Thu, 24 Jan 2019

Package ranger updated to version 0.11.1 with previous version 0.11.0 dated 2019-01-21

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix') can be directly analyzed.
Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>

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Package mlVAR updated to version 0.4.2 with previous version 0.4.1 dated 2018-08-26

Title: Multi-Level Vector Autoregression
Description: Estimates the multi-level vector autoregression model on time-series data. Three network structures are obtained: temporal networks, contemporaneous networks and between-subjects networks.
Author: Sacha Epskamp, Marie K. Deserno and Laura F. Bringmann
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package lulcc updated to version 1.0.3 with previous version 1.0.2 dated 2017-03-27

Title: Land Use Change Modelling in R
Description: Classes and methods for spatially explicit land use change modelling in R.
Author: Simon Moulds <sim.moulds@gmail.com>
Maintainer: Simon Moulds <sim.moulds@gmail.com>

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Package eurostat updated to version 3.3.1.2 with previous version 3.3.1.1 dated 2019-01-23

Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database <http://ec.europa.eu/eurostat> together with search and manipulation utilities.
Author: Leo Lahti [aut, cre], Janne Huovari [aut], Markus Kainu [aut], Przemyslaw Biecek [aut], Joona Lehtomaki [ctb], Francois Briatte [ctb], Oliver Reiter [ctb]
Maintainer: ORPHANED

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Package bootnet updated to version 1.2 with previous version 1.1.0 dated 2018-07-27

Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures and centrality indices. Allows for flexible specification of any undirected network estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler', 'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp [aut, cre], Eiko I. Fried [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package qgam updated to version 1.2.3 with previous version 1.2.2 dated 2018-05-28

Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2017) <arXiv:1707.03307>. Differently from 'quantreg', the smoothing parameters are estimated automatically by marginal loss minimization, while the regression coefficients are estimated using either PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian credible intervals of the estimated effects have approximately the correct coverage. The main function is qgam() which is similar to gam() in 'mgcv', but fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre], Simon N. Wood [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

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Package ordinalForest updated to version 2.3 with previous version 2.2 dated 2018-07-16

Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal Target Variables
Description: The ordinal forest (OF) method allows ordinal regression with high-dimensional and low-dimensional data. After having constructed an OF prediction rule using a training dataset, it can be used to predict the values of the ordinal target variable for new observations. Moreover, by means of the (permutation-based) variable importance measure of OF, it is also possible to rank the covariates with respect to their importances in the prediction of the values of the ordinal target variable. OF is presented in Hornung (2019). The main functions of the package are: ordfor() (construction of OF) and predict.ordfor() (prediction of the target variable values of new observations). References: Hornung R. (2019) Ordinal Forests. Journal of Classification, <doi:10.1007/s00357-018-9302-x>.
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>

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Package DriftBurstHypothesis updated to version 0.1.1 with previous version 0.1 dated 2019-01-02

Title: Calculates the Test-Statistic for the Drift Burst Hypothesis
Description: Calculates the T-Statistic for the drift burst hypothesis from the working paper Christensen, Oomen and Reno (2018) <DOI:10.2139/ssrn.2842535>. The authors' MATLAB code is available upon request, see: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2842535>.
Author: Emil Sjoerup
Maintainer: Emil Sjoerup <emilsjoerup@live.dk>

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Package cdcfluview updated to version 0.9.0 with previous version 0.7.0 dated 2017-11-14

Title: Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal
Description: The 'U.S.' Centers for Disease Control and Prevention (CDC) maintain a portal <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing state, regional and national influenza statistics as well as mortality surveillance data. The web interface makes it difficult and time-consuming to select and retrieve influenza data. Tools are provided to access the data provided by the portal's underlying 'API'.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Craig McGowan [ctb] (<https://orcid.org/0000-0002-6298-0185>), JJ Chen [ctb] (<https://orcid.org/0000-0001-8482-8398>), Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>), James Turtle [ctb] (<https://orcid.org/0000-0003-0735-7769>)
Maintainer: Bob Rudis <bob@rud.is>

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Package RNeXML updated to version 2.3.0 with previous version 2.2.0 dated 2018-11-01

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>), Kseniia Shumelchyk [aut], Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package iNEXT updated to version 2.0.19 with previous version 2.0.18 dated 2018-12-15

Title: Interpolation and Extrapolation for Species Diversity
Description: Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation of species diversity (Hill numbers) for individual-based (abundance) data or sampling-unit- based (incidence) data.
Author: T. C. Hsieh, K. H. Ma and Anne Chao
Maintainer: T. C. Hsieh <euler96@gmail.com>

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Package BNSL updated to version 0.1.4 with previous version 0.1.3 dated 2017-09-18

Title: Bayesian Network Structure Learning
Description: From a given data frame, this package learns its Bayesian network structure based on a selected score.
Author: Joe Suzuki and Jun Kawahara
Maintainer: Joe Suzuki <j-suzuki@sigmath.es.osaka-u.ac.jp>

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Package boostSeq (with last version 1.0) was removed from CRAN

