Wed, 17 May 2023

Package seeker updated to version 1.1.2 with previous version 1.1.1 dated 2023-05-05

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>

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Package OrdCD updated to version 1.1.2 with previous version 1.1.1 dated 2023-02-11

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>

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Package multid updated to version 0.8.0 with previous version 0.7.1 dated 2022-12-21

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>

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Package MBSP updated to version 4.0 with previous version 3.0 dated 2022-08-11

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>

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Package logitr updated to version 1.1.0 with previous version 1.0.1 dated 2023-02-19

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>

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Package ChannelAttribution updated to version 2.0.7 with previous version 2.0.6 dated 2022-11-23

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>

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Package spBayesSurv updated to version 1.1.7 with previous version 1.1.6 dated 2022-05-14

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>

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Package RNifti updated to version 1.5.0 with previous version 1.4.5 dated 2023-01-30

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>

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Package symbol.equation.gpt updated to version 1.1.3 with previous version 1.1.2 dated 2023-04-27

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>

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Package geouy updated to version 0.2.7 with previous version 0.2.6 dated 2022-10-05

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>

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Package DDIwR updated to version 0.14 with previous version 0.13 dated 2022-09-28

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>

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Package waywiser updated to version 0.4.0 with previous version 0.3.0 dated 2023-03-19

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>

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Package sits updated to version 1.4.0 with previous version 1.3.0 dated 2023-03-17

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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Package Robyn updated to version 3.10.3 with previous version 3.9.0 dated 2023-02-08

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

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More information about Robyn at CRAN
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Package qfa updated to version 2.0 with previous version 1.2 dated 2023-01-13

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>

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Package CP updated to version 1.7 with previous version 1.6 dated 2016-06-29

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>

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Package ubms updated to version 1.2.3 with previous version 1.2.2 dated 2022-11-10

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>

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Package spatialsample updated to version 0.4.0 with previous version 0.3.0 dated 2023-01-17

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>

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Package PTXQC updated to version 1.0.16 with previous version 1.0.15 dated 2023-04-25

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>

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Package mFD updated to version 1.0.4 with previous version 1.0.3 dated 2022-11-28

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>

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Package HYPEtools updated to version 1.4.0 with previous version 1.3.0 dated 2023-04-05

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>

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Package CEOdata updated to version 1.3.1 with previous version 1.3.0.1 dated 2023-02-01

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

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New package cascadeSelect with initial version 1.0.0
Package: cascadeSelect
Title: A Cascade Select Input for 'Shiny'
Version: 1.0.0
Description: Provides a cascade select widget for usage in 'Shiny' applications. This is useful for selection of hierarchical choices (e.g. continent, country, city). It is taken from the 'JavaScript' library 'PrimeReact'.
License: GPL-3
Depends: R (>= 2.10)
Imports: fontawesome, grDevices, htmltools, reactR, shiny
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-05-17 11:50:50 UTC; stla
Author: Stephane Laurent [aut, cre], PrimeTek Informatics [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2023-05-17 15:10:02 UTC

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New package chemdeg with initial version 0.1.2
Package: chemdeg
Title: Analysis of Chemical Degradation Kinetic Data
Version: 0.1.2
Description: A collection of functions that have been developed to assist experimenter in modeling chemical degradation kinetic data. The selection of the appropriate degradation model and parameter estimation is carried out automatically as far as possible and is driven by a rigorous statistical interpretation of the results. The package integrates already available goodness-of-fit statistics for nonlinear models. In addition it allows data fitting with the nonlinear first-order multi-target (FOMT) model.
License: GPL (>= 3)
URL: https://github.com/migliomatte/chemdeg, https://migliomatte.github.io/chemdeg/
BugReports: https://github.com/migliomatte/chemdeg/issues
Depends: R (>= 2.10)
Imports: graphics, MASS, methods, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), tibble
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-05-17 09:35:04 UTC; matteo
Author: Matteo Migliorini [aut, cre, cph], Roberto Chignola [aut]
Maintainer: Matteo Migliorini <matteo.migliorini@univr.it>
Repository: CRAN
Date/Publication: 2023-05-17 14:50:02 UTC

