Mon, 15 Oct 2018

Package marmap updated to version 1.0.2 with previous version 1.0.1 dated 2018-09-22

Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <http://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <http://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>

Diff between marmap versions 1.0.1 dated 2018-09-22 and 1.0.2 dated 2018-10-15

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Package crminer updated to version 0.2.0 with previous version 0.1.4 dated 2017-08-12

Title: Fetch 'Scholary' Full Text from 'Crossref'
Description: Text mining client for 'Crossref' (<https://crossref.org>). Includes functions for getting getting links to full text of articles, fetching full text articles from those links or Digital Object Identifiers ('DOIs'), and text extraction from 'PDFs'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package cosinor2 updated to version 0.2.1 with previous version 0.2.0 dated 2018-10-01

Title: Extended Tools for Cosinor Analysis of Rhythms
Description: Statistical procedures for calculating population–mean cosinor, non–stationary cosinor, estimation of best–fitting period, tests of population rhythm differences and more. See Cornélissen, G. (2014). <doi:10.1186/1742-4682-11-16>.
Author: Augustin Mutak <mutak94@gmail.com>
Maintainer: Augustin Mutak <mutak94@gmail.com>

Diff between cosinor2 versions 0.2.0 dated 2018-10-01 and 0.2.1 dated 2018-10-15

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Package ungroup updated to version 1.1.1 with previous version 1.1.0 dated 2018-09-30

Title: Penalized Composite Link Model for Efficient Estimation of Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data) assuming that counts are Poisson distributed and that the underlying sequence on a fine grid to be estimated is smooth. The method is based on the composite link model and estimation is achieved by maximizing a penalized likelihood. Smooth detailed sequences of counts and rates are so estimated from the binned counts. Ungrouping binned data can be desirable for many reasons: Bins can be too coarse to allow for accurate analysis; comparisons can be hindered when different grouping approaches are used in different histograms; and the last interval is often wide and open-ended and, thus, covers a lot of information in the tail area. Age-at-death distributions grouped in age classes and abridged life tables are examples of binned data. Because of modest assumptions, the approach is suitable for many demographic and epidemiological applications. For a detailed description of the method and applications see Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>), Silvia Rizzi [aut], Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>), Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>

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Package hdme updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-19

Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for measurement error problems (aka. errors-in-variables). The package contains a version of the lasso (L1-penalization) which corrects for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>). It also contains an implementation of the Generalized Matrix Uncertainty Selector, which is a version the (Generalized) Dantzig Selector for the case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package define updated to version 0.2.8 with previous version 0.2.7 dated 2018-03-13

Title: Create FDA-Style Data and Program Definitions
Description: Creates a directory of archived files with a descriptive 'PDF' document at the root level (i.e. 'define.pdf') containing tables of definitions of data items and relative-path hyperlinks to the documented files. Converts file extensions to 'txt' per FDA expectations and converts 'CSV' files to 'SAS' Transport format. Relies on data item descriptors stored as per R package 'spec'. See 'package?define'. See also '?define'. Requires a compatible installation of 'pdflatex', e.g. <https://miktex.org/>.
Author: Tim Bergsma [aut, cre], Scott Pivirotto [ctb]
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package decisionSupport updated to version 1.103.8 with previous version 1.103.7 dated 2018-05-15

Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based decision making processes using Monte Carlo simulations. Decision support is given on two levels: (i) The actual decision level is to choose between two alternatives under probabilistic uncertainty. This package calculates the optimal decision based on maximizing expected welfare. (ii) The meta decision level is to allocate resources to reduce the uncertainty in the underlying decision problem, i.e to increase the current information to improve the actual decision making process. This problem is dealt with using the Value of Information Analysis. The Expected Value of Information for arbitrary prospective estimates can be calculated as well as Individual Expected Value of Perfect Information. The probabilistic calculations are done via Monte Carlo simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (ICRAF), Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting), World Agroforesrtry Centre (ICRAF) [cph]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package stormwindmodel updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-09

Title: Model Tropical Cyclone Wind Speeds
Description: Allows users to input tracking data for a hurricane or other tropical storm, along with a data frame of grid points at which to model wind speeds. Functions in this package will then calculate wind speeds at each point based on wind model equations. This modeling framework is currently set up to model winds for North American locations with Atlantic basin storms. This work was supported in part by grants from the National Institute of Environmental Health Sciences (R00ES022631), the National Science Foundation (1331399), and the Department of Energy (DE-FG02-08ER64644).
Author: Brooke Anderson [aut, cre], Andrea Schumacher [aut], Seth Guikema [aut], Steven Quiring [aut], Joshua Ferreri [aut], Andrea Staid [ctb], Michael Guo [ctb], Lei Ming [ctb], Laiyin Zhu [ctb]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>

Diff between stormwindmodel versions 0.1.0 dated 2017-01-09 and 0.1.1 dated 2018-10-15

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 stormwindmodel-0.1.1/stormwindmodel/DESCRIPTION                                                                          |   27 
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 stormwindmodel-0.1.1/stormwindmodel/build/vignette.rds                                                                   |binary
 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Details.R                                                                   |   47 
 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Details.Rmd                                                                 |   50 
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 stormwindmodel-0.1.1/stormwindmodel/inst/doc/Overview.R                                                                  |   65 
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 stormwindmodel-0.1.1/stormwindmodel/man/add_forward_speed.Rd                                                             |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/add_inflow.Rd                                                                    |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/add_storm_track.Rd                                                               |    5 
 stormwindmodel-0.1.1/stormwindmodel/man/add_wind_radii.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_R1.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_and_summarize_grid_wind.Rd                                                  |    8 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_bearing.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_forward_speed.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_gradient_speed.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/calc_grid_wind.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/check_over_land.Rd                                                               |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/county_points.Rd                                                                 |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/create_full_track.Rd                                                             |    4 
 stormwindmodel-0.1.1/stormwindmodel/man/degrees_to_radians.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/figures                                                                          |only
 stormwindmodel-0.1.1/stormwindmodel/man/floyd_tracks.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/get_grid_winds.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/gradient_to_surface.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/interp_track.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/katrina_tracks.Rd                                                                |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/landmask.Rd                                                                      |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/latlon_to_km.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/map_wind.Rd                                                                      |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/radians_to_degrees.Rd                                                            |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/remove_forward_speed.Rd                                                          |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/solve_for_xi.Rd                                                                  |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/summarize_grid_wind.Rd                                                           |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will1.Rd                                                                         |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10a.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10b.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will10c.Rd                                                                       |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will1a.Rd                                                                        |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will2.Rd                                                                         |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will3_deriv_func.Rd                                                              |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will3_right.Rd                                                                   |    1 
 stormwindmodel-0.1.1/stormwindmodel/man/will7a.Rd                                                                        |    1 
 stormwindmodel-0.1.1/stormwindmodel/vignettes/Details.Rmd                                                                |   50 
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Package dLagM updated to version 1.0.8 with previous version 1.0.7 dated 2018-09-27

Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>

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Sun, 14 Oct 2018

Package paran updated to version 1.5.2 with previous version 1.5.1 dated 2012-09-10

Title: Horn's Test of Principal Components/Factors
Description: An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>

Diff between paran versions 1.5.1 dated 2012-09-10 and 1.5.2 dated 2018-10-14

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Package analytics updated to version 3.0 with previous version 2.0 dated 2017-06-14

Title: Regression Outlier Detection, Stationary Bootstrap, Testing Weak Stationarity, NA Imputation, and Other Tools for Data Analysis
Description: Current version includes outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, missing value imputation, column/rows sums/means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.
Author: Albert Dorador
Maintainer: Albert Dorador <albert.dorador.chalar@gmail.com>

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Package sjPlot updated to version 2.6.1 with previous version 2.6.0 dated 2018-08-23

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Carsten Schwemmer [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package wTO updated to version 1.6.2 with previous version 1.6.1 dated 2018-06-28

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>

Diff between wTO versions 1.6.1 dated 2018-06-28 and 1.6.2 dated 2018-10-14

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Package GetDFPData updated to version 1.2 with previous version 1.0 dated 2018-08-28

Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>. These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetDFPData versions 1.0 dated 2018-08-28 and 1.2 dated 2018-10-14

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Package fuzzyreg updated to version 0.4 with previous version 0.3 dated 2018-06-07

Title: Fuzzy Linear Regression
Description: Estimators for fuzzy linear regression. The functions estimate parameters of fuzzy linear regression models with crisp or fuzzy independent variables (triangular fuzzy numbers are supported). Implements multiple methods for parameter estimation and algebraic operations with triangular fuzzy numbers. Includes functions for summarising, printing and plotting the model fit. Calculates predictions from the model and total error of fit. Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>, Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>, Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>, Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>, Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>.
Author: Pavel Skrabanek [aut, cph], Natalia Martinkova [aut, cre, cph]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>

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Package vimp updated to version 1.1.4 with previous version 1.1.3 dated 2018-10-02

Title: Nonparametric Variable Importance
Description: Calculate point estimates of and valid confidence intervals for nonparametric variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (2017) <https://biostats.bepress.com/uwbiostat/paper422/>.
Author: Brian D. Williamson [aut, cre], Noah Simon [aut], Marco Carone [aut]
Maintainer: Brian D. Williamson <brianw26@uw.edu>

Diff between vimp versions 1.1.3 dated 2018-10-02 and 1.1.4 dated 2018-10-14

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Package RcppCCTZ updated to version 0.2.5 with previous version 0.2.4 dated 2018-10-06

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package pricesensitivitymeter updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-12

Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price Sensitivity Meter in R, which is a survey-based approach to analyze consumer price preferences and sensitivity (van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>

Diff between pricesensitivitymeter versions 0.3.2 dated 2018-05-12 and 0.3.3 dated 2018-10-14

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Package touch updated to version 0.1-4 with previous version 0.1-3 dated 2016-12-17

Title: Tools of Utilization and Cost in Healthcare
Description: R implementation of the software tools developed in the H-CUP (Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov> and AHRQ (Agency for Healthcare Research and Quality) <https://www.ahrq.gov>. It currently contains functions for mapping ICD-9 codes to the AHRQ comorbidity measures and translating ICD-9 (resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General Equivalence Mappings) from CMS (Centers for Medicare and Medicaid Services).
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>), Yan Li [aut], Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

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Sat, 13 Oct 2018

Package treemapify updated to version 2.5.2 with previous version 2.5.1 dated 2018-10-06

Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins <david@wilkox.org>
Maintainer: David Wilkins <david@wilkox.org>

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Package scBio updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-07

Title: Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>

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Package Rnightlights updated to version 0.2.3 with previous version 0.2.2 dated 2018-07-24

Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics from satellite nightlight rasters downloaded from the United States National Oceanic and Atmospheric Administration (<http://www.noaa.gov>) free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly nightlight raster data are supported. Satellite nightlight raster tiles are downloaded and cropped to the country boundaries using shapefiles from the GADM database of Global Administrative Areas (<http://gadm.org>). Zonal statistics are then calculated at the lowest administrative boundary for the selected country and cached locally for future retrieval. Finally, a simple data explorer/browser is included that allows one to visualize the cached data e.g. graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>

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Package MRPC updated to version 2.0.0 with previous version 1.0.0 dated 2018-08-14

Title: Mendelian Randomization (MR) Based PC Algorithm
Description: Infer causal graphs using the principle of Mendelian randomization-based PC (MRPC) algorithm. See Badsha and Fu (2018) <doi:10.1101/171348>,Badsha et al. (2018) <arXiv:1806.01899>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mdbadsha@uidaho.edu>

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Package MetFns updated to version 3.2.2 with previous version 3.2.1 dated 2018-08-23

Title: Analysis of Visual Meteor Data
Description: Functions for selection of visual meteor data, calculations of Zenithal Hourly Rate (ZHR) and population index, graphics of population index, ZHR and magnitude distribution.
Author: Kristina Veljkovic
Maintainer: Kristina Veljkovic <mackikac@gmail.com>

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Package tm1r updated to version 1.0.2 with previous version 1.0.1 dated 2018-08-09

Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>

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Package scriptexec updated to version 0.2.3 with previous version 0.2.2 dated 2018-10-01

Title: Execute Native Scripts
Description: Run complex native scripts with a single command, similar to system commands.
Author: Sagie Gur-Ari [aut, cre]
Maintainer: Sagie Gur-Ari <sagiegurari@gmail.com>

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Package GSED updated to version 1.10 with previous version 1.9 dated 2018-09-26

Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

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Package xSub updated to version 2.0.1 with previous version 0.0.1 dated 2017-10-11

Title: Cross-National Data on Sub-National Violence
Description: Tools to download and merge data files on sub-national conflict, violence and protests from <http://www.x-sub.org>.
Author: Yuri Zhukov [cre], Christian Davenport [aut], Nadiya Kostyuk [aut]
Maintainer: Yuri Zhukov <zhukov@umich.edu>

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Package refuge updated to version 0.2.0 with previous version 0.1.1 dated 2018-04-20

Title: Locate Trans and Intersex-Friendly Toilets
Description: Access the 'Refuge' API, a web-application for locating trans and intersex-friendly restrooms, including unisex and accessible restrooms. Includes data on the location of restrooms, along with directions, comments, user ratings and amenities. Coverage is global, but data is most comprehensive in the United States. See <https://www.refugerestrooms.org/api/docs/> for full API documentation.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>)
Maintainer: Evan Odell <evanodell91@gmail.com>

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Package REAT updated to version 2.0.3 with previous version 2.0.2 dated 2018-10-04

Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

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Package UCSCXenaTools updated to version 0.2.5 with previous version 0.2.4 dated 2018-09-12

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package testthat updated to version 2.0.1 with previous version 2.0.0 dated 2017-12-13

Title: Unit Testing for R
Description: Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd], R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package SCINA updated to version 1.0.1 with previous version 1.0.0 dated 2018-10-08

Title: A Semi-Supervised Category Identification and Assignment Tool
Description: An automatic cell type detection and assignment algorithm for single cell RNA-Seq and Cytof/FACS data. 'SCINA' is capable of assigning cell type identities to a pool of cells profiled by scRNA-Seq or Cytof/FACS data with prior knowledge of markers, such as genes and protein symbols that are highly or lowly expressed in each category.
Author: Ze Zhang
Maintainer: Ze Zhang <Ze.Zhang@utsouthwestern.edu>

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Package psychmeta updated to version 2.2.1 with previous version 2.2.0 dated 2018-09-18

Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre], Brenton M. Wiernik [aut], Michael T. Brannick [ctb] (Testing), Jack Kostal [ctb] (Code for reshape_mat2dat function), Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots), John Sakaluk [ctb] (Code for funnel and forest plots), Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>

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Package hoardr updated to version 0.5.0 with previous version 0.2.0 dated 2017-05-09

Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between hoardr versions 0.2.0 dated 2017-05-09 and 0.5.0 dated 2018-10-13

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Fri, 12 Oct 2018

Package mase updated to version 0.1.2 with previous version 0.1.1 dated 2018-06-14

