Wed, 06 Jan 2021

Package TSSS updated to version 1.3.1 with previous version 1.2.4 dated 2019-04-22

Title: Time Series Analysis with State Space Model
Description: Functions for statistical analysis, modeling and simulation of time series with state space model, based on the methodology in Kitagawa (2020, ISBN: 978-0-367-18733-0).
Author: The Institute of Statistical Mathematics, based on the program by Genshiro Kitagawa
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>

Diff between TSSS versions 1.2.4 dated 2019-04-22 and 1.3.1 dated 2021-01-06

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More information about TSSS at CRAN
Permanent link

Package TraitStats updated to version 1.0.1 with previous version 1.0.0 dated 2020-11-30

Title: Statistical Data Analysis for Randomized Block Design Experiments
Description: Functions for analysis of bulk data generated from experiments in Randomized block design as per Panse and Sukhatme (1954) <https://books.google.co.in/books?id=Efo9AAAAYAAJ>. Computes analysis of variance; Descriptive statistics parameter like Mean, Minimum, Maximum, CV, Standard error of mean, Standard Error of deviation, CD; Genetic parameter statistics Genotypic Coefficient of Variation, Phenotypic Coefficient of Variation, Heritability in broad sense, Genetic Advance and Genetic Advance per cent mean; Variance and Co-variance matrix of genotypic, phenotypic and environmental; Correlation of genotypic, phenotypic and environmental. Further includes directly publication ready tables.
Author: Nitesh Shirur Devaraja [aut, cre], Parashuram Patroti [aut], Shilpa Parashuram [aut], Manoj Katiyar [ctb], Aravind J [ctb] (Reference material of augmentedRCBD), Sunil Kumar [ctb]
Maintainer: Nitesh Shirur Devaraja <mail@niteshgpb.in>

Diff between TraitStats versions 1.0.0 dated 2020-11-30 and 1.0.1 dated 2021-01-06

 DESCRIPTION               |    8 ++---
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 4 files changed, 39 insertions(+), 39 deletions(-)

More information about TraitStats at CRAN
Permanent link

Package SHAPforxgboost updated to version 0.1.0 with previous version 0.0.4 dated 2020-05-14

Title: SHAP Plots for 'XGBoost'
Description: Aid in visual data investigations using SHAP (SHapley Additive exPlanation) visualization plots for 'XGBoost' and 'LightGBM'. It provides summary plot, dependence plot, interaction plot, and force plot and relies on the SHAP implementation provided by 'XGBoost' and 'LightGBM'. Please refer to 'slundberg/shap' for the original implementation of SHAP in 'Python'.
Author: Yang Liu [aut, cre] (<https://orcid.org/0000-0001-6557-6439>), Allan Just [aut, ctb] (<https://orcid.org/0000-0003-4312-5957>)
Maintainer: Yang Liu <lyhello@gmail.com>

Diff between SHAPforxgboost versions 0.0.4 dated 2020-05-14 and 0.1.0 dated 2021-01-06

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More information about SHAPforxgboost at CRAN
Permanent link

Package sars updated to version 1.3.2 with previous version 1.3.0 dated 2020-10-06

Title: Fit and Compare Species-Area Relationship Models Using Multimodel Inference
Description: Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] (<https://orcid.org/0000-0002-7624-244X>), Francois Guilhaumon [aut] (<https://orcid.org/0000-0003-4707-8932>), Kevin Cazelles [rev] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Thomas J. Matthews <txm676@gmail.com>

Diff between sars versions 1.3.0 dated 2020-10-06 and 1.3.2 dated 2021-01-06

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More information about sars at CRAN
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Package SARP.moodle updated to version 0.8.6 with previous version 0.8.1 dated 2020-05-15

Title: XML Output Functions for Easy Creation of Moodle Questions
Description: Provides a set of basic functions for creating Moodle XML output files suited for importing questions in Moodle (a learning management system, see <https://moodle.org/> for more information).
Author: Emmanuel Curis [aut, cre, cph] (<https://orcid.org/0000-0001-8382-1493>), Virginie Lasserre [ctb]
Maintainer: Emmanuel Curis <emmanuel.curis@parisdescartes.fr>

Diff between SARP.moodle versions 0.8.1 dated 2020-05-15 and 0.8.6 dated 2021-01-06

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Package MRReg updated to version 0.1.3 with previous version 0.1.2 dated 2020-09-12

Title: MDL Multiresolution Linear Regression Framework
Description: We provide the framework to analyze multiresolution partitions (e.g. country, provinces, subdistrict) where each individual data point belongs to only one partition in each layer (e.g. i belongs to subdistrict A, province P, and country Q). We assume that a partition in a higher layer subsumes lower-layer partitions (e.g. a nation is at the 1st layer subsumes all provinces at the 2nd layer). Given N individuals that have a pair of real values (x,y) that generated from independent variable X and dependent variable Y. Each individual i belongs to one partition per layer. Our goal is to find which partitions at which highest level that all individuals in the these partitions share the same linear model Y=f(X) where f is a linear function. The framework deploys the Minimum Description Length principle (MDL) to infer solutions. The publication of this package is at Chainarong Amornbunchornvej, Navaporn Surasvadi, Anon Plangprasopchok, and Suttipong Thajchayapong (2021) <doi:10.1145/3424670>.
Author: Chainarong Amornbunchornvej [aut, cre] (<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>

Diff between MRReg versions 0.1.2 dated 2020-09-12 and 0.1.3 dated 2021-01-06

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More information about MRReg at CRAN
Permanent link

Package garma updated to version 0.9.7 with previous version 0.9.6 dated 2020-10-29

Title: Fitting and Forecasting Gegenbauer ARMA Time Series Models
Description: Methods for estimating univariate long memory-seasonal/cyclical Gegenbauer time series processes. See for example (2018) <doi:10.1214/18-STS649>. Refer to the vignette for details of fitting these processes.
Author: Richard Hunt [aut, cre]
Maintainer: Richard Hunt <maint@huntemail.id.au>

Diff between garma versions 0.9.6 dated 2020-10-29 and 0.9.7 dated 2021-01-06

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Package emba updated to version 0.1.8 with previous version 0.1.7 dated 2020-09-22

Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for biomarker discovery in cancer cell networks. The package allows to easily load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug combinations in cancer cell lines (developed by the DrugLogics research group in NTNU). It has generic functions that can be used to split a boolean model dataset to model groups with regards to the models predictive performance (number of true positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set of gold standard synergies and find the average activity difference per network node between all model group pairs. Thus, given user-specific thresholds, important nodes (biomarkers) can be accessed in the sense that they make the models predict specific synergies (synergy biomarkers) or have better performance in general (performance biomarkers). Lastly, if the boolean models have a specific equation form and differ only in their link operator, link operator biomarkers can also be found.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>

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Package dexterMST updated to version 0.9.2 with previous version 0.9.0 dated 2020-06-24

Title: CML and Bayesian Calibration of Multistage Tests
Description: Conditional Maximum Likelihood Calibration and data management of multistage tests. Supports polytomous items and incomplete designs with linear as well as multistage tests. Extended Nominal Response and Interaction models, DIF and profile analysis. See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
Author: Timo Bechger [aut, cre], Jesse Koops [aut], Ivailo Partchev [aut], Gunter Maris [aut], Robert Zwitser [ctb]
Maintainer: Timo Bechger <tmbechger@gmail.com>

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Package outForest updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-13

Title: Multivariate Outlier Detection and Replacement
Description: Provides a random forest based implementation of the method described in Chapter 7.1.2 (Regression model based anomaly detection) of Chandola et al. (2009) <doi:10.1145/1541880.1541882>. It works as follows: Each numeric variable is regressed onto all other variables by a random forest. If the scaled absolute difference between observed value and out-of-bag prediction of the corresponding random forest is suspiciously large, then a value is considered an outlier. The package offers different options to replace such outliers, e.g. by realistic values found via predictive mean matching. Once the method is trained on a reference data, it can be applied to new data.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package GPvam updated to version 3.0-7 with previous version 3.0-5 dated 2018-04-18

Title: Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl, Yan Yang, and Sharon Lohr
Maintainer: Andrew Karl <akarl@asu.edu>

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Package SlidingWindows updated to version 0.1.9 with previous version 0.1.7 dated 2020-11-01

Title: Methods for Time Series Analysis
Description: A collection of functions to perform Detrended Fluctuation Analysis (DFA exponent), GUEDES et al. (2019) <doi:10.1016/j.physa.2019.04.132> , Detrended cross-correlation coefficient (RHODCCA), GUEDES & ZEBENDE (2019) <doi:10.1016/j.physa.2019.121286>, DMCA cross-correlation coefficient and Multiple Detrended cross-correlation coefficient (DMC), ZEBENDE & SILVA-FILHO (2018) <doi:10.1016/j.physa.2018.06.119>, both with sliding windows approach.
Author: Everaldo Freitas Guedes [aut, cre] (<https://orcid.org/0000-0002-2986-7367>), Ivan Costa da Cunha Lima [aut] (<https://orcid.org/0000-0002-4525-2346>), Gilney Figueira Zebende [aut] (<https://orcid.org/0000-0003-2420-9805>), AloĆ­sio Machado Silva-Filho [aut] (<https://orcid.org/0000-0001-8250-1527>)
Maintainer: Everaldo Freitas Guedes <efgestatistico@gmail.com>

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Package ibelief updated to version 1.3.1 with previous version 1.3 dated 2019-10-25

Title: Belief Function Implementation
Description: Some basic functions to implement belief functions including: transformation between belief functions using the method introduced by Philippe Smets <arXiv:1304.1122>, evidence combination, evidence discounting, decision-making, and constructing masses. Currently, thirteen combination rules and six decision rules are supported. It can also be used to generate different types of random masses when working on belief combination and conflict management.
Author: Kuang Zhou <kzhoumath@163.com>; Arnaud Martin <arnaud.martin@univ-rennes1.fr>
Maintainer: Kuang Zhou <kzhoumath@163.com>

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Package gbfs updated to version 1.3.6 with previous version 1.3.5 dated 2020-11-05

Title: Interface with Live Bikeshare Data
Description: Supplies a set of functions to interface with bikeshare data following the General Bikeshare Feed Specification, allowing users to query and accumulate tidy datasets for specified cities/bikeshare programs.
Author: Simon P. Couch [aut, cre], Kaelyn Rosenberg [aut], Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>

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Package spcosa updated to version 0.3-10 with previous version 0.3-9 dated 2020-01-13

Title: Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means. See Walvoort et al. (2010) <doi:10.1016/j.cageo.2010.04.005> for details.
Author: Dennis Walvoort [aut, cre, cph], Dick Brus [aut, cph], Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>

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Package mully updated to version 2.1.31 with previous version 2.1.30 dated 2020-12-15

