08169>.
Author: Marc Burri [aut, cre, cph] ,
Philipp Wegmueller [aut, cph]
Maintainer: Marc Burri <marc.burri91@gmail.com>
Diff between reviser versions 0.2.0 dated 2026-08-22 and 0.3.0 dated 2026-09-02
reviser-0.2.0/reviser/man/coef.jvn_model.Rd |only reviser-0.2.0/reviser/man/coef.kk_model.Rd |only reviser-0.2.0/reviser/man/fitted.jvn_model.Rd |only reviser-0.2.0/reviser/man/fitted.kk_model.Rd |only reviser-0.2.0/reviser/man/logLik.jvn_model.Rd |only reviser-0.2.0/reviser/man/logLik.kk_model.Rd |only reviser-0.2.0/reviser/man/nobs.jvn_model.Rd |only reviser-0.2.0/reviser/man/nobs.kk_model.Rd |only reviser-0.2.0/reviser/man/plot.jvn_model.Rd |only reviser-0.2.0/reviser/man/plot.kk_model.Rd |only reviser-0.2.0/reviser/man/plot.tbl_pubdate.Rd |only reviser-0.2.0/reviser/man/plot.tbl_release.Rd |only reviser-0.2.0/reviser/man/predict.jvn_model.Rd |only reviser-0.2.0/reviser/man/predict.kk_model.Rd |only reviser-0.2.0/reviser/man/print.jvn_model.Rd |only reviser-0.2.0/reviser/man/print.kk_model.Rd |only reviser-0.2.0/reviser/man/print.tbl_pubdate.Rd |only reviser-0.2.0/reviser/man/print.tbl_release.Rd |only reviser-0.2.0/reviser/man/residuals.jvn_model.Rd |only reviser-0.2.0/reviser/man/residuals.kk_model.Rd |only reviser-0.2.0/reviser/man/summary.jvn_model.Rd |only reviser-0.2.0/reviser/man/summary.kk_model.Rd |only reviser-0.2.0/reviser/man/summary.tbl_pubdate.Rd |only reviser-0.2.0/reviser/man/summary.tbl_release.Rd |only reviser-0.2.0/reviser/man/tbl_sum.tbl_pubdate.Rd |only reviser-0.2.0/reviser/man/tbl_sum.tbl_release.Rd |only reviser-0.2.0/reviser/man/vcov.jvn_model.Rd |only reviser-0.2.0/reviser/man/vcov.kk_model.Rd |only reviser-0.3.0/reviser/DESCRIPTION | 8 reviser-0.3.0/reviser/MD5 | 134 - reviser-0.3.0/reviser/NAMESPACE | 45 reviser-0.3.0/reviser/NEWS.md | 143 + reviser-0.3.0/reviser/R/data-vintages.R | 16 reviser-0.3.0/reviser/R/graphs.R | 97 - reviser-0.3.0/reviser/R/jvn.R | 345 +--- reviser-0.3.0/reviser/R/kk.R | 220 -- reviser-0.3.0/reviser/R/model-methods.R | 827 +++++----- reviser-0.3.0/reviser/R/reviser-package.R | 1 reviser-0.3.0/reviser/R/revisions.R | 12 reviser-0.3.0/reviser/R/utils.R | 441 +---- reviser-0.3.0/reviser/R/vintage-methods.R |only reviser-0.3.0/reviser/README.md | 14 reviser-0.3.0/reviser/data/gdp.rda |binary reviser-0.3.0/reviser/inst/CITATION | 20 reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-jvn.R | 21 reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-jvn.Rmd | 38 reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-jvn.html | 205 +- reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-kk.R | 11 reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-kk.Rmd | 25 reviser-0.3.0/reviser/inst/doc/nowcasting-revisions-kk.html | 164 + reviser-0.3.0/reviser/inst/doc/reviser.html | 249 +-- reviser-0.3.0/reviser/inst/doc/revision-analysis.html | 26 reviser-0.3.0/reviser/man/coef.revision_model.Rd |only reviser-0.3.0/reviser/man/diagnose.revision_summary.Rd | 2 reviser-0.3.0/reviser/man/figures/README-readme-example-1.png |binary reviser-0.3.0/reviser/man/fitted.revision_model.Rd |only reviser-0.3.0/reviser/man/gdp.Rd | 17 reviser-0.3.0/reviser/man/jvn_nowcast.Rd | 38 reviser-0.3.0/reviser/man/kk_nowcast.Rd | 36 reviser-0.3.0/reviser/man/logLik.revision_model.Rd |only reviser-0.3.0/reviser/man/nobs.revision_model.Rd |only reviser-0.3.0/reviser/man/plot.revision_model.Rd |only reviser-0.3.0/reviser/man/plot.tbl_vintage.Rd |only reviser-0.3.0/reviser/man/plot_vintages.Rd | 3 reviser-0.3.0/reviser/man/predict.revision_model.Rd |only reviser-0.3.0/reviser/man/print.revision_model.Rd |only reviser-0.3.0/reviser/man/print.tbl_vintage.Rd |only reviser-0.3.0/reviser/man/residuals.revision_model.Rd |only reviser-0.3.0/reviser/man/reviser-package.Rd | 3 reviser-0.3.0/reviser/man/revision_model.Rd |only reviser-0.3.0/reviser/man/states.Rd | 47 reviser-0.3.0/reviser/man/summary.revision_model.Rd |only reviser-0.3.0/reviser/man/summary.tbl_vintage.Rd |only reviser-0.3.0/reviser/man/tbl_sum.tbl_vintage.Rd |only reviser-0.3.0/reviser/man/tbl_vintage.Rd |only reviser-0.3.0/reviser/man/theme_reviser.Rd | 14 reviser-0.3.0/reviser/man/validate_vintages.Rd | 38 reviser-0.3.0/reviser/man/vcov.revision_model.Rd |only reviser-0.3.0/reviser/man/vintages_long.Rd | 23 reviser-0.3.0/reviser/man/vintages_wide.Rd | 10 reviser-0.3.0/reviser/tests/testthat/helper-runtime.R | 12 reviser-0.3.0/reviser/tests/testthat/test-graphs.R | 12 reviser-0.3.0/reviser/tests/testthat/test-kk.R | 4 reviser-0.3.0/reviser/tests/testthat/test-model-methods.R |only reviser-0.3.0/reviser/tests/testthat/test-revisions-panel.R |only reviser-0.3.0/reviser/tests/testthat/test-utils.R | 49 reviser-0.3.0/reviser/tests/testthat/test-vintage-methods.R |only reviser-0.3.0/reviser/vignettes/nowcasting-revisions-jvn.Rmd | 38 reviser-0.3.0/reviser/vignettes/nowcasting-revisions-kk.Rmd | 25 reviser-0.3.0/reviser/vignettes/precomputed/nowcasting-revisions-jvn-fit.rds |binary reviser-0.3.0/reviser/vignettes/precomputed/nowcasting-revisions-kk-efficient-release.rds |binary reviser-0.3.0/reviser/vignettes/precomputed/nowcasting-revisions-kk-fit.rds |binary 92 files changed, 1669 insertions(+), 1764 deletions(-)