Title: Model-Assisted Survey Estimators
Description: A set of model-assisted survey estimators and corresponding variance estimators for single stage, unequal probability, without replacement sampling designs. All of the estimators can be written as a generalized regression estimator with the Horvitz-Thompson, ratio, post-stratified, and regression estimators summarized by Sarndal et al. (1992, ISBN:978-0-387-40620-6). Two of the estimators employ a statistical learning model as the assisting model: the elastic net regression estimator, which is an extension of the lasso regression estimator given by McConville et al. (2017) <doi:10.1093/jssam/smw041>, and the regression tree estimator described in McConville and Toth (2017) <arXiv:1712.05708>. The variance estimators which approximate the joint inclusion probabilities can be found in Berger and Tille (2009) <doi:10.1016/S0169-7161(08)00002-3> and the bootstrap variance estimator is presented in Mashreghi et al. (2016) <doi:10.1214/16-SS113>.
Author: Kelly McConville [aut, cre, cph], Becky Tang [aut], George Zhu [aut], Sida Li [ctb], Shirley Chueng [ctb], Daniell Toth [ctb, cph] (Author and copyright holder of treeDesignMatrix helper function)
Maintainer: Kelly McConville <mcconville@reed.edu>

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Package BOIN updated to version 2.6.4 with previous version 2.6.3 dated 2018-04-10

Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

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Package nlts updated to version 1.0-2 with previous version 0.2-2 dated 2017-08-28

Title: Nonlinear Time Series Analysis
Description: R functions for (non)linear time series analysis with an emphasis on nonparametric autoregression and order estimation, and tests for linearity / additivity.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package icr updated to version 0.5.7 with previous version 0.5.6 dated 2018-07-24

Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder reliability coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb] (author of the C++ RNG code)
Maintainer: Alexander Staudt <staudtlex@live.de>

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Package comperes updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-11

Title: Manage Competition Results
Description: Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package bayesPop updated to version 7.0-0 with previous version 6.2-4 dated 2018-03-16

Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package rococo updated to version 1.1.7 with previous version 1.1.5 dated 2017-07-08

Title: Robust Rank Correlation Coefficient and Test
Description: Provides the robust gamma rank correlation coefficient as introduced by Bodenhofer, Krone, and Klawonn (2013) <DOI:10.1016/j.ins.2012.11.026> along with a permutation-based rank correlation test. The rank correlation coefficient and the test are explicitly designed for dealing with noisy numerical data.
Author: Martin Krone, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

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Package Phase123 updated to version 1.7 with previous version 1.5 dated 2018-03-28

Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>

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Package egoTERGM updated to version 2.0.1 with previous version 1.0.0 dated 2018-04-25

Title: Estimation of Ego-Temporal Exponential Random Graph Models via Expectation Maximization (EM)
Description: Estimation of ego-temporal exponential random graph models with two-stage estimation including initialization through k-means clustering on temporal exponential random graph model parameters and EM as per Campbell (2018) <doi:10.7910/DVN/TWHEZ9>.
Author: Benjamin W. Campbell [aut, cre], Michael Salter-Townshend [ctb], Thomas Brendan Murphy [ctb]
Maintainer: Benjamin W. Campbell <campbell.1721@osu.edu>

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Package crqa updated to version 1.0.9 with previous version 1.0.8 dated 2018-08-19

Title: Cross-Recurrence Quantification Analysis for Categorical and Continuous Time-Series
Description: Cross-recurrence quantification analysis of two time-series, of either categorical or continuous values. It provides different methods for profiling cross-recurrence, i.e., only looking at the diagonal recurrent points, as well as more in-depth measures of the whole cross-recurrence plot, e.g., recurrence rate. Please refer to by Coco and Dale (2014) <doi:10.3389/fpsyg.2014.00510> for further details about the method.
Author: Moreno I. Coco and Rick Dale with contributions of James D. Dixon and John Nash
Maintainer: Moreno I. Coco <moreno.cocoi@gmail.com>

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Package TBFmultinomial updated to version 0.1.3 with previous version 0.1.2 dated 2018-08-23

Title: TBF Methodology Extension for Multinomial Outcomes
Description: Extends the test-based Bayes factor (TBF) methodology to multinomial regression models and discrete time-to-event models with competing risks. The TBF methodology has been well developed and implemented for the generalised linear model [Held et al. (2015) <doi:10.1214/14-STS510>] and for the Cox model [Held et al. (2016) <doi:10.1002/sim.7089>].
Author: Rachel Heyard [aut, cre]
Maintainer: Rachel Heyard <rachel.heyard@uzh.ch>

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Package PxWebApiData updated to version 0.2.0 with previous version 0.1.0 dated 2018-06-06

Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Øyvind Langsrud and Jan Bruusgaard
Maintainer: Øyvind Langsrud <oyl@ssb.no>

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Package binb updated to version 0.0.3 with previous version 0.0.2 dated 2018-09-27

Title: 'binb' is not 'Beamer'
Description: A collection of 'LaTeX' styles using 'Beamer' customization for pdf-based presentation slides in 'RMarkdown'. At present it contains 'RMarkdown' adaptations of the LaTeX themes 'Metropolis' (formerly 'mtheme') theme by Matthias Vogelgesang and others (now included in 'TeXLive'), the 'IQSS' by Ista Zahn (which is included here), and the 'Monash' theme by Rob J Hyndman. Additional (free) fonts may be needed: 'Metropolis' prefers 'Fira', and 'IQSS' requires 'Libertinus'.
Author: Dirk Eddelbuettel, Ista Zahn and Rob Hyndman
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package mMPA updated to version 1.2.0 with previous version 0.1.0 dated 2017-03-22

Title: Implementation of Marker-Assisted Mini-Pooling with Algorithm
Description: To determine the number of quantitative assays needed for a sample of data using pooled testing methods, which include mini-pooling (MP), MP with algorithm (MPA), and marker-assisted MPA (mMPA). To estimate the number of assays needed, the package also provides a tool to conduct Monte Carlo (MC) to simulate different orders in which the sample would be collected to form pools. Using MC avoids the dependence of the estimated number of assays on any specific ordering of the samples to form pools.
Author: "Tao Liu, PhD <tliu@stat.brown.edu> [aut, cre]" "Yizhen Xu, ScM <yizhen_xu@brown.edu> [aut]"
Maintainer: "Tao Liu, PhD" <tliu@stat.brown.edu>

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Package mrfDepth updated to version 1.0.10 with previous version 1.0.9 dated 2018-09-26

Title: Depth Measures in Multivariate, Regression and Functional Settings
Description: Tools to compute depth measures and implementations of related tasks such as outlier detection, data exploration and classification of multivariate, regression and functional data.
Author: Pieter Segaert [aut], Mia Hubert [aut], Peter Rousseeuw [aut], Jakob Raymaekers [aut, cre], Kaveh Vakili [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>

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Package komaletter updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-13

Title: Simple yet Flexible Letters via the 'KOMA-Script LaTeX Bundle'
Description: An R Markdown template for writing beautiful yet versatile letters, using the 'KOMA-Script' letter class 'scrlttr2' and an adaptation of the 'pandoc-letter' template. 'scrlttr2' provides layouts for many different window envelope types and the possibility to define your own.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>), Dirk Eddelbuettel [aut], Aaron Wolen [aut]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>

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Package ExPanDaR updated to version 0.3.0 with previous version 0.2.0 dated 2018-05-11

Title: Explore Panel Data Interactively
Description: Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory panel data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can also use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.
Author: Joachim Gassen [aut, cre] (<https://orcid.org/0000-0003-4364-2911>)
Maintainer: Joachim Gassen <gassen@wiwi.hu-berlin.de>

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Package trackeR updated to version 1.2.0 with previous version 1.1 dated 2018-09-24

Title: Infrastructure for Running, Cycling and Swimming Data from GPS-Enabled Tracking Devices
Description: Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>), Hannah Frick [aut] (<https://orcid.org/0000-0002-6049-5258>), Robin Hornak [aut]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package bamlss updated to version 1.0-1 with previous version 1.0-0 dated 2018-04-13

Title: Bayesian Additive Models for Location Scale and Shape (and Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2017) <doi:10.1080/10618600.2017.1407325>.
Author: Nikolaus Umlauf [aut, cre], Nadja Klein [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Meike Koehler [aut], Thorsten Simon [ctb], Stanislaus Stadlmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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Package ddsPLS updated to version 1.0.1 with previous version 1.0.0 dated 2018-09-19

Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>

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Package survey updated to version 3.34 with previous version 3.33-2 dated 2018-03-12

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

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Package SQRL updated to version 0.5.0 with previous version 0.4.0 dated 2018-06-03

Title: Database Query Interfaces
Description: Facilitates interaction with 'ODBC' data sources.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>

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Package bayesTFR updated to version 6.2-0 with previous version 6.1-2 dated 2018-01-19

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Thu, 11 Oct 2018

Package globals updated to version 0.12.4 with previous version 0.12.3 dated 2018-09-17

Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package ttScreening updated to version 1.6 with previous version 1.5 dated 2014-11-14

Title: Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples
Description: A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.
Author: Meredith Ray, Xin Tong, Hongmei Zhang
Maintainer: Meredith Ray <maray@memphis.edu>

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Package ITNr updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-26

Title: Analysis of the International Trade Network
Description: Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
Author: Matthew Smith
Maintainer: Matthew Smith <matt_smith.90@hotmail.co.uk>

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Package remotes updated to version 2.0.0 with previous version 1.1.1 dated 2017-12-20

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package is a lightweight replacement of the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package pkgload updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-07

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <james.hester@rstudio.com>

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Package dslabs updated to version 0.5.0 with previous version 0.4.0 dated 2018-08-02

Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>

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Package VBLPCM updated to version 2.4.5 with previous version 2.4.4 dated 2015-12-18

Title: Variational Bayes Latent Position Cluster Model for Networks
Description: Fit and simulate latent position and cluster models for network data, using a fast Variational Bayes approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend <mike.saltertownshend@gmail.com>

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Package sysfonts updated to version 0.8 with previous version 0.7.2 dated 2018-01-16

Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package Rlabkey updated to version 2.2.3 with previous version 2.2.2 dated 2018-07-12

Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <http://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package GetLattesData updated to version 1.2 with previous version 1.1 dated 2018-08-19

Title: Reading Bibliometric Data from Lattes Platform
Description: A simple API for downloading and reading xml data directly from Lattes <http://lattes.cnpq.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetLattesData versions 1.1 dated 2018-08-19 and 1.2 dated 2018-10-11

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Package tidyLPA updated to version 0.2.2 with previous version 0.2.1 dated 2018-10-11

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Caspar van Lissa [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package Rodam updated to version 0.1.4 with previous version 0.1.3 dated 2018-06-01

Title: Wrapper Functions for 'ODAM' (Open Data for Access and Mining) Web Services
Description: 'ODAM' (Open Data for Access and Mining) is a framework that implements a simple way to make research data broadly accessible and fully available for reuse, including by a script language such as R. The main purpose is to make a data set accessible online with a minimal effort from the data provider, and to allow any scientists or bioinformaticians to be able to explore the data set and then extract a subpart or the totality of the data according to their needs. The Rodam package has only one class, 'odamws', that provides methods to allow you to retrieve online data using 'ODAM' Web Services. This obviously requires that data are implemented according the 'ODAM' approach , namely that the data subsets were deposited in the suitable data repository in the form of TSV files associated with their metadata also described in TSV files. See <http://www.slideshare.net/danieljacob771282/odam-open-data-access-and-mining>.
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>)
Maintainer: Daniel Jacob <daniel.jacob@inra.fr>

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Package GSODR updated to version 1.2.3 with previous version 1.2.2 dated 2018-08-17

Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI') for use in R. Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity are calculated from the original data and included in the final data set. The resulting data include station identification information, state, country, latitude, longitude, elevation, weather observations and associated flags. Additional data are included with this R package: a list of elevation values for stations between -60 and 60 degrees latitude derived from the Shuttle Radar Topography Measuring Mission ('SRTM'). For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package FLightR updated to version 0.4.7 with previous version 0.4.6 dated 2017-03-14

Title: A Package for Reconstructing Animal Paths from Solar Geolocation Loggers
Description: Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology (Rakhimberdiev et al., 2015)<doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution (Rakhimberdiev et al., 2017)<doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology (Rakhimberdiev et al. 2016)<doi:10.1111/jav.00891>.
Author: Eldar Rakhimberdiev [aut, cre], Anatoly Saveliev [aut], Julia Karagicheva [aut], Simeon Lisovski [ctb]
Maintainer: Eldar Rakhimberdiev <eldar@nioz.nl>

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Package stacomiR updated to version 0.5.4.0 with previous version 0.5.3.1 dated 2018-01-04

Title: Fish Migration Monitoring
Description: Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Agency for Biodiversity (AFB) institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Author: Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>

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More information about stacomiR at CRAN
Permanent link

Package polyCub updated to version 0.7.0 with previous version 0.6.1 dated 2017-10-02

Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable functions f(x,y) over simple closed polygonal domains. The following cubature methods are implemented: product Gauss cubature (Sommariva and Vianello, 2007, <doi:10.1007/s10543-007-0131-2>), the simple two-dimensional midpoint rule (wrapping 'spatstat' functions), adaptive cubature for radially symmetric functions via line integrate() along the polygon boundary (Meyer and Held, 2014, <doi:10.1214/14-AOAS743>, Supplement B), and integration of the bivariate Gaussian density based on a triangulation of the polygonal domain. For simple integration along the axes, the packages 'cubature' and 'R2Cuba' are more appropriate.
Author: Sebastian Meyer [aut, cre, trl] (<https://orcid.org/0000-0002-1791-9449>), Leonhard Held [ths], Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>

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Package partialCI updated to version 1.2.0 with previous version 1.1.1 dated 2018-03-06

Title: Partial Cointegration
Description: A collection of time series is partially cointegrated if a linear combination of these time series can be found so that the residual spread is partially autoregressive - meaning that it can be represented as a sum of an autoregressive series and a random walk. This concept is useful in modeling certain sets of financial time series and beyond, as it allows for the spread to contain transient and permanent components alike. Partial cointegration has been introduced by Clegg and Krauss (2017) <doi:10.1080/14697688.2017.1370122>, along with a large-scale empirical application to financial market data. The partialCI package comprises estimation, testing, and simulation routines for partial cointegration models in state space. Clegg et al. (2017) <https://hdl.handle.net/10419/150014> provide an in in-depth discussion of the package functionality as well as illustrating examples in the fields of finance and macroeconomics.
Author: Matthew Clegg [aut], Christopher Krauss [aut], Jonas Rende [cre, aut]
Maintainer: Jonas Rende <jonas.rende@fau.de>

Diff between partialCI versions 1.1.1 dated 2018-03-06 and 1.2.0 dated 2018-10-11

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Package drfit updated to version 0.7.2 with previous version 0.7.1 dated 2017-07-19

Title: Dose-Response Data Evaluation
Description: A somewhat outdated package of basic and easy-to-use functions for fitting dose-response curves to continuous dose-response data, calculating some toxicological parameters and plotting the results. Please consider using the more powerful and actively developed 'drc' package. Functions that are fitted are the cumulative density function of the log-normal distribution ('probit' fit), of the logistic distribution ('logit' fit), of the Weibull distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving dose-response data retrieved from a database accessed via 'odbc' are included. As an alternative to the original fitting methods, the algorithms from the 'drc' package can be used.
Author: Johannes Ranke [aut, cre] (<https://orcid.org/0000-0003-4371-6538>)
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

