Thu, 09 Feb 2017

Package funcy updated to version 0.8.6 with previous version 0.8.5 dated 2016-05-11

Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre], Dominik Ernst [ctb], Madison Giacofci [ctb], Sophie Lambert-Lacroix [ctb], Guillemette Marot [ctb], Franck Picard [ctb], Nicoleta Serban [ctb], Huijing Jiang [ctb], Gareth James [ctb], Catherine Sugar [ctb], Hans-Georg Mueller [ctb], Jie Peng [ctb], Chiou Jeng-Min [ctb], Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>

Diff between funcy versions 0.8.5 dated 2016-05-11 and 0.8.6 dated 2017-02-09

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Package rptR updated to version 0.9.1 with previous version 0.9.0 dated 2016-09-23

Title: Repeatability Estimation for Gaussian and Non-Gaussian Data
Description: R functions for estimating repeatability (intra-class correlation) from gaussian, binary, proportion and count data.
Author: Holger Schielzeth <holger.schielzeth@uni-jena.de>, Martin Stoffel <martin.adam.stoffel@gmail.com>, Shinichi Nakagawa <s.nakagawa@unsw.edu.au>
Maintainer: Martin Stoffel <martin.adam.stoffel@gmail.com>

Diff between rptR versions 0.9.0 dated 2016-09-23 and 0.9.1 dated 2017-02-09

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Package devEMF updated to version 3.3 with previous version 3.2 dated 2017-02-03

Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>

Diff between devEMF versions 3.2 dated 2017-02-03 and 3.3 dated 2017-02-09

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Package assertable updated to version 0.2.1 with previous version 0.2.0 dated 2017-01-27

Title: Verbose Assertions for Tabular Data (Data.frames and Data.tables)
Description: Simple, flexible, assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, assertable is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, assertable includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.
Author: Grant Nguyen
Maintainer: Grant Nguyen <gngu@uw.edu>

Diff between assertable versions 0.2.0 dated 2017-01-27 and 0.2.1 dated 2017-02-09

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Package GRANBase updated to version 1.2.1 with previous version 1.2.0 dated 2016-10-24

Title: Creating Continuously Integrated Package Repositories from Manifests
Description: Repository based tools for department and analysis level reproducibility. 'GRANBase' allows creation of custom branched, continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

Diff between GRANBase versions 1.2.0 dated 2016-10-24 and 1.2.1 dated 2017-02-09

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New package Tnseq with initial version 0.1.1
Package: Tnseq
Version: 0.1.1
Date: 2017-2-1
Title: Identification of Conditionally Essential Genes in Transposon Sequencing Studies
Author: Lili Zhao <zhaolili@umich.edu>
Maintainer: Lili Zhao <zhaolili@umich.edu>
Imports: methods, limma, edgeR, Ckmeans.1d.dp, Biobase
Depends: DESeq
Description: Identification of conditionally essential genes using high-throughput sequencing data from transposon mutant libraries.
License: GPL (>= 3)
LazyData: TRUE
NeedsCompilation: no
Packaged: 2017-02-08 16:56:08 UTC; zhaolili
Repository: CRAN
Date/Publication: 2017-02-09 19:42:38

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New package som.nn with initial version 1.0.3
Package: som.nn
Type: Package
Title: Topological k-NN Classifier Based on Self-Organising Maps
Version: 1.0.3
Author: Andreas Dominik
Maintainer: Andreas Dominik <andreas.dominik@mni.thm.de>
Encoding: UTF-8
Depends:
Imports: hexbin, class, kohonen, som, methods, graphics, grDevices, stats, utils
Description: A topological version of k-NN: An abstract model is build as 2-dimensional self-organising map. Samples of unknown class are predicted by mapping them on the SOM and analysing class membership of neurons in the neighbourhood.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-02-09 10:04:33 UTC; andreas
Repository: CRAN
Date/Publication: 2017-02-09 19:50:17

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Package party updated to version 1.2-1 with previous version 1.2-0 dated 2017-02-06

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available. The methods are described in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008) <doi:10.1198/106186008X319331> and Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between party versions 1.2-0 dated 2017-02-06 and 1.2-1 dated 2017-02-09

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Package biomartr updated to version 0.3.0 with previous version 0.2.1 dated 2016-12-15

Title: Genomic Data Retrieval
Description: Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' (Yates et al. (2016) <doi:10.1093/nar/gkv1157>) databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

Diff between biomartr versions 0.2.1 dated 2016-12-15 and 0.3.0 dated 2017-02-09

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Package RSurvey updated to version 0.9.0 with previous version 0.8-3 dated 2015-02-20