Title: Offline Taxonomic Name Matching Against Darwin Core Backbones
Description: Match taxonomic names against locally stored Darwin Core backbone
databases ('WFO', 'COL', 'GBIF', 'ITIS', 'NCBI Taxonomy', 'Open Tree of Life',
'WoRMS', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase',
'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP',
'Mammal Diversity Database', 'AviList', 'LPSN'). Provides offline fuzzy and
exact matching with synonym resolution, hybrid name detection, and a unified
output schema across all sources. All heavy computation runs in the 'vectra'
C11 columnar engine.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between taxify versions 0.4.0 dated 2026-07-23 and 0.5.0 dated 2026-09-02
DESCRIPTION | 17 MD5 | 485 - NAMESPACE | 351 NEWS.md | 3166 ++++---- R/add-alpine-carabids.R |only R/add-betsi-collembola-body-length.R |only R/add-betsi-collembola-traits.R |only R/add-betsi-earthworm-traits.R |only R/add-chowdhury.R |only R/add-eberswalde.R |only R/add-ecomorphosis.R |only R/add-ellers-collembola.R |only R/add-faprotax.R |only R/add-finand.R |only R/add-fishbase.R | 35 R/add-hybrid-info.R | 13 R/add-hydraulics.R |only R/add-imageomics-neon.R |only R/add-inrae-collembola-traits.R |only R/add-monograph-collembola-body-length.R |only R/add-noddb.R |only R/add-plazi-collembola-body-length.R |only R/add-sealifebase.R | 32 R/add-sworm.R |only R/add-trait.R | 675 - R/add-virion.R |only R/backbones.R | 833 +- R/backend.R | 2034 ++--- R/backends-registry.R | 186 R/browse.R | 2 R/cache.R | 4 R/cite.R | 596 - R/content-store.R |only R/disambiguate-authorship.R | 230 R/download.R | 856 +- R/downstream.R | 2 R/enrichment-meta.R | 84 R/enrichment.R | 3864 ++++++---- R/lock.R | 659 + R/manifest.R | 675 - R/parse-name.R | 467 - R/pick.R | 207 R/region.R | 18 R/taxify-result.R | 438 - R/taxify.R | 2718 +++---- R/trait-registry.R | 703 + README.md | 583 - inst/doc/backbones.R | 5 inst/doc/backbones.Rmd | 1780 ++-- inst/doc/backbones.html | 199 inst/doc/custom-data.R | 18 inst/doc/custom-data.Rmd | 23 inst/doc/custom-data.html | 243 inst/doc/enrichments.R | 7 inst/doc/enrichments.Rmd | 5257 +++++++------- inst/doc/enrichments.html | 1253 +-- inst/doc/fuzzy-matching.R | 1 inst/doc/fuzzy-matching.Rmd | 8 inst/doc/fuzzy-matching.html | 24 inst/doc/hybrids-and-aggregates.R | 4 inst/doc/hybrids-and-aggregates.Rmd | 79 inst/doc/hybrids-and-aggregates.html | 205 inst/doc/inspecting-names.R | 6 inst/doc/inspecting-names.Rmd | 57 inst/doc/inspecting-names.html | 106 inst/doc/large-scale.R | 12 inst/doc/large-scale.Rmd | 1584 ++-- inst/doc/large-scale.html | 437 - inst/doc/migration.R | 9 inst/doc/migration.Rmd | 1009 +- inst/doc/migration.html | 132 inst/doc/quickstart.R | 4 inst/doc/quickstart.Rmd | 1004 +- inst/doc/quickstart.html | 148 inst/doc/regions.R | 3 inst/doc/regions.Rmd | 11 inst/doc/regions.html | 20 inst/exampledb/enrichment/austraits/latest/austraits.vtr |binary inst/exampledb/enrichment/bien/latest/bien.vtr |binary inst/manifest.json | 5484 ++++++++++++--- man/add_algae_traits.Rd | 112 man/add_alien_first_records.Rd | 124 man/add_alpine_carabids.Rd |only man/add_amniote.Rd | 110 man/add_amphibio.Rd | 116 man/add_anage.Rd | 106 man/add_animaltraits.Rd | 90 man/add_arctic_traits.Rd | 80 man/add_arthropod_traits.Rd | 108 man/add_austraits.Rd | 118 man/add_avonet.Rd | 112 man/add_bacdive.Rd | 106 man/add_bee_ostwald.Rd | 80 man/add_bet.Rd | 116 man/add_betsi_collembola_body_length.Rd |only man/add_betsi_collembola_traits.Rd |only man/add_betsi_earthworm_traits.Rd |only man/add_beukhof.Rd | 82 man/add_bien.Rd | 120 man/add_birdbase.Rd | 116 man/add_blanchard.Rd | 78 man/add_brot.Rd | 84 man/add_bryoatt.Rd | 118 man/add_ccdb.Rd | 124 man/add_cefas_btrait.Rd | 110 man/add_chelonians.Rd | 112 man/add_chowdhury.Rd |only man/add_classification.Rd | 88 man/add_clopla.Rd | 128 man/add_col_info.Rd | 94 man/add_combine.Rd | 102 man/add_combine_imputed.Rd | 118 man/add_combine_reported.Rd | 142 man/add_common_names.Rd | 118 man/add_copepod_traits.Rd | 100 man/add_coral_traits.Rd | 108 man/add_data.Rd | 238 man/add_diaz_traits.Rd | 88 man/add_disperse.Rd | 88 man/add_eberswalde.Rd |only man/add_ecomorphosis.Rd |only man/add_edwards_phyto.Rd | 112 man/add_eive.Rd | 100 man/add_ellers_collembola.Rd |only man/add_elton_traits.Rd | 130 man/add_epa_freshwater.Rd | 108 man/add_eupolltrait.Rd | 78 man/add_eurobat.Rd | 106 man/add_faprotax.Rd |only man/add_finand.Rd |only man/add_fishbase.Rd | 130 man/add_fishmorph.Rd | 128 man/add_fishtraits.Rd | 112 man/add_freshwater_insects_conus.Rd | 106 man/add_frugivoria.Rd | 78 man/add_fungal_traits.Rd | 122 man/add_fungalroot.Rd | 104 man/add_funguild.Rd | 112 man/add_gbif_info.Rd | 80 man/add_gidias.Rd | 228 man/add_globi.Rd | 110 man/add_globtherm.Rd | 96 man/add_glonaf.Rd | 116 man/add_gmpd.Rd | 124 man/add_gwdd.Rd | 90 man/add_homerange.Rd | 76 man/add_hosts.Rd | 92 man/add_huang_amph.Rd | 80 man/add_hybrid_info.Rd | 85 man/add_hydraulics.Rd |only man/add_imageomics_neon.Rd |only man/add_inrae_collembola_traits.Rd |only man/add_invacost.Rd | 108 man/add_italic.Rd | 102 man/add_iucn.Rd | 92 man/add_kew_cvalues.Rd | 118 man/add_kew_sid.Rd | 106 man/add_leda.Rd | 130 man/add_leptraits.Rd | 102 man/add_madin.Rd | 100 man/add_monograph_collembola_body_length.Rd |only man/add_nesttrait.Rd | 82 man/add_noddb.Rd |only man/add_nztd.Rd | 78 man/add_octocoral.Rd | 80 man/add_odonata.Rd | 76 man/add_pantheria.Rd | 102 man/add_parravicini.Rd | 76 man/add_pelagic.Rd | 80 man/add_phylacine.Rd | 126 man/add_pignatti.Rd | 110 man/add_plantatt.Rd | 120 man/add_plazi_collembola_body_length.Rd |only man/add_pottier.Rd | 82 man/add_quimbayo.Rd | 82 man/add_ramond.Rd | 108 man/add_repttraits.Rd | 144 man/add_rimet_phyto.Rd | 80 man/add_saproxylic.Rd | 80 man/add_sealifebase.Rd | 131 man/add_sharkipedia.Rd | 102 man/add_sheld.Rd | 78 man/add_spider_traits.Rd | 108 man/add_sworm.Rd |only man/add_tetradensity.Rd | 74 man/add_thermofresh.Rd | 94 man/add_trait.Rd | 8 man/add_tree_of_sex.Rd | 100 man/add_usda_fungus_host.Rd | 94 man/add_useful_plants.Rd | 104 man/add_virion.Rd |only man/add_wcvp.Rd | 112 man/add_wfo_info.Rd | 74 man/add_zooplankton.Rd | 82 man/candidate_order.Rd |only man/children.Rd | 82 man/cite.Rd | 62 man/class2tree.Rd | 106 man/comm2sci.Rd | 134 man/downstream.Rd | 96 man/enrichment_cols.Rd | 58 man/enrichment_groups.Rd | 74 man/export_data.Rd | 72 man/gift_traits.Rd | 60 man/id2name.Rd | 112 man/inspect.Rd | 230 man/install_backbones.Rd | 70 man/list_backbones.Rd | 71 man/list_enrichments.Rd | 52 man/lookup_genus.Rd | 36 man/lowest_common.Rd | 82 man/parse_name.Rd | 114 man/print.taxify_result.Rd | 40 man/reconcile.Rd | 132 man/sci2comm.Rd | 122 man/score_candidates.Rd | 27 man/sub-.taxify_result.Rd | 54 man/summary.taxify_result.Rd | 44 man/synonyms.Rd | 100 man/taxify-package.Rd | 56 man/taxify.Rd | 556 - man/taxify_candidates.Rd | 100 man/taxify_clear_cache.Rd | 30 man/taxify_data_dir.Rd | 46 man/taxify_databases.Rd | 68 man/taxify_download.Rd | 94 man/taxify_download_enrichment.Rd | 95 man/taxify_load_register.Rd | 54 man/taxify_lock.Rd | 90 man/taxify_refresh_manifest.Rd | 32 man/taxify_register_coverage.Rd | 40 man/taxify_restore.Rd | 103 man/taxify_store.Rd |only man/upstream.Rd | 108 tests/testthat/helper-grain.R | 6 tests/testthat/helper-mock-coverage.R | 77 tests/testthat/test-add-trait.R | 3 tests/testthat/test-backbone-content-id.R | 35 tests/testthat/test-backbones.R | 90 tests/testthat/test-content-store.R |only tests/testthat/test-cross-backbone-recovery.R |only tests/testthat/test-default-backend.R | 172 tests/testthat/test-enrich-by-group-authorship.R |only tests/testthat/test-enrichment-content-id.R | 91 tests/testthat/test-extensions.R | 9 tests/testthat/test-fuzzy-boundary.R | 611 - tests/testthat/test-gap-verbs.R | 720 + tests/testthat/test-gbif.R | 424 - tests/testthat/test-infra-marker-recovery.R |only tests/testthat/test-manifest.R | 21 tests/testthat/test-match.R | 915 +- tests/testthat/test-new-verbs.R | 528 - tests/testthat/test-quality-staged-chain.R |only tests/testthat/test-register.R | 630 - tests/testthat/test-source-date.R |only tests/testthat/test-trait-registry.R | 195 vignettes/backbones.Rmd | 1780 ++-- vignettes/custom-data.Rmd | 23 vignettes/enrichments.Rmd | 5257 +++++++------- vignettes/fuzzy-matching.Rmd | 8 vignettes/hybrids-and-aggregates.Rmd | 79 vignettes/inspecting-names.Rmd | 57 vignettes/large-scale.Rmd | 1584 ++-- vignettes/migration.Rmd | 1009 +- vignettes/quickstart.Rmd | 1004 +- vignettes/regions.Rmd | 11 266 files changed, 37550 insertions(+), 30318 deletions(-)
Title: Modular Monte Carlo Risk Analysis
Description: Framework for building modular Monte Carlo risk analysis models. It extends the capabilities of 'mc2d' to facilitate working with multiple risk pathways, variates and scenarios. It provides tools to organize risk analysis in independent flexible modules, align multivariate mcnodes, automate the creation of mcnodes, visualise model structure, assess convergence, and perform sensitivity analysis. For more details see Ciria (2026) <https://nataliaciria.com/mcmodule/>.
