Thu, 18 Apr 2019

Package StratigrapheR updated to version 0.0.4 with previous version 0.0.3 dated 2019-03-22

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>

Diff between StratigrapheR versions 0.0.3 dated 2019-03-22 and 0.0.4 dated 2019-04-18

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Package MetaCycle updated to version 1.2.0 with previous version 1.1.0 dated 2015-12-04

Title: Evaluate Periodicity in Large Scale Data
Description: There are two functions-meta2d and meta3d for detecting rhythmic signals from time-series datasets. For analyzing time-series datasets without individual information, 'meta2d' is suggested, which could incorporates multiple methods from ARSER, JTK_CYCLE and Lomb-Scargle in the detection of interested rhythms. For analyzing time-series datasets with individual information, 'meta3d' is suggested, which takes use of any one of these three methods to analyze time-series data individual by individual and gives out integrated values based on analysis result of each individual.
Author: Gang Wu [aut, cre], Ron Anafi [aut, ctb], John Hogenesch [aut, ctb], Michael Hughes [aut, ctb], Karl Kornacker [aut, ctb], Xavier Li [aut, ctb], Matthew Carlucci [aut, ctb]
Maintainer: Gang Wu <wggucas@gmail.com>

Diff between MetaCycle versions 1.1.0 dated 2015-12-04 and 1.2.0 dated 2019-04-18

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More information about MetaCycle at CRAN
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Package CrossVA updated to version 0.9.6 with previous version 0.9.5 dated 2019-01-19

Title: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.
Author: Eungang Choi [aut], Sam Clark [aut], Zehang Li [aut], Jason Thomas [aut, cre]
Maintainer: Jason Thomas <jarathomas@gmail.com>

Diff between CrossVA versions 0.9.5 dated 2019-01-19 and 0.9.6 dated 2019-04-18

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Package caret updated to version 6.0-83 with previous version 6.0-82 dated 2019-03-26

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau, Andrew Ziem, Luca Scrucca, Yuan Tang, Can Candan, and Tyler Hunt.
Maintainer: Max Kuhn <mxkuhn@gmail.com>

Diff between caret versions 6.0-82 dated 2019-03-26 and 6.0-83 dated 2019-04-18

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More information about caret at CRAN
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Package blockseg updated to version 0.5.2 with previous version 0.5.0 dated 2018-07-03

Title: Two Dimensional Change-Points Detection
Description: Segments a matrix in blocks with constant values. BRAULT V, CHIQUET J. and LEVY-LEDUC C. (2017) <doi:10.1214/17-EJS1270>.
Author: Julien Chiquet [aut] (<https://orcid.org/0000-0002-3629-3429>), Vincent Brault [aut, cre] (<https://orcid.org/0000-0003-4228-6687>)
Maintainer: Vincent Brault <vincent.brault@univ-grenoble-alpes.fr>

Diff between blockseg versions 0.5.0 dated 2018-07-03 and 0.5.2 dated 2019-04-18

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Package akmedoids updated to version 0.1.1 with previous version 0.1.0 dated 2019-03-24

Title: Anchored Kmedoids for Longitudinal Data Clustering
Description: Advances a novel adaptation of longitudinal k-means clustering technique (Genolini et al. (2015) <doi:10.18637/jss.v065.i04>) for grouping trajectories based on the similarities of their long-term trends and determines the optimal solution based on the Calinski-Harabatz criterion (Calinski and Harabatz (1974) <doi:10.1080/03610927408827101>). Includes functions to extract descriptive statistics and generate a visualisation of the resulting groups, drawing methods from the 'ggplot2' library (Wickham H. (2016) <doi:10.1007/978-3-319-24277-4>). The package also includes a number of other useful functions for exploring and manipulating longitudinal data prior to the clustering process.
Author: Monsuru Adepeju [cre, aut], Samuel Langton [aut], Jon Bannister [aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>

Diff between akmedoids versions 0.1.0 dated 2019-03-24 and 0.1.1 dated 2019-04-18