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

2012-08-11 1.0

Permanent link
Package Sleuth2 updated to version 2.0-5 with previous version 2.0-4.1 dated 2019-01-23

Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Author: Original by F.L. Ramsey and D.W. Schafer; modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach; vignettes contributed by Nicholas Horton, Kate Aloisio and Ruobing Zhang, with corrections by Randall Pruim
Maintainer: Berwin A Turlach <Berwin.Turlach@gmail.com>

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Package ROI.plugin.deoptim updated to version 0.3-2 with previous version 0.3-0 dated 2017-10-23

Title: 'DEoptim' and 'DEoptimR' Plugin for the 'R' Optimization Interface
Description: Enhances the R Optimization Infrastructure ('ROI') package with the 'DEoptim' and 'DEoptimR' package. 'DEoptim' is used for unconstrained optimization and 'DEoptimR' for constrained optimization.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>

Diff between ROI.plugin.deoptim versions 0.3-0 dated 2017-10-23 and 0.3-2 dated 2019-01-24

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Package lorentz updated to version 1.0-1 with previous version 1.0-0 dated 2018-10-08

Title: The Lorentz Transform in Relativistic Physics
Description: This package furnishes functionality to work with Lorentz transforms in special relativity. It also implements the gyrogroup structure of three-velocities following Ungar (2006) <doi:10.1088/0143-0807/27/3/L02>. For general relativity, see the 'schwarzschild' package.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package cIRT updated to version 1.3.0 with previous version 1.2.1 dated 2017-04-26

Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steven Andrew Culpepper [aut, cph] (<https://orcid.org/0000-0003-4226-6176>), James Joseph Balamuta [aut, cph, cre] (<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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2018-03-15 0.1.1
2018-02-27 0.1.0
2017-12-01 0.0.1

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2017-10-29 1.0.0

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Package TR8 (with last version 0.9.19) was removed from CRAN

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2018-12-01 0.9.19
2017-09-14 0.9.18
2017-03-16 0.9.16
2016-12-14 0.9.15
2016-03-31 0.9.14
2015-03-22 0.9.13
2015-03-04 0.9.12

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Package mcglm (with last version 0.4.0) was removed from CRAN

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2018-04-10 0.4.0
2016-06-13 0.3.0

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Package glycanr (with last version 0.3.1) was removed from CRAN

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2018-07-30 0.3.1

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Package NetLogoR (with last version 0.3.4) was removed from CRAN

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2018-10-07 0.3.4
2018-06-07 0.3.3
2018-02-12 0.3.2
2018-02-05 0.3.1

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2018-07-05 0.2.1

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2018-11-20 2.7.6
2018-11-09 2.7.4
2018-06-25 2.6.5
2018-06-10 2.6.4
2017-10-18 2.5.0
2017-05-17 2.4.0
2017-04-06 2.3.1
2017-03-07 2.3.0
2017-01-23 2.2.0
2017-01-07 2.1.1
2016-12-22 2.1.0
2016-11-19 2.0.0
2016-06-15 1.1.6
2016-02-25 1.1.5.2
2016-02-17 1.1.5.1
2015-12-16 1.1.5
2015-10-12 1.1.3
2015-08-10 1.1.1

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

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2018-11-19 0.1.0

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2018-03-05 1.2.0
2017-08-28 1.1.3
2017-01-23 1.1.1
2016-11-22 1.1.0
2016-08-16 1.0.5
2016-04-05 1.0.4
2016-03-07 1.0.3
2016-02-06 1.0.2
2016-01-24 1.0.1
2015-12-27 1.0.0

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Package sdpt3r (with last version 0.2) was removed from CRAN

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2018-10-16 0.1.0

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2018-12-18 0.6.0

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2018-12-03 1.1.7.4
2018-09-13 1.1.7.1
2018-08-24 1.1.6
2018-03-21 1.1.1
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2018-10-23 0.2.1
2018-06-17 0.2.0
2018-01-12 0.1.1
2018-01-08 0.1.0

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Package MScombine updated to version 1.3 with previous version 1.2 dated 2018-12-20

Title: Combine Data from Positive and Negative Ionization Mode Finding Common Entities
Description: Find common entities detected in both positive and negative ionization mode, delete this entity in the less sensible mode and combine both matrices.
Author: Monica Calderon-Santiago
Maintainer: Monica Calderon-Santiago <b42casam@uco.es>

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Package rabi updated to version 1.0.0 with previous version 0.1.0 dated 2017-10-18

Title: Generate Codes to Uniquely and Robustly Identify Individuals for Animal Behavior Studies
Description: Facilitates the design and generation of optimal color (or symbol) codes that can be used to mark and identify individual animals. These codes are made such that the IDs are robust to partial erasure: even if sections of the code are lost, the entire identity of the animal can be reconstructed. Thus, animal subjects are not confused and no ambiguity is introduced.
Author: Andrew Taylor Burchill [aut, cre], Theodore P. Pavlic [ctb]
Maintainer: Andrew Taylor Burchill <andrew.burchill@asu.edu>

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Package STMotif (with last version 1.0.1) was removed from CRAN

