Wed, 06 Apr 2016

Package photobiology updated to version 0.9.7 with previous version 0.9.6 dated 2016-04-02

Title: 'Photobiological' Calculations
Description: Definitions of classes, methods, operators and functions for use in 'photobiology' and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted 'irradiances'/doses, 'fluence' rates, 'transmittance', 'reflectance', 'absorptance', 'absorbance' and diverse ratios and other derived quantities from spectral data. Local 'maxima' and 'minima'. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package taxize updated to version 0.7.5 with previous version 0.7.4 dated 2016-03-08

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

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Package tablaxlsx updated to version 1.0.9 with previous version 1.0.8 dated 2016-03-10

Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>

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Package pogit updated to version 1.1.0 with previous version 1.0.1 dated 2015-07-14

Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>

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Package palettetown updated to version 0.1.1 with previous version 0.1.0 dated 2015-09-07

Title: Use Pokemon Inspired Colour Palettes
Description: Use Pokemon(R) inspired palettes with additional 'ggplot2' scales. Palettes are the colours in each Pokemon's sprite, ordered by how common they are in the image. The first 386 Pokemon are currently provided.
Author: Tim Lucas
Maintainer: Tim Lucas <timcdlucas@gmail.com>

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Package MixtureInf updated to version 1.1 with previous version 1.0-1 dated 2013-03-18

Title: Inference for Finite Mixture Models
Description: Functions for computing the penalized maximum likelihood estimate (PMLE) or maximum likelihood estimate (MLE), testing the order of a finite mixture model using EM-test, drawing histogram of observations and the fitted density or probability mass function of the mixture model.
Author: Shaoting Li, Jiahua Chen and Pengfei Li.
Maintainer: Davor Cubranic <cubranic@stat.ubc.ca>

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Package geoknife updated to version 1.3.0 with previous version 1.2.1 dated 2016-02-18

Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web-enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre], Jordan Walker [aut], Alison Appling [aut], David Blodgett [aut], Emily Read [aut], Luke Winslow [aut]
Maintainer: Jordan Read <jread@usgs.gov>

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Package sem updated to version 3.1-7 with previous version 3.1-6 dated 2015-06-10

Title: Structural Equation Models
Description: Functions for fitting general linear structural equation models (with observed and latent variables) using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre], Zhenghua Nie [aut], Jarrett Byrnes [aut], Michael Culbertson [ctb], Saikat DebRoy [ctb], Michael Friendly [ctb], Goodrich Benjamin [ctb], Richard H. Jones [ctb], Adam Kramer [ctb], Georges Monette [ctb], R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package RcmdrPlugin.survival updated to version 1.1-0 with previous version 1.0-5 dated 2015-02-03

Title: R Commander Plug-in for the 'survival' Package
Description: An R Commander plug-in for the survival package, with dialogs for Cox models, parametric survival regression models, estimation of survival curves, and testing for differences in survival curves, along with data-management facilities and a variety of tests, diagnostics and graphs.
Author: John Fox
Maintainer: John Fox <jfox@mcmaster.ca>

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Package molaR updated to version 2.2 with previous version 2.1 dated 2016-03-01

Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy, relief index, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>

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New package island with initial version 0.1.2
Package: island
Type: Package
Title: Stochastic Island Biogeography Theory Made Easy
Version: 0.1.2
Date: 2016-04-06
Authors@R: c(person("Vicente","Jimenez",email="vicente.jimenez.ontiveros@gmail.com",role=c("aut","cre")), person("David","Alonso", email = "dalonso@ceab.csic.es", role = "aut"))
Description: Tools to develop stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <DOI:10.1023/A:1016393430551> and extensions. The package implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulate community assembly, and perform model selection.
NeedsCompilation: no
Depends: R (>= 3.0.0), stats, utils
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Packaged: 2016-04-06 16:00:38 UTC; usercluster
Author: Vicente Jimenez [aut, cre], David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-06 18:18:53

