Sun, 05 Feb 2017

Package LSDinterface updated to version 0.3.0 with previous version 0.2.3 dated 2017-01-20

Title: Reading LSD Results (.res) Files
Description: Interfaces R with LSD. Reads object-oriented data in results files (.res) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallelization of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <http://labsimdev.org>).
Author: Marcelo C. Pereira
Maintainer: Marcelo C. Pereira <marcelocpereira@uol.com.br>

Diff between LSDinterface versions 0.2.3 dated 2017-01-20 and 0.3.0 dated 2017-02-05

 DESCRIPTION          |   12 +-
 MD5                  |   14 +--
 NAMESPACE            |    2 
 R/LSDinterface.R     |  231 +++++++++++++++++++++++++++++++++++++++------------
 build/partial.rdb    |binary
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 man/read.4d.lsd.Rd   |    5 -
 man/read.list.lsd.Rd |    6 +
 8 files changed, 207 insertions(+), 68 deletions(-)

More information about LSDinterface at CRAN
Permanent link

New package LinkageMapView with initial version 1.0.0
Package: LinkageMapView
Type: Package
Title: Plot Linkage Group Maps with Quantitative Trait Loci
Version: 1.0.0
Authors@R: person("Lisa", "Ouellette", email = "louellet@uncc.edu", role = c("aut", "cre"))
Description: Produces high resolution, publication ready linkage maps and quantitative trait loci maps. Input can be output from 'R/qtl', simple text or comma delimited files. Output is currently a portable document file.
URL: https://github.com/louellette/LinkageMapView
BugReports: https://github.com/louellette/LinkageMapView/issues
License: GPL-3
LazyData: TRUE
Imports: plotrix (>= 3.6-3), grDevices, graphics, utils
Suggests: qtl (>= 1.39-5), rmarkdown
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-02-05 18:32:58 UTC; Lisa
Author: Lisa Ouellette [aut, cre]
Maintainer: Lisa Ouellette <louellet@uncc.edu>
Repository: CRAN
Date/Publication: 2017-02-06 00:53:23

More information about LinkageMapView at CRAN
Permanent link

Package lidR updated to version 1.1.0 with previous version 1.0.2 dated 2016-12-31

Title: Airborne LiDAR Data Manipulation and Visualization for Forestry Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph], David Auty [aut, ctb] (Reviews the documentation), Florian De Boissieu [ctb] (Fixed bugs and improved catalog features), Andrew Sánchez Meador [ctb] (Helped to review the documentation)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

Diff between lidR versions 1.0.2 dated 2016-12-31 and 1.1.0 dated 2017-02-05

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More information about lidR at CRAN
Permanent link

New package BayesianTools with initial version 0.1.0
Package: BayesianTools
Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Version: 0.1.0
Date: 2017-02-5
Authors@R: c(person("Florian", "Hartig", email = "florian.hartig@biologie.uni-regensburg.de", role = c("aut", "cre")), person("Francesco", "Minunno", role = c("aut")), person("Stefan", " Paul", role = c("aut") ), person("David", "Cameron", role = "ctb"))
Author: Florian Hartig [aut, cre], Francesco Minunno [aut], Stefan Paul [aut], David Cameron [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Description: General-purpose MCMC and SMC samplers, as well as plot and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Depends: R (>= 3.1.2)
License: CC BY-SA 4.0
Imports: coda, vioplot, emulator, mvtnorm, IDPmisc, Rcpp, ellipse, numDeriv, msm, MASS, Matrix, stats, utils, graphics
Suggests: DEoptim, lhs, sensitivity, knitr, rmarkdown, roxygen2, testthat, gap
LinkingTo: Rcpp
LazyData: true
RoxygenNote: 6.0.0
URL: https://github.com/florianhartig/BayesianTools
BugReports: https://github.com/florianhartig/BayesianTools/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-02-05 21:17:28 UTC; Florian
Repository: CRAN
Date/Publication: 2017-02-06 00:42:53

More information about BayesianTools at CRAN
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Package WikidataR updated to version 1.2.0 with previous version 1.1.0 dated 2016-06-13

Title: API Client Library for 'Wikidata'
Description: An API client for the Wikidata <http://wikidata.org/> store of semantic data.
Author: Oliver Keyes [aut, cre], Serena Signorelli [aut, cre], Christian Graul [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>