Title: Create, Modify and Visualize Multi-Layered Networks
Description: Allows the user to create graph with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.
Author: Zaynab Hammoud
Maintainer: Zaynab Hammoud <zaynabhassanhammoud@gmail.com>

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Package libr updated to version 1.1.1 with previous version 1.0.1 dated 2020-12-09

Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries, generate data dictionaries, and simulate a data step. The libname() function will load a directory of data into a library in one line of code. The dictionary() function will generate data dictionaries for individual data frames or an entire library. And the datestep() function will perform row-by-row data processing.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>

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Package lamW updated to version 2.0.0 with previous version 1.3.3 dated 2020-06-26

Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function (Corless et al, 1996) <doi:10.1007/BF02124750> without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package fdrtool updated to version 1.2.16 with previous version 1.2.15 dated 2015-07-08

Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Description: Estimates both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>

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Package primer updated to version 1.2.0 with previous version 1.1.1 dated 2019-10-07

Title: Functions and Data for the Book, a Primer of Ecology with R
Description: Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.
Author: M H H Stevens
Maintainer: Hank Stevens <hank.stevens@miamioh.edu>

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Package jmcm updated to version 0.2.3 with previous version 0.2.2 dated 2020-07-28

Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Armadillo' C++ library for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre], Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>

Diff between jmcm versions 0.2.2 dated 2020-07-28 and 0.2.3 dated 2021-01-06

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Package nbTransmission updated to version 1.1.2 with previous version 1.1.1 dated 2020-07-13

Title: Naive Bayes Transmission Analysis
Description: Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.
Author: Sarah V Leavitt [aut, cre, cph]
Maintainer: Sarah V Leavitt <sv1205@bu.edu>

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Package MEDseq updated to version 1.2.1 with previous version 1.2.0 dated 2020-11-21

Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2019) <arXiv:1908.07963>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>), Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>), Raffaella Piccarreta [ctb], Isobel Claire Gormley [ctb] (<https://orcid.org/0000-0001-7713-681X>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>

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Package compareDF updated to version 2.3.1 with previous version 2.3.0 dated 2020-08-26

Title: Do a Git Style Diff of the Rows Between Two Dataframes with Similar Structure
Description: Compares two dataframes which have the same column structure to show the rows that have changed. Also gives a git style diff format to quickly see what has changed in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>

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Package qs updated to version 0.23.5 with previous version 0.23.4 dated 2020-11-25

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd, lz4 and xxHash code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library), Bryce Chamberlain [ctb] (qsavem and qload functions)
Maintainer: Travers Ching <traversc@gmail.com>

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Package nardl updated to version 0.1.6 with previous version 0.1.5 dated 2018-05-07

Title: Nonlinear Cointegrating Autoregressive Distributed Lag Model
Description: Computes the nonlinear cointegrating autoregressive distributed lag model with automatic bases aic and bic lags selection of independent variables proposed by (Shin, Yu & Greenwood-Nimmo, 2014 <doi:10.1007/978-1-4899-8008-3_9>).
Author: Taha Zaghdoudi
Maintainer: Taha Zaghdoudi <zedtaha@gmail.com>

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Package gdtools updated to version 0.2.3 with previous version 0.2.2 dated 2020-04-03

Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre], Hadley Wickham [aut], Lionel Henry [aut], Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>), Yixuan Qiu [ctb], R Core Team [cph] (Cairo code from X11 device), RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package tsdb updated to version 1.0-0 with previous version 0.7-4 dated 2020-08-26

Title: Terribly-Simple Data Base for Time Series
Description: A terribly-simple data base for numeric time series, written purely in R, so no external database-software is needed. Series are stored in plain-text files (the most-portable and enduring file type) in CSV format. Timestamps are encoded using R's native numeric representation for 'Date'/'POSIXct', which makes them fast to parse, but keeps them accessible with other software. The package provides tools for saving and updating series in this standardised format, for retrieving and joining data, for summarising files and directories, and for coercing series from and to other data types (such as 'zoo' series).
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>

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Package tidytext updated to version 0.3.0 with previous version 0.2.6 dated 2020-09-20

Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Using tidy data principles can make many text mining tasks easier, more effective, and consistent with tools already in wide use. Much of the infrastructure needed for text mining with tidy data frames already exists in packages like 'dplyr', 'broom', 'tidyr', and 'ggplot2'. In this package, we provide functions and supporting data sets to allow conversion of text to and from tidy formats, and to switch seamlessly between tidy tools and existing text mining packages.
Author: Gabriela De Queiroz [ctb], Colin Fay [ctb] (<https://orcid.org/0000-0001-7343-1846>), Emil Hvitfeldt [ctb], Os Keyes [ctb] (<https://orcid.org/0000-0001-5196-609X>), Kanishka Misra [ctb], Tim Mastny [ctb], Jeff Erickson [ctb], David Robinson [aut], Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Julia Silge <julia.silge@gmail.com>

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Package Matrix updated to version 1.3-2 with previous version 1.3-0 dated 2020-12-22

Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut], Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Timothy A. Davis [ctb] (SuiteSparse and 'cs' C libraries, notably CHOLMOD, AMD; collaborators listed in dir(pattern = '^[A-Z]+[.]txt$', full.names=TRUE, system.file('doc', 'SuiteSparse', package='Matrix'))), Jens OehlschlƤgel [ctb] (initial nearPD()), Jason Riedy [ctb] (condest() and onenormest() for octave, Copyright: Regents of the University of California), R Core Team [ctb] (base R matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>

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Package IFAA updated to version 1.0.1 with previous version 1.0.0 dated 2020-11-04

Title: Robust Analysis for Absolute Abundance in Microbiome
Description: A novel approach to make inference on the association of covariates with the absolute abundance (AA) of 'microbiome' in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA (even if AA data is not available) because the ratio of two RA is equal ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential 'confounders'. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. This algorithm finds optimal reference 'taxa/OTU (Operational Taxonomic Unit)/ASV (Amplicon Sequence Bariant)' and uses permutation to control FDR (False Discovery Rate).
Author: Zhigang Li [aut, cre]
Maintainer: Zhigang Li <zhigang.li@ufl.edu>

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Package gggibbous updated to version 0.1.1 with previous version 0.1.0 dated 2019-12-02

Title: Moon Charts, a Pie Chart Alternative
Description: Moon charts are like pie charts except that the proportions are shown as crescent or gibbous portions of a circle, like the lit and unlit portions of the moon. As such, they work best with only one or two groups. 'gggibbous' extends 'ggplot2' to allow for plotting multiple moon charts in a single panel and does not require a square coordinate system.
Author: Michael Bramson [aut, cre]
Maintainer: Michael Bramson <mnbramson@gmail.com>

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Package corHMM updated to version 2.6 with previous version 2.5 dated 2020-11-24

Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Jeffrey Oliver [aut], James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>

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Package chillR updated to version 0.72.2 with previous version 0.72 dated 2020-12-10

Title: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.
Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package xfun updated to version 0.20 with previous version 0.19 dated 2020-10-30

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>), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim BrĆ¼ggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package tools4uplift updated to version 1.0.0 with previous version 0.1-1 dated 2019-01-29

Title: Tools for Uplift Modeling
Description: Uplift modeling aims at predicting the causal effect of an action such as a marketing campaign on a particular individual. In order to simplify the task for practitioners in uplift modeling, we propose a combination of tools that can be separated into the following ingredients: i) quantization, ii) visualization, iii) variable selection, iv) parameters estimation and, v) model validation. For more details, see <https://dms.umontreal.ca/~murua/research/UpliftRegression.pdf>.
Author: Mouloud Belbahri, Olivier Gandouet, Alejandro Murua, Vahid Partovi Nia
Maintainer: Mouloud Belbahri <mouloud.belbahri@gmail.com>

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Package sommer updated to version 4.1.2 with previous version 4.1.1 dated 2020-09-30

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

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Package SimplicialCubature updated to version 1.3 with previous version 1.2 dated 2016-05-16

Title: Integration of Functions Over Simplices
Description: Provides methods to integrate functions over m-dimensional simplices in n-dimensional Euclidean space. There are exact methods for polynomials and adaptive methods for integrating an arbitrary function.
Author: John P. Nolan, with parts adapted from Fortran and matlab code by Alan Genz
Maintainer: John P. Nolan <jpnolan@american.edu>

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Package rvinecopulib updated to version 0.5.5.1.1 with previous version 0.5.5.1.0 dated 2020-11-23

Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine copula modeling. The 'rvinecopulib' package implements the core features of the popular 'VineCopula' package, in particular inference algorithms for both vine copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker and more modern API, improved performances, especially in high dimensions, nonparametric and multi-parameter families, and the ability to model discrete variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only C++ library (currently version 0.5.5). Thus users do not need to install 'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre], Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>

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Package rticles updated to version 0.18 with previous version 0.17 dated 2020-11-01

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] (<https://orcid.org/0000-0002-8319-7624>), Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>), MDPI [aut, cph], Taylor and Francis [aut, cph], Oğuzhan Ɩğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel NĆ¼st [aut, cph] (<https://orcid.org/0000-0002-0024-5046>), Petter Uvesten [aut, cph], Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>), John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>), Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>), Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Duncan Luguern [aut], David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000), Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>), Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>), Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>), Alfredo HernĆ”ndez [ctb] (<https://orcid.org/0000-0002-2660-4545>), Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rticles versions 0.17 dated 2020-11-01 and 0.18 dated 2021-01-06

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 rticles-0.18/rticles/NEWS.md                                                                         |   19 ++
 rticles-0.18/rticles/R/article.R                                                                     |    2 
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Package rgbif updated to version 3.4.2 with previous version 3.4.0 dated 2020-12-03

Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <https://www.gbif.org/developer/summary>). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>), Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>), Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>), Laurens Geffert [ctb], Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>), Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>), rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rgbif versions 3.4.0 dated 2020-12-03 and 3.4.2 dated 2021-01-06

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Permanent link

Package poppr updated to version 2.8.7 with previous version 2.8.6 dated 2020-06-02

Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and GrĆ¼nwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and GrĆ¼nwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>), Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>), Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>), Jonah C. Brooks [aut], Stacy A. Krueger-Hadfield [ctb] (<https://orcid.org/0000-0002-7324-7448>), Erik Sotka [ctb], Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>), Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>), FrĆ©dĆ©ric D. Chevalier [ctb] (<https://orcid.org/0000-0003-2611-8106>), Niklaus J. GrĆ¼nwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

Diff between poppr versions 2.8.6 dated 2020-06-02 and 2.8.7 dated 2021-01-06

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Package paletteer updated to version 1.3.0 with previous version 1.2.0 dated 2020-06-07

Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

Diff between paletteer versions 1.2.0 dated 2020-06-07 and 1.3.0 dated 2021-01-06

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Package pairwise updated to version 0.5.0-2 with previous version 0.5.0-1 dated 2020-12-02

Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

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Package MoEClust updated to version 1.3.3 with previous version 1.3.2 dated 2020-11-17

