Tue, 23 Oct 2018

Package tsmp updated to version 0.3.2 with previous version 0.3.1 dated 2018-09-10

Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept that was created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] (<https://orcid.org/0000-0002-5301-8672>), Michael Yeh [res, ccp, ctb] (<https://orcid.org/0000-0002-9807-2963>), Diego Silva [res, ccp, ctb] (<https://orcid.org/0000-0002-5184-9413>), Yan Zhu [res, ccp, ctb] (<https://orcid.org/0000-0002-5952-2108>), Hoang Dau [res, ccp, ctb] (<https://orcid.org/0000-0003-2439-5185>)
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>

Diff between tsmp versions 0.3.1 dated 2018-09-10 and 0.3.2 dated 2018-10-23

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Package projpred updated to version 1.1.0 with previous version 1.0.0 dated 2018-09-18

Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models (see, Piironen, Paasiniemi and Vehtari, 2018, <arXiv:1810.02406>). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the package vignette for more information and examples.
Author: Juho Piironen [cre, aut], Markus Paasiniemi [aut], Aki Vehtari [aut], Jonah Gabry [ctb], Paul-Christian Bürkner [ctb]
Maintainer: Juho Piironen <juho.piironen@aalto.fi>

Diff between projpred versions 1.0.0 dated 2018-09-18 and 1.1.0 dated 2018-10-23

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Package kyotil updated to version 2018.10-17 with previous version 2018.7-16 dated 2018-08-07

Title: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre], Krisztian Sebestyen [aut], Jason Becker [ctb], Bendix Carstensen [ctb], Daryl Morris [ctb], Josh Pasek [ctb], Dennis Chao [ctb], Andri Signorell [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>

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Package geodetector updated to version 1.0-3 with previous version 1.0-2 dated 2018-08-18

Title: Stratified Heterogeneity Measure, Dominant Driving Force Detection, Interaction Relationship Investigation
Description: Spatial stratified heterogeneity (SSH), referring to the within strata are more similar than the between strata, a model with global parameters would be confounded if input data is SSH. Note that the "spatial" here can be either geospatial or the space in mathematical meaning. Geographical detector is a novel tool to investigate SSH: (1) measure and find SSH of a variable Y; (2) test the power of determinant X of a dependent variable Y according to the consistency between their spatial distributions; and (3) investigate the interaction between two explanatory variables X1 and X2 to a dependent variable Y (Wang et al 2014 <doi:10.1080/13658810802443457>, Wang, Zhang, and Fu 2016 <doi:10.1016/j.ecolind.2016.02.052>).
Author: Chengdong Xu [aut, cre], Jinfeng Wang [aut], Yue Hou [ctb], Qian Yin [ctb]
Maintainer: Chengdong Xu <xucd@Lreis.ac.cn>

Diff between geodetector versions 1.0-2 dated 2018-08-18 and 1.0-3 dated 2018-10-23

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Package xaringan updated to version 0.8 with previous version 0.7 dated 2018-07-10

Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Claus Thorn Ekstrøm [ctb], Daniel Anderson [ctb], Dawei Lang [ctb], Garrick Aden-Buie [ctb], John Little [ctb], Joseph Casillas [ctb], Michael Wayne Kearney [ctb], Nan-Hung Hsieh [ctb], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/default.css), Patrick Schratz [ctb], Sean Lopp [ctb], Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>), Emi Tanaka [ctb], Yongfu Liao [ctb], Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between xaringan versions 0.7 dated 2018-07-10 and 0.8 dated 2018-10-23

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Package isdparser updated to version 0.3.0 with previous version 0.2.0 dated 2017-01-18

Title: Parse 'NOAA' Integrated Surface Data Files
Description: Tools for parsing 'NOAA' Integrated Surface Data ('ISD') files, described at <https://www.ncdc.noaa.gov/isd>. Data includes for example, wind speed and direction, temperature, cloud data, sea level pressure, and more. Includes data from approximately 35,000 stations worldwide, though best coverage is in North America/Europe/Australia. Data is stored as variable length ASCII character strings, with most fields optional. Included are tools for parsing entire files, or individual lines of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between isdparser versions 0.2.0 dated 2017-01-18 and 0.3.0 dated 2018-10-23

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Package reshape updated to version 0.8.8 with previous version 0.8.7 dated 2017-08-06

Title: Flexibly Reshape Data
Description: Flexibly restructure and aggregate data using just two functions: melt and cast.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between reshape versions 0.8.7 dated 2017-08-06 and 0.8.8 dated 2018-10-23