Title: Geographic Information System Application
Description: A geographic information system (GIS) graphical user interface (GUI) that provides data viewing, management, and analysis tools.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>

Diff between RSurvey versions 0.8-3 dated 2015-02-20 and 0.9.0 dated 2017-02-09

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Package rLDCP updated to version 1.0.1 with previous version 1.0.0 dated 2016-12-23

Title: Text Generation from Data
Description: Linguistic Descriptions of Complex Phenomena (LDCP) is an architecture and methodology that allows us to model complex phenomena, interpreting input data, and generating automatic text reports customized to the user needs (see <doi:10.1016/j.ins.2016.11.002> and <doi:10.1007/s00500-016-2430-5>). The proposed package contains a set of methods that facilitates the development of LDCP systems. It main goal is increasing the visibility and practical use of this research line.
Author: Patricia Conde-Clemente [aut, cre], Jose M. Alonso [aut], Gracian Trivino [aut]
Maintainer: Patricia Conde-Clemente <patricia.condeclemente@gmail.com>

Diff between rLDCP versions 1.0.0 dated 2016-12-23 and 1.0.1 dated 2017-02-09

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New package optbdmaeAT with initial version 1.0.1
Package: optbdmaeAT
Version: 1.0.1
Date: 2017-02-07
Title: Optimal Block Designs for Two-Colour cDNA Microarray Experiments
Author: Dibaba Bayisa Gemechu, Legesse Kassa Debusho, and Linda Haines
Maintainer: Dibaba Bayisa Gemechu <diboobayu@gmail.com>
Depends: R (>= 3.3.1), MASS, Matrix, igraph, tcltk
License: GPL-2
Description: Computes A-, MV-, D- and E-optimal or near-optimal block designs for two-colour cDNA microarray experiments using the linear fixed effects and mixed effects models where the interest is in a comparison of all possible elementary treatment contrasts. The algorithms used in this package are based on the treatment exchange and array exchange algorithms of Debusho, Gemechu and Haines (2016, unpublished). The package also provides an optional method of using the graphical user interface (GUI) R package tcltk to ensure that it is user friendly.
NeedsCompilation: no
Packaged: 2017-02-09 07:59:16 UTC; Dibaba B Gemechu
Repository: CRAN
Date/Publication: 2017-02-09 18:27:01

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Package bnlearn updated to version 4.1 with previous version 4.0 dated 2016-05-16

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with the latest bugfixes are available from <http://www.bnlearn.com>.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>

Diff between bnlearn versions 4.0 dated 2016-05-16 and 4.1 dated 2017-02-09

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New package aniDom with initial version 0.1
Package: aniDom
Type: Package
Title: Inferring Dominance Hierarchies and Estimating Uncertainty
Version: 0.1
Date: 2017-02-08
Author: Damien R. Farine and Alfredo Sanchez-Tojar
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Description: Provides: (1) Tools to infer dominance hierarchies based on calculating Elo scores, but with custom functions to improve estimates in animals with relatively stable dominance ranks. (2) Tools to plot the shape of the dominance hierarchy and estimate the uncertainty of a given data set.
License: GPL-2
Imports: rptR
NeedsCompilation: no
Packaged: 2017-02-09 14:56:47 UTC; damienfarine
Repository: CRAN
Date/Publication: 2017-02-09 18:26:07

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Package actuar updated to version 2.1-0 with previous version 2.0-0 dated 2016-11-12

Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science: modeling of loss distributions; risk theory and ruin theory; simulation of compound models, discrete mixtures and compound hierarchical models; credibility theory. Support for many additional probability distributions to model insurance loss amounts and loss frequency: 19 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete distribution; zero-truncated and zero-modified extensions of the standard discrete distributions. Support for phase-type distributions commonly used to compute ruin probabilities.
Author: Vincent Goulet [cre, aut], S├ębastien Auclair [ctb], Christophe Dutang [aut], Xavier Milhaud [ctb], Tommy Ouellet [ctb], Louis-Philippe Pouliot [ctb], Mathieu Pigeon [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

Diff between actuar versions 2.0-0 dated 2016-11-12 and 2.1-0 dated 2017-02-09

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Package RVsharing updated to version 1.7.0 with previous version 1.6.0 dated 2016-06-17

Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>

Diff between RVsharing versions 1.6.0 dated 2016-06-17 and 1.7.0 dated 2017-02-09

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Package RHRV updated to version 4.2.3 with previous version 4.2.2 dated 2016-11-15

