Tue, 19 Feb 2019

Package robCompositions updated to version 2.0.10 with previous version 2.0.9 dated 2018-11-08

Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data including robust methods, imputation, methods to replace rounded zeros, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.
Author: Matthias Templ [aut, cre], Karel Hron [aut], Peter Filzmoser [aut], Petra Kynclova [ctb], Jan Walach [ctb], Veronika Pintar [ctb], Jiajia Chen [ctb], Dominika Miksova [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between robCompositions versions 2.0.9 dated 2018-11-08 and 2.0.10 dated 2019-02-19

 robCompositions-2.0.10/robCompositions/DESCRIPTION                           |   12 
 robCompositions-2.0.10/robCompositions/MD5                                   |  179 ++++------
 robCompositions-2.0.10/robCompositions/NEWS                                  |   10 
 robCompositions-2.0.10/robCompositions/R/aDist.R                             |    6 
 robCompositions-2.0.10/robCompositions/R/addLR.R                             |    8 
 robCompositions-2.0.10/robCompositions/R/addLRinv.R                          |    6 
 robCompositions-2.0.10/robCompositions/R/balZav.R                            |   11 
 robCompositions-2.0.10/robCompositions/R/balances.R                          |    6 
 robCompositions-2.0.10/robCompositions/R/biplot.factanal.R                   |    4 
 robCompositions-2.0.10/robCompositions/R/biplot.pcaCoDa.R                    |    4 
 robCompositions-2.0.10/robCompositions/R/ced.R                               |   12 
 robCompositions-2.0.10/robCompositions/R/cenLR.R                             |   12 
 robCompositions-2.0.10/robCompositions/R/cenLRinv.R                          |    6 
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 robCompositions-2.0.10/robCompositions/R/daCoDa.R                            |   10 
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 robCompositions-2.0.10/robCompositions/R/dataSets.R                          |    2 
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 robCompositions-2.0.10/robCompositions/R/impCoda.R                           |    4 
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 robCompositions-2.0.10/robCompositions/R/rdcm.R                              |    7 
 robCompositions-2.0.10/robCompositions/R/stats.R                             |    9 
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 robCompositions-2.0.10/robCompositions/man/ced.Rd                            |   10 
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 robCompositions-2.0.10/robCompositions/man/daCoDa.Rd                         |   10 
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 91 files changed, 519 insertions(+), 604 deletions(-)

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Package ssizeRNA updated to version 1.3.1 with previous version 1.2.9 dated 2017-01-09

Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>

Diff between ssizeRNA versions 1.2.9 dated 2017-01-09 and 1.3.1 dated 2019-02-19

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Package sampleSelection updated to version 1.2-2 with previous version 1.2-0 dated 2017-12-07

Title: Sample Selection Models
Description: Two-step and maximum likelihood estimation of Heckman-type sample selection models: standard sample selection models (Tobit-2), endogenous switching regression models (Tobit-5), sample selection models with binary dependent outcome variable, interval regression with sample selection (only ML estimation), and endogenous treatment effects models.
Author: Arne Henningsen [aut, cre], Ott Toomet [aut], Sebastian Petersen [ctb]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between sampleSelection versions 1.2-0 dated 2017-12-07 and 1.2-2 dated 2019-02-19

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New package pgdraw with initial version 1.1
Package: pgdraw
Type: Package
Title: Generate Random Samples from the Polya-Gamma Distribution
Version: 1.1
Date: 2019-02-19
Author: Daniel F. Schmidt [aut, cph, cre], Enes Makalic [aut, cph]
Maintainer: Daniel F. Schmidt <daniel.schmidt@monash.edu>
Description: Generates random samples from the Polya-Gamma distribution using an implementation of the algorithm described in J. Windle's PhD thesis (2013) <https://repositories.lib.utexas.edu/bitstream/handle/2152/21842/WINDLE-DISSERTATION-2013.pdf>. The underlying implementation is in C.
License: GPL (>= 3)
Imports: Rcpp (>= 0.12.16)
NeedsCompilation: yes
LinkingTo: Rcpp
Authors@R: c( person("Daniel F. Schmidt", email="daniel.schmidt@monash.edu", role = c("aut","cph","cre")), person("Enes Makalic", email="emakalic@unimelb.edu.au", role=c("aut","cph")) )
RoxygenNote: 6.1.0
Packaged: 2019-02-19 01:26:45 UTC; dschmidt
Repository: CRAN
Date/Publication: 2019-02-19 13:00:03 UTC

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Package geonames updated to version 0.999 with previous version 0.998 dated 2014-12-19

Title: Interface to the "Geonames" Spatial Query Web Service
Description: The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.
Author: Barry Rowlingson
Maintainer: Barry Rowlingson <b.rowlingson@gmail.com>

Diff between geonames versions 0.998 dated 2014-12-19 and 0.999 dated 2019-02-19

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Package ssh updated to version 0.4 with previous version 0.3 dated 2018-10-07

Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between ssh versions 0.3 dated 2018-10-07 and 0.4 dated 2019-02-19

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Package bupaR updated to version 0.4.2 with previous version 0.4.1 dated 2018-07-01

Title: Business Process Analysis in R
Description: Comprehensive Business Process Analysis toolkit. Creates S3-class for event log objects, and related handler functions. Imports related packages for filtering event data, computation of descriptive statistics, handling of 'Petri Net' objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>

Diff between bupaR versions 0.4.1 dated 2018-07-01 and 0.4.2 dated 2019-02-19

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Package ggvoronoi (with last version 0.8.2) was removed from CRAN

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

2018-11-15 0.8.2
2018-10-04 0.8.1
2018-07-20 0.8.0

Permanent link
Package longpower (with last version 1.0-16.1) was removed from CRAN

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

2018-09-11 1.0-16.1
2016-07-25 1.0-16
2016-05-17 1.0-15
2015-01-16 1.0-11
2013-09-14 1.0-10
2013-06-17 1.0-9
2013-05-28 1.0-8
2013-05-22 1.0-7
2013-01-23 1.0-4
2013-01-11 1.0-3
2012-05-31 1.0-2
2010-09-01 1.0-1

Permanent link
Package ubeR (with last version 0.1.4) was removed from CRAN

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

2017-02-16 0.1.4
2016-10-22 0.1.3

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Package rockchalk updated to version 1.8.140 with previous version 1.8.129 dated 2018-11-09

Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in <http://pj.freefaculty.org/guides>. Includes regression diagnostics, regression tables, and plots of interactions and "moderator" variables. The emphasis is on "mean-centered" and "residual-centered" predictors. The vignette 'rockchalk' offers a fairly comprehensive overview. The vignette 'Rstyle' has advice about coding in R. The package title 'rockchalk' refers to our school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre], Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>

Diff between rockchalk versions 1.8.129 dated 2018-11-09 and 1.8.140 dated 2019-02-19

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Package perturbR updated to version 0.1.3 with previous version 0.1.2 dated 2018-07-27

Title: Random Perturbation of Count Matrices
Description: The perturbR() function incrementally perturbs network edges (using the rewireR function)and compares the resulting community detection solutions from the rewired networks with the solution found for the original network. These comparisons aid in understanding the stability of the original solution. The package requires symmetric, weighted (specifically, count) matrices/networks.
Author: KM Gates [aut, cre], Zachary Fisher [aut], Cara Arizmendi [aut]
Maintainer: KM Gates <gateskm@email.unc.edu>

Diff between perturbR versions 0.1.2 dated 2018-07-27 and 0.1.3 dated 2019-02-19

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Package idealstan updated to version 0.7.0 with previous version 0.5.1 dated 2018-12-06

Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (www.mc-stan.org).
Author: Robert Kubinec [aut, cre], Jonah Gabry [ctb], Ben Goodrich [ctb], Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>

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Package relMix updated to version 1.3 with previous version 1.2.3 dated 2017-04-03

Title: Relationship Inference for DNA Mixtures
Description: Makes relationship inference involving DNA mixtures with unknown profiles.
Author: Guro Dorum, Elias Hernandis, Navreet Kaur, Thore Egeland
Maintainer: Guro Dorum <guro.dorum@gmail.com>

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Package haven updated to version 2.1.0 with previous version 2.0.0 dated 2018-11-21

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package divDyn updated to version 0.7.1 with previous version 0.7.0 dated 2019-01-08

Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis, John Alroy, Carl J. Reddin, Wolfgang Kiessling
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>

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Package CB2 updated to version 1.1 with previous version 1.0 dated 2019-02-11

Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2018) <doi:10.1101/309302> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>

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Package palasso (with last version 0.0.2) was removed from CRAN

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

2018-10-27 0.0.2
2018-05-31 0.0.1

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Package birdnik (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:

2018-05-27 0.1.1
2016-08-14 0.1.0

Permanent link
Package ellipsis updated to version 0.1.0 with previous version 0.0.2 dated 2019-01-09

Title: Tools for Working with ...
Description: In S3 generics, it's useful to take ... so that methods can have additional argument. But this flexibility comes at a cost: misspelled arguments will be silently ignored. The ellipsis packages is an experiment that allows a generic to warn if any arguments passed in ... are not used.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between ellipsis versions 0.0.2 dated 2019-01-09 and 0.1.0 dated 2019-02-19

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Package afex updated to version 0.23-0 with previous version 0.22-1 dated 2018-09-24

Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), automatically aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() provides a high-level interface for interaction or one-way plots using ggplot2, combining raw data and model estimates. afex uses type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>), Ben Bolker [aut], Jake Westfall [aut], Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>), Søren Højsgaard [ctb], John Fox [ctb], Michael A. Lawrence [ctb], Ulf Mertens [ctb], Jonathon Love [ctb], Russell Lenth [ctb], Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>

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Mon, 18 Feb 2019

Package windfarmGA updated to version 2.2.1 with previous version 1.2.1 dated 2018-03-24

Title: Genetic Algorithm for Wind Farm Layout Optimization
Description: The genetic algorithm is designed to optimize small wind farms with irregular shapes. The algorithm works with a fixed amount of turbines, a fixed rotor radius and a mean wind speed value for every incoming wind direction. If required, it can include a terrain effect model which downloads an 'SRTM' elevation model automatically and loads a Corine Land Cover raster, which has to be downloaded previously. Further information can be found in the description of the function 'windfarmGA'. To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can be used. The function 'windfarmGA' checks the user inputs interactively and then runs the function 'genAlgo'. If the input parameters are already known, an optimization can be run directly via the function 'genAlgo'. Their output is identical.
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>

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Permanent link

New package interactions with initial version 1.0.0
Package: interactions
Type: Package
Title: Comprehensive, User-Friendly Toolkit for Probing Interactions
Version: 1.0.0
Authors@R: person(c("Jacob","A."), "Long", email = "long.1377@osu.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1582-6214"))
Description: A suite of functions for conducting and interpreting analysis of statistical interaction in regression models that was formerly part of the 'jtools' package. Functionality includes visualization of two- and three-way interactions among continuous and/or categorical variables as well as calculation of "simple slopes" and Johnson-Neyman intervals. These capabilities are implemented for generalized linear models in addition to the standard linear regression context.
URL: https://interactions.jacob-long.com
BugReports: https://github.com/jacob-long/interactions/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, crayon, cli, jtools (>= 2.0.0), rlang
Suggests: brms, broom, cowplot, ggstance, glue, huxtable (>= 3.0.0), lme4, rstanarm, sandwich, survey, knitr, rmarkdown, rmdformats, testthat
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-09 14:06:52 UTC; jlong
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <long.1377@osu.edu>
Repository: CRAN
Date/Publication: 2019-02-18 23:20:03 UTC

More information about interactions at CRAN
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Package tidygraph updated to version 1.1.2 with previous version 1.1.1 dated 2018-11-20

Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between tidygraph versions 1.1.1 dated 2018-11-20 and 1.1.2 dated 2019-02-18

 DESCRIPTION     |   10 +++++-----
 MD5             |   10 +++++-----
 NEWS.md         |   21 ++++++++++++++++++++-
 R/morphers.R    |    7 +++++--
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 6 files changed, 39 insertions(+), 17 deletions(-)

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Package shinyWidgets updated to version 0.4.5 with previous version 0.4.4 dated 2018-11-05

Title: Custom Inputs Widgets for Shiny
Description: Some custom inputs widgets to use in Shiny applications, like a toggle switch to replace checkboxes. And other components to pimp your apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], David Granjon [aut] (jQuery Knob shiny interface & sliders appearance), Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), SnapAppointments [cph] (bootstrap-select), Mattia Larentis [ctb, cph] (Bootstrap Switch), Emanuele Marchi [ctb, cph] (Bootstrap Switch), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Flatlogic [cph] (Awesome Bootstrap Checkbox), mouse0270 [ctb, cph] (Material Design Switch), Tristan Edwards [ctb, cph] (SweetAlert), Fabian Lindfors [ctb, cph] (multi.js), Anthony Terrien [ctb, cph] (jQuery Knob), Daniel Eden [ctb, cph] (animate.css), Ganapati V S [ctb, cph] (bttn.css), Brian Grinstead [ctb, cph] (Spectrum), Lokesh Rajendran [ctb, cph] (pretty-checkbox), Leon Gersen [ctb, cph] (wnumb & noUiSlider), Timofey Marochkin [ctb, cph] (air-datepicker), Tobias Ahlin [ctb, cph] (CSS spin)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinyWidgets versions 0.4.4 dated 2018-11-05 and 0.4.5 dated 2019-02-18

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New package segmenTier with initial version 0.1.2
Package: segmenTier
Type: Package
Title: Similarity-Based Segmentation of Multidimensional Signals
Version: 0.1.2
Author: Rainer Machne, Douglas B. Murray, Peter F. Stadler
URL: https://github.com/raim/segmenTier
BugReports: https://github.com/raim/segmenTier/issues
Maintainer: Rainer Machne <raim@tbi.univie.ac.at>
Description: A dynamic programming solution to segmentation based on maximization of arbitrary similarity measures within segments. The general idea, theory and this implementation are described in Machne, Murray & Stadler (2017) <doi:10.1038/s41598-017-12401-8>. In addition to the core algorithm, the package provides time-series processing and clustering functions as described in the publication. These are generally applicable where a `k-means` clustering yields meaningful results, and have been specifically developed for clustering of the Discrete Fourier Transform of periodic gene expression data (`circadian' or `yeast metabolic oscillations'). This clustering approach is outlined in the supplemental material of Machne & Murray (2012) <doi:10.1371/journal.pone.0037906>), and here is used as a basis of segment similarity measures. Notably, the time-series processing and clustering functions can also be used as stand-alone tools, independent of segmentation, e.g., for transcriptome data already mapped to genes.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.7)
Suggests: flowMerge, flowClust, flowCore, knitr, rmarkdown
LinkingTo: Rcpp
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-02-09 13:04:24 UTC; raim
Repository: CRAN
Date/Publication: 2019-02-18 23:00:03 UTC