Author: Natalia Ciria [aut, cre, cph] ,
Alberto Allepuz [ths] ,
Giovanna Ciaravino [ths]
Maintainer: Natalia Ciria <nataliaciria@hotmail.com>
Diff between mcmodule versions 1.3.0 dated 2026-05-25 and 1.3.1 dated 2026-09-02
DESCRIPTION | 8 MD5 | 55 NAMESPACE | 1 NEWS.md | 34 R/get_node_list.R | 2 R/mc_analysis.R | 3053 ++++++++++++++++------------------ R/mc_network.R | 2 R/mc_plot.R | 71 R/totals.R | 81 README.md | 268 +- inst/doc/mcmodule.R | 59 inst/doc/mcmodule.Rmd | 82 inst/doc/mcmodule.html | 273 ++- inst/doc/multivariate_operations.html | 26 inst/doc/sensitivity_analysis.Rmd | 26 inst/doc/sensitivity_analysis.html | 176 + man/agg_totals.Rd | 49 man/agg_variates.Rd |only man/mc_network.Rd | 2 man/mcmodule_corr.Rd | 2 tests/testthat/test-add_prefix.R | 2 tests/testthat/test-dim_match.R | 4 tests/testthat/test-eval_module.R | 2 tests/testthat/test-mc_analysis.R | 7 tests/testthat/test-mc_compare.R | 6 tests/testthat/test-totals.R | 63 vignettes/mcmodule.Rmd | 82 vignettes/references.bib | 69 vignettes/sensitivity_analysis.Rmd | 26 29 files changed, 2384 insertions(+), 2147 deletions(-)
Title: Convex Optimal Designs for Group Testing Experiments
Description: Finite candidate-set approximate optimal designs for group
testing and related experiments, using convex optimization and equivalence
checks. Implements the information matrix and cost structure for the
prevalence / sensitivity / specificity model used in Huang and colleagues
(2020), as in Chi-Kuang Yeh, Weng Kee Wong, and Julie Zhou (<doi:10.48550/arXiv.2508.08445>).
Author: Chi-Kuang Yeh [aut, cre] ,
Julie Zhou [aut],
Weng Kee Wong [ctb]
Maintainer: Chi-Kuang Yeh <cyeh@gsu.edu>
Diff between gtDesign versions 0.1.0 dated 2026-04-09 and 0.1.1 dated 2026-09-02
gtDesign-0.1.0/gtDesign/inst/WORDLIST |only gtDesign-0.1.1/gtDesign/DESCRIPTION | 10 +- gtDesign-0.1.1/gtDesign/MD5 | 16 ++-- gtDesign-0.1.1/gtDesign/NAMESPACE | 12 +-- gtDesign-0.1.1/gtDesign/R/rounding_gt_budget.R | 16 +++- gtDesign-0.1.1/gtDesign/README.md | 38 +++++----- gtDesign-0.1.1/gtDesign/inst/examples |only gtDesign-0.1.1/gtDesign/man/plot_equivalence.Rd | 2 gtDesign-0.1.1/gtDesign/tests/testthat/test-huang2020-paper.R | 4 - 9 files changed, 60 insertions(+), 38 deletions(-)
Title: A Unified Tidy Interface to R's Machine Learning Ecosystem
Description: Provides a unified tidyverse-compatible interface to R's machine
learning ecosystem - from data ingestion to model publishing. The tl_read()
family reads data from files ('CSV', 'Excel', 'Parquet', 'JSON'), databases
('SQLite', 'PostgreSQL', 'MySQL', 'BigQuery'), and cloud sources ('S3',
'GitHub', 'Kaggle'). The tl_model() function wraps established
implementations from 'glmnet', 'randomForest', 'xgboost', 'e1071', 'rpart',
'gbm', 'nnet', 'cluster', 'dbscan', and others with consistent function
signatures and tidy tibble output. Results flow into unified 'ggplot2'-based
visualization and optional formatted 'gt' tables via the tl_table() family.
The underlying algorithms are unchanged; 'tidylearn' simply makes them
easier to use together. Access raw model objects via the $fit slot for a
supervised method, or $fit$model for an unsupervised one.
Methods include random forests Breiman (2001) <doi:10.1023/A:1010933404324>,
LASSO regression Tibshirani (1996) <doi:10.1111/j.2517-6161 [...truncated...]