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Package rbacon updated to version 3.1.0 with previous version 3.0.0 dated 2022-12-22

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>

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Package phosphoricons updated to version 0.2.0 with previous version 0.1.2 dated 2022-04-11

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>

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More information about phosphoricons at CRAN
Permanent link

Package GGIRread updated to version 0.2.7 with previous version 0.2.6 dated 2022-12-05

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

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More information about GGIRread at CRAN
Permanent link

Package eplusr updated to version 0.16.0 with previous version 0.15.3 dated 2022-11-20

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

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More information about eplusr at CRAN
Permanent link

Package DescTools updated to version 0.99.49 with previous version 0.99.48 dated 2023-02-19

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

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More information about DescTools at CRAN
Permanent link

Package wdnet updated to version 1.1.0 with previous version 1.0.0 dated 2023-01-19

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

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More information about wdnet at CRAN
Permanent link

New package volcano3D with initial version 2.0.9
Package: volcano3D
Title: 3D Volcano Plots and Polar Plots for Three-Class Data
Version: 2.0.9
Maintainer: Katriona Goldmann <katrionagoldmann@gmail.com>
URL: https://katrionagoldmann.github.io/volcano3D/index.html, https://github.com/KatrionaGoldmann/volcano3D
BugReports: https://github.com/KatrionaGoldmann/volcano3D/issues
Description: Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.
Language: en-gb
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-17 10:02:31 UTC; kgoldmann
Imports: plotly, ggplot2, ggpubr, htmlwidgets, magrittr, methods, Rfast, rlang, matrixTests
Suggests: DESeq2, edgeR, limma, qvalue, SummarizedExperiment, knitr, rmarkdown, kableExtra, usethis, easylabel
Author: Katriona Goldmann [aut, cre] , Myles Lewis [aut]
Repository: CRAN
Date/Publication: 2023-05-17 11:00:02 UTC

More information about volcano3D at CRAN
Permanent link

New package stabiliser with initial version 1.0.6
Package: stabiliser
Title: Stabilising Variable Selection
Version: 1.0.6
Description: A stable approach to variable selection through stability selection and the use of a permutation-based objective stability threshold. Lima et al (2021) <doi:10.1038/s41598-020-79317-8>, Meinshausen and Buhlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.0)
Suggests: rmarkdown, testthat (>= 3.0.0), markdown
Imports: glmnet, dplyr, bigstep, rsample, tibble, purrr, tidyr, stringr, ggplot2, broom, caret, ncvreg, knitr, Hmisc, expss, lme4, matrixStats, recipes, lmerTest
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-17 09:39:37 UTC; svzrh2
Author: Robert Hyde [aut, cre] , Martin Green [aut], Eliana Lima [aut]
Maintainer: Robert Hyde <robert.hyde4@nottingham.ac.uk>
Repository: CRAN
Date/Publication: 2023-05-17 11:00:05 UTC

More information about stabiliser at CRAN
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Package s2 updated to version 1.1.4 with previous version 1.1.3 dated 2023-04-27

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

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 7 files changed, 24 insertions(+), 14 deletions(-)

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Package scattermore updated to version 1.1 with previous version 1.0 dated 2023-05-03

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

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Package rrcov updated to version 1.7-3 with previous version 1.7-2 dated 2022-10-24

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

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New package rotatogram with initial version 0.1.3
Package: rotatogram
Title: A Non-Axis-Dominant Association Plotting Tool
Version: 0.1.3
Description: A rotatogram is a method of displaying an association which is axis non-dominant. This is achieved in two ways: First, the method of estimating the slope and intercept uses the least-products method rather than more typical least squared error for the "dependent" variable. The least products method has no "dependent" variable and is scale independent. Second, the plot is rotated such that the resulting regression line is vertical, reducing the suggestion that the vertical axis is the dominant one. The slope can be read relative to either axis equally.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2,stats,grid
NeedsCompilation: no
Packaged: 2023-05-16 22:33:09 UTC; noahh
Author: Noah Haber [aut, cre]
Maintainer: Noah Haber <noahhaber@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-17 09:00:02 UTC

