Mon, 11 Feb 2019

Package tourr updated to version 0.5.6 with previous version 0.5.5 dated 2017-08-02

Title: Implement Tour Methods in R Code
Description: Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Author: Hadley Wickham [aut, ctb], Di Cook [aut, cre], Nick Spyrison [ctb], Ursula Laa [ctb]
Maintainer: Di Cook <dicook@monash.edu>

Diff between tourr versions 0.5.5 dated 2017-08-02 and 0.5.6 dated 2019-02-11

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Package ktsolve updated to version 1.1.1 with previous version 1.1 dated 2013-09-23

Title: Configurable Function for Solving Families of Nonlinear Equations
Description: This is designed for use with an arbitrary set of equations with an arbitrary set of unknowns. The user selects "fixed" values for enough unknowns to leave as many variables as there are equations, which in most cases means the system is properly defined and a unique solution exists. The function, the fixed values and initial values for the remaining unknowns are fed to a nonlinear backsolver. The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>

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Package IDPmisc updated to version 1.1.19 with previous version 1.1.18 dated 2018-10-02

Title: 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'
Description: Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Author: Rene Locher [aut, cre], Andreas Ruckstuhl [ctb]
Maintainer: Rene Locher <rene.locher@zhaw.ch>

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Package forecastHybrid updated to version 4.2.17 with previous version 4.1.16 dated 2018-12-19

Title: Convenient Functions for Ensemble Time Series Forecasts
Description: Convenient functions for ensemble forecasts in R combining approaches from the 'forecast' package. Forecasts generated from auto.arima(), ets(), thetaf(), nnetar(), stlm(), tbats(), and snaive() can be combined with equal weights, weights based on in-sample errors (introduced by Bates & Granger (1969) <doi:10.1057/jors.1969.103>), or cross-validated weights. Cross validation for time series data with user-supplied models and forecasting functions is also supported to evaluate model accuracy.
Author: David Shaub [aut, cre], Peter Ellis [aut]
Maintainer: David Shaub <davidshaub@gmx.com>

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Package emdbook updated to version 1.3.11 with previous version 1.3.10 dated 2018-05-19

Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker [aut, cre], Sang Woo Park [ctb], James Vonesh [dtc], Jacqueline Wilson [dtc], Russ Schmitt [dtc], Sally Holbrook [dtc], James D. Thomson [dtc], R. Scot Duncan [dtc]
Maintainer: Ben Bolker <bolker@mcmaster.ca>

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Package autocogs updated to version 0.1.2 with previous version 0.1.1 dated 2018-09-21

Title: Automatic Cognostic Summaries
Description: Automatically calculates cognostic groups for plot objects and list column plot objects. Results are returned in a nested data frame.
Author: Barret Schloerke [aut], Ryan Hafen [ths, cre]
Maintainer: Ryan Hafen <rhafen@gmail.com>

Diff between autocogs versions 0.1.1 dated 2018-09-21 and 0.1.2 dated 2019-02-11

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Package ctmm updated to version 0.5.5 with previous version 0.5.4 dated 2019-02-08

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, and Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

Diff between ctmm versions 0.5.4 dated 2019-02-08 and 0.5.5 dated 2019-02-11

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Package cgmanalysis updated to version 2.2 with previous version 2.1 dated 2018-12-17

Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>

Diff between cgmanalysis versions 2.1 dated 2018-12-17 and 2.2 dated 2019-02-11

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New package rPACI with initial version 0.1.1
Package: rPACI
Title: Placido Analysis of Corneal Irregularity
Version: 0.1.1
Authors@R: c( person(given = "Darío", family = "Ramos-López", role = c("aut", "cre"), email = "dario.ramos.lopez@urjc.es"), person(given = "Ana D.", family = "Maldonado", role = c("aut"), email = "ana.d.maldonado@ual.es"))
Description: Analysis of corneal data obtained from a Placido disk corneal topographer with calculation of irregularity indices. A corneal topographer is an ophthalmic clinical device that obtains measurements in the cornea (the anterior part of the eye). A Placido disk corneal topographer makes use of the Placido disk (Rowsey et al. (1981), <doi:10.1001/archopht.1981.03930011093022>, Rand et al. (1997), <doi:10.1016/S0886-3350(99)00355-7>), which produce a circular pattern of measurement nodes. The raw information measured by such a topographer is used by practitioners to analyze curvatures, to study optical aberrations, or to diagnose specific conditions of the eye. The rPACI package allows the calculation of the corneal irregularity indices described in Ramos-Lopez et al. (2013), <doi:10.1097/OPX.0b013e3182843f2a>, and that were firstly introduced in Ramos-Lopez et al. (2011), <doi:10.1097/OPX.0b013e3182843f2a>. It provides a simple interface to read corneal topography data files as exported by a typical Placido disk topographer, to compute the irregularity indices mentioned before, and to display summary plots that are easy to interpret for a clinician.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1.9000
NeedsCompilation: no
Packaged: 2019-02-05 16:04:34 UTC; Usuario
Author: Darío Ramos-López [aut, cre], Ana D. Maldonado [aut]
Maintainer: Darío Ramos-López <dario.ramos.lopez@urjc.es>
Repository: CRAN
Date/Publication: 2019-02-11 21:40:03 UTC