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New package haplotyper with initial version 0.1
Package: haplotyper
Type: Package
Title: Tool for Clustering Genotypes in Haplotypes
Version: 0.1
Date: 2016-03-28
Author: Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Maintainer: Gaston Quero <gastonquero@gmail.com>
Description: Function to identify haplotypes within QTL (Quantitative Trait Loci). One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within the QTL. This function groups together all individuals of a population with the same haplotype. Each group contains individual with the same allele in each SNP, whether or not missing data. Thus, haplotyper groups individuals, that to be imputed, have a non-zero probability of having the same alleles in the entire sequence of SNP's. Moreover, haplotyper calculates such probability from relative frequencies.
Depends: R (>= 2.10)
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: graphics, utils
NeedsCompilation: no
Packaged: 2016-04-06 14:44:27 UTC; GQ
Repository: CRAN
Date/Publication: 2016-04-06 17:23:47

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Package cape updated to version 2.0.1 with previous version 2.0 dated 2016-03-29

Title: Combined Analysis of Pleiotropy and Epistasis
Description: Combines complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Maintainer: Anna L. Tyler <Anna.Tyler@jax.org>

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More information about cape at CRAN
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Package rmetasim updated to version 3.0.4 with previous version 3.0.2 dated 2016-03-29

Title: An Individual-Based Population Genetic Simulation Environment
Description: An interface between R and the metasim simulation engine. The simulation environment is documented in: "Strand, A.(2002) <DOI:10.1046/j.1471-8286.2002.00208.x> Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. Mol. Ecol. Notes. Please see the vignettes CreatingLandscapes and Simulating to get some ideas on how to use the packages. See the rmetasim vignette to get an overview and to see important changes to the code in the most recent version.
Author: Allan Strand <stranda@cofc.edu>, James Niehaus
Maintainer: Allan Strand <stranda@cofc.edu>

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New package pop.wolf with initial version 0.1
Package: pop.wolf
Type: Package
Title: Models for Simulating Wolf Populations
Version: 0.1
Date: 2016-04-05
Authors@R: c(person("Guillaume", "Chapron", role = c("aut", "cre"), email = "guillaume.chapron@slu.se"), person("Camilla", "Wikenros", role = "ctb"), person("Olof", "Liberg", role = "ctb"), person("Øystein", "Flagstad", role = "ctb"), person("Cyril", "Milleret", role = "ctb"), person("Johan", "Månsson", role = "ctb"), person("Linn", "Svensson", role = "ctb"), person("Barbara", "Zimmermann", role = "ctb"), person("Mikael", "Åkesson", role = "ctb"), person("Petter", "Wabakken", role = "ctb"), person("Håkan", "Sand", role = "ctb"))
Author: Guillaume Chapron [aut, cre], Camilla Wikenros [ctb], Olof Liberg [ctb], Øystein Flagstad [ctb], Cyril Milleret [ctb], Johan Månsson [ctb], Linn Svensson [ctb], Barbara Zimmermann [ctb], Mikael Åkesson [ctb], Petter Wabakken [ctb], Håkan Sand [ctb]
Maintainer: Guillaume Chapron <guillaume.chapron@slu.se>
Description: Simulate the dynamic of wolf populations using a specific Individual-Based Model (IBM) compiled in C.
License: GPL-3
Depends: parallel, abind
NeedsCompilation: yes
LazyData: true
Encoding: UTF-8
Packaged: 2016-04-06 13:18:44 UTC; Guillaume
Repository: CRAN
Date/Publication: 2016-04-06 16:21:30

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Permanent link

New package PhysActBedRest with initial version 1.0
Package: PhysActBedRest
Type: Package
Title: Marks Periods of 'Bedrest' in Actigraph Accelerometer Data
Version: 1.0
Date: 2016-4-5
Author: J. Dustin Tracy, Zhiyi Xu, Sari Acra, Kong Y. Chen, Maciej S. Buchowski
Maintainer: J. Dustin Tracy <jtracy2@student.gsu.edu>
Depends: R (>= 2.10), chron, stringr
Imports: lubridate
Description: Contains a function to categorize accelerometer readings collected in free-living (e.g., for 24 hours/day for 7 days), preprocessed and compressed as counts (unit-less value) in a specified time period termed epoch (e.g., 1 minute) as either bedrest (sleep) or active. The input is a matrix with a timestamp column and a column with number of counts per epoch. The output is the same dataframe with an additional column termed bedrest. In the bedrest column each line (epoch) contains a function-generated classification 'br' or 'a' denoting bedrest/sleep and activity, respectively. The package is designed to be used after wear/nonwear marking function in the 'PhysicalActivity' package.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2016-04-06 13:50:34 UTC; Dustin
Repository: CRAN
Date/Publication: 2016-04-06 16:21:27