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Package prolific.api updated to version 0.5.1 with previous version 0.5 dated 2022-10-19

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

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New package pheble with initial version 0.1.0
Package: pheble
Title: Classifying High-Dimensional Phenotypes with Ensemble Learning
Version: 0.1.0
Description: A system for binary and multi-class classification of high-dimensional phenotypic data using ensemble learning. By combining predictions from different classification models, this package attempts to improve performance over individual learners. The pre-processing, training, validation, and testing are performed end-to-end to minimize user input and simplify the process of classification.
License: GPL (>= 3)
Encoding: UTF-8
Imports: adabag, base, C50, caret, caTools, data.table, doParallel, dplyr, e1071, earth, evtree, frbs, glmnet, gmodels, hda, HDclassif, ipred, kernlab, kknn, klaR, magrittr, MASS, Matrix, mda, MLmetrics, nnet, parallel, party, pls, randomForest, rpartScore, sparseLDA, stats, themis, utils
Depends: R (>= 2.10)
LazyData: true
Suggests: h2o
NeedsCompilation: no
Packaged: 2023-05-16 20:35:33 UTC; bhlab
Author: Jay Devine [aut, cre, cph], Bened'ikt Hallgrimsson [aut]
Maintainer: Jay Devine <jay.devine1@ucalgary.ca>
Repository: CRAN
Date/Publication: 2023-05-17 08:50:11 UTC

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New package mdir with initial version 0.9.0
Package: mdir
Title: Bayesian Model-Based Clustering of Multi-Modal Data
License: GPL-3
Version: 0.9.0
Date: 2023-05-16
Description: Integrative clustering and semi-supervised prediction. This package includes a 'C++' implementation of both semi-supervised and unsupervised Multiple Dataset Integration (MDI; Kirk et al., 2012 <https://doi-org.ezp.lib.cam.ac.uk/10.1093/bioinformatics/bts595>), an extension of Bayesian mixture models to the integrative (multiple dataset or multi-modal) setting such as multi-omics analysis. The package also includes Bayesian mixture models. Densities allowed within MDI and the mixture model are Gaussian with full and diagonal covariance matrices, categorical, Gaussian with a Gaussian process (GP) prior on the mean parameter. The GP model implemented canonly handle data with common time points of equal separation. The Gaussian and GP models can be augmented with a global multivariate t distribution to handle outliers.
Imports: Rcpp (>= 1.0.6), RcppParallel, ggplot2, stringr, tidyr, salso
LinkingTo: Rcpp, RcppArmadillo, testthat, RcppParallel
Suggests: xml2
SystemRequirements: GNU make
Encoding: UTF-8
URL: https://github.com/stcolema/mdir
BugReports: https://github.com/stcolema/mdir/issues
NeedsCompilation: yes
Packaged: 2023-05-16 13:51:58 UTC; stephen
Author: Stephen Coleman [aut, cre], Paul Kirk [aut], Chris Wallace [aut], Oliver Crook [aut]
Maintainer: Stephen Coleman <stcolema@tcd.ie>
Repository: CRAN
Date/Publication: 2023-05-17 08:40:02 UTC

