Thu, 26 May 2016

Package texmexseq updated to version 0.2 with previous version 0.1 dated 2015-03-11

Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>

Diff between texmexseq versions 0.1 dated 2015-03-11 and 0.2 dated 2016-05-26

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Package spfrontier updated to version 0.2.3 with previous version 0.1.12 dated 2014-12-21

Title: Spatial Stochastic Frontier Models
Description: A set of tools for estimation of various spatial specifications of stochastic frontier models.
Author: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Maintainer: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>

Diff between spfrontier versions 0.1.12 dated 2014-12-21 and 0.2.3 dated 2016-05-26

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Package PST updated to version 0.88 with previous version 0.86 dated 2015-02-18

Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@unige.ch>

Diff between PST versions 0.86 dated 2015-02-18 and 0.88 dated 2016-05-26

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Package HTSCluster updated to version 2.0.8 with previous version 2.0.4 dated 2014-08-26

Title: Clustering High-Throughput Transcriptome Sequencing (HTS) Data
Description: A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau
Maintainer: Andrea Rau <andrea.rau@jouy.inra.fr>

Diff between HTSCluster versions 2.0.4 dated 2014-08-26 and 2.0.8 dated 2016-05-26

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Package DiversityOccupancy updated to version 1.0.4 with previous version 1.0.3 dated 2016-05-12

Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre], Dylan Kesler [aut], Nicole Michel [ctb], Mike Meredith [ctb]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>

Diff between DiversityOccupancy versions 1.0.3 dated 2016-05-12 and 1.0.4 dated 2016-05-26

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New package CHFF with initial version 0.1.0
Package: CHFF
Type: Package
Title: Closest History Flow Field Forecasting for Bivariate Time Series
Version: 0.1.0
Author: Patrick Fleming
Maintainer: Kyle A. Caudle <kyle.caudle@sdsmt.edu>
Description: The software matches the current history to the closest history in a time series to build a forecast.
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-26 17:06:11 UTC; kcaudle
Repository: CRAN
Date/Publication: 2016-05-26 23:10:00

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New package BetaBit with initial version 1.2.1
Package: BetaBit
Title: Mini Games from Adventures of Beta and Bit
Version: 1.2.1
Authors@R: c( person("Przemysław", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut", "cre")), person("Witold", "Chodor", email = "witoldchodor@gmail.com", role = c("trl")), person("Katarzyna", "Fak", role = c("aut")), person("Foundation", "SmarterPoland.pl", email = "smarterpoland@gmail.com", role = c("cph")))
Description: Two games: proton and frequon. Both are console-based data-crunching games for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. You have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. The knowledge of 'dplyr' package is not required but may be very helpful. This game is linked with the ,,Pietraszko's Cave'' story available at <http://biecek.pl/BetaBit/Warsaw>. It's a part of Beta and Bit series. You will find more about the Beta and Bit series at <http://betabit.wiki>.
Depends: R (>= 3.0.0)
Imports: digest
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 17:14:41 UTC; pbiecek
Author: Przemysław Biecek [aut, cre], Witold Chodor [trl], Katarzyna Fak [aut], Foundation SmarterPoland.pl [cph]
Maintainer: Przemysław Biecek <przemyslaw.biecek@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 23:09:59

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Package vcfR updated to version 1.1.0 with previous version 1.0.0 dated 2016-02-22

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

Diff between vcfR versions 1.0.0 dated 2016-02-22 and 1.1.0 dated 2016-05-26

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Package unfoldr updated to version 0.5.5 with previous version 0.5.1 dated 2016-05-04

Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in the estimation of the joint size-shape-orientation distribution of spheroidal shaped particles based on the same measured quantities of corresponding planar section profiles. A single trivariate discretized version of the (stereological) integral equation in the case of prolate and oblate spheroids is solved numerically by the EM algorithm. The estimation of diameter distribution of spheres from planar sections (Wicksell's corpuscle problem) is also implemented. Further, the package provides routines for the simulation of a Poisson germ- grain process with either spheroids, spherocylinders or spheres as grains together with functions for planar sections. For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

Diff between unfoldr versions 0.5.1 dated 2016-05-04 and 0.5.5 dated 2016-05-26

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More information about unfoldr at CRAN
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Package Qtools updated to version 1.1 with previous version 1.0 dated 2016-02-04

Title: Utilities for Quantiles
Description: This is a collection of functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, and restricted quantile regression.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

Diff between Qtools versions 1.0 dated 2016-02-04 and 1.1 dated 2016-05-26

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Package rfoaas updated to version 0.1.9 with previous version 0.1.8 dated 2015-10-24

Title: R Interface to 'FOAAS'
Description: R access to the 'FOAAS' (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between rfoaas versions 0.1.8 dated 2015-10-24 and 0.1.9 dated 2016-05-26

