Title: Simplified Fetching and Processing of Microarray and RNA-Seq
Data
Description: Wrapper around various existing tools and command-line interfaces,
providing a standard interface, simple parallelization, and detailed logging.
For microarray data, maps probe sets to standard gene IDs, building on
'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>,
'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>,
Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>,
and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>.
For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology
Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and
quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>,
performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>,
quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197& [...truncated...]
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between seeker versions 1.1.1 dated 2023-05-05 and 1.1.2 dated 2023-05-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/introduction.html | 4 ++-- inst/doc/reproducibility.html | 4 ++-- tests/testthat/test-fetch.R | 3 +++ 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Ordinal Causal Discovery
Description: Algorithms for ordinal causal discovery. This package aims to enable users to discover causality for observational ordinal categorical data with greedy and exhaustive search. See Ni, Y., & Mallick, B. (2022) <https://proceedings.mlr.press/v180/ni22a/ni22a.pdf> "Ordinal Causal Discovery. Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence, (UAI 2022), PMLR 180:1530–1540".
Author: Yang Ni [aut, cre]
Maintainer: Yang Ni <yni@stat.tamu.edu>
Diff between OrdCD versions 1.1.1 dated 2023-02-11 and 1.1.2 dated 2023-05-17
OrdCD-1.1.1/OrdCD/man/OCD.Rd |only OrdCD-1.1.2/OrdCD/DESCRIPTION | 10 +++--- OrdCD-1.1.2/OrdCD/MD5 | 10 +++--- OrdCD-1.1.2/OrdCD/NAMESPACE | 2 - OrdCD-1.1.2/OrdCD/R/functions_v4.R | 56 +++++++++++++++++++++++++++++-------- OrdCD-1.1.2/OrdCD/README.md | 4 +- OrdCD-1.1.2/OrdCD/man/OrdCD.Rd |only 7 files changed, 58 insertions(+), 24 deletions(-)
Title: Multivariate Difference Between Two Groups
Description: Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Lönnqvist & Ilmarinen (2021) <doi:10.1007/s11109-021-09681-2> and Ilmarinen et al. (2022) <doi:10.1177/08902070221088155>.
Includes tools that help in understanding difference score reliability, predictions of difference score variables, conditional intra-class correlations, and heterogeneity of variance estimates. Package development was supported by the Academy of Finland research grant 338891.
Author: Ville-Juhani Ilmarinen [aut, cre]
Maintainer: Ville-Juhani Ilmarinen <vj.ilmarinen@gmail.com>
Diff between multid versions 0.7.1 dated 2022-12-21 and 0.8.0 dated 2023-05-17
DESCRIPTION | 8 MD5 | 42 - NAMESPACE | 3 NEWS.md | 10 R/D_regularized.R | 4 R/D_regularized_out.R | 51 + R/ddsc_sem.R |only R/diff_two_dep_cors.R |only R/sem_dadas.R | 4 R/value_correlation.R |only README.md | 58 - build/vignette.rds |binary inst/CITATION | 9 inst/doc/multivariate_sex_differences_in_personality.R | 1 inst/doc/multivariate_sex_differences_in_personality.Rmd | 64 -- inst/doc/multivariate_sex_differences_in_personality.html | 433 +++++++------- man/D_regularized.Rd | 4 man/D_regularized_out.Rd | 2 man/ddsc_sem.Rd |only man/diff_two_dep_cors.Rd |only man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/sem_dadas.Rd | 4 man/value_correlation.Rd |only vignettes/multivariate_sex_differences_in_personality.Rmd | 64 -- 25 files changed, 400 insertions(+), 361 deletions(-)
Title: Multivariate Bayesian Model with Shrinkage Priors
Description: Gibbs sampler for fitting multivariate Bayesian linear regression with shrinkage priors (MBSP), using the three parameter beta normal family. The method is described in Bai and Ghosh (2018) <doi:10.1016/j.jmva.2018.04.010>.
Author: Ray Bai, Malay Ghosh
Maintainer: Ray Bai <raybaistat@gmail.com>
Diff between MBSP versions 3.0 dated 2022-08-11 and 4.0 dated 2023-05-17
DESCRIPTION | 10 +-- MD5 | 8 +- NAMESPACE | 2 R/MBSP.R | 168 ++++++++++++++++++++++++++++++++++++++++++++++++------------ man/MBSP.Rd | 78 +++++++++++++++++---------- 5 files changed, 196 insertions(+), 70 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph]
,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.0.1 dated 2023-02-19 and 1.1.0 dated 2023-05-17
logitr-1.0.1/logitr/R/tools.R |only logitr-1.1.0/logitr/DESCRIPTION | 8 logitr-1.1.0/logitr/MD5 | 46 - logitr-1.1.0/logitr/NAMESPACE | 2 logitr-1.1.0/logitr/NEWS.md | 6 logitr-1.1.0/logitr/R/inputChecks.R | 15 logitr-1.1.0/logitr/R/predict.R | 181 ++-- logitr-1.1.0/logitr/R/utils.R |only logitr-1.1.0/logitr/build/partial.rdb |binary logitr-1.1.0/logitr/build/vignette.rds |binary logitr-1.1.0/logitr/inst/doc/basic_usage.html | 68 - logitr-1.1.0/logitr/inst/doc/data_formatting.html | 25 logitr-1.1.0/logitr/inst/doc/interactions.html | 24 logitr-1.1.0/logitr/inst/doc/mnl_models.html | 44 - logitr-1.1.0/logitr/inst/doc/mnl_models_weighted.html | 12 logitr-1.1.0/logitr/inst/doc/mxl_models.html | 18 logitr-1.1.0/logitr/inst/doc/predict.R | 9 logitr-1.1.0/logitr/inst/doc/predict.Rmd | 11 logitr-1.1.0/logitr/inst/doc/predict.html | 71 - logitr-1.1.0/logitr/inst/doc/summarizing_results.html | 688 +++++++++--------- logitr-1.1.0/logitr/man/ci.Rd |only logitr-1.1.0/logitr/man/fquantile.Rd | 2 logitr-1.1.0/logitr/man/logit_probs.Rd |only logitr-1.1.0/logitr/man/predict.logitr.Rd | 49 + logitr-1.1.0/logitr/man/statusCodes.Rd | 2 logitr-1.1.0/logitr/vignettes/predict.Rmd | 11 26 files changed, 683 insertions(+), 609 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>
Diff between ChannelAttribution versions 2.0.6 dated 2022-11-23 and 2.0.7 dated 2023-05-17
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 28 ++++++++++++++-------------- R/ChannelAttribution.R | 38 +++++++++++++++++++++++++++++--------- build/partial.rdb |binary man/ChannelAttribution-package.Rd | 4 ++-- man/auto_markov_model.Rd | 3 ++- man/choose_order.Rd | 4 ++-- man/heuristic_models.Rd | 3 ++- man/markov_model.Rd | 3 ++- man/transition_matrix.Rd | 3 ++- src/ChannelAttribution.cpp | 2 +- src/ChannelAttribution.h | 2 +- src/Makevars | 1 - src/Makevars.win | 1 - 15 files changed, 62 insertions(+), 40 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.
Author: Haiming Zhou [aut, cre, cph],
Timothy Hanson [aut]
Maintainer: Haiming Zhou <haiming2019@gmail.com>
Diff between spBayesSurv versions 1.1.6 dated 2022-05-14 and 1.1.7 dated 2023-05-17
DESCRIPTION | 14 +++++++------- MD5 | 38 +++++++++++++++++++------------------- src/spSurv_AFT_BP.cpp | 24 ++++++++++++------------ src/spSurv_AFT_MPT.cpp | 24 ++++++++++++------------ src/spSurv_AH_BP.cpp | 24 ++++++++++++------------ src/spSurv_DDP_tools.cpp | 10 +++++----- src/spSurv_LDTFP_tools.cpp | 8 ++++---- src/spSurv_PHPOAFT_BP.cpp | 32 ++++++++++++++++---------------- src/spSurv_PH_BP.cpp | 24 ++++++++++++------------ src/spSurv_PH_MPT.cpp | 24 ++++++++++++------------ src/spSurv_PO_BP.cpp | 24 ++++++++++++------------ src/spSurv_PO_MPT.cpp | 24 ++++++++++++------------ src/spSurv_SpatDens.cpp | 10 +++++----- src/spSurv_anovaDDP.cpp | 2 +- src/spSurv_frailtyLDTFP.cpp | 2 +- src/spSurv_frailty_GRF_LDTFP.cpp | 2 +- src/spSurv_indeptCoxph.cpp | 12 ++++++------ src/spSurv_nonfrailtyLDTFP.cpp | 2 +- src/spSurv_spCopulaCoxph.cpp | 6 +++--- src/spSurv_spCopulaDDP.cpp | 2 +- 20 files changed, 154 insertions(+), 154 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.4.5 dated 2023-01-30 and 1.5.0 dated 2023-05-17
DESCRIPTION | 10 MD5 | 42 +- NEWS | 17 + R/nifti.R | 27 + R/viewer.R | 24 - inst/include/RNifti.h | 2 inst/include/RNifti/NiftiImage.h | 8 inst/include/RNifti/NiftiImage_impl.h | 39 ++ inst/include/RNiftiAPI.h | 12 inst/include/niftilib/nifti1.h | 8 inst/include/niftilib/nifti1_io.h | 20 - inst/include/niftilib/nifti1_io_version.h |only inst/include/niftilib/nifti2.h | 6 inst/include/niftilib/nifti2_io.h | 29 +- inst/include/niftilib/nifti2_io_version.h |only inst/include/znzlib/znzlib.h | 21 + man/asNifti.Rd | 3 man/writeNifti.Rd | 20 + src/main.cpp | 6 src/niftilib/nifti1_io.c | 396 ++++++++++++++++++--------- src/niftilib/nifti2_io.c | 426 ++++++++++++++++++------------ src/znzlib/znzlib.c | 12 src/zzz.c | 4 23 files changed, 739 insertions(+), 393 deletions(-)
Title: Powerful User Interface to Build Equations and Add Symbols
Description: User Interface for adding symbols, smileys, arrows, building mathematical equations using 'LaTeX' or 'r2symbols'. Built for use in development of 'Markdown' and 'Shiny' Outputs.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between symbol.equation.gpt versions 1.1.2 dated 2023-04-27 and 1.1.3 dated 2023-05-17
symbol.equation.gpt-1.1.2/symbol.equation.gpt/inst/lib/introduction.md |only symbol.equation.gpt-1.1.3/symbol.equation.gpt/DESCRIPTION | 6 ++-- symbol.equation.gpt-1.1.3/symbol.equation.gpt/MD5 | 13 ++++------ symbol.equation.gpt-1.1.3/symbol.equation.gpt/NEWS.md | 7 +++++ symbol.equation.gpt-1.1.3/symbol.equation.gpt/README.md | 4 +-- symbol.equation.gpt-1.1.3/symbol.equation.gpt/inst/doc/using_equations_symbols_r.html | 4 +-- symbol.equation.gpt-1.1.3/symbol.equation.gpt/inst/lib/req_pack.ob |binary symbol.equation.gpt-1.1.3/symbol.equation.gpt/inst/rstudio/addins.dcf | 4 +-- 8 files changed, 22 insertions(+), 16 deletions(-)
More information about symbol.equation.gpt at CRAN
Permanent link
Title: Geographic Information of Uruguay
Description: The toolbox have functions to load and process geographic information for Uruguay.
And extra-function to get address coordinates and orthophotos through the uruguayan 'IDE' API <https://www.gub.uy/infraestructura-datos-espaciales/tramites-y-servicios/servicios/sistema-unico-direcciones-geograficas>.
Author: Richard Detomasi [aut, cre, cph]
,
Ministerio de Desarrollo Social, Uruguay [dtc],
Infraestrutura de Datos Espaciales, Uruguay [dtc],
Servicio Geografico Militar, Uruguay [dtc],
Ministerio de Transporte y Obras Publicas, Uruguay [dtc],
Instituto [...truncated...]