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New package Ropj with initial version 0.1-1
Package: Ropj
Type: Package
Title: Import Origin(R) Project Files
Version: 0.1-1
Date: 2019-02-06
Authors@R: c(person('Miquel', 'Garriga', email = 'gbmiquel@gmail.com', role = c('aut', 'cph')), person('Stefan', 'Gerlach', email = 'stefan.gerlach@uni-konstanz.de', role = c('aut', 'cph')), person('Ion', 'Vasilief', email = 'ion_vasilief@yahoo.fr', role = c('aut', 'cph')), person('Alex', 'Kargovsky', email = 'kargovsky@yumr.phys.msu.su', role = c('aut', 'cph')), person('Knut', 'Franke', email = 'Knut.Franke@gmx.de', role = c('ctb', 'cph')), person('Alexander', 'Semke', email = 'alexander.semke@web.de', role = c('ctb', 'cph')), person('Tilman', 'Benkert', email = 'thzs@gmx.net', role = c('ctb', 'cph')), person('Kasper', 'Peeters', email = 'kasper.peeters@aei.mpg.de', role = c('ctb', 'cph')), person('Russell', 'Standish', role = c('ctb', 'cph')), person('Ivan', 'Krylov', email = 'krylov.r00t@gmail.com', role = c('cre', 'cph')))
Description: Read the data from Origin(R) project files ('*.opj') <https://www.originlab.com/doc/User-Guide/Origin-File-Types>. For now, only spreadsheet objects are imported as data frames and no export is planned. More object types may be available to be imported later.
License: GPL (>= 3)
Imports: Rcpp (>= 1.0.0)
LinkingTo: Rcpp
URL: https://github.com/aitap/Ropj
BugReports: https://github.com/aitap/Ropj/issues
NeedsCompilation: yes
Packaged: 2019-02-06 15:12:05 UTC; aitap
Author: Miquel Garriga [aut, cph], Stefan Gerlach [aut, cph], Ion Vasilief [aut, cph], Alex Kargovsky [aut, cph], Knut Franke [ctb, cph], Alexander Semke [ctb, cph], Tilman Benkert [ctb, cph], Kasper Peeters [ctb, cph], Russell Standish [ctb, cph], Ivan Krylov [cre, cph]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-11 21:33:22 UTC

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New package HRW with initial version 1.0-3
Package: HRW
Version: 1.0-3
Date: 2019-02-06
Title: Datasets, Functions and Scripts for Semiparametric Regression Supporting Harezlak, Ruppert & Wand (2018)
Authors@R: c(person("Jaroslaw", "Harezlak", role = "aut", email = "harezlak@iu.edu"), person("David", "Ruppert", role = "aut", email = "dr24@cornell.edu"), person("Matt P.", "Wand", role = c("aut","cre"), email = "matt.wand@uts.edu.au"))
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Depends: R (>= 2.10), KernSmooth, grDevices, graphics, splines, stats
Suggests: fields, lattice, mgcv
Description: The book "Semiparametric Regression with R" by J. Harezlak, D. Ruppert & M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets and scripts to explain semiparametric regression concepts. Each of the book's scripts are contained in this package as well as datasets that are not within other R packages. Functions that aid semiparametric regression analysis are also included.
License: GPL (>= 2)
LazyData: TRUE
NeedsCompilation: no
Packaged: 2019-02-06 11:25:33 UTC; mwand
Author: Jaroslaw Harezlak [aut], David Ruppert [aut], Matt P. Wand [aut, cre]
Repository: CRAN
Date/Publication: 2019-02-11 21:33:31 UTC

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Package HeritSeq updated to version 1.0.1 with previous version 1.0.0 dated 2017-01-04

Title: Heritability of Gene Expression for Next-Generation Sequencing
Description: Statistical framework to analyze heritability of gene expression based on next-generation sequencing data and simulating sequencing reads. Variance partition coefficients (VPC) are computed using linear mixed effects and generalized linear mixed effects models. Compound Poisson and negative binomial models are included. Reference: Rudra, Pratyaydipta, et al. "Model based heritability scores for high-throughput sequencing data." BMC bioinformatics 18.1 (2017): 143.
Author: W. Jenny Shi [aut, cre], Pamela Russell [aut], Pratyaydipta Rudra [aut, cre], Brian Vestal [aut, cre], Katerina Kechris [aut], Laura Saba [aut]
Maintainer: W. Jenny Shi <wjennyshi@gmail.com>