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2018-11-09 1.0.1
2018-10-22 1.0.0
2018-08-24 0.1.1
2018-08-07 0.1.0

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Package spongebob updated to version 0.2.0 with previous version 0.1 dated 2019-01-12

Title: Spongebob-Case Converter : spOngEboB-CASe CoNVertOR
Description: Convert character strings to Spongebob case. CoNVErt ChaRaCTer StRINgs TO spONGebOB caSE.
Author: Jay Qi [aut, cre]
Maintainer: Jay Qi <jayqi.opensource@gmail.com>

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Package spc4sts updated to version 0.4.0 with previous version 0.3.1 dated 2018-04-09

Title: Statistical Process Control for Stochastic Textured Surfaces
Description: Provides statistical process control tools for stochastic textured surfaces. The current version supports the following tools: (1) generic modeling of stochastic textured surfaces. (2) local defect monitoring and diagnostics in stochastic textured surfaces, which was proposed by Bui and Apley (2018a) <doi:10.1080/00401706.2017.1302362>. (3) global change monitoring in the nature of stochastic textured surfaces, which was proposed by Bui and Apley (2018b) <doi:10.1080/00224065.2018.1507559>. (4) computation of dissimilarity matrix of stochastic textured surface images.
Author: Anh Bui [aut, cre] and Daniel Apley [ths]
Maintainer: Anh Bui <atbui@u.northwestern.edu>

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Package mdsstat updated to version 0.2.2 with previous version 0.2.1 dated 2018-12-11

Title: Statistical Trending for Medical Devices Surveillance
Description: A collection of common statistical algorithms used in active surveillance of medical device events. Context includes post-market surveillance, pharmacovigilance, signal detection and trending, and regulatory reporting. Primary inputs are device-event time series. Outputs include trending results with the ability to run multiple algorithms at once. This package works well with the 'mds' package, but does not require it.
Author: Gary Chung [aut, cre], Stephane Bottine [ctb] ((derived code from 'SPRT' package)), Ismaïl Ahmed [ctb] ((derived code from 'PhViD' package)), John Ihrie [ctb] ((derived code from 'openEBGM' package))
Maintainer: Gary Chung <gchung05@gmail.com>

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Wed, 23 Jan 2019

New package ZVCV with initial version 1.0.0
Package: ZVCV
Type: Package
Title: Zero-Variance Control Variates
Version: 1.0.0
Date: 2018-12-20
Authors@R: c(person("Leah F.","South",role=c("aut","cre"),email="leah.south@hdr.qut.edu.au",comment = c(ORCID = "0000-0002-5646-2963")))
Description: Zero-variance control variates (ZV-CV, Mira et al. (2013) <doi:10.1007/s11222-012-9344-6>) is a post-processing method to reduce the variance of Monte Carlo estimators of expectations using the derivatives of the log target. Once the derivatives are available, the only additional computational effort is in solving a linear regression problem. Recently, this method has been extended to higher dimensions using regularisation (South et al., 2018 <arXiv:1811.05073>). This package can be used to easily perform ZV-CV or regularised ZV-CV when a set of samples, derivatives and function evaluations are available. Additional functions for applying ZV-CV to two estimators for the normalising constant of the posterior distribution in Bayesian statistics are also supplied.
License: GPL (>= 2)
LazyLoad: yes
Imports: Rcpp (>= 0.11.0), glmnet, abind, mvtnorm, partitions, stats
LinkingTo: Rcpp, RcppArmadillo
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-01-16 02:03:43 UTC; n8001626
Author: Leah F. South [aut, cre] (<https://orcid.org/0000-0002-5646-2963>)
Maintainer: Leah F. South <leah.south@hdr.qut.edu.au>
Repository: CRAN
Date/Publication: 2019-01-24 00:00:02 UTC

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Package rym updated to version 0.5.2 with previous version 0.5.1 dated 2019-01-17

Title: R Interface to Yandex Metrica API
Description: Allows work with 'Management API' for load counters, segments, filters, user permissions and goals list from Yandex Metrica, 'Reporting API' allows you to get information about the statistics of site visits and other data without using the web interface, 'Logs API' allows to receive non-aggregated data and 'Compatible with Google Analytics Core Reporting API v3' allows receive information about site traffic and other data using field names from Google Analytics Core API. For more information see official documents <https://tech.yandex.ru/metrika/doc/api2/concept/about-docpage/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package ROI updated to version 0.3-2 with previous version 0.3-1 dated 2018-01-26

Title: R Optimization Infrastructure
Description: The R Optimization Infrastructure ('ROI') is a sophisticated framework for handling optimization problems in R. More information can be found on the 'ROI' homepage <http://roi.r-forge.r-project.org/>.
Author: Kurt Hornik [aut], David Meyer [aut], Florian Schwendinger [aut], Stefan Theussl [aut, cre], Diethelm Wuertz [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>