Maintainer: Richard Detomasi <richard.detomasi@gmail.com>
Diff between geouy versions 0.2.6 dated 2022-10-05 and 0.2.7 dated 2023-05-17
DESCRIPTION | 10 ++--- MD5 | 37 ++++++++++----------- NEWS.md | 6 +++ R/plot_geouy.R | 2 - R/utils.R | 2 - R/which_uy.R | 2 - build/vignette.rds |binary data/metadata.rda |binary inst/doc/geouy.html | 4 +- inst/tutorials |only man/geouy.Rd | 26 +++++++------- man/is.uy32721.Rd | 64 ++++++++++++++++++------------------ man/is.uy4326.Rd | 64 ++++++++++++++++++------------------ man/is.uy5381.Rd | 64 ++++++++++++++++++------------------ man/is.uy5382.Rd | 64 ++++++++++++++++++------------------ man/mvd_barrios_grid.Rd | 62 +++++++++++++++++------------------ man/pipe.Rd | 24 ++++++------- man/plot_geouy.Rd | 76 +++++++++++++++++++++---------------------- man/reverse_ide_uy.Rd | 84 ++++++++++++++++++++++++------------------------ man/uy_deptos_grid.Rd | 62 +++++++++++++++++------------------ 20 files changed, 330 insertions(+), 323 deletions(-)
Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative)
related inputs and outputs. Converts data files to and from DDI, SPSS,
Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between DDIwR versions 0.13 dated 2022-09-28 and 0.14 dated 2023-05-17
DDIwR-0.13/DDIwR/R/getDecimals.R |only DDIwR-0.14/DDIwR/DESCRIPTION | 15 DDIwR-0.14/DDIwR/MD5 | 74 +-- DDIwR-0.14/DDIwR/R/DDIwR_package.R | 64 -- DDIwR-0.14/DDIwR/R/checkType.R | 28 - DDIwR-0.14/DDIwR/R/cleanup.R | 25 - DDIwR-0.14/DDIwR/R/collectMetadata.R | 31 - DDIwR-0.14/DDIwR/R/convert.R | 236 +++++---- DDIwR-0.14/DDIwR/R/exportDDI.R | 316 +++++++------ DDIwR-0.14/DDIwR/R/getDelimiter.R | 83 +-- DDIwR-0.14/DDIwR/R/getEnter.R | 81 +-- DDIwR-0.14/DDIwR/R/getFiles.R | 250 ++++------ DDIwR-0.14/DDIwR/R/getFormat.R | 53 -- DDIwR-0.14/DDIwR/R/getMetadata.R | 132 +++-- DDIwR-0.14/DDIwR/R/getXML.R | 25 - DDIwR-0.14/DDIwR/R/makeXML.R | 25 - DDIwR-0.14/DDIwR/R/make_labelled.R | 43 - DDIwR-0.14/DDIwR/R/onAttach.R | 25 - DDIwR-0.14/DDIwR/R/recodeCharcat.R | 41 - DDIwR-0.14/DDIwR/R/recodeMissings.R | 101 ++-- DDIwR-0.14/DDIwR/R/replaceTicks.R | 25 - DDIwR-0.14/DDIwR/R/setupfile.R | 783 ++++++++++++++------------------- DDIwR-0.14/DDIwR/R/splitrows.R | 76 +-- DDIwR-0.14/DDIwR/R/sysdata.rda |only DDIwR-0.14/DDIwR/R/treatPath.R | 57 +- DDIwR-0.14/DDIwR/R/writeMetadata.R | 66 +- DDIwR-0.14/DDIwR/R/writeRlist.R | 248 +++++----- DDIwR-0.14/DDIwR/inst/ChangeLog | 10 DDIwR-0.14/DDIwR/inst/WORDLIST |only DDIwR-0.14/DDIwR/man/DDIwR_package.Rd | 27 - DDIwR-0.14/DDIwR/man/convert.Rd | 124 +++-- DDIwR-0.14/DDIwR/man/exportDDI.Rd | 100 ++-- DDIwR-0.14/DDIwR/man/getMetadata.Rd | 26 - DDIwR-0.14/DDIwR/man/recodeCharcat.Rd | 11 DDIwR-0.14/DDIwR/man/recodeMissings.Rd | 13 DDIwR-0.14/DDIwR/man/setupfile.Rd | 55 +- DDIwR-0.14/DDIwR/tests |only 37 files changed, 1486 insertions(+), 1783 deletions(-)
Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.3.0 dated 2023-03-19 and 0.4.0 dated 2023-05-17
DESCRIPTION | 10 MD5 | 162 NAMESPACE | 2 NEWS.md | 34 R/area_of_applicability.R | 6 R/local_moran.R | 24 R/misc.R | 10 R/misc_yardstick.R | 88 R/multi_scale.R | 255 R/waywiser-package.R | 5 README.md | 31 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 28 inst/doc/multi-scale-assessment.html | 4 inst/doc/residual-autocorrelation.html | 10 inst/doc/waywiser.Rmd | 2 inst/doc/waywiser.html | 26 inst/srr_template_nonspatial_yardstick.R | 106 man/figures/logo.png |binary man/ww_multi_scale.Rd | 25 tests/testthat/_snaps/area_of_applicability.md | 47 tests/testthat/_snaps/local_geary.md | 4 tests/testthat/_snaps/local_getis.md | 8 tests/testthat/_snaps/local_moran.md | 96 tests/testthat/_snaps/misc.md | 63 tests/testthat/_snaps/misc_yardstick.md | 42 tests/testthat/_snaps/multi_scale.md | 89 tests/testthat/_snaps/srr-ww_agreement_coefficient.md | 104 tests/testthat/_snaps/srr-ww_area_of_applicability.md | 108 tests/testthat/_snaps/srr-ww_global_geary_c.md | 90 tests/testthat/_snaps/srr-ww_global_geary_pvalue.md | 90 tests/testthat/_snaps/srr-ww_global_moran_i.md | 90 tests/testthat/_snaps/srr-ww_global_moran_pvalue.md | 90 tests/testthat/_snaps/srr-ww_local_geary_c.md | 100 tests/testthat/_snaps/srr-ww_local_geary_pvalue.md | 100 tests/testthat/_snaps/srr-ww_local_getis_ord_g.md | 100 tests/testthat/_snaps/srr-ww_local_getis_ord_g_pvalue.md | 100 tests/testthat/_snaps/srr-ww_local_moran_i.md |26196 +++------- tests/testthat/_snaps/srr-ww_local_moran_pvalue.md |23532 +++----- tests/testthat/_snaps/srr-ww_systematic_agreement_coefficient.md | 104 tests/testthat/_snaps/srr-ww_systematic_mpd.md | 104 tests/testthat/_snaps/srr-ww_systematic_mse.md | 104 tests/testthat/_snaps/srr-ww_systematic_rmpd.md | 104 tests/testthat/_snaps/srr-ww_systematic_rmse.md | 104 tests/testthat/_snaps/srr-ww_unsystematic_agreement_coefficient.md | 104 tests/testthat/_snaps/srr-ww_unsystematic_mpd.md | 104 tests/testthat/_snaps/srr-ww_unsystematic_mse.md | 104 tests/testthat/_snaps/srr-ww_unsystematic_rmpd.md | 104 tests/testthat/_snaps/srr-ww_unsystematic_rmse.md | 104 tests/testthat/_snaps/srr-ww_willmott_d.md | 104 tests/testthat/_snaps/srr-ww_willmott_d1.md | 104 tests/testthat/_snaps/srr-ww_willmott_dr.md | 104 tests/testthat/_snaps/tidy_importance.md | 10 tests/testthat/test-local_moran.R | 4 tests/testthat/test-misc.R | 6 tests/testthat/test-multi_scale.R | 43 tests/testthat/test-srr-ww_agreement_coefficient.R | 108 tests/testthat/test-srr-ww_global_geary_c.R | 2 tests/testthat/test-srr-ww_global_geary_pvalue.R | 2 tests/testthat/test-srr-ww_global_moran_i.R | 2 tests/testthat/test-srr-ww_global_moran_pvalue.R | 2 tests/testthat/test-srr-ww_local_geary_c.R | 2 tests/testthat/test-srr-ww_local_geary_pvalue.R | 26 tests/testthat/test-srr-ww_local_getis_ord_g.R | 2 tests/testthat/test-srr-ww_local_getis_ord_g_pvalue.R | 26 tests/testthat/test-srr-ww_local_moran_i.R | 2 tests/testthat/test-srr-ww_local_moran_pvalue.R | 2 tests/testthat/test-srr-ww_systematic_agreement_coefficient.R | 108 tests/testthat/test-srr-ww_systematic_mpd.R | 108 tests/testthat/test-srr-ww_systematic_mse.R | 108 tests/testthat/test-srr-ww_systematic_rmpd.R | 108 tests/testthat/test-srr-ww_systematic_rmse.R | 108 tests/testthat/test-srr-ww_unsystematic_agreement_coefficient.R | 108 tests/testthat/test-srr-ww_unsystematic_mpd.R | 108 tests/testthat/test-srr-ww_unsystematic_mse.R | 108 tests/testthat/test-srr-ww_unsystematic_rmpd.R | 108 tests/testthat/test-srr-ww_unsystematic_rmse.R | 108 tests/testthat/test-srr-ww_willmott_d.R | 108 tests/testthat/test-srr-ww_willmott_d1.R | 108 tests/testthat/test-srr-ww_willmott_dr.R | 108 vignettes/waywiser.Rmd | 2 82 files changed, 19944 insertions(+), 34930 deletions(-)
Title: Satellite Image Time Series Analysis for Earth Observation Data
Cubes
Description: An end-to-end toolkit for land use and land cover classification
using big Earth observation data, based on machine learning methods
applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>.
Builds regular data cubes from collections in AWS, Microsoft Planetary Computer,
Brazil Data Cube, and Digital Earth Africa using the Spatio-temporal Asset Catalog (STAC)
protocol (<https://stacspec.org/> and the 'gdalcubes' R package
developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>.
Supports visualization methods for images and time series and
smoothing filters for dealing with noisy time series.
Includes functions for quality assessment of training samples using self-organized maps
as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>.
Provides machine learning methods including support vector machines,
random forests, extreme gradient boosting, multi-layer perceptrons,
temporal convolutional neu [...truncated...]
Author: Rolf Simoes [aut],
Gilberto Camara [aut, cre],
Felipe Souza [aut],
Lorena Santos [aut],
Pedro Andrade [aut],
Karine Ferreira [aut],
Alber Sanchez [aut],
Gilberto Queiroz [aut]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between sits versions 1.3.0 dated 2023-03-17 and 1.4.0 dated 2023-05-17
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390 ++- sits-1.4.0/sits/tests/testthat/test-file_info.R | 10 sits-1.4.0/sits/tests/testthat/test-labels.R | 10 sits-1.4.0/sits/tests/testthat/test-mixture_model.R | 32 sits-1.4.0/sits/tests/testthat/test-ml.R | 10 sits-1.4.0/sits/tests/testthat/test-mosaic.R |only sits-1.4.0/sits/tests/testthat/test-parallel.R | 1 sits-1.4.0/sits/tests/testthat/test-plot.R | 71 sits-1.4.0/sits/tests/testthat/test-raster.R | 798 ++----- sits-1.4.0/sits/tests/testthat/test-reclassify.R |only sits-1.4.0/sits/tests/testthat/test-regularize.R |only sits-1.4.0/sits/tests/testthat/test-roi.R | 20 sits-1.4.0/sits/tests/testthat/test-segmentation.R |only sits-1.4.0/sits/tests/testthat/test-tibble.R | 4 sits-1.4.0/sits/tests/testthat/test-tuning.R | 100 sits-1.4.0/sits/tests/testthat/test-uncertainty.R | 8 sits-1.4.0/sits/tests/testthat/test-variance.R |only sits-1.4.0/sits/tests/testthat/test-view.R | 47 178 files changed, 3471 insertions(+), 2343 deletions(-)
Title: Semi-Automated Marketing Mix Modeling (MMM) from Meta Marketing
Science
Description: Semi-Automated Marketing Mix Modeling (MMM) aiming to reduce human bias by means of ridge regression and evolutionary algorithms, enables actionable decision making providing a budget allocation and diminishing returns curves and allows ground-truth calibration to account for causation.
Author: Gufeng Zhou [aut],
Leonel Sentana [aut],
Igor Skokan [aut],
Bernardo Lares [cre, aut],
Meta Platforms, Inc. [cph, fnd]
Maintainer: Bernardo Lares <bernardolares@meta.com>
Diff between Robyn versions 3.9.0 dated 2023-02-08 and 3.10.3 dated 2023-05-17
DESCRIPTION | 8 MD5 | 62 +- NAMESPACE | 8 R/allocator.R | 1024 +++++++++++++++++++++++++++-------------- R/calibration.R | 41 - R/checks.R | 245 +++++++-- R/clusters.R | 33 - R/convergence.R | 34 - R/exports.R | 9 R/imports.R | 12 R/inputs.R | 34 - R/json.R | 40 + R/model.R | 249 +++------ R/outputs.R | 43 + R/pareto.R | 241 +++++---- R/plots.R | 626 ++++++++++++++++++------- R/refresh.R | 14 R/response.R | 231 ++++++--- R/transformation.R | 124 ++++ README.md | 2 data/dt_simulated_weekly.RData |binary man/adstocks.Rd | 15 man/robyn_allocator.Rd | 105 +--- man/robyn_clusters.Rd | 3 man/robyn_converge.Rd | 14 man/robyn_inputs.Rd | 4 man/robyn_mmm.Rd | 16 man/robyn_outputs.Rd | 14 man/robyn_response.Rd | 24 man/robyn_run.Rd | 11 man/robyn_train.Rd | 11 man/robyn_write.Rd | 6 32 files changed, 2178 insertions(+), 1125 deletions(-)
Title: Quantile-Frequency Analysis (QFA) of Time Series
Description: Quantile-frequency analysis (QFA) of univariate or multivariate time series based on trigonometric quantile regression. See Li, T.-H. (2012) "Quantile periodograms", Journal of the American Statistical Association, 107, 765–776, <doi:10.1080/01621459.2012.682815>; Li, T.-H. (2014) Time Series with Mixed Spectra, CRC Press, <doi:10.1201/b15154>; Li, T.-H. (2022) "Quantile Fourier transform, quantile series, and nonparametric estimation of quantile spectra", <doi:10.48550/arXiv.2211.05844>.
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl@us.ibm.com>
Diff between qfa versions 1.2 dated 2023-01-13 and 2.0 dated 2023-05-17
qfa-1.2/qfa/R/qfa1.2.R |only qfa-1.2/qfa/man/qper2qcoh.Rd |only qfa-2.0/qfa/DESCRIPTION | 14 ++++----- qfa-2.0/qfa/MD5 | 51 ++++++++++++++++++++++++------------ qfa-2.0/qfa/NAMESPACE | 20 +++++++++++++- qfa-2.0/qfa/R/qfa2.0.R |only qfa-2.0/qfa/man/ar2qspec.Rd |only qfa-2.0/qfa/man/qacf.Rd |only qfa-2.0/qfa/man/qdft.Rd | 4 +- qfa-2.0/qfa/man/qdft2qacf.Rd | 14 ++++----- qfa-2.0/qfa/man/qdft2qper.Rd | 12 ++++---- qfa-2.0/qfa/man/qdft2qser.Rd | 12 ++++---- qfa-2.0/qfa/man/qfa.plot.Rd | 8 ++--- qfa-2.0/qfa/man/qkl.divergence.Rd | 8 ++--- qfa-2.0/qfa/man/qper.Rd |only qfa-2.0/qfa/man/qper2.Rd |only qfa-2.0/qfa/man/qser.Rd |only qfa-2.0/qfa/man/qser2ar.Rd |only qfa-2.0/qfa/man/qser2sar.Rd |only qfa-2.0/qfa/man/qsmooth.qdft.Rd | 13 ++++----- qfa-2.0/qfa/man/qsmooth.qper.Rd | 21 +++++++------- qfa-2.0/qfa/man/qspec.ar.Rd |only qfa-2.0/qfa/man/qspec.lw.Rd | 24 ++++++++-------- qfa-2.0/qfa/man/qspec.lwqs.Rd |only qfa-2.0/qfa/man/qspec.qslw.Rd |only qfa-2.0/qfa/man/qspec.sar.Rd |only qfa-2.0/qfa/man/qspec.sqrlw.Rd |only qfa-2.0/qfa/man/qspec2qcoh.Rd |only qfa-2.0/qfa/man/sar.eq.bootstrap.Rd |only qfa-2.0/qfa/man/sar.eq.test.Rd |only qfa-2.0/qfa/man/sar.gc.bootstrap.Rd |only qfa-2.0/qfa/man/sar.gc.coef.Rd |only qfa-2.0/qfa/man/sar.gc.test.Rd |only qfa-2.0/qfa/man/sqdft.Rd | 11 ++++--- qfa-2.0/qfa/man/sqr.fit.Rd | 6 ++-- qfa-2.0/qfa/man/tqr.fit.Rd | 2 - qfa-2.0/qfa/man/tsqr.fit.Rd | 2 - 37 files changed, 129 insertions(+), 93 deletions(-)
Title: Conditional Power Calculations
Description: Functions for calculating the conditional power
for different models in survival time analysis
within randomized clinical trials
with two different treatments to be compared
and survival as an endpoint.
Author: Andreas Kuehnapfel
Maintainer: Andreas Kuehnapfel <andreas.kuehnapfel@imise.uni-leipzig.de>
Diff between CP versions 1.6 dated 2016-06-29 and 1.7 dated 2023-05-17
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/CP-package.Rd | 14 ++++++++------ 3 files changed, 15 insertions(+), 13 deletions(-)
Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence
via the 'rstan' package, the R interface to the 'Stan' C++ library.
Supported models include single-season occupancy, dynamic occupancy, and
N-mixture abundance models. Covariates on model parameters are specified
using a formula-based interface similar to package 'unmarked', while also
allowing for estimation of random slope and intercept terms. References:
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between ubms versions 1.2.2 dated 2022-11-10 and 1.2.3 dated 2023-05-17
DESCRIPTION | 20 ++-- MD5 | 40 ++++----- NAMESPACE | 3 NEWS.md | 7 + R/distsamp.R | 17 ++-- R/gof.R | 12 +- R/plot_effects.R | 16 ++- R/plot_posteriors.R | 6 - R/residuals.R | 17 ++-- R/spatial.R | 17 ++-- build/vignette.rds |binary inst/doc/ubms.R | 8 - inst/doc/ubms.Rmd | 17 ++-- inst/doc/ubms.html | 133 ++++++++++++++++---------------- inst/stan/include/functions_priors.stan | 16 ++- man/gof.Rd | 6 - src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_colext.R | 2 tests/testthat/test_fitlist.R | 2 vignettes/ubms.Rmd | 17 ++-- 21 files changed, 199 insertions(+), 161 deletions(-)
Title: Spatial Resampling Infrastructure
Description: Functions and classes for spatial resampling to use with the
'rsample' package, such as spatial cross-validation (Brenning, 2012)
<doi:10.1109/IGARSS.2012.6352393>. The scope of 'rsample' and
'spatialsample' is to provide the basic building blocks for creating
and analyzing resamples of a spatial data set, but neither package
includes functions for modeling or computing statistics. The resampled
spatial data sets created by 'spatialsample' do not contain much
overhead in memory.