Diff between WikidataR versions 1.1.0 dated 2016-06-13 and 1.2.0 dated 2017-02-05

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Package random updated to version 0.2.6 with previous version 0.2.5 dated 2015-06-30

Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG website created by Mads Haahr samples atmospheric noise via radio tuned to an unused broadcasting frequency together with a skew correction algorithm due to John von Neumann. More background is available in the included vignette based on an essay by Mads Haahr. In its current form, the package offers functions to retrieve random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between random versions 0.2.5 dated 2015-06-30 and 0.2.6 dated 2017-02-05

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More information about random at CRAN
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Package pROC updated to version 1.9.1 with previous version 1.8 dated 2015-05-05

Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut], Natacha Turck [aut], Alexandre Hainard [aut], Natalia Tiberti [aut], Frédérique Lisacek [aut], Jean-Charles Sanchez [aut], Markus Müller [aut], Stefan Siegert [ctb] (Fast DeLong code)
Maintainer: Xavier Robin <robin@lindinglab.org>

Diff between pROC versions 1.8 dated 2015-05-05 and 1.9.1 dated 2017-02-05

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Package braQCA updated to version 0.9.9.6 with previous version 0.9.9.4 dated 2016-10-11

Title: Bootstrapped Robustness Assessment for Qualitative Comparative Analysis
Description: Test the robustness of a user's Qualitative Comparative Analysis solutions to randomness, using the bootstrapped assessment: baQCA(). This package also includes a function that provides recommendations for improving solutions to reach typical significance levels: brQCA(). After applying recommendations from brQCA(), QCAdiff() shows which cases are excluded from the final result.
Author: C. Ben Gibson [aut, cre], Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>

Diff between braQCA versions 0.9.9.4 dated 2016-10-11 and 0.9.9.6 dated 2017-02-05

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Package rlas updated to version 1.1.0 with previous version 1.0.3 dated 2016-12-28

Title: Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3.
Author: Jean-Romain Roussel [aut, cre, cph], Martin Isenburg [cph] (Is the author of the LASlib and LASzip libraries), David Auty [ctb] (Reviewed the documentation), Pierrick Marie [ctb] (Helped to compile LASlib code in R), Florian De Boissieu [ctb] (Enable support of .lax file)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

Diff between rlas versions 1.0.3 dated 2016-12-28 and 1.1.0 dated 2017-02-05

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Package missDeaths updated to version 2.0 with previous version 1.2 dated 2015-08-09

Title: Simulating and Analyzing Time to Event Data in the Presence of Population Mortality
Description: Implements two methods: a nonparametric risk adjustment and a data imputation method that use general population mortality tables to allow a correct analysis of time to disease recurrence. Also includes a powerful set of object oriented survival data simulation functions.
Author: Tomaz Stupnik [aut, cre], Maja Pohar Perme [ctb]
Maintainer: Tomaz Stupnik <tomaz.stupnik@guest.arnes.si>

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More information about missDeaths at CRAN
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Package eulerr updated to version 1.1.0 with previous version 1.0.0 dated 2016-12-10

Title: Area-Proportional Euler Diagrams
Description: If possible, generates exactly area-proportional Euler diagrams, or otherwise approximately proportional diagrams using numerical optimization. A Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johanlarsson@outlook.com>

Diff between eulerr versions 1.0.0 dated 2016-12-10 and 1.1.0 dated 2017-02-05

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More information about eulerr at CRAN
Permanent link

Package FRK (with last version 0.1.1) was removed from CRAN

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

2017-02-05 0.1.1

Permanent link
New package mbrglm with initial version 0.0.1
Package: mbrglm
Type: Package
Title: Median Bias Reduction in Binomial-Response GLMs
Version: 0.0.1
Date: 2017-02-05
Author: Euloge Clovis Kenne Pagui, Nicola Sartori and Alessandra Salvan
Maintainer: Euloge C. Kenne Pagui <kenne@stat.unipd.it>
Description: Fit generalized linear models with binomial responses using a median modified score approach (Kenne Pagui et al., 2016, <https://arxiv.org/abs/1604.04768>) to median bias reduction. This method respects equivariance under reparameterizations for each parameter component and also solves the infinite estimates problem (data separation).
License: GPL-2
Suggests: brglm
Depends: R (>= 2.6.0), nleqslv, enrichwith
NeedsCompilation: yes
Packaged: 2017-02-05 07:42:35 UTC; nicolasartori
Repository: CRAN
Date/Publication: 2017-02-05 16:07:53