Author: Cesaire Tobias [aut, cre]
Maintainer: Cesaire Tobias <cesaire@sheetsolved.com>
Diff between tidylearn versions 0.4.0 dated 2026-08-03 and 0.5.0 dated 2026-09-02
DESCRIPTION | 30 MD5 | 266 +++--- NAMESPACE | 4 NEWS.md | 762 +++++++++++++++++ R/cloud-consent.R |only R/cloud-cost.R |only R/cloud-endpoint.R |only R/cloud-serialize.R |only R/compute-advisor.R | 4 R/compute-detection.R | 3 R/core.R | 346 +++++++ R/diagnostics.R | 231 ++++- R/integration.R | 26 R/interactions.R | 57 + R/metrics.R | 132 ++ R/pipeline.R | 701 ++++++++++++--- R/preprocessing.R | 51 + R/read-backends.R | 234 ++++- R/read.R | 34 R/supervised-classification.R | 64 + R/supervised-deep-learning.R | 43 R/supervised-neural-networks.R | 53 + R/supervised-regularization.R | 25 R/supervised-svm.R | 59 - R/supervised-trees.R | 140 +-- R/supervised-xgboost.R | 199 +++- R/tuning.R | 237 ++++- R/unsupervised-clustering.R | 14 R/unsupervised-dbscan.R | 45 - R/unsupervised-distance.R | 21 R/unsupervised-hclust.R | 31 R/unsupervised-market-basket.R | 5 R/unsupervised-mds.R | 46 - R/unsupervised-pca.R | 92 +- R/unsupervised-validation.R | 2 R/utils.R | 575 +++++++++++- R/visualization.R | 73 + R/workflows.R | 140 ++- README.md | 137 ++- build/vignette.rds |binary inst/CITATION | 42 inst/WORDLIST | 53 + inst/doc/automl.R | 464 +++------- inst/doc/automl.Rmd | 674 +++++---------- inst/doc/automl.html | 902 ++++++++------------ inst/doc/compute-backends.R |only inst/doc/compute-backends.Rmd |only inst/doc/compute-backends.html |only inst/doc/data-ingestion.html | 16 inst/doc/diagnostics.R |only inst/doc/diagnostics.Rmd |only inst/doc/diagnostics.html |only inst/doc/getting-started.R | 10 inst/doc/getting-started.Rmd | 90 +- inst/doc/getting-started.html | 151 +-- inst/doc/integration-workflows.R | 45 - inst/doc/integration-workflows.Rmd | 148 +-- inst/doc/integration-workflows.html | 506 ++--------- inst/doc/market-basket.R |only inst/doc/market-basket.Rmd |only inst/doc/market-basket.html |only inst/doc/reporting.Rmd | 36 inst/doc/reporting.html | 1285 ++++++++++++++--------------- inst/doc/supervised-learning.R | 16 inst/doc/supervised-learning.Rmd | 52 - inst/doc/supervised-learning.html | 172 +-- inst/doc/tuning-and-pipelines.R |only inst/doc/tuning-and-pipelines.Rmd |only inst/doc/tuning-and-pipelines.html |only inst/doc/unsupervised-learning.R | 363 +++----- inst/doc/unsupervised-learning.Rmd | 565 +++++++----- inst/doc/unsupervised-learning.html | 1022 +++++++++++------------ inst/examples/unified_workflow.R | 32 inst/security/threat-model.md | 448 ++++++++-- man/get_pca_loadings.Rd | 3 man/get_pca_variance.Rd | 6 man/plot_mds.Rd | 4 man/predict.tidylearn_transfer.Rd | 2 man/print.tidylearn_automl.Rd | 12 man/print.tidylearn_compute_advice.Rd | 5 man/print.tidylearn_gpu_check.Rd | 4 man/recommend_products.Rd | 5 man/suggest_eps.Rd | 2 man/tidy_dbscan.Rd | 88 - man/tidy_pca_biplot.Rd | 3 man/tidylearn-cloud-consent.Rd |only man/tidylearn-cloud-cost.Rd |only man/tidylearn-cloud-endpoint.Rd |only man/tidylearn-cloud-serialize.Rd |only man/tidylearn-core.Rd | 4 man/tidylearn-package.Rd | 3 man/tl_anomaly_aware.Rd | 7 man/tl_check_assumptions.Rd | 66 - man/tl_cloud_allow_host.Rd |only man/tl_cloud_allowed_hosts.Rd |only man/tl_cloud_consent.Rd |only man/tl_cloud_jobs.Rd |only man/tl_compare_pipeline_models.Rd | 16 man/tl_cv.Rd | 11 man/tl_event_level_args.Rd |only man/tl_fit_deep.Rd | 6 man/tl_fit_forest.Rd | 6 man/tl_fit_svm.Rd | 5 man/tl_interaction_effects.Rd | 28 man/tl_model.Rd | 23 man/tl_pipeline.Rd | 88 - man/tl_plot_cv_results.Rd | 9 man/tl_plot_interaction.Rd | 12 man/tl_plot_nn_tuning.Rd | 18 man/tl_plot_xgboost_shap_dependence.Rd | 14 man/tl_plot_xgboost_tree.Rd | 11 man/tl_predict_boost.Rd | 56 - man/tl_predict_pipeline.Rd | 20 man/tl_predict_xgboost.Rd | 19 man/tl_read_kaggle.Rd | 6 man/tl_read_zip.Rd | 5 man/tl_semisupervised.Rd | 7 man/tl_stratified_models.Rd | 7 man/tl_transfer_learning.Rd | 9 man/tl_tune_nn.Rd | 14 man/tl_tune_random.Rd | 16 man/tl_tune_xgboost.Rd | 28 tests/testthat.R | 45 - tests/testthat/setup.R | 37 tests/testthat/test-cloud-cost.R |only tests/testthat/test-cloud-guards.R |only tests/testthat/test-cloud-roundtrip.R |only tests/testthat/test-cloud-serialize.R |only tests/testthat/test-core.R | 176 ++- tests/testthat/test-degenerate-specs.R |only tests/testthat/test-diagnostics.R | 665 ++++++++------- tests/testthat/test-examples.R |only tests/testthat/test-integration.R | 17 tests/testthat/test-leakage-and-guards.R |only tests/testthat/test-metrics-correctness.R |only tests/testthat/test-predict-contract.R |only tests/testthat/test-read.R | 137 ++- tests/testthat/test-supervised.R | 258 +++++ tests/testthat/test-tuning.R | 210 ++++ tests/testthat/test-unsupervised-predict.R | 140 +++ tests/testthat/test-unsupervised.R | 162 +++ tests/testthat/test-visualization.R | 514 ++++++----- tests/testthat/test-workflows.R | 59 + vignettes/automl.Rmd | 674 +++++---------- vignettes/compute-backends.Rmd |only vignettes/diagnostics.Rmd |only vignettes/getting-started.Rmd | 90 +- vignettes/integration-workflows.Rmd | 148 +-- vignettes/market-basket.Rmd |only vignettes/reporting.Rmd | 36 vignettes/supervised-learning.Rmd | 52 - vignettes/tuning-and-pipelines.Rmd |only vignettes/unsupervised-learning.Rmd | 565 +++++++----- 153 files changed, 10478 insertions(+), 6129 deletions(-)
Title: Utilities for Joining Dataframes with Inexact Matching
Description: Provides functions for joining data frames based on inexact
criteria, including string distance, Manhattan distance, Euclidean
distance, and interval overlap. This API is designed as a modern,
performance-oriented alternative to the 'fuzzyjoin' package (Robinson 2026)
<doi:10.32614/CRAN.package.fuzzyjoin>. String distance functions utilizing
'q-grams' are adapted with permission from the 'textdistance' 'Rust' crate
(Orsinium 2024) <https://docs.rs/textdistance/latest/textdistance/>. Other
string distance calculations rely on the 'rapidfuzz' 'Rust' crate (Bachmann
2023) <https://docs.rs/rapidfuzz/0.5.0/rapidfuzz/>. Interval joins are
backed by a Adelson-Velsky and Landis tree as implemented by the 'interavl'
'Rust' crate <https://docs.rs/interavl/0.5.0/interavl/>.