More information about segmenTier at CRAN
Permanent link

Package nonmem2R updated to version 0.2.1 with previous version 0.1.10 dated 2018-09-26

Title: Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>

Diff between nonmem2R versions 0.1.10 dated 2018-09-26 and 0.2.1 dated 2019-02-18

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More information about nonmem2R at CRAN
Permanent link

Package ggsn updated to version 0.5.0 with previous version 0.4.0 dated 2017-03-20

Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or 'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers, meters, nautical miles, or statue miles, to maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>

Diff between ggsn versions 0.4.0 dated 2017-03-20 and 0.5.0 dated 2019-02-18

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More information about ggsn at CRAN
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Package modelr updated to version 0.1.4 with previous version 0.1.3 dated 2019-02-05

Title: Modelling Functions that Work with the Pipe
Description: Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between modelr versions 0.1.3 dated 2019-02-05 and 0.1.4 dated 2019-02-18

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Package flexmix updated to version 2.3-15 with previous version 2.3-14 dated 2017-04-28

Title: Flexible Mixture Modeling
Description: A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
Author: Bettina Gruen [aut, cre] (<https://orcid.org/0000-0001-7265-4773>), Friedrich Leisch [aut] (<https://orcid.org/0000-0001-7278-1983>), Deepayan Sarkar [ctb] (<https://orcid.org/0000-0003-4107-1553>), Frederic Mortier [ctb], Nicolas Picard [ctb] (<https://orcid.org/0000-0001-5548-9171>)
Maintainer: Bettina Gruen <Bettina.Gruen@jku.at>

Diff between flexmix versions 2.3-14 dated 2017-04-28 and 2.3-15 dated 2019-02-18

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More information about flexmix at CRAN
Permanent link

Package nonneg.cg updated to version 0.1.1 with previous version 0.1 dated 2019-01-27

Title: Non-Negative Conjugate-Gradient Minimizer
Description: Minimize a differentiable function subject to all the variables being non-negative (i.e. >= 0), using a Conjugate-Gradient algorithm based on a modified Polak-Ribiere-Polyak formula as described in (Li, Can, 2013, <https://www.hindawi.com/journals/jam/2013/986317/abs/>).
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between nonneg.cg versions 0.1 dated 2019-01-27 and 0.1.1 dated 2019-02-18

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Package libcoin updated to version 1.0-3 with previous version 1.0-2 dated 2018-12-13

Title: Linear Test Statistics for Permutation Inference
Description: Basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This package must not be used by end-users. CRAN package 'coin' implements all user interfaces and is ready to be used by anyone.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between libcoin versions 1.0-2 dated 2018-12-13 and 1.0-3 dated 2019-02-18

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Permanent link

Package poplite updated to version 0.99.21 with previous version 0.99.19 dated 2017-10-12

Title: Tools for Simplifying the Population and Querying of SQLite Databases
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
Author: Daniel Bottomly [cre, aut], Shannon McWeeney [aut], Beth Wilmot [aut]
Maintainer: Daniel Bottomly <bottomly@ohsu.edu>

Diff between poplite versions 0.99.19 dated 2017-10-12 and 0.99.21 dated 2019-02-18

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More information about poplite at CRAN
Permanent link

Package rayshader updated to version 0.10.0 with previous version 0.5.1 dated 2018-09-11

Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing, spherical texture mapping, lambertian reflectance, and ambient occlusion to produce hillshades of elevation matrices. Includes water detection and layering functions, programmable color palette generation, several built-in textures, 2D and 3D plotting options, and the ability to export 3D maps to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

Diff between rayshader versions 0.5.1 dated 2018-09-11 and 0.10.0 dated 2019-02-18

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More information about rayshader at CRAN
Permanent link

Package lwgeom updated to version 0.1-6 with previous version 0.1-5 dated 2018-12-07

Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Colin Rundel [ctb], Andy Teucher [ctb], liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between lwgeom versions 0.1-5 dated 2018-12-07 and 0.1-6 dated 2019-02-18

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More information about lwgeom at CRAN
Permanent link

Package SAM updated to version 1.1.0 with previous version 1.0.5 dated 2014-02-12

Title: Sparse Additive Modelling
Description: Computationally efficient tools for high dimensional predictive modeling (regression and classification). SAM is short for sparse additive modeling, and adopts the computationally efficient basis spline technique. We solve the optimization problems by various computational algorithms including the block coordinate descent algorithm, fast iterative soft-thresholding algorithm, and newton method. The computation is further accelerated by warm-start and active-set tricks.
Author: Haoming Jiang, Yukun Ma, Xinyu Fei, Tuo Zhao, Xingguo Li, Han Liu, and Kathryn Roeder
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>

Diff between SAM versions 1.0.5 dated 2014-02-12 and 1.1.0 dated 2019-02-18

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More information about SAM at CRAN
Permanent link

Package dkanr updated to version 0.1.3 with previous version 0.1.2 dated 2018-07-12

Title: Client for the 'DKAN' API
Description: Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.
Author: Tony Fujs [aut, cre], Meera Desai [aut], Karthik Ramanathan [aut]
Maintainer: Tony Fujs <tonyfujs@gmail.com>

Diff between dkanr versions 0.1.2 dated 2018-07-12 and 0.1.3 dated 2019-02-18

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More information about dkanr at CRAN
Permanent link

New package swephR with initial version 0.1.5
Package: swephR
Type: Package
Title: High Precision Swiss Ephemeris
Version: 0.1.5
Authors@R: c( person("Ralf", "Stubner", email = "ralf.stubner@gmail.com", role = c("aut", "cre")), person("Victor", "Reijs", role = "aut"), person("Authors and copyright holder of the Swiss Ephemeris", role = c("aut", "cph"), comment = "see LICENSE for details"))
Description: The Swiss Ephemeris is a high precision ephemeris based upon the DE431 ephemerides from NASA's JPL. It covers the time range 13201 BC to AD 17191. This package uses the semi-analytic theory by Steve Moshier. For faster and more accurate calculations, the compressed Swiss Ephemeris data is available in the 'swephRdata' package. To access this data package, run 'install.packages("swephRdata", repos = "https://rstub.github.io/drat/", type = "source")'. The size of the 'swephRdata' package is approximately 115 MB. The user can also use the original JPL DE431 data.
License: AGPL | file LICENSE
Imports: Rcpp (>= 0.12.18)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Suggests: testthat, swephRdata, knitr, rmarkdown
Encoding: UTF-8
URL: https://github.com/rstub/swephR/, http://www.astro.com/swisseph/
BugReports: https://github.com/rstub/swephR/issues/
Additional_repositories: https://rstub.github.io/drat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-02-09 11:50:37 UTC; ralf
Author: Ralf Stubner [aut, cre], Victor Reijs [aut], Authors and copyright holder of the Swiss Ephemeris [aut, cph] (see LICENSE for details)
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-18 15:00:03 UTC

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New package pcgen with initial version 0.2.0
Package: pcgen
Type: Package
Title: Reconstruction of Causal Networks for Data with Random Genetic Effects
Version: 0.2.0
Author: Willem Kruijer, Pariya Behrouzi, Maria Xose Rodriguez-Alvarez
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Depends: R (>= 3.1.0)
Imports: pcalg, graph, Matrix, stats, MASS, utils, Hmisc, methods, lme4, sommer, ggm
Description: Implements the pcgen algorithm, which is a modified version of the standard pc-algorithm, with specific conditional independence tests and modified orientation rules. pcgen extends the approach of Valente et al. (2010) <doi:10.1534/genetics.109.112979> with reconstruction of direct genetic effects.
License: GPL-3
Date: 2019-02-18
NeedsCompilation: no
Packaged: 2019-02-18 13:27:37 UTC; behro001
Repository: CRAN
Date/Publication: 2019-02-18 14:50:03 UTC

More information about pcgen at CRAN
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New package LongMemoryTS with initial version 0.1.0
Package: LongMemoryTS
Type: Package
Title: Long Memory Time Series
Version: 0.1.0
Date: 2019-01-18
Authors@R: c(person("Christian", "Leschinski", email="christian_leschinski@gmx.de", role=c("aut", "cre")), person("Michelle", "Voges", email="voges@statistik.uni-hannover.de", role="ctb"), person("Kai", "Wenger", email="wenger@statistik.uni-hannover.de", role="ctb"))
Description: Long Memory Time Series is a collection of functions for estimation, simulation and testing of long memory processes, spurious long memory processes and fractionally cointegrated systems.
License: GPL-2
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, stats, longmemo, partitions, fracdiff, mvtnorm
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-02-09 13:31:27 UTC; Christian
Author: Christian Leschinski [aut, cre], Michelle Voges [ctb], Kai Wenger [ctb]
Maintainer: Christian Leschinski <christian_leschinski@gmx.de>
Repository: CRAN
Date/Publication: 2019-02-18 14:40:03 UTC

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New package imageviewer with initial version 0.1.0
Package: imageviewer
Title: Simple 'htmlwidgets' Image Viewer with WebGL Brightness/Contrast
Version: 0.1.0
Author: Iakov Pustilnik [aut, cre], Denis Rastegaev [aut]
Maintainer: Iakov Pustilnik <xyapus@gmail.com>
URL: https://github.com/yapus/imageviewer
BugReports: https://github.com/yapus/imageviewer/issues
Authors@R: c( person("Iakov", "Pustilnik", email = "xyapus@gmail.com", role = c("aut", "cre")), person("Denis", "Rastegaev", email = "leda82@gmail.com", role = "aut") )
Description: Display a 2D-matrix data as a interactive zoomable gray-scale image viewer, providing tools for manual data inspection. The viewer window shows cursor guiding lines and a corresponding data slices for both axes at the current cursor position. A tool-bar allows adjusting image display brightness/contrast through WebGL filters and performing basic high-pass/low-pass filtering.
Depends: R (>= 3.4), htmlwidgets
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-09 07:19:14 UTC; 2can
Repository: CRAN
Date/Publication: 2019-02-18 14:50:40 UTC

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New package DTAT with initial version 0.3-0
Package: DTAT
Type: Package
Title: Dose Titration Algorithm Tuning
Version: 0.3-0
Date: 2019-02-08
Authors@R: person("David C.", "Norris" , role = c("aut", "cre") , email = "david@precisionmethods.guru" )
Maintainer: David C. Norris <david@precisionmethods.guru>
Depends: R (>= 3.4.0), survival
Imports: km.ci, pomp, Hmisc, data.table, dplyr, r2d3, shiny, jsonlite, methods
Suggests: knitr, rmarkdown, lattice, latticeExtra, widgetframe, tidyr, RColorBrewer
Description: DTAT is a methodologic framework allowing dose individualization to be conceived as a continuous learning process that begins in early-phase clinical trials and continues throughout drug development, on into clinical practice. This package includes code that researchers may use to reproduce or extend key results of the DTAT research programme, plus tools for trialists to design and simulate a '3+3/PC' dose-finding study. Please see Norris (2017) <doi:10.12688/f1000research.10624.3> and Norris (2017) <doi:10.1101/240846>.
URL: https://osf.io/5479p/
License: MIT + file LICENSE
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-02-08 12:05:34 UTC; david
Author: David C. Norris [aut, cre]
Repository: CRAN
Date/Publication: 2019-02-18 14:40:10 UTC

More information about DTAT at CRAN
Permanent link

New package Cascade with initial version 1.7
Package: Cascade
Type: Package
Title: Selection, Reverse-Engineering and Prediction in Cascade Networks
Version: 1.7
Date: 2019-02-09
Depends: R (>= 2.10)
Imports: abind, animation, cluster, grid, igraph, lars, lattice, limma, magic, methods, nnls, splines, stats4, survival, tnet, VGAM
Suggests: R.rsp, CascadeData, knitr
Authors@R: c( person(given = "Frederic", family= "Bertrand", role = c("cre", "aut"), email = "frederic.bertrand@math.unistra.fr", comment = c(ORCID = "0000-0002-0837-8281")), person(given = "Myriam", family= "Maumy-Bertrand", role = c("aut"), email = "myriam.maumy-bertrand@math.unistra.fr", comment = c(ORCID = "0000-0002-4615-1512")), person(given = "Laurent", family= "Vallat", role = c("ctb"), email = "vallat@unistra.fr"), person(given = "Nicolas", family= "Jung", role = c("ctb"), email = "nicolas.jung@unistra.fr"))
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>), Laurent Vallat [ctb], Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
License: GPL (>= 2)
Encoding: UTF-8
Collate: global.R micro_array.R network.R micro_array-network.R micropredict.R
Classification/MSC: 62J05, 62J07, 62J99, 92C42
VignetteBuilder: R.rsp
RoxygenNote: 6.1.1
URL: http://www-irma.u-strasbg.fr/~fbertran/, https://github.com/fbertran/Cascade
BugReports: https://github.com/fbertran/Cascade/issues
NeedsCompilation: no
Packaged: 2019-02-09 02:24:24 UTC; fbertran
Repository: CRAN
Date/Publication: 2019-02-18 14:50:52 UTC

More information about Cascade at CRAN
Permanent link

New package bdchecks with initial version 0.1.7
Package: bdchecks
Title: Biodiversity Data Checks
Description: Supplies a Shiny app and a set of functions to perform and managing data checks for biodiversity data.
Version: 0.1.7
Date: 2019-02-07
License: GPL-3 | file LICENSE
URL: https://github.com/bd-R/bdchecks
BugReports: https://github.com/bd-R/bdchecks/issues
Authors@R: c( person( "Povilas", "Gibas", email = "povilasgibas@gmail.com", role = c("aut", "cre"), comment = c(ORCID = '0000-0001-5311-6021')), person( "Tomer", "Gueta", email = "tomer.gu@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0003-1557-8596')), person( "Vijay", "Barve", , email = "vijay.barve@gmail.com", role = c("aut"), comment = c(ORCID = '0000-0002-4852-2567')), person( "Thiloshon", "Nagarajah", email = "thiloshon@gmail.com", role = c("aut")), person( "Yohay", "Carmel", email = "yohay@cv.technion.ac.il", role = c("aut"), comment = c(ORCID = '0000-0002-5883-0184')) )
Depends: R (>= 2.10)
Imports: bdDwC, DT, data.table, finch, methods, knitr, rgbif, shiny, shinyBS, shinydashboard, shinyjs, spocc, yaml
LazyData: true
RoxygenNote: 6.1.1
Encoding: UTF-8
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2019-02-09 09:38:55 UTC; pogibas
Author: Povilas Gibas [aut, cre] (<https://orcid.org/0000-0001-5311-6021>), Tomer Gueta [aut] (<https://orcid.org/0000-0003-1557-8596>), Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Thiloshon Nagarajah [aut], Yohay Carmel [aut] (<https://orcid.org/0000-0002-5883-0184>)
Maintainer: Povilas Gibas <povilasgibas@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-18 15:00:07 UTC