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

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Daijiang Li [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package tinytex updated to version 0.9 with previous version 0.8 dated 2018-08-30

Title: Helper Functions to Install and Maintain 'TeX Live', and Compile 'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), RStudio, Inc. [cph], Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package servr updated to version 0.11 with previous version 0.10 dated 2018-05-30

Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Carson Sievert [ctb], Jesse Anderson [ctb], Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package RMixpanel updated to version 0.7-1 with previous version 0.7-0 dated 2018-10-19

Title: API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner [aut, cre, cph], ProSiebenSat.1 Digital GmbH [cph], BCG Digital Ventures GmbH [cph]
Maintainer: Meinhard Ploner <meinhard.ploner@gmail.com>

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Package DEploid updated to version 0.5.2 with previous version 0.5.1 dated 2018-10-21

Title: Deconvolute Mixed Genomes with Unknown Proportions
Description: Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.
Author: Joe Zhu [aut, cre, cph], Jacob Almagro-Garcia [aut, cph], Gil McVean [aut, cph], University of Oxford [cph], Yinghan Liu [ctb], CodeCogs Zyba Ltd [com, cph], Deepak Bandyopadhyay [com, cph], Lutz Kettner [com, cph]
Maintainer: Joe Zhu <joe.zhu@bdi.ox.ac.uk>

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Package blogdown updated to version 0.9 with previous version 0.8 dated 2018-07-15

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Beilei Bian [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], JJ Allaire [ctb], Kevin Ushey [ctb], Leonardo Collado-Torres [ctb], Xianying Tan [ctb], RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between blogdown versions 0.8 dated 2018-07-15 and 0.9 dated 2018-10-23

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Package PSPManalysis updated to version 0.2.1 with previous version 0.2.0 dated 2018-06-17

Title: Analysis of Physiologically Structured Population Models
Description: Performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level. A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity. M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>. O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>. A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>.
Author: Andre M. de Roos [aut, cre], Ernst Hairer [ctb], Gerhard Wanner [ctb]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>

Diff between PSPManalysis versions 0.2.0 dated 2018-06-17 and 0.2.1 dated 2018-10-23

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Package SuperRanker updated to version 1.1.1 with previous version 1.1.0 dated 2018-01-13

Title: Sequential Rank Agreement
Description: Tools for analysing the agreement of two or more rankings of the same items. Examples are importance rankings of predictor variables and risk predictions of subjects. Benchmarks for agreement are computed based on random permutation and bootstrap.
Author: Claus Thorn Ekstrøm and Thomas Alexander Gerds
Maintainer: Claus Thorn Ekstrøm <ekstrom@sund.ku.dk>

Diff between SuperRanker versions 1.1.0 dated 2018-01-13 and 1.1.1 dated 2018-10-23

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Package extraDistr updated to version 1.8.10 with previous version 1.8.9 dated 2018-06-05

Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions. This package implements the following distributions: Bernoulli, beta-binomial, beta-negative binomial, beta prime, Bhattacharjee, Birnbaum-Saunders, bivariate normal, bivariate Poisson, categorical, Dirichlet, Dirichlet-multinomial, discrete gamma, discrete Laplace, discrete normal, discrete uniform, discrete Weibull, Frechet, gamma-Poisson, generalized extreme value, Gompertz, generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t, Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy, Laplace, location-scale t, logarithmic, Lomax, multivariate hypergeometric, multinomial, negative hypergeometric, non-standard beta, normal mixture, Poisson mixture, Pareto, power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam, slash, triangular, truncated binomial, truncated normal, truncated Poisson, Tukey lambda, Wald, zero-inflated binomial, zero-inflated negative binomial, zero-inflated Poisson.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>

Diff between extraDistr versions 1.8.9 dated 2018-06-05 and 1.8.10 dated 2018-10-23

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Permanent link

Package websearchr updated to version 0.0.3 with previous version 0.0.2 dated 2017-10-29

Title: Access Domains and Search Popular Websites
Description: Functions that allow for accessing domains and a number of search engines.
Author: Florian S. Schaffner [aut, cre] (<https://orcid.org/0000-0003-3352-6191>), Charles Crabtree [ctb]
Maintainer: Florian S. Schaffner <florian.schaffner@outlook.com>

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Package walker updated to version 0.2.3 with previous version 0.2.2 dated 2018-10-16

Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression coefficients can vary over time as random walks. Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, walker uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between walker versions 0.2.2 dated 2018-10-16 and 0.2.3 dated 2018-10-23