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Package antaresViz updated to version 0.15.0 with previous version 0.14.0 dated 2018-06-12

Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations. You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
Author: Jalal-Edine ZAWAM [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], Baptiste SEGUINOT [ctb], RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>

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Package tidyLPA updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-13

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Caspar van Lissa [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package RMCriteria updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-13

Title: Multicriteria Package
Description: Provides a methodology to solve most of multicriteria ranking problems using partial and total pre-order from Promethee methods. Albuquerque & Montenegro (2015) <doi:10.1080/03610926.2014.942432>.
Author: Pedro Albuquerque and Gustavo Monteiro
Maintainer: Pedro Albuquerque <pedroa@unb.br>

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Package itunesr updated to version 0.1.3 with previous version 0.1.2 dated 2018-09-14

Title: Access iTunes App Store Ratings and Reviews using R
Description: To enable 'iOS' App Developers to access iTunes App Store Ratings and Reviews using R to extract Basic App Information and Reviews submitted by their App users, Since Apple Store does not provide this straightforward.
Author: AbdulMajedRaja RS [aut, cre]
Maintainer: AbdulMajedRaja RS <amrrs.data@gmail.com>

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Package BatchGetSymbols updated to version 2.2 with previous version 2.1 dated 2018-05-08

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo or Google Finance.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package wevid updated to version 0.5.1 with previous version 0.4.2 dated 2018-06-15

Title: Quantifying Performance of a Binary Classifier Through Weight of Evidence
Description: The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test (McKeigue (2018), <doi:10.1177/0962280218776989>). The package can be used with any test dataset on which you have observed case-control status and have computed prior and posterior probabilities of case status using a model learned on a training dataset. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Author: Paul McKeigue [aut] (<https://orcid.org/0000-0002-5217-1034>), Marco Colombo [ctb, cre] (<https://orcid.org/0000-0001-6672-0623>)
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>

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Package tidyselect updated to version 0.2.5 with previous version 0.2.4 dated 2018-02-26

Title: Select from a Set of Strings
Description: A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package bayesmeta updated to version 2.3 with previous version 2.2 dated 2018-04-12

Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.
Author: Christian Roever [aut, cre] (<https://orcid.org/0000-0002-6911-698X>), Tim Friede [ctb] (<https://orcid.org/0000-0001-5347-7441>)
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>

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Package GROAN updated to version 1.2.0 with previous version 1.1.0 dated 2017-10-07

Title: Genomic Regression Workbench
Description: Workbench for testing genomic regression accuracy on (optionally noisy) phenotypes.
Author: Nelson Nazzicari & Filippo Biscarini
Maintainer: Nelson Nazzicari <nelson.nazzicari@gmail.com>

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Package FisherEM updated to version 1.5.1 with previous version 1.5 dated 2018-10-09

Title: The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data
Description: The FisherEM algorithm, proposed by Bouveyron & Brunet (201) <doi:10.1007/s11222-011-9249-9>, is an efficient method for the clustering of high-dimensional data. FisherEM models and clusters the data in a discriminative and low-dimensional latent subspace. It also provides a low-dimensional representation of the clustered data. A sparse version of Fisher-EM algorithm is also provided.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

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Package eplusr updated to version 0.9.3 with previous version 0.9.2 dated 2018-09-30

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] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuanjia@cqu.edu.cn>

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Package docopt updated to version 0.6.1 with previous version 0.6 dated 2018-08-03

Title: Command-Line Interface Specification Language
Description: Define a command-line interface by just giving it a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package ggeffects updated to version 0.6.0 with previous version 0.5.0 dated 2018-08-11

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are ggpredict() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package ncf updated to version 1.2-6 with previous version 1.2-5 dated 2018-05-24

Title: Spatial Covariance Functions
Description: R functions for analyzing spatial (cross-)covariance: the nonparametric (cross-)covariance function, the spline correlogram, the nonparametric phase coherence function, local indicators of spatial association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre], Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package EcoVirtual updated to version 1.1 with previous version 1.0 dated 2016-06-29

Title: Simulation of Ecological Models
Description: Computer simulations of classical ecological models as a learning resource.
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado <ecovirtualpackage@gmail.com>
Maintainer: Alexandre Adalardo de Oliveira <ecovirtualpackage@gmail.com>

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Package CAST updated to version 0.3.0 with previous version 0.2.1 dated 2018-07-12

Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut], Chris Reudenbach [ctb], Marvin Ludwig [ctb], Thomas Nauss [ctb]
Maintainer: Hanna Meyer <hanna.meyer@geo.uni-marburg.de>

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Wed, 10 Oct 2018

Package RSDA updated to version 2.0.8 with previous version 2.0.7 dated 2018-10-05

Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>

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Package clhs updated to version 0.7-0 with previous version 0.6-0 dated 2018-04-12

Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728-46>).
Author: Pierre Roudier [aut, cre], Colby Brugnard [ctb], Dylan Beaudette [ctb], Benjamin Louis [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>

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Package BiocManager updated to version 1.30.3 with previous version 1.30.2 dated 2018-08-24

Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>

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Package GetHFData updated to version 1.6 with previous version 1.5 dated 2017-11-28

Title: Download and Aggregate High Frequency Trading Data from Bovespa
Description: Downloads and aggregates high frequency trading data for Brazilian instruments directly from Bovespa ftp site <ftp://ftp.bmf.com.br/MarketData/>.
Author: Marcelo Perlin [aut, cre], Henrique Ramos [ctb]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package ca updated to version 0.71 with previous version 0.70 dated 2016-12-14

Title: Simple, Multiple and Joint Correspondence Analysis
Description: Computation and visualization of simple, multiple and joint correspondence analysis.
Author: Michael Greenacre [aut], Oleg Nenadic [aut, cre], Michael Friendly [ctb]
Maintainer: Oleg Nenadic <onenadi@uni-goettingen.de>

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Package rcheology updated to version 3.5.1.1 with previous version 3.5.1.0 dated 2018-07-20

Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package emdi updated to version 1.1.4 with previous version 1.1.3 dated 2018-07-24

Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation and the model-based approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel.
Author: Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Natalia Rojas-Perilla [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>

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Package breathteststan updated to version 0.4.4 with previous version 0.4.3 dated 2018-07-30

Title: Stan-Based Fit to Gastric Emptying Curves
Description: Stan-based curve-fitting function for use with package 'breathtestcore' by the same author. Stan functions are refactored here for easier testing.
Author: Dieter Menne [aut, cre], Menne Biomed Consulting Tuebingen [cph], Benjamin Misselwitz [fnd], Mark Fox [fnd], University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>

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Package digest updated to version 0.6.18 with previous version 0.6.17 dated 2018-09-12

Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang, Viliam Simko, Kurt Hornik and Radford Neal.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between digest versions 0.6.17 dated 2018-09-12 and 0.6.18 dated 2018-10-10

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Package rhierbaps updated to version 1.1.0 with previous version 1.0.0 dated 2018-07-20

Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
Author: Gerry Tonkin-Hill [cre, aut]
Maintainer: Gerry Tonkin-Hill <g.tonkinhill@gmail.com>

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Package MTS updated to version 1.0 with previous version 0.33 dated 2015-02-12

Title: All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models
Description: Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index, transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
Author: Ruey S. Tsay and David Wood
Maintainer: Ruey S. Tsay <ruey.tsay@chicagobooth.edu>

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Package tsibble updated to version 0.5.3 with previous version 0.5.2 dated 2018-09-11

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage temporal-context data in a data-centric format, which is built on top of the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal data, including counting and filling time gaps, aggregate over calendar periods, performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package smcfcs updated to version 1.3.1 with previous version 1.3.0 dated 2017-06-03

Title: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Author: Jonathan Bartlett [aut, cre], Ruth Keogh [aut]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>

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Package CutpointsOEHR updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-06

Title: Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model
Description: Use optimal equal-HR method to determine two optimal cutpoints of a continuous predictor that has a U-shaped relationship with survival outcomes based on Cox regression model. The optimal equal-HR method estimates two optimal cut-points that have approximately the same log hazard value based on Cox regression model and divides individuals into different groups according to their HR values.
Author: Yimin Chen, Zhang Jinxin
Maintainer: Yimin Chen <chenyimin0226@126.com>

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Package hNMF updated to version 0.8 with previous version 0.6 dated 2018-06-01

Title: Hierarchical Non-Negative Matrix Factorization
Description: Hierarchical and single-level non-negative matrix factorization. Several NMF algorithms are available.
Author: Nicolas Sauwen
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>

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Package airGR updated to version 1.0.15.2 with previous version 1.0.14.1 dated 2018-09-28

Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>), Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>), Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>), Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>), Claude Michel [aut, ths], Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>), François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>, 'Parameter estimation' vignettes), Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>), Nicolas Le Moine [ctb], Thibaut Mathevet [ctb], Safouane Mouelhi [ctb], Ludovic Oudin [ctb], Raji Pushpalatha [ctb], Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>

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Package Surrogate updated to version 1.0 with previous version 0.9 dated 2018-06-09

Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package spotGUI updated to version 0.2.1 with previous version 0.2.0 dated 2018-06-01

Title: Graphical User Interface for the Package 'SPOT'
Description: A graphical user interface for the Sequential Parameter Optimization Toolbox (package 'SPOT'). It includes a quick, graphical setup for spot, interactive 3D plots, export possibilities and more.
Author: Frederik Rehbach [aut, cre], Martin Zaefferer [aut], Thomas Bartz-Beielstein [ctb], Andreas Fischbach [ctb], Lorenzo Gentile [ctb]
Maintainer: Frederik Rehbach <frederik.rehbach@th-koeln.de>

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Package wooldridge updated to version 1.3.1 with previous version 1.3.0 dated 2018-04-09

Title: 111 Data Sets from "Introductory Econometrics: A Modern Approach, 6e" by Jeffrey M. Wooldridge
Description: Students learning both econometrics and R may find the introduction to both challenging. However, if the text is "Introductory Econometrics: A Modern Approach" by Jeffrey M. Wooldridge, they are in luck! The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have all been compressed to a fraction of their original size and are well documented. Documentation files contain the page numbers of the text where each set is used, the original source, time of publication, and notes suggesting ideas for further exploratory data analysis and research. If one need's to brush-up on model syntax, a vignette contains R solutions to examples from each chapter of the text. Data sets are from the 6th edition (Wooldridge 2016, ISBN-13: 978-1-305-27010-7), and are backwards compatible with all versions of the text.
Author: Justin M. Shea [aut, cre], Kennth H. Brown [ctb]
Maintainer: Justin M. Shea <jshea@roosevelt.edu>

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Package NetworkChange updated to version 0.4 with previous version 0.3 dated 2017-08-19

Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov multilinear tensor regression model (Park and Sohn, 2017, <http://jhp.snu.ac.kr/NetworkChange.pdf>). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.
Author: Jong Hee Park [aut,cre], Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

Diff between NetworkChange versions 0.3 dated 2017-08-19 and 0.4 dated 2018-10-10

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Tue, 09 Oct 2018

Package StereoMorph updated to version 1.6.2 with previous version 1.6.1 dated 2017-03-14

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between StereoMorph versions 1.6.1 dated 2017-03-14 and 1.6.2 dated 2018-10-09

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Package msigdbr updated to version 6.2.1 with previous version 6.1.1 dated 2018-04-12

Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets typically used with the 'Gene Set Enrichment Analysis' (GSEA) software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>) in a standard R data frame with key-value pairs. Included are the original human gene symbols and Entrez IDs as well as the equivalents for various frequently studied model organisms such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>

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Package microbenchmark updated to version 1.4-5 with previous version 1.4-4 dated 2018-01-24

Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare the execution time of R expressions.
Author: Olaf Mersmann [aut], Claudia Beleites [ctb], Rainer Hurling [ctb], Ari Friedman [ctb], Joshua M. Ulrich [cre]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>

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Package BayesGOF updated to version 5.2 with previous version 5.1 dated 2018-10-05

Title: Bayesian Modeling via Frequentist Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>

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Package RndTexExams updated to version 1.5 with previous version 1.4.1 dated 2018-01-13

Title: Build and Grade Multiple Choice Exams with Randomized Content
Description: Using as input a 'LaTeX' file with a multiple choice exam, this package will produce several versions with randomized contents of the same exam. Functions for grading are also available.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package evaluate updated to version 0.12 with previous version 0.11 dated 2018-07-17

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package rticles updated to version 0.6 with previous version 0.5 dated 2018-07-06

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph], Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph], MDPI [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package tsBSS updated to version 0.5.2 with previous version 0.5.1 dated 2018-06-25

Title: Blind Source Separation and Supervised Dimension Reduction for Time Series
Description: Different estimates are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>

Diff between tsBSS versions 0.5.1 dated 2018-06-25 and 0.5.2 dated 2018-10-09

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Package EFAutilities updated to version 1.2.3 with previous version 1.2.2 dated 2018-05-21

Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis are included in this package. In particular, it computes standard errors for parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>

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Package intsvy updated to version 2.3 with previous version 2.2 dated 2018-09-20

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Author: Daniel Caro <dcarov@gmail.com>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <dcarov@gmail.com>

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Package bayou updated to version 2.1.1 with previous version 2.1 dated 2018-06-07

Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>

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Package dynamichazard updated to version 0.6.0 with previous version 0.5.3 dated 2018-07-01

Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using state space models. The first implemented model is described in Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994) <doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the Extended Kalman filter is replaced by an unscented Kalman filter and other options including particle filters. The implemented particle filters support more general state space models.
Author: Benjamin Christoffersen [cre, aut], Alan Miller [cph], Anthony Williams [cph], Boost developers [cph], R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

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 DESCRIPTION                                                                    |    9 
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 R/RcppExports.R                                                                |   24 
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 man/plot.ddhazard.Rd                                                           |    2 
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 man/static_glm.Rd                                                              |    2 
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 src/arma_BLAS_LAPACK.h                                                         |    4 
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 src/bigglm_wrapper.h                                                           |   14 
 src/ddhazard.h                                                                 |   48 
 src/ddhazard/EKF_solver.cpp                                                    |   61 
 src/ddhazard/GMA_solver.cpp                                                    |   15 
 src/ddhazard/SMA_solver.cpp                                                    |   32 
 src/ddhazard/UKF_solver.cpp                                                    |   42 
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 src/for_tests.cpp                                                              |   54 
 src/lin_maps.cpp                                                               |   78 
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 src/loglike.cpp                                                                |   45 
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 tests/testthat/test_loglike.R                                                  |   58 
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 tests/testthat/test_predict.R                                                  |   13 
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 tests/testthat/test_summary.R                                                  |    8 
 tests/testthat/test_test_utils.R                                               |    4 
 tests/testthat/test_weights.R                                                  |   13 
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 vignettes/Diagnostics.Rmd                                                      |   20 
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Package cffdrs updated to version 1.8.1 with previous version 1.7.6 dated 2017-04-06

Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System. Some functions have two versions, table and raster based.
Author: Xianli Wang, Alan Cantin, Marc-André Parisien, Mike Wotton, Kerry Anderson, Brett Moore, Tom Schiks, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>

Diff between cffdrs versions 1.7.6 dated 2017-04-06 and 1.8.1 dated 2018-10-09

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Package rjags updated to version 4-7 with previous version 4-6 dated 2016-02-19

Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>

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Package bibliometrix updated to version 2.0.1 with previous version 2.0.0 dated 2018-09-10

Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>), Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Cochrane Library (<http://www.cochranelibrary.com/>) and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

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Package PAC updated to version 1.1.0 with previous version 1.0.10 dated 2018-03-06

Title: Partition-Assisted Clustering and Multiple Alignments of Networks
Description: Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.
Author: Ye Henry Li, Dangna Li
Maintainer: Ye Henry Li <hlowl2@gmail.com>

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Package mindr updated to version 1.1.5 with previous version 1.1.0 dated 2017-07-19

Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package dglars updated to version 2.1.0 with previous version 2.0.1 dated 2018-04-24

Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

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Package nucim updated to version 1.0.6 with previous version 1.0.0 dated 2016-12-05

Title: Nucleome Imaging Toolbox
Description: Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <stats@volkerschmid.de>

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Package funData updated to version 1.3-2 with previous version 1.3-1 dated 2018-10-02

Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with utility functions.
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>

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Package reReg updated to version 1.1.5 with previous version 1.1.4 dated 2018-05-30

Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time data. Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, Lin et al. (2000) <doi:10.1111/1467-9868.00259>, Wang et al. (2001) <doi:10.1198/016214501753209031>, Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, Huang and Wang (2004) <doi:10.1198/016214504000001033>, and more.
Author: Sy Han (Steven) Chiou [aut, cre], Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>

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Package rmgarch updated to version 1.3-5 with previous version 1.3-0 dated 2015-12-28

Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

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Package Bolstad updated to version 0.2-40 with previous version 0.2-39 dated 2018-08-29

Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to Bayesian Statistics, Bolstad, W.M. (2017), John Wiley & Sons ISBN 978-1-118-09156-2.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>

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Package aphid updated to version 1.3.0 with previous version 1.2.0 dated 2018-08-14

Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>

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Mon, 08 Oct 2018

Package cladoRcpp updated to version 0.15 with previous version 0.14.4 dated 2014-05-18

Title: C++ Implementations of Phylogenetic Cladogenesis Calculations
Description: Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>

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Package pmml updated to version 1.5.6 with previous version 1.5.5 dated 2018-07-06

Title: Generate PMML for Various Models
Description: The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler (arules), Software AG, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>

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Package funHDDC updated to version 2.2.0 with previous version 2.1.0 dated 2018-08-13

Title: Univariate and Multivariate Model-Based Clustering in Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Schmutz et al., 2018) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

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Package weathercan updated to version 0.2.8 with previous version 0.2.7 dated 2018-07-05

Title: Download Weather Data from the Environment and Climate Change Canada Website
Description: Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<http://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>), Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>

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Package billboarder updated to version 0.2.4 with previous version 0.2.3 dated 2018-08-07

Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package sommer updated to version 3.6 with previous version 3.5 dated 2018-07-02

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous variance models (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson, and Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple relationship matrices or other covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

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Package ndtv updated to version 0.12.3 with previous version 0.12.2 dated 2018-05-13

Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut], Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>

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Package CopyDetect updated to version 1.3 with previous version 1.2 dated 2016-04-27

Title: Computing Response Similarity Indices for Multiple-Choice Tests
Description: Contains several IRT and non-IRT based response similarity indices proposed in the literature for multiple-choice examinations such as the Omega index, Wollack (1997) <doi:10.1177/01466216970214002>; Generalized Binomial Test, van der Linden & Sotaridona (2006) <doi:10.3102/10769986031003283>; K index, K1 and K2 indices, Sotaridona & Meijer (2002) <doi:10.1111/j.1745-3984.2002.tb01138.x>; and S1 and S2 indices, Sotaridona & Meijer (2003) <doi:10.1111/j.1745-3984.2003.tb01096.x>.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>

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Package stylo updated to version 0.6.8 with previous version 0.6.7 dated 2018-05-26

Title: Stylometric Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>

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Package InvariantCausalPrediction updated to version 0.7-2 with previous version 0.7-1 dated 2017-10-03

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

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Package cdata updated to version 1.0.2 with previous version 1.0.1 dated 2018-09-22

Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . Based on the 'DBI' database interface.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package useful updated to version 1.2.6 with previous version 1.2.5 dated 2018-06-09

Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a data.frame, constructing formulas from text and building design and response matrices.
Author: Jared P. Lander [cre, aut], Nicholas Galasinao [ctb], Joshua Kraut [ctb], Daniel Chen [ctb]
Maintainer: Jared P. Lander <packages@jaredlander.com>

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Package bookdownplus updated to version 1.5.1 with previous version 1.4.6 dated 2018-09-10

Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package solvebio updated to version 2.6.0 with previous version 2.5.1 dated 2018-07-10

Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>

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Package SPUTNIK updated to version 1.0.4.1 with previous version 1.0.3.4 dated 2018-09-18

Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>

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Package easyreg updated to version 2.0 with previous version 1.0 dated 2016-10-13

Title: Easy Regression
Description: Performs analysis of regression in simple designs with quantitative treatments, including mixed models and non linear models.
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>

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Package ggspectra updated to version 0.3.0 with previous version 0.2.4-1 dated 2018-05-07

Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, and stats for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and plot() methods for spectral data stored in objects of the classes defined in package 'photobiology' and a plot() method for objects of class "waveband", also defined in package 'photobiology'. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package deming updated to version 1.3 with previous version 1.2 dated 2018-06-19

Title: Deming, Thiel-Sen and Passing-Bablock Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>

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Package qle updated to version 0.18 with previous version 0.17 dated 2018-03-16

Title: Simulation-Based Quasi-Likelihood Estimation
Description: A simulation-based quasi-likelihood method (Baaske, M., Ballani, F., v.d. Boogaart, K.G. (2014) <doi:10.5566/ias.v33.p107-119>) for parameter estimation of parametric statistical models for which closed-form representations of distributional characteristics are unavailable and can only be obtained by computationally intensive simulations of the model.
Author: Markus Baaske [aut, cre, cph], K. Gerald van den Boogaart [ths]
Maintainer: Markus Baaske <markus.baaske@uni-jena.de>

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Package comorbidity updated to version 0.2.0 with previous version 0.1.1 dated 2018-03-30

Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Hojjat Salmasian [ctb] (ICD-9-CM scores)
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>

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Package coda updated to version 0.19-2 with previous version 0.19-1 dated 2016-12-08

Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles [aut], Karen Vines [aut], Deepayan Sarkar [aut], Douglas Bates [aut], Russell Almond [aut], Arni Magnusson [aut]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>

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Package princurve updated to version 2.1.3 with previous version 2.1.2.1 dated 2018-08-02

Title: Fits a Principal Curve in Arbitrary Dimension
Description: Fitting a principal curve to a data matrix in arbitrary dimensions.
Author: Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (HenrikBengtsson), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package prais updated to version 1.0.0 with previous version 0.1.1 dated 2015-03-19

Title: Prais-Winsten Estimator for AR(1) Serial Correlation
Description: The Prais-Winsten estimator takes into account AR(1) serial correlation of the errors in a linear regression model. The procedure recursively estimates the coefficients and the error autocorrelation of the specified model until sufficient convergence of the AR(1) coefficient is attained.
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <prais.r@outlook.com>

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Package PPCI updated to version 0.1.3 with previous version 0.1.2 dated 2018-03-15

Title: Projection Pursuit for Cluster Identification
Description: Implements recently developed projection pursuit algorithms for finding optimal linear cluster separators. The clustering algorithms use optimal hyperplane separators based on minimum density, Pavlidis et. al (2016) <https://jmlr.csail.mit.edu/papers/volume17/15-307/15-307.pdf>; minimum normalised cut, Hofmeyr (2017) <doi:10.1109/TPAMI.2016.2609929>; and maximum variance ratio clusterability, Hofmeyr and Pavlidis (2015) <doi:10.1109/SSCI.2015.116>.
Author: David Hofmeyr <dhofmeyr@sun.ac.za> [aut, cre] Nicos Pavlidis <n.pavlidis@lancaster.ac.uk> [aut]
Maintainer: David Hofmeyr <dhofmeyr@sun.ac.za>

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Package EpiStats updated to version 1.2 with previous version 1.1 dated 2018-06-05

Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists. They include commands for measures of association and impact for case control studies and cohort studies. They may be particularly useful for outbreak investigations and include univariate and stratified analyses. The functions for cohort studies include the CS(), CSTable() and CSInter() commands. The functions for case control studies include the CC(), CCTable() and CCInter() commands.
Author: Jean Pierre Decorps [aut, cre], Esther Kissling [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>

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Package DiceKriging updated to version 1.5.6 with previous version 1.5.5 dated 2015-04-24

Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant <roustant@emse.fr>

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Package devRate updated to version 0.1.9 with previous version 0.1.8 dated 2018-07-06

Title: Quantify the Relationship Between Development Rate and Temperature in Ectotherms
Description: A set of functions to quantify the relationship between development rate and temperature and to build phenological models. The package comprises a set of models and estimated parameters borrowed from a literature review in ectotherms. The methods and literature review are described in Rebaudo et al. (2018) <doi:10.1111/2041-210X.12935> and Rebaudo and Rabhi (2018) <doi:10.1111/eea.12693>. An example can be found in Rebaudo et al. (2017) <doi:10.1007/s13355-017-0480-5>.
Author: Francois Rebaudo [aut, cre] (2016-2018), Camila Benavides [ctb] (M2 student; 2018), Tanusson Selvarajah [ctb] (L2 student; 2018), Nicolas Bonnal [ctb] (M1 student; 2018), Badre Rabhi [ctb] (L2 student; 2017), Quentin Struelens [ctb] (VIA; 2016)
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>

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Package sptemExp updated to version 0.1.3 with previous version 0.1.1 dated 2017-09-01

Title: Constrained Spatiotemporal Mixed Models for Exposure Estimation
Description: The approach of constrained spatiotemporal mixed models is to make reliable estimation of air pollutant concentrations at high spatiotemporal resolution (Li, L., Zhang, J., Meng, X., Fang, Y., Ge, Y., Wang, J., Wang, C., Wu, J., Kan, H. (2018) <doi.org/10.1016/j.rse.2018.09.001>; Li, L., Lurmann, F., Habre, R., Urman, R., Rappaport, E., Ritz, B., Chen, J., Gilliland, F., Wu, J., (2017) <doi:10.1021/acs.est.7b01864>). This package is an extensive tool for this modeling approach with support of block Kriging (Goovaerts, P. (1997) <http://www.gbv.de/dms/goettingen/229148123.pdf>) and uses the PM2.5 modeling as examples. It provides the following functionality: (1) Extraction of covariates from the satellite images such as GeoTiff and NC4 raster; (2) Generation of temporal basis functions to simulate the seasonal trends in the study regions; (3) Generation of the regional monthly or yearly means of air pollutant concentration; (4) Generation of Thiessen polygons and spatial effect modeling; (5) Ensemble modeling for spatiotemporal mixed models, supporting multi-core parallel computing; (6) Integrated predictions with or without weights of the model's performance, supporting multi-core parallel computing; (7) Constrained optimization to interpolate the missing values; (8) Generation of the grid surfaces of air pollutant concentration estimates at high resolution; (9) Block Kriging for regional mean estimation at multiple scales.
Author: Lianfa Li,
Maintainer: Lianfa Li <lspatial@gmail.com>

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Package c212 updated to version 0.94 with previous version 0.93 dated 2017-04-06

Title: Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)
Description: Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class.The package title c212 is in reference to the original Engineering and Physical Sciences Research Council (UK) funded project which was named CASE 2/12.
Author: Raymond Carragher <raymond.carragher@strath.ac.uk>
Maintainer: Raymond Carragher <raymond.carragher@strath.ac.uk>

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Package psda updated to version 1.0.1 with previous version 1.0.0 dated 2017-09-05

Title: Polygonal Symbolic Data Analysis
Description: An implementation of symbolic polygonal data analysis. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation. In addition, transformation of the data in polygons. Empirical probability distribution function based on polygonal histogram and regression models are presented.
Author: Wagner Silva [aut, cre, ths], Renata Souza [aut], Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>

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Sun, 07 Oct 2018

Package SamplingStrata updated to version 1.3 with previous version 1.2 dated 2018-02-18

Title: Optimal Stratification of Sampling Frames for Multipurpose Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen, Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>

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Package hdf5r updated to version 1.0.1 with previous version 1.0.0 dated 2017-10-25

Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre], Mario Annau [aut], Novartis Institute for BioMedical Research (NIBR) [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>

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Package wallace updated to version 1.0.6 with previous version 1.0.5 dated 2018-06-22

Title: A Modular Platform for Reproducible Modeling of Species Niches and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre], Gonzalo E. Pinilla-Buitrago [aut], Bruno Vilela [aut], Matthew E. Aiello-Lammens [aut], Robert Muscarella [aut], Cory Merow [aut], Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>

Diff between wallace versions 1.0.5 dated 2018-06-22 and 1.0.6 dated 2018-10-07

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 wallace-1.0.6/wallace/README.md                                      |    6 
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Package StanHeaders updated to version 2.18.0 with previous version 2.17.2 dated 2018-01-20

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code or function documentation. There is a shared object containing part of the 'CVODES' library, but it is not accessible from R. 'StanHeaders' is only 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 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
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], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between StanHeaders versions 2.17.2 dated 2018-01-20 and 2.18.0 dated 2018-10-07

