Sun, 28 Mar 2021

Package srvyr updated to version 1.0.1 with previous version 1.0.0 dated 2020-12-01

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre], Thomas Lumley [ctb], Tomasz Żółtak [ctb], Ben Schneider [aut, ctb], Pavel N. Krivitsky [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 1.0.0 dated 2020-12-01 and 1.0.1 dated 2021-03-28

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Package simsem updated to version 0.5-16 with previous version 0.5-15 dated 2020-02-12

Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut], Patrick Miller [aut], Alexander Schoemann [aut] (<https://orcid.org/0000-0002-8479-8798>), Terrence D. Jorgensen [aut, cre] (<https://orcid.org/0000-0001-5111-6773>), Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>

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Package divest updated to version 0.10.0 with previous version 0.9.0 dated 2020-09-04

Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] (<https://orcid.org/0000-0002-6608-0619>), Chris Rorden [aut], Martin J Fiedler [cph], Cong Xu [cph], Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>

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Package fsbrain updated to version 0.4.2 with previous version 0.4.1 dated 2021-01-20

Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>

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Package gausscov updated to version 0.1.0 with previous version 0.0.13 dated 2021-02-26

Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>

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Package deaR updated to version 1.2.3 with previous version 1.2.2 dated 2020-12-11

Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models.See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>

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Package poorman updated to version 0.2.5 with previous version 0.2.4 dated 2020-11-27

Title: A Poor Man's Dependency Free Recreation of 'dplyr'
Description: A replication of key functionality from 'dplyr' and the wider 'tidyverse' using only 'base'.
Author: Nathan Eastwood [aut, cre]
Maintainer: Nathan Eastwood <nathan.eastwood@icloud.com>

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Package strucchangeRcpp updated to version 1.5-3-1.0.1 with previous version 1.5-3-1.0.0 dated 2021-03-24

Title: Testing, Monitoring, and Dating Structural Changes: C++ Version
Description: A fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. 'strucchangeRcpp' features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.
Author: Dainius Masiliunas [aut, cre] (<https://orcid.org/0000-0001-5654-1277>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Marius Appel [aut], Friedrich Leisch [aut], Kurt Hornik [aut], Christian Kleiber [aut], Andrei Mirt [ctb] (<https://orcid.org/0000-0003-3654-2090>), Bruce Hansen [ctb], Edgar C. Merkle [ctb]
Maintainer: Dainius Masiliunas <pastas4@gmail.com>

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Package stats19 updated to version 1.4.1 with previous version 1.4.0 dated 2021-03-15

Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979, the types (including make and model) of vehicles involved and the consequential casualties. The statistics relate only to personal casualties on public roads that are reported to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See the Department for Transport website <https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>), Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>), David Ranzolin [rev], Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>), Ivo Wengraf [ctb], RAC Foundation [fnd]
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package GNRS updated to version 0.2.0 with previous version 0.1.1 dated 2021-01-22

Title: Access the 'Geographic Name Resolution Service'
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Author: Brad Boyle [aut], Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>

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Package GauPro updated to version 0.2.3 with previous version 0.2.2 dated 2017-09-11

Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes are commonly used in computer experiments to fit an interpolating model. The model is stored as an 'R6' object and can be easily updated with new data. There are options to run in parallel (not for Windows), and 'Rcpp' has been used to speed up calculations. Other R packages that perform similar calculations include 'laGP', 'DiceKriging', 'GPfit', and 'mlegp'.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>

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Package foqat updated to version 1.6.4 with previous version 1.6.2 dated 2021-03-18

Title: Field Observation Quick Analysis Toolkit
Description: Tools for quickly processing and analyzing field observation data and air quality data. This tools contain functions that facilitate analysis in atmospheric chemistry (especially in ozone pollution). Some functions of time series are also applicable to other fields. For detail please view homepage<https://github.com/tianshu129/foqat>. Scientific Reference: 1. The Hydroxyl Radical (OH) Reactivity: Roger Atkinson and Janet Arey (2003) <doi:10.1021/cr0206420>. 2. Ozone Formation Potential (OFP): <https://ww3.arb.ca.gov/regact/2009/mir2009/mir10.pdf>. 3. TUV model: <https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model>.
Author: Tianshu Chen
Maintainer: Tianshu Chen <tianshu129@163.com>