Author: Michael Mahoney [aut, cre] ,
Julia Silge [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between spatialsample versions 0.3.0 dated 2023-01-17 and 0.4.0 dated 2023-05-17
spatialsample-0.3.0/spatialsample/R/0_imports.R |only spatialsample-0.4.0/spatialsample/DESCRIPTION | 27 spatialsample-0.4.0/spatialsample/LICENSE | 4 spatialsample-0.4.0/spatialsample/MD5 | 90 - spatialsample-0.4.0/spatialsample/NAMESPACE | 13 spatialsample-0.4.0/spatialsample/NEWS.md | 7 spatialsample-0.4.0/spatialsample/R/autoplot.R | 24 spatialsample-0.4.0/spatialsample/R/buffer.R | 1 spatialsample-0.4.0/spatialsample/R/checks.R | 1 spatialsample-0.4.0/spatialsample/R/compat-vctrs-helpers.R | 3 spatialsample-0.4.0/spatialsample/R/spatial_block_cv.R | 19 spatialsample-0.4.0/spatialsample/R/spatial_clustering_cv.R | 5 spatialsample-0.4.0/spatialsample/R/spatial_nndm_cv.R |only spatialsample-0.4.0/spatialsample/R/spatial_vfold_cv.R | 35 spatialsample-0.4.0/spatialsample/R/spatialsample-package.R |only spatialsample-0.4.0/spatialsample/R/zzz-compat-vctrs-spatial_nndm_cv.R |only spatialsample-0.4.0/spatialsample/README.md | 6 spatialsample-0.4.0/spatialsample/build/partial.rdb |binary spatialsample-0.4.0/spatialsample/build/vignette.rds |binary spatialsample-0.4.0/spatialsample/inst/CITATION |only spatialsample-0.4.0/spatialsample/inst/doc/spatialsample.R | 19 spatialsample-0.4.0/spatialsample/inst/doc/spatialsample.Rmd | 19 spatialsample-0.4.0/spatialsample/inst/doc/spatialsample.html | 89 - spatialsample-0.4.0/spatialsample/man/figures/README-2022-06-12_boston-anim-.gif |binary spatialsample-0.4.0/spatialsample/man/figures/README-2022-06-12_boston_static-1.png |binary spatialsample-0.4.0/spatialsample/man/figures/logo.png |binary spatialsample-0.4.0/spatialsample/man/reexports.Rd | 2 spatialsample-0.4.0/spatialsample/man/spatial_clustering_cv.Rd | 4 spatialsample-0.4.0/spatialsample/man/spatial_nndm_cv.Rd |only spatialsample-0.4.0/spatialsample/man/spatialsample-package.Rd | 6 spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/autoplot/block-split-plots.svg | 810 +++++----- spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/autoplot/buffered-llo-split-plot.svg | 210 +- spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/autoplot/buffered-rsample-plot.svg | 720 ++++---- spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/autoplot/buffered-vfold-split.svg | 172 +- spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/autoplot/cluster-split-plots.svg | 688 ++++---- spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/buffer.md | 4 spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/compat-vctrs.md | 43 spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/spatial_block_cv.md | 6 spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/spatial_nndm_cv.md |only spatialsample-0.4.0/spatialsample/tests/testthat/_snaps/spatial_vfold_cv.md | 4 spatialsample-0.4.0/spatialsample/tests/testthat/helper-rset.R | 1 spatialsample-0.4.0/spatialsample/tests/testthat/test-autoplot.R | 1 spatialsample-0.4.0/spatialsample/tests/testthat/test-buffer.R | 6 spatialsample-0.4.0/spatialsample/tests/testthat/test-compat-dplyr.R | 4 spatialsample-0.4.0/spatialsample/tests/testthat/test-misc.R | 8 spatialsample-0.4.0/spatialsample/tests/testthat/test-spatial_block_cv.R | 5 spatialsample-0.4.0/spatialsample/tests/testthat/test-spatial_clustering_cv.R | 3 spatialsample-0.4.0/spatialsample/tests/testthat/test-spatial_nndm_cv.R |only spatialsample-0.4.0/spatialsample/tests/testthat/test-spatial_vfold_cv.R | 14 spatialsample-0.4.0/spatialsample/vignettes/spatialsample.Rmd | 19 50 files changed, 1571 insertions(+), 1521 deletions(-)
Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.0.15 dated 2023-04-25 and 1.0.16 dated 2023-05-17
DESCRIPTION | 8 +++--- MD5 | 25 ++++++++++---------- NEWS | 3 ++ R/MQDataReader.R | 34 +++++++++++++++++++++++++--- R/qcMetric_PAR.R | 5 ++-- README.md | 4 +-- inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 +-- inst/doc/PTXQC-CustomizeReport.html | 4 +-- inst/doc/PTXQC-DragNDrop.html | 4 +-- inst/doc/PTXQC-FAQ.html | 4 +-- inst/doc/PTXQC-Input_And_Output_Data.html | 4 +-- inst/doc/PTXQC-ListOfMetrics.html | 4 +-- man/MQDataReader-class.Rd | 2 + man/getFileEncoding.Rd |only 14 files changed, 70 insertions(+), 35 deletions(-)
Title: Compute and Illustrate the Multiple Facets of Functional
Diversity
Description: Computing functional traits-based distances between pairs of
species for species gathered in assemblages allowing to build several
functional spaces. The package allows to compute functional diversity
indices assessing the distribution of species (and of their dominance) in a
given functional space for each assemblage and the overlap between
assemblages in a given functional space, see: Chao et al. (2018)
<doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>,
Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al.
(2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009)
<doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included.
Visit the 'mFD' website for more information, documentation and examples.
Author: Camille Magneville [aut, cre, cph]
,
Nicolas Loiseau [aut] ,
Camille Albouy [aut] ,
Nicolas Casajus [aut] ,
Thomas Claverie [aut] ,
Arthur Escalas [aut] ,
Fabien Leprieur [aut] ,
Eva Maire [aut] ,
David Mouillot [aut] ,
Sebastien Villeger [aut]
Maintainer: Camille Magneville <camille.magneville@gmail.com>
Diff between mFD versions 1.0.3 dated 2022-11-28 and 1.0.4 dated 2023-05-17
DESCRIPTION | 8 MD5 | 37 NEWS.md | 76 R/alpha_indiv_ind_computation.R | 2 R/funct_dist_computation.R | 11 R/sp_to_FE.R | 2 README.md | 18 build/partial.rdb |only build/vignette.rds |binary inst/doc/Compute_and_interpret_quality_of_functional_spaces.html | 362 ++- inst/doc/Compute_functional_hill_indices.html | 287 +- inst/doc/Continuous_traits_framework.Rmd | 8 inst/doc/Continuous_traits_framework.html | 261 +- inst/doc/Customised_plots.html | 481 +++- inst/doc/How_to_deal_with_Functional_Entities.html | 291 +- inst/doc/mFD_general_workflow.Rmd | 6 inst/doc/mFD_general_workflow.html | 994 +++++++--- man/mFD-package.Rd | 2 vignettes/Continuous_traits_framework.Rmd | 8 vignettes/mFD_general_workflow.Rmd | 6 20 files changed, 2008 insertions(+), 852 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.
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 1.3.0 dated 2023-04-05 and 1.4.0 dated 2023-05-17
DESCRIPTION | 18 - MD5 | 40 +-- NAMESPACE | 5 NEWS.md | 16 + R/function_PlotBasinOutput.R | 50 ++-- R/function_PlotMapOutput.R | 18 - R/function_PlotMapPoints.R | 71 ++++-- R/function_PlotPerformanceByAttribute.R | 376 +++++++++++++++++++++++--------- R/functioncollection_import.R | 2 R/sysdata.rda |binary inst/doc/basin_network.html | 2 inst/doc/plot_map_statistics.R | 17 + inst/doc/plot_map_statistics.Rmd | 20 + inst/doc/plot_map_statistics.html | 22 + inst/visualize_map_output/server.R | 4 inst/visualize_map_points/server.R | 25 +- man/PlotMapOutput.Rd | 2 man/PlotMapPoints.Rd | 3 man/PlotPerformanceByAttribute.Rd | 28 ++ man/ReadSubass.Rd | 2 vignettes/plot_map_statistics.Rmd | 20 + 21 files changed, 550 insertions(+), 191 deletions(-)
Title: Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion
Polls in Catalonia
Description: Easy and convenient access to the datasets of the
"Centre d'Estudis d'Opinio", the Catalan institution for polling and public
opinion. The package uses the data stored in the servers of the CEO and returns
it in a tidy format.
Author: Xavier Fernandez-i-Marin [aut, cre]
Maintainer: Xavier Fernandez-i-Marin <xavier.fim@gmail.com>
Diff between CEOdata versions 1.3.0.1 dated 2023-02-01 and 1.3.1 dated 2023-05-17
DESCRIPTION | 6 MD5 | 26 NEWS | 17 R/zzz.R | 3 build/vignette.rds |binary inst/doc/cheatsheet.pdf |binary inst/doc/using_CEOdata.R | 17 inst/doc/using_CEOdata.Rmd | 28 inst/doc/using_CEOdata.html | 440 +++++----- inst/doc/working_with_survey_data_using_the_CEOdata_package.R | 34 inst/doc/working_with_survey_data_using_the_CEOdata_package.Rmd | 33 inst/doc/working_with_survey_data_using_the_CEOdata_package.html | 56 - vignettes/using_CEOdata.Rmd | 28 vignettes/working_with_survey_data_using_the_CEOdata_package.Rmd | 33 14 files changed, 445 insertions(+), 276 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph]
,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 3.0.0 dated 2022-12-22 and 3.1.0 dated 2023-05-17
DESCRIPTION | 8 MD5 | 92 NAMESPACE | 5 NEWS.md | 16 R/Bacon.R | 119 - R/MCMC.R | 40 R/accrate.R | 21 R/agedepth.R | 70 R/calc.R | 78 R/calibrate.R | 9 R/forplum.R | 6 R/internal_plots.R | 73 R/read_write.R | 116 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 5 inst/doc/FAQ.R | 8 inst/doc/FAQ.Rmd | 36 inst/doc/FAQ.html | 574 ++++- inst/doc/contents.html | 210 + inst/doc/foldersfiles.html | 411 +++ inst/doc/intro.Rmd | 3 inst/doc/intro.html | 392 +++ inst/doc/postrun.html | 384 ++- inst/doc/priorssettings.Rmd | 6 inst/doc/priorssettings.html | 407 +++ inst/extdata/Cores/MSB2K/MSB2K_21.out | 3600 +++++++++++++++------------------- man/Bacon.Rd | 56 man/accrate.age.Rd | 5 man/accrate.depth.Rd | 4 man/agedepth.Rd | 46 man/calib.plot.Rd | 3 man/scissors.Rd | 14 man/set.initvals.Rd |only man/squeeze.Rd |only man/stretch.Rd |only man/thinner.Rd | 14 src/bacon.cpp | 1 src/cal.h | 130 - src/gauss.cpp |only src/input.cpp | 71 src/input.h | 23 src/ranfun.cpp | 14 src/ranfun.h | 10 src/twalk.h | 2 src/vector.cpp | 1 vignettes/FAQ.Rmd | 36 vignettes/intro.Rmd | 3 vignettes/priorssettings.Rmd | 6 49 files changed, 4414 insertions(+), 2714 deletions(-)
Title: 'Phosphor' Icons for R
Description: Use 'Phosphor' icons in 'shiny' applications or 'rmarkdown' documents. Icons are available in
5 different weights and can be customized by setting color, size, orientation and more.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Phosphor Icons [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between phosphoricons versions 0.1.2 dated 2022-04-11 and 0.2.0 dated 2023-05-17
DESCRIPTION | 8 LICENSE | 4 MD5 | 77 +++++--- NAMESPACE | 32 +-- NEWS.md | 24 +- R/ph.R | 225 +++++++++++++------------- R/ph_i.R | 141 ++++++++-------- R/search.R | 84 ++++----- R/sysdata.rda |binary R/utils.R | 85 ++++++--- R/waffle.R | 240 +++++++++++++-------------- README.md | 285 ++++++++++++++++----------------- inst/assets/css/Phosphor-Bold.woff |only inst/assets/css/Phosphor-Bold.woff2 |only inst/assets/css/Phosphor-Duotone.woff |only inst/assets/css/Phosphor-Duotone.woff2 |only inst/assets/css/Phosphor-Fill.woff |only inst/assets/css/Phosphor-Fill.woff2 |only inst/assets/css/Phosphor-Light.woff |only inst/assets/css/Phosphor-Light.woff2 |only inst/assets/css/Phosphor-Thin.woff |only inst/assets/css/Phosphor-Thin.woff2 |only inst/assets/css/Phosphor.woff |only inst/assets/css/Phosphor.woff2 |only inst/assets/css/icons.min.css | 2 inst/assets/css/size.scss |only inst/tinytest/test_ph.R | 50 ++--- inst/tinytest/test_ph_fill.R | 74 ++++---- inst/tinytest/test_ph_i.R | 46 ++--- inst/tinytest/test_search.R | 24 +- inst/tinytest/test_waffle.R | 162 +++++++++--------- man/figures/icon-fill-perc-1.svg | 22 +- man/figures/icon-fill-perc-2.svg | 22 +- man/figures/lightning-bold-gold.svg | 6 man/figures/lightning-bold.svg | 6 man/figures/lightning-fill.svg | 6 man/figures/lightning-light.svg | 6 man/figures/lightning-regular.svg | 6 man/figures/lightning-thin.svg | 6 man/html_dependency_phosphor.Rd | 80 ++++----- man/ph.Rd | 108 ++++++------ man/ph_fill.Rd | 94 +++++----- man/ph_i.Rd | 88 +++++----- man/search_icon.Rd | 46 ++--- man/waffle_icon.Rd | 124 +++++++------- tests/tinytest.R | 10 - 46 files changed, 1121 insertions(+), 1072 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, binary data from GENEA devices (not for sale), and .cwa-format and .wav-format data from 'Axivity' <https://axivity.com>. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 0.2.6 dated 2022-12-05 and 0.2.7 dated 2023-05-17
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- R/readAxivity.R | 57 +++++++++++++++++++++----------------- R/readGENEActiv.R | 3 -- R/readWav.R | 71 +++++++++++++++++++++++++++++++++++------------- inst/NEWS.Rd | 12 ++++++-- man/GGIRread-package.Rd | 4 +- src/GENEActivReader.cpp | 27 +++++------------- 8 files changed, 117 insertions(+), 79 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] ,
Adrian Chong [aut]
Maintainer: Hongyuan Jia <hongyuanjia@cqust.edu.cn>
Diff between eplusr versions 0.15.3 dated 2022-11-20 and 0.16.0 dated 2023-05-17
DESCRIPTION | 18 MD5 | 177 NAMESPACE | 16 NEWS.md | 27 R/assert.R | 372 - R/constants.R | 15 R/diagram.R | 120 R/epw.R | 4328 +++++++-------- R/err.R | 850 +- R/format.R | 2432 ++++---- R/geom.R | 1474 ++--- R/group.R | 3418 +++++------ R/idd.R | 2764 ++++----- R/iddobj.R | 3958 ++++++------- R/idf.R | 7967 +++++++++++++-------------- R/idfobj-sch.R | 1156 ++-- R/idfobj.R | 4092 +++++++------- R/impl-epw.R | 53 R/impl-geom.R | 3579 ++++++------ R/impl-idd.R | 2160 +++---- R/impl-iddobj.R | 226 R/impl-idf.R | 40 R/impl-idfobj-sch.R | 2008 +++---- R/impl-idfobj.R | 508 - R/impl-sql.R | 5 R/impl-viewer.R | 1917 +++--- R/impl.R | 616 +- R/install.R | 1786 +++--- R/job.R | 2857 +++++----- R/options.R | 488 - R/param.R | 1842 +++--- R/parse.R | 3294 +++++------ R/rdd.R | 812 +- R/reload.R | 246 R/run.R | 4980 ++++++++--------- R/sql.R | 1288 ++-- R/sysdata.rda |binary R/transition.R | 9709 +++++++++++++++++----------------- R/units.R | 392 - R/utils.R | 1021 +-- R/validate.R | 1530 ++--- R/viewer.R | 1797 +++--- README.md | 415 - inst/CITATION | 33 man/Idf.Rd | 2 man/IdfGeometry.Rd | 6 man/IdfViewer.Rd | 6 man/as_EpwDate.Rd |only man/read_epw.Rd | 100 man/read_idf.Rd | 154 man/use_idd.Rd | 234 tests/testthat.R | 10 tests/testthat/helper-copy.R | 72 tests/testthat/helper-eplus.R | 10 tests/testthat/helper-text.R | 224 tests/testthat/helper-transition.R | 26 tests/testthat/test-assert.R | 42 tests/testthat/test-diagram.R | 29 tests/testthat/test-epw.R | 170 tests/testthat/test-format.R | 995 +-- tests/testthat/test-geom.R | 93 tests/testthat/test-group.R | 448 - tests/testthat/test-idd.R | 571 - tests/testthat/test-iddobj.R | 603 +- tests/testthat/test-idf.R | 2719 ++++----- tests/testthat/test-idfobj-sch.R | 682 +- tests/testthat/test-idfobj.R | 1285 ++-- tests/testthat/test-impl-epw.R | 994 +-- tests/testthat/test-impl-geom.R | 570 + tests/testthat/test-impl-idd.R | 746 +- tests/testthat/test-impl-iddobj.R | 254 tests/testthat/test-impl-idf.R | 5256 +++++++++--------- tests/testthat/test-impl-idfobj-sch.R | 634 +- tests/testthat/test-impl-idfobj.R | 422 - tests/testthat/test-impl-viewer.R | 192 tests/testthat/test-impl.R | 261 tests/testthat/test-install.R | 70 tests/testthat/test-job.R | 252 tests/testthat/test-options.R | 63 tests/testthat/test-param.R | 430 - tests/testthat/test-parse.R | 1155 ++-- tests/testthat/test-rdd.R | 114 tests/testthat/test-reload.R | 188 tests/testthat/test-run.R | 273 tests/testthat/test-sql.R | 370 - tests/testthat/test-transition.R | 5175 +++++++++--------- tests/testthat/test-units.R | 28 tests/testthat/test-utils.R | 226 tests/testthat/test-validate.R | 522 - tests/testthat/test-viewer.R | 139 90 files changed, 52357 insertions(+), 51244 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in ab [...truncated...]