More information about bdchecks at CRAN
Permanent link

Package RandomFields updated to version 3.3.1 with previous version 3.3 dated 2019-02-14

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.3 dated 2019-02-14 and 3.3.1 dated 2019-02-18

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More information about RandomFields at CRAN
Permanent link

Package geometry updated to version 0.4.0 with previous version 0.3-6 dated 2015-09-09

Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees), C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Robert B. Gramacy [cph, aut], Pavlo Mozharovskyi [cph, aut], David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

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Package zCompositions updated to version 1.2.0 with previous version 1.1.2 dated 2018-11-06

Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets.
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>

Diff between zCompositions versions 1.1.2 dated 2018-11-06 and 1.2.0 dated 2019-02-18

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New package phenofit with initial version 0.2.0
Package: phenofit
Type: Package
Title: Extract Remote Sensing Vegetation Phenology
Version: 0.2.0
Authors@R: c( person("Dongdong", "Kong", role = c("aut", "cre"), email = "kongdd.sysu@gmail.com"), person("Mingzhong", "Xiao", role = c("aut"), email = "xmingzh@mail2.sysu.edu.cn"), person("Yongqiang", "Zhang", role = c("aut"), email = "yongqiang.zhang2014@gmail.com"), person("Xihui", "Gu", role = c("aut"), email = "guxh@cug.edu.cn"), person("Jianjian", "Cui", role = c("aut"), email = "cuijj6@mail2.sysu.edu.cn"))
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods.
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.1)
Imports: Rcpp, tibble, dplyr, purrr, stringr, tidyr, ggplot2, lubridate, data.table, spam, grid, gridExtra, magrittr, plyr, reshape2, zoo, optimx, ucminf, numDeriv, grDevices, utils, stats, DT
Suggests: knitr, rmarkdown, testthat
URL: https://github.com/kongdd/phenofit
BugReports: https://github.com/kongdd/phenofit/issues
NeedsCompilation: yes
Packaged: 2019-02-08 23:37:39 UTC; kongdd
Author: Dongdong Kong [aut, cre], Mingzhong Xiao [aut], Yongqiang Zhang [aut], Xihui Gu [aut], Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-18 11:50:04 UTC

More information about phenofit at CRAN
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Package catlearn updated to version 0.6.1 with previous version 0.6 dated 2018-07-17

Title: Formal Psychological Models of Categorization and Learning
Description: Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.
Author: Andy Wills, Lenard Dome, Charlotte Edmunds, Garrett Honke, Angus Inkster, René Schlegelmilch, Stuart Spicer
Maintainer: Andy Wills <andy@willslab.co.uk>

Diff between catlearn versions 0.6 dated 2018-07-17 and 0.6.1 dated 2019-02-18

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Package VGAM updated to version 1.1-1 with previous version 1.0-6 dated 2018-08-18

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

Diff between VGAM versions 1.0-6 dated 2018-08-18 and 1.1-1 dated 2019-02-18

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 VGAM-1.1-1/VGAM/MD5                          |  771 +++++++++++++--------------
 VGAM-1.1-1/VGAM/NAMESPACE                    |   28 
 VGAM-1.1-1/VGAM/NEWS                         |   84 +-
 VGAM-1.1-1/VGAM/R/Links.R                    |    2 
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 VGAM-1.1-1/VGAM/R/family.basics.R            |   43 +
 VGAM-1.1-1/VGAM/R/family.binomial.R          |   54 -
 VGAM-1.1-1/VGAM/R/family.bivariate.R         |   70 +-
 VGAM-1.1-1/VGAM/R/family.categorical.R       |  105 +--
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 VGAM-1.1-1/VGAM/R/family.exp.R               |    4 
 VGAM-1.1-1/VGAM/R/family.extremes.R          |   54 -
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 VGAM-1.1-1/VGAM/R/family.maths.R             |only
 VGAM-1.1-1/VGAM/R/family.mixture.R           |   10 
 VGAM-1.1-1/VGAM/R/family.nbd.R               |   84 +-
 VGAM-1.1-1/VGAM/R/family.nonlinear.R         |    2 
 VGAM-1.1-1/VGAM/R/family.normal.R            |  205 ++++---
 VGAM-1.1-1/VGAM/R/family.oneinf.R            |   36 -
 VGAM-1.1-1/VGAM/R/family.others.R            |   25 
 VGAM-1.1-1/VGAM/R/family.positive.R          |   43 -
 VGAM-1.1-1/VGAM/R/family.qreg.R              |  189 ++++--
 VGAM-1.1-1/VGAM/R/family.rcim.R              |   18 
 VGAM-1.1-1/VGAM/R/family.rcqo.R              |    2 
 VGAM-1.1-1/VGAM/R/family.robust.R            |   12 
 VGAM-1.1-1/VGAM/R/family.rrr.R               |   40 -
 VGAM-1.1-1/VGAM/R/family.sur.R               |    4 
 VGAM-1.1-1/VGAM/R/family.survival.R          |    6 
 VGAM-1.1-1/VGAM/R/family.ts.R                |   42 -
 VGAM-1.1-1/VGAM/R/family.univariate.R        |  566 +++++++++++++++----
 VGAM-1.1-1/VGAM/R/family.vglm.R              |    2 
 VGAM-1.1-1/VGAM/R/family.zeroinf.R           |  103 +--
 VGAM-1.1-1/VGAM/R/fittedvlm.R                |    2 
 VGAM-1.1-1/VGAM/R/formula.vlm.q              |    2 
 VGAM-1.1-1/VGAM/R/generic.q                  |    2 
 VGAM-1.1-1/VGAM/R/getxvlmaug.R               |    2 
 VGAM-1.1-1/VGAM/R/hdeff.R                    |  166 +++++
 VGAM-1.1-1/VGAM/R/links.q                    |  283 +++++++--
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 VGAM-1.1-1/VGAM/R/lrp.R                      |    2 
 VGAM-1.1-1/VGAM/R/lrwaldtest.R               |    2 
 VGAM-1.1-1/VGAM/R/model.matrix.vglm.q        |    2 
 VGAM-1.1-1/VGAM/R/mux.q                      |    2 
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 VGAM-1.1-1/VGAM/R/plot.vgam.R                |    2 
 VGAM-1.1-1/VGAM/R/plot.vglm.R                |    2 
 VGAM-1.1-1/VGAM/R/predict.vgam.q             |    2 
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 VGAM-1.1-1/VGAM/R/print.vglm.q               |    2 
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 VGAM-1.1-1/VGAM/R/qtplot.q                   |    2 
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 VGAM-1.1-1/VGAM/R/rrvglm.R                   |    2 
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 VGAM-1.1-1/VGAM/R/smart.R                    |    2 
 VGAM-1.1-1/VGAM/R/summary.vgam.q             |   21 
 VGAM-1.1-1/VGAM/R/summary.vglm.q             |   24 
 VGAM-1.1-1/VGAM/R/summary.vlm.q              |    2 
 VGAM-1.1-1/VGAM/R/vcov.pvgam.R               |    2 
 VGAM-1.1-1/VGAM/R/vgam.R                     |    2 
 VGAM-1.1-1/VGAM/R/vgam.control.q             |    3 
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 VGAM-1.1-1/VGAM/R/vgam.match.q               |    2 
 VGAM-1.1-1/VGAM/R/vglm.R                     |    2 
 VGAM-1.1-1/VGAM/R/vglm.control.q             |    2 
 VGAM-1.1-1/VGAM/R/vglm.fit.q                 |   17 
 VGAM-1.1-1/VGAM/R/vlm.R                      |    2 
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 VGAM-1.1-1/VGAM/R/vsmooth.spline.q           |    2 
 VGAM-1.1-1/VGAM/R/wald0.R                    |    2 
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 VGAM-1.1-1/VGAM/data/finney44.rda            |binary
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 VGAM-1.1-1/VGAM/inst/doc/crVGAM.pdf          |binary
 VGAM-1.1-1/VGAM/man/A1A2A3.Rd                |    9 
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 VGAM-1.1-1/VGAM/man/AB.Ab.aB.ab.Rd           |    2 
 VGAM-1.1-1/VGAM/man/ABO.Rd                   |    2 
 VGAM-1.1-1/VGAM/man/AR1.Rd                   |    8 
 VGAM-1.1-1/VGAM/man/AR1EIM.Rd                |    4 
 VGAM-1.1-1/VGAM/man/AR1UC.Rd                 |    2 
 VGAM-1.1-1/VGAM/man/CommonVGAMffArguments.Rd |  106 ++-
 VGAM-1.1-1/VGAM/man/Links.Rd                 |  119 ++--
 VGAM-1.1-1/VGAM/man/MNSs.Rd                  |    6 
 VGAM-1.1-1/VGAM/man/R2latvar.Rd              |   14 
 VGAM-1.1-1/VGAM/man/VGAM-package.Rd          |   14 
 VGAM-1.1-1/VGAM/man/acat.Rd                  |    8 
 VGAM-1.1-1/VGAM/man/alaplace3.Rd             |   20 
 VGAM-1.1-1/VGAM/man/amlbinomial.Rd           |    4 
 VGAM-1.1-1/VGAM/man/amlexponential.Rd        |    6 
 VGAM-1.1-1/VGAM/man/amlpoisson.Rd            |    2 
 VGAM-1.1-1/VGAM/man/anovavglm.Rd             |   14 
 VGAM-1.1-1/VGAM/man/bellff.Rd                |    4 
 VGAM-1.1-1/VGAM/man/benini.Rd                |   16 
 VGAM-1.1-1/VGAM/man/beniniUC.Rd              |    2 
 VGAM-1.1-1/VGAM/man/betaII.Rd                |    2 
 VGAM-1.1-1/VGAM/man/betaR.Rd                 |    6 
 VGAM-1.1-1/VGAM/man/betabinomial.Rd          |    6 
 VGAM-1.1-1/VGAM/man/betabinomialff.Rd        |    8 
 VGAM-1.1-1/VGAM/man/betaff.Rd                |   14 
 VGAM-1.1-1/VGAM/man/betageometric.Rd         |    2 
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 VGAM-1.1-1/VGAM/man/biamhcop.Rd              |    4 
 VGAM-1.1-1/VGAM/man/biclaytoncop.Rd          |    4 
 VGAM-1.1-1/VGAM/man/bifgmcop.Rd              |    4 
 VGAM-1.1-1/VGAM/man/bifgmexp.Rd              |    2 
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 VGAM-1.1-1/VGAM/man/bigamma.mckay.Rd         |    2 
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 VGAM-1.1-1/VGAM/man/binom2.or.Rd             |   14 
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 VGAM-1.1-1/VGAM/man/binom2.rhoUC.Rd          |    6 
 VGAM-1.1-1/VGAM/man/binomialff.Rd            |   11 
 VGAM-1.1-1/VGAM/man/binormal.Rd              |   12 
 VGAM-1.1-1/VGAM/man/binormalcop.Rd           |    4 
 VGAM-1.1-1/VGAM/man/biplackettcop.Rd         |    2 
 VGAM-1.1-1/VGAM/man/bisa.Rd                  |    2 
 VGAM-1.1-1/VGAM/man/bistudentt.Rd            |    2 
 VGAM-1.1-1/VGAM/man/borel.tanner.Rd          |    2 
 VGAM-1.1-1/VGAM/man/calibrate.Rd             |   16 
 VGAM-1.1-1/VGAM/man/calibrate.qrrvglm.Rd     |   26 
 VGAM-1.1-1/VGAM/man/cao.Rd                   |    4 
 VGAM-1.1-1/VGAM/man/cardioid.Rd              |    6 
 VGAM-1.1-1/VGAM/man/cauchitlink.Rd           |only
 VGAM-1.1-1/VGAM/man/cauchy.Rd                |    4 
 VGAM-1.1-1/VGAM/man/cens.gumbel.Rd           |    2 
 VGAM-1.1-1/VGAM/man/cens.normal.Rd           |    2 
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 VGAM-1.1-1/VGAM/man/constraints.Rd           |    6 
 VGAM-1.1-1/VGAM/man/cqo.Rd                   |    4 
 VGAM-1.1-1/VGAM/man/cratio.Rd                |   12 
 VGAM-1.1-1/VGAM/man/cumulative.Rd            |   48 +
 VGAM-1.1-1/VGAM/man/dagum.Rd                 |    2 
 VGAM-1.1-1/VGAM/man/diffzeta.Rd              |    4 
 VGAM-1.1-1/VGAM/man/dirichlet.Rd             |    2 
 VGAM-1.1-1/VGAM/man/dirmul.old.Rd            |    2 
 VGAM-1.1-1/VGAM/man/dirmultinomial.Rd        |    2 
 VGAM-1.1-1/VGAM/man/double.cens.normal.Rd    |    2 
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 VGAM-1.1-1/VGAM/man/expexpff.Rd              |    2 
 VGAM-1.1-1/VGAM/man/expexpff1.Rd             |    2 
 VGAM-1.1-1/VGAM/man/expgeometric.Rd          |    4 
 VGAM-1.1-1/VGAM/man/explink.Rd               |    7 
 VGAM-1.1-1/VGAM/man/explogff.Rd              |    4 
 VGAM-1.1-1/VGAM/man/exponential.Rd           |    9 
 VGAM-1.1-1/VGAM/man/exppoisson.Rd            |    2 
 VGAM-1.1-1/VGAM/man/felix.Rd                 |    2 
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 VGAM-1.1-1/VGAM/man/fittedvlm.Rd             |    2 
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 VGAM-1.1-1/VGAM/man/gamma1.Rd                |   26 
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 VGAM-1.1-1/VGAM/man/genpoisson.Rd            |    8 
 VGAM-1.1-1/VGAM/man/genrayleigh.Rd           |    2 
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 VGAM-1.1-1/VGAM/man/gordlink.Rd              |only
 VGAM-1.1-1/VGAM/man/gpd.Rd                   |   10 
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 VGAM-1.1-1/VGAM/man/hspider.Rd               |    2 
 VGAM-1.1-1/VGAM/man/huber.Rd                 |    2 
 VGAM-1.1-1/VGAM/man/hyperg.Rd                |    2 
 VGAM-1.1-1/VGAM/man/hypersecant.Rd           |    6 
 VGAM-1.1-1/VGAM/man/hzeta.Rd                 |    2 
 VGAM-1.1-1/VGAM/man/identitylink.Rd          |   15 
 VGAM-1.1-1/VGAM/man/inv.binomial.Rd          |    4 
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 VGAM-1.1-1/VGAM/man/leipnik.Rd               |    8 
 VGAM-1.1-1/VGAM/man/lerch.Rd                 |   55 +
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 VGAM-1.1-1/VGAM/man/lgammaff.Rd              |    4 
 VGAM-1.1-1/VGAM/man/lindley.Rd               |    2 
 VGAM-1.1-1/VGAM/man/linkfun.Rd               |    2 
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 VGAM-1.1-1/VGAM/man/lms.bcg.Rd               |    2 
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New package telefit with initial version 1.0.1
Package: telefit
Type: Package
Title: Estimation and Prediction for Remote Effects Spatial Process Models
Version: 1.0.1
Date: 2019-02-15
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@colostate.edu>
Description: Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
License: GPL-3
Depends: R (>= 3.0.2)
Imports: abind, coda, cowplot, doRNG, dplyr, fields, itertools, mvtnorm, raster, scoringRules, stringr, foreach, ggplot2, gtable, reshape2, scales, sp, SDMTools
LinkingTo: Rcpp (>= 0.12.4), RcppArmadillo, RcppEigen (>= 0.3.3.3.1)
RoxygenNote: 6.1.1
Suggests: testthat
LazyData: true
SystemRequirements: A system with a recent-enough C++11 compiler (such as g++-4.8 or later).
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2019-02-15 22:34:18 UTC; pointdex
Repository: CRAN
Date/Publication: 2019-02-18 10:50:03 UTC