 StanHeaders-2.17.2/StanHeaders/inst/include/cvodes/cvodes_band.h                                                  |only
 StanHeaders-2.17.2/StanHeaders/inst/include/cvodes/cvodes_dense.h                                                 |only
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 StanHeaders-2.17.2/StanHeaders/man                                                                                |only
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 StanHeaders-2.18.0/StanHeaders/DESCRIPTION                                                                        |   15 
 StanHeaders-2.18.0/StanHeaders/MD5                                                                                | 2920 +++++-----
 StanHeaders-2.18.0/StanHeaders/build                                                                              |only
 StanHeaders-2.18.0/StanHeaders/inst/CITATION                                                                      |    6 
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 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes.h                                                       |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes_bandpre.h                                               |  305 -
 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes_bbdpre.h                                                |  576 -
 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes_diag.h                                                  |    3 
 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes_direct.h                                                |  589 --
 StanHeaders-2.18.0/StanHeaders/inst/include/cvodes/cvodes_spils.h                                                 |  888 +--
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 StanHeaders-2.18.0/StanHeaders/inst/include/nvector/nvector_parallel.h                                            |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/nvector/nvector_parhyp.h                                              |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/nvector/nvector_petsc.h                                               |   50 
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 StanHeaders-2.18.0/StanHeaders/inst/include/nvector/nvector_serial.h                                              |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/nvector/raja                                                          |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/io/program_reader.hpp                                        |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast.hpp                                                 |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/base_expr_type.hpp                                  |  233 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/expr_type.hpp                                       |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/expr_type_def.hpp                                   |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/generate_expression.hpp                         |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis.hpp                       |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis_def.hpp                   |    7 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis.hpp                                 |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis_def.hpp                             |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/indexed_type.hpp                                |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/indexed_type_def.hpp                            |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing_def.hpp                     |   13 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable_def.hpp                           |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis.hpp                                  |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis_def.hpp                              |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis.hpp                      |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis_def.hpp                  |   19 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/print_scope_def.hpp                             |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive_def.hpp                       |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_def.hpp                            |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis.hpp                            |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis_def.hpp                        |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis.hpp                              |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis_def.hpp                          |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/fun/write_base_expr_type_def.hpp                    |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/ill_formed_type.hpp                                 |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/int_type.hpp                                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/matrix_type.hpp                                     |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/assgn.hpp                                      |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/assgn_def.hpp                                  |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/cholesky_corr_var_decl_def.hpp                 |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/cholesky_factor_var_decl_def.hpp               |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/corr_matrix_var_decl_def.hpp                   |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/cov_matrix_var_decl_def.hpp                    |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/double_literal_def.hpp                         |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/double_var_decl_def.hpp                        |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/expression.hpp                                 |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/expression_def.hpp                             |    9 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/fun_def.hpp                                    |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal_def.hpp                            |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/int_var_decl_def.hpp                           |    4 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/ordered_var_decl_def.hpp                       |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/positive_ordered_var_decl_def.hpp              |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_var_decl_def.hpp                    |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/simplex_var_decl_def.hpp                       |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/statement.hpp                                  |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/statement_def.hpp                              |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/unit_vector_var_decl_def.hpp                   |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/node/vector_var_decl_def.hpp                        |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/origin_block.hpp                                    |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/row_vector_type.hpp                                 |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/scope.hpp                                           |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/scope_def.hpp                                       |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_arg_type.hpp                          |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures.hpp                        |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures_def.hpp                    |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast/vector_type.hpp                                     |only
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/ast_def.cpp                                             |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/compile_functions.hpp                                   |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/compiler.hpp                                            |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/function_signatures.h                                   | 1509 ++---
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator.hpp                                           |    1 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/constants.hpp                                 |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/constrained_param_names_visgen.hpp            |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/dump_member_var_visgen.hpp                    |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/expression_visgen.hpp                         |  122 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/fun_scalar_type.hpp                           |    2 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_constructor.hpp                      |   15 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_cpp.hpp                              |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_eigen_index_expression.hpp           |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_expression.hpp                       |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_fun_inst_templ_params.hpp            |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function.hpp                         |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function_arguments.hpp               |    3 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function_body.hpp                    |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation.hpp           |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_body.hpp      |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_name.hpp      |    1 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_functions.hpp                        |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr.hpp                     |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_initializer.hpp                      |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decls.hpp                  |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_inits.hpp                  |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_log_prob.hpp                         |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_quoted_expression.hpp                |    3 
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 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_standalone_functions.hpp             |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_statement.hpp                        |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_statements.hpp                       |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_method.hpp |   12 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_context_size.hpp            |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_positive.hpp                |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_var_resizing.hpp                     |    3 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/generate_write_array_method.hpp               |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/has_only_int_args.hpp                         |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/idx_user_visgen.hpp                           |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/idx_visgen.hpp                                |   15 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/init_local_var_visgen.hpp                     |   97 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/init_visgen.hpp                               |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/is_numbered_statement_vis.hpp                 |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/local_var_decl_visgen.hpp                     |  102 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/local_var_init_nan_visgen.hpp                 |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/printable_visgen.hpp                          |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/set_param_ranges_visgen.hpp                   |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/statement_visgen.hpp                          |  278 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/unconstrained_param_names_visgen.hpp          |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/validate_transformed_params_visgen.hpp        |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/validate_var_decl_visgen.hpp                  |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/write_array_vars_visgen.hpp                   |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/write_array_visgen.hpp                        |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/generator/write_dims_visgen.hpp                         |    7 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_def.hpp                      |   13 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions.hpp                           |  116 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp                       |  892 +--
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp                          |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp                      |  192 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar.hpp                               |    5 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp                           |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp                                     |    3 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/mcmc/chains.hpp                                              |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/base_xhmc.hpp                                  |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/model/standalone_functions_header.hpp                        |    1 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/optimize/bfgs.hpp                                   |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/optimize/lbfgs.hpp                                  |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/optimize/newton.hpp                                 |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/util/gq_writer.hpp                                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/util/initialize.hpp                                 |  399 -
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/services/util/mcmc_writer.hpp                                |  482 -
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/variational/advi.hpp                                         |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/src/stan/version.hpp                                                  |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/arr/fun/log_sum_exp.hpp                                 |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/arr/fun/sum.hpp                                         |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/arr/fun/to_fvar.hpp                                     |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/fvar.hpp                                           |  555 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_addition.hpp                              |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_division.hpp                              |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_equal.hpp                                 |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_greater_than.hpp                          |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_greater_than_or_equal.hpp                 |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_less_than.hpp                             |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_less_than_or_equal.hpp                    |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_logical_and.hpp                           |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_logical_or.hpp                            |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_multiplication.hpp                        |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_not_equal.hpp                             |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_subtraction.hpp                           |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_unary_minus.hpp                           |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_unary_not.hpp                             |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/operator_unary_plus.hpp                            |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/core/std_numeric_limits.hpp                             |  172 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/Eigen_NumTraits.hpp                             |  111 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_product.hpp                         |   91 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_self.hpp                            |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/crossprod.hpp                                   |   21 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/determinant.hpp                                 |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/divide.hpp                                      |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_product.hpp                                 |  299 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_self.hpp                                    |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/inverse.hpp                                     |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_determinant.hpp                             |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_softmax.hpp                                 |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_sum_exp.hpp                                 |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left.hpp                                |  163 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_ldlt.hpp                           |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_tri_low.hpp                        |  195 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right.hpp                               |  166 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right_tri_low.hpp                       |  192 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply.hpp                                    |  233 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply_lower_tri_self_transpose.hpp           |   31 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_Q.hpp                                        |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_R.hpp                                        |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/quad_form_sym.hpp                               |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_product.hpp                            |   85 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_self.hpp                               |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/softmax.hpp                                     |   71 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/squared_distance.hpp                            |  300 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/sum.hpp                                         |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/tcrossprod.hpp                                  |   21 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/to_fvar.hpp                                     |   59 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/trace_gen_quad_form.hpp                         |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/trace_quad_form.hpp                             |   59 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/typedefs.hpp                                    |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/unit_vector_constrain.hpp                       |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/functor/gradient.hpp                                |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/functor/hessian.hpp                                 |  117 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/functor/jacobian.hpp                                |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/meta/operands_and_partials.hpp                      |  201 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/mat/vectorize/apply_scalar_unary.hpp                    |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal.hpp                                                |    1 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi.hpp                                        |   21 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi_approx.hpp                                 |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/abs.hpp                                        |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/acos.hpp                                       |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/acosh.hpp                                      |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/asin.hpp                                       |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/asinh.hpp                                      |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan.hpp                                       |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan2.hpp                                      |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/atanh.hpp                                      |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_first_kind.hpp                          |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_second_kind.hpp                         |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/binary_log_loss.hpp                            |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/binomial_coefficient_log.hpp                   |  117 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/cbrt.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/ceil.hpp                                       |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/cos.hpp                                        |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/cosh.hpp                                       |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/digamma.hpp                                    |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/erf.hpp                                        |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/erfc.hpp                                       |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp.hpp                                        |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp2.hpp                                       |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/expm1.hpp                                      |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fabs.hpp                                       |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/falling_factorial.hpp                          |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fdim.hpp                                       |  103 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/floor.hpp                                      |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fma.hpp                                        |  239 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmax.hpp                                       |  153 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmin.hpp                                       |  106 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmod.hpp                                       |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_p.hpp                                    |  146 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_q.hpp                                    |  158 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/grad_inc_beta.hpp                              |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/hypot.hpp                                      |  120 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inc_beta.hpp                                   |   33 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv.hpp                                        |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_Phi.hpp                                    |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_cloglog.hpp                                |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_logit.hpp                                  |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_sqrt.hpp                                   |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_square.hpp                                 |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_inf.hpp                                     |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_nan.hpp                                     |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/lbeta.hpp                                      |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/lgamma.hpp                                     |   31 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/lmgamma.hpp                                    |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log.hpp                                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log10.hpp                                      |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m.hpp                                      |   13 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_exp.hpp                                  |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_inv_logit.hpp                            |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p.hpp                                      |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p_exp.hpp                                  |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log2.hpp                                       |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_diff_exp.hpp                               |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_falling_factorial.hpp                      |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit.hpp                              |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit_diff.hpp                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_mix.hpp                                    |  425 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_rising_factorial.hpp                       |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_sum_exp.hpp                                |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/logit.hpp                                      |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_first_kind.hpp                 |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_second_kind.hpp                |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/multiply_log.hpp                               |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/owens_t.hpp                                    |  114 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/pow.hpp                                        |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/primitive_value.hpp                            |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/rising_factorial.hpp                           |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/round.hpp                                      |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/sin.hpp                                        |   19 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/sinh.hpp                                       |   19 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/sqrt.hpp                                       |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/square.hpp                                     |   15 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/tan.hpp                                        |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/tanh.hpp                                       |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/tgamma.hpp                                     |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/to_fvar.hpp                                    |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/trigamma.hpp                                   |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/trunc.hpp                                      |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of.hpp                                   |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of_rec.hpp                               |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/meta/ad_promotable.hpp                             |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/meta/is_fvar.hpp                                   |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/meta/operands_and_partials.hpp                     |  171 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/fwd/scal/meta/partials_type.hpp                             |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/gpu                                                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp                                      |  504 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/fun/typedefs.hpp                                    |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/derivative.hpp                              |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/finite_diff_grad_hessian.hpp                |  149 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_hessian.hpp                            |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_tr_mat_times_hessian.hpp               |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/gradient_dot_vector.hpp                     |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian.hpp                                 |  125 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian_times_vector.hpp                    |   81 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/mix/mat/functor/partial_derivative.hpp                      |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr.hpp                                                |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/err/check_matching_sizes.hpp                       |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/err/check_nonzero_size.hpp                         |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/err/check_opencl.hpp                               |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/err/check_ordered.hpp                              |   66 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/array_builder.hpp                              |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/common_type.hpp                                |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/dot.hpp                                        |   19 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/dot_self.hpp                                   |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/fill.hpp                                       |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/inverse_softmax.hpp                            |   68 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/log_sum_exp.hpp                                |   61 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_elements.hpp                           |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar.hpp                             |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar_type.hpp                        |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/rep_array.hpp                                  |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/scaled_add.hpp                                 |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_asc.hpp                                   |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_desc.hpp                                  |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/sub.hpp                                        |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/sum.hpp                                        |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of.hpp                                   |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of_rec.hpp                               |   73 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_observer.hpp                   |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_system.hpp                     |  268 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_1d.hpp                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp                     |  236 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/mpi_cluster.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/mpi_cluster_inst.cpp                       |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/mpi_command.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/functor/mpi_distributed_apply.hpp                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/VectorBuilderHelper.hpp                       |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/contains_std_vector.hpp                       |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/get.hpp                                       |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/index_type.hpp                                |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant_struct.hpp                        |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/is_std_vector.hpp                             |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/is_vector.hpp                                 |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/length.hpp                                    |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/scalar_type.hpp                               |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/arr/meta/value_type.hpp                                |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat.hpp                                                |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp                      |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp                 |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_column_index.hpp                         |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp                          |  107 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp                           |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_ldlt_factor.hpp                          |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp                     |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_matching_dims.hpp                        |  110 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_multiplicable.hpp                        |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_ordered.hpp                              |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp                         |  144 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp                     |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_positive_ordered.hpp                     |   65 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_range.hpp                                |  155 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_row_index.hpp                            |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_simplex.hpp                              |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp                          |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_square.hpp                               |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_std_vector_index.hpp                     |   60 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp                            |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp                          |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_vector.hpp                               |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/constraint_tolerance.hpp                       |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/err/validate_non_negative_index.hpp                |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/LDLT_factor.hpp                                |  231 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/Phi.hpp                                        |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/Phi_approx.hpp                                 |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/accumulator.hpp                                |  208 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/acos.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/acosh.hpp                                      |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/add.hpp                                        |  136 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/add_diag.hpp                                   |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/append_array.hpp                               |  121 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/append_col.hpp                                 |  414 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/append_row.hpp                                 |  398 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/asin.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/asinh.hpp                                      |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp                                     |  326 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/atan.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/atanh.hpp                                      |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/autocorrelation.hpp                            |  289 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/autocovariance.hpp                             |  166 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/block.hpp                                      |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cbrt.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/ceil.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/chol2inv.hpp                                   |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp                    |  137 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_free.hpp                         |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp                         |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_constrain.hpp                  |  145 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_free.hpp                       |   63 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/col.hpp                                        |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cols.hpp                                       |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/columns_dot_product.hpp                        |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/columns_dot_self.hpp                           |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/common_type.hpp                                |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_constrain.hpp                      |  164 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_free.hpp                           |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cos.hpp                                        |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cosh.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp                               |  303 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp                       |  156 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain_lkj.hpp                   |  149 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free.hpp                            |   95 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free_lkj.hpp                        |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/crossprod.hpp                                  |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp                              |   75 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp                              |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp                              |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp                    |  198 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp                        |  105 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_u_to_z.hpp                                 |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cumulative_sum.hpp                             |   96 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/determinant.hpp                                |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_matrix.hpp                                |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_post_multiply.hpp                         |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_pre_multiply.hpp                          |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/diagonal.hpp                                   |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/digamma.hpp                                    |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/dims.hpp                                       |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/distance.hpp                                   |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/divide.hpp                                     |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_product.hpp                                |   87 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_self.hpp                                   |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/eigenvalues_sym.hpp                            |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/eigenvectors_sym.hpp                           |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_divide.hpp                                 |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_multiply.hpp                               |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/erf.hpp                                        |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/erfc.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/exp.hpp                                        |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/exp2.hpp                                       |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/expm1.hpp                                      |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/fabs.hpp                                       |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_U.hpp                                   |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_cov_matrix.hpp                          |   85 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/fill.hpp                                       |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/floor.hpp                                      |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/get_base1.hpp                                  |  690 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/get_base1_lhs.hpp                              |  692 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/get_lp.hpp                                     |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_dot_prod_cov.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_periodic_cov.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/head.hpp                                       |  121 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/initialize.hpp                                 |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv.hpp                                        |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_Phi.hpp                                    |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_cloglog.hpp                                |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_logit.hpp                                  |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_sqrt.hpp                                   |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_square.hpp                                 |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse.hpp                                    |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse_spd.hpp                                |   59 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/lgamma.hpp                                     |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log.hpp                                        |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log10.hpp                                      |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m.hpp                                      |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m_exp.hpp                                  |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m_inv_logit.hpp                            |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1p.hpp                                      |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1p_exp.hpp                                  |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log2.hpp                                       |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant.hpp                            |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant_ldlt.hpp                       |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_determinant_spd.hpp                        |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_inv_logit.hpp                              |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_mix.hpp                                    |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_softmax.hpp                                |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log_sum_exp.hpp                                |   65 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/logit.hpp                                      |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/make_nu.hpp                                    |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp.hpp                                 |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp                             |   61 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_multiply.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_pade.hpp                            |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/max.hpp                                        |   96 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left.hpp                               |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_ldlt.hpp                          |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_spd.hpp                           |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri.hpp                           |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri_low.hpp                       |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right.hpp                              |   63 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_ldlt.hpp                         |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_spd.hpp                          |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri.hpp                          |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri_low.hpp                      |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/mean.hpp                                       |   66 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/min.hpp                                        |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/minus.hpp                                      |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply.hpp                                   |  138 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply_lower_tri_self_transpose.hpp          |   61 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/num_elements.hpp                               |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/opencl_copy.hpp                                |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_constrain.hpp                          |  111 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_free.hpp                               |   65 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_constrain.hpp                 |  108 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_free.hpp                      |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/prod.hpp                                       |   60 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_common.hpp                             |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_elements.hpp                           |   98 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar.hpp                             |  170 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar_type.hpp                        |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_Q.hpp                                       |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_R.hpp                                       |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_Q.hpp                                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_R.hpp                                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form.hpp                                  |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp                             |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_sym.hpp                              |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp                                       |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_L.hpp                                |  184 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_matrix.hpp                           |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/read_cov_L.hpp                                 |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/read_cov_matrix.hpp                            |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_matrix.hpp                                 |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_row_vector.hpp                             |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_vector.hpp                                 |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/resize.hpp                                     |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/round.hpp                                      |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/row.hpp                                        |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rows.hpp                                       |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rows_dot_product.hpp                           |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rows_dot_self.hpp                              |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/scale_matrix_exp_multiply.hpp                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sd.hpp                                         |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/segment.hpp                                    |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_constrain.hpp                          |  147 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_free.hpp                               |   71 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sin.hpp                                        |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/singular_values.hpp                            |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sinh.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/size.hpp                                       |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/softmax.hpp                                    |  102 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_asc.hpp                                   |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_desc.hpp                                  |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices.hpp                               |  126 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_asc.hpp                           |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_desc.hpp                          |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sqrt.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/square.hpp                                     |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/squared_distance.hpp                           |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/stan_print.hpp                                 |  103 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_col.hpp                                    |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_row.hpp                                    |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/subtract.hpp                                   |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sum.hpp                                        |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tail.hpp                                       |  119 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tan.hpp                                        |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tanh.hpp                                       |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tcrossprod.hpp                                 |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tgamma.hpp                                     |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_1d.hpp                                |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_2d.hpp                                |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_matrix.hpp                                  |  404 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_row_vector.hpp                              |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_vector.hpp                                  |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trace.hpp                                      |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_inv_quad_form_ldlt.hpp               |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_quad_form.hpp                        |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_inv_quad_form_ldlt.hpp                   |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_quad_form.hpp                            |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/transpose.hpp                                  |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trigamma.hpp                                   |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/trunc.hpp                                      |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/typedefs.hpp                                   |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_constrain.hpp                      |   87 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_free.hpp                           |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of.hpp                                   |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of_rec.hpp                               |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/variance.hpp                                   |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_covar_estimator.hpp                    |   75 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_var_estimator.hpp                      |   75 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_gradient.hpp                   |  139 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian.hpp                    |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect.hpp                               |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_combine.hpp                       |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_concurrent.hpp                    |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_mpi.hpp                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_reduce.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/functor/mpi_parallel_call.hpp                      |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/append_return_type.hpp                        |  131 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/broadcast_array.hpp                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/get.hpp                                       |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/index_type.hpp                                |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant_struct.hpp                        |   19 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector.hpp                                 |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector_like.hpp                            |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/length.hpp                                    |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/length_mvt.hpp                                |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/operands_and_partials.hpp                     |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/scalar_type.hpp                               |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/seq_view.hpp                                  |  316 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/value_type.hpp                                |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/meta/vector_seq_view.hpp                           |  230 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_lpmf.hpp                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_log.hpp                           |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_log.hpp                     |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_lpmf.hpp                    |  129 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_rng.hpp                     |   63 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_lpmf.hpp                          |  147 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_rng.hpp                           |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_log.hpp                             |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp                            |  168 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_rng.hpp                             |  115 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_log.hpp                      |  299 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_lpdf.hpp                     |  654 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_log.hpp                           |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_lpdf.hpp                          |  196 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_rng.hpp                           |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp                     |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_lpdf.hpp                    |   98 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_rng.hpp                     |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_log.hpp                              |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_lpdf.hpp                             |  141 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_rng.hpp                              |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_log.hpp                               |  109 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_lpdf.hpp                              |  200 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_log.hpp                    |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_lpdf.hpp                   |  170 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_log.hpp                     |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_lpdf.hpp                    |  162 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_log.hpp                              |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_lpdf.hpp                             |  159 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_log.hpp                 |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_lpdf.hpp                |  255 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_rng.hpp                 |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_log.hpp                          |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_lpdf.hpp                         |  191 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_log.hpp                     |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_lpdf.hpp                    |  191 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_rng.hpp                          |  115 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_log.hpp                       |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_lpdf.hpp                      |  241 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_rng.hpp                       |  119 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_log.hpp                           |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_lpmf.hpp                          |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_rng.hpp                           |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_lpmf.hpp               |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_lpdf.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_log.hpp                      |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_lpmf.hpp                     |  278 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_rng.hpp                      |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_log.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_lpmf.hpp                       |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_rng.