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Package DSAIRM updated to version 0.5.5 with previous version 0.5.0 dated 2019-01-17

Title: Dynamical Systems Approach to Immune Response Modeling
Description: A collection of 'shiny' apps that allow for the simulation and exploration of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models. The development of this package was partially supported by NIH grant U19AI117891.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>), Spencer Hall [ctb], Sina Solaimanpour [ctb], Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>

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Package tibbletime updated to version 0.1.2 with previous version 0.1.1 dated 2018-01-30

Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension that allows for the creation of time aware tibbles. Some immediate advantages of this include: the ability to perform time-based subsetting on tibbles, quickly summarising and aggregating results by time periods, and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre], Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between tibbletime versions 0.1.1 dated 2018-01-30 and 0.1.2 dated 2019-02-11

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Package BEACH updated to version 1.3.1 with previous version 1.2.1 dated 2018-02-22

Title: Biometric Exploratory Analysis Creation House
Description: A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.
Author: Danni Yu [aut, cre], Michael Man [aut], ChenChen Yu [com]
Maintainer: Danni Yu <danni.yu@gmail.com>

Diff between BEACH versions 1.2.1 dated 2018-02-22 and 1.3.1 dated 2019-02-11

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 16 files changed, 2612 insertions(+), 2436 deletions(-)

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New package uclust with initial version 0.1.0
Package: uclust
Title: Clustering and Classification Inference with U-Statistics
Version: 0.1.0
Authors@R: c(person("Gabriela","Cybis",email="gcybis@gmail.com",role=c("aut","cre")), person("Marcio","Valk",email="marciovalk@gmail.com",role="aut"), person("Kazuki","Yokoyama",email="gcybis@gmail.com",role="ctb"))
Description: Clustering and classification inference for high dimension low sample size (HDLSS) data with U-statistics. The package contains implementations of nonparametric statistical tests for sample homogeneity, group separation, clustering, and classification of multivariate data. The methods have high statistical power and are tailored for data in which the dimension L is much larger than sample size n. See Gabriela B. Cybis, Marcio Valk and Sílvia RC Lopes (2018) <doi:10.1080/00949655.2017.1374387> and Marcio Valk and Gabriela B. Cybis (2018) <arXiv:1805.12179>.
Depends: R (>= 3.4.0),dendextend,robcor
Imports:
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-02-05 13:26:44 UTC; Gabriela
Author: Gabriela Cybis [aut, cre], Marcio Valk [aut], Kazuki Yokoyama [ctb]
Maintainer: Gabriela Cybis <gcybis@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-11 16:00:03 UTC

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Package StatCharrms updated to version 0.90.92 with previous version 0.90.91 dated 2018-06-10

Title: Statistical Analysis of Chemistry, Histopathology, and Reproduction Endpoints Including Repeated Measures and Multi-Generation Studies
Description: A front end for the statistical analyses involved in the tier II endocrine disruptor screening program. The analyses available to this package are: Rao-Scott adjusted Cochran-Armitage test for trend By Slices (RSCABS), a Standard Cochran-Armitage test for trend By Slices (SCABS), mixed effects Cox proportional model, Jonckheere-Terpstra step down trend test Dunn test, one way ANOVA, weighted ANOVA, mixed effects ANOVA, repeated measures ANOVA, and Dunnett test.
Author: Joe Swintek [aut, cre], Kevin Flynn [ctb], Jon Haselman [ctb], Maki Sakurai [ctb]
Maintainer: Joe Swintek <swintek.joe@epa.gov>

Diff between StatCharrms versions 0.90.91 dated 2018-06-10 and 0.90.92 dated 2019-02-11

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Package smicd updated to version 1.0.3 with previous version 1.0.2 dated 2018-09-10

Title: Statistical Methods for Interval Censored Data
Description: Functions that provide statistical methods for interval censored (grouped) data. The package supports the estimation of linear and linear mixed regression models with interval censored dependent variables. Parameter estimates are obtained by a stochastic expectation maximization algorithm. Furthermore, the package enables the direct (without covariates) estimation of statistical indicators from interval censored data via an iterative kernel density algorithm. Survey and Organisation for Economic Co-operation and Development (OECD) weights can be included into the direct estimation (see, Groß, M., U. Rendtel, T. Schmid, S. Schmon, and N. Tzavidis (2017) <doi:10.1111/rssa.12179>).
Author: Paul Walter
Maintainer: Paul Walter <paul.walter@fu-berlin.de>