Author: Andri Signorell [aut, cre],
Ken Aho [ctb],
Andreas Alfons [ctb],
Nanina Anderegg [ctb],
Tomas Aragon [ctb],
Chandima Arachchige [ctb],
Antti Arppe [ctb],
Adrian Baddeley [ctb],
Kamil Barton [ctb],
Ben Bolker [ctb],
Hans W. Borchers [ctb],
Frederico C [...truncated...]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.48 dated 2023-02-19 and 0.99.49 dated 2023-05-17
DESCRIPTION | 10 MD5 | 28 NAMESPACE | 7 NEWS | 28 R/Desc.R | 3550 +++++++++++++++++++++++++--------------------- R/DescTools.r | 9 R/StatsAndCIs.r | 122 + R/Tests.r | 92 - README.md | 5 build/vignette.rds |binary man/BinomCI.Rd | 14 man/BreuschGodfreyTest.Rd | 2 man/DurbinWatsonTest.Rd | 5 man/MultinomCI.Rd | 35 tests/misc.R | 40 15 files changed, 2303 insertions(+), 1644 deletions(-)
Title: Weighted and Directed Networks
Description: Implementations of network analysis including
(1) assortativity coefficient of weighted and directed networks,
Yuan, Yan and Zhang (2021) <doi:10.1093/comnet/cnab017>,
(2) centrality measures for weighted and directed networks,
Opsahl, Agneessens and Skvoretz (2010) <doi:10.1016/j.socnet.2010.03.006>,
Zhang, Wang and Yan (2022) <doi:10.1016/j.physa.2021.126438>,
(3) clustering coefficient of weighted and directed networks,
Fagiolo (2007) <doi:10.1103/PhysRevE.76.026107> and
Clemente and Grassi (2018) <doi:10.1016/j.chaos.2017.12.007>,
(4) rewiring networks with given assortativity coefficients,
Wang, Yan, Yuan and Zhang (2022) <doi:10.1007/s11222-022-10161-8>,
(5) preferential attachment network generation.
Author: Yelie Yuan [aut, cre],
Tiandong Wang [aut],
Jun Yan [aut],
Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>
Diff between wdnet versions 1.0.0 dated 2023-01-19 and 1.1.0 dated 2023-05-17
wdnet-1.0.0/wdnet/R/rpanet_general.R |only wdnet-1.0.0/wdnet/R/rpanet_simple.R |only wdnet-1.0.0/wdnet/man/adj_to_edge.Rd |only wdnet-1.0.0/wdnet/man/edge_to_adj.Rd |only wdnet-1.0.0/wdnet/man/rpanet_general.Rd |only wdnet-1.0.0/wdnet/man/rpanet_simple.Rd |only wdnet-1.1.0/wdnet/DESCRIPTION | 13 wdnet-1.1.0/wdnet/MD5 | 160 ++--- wdnet-1.1.0/wdnet/NAMESPACE | 18 wdnet-1.1.0/wdnet/NEWS.md | 7 wdnet-1.1.0/wdnet/R/RcppExports.R | 74 +- wdnet-1.1.0/wdnet/R/assortativity.R | 296 +++++---- wdnet-1.1.0/wdnet/R/centrality.R | 449 +++++++------- wdnet-1.1.0/wdnet/R/cls_rpacontrol.R |only wdnet-1.1.0/wdnet/R/cls_wdnet.R |only wdnet-1.1.0/wdnet/R/clustercoef.R | 185 +++--- wdnet-1.1.0/wdnet/R/compile_pref.R | 68 +- wdnet-1.1.0/wdnet/R/joint_dist.R | 327 ++++++---- wdnet-1.1.0/wdnet/R/rewire.R | 546 ++++++++++-------- wdnet-1.1.0/wdnet/R/rpa_control.R | 413 +++++++++---- wdnet-1.1.0/wdnet/R/rpanet.R | 371 +++++++----- wdnet-1.1.0/wdnet/R/rpanet_internal.R |only wdnet-1.1.0/wdnet/R/utils.R | 72 +- wdnet-1.1.0/wdnet/R/wdnet-package.R | 62 +- wdnet-1.1.0/wdnet/README.md | 60 - wdnet-1.1.0/wdnet/man/adj_to_edgelist.Rd |only wdnet-1.1.0/wdnet/man/adj_to_wdnet.Rd |only wdnet-1.1.0/wdnet/man/assortcoef.Rd | 130 ++-- wdnet-1.1.0/wdnet/man/centrality.Rd | 253 ++++---- wdnet-1.1.0/wdnet/man/closeness_c.Rd | 110 +-- wdnet-1.1.0/wdnet/man/clustcoef.Rd | 136 ++-- wdnet-1.1.0/wdnet/man/compile_pref_func.Rd | 2 wdnet-1.1.0/wdnet/man/create_wdnet.Rd |only wdnet-1.1.0/wdnet/man/degree_c.Rd | 80 +- wdnet-1.1.0/wdnet/man/dprewire.Rd | 219 +++---- wdnet-1.1.0/wdnet/man/dprewire.range.Rd | 137 ++-- wdnet-1.1.0/wdnet/man/dprewire_directed.Rd | 83 +- wdnet-1.1.0/wdnet/man/dprewire_directed_cpp.Rd | 107 +-- wdnet-1.1.0/wdnet/man/dprewire_undirected.Rd | 82 +- wdnet-1.1.0/wdnet/man/dprewire_undirected_cpp.Rd | 105 +-- wdnet-1.1.0/wdnet/man/dw_assort.Rd | 69 +- wdnet-1.1.0/wdnet/man/dw_feature_assort.Rd | 75 +- wdnet-1.1.0/wdnet/man/edgelist_to_adj.Rd |only wdnet-1.1.0/wdnet/man/edgelist_to_wdnet.Rd |only wdnet-1.1.0/wdnet/man/fill_weight_cpp.Rd | 4 wdnet-1.1.0/wdnet/man/get_constr.Rd | 48 - wdnet-1.1.0/wdnet/man/get_dist.Rd | 50 - wdnet-1.1.0/wdnet/man/get_eta_directed.Rd | 85 +- wdnet-1.1.0/wdnet/man/get_eta_undirected.Rd | 72 +- wdnet-1.1.0/wdnet/man/get_values.Rd | 48 - wdnet-1.1.0/wdnet/man/igraph_to_wdnet.Rd |only wdnet-1.1.0/wdnet/man/is_rpacontrol.Rd |only wdnet-1.1.0/wdnet/man/is_wdnet.Rd |only wdnet-1.1.0/wdnet/man/plot.wdnet.Rd |only wdnet-1.1.0/wdnet/man/plus-.rpacontrol.Rd | 14 wdnet-1.1.0/wdnet/man/print.rpacontrol.Rd |only wdnet-1.1.0/wdnet/man/print.wdnet.Rd |only wdnet-1.1.0/wdnet/man/print_control_details.Rd |only wdnet-1.1.0/wdnet/man/print_control_preference.Rd |only wdnet-1.1.0/wdnet/man/rpa_control_default.Rd |only wdnet-1.1.0/wdnet/man/rpa_control_edgeweight.Rd | 18 wdnet-1.1.0/wdnet/man/rpa_control_list.Rd |only wdnet-1.1.0/wdnet/man/rpa_control_newedge.Rd | 34 - wdnet-1.1.0/wdnet/man/rpa_control_preference.Rd | 49 - wdnet-1.1.0/wdnet/man/rpa_control_reciprocal.Rd | 10 wdnet-1.1.0/wdnet/man/rpa_control_scenario.Rd | 4 wdnet-1.1.0/wdnet/man/rpacontrol.Rd |only wdnet-1.1.0/wdnet/man/rpanet.Rd | 213 +++---- wdnet-1.1.0/wdnet/man/rpanet.internal.Rd |only wdnet-1.1.0/wdnet/man/rpanet_bag_cpp.Rd | 10 wdnet-1.1.0/wdnet/man/rpanet_binary_directed.Rd | 10 wdnet-1.1.0/wdnet/man/rpanet_binary_undirected_cpp.Rd | 4 wdnet-1.1.0/wdnet/man/rpanet_linear_directed_cpp.Rd | 8 wdnet-1.1.0/wdnet/man/rpanet_linear_undirected_cpp.Rd | 4 wdnet-1.1.0/wdnet/man/sample_node_cpp.Rd | 4 wdnet-1.1.0/wdnet/man/wdnet.Rd | 35 + wdnet-1.1.0/wdnet/man/wdnet_to_igraph.Rd |only wdnet-1.1.0/wdnet/man/wpr.Rd | 78 +- wdnet-1.1.0/wdnet/src/Makevars | 1 wdnet-1.1.0/wdnet/src/Makevars.win | 1 wdnet-1.1.0/wdnet/src/RcppExports.cpp | 52 - wdnet-1.1.0/wdnet/src/rewire.cpp | 94 +-- wdnet-1.1.0/wdnet/src/rpanet_bag.cpp | 258 ++++---- wdnet-1.1.0/wdnet/src/rpanet_binary_directed.cpp | 28 wdnet-1.1.0/wdnet/src/rpanet_binary_linear.h | 2 wdnet-1.1.0/wdnet/src/rpanet_binary_linear_utils.cpp | 8 wdnet-1.1.0/wdnet/src/rpanet_binary_undirected.cpp | 34 - wdnet-1.1.0/wdnet/src/rpanet_linear_directed.cpp | 146 ++-- wdnet-1.1.0/wdnet/src/rpanet_linear_undirected.cpp | 26 wdnet-1.1.0/wdnet/src/utils.cpp | 34 - wdnet-1.1.0/wdnet/tests/testthat.R | 8 wdnet-1.1.0/wdnet/tests/testthat/test-assortativity.R |only wdnet-1.1.0/wdnet/tests/testthat/test-centrality.R |only wdnet-1.1.0/wdnet/tests/testthat/test-clustecoef.R |only wdnet-1.1.0/wdnet/tests/testthat/test-rewire.R |only wdnet-1.1.0/wdnet/tests/testthat/test-rpanet.R | 273 ++++++--- wdnet-1.1.0/wdnet/tests/testthat/test-wdnet-igraph.R |only 97 files changed, 3633 insertions(+), 2843 deletions(-)
Title: Spherical Geometry Operators Using the S2 Geometry Library
Description: Provides R bindings for Google's s2 library for geometric calculations on
the sphere. High-performance constructors and exporters provide high compatibility
with existing spatial packages, transformers construct new geometries from existing
geometries, predicates provide a means to select geometries based on spatial
relationships, and accessors extract information about geometries.
Author: Dewey Dunnington [aut] ,
Edzer Pebesma [aut, cre] ,
Ege Rubak [aut],
Jeroen Ooms [ctb] ,
Google, Inc. [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between s2 versions 1.1.3 dated 2023-04-27 and 1.1.4 dated 2023-05-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/partial.rdb |binary src/s2/s2region_coverer.h | 9 +++++++-- tests/testthat/test-s2-accessors.R | 2 +- tests/testthat/test-s2-lnglat.R | 5 +++-- 7 files changed, 24 insertions(+), 14 deletions(-)
Title: Scatterplots with More Points
Description: C-based conversion of large scatterplot data to rasters plus other
operations such as data blurring or data alpha blending. Speeds up
plotting of data with millions of points.
Author: Tereza Kulichova [aut],
Mirek Kratochvil [aut, cre]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between scattermore versions 1.0 dated 2023-05-03 and 1.1 dated 2023-05-17
scattermore-1.0/scattermore/inst/doc/histogram_lines.R |only scattermore-1.0/scattermore/inst/doc/histogram_lines.Rmd |only scattermore-1.0/scattermore/inst/doc/histogram_lines.html |only scattermore-1.0/scattermore/inst/doc/histogram_points.R |only scattermore-1.0/scattermore/inst/doc/histogram_points.Rmd |only scattermore-1.0/scattermore/inst/doc/histogram_points.html |only scattermore-1.0/scattermore/inst/doc/merge_and_blend.R |only scattermore-1.0/scattermore/inst/doc/merge_and_blend.Rmd |only scattermore-1.0/scattermore/inst/doc/merge_and_blend.html |only scattermore-1.0/scattermore/inst/doc/rgbwt_lines.R |only scattermore-1.0/scattermore/inst/doc/rgbwt_lines.Rmd |only scattermore-1.0/scattermore/inst/doc/rgbwt_lines.html |only scattermore-1.0/scattermore/inst/doc/rgbwt_points.R |only scattermore-1.0/scattermore/inst/doc/rgbwt_points.Rmd |only scattermore-1.0/scattermore/inst/doc/rgbwt_points.html |only scattermore-1.0/scattermore/vignettes/histogram_lines.Rmd |only scattermore-1.0/scattermore/vignettes/histogram_points.Rmd |only scattermore-1.0/scattermore/vignettes/merge_and_blend.Rmd |only scattermore-1.0/scattermore/vignettes/rgbwt_lines.Rmd |only scattermore-1.0/scattermore/vignettes/rgbwt_points.Rmd |only scattermore-1.1/scattermore/DESCRIPTION | 6 scattermore-1.1/scattermore/MD5 | 93 +++---- scattermore-1.1/scattermore/NAMESPACE | 73 ++--- scattermore-1.1/scattermore/R/apply_kernel_histogram.R | 55 +--- scattermore-1.1/scattermore/R/apply_kernel_rgbwt.R | 67 +---- scattermore-1.1/scattermore/R/blend_rgba_float.R | 34 +- scattermore-1.1/scattermore/R/default_kernel.R |only scattermore-1.1/scattermore/R/globals.R | 12 scattermore-1.1/scattermore/R/histogram_to_rgbwt.R | 44 +-- scattermore-1.1/scattermore/R/merge_rgbwt.R | 28 +- scattermore-1.1/scattermore/R/rgba_float_to_rgba_int.R | 23 - scattermore-1.1/scattermore/R/rgba_int_to_raster.R | 8 scattermore-1.1/scattermore/R/rgbwt_to_rgba_float.R | 24 - scattermore-1.1/scattermore/R/rgbwt_to_rgba_int.R | 24 - scattermore-1.1/scattermore/R/scatter_lines_histogram.R | 55 +--- scattermore-1.1/scattermore/R/scatter_lines_rgbwt.R | 63 ++-- scattermore-1.1/scattermore/R/scatter_points_histogram.R | 37 +- scattermore-1.1/scattermore/R/scatter_points_rgbwt.R | 128 ++++------ scattermore-1.1/scattermore/R/scattermore.R | 5 scattermore-1.1/scattermore/build/vignette.rds |binary scattermore-1.1/scattermore/inst/doc/low_level_interface.R |only scattermore-1.1/scattermore/inst/doc/low_level_interface.Rmd |only scattermore-1.1/scattermore/inst/doc/low_level_interface.html |only scattermore-1.1/scattermore/man/apply_kernel_histogram.Rd | 68 ++--- scattermore-1.1/scattermore/man/apply_kernel_rgbwt.Rd | 72 ++--- scattermore-1.1/scattermore/man/blend_rgba_float.Rd | 34 +- scattermore-1.1/scattermore/man/histogram_to_rgbwt.Rd | 51 ++- scattermore-1.1/scattermore/man/merge_rgbwt.Rd | 35 +- scattermore-1.1/scattermore/man/rgba_float_to_rgba_int.Rd | 6 scattermore-1.1/scattermore/man/rgba_int_to_raster.Rd | 6 scattermore-1.1/scattermore/man/rgbwt_to_rgba_float.Rd | 5 scattermore-1.1/scattermore/man/rgbwt_to_rgba_int.Rd | 7 scattermore-1.1/scattermore/man/scatter_lines_histogram.Rd | 34 -- scattermore-1.1/scattermore/man/scatter_lines_rgbwt.Rd | 37 +- scattermore-1.1/scattermore/man/scatter_points_histogram.Rd | 23 - scattermore-1.1/scattermore/man/scatter_points_rgbwt.Rd | 88 +++--- scattermore-1.1/scattermore/src/histogram_to_rgbwt.cpp | 38 +- scattermore-1.1/scattermore/src/scatter_lines_impl.h | 62 ++-- scattermore-1.1/scattermore/src/scatters.h | 2 scattermore-1.1/scattermore/vignettes/low_level_interface.Rmd |only 60 files changed, 584 insertions(+), 763 deletions(-)
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point:
principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>),
linear and quadratic discriminant analysis (Todorov and Pires (2007)),
multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>),
outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).