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Package RcppTOML updated to version 0.1.4 with previous version 0.1.3 dated 2017-04-25

Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format (described at <https://github.com/toml-lang/toml>) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppTOML versions 0.1.3 dated 2017-04-25 and 0.1.4 dated 2018-10-23

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Package SPUTNIK updated to version 1.1 with previous version 1.0.4.1 dated 2018-10-08

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>

Diff between SPUTNIK versions 1.0.4.1 dated 2018-10-08 and 1.1 dated 2018-10-23

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Package prettyR updated to version 2.2-2 with previous version 2.2 dated 2015-10-20

Title: Pretty Descriptive Stats
Description: Functions for conventionally formatting descriptive stats, reshaping data frames and formatting R output as HTML.
Author: Jim Lemon <drjimlemon@gmail.com>, Philippe Grosjean <phgrosjean@sciviews.org>
Maintainer: Jim Lemon <drjimlemon@gmail.com>

Diff between prettyR versions 2.2 dated 2015-10-20 and 2.2-2 dated 2018-10-23

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Package brms updated to version 2.6.0 with previous version 2.5.0 dated 2018-09-16

Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package tm1r updated to version 1.1.0 with previous version 1.0.3 dated 2018-10-16

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>

Diff between tm1r versions 1.0.3 dated 2018-10-16 and 1.1.0 dated 2018-10-23

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Package matchingMarkets updated to version 0.3-6 with previous version 0.3-5 dated 2018-02-23

Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for the sample selection bias from observed outcomes in matching markets. This includes one-sided matching of agents into groups as well as two-sided matching of students to schools. The package also contains algorithms to find stable matchings in the three most common matching problems: the stable roommates problem, the college admissions problem, and the house allocation problem.
Author: Thilo Klein [aut, cre], Sven Giegerich [ctb], Alexander Sauer [ctb]
Maintainer: Thilo Klein <thilo@klein.uk>

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Package FunChisq updated to version 2.4.5-2 with previous version 2.4.5-1 dated 2018-06-16

Title: Chi-Square and Exact Tests for Model-Free Functional Dependency
Description: Statistical hypothesis testing methods for model-free functional dependency using asymptotic chi-square or exact distributions. Functional chi-squares are asymmetric and functionally optimal, unique from other related statistics. Tests in this package reveal evidence for causality based on the causality-by-functionality principle. They include asymptotic functional chi-square tests, an exact functional test, a comparative functional chi-square test, and also a comparative chi-square test. The normalized non-constant functional chi-square test was used by Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. For continuous data, these tests offer an advantage over regression analysis when a parametric functional form cannot be assumed; for categorical data, they provide a novel means to assess directional dependency not possible with symmetrical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang [aut], Hua Zhong [aut], Ruby Sharma [aut], Sajal Kumar [aut], Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package bigmatch updated to version 0.4.1 with previous version 0.3.1 dated 2018-07-11

Title: Making Optimal Matching Size-Scalable Using Optimal Calipers
Description: Implements optimal matching with near-fine balance in large observational studies with the use of optimal calipers to get a sparse network. The caliper is optimal in the sense that it is as small as possible such that a matching exists. The main functions in the 'bigmatch' package are optcal() to find the optimal caliper, optconstant() to find the optimal number of nearest neighbors and nfmatch() to find a near-fine balance match with a caliper and a restriction on number of nearest neighbors. Glover, F. (1967). <DOI:10.1002/nav.3800140304>. Lipski, W., Jr, and Preparata, F. P. (1981). <DOI:10.1007/BF00264533>. Rosenbaum, P.R. (1989). <DOI:10.1080/01621459.1989.10478868>. Yang, D., Small, D. S., Silber, J. H., and Rosenbaum, P. R. (2012). <DOI:10.1111/j.1541-0420.2011.01691.x>.
Author: Ruoqi Yu
Maintainer: Ruoqi Yu <ruoqiyu@wharton.upenn.edu>

Diff between bigmatch versions 0.3.1 dated 2018-07-11 and 0.4.1 dated 2018-10-23

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Package RPresto updated to version 1.3.2 with previous version 1.3.1 dated 2018-09-10

Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is an open source distributed SQL query engine for running interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut, cre], Sergey Goder [aut], John Myles White [ctb]
Maintainer: Onur Ismail Filiz <onur@fb.com>

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Package analogue updated to version 0.17-1 with previous version 0.17-0 dated 2016-02-28

Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>), Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

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