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Package pbmcapply updated to version 1.2.1 with previous version 1.2.0 dated 2017-02-04

Title: Tracking the Progress of Mc*pply with Progress Bar
Description: A light-weight package helps you track and visualize the progress of parallel version of vectorized R functions (mc*apply). The package works on *nix (Linux, Unix such as macOS) system only due to the lack of fork() functionality, which is essential for mc*apply, on Windows.
Author: Kevin Kuang (aut), Francesco Napolitano (ctb)
Maintainer: Kevin kuang <kvn.kuang@mail.utoronto.ca>

Diff between pbmcapply versions 1.2.0 dated 2017-02-04 and 1.2.1 dated 2017-02-05

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New package odbc with initial version 1.0.0
Package: odbc
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Version: 1.0.0
Authors@R: c( person("Jim", "Hester", , "james.hester@rstudio.com", role = c("aut", "cre")), person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut")), person(family = "lexicalunit", role = c("cph"), comment = "nanodbc library"), person(family = "RStudio", role = c("cph", "fnd")) )
Description: A DBI-compatible interface to ODBC databases.
License: MIT + file LICENSE
LazyData: true
Imports: DBI (>= 0.3.0), methods, Rcpp, blob
LinkingTo: Rcpp, BH
RoxygenNote: 5.0.1.9000
URL: https://github.com/rstats-db/odbc
BugReports: https://github.com/rstats-db/odbc/issues
SystemRequirements: An ODBC3 driver manager and drivers.
Suggests: tibble, DBItest, testthat, covr
Collate: 'odbc.R' 'Driver.R' 'Connection.R' 'RcppExports.R' 'Result.R' 'Table.R' 'utils.R' 'zzz.R'
NeedsCompilation: yes
Packaged: 2017-02-03 13:50:22 UTC; jhester
Author: Jim Hester [aut, cre], Hadley Wickham [aut], lexicalunit [cph] (nanodbc library), RStudio [cph, fnd]
Maintainer: Jim Hester <james.hester@rstudio.com>
Repository: CRAN
Date/Publication: 2017-02-05 13:41:55

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New package FRK with initial version 0.1.1
Package: FRK
Type: Package
Title: Fixed Rank Kriging
Version: 0.1.1
Date: 2017-01-21
Authors@R: c( person("Andrew", "Zammit-Mangion", , "andrewzm@gmail.com", c("aut", "cre","cph")) )
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
VignetteBuilder: knitr
Description: Fixed Rank Kriging is a tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach, discussed in Cressie and Johannesson (2008), decomposes the field, and hence the covariance function, using a fixed set of n basis functions, where n is typically much smaller than the number of data points (or polygons) m. The method naturally allows for non-stationary, anisotropic covariance functions and the use of observations with varying support (with known error variance). The projected field is a key building block of the Spatial Random Effects (SRE) model, on which this package is based. The package FRK provides helper functions to model, fit, and predict using an SRE with relative ease. Reference: Cressie, N. and Johannesson, G. (2008) <DOI:10.1111/j.1467-9868.2007.00633.x>.
BugReports: http://github.com/andrewzm/FRK/issues
Depends: R (>= 3.1)
Suggests: covr, gstat, INLA, knitr, mapproj, parallel, rgeos, spdep, splancs, testthat, verification
Enhances: dggrids
Additional_repositories: https://andrewzm.github.io/dggrids-repo, http://www.math.ntnu.no/inla/R/stable
Imports: digest, dplyr, Matrix, methods, ggplot2, grDevices, plyr, sp, spacetime, stats, Rcpp, utils
License: GPL (>= 2.1)
NeedsCompilation: yes
LazyData: true
RoxygenNote: 5.0.1
LinkingTo: Rcpp
Packaged: 2017-02-03 16:07:42 UTC; andrew
Author: Andrew Zammit-Mangion [aut, cre, cph]
Repository: CRAN
Date/Publication: 2017-02-05 13:46:34