Author: Jon Downs [aut, cre],
The authors of the dependency Rust crates [ctb, cph]
Maintainer: Jon Downs <jon@jondowns.net>
Diff between fozziejoin versions 0.0.13 dated 2026-03-09 and 0.0.16 dated 2026-09-02
DESCRIPTION | 10 - MD5 | 54 +++++----- NEWS.md | 20 +++ R/fozzie_string_join.R | 6 - README.md | 64 ++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/overview.R | 3 inst/doc/overview.Rmd | 4 inst/doc/overview.html | 36 +++--- inst/doc/string_dist_benchmarking.R | 17 ++- inst/doc/string_dist_benchmarking.Rmd | 21 ++-- inst/doc/string_dist_benchmarking.html | 107 ++++++++++---------- man/fozzie_string_join_family.Rd | 12 -- man/fozziejoin-package.Rd | 5 src/Makevars.win.in | 2 src/rust/Cargo.lock | 56 ++++++++-- src/rust/Cargo.toml | 2 src/rust/src/merge/mod.rs | 2 src/rust/src/string/ngram/jaccard.rs | 131 +++++++++++++++---------- src/rust/vendor.tar.xz |binary tests/testthat/setup.R | 1 tests/testthat/test_fozzie_difference_join.R | 26 ---- tests/testthat/test_fozzie_string_inner_join.R | 51 +++------ tests/testthat/test_fozzie_temporal_join.R | 16 +-- tools/config.R | 11 ++ vignettes/overview.Rmd | 4 vignettes/string_dist_benchmarking.Rmd | 21 ++-- 28 files changed, 369 insertions(+), 313 deletions(-)
Title: Access and Analyse 'VALD' Data via Our External 'APIs'
Description: Provides helper functions and wrappers to simplify authentication,
data retrieval, and result processing from the 'VALD' 'APIs'.
Designed to streamline integration for analysts and researchers working
with 'VALD's external 'APIs'.
For further documentation on integrating with 'VALD' 'APIs', see:
<https://support.vald.com/hc/en-au/articles/23415335574553-How-to-integrate-with-VALD-APIs>.
For a step-by-step guide to using this package, see:
<https://support.vald.com/hc/en-au/articles/48730811824281-A-guide-to-using-the-valdr-R-package>.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdr versions 3.0.0 dated 2026-04-22 and 4.0.0 dated 2026-09-02
DESCRIPTION | 6 MD5 | 73 + NAMESPACE | 8 R/config.R | 50 - R/dev |only R/dynamo_tests.R |only R/dynamo_tests_by_id.R |only R/forceframe_tests_by_id.R | 6 R/humantrak_reps_by_id.R |only R/humantrak_test_type_metrics.R |only R/humantrak_tests.R |only R/nordbord_tests_by_id.R | 4 R/profiles.R | 4 R/profiles_by_id.R |only R/session.R | 250 +++++- R/utils.R | 767 ++++++++++++++++++- man/dot-build_dynamo_asymmetries_df.Rd |only man/dot-build_dynamo_df.Rd |only man/dot-build_dynamo_ratios_df.Rd |only man/dot-build_dynamo_repetition_type_summaries_df.Rd |only man/dot-build_dynamo_repetitions_df.Rd |only man/dot-build_humantrak_df.Rd |only man/dot-build_humantrak_metric_groups_df.Rd |only man/dot-build_humantrak_repetition_counts_df.Rd |only man/dot-build_humantrak_repetitions_df.Rd |only man/dot-build_humantrak_summary_measurements_df.Rd |only man/dot-build_humantrak_test_type_metrics_df.Rd |only man/dot-build_profile_details_df.Rd |only man/dot-extract_nested_character_list.Rd |only man/get_dynamo_data.Rd |only man/get_dynamo_test_by_id.Rd |only man/get_dynamo_tests.Rd |only man/get_dynamo_tests_by_id.Rd |only man/get_dynamo_tests_only.Rd |only man/get_forceframe_repetitions_by_id.Rd | 2 man/get_forceframe_test_by_id.Rd | 2 man/get_forceframe_tests_by_id.Rd | 3 man/get_humantrak_data.Rd |only man/get_humantrak_repetitions_by_id.Rd |only man/get_humantrak_reps_by_id.Rd |only man/get_humantrak_test_type_metrics.Rd |only man/get_humantrak_test_type_metrics_only.Rd |only man/get_humantrak_tests.Rd |only man/get_humantrak_tests_only.Rd |only man/get_nordbord_test_by_id.Rd | 2 man/get_nordbord_tests_by_id.Rd | 3 man/get_nordbord_tests_only.Rd | 2 man/get_profile_by_id.Rd |only man/get_profiles_by_id.Rd |only man/get_profiles_groups_categories.Rd | 4 man/get_profiles_groups_categories_mapping.Rd | 13 man/load_credentials.Rd | 14 tests/testthat/test-12-dynamo-humantrak-builders.R |only tests/testthat/test-13-profile-by-id.R |only tests/testthat/test-14-dynamo-long-form.R |only tests/testthat/test-15-humantrak-relational.R |only tests/testthat/test-16-new-retrieval-visibility.R |only 57 files changed, 1107 insertions(+), 106 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <https://www.openstreetmap.org/>,
Bing Maps <https://www.bing.com/maps> and other tiled map sources. Use to create
basemaps quickly and add hillshade to vector-based maps.