Title: Gaussian Parsimonious Clustering Models with Covariates and a Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>), Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>

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Package mlr3measures updated to version 0.3.1 with previous version 0.3.0 dated 2020-10-05

Title: Performance Measures for 'mlr3'
Description: Implements multiple performance measures for supervised learning. Includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what the best and worst possible performances scores are.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Martin Binder [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

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Package micEcon updated to version 0.6-16 with previous version 0.6-14 dated 2017-03-16

Title: Microeconomic Analysis and Modelling
Description: Various tools for microeconomic analysis and microeconomic modelling, e.g. estimating quadratic, Cobb-Douglas and Translog functions, calculating partial derivatives and elasticities of these functions, and calculating Hessian matrices, checking curvature and preparing restrictions for imposing monotonicity of Translog functions.
Author: Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

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Package mdsr updated to version 0.2.4 with previous version 0.2.3 dated 2020-11-10

Title: Complement to 'Modern Data Science with R'
Description: A complement to *Modern Data Science with R*, both the first (ISBN: 978-1498724487, publisher URL: <https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9781498724487>) and second editions (ISBN: 978-0367191498, publisher URL: <https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9780367191498>). This package contains data and code to complete exercises and reproduce examples from the text. It also facilitates connections to the SQL database server used in the book. Both editions of the book are supported by this package.
Author: Benjamin S. Baumer [aut, cre] (<https://orcid.org/0000-0002-3279-0516>), Nicholas Horton [aut] (<https://orcid.org/0000-0003-3332-4311>), Daniel Kaplan [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>

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Package MDFS updated to version 1.1.0 with previous version 1.0.5 dated 2019-11-10

Title: MultiDimensional Feature Selection
Description: Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs.
Author: Radosław Piliszek [aut, cre], Krzysztof Mnich [aut], Paweł Tabaszewski [aut], Szymon Migacz [aut], Andrzej Sułecki [aut], Witold Remigiusz Rudnicki [aut]
Maintainer: Radosław Piliszek <r.piliszek@uwb.edu.pl>

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Package fmtr updated to version 1.4.1 with previous version 1.3.0 dated 2020-11-16

Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply formats to data frames or vectors. The package aims to provide to functionality similar to that of SASĀ® formats. Formats are assigned to the format attribute on data frame columns. Then when the fdata() function is called, a new data frame is created with the column data formatted as specified. The package also contains a value() function to create a user-defined format, similar to a SASĀ® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>

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Package equaltestMI updated to version 0.6.1 with previous version 0.6.0 dated 2020-06-05

Title: Examine Measurement Invariance via Equivalence Testing and Projection Method
Description: Functions for examining measurement invariance via equivalence testing are included in this package. The traditionally used RMSEA (Root Mean Square Error of Approximation) cutoff values are adjusted based on simulation results. In addition, a projection-based method is implemented to test the equality of latent factor means across groups without assuming the equality of intercepts. For more information, see Yuan, K. H., & Chan, W. (2016) <doi:10.1037/met0000080>, Deng, L., & Yuan, K. H. (2016) <doi:10.1007/s11336-015-9491-8>, and Jiang, G., Mai, Y., & Yuan, K. H. (2017) <doi:10.3389/fpsyg.2017.01823>.
Author: Ge Jiang [aut, cre], Yujiao Mai [aut], Ke-Hai Yuan [ctb]
Maintainer: Ge Jiang <gejiang2@illinois.edu>

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Package DT updated to version 0.17 with previous version 0.16 dated 2020-10-13

Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre], Joe Cheng [aut], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib), SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>

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Package dexter updated to version 1.1.2 with previous version 1.1.1 dated 2020-11-13

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Jesse Koops <jesse.koops@cito.nl>

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Package clusterSim updated to version 0.49-2 with previous version 0.49-1 dated 2020-07-20

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

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Package castor updated to version 1.6.5 with previous version 1.6.4 dated 2020-10-26

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package bayesDP updated to version 1.3.4 with previous version 1.3.3 dated 2020-02-03

Title: Tools for the Bayesian Discount Prior Function
Description: Functions for data augmentation using the Bayesian discount prior method for single arm and two-arm clinical trials, as described in Haddad et al. (2017) <doi:10.1080/10543406.2017.1300907>. The discount power prior methodology was developed in collaboration with the The Medical Device Innovation Consortium (MDIC) Computer Modeling & Simulation Working Group.
Author: Shawn Balcome [aut], Donnie Musgrove [aut], Tarek Haddad [aut], Graeme L. Hickey [cre, aut] (<https://orcid.org/0000-0002-4989-0054>), Christopher Jackson [ctb] (For the ppexp R code that was ported to C++.)
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>

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Package actuar updated to version 3.1-0 with previous version 3.0-0 dated 2020-06-05

Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. Support for many additional probability distributions to model insurance loss size and frequency: 23 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. Support for phase-type distributions commonly used to compute ruin probabilities.
Author: Vincent Goulet [cre, aut], SĆ©bastien Auclair [ctb], Christophe Dutang [aut], Nicholas Langevin [ctb], Xavier Milhaud [ctb], Tommy Ouellet [ctb], Alexandre Parent [ctb], Mathieu Pigeon [aut], Louis-Philippe Pouliot [ctb], Jeffrey A. Ryan [aut] (Package API), Robert Gentleman [aut] (Parts of the R to C interface), Ross Ihaka [aut] (Parts of the R to C interface), R Core Team [aut] (Parts of the R to C interface), R Foundation [aut] (Parts of the R to C interface)
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

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Package RobustBayesianCopas updated to version 2.0 with previous version 1.0 dated 2020-05-12

Title: Robust Bayesian Copas Selection Model
Description: Fits the robust Bayesian Copas (RBC) selection model of Bai et al. (2020) <arXiv:2005.02930> for correcting and quantifying publication bias in univariate meta-analysis. Also fits standard random effects meta-analysis and the Copas-like selection model of Ning et al. (2017) <doi:10.1093/biostatistics/kxx004>.
Author: Ray Bai
Maintainer: Ray Bai <raybaistat@gmail.com>

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Package odds.n.ends updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-12

Title: Odds Ratios, Contingency Table, and Model Significance from a Generalized Linear Model Object
Description: Computes odds ratios and 95% confidence intervals from a generalized linear model object. It also computes model significance with the chi-squared statistic and p-value and it computes model fit using a contingency table to determine the percent of observations for which the model correctly predicts the value of the outcome. Calculates model sensitivity and specificity.
Author: Jenine Harris [aut, cre]
Maintainer: Jenine Harris <harrisj@wustl.edu>

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Package lawn updated to version 0.6.0 with previous version 0.5.0 dated 2019-02-01

Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (<https://turfjs.org>) for 'geospatial' analysis. The package revolves around using 'GeoJSON' data. Functions are included for creating 'GeoJSON' data objects, measuring aspects of 'GeoJSON', and combining, transforming, and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Jeff Hollister [aut], Morgan Herlocker [cph], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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More information about lawn at CRAN
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Package iriR updated to version 0.2.1 with previous version 0.1.0 dated 2020-11-09

Title: Global Innovation Through Company Level Data
Description: Researchers and analysts have access to more than 7,500 innovative companies worldwide, which are or have been part of the top 1,000 innovative companies. They can access the six parameters that compose the global IRI Scoreboard's data on R&D: Country, Year, Company's name, Industry, Indicator and Company's rank. Please cite: Warin, Th. (2020) "iiriR: An R Package for the EU Industrial R&D Investment Scoreboard", <doi:10.6084/m9.figshare.11774640.v5>.
Author: Thierry Warin [aut, cre] (<https://orcid.org/0000-0002-5921-3428>)
Maintainer: Thierry Warin <thierry.warin@hec.ca>

Diff between iriR versions 0.1.0 dated 2020-11-09 and 0.2.1 dated 2021-01-06

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More information about iriR at CRAN
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Package ggmsa updated to version 0.0.5 with previous version 0.0.4 dated 2020-05-28

Title: Plot Multiple Sequence Alignment using 'ggplot2'
Description: Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Lang Zhou [aut], Huina Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggmsa versions 0.0.4 dated 2020-05-28 and 0.0.5 dated 2021-01-06

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Permanent link

Package ExpDes.pt updated to version 1.2.1 with previous version 1.2.0 dated 2018-05-17

Title: Pacote Experimental Designs (Portugues)
Description: Pacote para anƔlise de delineamentos experimentais (DIC, DBC e DQL), experimentos em esquema fatorial duplo (em DIC e DBC), experimentos em parcelas subdivididas (em DIC e DBC), experimentos em esquema fatorial duplo com um tratamento adicional (em DIC e DBC), experimentos em fatorial triplo (em DIC e DBC) e experimentos em esquema fatorial triplo com um tratamento adicional (em DIC e DBC), fazendo analise de variancia e comparacao de multiplas medias (para tratamentos qualitativos), ou ajustando modelos de regressao ate a terceira potencia (para tratamentos quantitativos); analise de residuos (Ferreira, Cavalcanti and Nogueira, 2014) <doi:10.4236/am.2014.519280>.
Author: Eric Batista Ferreira, Portya Piscitelli Cavalcanti, Denismar Alves Nogueira
Maintainer: Eric Batista Ferreira <eric.ferreira@unifal-mg.edu.br>

Diff between ExpDes.pt versions 1.2.0 dated 2018-05-17 and 1.2.1 dated 2021-01-06

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 ExpDes.pt-1.2.1/ExpDes.pt/man/ex5.Rd               |   67 ++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/ex6.Rd               |   60 ++--
 ExpDes.pt-1.2.1/ExpDes.pt/man/ex7.Rd               |   69 ++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/ex8.Rd               |   70 ++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/ex9.Rd               |   68 ++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/exnl.Rd              |only
 ExpDes.pt-1.2.1/ExpDes.pt/man/faixas.Rd            |  133 +++++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat2.ad.dbc.Rd       |  178 ++++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat2.ad.dic.Rd       |  186 ++++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat2.dbc.Rd          |  170 +++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat2.dic.Rd          |  168 +++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat3.ad.dbc.Rd       |  186 ++++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat3.ad.dic.Rd       |  187 ++++++++------
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat3.dbc.Rd          |  176 ++++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/fat3.dic.Rd          |  173 +++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/ginv.Rd              |   73 ++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/graficos.Rd          |  133 +++++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/han.Rd               |  115 ++++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/lastC.Rd             |   84 ++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/layard.Rd            |  120 ++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/levene.Rd            |  121 ++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/lsd.Rd               |  123 +++------
 ExpDes.pt-1.2.1/ExpDes.pt/man/lsdb.Rd              |  122 +++------
 ExpDes.pt-1.2.1/ExpDes.pt/man/oneilldbc.Rd         |  111 +++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/oneillmathews.Rd     |  121 ++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/order.group.Rd       |  120 +++------
 ExpDes.pt-1.2.1/ExpDes.pt/man/order.stat.SNK.Rd    |   95 ++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/plotres.Rd           |   85 +++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/psub2.dbc.Rd         |  163 +++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/psub2.dic.Rd         |  165 +++++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/reg.nl.Rd            |   90 +++---
 ExpDes.pt-1.2.1/ExpDes.pt/man/reg.poly.Rd          |  106 +++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/respAd.Rd            |   46 +--
 ExpDes.pt-1.2.1/ExpDes.pt/man/samiuddin.Rd         |  115 ++++----
 ExpDes.pt-1.2.1/ExpDes.pt/man/scottknott.Rd        |  130 ++++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/secaAd.Rd            |   46 +--
 ExpDes.pt-1.2.1/ExpDes.pt/man/snk.Rd               |  125 +++------
 ExpDes.pt-1.2.1/ExpDes.pt/man/tapply.stat.Rd       |   95 ++-----
 ExpDes.pt-1.2.1/ExpDes.pt/man/tukey.Rd             |  133 ++++-----
 115 files changed, 5493 insertions(+), 3610 deletions(-)