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New package ETASbootstrap with initial version 0.1.0
Package: ETASbootstrap
Title: Bootstrap Confidence Interval Estimation for 'ETAS' Model Parameters
Description: The 2-D spatial and temporal Epidemic Type Aftershock Sequence ('ETAS') Model is widely used to 'decluster' earthquake data catalogs. Usually, the calculation of standard errors of the 'ETAS' model parameter estimates is based on the Hessian matrix derived from the log-likelihood function of the fitted model. However, when an 'ETAS' model is fitted to a local data set over a time period that is limited or short, the standard errors based on the Hessian matrix may be inaccurate. It follows that the asymptotic confidence intervals for parameters may not always be reliable. As an alternative, this package allows the building of bootstrap confidence intervals based on empirical quantiles for the parameters of the 2-D spatial and temporal 'ETAS' model.
Version: 0.1.0
Author: Renjie Peng [aut, cre], Pierre Dutilleul [aut] , Christian Genest [aut]
Maintainer: Renjie Peng <renjie.peng@mail.mcgill.ca>
Depends: R (>= 3.3.0)
Imports: ETAS (>= 0.5.1), MASS (>= 7.3.58.2), stats (>= 4.2.2), utils (>= 4.2.2)
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-05-16 20:10:33 UTC; rjpeng
Repository: CRAN
Date/Publication: 2023-05-17 08:50:14 UTC

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New package agena.ai with initial version 1.0.0
Package: agena.ai
Title: R Wrapper for 'agena.ai' API
Version: 1.0.0
Description: An R wrapper for 'agena.ai' <https://www.agena.ai> which provides users capabilities to work with 'agena.ai' using the R environment. Users can create Bayesian network models from scratch or import existing models in R and export to 'agena.ai' cloud or local API for calculations.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rjson, httr, openxlsx, Rgraphviz, methods, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-16 22:05:53 UTC; erhan
Author: Erhan Pisirir [aut], Eugene Dementiev [aut, cre], Martin Neil [aut, cph]
Maintainer: Eugene Dementiev <support@agenarisk.com>
Repository: CRAN
Date/Publication: 2023-05-17 09:00:05 UTC

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Package StanHeaders updated to version 2.26.25 with previous version 2.21.0-7 dated 2020-12-17

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>

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 StanHeaders-2.26.25/StanHeaders/MD5                                                                                 | 3791 +++++-----
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 StanHeaders-2.26.25/StanHeaders/inst/CITATION                                                                       |    4 
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 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
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/fwd/core/std_numeric_limits.hpp                              |    2 
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 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
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 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 
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 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 
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 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 
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 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 
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 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
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/categorical_logit_glm_lpmf.hpp                   |  161 
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/col.hpp                                          |only
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/gumbel_lpdf.hpp                                  |only
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 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 
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 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
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 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
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 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
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 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 
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/sub_col.hpp                                      |only
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/opencl/prim/uniform_lpdf.hpp                                 |only
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 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
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 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
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_equal_equal.hpp                           |only
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/core/operator_subtraction.hpp                           |only
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 StanHeaders-2.26.25/StanHeaders/inst/include/stan/math/prim/err                                                     |only
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 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
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 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 
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 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 
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 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 
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 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
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 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 
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Permanent link

Package spatstat updated to version 3.0-6 with previous version 3.0-5 dated 2023-04-22

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

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More information about spatstat at CRAN
Permanent link

Package RAMClustR updated to version 1.3.0 with previous version 1.2.4 dated 2022-04-13

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

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Package mmodely updated to version 0.2.5 with previous version 0.2.2 dated 2022-11-06

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>

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Package kernelshap updated to version 0.3.7 with previous version 0.3.6 dated 2023-05-03

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>

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Package drhur updated to version 1.1.0 with previous version 1.0.0 dated 2022-10-17

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>

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Package crul updated to version 1.4.0 with previous version 1.3 dated 2022-09-03

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>

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Package conf updated to version 1.8.0 with previous version 1.7.1 dated 2022-05-20

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>

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Package NNS updated to version 0.9.8 with previous version 0.9.7 dated 2023-04-11

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>

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2023-05-03 2.5.0
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Package WeightedCluster updated to version 1.6-2 with previous version 1.6-0 dated 2021-10-05

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>

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Package deldir updated to version 1.0-9 with previous version 1.0-6 dated 2021-10-23

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>

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Package svrep updated to version 0.5.1 with previous version 0.5.0 dated 2023-02-07

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>

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Package ssdtools updated to version 1.0.4 with previous version 1.0.3 dated 2023-04-12

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>

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Package ausplotsR updated to version 1.2.9 with previous version 1.2.8 dated 2023-03-23

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>

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