See also Todorov and Filzmoser (2009) <ISBN-13:978-3838108148>,
Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and
Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Author: Valentin Todorov [aut, cre]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between rrcov versions 1.7-2 dated 2022-10-24 and 1.7-3 dated 2023-05-17
ChangeLog | 8 ++++ DESCRIPTION | 10 ++--- MD5 | 68 ++++++++++++++++++++-------------------- R/CovRobust.R | 45 +++++++++++++++++--------- R/datadoc.R | 48 +++++++++++++++++++++++++++- R/plot-utils.R | 17 +++++----- README.md | 24 +++++++++++++- build/partial.rdb |binary data/Appalachia.rda |binary data/Cascades.rda |binary data/OsloTransect.rda |binary data/bus.rda |binary data/bushmiss.rda |binary data/diabetes.rda |binary data/fish.rda |binary data/fruit.rda |binary data/hemophilia.rda |binary data/ionosphere.rda |only data/lmom32.rda |binary data/lmom33.rda |binary data/machines.rda |binary data/maryo.rda |binary data/octane.rda |binary data/olitos.rda |binary data/pottery.rda |binary data/rice.rda |binary data/salmon.rda |binary data/soil.rda |binary data/un86.rda |binary data/wages.rda |binary data/wolves.rda |binary inst/Citation | 32 +++++++------------ inst/NEWS.Rd | 11 +++++- man/ionosphere.Rd |only man/olitos.Rd | 2 - src/fsada.f | 84 +++++++++++++++++++++++++------------------------- 36 files changed, 220 insertions(+), 129 deletions(-)
Title: A User-Friendly Interface for Accessing the Prolific API
Description: A user-friendly interface for creating and managing empirical crowd-sourcing studies via API access to <https://www.prolific.co>.
Author: Simon Lenau [aut, cre]
Maintainer: Simon Lenau <lenau@cispa.de>
Diff between prolific.api versions 0.5 dated 2022-10-19 and 0.5.1 dated 2023-05-17
DESCRIPTION | 8 MD5 | 46 ++-- R/CLASS_api_access.R | 16 - R/CLASS_prolific_prescreener.R | 27 +- R/CLASS_prolific_study.R | 17 - R/METHODS_Internals.R | 8 R/METHODS_api_access.R | 251 +++++++++------------ R/METHODS_prolific_prescreener.R | 21 + R/METHODS_prolific_study.R | 209 +++++++++--------- R/UTILS_FieldAccess.R | 43 +++ R/UTILS_api_access.R | 17 + R/UTILS_misc.R | 43 ++- R/UTILS_prolific_prescreener.R | 14 + R/UTILS_prolific_study.R | 3 build/vignette.rds |binary inst/doc/prolificapi-package.R | 5 inst/doc/prolificapi-package.Rmd | 41 ++- inst/doc/prolificapi-package.html | 355 ++++++++++++++++--------------- vignettes/_list_fields_methods.R | 5 vignettes/_list_prescreeners.R | 4 vignettes/_prolificapi-package-chunks.R | 4 vignettes/list_of_prescreeners.RData |binary vignettes/prolificapi-package.Rmd | 41 ++- vignettes/prolificapi-package.precompile | 5 24 files changed, 639 insertions(+), 544 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 2.21.0-7 dated 2020-12-17 and 2.26.25 dated 2023-05-17
StanHeaders-2.21.0-7/StanHeaders/inst/include/nvector/cuda |only StanHeaders-2.21.0-7/StanHeaders/inst/include/nvector/nvector_mpicuda.h |only StanHeaders-2.21.0-7/StanHeaders/inst/include/nvector/nvector_mpiraja.h |only StanHeaders-2.21.0-7/StanHeaders/inst/include/nvector/raja |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/arr |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/arr.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/mat |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/mat.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/scal |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/fwd/scal.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/mix/arr.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/mix/mat |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/mix/scal.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/copy_triangular.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/diagonal_multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/err/check_matching_dims.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/err/check_square.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/err/check_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/identity.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/is_matrix_cl.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/bernoulli_logit_glm_lpmf.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/copy_triangular.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/fill.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/identity.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/normal_id_glm_lpdf.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/poisson_log_glm_lpmf.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/sub_block.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/subtract.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/kernels/transpose.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/opencl.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/prim/add.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/prim/subtract.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/prim/transpose.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/sub_block.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/opencl/zeros.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/err |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/array_builder.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/common_type.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/dot.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/dot_self.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/fill.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/inverse_softmax.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/log_sum_exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_elements.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar_type.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/rep_array.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/scaled_add.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_asc.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_desc.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/sub.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of_rec.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/fun/vec_concat.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/functor |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/arr/meta |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/eigen_plugins.h |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_column_index.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_size_mvt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_sizes_mvt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_finite.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_flag_sundials.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_matching_dims.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_multiplicable.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_nonempty.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_ordered.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_positive_ordered.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_range.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_row_index.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_simplex.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_square.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_std_vector_index.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/check_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/constraint_tolerance.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor_corr.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_column_index.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_corr_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_ldlt_factor.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_lower_triangular.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_mat_finite.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_matching_dims.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_pos_definite.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_square.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_symmetric.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/is_unit_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/err/validate_non_negative_index.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/MatrixExponential.h |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/Phi.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/Phi_approx.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/accumulator.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/acos.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/acosh.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/add.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/add_diag.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/append_array.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/append_col.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/append_row.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/asin.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/asinh.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/atan.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/atanh.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/block.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cbrt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/ceil.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/chol2inv.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/col.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cols.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/columns_dot_product.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/columns_dot_self.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/common_type.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cos.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cosh.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain_lkj.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free_lkj.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/crossprod.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_u_to_z.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/cumulative_sum.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/determinant.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_post_multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_pre_multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/diagonal.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/digamma.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/dims.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/distance.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/divide.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/divide_columns.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_product.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_self.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/eigenvalues_sym.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/eigenvectors_sym.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_divide.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/erf.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/erfc.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/exp2.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/expm1.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/fabs.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_U.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_cov_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/fill.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/floor.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/get_base1.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/get_base1_lhs.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/get_lp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_dot_prod_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exp_quad_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exponential_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern32_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern52_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_periodic_cov.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/head.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/initialize.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_Phi.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_cloglog.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_logit.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_sqrt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_square.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse_spd.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/lgamma.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log10.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m_exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m_inv_logit.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log1p.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log1p_exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log2.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant_spd.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_inv_logit.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_mix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_softmax.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/log_sum_exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/logit.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/make_nu.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_pade.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/max.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_ldlt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_spd.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri_low.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_ldlt.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_spd.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri_low.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/min.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/minus.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply_lower_tri_self_transpose.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/num_elements.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_constrain.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_free.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/prod.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_common.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_elements.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar_type.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_Q.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_R.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_Q.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_R.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_sym.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_L.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/read_cov_L.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/read_cov_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_matrix.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_row_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_vector.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/resize.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/round.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/row.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rows.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rows_dot_product.hpp |only StanHeaders-2.21.0-7/StanHeaders/inst/include/stan/math/prim/mat/fun/rows_dot_self.hpp |only 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StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes.h | 48 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_bandpre.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_bbdpre.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_diag.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_direct.h | 28 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_ls.h | 39 StanHeaders-2.26.25/StanHeaders/inst/include/cvodes/cvodes_spils.h | 42 StanHeaders-2.26.25/StanHeaders/inst/include/idas/idas.h | 35 StanHeaders-2.26.25/StanHeaders/inst/include/idas/idas_bbdpre.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/idas/idas_direct.h | 26 StanHeaders-2.26.25/StanHeaders/inst/include/idas/idas_ls.h | 10 StanHeaders-2.26.25/StanHeaders/inst/include/idas/idas_spils.h | 70 StanHeaders-2.26.25/StanHeaders/inst/include/kinsol/kinsol.h | 7 StanHeaders-2.26.25/StanHeaders/inst/include/kinsol/kinsol_bbdpre.h | 2 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StanHeaders-2.26.25/StanHeaders/inst/include/nvector/nvector_pthreads.h | 31 StanHeaders-2.26.25/StanHeaders/inst/include/nvector/nvector_raja.h | 114 StanHeaders-2.26.25/StanHeaders/inst/include/nvector/nvector_serial.h | 25 StanHeaders-2.26.25/StanHeaders/inst/include/nvector/nvector_trilinos.h | 18 StanHeaders-2.26.25/StanHeaders/inst/include/nvector/trilinos/SundialsTpetraVectorInterface.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/nvector/trilinos/SundialsTpetraVectorKernels.hpp | 320 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/analyze/mcmc/autocovariance.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_effective_sample_size.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/command/stanc_helper.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/array_var_context.hpp | 24 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/chained_var_context.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/cmd_line.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/dump.hpp | 41 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/empty_var_context.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/random_var_context.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/reader.hpp | 624 + StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/util.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/validate_dims.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/var_context.hpp | 52 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/io/writer.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_control.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/node/assgn.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_control.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/node/lub_idx.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/node/while_statement.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/scope.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures.hpp | 14 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/ast/variable_map.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator.hpp | 1 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/expression_visgen.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_cpp.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_function_functor.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_functor_arguments.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decl_inits.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_model_compile_info_method.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_set_param_ranges.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_statement.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_transform_inits_method.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_array.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_method.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_using.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_using_namespace.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_usings.hpp | 1 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_nonnegative.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/generate_void_statement.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/idx_user_visgen.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_type.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar_def.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_def.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_def.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_def.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/chains.hpp | 33 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/covar_adaptation.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/base_hmc.hpp | 29 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/ps_point.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_metric.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/impl_leapfrog.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/base_nuts_classic.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/static/base_static_hmc.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/base_static_uniform.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_dense_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_diag_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_softabs_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_unit_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/base_xhmc.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/dense_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/diag_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/softabs_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/unit_e_xhmc.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/sample.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/stepsize_adaptation.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/stepsize_adapter.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/stepsize_covar_adapter.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/stepsize_var_adapter.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/var_adaptation.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/mcmc/windowed_adaptation.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/grad_tr_mat_times_hessian.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/gradient.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/gradient_dot_vector.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/hessian.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/hessian_times_vector.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/access_helpers.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/deep_copy.hpp | 49 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/index.hpp | 18 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/index_list.hpp | 60 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/lvalue.hpp | 1065 ++ StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/lvalue_varmat.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/rvalue.hpp | 892 +- StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/rvalue_at.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/rvalue_index_size.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/rvalue_return.hpp | 32 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/indexing/rvalue_varmat.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/log_prob_grad.hpp | 21 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/log_prob_propto.hpp | 24 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/model_base.hpp | 16 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/model_functional.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/model_header.hpp | 1 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/prob_grad.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/model/standalone_functions_header.hpp | 1 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/optimization/bfgs_update.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp | 20 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/optimization/newton.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/diagnose/diagnose.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/experimental/advi/defaults.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/experimental/advi/fullrank.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/experimental/advi/meanfield.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/optimize/bfgs.hpp | 12 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/optimize/defaults.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/optimize/lbfgs.hpp | 21 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/optimize/newton.hpp | 15 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/fixed_param.hpp | 18 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e_adapt.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e_adapt.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e_adapt.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e_adapt.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e_adapt.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e_adapt.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp | 38 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/create_unit_e_dense_inv_metric.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/generate_transitions.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/initialize.hpp | 17 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/read_dense_inv_metric.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/read_diag_inv_metric.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/run_adaptive_sampler.hpp | 22 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/run_sampler.hpp | 22 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/validate_dense_inv_metric.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/services/util/validate_diag_inv_metric.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/variational/advi.hpp | 28 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/variational/base_family.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/variational/print_progress.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/src/stan/version.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math.hpp | 17 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/fvar.hpp | 44 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/operator_division.hpp | 61 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/operator_logical_and.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/operator_logical_or.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/std_complex.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/std_iterator_traits.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/std_numeric_limits.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/fun |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/fun.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/functor |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/functor.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/meta |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/meta.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/fun |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/fun.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/functor |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/functor.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/mat.hpp | 26 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/mix/meta.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/buffer_types.hpp | 26 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/cholesky_decompose.hpp | 44 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/copy.hpp | 266 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_diagonal_zeros.hpp | 14 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_invalid_matrix_view.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_mat_size_one.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_nan.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_opencl.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_symmetric.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/err/check_triangular.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/is_constant.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernel_cl.hpp | 172 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernel_generator |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernel_generator.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/add.hpp | 53 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/batch_identity.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/categorical_logit_glm_lpmf.hpp | 12 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/check_diagonal_zeros.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/check_nan.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/check_symmetric.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/cholesky_decompose.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/copy.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/Phi.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/Phi_approx.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/beta.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/binomial_coefficient_log.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/digamma.hpp | 187 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_Phi.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_logit.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/inv_square.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lbeta.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lgamma_stirling.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/lgamma_stirling_diff.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m_exp.hpp | 51 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1m_inv_logit.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log1p_exp.hpp | 41 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_diff_exp.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_inv_logit.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/log_inv_logit_diff.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/logit.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/multiply_log.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions/trigamma.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/diag_inv.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/divide_columns.hpp | 28 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/fill_strict_tri.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/gp_exp_quad_cov.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/helpers.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/inv_lower_tri_multiply.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/matrix_multiply.hpp | 54 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/multiply_transpose.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/neg_binomial_2_log_glm_lpmf.hpp | 35 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/neg_rect_lower_tri_multiply.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/ordered_logistic_glm_lpmf.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/pack.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/rep_matrix.