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New package portalr with initial version 0.2.1
Package: portalr
Title: Create Useful Summaries of the Portal Data
Version: 0.2.1
Authors@R: c(person(c("Glenda", "M."), "Yenni", role = c("aut", "cre"), email = "glenda@weecology.org", comment = c(ORCID = "0000-0001-6969-1848")), person("Hao", "Ye", role = c("aut"), comment = c(ORCID = "0000-0002-8630-1458")), person(c("Erica", "M."), "Christensen", role = c("aut"), comment = c(ORCID = "0000-0002-5635-2502")), person(c("Juniper", "L."), "Simonis", role = c("aut"), comment = c(ORCID = "0000-0001-9798-0460")), person(c("Ellen", "K."), "Bledsoe", role = c("aut"), comment = c(ORCID = "0000-0002-3629-7235")), person(c("Renata", "M."), "Diaz", role = c("aut"), comment = c(ORCID = "0000-0003-0803-4734")), person(c("Shawn", "D."), "Taylor", role = c("aut"), comment = c(ORCID = "0000-0002-6178-6903")), person(c("Ethan", "P,"), "White", role = c("aut"), comment = c(ORCID = "0000-0001-6728-7745")), person(c("S.K.", "Morgan"), "Ernest", role = c("aut"), comment = c(ORCID = "0000-0002-6026-8530")))
Description: Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahua desert. The raw data files can be found at <https://github.com/weecology/portaldata>.
License: MIT + file LICENSE
URL: https://weecology.github.io/portalr/, https://github.com/weecology/portalr
BugReports: https://github.com/weecology/portalr/issues
LazyData: true
Depends: R (>= 3.2.3)
Imports: dplyr, ggplot2, tidyr, zoo, lubridate, magrittr, httr, rlang, forecast, lunar, jsonlite, tibble
Suggests: httptest, digest, tidyverse, cowplot, knitr, rmarkdown, pkgdown, covr
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-01-23 19:54:53 UTC; GlendaYenni
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>), Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>), Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>), Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>), Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>), Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>), Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>), Ethan P, White [aut] (<https://orcid.org/0000-0001-6728-7745>), S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>)
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Repository: CRAN
Date/Publication: 2019-01-23 22:50:35 UTC

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Package kutils updated to version 1.60 with previous version 1.45 dated 2018-05-19

Title: Project Management Tools
Description: Tools for data importation, recoding, and inspection that are used at the University of Kansas Center for Research Methods and Data Analysis. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding. We are eager to have community feedback about the variable key and the vignette about it.
Author: Paul Johnson [aut, cre], Benjamin Kite [aut], Charles Redmon [aut], Jared Harpole [ctb], Kenna Whitley [ctb], Po-Yi Chen [ctb], Shadi Pirhosseinloo [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>

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New package blscrapeR with initial version 3.1.5
Package: blscrapeR
Type: Package
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Version: 3.1.5
Authors@R: person("Kris", "Eberwein", email = "eberwein@knights.ucf.edu", role = c("aut", "cre"))
Description: Scrapes various data from <https://www.bls.gov/>. The U.S. Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Depends: R (>= 3.3.0)
Imports: httr, jsonlite, ggplot2, magrittr, utils, stats, grDevices, dplyr, purrr, tibble, stringr
Suggests: testthat, knitr, rmarkdown
License: MIT + file LICENSE
URL: https://github.com/keberwein/blscrapeR
BugReports: https://github.com/keberwein/blscrapeR/issues
LazyData: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-01-23 20:20:57 UTC; mediacenter
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Repository: CRAN
Date/Publication: 2019-01-23 22:50:59 UTC

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Package asbio updated to version 1.5-5 with previous version 1.5-4 dated 2019-01-09

Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>

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Package taxotools updated to version 0.0.5 with previous version 0.0.4 dated 2018-09-28

Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>

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Package rtext updated to version 0.1.21 with previous version 0.1.20 dated 2016-11-01

Title: R6 Objects for Text and Data
Description: For natural language processing and analysis of qualitative text coding structures which provide a way to bind together text and text data are fundamental. The package provides such a structure and accompanying methods in form of R6 objects. The 'rtext' class allows for text handling and text coding (character or regex based) including data updates on text transformations as well as aggregation on various levels. Furthermore, the usage of R6 enables inheritance and passing by reference which should enable 'rtext' instances to be used as back-end for R based graphical text editors or text coding GUIs.
Author: Peter Meissner [aut, cre], Ulrich Sieberer [cph], University of Konstanz [cph]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

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Package episheet updated to version 0.4.0 with previous version 0.3.0 dated 2018-10-22

Title: Rothman's Episheet
Description: A collection of R functions supporting the text book Modern Epidemiology, Second Edition, by Kenneth J.Rothman and Sander Greenland. ISBN 13: 978-0781755641 See <http://www.krothman.org/> for more information.
Author: James Black [aut, cre], Ken Rothman [cph], Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>)
Maintainer: James Black <james@epijim.uk>

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Package freqweights (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:

2017-05-12 1.0.4
2017-04-18 1.0.3
2015-06-22 1.0.2
2014-10-09 1.0.1
2014-09-01 0.1.1
2014-05-21 0.1.0
2014-04-13 0.0.1