Title: Heart Rate Variability Analysis of ECG Data
Description: Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis.
Author: Leandro Rodriguez-Linares [aut, cre], Xose Vila [aut], Maria Jose Lado [aut], Arturo Mendez [aut], Abraham Otero [aut], Constantino Antonio Garcia [aut], Matti Lassila [ctb]
Maintainer: Leandro Rodriguez-Linares <leandro@uvigo.es>

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Package paramGUI updated to version 2.1.1 with previous version 2.1 dated 2017-02-06

Title: A Shiny GUI for some Parameter Estimation Examples
Description: Allows specification and fitting of some parameter estimation examples inspired by time-resolved spectroscopy via a Shiny GUI.
Author: Joris Snellenburg [cre, aut], Katharine Mullen [aut], Ivo van Stokkum [aut]
Maintainer: Joris Snellenburg <j.snellenburg@vu.nl>

Diff between paramGUI versions 2.1 dated 2017-02-06 and 2.1.1 dated 2017-02-09

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Package naptime updated to version 1.2.2 with previous version 1.2.0 dated 2016-12-01

Title: A Flexible and Robust Sys.sleep() Replacement
Description: Provides a near drop-in replacement for base::Sys.sleep() that allows more types of input to produce delays in the execution of code and can silence/prevent typical sources of error.
Author: Russell S. Pierce [aut, cre], Timothy Gann [aut]
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>

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Package Zelig updated to version 5.0-15 with previous version 5.0-14 dated 2017-01-31

Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common statistical models found across packages into a unified interface, and provides a common architecture for estimation and interpretation, as well as bridging functions to absorb increasingly more models into the collective library. Zelig allows each individual package, for each statistical model, to be accessed by a common uniformly structured call and set of arguments. Moreover, Zelig automates all the surrounding building blocks of a statistical work-flow--procedures and algorithms that may be essential to one user's application but which the original package developer did not use in their own research and might not themselves support. These include bootstrapping, jackknifing, and re-weighting of data. In particular, Zelig automatically generates predicted and simulated quantities of interest (such as relative risk ratios, average treatment effects, first differences and predicted and expected values) to interpret and visualize complex models.
Author: Christine. Choirat [aut], Christopher Gandrud [aut, cre], James Honaker [aut], Kosuke Imai [aut], Gary King [aut], Olivia Lau [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>

Diff between Zelig versions 5.0-14 dated 2017-01-31 and 5.0-15 dated 2017-02-09

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Package seqMeta updated to version 1.6.7 with previous version 1.6.6 dated 2016-09-26

Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Maintainer: Brian Davis <Brian.Davis281@gmail.com>

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Package anytime updated to version 0.2.1 with previous version 0.2.0 dated 2016-12-24

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package TreatmentSelection updated to version 2.0.3 with previous version 1.2.0 dated 2016-01-15

Title: Evaluate Treatment Selection Biomarkers
Description: A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations. Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>

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Package pubmed.mineR updated to version 1.0.8 with previous version 1.0.7 dated 2017-01-05

Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>

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Package ziphsmm updated to version 1.0.3 with previous version 1.0.2 dated 2017-01-27

Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly maximizing the log likelihood function. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>

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Package mrMLM updated to version 2.1 with previous version 2.0 dated 2016-12-20

Title: Multi-Locus Random-SNP-Effect Mixed Linear Model for Genome-Wide Association Studies and Linkage Analyses
Description: Conduct multi-locus GWAS and multi-locus QTL mapping under the framework of random-SNP-effect mixed linear model (mrMLM). First, each position (or marker) on the genome is scanned by mrMLM algorithm. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers (or QTL) that are potentially associated with the trait are included in a multi-locus model, their effects are estimated by empirical Bayes and true QTN or QTL are identified by likelihood ratio test.
Author: Wenlong Ren,Yuanli Ni,Shibo Wang,Yangjun Wen,Bo Huang and Yuanming Zhang
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

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Package haploR updated to version 1.4.2 with previous version 1.4.1 dated 2016-12-31

Title: Query HaploReg and RegulomeDB
Description: A set of utilities for querying HaploReg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> and RegulomeDB <http://www.regulomedb.org> web-based tools. The package connects to Haploreg or RegulomeDB, searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Author: I. Y. Zhbannikov, K. G. Arbeev, A. I. Yashin
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

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Package dunn.test updated to version 1.3.3 with previous version 1.3.2 dated 2016-01-06

Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>

Diff between dunn.test versions 1.3.2 dated 2016-01-06 and 1.3.3 dated 2017-02-09

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Package conover.test updated to version 1.1.2 with previous version 1.1.1 dated 2016-01-06

Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>

Diff between conover.test versions 1.1.1 dated 2016-01-06 and 1.1.2 dated 2017-02-09

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