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More information about akmedoids at CRAN
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Package xtensor updated to version 0.11.0-0 with previous version 0.10.1-0 dated 2019-03-18

Title: Headers for the 'xtensor' Library
Description: The 'xtensor' C++ library for numerical analysis with multi-dimensional array expressions is provided as a header-only C++14 library. It offers an extensible expression system enabling lazy broadcasting; an API following the idioms of the C++ standard library; and tools to manipulate array expressions and build upon 'xtensor'.
Author: Johan Mabille, Sylvain Corlay and Wolf Vollprecht
Maintainer: Sylvain Corlay <sylvain.corlay@gmail.com>

Diff between xtensor versions 0.10.1-0 dated 2019-03-18 and 0.11.0-0 dated 2019-04-18

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Package textmineR updated to version 3.0.4 with previous version 3.0.3 dated 2019-03-22

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Author: Tommy Jones [aut, cre], William Doane [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>

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Package SDMTools updated to version 1.1-221.1 with previous version 1.1-221 dated 2014-08-05

Title: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
Description: This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.. This package was made possible in part by financial support from the Australian Research Council & ARC Research Network for Earth System Science.
Author: Jeremy VanDerWal, Lorena Falconi, Stephanie Januchowski, Luke Shoo and Collin Storlie
Maintainer: ORPHANED

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Package plotGMM updated to version 0.2.0 with previous version 0.1.0 dated 2018-12-25

Title: Tools for Visualizing Gaussian Mixture Models
Description: The main function, plot_GMM, is used for plotting output from Gaussian mixture models, including both densities and overlaying mixture weight component curves from the fit GMM. The package includes another function, plot_mix_comps, which is used in the plot_GMM function, and can be used in any plot generated by the user for overlaying mixture component curves from Gaussian mixture models. For the plot_mix_comps function, usage most often will be specifying the "fun" argument within "stat_function" in a ggplot2 object.
Author: Philip Waggoner [aut, cre], Fong Chan [aut]
Maintainer: Philip Waggoner <philip.waggoner@gmail.com>

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Package PHEindicatormethods updated to version 1.1.1 with previous version 1.0.8 dated 2018-07-30

Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and their confidence intervals using methods approved for use in the production of Public Health England indicators such as those presented via Fingertips (<http://fingertips.phe.org.uk/>). It provides functions for the generation of proportions, crude rates, means, directly standardised rates, indirectly standardised rates, standardised mortality ratios, slope and relative index of inequality and life expectancy. Statistical methods are referenced in the following publications. Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>. Dobson et al (1991) <doi:10.1002/sim.4780100317>. Armitage P, Berry G (2002) <doi:10.1002/9780470773666>. Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>. Altman DG et al (2000, ISBN: 978-0-727-91375-3). Chiang CL. (1968, ISBN: 978-0-882-75200-6). Newell C. (1994, ISBN: 978-0-898-62451-9). Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>. Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>. Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
Author: Anderson Georgina [aut, cre], Fox Sebastian [ctb], Francis Matthew [ctb], Fryers Paul [ctb], Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>

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Package GerminaR updated to version 1.3 with previous version 1.2 dated 2017-10-25

Title: Germination Indices and Graphics for Seed Germination in Ecophysiological Studies
Description: The aim of GerminaR consists of the assessment of different seed germination indices and visualization techniques that provide a robust approach for germination data analysis.
Author: Flavio Lozano Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>), Omar Benites Alfaro [aut] (<https://orcid.org/0000-0002-6852-9598>), Denise Garcia de Santana [ctb], Marli A. Ranal [ctb], Marcelo F. Pompelli [aut, ths] (<https://orcid.org/0000-0002-4408-6374>), Federal University of Pernambuco [cph] (Register of application), Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano Isla <flavjack@gmail.com>

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Package GeneCycle updated to version 1.1.3 with previous version 1.1.2 dated 2012-04-16

Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert et al. (2004) <doi.org/10.1093/bioinformatics/btg364>, Ahdesmaki et al. (2005) <DOI:10.1186/1471-2105-6-117> and Ahdesmaki et al. (2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically expressed genes from gene expression time series data.
Author: Miika Ahdesmaki, Konstantinos Fokianos, and Korbinian Strimmer.
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>

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Package bzinb updated to version 1.0.1 with previous version 1.0.0 dated 2019-04-10

Title: Bivariate Zero-Inflated Negative Binomial Model Estimator
Description: Provides a maximum likelihood estimation of Bivariate Zero-Inflated Negative Binomial (BZINB) model or the nested model parameters. Also estimates the underlying correlation of the a pair of count data. See Cho, H., Preisser, J., Liu, C., and Wu, D. (In preparation) for details.
Author: Hunyong Cho, Chuwen Liu, Jinyoung Park, Di Wu
Maintainer: Hunyong Cho <hunycho@live.unc.edu>

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Package cba updated to version 0.2-21 with previous version 0.2-20 dated 2019-03-04

Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>

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Package PDFEstimator updated to version 0.1-3 with previous version 0.1-2 dated 2019-04-08

Title: Nonparametric Probability Density Estimator
Description: Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>

Diff between PDFEstimator versions 0.1-2 dated 2019-04-08 and 0.1-3 dated 2019-04-18

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Package MiDA updated to version 0.1.2 with previous version 0.1.0 dated 2019-03-04

Title: Microarray Data Analysis
Description: Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.
Author: Elena Filatova [aut, cre], Nikolai Sakharnov [dtc], Dmitry Knyazev [dtc], Oleg Utkin [dtc], Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia [fnd]
Maintainer: Elena Filatova <filatova@nniiem.ru>

Diff between MiDA versions 0.1.0 dated 2019-03-04 and 0.1.2 dated 2019-04-18

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Package expperm updated to version 1.1 with previous version 1.0 dated 2019-04-07

Title: Computing Expectations and Marginal Likelihoods for Permutations
Description: A set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper 'Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.
Author: Ben Powell
Maintainer: Ben Powell <ben.powell@york.ac.uk>

Diff between expperm versions 1.0 dated 2019-04-07 and 1.1 dated 2019-04-18

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Package deisotoper updated to version 0.0.7 with previous version 0.0.3 dated 2017-12-19

Title: Detection of Isotope Pattern of a Mass Spectrometric Measurement
Description: Provides a low-level interface for a deisotoper container implemented in the 'Java' programming language and means of S3 helper functions for plotting and debugging isotopes of mass spectrometric data. The deisotoper algorithm detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.
Author: Christian Panse [cre, aut] (<https://orcid.org/0000-0003-1975-3064>), Lucas Schmidt [ctb, aut] (<https://orcid.org/0000-0003-4496-0487>), Witold E. Wolski [ctb, aut] (<https://orcid.org/0000-0002-6468-120X>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

Diff between deisotoper versions 0.0.3 dated 2017-12-19 and 0.0.7 dated 2019-04-18

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 R/onAttach.R                                                                             |    9 
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 tests/testthat/test-deisotoper.R                                                         |    8 
 vignettes/deisotoper.Rnw                                                                 |   28 
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Package UCSCXenaTools updated to version 1.2.1 with previous version 1.2.0 dated 2019-03-31

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

Diff between UCSCXenaTools versions 1.2.0 dated 2019-03-31 and 1.2.1 dated 2019-04-18

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Package pammtools updated to version 0.1.11 with previous version 0.1.9 dated 2019-03-14

Title: Piece-Wise Exponential Additive Mixed Modeling Tools
Description: The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and Scheipl (2018) <doi: 10.1177/1471082X17748083>) is a powerful model class for survival analysis, based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender et. al. (2018) <doi:10.1093/biostatistics/kxy003>. pammtools provides tidy workflow for survival analysis with PAMMs, including data transformation and other pre- and post-processing functions as well as visualization.
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>), Fabian Scheipl [aut]
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>

Diff between pammtools versions 0.1.9 dated 2019-03-14 and 0.1.11 dated 2019-04-18