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Package simglm updated to version 0.7.2 with previous version 0.7.1 dated 2018-07-25

Title: Simulate Models Based on the Generalized Linear Model
Description: Easily simulates regression models, including both simple regression and generalized linear mixed models with up to three level of nesting. Power simulations that are flexible allowing the specification of missing data, unbalanced designs, and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>

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Package prc updated to version 2019.1-23 with previous version 2018.8-17 dated 2018-08-17

Title: Paired Response Curve
Description: Estimation, prediction and testing for analyzing serial dilution assay data (Fong and Yu 2015 <DOI:10.1080/19466315.2015.1093019>) using paired response curve, which is a model of the nonlinear functional relationship between experimental outcomes measured at two different dilutions.
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>

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Package ggmcmc updated to version 1.1.1 with previous version 1.1 dated 2016-06-28

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: ORPHANED

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Package mrgsolve updated to version 0.9.0 with previous version 0.8.12 dated 2018-04-27

Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>), Alan C Hindmarsh [ctb], Linda R Petzold [ctb], Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>

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More information about mrgsolve at CRAN
Permanent link

Package landscapemetrics updated to version 0.3.1 with previous version 0.3 dated 2018-12-07

Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>), Laura J. Graham [ctb] (Input on package structure), Jeffrey Hollister [ctb] (Input on package structure), Kimberly A. With [ctb] (Input on package structure), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function), Jeremy VanDerWal [ctb] (Original author of underlying C code for get_patches() function), Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>

Diff between landscapemetrics versions 0.3 dated 2018-12-07 and 0.3.1 dated 2019-01-23

 DESCRIPTION                                       |    6 
 MD5                                               |  646 +--
 NEWS.md                                           |  107 
 R/calculate_lsm.R                                 |  775 ++--
 R/check_landscape.R                               |  310 -
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 R/get_nearestneighbour.R                          |  150 
 R/get_patches.R                                   |  582 +--
 R/get_unique_values.R                             |  434 +-
 R/landscapemetrics-package.R                      |  103 
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 R/lsm_c_ai.R                                      |  294 -
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 R/lsm_c_split.R                                   |  270 -
 R/lsm_c_tca.R                                     |  284 -
 R/lsm_c_te.R                                      |  438 +-
 R/lsm_l_ai.R                                      |  260 -
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 R/lsm_l_condent.R                                 |  312 -
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More information about landscapemetrics at CRAN
Permanent link

Package mgcViz updated to version 0.1.3 with previous version 0.1.1 dated 2018-06-30

Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre], Raphael Nedellec [aut], Yannig Goude [ctb], Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

Diff between mgcViz versions 0.1.1 dated 2018-06-30 and 0.1.3 dated 2019-01-23

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Package Rmosek updated to version 1.3.1 with previous version 1.3.0 dated 2019-01-18

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 MachineShop updated to version 1.1.0 with previous version 1.0.0 dated 2019-01-02

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 fitdistrplus updated to version 1.0-14 with previous version 1.0-11 dated 2018-09-10

Title: Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available. See e.g. Casella & Berger (2002). Statistical inference. Pacific Grove.
Author: Marie-Laure Delignette-Muller [aut], Christophe Dutang [aut], Regis Pouillot [ctb], Jean-Baptiste Denis [ctb], Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Package phylosignal updated to version 1.2.1 with previous version 1.2 dated 2018-01-10

Title: Exploring the Phylogenetic Signal in Continuous Traits
Description: A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
Author: Francois Keck <francois.keck@gmail.com>
Maintainer: ORPHANED

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Package eurostat updated to version 3.3.1.1 with previous version 3.3.1 dated 2018-11-24

Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database <http://ec.europa.eu/eurostat> together with search and manipulation utilities.
Author: Leo Lahti [aut, cre], Janne Huovari [aut], Markus Kainu [aut], Przemyslaw Biecek [aut], Joona Lehtomaki [ctb], Francois Briatte [ctb], Oliver Reiter [ctb]
Maintainer: ORPHANED

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Package surveydata updated to version 0.2.3 with previous version 0.2.2 dated 2018-12-06

Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the survey responses, but also the survey metadata, e.g. the original survey questions and the answer options. The 'surveydata' package makes it easy to keep track of this metadata, and to easily extract columns with specific questions.
Author: Andrie de Vries [aut, cre, cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>

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Package colorednoise updated to version 1.0.4 with previous version 1.0.3 dated 2018-06-01

Title: Simulate Temporally Autocorrelated Populations
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one. This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.
Author: Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>)
Maintainer: Julia Pilowsky <jap2178@caa.columbia.edu>

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Package Sleuth3 updated to version 1.0-2.1 with previous version 1.0-2 dated 2016-06-15

Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer; modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach; vignettes contributed by Nicholas Horton, Linda Loi, Kate Aloisio and Ruobing Zhang, with corrections by Randall Pruim
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Package Sleuth2 updated to version 2.0-4.1 with previous version 2.0-4 dated 2016-06-15

Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Author: Original by F.L. Ramsey and D.W. Schafer; modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach; vignettes contributed by Nicholas Horton, Kate Aloisio and Ruobing Zhang, with corrections by Randall Pruim
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Package missMDA updated to version 1.14 with previous version 1.13 dated 2018-06-25

Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA or MCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>

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Package imager updated to version 0.41.2 with previous version 0.41.1 dated 2018-05-30

Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Author: Simon Barthelme [aut, cre], David Tschumperle [ctb], Jan Wijffels [ctb], Haz Edine Assemlal [ctb]
Maintainer: ORPHANED

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Package getTBinR updated to version 0.5.7 with previous version 0.5.6 dated 2018-11-15

Title: Get WHO Tuberculosis Data
Description: Facilitates easy import of analysis ready World Health Organisation Tuberculosis data and provides plotting functions for exploratory data analysis.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>)
Maintainer: Sam Abbott <contact@samabbott.co.uk>

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Package spmoran updated to version 0.1.6.1 with previous version 0.1.6 dated 2018-10-06

Title: Moran's Eigenvector-Based Spatial Regression Models
Description: Functions for estimating Moran's eigenvector-based spatial regression models. For details see Murakami (2018) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>

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Package logging updated to version 0.9-106 with previous version 0.9-105 dated 2019-01-16

Title: R Logging Package
Description: Pure R implementation of the ubiquitous log4j package. It offers hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.
Author: Mario Frasca [aut], Walerian Sokolowski [cre]
Maintainer: Walerian Sokolowski <r-logging@wlogsolutions.com>

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Package BHSBVAR updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-19

Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for running Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>

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New package woeR with initial version 0.2.1
Package: woeR
Title: Weight of Evidence Based Segmentation of a Variable
Version: 0.2.1
Author: Kashish Soien
Maintainer: Kashish Soien <kashish.soien19@gmail.com>
Description: Segment a numeric variable based on a dichotomous dependent variable by using the weight of evidence (WOE) approach (Ref: Siddiqi, N. (2006) <doi:10.1002/9781119201731.biblio>). The underlying algorithm adopts a recursive approach to create segments that are diverse in respect of their WOE values and meet the demands of user-defined parameters. The algorithm also aims to maintain a monotonic trend in WOE values of consecutive segments. As such, it can be particularly helpful in improving robustness of linear and logistic regression models.
Imports: dplyr
Suggests: smbinning
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
BugReports: https://github.com/kraken19/woeR/issues
NeedsCompilation: no
Packaged: 2019-01-23 00:15:53 UTC; kashish
Repository: CRAN
Date/Publication: 2019-01-23 08:30:04 UTC

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Package tram updated to version 0.2-4 with previous version 0.2-3 dated 2018-09-18

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package homomorpheR updated to version 0.2-2 with previous version 0.2-1 dated 2017-04-28

Title: Homomorphic Computations in R
Description: Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.
Author: Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>

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Package ggmap updated to version 2.6.2 with previous version 2.6.1 dated 2016-01-22

Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.
Author: David Kahle [aut, cre], Hadley Wickham [aut]
Maintainer: ORPHANED

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Package BART updated to version 2.2 with previous version 2.1 dated 2018-11-30

Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut], Rodney Sparapani [aut, cre], Robert Gramacy [aut], Charles Spanbauer [aut], Matthew Pratola [aut]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>

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Package natserv updated to version 0.3.0 with previous version 0.1.4 dated 2017-01-03

Title: 'NatureServe' Interface
Description: Interface to 'NatureServe' (<http://www.natureserve.org>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package g3viz updated to version 0.1.4 with previous version 0.1.3 dated 2018-08-30

Title: Visualize Genomic Mutation Data Using an Interactive Lollipop Diagram
Description: R interface for 'g3viz' JavaScript library. Using an interactive lollipop diagram to visualize genomic mutation data in a web browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <phoeguo@gmail.com>

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Package face updated to version 0.1-5 with previous version 0.1-4 dated 2018-01-19

Title: Fast Covariance Estimation for Sparse Functional Data
Description: We implement the Fast Covariance Estimation for Sparse Functional Data paper published in Statistics and Computing <doi: 10.1007/s11222-017-9744-8>.
Author: Luo Xiao [aut,cre], Cai Li [aut], William Checkley [aut], Ciprian Crainiceanu [aut]
Maintainer: Luo Xiao <lxiao5@ncsu.edu>

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Package easyPubMed updated to version 2.11 with previous version 2.5 dated 2018-05-06

Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>

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Package carfima updated to version 2.0.1 with previous version 2.0.0 dated 2018-11-01