More information about ExpDes.pt at CRAN
Permanent link

Package ExpDes updated to version 1.2.1 with previous version 1.2.0 dated 2018-05-17

Title: Experimental Designs Package
Description: Package for analysis of simple experimental designs (CRD, RBD and LSD), experiments in double factorial schemes (in CRD and RBD), experiments in a split plot in time schemes (in CRD and RBD), experiments in double factorial schemes with an additional treatment (in CRD and RBD), experiments in triple factorial scheme (in CRD and RBD) and experiments in triple factorial schemes with an additional treatment (in CRD and RBD), performing the analysis of variance and means comparison by fitting regression models until the third power (quantitative treatments) or by a multiple comparison test, Tukey test, test of Student-Newman-Keuls (SNK), Scott-Knott, Duncan test, t test (LSD) and Bonferroni t test (protected LSD) - for qualitative treatments; residual analysis (Ferreira, Cavalcanti and Nogueira, 2014) <doi:10.4236/am.2014.519280>.
Author: Eric Batista Ferreira, Portya Piscitelli Cavalcanti, Denismar Alves Nogueira
Maintainer: Eric Batista Ferreira <eric.ferreira@unifal-mg.edu.br>

Diff between ExpDes versions 1.2.0 dated 2018-05-17 and 1.2.1 dated 2021-01-06

 ExpDes-1.2.0/ExpDes/R/ExpDes-internal.R   |only
 ExpDes-1.2.0/ExpDes/R/ccboot.R            |only
 ExpDes-1.2.0/ExpDes/R/ccf.R               |only
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 ExpDes-1.2.0/ExpDes/man/ExpDes-package.Rd |only
 ExpDes-1.2.0/ExpDes/man/ccf.Rd            |only
 ExpDes-1.2.0/ExpDes/man/ex_nl.Rd          |only
 ExpDes-1.2.1/ExpDes/DESCRIPTION           |   21 +-
 ExpDes-1.2.1/ExpDes/MD5                   |  232 +++++++++++++++---------------
 ExpDes-1.2.1/ExpDes/NAMESPACE             |   84 +++++++++-
 ExpDes-1.2.1/ExpDes/R/anscombetukey.R     |   62 ++++++--
 ExpDes-1.2.1/ExpDes/R/bartlett.R          |   48 ++++--
 ExpDes-1.2.1/ExpDes/R/ccF.r               |only
 ExpDes-1.2.1/ExpDes/R/ccboot.r            |only
 ExpDes-1.2.1/ExpDes/R/crd.R               |   74 ++++++++-
 ExpDes-1.2.1/ExpDes/R/duncan.R            |   21 ++
 ExpDes-1.2.1/ExpDes/R/est21Ad.r           |only
 ExpDes-1.2.1/ExpDes/R/ex.r                |only
 ExpDes-1.2.1/ExpDes/R/ex1.r               |only
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 ExpDes-1.2.1/ExpDes/R/ex9.r               |only
 ExpDes-1.2.1/ExpDes/R/exnl.r              |only
 ExpDes-1.2.1/ExpDes/R/fat2.ad.crd.R       |   89 +++++++++--
 ExpDes-1.2.1/ExpDes/R/fat2.ad.rbd.R       |  119 +++++++++++----
 ExpDes-1.2.1/ExpDes/R/fat2.crd.R          |  108 ++++++++++---
 ExpDes-1.2.1/ExpDes/R/fat2.rbd.R          |   94 +++++++++---
 ExpDes-1.2.1/ExpDes/R/fat3.ad.crd.R       |  175 +++++++++++++++-------
 ExpDes-1.2.1/ExpDes/R/fat3.ad.rbd.R       |  171 ++++++++++++++--------
 ExpDes-1.2.1/ExpDes/R/fat3.crd.R          |  218 +++++++++++++++++-----------
 ExpDes-1.2.1/ExpDes/R/fat3.rbd.R          |  169 ++++++++++++++-------
 ExpDes-1.2.1/ExpDes/R/ginv.R              |   16 ++
 ExpDes-1.2.1/ExpDes/R/graphics.R          |   40 ++++-
 ExpDes-1.2.1/ExpDes/R/han.R               |   36 ++++
 ExpDes-1.2.1/ExpDes/R/lastC.R             |   18 ++
 ExpDes-1.2.1/ExpDes/R/latsd.R             |   68 +++++++-
 ExpDes-1.2.1/ExpDes/R/layard.R            |   34 ++++
 ExpDes-1.2.1/ExpDes/R/levene.R            |   36 ++++
 ExpDes-1.2.1/ExpDes/R/lsd.R               |   32 ++++
 ExpDes-1.2.1/ExpDes/R/lsdb.R              |   31 ++++
 ExpDes-1.2.1/ExpDes/R/oneilldbc.R         |   36 ++++
 ExpDes-1.2.1/ExpDes/R/oneillmathews.R     |   38 ++++
 ExpDes-1.2.1/ExpDes/R/order.group.R       |   28 +++
 ExpDes-1.2.1/ExpDes/R/order.stat.SNK.R    |   22 ++
 ExpDes-1.2.1/ExpDes/R/plotres.R           |   31 +++-
 ExpDes-1.2.1/ExpDes/R/rbd.R               |   76 +++++++++
 ExpDes-1.2.1/ExpDes/R/reg.nl.R            |  160 +++++++++++---------
 ExpDes-1.2.1/ExpDes/R/reg.poly.R          |   35 +++-
 ExpDes-1.2.1/ExpDes/R/respAd.r            |only
 ExpDes-1.2.1/ExpDes/R/samiuddin.R         |   36 ++++
 ExpDes-1.2.1/ExpDes/R/scottknott.R        |   50 +++++-
 ExpDes-1.2.1/ExpDes/R/secaAd.r            |only
 ExpDes-1.2.1/ExpDes/R/snk.R               |   28 +++
 ExpDes-1.2.1/ExpDes/R/split2.crd.R        |  114 ++++++++++----
 ExpDes-1.2.1/ExpDes/R/split2.rbd.R        |  111 ++++++++++----
 ExpDes-1.2.1/ExpDes/R/strip.R             |   95 +++++++++---
 ExpDes-1.2.1/ExpDes/R/tapply.stat.R       |   20 ++
 ExpDes-1.2.1/ExpDes/R/tukey.R             |   39 +++++
 ExpDes-1.2.1/ExpDes/data/est21Ad.rda      |binary
 ExpDes-1.2.1/ExpDes/data/ex.rda           |binary
 ExpDes-1.2.1/ExpDes/data/ex1.rda          |binary
 ExpDes-1.2.1/ExpDes/data/ex2.rda          |binary
 ExpDes-1.2.1/ExpDes/data/ex3.rda          |binary
 ExpDes-1.2.1/ExpDes/data/ex4.rda          |binary
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 ExpDes-1.2.1/ExpDes/data/ex6.rda          |binary
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 ExpDes-1.2.1/ExpDes/data/respAd.rda       |binary
 ExpDes-1.2.1/ExpDes/data/secaAd.rda       |binary
 ExpDes-1.2.1/ExpDes/man/anscombetukey.Rd  |  116 ++++++---------
 ExpDes-1.2.1/ExpDes/man/bartlett.Rd       |  121 +++++++--------
 ExpDes-1.2.1/ExpDes/man/ccF.Rd            |only
 ExpDes-1.2.1/ExpDes/man/ccboot.Rd         |  114 +++++++-------
 ExpDes-1.2.1/ExpDes/man/crd.Rd            |  166 ++++++++++++---------
 ExpDes-1.2.1/ExpDes/man/duncan.Rd         |   96 +++++-------
 ExpDes-1.2.1/ExpDes/man/est21Ad.Rd        |   45 ++---
 ExpDes-1.2.1/ExpDes/man/ex.Rd             |   58 +++----
 ExpDes-1.2.1/ExpDes/man/ex1.Rd            |   63 ++++----
 ExpDes-1.2.1/ExpDes/man/ex2.Rd            |   64 ++++----
 ExpDes-1.2.1/ExpDes/man/ex3.Rd            |   66 ++++----
 ExpDes-1.2.1/ExpDes/man/ex4.Rd            |   82 +++++-----
 ExpDes-1.2.1/ExpDes/man/ex5.Rd            |   67 ++++----
 ExpDes-1.2.1/ExpDes/man/ex6.Rd            |   60 +++----
 ExpDes-1.2.1/ExpDes/man/ex7.Rd            |   69 ++++----
 ExpDes-1.2.1/ExpDes/man/ex8.Rd            |   71 +++++----
 ExpDes-1.2.1/ExpDes/man/ex9.Rd            |   68 ++++----
 ExpDes-1.2.1/ExpDes/man/exnl.Rd           |only
 ExpDes-1.2.1/ExpDes/man/fat2.ad.crd.Rd    |  174 +++++++++++++---------
 ExpDes-1.2.1/ExpDes/man/fat2.ad.rbd.Rd    |  166 +++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat2.crd.Rd       |  158 ++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat2.rbd.Rd       |  157 ++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat3.ad.crd.Rd    |  176 ++++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat3.ad.rbd.Rd    |  173 ++++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat3.crd.Rd       |  157 ++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/fat3.rbd.Rd       |  162 +++++++++++++-------
 ExpDes-1.2.1/ExpDes/man/ginv.Rd           |   70 ++++-----
 ExpDes-1.2.1/ExpDes/man/graphics.Rd       |  126 +++++++++-------
 ExpDes-1.2.1/ExpDes/man/han.Rd            |  115 ++++++--------
 ExpDes-1.2.1/ExpDes/man/lastC.Rd          |   82 ++++------
 ExpDes-1.2.1/ExpDes/man/latsd.Rd          |  151 +++++++++++--------
 ExpDes-1.2.1/ExpDes/man/layard.Rd         |  117 ++++++---------
 ExpDes-1.2.1/ExpDes/man/levene.Rd         |  114 +++++++-------
 ExpDes-1.2.1/ExpDes/man/lsd.Rd            |  106 ++++++-------
 ExpDes-1.2.1/ExpDes/man/lsdb.Rd           |  107 ++++++-------
 ExpDes-1.2.1/ExpDes/man/oneilldbc.Rd      |  110 ++++++--------
 ExpDes-1.2.1/ExpDes/man/oneillmathews.Rd  |  118 +++++++--------
 ExpDes-1.2.1/ExpDes/man/order.group.Rd    |  104 ++++++-------
 ExpDes-1.2.1/ExpDes/man/order.stat.SNK.Rd |   86 ++++-------
 ExpDes-1.2.1/ExpDes/man/plotres.Rd        |   82 ++++------
 ExpDes-1.2.1/ExpDes/man/rbd.Rd            |  177 +++++++++++++---------
 ExpDes-1.2.1/ExpDes/man/reg.nl.Rd         |   87 +++++------
 ExpDes-1.2.1/ExpDes/man/reg.poly.Rd       |   93 +++++-------
 ExpDes-1.2.1/ExpDes/man/respAd.Rd         |   45 ++---
 ExpDes-1.2.1/ExpDes/man/samiuddin.Rd      |  116 ++++++---------
 ExpDes-1.2.1/ExpDes/man/scottknott.Rd     |  113 +++++++-------
 ExpDes-1.2.1/ExpDes/man/secaAd.Rd         |   46 ++---
 ExpDes-1.2.1/ExpDes/man/snk.Rd            |  104 ++++++-------
 ExpDes-1.2.1/ExpDes/man/split2.crd.Rd     |  157 ++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/split2.rbd.Rd     |  156 ++++++++++++--------
 ExpDes-1.2.1/ExpDes/man/strip.Rd          |  143 ++++++++++--------
 ExpDes-1.2.1/ExpDes/man/tapply.stat.Rd    |   86 ++++-------
 ExpDes-1.2.1/ExpDes/man/tukey.Rd          |  128 ++++++++--------
 130 files changed, 5220 insertions(+), 3283 deletions(-)