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Package yardstick updated to version 0.0.8 with previous version 0.0.7 dated 2020-07-13

Title: Tidy Characterizations of Model Performance
Description: Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).
Author: Max Kuhn [aut], Davis Vaughan [aut, cre], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

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Package spatstat.linnet updated to version 2.1-1 with previous version 2.0-0 dated 2021-03-18

Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network and provides functionality for geometrical operations, data analysis and modelling of data on a linear network, in the 'spatstat' family of packages. Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks. Data types defined on a network include point patterns, pixel images, functions, and tessellations. Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the function lppm() similar to glm(). Only Poisson models are implemented so far. Models may involve dependence on covariates and dependence on marks. Models are fitted by maximum likelihood. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots. Random point patterns on a network can be generated using a variety of models.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut], Ottmar Cronie [ctb], Tilman Davies [ctb], Greg McSwiggan [ctb], Suman Rakshit [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package rgeoprofile updated to version 0.2.1 with previous version 0.2.0 dated 2020-05-28

Title: Geographic Profiling Methods for Serial Crime Analysis
Description: An implementation of functions for the analysis of serial crime incidents. The package implements algorithms for the geographical profiling of serial incidents in attempt to prioritize the area in which the anchor point or home base of the perpetrator is located. The geographic profiling methods in the package are implemented based upon the 'Dragnet' software by Canter, Coffey, Huntley, and Missen (2000) <doi:10.1023/A:1007551316253>, the 'CrimeStat' software by Levine (2013) <https://nij.ojp.gov/topics/articles/crimestat-spatial-statistics-program-analysis-crime-incident-locations>, and the criminal geographic targeting model outlined in Rossmo (2000, ISBN:978-0849381294) and Rossmo (1995) <http://summit.sfu.ca/item/6820>.
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspaulding02@hamline.edu>

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Package pbm updated to version 1.2.1 with previous version 1.1.0 dated 2018-03-05

Title: Protein Binding Models
Description: Binding models which are useful when analysing protein-ligand interactions by techniques such as Biolayer Interferometry (BLI) or Surface Plasmon Resonance (SPR). Naman B. Shah, Thomas M. Duncan (2014) <doi:10.3791/51383>. Hoang H. Nguyen et al. (2015) <doi:10.3390/s150510481>. After initial binding parameters are known, binding curves can be simulated and parameters can be varied. The models within this package may also be used to fit a curve to measured binding data using non-linear regression.
Author: Jonathan Davies [aut, cre] (<https://orcid.org/0000-0002-4986-8594>)
Maintainer: Jonathan Davies <jonathanrd@gmail.com>

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Package MATA updated to version 0.7.1 with previous version 0.7.0 dated 2021-03-21

Title: Model-Averaged Tail Area (MATA) Confidence Interval and Distribution
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, and MATA-Wald confidence densities and distributions, which are constructed using single-model frequentist estimators and model weights. See Turek and Fletcher (2012) <doi:10.1016/j.csda.2012.03.002> and Fletcher et al (2019) <doi:10.1007/s10651-019-00432-5> for details.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>

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Package kim updated to version 0.2.172 with previous version 0.2.133 dated 2021-03-14