Diff between smicd versions 1.0.2 dated 2018-09-10 and 1.0.3 dated 2019-02-11

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New package rrum with initial version 0.2.0
Package: rrum
Type: Package
Title: Bayesian Estimation of the Reduced Reparameterized Unified Model with Gibbs Sampling
Version: 0.2.0
Authors@R: c( person("Steven Andrew", "Culpepper", email = "sculpepp@illinois.edu", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-4226-6176") ), person("Aaron", "Hudson", email = "awhudson@uw.edu", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-9731-2224") ), person("James Joseph", "Balamuta", email = "balamut2@illinois.edu", role = c("aut", "cph", "cre"), comment = c(ORCID = "0000-0003-2826-8458") ) )
Description: Implementation of Gibbs sampling algorithm for Bayesian Estimation of the Reduced Reparameterized Unified Model ('rrum'), described by Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>.
License: GPL (>= 2)
Depends: R (>= 3.4.0), simcdm (>= 0.1.0)
Imports: Rcpp (>= 1.0.0)
LinkingTo: Rcpp, RcppArmadillo (>= 0.9.200), rgen, simcdm
RoxygenNote: 6.1.1
Suggests: testthat, covr
SystemRequirements: C++11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2019-02-05 22:55:59 UTC; ronin
Author: Steven Andrew Culpepper [aut, cph] (<https://orcid.org/0000-0003-4226-6176>), Aaron Hudson [aut, cph] (<https://orcid.org/0000-0002-9731-2224>), James Joseph Balamuta [aut, cph, cre] (<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Repository: CRAN
Date/Publication: 2019-02-11 16:10:05 UTC

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New package metaMix with initial version 0.3
Package: metaMix
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Version: 0.3
Author: Sofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
Maintainer: Sofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
Depends: R (>= 3.2)
Imports: data.table (>= 1.9.2), Matrix, gtools, Rmpi, ggplot2
Suggests: knitr
VignetteBuilder: knitr
Description: Resolves complex metagenomic mixtures by analysing deep sequencing data, using a mixture model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture.
License: GPL-3
LazyData: true
SystemRequirements: Open MPI (>=1.4.3)
RoxygenNote: 6.1.1
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2019-02-07 15:41:40 UTC; sophia
Repository: CRAN
Date/Publication: 2019-02-11 16:20:03 UTC

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New package matsindf with initial version 0.3.0
Package: matsindf
Type: Package
Title: Matrices in data frames
Version: 0.3.0
Date: 2019-01-26
Authors@R: c(person("Matthew", "Heun", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7438-214X"), email = "matthew.heun@me.com"))
Maintainer: Matthew Heun <matthew.heun@me.com>
Description: Provides functions to collapse a tidy data frame into matrices in a data frame and expand a data frame of matrices into a tidy data frame.
License: MIT + file LICENSE
Language: en-US
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 2.10)
Imports: dplyr, magrittr, matsbyname, purrr, rlang, rlist, tibble, tidyr
Suggests: ggplot2, knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
URL: https://github.com/MatthewHeun/matsindf
BugReports: https://github.com/MatthewHeun/matsindf/issues
NeedsCompilation: no
Packaged: 2019-02-05 14:59:35 UTC; mkh2
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Repository: CRAN
Date/Publication: 2019-02-11 16:00:11 UTC

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New package leiden with initial version 0.2.3
Package: leiden
Type: Package
Title: Implementation of the 'Python leidenalg' Module
Version: 0.2.3
Date: 2019-02-05
Author: Tom Kelly <tom.kelly@riken.jp>
Maintainer: Tom Kelly <tom.kelly@riken.jp>
Description: Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
License: GPL-3
URL: https://github.com/TomKellyGenetics/leiden
Imports: reticulate
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: covr, testthat, spelling, knitr, rmarkdown, igraph, RColorBrewer
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-05 12:54:48 UTC; tom
Repository: CRAN
Date/Publication: 2019-02-11 16:53:22 UTC

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New package CB2 with initial version 1.0
Package: CB2
Type: Package
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Version: 1.0
Date: 2019-01-30
Authors@R: c(person(given = "Hyun-Hwan", family = "Jeong", role = c("aut", "cre"), email = "hyun-hwan.jeong@bcm.edu"))
Description: Provides functions of a statistical hypothesis test for hit gene identification and a mapping algorithm to quantify sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2018) <doi:10.1101/309302>.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Imports: Rcpp (>= 0.12.16), metap, magrittr, dplyr, tibble, stringr, ggplot2, tidyr, glue
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.1
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-02-05 17:57:58 UTC; hyunhwan
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>
Repository: CRAN
Date/Publication: 2019-02-11 16:23:19 UTC