More information about ExpDes at CRAN
Permanent link

Package EpiReport updated to version 1.0.0 with previous version 0.1.1 dated 2020-05-11

Title: Epidemiological Report
Description: Drafting an epidemiological report in 'Microsoft Word' format for a given disease, similar to the Annual Epidemiological Reports published by the European Centre for Disease Prevention and Control. Through standalone functions, it is specifically designed to generate each disease specific output presented in these reports and includes: - Table with the distribution of cases by Member State over the last five years; - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, by month, over the past five years; - Trend plot with the trend and number of cases at the European Union / European Economic Area level, by month, over the past five years; - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level. Two types of datasets can be used: - The default dataset of dengue 2015-2019 data; - Any dataset specified as described in the vignette.
Author: Lore Merdrignac [aut, ctr, cre] (Author of the package and original code), Tommi Karki [aut, fnd], Esther Kissling [aut, ctr], Joana Gomes Dias [aut, fnd] (Project manager)
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>

Diff between EpiReport versions 0.1.1 dated 2020-05-11 and 1.0.0 dated 2021-01-06

 DESCRIPTION                         |   21 +-
 MD5                                 |   84 +++++---
 NAMESPACE                           |   11 +
 R/AER_age_gender_bar.R              |  234 +++++++++++++---------
 R/AER_maps.R                        |   53 ++---
 R/AER_report.R                      |  156 ++++++++-------
 R/AER_seasonality_graph.R           |  118 +++++++----
 R/AER_table.R                       |  147 +++++++++++---
 R/AER_trend_graph.R                 |  100 ++++++---
 R/EcdcColors.R                      |only
 R/data.R                            |   39 +++
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 vignettes/EpiReport_Vignette.Rmd    |   37 +++
 53 files changed, 1175 insertions(+), 657 deletions(-)

More information about EpiReport at CRAN
Permanent link

Package yamlme updated to version 0.1.1 with previous version 0.1.0 dated 2020-12-16

Title: Writing 'YAML' Headers for 'R-Markdown' Documents
Description: Setting layout through 'YAML' headers in 'R-Markdown' documents, enabling their automatic generation. Functions and methods may summarize 'R' objects in automatic reports, for instance check-lists and further reports applied to the packages 'taxlist' and 'vegtable'.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>), Bisrat Haile Gebrekidan [ctb]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>

Diff between yamlme versions 0.1.0 dated 2020-12-16 and 0.1.1 dated 2021-01-06

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 24 files changed, 584 insertions(+), 707 deletions(-)

More information about yamlme at CRAN
Permanent link

Package NADIA updated to version 0.4.1 with previous version 0.4.0 dated 2020-11-23

Title: NA Data Imputation Algorithms
Description: Creates a uniform interface for several advanced imputations missing data methods. Every available method can be used as a part of 'mlr3' pipelines which allows easy tuning and performance evaluation. Most of the used functions work separately on the training and test sets (imputation is trained on the training set and impute training data. After that imputation is again trained on the test set and impute test data).
Author: Jan Borowski, Piotr Fic
Maintainer: Jan Borowski <janborowka7@gmail.com>

Diff between NADIA versions 0.4.0 dated 2020-11-23 and 0.4.1 dated 2021-01-06

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 NADIA-0.4.1/NADIA/DESCRIPTION                                   |   13 
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 NADIA-0.4.1/NADIA/NAMESPACE                                     |  115 -
 NADIA-0.4.1/NADIA/R/PipeOPAmelia.R                              |  461 ++---
 NADIA-0.4.1/NADIA/R/PipeOPVIM_IRMI.R                            |  407 ++--
 NADIA-0.4.1/NADIA/R/PipeOPmissForest.R                          |  455 ++---
 NADIA-0.4.1/NADIA/R/PipeOpHist_B.R                              |  108 -
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 NADIA-0.4.1/NADIA/R/PipeOpMedian_B.R                            |  101 -
 NADIA-0.4.1/NADIA/R/PipeOpMice.R                                |  500 ++---
 NADIA-0.4.1/NADIA/R/PipeOpMice_A.R                              |  504 ++---
 NADIA-0.4.1/NADIA/R/PipeOpMissMDA_PCA_MCA_FMAD.R                |  443 ++---
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 NADIA-0.4.1/NADIA/R/PipeOpSimulateMissings.R                    |  173 +-
 NADIA-0.4.1/NADIA/R/PipeOpSoftImpute.R                          |  409 ++--
 NADIA-0.4.1/NADIA/R/PipeOpVIM_HD.R                              |  355 ++--
 NADIA-0.4.1/NADIA/R/PipeOpVIM_kNN.R                             |  370 ++--
 NADIA-0.4.1/NADIA/R/PipeOpVIM_regrImp.R                         |  385 ++--
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Package logr updated to version 1.2.1 with previous version 1.1.1 dated 2020-10-10

Title: Creates Log Files
Description: Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>

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Package AnchorRegression updated to version 0.1.3 with previous version 0.1.1 dated 2020-12-09

Title: Perform AnchorRegression
Description: Performs AnchorRegression proposed by RothenhƤusler et al. 2020. The code is adapted from the original paper repository. (<https://github.com/rothenhaeusler/anchor-regression>) The code was developed independently from the authors of the paper.
Author: Simon Zimmermann
Maintainer: Simon Zimmermann <zimmersi@hu-berlin.de>

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Package minidown updated to version 0.0.3 with previous version 0.0.2 dated 2020-09-30

Title: Create Simple Yet Powerful HTML Documents with Light Weight CSS Frameworks
Description: Create minimal, responsive, and style-agnostic HTML documents with the lightweight CSS frameworks such as 'sakura', 'Water.css', and 'mini.css'. Powerful features include floating table of contents as a sidebar, code folding of source, output, message, warning, and error, and accordion menus. They work without JavaScript.
Author: Atsushi Yasumoto [aut, cph, cre] (<https://orcid.org/0000-0002-8335-495X>), Angelos Chalaris [aut] (mini.css), Mitesh Shah [aut] (sakura), Kognise [aut] (Water.css)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>

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Package lefko3 updated to version 3.2.0 with previous version 3.1.2 dated 2020-11-16

Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological analyses. Specializes on the construction of historical matrices, which are 2d matrices comprising 3 time intervals of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices. Methodology based on Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre] (<https://orcid.org/0000-0002-5234-3131>), Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>

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Package extRatum updated to version 1.0.2 with previous version 1.0.1 dated 2021-01-04

Title: Summary Statistics for Geospatial Features
Description: Provides summary statistics of local geospatial features within a given geographic area. It does so by calculating the area covered by a target geospatial feature (i.e. buildings, parks, lakes, etc.). The geospatial features can be of any type of geospatial data, including point, polygon or line data.
Author: Nikos Patias [aut, cre] (<https://orcid.org/0000-0002-6542-2330>), Francisco Rowe [aut]
Maintainer: Nikos Patias <n.patias@liverpool.ac.uk>

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Package COVID19 updated to version 2.3.2 with previous version 2.3.1 dated 2020-10-12

Title: R Interface to COVID-19 Data Hub
Description: Download COVID-19 data across governmental sources at national, regional, and city level, as described in Guidotti and Ardia (2020) <doi:10.21105/joss.02376>. Includes the time series of vaccines, tests, cases, deaths, recovered, hospitalizations, intensive therapy, and policy measures by 'Oxford COVID-19 Government Response Tracker' <https://www.bsg.ox.ac.uk/research/research-projects/coronavirus-government-response-tracker>. Provides a seamless integration with 'World Bank Open Data' <https://data.worldbank.org/>, 'Google Mobility Reports' <https://www.google.com/covid19/mobility/>, 'Apple Mobility Reports' <https://covid19.apple.com/mobility>.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>), David Ardia [ctb] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>

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Package sfdct updated to version 0.1.0 with previous version 0.0.6 dated 2018-03-23

Title: Constrained Triangulation for Simple Features
Description: Build a constrained Delaunay triangulation from simple features objects, applying constraints based on input line segments, and triangle properties including maximum area, minimum internal angle. The triangulation code in 'RTriangle' uses the method of Cheng, Dey and Shewchuk (2012, ISBN:9781584887300). For a low-dependency alternative with low-quality path-based constrained triangulation see <https://CRAN.R-project.org/package=decido> and for high-quality configurable triangulation see <https://CRAN.R-project.org/package=anglr>.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package sf updated to version 0.9-7 with previous version 0.9-6 dated 2020-09-13

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations. Optionally uses the 's2' package for spherical geometry operations on geographic coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Etienne Racine [ctb], Michael Sumner [ctb], Ian Cook [ctb], Tim Keitt [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Kirill MĆ¼ller [ctb], Thomas Lin Pedersen [ctb], Dan Baston [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package robmed updated to version 0.8.0 with previous version 0.7.0 dated 2020-06-08

Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package pencal updated to version 0.2.1 with previous version 0.1.2 dated 2020-12-04

Title: Penalized Regression Calibration (PRC)
Description: Computes the penalized regression calibration (PRC) method, that allows to predict survival using high-dimensional longitudinal predictors. PRC is described in Signorelli et al. (in review).
Author: Mirko Signorelli [aut, cre, cph] (<https://orcid.org/0000-0002-8102-3356>), Pietro Spitali [ctb], Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

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Package micEconCES updated to version 1.0-0 with previous version 0.9-8 dated 2014-04-23

Title: Analysis with the Constant Elasticity of Substitution (CES) Function
Description: Tools for econometric analysis and economic modelling with the traditional two-input Constant Elasticity of Substitution (CES) function and with nested CES functions with three and four inputs. The econometric estimation can be done by the Kmenta approximation, or non-linear least-squares using various gradient-based or global optimisation algorithms. Some of these algorithms can constrain the parameters to certain ranges, e.g. economically meaningful values. Furthermore, the non-linear least-squares estimation can be combined with a grid-search for the rho-parameter(s).
Author: Arne Henningsen and Geraldine Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

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Package helda updated to version 1.1.5 with previous version 1.1.3 dated 2020-06-13

Title: Preprocess Data and Get Better Insights from Machine Learning Models
Description: The main focus is on preprocessing and data visualization of machine learning models performances. Some functions allow to fill in gaps in time series using linear interpolation on panel data, some functions permit to draw lift effect and lift curve in order to benchmark machine learning models or you can even find the optimal number of clusters in agglomerative clustering algorithm.
Author: Simon Corde [aut, cre]
Maintainer: Simon Corde <simon.corde@hotmail.fr>

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Package heatmap3 updated to version 1.1.9 with previous version 1.1.7 dated 2020-03-03

Title: An Improved Heatmap Package
Description: An improved heatmap package. Completely compatible with the original R function 'heatmap', and provides more powerful and convenient features.
Author: Shilin Zhao, Linlin Yin, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao <shilin.zhao@vanderbilt.edu>

Diff between heatmap3 versions 1.1.7 dated 2020-03-03 and 1.1.9 dated 2021-01-06

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Package ggroups updated to version 2.1.0 with previous version 2.0.3 dated 2020-03-19

Title: Pedigree and Genetic Groups
Description: Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, calculating inbreeding coefficients (Meuwissen & Luo, 1992 <doi:10.1186/1297-9686-24-4-305>), as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Author: Mohammad Ali Nilforooshan [aut, cre] (<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>

Diff between ggroups versions 2.0.3 dated 2020-03-19 and 2.1.0 dated 2021-01-06

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New package footprint with initial version 0.1
Package: footprint
Title: Calculate Air Travel Emissions
Version: 0.1
Authors@R: c(person(given = "Anthony", family = "Schmidt", role = c("aut", "cre"), email = "aschmi11@utk.edu", comment = c(ORCID = "0000-0003-4478-0638")), person(given = "Kasia", family = "Kulma", role = "aut", email = "katarzyna.kulma@gmail.com"))
Description: A handy tool to calculate carbon footprints from air travel based on three-letter International Air Transport Association (IATA) airport codes or latitude and longitude. footprint first calculates the great-circle distance between departure and arrival destinations. It then uses the Department of Environment, Food & Rural Affairs (DEFRA) greenhouse gas conversion factors for business air travel to estimate the carbon footprint. These conversion factors consider trip length, flight class (e.g. economy, business), and emissions metric (e.g. carbon dioxide equivalent, methane).
License: CC0
URL: https://github.com/acircleda/footprint
BugReports: https://github.com/acircleda/footprint/issues
Depends: R (>= 3.5.0)
Imports: airportr, dplyr, magrittr, rlang
Suggests: devtools, knitr, rmarkdown, testthat (>= 2.1.0), tibble, covr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-04 16:54:42 UTC; aschmidt
Author: Anthony Schmidt [aut, cre] (<https://orcid.org/0000-0003-4478-0638>), Kasia Kulma [aut]
Maintainer: Anthony Schmidt <aschmi11@utk.edu>
Repository: CRAN
Date/Publication: 2021-01-06 10:40:02 UTC

More information about footprint at CRAN
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Package disastr.api updated to version 1.0.2 with previous version 1.0.1 dated 2021-01-05

Title: Automated Retrieval of Disaster Event Data
Description: Access and manage the application programming interface (API) of the United Nations Office for the Coordination of Humanitarian Affairs' (OCHA) ReliefWeb disaster events at <https://reliefweb.int/disasters/>. The package offers functionality to retrieve a user-defined sample of disaster events from ReliefWeb, providing an easy alternative to scraping the ReliefWeb website. It enables a seamless integration of regular data updates into the research work flow.
Author: Christoph Dworschak [aut, cre] (<https://orcid.org/0000-0003-0196-9545>)
Maintainer: Christoph Dworschak <c.dworschak@essex.ac.uk>

Diff between disastr.api versions 1.0.1 dated 2021-01-05 and 1.0.2 dated 2021-01-06

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Package cmfrec updated to version 2.4.1 with previous version 2.3.0 dated 2020-11-23

Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization, Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the product of two low-dimensional matrices aided with secondary information matrices about rows and/or columns of 'X' which are also factorized using the same latent components. The intended usage is for recommender systems, dimensionality reduction, and missing value imputation. Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky, (2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model, (Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>), or the enhanced model with 'implicit features' (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009) <doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver (Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>), providing efficient methods for sparse and dense data, and mixtures thereof. Supports L1 and L2 regularization in the main models, offers alternative most-popular and content-based models, and implements functionality for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph], Jorge Nocedal [cph], Naoaki Okazaki [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between cmfrec versions 2.3.0 dated 2020-11-23 and 2.4.1 dated 2021-01-06

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Package AMR updated to version 1.5.0 with previous version 1.4.0 dated 2020-10-08

Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) <doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alexander W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Gwen Knight [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Sofia Ny [ctb], Rogier P. Schade [ctb], Dennis Souverein [ctb], Anthony Underwood [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between AMR versions 1.4.0 dated 2020-10-08 and 1.5.0 dated 2021-01-06

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New package SAMGEP with initial version 0.1.0-1
Package: SAMGEP
Type: Package
Title: A Semi-Supervised Method for Prediction of Phenotype Event Times
Version: 0.1.0-1
Authors@R: c( person("Yuri", "Ahuja", role = c("aut", "cre"), email = "Yuri_Ahuja@hms.harvard.edu"), person("Tianxi", "Cai", role = c("aut")), person(family = "PARSE LTD", role = c("aut")) )
Description: A novel semi-supervised machine learning algorithm to predict phenotype event times using Electronic Health Record (EHR) data.
URL: https://github.com/celehs/SAMGEP
BugReports: https://github.com/celehs/SAMGEP/issues
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Depends: R (>= 3.5.0)
Imports: stats, mvtnorm, nlme, pROC, abind, nloptr, foreach, doParallel, parallel, Rcpp
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2021-01-04 02:54:21 UTC; yuriahuja
Author: Yuri Ahuja [aut, cre], Tianxi Cai [aut], PARSE LTD [aut]
Maintainer: Yuri Ahuja <Yuri_Ahuja@hms.harvard.edu>
Repository: CRAN
Date/Publication: 2021-01-06 10:00:02 UTC

More information about SAMGEP at CRAN
Permanent link

Package RobinHood updated to version 1.5 with previous version 1.4 dated 2020-05-23

Title: Interface for the RobinHood.com No Commission Investing Platform
Description: Execute API calls to the RobinHood <https://robinhood.com> investing platform. Functionality includes accessing account data and current holdings, retrieving investment statistics and quotes, placing and canceling orders, getting market trading hours, searching investments by popular tag, and interacting with watch lists.
Author: Joseph Blubaugh
Maintainer: Joseph Blubaugh <jestonblu@gmail.com>

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New package ProSGPV with initial version 0.1.0
Package: ProSGPV
Title: Penalized Regression with Second-Generation P-Values
Version: 0.1.0
Authors@R: c(person(given = "Yi", family = "Zuo", role = c("aut", "cre"), email = "yi.zuo@vanderbilt.edu", comment = c(ORCID = "0000-0002-6643-8326")), person("Thomas", "Stewart", email = "thomas.stewart@vanderbilt.edu", role = c("aut")), person("Jeffrey", "Blume", email = "j.blume@vanderbilt.edu", role = c("aut")) )
Maintainer: Yi Zuo <yi.zuo@vanderbilt.edu>
Description: Implementation of penalized regression with second-generation p-values for variable selection. The one-stage algorithm is extremely fast and the two-stage algorithm has lower parameter estimation bias when data are highly correlated. S3 methods print(), summary(), coef(), and predict() are available for both algorithms, and S3 method plot() is available for the two-stage algorithm. Technical details of the algorithms can be found at <arXiv:2012.07941>.
Depends: R (>= 3.5.0), glmnet
Imports: MASS
License: GPL-3
Encoding: UTF-8
URL: https://github.com/zuoyi93/ProSGPV, https://arxiv.org/abs/2012.07941
BugReports: https://github.com/zuoyi93/ProSGPV/issues
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-04 14:04:41 UTC; buzzzuoyi
Author: Yi Zuo [aut, cre] (<https://orcid.org/0000-0002-6643-8326>), Thomas Stewart [aut], Jeffrey Blume [aut]
Repository: CRAN
Date/Publication: 2021-01-06 09:50:05 UTC

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Package periscope updated to version 0.5.3 with previous version 0.5.2 dated 2020-09-21

Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework including a variety of developer convenience functions with the goal of both streamlining robust application development while assisting with creating a consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre], Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer), Ger Inberg [ctb], Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>

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New package noisyr with initial version 0.1.0
Package: noisyr
Type: Package
Title: Noise Quantification in High Throughput Sequencing Output
Version: 0.1.0
Authors@R: c( person("Ilias", "Moutsopoulos", , "im383@cam.ac.uk", c("aut", "cre")), person("Irina", "Mohorianu", , "iim22@cam.ac.uk", role = c("aut","ctb")), person("Hajk-Georg", "Drost", , "hajk-georg.drost@tuebingen.mpg.de", role="ctb"), person("Elze", "Lauzikaite", , "el523@cam.ac.uk", role = "ctb") )
Maintainer: Ilias Moutsopoulos <im383@cam.ac.uk>
Description: Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output.
Depends: R (>= 3.1.2)
Imports: utils, grDevices, tibble, dplyr,magrittr, ggplot2, preprocessCore, IRanges, GenomicRanges, Rsamtools, philentropy, doParallel, foreach
Suggests: testthat, roxygen2
License: GPL-2
Encoding: UTF-8
LazyData: true
URL: https://github.com/Core-Bioinformatics/noisyR
BugReports: https://github.com/Core-Bioinformatics/noisyR/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-01-04 14:56:17 UTC; Ilias Moutsopoulos
Author: Ilias Moutsopoulos [aut, cre], Irina Mohorianu [aut, ctb], Hajk-Georg Drost [ctb], Elze Lauzikaite [ctb]
Repository: CRAN
Date/Publication: 2021-01-06 09:50:02 UTC