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 robust two-way analysis of variance. Selected References: Canty & Ripley (2021) <https://CRAN.R-project.org/package=boot>. Cohen (1988) <doi:10.4324/9780203771587>. Dinno (2018) <https://CRAN.R-project.org/package=paran>. Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>. Edwards et al. (2020) <https://CRAN.R-project.org/package=lemon>. Fox et al. (2020) <https://CRAN.R-project.org/package=car>. Hester et al. (2020) <https://CRAN.R-project.org/package=remotes>. Ioannidis (2005) <doi:10.1371/journal.pmed.0020124> Kim (2021) <doi:10.5281/zenodo.4641436>. Kim (2020) <https://CRAN.R-project.org/package=ezr>. Long (2020) <https://CRAN.R-project.org/package=interactions>. Mair & Wilcox (2021) <https://CRAN.R-project.org/package=WRS2>. Pasek et al. (2020) <https://CRAN.R-project.org/package=weights>. Simmons et al. (2011) <doi:10.1177/0956797611417632>. Tingley et al. (2019) <https://CRAN.R-project.org/package=mediation>. Torchiano (2020) <https://CRAN.R-project.org/package=effsize>. Wickham et al. (2020) <https://CRAN.R-project.org/package=ggplot2>. Wilke (2021) <https://CRAN.R-project.org/package=ggridges>.
Author: Jin Kim [aut, cre] (<https://orcid.org/0000-0002-5013-3958>)
Maintainer: Jin Kim <jin.m.kim@yale.edu>

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Package GDAtools updated to version 1.6 with previous version 1.5 dated 2020-05-17

Title: A Toolbox for Geometric Data Analysis and More
Description: Contains functions for 'specific' Multiple Correspondence Analysis, Class Specific Analysis, Multiple Factor Analysis, 'standardized' MCA, computing and plotting structuring factors and concentration ellipses, inductive tests and others tools for Geometric Data Analysis (Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0>). It also provides functions for the translation of logit models coefficients into percentages (Deauvieau (2010) <doi:10.1177/0759106309352586>), weighted contingency tables, an association measure for contingency tables ("Percentages of Maximum Deviation from Independence", aka PEM, see Cibois (1993) <doi:10.1177/075910639304000103>) and some tools to measure bivariate associations between variables (phi, Cramér V, correlation coefficient, eta-squared...).
Author: Nicolas Robette
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>

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Package ftExtra updated to version 0.2.0 with previous version 0.1.1 dated 2021-01-27

Title: Extensions for 'Flextable'
Description: Build display tables easily by extending the functionality of the 'flextable' package. Features include spanning header, grouping rows, parsing markdown and so on.
Author: Atsushi Yasumoto [aut, cph, cre] (<https://orcid.org/0000-0002-8335-495X>), David Gohel [ctb], Romain François [ctb] (<https://orcid.org/0000-0002-2444-4226>)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>

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Package sn updated to version 2.0.0 with previous version 1.6-2 dated 2020-05-26

Title: The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t and the SUN families. For the skew-normal and the skew-t distributions, statistical methods are provided for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini [aut, cre] (<https://orcid.org/0000-0002-7583-1269>)
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package acled.api updated to version 1.1.3 with previous version 1.1.2 dated 2021-03-04

Title: Automated Retrieval of ACLED Conflict Event Data
Description: Access and manage the application programming interface (API) of the Armed Conflict Location & Event Data Project (ACLED) at <https://acleddata.com/>. The package makes it easy to retrieve a user-defined sample (or all of the available data) of ACLED, enabling a seamless integration of regular data updates into the research work flow. It requires a minimal number of dependencies. See the package's README file for a note on replicability when drawing on ACLED data. When using this package, you acknowledge that you have read ACLED's terms and conditions of use, and that you agree with their attribution requirements.
Author: Christoph Dworschak [aut, cre] (<https://orcid.org/0000-0003-0196-9545>), Rob Williams [ctb] (<https://orcid.org/0000-0001-9259-3883>)
Maintainer: Christoph Dworschak <c.dworschak@essex.ac.uk>

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Package MRReg updated to version 0.1.4 with previous version 0.1.3 dated 2021-01-06

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>

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Package anndata updated to version 0.7.5.2 with previous version 0.7.5.1 dated 2021-02-02