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Package scriptName (with last version 1.0.0) was removed from CRAN

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

2018-04-10 1.0.0

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Package Rpolyhedra (with last version 0.4.0) was removed from CRAN

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

2019-01-04 0.4.0
2018-11-30 0.3.0
2018-10-05 0.2.8
2018-10-02 0.2.7
2018-07-10 0.2.6
2018-07-03 0.2.5
2018-03-21 0.2.4
2018-03-17 0.2.3
2018-03-15 0.2.2
2018-03-13 0.2.1
2017-11-02 0.1.0

Permanent link
Package EloChoice (with last version 0.29) was removed from CRAN

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

2015-10-12 0.29
2015-10-11 0.28

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Package frite (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:

2018-07-01 0.1.0

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New package STMotif with initial version 1.0.2
Package: STMotif
Type: Package
Title: Discovery of Motifs in Spatial-Time Series
Version: 1.0.2
Authors@R: c( person("Amin", "Bazaz", role = c("aut"), comment = "Polytech'Montpellier"), person("Heraldo", "Borges", email = "stmotif@eic.cefet-rj.br", role = c("aut", "cre"), comment = "CEFET/RJ"), person("Eduardo", "Ogasawara", role = c("aut"), comment = "CEFET/RJ"))
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>
Description: Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats, ggplot2, reshape2, scales, grDevices, RColorBrewer, shiny
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-10 18:07:36 UTC; heraldoborges
Author: Amin Bazaz [aut] (Polytech'Montpellier), Heraldo Borges [aut, cre] (CEFET/RJ), Eduardo Ogasawara [aut] (CEFET/RJ)
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2019-02-11 15:13:14 UTC

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Package compareDF updated to version 1.7.1 with previous version 1.7.0 dated 2018-10-25

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

Diff between compareDF versions 1.7.0 dated 2018-10-25 and 1.7.1 dated 2019-02-11

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Package tidytidbits updated to version 0.2.0 with previous version 0.1.0 dated 2018-08-24

Title: A Collection of Tools and Helpers Extending the Tidyverse
Description: A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages. This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of 'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count, various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks, saving to PDF and PNG from a pipe and various small utilities.
Author: Marcel Wiesweg [aut, cre]
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>

Diff between tidytidbits versions 0.1.0 dated 2018-08-24 and 0.2.0 dated 2019-02-11

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New package Rfssa with initial version 0.0.1
Package: Rfssa
Type: Package
Title: Functional Singular Spectrum Analysis
Version: 0.0.1
Authors@R: c( person("Hossein", "Haghbin", email = "haghbinh@gmail.com", role = c("aut", "cre")), person("Seyed Morteza", "Najibi", email = "mnajibi@shirazu.ac.ir", role = "aut"))
Maintainer: Hossein Haghbin <haghbinh@gmail.com>
URL: https://github.com/haghbinh/Rfssa.git
Description: Methods and tools for implementing functional singular spectrum analysis for functional time series as described in Haghbin H., Najibi, S.M., Mahmoudvand R., Maadooliat M. (2019). Functional singular spectrum Analysis. Manuscript submitted for publication.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.1.1
Imports: Rcpp, fda, lattice, plot3D,
LinkingTo: Rcpp, RcppArmadillo,
Suggests: knitr,
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2019-02-05 06:12:25 UTC; Hossein
Author: Hossein Haghbin [aut, cre], Seyed Morteza Najibi [aut]
Repository: CRAN
Date/Publication: 2019-02-11 14:13:16 UTC

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New package IrregLong with initial version 0.1.0
Package: IrregLong
Type: Package
Title: Analysis of Longitudinal Data with Irregular Observation Times
Version: 0.1.0
Date: 2019-01-28
Author: Eleanor Pullenayegum
Maintainer: Eleanor Pullenayegum <eleanor.pullenayegum@sickkids.ca>
Description: Analysis of longitudinal data for which the times of observation are random variables that are potentially associated with the outcome process. The package includes inverse-intensity weighting methods (Lin H, Scharfstein DO, Rosenheck RA (2004) <doi:10.1111/j.1467-9868.2004.b5543.x>) and multiple outputation (Pullenayegum EM (2016) <doi:10.1002/sim.6829>).
Depends: R (>= 2.10)
Imports: survival, geepack, frailtypack
License: GPL-3
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, nlme, MEMSS
VignetteBuilder: knitr
LazyData: true
Language: en-GB
NeedsCompilation: no
Packaged: 2019-02-05 01:13:03 UTC; Eleanor Pullenayegum
Repository: CRAN
Date/Publication: 2019-02-11 14:03:20 UTC