Author: Dewey Dunnington [aut, cre] ,
Timothee Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.3.1 dated 2026-01-21 and 0.3.2 dated 2026-09-02
DESCRIPTION | 8 +++---- MD5 | 10 ++++----- NEWS.md | 5 ++++ R/deprecated.R | 42 +++++++++++++++++++++++++++++---------- man/deprecated.Rd | 10 +++++++-- tests/testthat/test-deprecated.R | 32 +++++++++++++++++++++++++++-- 6 files changed, 84 insertions(+), 23 deletions(-)
Title: Read and Write ODS Files
Description: Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten [aut],
Chung-hong Chan [aut, cre] ,
Peter Brohan [aut],
Detlef Steuer [aut] ,
Thomas J. Leeper [aut] ,
John Foster [ctb],
Sergio Oller [ctb],
Jim Hester [ctb] ,
Stephen Watts [ctb],
Arthur Katossky [ctb],
Stas Malavin [ctb],
Dunca [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 2.3.5 dated 2026-04-13 and 2.3.6 dated 2026-09-02
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 4 README.md | 10 - src/cpp11.cpp | 8 src/get_sheet_names.cpp | 11 - src/is_ods.cpp | 3 src/read_flat_ods_.cpp | 9 src/read_ods_.cpp | 7 src/splice.cpp | 236 ++++++++------------------ src/splice.h | 11 - src/write_sheet_file_.cpp | 6 tests/testthat/test_read_ods.R | 4 tests/testthat/test_write_ods_append_update.R | 14 + 14 files changed, 141 insertions(+), 216 deletions(-)
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.7 dated 2026-05-23 and 0.1.0 dated 2026-09-02
readNSx-0.0.7/readNSx/R/hdf5-alternative.R |only readNSx-0.1.0/readNSx/DESCRIPTION | 14 readNSx-0.1.0/readNSx/MD5 | 32 readNSx-0.1.0/readNSx/NEWS.md | 29 readNSx-0.1.0/readNSx/R/bci2000.R | 8 readNSx-0.1.0/readNSx/R/blackrock.R | 11 readNSx-0.1.0/readNSx/R/cpp11.R | 40 readNSx-0.1.0/readNSx/R/hdf5.R | 652 +++++--------- readNSx-0.1.0/readNSx/R/nsx.R | 2 readNSx-0.1.0/readNSx/R/specifications.R | 2 readNSx-0.1.0/readNSx/R/validators.R | 2 readNSx-0.1.0/readNSx/build/vignette.rds |binary readNSx-0.1.0/readNSx/man/import_nsp.Rd | 14 readNSx-0.1.0/readNSx/src/Makevars |only readNSx-0.1.0/readNSx/src/cpp11.cpp | 122 ++ readNSx-0.1.0/readNSx/src/h5native.cpp |only readNSx-0.1.0/readNSx/tests/testthat/golden-hdf5r.h5 |only readNSx-0.1.0/readNSx/tests/testthat/test-h5-allocation.R | 85 - readNSx-0.1.0/readNSx/tests/testthat/test-h5.R |only readNSx-0.1.0/readNSx/tests/testthat/test-hdf5r-compat.R |only 20 files changed, 487 insertions(+), 526 deletions(-)
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).
Author: Hung Nguyen [aut],
Bang Tran [aut],
Duc Tran [aut],
Tin Nguyen [aut],
Van-Dung Pham [cre]
Maintainer: Van-Dung Pham <dvp0001@wayne.edu>
Diff between PINSPlus versions 2.0.9 dated 2025-07-29 and 2.0.10 dated 2026-09-02
DESCRIPTION | 14 +- MD5 | 4 inst/doc/PINSPlus.html | 260 ++++++++++++++++++++++++------------------------- 3 files changed, 138 insertions(+), 140 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.5.1 dated 2026-07-27 and 1.5.2 dated 2026-09-02
nhdplusTools-1.5.1/nhdplusTools/build/vignette.rds |only nhdplusTools-1.5.1/nhdplusTools/inst/doc |only nhdplusTools-1.5.1/nhdplusTools/vignettes |only nhdplusTools-1.5.2/nhdplusTools/DESCRIPTION | 13 nhdplusTools-1.5.2/nhdplusTools/MD5 | 202 ++++------ nhdplusTools-1.5.2/nhdplusTools/NEWS.md | 5 nhdplusTools-1.5.2/nhdplusTools/R/A_nhdplusTools.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/calc_network.R | 32 - nhdplusTools-1.5.2/nhdplusTools/R/discover_nhdplus.R | 11 nhdplusTools-1.5.2/nhdplusTools/R/downloading_tools.R | 38 - nhdplusTools-1.5.2/nhdplusTools/R/get_codes.R | 92 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_drainage_area_estimates.R | 8 nhdplusTools-1.5.2/nhdplusTools/R/get_geoconnex.R | 24 - nhdplusTools-1.5.2/nhdplusTools/R/get_hydro.R | 61 --- nhdplusTools-1.5.2/nhdplusTools/R/get_network.R | 84 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_nhdplus.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/get_nhdplushr.R | 63 --- nhdplusTools-1.5.2/nhdplusTools/R/get_nldi.R | 83 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_oaproc.R | 136 ------ nhdplusTools-1.5.2/nhdplusTools/R/get_path_lengths.R | 26 - nhdplusTools-1.5.2/nhdplusTools/R/get_paths.R | 47 -- nhdplusTools-1.5.2/nhdplusTools/R/get_vaa.R | 29 - nhdplusTools-1.5.2/nhdplusTools/R/index_nhdplus.R | 81 ---- nhdplusTools-1.5.2/nhdplusTools/R/map_nhdplus.R | 15 nhdplusTools-1.5.2/nhdplusTools/R/plot_nhdplus.R | 77 --- nhdplusTools-1.5.2/nhdplusTools/R/prep_nhdplus.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/rebuild_topology.R | 19 nhdplusTools-1.5.2/nhdplusTools/R/rescale_catchments.R | 27 - nhdplusTools-1.5.2/nhdplusTools/R/run_plus_attributes.R | 14 nhdplusTools-1.5.2/nhdplusTools/R/subset_nhdplus.R | 91 ---- nhdplusTools-1.5.2/nhdplusTools/man/add_plus_network_attributes.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/align_nhdplus_names.Rd | 12 nhdplusTools-1.5.2/nhdplusTools/man/calculate_arbolate_sum.Rd | 17 nhdplusTools-1.5.2/nhdplusTools/man/calculate_total_drainage_area.Rd | 17 nhdplusTools-1.5.2/nhdplusTools/man/disambiguate_flowline_indexes.Rd | 39 - nhdplusTools-1.5.2/nhdplusTools/man/discover_geoconnex_reference.Rd | 6 nhdplusTools-1.5.2/nhdplusTools/man/discover_nhdplus_id.Rd | 12 nhdplusTools-1.5.2/nhdplusTools/man/download_nhd.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/download_nhdplushr.Rd | 13 nhdplusTools-1.5.2/nhdplusTools/man/download_nhdplusv2.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/download_rf1.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/download_wbd.Rd | 63 +-- nhdplusTools-1.5.2/nhdplusTools/man/get_3dhp.Rd | 41 -- nhdplusTools-1.5.2/nhdplusTools/man/get_DD.