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul_diagonal.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/triangular_transpose.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/kernels/unpack.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/matrix_cl.hpp | 491 - StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/matrix_cl_view.hpp | 20 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/multiply_transpose.hpp | 18 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/opencl_context.hpp | 204 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/pinned_matrix.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/plain_type.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/add_diag.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_logit_glm_lpmf.hpp | 211 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_logit_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/bernoulli_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/beta_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/beta_proportion_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/binomial_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/block.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/categorical_logit_glm_lpmf.hpp | 161 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/cauchy_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/chi_square_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/cholesky_decompose.hpp | 12 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/col.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/cols.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/columns_dot_product.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/columns_dot_self.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/crossprod.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/diag_matrix.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/diag_post_multiply.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/diag_pre_multiply.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/dims.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/distance.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/divide.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/divide_columns.hpp | 23 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/dot_product.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/dot_self.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/double_exponential_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/exp_mod_normal_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/exponential_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/frechet_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/gamma_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/gp_exp_quad_cov.hpp | 11 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/head.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/inv.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/inv_chi_square_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/inv_cloglog.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/inv_gamma_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/inv_sqrt.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/logistic_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/lognormal_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/mdivide_left_tri_low.hpp | 30 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/mdivide_right_tri_low.hpp | 18 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/mean.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/multiply.hpp | 214 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_log_glm_lpmf.hpp | 259 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_log_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_2_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/neg_binomial_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/normal_id_glm_lpdf.hpp | 298 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/normal_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/num_elements.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/ordered_logistic_glm_lpmf.hpp | 162 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/pareto_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/pareto_type_2_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/poisson_log_glm_lpmf.hpp | 202 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/poisson_log_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/poisson_lpmf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rayleigh_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rep_matrix.hpp | 15 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rep_row_vector.hpp | 7 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rep_vector.hpp | 7 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/row.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rows.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rows_dot_product.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/rows_dot_self.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/scaled_inv_chi_square_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/segment.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/sign.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/size.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/skew_normal_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/squared_distance.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/std_normal_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/student_t_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/sub_col.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/sub_row.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/sum.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/tail.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/tcrossprod.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/uniform_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/weibull_lpdf.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/ref_type_for_opencl.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/rev |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/rev.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/scalar_type.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/to_ref_for_opencl.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/tri_inverse.hpp | 76 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/triangular_transpose.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/value_type.hpp | 6 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/zeros_strict_tri.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/arr/fun/sum.hpp | 27 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/complex_base.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/init_threadpool_tbb.hpp | 37 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_addition.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_division.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_equal_equal.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_minus.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_multiplication.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_not_equal.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_plus.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_subtraction.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/eigen_plugins.h |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/err |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/err.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/fun |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/fun.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/functor |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/functor.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat.hpp | 340 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/err/check_ldlt_factor.hpp | 42 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp | 64 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/Eigen.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/LDLT_factor.hpp | 130 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/autocorrelation.hpp | 199 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/autocovariance.hpp | 123 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp | 53 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp | 55 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp | 49 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant_ldlt.hpp | 18 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/mean.hpp | 42 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/sum.hpp | 27 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_inv_quad_form_ldlt.hpp | 33 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/mat/fun/variance.hpp | 61 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/meta |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/meta.hpp | 296 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/prob |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/prob.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal.hpp | 419 - StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_finite.hpp | 52 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater_or_equal.hpp | 70 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_nonnegative.hpp | 56 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_not_nan.hpp | 55 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive.hpp | 82 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/err/check_size_match.hpp | 68 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/meta/include_summand.hpp | 57 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/meta/max_size_mvt.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/scal/meta/return_type.hpp | 49 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core.hpp | 17 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/Eigen_NumTraits.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/accumulate_adjoints.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/arena_allocator.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/arena_matrix.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/autodiffstackstorage.hpp | 22 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/build_vari_array.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/callback_vari.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/chainable_object.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/chainablestack.hpp | 7 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/count_vars.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/deep_copy_vars.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/grad.hpp | 38 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/init_chainablestack.hpp | 20 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/matrix_vari.hpp | 19 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/nested_rev_autodiff.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp | 253 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_divide_equal.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp | 79 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_equal.hpp | 39 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_greater_than.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_greater_than_or_equal.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_less_than.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_less_than_or_equal.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_logical_and.hpp | 15 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_logical_or.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_minus_equal.hpp | 17 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_multiplication.hpp | 31 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_multiply_equal.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_not_equal.hpp | 42 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_plus_equal.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp | 310 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_unary_decrement.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_unary_increment.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp | 13 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_unary_not.hpp | 1 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/operator_unary_plus.hpp | 9 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/precomp_v_vari.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/precomp_vv_vari.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/precomp_vvv_vari.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/precomputed_gradients.hpp | 160 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/print_stack.hpp | 10 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/profiling.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/read_var.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/recover_memory_nested.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/reverse_pass_callback.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/save_varis.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/scoped_chainablestack.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp | 8 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/start_nested.hpp | 3 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/std_complex.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/std_isinf.hpp | 4 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/std_isnan.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/std_iterator_traits.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/std_numeric_limits.hpp | 98 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/stored_gradient_vari.hpp | 2 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/typedefs.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/var.hpp | 986 ++ StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/vari.hpp | 858 ++ StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/vector_vari.hpp | 7 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/core/zero_adjoints.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/fun |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/fun.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/functor |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/functor.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/mat.hpp | 78 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/meta |only StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/rev/meta.hpp | 16 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/version.hpp | 5 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_band.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_config.h | 178 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_config.in | 152 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_cuda_policies.hpp |only StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_dense.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_direct.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_export.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_fconfig.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_fnvector.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_futils.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_iterative.h | 8 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_lapack.h | 231 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_linearsolver.h | 95 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_math.h | 33 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_matrix.h | 37 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_memory.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_mpi_types.h | 16 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_nonlinearsolver.h | 53 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_nvector.h | 107 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_nvector_senswrapper.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_types.h | 19 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_version.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sundials/sundials_xbraid.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sundials_debug.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_band.h | 15 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_dense.h | 7 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_klu.h | 34 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_lapackband.h | 25 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_lapackdense.h | 25 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_pcg.h | 36 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_spbcgs.h | 41 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_spfgmr.h | 41 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_spgmr.h | 42 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_sptfqmr.h | 34 StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_superludist.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sunlinsol/sunlinsol_superlumt.h | 29 StanHeaders-2.26.25/StanHeaders/inst/include/sunmatrix/sunmatrix_band.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sunmatrix/sunmatrix_cusparse.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sunmatrix/sunmatrix_dense.h | 2 StanHeaders-2.26.25/StanHeaders/inst/include/sunmatrix/sunmatrix_slunrloc.h |only StanHeaders-2.26.25/StanHeaders/inst/include/sunmatrix/sunmatrix_sparse.h | 5 StanHeaders-2.26.25/StanHeaders/inst/include/sunmemory |only StanHeaders-2.26.25/StanHeaders/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 59 StanHeaders-2.26.25/StanHeaders/inst/include/sunnonlinsol/sunnonlinsol_newton.h | 18 StanHeaders-2.26.25/StanHeaders/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h |only StanHeaders-2.26.25/StanHeaders/inst/stanc.js |only StanHeaders-2.26.25/StanHeaders/src/Makevars | 18 StanHeaders-2.26.25/StanHeaders/src/Makevars.win | 18 StanHeaders-2.26.25/StanHeaders/src/cvodes/LICENSE | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/README.md |only StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodea.c | 328 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodea_io.c | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes.c | 3132 ++++---- StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_bandpre.c | 122 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_bandpre_impl.h | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_bbdpre.c | 164 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_bbdpre_impl.h | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_diag.c | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_diag_impl.h | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_direct.c | 7 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_impl.h | 392 - StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_io.c | 451 - StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_ls.c | 819 +- StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_ls_impl.h | 41 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_nls.c | 56 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_nls_sim.c | 75 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_nls_stg.c | 39 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_nls_stg1.c | 23 StanHeaders-2.26.25/StanHeaders/src/cvodes/cvodes_spils.c | 2 StanHeaders-2.26.25/StanHeaders/src/cvodes/fmod |only StanHeaders-2.26.25/StanHeaders/src/idas/LICENSE | 2 StanHeaders-2.26.25/StanHeaders/src/idas/README.md |only StanHeaders-2.26.25/StanHeaders/src/idas/fmod |only StanHeaders-2.26.25/StanHeaders/src/idas/idaa.c | 533 - StanHeaders-2.26.25/StanHeaders/src/idas/idaa_io.c | 8 StanHeaders-2.26.25/StanHeaders/src/idas/idas.c | 1955 ++--- StanHeaders-2.26.25/StanHeaders/src/idas/idas_bbdpre.c | 149 StanHeaders-2.26.25/StanHeaders/src/idas/idas_bbdpre_impl.h | 2 StanHeaders-2.26.25/StanHeaders/src/idas/idas_direct.c | 2 StanHeaders-2.26.25/StanHeaders/src/idas/idas_ic.c | 2 StanHeaders-2.26.25/StanHeaders/src/idas/idas_impl.h | 483 - StanHeaders-2.26.25/StanHeaders/src/idas/idas_io.c | 345 StanHeaders-2.26.25/StanHeaders/src/idas/idas_ls.c | 388 - StanHeaders-2.26.25/StanHeaders/src/idas/idas_ls_impl.h | 16 StanHeaders-2.26.25/StanHeaders/src/idas/idas_nls.c | 69 StanHeaders-2.26.25/StanHeaders/src/idas/idas_nls_sim.c | 80 StanHeaders-2.26.25/StanHeaders/src/idas/idas_nls_stg.c | 33 StanHeaders-2.26.25/StanHeaders/src/idas/idas_spils.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/LICENSE | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/README.md |only StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinband.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinbbd.c | 18 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinbbd.h | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkindense.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinjtimes.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinnulllinsol.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinnullmatrix.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinpreco.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinsol.c | 12 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinsol.h | 4 StanHeaders-2.26.25/StanHeaders/src/kinsol/fcmix/fkinsparse.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/fmod |only StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol.c | 1169 +-- StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_bbdpre.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_bbdpre_impl.h | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_direct.c | 2 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_impl.h | 156 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_io.c | 115 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_ls.c | 200 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_ls_impl.h | 9 StanHeaders-2.26.25/StanHeaders/src/kinsol/kinsol_spils.c | 2 StanHeaders-2.26.25/StanHeaders/src/nvector/cuda/VectorArrayKernels.cuh |only StanHeaders-2.26.25/StanHeaders/src/nvector/cuda/VectorKernels.cuh |only StanHeaders-2.26.25/StanHeaders/src/nvector/cuda/nvector_cuda.cu | 2224 ++++- StanHeaders-2.26.25/StanHeaders/src/nvector/hip |only StanHeaders-2.26.25/StanHeaders/src/nvector/manyvector |only StanHeaders-2.26.25/StanHeaders/src/nvector/mpiplusx |only StanHeaders-2.26.25/StanHeaders/src/nvector/openmp/fmod |only StanHeaders-2.26.25/StanHeaders/src/nvector/openmp/fnvector_openmp.c | 22 StanHeaders-2.26.25/StanHeaders/src/nvector/openmp/fnvector_openmp.h | 2 StanHeaders-2.26.25/StanHeaders/src/nvector/openmp/nvector_openmp.c | 476 - StanHeaders-2.26.25/StanHeaders/src/nvector/openmpdev/nvector_openmpdev.c | 319 StanHeaders-2.26.25/StanHeaders/src/nvector/parallel/fmod |only StanHeaders-2.26.25/StanHeaders/src/nvector/parallel/fnvector_parallel.c | 42 StanHeaders-2.26.25/StanHeaders/src/nvector/parallel/fnvector_parallel.h | 2 StanHeaders-2.26.25/StanHeaders/src/nvector/parallel/nvector_parallel.c | 505 - StanHeaders-2.26.25/StanHeaders/src/nvector/parhyp/nvector_parhyp.c | 525 - StanHeaders-2.26.25/StanHeaders/src/nvector/petsc/nvector_petsc.c | 480 - StanHeaders-2.26.25/StanHeaders/src/nvector/pthreads/fmod |only StanHeaders-2.26.25/StanHeaders/src/nvector/pthreads/fnvector_pthreads.c | 22 StanHeaders-2.26.25/StanHeaders/src/nvector/pthreads/fnvector_pthreads.h | 2 StanHeaders-2.26.25/StanHeaders/src/nvector/pthreads/nvector_pthreads.c | 458 - StanHeaders-2.26.25/StanHeaders/src/nvector/raja/nvector_raja.cpp |only StanHeaders-2.26.25/StanHeaders/src/nvector/serial/fmod |only StanHeaders-2.26.25/StanHeaders/src/nvector/serial/fnvector_serial.c | 22 StanHeaders-2.26.25/StanHeaders/src/nvector/serial/fnvector_serial.h | 2 StanHeaders-2.26.25/StanHeaders/src/nvector/serial/nvector_serial.c | 300 StanHeaders-2.26.25/StanHeaders/src/nvector/trilinos/nvector_trilinos.cpp | 336 StanHeaders-2.26.25/StanHeaders/src/sundials/fmod |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_band.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_cuda.h |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_cuda_kernels.cuh |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_debug.h |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_dense.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_direct.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_futils.c |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_hip.h |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_hip_kernels.hip.hpp |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_iterative.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_linearsolver.c | 131 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_math.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_matrix.c | 119 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_memory.c |only StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_nonlinearsolver.c | 97 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_nvector.c | 460 + StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_nvector_senswrapper.c | 2 StanHeaders-2.26.25/StanHeaders/src/sundials/sundials_version.c | 30 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/band/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/band/fsunlinsol_band.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/band/fsunlinsol_band.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/band/sunlinsol_band.c | 168 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/cusolversp |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/dense/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/dense/fsunlinsol_dense.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/dense/fsunlinsol_dense.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/dense/sunlinsol_dense.c | 161 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/klu/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/klu/fsunlinsol_klu.c | 14 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/klu/fsunlinsol_klu.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/klu/sunlinsol_klu.c | 239 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackband/fsunlinsol_lapackband.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackband/fsunlinsol_lapackband.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackband/sunlinsol_lapackband.c | 183 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackdense/fsunlinsol_lapackdense.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackdense/fsunlinsol_lapackdense.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/lapackdense/sunlinsol_lapackdense.c | 171 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/pcg/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/pcg/fsunlinsol_pcg.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/pcg/fsunlinsol_pcg.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/pcg/sunlinsol_pcg.c | 300 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spbcgs/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spbcgs/fsunlinsol_spbcgs.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spbcgs/fsunlinsol_spbcgs.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spbcgs/sunlinsol_spbcgs.c | 326 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spfgmr/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spfgmr/fsunlinsol_spfgmr.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spfgmr/fsunlinsol_spfgmr.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spfgmr/sunlinsol_spfgmr.c | 404 - StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spgmr/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spgmr/fsunlinsol_spgmr.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spgmr/fsunlinsol_spgmr.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/spgmr/sunlinsol_spgmr.c | 437 - StanHeaders-2.26.25/StanHeaders/src/sunlinsol/sptfqmr/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/sptfqmr/fsunlinsol_sptfqmr.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/sptfqmr/fsunlinsol_sptfqmr.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/sptfqmr/sunlinsol_sptfqmr.c | 358 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/superludist |only StanHeaders-2.26.25/StanHeaders/src/sunlinsol/superlumt/fsunlinsol_superlumt.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/superlumt/fsunlinsol_superlumt.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunlinsol/superlumt/sunlinsol_superlumt.c | 310 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/band/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunmatrix/band/fsunmatrix_band.c | 26 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/band/fsunmatrix_band.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/band/sunmatrix_band.c | 145 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/cusparse |only StanHeaders-2.26.25/StanHeaders/src/sunmatrix/dense/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunmatrix/dense/fsunmatrix_dense.c | 17 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/dense/fsunmatrix_dense.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/dense/sunmatrix_dense.c | 123 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/slunrloc |only StanHeaders-2.26.25/StanHeaders/src/sunmatrix/sparse/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunmatrix/sparse/fsunmatrix_sparse.c | 29 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/sparse/fsunmatrix_sparse.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunmatrix/sparse/sunmatrix_sparse.c | 453 - StanHeaders-2.26.25/StanHeaders/src/sunmemory |only StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/fixedpoint/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/fixedpoint/fsunnonlinsol_fixedpoint.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c | 229 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/newton/fmod |only StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/newton/fsunnonlinsol_newton.c | 2 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/newton/fsunnonlinsol_newton.h | 2 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/newton/sunnonlinsol_newton.c | 194 StanHeaders-2.26.25/StanHeaders/src/sunnonlinsol/petscsnes |only StanHeaders-2.26.25/StanHeaders/vignettes/stanmath.Rmd | 15 1126 files changed, 25497 insertions(+), 17698 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.0-5 dated 2023-04-22 and 3.0-6 dated 2023-05-17
DESCRIPTION | 14 +-- MD5 | 32 ++++---- NEWS | 9 ++ inst/doc/bugfixes.R | 18 ++-- inst/doc/bugfixes.Rnw | 20 ++++- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 12 +-- inst/doc/updates.Rnw | 167 +++++++++++++++++++++++++++++++++++++++++----- inst/doc/updates.pdf |binary man/spatstat-package.Rd | 2 vignettes/bugfixes.Rnw | 20 ++++- vignettes/updates.Rnw | 167 +++++++++++++++++++++++++++++++++++++++++----- 17 files changed, 385 insertions(+), 77 deletions(-)
Title: Mass Spectrometry Metabolomics Feature Clustering and
Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry data <DOI: 10.1021/ac501530d>.