More information about IrregLong at CRAN
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New package expSBM with initial version 1.0
Package: expSBM
Type: Package
Title: An Exponential Stochastic Block Model for Interaction Lengths
Version: 1.0
Date: 2019-02-04
Authors@R: c(person("Riccardo", "Rastelli", role = c("aut", "cre"), email = "riccardoras@gmail.com", comment = c(ORCID = "0000-0003-0982-2935")), person("Michael", "Fop", role = "aut", comment = c(ORCID = "0000-0003-3936-2757")))
Description: Given a continuous-time dynamic network, this package allows one to fit a stochastic blockmodel where nodes belonging to the same group create interactions and non-interactions of similar lengths. This package implements the methodology described by R. Rastelli and M. Fop (2019) <arXiv:1901.09828>.
License: GPL-3
Imports: Rcpp (>= 0.12.10), mclust, gtools
LinkingTo: Rcpp, RcppArmadillo
LazyData: TRUE
NeedsCompilation: yes
Packaged: 2019-02-04 22:41:52 UTC; riccardo
Author: Riccardo Rastelli [aut, cre] (<https://orcid.org/0000-0003-0982-2935>), Michael Fop [aut] (<https://orcid.org/0000-0003-3936-2757>)
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-11 14:03:17 UTC

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Package DJL updated to version 2.9.1 with previous version 2.9 dated 2019-02-05

Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics. Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>

Diff between DJL versions 2.9 dated 2019-02-05 and 2.9.1 dated 2019-02-11

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More information about DJL at CRAN
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New package TmCalculator with initial version 1.0.0
Package: TmCalculator
Type: Package
Title: Melting Temperature of Nucleic Acid Sequences
Version: 1.0.0
Date: 2019-01-25
Author: Junhui Li
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Description: The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <PMID:11673362>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).
License: GPL (>= 2)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2019-02-05 05:10:32 UTC; lenovo
Repository: CRAN
Date/Publication: 2019-02-11 13:53:18 UTC

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New package calendar with initial version 0.0.1
Package: calendar
Title: Create, Read, Write, and Work with 'iCalander' Files, Calendars and Scheduling Data
Version: 0.0.1
Authors@R: c( person("Robin", "Lovelace", email = "rob00x@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5679-6536")), person("Layik", "Hama", email = "layik.hama@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-1912-4890")) )
Description: Provides function to create, read, write, and work with 'iCalander' files (which typically have '.ics' or '.ical' extensions), and the scheduling data, calendars and timelines of people, organisations and other entities that they represent. 'iCalendar' is an open standard for exchanging calendar and scheduling information between users and computers, described at <https://icalendar.org/>.
Depends: R (>= 3.4.0)
License: Apache License (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: testthat, knitr, rmarkdown
Imports: methods, tibble, lubridate
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-05 11:59:18 UTC; robin
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-11 13:53:13 UTC

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Package AdhereR updated to version 0.4.1 with previous version 0.4 dated 2019-02-10

Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care Data and visualization of individual medication histories and adherence patterns. The package implements a set of S3 classes and functions consistent with current adherence guidelines and definitions. It allows the computation of different measures of adherence (as defined in the literature, but also several original ones), their publication-quality plotting, the estimation of event duration and time to initiation, the interactive exploration of patient medication history and the real-time estimation of adherence given various parameter settings. It scales from very small datasets stored in flat CSV files to very large databases and from single-thread processing on mid-range consumer laptops to parallel processing on large heterogeneous computing clusters. It exposes a standardized interface allowing it to be used from other programming languages and platforms, such as Python.
Author: Dan Dediu [aut, cre], Alexandra Dima [aut], Samuel Allemann [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>

Diff between AdhereR versions 0.4 dated 2019-02-10 and 0.4.1 dated 2019-02-11

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Package VIM updated to version 4.8.0 with previous version 4.7.0 dated 2017-04-11

Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Author: Matthias Templ [aut, cre], Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>), Andreas Alfons [aut], Bernd Prantner [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between VIM versions 4.7.0 dated 2017-04-11 and 4.8.0 dated 2019-02-11

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 VIM-4.8.0/VIM/man/marginmatrix.Rd       |  155 +-
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 61 files changed, 5229 insertions(+), 5067 deletions(-)

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Package kaphom updated to version 0.3 with previous version 0.2 dated 2017-10-26

Title: Test the Homogeneity of Kappa Statistics
Description: Tests the homogeneity of intraclass kappa statistics obtained from independent studies or a stratified study with binary results. It is desired to compare the kappa statistics obtained in multi-center studies or in a single stratified study to give a common or summary kappa using all available information. If the homogeneity test of these kappa statistics is not rejected, then it is possible to make inferences over a single kappa statistic that summarizes all the studies. Muammer Albayrak, Kemal Turhan, Yasemin Yavuz, Zeliha Aydin Kasap (2019) <doi:10.1080/03610918.2018.1538457> Jun-mo Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005) <doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura McSweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner, Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>.
Author: Muammer Albayrak
Maintainer: Muammer Albayrak <m.albayrak@ktu.edu.tr>

