Sat, 13 Jun 2015

Package smbinning updated to version 0.2 with previous version 0.1 dated 2015-02-15

Title: Optimal Binning for Scoring Modeling
Description: It categorizes a numeric variable into bins mapped to a binary target variable for its ulterior usage in scoring modeling. Its purpose is to automate the time consuming process of selecting the right cut points, quickly calculate metrics such as Weight of Evidence and Information Value; and also document SQL codes, tables, and plots used throughout the development stage. The package also allows users to establish their own cut points for numeric characteristics and run the analysis for categorical variables.
Author: Herman Jopia
Maintainer: Herman Jopia <hjopia@gmail.com>

Diff between smbinning versions 0.1 dated 2015-02-15 and 0.2 dated 2015-06-13

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 8 files changed, 500 insertions(+), 42 deletions(-)

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Package peacots updated to version 1.2 with previous version 1.1 dated 2014-10-29

Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@math.ubc.ca>

Diff between peacots versions 1.1 dated 2014-10-29 and 1.2 dated 2015-06-13

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Package MPTinR updated to version 1.9.2 with previous version 1.8.0 dated 2015-04-30

Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>

Diff between MPTinR versions 1.8.0 dated 2015-04-30 and 1.9.2 dated 2015-06-13

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Package blme updated to version 1.0-4 with previous version 1.0-3 dated 2015-05-30

Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. Extends 'lme4' by Douglas Bates, Martin Maechler, Ben Bolker, and Steve Walker.
Author: Vincent Dorie <vjd4@nyu.edu>
Maintainer: Vincent Dorie <vjd4@nyu.edu>

Diff between blme versions 1.0-3 dated 2015-05-30 and 1.0-4 dated 2015-06-13

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New package mmtfa with initial version 0.1
Package: mmtfa
Type: Package
Title: Model-Based Clustering and Classification with Mixtures of Modified t Factor Analyzers
Version: 0.1
Date: 2015-06-13
Author: Jeffrey L. Andrews, Paul D. McNicholas, and Mathieu Chalifour
Maintainer: Jeffrey L. Andrews <jeffrey.andrews@macewan.ca>
Description: Fits a family of mixtures of multivariate t-distributions under a continuous t-distributed latent variable structure for the purpose of clustering or classification. The alternating expectation-conditional maximization algorithm is used for parameter estimation.
License: GPL (>= 2)
LazyLoad: yes
Imports: parallel, mvnfast, matrixStats
Packaged: 2015-06-13 21:10:01 UTC; jandrews
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-14 00:22:42

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Package beepr updated to version 1.2 with previous version 1.1 dated 2014-06-26

Title: Easily Play Notification Sounds on any Platform
Description: The sole function of this package is beep(), with the purpose to make it easy to play notification sounds on whatever platform you are on. It is intended to be useful, for example, if you are running a long analysis in the background and want to know when it is ready.
Author: Rasmus Bååth <rasmus.baath@gmail.com>
Maintainer: Rasmus Bååth <rasmus.baath@gmail.com>

Diff between beepr versions 1.1 dated 2014-06-26 and 1.2 dated 2015-06-13

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Package taxize updated to version 0.6.0 with previous version 0.5.2 dated 2014-12-19

Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Zachary Foster [aut], Carl Boettiger [aut], Karthik Ram [aut], Ignasi Bartomeus [aut], John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between taxize versions 0.5.2 dated 2014-12-19 and 0.6.0 dated 2015-06-13