Author: Corey D. Broeckling [aut] ,
Fayyaz Afsar [aut],
Steffen Neumann [aut],
Asa Ben-Hur [aut],
Jessica Prenni [aut],
Helge Hecht [cre] ,
Matej Trojak [ctb],
Zargham Ahmad [ctb]
Maintainer: Helge Hecht <helge.hecht@recetox.muni.cz>
Diff between RAMClustR versions 1.2.4 dated 2022-04-13 and 1.3.0 dated 2023-05-17
RAMClustR-1.2.4/RAMClustR/R/rc.feature.cv.filter.R |only RAMClustR-1.2.4/RAMClustR/tests/testthat/testdata/ramclustObj.rds |only RAMClustR-1.3.0/RAMClustR/ChangeLog | 9 RAMClustR-1.3.0/RAMClustR/DESCRIPTION | 50 RAMClustR-1.3.0/RAMClustR/MD5 | 178 RAMClustR-1.3.0/RAMClustR/NAMESPACE | 28 RAMClustR-1.3.0/RAMClustR/R/RCQC.R | 6 RAMClustR-1.3.0/RAMClustR/R/adap.to.rc.R |only RAMClustR-1.3.0/RAMClustR/R/annotate.R | 56 RAMClustR-1.3.0/RAMClustR/R/calculate.similarity.R | 32 RAMClustR-1.3.0/RAMClustR/R/defineExperiment.R | 392 RAMClustR-1.3.0/RAMClustR/R/get.taxon.cids.R |only RAMClustR-1.3.0/RAMClustR/R/import.MSFinder.formulas.R | 27 RAMClustR-1.3.0/RAMClustR/R/import.MSFinder.structures.R | 3 RAMClustR-1.3.0/RAMClustR/R/import.adap.kdb.R | 4 RAMClustR-1.3.0/RAMClustR/R/import.msfinder.mssearch.R | 30 RAMClustR-1.3.0/RAMClustR/R/mergeRCobjects.R | 69 RAMClustR-1.3.0/RAMClustR/R/ramclustR.R | 972 RAMClustR-1.3.0/RAMClustR/R/rc.calibrate.ri.R | 2 RAMClustR-1.3.0/RAMClustR/R/rc.cmpd.filter.blanks.R |only RAMClustR-1.3.0/RAMClustR/R/rc.cmpd.get.classyfire.R | 8 RAMClustR-1.3.0/RAMClustR/R/rc.cmpd.get.pathways.R |only RAMClustR-1.3.0/RAMClustR/R/rc.cmpd.get.pubchem.R | 64 RAMClustR-1.3.0/RAMClustR/R/rc.expand.sample.names.R | 10 RAMClustR-1.3.0/RAMClustR/R/rc.export.msp.rc.R | 4 RAMClustR-1.3.0/RAMClustR/R/rc.feature.filter.blanks.R | 355 RAMClustR-1.3.0/RAMClustR/R/rc.feature.filter.cv.R | 282 RAMClustR-1.3.0/RAMClustR/R/rc.feature.normalize.batch.qc.R |only RAMClustR-1.3.0/RAMClustR/R/rc.feature.normalize.qc.R | 391 RAMClustR-1.3.0/RAMClustR/R/rc.feature.normalize.quantile.R |only RAMClustR-1.3.0/RAMClustR/R/rc.feature.normalize.tic.R | 108 RAMClustR-1.3.0/RAMClustR/R/rc.feature.replace.na.R | 244 RAMClustR-1.3.0/RAMClustR/R/rc.get.csv.data.R |only RAMClustR-1.3.0/RAMClustR/R/rc.get.df.data.R |only RAMClustR-1.3.0/RAMClustR/R/rc.get.xmcs.data.R | 353 RAMClustR-1.3.0/RAMClustR/R/rc.qc.R | 20 RAMClustR-1.3.0/RAMClustR/R/rc.ramclustr.R | 213 RAMClustR-1.3.0/RAMClustR/R/rc.remove.qc.R | 96 RAMClustR-1.3.0/RAMClustR/R/rc.restore.qc.samples.R | 28 RAMClustR-1.3.0/RAMClustR/R/write.methods.R | 7 RAMClustR-1.3.0/RAMClustR/R/write.msp.R | 3 RAMClustR-1.3.0/RAMClustR/README.md | 102 RAMClustR-1.3.0/RAMClustR/build/vignette.rds |binary RAMClustR-1.3.0/RAMClustR/inst/doc/RAMClustR.R | 2 RAMClustR-1.3.0/RAMClustR/inst/doc/RAMClustR.Rmd | 2 RAMClustR-1.3.0/RAMClustR/inst/doc/RAMClustR.html | 130 RAMClustR-1.3.0/RAMClustR/inst/extdata/featDefinition.rds |only RAMClustR-1.3.0/RAMClustR/inst/extdata/featValues.rds |only RAMClustR-1.3.0/RAMClustR/inst/extdata/phenoData.csv |only RAMClustR-1.3.0/RAMClustR/inst/extdata/phenoData_df.rds |only RAMClustR-1.3.0/RAMClustR/man/adap.to.rc.Rd |only RAMClustR-1.3.0/RAMClustR/man/add_params.Rd |only RAMClustR-1.3.0/RAMClustR/man/check_arguments_filter.blanks.Rd |only RAMClustR-1.3.0/RAMClustR/man/check_arguments_filter.cv.Rd |only 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Title: Modeling Multivariate Origins Determinants - Evolutionary
Lineages in Ecology
Description: Perform multivariate modeling of evolved traits, with special attention to
understanding the interplay of the multi-factorial determinants of their origins
in complex ecological settings (Stephens, 2007 <doi:10.1016/j.tree.2006.12.003>).
This software primarily concentrates on phylogenetic regression analysis, enabling
implementation of tree transformation averaging and visualization functionality.
Functions additionally support information theoretic approaches
(Grueber, 2011 <doi:10.1111/j.1420-9101.2010.02210.x>;
Garamszegi, 2011 <doi:10.1007/s00265-010-1028-7>)
such as model averaging and selection of phylogenetic models.
Accessory functions are also implemented for coef standardization (Cade 2015),
selection uncertainty, and variable importance (Burnham & Anderson 2000).
There are other numerous functions for visualizing confounded variables,
plotting phylogenetic trees, as well as reporting and exporting modeling results.
Lastly, as challenges to ecology are [...truncated...]
Author: David M Schruth
Maintainer: David M Schruth <dschruth@anthropoidea.org>
Diff between mmodely versions 0.2.2 dated 2022-11-06 and 0.2.5 dated 2023-05-17
mmodely-0.2.2/mmodely/R/AIC.R |only mmodely-0.2.2/mmodely/man/distro.dots.modsel.Rd |only mmodely-0.2.2/mmodely/man/weight.AIC.Rd |only mmodely-0.2.5/mmodely/DESCRIPTION | 12 - mmodely-0.2.5/mmodely/MD5 | 50 ++--- mmodely-0.2.5/mmodely/NAMESPACE | 4 mmodely-0.2.5/mmodely/R/IC.R |only mmodely-0.2.5/mmodely/R/models.R | 2 mmodely-0.2.5/mmodely/R/pgls.R | 87 ++++++---- mmodely-0.2.5/mmodely/R/phylogeny.R | 2 mmodely-0.2.5/mmodely/R/plotting.R | 23 +- mmodely-0.2.5/mmodely/R/standarize.R |only mmodely-0.2.5/mmodely/build/vignette.rds |binary mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.R | 42 ++-- mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.Rnw | 27 ++- mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.pdf |binary mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.R | 58 +++--- mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.Rnw | 40 ++-- mmodely-0.2.5/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.pdf |binary mmodely-0.2.5/mmodely/man/average.fit.models.Rd | 15 + mmodely-0.2.5/mmodely/man/calc.q2n.ratio.Rd |only mmodely-0.2.5/mmodely/man/get.model.combos.Rd | 2 mmodely-0.2.5/mmodely/man/pgls.iter.Rd | 2 mmodely-0.2.5/mmodely/man/plot.pgls.R2AIC.Rd | 6 mmodely-0.2.5/mmodely/man/plot.pgls.iters.Rd | 2 mmodely-0.2.5/mmodely/man/select.best.models.Rd | 4 mmodely-0.2.5/mmodely/man/sparge.modsel.Rd |only mmodely-0.2.5/mmodely/man/weight.IC.Rd |only mmodely-0.2.5/mmodely/vignettes/Schruth-mmodely-vignette-Vision.Rnw | 27 ++- mmodely-0.2.5/mmodely/vignettes/Schruth-mmodely-vignette-Vocal.Rnw | 40 ++-- 30 files changed, 273 insertions(+), 172 deletions(-)
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee
(2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert
and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>. For
models with up to eight features, the results are exact regarding the
selected background data. Otherwise, an almost exact hybrid algorithm
involving iterative sampling is used. The package plays well together
with meta-learning packages like 'tidymodels', 'caret' or 'mlr3'.
Visualizations can be done using the R package 'shapviz'.
Author: Michael Mayer [aut, cre],
David Watson [aut],
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.3.6 dated 2023-05-03 and 0.3.7 dated 2023-05-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/kernelshap.R | 18 +++++++++++------- man/kernelshap.Rd | 18 +++++++++++------- 5 files changed, 35 insertions(+), 21 deletions(-)
Title: Learning R with Dr. Hu
Description: Tutarials of R learning easily and happily.
Author: Yue Hu [aut, cre],
Xinyi Ye [ctb, trl],
Yufei Sun [ctb]
Maintainer: Yue Hu <yuehu@tsinghua.edu.cn>
Diff between drhur versions 1.0.0 dated 2022-10-17 and 1.1.0 dated 2023-05-17
drhur-1.0.0/drhur/inst/tutorials/calculate_cn/calculate_cn.html |only drhur-1.0.0/drhur/inst/tutorials/describe_cn |only drhur-1.0.0/drhur/inst/tutorials/play_cn/play_cn.html |only drhur-1.0.0/drhur/inst/tutorials/visualize_cn/visualize_cn.html |only drhur-1.0.0/drhur/inst/tutorials/visualize_cn/visualize_cn_files |only drhur-1.0.0/drhur/inst/tutorials/wrangle_cn/images/wvs7.jfif |only drhur-1.0.0/drhur/inst/tutorials/wrangle_cn/wrangle_cn.html |only drhur-1.1.0/drhur/DESCRIPTION | 19 drhur-1.1.0/drhur/LICENSE | 2 drhur-1.1.0/drhur/MD5 | 63 drhur-1.1.0/drhur/NAMESPACE | 8 drhur-1.1.0/drhur/NEWS.md | 12 drhur-1.1.0/drhur/R/drhur.R | 50 drhur-1.1.0/drhur/R/wvs7.R | 74 drhur-1.1.0/drhur/README.md | 38 drhur-1.1.0/drhur/build/vignette.rds |binary drhur-1.1.0/drhur/inst/doc/drhur-vignette.R | 55 drhur-1.1.0/drhur/inst/doc/drhur-vignette.Rmd | 160 - drhur-1.1.0/drhur/inst/doc/drhur-vignette.html | 1129 +++------ drhur-1.1.0/drhur/inst/doc/drhur-vignette_cn.R |only drhur-1.1.0/drhur/inst/doc/drhur-vignette_cn.Rmd |only drhur-1.1.0/drhur/inst/doc/drhur-vignette_cn.html |only drhur-1.1.0/drhur/inst/tutorials/calculate_cn/calculate_cn.Rmd | 956 +++---- drhur-1.1.0/drhur/inst/tutorials/calculate_en |only drhur-1.1.0/drhur/inst/tutorials/play_cn/play_cn.Rmd | 1213 +++++----- drhur-1.1.0/drhur/inst/tutorials/play_en |only drhur-1.1.0/drhur/inst/tutorials/visualize_cn/visualize_cn.Rmd | 1057 ++++---- drhur-1.1.0/drhur/inst/tutorials/visualize_en |only drhur-1.1.0/drhur/inst/tutorials/wrangle_cn/images/wvs7.png |only drhur-1.1.0/drhur/inst/tutorials/wrangle_cn/wrangle_cn.Rmd | 1072 ++++---- drhur-1.1.0/drhur/inst/tutorials/wrangle_en |only drhur-1.1.0/drhur/man/drhur.Rd | 51 drhur-1.1.0/drhur/man/wvs7.Rd | 96 drhur-1.1.0/drhur/vignettes/drhur-vignette.Rmd | 160 - drhur-1.1.0/drhur/vignettes/drhur-vignette_cn.Rmd |only 35 files changed, 3032 insertions(+), 3183 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.se/libcurl/>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 1.3 dated 2022-09-03 and 1.4.0 dated 2023-05-17
DESCRIPTION | 8 MD5 | 168 +++++------ NEWS.md | 8 R/async-queue.R | 25 - R/async.R | 51 ++- R/asyncvaried.R | 108 +++++-- R/auth.R | 4 R/client.R | 12 R/content-types.R | 6 R/cookies.R | 4 R/curl-options.R | 2 R/handle.R | 4 R/hooks.R | 8 R/http-headers.R | 6 R/httprequest.R | 57 +++ R/make_url.R | 24 - R/mocking.R | 2 R/ok.R | 6 R/response.R | 8 R/set.R | 12 R/upload.R | 2 R/verbs.R | 47 +-- R/writing-options.R | 28 - build/vignette.rds |binary inst/doc/async.Rmd | 113 ++----- inst/doc/async.html | 302 +++++++++----------- inst/doc/best-practices-api-packages.Rmd | 8 inst/doc/best-practices-api-packages.html | 133 ++++----- inst/doc/choosing-a-client.Rmd | 8 inst/doc/choosing-a-client.html | 8 inst/doc/crul.Rmd | 124 ++++---- inst/doc/crul.html | 389 ++++++++++++++------------- inst/doc/curl-options.Rmd | 16 - inst/doc/curl-options.html | 223 +++++++-------- inst/doc/how-to-use-crul.Rmd | 22 - inst/doc/how-to-use-crul.html | 267 +++++++++--------- man/Async.Rd | 67 +++- man/AsyncQueue.Rd | 21 - man/AsyncVaried.Rd | 43 +- man/HttpClient.Rd | 20 - man/HttpRequest.Rd | 72 ++++ man/HttpResponse.Rd | 10 man/Paginator.Rd | 2 man/auth.Rd | 4 man/content-types.Rd | 6 man/cookies.Rd | 4 man/crul-options.Rd | 12 man/curl-options.Rd | 2 man/handle.Rd | 4 man/hooks.Rd | 8 man/http-headers.Rd | 6 man/mock.Rd | 2 man/ok.Rd | 6 man/upload.Rd | 2 man/url_build.Rd | 22 - man/verb-DELETE.Rd | 7 man/verb-GET.Rd | 10 man/verb-HEAD.Rd | 7 man/verb-PATCH.Rd | 7 man/verb-POST.Rd | 9 man/verb-PUT.Rd | 7 man/writing-options.Rd | 28 - tests/testthat/helper-crul.R | 11 tests/testthat/test-async.R | 17 + tests/testthat/test-asyncqueue.R | 16 - tests/testthat/test-asyncvaried.R | 16 - tests/testthat/test-client-hooks.R | 6 tests/testthat/test-client.R | 4 tests/testthat/test-content-type.R | 4 tests/testthat/test-response.R | 2 tests/testthat/test-retry.R | 8 tests/testthat/test-url_build_parse.R | 9 tests/testthat/test-utils.R | 4 vignettes/async.Rmd | 113 ++----- vignettes/async.Rmd.og | 12 vignettes/best-practices-api-packages.Rmd | 8 vignettes/best-practices-api-packages.Rmd.og | 6 vignettes/choosing-a-client.Rmd | 8 vignettes/choosing-a-client.Rmd.og | 6 vignettes/crul.Rmd | 124 ++++---- vignettes/crul.Rmd.og | 11 vignettes/curl-options.Rmd | 16 - vignettes/curl-options.Rmd.og | 14 vignettes/how-to-use-crul.Rmd | 22 - vignettes/how-to-use-crul.Rmd.og | 2 85 files changed, 1609 insertions(+), 1431 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations, (3) calculating confidence intervals and the associated
actual coverage for binomial proportions, and 4) calculating the support values and the
probability mass function of the Kaplan-Meier product-limit estimator. Each is given in
greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif,
weibull) corresponding to a user-given complete or right-censored dataset and level of
significance. The crplot() algorithm plots more points in areas of greater curvature to
ensure a smooth appearance throughout the confidence region boundary. An alternative
heuristic plots a specified number of points at roughly uniform intervals along its boundary.