Title: 'anndata' for R
Description: A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [ccp] (<https://orcid.org/0000-0002-0369-2888>, flying-sheep), Alex Wolf [ccp] (<https://orcid.org/0000-0002-8760-7838>, falexwolf), Isaac Virshup [ccp] (ivirshup), Sergei Rybakov [ccp] (Koncopd), Robrecht Cannoodt [aut, ctb, cre, cph] (<https://orcid.org/0000-0003-3641-729X>, rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package radiomics (with last version 0.1.3) was removed from CRAN

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2018-03-30 0.1.3

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Package ForestTools (with last version 0.2.1) was removed from CRAN

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

2020-05-06 0.2.1
2018-04-04 0.2.0
2017-09-08 0.1.5
2017-04-17 0.1.4
2017-03-20 0.1.2
2017-03-06 0.1.1
2017-01-21 0.1.0

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Package OutlierDetection (with last version 0.1.1) was removed from CRAN

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

2019-06-15 0.1.1
2019-02-07 0.1.0

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Package highriskzone (with last version 1.4.5) was removed from CRAN

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

2018-07-11 1.4.5
2017-11-27 1.4-2
2017-08-21 1.4-1
2016-03-11 1.3-1
2015-11-16 1.3
2015-07-22 1.2

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Package targets updated to version 0.3.1 with previous version 0.3.0 dated 2021-03-27

Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R, the 'targets' package brings together function-oriented programming and 'Make'-like declarative workflows. It analyzes the dependency relationships among the tasks of a workflow, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results match the underlying code and data. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Matthew T. Warkentin [ctb], Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>), Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>), Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package table1 updated to version 1.3 with previous version 1.2.1 dated 2020-11-26

Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>

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Package spatialEco updated to version 1.3-6 with previous version 1.3-5 dated 2021-01-10

Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling and modelling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre], Melanie A. Murphy [ctb], Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

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Package simpleMLP updated to version 1.0.0 with previous version 0.2.0 dated 2021-02-11

Title: Simple Multilayer Perceptron Neural Network
Description: Create and train a multilayer perceptron, a type of feedforward, fully connected neural network. Features 2 ReLU hidden layers. Learn more about about the activation functions and backpropagation used by this network in Goodfellow et al. (2016, ISBN: 9780262035613) "Deep Learning".
Author: Cullen Pu [aut, cre]
Maintainer: Cullen Pu <cullenpu@gmail.com>

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Package RcppSpdlog updated to version 0.0.5 with previous version 0.0.4 dated 2020-12-11

Title: 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides many desirable features. This package bundles these header files for easy use by R packages via a simple 'LinkingTo:' inclusion.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package rBiasCorrection updated to version 0.2.8 with previous version 0.2.7 dated 2021-03-01

Title: Correct Bias in DNA Methylation Analyses
Description: Implementation of the algorithms (with minor modifications) to correct bias in quantitative DNA methylation analyses as described by Moskalev et al. (2011) <doi:10.1093/nar/gkr213>.
Author: Lorenz A. Kapsner [cre, aut, cph] (<https://orcid.org/0000-0003-1866-860X>), Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>

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Package psychTools updated to version 2.1.3 with previous version 2.0.8 dated 2020-08-12

Title: Tools to Accompany the 'psych' Package for Psychological Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>

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Package PoissonBinomial updated to version 1.2.3 with previous version 1.2.2 dated 2021-03-12

Title: Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>

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Package oce updated to version 1.4-0 with previous version 1.3-0 dated 2021-01-29

Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively in Dan Kelley's book Oceanographic Analysis with R, published in 2018 by 'Springer-Verlag' with ISBN 978-1-4939-8842-6.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>), Clark Richards [aut] (<https://orcid.org/0000-0002-7833-206X>), Chantelle Layton [ctb] (<https://orcid.org/0000-0002-3199-5763>, curl() coauthor), British Geological Survey [ctb, cph] (magnetic-field subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>

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Package mrgsolve updated to version 0.11.0 with previous version 0.10.7 dated 2020-12-09

Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>), Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Dilawar Singh [ctb], Felicien Le Louedec [ctb] (<https://orcid.org/0000-0003-3699-2729>), Timothy Waterhouse [ctb] (<https://orcid.org/0000-0002-0954-9660>), Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>

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Package hht updated to version 2.1.4 with previous version 2.1.3 dated 2016-05-18

Title: The Hilbert-Huang Transform: Tools and Methods
Description: Builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis. The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum.
Author: Daniel C. Bowman [aut, cre], Jonathan M. Lees [ctb]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>

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Package fontawesome updated to version 0.2.0 with previous version 0.1.0 dated 2021-02-22

Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>

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Package EDOIF updated to version 0.1.3 with previous version 0.1.2 dated 2020-11-07

Title: Empirical Distribution Ordering Inference Framework (EDOIF)
Description: A non-parametric framework based on estimation statistics principle. Its main purpose is to infer orders of empirical distributions from different categories based on a probability of finding a value in one distribution that is greater than an expectation of another distribution. Given a set of ordered-pair of real-category values the framework is capable of 1) inferring orders of domination of categories and representing orders in the form of a graph; 2) estimating magnitude of difference between a pair of categories in forms of mean-difference confidence intervals; and 3) visualizing domination orders and magnitudes of difference of categories. The publication of this package is at Chainarong Amornbunchornvej, Navaporn Surasvadi, Anon Plangprasopchok, and Suttipong Thajchayapong (2020) <doi:10.1016/j.heliyon.2020.e05435>.
Author: Chainarong Amornbunchornvej [aut, cre] (<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>

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Package dialrjars updated to version 8.12.20 with previous version 8.12.19 dated 2021-03-16

Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the 'dialr' package.
Author: Danny Smith [aut, cre], Google Inc. [ctb, cph] (libphonenumber), Vonage Holdings Corp. [ctb, cph] (libphonenumber), Ian Galpin [ctb, cph] (libphonenumber), Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>

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Package DHARMa updated to version 0.4.0 with previous version 0.3.4 dated 2021-03-23

Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB' 'GLMMadaptive' and 'spaMM', generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>), Lukas Lohse [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

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Package csppData updated to version 0.1.2 with previous version 0.1.0 dated 2020-12-17

Title: Data Only: The Correlates of State Policy Project Dataset
Description: Contains the Correlates of State Policy Project dataset (+ codebook) assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy> used by the 'cspp' package. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States.
Author: Caleb Lucas (https://caleblucas.com/) and Joshua McCrain (http://joshuamccrain.com/)
Maintainer: Josh McCrain <josh.mccrain@gmail.com>

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Package caTools updated to version 1.18.2 with previous version 1.18.1 dated 2021-01-11

Title: Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
Author: Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>

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Package callr updated to version 3.6.0 with previous version 3.5.1 dated 2020-10-13

Title: Call R from R
Description: It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>), Winston Chang [aut], RStudio [cph, fnd], Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package BiocManager updated to version 1.30.12 with previous version 1.30.10 dated 2019-11-16

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

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Package IDSpatialStats (with last version 0.3.10) was removed from CRAN

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

2019-11-15 0.3.10
2018-06-12 0.3.5
2018-06-05 0.3.4
2016-09-19 0.2.2
2016-05-10 0.2.1
2016-05-09 0.2

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Package ENMTools (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:

2020-11-20 1.0.2
2020-08-28 1.0.1
2020-07-29 1.0

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Package foster (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:

2020-11-05 0.1.0

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Package stpp (with last version 2.0-4) was removed from CRAN

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

2020-04-06 2.0-4

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Package expp (with last version 1.2.4) was removed from CRAN

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

2019-02-03 1.2.4

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Package windfarmGA (with last version 2.3.0) was removed from CRAN

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2020-10-20 2.3.0
2019-12-16 2.2.3
2019-08-27 2.2.2
2019-02-18 2.2.1
2018-03-24 1.2.1
2018-03-11 1.2
2017-07-27 1.1.1
2017-07-09 1.1
2017-06-24 1.0