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 taxize-0.6.0/taxize/DESCRIPTION                                                    |   41 
 taxize-0.6.0/taxize/LICENSE                                                        |    4 
 taxize-0.6.0/taxize/MD5                                                            |  553 +++++-----
 taxize-0.6.0/taxize/NAMESPACE                                                      |   12 
 taxize-0.6.0/taxize/NEWS                                                           |   58 +
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 taxize-0.6.0/taxize/R/apg_lookup.R                                                 |   33 
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 taxize-0.6.0/taxize/R/comm2sci.R                                                   |   33 
 taxize-0.6.0/taxize/R/downstream.R                                                 |   18 
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 taxize-0.6.0/taxize/R/eol_pages.R                                                  |   31 
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 taxize-0.6.0/taxize/R/genbank2uid.R                                                |   39 
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 taxize-0.6.0/taxize/R/get_colid.R                                                  |  133 +-
 taxize-0.6.0/taxize/R/get_eolid.R                                                  |   97 -
 taxize-0.6.0/taxize/R/get_gbifid.R                                                 |  170 ++-
 taxize-0.6.0/taxize/R/get_ids.R                                                    |   13 
 taxize-0.6.0/taxize/R/get_nbnid.R                                                  |    5 
 taxize-0.6.0/taxize/R/get_tpsid.R                                                  |  116 +-
 taxize-0.6.0/taxize/R/get_tsn.R                                                    |   24 
 taxize-0.6.0/taxize/R/get_ubioid.R                                                 |  165 ++
 taxize-0.6.0/taxize/R/get_uid.R                                                    |  162 ++
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 taxize-0.6.0/taxize/R/itis.R                                                       |  366 ++----
 taxize-0.6.0/taxize/R/itis_acceptname.R                                            |   12 
 taxize-0.6.0/taxize/R/itis_native.R                                                |    8 
 taxize-0.6.0/taxize/R/itis_terms.R                                                 |   16 
 taxize-0.6.0/taxize/R/names_list.r                                                 |    2 
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 taxize-0.6.0/taxize/R/nbn_search.R                                                 |    2 
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 taxize-0.6.0/taxize/R/ping.R                                                       |    7 
 taxize-0.6.0/taxize/R/rankagg.R                                                    |    4 
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 taxize-0.6.0/taxize/R/resolve.R                                                    |   12 
 taxize-0.6.0/taxize/R/sci2comm.R                                                   |    6 
 taxize-0.6.0/taxize/R/synonyms.R                                                   |  155 ++
 taxize-0.6.0/taxize/R/tax_agg.R                                                    |   16 
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 taxize-0.6.0/taxize/R/taxize_cite.R                                                |  263 ++++
 taxize-0.6.0/taxize/R/tnrs.R                                                       |   22 
 taxize-0.6.0/taxize/R/tp_accnames.R                                                |   19 
 taxize-0.6.0/taxize/R/tp_classification.R                                          |    6 
 taxize-0.6.0/taxize/R/tp_dist.R                                                    |   17 
 taxize-0.6.0/taxize/R/tp_refs.R                                                    |    9 
 taxize-0.6.0/taxize/R/tp_search.R                                                  |   20 
 taxize-0.6.0/taxize/R/tp_summary.R                                                 |   10 
 taxize-0.6.0/taxize/R/tp_synonyms.R                                                |   23 
 taxize-0.6.0/taxize/R/tpl_families.r                                               |   21 
 taxize-0.6.0/taxize/R/tpl_get.r                                                    |   54 
 taxize-0.6.0/taxize/R/tpl_search.r                                                 |   29 
 taxize-0.6.0/taxize/R/ubio_search.R                                                |   26 
 taxize-0.6.0/taxize/R/upstream.R                                                   |   16 
 taxize-0.6.0/taxize/R/vascan_search.r                                              |    5 
 taxize-0.6.0/taxize/R/zzz.R                                                        |   37 
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 taxize-0.6.0/taxize/man/get_ids.Rd                                                 |    7 
 taxize-0.6.0/taxize/man/get_nbnid.Rd                                               |    7 
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 taxize-0.6.0/taxize/man/get_tpsid.Rd                                               |   41 
 taxize-0.6.0/taxize/man/get_tsn.Rd                                                 |   26 
 taxize-0.6.0/taxize/man/get_ubioid.Rd                                              |   47 
 taxize-0.6.0/taxize/man/get_uid.Rd                                                 |   55 
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 taxize-0.6.0/taxize/man/getkey.Rd                                                  |    2 
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 taxize-0.6.0/taxize/man/gni_search.Rd                                              |    2 
 taxize-0.6.0/taxize/man/gnr_datasources.Rd                                         |    4 
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More information about taxize at CRAN
Permanent link