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New package orders with initial version 0.1.0
Package: orders
Type: Package
Title: Sampling from Order Statistics of New Families of Distributions
Version: 0.1.0
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Description: Set of tools to generate samples of order statistics from new families of distributions. The main references for this package are: Gentle, J. (2009), Computational Statistics, Springer-Verlag and Naradajah, S. and Rocha, R. (2016), Newdistns: An R Package for New Families of Distributions, Journal of Statistical Software. The families of distributions are: Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modi???ed beta G distributions, and exponentiated exponential Poisson G distributions.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: Newdistns
NeedsCompilation: no
Packaged: 2019-02-08 23:26:30 UTC; Carlos
Repository: CRAN
Date/Publication: 2019-02-18 10:30:03 UTC

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Package maptools updated to version 0.9-5 with previous version 0.9-4 dated 2018-09-19

Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Nick Bearman [ctb], Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stéphane Dray [ctb], David Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb], Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb], Kent Johnson [ctb], Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai [ctb], Edzer Pebesma [ctb], Oscar Perpiñán Lamigueiro [ctb], Ethan Plunkett [ctb], Tom Short [ctb], Greg Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between maptools versions 0.9-4 dated 2018-09-19 and 0.9-5 dated 2019-02-18

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New package fiberLD with initial version 0.1-6
Encoding: UTF-8
Package: fiberLD
Version: 0.1-6
Author: Natalya Pya Arnqvist[aut, cre], Sara Sjöstedt de Luna [aut] Konrad Abramowicz [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Title: Fiber Length Determination
Date: 2019-02-08
Description: Routines for estimating tree fiber (tracheid) length distributions in the standing tree based on increment core samples. Two types of data can be used with the package, increment core data measured by means of an optical fiber analyzer (OFA), e.g. such as the Kajaani Fiber Lab, or measured by microscopy. Increment core data analyzed by OFAs consist of the cell lengths of both cut and uncut fibres (tracheids) and fines (such as ray parenchyma cells) without being able to identify which cells are cut or if they are fines or fibres. The microscopy measured data consist of the observed lengths of the uncut fibres in the increment core. A censored version of a mixture of the fine and fiber length distributions is proposed to fit the OFA data, under distributional assumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>. The package offers two choices for the assumptions of the underlying density functions of the true fiber (fine) lenghts of those fibers (fines) that at least partially appear in the increment core, being the generalized gamma and the log normal densities.
Depends: R (>= 2.15.0)
Imports: stats, graphics, Matrix, VGAM, parallel, foreach, doParallel
Suggests: MASS
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2019-02-08 21:07:16 UTC; natalya
Repository: CRAN
Date/Publication: 2019-02-18 10:30:10 UTC

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Package tsibble updated to version 0.7.0 with previous version 0.6.2 dated 2018-12-12

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage temporal data in a data-centric format, which is built on top of the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal data, including counting and filling in time gaps, aggregate over calendar periods, performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package Spectrum updated to version 0.3 with previous version 0.2 dated 2019-02-11

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

Diff between Spectrum versions 0.2 dated 2019-02-11 and 0.3 dated 2019-02-18

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New package SPAS with initial version 2019.2
Package: SPAS
Type: Package
Title: Stratified-Petersen Analysis System
Version: 2019.2
Date: 2019-02-06
Author: Carl James Schwarz
Maintainer: Carl James Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Depends:
Imports: BB, MASS, Matrix, msm, numDeriv, plyr
Description: The Stratified-Petersen Analysis System (SPAS) is designed to estimate abundance in two-sample capture-recapture experiments where the capture and recaptures are stratified. This is a generalization of the simple Lincoln-Petersen estimator. Strata may be defined in time or in space or both, and the s strata in which marking takes place may differ from the t strata in which recoveries take place. When s=t, SPAS reduces to the method described by Darroch (1961) <https://www.jstor.org/stable/2332748>. When s<t, SPAS implements the methods described in Plante, Rivest, and Tremblay (1988) <https://www.jstor.org/stable/2533994>. Schwarz and Taylor (1998) <doi:10.1139/f97-238> describe the use of SPAS in estimating return of salmon stratified by time and geography. A related package, BTSPAS, deals with temporal stratification where a spline is used to model the distribution of the population over time as it passes the second capture location. This is the R-version of the (now obsolete) standalone Windows program available at <http://www.cs.umanitoba.ca/~popan/spas/spas_home.html>.
License: GPL (>= 2)
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-07 06:25:06 UTC; carlschwarz
Repository: CRAN
Date/Publication: 2019-02-18 09:30:02 UTC

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New package SMITIDvisu with initial version 0.0.3
Package: SMITIDvisu
Type: Package
Title: Visualize Data for Host and Viral Population from 'SMITIDstruct' using HTMLwidgets
Version: 0.0.3
Authors@R: person("Jean-Francois", "Rey", email = "jean-francois.rey@inra.fr", role = c("aut", "cre"))
Description: Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using HTMLwidgets. It mainly using D3JS javascript framework.
Date: 2019-02-03
Depends: R (>= 3.4.0), utils
LinkingTo: Rcpp
NeedsCompilation: yes
SystemRequirements: C++11
Biarch: true
License: GPL (>= 3) | file LICENSE
URL: https://informatique-mia.inra.fr/biosp/anr-smitid-project, https://gitlab.paca.inra.fr/SMITID/visu
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.11.0), htmlwidgets (>= 0.3.2), yaml (>= 2.1.16), jsonlite (>= 1.5.0), magrittr
Suggests: SMITIDstruct, knitr, shiny
RoxygenNote: 6.1.0
Packaged: 2019-02-08 13:24:25 UTC; jfrey
Author: Jean-Francois Rey [aut, cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
Repository: CRAN
Date/Publication: 2019-02-18 09:40:07 UTC

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New package PUPAIM with initial version 0.1.0
Package: PUPAIM
Type: Package
Title: 'A Collection of Physical and Chemical Adsorption Isotherm Models'
Version: 0.1.0
Author: John Ray V. Saroyda/Ranya Yyan S. Cruz/Roel Joseph C. Antonio/Chester C. Deocaris
Maintainer: Chester Deocaris <ccdeocaris@pup.edu.ph>
Description: Adsorption isotherm equations are linearized plots of different solid-liquid phase equilibria used in calculating different parameters related to the adsorption process. Isotherm equations deals with physical adsorption of gases and vapor and gives the most important characteristics of industrial adsorbents that include pore volume, pore size or energy distribution. PUPAIM has 28 documented adsorption isotherm models listed by Dabrowski (2001) <doi:10.1016/S0001-8686(00)00082-8> and Ayawei et al.(2017) <doi:10.1155/2017/3039817>. These models could be easily fitted in R using adsorption data (Ce and Qe) obtained from experiments.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R(>= 3.4.0)
Imports: FSA, Metrics, minpack.lm, stats, graphics
NeedsCompilation: no
Packaged: 2019-02-08 12:46:18 UTC; Joseph
Repository: CRAN
Date/Publication: 2019-02-18 09:40:10 UTC

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New package optimos.prime with initial version 0.1.0
Package: optimos.prime
Type: Package
Title: Optimos Prime Helps Calculate Autoecological Data for Biological Species
Version: 0.1.0
Authors@R: c( person("María Belén", "Sathicq", email = "mbelen@ilpla.edu.ar", role = "aut"), person("María Mercedes", "Nicolosi Gelis", email = "mercedesnicolosi@ilpla.edu.ar", role = "aut"), person("Joaquín", "Cochero", email = "jcochero@ilpla.edu.ar", role = "cre"))
Maintainer: Joaquín Cochero <jcochero@ilpla.edu.ar>
Description: Calculates autoecological data (optima and tolerance ranges) of a biological species given an environmental matrix. The package calculates by weighted averaging, using the number of occurrences to adjust the tolerance assigned to each taxon to estimate optima and tolerance range in cases where taxa have unequal occurrences. See the detailed methodology by Birks et al. (1990) <doi:10.1098/rstb.1990.0062>, and a case example by Potapova and Charles (2003) <doi:10.1046/j.1365-2427.2003.01080.x>.
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1.9000
Depends: ggplot2, tidyverse, plotly
NeedsCompilation: no
Packaged: 2019-02-08 17:18:13 UTC; Juaco
Author: María Belén Sathicq [aut], María Mercedes Nicolosi Gelis [aut], Joaquín Cochero [cre]
Repository: CRAN
Date/Publication: 2019-02-18 09:50:03 UTC

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New package opalr with initial version 1.0.0
Package: opalr
Version: 1.0.0
Title: Opal R and Datashield Utils
Authors@R: c(person(given = "Yannick", family = "Marcon", role = c("aut", "cre"), email = "yannick.marcon@obiba.org", comment = c(ORCID = "0000-0003-0138-2023")), person(given = "Amadou", family = "Gaye", role = "ctb", comment = c(ORCID = "0000-0002-1180-2792")), person("OBiBa group", role="cph", email="info@obiba.org"))
Depends: R (>= 3.1), httr
Imports: xml2, jsonlite, mime
Suggests: e1071, knitr, knitrBootstrap, rmarkdown
Description: Data integration Web application for biobanks by OBiBa. Opal is OBiBa's core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. Opal is such a central repository. It can import, process, validate, query, analyze, report, and export data. Opal is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks.
License: GPL-3
URL: https://www.obiba.org/ https://www.obiba.org/pages/products/opal/ https://academic.oup.com/ije/article/46/5/1372/4102813
BugReports: https://github.com/obiba/opalr
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-02-08 16:46:59 UTC; yannick
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>), Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>), OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Repository: CRAN
Date/Publication: 2019-02-18 10:00:08 UTC

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New package nsga3 with initial version 0.0.3
Package: nsga3
Type: Package
Title: An Implementation of Non-Dominated Sorting Genetic Algorithm III for Feature Selection
Version: 0.0.3
Author: Artem Shramko
Maintainer: Artem Shramko <art.shramko@gmail.com>
Description: An adaptation of Non-dominated Sorting Genetic Algorithm III for multi objective feature selection tasks. Non-dominated Sorting Genetic Algorithm III is a genetic algorithm that solves multiple optimization problems simultaneously by applying a non-dominated sorting technique. It uses a reference points based selection operator to explore solution space and preserve diversity. See the original paper by K. Deb and H. Jain (2014) <DOI:10.1109/TEVC.2013.2281534> for a detailed description.
Depends: R (>= 2.10.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: mlr, parallelMap, rPref, xgboost
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-08 16:47:37 UTC; user
Repository: CRAN
Date/Publication: 2019-02-18 10:00:15 UTC

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New package mixsqp with initial version 0.1-97
Encoding: UTF-8
Type: Package
Package: mixsqp
Version: 0.1-97
Date: 2019-02-08
Title: Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
Authors@R: c(person("Youngseok","Kim",role="aut", email="youngseok@uchicago.edu"), person("Peter","Carbonetto",role=c("aut","cre"), email="peter.carbonetto@gmail.com"), person("Mihai","Anitescu",role="aut"), person("Matthew","Stephens",role="aut"), person("Jason","Willwerscheid",role="ctb"), person("Jean","Morrison",role="ctb"))
URL: https://github.com/stephenslab/mixsqp
BugReports: https://github.com/stephenslab/mixsqp/issues
SystemRequirements: C++11
Depends: R (>= 3.3.0)
Description: Provides optimization algorithms based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithms are expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly in large data sets. The algorithms are described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2012) <arXiv:1806.01412>.
License: MIT + file LICENSE
Imports: stats, Rcpp (>= 0.12.15)
Suggests: REBayes, Rmosek, testthat, knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
LazyData: true
NeedsCompilation: yes
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Packaged: 2019-02-08 13:57:28 UTC; pcarbo
Author: Youngseok Kim [aut], Peter Carbonetto [aut, cre], Mihai Anitescu [aut], Matthew Stephens [aut], Jason Willwerscheid [ctb], Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-18 09:40:03 UTC

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Package SDLfilter updated to version 1.2.0 with previous version 1.1.1 dated 2018-06-20

Title: Filtering Satellite-Derived Locations
Description: Functions to filter GPS and/or Argos locations. The provided filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as proposed in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <takahiro.shimada@my.jcu.edu.au>

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Package ggstatsplot updated to version 0.0.9 with previous version 0.0.8 dated 2019-01-07