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Package inctools updated to version 1.0.5 with previous version 1.0.3 dated 2016-05-18

Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross- sectional surveys and for calibrating tests for recent infection.
Author: Alex Welte [aut], Eduard Grebe [cre, aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Cari Van Schalkwyk [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [ctb], Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>

Diff between inctools versions 1.0.3 dated 2016-05-18 and 1.0.5 dated 2016-05-26

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Package imputeMulti updated to version 0.4.6 with previous version 0.4.5 dated 2016-05-05

Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

Diff between imputeMulti versions 0.4.5 dated 2016-05-05 and 0.4.6 dated 2016-05-26

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New package heatmaply with initial version 0.3.2
Package: heatmaply
Type: Package
Title: Interactive Heat Maps Using 'plotly'
Version: 0.3.2
Date: 2016-05-25
Authors@R: c(person("Tal", "Galili", role = c("aut", "cre", "cph"), email = "tal.galili@gmail.com", comment = "http://www.r-statistics.com"))
Description: Create interactive heatmaps that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms. Heatmaps are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive heatmaps allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the heatmap by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar heatmaps as 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), and the ability to zoom from the dendrogram panes.
Depends: R (>= 3.0.0), plotly (>= 3.6.0), viridis
Imports: ggplot2, dendextend, magrittr (>= 1.0.1), reshape2, scales, utils, stats
Suggests: knitr, rmarkdown, gplots
VignetteBuilder: knitr
License: GPL-2 | GPL-3
URL: https://cran.r-project.org/package=heatmaply, https://github.com/talgalili/heatmaply/, http://www.r-statistics.com/tag/heatmaply/
BugReports: https://github.com/talgalili/heatmaply/issues
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 07:40:04 UTC; junior
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com)
Maintainer: Tal Galili <tal.galili@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:50:25

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Package Haplin updated to version 6.0.1 with previous version 6.0 dated 2016-05-25

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>

Diff between Haplin versions 6.0 dated 2016-05-25 and 6.0.1 dated 2016-05-26

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Package ecospat updated to version 2.0 with previous version 1.1 dated 2015-03-06

Title: Spatial Ecology Miscellaneous Methods
Description: Colection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly., written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut], Valeria Di Cola [cre, aut], Blaise Petitpierre [ctb], Frank Breiner [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Daniel Scherrer [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeria.dicola@unil.ch>

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New package fakeR with initial version 1.0
Package: fakeR
Type: Package
Title: Simulates Data from a Data Frame of Different Variable Types
Version: 1.0
Date: 2016-05-25
Authors@R: c(person("Lily", "Zhang", email = "lilyhzhang1029@gmail.com", role = c("aut", "cre")), person("Dustin","Tingley", email = "dtingley@gov.harvard.edu", role = c("aut")))
Description: Generates fake data from a dataset of different variable types. The package contains the functions simulate_dataset and simulate_dataset_ts to simulate time-independent and time-dependent data. It randomly samples character and factor variables from contingency tables and numeric and ordered factors from a multivariate normal distribution. It currently supports the simulation of stationary and zero-inflated count time series.
License: CC0
Imports: mvtnorm, polycor, pscl, VGAM, stats
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-26 06:59:29 UTC; lilyzhang
Author: Lily Zhang [aut, cre], Dustin Tingley [aut]
Maintainer: Lily Zhang <lilyhzhang1029@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:54:23

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Package ddst updated to version 1.4 with previous version 1.03 dated 2012-08-19

Title: Data Driven Smooth Tests
Description: Smooth testing of goodness of fit. These tests are data driven (alternative hypothesis is dynamically selected based on data). In this package you will find various tests for exponent, Gaussian, Gumbel and uniform distribution.
Author: Przemyslaw Biecek (R code), Teresa Ledwina (support, descriptions)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between ddst versions 1.03 dated 2012-08-19 and 1.4 dated 2016-05-26

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Package climtrends updated to version 1.0.6 with previous version 1.0.5 dated 2015-09-20

Title: Statistical Methods for Climate Sciences
Description: Absolute homogeneity tests SNHT absolute 1-breaks, 1-break, SD different from 1, 2-breaks, Buishand, Pettitt, von Neumann ratio and ratio-rank, Worsley, and Craddock, Relative homogeneity tests SNHT absolute 1-breaks, 1-break SD different from 1, 2-breaks, Peterson and Easterling, and Vincent, Differences in scale between two groups Siegel–Tukey, Create reference time series mean, weights/correlation, finding outliers Grubbs, ESD, MAD, Tietjen Moore, Hampel, etc.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>

Diff between climtrends versions 1.0.5 dated 2015-09-20 and 1.0.6 dated 2016-05-26

