Mon, 01 Jun 2020

Package vpc updated to version 1.2.1 with previous version 1.2.0 dated 2020-05-07

Title: Create Visual Predictive Checks
Description: Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.
Author: Ron Keizer <ronkeizer@gmail.com>
Maintainer: Ron Keizer <ronkeizer@gmail.com>

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Package StratigrapheR updated to version 1.1.0 with previous version 1.0.1 dated 2020-03-20

Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions based on R base graphics, interval management functions and svg importation functions among others. Also include stereographic projection functions, and other functions made to deal with large datasets while keeping options to get into the details of the data. When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, Litholog generation with the StratigrapheR package and signal decomposition for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21, EGU2019-5520, 2019, EGU General Assembly 2019. <http://hdl.handle.net/2268/234402> The palaeomagnetism functions are based on: Tauxe, L., 2010. Essentials of Paleomagnetism. University of California Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>; Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge University Press, 289 pp.; Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205, <doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>

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Package LPKsample updated to version 2.1 with previous version 2.0 dated 2018-09-20

Title: LP Nonparametric High Dimensional K-Sample Comparison
Description: LP nonparametric high-dimensional K-sample comparison method that includes (i) confirmatory test, (ii) exploratory analysis, and (iii) options to output a data-driven LP-transformed matrix for classification. The primary reference is Mukhopadhyay, S. and Wang, K. (2020, Biometrika); <arXiv:1810.01724>.
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kaijunwang.19@gmail.com>

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Package DisImpact updated to version 0.0.9 with previous version 0.0.8 dated 2020-04-28

Title: Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index. California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>. California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>

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Package smoothedLasso updated to version 1.2 with previous version 1.1 dated 2020-05-31

Title: Smoothed LASSO Regression via Nesterov Smoothing
Description: We provide full functionality to compute smoothed LASSO regression estimates. For this, the LASSO objective function is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified LASSO objective function with explicit gradients everywhere. The smoothed objective function and its gradient are used to minimize it via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed LASSO objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed LASSO objective function as well as on their respective minimizers. A progressive smoothing approach is provided which iteratively smoothes the LASSO, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>

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Package bujar updated to version 0.2-8 with previous version 0.2-7 dated 2019-11-12

Title: Buckley-James Regression for Survival Data with High-Dimensional Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.
Author: Zhu Wang <https://orcid.org/0000-0002-0773-0052> and others (see COPYRIGHTS)
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

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Package bimets updated to version 1.5.1 with previous version 1.5.0 dated 2020-05-29

Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization.
Author: Andrea Luciani [aut, cre], Roberto Stok [aut], Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>

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Package tidyRSS updated to version 2.0.2 with previous version 2.0.1 dated 2020-03-07

Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom and JSON feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>

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Package phytools updated to version 0.7-47 with previous version 0.7-20 dated 2020-03-19

Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>

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Package mpath updated to version 0.3-26 with previous version 0.3-25 dated 2020-04-22

Title: Regularized Linear Models
Description: Algorithms optimize penalized models. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial regression models and robust models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD), minimax concave penalty (MCP), and each possibly combining with L_2 penalty. See Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>, Wang et al. (2016) <doi:10.1177/0962280214530608>, Wang (2019) <arXiv:1912.11119>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

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Package malariaAtlas updated to version 1.0.1 with previous version 1.0.0 dated 2020-02-24

Title: An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
Description: A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Author: Daniel Pfeffer [aut] (<https://orcid.org/0000-0002-2204-3488>), Tim Lucas [aut, cre] (<https://orcid.org/0000-0003-4694-8107>), Daniel May [aut] (<https://orcid.org/0000-0003-0005-2452>), Suzanne Keddie [aut] (<https://orcid.org/0000-0003-1254-7794>), Jen Rozier [aut] (<https://orcid.org/0000-0002-2610-7557>), Oliver Watson [aut] (<https://orcid.org/0000-0003-2374-0741>), Harry Gibson [aut] (<https://orcid.org/0000-0001-6779-3250>), Nick Golding [ctb], David Smith [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>

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Package FKF updated to version 0.1.6 with previous version 0.1.5 dated 2018-07-20

Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman filter, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.
Author: David Luethi [aut], Philipp Erb [aut], Simon Otziger [aut], Paul Smith [cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>

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Package rstantools updated to version 2.1.0 with previous version 2.0.0 dated 2019-09-14

Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing with 'Stan' <https://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and vignettes with recommendations for developers.
Author: Jonah Gabry [aut, cre], Ben Goodrich [aut], Martin Lysy [aut], Stefan Siegert [ctb], Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

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Package mrbin updated to version 1.4.2 with previous version 1.4.1 dated 2020-05-20

Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science research. The package (<http://www.kleinomicslab.com/software>) converts 1D or 2D data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, are replaced by positive values. All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>

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Package Umpire updated to version 2.0.3 with previous version 2.0.1 dated 2020-04-27

Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes, Jiexin Zhang, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package tadaatoolbox updated to version 0.17.0 with previous version 0.16.1 dated 2018-11-23

Title: Helpers for Data Analysis and Presentation Focused on Undergrad Psychology
Description: A teaching project for the display of statistical tests as well as some convenience functions for data cleanup. The primary components are the functions prefixed with 'tadaa_', which are built to work in an interactive environment, but also print markdown tables powered by 'pixiedust' for the creation of 'RMarkdown' reports. This package is no longer actively developed.
Author: Lukas Burk [aut, cre] (<https://orcid.org/0000-0001-7528-3795>), Tobias Anton [aut], Daniel Lüdecke [ctb], Gesa Graf [ctb]
Maintainer: Lukas Burk <lukas@tadaa-data.de>

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Package smoothSurv updated to version 2.3 with previous version 2.2 dated 2020-05-18

Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between smoothSurv versions 2.2 dated 2020-05-18 and 2.3 dated 2020-06-01

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Package DecomposeR updated to version 1.0.2 with previous version 1.0.1 dated 2020-04-01

Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new algorithm, extricate, that performs EEMD in seconds, a linear interpolation algorithm using the greatest rational common divisor of depth or time, different algorithms to compute instantaneous amplitude, frequency and ratios of frequencies, and functions to verify and visualise the outputs. The functions were developed during the CRASH project (Checking the Reproducibility of Astrochronology in the Hauterivian). When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, "Litholog generation with the 'StratigrapheR' package and signal decomposition for cyclostratigraphic purposes". Geophysical Research Abstracts Vol. 21, EGU2019-5520, 2019, EGU General Assembly 2019. <http://hdl.handle.net/2268/234402>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>

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Package PKNCA updated to version 0.9.4 with previous version 0.9.3 dated 2020-04-12

Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] (<https://orcid.org/0000-0002-5759-428X>), Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>

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Package clean updated to version 2.0.0 with previous version 1.1.0 dated 2019-08-20

Title: Fast and Easy Data Cleaning
Description: A wrapper around the new 'cleaner' package, that allows data cleaning functions for classes 'logical', 'factor', 'numeric', 'character', 'currency' and 'Date' to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

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Package sergeant updated to version 0.9.0 with previous version 0.5.2 dated 2017-07-17

Title: Tools to Transform and Query Data with Apache Drill
Description: Apache Drill is a low-latency distributed query engine designed to enable data exploration and analysis on both relational and non-relational data stores, scaling to petabytes of data. Methods are provided that enable working with Apache Drill instances via the REST API, DBI methods and using 'dplyr'/'dbplyr' idioms. Helper functions are included to facilitate using official Drill Docker images/containers.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Edward Visel [ctb], Andy Hine [ctb], Scott Came [ctb], David Severski [ctb] (<https://orcid.org/0000-0001-7867-0459>), James Lamb [ctb]
Maintainer: Bob Rudis <bob@rud.is>

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Package haven updated to version 2.3.1 with previous version 2.3.0 dated 2020-05-24

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between haven versions 2.3.0 dated 2020-05-24 and 2.3.1 dated 2020-06-01

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Package hexSticker updated to version 0.4.7 with previous version 0.4.6 dated 2019-05-20

Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre], Laurent Gatto [ctb], Johannes Rainer [ctb], Sebastian Gibb [ctb], Robert Corty [ctb], Thomas Neitmann [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package cleaner updated to version 1.5.0 with previous version 1.4.0 dated 2020-04-01

Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes logical, factor, numeric, character, currency and Date to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

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Package aws.signature updated to version 0.6.0 with previous version 0.5.2 dated 2019-08-08

Title: Amazon Web Services Request Signatures
Description: Generates version 2 and version 4 request signatures for Amazon Web Services ('AWS') <https://aws.amazon.com/> Application Programming Interfaces ('APIs') and provides a mechanism for retrieving credentials from environment variables, 'AWS' credentials files, and 'EC2' instance metadata. For use on 'EC2' instances, users will need to install the suggested package 'aws.ec2metadata' <https://cran.r-project.org/package=aws.ec2metadata>.
Author: Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Jonathan Stott [cre, aut], Mike Kaminsky [ctb]
Maintainer: Jonathan Stott <jonathan.stott@magairports.com>

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Package shinyWidgets updated to version 0.5.3 with previous version 0.5.2 dated 2020-05-14

Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], David Granjon [aut], Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), SnapAppointments [cph] (bootstrap-select), Mattia Larentis [ctb, cph] (Bootstrap Switch), Emanuele Marchi [ctb, cph] (Bootstrap Switch), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Flatlogic [cph] (Awesome Bootstrap Checkbox), mouse0270 [ctb, cph] (Material Design Switch), Tristan Edwards [ctb, cph] (SweetAlert), Fabian Lindfors [ctb, cph] (multi.js), Anthony Terrien [ctb, cph] (jQuery Knob), Daniel Eden [ctb, cph] (animate.css), Ganapati V S [ctb, cph] (bttn.css), Brian Grinstead [ctb, cph] (Spectrum), Lokesh Rajendran [ctb, cph] (pretty-checkbox), Leon Gersen [ctb, cph] (wnumb & noUiSlider), Timofey Marochkin [ctb, cph] (air-datepicker), Tobias Ahlin [ctb, cph] (CSS spin), atomiks [ctb, cph] (tippy.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package ggpmisc updated to version 0.3.5 with previous version 0.3.4 dated 2020-04-22

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", "plot" and "grob" add insets to plots using native data coordinates, while "table_npc", "plot_npc" and "grob_npc" do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: locate and tag peaks and valleys; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package collections updated to version 0.3.2 with previous version 0.3.1 dated 2020-04-30

Title: High Performance Container Data Types
Description: Provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre], Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package sen2r updated to version 1.3.5 with previous version 1.3.4 dated 2020-04-22

Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images and perform preliminary processing operations. 'sen2r' provides the instruments required to easily perform (and eventually automate) the steps necessary to build a complete Sentinel-2 processing chain. A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>), Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>

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Package Delaporte updated to version 7.0.3 with previous version 7.0.2 dated 2019-05-17

Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Delaporte versions 7.0.2 dated 2019-05-17 and 7.0.3 dated 2020-06-01

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Package sigminer updated to version 1.0.6 with previous version 1.0.5 dated 2020-05-14

Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>), Tao Wu [aut, ctb], Ziyu Tao [aut, ctb], Geoffrey Macintyre [ctb], Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package blocksdesign updated to version 4.1 with previous version 4.0 dated 2020-05-06

Title: Nested and Crossed Block Designs for Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal treatment and block designs for linear treatment models with crossed or nested block factors. The treatment design can be any arbitrary linear model defined by a treatment model formula and the block design can be any feasible combination of crossed or nested block factors. The block design factors are optimized sequentially and the levels of each successive block factor are optimized within the levels of each preceding block factor. Crossed block designs with non-singular interaction effects are optimized using a weighting scheme that allows for differential weighting of first and second-order block effects. Outputs include a table showing the allocation of treatments to blocks and tables showing the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>

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Package Evapotranspiration updated to version 1.15 with previous version 1.14 dated 2019-05-31

Title: Modelling Actual, Potential and Reference Crop Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo [aut, cre] <danlu.guo@adelaide.edu.au>, Seth Westra [aut] <swestra@civeng.adelaide.edu.au>, Tim Peterson [ctb] <tim.peterson@monash.edu>
Maintainer: Danlu Guo <danlu.guo@unimelb.edu.au>

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