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis. of continuous (violin plots, scatterplots, histograms) or categorical (pie and bar charts) data. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [aut, ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package cchs updated to version 0.4.1 with previous version 0.4.0 dated 2017-08-26

Title: Cox Model for Case-Cohort Data with Stratified Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones
Maintainer: E. Jones <edmundjones79@gmail.com>

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Package openVA updated to version 1.0.8 with previous version 1.0.7 dated 2018-09-13

Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@gmail.com>

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Package JuliaCall updated to version 0.16.4 with previous version 0.16.2 dated 2019-01-02

Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia', which is a high-level, high-performance dynamic programming language for numerical computing, see <https://julialang.org/> for more information. It provides a high-level interface as well as a low-level interface. Using the high level interface, you could call any 'Julia' function just like any R function with automatic type conversion. Using the low level interface, you could deal with C-level SEXP directly while enjoying the convenience of using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre], Randy Lai [ctb], Dmitri Grominski [ctb], Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>

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Sun, 17 Feb 2019

Package LPCM updated to version 0.46-1 with previous version 0.45-0 dated 2015-09-22

Title: Local Principal Curve Methods
Description: Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering.
Author: Jochen Einbeck and Ludger Evers
Maintainer: Jochen Einbeck <jochen.einbeck@durham.ac.uk>

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Package funtimes updated to version 6.0 with previous version 5.0 dated 2018-02-04

Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich [aut, cre], Yulia R. Gel [aut], Calvin Chu [ctb], Xin Huang [ctb], Ethan D. Schaeffer [ctb], Srishti Vishwakarma [ctb], Xingyu Wang [ctb]
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>

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Package survELtest updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-16

Title: Comparing Multiple Survival Functions with Crossing Hazards in R
Description: Contains routines for computing the one-sided/two-sided integrated/maximally selected EL statistics for simultaneous testing, the one-sided/two-sided EL tests for pointwise testing, and an initial test that precedes one-sided testing to exclude the possibility of crossings or alternative orderings.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>

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Package rqdatatable updated to version 1.1.3 with previous version 1.1.2 dated 2018-12-17

Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package tableone updated to version 0.10.0 with previous version 0.9.3 dated 2018-04-29

Title: Create 'Table 1' to Describe Baseline Characteristics
Description: Creates 'Table 1', i.e., description of baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. Weighted data are supported via the 'survey' package. See 'github' for a screen cast. 'tableone' was inspired by descriptive statistics functions in 'Deducer' , a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida [cre, aut] (<https://orcid.org/0000-0002-2030-3549>), Jonathan J Chipman [ctb], Justin Bohn [ctb], Lucy DAgostino McGowan [ctb], Malcolm Barrett [ctb], Rune Haubo B Christensen [ctb], gbouzill [ctb]
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>

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Package ThreeArmedTrials updated to version 1.0-3 with previous version 1.0-0 dated 2016-05-17

Title: Design and Analysis of Clinical Non-Inferiority or Superiority Trials with Active and Placebo Control
Description: Design and analyze three-arm non-inferiority or superiority trials which follow a gold-standard design, i.e. trials with an experimental treatment, an active, and a placebo control. Method for the following distributions are implemented: Poisson (Mielke and Munk (2009) <arXiv:0912.4169>), negative binomial (Muetze et al. (2016) <doi:10.1002/sim.6738>), normal (Pigeot et al. (2003) <doi:10.1002/sim.1450>; Hasler et al. (2009) <doi:10.1002/sim.3052>), binary (Friede and Kieser (2007) <doi:10.1002/sim.2543>), nonparametric (Muetze et al. (2017) <doi:10.1002/sim.7176>), exponential (Mielke and Munk (2009) <arXiv:0912.4169>).
Author: Tobias Mütze [aut, cre] (<https://orcid.org/0000-0002-4111-1941>), Tim Friede [ctb]
Maintainer: Tobias Mütze <tobias.muetze@outlook.com>

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Package MSPRT updated to version 2.0 with previous version 1.0 dated 2018-09-17

Title: Modified Sequential Probability Ratio Test (MSPRT)
Description: A modified SPRT (MSPRT) can be designed and implemented with the help of this package. In a MSPRT design, (i) the maximum sample size of an experiment is fixed prior to the start of an experiment; (ii) the alternative hypothesis used to define the rejection region of the test is derived from the size of the test (Type I error), the maximum available sample size (N), and (iii) the targeted Type 2 error (equals to 1 minus the power) is also prespecified. Given these values, the MSPRT is defined in a manner very similar to Wald's initial proposal. This test can reduce the average sample size required to perform statistical hypothesis tests at the specified level of significance and power. This package implements one-sample proportion tests, one-sample Z-tests, one-sample T-tests, two-sample Z-tests and two-sample T-tests. A user guidance for this package is provided here. One can also refer to the supplemental information for the same.
Author: Sandipan Pramanik [aut, cre], Valen E. Johnson [aut], Anirban Bhattacharya [aut]
Maintainer: Sandipan Pramanik <sandy@stat.tamu.edu>

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Package BAwiR updated to version 1.2 with previous version 1.1.3 dated 2018-09-24

Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly web scraping and visualization. Data were obtained from <http://www.euroleague.net/>, <http://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games and maps of nationalities.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

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Package sloop updated to version 1.0.1 with previous version 1.0.0 dated 2018-10-30

Title: Helpers for 'OOP' in R
Description: A collection of helper functions designed to help you to better understand object oriented programming in R, particularly using 'S3'.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package congressbr updated to version 0.2.0 with previous version 0.1.8 dated 2019-01-29

Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/> respectively.
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>

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Package quadprogXT updated to version 0.0.4 with previous version 0.0.3 dated 2018-05-22

Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre]
Maintainer: Bob Harlow <rharlow86@gmail.com>

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Package forcats updated to version 0.4.0 with previous version 0.3.0 dated 2018-02-19

Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package pivottabler updated to version 1.1.0 with previous version 1.0.0 dated 2018-10-17

Title: Create Pivot Tables in R
Description: Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>

Diff between pivottabler versions 1.0.0 dated 2018-10-17 and 1.1.0 dated 2019-02-17

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Package foghorn updated to version 1.1.0 with previous version 1.0.2 dated 2018-04-14

Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results in your R terminal.
Author: Francois Michonneau [aut, cre], Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

Diff between foghorn versions 1.0.2 dated 2018-04-14 and 1.1.0 dated 2019-02-17

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Package nasapower updated to version 1.0.7 with previous version 1.0.5 dated 2019-02-02

Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>), Hazel Kavili [rev], Alison Boyer [rev]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

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More information about nasapower at CRAN
Permanent link

Package AGread updated to version 0.2.0 with previous version 0.1.2 dated 2018-04-19

Title: Read Data Files from ActiGraph Monitors
Description: Standardize the process of bringing various modes of output files into R. For more information, see: <https://actigraph.desk.com/customer/en/portal/articles/2515800-what-do-the-different-mode-numbers-mean-in-a-csv-or-dat-file->. Additionally, processes are provided to read and minimally pre- process raw data from primary accelerometer and inertial measurement unit files, as well as binary .gt3x files. ActiGraph monitors are used to estimate physical activity outcomes via body-worn sensors that measure (e.g.) acceleration or rotational velocity.
Author: Paul R. Hibbing [aut, cre], Vincent T. van Hees [ctb], Samuel R. LaMunion [ctb]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>

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Sat, 16 Feb 2019

Package netgwas updated to version 1.8.1 with previous version 1.7.0 dated 2018-08-13

Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. We use conditional independence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <arXiv:1710.01063>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>

Diff between netgwas versions 1.7.0 dated 2018-08-13 and 1.8.1 dated 2019-02-16

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More information about netgwas at CRAN
Permanent link

New package mlbgameday with initial version 0.1.4
Package: mlbgameday
Title: Tools to Gather Data from Major League Baseball Advanced Media
Version: 0.1.4
Authors@R: person("Kris", "Eberwein", email = "eberwein@knights.ucf.edu", role = c("aut", "cre"))
Description: Multi-core processing of data from Major League Baseball Advanced Media <http://gd2.mlb.com/components/game/mlb/>. Additional tools to parallel process large data sets and write them to a database.
Depends: R (>= 3.3.0)
Imports: magrittr, xml2, dplyr, stringr, purrr, tidyr, utils, stats, foreach, iterators, parallel, doParallel, DBI
Suggests: testthat, knitr, rmarkdown, ggplot2, RSQLite, dbplyr
License: MIT + file LICENSE
URL: https://github.com/keberwein/mlbgameday
BugReports: https://github.com/keberwein/mlbgameday/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-16 19:18:45 UTC; mediacenter
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Repository: CRAN
Date/Publication: 2019-02-16 23:30:08 UTC

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Package optionstrat updated to version 1.1.0 with previous version 1.0.0 dated 2018-12-09

Title: Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies
Description: Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>

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Package matsbyname updated to version 0.4.10 with previous version 0.4.9 dated 2019-01-25

Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>

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Package CuCubes (with last version 0.1.0) was removed from CRAN

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

2016-12-09 0.1.0

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Package ezpickr updated to version 1.0.1 with previous version 1.0.0 dated 2019-02-02

Title: Import Various Data File Types as a Rectangular Form Using a File Picker Dialogue Box
Description: Easy data importing for the most frequently used file formats in a 'tibble' form.
Author: JooYoung Seo [aut, cre], Soyoung Choi [aut], hyun seung Lee [ctb], Jonghoen Kim [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>

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Package SignifReg updated to version 1.1 with previous version 1.0 dated 2017-02-01

Title: Consistent Significance Controlled Variable Selection in Linear Regression
Description: Provide consistent significance controlled variable selection procedure with different directions (forward, backward, stepwise) based on diverse criteria (Mallows' Cp, AIC, BIC, adjusted r-square, p-value). The algorithm selects a final model with only significant variables based on a correction choice of False Discovery Rate, Bonferroni, or no correction.
Author: Jongwook Kim, Adriano Zanin Zambom
Maintainer: Jongwook Kim <jongwook226@gmail.com>

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Package ROI.plugin.neos updated to version 0.3-1 with previous version 0.3-0 dated 2018-06-19

Title: 'NEOS' Plug-in for the 'R' Optimization Interface
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package with a connection to the 'neos' server. 'ROI' optimization problems can be directly be sent to the 'neos' server and solution obtained in the typical 'ROI' style.
Author: Ronald Hochreiter [aut], Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>

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Package hoa updated to version 2.1.4.1 with previous version 2.1.4 dated 2015-08-11

Title: Higher Order Likelihood Inference
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>

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Package ipcwswitch updated to version 1.0.2 with previous version 1.0.1 dated 2018-11-16

Title: Inverse Probability of Censoring Weights to Deal with Treatment Switch in Randomized Clinical Trials
Description: Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.
Author: Nathalie Graffeo [aut, cre], Aurelien Latouche [aut], Sylvie Chevret [aut]
Maintainer: Nathalie Graffeo <nathalie.graffeo@univ-amu.fr>

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Package rPref updated to version 1.3 with previous version 1.2 dated 2016-12-18

Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al. (2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations known as database preferences (see Kießling (2002) <doi:10.1016/B978-155860869-6/50035-4>).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>

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Package WRSS updated to version 2.2 with previous version 2.1 dated 2019-01-21

Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary storage and hydropower water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

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Package areaplot updated to version 1.2-1 with previous version 1.2-0 dated 2017-10-18

Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add polygons to existing plots. A variety of input formats are supported, including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

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Fri, 15 Feb 2019

Package ggmcmc updated to version 1.2 with previous version 1.1.1 dated 2019-01-23

Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of Markov Chain Monte Carlo simulations, as well as for graphically display results from full MCMC analysis. The package also facilitates the graphical interpretation of models by providing flexible functions to plot the results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>

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Package FNN updated to version 1.1.3 with previous version 1.1.2.2 dated 2018-12-10

Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford (cover tree library), Sunil Arya and David Mount (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>

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Package chillR updated to version 0.70.14 with previous version 0.70.12 dated 2018-12-18

Title: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi.org/10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi.org/10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package psychmeta updated to version 2.3.1 with previous version 2.3.0 dated 2019-01-09

Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre], Brenton M. Wiernik [aut], Michael T. Brannick [ctb] (Testing), Jack Kostal [ctb] (Code for reshape_mat2dat function), Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots), John Sakaluk [ctb] (Code for funnel and forest plots), Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>

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Package neo4r updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-27

Title: A 'Neo4J' Driver
Description: A Modern and Flexible 'Neo4J' Driver, allowing you to query data on a 'Neo4J' server and handle the results in R. It's modern in the sense it provides a driver that can be easily integrated in a data analysis workflow, especially by providing an API working smoothly with other data analysis and graph packages. It's flexible in the way it returns the results, by trying to stay as close as possible to the way 'Neo4J' returns data. That way, you have the control over the way you will compute the results. At the same time, the result is not too complex, so that the "heavy lifting" of data wrangling is not left to the user.
Author: Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>), ThinkR [cph], Neo4J [spn]
Maintainer: Colin Fay <contact@colinfay.me>

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Package gganimate updated to version 1.0.1 with previous version 1.0.0 dated 2019-01-02

Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre], David Robinson [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package finalfit updated to version 0.9.0 with previous version 0.8.9 dated 2018-12-18

Title: Quickly Create Elegant Regression Results Tables and Plots when Modelling
Description: Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre], Tom Drake [aut], Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>

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Package ruler updated to version 0.2.0 with previous version 0.1.4 dated 2018-12-05

Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and tidy reports. This package offers a framework for exploring and validating data frame like objects using 'dplyr' grammar of data manipulation.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package rotl updated to version 3.0.7 with previous version 3.0.6 dated 2019-01-20

Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Author: Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package ahpsurvey updated to version 0.4.0 with previous version 0.3.0 dated 2018-12-17

Title: Analytic Hierarchy Process for Survey Data
Description: The Analytic Hierarchy Process is a versatile multi-criteria decision-making tool introduced by Saaty (1987) <doi:10.1016/0270-0255(87)90473-8> that allows decision-makers to weigh attributes and evaluate alternatives presented to them. This package provides a consistent methodology for researchers to reformat data and run analytic hierarchy process in R on data that are formatted using the survey data entry mode. It is optimized for performing the analytic hierarchy process with many decision-makers, and provides tools and options for researchers to aggregate individual preferences and test multiple options. It also allows researchers to quantify, visualize and correct for inconsistency in the decision-maker's comparisons.
Author: Frankie Cho [aut, cre]
Maintainer: Frankie Cho <htcho@connect.hku.hk>