Both heuristics build upon the radial profile log-likelihood ratio technique for plotting
confid [...truncated...]
Author: Christopher Weld [aut, cre] ,
Kexin Feng [aut],
Hayeon Park [aut],
Yuxin Qin [aut],
Heather Sasinowska [aut],
Lawrence Leemis [aut],
Yuan Chang [ctb],
Brock Crook [ctb],
Chris Kuebler [ctb],
Andrew Loh [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>
Diff between conf versions 1.7.1 dated 2022-05-20 and 1.8.0 dated 2023-05-17
DESCRIPTION | 44 +- MD5 | 28 + NAMESPACE | 5 R/conf-package.R | 21 - R/km.outcomes.R |only R/km.pmf.R |only R/km.support.R |only R/km.surv.R |only R/support.R |only build/vignette.rds |binary inst/CITATION | 37 -- inst/doc/coversim.html | 608 ++++++++++++++++++++++------------ inst/doc/crplot.html | 648 ++++++++++++++++++++++++------------ inst/doc/crplot_advanced.html | 746 +++++++++++++++++++++++++++++------------- man/conf.Rd | 21 - man/km.outcomes.Rd |only man/km.pmf.Rd |only man/km.support.Rd |only man/km.surv.Rd |only man/support.Rd |only 20 files changed, 1450 insertions(+), 708 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.9.7 dated 2023-04-11 and 0.9.8 dated 2023-05-17
DESCRIPTION | 8 - MD5 | 69 ++++++------- R/ANOVA.R | 30 +++-- R/ARMA.R | 22 ++-- R/ARMA_optim.R | 14 +- R/Binary_ANOVA.R | 65 +++++------- R/Boost.R | 22 ++-- R/Copula.R | 38 ++++--- R/Dependence.R | 1 R/Multivariate_Regression.R | 43 ++++++-- R/Normalization.R | 31 +++-- R/Partial_Moments.R | 2 R/Regression.R | 30 ++++- R/Stack.R | 24 +++- R/dy_dx.R | 99 +++++++------------ README.md | 4 inst/doc/NNSvignette_Classification.R | 2 inst/doc/NNSvignette_Classification.Rmd | 2 inst/doc/NNSvignette_Classification.html | 4 inst/doc/NNSvignette_Clustering_and_Regression.R | 37 +++---- inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 37 +++---- inst/doc/NNSvignette_Clustering_and_Regression.html | 93 +++++++++-------- inst/doc/NNSvignette_Correlation_and_Dependence.html | 6 - inst/doc/NNSvignette_Forecasting.R | 18 +-- inst/doc/NNSvignette_Forecasting.Rmd | 92 +++++++++-------- inst/doc/NNSvignette_Forecasting.html | 4 man/NNS.boost.Rd | 5 man/NNS.norm.Rd | 9 + man/NNS.reg.Rd | 8 + man/NNS.stack.Rd | 6 + man/dy.dx.Rd | 6 - tests/testthat/test_Copula.R | 6 - vignettes/NNSvignette_Classification.Rmd | 2 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 37 +++---- vignettes/NNSvignette_Forecasting.Rmd | 92 +++++++++-------- vignettes/images |only 36 files changed, 537 insertions(+), 431 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-03 2.5.0
2021-07-16 2.1.7
2021-05-25 2.1.5
2021-05-22 2.1.4
2021-02-12 2.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-15 0.1.0
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting (fuzzy) clusters of state sequences. Parametric bootstraps methods to validate typology of sequences are also provided.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.6-0 dated 2021-10-05 and 1.6-2 dated 2023-05-17
DESCRIPTION | 13 ++---- MD5 | 32 +++++++------- NAMESPACE | 7 +++ NEWS | 11 +++++ R/seqnullcqi.R | 78 ++++++++++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 +- inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary man/seqnullcqi.Rd | 6 +- man/wcAggregateCases.Rd | 3 + src/clusterquality.cpp | 2 src/clusterqualitybody.cpp | 10 ++-- src/init.c | 2 src/kmedoidbasebody.cpp | 4 - 17 files changed, 125 insertions(+), 49 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations. Summarises information about
the tiles of the tessellation. Calculates the centroidal
Voronoi (Dirichlet) tessellation using Lloyd's algorithm.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 1.0-6 dated 2021-10-23 and 1.0-9 dated 2023-05-17
deldir-1.0-6/deldir/inst/ratfor |only deldir-1.0-9/deldir/ChangeLog | 55 ++++++++++++++ deldir-1.0-9/deldir/DESCRIPTION | 8 +- deldir-1.0-9/deldir/MD5 | 108 +++++++++++++++-------------- deldir-1.0-9/deldir/R/First.R | 43 ++++++----- deldir-1.0-9/deldir/R/deldir.R | 53 +++++++++++--- deldir-1.0-9/deldir/R/getNbrs.R |only deldir-1.0-9/deldir/R/insidePoly.R |only deldir-1.0-9/deldir/R/insideRect.R |only deldir-1.0-9/deldir/R/plot.deldir.R | 32 +++++++- deldir-1.0-9/deldir/R/plot.tile.list.R | 81 ++++++++++++--------- deldir-1.0-9/deldir/R/print.tileInfo.R | 41 ++++++++--- deldir-1.0-9/deldir/R/tile.list.R | 35 ++++----- deldir-1.0-9/deldir/R/tileInfo.R | 28 ++++++- deldir-1.0-9/deldir/data/grapherXmpl.rda |binary deldir-1.0-9/deldir/data/niProperties.rda |binary deldir-1.0-9/deldir/data/seaweed.rda |binary deldir-1.0-9/deldir/data/toyPattern.rda |binary deldir-1.0-9/deldir/data/volTriPoints.rda |binary deldir-1.0-9/deldir/inst/Ratfor |only deldir-1.0-9/deldir/man/deldir-internal.Rd | 4 + deldir-1.0-9/deldir/man/deldir.Rd | 48 ++++++++++-- deldir-1.0-9/deldir/man/getNbrs.Rd |only deldir-1.0-9/deldir/man/plot.deldir.Rd | 62 +++++++++------- deldir-1.0-9/deldir/man/plot.tile.list.Rd | 92 +++++++++++++++--------- deldir-1.0-9/deldir/man/print.tileInfo.Rd | 53 +++++++++----- deldir-1.0-9/deldir/man/seaweed.Rd | 2 deldir-1.0-9/deldir/man/tileInfo.Rd | 18 +++- deldir-1.0-9/deldir/man/tilePerim.Rd | 2 29 files changed, 513 insertions(+), 252 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.5.0 dated 2023-02-07 and 0.5.1 dated 2023-05-17
DESCRIPTION | 6 MD5 | 63 +++--- NEWS.md | 12 + R/as_bootstrap_design.R | 12 - R/calibrate_to_estimate.R | 20 + R/calibrate_to_sample.R | 22 ++ R/generalized_bootstrap.R | 176 ++++++++-------- R/quadratic_forms.R | 271 ++++++++++++++++++++++---- R/quadratic_forms_of_survey_design_objects.R | 103 ++------- R/stack_replicate_designs.R | 10 README.md | 24 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/doc/nonresponse-adjustments.Rmd | 2 inst/doc/nonresponse-adjustments.html | 4 man/as_bootstrap_design.Rd | 3 man/as_gen_boot_design.Rd | 88 ++++++-- man/calibrate_to_estimate.Rd | 17 + man/calibrate_to_sample.Rd | 17 + man/get_design_quad_form.Rd | 69 +++++- man/make_gen_boot_factors.Rd | 12 + man/make_ppswor_approx_matrix.Rd |only man/make_quad_form_matrix.Rd | 95 ++++++++- man/make_twophase_quad_form.Rd | 2 man/shift_weight.Rd | 46 ++-- tests/testthat/test-as_bootstrap_design.R | 31 ++ tests/testthat/test-calibrate_to_estimate.R | 26 ++ tests/testthat/test-calibrate_to_sample.R | 21 +- tests/testthat/test-generalized-bootstrap.R | 61 +++++ tests/testthat/test-quadratic-forms.R | 77 ++++++- tests/testthat/test-stack_replicate_designs.R | 15 + vignettes/nonresponse-adjustments.Rmd | 2 33 files changed, 976 insertions(+), 337 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al.(2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
Weibull to censored and/or weighted data. Multiple distributions can
be averaged using Akaike Information Criteria. Confidence intervals
on hazard concentrations and proportions are produced by parametric
bootstrapping.
Author: Joe Thorley [aut, cre, ctr] ,
Carl Schwarz [aut, ctr],
Rebecca Fisher [ctb],
David Fox [ctb],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb], [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 1.0.3 dated 2023-04-12 and 1.0.4 dated 2023-05-17
DESCRIPTION | 14 MD5 | 201 - NEWS.md | 6 R/pqr.R | 2 R/test-helpers.R | 21 README.md | 16 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/distributions.html | 6 inst/doc/exposure-plots.html | 4 inst/doc/faqs.html | 4 inst/doc/small-sample-bias-ref.html | 4 inst/doc/ssdtools.html | 4 man/ssdtools-package.Rd | 4 tests/testthat/_snaps/burrIII3/hc_chloride.csv | 2 tests/testthat/_snaps/burrIII3/hc_uranium.csv | 2 tests/testthat/_snaps/burrIII3/tidy_anon_e.csv | 6 tests/testthat/_snaps/coef/coef.csv | 30 tests/testthat/_snaps/data/boron_stable.csv | 30 tests/testthat/_snaps/data/boron_unstable.csv | 18 tests/testthat/_snaps/fit/min_pmix5.csv | 20 tests/testthat/_snaps/fit/min_pmix_05.csv | 12 tests/testthat/_snaps/fit/tidy_gamma_unstable.csv |only tests/testthat/_snaps/fit/tidy_pmix0.csv | 20 tests/testthat/_snaps/fit/tidy_stable_anon_e.csv | 30 tests/testthat/_snaps/fit/tidy_stable_computable.csv | 26 tests/testthat/_snaps/fit/tidy_stable_rescale.csv | 30 tests/testthat/_snaps/fit/tidy_unstable_anon_e.csv | 14 tests/testthat/_snaps/glance/fit.csv | 6 tests/testthat/_snaps/glance/fit_cens.csv | 6 tests/testthat/_snaps/glance/fit_cens_n.csv | 6 tests/testthat/_snaps/glance/glance.csv | 12 tests/testthat/_snaps/gof/gof.csv | 12 tests/testthat/_snaps/gof/gof_pvalue_mixture.csv | 2 tests/testthat/_snaps/gof/gof_statistic.csv | 12 tests/testthat/_snaps/gof/gof_statistic_mixture.csv | 2 tests/testthat/_snaps/gompertz/hc_prob.csv | 2 tests/testthat/_snaps/hc-burrlioz/hc_boron.csv | 2 tests/testthat/_snaps/hc-burrlioz/hc_burrIII3.csv | 2 tests/testthat/_snaps/hc-burrlioz/hc_burrIII3_parametric.csv | 2 tests/testthat/_snaps/hc/hc.csv | 14 tests/testthat/_snaps/hc/hc138.csv | 4 tests/testthat/_snaps/hc/hc145.csv | 2 tests/testthat/_snaps/hc/hc153.csv | 198 - tests/testthat/_snaps/hc/hc161.csv | 198 - tests/testthat/_snaps/hc/hc168.csv | 12 tests/testthat/_snaps/hc/hc_1.csv | 2 tests/testthat/_snaps/hc/hc_30.csv | 4 tests/testthat/_snaps/hc/hc_boron.csv | 4 tests/testthat/_snaps/hc/hc_burrIII3.csv | 4 tests/testthat/_snaps/hc/hc_burrIII3_parametric.csv | 4 tests/testthat/_snaps/hc/hc_cis.csv | 2 tests/testthat/_snaps/hc/hc_cis_chloride50.csv | 6 tests/testthat/_snaps/hc/hc_cis_level08.csv | 2 tests/testthat/_snaps/hc/hc_err.csv | 4 tests/testthat/_snaps/hc/hc_err_avg.csv | 4 tests/testthat/_snaps/hc/hc_err_na.csv | 4 tests/testthat/_snaps/hc/hc_err_two.csv | 6 tests/testthat/_snaps/hc/hc_nonpara.csv | 4 tests/testthat/_snaps/hc/hc_para.csv | 2 tests/testthat/_snaps/hc/hc_para_small.csv | 2 tests/testthat/_snaps/hp/hp.csv | 12 tests/testthat/_snaps/hp/hp106.csv | 2 tests/testthat/_snaps/hp/hp114.csv | 12 tests/testthat/_snaps/hp/hp81.csv | 2 tests/testthat/_snaps/hp/hp89.csv | 4 tests/testthat/_snaps/hp/hp98.csv | 2 tests/testthat/_snaps/hp/hp_1.csv | 2 tests/testthat/_snaps/hp/hp_30.csv | 4 tests/testthat/_snaps/hp/hp_err.csv | 4 tests/testthat/_snaps/hp/hp_err_avg.csv | 4 tests/testthat/_snaps/hp/hp_err_na.csv | 4 tests/testthat/_snaps/hp/hp_err_two.csv | 6 tests/testthat/_snaps/hp/hp_nonpara.csv | 4 tests/testthat/_snaps/hp/hp_para.csv | 4 tests/testthat/_snaps/invpareto/anon_a.csv | 4 tests/testthat/_snaps/invpareto/hc_boron.csv | 2 tests/testthat/_snaps/lnorm-lnorm/tidy_anonb.csv | 10 tests/testthat/_snaps/plot-cf/ccme_boron.png |binary tests/testthat/_snaps/predict/pred_cis.csv | 198 - tests/testthat/_snaps/predict/pred_cis_burrlioz.csv | 198 - tests/testthat/_snaps/predict/pred_dists.csv | 198 - tests/testthat/_snaps/predict/pred_notaverage.csv | 1188 +++++------ tests/testthat/_snaps/schwarz-tillmans/gof.csv | 12 tests/testthat/_snaps/schwarz-tillmans/hc.csv | 12 tests/testthat/_snaps/schwarz-tillmans/hc_avg.csv | 2 tests/testthat/_snaps/tidy/tidy.csv | 30 tests/testthat/_snaps/weibull/hc_anona.csv | 2 tests/testthat/_snaps/weibull/tidy.csv | 8 tests/testthat/_snaps/weibull/tidy_anona.csv | 8 tests/testthat/test-burrIII3.R | 9 tests/testthat/test-fit.R | 31 tests/testthat/test-ggplot.R | 2 tests/testthat/test-gompertz-deprecated.R | 3 tests/testthat/test-gompertz.R | 3 tests/testthat/test-hc-burrlioz.R | 3 tests/testthat/test-hc.R | 49 tests/testthat/test-hp.R | 32 tests/testthat/test-lgumbel-deprecated.R | 3 tests/testthat/test-lnorm-lnorm.R | 3 tests/testthat/test-ssd-plot.R | 8 vignettes/references.bib | 1 102 files changed, 1639 insertions(+), 1521 deletions(-)
Title: TERN AusPlots Analysis Package
Description: Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-land-observatory/ecosystem-surveillance-and-environmental-monitoring/>).
Author: Greg Guerin [aut, cre],
Tom Saleeba [aut],
Samantha Munroe [aut],
Bernardo Blanco-Martin [aut],
Irene Martin-Fores [aut],
Walid Al Naim [ctb],
Andrew Tokmakoff [aut]
Maintainer: Greg Guerin <ggueri01@gmail.com>
Diff between ausplotsR versions 1.2.8 dated 2023-03-23 and 1.2.9 dated 2023-05-17
DESCRIPTION | 16 - MD5 | 8 NAMESPACE | 4 R/ausplots_queries.r | 526 +++++++++++++++++++++++++++------------------- inst/doc/start_guide.html | 189 +++++++++------- 5 files changed, 431 insertions(+), 312 deletions(-)