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Package outbreaks updated to version 1.2.0 with previous version 1.1.0 dated 2016-11-23

Title: A Collection of Disease Outbreak Data
Description: Empirical or simulated disease outbreak data, provided either as RData or as text files.
Author: Thibaut Jombart [aut], Simon Frost [aut], Pierre Nouvellet [aut], Finlay Campbell [aut, cre], Bertrand Sudre [aut]
Maintainer: Finlay Campbell <f.campbell15@imperial.ac.uk>

Diff between outbreaks versions 1.1.0 dated 2016-11-23 and 1.2.0 dated 2017-02-05

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More information about outbreaks at CRAN
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New package glmnetUtils with initial version 1.0.0
Package: glmnetUtils
Type: Package
Version: 1.0.0
Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for elasticnet regression, a method for cross-validating the alpha parameter, and other quality-of-life tools.
Imports: stats, graphics, grDevices, glmnet, parallel, Matrix
Suggests: knitr, rmarkdown, MASS, doParallel, testthat
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi@microsoft.com>
NeedsCompilation: no
VignetteBuilder: knitr
Copyright: Microsoft
License: GPL-2
Collate: 'glmnetUtils.r' 'cvAlpha.r' 'cvGlmnetFormula.r' 'glmnetFormula.r' 'makeModelComponents.r'
RoxygenNote: 5.0.1
Packaged: 2017-02-05 03:08:55 UTC; hongooi
Repository: CRAN
Date/Publication: 2017-02-05 09:55:26

More information about glmnetUtils at CRAN
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New package Wrapped with initial version 1.0
Package: Wrapped
Type: Package
Title: Computes Pdf, Cdf, Quantile, Random Numbers and Provides Estimation for 40 Univariate Wrapped Distributions
Version: 1.0
Date: 2017-01-31
Author: Saralees Nadarajah, Yuanyuan Zhang
Maintainer: Saralees Nadarajah <mbbsssn2@manchester.ac.uk>
Depends: R (>= 3.0.1)
Imports: AdequacyModel, evd, sn, ald, NormalLaplace, GeneralizedHyperbolic, glogis, irtProb, sld, normalp, gamlss.dist, sgt, SkewHyperbolic, fBasics, cubfits, lqmm, LCA, GEVStableGarch, VarianceGamma, VGAM, ordinal
Description: Computes the probability density function, cumulative distribution function, quantile function and random numbers for 40 univariate wrapped distributions. They include the wrapped normal, wrapped Gumbel, wrapped logistic, wrapped t, wrapped Cauchy, wrapped skew normal, wrapped skew t, wrapped asymmetric Laplace, wrapped normal Laplace, wrapped skew Laplace, wrapped skew logistic, wrapped exponential power, wrapped skew power exponential, wrapped power exponential t, wrapped skew generalized t, wrapped skew hyperbolic, wrapped generalized hyperbolic Student t, wrapped power hyperbola logistic, wrapped Kiener, wrapped Laplace mixture, wrapped skew Laplace, wrapped polynomial tail Laplace, wrapped generalized asymmetric t, wrapped variance gamma, wrapped normal inverse gamma, wrapped skew Cauchy, wrapped slash, wrapped ex Gaussian, wrapped stable and wrapped log gamma distributions. Also given are maximum likelihood estimates of the parameters, standard errors, 95 percent confidence intervals, log-likelihood values, AIC values, CAIC values, BIC values, HQIC values, values of the W statistic, values of the A statistic, values of the KS tatistic and the associated p-value.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2017-02-03 19:16:57 UTC; Saraleesan
Repository: CRAN
Date/Publication: 2017-02-05 08:51:11

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Package WikipediR updated to version 1.5.0 with previous version 1.4.0 dated 2016-06-13

Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve page text, information about users or the history of pages, and elements of the category tree.
Author: Oliver Keyes [aut, cre], Brock Tilbert [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>

Diff between WikipediR versions 1.4.0 dated 2016-06-13 and 1.5.0 dated 2017-02-05