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Package hse updated to version 0.0-26 with previous version 0.0-14 dated 2020-11-30

Title: The hse Distribution
Description: Density (probability), distribution, inverse distribution (quantile) and random data generation functions for the hse ("hope springs eternal") distribution. Maximum likelihood estimation of parameters. Plotting of the probability mass function, from specified parameters or from a maximum likelihood fit, and of the likelihood surface. Fisher information, different estimates of the hessian of the log likelihood and Monte Carlo estimation of the covariance matrix of the maximum likelihood parameter estimates. Goodness of fit tests.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package vote updated to version 2.1-0 with previous version 2.0-2 dated 2020-12-12

Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including the single transferable vote or ranked choice (Newland and F.S. Britton, 1997; ISBN: 0903291185), approval, score, plurality, condorcet and two-round runoff methods.
Author: Hana Sevcikova, Bernard Silverman, Adrian Raftery
Maintainer: Hana Sevcikova<hanas@uw.edu>

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Package postcards updated to version 0.2.0 with previous version 0.1.0 dated 2020-12-14

Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>

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Package polyRAD updated to version 1.3 with previous version 1.2 dated 2020-05-12

Title: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020) <doi:10.1101/2020.01.11.902890>.
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>), U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>

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Package peruse updated to version 0.2.0 with previous version 0.1.0 dated 2020-12-21

Title: Sequence Iteration and Set Comprehension
Description: A friendly API for sequence iteration and set comprehension, and a tool for constructing and manipulating hash-table based data sets.
Author: Jacob Goldsmith [aut, cre]
Maintainer: Jacob Goldsmith <jacobg314@hotmail.com>

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Package mlflow updated to version 1.13.1 with previous version 1.12.1 dated 2020-11-19

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

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Package cir updated to version 2.1.1 with previous version 2.1.0 dated 2020-12-07

Title: Centered Isotonic Regression and Dose-Response Utilities
Description: Isotonic regression (IR) and its improvement: centered isotonic regression (CIR). CIR is recommended in particular with small samples. Also, interval estimates for both, and additional utilities such as plotting dose-response data.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <aoron@idmod.org>

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Package cgwtools updated to version 3.3 with previous version 3.2 dated 2020-09-07

Title: Miscellaneous Tools
Description: Functions for performing quick observations or evaluations of data, including a variety of ways to list objects by size, class, etc. The functions 'seqle' and 'reverse.seqle' mimic the base 'rle' but can search for linear sequences. The function 'splatnd' allows the user to generate zero-argument commands without the need for 'makeActiveBinding' . Functions provided to convert from any base to any other base, and to find the n-th greatest max or n-th least min. In addition, functions which mimic Unix shell commands, including 'head', 'tail' ,'pushd' ,and 'popd'.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>

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Package germanpolls (with last version 0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-04-30 0.3
2019-01-08 0.2

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Package sarsop (with last version 0.6.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-12 0.6.6
2020-08-03 0.6.5

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Package rjpdmp (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-10 0.1.0

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Package opentimsr (with last version 1.0.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-10 1.0.2

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Package eBsc (with last version 4.12) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-11-24 4.12

Permanent link
Package covidregionaldata (with last version 0.8.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-12 0.8.2
2020-08-27 0.6.0
2020-07-24 0.5.0

Permanent link
Package doc2vec (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-10 0.1.0

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Package biClassify (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-14 1.0

Permanent link
Package plater updated to version 1.0.3 with previous version 1.0.2 dated 2020-03-24

Title: Read, Tidy, and Display Data from Microtiter Plates
Description: Tools for interacting with data from experiments done in microtiter plates. Easily read in plate-shaped data and convert it to tidy format, combine plate-shaped data with tidy data, and view tidy data in plate shape.
Author: Sean Hughes [aut, cre] (<https://orcid.org/0000-0002-9409-9405>)
Maintainer: Sean Hughes <smhughes@uw.edu>