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Package AnalyzeTS updated to version 1.9 with previous version 1.8 dated 2016-04-04

Title: Analyze Time Series
Description: Main function of package is helped to analyze time series, peculiar is fuzzy time series. The package can calculate AIC value of common time series models and propose the best models according AIC values. To fuzzy time series by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models, also can fuzzy and forecast time series by Abbasov-Mamedova model.
Author: Tran Thi Ngoc Han <tranthingochan01011994@gmail.com>_ Doan Hai Nghi <Hainghi1426262609121094@gmail.com> _ Mai Thi Hong Diem <maidiemks@gmail.com> _ Nguyen Thi Diem My <myntdhg@gmail.com> _ Hong Viet Minh <hongvietminh@gmail.com> _ Vo Van Tai <vvtai@ctu.edu.vn>
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>

Diff between AnalyzeTS versions 1.8 dated 2016-04-04 and 1.9 dated 2016-05-26

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Package intcox (with last version 0.9.3) was removed from CRAN

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

2013-02-25 0.9.3

Permanent link
Package replicationInterval updated to version 2.0.1 with previous version 1.0.0 dated 2015-07-07

Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the question of whether the results of a replication study are consistent with the original published study. One solution to this problem is to examine the effect size from the original study and generate the range of effect sizes that could reasonably be obtained (due to random sampling) in a replication attempt (i.e., calculate a replication interval). If a replication effect size falls outside the replication interval, then that effect likely did not occur due to the effects of sampling error alone. Alternatively, if a replication effect size falls within the replication interval, then the replication effect could have reasonably occurred due to the effects of sampling error alone. This package has functions that calculate the replication interval for the correlation (i.e., r), standardized mean difference (i.e., d-value), and mean. The calculations used in version 2.0.0 and onward differ from past calculations due to feedback during the journal review process. The new calculations allow for a more precise interpretation of the replication interval.
Author: David Stanley
Maintainer: David Stanley <dstanley@uoguelph.ca>

Diff between replicationInterval versions 1.0.0 dated 2015-07-07 and 2.0.1 dated 2016-05-26

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Package GSODR updated to version 0.1.6 with previous version 0.1.5 dated 2016-05-16

Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean, reformat and create new variables from the USA National Climatic Data Center (NCDC) Global Surface Summary of the Day (GSOD) weather stations data, <https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>. The function, get_GSOD(), retrieves data from the GSOD ftp site and reformats it from United States Customary System (USCS) units to International System of Units (SI), also for convenience elevation is converted from decimetres to metres. Stations are individually checked for number of missing days, as defined by the user, to assure data quality. Stations with too many missing observations are omitted from final file. Stations with missing latitude or longitude or values for both of 0 are omitted. Also omitted are stations with a latitude of < -90 or > 90 or longitude of < - 180 or > 180. Output is returned as a comma-separated values (CSV) file written to disk in a location selected by the user, which summarises each year by station and includes new variables: actual vapor pressure, saturation vapor pressure and relative humidity are calculated from the original GSOD data. The resulting files can be as large as 500mb depending on the user's stringency for missing data and geographic area of interest. Be sure to have sufficient RAM and disk space as well as a reasonably fast internet connection to use this package to perform this operation. However, for much smaller and more manageable data sets, an individual country of interest may be selected as well as only stations falling between -60/60 degrees latitude for agroclimatology work or individual stations if the station ID is known. The resulting files include station data (e.g., station name, country, latitude, longitude, elevation) for use in a geographic information system (GIS). The function was largely based on T. Hengl's 'getGSOD.R' script, available from <http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements to be more cross-platform, faster and more flexible. See the GSOD readme.txt <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre], Tomislav Hengl [ctb], Andy Nelson [ctb], Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>

Diff between GSODR versions 0.1.5 dated 2016-05-16 and 0.1.6 dated 2016-05-26

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Package forecTheta updated to version 2.2 with previous version 2.1 dated 2016-03-07

Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>

Diff between forecTheta versions 2.1 dated 2016-03-07 and 2.2 dated 2016-05-26

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Package elliptic updated to version 1.3-7 with previous version 1.3-5 dated 2014-11-05

Title: Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between elliptic versions 1.3-5 dated 2014-11-05 and 1.3-7 dated 2016-05-26

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Package Davies updated to version 1.1-9 with previous version 1.1-8 dated 2012-11-07

Title: The Davies Quantile Function
Description: Various utilities for the Davies distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between Davies versions 1.1-8 dated 2012-11-07 and 1.1-9 dated 2016-05-26

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Package contfrac updated to version 1.1-10 with previous version 1.1-9 dated 2013-01-21

Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between contfrac versions 1.1-9 dated 2013-01-21 and 1.1-10 dated 2016-05-26

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