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New package RiskPortfolios with initial version 2.1.1
Package: RiskPortfolios
Version: 2.1.1
Date: 2017-02-03
Title: Computation of Risk-Based Portfolios
Authors@R: c(person("David", "Ardia", role = c("aut", "cre"), email = "david.ardia.ch@gmail.com"), person("Kris", "Boudt", role = "aut"), person("Jean-Philippe", "Gagnon-Fleury", role = "aut"))
Author: David Ardia [aut, cre], Kris Boudt [aut], Jean-Philippe Gagnon-Fleury [aut]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Imports: MASS, quadprog, nloptr
Description: Collection of functions designed to compute risk-based portfolios as described in Ardia et al. (2016) <doi:10.2139/ssrn.2650644> and Ardia et al. (2017) <doi:10.21105/joss.00171>.
License: GPL (>= 2)
BugReports: https://github.com/ArdiaD/RiskPortfolios/issues
URL: https://github.com/ArdiaD/RiskPortfolios
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-02-05 00:55:03 UTC; ardiad
Repository: CRAN
Date/Publication: 2017-02-05 08:41:41

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Package jmvcore updated to version 0.3.3 with previous version 0.2.2 dated 2017-01-05

Title: Dependencies for the 'jamovi' Framework
Description: 'jamovi' is a framework for creating rich interactive statistical analyses (see <https://www.jamovi.org> for more information). This package represents the core libraries which jamovi analyses written in R depend upon.
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>

Diff between jmvcore versions 0.2.2 dated 2017-01-05 and 0.3.3 dated 2017-02-05

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New package IMIFA with initial version 1.1.0
Package: IMIFA
Type: Package
Date: 2017-02-02
Title: Fitting, Diagnostics, and Plotting Functions for Infinite Mixtures of Infinite Factor Analysers and Related Models
Version: 1.1.0
Authors@R: c(person("Keefe", "Murphy", email = "keefe.murphy@ucd.ie", role = c("aut", "cre")), person("Isobel Claire", "Gormley", role = "ctb"), person("Cinzia", "Viroli", role = "ctb"))
Description: Provides flexible Gibbs sampler functions for fitting Infinite Mixtures of Infinite Factor Analysers and related models, introduced by Murphy et al. (2017) <https://arxiv.org/abs/1701.07010>, which conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors. Model-specific diagnostic tools are also provided, as well as many options for plotting results and conducting posterior inference on parameters of interest.
Depends: R (>= 3.3.2)
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/Keefe-Murphy/IMIFA
Imports: abind, corpcor, e1071, gclus, graphics, grDevices, matrixcalc, matrixStats, mclust, MCMCpack, mvnfast, plotrix, Rfast, slam, stats, utils, viridis
Suggests: Rmpfr, gmp, knitr, rmarkdown
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-02-03 16:28:06 UTC; Keefe
Author: Keefe Murphy [aut, cre], Isobel Claire Gormley [ctb], Cinzia Viroli [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Repository: CRAN
Date/Publication: 2017-02-05 08:44:23

More information about IMIFA at CRAN
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Package fmdates updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-08

Title: Financial Market Date Calculations
Description: Implements common date calculations relevant for specifying the economic nature of financial market contracts that are typically defined by International Swap Dealer Association (ISDA, <http://www2.isda.org>) legal documentation. This includes methods to check whether dates are business days in certain locales, functions to adjust and shift dates and time length (or day counter) calculations.
Author: Imanuel Costigan <i.costigan@me.com>
Maintainer: Imanuel Costigan <i.costigan@me.com>

Diff between fmdates versions 0.1.0 dated 2017-01-08 and 0.1.1 dated 2017-02-05

 DESCRIPTION                     |   20 ++++++------
 MD5                             |   22 +++++++-------
 NEWS                            |    5 +++
 R/calendar-methods.R            |    5 ---
 R/date-methods.R                |    3 +
 R/yyy-assertion-helpers.R       |    6 +++
 README.md                       |    2 -
 inst/doc/dates.html             |    4 +-
 tests/testthat/test-adjusters.R |only
 tests/testthat/test-calendars.R |   62 ++++++++++++++++------------------------
 tests/testthat/test-counters.R  |    1 
 tests/testthat/test-schedule.R  |   16 ++++++++++
 tests/testthat/test-shifters.R  |only
 13 files changed, 80 insertions(+), 66 deletions(-)

More information about fmdates at CRAN
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