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Package BDgraph updated to version 2.55 with previous version 2.54 dated 2019-01-21

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Letac et al. (2018) <arXiv:1706.04416>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>, Ernst Wit [aut], Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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Package MATA updated to version 0.4 with previous version 0.3 dated 2015-04-18

Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, which are constructed using single-model estimators and model weights. See Turek and Fletcher (2012) <doi:10.1016/j.csda.2012.03.002> for details.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>

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Package MachineShop updated to version 1.2.0 with previous version 1.1.0 dated 2019-01-23

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package walker updated to version 0.2.4 with previous version 0.2.3-1 dated 2018-11-09

Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression coefficients can vary over time as random walks. Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, walker uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package visdat updated to version 0.5.3 with previous version 0.5.2 dated 2018-12-10

Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>), Sean Hughes [rev] (<https://orcid.org/0000-0002-9409-9405>, Sean Hughes reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Mara Averick [rev] (Mara Averick reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Stuart Lee [ctb], Earo Wang [ctb], Nic Crane [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package scopr updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-29

Title: Read Ethoscope Data
Description: Handling of behavioural data from the Ethoscope platform (Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>). Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables such as xy coordinates, dimensions and speed. This package is part of the rethomics framework <http://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>

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Package rwty updated to version 1.0.2 with previous version 1.0.1 dated 2016-06-22

Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Description: Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.
Author: Dan Warren [aut, cre], Anthony Geneva [aut], Rob Lanfear [aut], Luke Harmon [ctb], April Wright [ctb], Diego Mallo [ctb], Klaus Schliep [ctb]
Maintainer: Dan Warren <dan.l.warren@gmail.com>

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Package readxl updated to version 1.3.0 with previous version 1.2.0 dated 2018-12-19

Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://github.com/evanmiller/libxls> and '.xlsx' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package purrrlyr updated to version 0.0.4 with previous version 0.0.3 dated 2018-05-29

Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and 'purrr' that formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre], Hadley Wickham [ctb], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package jstable updated to version 0.7.9 with previous version 0.7.7 dated 2019-02-03

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package irg updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-04

Title: Instantaneous Rate of Green Up
Description: Fits a double logistic function to NDVI time series and calculates instantaneous rate of green (IRG) according to methods described in Bischoff et al. (2012) <doi:10.1086/667590>.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>

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Package dplyr updated to version 0.8.0.1 with previous version 0.8.0 dated 2019-02-14

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package stats19 updated to version 0.2.0 with previous version 0.1.1 dated 2019-01-17

Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979, the types (including make and model) of vehicles involved and the consequential casualties. The statistics relate only to personal casualties on public roads that are reported to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See the Department for Transportation website <https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Malcolm Morgan [aut], Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>), Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>), David Ranzolin [rev], Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package naniar updated to version 0.4.2 with previous version 0.4.1 dated 2018-11-20

Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>), Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>), Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>), Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>), Mitchell O'Hara-Wild [ctb], Jim Hester [ctb], Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package jskm updated to version 0.3.0 with previous version 0.2.7 dated 2019-02-01

Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package dbhydroR updated to version 0.2-7 with previous version 0.2-6 dated 2018-07-19

Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water Management District's 'DBHYDRO' database at <https://www.sfwmd.gov/science-data/dbhydro>, with functions for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package castor updated to version 1.3.5 with previous version 1.3.4 dated 2018-08-16

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package kinfit (with last version 1.1.14) was removed from CRAN

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

2015-07-04 1.1.14
2014-11-25 1.1.13
2013-11-27 1.1.12
2012-06-30 1.1.09
2011-11-09 1.1.06
2011-09-02 1.1.04
2011-03-21 1.0.8
2010-12-23 1.0.6
2010-05-01 1.0

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Package udpipe updated to version 0.8.1 with previous version 0.8 dated 2018-12-09

Title: Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <http://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph], BNOSAC [cph], Institute of Formal and Applied Linguistics, Faculty of Mathematics and Physics, Charles University in Prague, Czech Republic [cph], Milan Straka [ctb, cph], Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>

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Package Rmosek updated to version 1.3.2 with previous version 1.3.1 dated 2019-01-23

Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization facilities of MOSEK available from the R-language. The interface supports large-scale optimization of many kinds: Mixed-integer and continuous linear, second-order cone, exponential cone and power cone optimization, as well as continuous semidefinite optimization. Rmosek and the R-language are open-source projects. MOSEK is a proprietary product, but unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>

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Package LLSR updated to version 0.0.2.12 with previous version 0.0.2.6 dated 2019-01-14

Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters, producing a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com> [aut, cre], Pedro Vitor Oliveira Menezes <pedrod841@hotmail.com> [dtc], Carla Corina dos Santos Porto <carlacorina@hotmail.com.br> [dtc], Jon George Huddleston <Jonathan.Huddleston@brunel.ac.uk> [rev], Elias Basile Tambourgi <eliastam@feq.unicamp.br> [rev]
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>

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Package bcmaps updated to version 0.18.0 with previous version 0.17.1 dated 2018-03-14

Title: Map Layers and Spatial Utilities for British Columbia
Description: Provides access to various spatial layers for B.C., such as administrative boundaries, natural resource management boundaries, etc. All layers are imported from the 'bcmapsdata' package as 'sf' or 'Spatial' objects through function calls in this package. All layers are in B.C. 'Albers' equal-area projection <http://spatialreference.org/ref/epsg/nad83-bc-albers/>, which is the B.C. government standard.
Author: Andy Teucher [aut, cre], Stephanie Hazlitt [aut], Sam Albers [aut], Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

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Package AzureStor updated to version 2.0.0 with previous version 1.0.0 dated 2018-12-25

Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS).
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package BacArena updated to version 1.8 with previous version 1.7 dated 2018-05-09

Title: Modeling Framework for Cellular Communities in their Environments
Description: Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.
Author: Eugen Bauer [aut], Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>

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Package SqlRender updated to version 1.6.0 with previous version 1.5.3 dated 2018-11-23

Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between SqlRender versions 1.5.3 dated 2018-11-23 and 1.6.0 dated 2019-02-15

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Package QuantumOps updated to version 2.4 with previous version 2.3 dated 2019-01-30

Title: Performs Common Linear Algebra Operations Used in Quantum Computing
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Contains all commonly used quantum gates, creates arbitrarily controlled versions of all gates, and can simulate complete or partial measurements of kets. Implements modular arithmetic commonly found in quantum algorithms and can convert functions into equivalent quantum gates. It can also simulate larger applications, including the Quantum Fourier Transform developed by Shor (1999), Shor's algorithm which factors numbers up to 21, Grover's algorithm (1996), and the training of a quantum neural network developed by Schuld (2018) which can classify the MNIST dataset.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

Diff between QuantumOps versions 2.3 dated 2019-01-30 and 2.4 dated 2019-02-15

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Package GWmodel updated to version 2.0-8 with previous version 2.0-7 dated 2019-02-02

Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>

Diff between GWmodel versions 2.0-7 dated 2019-02-02 and 2.0-8 dated 2019-02-15

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Thu, 14 Feb 2019

Package cdata updated to version 1.0.6 with previous version 1.0.5 dated 2019-01-20

Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . Works on in-memory data or on remote data using 'rquery' and the 'DBI' database interface.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between cdata versions 1.0.5 dated 2019-01-20 and 1.0.6 dated 2019-02-14

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Package triangle updated to version 0.12 with previous version 0.11 dated 2017-10-02

Title: Provides the Standard Distribution Functions for the Triangle Distribution
Description: Provides the "r, q, p, and d" distribution functions for the triangle distribution.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>

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Package RandomFieldsUtils updated to version 0.5.1 with previous version 0.5 dated 2019-02-10

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.5 dated 2019-02-10 and 0.5.1 dated 2019-02-14

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Package RandomFields updated to version 3.3 with previous version 3.1.50 dated 2017-04-17

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.1.50 dated 2017-04-17 and 3.3 dated 2019-02-14

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 RandomFields-3.3/RandomFields/man/RMfractdiff.Rd                       |  114 
 RandomFields-3.3/RandomFields/man/RMfractgauss.Rd                      |   11 
 RandomFields-3.3/RandomFields/man/RMgauss.Rd                           |  155 
 RandomFields-3.3/RandomFields/man/RMgencauchy.Rd                       |  196 
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 RandomFields-3.3/RandomFields/man/RMlgd.Rd                             |  136 
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 RandomFields-3.3/RandomFields/man/RMmastein.Rd                         |  197 
 RandomFields-3.3/RandomFields/man/RMmatern.Rd                          |  335 
 RandomFields-3.3/RandomFields/man/RMmatrix.Rd                          |  177 
 RandomFields-3.3/RandomFields/man/RMmodel-class.Rd                     |  432 
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 RandomFields-3.3/RandomFields/man/RMmodelExt-class.Rd                  |  248 
 RandomFields-3.3/RandomFields/man/RMmodelgenerator-class.Rd            |  444 
 RandomFields-3.3/RandomFields/man/RMmodelsAdvanced.Rd                  |  496 
 RandomFields-3.3/RandomFields/man/RMmodelsAuxiliary.Rd                 |  244 
 RandomFields-3.3/RandomFields/man/RMmodelsMultivariate.Rd              |  240 
 RandomFields-3.3/RandomFields/man/RMmodelsNonstatationary.Rd           |  110 
 RandomFields-3.3/RandomFields/man/RMmodelsSpaceTime.Rd                 |  177 
 RandomFields-3.3/RandomFields/man/RMmodelsSphere.Rd                    |  246 
 RandomFields-3.3/RandomFields/man/RMmodelsTailcorrelation.Rd           |  226 
 RandomFields-3.3/RandomFields/man/RMmodelsTrend.Rd                     |  131 
 RandomFields-3.3/RandomFields/man/RMmppplus.Rd                         |  105 
 RandomFields-3.3/RandomFields/man/RMmqam.Rd                            |  149 
 RandomFields-3.3/RandomFields/man/RMmult.Rd                            |  151 
 RandomFields-3.3/RandomFields/man/RMmultiquad.Rd                       |  171 
 RandomFields-3.3/RandomFields/man/RMnatsc.Rd                           |   89 
 RandomFields-3.3/RandomFields/man/RMnonstwm.Rd                         |  127 
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 RandomFields-3.3/RandomFields/man/RMnugget.Rd                          |  128 
 RandomFields-3.3/RandomFields/man/RMoesting.Rd                         |   15 
 RandomFields-3.3/RandomFields/man/RMparswm.Rd                          |   20 
 RandomFields-3.3/RandomFields/man/RMpenta.Rd                           |  122 
 RandomFields-3.3/RandomFields/man/RMplus.Rd                            |  119 
 RandomFields-3.3/RandomFields/man/RMpoissonpoly.Rd                     |  146 
 RandomFields-3.3/RandomFields/man/RMpolynome.Rd                        |  118 
 RandomFields-3.3/RandomFields/man/RMpower.Rd                           |   11 
 RandomFields-3.3/RandomFields/man/RMprod.Rd                            |  125 
 RandomFields-3.3/RandomFields/man/RMqam.Rd                             |  144 
 RandomFields-3.3/RandomFields/man/RMqexp.Rd                            |  102 
 RandomFields-3.3/RandomFields/man/RMrational.Rd                        |   80 
 RandomFields-3.3/RandomFields/man/RMrotat.Rd                           |  105 
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 RandomFields-3.3/RandomFields/man/RMschur.Rd                           |  126 
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 RandomFields-3.3/RandomFields/man/RMsinepower.Rd                       |  146 
 RandomFields-3.3/RandomFields/man/RMspheric.Rd                         |  121 
 RandomFields-3.3/RandomFields/man/RMstable.Rd                          |  205 
 RandomFields-3.3/RandomFields/man/RMstein.Rd                           |  126 
 RandomFields-3.3/RandomFields/man/RMstp.Rd                             |  174 
 RandomFields-3.3/RandomFields/man/RMstrokorb.Rd                        |  172 
 RandomFields-3.3/RandomFields/man/RMsum.Rd                             |  109 
 RandomFields-3.3/RandomFields/man/RMtbm.Rd                             |  215 
 RandomFields-3.3/RandomFields/man/RMtrafo.Rd                           |  331 
 RandomFields-3.3/RandomFields/man/RMtrend.Rd                           |  428 
 RandomFields-3.3/RandomFields/man/RMtruncsupport.Rd                    |  111 
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 RandomFields-3.3/RandomFields/man/RMvector.Rd                          |  150 
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 RandomFields-3.3/RandomFields/man/RPbernoulli.Rd                       |  159 
 RandomFields-3.3/RandomFields/man/RPbrownresnick.Rd                    |  251 
 RandomFields-3.3/RandomFields/man/RPchi2.Rd                            |  107 
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 RandomFields-3.3/RandomFields/man/RPcoin.Rd                            |  203 
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 RandomFields-3.3/RandomFields/man/RPgauss.Rd                           |  226 
 RandomFields-3.3/RandomFields/man/RPhyperplane.Rd                      |  207 
 RandomFields-3.3/RandomFields/man/RPmaxstable.Rd                       |  223 
 RandomFields-3.3/RandomFields/man/RPmaxstableAdvanced.Rd               |   10 
 RandomFields-3.3/RandomFields/man/RPnugget.Rd                          |  269 
 RandomFields-3.3/RandomFields/man/RPopitz.Rd                           |  147 
 RandomFields-3.3/RandomFields/man/RPpoisson.Rd                         |  129 
 RandomFields-3.3/RandomFields/man/RPschlather.Rd                       |  203 
 RandomFields-3.3/RandomFields/man/RPsequential.Rd                      |  208 
 RandomFields-3.3/RandomFields/man/RPsmith.Rd                           |  260 
 RandomFields-3.3/RandomFields/man/RPspecific.Rd                        |  230 
 RandomFields-3.3/RandomFields/man/RPspectral.Rd                        |  227 
 RandomFields-3.3/RandomFields/man/RPt.Rd                               |  125 
 RandomFields-3.3/RandomFields/man/RPtbm.Rd                             |  394 
 RandomFields-3.3/RandomFields/man/RR.Rd                                |  227 
 RandomFields-3.3/RandomFields/man/RRdeterm.Rd                          |   89 
 RandomFields-3.3/RandomFields/man/RRdistr.Rd                           |  212 
 RandomFields-3.3/RandomFields/man/RRgauss.Rd                           |  104 
 RandomFields-3.3/RandomFields/man/RRloc.Rd                             |  113 
 RandomFields-3.3/RandomFields/man/RRmcmc.Rd                            |  156 
 RandomFields-3.3/RandomFields/man/RRrectangular.Rd                     |  198 
 RandomFields-3.3/RandomFields/man/RRspherical.Rd                       |   93 
 RandomFields-3.3/RandomFields/man/RRunif.Rd                            |  117 
 RandomFields-3.3/RandomFields/man/RandomFields.Rd                      |  650 -
 RandomFields-3.3/RandomFields/man/conventional2RFspDataFrame.Rd        |  113 
 RandomFields-3.3/RandomFields/man/fitgauss.Rd                          |  175 
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 RandomFields-3.3/RandomFields/man/soil.Rd                              |  225 
 RandomFields-3.3/RandomFields/man/sp2RF.Rd                             |  119 
 RandomFields-3.3/RandomFields/man/weather.Rd                           |  142 
 RandomFields-3.3/RandomFields/src/AutoRandomFields.cc                  |  120 
 RandomFields-3.3/RandomFields/src/AutoRandomFields.h                   |  385 
 RandomFields-3.3/RandomFields/src/Brown.cc                             | 1557 +-
 RandomFields-3.3/RandomFields/src/Coordinate_systems.cc                |  999 -
 RandomFields-3.3/RandomFields/src/Coordinate_systems.h                 |  202 
 RandomFields-3.3/RandomFields/src/D.H.cc                               |   11 
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 RandomFields-3.3/RandomFields/src/Gneiting.cc                          | 1204 --
 RandomFields-3.3/RandomFields/src/Huetchen.cc                          | 2026 +--
 RandomFields-3.3/RandomFields/src/InternalCov.cc                       | 2961 ++---
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 RandomFields-3.3/RandomFields/src/KeyInfo.cc                           | 1718 +--
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 RandomFields-3.3/RandomFields/src/Specific.cc                          |  190 
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 RandomFields-3.3/RandomFields/src/auxiliary.h                          |   59 
 RandomFields-3.3/RandomFields/src/auxiliary2.h                         |    6 
 RandomFields-3.3/RandomFields/src/avltr_modified.cc                    |  141 
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 RandomFields-3.3/RandomFields/src/direct.cc                            |  273 
 RandomFields-3.3/RandomFields/src/empvario.cc                          |  622 -
 RandomFields-3.3/RandomFields/src/extremes.cc                          | 1554 +-
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 RandomFields-3.3/RandomFields/src/fftVario.cc                          |   86 
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 RandomFields-3.3/RandomFields/src/gausslikeli.cc                       |  491 
 RandomFields-3.3/RandomFields/src/getNset.cc                           | 2933 +----
 RandomFields-3.3/RandomFields/src/hyperplan.cc                         |  231 
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 RandomFields-3.3/RandomFields/src/kleinkram.cc                         |  292 
 RandomFields-3.3/RandomFields/src/kleinkram.h                          |   21 
 RandomFields-3.3/RandomFields/src/metropolis.cc                        |   37 
 RandomFields-3.3/RandomFields/src/nugget.cc                            |  566 -
 RandomFields-3.3/RandomFields/src/operator.cc                          | 5575 ++++------
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 RandomFields-3.3/RandomFields/src/spectral.cc                          |  186 
 RandomFields-3.3/RandomFields/src/startGetNset.cc                      | 1085 +
 RandomFields-3.3/RandomFields/src/startGetNset.h                       |only
 RandomFields-3.3/RandomFields/src/tbm.cc                               |  545 
 RandomFields-3.3/RandomFields/src/trend.cc                             | 1338 --
 RandomFields-3.3/RandomFields/src/userinterfaces.cc                    | 2983 +----
 RandomFields-3.3/RandomFields/src/variogramAndCo.cc                    |  745 -
 RandomFields-3.3/RandomFields/src/variogramAndCo.h                     |  249 
 RandomFields-3.3/RandomFields/src/xport_import.cc                      |only
 RandomFields-3.3/RandomFields/src/xport_import.h                       |only
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 RandomFields-3.3/RandomFields/src/zzz.c                                |   84 
 373 files changed, 48282 insertions(+), 51036 deletions(-)