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp                      |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_log.hpp                               |  105 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_lpdf.hpp                              |  179 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_rng.hpp                               |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/mat/vectorize/apply_scalar_unary.hpp                   |  285 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal.hpp                                               |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_2F1_converges.hpp                       |  124 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_3F2_converges.hpp                       |  156 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_bounded.hpp                             |  155 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_size.hpp                     |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_sizes.hpp                    |  261 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_finite.hpp                              |   87 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater.hpp                             |  128 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater_or_equal.hpp                    |  130 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_less.hpp                                |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_less_or_equal.hpp                       |  128 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_nonnegative.hpp                         |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_not_nan.hpp                             |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive.hpp                            |   95 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_finite.hpp                     |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_size.hpp                       |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/check_size_match.hpp                          |  130 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error.hpp                              |  101 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error_vec.hpp                          |  126 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument.hpp                          |  116 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument_vec.hpp                      |  128 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/out_of_range.hpp                              |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/err/system_error.hpp                              |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/F32.hpp                                       |  148 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi.hpp                                       |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi_approx.hpp                                |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/abs.hpp                                       |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/acosh.hpp                                     |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/as_bool.hpp                                   |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/asinh.hpp                                     |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/atanh.hpp                                     |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_first_kind.hpp                         |   71 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_second_kind.hpp                        |   73 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/binary_log_loss.hpp                           |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/binomial_coefficient_log.hpp                  |  137 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/boost_policy.hpp                              |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/cbrt.hpp                                      |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/choose.hpp                                    |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/common_type.hpp                               |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/constants.hpp                                 |  309 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_constrain.hpp                            |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_free.hpp                                 |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/digamma.hpp                                   |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/distance.hpp                                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/divide.hpp                                    |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/erf.hpp                                       |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/erfc.hpp                                      |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/exp.hpp                                       |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/exp2.hpp                                      |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/expm1.hpp                                     |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/falling_factorial.hpp                         |  119 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/fdim.hpp                                      |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/fill.hpp                                      |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/fma.hpp                                       |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/fmax.hpp                                      |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/fmin.hpp                                      |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_p.hpp                                   |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_q.hpp                                   |   97 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_2F1.hpp                                  |  160 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_F32.hpp                                  |  216 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_inc_beta.hpp                             |   43 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_beta.hpp                         |   68 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_gamma.hpp                        |  182 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_lower_inc_gamma.hpp                  |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/hypot.hpp                                     |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/ibeta.hpp                                     |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_constrain.hpp                        |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_free.hpp                             |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/if_else.hpp                                   |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta.hpp                                  |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_dda.hpp                              |  156 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddb.hpp                              |  144 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddz.hpp                              |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/int_step.hpp                                  |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv.hpp                                       |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_Phi.hpp                                   |  133 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_cloglog.hpp                               |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_logit.hpp                                 |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_sqrt.hpp                                  |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_square.hpp                                |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/is_inf.hpp                                    |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/is_integer.hpp                                |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nan.hpp                                    |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nonpositive_integer.hpp                    |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/is_uninitialized.hpp                          |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_constrain.hpp                              |  110 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_free.hpp                                   |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lbeta.hpp                                     |  112 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/ldexp.hpp                                     |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lgamma.hpp                                    |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lmgamma.hpp                                   |  112 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log.hpp                                       |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m.hpp                                     |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_exp.hpp                                 |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_inv_logit.hpp                           |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p.hpp                                     |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p_exp.hpp                                 |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log2.hpp                                      |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_diff_exp.hpp                              |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_falling_factorial.hpp                     |  105 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit.hpp                             |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit_diff.hpp                        |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_mix.hpp                                   |   87 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_modified_bessel_first_kind.hpp            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_rising_factorial.hpp                      |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_sum_exp.hpp                               |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_and.hpp                               |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_eq.hpp                                |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gt.hpp                                |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gte.hpp                               |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lt.hpp                                |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lte.hpp                               |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_negation.hpp                          |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_neq.hpp                               |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_or.hpp                                |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/logit.hpp                                     |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_constrain.hpp                             |  250 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_free.hpp                                  |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_first_kind.hpp                |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_second_kind.hpp               |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/modulus.hpp                                   |   16 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/multiply_log.hpp                              |  102 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/owens_t.hpp                                   |  107 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_constrain.hpp                        |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_free.hpp                             |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/primitive_value.hpp                           |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_constrain.hpp                            |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_free.hpp                                 |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_elements.hpp                          |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar.hpp                            |  117 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar_type.hpp                       |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/rising_factorial.hpp                          |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/round.hpp                                     |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/sign.hpp                                      |   15 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/size_zero.hpp                                 |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/square.hpp                                    |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/squared_distance.hpp                          |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/step.hpp                                      |   54 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/tgamma.hpp                                    |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/trigamma.hpp                                  |  233 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/trunc.hpp                                     |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_constrain.hpp                              |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_free.hpp                                   |   68 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of.hpp                                  |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of_rec.hpp                              |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/StdVectorBuilder.hpp                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilder.hpp                            |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilderHelper.hpp                      |   93 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/ad_promotable.hpp                            |  251 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/broadcast_array.hpp                          |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/child_type.hpp                               |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_fvar.hpp                            |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_nonconstant_struct.hpp              |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_vector.hpp                          |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/error_index.hpp                              |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/get.hpp                                      |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/include_summand.hpp                          |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/index_type.hpp                               |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant.hpp                              |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp                       |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_fvar.hpp                                  |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_std_vector.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var.hpp                                   |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var_or_arithmetic.hpp                     |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector.hpp                                |   17 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector_like.hpp                           |   95 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/length.hpp                                   |    9 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/length_mvt.hpp                               |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/likely.hpp                                   |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/max_size.hpp                                 |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/max_size_mvt.hpp                             |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/operands_and_partials.hpp                    |  215 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_return_type.hpp                     |   31 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_type.hpp                            |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/return_type.hpp                              |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_seq_view.hpp                          |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type.hpp                              |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type_pre.hpp                          |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/size_of.hpp                                  |   35 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/meta/value_type.hpp                               |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_ccdf_log.hpp                       |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf.hpp                            |  128 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf_log.hpp                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lccdf.hpp                          |  120 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lcdf.hpp                           |  120 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_log.hpp                            |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_log.hpp                      |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_lpmf.hpp                     |  157 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_rng.hpp                      |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lpmf.hpp                           |  189 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_rng.hpp                            |   81 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_ccdf_log.hpp                   |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf.hpp                        |  253 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf_log.hpp                    |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lccdf.hpp                      |  234 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lcdf.hpp                       |  233 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_log.hpp                        |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lpmf.hpp                       |  293 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_rng.hpp                        |   81 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_ccdf_log.hpp                            |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf.hpp                                 |  239 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf_log.hpp                             |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lccdf.hpp                               |  217 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lcdf.hpp                                |  220 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_log.hpp                                 |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lpdf.hpp                                |  318 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_rng.hpp                                 |  134 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_ccdf_log.hpp                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf.hpp                             |  163 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lccdf.hpp                           |  157 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lcdf.hpp                            |  157 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_log.hpp                             |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_log.hpp                       |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_lpmf.hpp                      |  193 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lpmf.hpp                            |  187 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_rng.hpp                             |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_ccdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf.hpp                               |  192 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf_log.hpp                           |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lccdf.hpp                             |  143 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lcdf.hpp                              |  144 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_log.hpp                               |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lpdf.hpp                              |  205 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_rng.hpp                               |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_ccdf_log.hpp                      |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf.hpp                           |  197 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf_log.hpp                       |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lccdf.hpp                         |  181 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lcdf.hpp                          |  181 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_log.hpp                           |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lpdf.hpp                          |  219 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_rng.hpp                           |   81 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_ccdf_log.hpp              |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf.hpp                   |  167 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf_log.hpp               |   21 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lccdf.hpp                 |  157 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lcdf.hpp                  |  153 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_log.hpp                   |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lpdf.hpp                  |  202 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_rng.hpp                   |   97 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_ccdf_log.hpp                  |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf.hpp                       |  217 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf_log.hpp                   |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lccdf.hpp                     |  194 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lcdf.hpp                      |  201 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_log.hpp                       |   51 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lpdf.hpp                      |  197 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_rng.hpp                       |   74 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_ccdf_log.hpp                     |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf.hpp                          |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf_log.hpp                      |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lccdf.hpp                        |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lcdf.hpp                         |   85 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_log.hpp                          |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lpdf.hpp                         |  163 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_rng.hpp                          |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_ccdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf.hpp                              |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lccdf.hpp                            |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lcdf.hpp                             |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_log.hpp                              |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lpdf.hpp                             |  203 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_rng.hpp                              |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_ccdf_log.hpp                           |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf.hpp                                |  224 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf_log.hpp                            |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lccdf.hpp                              |  175 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lcdf.hpp                               |  172 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_log.hpp                                |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lpdf.hpp                               |  247 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_rng.hpp                                |   91 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_ccdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf.hpp                               |  156 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf_log.hpp                           |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lccdf.hpp                             |  136 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lcdf.hpp                              |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_log.hpp                               |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lpdf.hpp                              |  182 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_rng.hpp                               |   83 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_log.hpp                       |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_lpmf.hpp                      |  108 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_rng.hpp                       |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_ccdf_log.hpp                  |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf.hpp                       |  205 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf_log.hpp                   |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lccdf.hpp                     |  190 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lcdf.hpp                      |  189 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_log.hpp                       |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lpdf.hpp                      |  208 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_rng.hpp                       |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_ccdf_log.hpp                       |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf.hpp                            |  236 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf_log.hpp                        |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lccdf.hpp                          |  183 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lcdf.hpp                           |  180 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_log.hpp                            |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lpdf.hpp                           |  242 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_rng.hpp                            |   81 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_ccdf_log.hpp                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf.hpp                             |  163 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lccdf.hpp                           |  135 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lcdf.hpp                            |  136 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_log.hpp                             |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lpdf.hpp                            |  205 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_rng.hpp                             |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_ccdf_log.hpp                       |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf.hpp                            |  146 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf_log.hpp                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lccdf.hpp                          |  122 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lcdf.hpp                           |  122 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_log.hpp                            |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lpdf.hpp                           |  229 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_rng.hpp                            |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_ccdf_log.hpp                  |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf.hpp                       |  193 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf_log.hpp                   |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lccdf.hpp                     |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lcdf.hpp                      |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log.hpp                       |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_log.hpp                   |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_lpmf.hpp                  |  192 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_rng.hpp                   |  129 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lpmf.hpp                      |  196 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_rng.hpp                       |  128 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_ccdf_log.hpp                    |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf.hpp                         |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf_log.hpp                     |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lccdf.hpp                       |  186 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lcdf.hpp                        |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_log.hpp                         |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lpmf.hpp                        |  257 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_rng.hpp                         |  117 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_ccdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf.hpp                               |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf_log.hpp                           |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lccdf.hpp                             |  140 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lcdf.hpp                              |  138 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_log.hpp                               |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lpdf.hpp                              |  197 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_rng.hpp                               |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_log.hpp                    |   57 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_lpdf.hpp                   |  278 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_ccdf_log.hpp                          |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf.hpp                               |  162 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf_log.hpp                           |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lccdf.hpp                             |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lcdf.hpp                              |  134 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_log.hpp                               |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lpdf.hpp                              |  192 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_rng.hpp                               |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_ccdf_log.hpp                   |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf.hpp                        |  202 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf_log.hpp                    |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lccdf.hpp                      |  171 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lcdf.hpp                       |  171 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_log.hpp                        |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lpdf.hpp                       |  220 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_rng.hpp                        |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_ccdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf.hpp                              |  120 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lccdf.hpp                            |  107 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lcdf.hpp                             |  108 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log.hpp                              |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_log.hpp                          |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_lpmf.hpp                         |  139 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_rng.hpp                          |   72 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lpmf.hpp                             |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_rng.hpp                              |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_ccdf_log.hpp                        |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf.hpp                             |  122 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lccdf.hpp                           |   99 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lcdf.hpp                            |  108 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_log.hpp                             |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lpdf.hpp                            |  139 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_rng.hpp                             |   65 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_ccdf_log.hpp           |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf.hpp                |  238 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf_log.hpp            |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lccdf.hpp              |  186 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lcdf.hpp               |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_log.hpp                |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lpdf.hpp               |  270 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_rng.hpp                |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_ccdf_log.hpp                     |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf.hpp                          |  183 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf_log.hpp                      |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lccdf.hpp                        |  152 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lcdf.hpp                         |  152 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_log.hpp                          |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lpdf.hpp                         |  211 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_rng.hpp                          |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_log.hpp                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_lpdf.hpp                          |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_ccdf_log.hpp                       |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf.hpp                            |  311 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf_log.hpp                        |   23 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lccdf.hpp                          |  294 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lcdf.hpp                           |  294 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_log.hpp                            |   95 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lpdf.hpp                           |  358 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_rng.hpp                            |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_ccdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf.hpp                              |  133 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lccdf.hpp                            |  116 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lcdf.hpp                             |  116 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_log.hpp                              |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lpdf.hpp                             |  189 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_rng.hpp                              |   67 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_log.hpp                            |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_lpdf.hpp                           |  185 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_rng.hpp                            |  137 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_ccdf_log.hpp                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf.hpp                              |  151 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf_log.hpp                          |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lccdf.hpp                            |  118 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lcdf.hpp                             |  127 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_log.hpp                              |   40 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lpdf.hpp                             |  238 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_rng.hpp                              |   91 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_log.hpp                               |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_lpdf.hpp                              |  304 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr.hpp                                                 |    2 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr/fun/log_sum_exp.hpp                                 |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr/fun/sum.hpp                                         |   97 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr/fun/to_var.hpp                                      |   56 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp                      | 1131 +--
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/arr/functor/integrate_1d.hpp                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/autodiffstackstorage.hpp                           |  123 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/chainable_alloc.hpp                                |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/chainablestack.hpp                                 |   12 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/ddv_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/dv_vari.hpp                                        |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/dvd_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/dvv_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/empty_nested.hpp                                   |   18 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/gevv_vvv_vari.hpp                                  |   89 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/grad.hpp                                           |   68 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/matrix_vari.hpp                                    |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/nested_size.hpp                                    |   14 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp                              |  207 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_divide_equal.hpp                          |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp                              |  221 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_equal.hpp                                 |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_greater_than.hpp                          |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_greater_than_or_equal.hpp                 |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_less_than.hpp                             |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_less_than_or_equal.hpp                    |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_logical_and.hpp                           |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_logical_or.hpp                            |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_minus_equal.hpp                           |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_multiplication.hpp                        |  205 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_multiply_equal.hpp                        |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_not_equal.hpp                             |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_plus_equal.hpp                            |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp                           |  228 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_unary_decrement.hpp                       |   98 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_unary_increment.hpp                       |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp                        |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_unary_not.hpp                             |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/operator_unary_plus.hpp                            |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/precomp_v_vari.hpp                                 |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/precomp_vv_vari.hpp                                |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/precomp_vvv_vari.hpp                               |   42 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/precomputed_gradients.hpp                          |  168 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/print_stack.hpp                                    |   45 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/recover_memory.hpp                                 |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/recover_memory_nested.hpp                          |   69 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints.hpp                          |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp                   |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/start_nested.hpp                                   |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/std_isinf.hpp                                      |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/std_isnan.hpp                                      |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/std_numeric_limits.hpp                             |  116 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/stored_gradient_vari.hpp                           |   87 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/v_vari.hpp                                         |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/var.hpp                                            |  855 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vari.hpp                                           |  276 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vd_vari.hpp                                        |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vdd_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vdv_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vector_vari.hpp                                    |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vv_vari.hpp                                        |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vvd_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/core/vvv_vari.hpp                                       |   29 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat.hpp                                                 |    6 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp                             |  661 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_alloc.hpp                                  |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_factor.hpp                                 |  254 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp                          |  501 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_product.hpp                         |   33 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_self.hpp                            |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/cov_exp_quad.hpp                                |  512 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/crossprod.hpp                                   |   25 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/determinant.hpp                                 |  108 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/divide.hpp                                      |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_product.hpp                                 |  453 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_self.hpp                                    |  139 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_periodic_cov.hpp                             |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/grad.hpp                                        |   47 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/initialize_variable.hpp                         |   59 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant.hpp                             |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_ldlt.hpp                        |   79 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_spd.hpp                         |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_softmax.hpp                                 |  189 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_sum_exp.hpp                                 |   83 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/matrix_exp_multiply.hpp                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left.hpp                                |  644 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_ldlt.hpp                           |  588 --
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_spd.hpp                            |  592 --
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_tri.hpp                            |  719 +-
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply.hpp                                    | 1213 ++--
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply_lower_tri_self_transpose.hpp           |   73 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form.hpp                                   |  240 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form_sym.hpp                               |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/rows_dot_product.hpp                            |   33 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/scale_matrix_exp_multiply.hpp                   |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/sd.hpp                                          |  142 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/softmax.hpp                                     |  151 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/squared_distance.hpp                            |  224 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/stan_print.hpp                                  |   10 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/sum.hpp                                         |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/tcrossprod.hpp                                  |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/to_var.hpp                                      |  160 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_inv_quad_form_ldlt.hpp                |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_quad_form.hpp                         |  213 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_inv_quad_form_ldlt.hpp                    |  321 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_quad_form.hpp                             |  163 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/typedefs.hpp                                    |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/unit_vector_constrain.hpp                       |  183 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/fun/variance.hpp                                    |  121 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver.hpp                          |  507 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_system.hpp                          |  290 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_integrator.hpp                       |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_ode_data.hpp                         |  375 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_utils.hpp                            |   91 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/gradient.hpp                                |  105 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp                     |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_bdf.hpp                       |  222 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/jacobian.hpp                                |   62 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/functor/map_rect_reduce.hpp                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/meta/operands_and_partials.hpp                      |  254 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/mat/vectorize/apply_scalar_unary.hpp                    |   52 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal.hpp                                                |    1 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi.hpp                                        |  119 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi_approx.hpp                                 |   94 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/abs.hpp                                        |   60 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/acos.hpp                                       |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp                                      |  110 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/as_bool.hpp                                    |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/asin.hpp                                       |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp                                      |  100 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/atan.hpp                                       |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/atan2.hpp                                      |  222 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp                                      |  110 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_first_kind.hpp                          |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_second_kind.hpp                         |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/binary_log_loss.hpp                            |  124 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_fpclassify.hpp                           |   38 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isfinite.hpp                             |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isinf.hpp                                |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isnan.hpp                                |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isnormal.hpp                             |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/calculate_chain.hpp                            |   12 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp                                       |   83 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/ceil.hpp                                       |   98 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/cos.hpp                                        |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/cosh.hpp                                       |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/digamma.hpp                                    |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp                                        |  103 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp                                       |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/exp.hpp                                        |   70 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/exp2.hpp                                       |   78 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp                                      |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fabs.hpp                                       |  102 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/falling_factorial.hpp                          |   77 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fdim.hpp                                       |  238 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/floor.hpp                                      |   98 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp                                        |  423 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fmax.hpp                                       |  228 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fmin.hpp                                       |  219 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fmod.hpp                                       |  245 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_p.hpp                                    |  206 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_q.hpp                                    |  106 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/grad_inc_beta.hpp                              |   58 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/hypot.hpp                                      |  199 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/ibeta.hpp                                      |  421 -
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/if_else.hpp                                    |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inc_beta.hpp                                   |   61 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv.hpp                                        |   64 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp                                    |   55 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_cloglog.hpp                                |   61 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_logit.hpp                                  |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_sqrt.hpp                                   |   66 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_square.hpp                                 |   66 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/is_inf.hpp                                     |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/is_nan.hpp                                     |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/is_uninitialized.hpp                           |   34 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/lgamma.hpp                                     |   50 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/lmgamma.hpp                                    |   39 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log.hpp                                        |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log10.hpp                                      |   88 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m.hpp                                      |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp                                  |   49 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_inv_logit.hpp                            |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p.hpp                                      |   48 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p_exp.hpp                                  |   37 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log2.hpp                                       |   86 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp                               |  123 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_falling_factorial.hpp                      |  119 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit.hpp                              |   28 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit_diff.hpp                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_mix.hpp                                    |  235 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_rising_factorial.hpp                       |   92 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_sum_exp.hpp                                |  103 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/logit.hpp                                      |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_first_kind.hpp                 |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_second_kind.hpp                |   41 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/multiply_log.hpp                               |  183 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp                                    |  165 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/pow.hpp                                        |  264 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/primitive_value.hpp                            |   24 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/rising_factorial.hpp                           |   73 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/round.hpp                                      |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/sin.hpp                                        |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/sinh.hpp                                       |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/sqrt.hpp                                       |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/square.hpp                                     |   76 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/squared_distance.hpp                           |   99 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/step.hpp                                       |   44 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/tan.hpp                                        |   80 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/tanh.hpp                                       |   84 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/tgamma.hpp                                     |  104 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/to_var.hpp                                     |   46 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/trigamma.hpp                                   |   26 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp                                      |   90 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of.hpp                                   |   36 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of_rec.hpp                               |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/meta/ad_promotable.hpp                             |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/meta/is_var.hpp                                    |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/meta/operands_and_partials.hpp                     |  205 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/rev/scal/meta/partials_type.hpp                             |   11 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan/math/version.hpp                                                 |   22 
 StanHeaders-2.18.0/StanHeaders/inst/include/stan_sundials_printf_override.hpp                                     |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_band.h                                              |   32 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_config.h                                            |    8 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_config.in                                           |   27 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_dense.h                                             |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_direct.h                                            |   53 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_fconfig.in                                          |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_fnvector.h                                          |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_iterative.h                                         |   30 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_klu_impl.h                                          |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_lapack.h                                            |   82 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_linearsolver.h                                      |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_math.h                                              |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_matrix.h                                            |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_mpi_types.h                                         |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_nvector.h                                           |   20 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_sparse.h                                            |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_spbcgs.h                                            |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_spgmr.h                                             |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_sptfqmr.h                                           |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_superlumt_impl.h                                    |    4 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_types.h                                             |   95 
 StanHeaders-2.18.0/StanHeaders/inst/include/sundials/sundials_version.h                                           |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sunlinsol                                                             |only
 StanHeaders-2.18.0/StanHeaders/inst/include/sunmatrix                                                             |only
 StanHeaders-2.18.0/StanHeaders/src/Makevars                                                                       |   19 
 StanHeaders-2.18.0/StanHeaders/src/Makevars.win                                                                   |   20 
 StanHeaders-2.18.0/StanHeaders/src/cvodes/CMakeLists.txt                                                          |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/LICENSE                                                                 |   17 
 StanHeaders-2.18.0/StanHeaders/src/cvodes/README                                                                  |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodea.c                                                                |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodea_io.c                                                             |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes.c                                                                |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_bandpre.c                                                        |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_bandpre_impl.h                                                   |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_bbdpre.c                                                         |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_bbdpre_impl.h                                                    |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_diag.c                                                           |only
 StanHeaders-2.18.0/StanHeaders/src/cvodes/cvodes_diag_impl.h                                                      |only
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Package SharpeR updated to version 1.2.0 with previous version 1.1.0 dated 2016-03-14

Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of assets, funds, and trading strategies, based on the Sharpe ratio and overfit of the same. Provides density, distribution, quantile and random generation of the Sharpe ratio distribution based on normal returns, as well as the optimal Sharpe ratio over multiple assets. Computes confidence intervals on the Sharpe and provides a test of equality of Sharpe ratios based on the Delta method.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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Package rmapzen updated to version 0.4.1 with previous version 0.4.0 dated 2018-08-28

Title: Client for 'Mapzen' and Related Map APIs
Description: Provides an interface to 'Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but 'rmapzen' can be set up to work with any provider who implements the Mapzen API.
Author: Tarak Shah [aut, cre], Daniel Possenriede [ctb]
Maintainer: Tarak Shah <tarak.shah@gmail.com>

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Package ratelimitr updated to version 0.4.1 with previous version 0.4.0 dated 2018-08-28

Title: Rate Limiting for R
Description: Allows to limit the rate at which one or more functions can be called.
Author: Tarak Shah
Maintainer: Tarak Shah <tarak.shah@gmail.com>

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Package lvm4net updated to version 0.2.1 with previous version 0.2 dated 2015-04-10

Title: Latent Variable Models for Networks
Description: Latent variable models for network data using fast inferential procedures.
Author: Isabella Gollini [aut, cre]
Maintainer: Isabella Gollini <igollini.stats@gmail.com>