Package phylocurve updated to version 1.2.0 with previous version 1.1.0 dated 2015-05-11

Title: Phylogenetic Comparative Methods for Function-Valued and Other High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

Diff between phylocurve versions 1.1.0 dated 2015-05-11 and 1.2.0 dated 2015-06-13

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More information about phylocurve at CRAN
Permanent link

Package nodiv updated to version 1.0.4 with previous version 1.0.3 dated 2015-03-26

Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>

Diff between nodiv versions 1.0.3 dated 2015-03-26 and 1.0.4 dated 2015-06-13

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More information about nodiv at CRAN
Permanent link

Package rmarkdown updated to version 0.7 with previous version 0.6.1 dated 2015-05-07

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between rmarkdown versions 0.6.1 dated 2015-05-07 and 0.7 dated 2015-06-13

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More information about rmarkdown at CRAN
Permanent link

Package polysat updated to version 1.4-0 with previous version 1.3-3 dated 2014-09-22

Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, POPDIST, STRand, and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise Fst values based on those frequencies, and export allele frequencies to SPAGeDi and adegenet. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>

Diff between polysat versions 1.3-3 dated 2014-09-22 and 1.4-0 dated 2015-06-13

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More information about polysat at CRAN
Permanent link

Package pkgKitten updated to version 0.1.3 with previous version 0.1.2 dated 2014-09-11

Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little packages which pass R package checks. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between pkgKitten versions 0.1.2 dated 2014-09-11 and 0.1.3 dated 2015-06-13

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More information about pkgKitten at CRAN
Permanent link

New package MM2Sdata with initial version 1.0.0
Package: MM2Sdata
Type: Package
Title: Gene Expression Datasets for the 'MM2S' Package
Version: 1.0.0
Date: 2015-05-14
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Description: Gene Expression datasets for the 'MM2S' package. Contains normalized expression data for Human Medulloblastoma ('GSE37418') as well as Mouse Medulloblastoma models ('GSE36594').
License: Artistic-2.0
Depends: R (>= 2.10), Biobase
Suggests: knitr
biocViews: MM2S, ExperimentData,ExpressionData, MicroarrayData
Packaged: 2015-06-12 16:16:00 UTC; DeenaGendoo
NeedsCompilation: no
URL: http://www.sciencedirect.com/science/article/pii/S0888754315000774
Repository: CRAN
Date/Publication: 2015-06-13 14:43:49

More information about MM2Sdata at CRAN
Permanent link

New package likelihoodAsy with initial version 0.40
Package: likelihoodAsy
Version: 0.40
Priority: optional
Title: Functions for Likelihood Asymptotics
Author: Ruggero Bellio and Donald Pierce
Maintainer: Ruggero Bellio <ruggero.bellio@uniud.it>
Depends: nleqslv, Rsolnp, alabama, pracma, cond
Description: Functions for computing the r and r* statistics for inference on an arbitrary scalar function of model parameters, plus some code for the (modified) profile likelihood.
Suggests: MASS, lme4, knitr
License: GPL (>= 2)
NeedsCompilation: no
LazyLoad: yes
VignetteBuilder: knitr
Packaged: 2015-06-13 10:30:12 UTC; ruggero
Repository: CRAN
Date/Publication: 2015-06-13 15:06:05

More information about likelihoodAsy at CRAN
Permanent link

Package installr updated to version 0.16.0 with previous version 0.15.17 dated 2015-06-03

Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and More!)
Description: R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Barry Rowlingson [ctb], Boris Hejblum [ctb], Dason [ctb], Felix Schonbrodt [ctb], G. Grothendieck [ctb], GERGELY DAROCZI [ctb], Heuristic Andrew [ctb], James [ctb] (http://stackoverflow.com/users/269476/james), Thomas Leeper [ctb] (http://thomasleeper.com/), VitoshKa [ctb], Yihui Xie [ctb] (http://yihui.name), Michael Friendly [ctb] (http://datavis.ca/), Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/), Dieter Menne [ctb], Tyler Hunt [ctb] (https://github.com/JackStat), Takekatsu Hiramura [ctb] (https://github.com/hiratake55), Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>

Diff between installr versions 0.15.17 dated 2015-06-03 and 0.16.0 dated 2015-06-13

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 man/package_authors.Rd                       |   33 ++--
 man/pkgDNLs_worldmapcolor.Rd                 |   24 +--
 man/read_RStudio_CRAN_data.Rd                |   38 ++---
 man/remove.installr.GUI.Rd                   |    5 
 man/remove_from_.First_in_Rprofile.site.Rd   |   16 +-
 man/rename_r_to_R.Rd                         |   32 ++--
 man/require2.Rd                              |   20 --
 man/restart_RGui.Rd                          |    4 
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 man/uninstall.packages.Rd                    |   23 +--
 man/up_folder.Rd                             |   12 -
 man/updateR.Rd                               |  132 +++++--------------
 man/xlsx2csv.Rd                              |   15 --
 94 files changed, 921 insertions(+), 1403 deletions(-)

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New package BIGDAWG with initial version 1.1
Package: BIGDAWG
Type: Package
Title: Case-Control Analysis of Multi-Allelic Loci
Version: 1.1
Date: 2015-06-11
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
URL: http://tools.immunogenomics.org/
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
License: GPL (>= 3)
LazyData: True
Depends: R (>= 2.10)
Imports: XML, haplo.stats, parallel
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-06-13 05:36:54 UTC; DPappas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-13 14:46:41

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Package Kernelheaping updated to version 0.9 with previous version 0.5 dated 2015-04-27

Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>

Diff between Kernelheaping versions 0.5 dated 2015-04-27 and 0.9 dated 2015-06-13

 Kernelheaping-0.5/Kernelheaping/data/students.R                 |only
 Kernelheaping-0.5/Kernelheaping/man/Rprx.Rd                     |only
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 Kernelheaping-0.9/Kernelheaping/MD5                             |   31 -
 Kernelheaping-0.9/Kernelheaping/NAMESPACE                       |    8 
 Kernelheaping-0.9/Kernelheaping/R/Kernelheaping.R               |   17 
 Kernelheaping-0.9/Kernelheaping/R/functions.R                   |  303 ++++++++--
 Kernelheaping-0.9/Kernelheaping/data/students.rda               |only
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 Kernelheaping-0.9/Kernelheaping/man/createSim.Kernelheaping.Rd  |    2 
 Kernelheaping-0.9/Kernelheaping/man/dbivr.Rd                    |only
 Kernelheaping-0.9/Kernelheaping/man/dheaping.Rd                 |    9 
 Kernelheaping-0.9/Kernelheaping/man/plot.Kernelheaping.Rd       |    2 
 Kernelheaping-0.9/Kernelheaping/man/plot.bivrounding.Rd         |only
 Kernelheaping-0.9/Kernelheaping/man/sim.Kernelheaping.Rd        |    4 
 Kernelheaping-0.9/Kernelheaping/man/simSummary.Kernelheaping.Rd |    2 
 Kernelheaping-0.9/Kernelheaping/man/students.Rd                 |    2 
 Kernelheaping-0.9/Kernelheaping/man/summary.Kernelheaping.Rd    |    2 
 Kernelheaping-0.9/Kernelheaping/man/tracePlots.Rd               |    2 
 19 files changed, 320 insertions(+), 100 deletions(-)

More information about Kernelheaping at CRAN
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