Diff between kaphom versions 0.2 dated 2017-10-26 and 0.3 dated 2019-02-11

 DESCRIPTION |   10 +++++-----
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 2 files changed, 6 insertions(+), 6 deletions(-)

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Package rdbnomics updated to version 0.4.6 with previous version 0.4.5 dated 2019-01-31

Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API (<https://db.nomics.world/>).
Author: Thomas Brand [aut], Sebastien Galais [cre, ctb]
Maintainer: Sebastien Galais <Sebastien.GALAIS@banque-france.fr>

Diff between rdbnomics versions 0.4.5 dated 2019-01-31 and 0.4.6 dated 2019-02-11

 DESCRIPTION             |    6 ++--
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Package Spectrum updated to version 0.2 with previous version 0.1 dated 2019-02-08

Title: Versatile Ultra-Fast Spectral Clustering for Single and Multi-View Data
Description: A versatile ultra-fast spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in dense regions in the graph. For integrating multi-view data and reducing noise we use a recently developed tensor product graph data integration and diffusion system. 'Spectrum' contains two techniques for finding the number of clusters (K); the classical eigengap method and a novel multimodality gap procedure. The multimodality gap analyses the distribution of the eigenvectors of the graph Laplacian to decide K and tune the kernel. 'Spectrum' is suited for clustering a wide range of complex data.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>

Diff between Spectrum versions 0.1 dated 2019-02-08 and 0.2 dated 2019-02-11

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New package sparsenet with initial version 1.3
Package: sparsenet
Type: Package
Title: Fit Sparse Linear Regression Models via Nonconvex Optimization
Version: 1.3
Date: 2019-02-01
Author: Rahul Mazumder [aut, cre], Trevor Hastie [aut, cre], Jerome Friedman [aut, cre]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Description: Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.
Depends: glmnet, Matrix (>= 1.0-6), shape
Imports: methods
License: GPL-2
NeedsCompilation: yes
URL: http://www.stanford.edu/~hastie/Papers/Sparsenet/jasa_MFH_final.pdf
Packaged: 2019-02-11 00:57:44 UTC; hastie
Repository: CRAN
Date/Publication: 2019-02-11 08:40:02 UTC

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New package sdpt3r with initial version 0.3
Package: sdpt3r
Type: Package
Title: Semi-Definite Quadratic Linear Programming Solver
Version: 0.3
Date: 2019-02-08
Author: Kim-Chuan Toh (Matlab/C), Micheal Todd (Matlab/C), Reha Tutunco (Matlab/C), Adam Rahman (R/C Headers), Timothy A. Davis (symamd C code), Stefan I. Larimore (symamd C code)
Maintainer: Adam Rahman <a45rahma@uwaterloo.ca>
Description: Solves the general Semi-Definite Linear Programming formulation using an R implementation of SDPT3 (K.C. Toh, M.J. Todd, and R.H. Tutuncu (1999) <doi:10.1080/10556789908805762>). This includes problems such as the nearest correlation matrix problem (Higham (2002) <doi:10.1093/imanum/22.3.329>), D-optimal experimental design (Smith (1918) <doi:10.2307/2331929>), Distance Weighted Discrimination (Marron and Todd (2012) <doi:10.1198/016214507000001120>), as well as graph theory problems including the maximum cut problem. Technical details surrounding SDPT3 can be found in R.H Tutuncu, K.C. Toh, and M.J. Todd (2003) <doi:10.1007/s10107-002-0347-5>.
License: GPL-2 | GPL-3
Depends: Matrix, R (>= 2.10)
RoxygenNote: 6.1.1
NeedsCompilation: yes
Imports: methods, stats
Packaged: 2019-02-09 00:45:34 UTC; adamr
Repository: CRAN
Date/Publication: 2019-02-11 08:50:03 UTC

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Package RVAideMemoire updated to version 0.9-72 with previous version 0.9-71 dated 2019-01-11

Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Herv
Maintainer: Maxime Herv <maxime.herve@univ-rennes1.fr>

Diff between RVAideMemoire versions 0.9-71 dated 2019-01-11 and 0.9-72 dated 2019-02-11

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Package mccmeiv updated to version 2.1 with previous version 2.0 dated 2019-02-06