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Package colorfindr updated to version 0.1.3 with previous version 0.1.0 dated 2018-09-30

Title: Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format Images
Description: Extracts colors from various image types, returns customized reports and plots treemaps and 3D scatterplots of image compositions. Selected colors and color ranges can be excluded from the analysis.
Author: David Zumbach [aut, cre]
Maintainer: David Zumbach <david.zumbach@gfzb.ch>

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Package ggwordcloud updated to version 0.2.0 with previous version 0.1.0 dated 2018-09-30

Title: A Wordcloud Geom for 'ggplot2'
Description: Provides a wordcloud text geom for 'ggplot2'. Texts are placed so that they do not overlap as in 'ggrepel'. The algorithm used is a variation around the one of 'wordcloud2.js'.
Author: Erwan Le Pennec [aut, cre], Kamil Slowikowski [aut]
Maintainer: Erwan Le Pennec <lepennec@gmail.com>

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Package NetLogoR updated to version 0.3.4 with previous version 0.3.3 dated 2018-06-07

Title: Build and Run Spatially Explicit Agent-Based Models
Description: Build and run spatially explicit agent-based models using only the R platform. 'NetLogoR' follows the same framework as the 'NetLogo' software (Wilensky, 1999 <http://ccl.northwestern.edu/netlogo/>) and is a translation in R of the structure and functions of 'NetLogo'. 'NetLogoR' provides new R classes to define model agents and functions to implement spatially explicit agent-based models in the R environment. This package allows benefiting of the fast and easy coding phase from the highly developed 'NetLogo' framework, coupled with the versatility, power and massive resources of the R software. Examples of three models (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>, Butterfly (Railsback and Grimm, 2012) and Wolf-Sheep-Predation <http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>) written using 'NetLogoR' are available. The 'NetLogo' code of the original version of these models is provided alongside. A programming guide inspired from the 'NetLogo' Programming Guide (<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>) equivalences are also available. NOTE: To increment 'time', these functions can use a for loop or can be integrated with a discrete event simulator, such as 'SpaDES' (<https://cran.r-project.org/package=SpaDES>). The suggested package 'fastshp' can be installed with 'install.packages("fastshp", repos = "https://rforge.net", type = "source")'.
Author: Sarah Bauduin [aut, cre] (<https://orcid.org/0000-0002-3252-5894>), Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>), Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>), Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Sarah Bauduin <sarahbauduin@hotmail.fr>

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Package diffeR updated to version 0.0-5 with previous version 0.0-4 dated 2015-12-29

Title: Metrics of Difference for Comparing Pairs of Maps or Pairs of Variables
Description: Metrics of difference for comparing pairs of variables or pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr. <rpontius@clarku.edu>, Ali Santacruz <asantacruzdelgado@clarku.edu>
Maintainer: Ali Santacruz <amsantac@unal.edu.co>

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Package antiword updated to version 1.2 with previous version 1.1 dated 2017-04-29

Title: Extract Text from Microsoft Word Documents
Description: Wraps the 'AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old 'doc' format, not the new xml based 'docx' format. Use the 'xml2' package to read the latter.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Adri van Os [cph] (Author 'antiword' utility)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package erhcv updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-12

Title: Equi-Rank Hierarchical Clustering Validation
Description: Assesses the statistical significance of clusters for a given dataset through bootstrapping and hypothesis testing of a given matrix of empirical Spearman's rho, based on the technique of S. Gaiser et al. (2010) <doi:10.1016/j.jmva.2010.07.008>.
Author: Simon-Pierre Gadoury <spgadou@me.com>
Maintainer: Simon-Pierre Gadoury <spgadou@me.com>

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Package ssh updated to version 0.3 with previous version 0.2 dated 2018-06-04

Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package summarytools updated to version 0.8.8 with previous version 0.8.7 dated 2018-07-23

Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>

Diff between summarytools versions 0.8.7 dated 2018-07-23 and 0.8.8 dated 2018-10-07

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Package ftsa updated to version 5.1 with previous version 5.0 dated 2018-09-15

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>

Diff between ftsa versions 5.0 dated 2018-09-15 and 5.1 dated 2018-10-07

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Package pollen updated to version 0.71.0 with previous version 0.70.0 dated 2018-02-25

Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), and calculation of growing degree days.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

Diff between pollen versions 0.70.0 dated 2018-02-25 and 0.71.0 dated 2018-10-07

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Package simukde updated to version 1.1.0 with previous version 1.0.0 dated 2018-07-05

Title: Simulation with Kernel Density Estimation
Description: Generates random values from a univariate and multivariate continuous distribution by using kernel density estimation based on a sample. Duong (2017) <doi:10.18637/jss.v021.i07>, Christian P. Robert and George Casella (2010 ISBN:978-1-4419-1575-7) <doi:10.1007/978-1-4419-1576-4>.
Author: MAKHGAL Ganbold [aut, cre], BAYARBAATAR Amgalan [aut]
Maintainer: MAKHGAL Ganbold <makhgal@seas.num.edu.mn>

Diff between simukde versions 1.0.0 dated 2018-07-05 and 1.1.0 dated 2018-10-07

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Package listviewer updated to version 2.1.0 with previous version 2.0.0 dated 2018-03-25

Title: 'htmlwidget' for Interactive Views of R Lists
Description: R lists, especially nested lists, can be very difficult to visualize or represent. Sometimes 'str()' is not enough, so this suite of htmlwidgets is designed to help see, understand, and maybe even modify your R lists. The function 'reactjson()' requires a package 'reactR' that can be installed from CRAN or <https://github.com/timelyportfolio/reactR>.
Author: Jos de Jong [aut, cph] (jsoneditor.js library in htmlwidgets/jsoneditor, http://github.com/josdejong/jsoneditor/), Mac Gainer [aut, cph] (react-json-view library in htmlwidgets/react-json, https://github.com/mac-s-g/react-json-view), Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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Package ijtiff updated to version 1.4.2 with previous version 1.4.1 dated 2018-09-24

Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Kent Johnson [aut], Simon Urbanek [ctb], Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>), Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>), Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between ijtiff versions 1.4.1 dated 2018-09-24 and 1.4.2 dated 2018-10-07

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Package DRIP updated to version 1.4 with previous version 1.3 dated 2018-06-01

Title: Discontinuous Regression and Image Processing
Description: This is a collection of functions for discontinuous regression analysis and image processing (DRIP). A recent addition is the blind image deblurring via jump-preserving extrapolation.
Author: Yicheng Kang <kangx276@umn.edu>
Maintainer: Yicheng Kang <kangx276@umn.edu>

Diff between DRIP versions 1.3 dated 2018-06-01 and 1.4 dated 2018-10-07

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Sat, 06 Oct 2018

Package bazar updated to version 1.0.10 with previous version 1.0.9 dated 2018-07-31

Title: Miscellaneous Basic Functions
Description: A collection of miscellaneous functions for copying objects to the clipboard ('Copy'); manipulating strings ('concat', 'mgsub', 'trim', 'verlan'); loading or showing packages ('library_with_dep', 'require_with_dep', 'sessionPackages'); creating or testing for named lists ('nlist', 'as.nlist', 'is.nlist'), formulas ('is.formula'), empty objects ('as.empty', 'is.empty'), whole numbers ('as.wholenumber', 'is.wholenumber'); testing for equality ('almost.equal', 'almost.zero') and computing uniqueness ('almost.unique'); getting modified versions of usual functions ('rle2', 'sumNA'); making a pause or a stop ('pause', 'stopif'); converting into a function ('as.fun'); providing a C like ternary operator ('condition %?% true %:% false'); finding packages and functions ('get_all_pkgs', 'get_all_funs'); and others ('erase', '%nin%', 'unwhich', 'top', 'bot', 'normalize').
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between bazar versions 1.0.9 dated 2018-07-31 and 1.0.10 dated 2018-10-06

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Package SSDforR updated to version 1.4.21 with previous version 1.4.20 dated 2018-09-25

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

Diff between SSDforR versions 1.4.20 dated 2018-09-25 and 1.4.21 dated 2018-10-06

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Package installr updated to version 0.21.0 with previous version 0.20.0 dated 2018-05-02

Title: Using R to Install Stuff (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Barry Rowlingson [ctb], Boris Hejblum [ctb], Dason [ctb], Felix Schonbrodt [ctb], G. Grothendieck [ctb], GERGELY DAROCZI [ctb], Heuristic Andrew [ctb], James [ctb] (http://stackoverflow.com/users/269476/james), Thomas Leeper [ctb] (http://thomasleeper.com/), VitoshKa [ctb], Yihui Xie [ctb] (http://yihui.name), Michael Friendly [ctb] (http://datavis.ca/), Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/), Dieter Menne [ctb], Tyler Hunt [ctb] (https://github.com/JackStat), Takekatsu Hiramura [ctb] (https://github.com/hiratake55), Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool), Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey), Tom Allard [ctb], ChingChuan Chen [ctb], Jonathan Hill [ctb], Chan-Yub Park [ctb] (https://github.com/mrchypark)
Maintainer: Tal Galili <tal.galili@gmail.com>

Diff between installr versions 0.20.0 dated 2018-05-02 and 0.21.0 dated 2018-10-06

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Package coalitions updated to version 0.6.5 with previous version 0.6.4 dated 2018-08-27

Title: Coalition Probabilities in Multi-Party Democracies
Description: An implementation of a MCMC method to calculate probabilities for a coalition majority based on survey results, see Bender and Bauer (2018) <doi:10.21105/joss.00606>.
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>), Alexander Bauer [aut] (<https://orcid.org/0000-0003-3495-5131>)
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>

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Package sdPrior updated to version 1.0-0 with previous version 0.6 dated 2018-07-07

Title: Scale-Dependent Hyperpriors in Structured Additive Distributional Regression
Description: Utility functions for scale-dependent and alternative hyperpriors. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. Hyperpriors for all effects can be elicitated within the package. Including complex tensor product interaction terms and variable selection priors. The basic model is explained in in Klein and Kneib (2016) <doi:10.1214/15-BA983>.
Author: Nadja Klein [aut, cre]
Maintainer: Nadja Klein <nadja.klein@hu-berlin.de>

Diff between sdPrior versions 0.6 dated 2018-07-07 and 1.0-0 dated 2018-10-06

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Package piggyback updated to version 0.0.8 with previous version 0.0.7 dated 2018-09-30

Title: Managing Larger Data on a GitHub Repository
Description: Because larger (> 50 MB) data files cannot easily be committed to git, a different approach is required to manage data associated with an analysis in a GitHub repository. This package provides a simple work-around by allowing larger (up to 2 GB) data files to piggyback on a repository as assets attached to individual GitHub releases. These files are not handled by git in any way, but instead are uploaded, downloaded, or edited directly by calls through the GitHub API. These data files can be versioned manually by creating different releases. This approach works equally well with public or private repositories. Data can be uploaded and downloaded programmatically from scripts. No authentication is required to download data from public repositories.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Mark Padgham [ctb] (<https://orcid.org/0000-0003-2172-5265>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package Opt5PL updated to version 0.1.1 with previous version 0.1.0 dated 2018-09-30

Title: Optimal Designs for the 5-Parameter Logistic Model
Description: Obtain and evaluate various optimal designs for the 3, 4, and 5-parameter logistic models. The optimal designs are obtained based on the numerical algorithm in Hyun, Wong, Yang (2018) <doi:10.18637/jss.v083.i05>.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Seung Won Hyun <yellowatom09@gmail.com>

Diff between Opt5PL versions 0.1.0 dated 2018-09-30 and 0.1.1 dated 2018-10-06

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Package mcbiopi updated to version 1.1.6 with previous version 1.1.5 dated 2018-09-15

Title: Matrix Computation Based Identification of Prime Implicants
Description: Computes the prime implicants or a minimal disjunctive normal form for a logic expression presented by a truth table or a logic tree. Has been particularly developed for logic expressions resulting from a logic regression analysis, i.e. logic expressions typically consisting of up to 16 literals, where the prime implicants are typically composed of a maximum of 4 or 5 literals.
Author: Holger Schwender
Maintainer: Holger Schwender <holger.schw@gmx.de>

Diff between mcbiopi versions 1.1.5 dated 2018-09-15 and 1.1.6 dated 2018-10-06

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Package umx updated to version 2.8.5 with previous version 2.8.0 dated 2018-06-19

Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models. See '?umx' for help, and file.show(system.file("NEWS", package="umx")) for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>

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More information about umx at CRAN
Permanent link

Package eixport updated to version 0.3.6 with previous version 0.3.0 dated 2018-03-01

Title: Export Emissions to Atmospheric Models
Description: Emissions are the mass of pollutants released into the atmosphere. Air quality models need emissions data, with spatial and temporal distribution, to represent air pollutant concentrations. This package, eixport, creates inputs for the air quality models 'WRF-Chem' Grell et al (2005) <doi:10.1016/j.atmosenv.2005.04.027>, 'BRAMS-SPM' Freitas et al (2005) <doi:10.1016/j.atmosenv.2005.07.017> and 'RLINE' Snyder et al (2013) <doi:10.1016/j.atmosenv.2013.05.074>. See the eixport website (<https://atmoschem.github.io/eixport/>) for more information, documentations and examples. More details in Ibarra-Espinosa et al (2018) <doi.org/10.21105/joss.00607>.
Author: Sergio Ibarra-Espinosa [aut, cre] (<https://orcid.org/0000-0002-3162-1905>), Daniel Schuch [aut] (<https://orcid.org/0000-0001-5977-4519>), Edmilson Freitas [ctb] (<https://orcid.org/0000-0001-8783-2747>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>

Diff between eixport versions 0.3.0 dated 2018-03-01 and 0.3.6 dated 2018-10-06

 DESCRIPTION                              |   29 ++--
 MD5                                      |   83 ++++++++----
 NAMESPACE                                |    6 
 NEWS.md                                  |   36 +++++
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 R/to_wrf.R                               |   28 ++--
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Package pdSpecEst updated to version 1.2.3 with previous version 1.2.2 dated 2018-07-10

Title: An Analysis Toolbox for Hermitian Positive Definite Matrices
Description: An implementation of data analysis tools for samples of symmetric or Hermitian positive definite matrices, such as collections of covariance matrices or spectral density matrices. The tools in this package can be used to perform: (i) intrinsic wavelet transforms for curves (1D) or surfaces (2D) of Hermitian positive definite matrices with applications to dimension reduction, denoising and clustering in the space of Hermitian positive definite matrices; and (ii) exploratory data analysis and inference for samples of positive definite matrices by means of intrinsic data depth functions and rank-based hypothesis tests in the space of Hermitian positive definite matrices.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

Diff between pdSpecEst versions 1.2.2 dated 2018-07-10 and 1.2.3 dated 2018-10-06

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Package RcppCCTZ updated to version 0.2.4 with previous version 0.2.3 dated 2017-06-20

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppCCTZ versions 0.2.3 dated 2017-06-20 and 0.2.4 dated 2018-10-06

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 48 files changed, 927 insertions(+), 379 deletions(-)

More information about RcppCCTZ at CRAN
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