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Package robustvarComp updated to version 0.1-5 with previous version 0.1-2 dated 2014-07-10

Title: Robust Estimation of Variance Component Models
Description: Robust Estimation of Variance Component Models by classic and composite robust procedures. The composite procedures are robust against outliers generated by the Independent Contamination Model.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it> and Victor J. Yohai <victoryohai@gmail.com>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>

Diff between robustvarComp versions 0.1-2 dated 2014-07-10 and 0.1-5 dated 2019-04-18

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Package Orcs updated to version 1.2.0 with previous version 1.1.1 dated 2019-02-28

Title: Omnidirectional R Code Snippets
Description: I tend to repeat the same code chunks over and over again. At first, this was fine for me and I paid little attention to such redundancies. A little later, when I got tired of manually replacing Linux filepaths with the referring Windows versions, and vice versa, I started to stuff some very frequently used work-steps into functions and, even later, into a proper R package. And that's what this package is - a hodgepodge of various R functions meant to simplify (my) everyday-life coding work without, at the same time, being devoted to a particular scope of application.
Author: Florian Detsch [cre, aut], Tim Appelhans [ctb], Baptiste Auguie [ctb], OpenStreetMap contributors [cph]
Maintainer: Florian Detsch <fdetsch@web.de>

Diff between Orcs versions 1.1.1 dated 2019-02-28 and 1.2.0 dated 2019-04-18

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Package R.filesets updated to version 2.13.0 with previous version 2.12.1 dated 2018-04-09

Title: Easy Handling of and Access to Files Organized in Structured Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.filesets versions 2.12.1 dated 2018-04-09 and 2.13.0 dated 2019-04-18

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Package nasapower updated to version 1.1.1 with previous version 1.1.0 dated 2019-04-10

Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>), Hazel Kavili [rev], Alison Boyer [rev]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

Diff between nasapower versions 1.1.0 dated 2019-04-10 and 1.1.1 dated 2019-04-18

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Package cOde updated to version 1.0.0 with previous version 0.4.1 dated 2018-08-08

Title: Automated C Code Generation for 'deSolve', 'bvpSolve'
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>

Diff between cOde versions 0.4.1 dated 2018-08-08 and 1.0.0 dated 2019-04-18

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 cOde-1.0.0/cOde/man/sensitivitiesSymb.Rd          |   64 ---
 21 files changed, 372 insertions(+), 585 deletions(-)

More information about cOde at CRAN
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Package clustree updated to version 0.4.0 with previous version 0.3.0 dated 2019-02-24

Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>), Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>), Andrea Rau [ctb], Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke.zappia@mcri.edu.au>

Diff between clustree versions 0.3.0 dated 2019-02-24 and 0.4.0 dated 2019-04-18

 DESCRIPTION                            |   28 +-
 MD5                                    |   43 ++--
 NAMESPACE                              |    3 
 NEWS.md                                |   19 +
 R/checks.R                             |only
 R/clustree.R                           |  211 ++++++----------------
 R/clustree_overlay.R                   |  108 ++++++++++-
 README.md                              |    3 
 build/vignette.rds                     |binary
 inst/CITATION                          |    2 
 inst/doc/clustree.R                    |   25 +-
 inst/doc/clustree.Rmd                  |   49 +++--
 inst/doc/clustree.html                 |  314 ++++++++++++++++++---------------
 man/assert_colour_node_aes.Rd          |    2 
 man/assert_node_aes.Rd                 |    2 
 man/assert_numeric_node_aes.Rd         |    2 
 man/check_node_aes_list.Rd             |    2 
 man/clustree.Rd                        |   10 -
 man/clustree_overlay.Rd                |   11 +
 tests/testthat/test-clustree-overlay.R |   36 ++-
 tests/testthat/test-clustree.R         |   28 ++
 vignettes/clustree.Rmd                 |   49 +++--
 vignettes/references.bib               |   93 +++++----
 23 files changed, 613 insertions(+), 427 deletions(-)

More information about clustree at CRAN
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