Title: Analysis of Matched Case Control Data with a Mismeasured Exposure that is Accompanied by Instrumental Variables
Description: Applying the methodology from Manuel et al. to estimate parameters using a matched case control data with a mismeasured exposure variable that is accompanied by instrumental variables (Submitted).
Author: Chris M Manuel, Samiran Sinha, and Suojin Wang
Maintainer: Chris M Manuel <cmmanuel@stat.tamu.edu>

Diff between mccmeiv versions 2.0 dated 2019-02-06 and 2.1 dated 2019-02-11

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Package lmerTest updated to version 3.1-0 with previous version 3.0-1 dated 2018-04-23

Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.
Author: Alexandra Kuznetsova [aut], Per Bruun Brockhoff [aut, ths, cre], Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>

Diff between lmerTest versions 3.0-1 dated 2018-04-23 and 3.1-0 dated 2019-02-11

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Package later updated to version 0.8.0 with previous version 0.7.5 dated 2018-09-18

Title: Utilities for Delaying Function Execution
Description: Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied.
Author: Joe Cheng [aut, cre], RStudio [cph], Winston Chang [aut], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)
Maintainer: Joe Cheng <joe@rstudio.com>

Diff between later versions 0.7.5 dated 2018-09-18 and 0.8.0 dated 2019-02-11

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 later-0.7.5/later/configure                     |only
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 later-0.8.0/later/MD5                           |   45 +++++++++++-------------
 later-0.8.0/later/NEWS.md                       |   10 +++++
 later-0.8.0/later/R/RcppExports.R               |    4 +-
 later-0.8.0/later/R/later.R                     |    9 +++-
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 later-0.8.0/later/src/init.c                    |    4 +-
 later-0.8.0/later/src/later.cpp                 |    6 +--
 later-0.8.0/later/src/later.h                   |    2 -
 later-0.8.0/later/src/later_posix.cpp           |   29 +++++++++------
 later-0.8.0/later/src/threadutils.h             |   38 ++++++++++----------
 later-0.8.0/later/src/timeconv.h                |    2 -
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 later-0.8.0/later/tests/testthat/test-run_now.R |   17 +++++++++
 28 files changed, 154 insertions(+), 87 deletions(-)

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Package corTest updated to version 0.9.7 with previous version 0.9.6 dated 2018-06-14

Title: Robust Tests for Equal Correlation
Description: There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. U are proportion to different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the passage New Statistical Methods for Constructing Robust Differential Correlation Networks (expected to be public).
Author: Danyang Yu, Weiliang Qiu, Zeyu Zhang, Kimberly Glass, Jessica Su, Dawn L. DeMeo, Kelan Tantisira, Scott T. Weiss
Maintainer: Danyang Yu <danyangyu@hnu.edu.cn>

Diff between corTest versions 0.9.6 dated 2018-06-14 and 0.9.7 dated 2019-02-11

 DESCRIPTION                 |   10 +++++-----
 MD5                         |   20 ++++++++++----------
 R/corTest.R                 |    7 ++++++-
 man/fisher_transfer_test.Rd |   13 ++++++++-----
 man/ghdist.Rd               |    4 ++--
 man/st1.Rd                  |    4 ++--
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 man/st4.Rd                  |    4 ++--
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 man/st6.Rd                  |    4 ++--
 11 files changed, 43 insertions(+), 35 deletions(-)

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Package protr updated to version 1.6-0 with previous version 1.5-2 dated 2018-11-22

Title: Generating Various Numerical Representation Schemes for Protein Sequences
Description: Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download> for more information.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>), Qing-Song Xu [aut], Dong-Sheng Cao [aut]
Maintainer: Nan Xiao <me@nanx.me>

Diff between protr versions 1.5-2 dated 2018-11-22 and 1.6-0 dated 2019-02-11

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 15 files changed, 667 insertions(+), 425 deletions(-)

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Package NAM updated to version 1.6.5 with previous version 1.6.4 dated 2018-09-29

Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between NAM versions 1.6.4 dated 2018-09-29 and 1.6.5 dated 2019-02-11

 DESCRIPTION                  |    8 -
 MD5                          |   28 ++---
 R/RcppExports.R              |   16 ++-
 R/gibbs.R                    |   25 ++--
 R/gmm.R                      |    4 
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 R/reml.R                     |   19 ++-
 R/snp.R                      |    2 
 inst/doc/gwa_description.pdf |binary
 inst/doc/vignette1.html      |    4 
 inst/doc/vignette2.html      |    4 
 man/Internals.Rd             |   17 ++-
 man/NAM-package.Rd           |    4 
 src/Functions.cpp            |  222 +++++++++++++++++++++++++++++++++++++++++--
 src/RcppExports.cpp          |   55 +++++++++-
 15 files changed, 354 insertions(+), 82 deletions(-)

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