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Package NNS updated to version 0.1.1 with previous version 0.1 dated 2016-04-05

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>

Diff between NNS versions 0.1 dated 2016-04-05 and 0.1.1 dated 2016-04-06

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Package maxstat updated to version 0.7-24 with previous version 0.7-23 dated 2015-07-01

Title: Maximally Selected Rank Statistics
Description: Maximally selected rank statistics with several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between maxstat versions 0.7-23 dated 2015-07-01 and 0.7-24 dated 2016-04-06

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New package FuzzyAHP with initial version 0.6.1
Package: FuzzyAHP
Type: Package
Title: (Fuzzy) AHP Calculation
Version: 0.6.1
Date: 2016-03-14
Authors@R: c(person("Jan", "Caha", email = "cahik@atlas.cz", role = c("aut", "cre")), person("Aneta", "Drážná", email = "", role = c("ctb", "com")))
URL: http://github.com/JanCaha/FuzzyAHP/
Description: Calculation of AHP (Analytic Hierarchy Process - <http://en.wikipedia.org/wiki/Analytic_hierarchy_process>) with classic and fuzzy weights based on Saaty's pairwise comparison method for determination of weights.
Encoding: UTF-8
Depends: R (>= 3.0.0), methods
Suggests: knitr
License: LGPL (>= 3)
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Collate: 'class-FuzzyData.R' 'class-PairwiseComparisonMatrix.R' 'class-FuzzyPairwiseComparisonMatrix.R' 'class-FuzzyWeights.R' 'class-Weights.R' 'function-bindFuzzyData.R' 'function-calculateAHP.R' 'function-calculateWeights.R' 'function-compare.R' 'function-consistencyRatio.R' 'function-defuzzify.R' 'function-getFuzzyNumbers.R' 'function-internal-optimization.R' 'function-print.R' 'function-strictConsistency.R' 'function-weakConsistency.R' 'package-FuzzyAHP.R'
NeedsCompilation: no
Packaged: 2016-04-05 09:41:13 UTC; Cahik
Author: Jan Caha [aut, cre], Aneta Drážná [ctb, com]
Maintainer: Jan Caha <cahik@atlas.cz>
Repository: CRAN
Date/Publication: 2016-04-06 15:31:29

More information about FuzzyAHP at CRAN
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Package covr updated to version 2.0.1 with previous version 1.2.0 dated 2015-06-25

Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally) upload the results to a coverage service like Codecov (http://codecov.io) or Coveralls (http://coveralls.io). Code coverage is a measure of the amount of code being exercised by the tests. It is an indirect measure of test quality. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/Fortran code.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Permanent link

Package infuser updated to version 0.2.3 with previous version 0.2.2 dated 2016-01-04

Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>

Diff between infuser versions 0.2.2 dated 2016-01-04 and 0.2.3 dated 2016-04-06

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New package spaero with initial version 0.1.0
Package: spaero
Title: Software for Project AERO
Version: 0.1.0
Authors@R: person("Eamon", "O'Dea", email = "odea35@gmail.com", role = c("aut", "cre"))
Description: Implements methods for anticipating the emergence and eradication of infectious diseases from surveillance time series. Also provides support for computational experiments testing the performance of such methods.
Depends: R (>= 3.2.1)
Imports: stats
License: GPL (>= 2)
LazyData: true
Suggests: earlywarnings (>= 1.0.59), lintr (>= 0.3.3), testthat (>= 0.11.0), np (>= 0.60.2), pomp (>= 1.2.2.1), knitr (>= 1.11), rmarkdown (>= 0.9.2)
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-04-06 03:32:57 UTC; eamon
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-06 09:43:13

More information about spaero at CRAN
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Package RNeo4j updated to version 1.6.4 with previous version 1.6.3 dated 2016-01-29

Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>

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New package MixRF with initial version 1.0
Package: MixRF
Title: A Random-Forest-Based Approach for Imputing Clustered Incomplete Data
Version: 1.0
Date: 2016-04-05
Author: Jiebiao Wang and Lin S. Chen
Maintainer: Jiebiao Wang <randel.wang@gmail.com>
Description: It offers random-forest-based functions to impute clustered incomplete data. The package is tailored for but not limited to imputing multitissue expression data, in which a gene's expression is measured on the collected tissues of an individual but missing on the uncollected tissues.
License: GPL
Depends: doParallel, randomForest, lme4, foreach
URL: https://github.com/randel/MixRF
BugReports: https://github.com/randel/MixRF/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-06 02:05:06 UTC; JWang
Repository: CRAN
Date/Publication: 2016-04-06 09:43:04

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Package hts updated to version 5.0 with previous version 4.5 dated 2015-06-28

Title: Hierarchical and Grouped Time Series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang, Alan Lee, Shanika Wickramasuriya
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>

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Package HH updated to version 3.1-30 with previous version 3.1-25 dated 2016-02-03

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>

Diff between HH versions 3.1-25 dated 2016-02-03 and 3.1-30 dated 2016-04-06

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New package BPEC with initial version 1.0
Package: BPEC
Type: Package
Title: Bayesian Phylogeographic and Ecological Clustering
Version: 1.0
Date: 2016-04-05
Author: Ioanna Manolopoulou, Axel Hille
Maintainer: Ioanna Manolopoulou <ioanna.manolopoulou@gmail.com>
Description: Model-based clustering for phylogeographic data comprising mtDNA sequences and geographical locations along with optional environmental characteristics, aiming to identify migration events that led to homogeneous population clusters.
Depends: ape,maps,igraph
Imports: mvtnorm,maptools,sp,R2G2,phytools,fields,coda,methods
License: GPL-2
LazyLoad: yes
Packaged: 2016-04-06 07:05:23 UTC; ioannamanolopoulou
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-04-06 09:49:06

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Package Bolstad updated to version 0.2-33 with previous version 0.2-32 dated 2016-03-22

Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to Bayesian Statistics, Bolstad, W.M. (2007), John Wiley & Sons ISBN 0-471-27020-2.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>

Diff between Bolstad versions 0.2-32 dated 2016-03-22 and 0.2-33 dated 2016-04-06

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Package biorxivr updated to version 0.1.3 with previous version 0.1.2 dated 2015-10-17

Title: Search and Download Papers from the bioRxiv Preprint Server
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>

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Package bdrift updated to version 1.2.2 with previous version 1.1.7 dated 2016-01-18

Title: Beta Drift Analysis
Description: Beta drift poses a serious challenge to asset managers and financial researchers. Beta drift causes problems in asset pricing models and can have serious ramifications for hedging attempts. Providing users with a tool that allows them to quantify beta drift and form educated opinions about it is the primary purpose of this package. This package contains the BDA() function that performs a beta drift analysis, typically for multi-factor asset pricing models. The BDA() function tests the underlying model parameters for drift across time, drift across model horizon, and applies a jackknife procedure to the baseline model. This allows the users to draw conclusions about the stability of model parameters or make inferences about the behavior of funds. For example, the drift of parameters for active funds could be interpreted as implicit style drift or, in the case of passive funds, management's inability to track a benchmark completely.
Author: Markus Peter Auer [aut, cre]
Maintainer: Markus Peter Auer <mp.auer@meanerreversion.com>

Diff between bdrift versions 1.1.7 dated 2016-01-18 and 1.2.2 dated 2016-04-06

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Package bayesboot updated to version 0.2.1 with previous version 0.2.0 dated 2016-02-18

Title: An Implementation of Rubin's (1981) Bayesian Bootstrap
Description: Functions for performing the Bayesian bootstrap as introduced by Rubin (1981) <doi:10.1214/aos/1176345338> and for summarizing the result. The implementation can handle both summary statistics that works on a weighted version of the data and summary statistics that works on a resampled data set.
Author: Rasmus Bååth [aut, cre]
Maintainer: Rasmus Bååth <rasmus.baath@gmail.com>

Diff between bayesboot versions 0.2.0 dated 2016-02-18 and 0.2.1 dated 2016-04-06

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Package RcppArmadillo updated to version 0.6.700.3.0 with previous version 0.6.600.4.0 dated 2016-03-16

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.6.600.4.0 dated 2016-03-16 and 0.6.700.3.0 dated 2016-04-06

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 34 files changed, 306 insertions(+), 159 deletions(-)

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