More information about RandomFields at CRAN
Permanent link

Package dplyr updated to version 0.8.0 with previous version 0.7.8 dated 2018-11-10

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between dplyr versions 0.7.8 dated 2018-11-10 and 0.8.0 dated 2019-02-14

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Package R.utils updated to version 2.8.0 with previous version 2.7.0 dated 2018-08-27

Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package GMCM updated to version 1.3.1 with previous version 1.3.0 dated 2018-12-15

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>

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New package cranly with initial version 0.3
Package: cranly
Title: Package Directives and Collaboration Networks in CRAN
Version: 0.3
Authors@R: c(person(given = "Ioannis", family = "Kosmidis", role = c("aut", "cre"), email = "ioannis.kosmidis@warwick.ac.uk", comment = c(ORCID = "0000-0003-1556-0302")))
Description: Provides core visualisations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organising the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualisations from the resulting networks. The package also provides functions to coerce the networks to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.
URL: https://github.com/ikosmidis/cranly
BugReports: https://github.com/ikosmidis/cranly/issues
Depends: R (>= 3.4.0)
Imports: visNetwork, colorspace, igraph, magrittr, stringr, ggplot2, countrycode
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-14 17:13:18 UTC; yiannis
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Repository: CRAN
Date/Publication: 2019-02-14 21:42:14 UTC

More information about cranly at CRAN
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Package rquery updated to version 1.3.1 with previous version 1.3.0 dated 2019-01-29

Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package R6 updated to version 2.4.0 with previous version 2.3.0 dated 2018-10-04

Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>

Diff between R6 versions 2.3.0 dated 2018-10-04 and 2.4.0 dated 2019-02-14

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Package icr updated to version 0.5.9 with previous version 0.5.8 dated 2018-10-21

Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder reliability coefficient alpha and bootstrapped uncertainty estimates (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb] (author of the C++ RNG code)
Maintainer: Alexander Staudt <staudtlex@live.de>

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Package brglm2 updated to version 0.5.1 with previous version 0.5.0 dated 2019-02-06

Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>), Kjell Konis [ctb], Euloge Clovis Kenne Pagui [ctb], Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package GetDFPData updated to version 1.5 with previous version 1.4 dated 2019-01-12

Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>. These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package qrandom updated to version 1.1 with previous version 1.0 dated 2019-01-10

Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API. The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies. By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers. The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793> and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>. The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package vardpoor updated to version 0.14.0 with previous version 0.12.0 dated 2018-09-20

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

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Package popkin updated to version 1.1.2 with previous version 1.0.5 dated 2018-01-26

Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Author: Alejandro Ochoa [aut, cre], John D. Storey [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>

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Package EBPRS updated to version 1.1.2 with previous version 1.0.1 dated 2018-11-03

Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <shuangsong0110@163.com>

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Package mapfuser (with last version 0.1.2) was removed from CRAN

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

2017-10-10 0.1.2

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Package monotonicity updated to version 1.2 with previous version 1.1 dated 2018-05-23

Title: Test for Monotonicity in Expected Asset Returns, Sorted by Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl] (<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package workflowr updated to version 1.2.0 with previous version 1.1.1 dated 2018-07-06

Title: A Framework for Reproducible and Collaborative Data Science
Description: Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.
Author: John Blischak [aut, cre] (<https://orcid.org/0000-0003-2634-9879>), Peter Carbonetto [aut] (<https://orcid.org/0000-0003-1144-6780>), Matthew Stephens [aut] (<https://orcid.org/0000-0001-5397-9257>), Luke Zappia [ctb] (Instructions for hosting with GitLab), Pierre Formont [ctb] (Support for hosting with Shiny Server), Tim Trice [ctb] (Instructions for sharing common code)
Maintainer: John Blischak <jdblischak@uchicago.edu>

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Package spongebob updated to version 0.3.0 with previous version 0.2.0 dated 2019-01-24

Title: SpongeBob-Case Converter : spOngEboB-CASe CoNVertOR
Description: Convert character strings to Mocking SpongeBob case <https://knowyourmeme.com/memes/mocking-spongebob> and show them off in fun ways. coNvErt CharACtER strInGs to MOckiNG spOngEbOb caSE <https://knowyourmeme.com/memes/mocking-spongebob> aND shOw tHem OFf IN Fun WayS.
Author: Jay Qi [aut, cre]
Maintainer: Jay Qi <jayqi.opensource@gmail.com>

Diff between spongebob versions 0.2.0 dated 2019-01-24 and 0.3.0 dated 2019-02-14

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Package rmytarget updated to version 2.1.3 with previous version 2.1.1 dated 2019-01-03

Title: Load Data from 'MyTarget API v2'
Description: Allows work with 'MyTarget API v2' <https://target.my.com/doc/apiv2/ru/detailed.html> and load data by ads, campaigns, agency clients and statistic from your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>

Diff between rmytarget versions 2.1.1 dated 2019-01-03 and 2.1.3 dated 2019-02-14

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More information about rmytarget at CRAN
Permanent link

Package popEpi updated to version 0.4.6 with previous version 0.4.5 dated 2018-05-16

Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models, rates, mean survival times, relative survival, and standardized incidence and mortality ratios (SIRs/SMRs), all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.
Author: Joonas Miettinen [aut, cre], Matti Rantanen [aut], Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>

Diff between popEpi versions 0.4.5 dated 2018-05-16 and 0.4.6 dated 2019-02-14

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New package mRMRe with initial version 2.0.9
Package: mRMRe
Type: Package
Title: "Parallelized Minimum Redundancy, Maximum Relevance (mRMR) Ensemble Feature Selection"
Version: 2.0.9
Date: 2019-02-13
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Description: "Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique with DOI: N De Jay et al. (2013) <doi:10.1093/bioinformatics/btt383>."
License: Artistic-2.0
Depends: R (>= 2.10), survival, igraph, methods
URL: http://www.pmgenomics.ca/bhklab/
NeedsCompilation: yes
Packaged: 2019-02-14 00:45:08 UTC; gangesh
Repository: CRAN
Date/Publication: 2019-02-14 09:20:14 UTC

More information about mRMRe at CRAN
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Package graphTweets updated to version 0.5.1 with previous version 0.5.0 dated 2018-08-25

Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets, also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>

Diff between graphTweets versions 0.5.0 dated 2018-08-25 and 0.5.1 dated 2019-02-14

 DESCRIPTION  |   17 ++++++++---------
 MD5          |    6 +++---
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More information about graphTweets at CRAN
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Package BoltzMM updated to version 0.1.4 with previous version 0.1.3 dated 2019-01-10

Title: Boltzmann Machines with MM Algorithms
Description: Provides probability computation, data generation, and model estimation for fully-visible Boltzmann machines. It follows the methods described in Nguyen and Wood (2016a) <doi:10.1162/NECO_a_00813> and Nguyen and Wood (2016b) <doi:10.1109/TNNLS.2015.2425898>.
Author: Andrew Thomas Jones, Hien Duy Nguyen, and Jessica Juanita Bagnall
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>

Diff between BoltzMM versions 0.1.3 dated 2019-01-10 and 0.1.4 dated 2019-02-14

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Package ddeploy (with last version 1.0.4) was removed from CRAN

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

2015-06-28 1.0.4
2015-05-08 1.0.2

Permanent link
Package SQRL updated to version 0.6.2 with previous version 0.6.1 dated 2019-02-01

Title: Database Query Interfaces
Description: Facilitates interaction with 'ODBC' data sources.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>

Diff between SQRL versions 0.6.1 dated 2019-02-01 and 0.6.2 dated 2019-02-14

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Package AzureContainers updated to version 1.0.1 with previous version 1.0.0 dated 2018-12-25

Title: Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'
Description: An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/overview/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'kubectl' and 'helm' commandline tools are provided.
Author: Hong Ooi [aut, cre], Bill Liang [ctb] (Assistance debugging MMLS on Kubernetes), Ramkumar Chandrasekaran [ctb] (Original blog article on Dockerising MMLS), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

Diff between AzureContainers versions 1.0.0 dated 2018-12-25 and 1.0.1 dated 2019-02-14

 DESCRIPTION               |    6 +++---
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Wed, 13 Feb 2019

Package ordinalCont updated to version 2.0.1 with previous version 2.0.0 dated 2018-11-21

Title: Ordinal Regression Analysis for Continuous Scales
Description: A regression framework for response variables which are continuous self-rating scales such as the Visual Analog Scale (VAS) used in pain assessment, or the Linear Analog Self-Assessment (LASA) scales in quality of life studies. These scales measure subjects' perception of an intangible quantity, and cannot be handled as ratio variables because of their inherent non-linearity. We treat them as ordinal variables, measured on a continuous scale. A function (the g function) connects the scale with an underlying continuous latent variable. The link function is the inverse of the CDF of the assumed underlying distribution of the latent variable. A variety of link functions are currently implemented.
Author: Maurizio Manuguerra [aut, cre], Gillian Heller [aut]
Maintainer: Maurizio Manuguerra <maurizio.manuguerra@mq.edu.au>

Diff between ordinalCont versions 2.0.0 dated 2018-11-21 and 2.0.1 dated 2019-02-13

 DESCRIPTION     |    7 ++++---
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Package RAMClustR updated to version 1.0.4 with previous version 1.0.0 dated 2019-01-18

Title: Mass Spectrometry Metabolomics Feature Clustering and Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectromery <DOI: 10.1021/ac501530d> data.
Author: Corey D. Broeckling, Fayyaz Afsar, Steffan Neumann, Asa Ben-Hur, Jessica Prenni.
Maintainer: "Broeckling,Corey" <Corey.Broeckling@ColoState.EDU>

Diff between RAMClustR versions 1.0.0 dated 2019-01-18 and 1.0.4 dated 2019-02-13

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Package xROI updated to version 0.9.13 with previous version 0.9.11 dated 2018-11-12

Title: Delineate Region of Interests (ROI's) and Extract Time-Series Data from Digital Repeat Photography Images
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>

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Package SoyNAM updated to version 1.6 with previous version 1.5 dated 2018-10-01

Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB). See <doi.org/10.1534/g3.118.200332> and <doi.org/10.1534/g3.117.300300>. BLUP function formats data for genome-wide prediction and association analysis.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Rouf Mian, Reka Howard, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah McHale, Perry Cregan, Qijian Song, Miguel Lopez, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

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Package paletteer updated to version 0.2.1 with previous version 0.2.0 dated 2019-02-04

Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

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Package NAM updated to version 1.7 with previous version 1.6.5 dated 2019-02-11

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

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Package lcc updated to version 1.0.1 with previous version 1.0 dated 2018-11-16

Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre], Rafael de Andrade Moral [aut], John Hinde [aut], Silvio Sandoval Zocchi [ctb], Clarice Garcia Borges Demetrio [ctb]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@usp.br>

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Package ethnobotanyR updated to version 0.1.4 with previous version 0.1.3 dated 2019-01-21

Title: Calculate Quantitative Ethnobotany Indices
Description: Calculate common quantitative ethnobotany indices to assess the cultural significance of plant species based on informant consensus. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <doi:10.1007/s12231-007-9004-5>.
Author: Cory Whitney
Maintainer: Cory Whitney <whitney.cory@gmail.com>

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Package logmult updated to version 0.7.1 with previous version 0.7.0 dated 2018-10-19

Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart. Functions allow computing the intrinsic association coefficient (and therefore the Altham index), including via the Bayes shrinkage estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Author: Milan Bouchet-Valat [aut, cre], Heather Turner [ctb], Michael Friendly [ctb], Jim Lemon [cph], Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

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Package stringi updated to version 1.3.1 with previous version 1.2.4 dated 2018-07-20

Title: Character String Processing Facilities
Description: Fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the 'ICU' (International Components for Unicode) library, the package provides 'R' users with platform-independent functions known to 'Java', 'Perl', 'Python', 'PHP', and 'Ruby' programmers. Available features include: pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, and many more.
Author: Marek Gagolewski [aut, cre], Bartek Tartanus [ctb], and other contributors (stringi source code); IBM, Unicode, Inc., and other contributors (ICU4C source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>

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More information about stringi at CRAN
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Package igraph updated to version 1.2.4 with previous version 1.2.3 dated 2019-02-10

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between igraph versions 1.2.3 dated 2019-02-10 and 1.2.4 dated 2019-02-13

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Package bWGR updated to version 1.6 with previous version 1.5.7 dated 2019-02-05

Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, with optional kernel term and sampling techniques as described by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between bWGR versions 1.5.7 dated 2019-02-05 and 1.6 dated 2019-02-13

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Package staRdom updated to version 1.0.12 with previous version 1.0.8 dated 2018-06-21

Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre], Daniel Graeber [aut, ctb], Stefan Preiner [ctb], Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>

Diff between staRdom versions 1.0.8 dated 2018-06-21 and 1.0.12 dated 2019-02-13

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Package rehh updated to version 2.0.4 with previous version 2.0.3 dated 2019-02-04

Title: Searching for Footprints of Selection using "Extended Haplotype Homozygosity" Based Tests
Description: Population genetic data in form of "Single Nucleotide Polymorphisms" (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. The concept of an "Extended Haplotype Homozygosity" (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several derived statistics designed for whole genome scans. The package provides functions to compute three of these, namely: "iHS" (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting selection within a single population as well as "Rsb" (Tang 2007) <doi:10.1371/journal.pbio.0050171> and "XP-EHH" (Sabeti 2007) <doi:10.1038/nature06250> to detect (differential) selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@inra.fr>

Diff between rehh versions 2.0.3 dated 2019-02-04 and 2.0.4 dated 2019-02-13

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Package ISOcodes updated to version 2019.02.13 with previous version 2018.06.29 dated 2018-06-30

Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes. Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859 character codes as well as the UN M.49 area codes.
Author: Christian Buchta [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between ISOcodes versions 2018.06.29 dated 2018-06-30 and 2019.02.13 dated 2019-02-13

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More information about ISOcodes at CRAN
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Package crseEventStudy updated to version 1.1 with previous version 1.0 dated 2018-11-15

Title: A Robust and Powerful Test of Abnormal Stock Returns in Long-Horizon Event Studies
Description: Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns' cross-sectional correlation, autocorrelation, and volatility clustering without power loss.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Seppo Pynnonen [aut]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package auth0 updated to version 0.1.1 with previous version 0.1.0 dated 2018-11-02

Title: Secure Authentication in Shiny with Auth0
Description: Uses Auth0 API (see <https://auth0.com> for more information) to use a simple and secure authentication system. It provides tools to log in and out a shiny application using social networks or a list of e-mails.
Author: Julio Trecenti [cre], Daniel Falbel [aut], José Jesus [ctb]
Maintainer: Julio Trecenti <julio.trecenti@gmail.com>

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Package rbacon updated to version 2.3.7 with previous version 2.3.6 dated 2019-01-17

Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre], J. Andres Christen [aut], Judith Esquivel Vazquez [ctb], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package qsub updated to version 1.1.0 with previous version 1.0.3 dated 2018-07-30

Title: Running Commands Remotely on 'Gridengine' Clusters
Description: Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package antaresRead updated to version 2.2.3 with previous version 2.2.2 dated 2019-01-21

Title: Import, Manipulate and Explore the Results of an 'Antares' Simulation
Description: Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
Author: Jalal-Edine ZAWAM [aut], Frederic Breant [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], RTE [cph]
Maintainer: Frederic Breant <frederic.breant@rte-france.com>

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Package rosr updated to version 0.0.4 with previous version 0.0.3 dated 2019-02-12

Title: Create Reproducible Research Projects
Description: Creates reproducible academic projects with integrated academic elements, including datasets, references, codes, images, manuscripts, dissertations, slides and so on. These elements are well connected so that they can be easily synchronized and updated.
Author: Peng Zhao [aut, cre]
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package DSsim updated to version 1.1.4 with previous version 1.1.3 dated 2018-06-27

Title: Distance Sampling Simulations
Description: Performs distance sampling simulations.It repeatedly generates instances of a user defined population within a given survey region, generates realisations of a survey design (currently these must be generated using Distance software in advance <http://distancesampling.org/>) and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This will allow users to select survey designs which will give them the best accuracy and precision given their expectations about population distribution. Any uncertainty in population distribution or population parameters can be included by running the different survey designs for a number of different population descriptions. An example simulation can be found in the help file for make.simulation.
Author: Laura Marshall <lhm@st-and.ac.uk>
Maintainer: Laura Marshall <lhm@st-and.ac.uk>

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Package carbonate updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-17

Title: Interact with 'carbon.js'
Description: Create beautiful images of source code using 'carbon.js'<https://carbon.now.sh/about>.
Author: Jonathan Sidi [aut, cre] (<https://orcid.org/0000-0002-4222-1819>)
Maintainer: Jonathan Sidi <yonicd@gmail.com>

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Package ALA4R updated to version 1.6.2 with previous version 1.6.0 dated 2018-05-22

Title: Atlas of Living Australia (ALA) Data and Resources in R
Description: The Atlas of Living Australia (ALA) provides tools to enable users of biodiversity information to find, access, combine and visualise data on Australian plants and animals; these have been made available from <http://ala.org.au/>. ALA4R provides a subset of the tools to be directly used within R. It enables the R community to directly access data and resources hosted by the ALA.
Author: Peggy Newman [aut, cre], Ben Raymond [aut], Jeremy VanDerWal [aut], Lee Belbin [aut], Michael Sumner [ctb], Tom August [ctb], John Baumgartner [ctb]
Maintainer: Peggy Newman <peggy.newman@csiro.au>

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Package qgraph updated to version 1.6.1 with previous version 1.6 dated 2019-01-24

Title: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre], Giulio Costantini [aut], Jonas Haslbeck [aut], Angelique O. J. Cramer [ctb], Lourens J. Waldorp [ctb], Verena D. Schmittmann [ctb], Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package philentropy updated to version 0.3.0 with previous version 0.2.0 dated 2018-05-22

Title: Similarity and Distance Quantification Between Probability Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

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Package spdep updated to version 1.0-2 with previous version 0.8-1 dated 2018-11-21

Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I', 'APLE', 'Gearys C', 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' Index, 'Getis/Ord' G and multicoloured join count statistics, local 'Moran's I' and 'Getis/Ord' G, 'saddlepoint' approximations, exact tests for global and local 'Moran's I' and 'LOSH' local indicators of spatial heteroscedasticity; and functions for estimating spatial simultaneous 'autoregressive' ('SAR') lag, error, general nested spatial and 'SARAR' models using maximum likelihood and 'MCMC', impact measures for lag, spatial 'Durbin', 'SLX', spatial 'Durbin' error, 'SARAR' and 'GNS' models, weighted and 'unweighted' 'SAR' and 'CAR' spatial regression models, semi-parametric and Moran 'eigenvector' spatial filtering, 'GM SAR' error models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb], Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stéphane Dray [ctb], Virgilio Gómez-Rubio [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas Lewin-Koh [ctb], Angela Li [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Abhirup Mallik [ctb, trl], Giovanni Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb], Michael Tiefelsdorf [ctb], René Westerholt [ctb], Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package mri updated to version 1.0.0 with previous version 0.1.1 dated 2015-07-22

Title: Modified Rand and Wallace Indices
Description: Provides modified Rand and Wallace indices for comparing two partitions, which are usually obtained on two different sets of units with a non-empty intercept. Splitting and merging of clusters have a different affects on the value of the indices.
Author: Marjan Cugmas [aut, cre]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>

Diff between mri versions 0.1.1 dated 2015-07-22 and 1.0.0 dated 2019-02-13

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New package survivalAnalysis with initial version 0.1.1
Package: survivalAnalysis
Type: Package
Title: High-Level Interface for Survival Analysis and Associated Plots
Version: 0.1.1
Author: Marcel Wiesweg [aut, cre]
Authors@R: person("Marcel", "Wiesweg", email = "marcel.wiesweg@uk-essen.de", role = c("aut", "cre"))
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>
Description: A high-level interface to perform survival analysis, including Kaplan-Meier analysis and log-rank tests and Cox regression. Aims at providing a clear and elegant syntax, support for use in a pipeline, structured output and plotting. Builds upon the 'survminer' package for Kaplan-Meier plots and provides a customizable implementation for forest plots. Kaplan & Meier (1958) <doi:10.1080/01621459.1958.10501452> Cox (1972) <JSTOR:2985181> Peto & Peto (1972) <doi:10.2307/2344317>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: grDevices, graphics, stats, utils, survival, rlang, dplyr, forcats, magrittr, purrr, stringr, tibble, tidyr, gridExtra, ggplot2 (>= 2.2.1), scales, survminer (> 0.4.0), cowplot, tidytidbits
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, tidyverse
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-12 15:23:56 UTC; wiesweg
Repository: CRAN
Date/Publication: 2019-02-13 09:40:04 UTC

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Package isqg updated to version 1.2 with previous version 1.1 dated 2018-05-08

Title: In Silico Quantitative Genetics
Description: Accomplish high performance simulations in quantitative genetics. The molecular genetic components are represented by R6/C++ classes and methods. Mimic the meiosis recombination and de novo genetic variability by means a count-location process (Karlin & Liberman, 1978) <doi:10.1073/pnas.75.12.6332>. The core computational algorithm is implemented using 'Boost' dynamic bitsets (Schaling, 2014) [ISBN:978-1937434366]. A mix between low and high level interfaces provides great flexibility and allows user defined extensions and a wide range of applications.
Author: Fernando H. Toledo [aut, cre], International Maize and Wheat Improvement Center [cph]
Maintainer: Fernando H. Toledo <f.toledo@cgiar.org>

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Package wru updated to version 0.1-8 with previous version 0.1-7 dated 2017-09-01

Title: Who are You? Bayesian Prediction of Racial Category Using Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation, and other attributes, such as gender and age. The method utilizes the Bayes' Rule to compute the posterior probability of each racial category for any given individual. The package implements methods described in Imai and Khanna (2015) "Improving Ecological Inference by Predicting Individual Ethnicity from Voter Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut]
Maintainer: Kabir Khanna <kabirkhanna@gmail.com>

Diff between wru versions 0.1-7 dated 2017-09-01 and 0.1-8 dated 2019-02-13

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Package qs updated to version 0.13.1 with previous version 0.12 dated 2019-02-08

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk. This package makes use of the 'zstd' library for compression and decompression. 'zstd' is created by Yann Collet and owned by Facebook, Inc.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures)
Maintainer: Travers Ching <traversc@gmail.com>

Diff between qs versions 0.12 dated 2019-02-08 and 0.13.1 dated 2019-02-13

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Package HierDpart updated to version 0.3.5 with previous version 0.2.0 dated 2019-01-31

Title: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems
Description: Miscellaneous R functions for calculating and decomposing hierarchical diversity metrics, including hierarchical allele richness (q=0), hierarchical exponential Shannon entropy (q=1), hierarchical heterozygosity (q=2) and genetic differentiation (Fst and Delta D). This package allows you to analyse spatial structured genetic data or species data under a unifying framework (Gaggiotti, O. E. et al, 2018, Evol Appl, 11:1176-1193; <DOI:10.1111/eva.12593>), which partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. It produces diversity profiles (q=0,1,2), hierarchical diversities and differentiation, as well as the the correlation between geographic distance and genetic differentiation.
Author: Xinghu Qin
Maintainer: Xinghu Qin <qinxinghu@gmail.com>

Diff between HierDpart versions 0.2.0 dated 2019-01-31 and 0.3.5 dated 2019-02-13

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Package CDECRetrieve (with last version 0.1.2) was removed from CRAN

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

2018-09-10 0.1.2
2018-05-15 0.1.1
2018-03-01 0.1.0

Permanent link
Package cati (with last version 0.99.2) was removed from CRAN

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

2018-05-09 0.99.2
2016-03-15 0.99.1
2015-05-29 0.99
2015-02-13 0.96
2014-06-24 0.8

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Package staplr updated to version 2.9.0 with previous version 2.2.0 dated 2018-05-08

Title: A Toolkit for PDF Files
Description: Provides function to manipulate PDF files: fill out PDF forms; merge multiple PDF files into one; remove selected pages from a file; rename multiple files in a directory; rotate entire pdf document; rotate selected pages of a pdf file; Select pages from a file; splits single input PDF document into individual pages; splits single input PDF document into parts from given points.
Author: Priyanga Dilini Talagala [aut, cre], Ogan Mancarci [aut], Daniel Padfield [aut], Granville Matheson [aut]
Maintainer: Priyanga Dilini Talagala <dilini.talagala@monash.edu>

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Package rlmDataDriven updated to version 0.2.0 with previous version 0.1.0 dated 2018-09-17

Title: Robust Regression with Data Driven Tuning Parameter
Description: Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.
Author: You-Gan Wang
Maintainer: The package maintainer <you-gan.wang@qut.edu.au>

Diff between rlmDataDriven versions 0.1.0 dated 2018-09-17 and 0.2.0 dated 2019-02-13

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