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_DM.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_UM.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_UT.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_catchment_characteristics.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/get_characteristics_metadata.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/get_drainage_area_estimates.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_elev_along_path.Rd | 27 - nhdplusTools-1.5.2/nhdplusTools/man/get_flowline_index.Rd | 30 - nhdplusTools-1.5.2/nhdplusTools/man/get_geoconnex_reference.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/get_levelpaths.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_nhdphr.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/get_nhdplus.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_nhdplushr.Rd | 24 - nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_basin.Rd | 34 - nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_feature.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_index.Rd | 18 nhdplusTools-1.5.2/nhdplusTools/man/get_path_lengths.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_path_members.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_pathlength.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_pfaf.Rd | 57 -- nhdplusTools-1.5.2/nhdplusTools/man/get_raindrop_trace.Rd | 18 nhdplusTools-1.5.2/nhdplusTools/man/get_sorted.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_split_catchment.Rd | 54 -- nhdplusTools-1.5.2/nhdplusTools/man/get_streamlevel.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/get_streamorder.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_terminal.Rd | 11 nhdplusTools-1.5.2/nhdplusTools/man/get_tocomid.Rd | 8 nhdplusTools-1.5.2/nhdplusTools/man/get_vaa.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_vaa_names.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_waterbody_index.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_wb_outlet.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_xs_point.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/get_xs_points.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/make_node_topology.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/make_standalone.Rd | 41 -- nhdplusTools-1.5.2/nhdplusTools/man/map_nhdplus.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/navigate_network.Rd | 28 - nhdplusTools-1.5.2/nhdplusTools/man/navigate_nldi.Rd | 30 - nhdplusTools-1.5.2/nhdplusTools/man/plot_nhdplus.Rd | 65 --- nhdplusTools-1.5.2/nhdplusTools/man/prepare_nhdplus.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/reexports.Rd | 2 nhdplusTools-1.5.2/nhdplusTools/man/rescale_catchment_characteristics.Rd | 158 +++---- nhdplusTools-1.5.2/nhdplusTools/man/subset_nhdplus.Rd | 76 --- nhdplusTools-1.5.2/nhdplusTools/man/subset_rpu.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/subset_vpu.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/tests/testthat.R | 8 90 files changed, 206 insertions(+), 2479 deletions(-)
Title: Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype
and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and
separate treatment of local (cis) and distant (trans) eQTLs.
For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
Author: Andrey A Shabalin [aut, cre]
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between MatrixEQTL versions 2.3 dated 2019-12-22 and 2.4 dated 2026-09-02
DESCRIPTION | 11 MD5 | 10 NAMESPACE | 18 R/Matrix_eQTL_engine.R | 4341 ++++++++++++++++++++++++------------------------ inst/CITATION | 30 man/Matrix_eQTL_main.Rd | 4 6 files changed, 2208 insertions(+), 2206 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.13.0 dated 2026-03-06 and 0.14.0 dated 2026-09-02
DESCRIPTION | 8 MD5 | 46 +-- NAMESPACE | 28 +- NEWS.md | 13 + R/deprecated.R | 204 ++++++++-------- R/ggcoef_model.R | 388 +++++++++++++++---------------- R/gglikert.R | 47 ++- R/weighted_quantile.R | 2 build/vignette.rds |binary inst/doc/ggcoef_model.html | 23 + inst/doc/stat_cross.html | 2 man/figures/README-unnamed-chunk-8-1.png |binary man/geom_connector.Rd | 4 man/ggcoef_model.Rd | 6 man/ggcoef_multicomponents.Rd | 310 ++++++++++++------------ man/gglikert.Rd | 20 + man/ggstats-package.Rd | 5 man/hex_bw.Rd | 5 man/pal_extender.Rd | 2 man/position_likert.Rd | 4 man/stat_cross.Rd | 2 man/stat_prop.Rd | 6 man/stat_weighted_mean.Rd | 2 tests/testthat/test-ggcoef_model.R | 16 - 24 files changed, 610 insertions(+), 533 deletions(-)
Title: Vectorised Computation of P-Values and Their Supports for
Several Discrete Statistical Tests
Description: Provides vectorised functions for computing p-values of various
common discrete statistical tests, as described e.g. in Agresti (2002)
<doi:10.1002/0471249688>, including their distributions. Exact and
approximate computation methods are provided. For exact ones, several
procedures of determining two-sided p-values are included, which are
outlined in more detail in Hirji (2006) <doi:10.1201/9781420036190>.
Author: Florian Junge [cre, aut] ,
Christina Kihn [aut],
Sebastian Doehler [ctb] ,
Guillermo Durand [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteTests versions 0.5.0 dated 2026-08-26 and 0.5.1 dated 2026-09-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/mann-whitney.R | 1 + src/mann_whitney.cpp | 10 +++++++--- 5 files changed, 24 insertions(+), 11 deletions(-)