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Package GSIF (with last version 0.5-5.1) was removed from CRAN

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2020-03-22 0.5-5.1
2019-01-04 0.5-5
2017-05-14 0.5-4
2016-07-22 0.5-3
2016-06-25 0.5-2
2016-05-03 0.5-1
2015-07-20 0.4-7
2015-05-11 0.4-6
2015-04-22 0.4-5
2015-01-30 0.4-4
2014-12-09 0.4-3
2014-11-10 0.4-2
2014-05-29 0.4-1
2014-05-04 0.4-0
2014-01-15 0.3-6
2013-11-15 0.3-5
2013-08-07 0.3-4
2013-06-24 0.3-3
2013-04-24 0.3-2
2013-04-18 0.3-1

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

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2020-07-27 0.1.0

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Package ppmlasso (with last version 1.1) was removed from CRAN

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2015-01-30 1.1

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Package Biolinv (with last version 0.1-2) was removed from CRAN

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2018-01-03 0.1-2
2017-02-03 0.1-1

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Package latticeDensity (with last version 1.1.6) was removed from CRAN

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2020-05-09 1.1.6

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Package geometr (with last version 0.2.5) was removed from CRAN

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2020-07-14 0.2.5

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Package TCIU (with last version 1.1.0) was removed from CRAN

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2020-09-18 1.1.0
2020-08-27 1.0.0

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Package GmAMisc (with last version 1.1.1) was removed from CRAN

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2020-03-19 1.1.1

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Package sbw (with last version 1.1.1) was removed from CRAN

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2020-06-23 1.1.1
2019-12-30 1.0

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Package pcoxtime updated to version 1.0.1 with previous version 1.0 dated 2021-02-15

Title: Penalized Cox Proportional Hazard Model for Time-Dependent Covariates
Description: Fits penalized models for both time-independent and time-dependent survival data. It fully implements elastic net and uses proximal gradient descent to solve the optimization problem. The package is an implementation of Steve Cygu and Benjamin M. Bolker. (2021) <arXiv:2102.02297>.
Author: Bicko Cygu [aut, cre] (<https://orcid.org/0000-0002-9284-8863>), Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>)
Maintainer: Bicko Cygu <cygubicko@gmail.com>

Diff between pcoxtime versions 1.0 dated 2021-02-15 and 1.0.1 dated 2021-03-28

 DESCRIPTION                     |    8 +-
 MD5                             |   34 ++++-----
 NAMESPACE                       |    9 +-
 R/methodfuns.R                  |    2 
 R/pcoxtime.R                    |    7 +
 R/pcoxtimecv.R                  |  151 +++++++++++++++++++++++-----------------
 R/pcoxtimeplots.R               |   43 +++++++----
 R/pkgsExport.R                  |    8 +-
 R/posthocfuns.R                 |   36 ++++++---
 man/concordScore.pcoxtime.Rd    |   14 ++-
 man/pcoxtime.Rd                 |    6 +
 man/pcoxtimecv.Rd               |    8 +-
 man/pkgsExport.Rd               |    4 -
 man/plot.Score.Rd               |    6 +
 man/predictRisk.pcoxtime.Rd     |    6 +
 man/predictSurvProb.pcoxtime.Rd |   12 ++-
 src/RcppExports.cpp             |    6 -
 src/helperfuns.cpp              |   21 ++---
 18 files changed, 237 insertions(+), 144 deletions(-)

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Package mlflow updated to version 1.15.0 with previous version 1.14.1 dated 2021-03-02

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>

Diff between mlflow versions 1.14.1 dated 2021-03-02 and 1.15.0 dated 2021-03-28

 DESCRIPTION                                |    6 +++---
 MD5                                        |    6 +++---
 R/tracking-experiments.R                   |    1 +
 tests/testthat/test-tracking-experiments.R |   27 +++++++++++++--------------
 4 files changed, 20 insertions(+), 20 deletions(-)

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