Diff between plater versions 1.0.2 dated 2020-03-24 and 1.0.3 dated 2021-01-06

 DESCRIPTION                                                         |   12 
 MD5                                                                 |  420 +--
 NAMESPACE                                                           |   15 
 NEWS.md                                                             |   54 
 R/add_plate.R                                                       |  265 +-
 R/check_plater_format.R                                             |   88 
 R/convert_plate_to_column.R                                         |  302 +-
 R/plate_utilities.R                                                 |  412 +--
 R/plater.R                                                          |   30 
 R/read_plate.R                                                      |  432 +--
 R/read_plates.R                                                     |  159 -
 R/view_plate.R                                                      |  452 ++--
 build/vignette.rds                                                  |binary
 inst/CITATION                                                       |   36 
 inst/doc/plater-basics.R                                            |  130 -
 inst/doc/plater-basics.Rmd                                          |  316 +-
 inst/doc/plater-basics.html                                         | 1092 +++++-----
 inst/extdata/example-1.csv                                          |   78 
 inst/extdata/example-2-part-A.csv                                   |  194 -
 inst/extdata/example-2-part-B.csv                                   |   58 
 inst/extdata/more-bacteria.csv                                      |   78 
 man/add_plate.Rd                                                    |   98 
 man/check_plater_format.Rd                                          |   50 
 man/plater.Rd                                                       |   36 
 man/read_plate.Rd                                                   |  140 -
 man/read_plates.Rd                                                  |   86 
 man/view_plate.Rd                                                   |   76 
 tests/testthat.R                                                    |    2 
 tests/testthat/test-add_plate.R                                     |  396 +--
 tests/testthat/test-convert_plate_to_column.R                       |  210 -
 tests/testthat/test-plate_utilities.R                               |  924 ++++----
 tests/testthat/test-read_plate.R                                    |  278 +-
 tests/testthat/test-read_plates.R                                   |  132 -
 tests/testthat/test-view_plate.R                                    |  532 ++--
 tests/testthat/testData/12/allWellIds.csv                           |    8 
 tests/testthat/testData/12/dontAddWhiteSpace.csv                    |    8 
 tests/testthat/testData/12/incorrectRowLabels.csv                   |    8 
 tests/testthat/testData/12/missingBottomRow.csv                     |    6 
 tests/testthat/testData/12/missingColumnsWithCorrectTitles.csv      |    8 
 tests/testthat/testData/12/missingMiddleRow.csv                     |    8 
 tests/testthat/testData/12/missingPlateNames.csv                    |   18 
 tests/testthat/testData/12/missingRightColumn.csv                   |    8 
 tests/testthat/testData/12/missingRowLabels.csv                     |    8 
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 tests/testthat/testData/12/oneExtraRow.csv                          |   10 
 tests/testthat/testData/12/oneFullOnePartEmpty.csv                  |   18 
 tests/testthat/testData/12/onePlateOneBlankRow.csv                  |    8 
 tests/testthat/testData/12/onePlateTwoBlankRows.csv                 |   10 
 tests/testthat/testData/12/oneWell.csv                              |    8 
 tests/testthat/testData/12/read_plates-validOne.csv                 |   18 
 tests/testthat/testData/12/read_plates-validTwo.csv                 |   18 
 tests/testthat/testData/12/twoPlatesNoBlankRow.csv                  |   18 
 tests/testthat/testData/12/twoPlatesOneBlankRow.csv                 |   20 
 tests/testthat/testData/12/twoPlatesTwoBlankRows.csv                |   20 
 tests/testthat/testData/12/validPlate.csv                           |    8 
 tests/testthat/testData/12/validPlateWithWhiteSpaceInRowNames.csv   |    8 
 tests/testthat/testData/12/weirdCharacters.csv                      |    8 
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 tests/testthat/testData/1536/incorrectRowLabels.csv                 |   66 
 tests/testthat/testData/1536/missingBottomRow.csv                   |   64 
 tests/testthat/testData/1536/missingColumnsWithCorrectTitles.csv    |   66 
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 tests/testthat/testData/1536/missingPlateNames.csv                  |  134 -
 tests/testthat/testData/1536/missingRightColumn.csv                 |   66 
 tests/testthat/testData/1536/missingRowLabels.csv                   |   66 
 tests/testthat/testData/1536/nonEmptyTopLeft.csv                    |   66 
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 tests/testthat/testData/1536/oneExtraRow.csv                        |   68 
 tests/testthat/testData/1536/oneFullOnePartEmpty.csv                |  134 -
 tests/testthat/testData/1536/onePlateOneBlankRow.csv                |   68 
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 tests/testthat/testData/1536/validPlate.csv                         |   66 
 tests/testthat/testData/1536/validPlateWithWhiteSpaceInRowNames.csv |   66 
 tests/testthat/testData/1536/weirdCharacters.csv                    |   66 
 tests/testthat/testData/1536/wellIdsAndEmptyWells.csv               |   66 
 tests/testthat/testData/24/allWellIds.csv                           |   10 
 tests/testthat/testData/24/dontAddWhiteSpace.csv                    |   10 
 tests/testthat/testData/24/incorrectRowLabels.csv                   |   10 
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 tests/testthat/testData/24/missingPlateNames.csv                    |   22 
 tests/testthat/testData/24/missingRightColumn.csv                   |   10 
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 tests/testthat/testData/24/validPlateWithWhiteSpaceInRowNames.csv   |   10 
 tests/testthat/testData/24/weirdCharacters.csv                      |   10 
 tests/testthat/testData/24/wellIdsAndEmptyWells.csv                 |   10 
 tests/testthat/testData/384/allWellIds.csv                          |   34 
 tests/testthat/testData/384/dontAddWhiteSpace.csv                   |   34 
 tests/testthat/testData/384/incorrectRowLabels.csv                  |   34 
 tests/testthat/testData/384/missingBottomRow.csv                    |   32 
 tests/testthat/testData/384/missingColumnsWithCorrectTitles.csv     |   34 
 tests/testthat/testData/384/missingMiddleRow.csv                    |   34 
 tests/testthat/testData/384/missingPlateNames.csv                   |   70 
 tests/testthat/testData/384/missingRightColumn.csv                  |   34 
 tests/testthat/testData/384/missingRowLabels.csv                    |   34 
 tests/testthat/testData/384/nonEmptyTopLeft.csv                     |   34 
 tests/testthat/testData/384/oneExtraColumn.csv                      |   34 
 tests/testthat/testData/384/oneExtraRow.csv                         |   36 
 tests/testthat/testData/384/oneFullOnePartEmpty.csv                 |   70 
 tests/testthat/testData/384/onePlateOneBlankRow.csv                 |   34 
 tests/testthat/testData/384/onePlateTwoBlankRows.csv                |   36 
 tests/testthat/testData/384/oneWell.csv                             |   34 
 tests/testthat/testData/384/read_plates-validOne.csv                |   70 
 tests/testthat/testData/384/read_plates-validTwo.csv                |   70 
 tests/testthat/testData/384/twoPlatesNoBlankRow.csv                 |   68 
 tests/testthat/testData/384/twoPlatesOneBlankRow.csv                |   70 
 tests/testthat/testData/384/twoPlatesTwoBlankRows.csv               |   72 
 tests/testthat/testData/384/validPlate.csv                          |   34 
 tests/testthat/testData/384/validPlateWithWhiteSpaceInRowNames.csv  |   34 
 tests/testthat/testData/384/weirdCharacters.csv                     |   34 
 tests/testthat/testData/384/wellIdsAndEmptyWells.csv                |   34 
 tests/testthat/testData/48/allWellIds.csv                           |   14 
 tests/testthat/testData/48/dontAddWhiteSpace.csv                    |   14 
 tests/testthat/testData/48/incorrectRowLabels.csv                   |   14 
 tests/testthat/testData/48/missingBottomRow.csv                     |   12 
 tests/testthat/testData/48/missingColumnsWithCorrectTitles.csv      |   14 
 tests/testthat/testData/48/missingMiddleRow.csv                     |   14 
 tests/testthat/testData/48/missingPlateNames.csv                    |   30 
 tests/testthat/testData/48/missingRightColumn.csv                   |   14 
 tests/testthat/testData/48/missingRowLabels.csv                     |   14 
 tests/testthat/testData/48/nonEmptyTopLeft.csv                      |   14 
 tests/testthat/testData/48/oneExtraColumn.csv                       |   14 
 tests/testthat/testData/48/oneExtraRow.csv                          |   16 
 tests/testthat/testData/48/oneFullOnePartEmpty.csv                  |   30 
 tests/testthat/testData/48/onePlateOneBlankRow.csv                  |   14 
 tests/testthat/testData/48/onePlateTwoBlankRows.csv                 |   16 
 tests/testthat/testData/48/oneWell.csv                              |   14 
 tests/testthat/testData/48/read_plates-validOne.csv                 |   30 
 tests/testthat/testData/48/read_plates-validTwo.csv                 |   30 
 tests/testthat/testData/48/twoPlatesNoBlankRow.csv                  |   30 
 tests/testthat/testData/48/twoPlatesOneBlankRow.csv                 |   32 
 tests/testthat/testData/48/twoPlatesTwoBlankRows.csv                |   32 
 tests/testthat/testData/48/validPlate.csv                           |   14 
 tests/testthat/testData/48/validPlateWithWhiteSpaceInRowNames.csv   |   14 
 tests/testthat/testData/48/weirdCharacters.csv                      |   14 
 tests/testthat/testData/48/wellIdsAndEmptyWells.csv                 |   14 
 tests/testthat/testData/6/allWellIds.csv                            |    6 
 tests/testthat/testData/6/dontAddWhiteSpace.csv                     |    6 
 tests/testthat/testData/6/incorrectRowLabels.csv                    |    6 
 tests/testthat/testData/6/missingBottomRow.csv                      |    4 
 tests/testthat/testData/6/missingColumnsWithCorrectTitles.csv       |    6 
 tests/testthat/testData/6/missingMiddleRow.csv                      |    6 
 tests/testthat/testData/6/missingPlateNames.csv                     |   14 
 tests/testthat/testData/6/missingRightColumn.csv                    |    6 
 tests/testthat/testData/6/missingRowLabels.csv                      |    6 
 tests/testthat/testData/6/nonEmptyTopLeft.csv                       |    6 
 tests/testthat/testData/6/oneExtraColumn.csv                        |    6 
 tests/testthat/testData/6/oneExtraRow.csv                           |    8 
 tests/testthat/testData/6/oneFullOnePartEmpty.csv                   |   14 
 tests/testthat/testData/6/onePlateOneBlankRow.csv                   |    6 
 tests/testthat/testData/6/onePlateTwoBlankRows.csv                  |   10 
 tests/testthat/testData/6/oneWell.csv                               |    6 
 tests/testthat/testData/6/read_plates-validOne.csv                  |   14 
 tests/testthat/testData/6/read_plates-validTwo.csv                  |   14 
 tests/testthat/testData/6/twoPlatesNoBlankRow.csv                   |   14 
 tests/testthat/testData/6/twoPlatesOneBlankRow.csv                  |   14 
 tests/testthat/testData/6/twoPlatesTwoBlankRows.csv                 |   18 
 tests/testthat/testData/6/validPlate.csv                            |    6 
 tests/testthat/testData/6/validPlateWithWhiteSpaceInRowNames.csv    |    6 
 tests/testthat/testData/6/weirdCharacters.csv                       |    6 
 tests/testthat/testData/6/wellIdsAndEmptyWells.csv                  |    6 
 tests/testthat/testData/96/allWellIds.csv                           |   18 
 tests/testthat/testData/96/dontAddWhiteSpace.csv                    |   18 
 tests/testthat/testData/96/incorrectRowLabels.csv                   |   18 
 tests/testthat/testData/96/missingBottomRow.csv                     |   16 
 tests/testthat/testData/96/missingColumnsWithCorrectTitles.csv      |   18 
 tests/testthat/testData/96/missingMiddleRow.csv                     |   18 
 tests/testthat/testData/96/missingPlateNames.csv                    |   38 
 tests/testthat/testData/96/missingRightColumn.csv                   |   18 
 tests/testthat/testData/96/missingRowLabels.csv                     |   18 
 tests/testthat/testData/96/nonEmptyTopLeft.csv                      |   18 
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 tests/testthat/testData/96/oneExtraRow.csv                          |   20 
 tests/testthat/testData/96/oneFullOnePartEmpty.csv                  |   38 
 tests/testthat/testData/96/onePlateOneBlankRow.csv                  |   20 
 tests/testthat/testData/96/onePlateTwoBlankRows.csv                 |   20 
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 tests/testthat/testData/96/read_plates-validOne.csv                 |   38 
 tests/testthat/testData/96/read_plates-validTwo.csv                 |   38 
 tests/testthat/testData/96/twoPlatesNoBlankRow.csv                  |   40 
 tests/testthat/testData/96/twoPlatesOneBlankRow.csv                 |   40 
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 tests/testthat/testData/96/weirdCharacters.csv                      |   18 
 tests/testthat/testData/96/wellIdsAndEmptyWells.csv                 |   18 
 tests/testthat/testData/numbers-and-text.csv                        |   18 
 vignettes/plater-basics.Rmd                                         |  316 +-
 211 files changed, 6561 insertions(+), 6498 deletions(-)

More information about plater at CRAN
Permanent link

Package NFLSimulatoR updated to version 0.3.0 with previous version 0.2.1 dated 2020-12-08

Title: Simulating Plays and Drives in the NFL
Description: The intent here is to enable the simulation of plays/drives and evaluate game-play strategies in the National Football League (NFL). Built-in strategies include going for it on fourth down and varying the proportion of passing/rushing plays during a drive. The user should be familiar with nflscrapR data before trying to write his/her own strategies. This work is inspired by a blog post by Mike Lopez, currently the Director of Data and Analytics at the NFL, Lopez (2019) <https://statsbylopez.netlify.app/post/resampling-nfl-drives/>.
Author: Ryan Elmore [cre, aut] (<https://orcid.org/0000-0002-0092-4532>), Ben Williams [aut] (<https://orcid.org/0000-0001-8474-5066>), Will Palmquist [aut] (<https://orcid.org/0000-0002-6100-0923>)
Maintainer: Ryan Elmore <Ryan.Elmore@du.edu>

Diff between NFLSimulatoR versions 0.2.1 dated 2020-12-08 and 0.3.0 dated 2021-01-06

 NFLSimulatoR-0.2.1/NFLSimulatoR/R/sample_drives_until_score.R    |only
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 12 files changed, 23 insertions(+), 12 deletions(-)

More information about NFLSimulatoR at CRAN
Permanent link

Package kim updated to version 0.2.35 with previous version 0.2.20 dated 2020-12-03

Title: Functions for Behavioral Science Researchers
Description: Miscellaneous functions to simplify and expedite analyses of experimental data. Examples include a function that plots sample means of groups in a factorial experimental design, a function that conducts robust regressions with bootstrapped samples, and a function that conducts two-way analysis of variance.
Author: Jin Kim [aut, cre] (<https://orcid.org/0000-0002-5013-3958>)
Maintainer: Jin Kim <jin.m.kim@yale.edu>

Diff between kim versions 0.2.20 dated 2020-12-03 and 0.2.35 dated 2021-01-06

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More information about kim at CRAN
Permanent link

Package ISRaD updated to version 1.7.8 with previous version 1.5.6 dated 2020-09-16

Title: Tools and Data for the International Soil Radiocarbon Database
Description: This is the central location for data and tools for the development, maintenance, analysis, and deployment of the International Soil Radiocarbon Database (ISRaD). ISRaD was developed as a collaboration between the U.S. Geological Survey Powell Center and the Max Planck Institute for Biogeochemistry. This R package provides tools for accessing and manipulating ISRaD data, compiling local data using the ISRaD data structure, and simple query and reporting functions for ISRaD. For more detailed information visit the ISRaD website at: <https://soilradiocarbon.org/>.
Author: Alison Hoyt [aut], Jeffrey Beem-Miller [aut, cre], Shane Stoner [aut], J. Grey Monroe [aut], Caitlin Hicks-Pries [aut], Paul A. Levine [aut]
Maintainer: Jeffrey Beem-Miller <jbeem@bgc-jena.mpg.de>

Diff between ISRaD versions 1.5.6 dated 2020-09-16 and 1.7.8 dated 2021-01-06

 DESCRIPTION                                   |   10 +-
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 R/QAQC.R                                      |   34 ++++--
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 inst/extdata/ISRaD_Master_Template.xlsx       |binary
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 man/Gaudinski_2001.Rd                         |    4 
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 tests/testthat/test-ISRaD.extra.fill_coords.R |   65 +++++++------
 tests/testthat/test-ISRaD.flatten.R           |    4 
 tests/testthat/test-ISRaD.rep.count.all.R     |    2 
 tests/testthat/test-ISRaD.rep.count.frc.R     |    2 
 tests/testthat/test-ISRaD.rep.entry.stats.R   |    2 
 tests/testthat/test-ISRaD.report.R            |    6 -
 tests/testthat/test-compile.R                 |   13 +-
 tests/testthat/test-qaqc.R                    |    2 
 tests/testthat/test-utils.R                   |   50 +++++-----
 35 files changed, 391 insertions(+), 248 deletions(-)

More information about ISRaD at CRAN
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