Title: Continuous-Time Fractionally Integrated ARMA Process for Irregularly Spaced Long-Memory Time Series Data
Description: We provide a toolbox to fit a continuous-time fractionally integrated ARMA process (CARFIMA) on univariate and irregularly spaced time series data via frequentist or Bayesian machinery. A general-order CARFIMA(p, H, q) model for p>q is specified in Tsai and Chan (2005) <doi:10.1111/j.1467-9868.2005.00522.x> and it involves (p+q+2) unknown model parameters, i.e., p AR parameters, q MA parameters, Hurst parameter H, and process uncertainty (standard deviation) sigma. The package produces their maximum likelihood estimates and asymptotic uncertainties using a global optimizer called the differential evolution algorithm. It also produces their posterior distributions via Metropolis within a Gibbs sampler equipped with adaptive Markov chain Monte Carlo for posterior sampling. These fitting procedures, however, may produce numerical errors if p>2. The toolbox also contains a function to simulate discrete time series data from CARFIMA(p, H, q) process given the model parameters and observation times.
Author: Hyungsuk Tak [aut] (<https://orcid.org/0000-0003-0334-8742>), Henghsiu Tsai [aut], Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>

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Package placement (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:

2016-07-27 0.1.1

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Package census (with last version 0.2.0) was removed from CRAN

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

2017-10-26 0.2.0
2017-10-23 0.1.0

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Package glmmBUGS (with last version 2.4.2) was removed from CRAN

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

2018-05-01 2.4.2
2016-09-21 2.4.0
2014-01-02 2.3
2012-01-13 2.0
2010-11-08 1.9
2010-10-19 1.8
2010-10-04 1.7
2009-10-18 1.6.4
2009-04-26 1.6
2009-01-13 1.5
2009-01-12 1.4
2008-11-25 1.2
2008-11-21 1.1
2008-09-09 1.0

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Package repijson (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:

2015-06-15 0.1.0

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Tue, 22 Jan 2019

Package NlinTS updated to version 1.3.7 with previous version 1.3.6 dated 2019-01-15

Title: Non Linear Time Series Analysis
Description: Models for non-linear time series analysis and causality detection. The main functionalities of this package consist of an implementation of the classical causality test (C.W.J.Granger 1980) <doi:10.1016/0165-1889(80)90069-X>, and a non-linear version of it based on feed-forward neural networks. This package contains also an implementation of the Transfer Entropy <doi:10.1103/PhysRevLett.85.461>, and the continuous Transfer Entropy using an approximation based on the k-nearest neighbors <doi:10.1103/PhysRevE.69.066138>. There are also some other useful tools, like the VARNN (Vector Auto-Regressive Neural Network) prediction model, the Augmented test of stationarity, and the discrete and continuous entropy and mutual information.
Author: Youssef Hmamouche [aut, cre], Sylvain Barthelemy [cph]
Maintainer: Youssef Hmamouche <hmamoucheyussef@gmail.com>

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Package emmeans updated to version 1.3.2 with previous version 1.3.1 dated 2018-12-13

Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and compact letter displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph], Henrik Singmann [ctb], Jonathon Love [ctb], Paul Buerkner [ctb], Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

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Package Rmpfr updated to version 0.7-2 with previous version 0.7-1 dated 2018-07-30

Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package pssmooth updated to version 1.0.2 with previous version 1.0.1 dated 2018-09-19

Title: Flexible and Efficient Evaluation of Principal Surrogates/Treatment Effect Modifiers
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB (2018), Inference on treatment effect modification by biomarker response in a three-phase sampling design, Biostatistics, kxy074 <doi:10.1093/biostatistics/kxy074>. The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response (see the flexible three-phase sampling design in the paper for details). Bootstrap-based procedures are available for pointwise and simultaneous confidence intervals and testing of four relevant hypotheses. Summary and plotting functions are provided for estimation results.
Author: Michal Juraska [aut, cre]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>

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Package nlaR updated to version 0.4.0 with previous version 0.3 dated 2018-07-13

Title: Interface to the National Lakes Assessment
Description: Client for programmatic access to the 2007 and 2012 National Lakes Assessment database <https://www.epa.gov/national-aquatic-resource-surveys/nla> containing data for hundreds of lakes in the lower 48 states of the contiguous US.
Author: Joseph Stachelek [aut, cre]
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package LAGOSNE updated to version 1.2.0 with previous version 1.1.0 dated 2017-12-12

Title: Interface to the Lake Multi-Scaled Geospatial and Temporal Database
Description: Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>), Samantha Oliver [aut] (<https://orcid.org/0000-0001-5668-1165>), Farzan Masrour [aut]
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package confreq updated to version 1.5.4-3 with previous version 1.5.1 dated 2016-12-28

Title: Configural Frequencies Analysis Using Log-Linear Modeling
Description: Offers several functions for Configural Frequencies Analysis (CFA), which is a useful statistical tool for the analysis of multiway contingency tables. CFA was introduced by G. A. Lienert as 'Konfigurations Frequenz Analyse - KFA'. Lienert, G. A. (1971). Die Konfigurationsfrequenzanalyse: I. Ein neuer Weg zu Typen und Syndromen. Zeitschrift für Klinische Psychologie und Psychotherapie, 19(2), 99–115.
Author: Joerg-Henrik Heine, R.W. Alexandrowicz (function stirling_cfa() ) and some package testing by Mark Stemmler
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

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Package assertr updated to version 2.6 with previous version 2.5 dated 2018-02-23

Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>

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Package fourPNO updated to version 1.0.5 with previous version 1.0.4 dated 2017-04-26

Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x> four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
Author: Steven Andrew Culpepper [aut, cre, cph] (<https://orcid.org/0000-0003-4226-6176>)
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>

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Package canvasXpress updated to version 1.22.9 with previous version 1.22.6 dated 2019-01-12

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <http://canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut], Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>

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New package wsyn with initial version 1.0.0
Package: wsyn
Version: 1.0.0
Type: Package
Title: Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields
Authors@R: c( person("Daniel C.", "Reuman", email = "reuman@ku.edu", role = c("aut", "cre")), person("Thomas L.", "Anderson", email="anderstl@gmail.com", role=c("aut")), person("Jonathan A.", "Walter", email = "jaw3es@virginia.edu", role=c("aut")), person("Lei", "Zhao", email = "lei.zhao@cau.edu.cn", role=c("aut")), person("Lawrence W.", "Sheppard", email="lwsheppard@ku.edu", role=c("aut")) )
Description: Tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. Some tools will be useful for studying community synchrony.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: fields (>= 9.6), graphics (>= 3.4.4), grDevices (>= 3.4.4), MASS (>= 7.3-47), stats (>= 3.4.4)
Suggests: knitr, mvtnorm, rmarkdown, testthat, vdiffr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2019-01-15 16:57:35 UTC; dreuman
Author: Daniel C. Reuman [aut, cre], Thomas L. Anderson [aut], Jonathan A. Walter [aut], Lei Zhao [aut], Lawrence W. Sheppard [aut]
Maintainer: Daniel C. Reuman <reuman@ku.edu>
Repository: CRAN
Date/Publication: 2019-01-22 18:10:03 UTC

More information about wsyn at CRAN
Permanent link

Package fulltext updated to version 1.2.0 with previous version 1.1.0 dated 2018-10-19

Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package qtl updated to version 1.44-9 with previous version 1.42-8 dated 2018-02-19

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman <broman@wisc.edu>

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Package mbir updated to version 1.3.5 with previous version 1.3.4 dated 2018-09-17

Title: Magnitude-Based Inferences
Description: Allows practitioners and researchers a wholesale approach for deriving magnitude-based inferences from raw data. A major goal of 'mbir' is to programmatically detect appropriate statistical tests to run in lieu of relying on practitioners to determine correct stepwise procedures independently.
Author: Kyle Peterson [aut, cre], Aaron Caldwell [aut]
Maintainer: Kyle Peterson <petersonkdon@gmail.com>

Diff between mbir versions 1.3.4 dated 2018-09-17 and 1.3.5 dated 2019-01-22

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Package RaceID updated to version 0.1.3 with previous version 0.1.2 dated 2018-11-13

Title: Identification of Cell Types and Inference of Lineage Trees from Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>

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Package Quartet updated to version 1.0.1 with previous version 1.0.0 dated 2019-01-16

Title: Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of bifurcating trees.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Andreas Sand [ant], Gerth Stølting Brodal [ant], Rolf Fagerberg [ant], Thomas Mailund [ant], Christian N. S. Pedersen [ant], Jens Johansen [ant], Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package diffeR updated to version 0.0-6 with previous version 0.0-5 dated 2018-10-07

Title: Metrics of Difference for Comparing Pairs of Maps or Pairs of Variables
Description: Metrics of difference for comparing pairs of variables or pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr. <rpontius@clarku.edu>, Ali Santacruz <asantacruzdelgado@clarku.edu>
Maintainer: Ali Santacruz <amsantac@unal.edu.co>

Diff between diffeR versions 0.0-5 dated 2018-10-07 and 0.0-6 dated 2019-01-22

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Package CoordinateCleaner updated to version 2.0-7 with previous version 2.0-3 dated 2018-10-24

Title: Automated Cleaning of Occurrence Records from Biological Collections
Description: Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets.
Author: Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)
Maintainer: Alexander Zizka <alexander.zizka@idiv.de>

Diff between CoordinateCleaner versions 2.0-3 dated 2018-10-24 and 2.0-7 dated 2019-01-22

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 NEWS.md                                                             |   40 
 R/CoordinateCleaner-package.R                                       |    5 
 R/cc_cap.R                                                          |    7 
 R/cc_cen.R                                                          |    2 
 R/cc_coun.R                                                         |    2 
 R/cc_outl.R                                                         |   27 
 R/cf_age.R                                                          |    2 
 R/cf_outl.R                                                         |    2 
 R/clean_coordinates.R                                               |    8 
 R/clean_fossils.R                                                   |    6 
 R/write_pyrate.R                                                    |    2 
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 man/cc_cap.Rd                                                       |    7 
 man/cc_cen.Rd                                                       |    5 
 man/cc_inst.Rd                                                      |    3 
 man/cc_outl.Rd                                                      |   13 
 man/cf_age.Rd                                                       |    2 
 man/cf_outl.Rd                                                      |    2 
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 man/clean_fossils.Rd                                                |    8 
 man/countryref.Rd                                                   |    5 
 man/write_pyrate.Rd                                                 |    2 
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Package tuneRanger updated to version 0.4 with previous version 0.3 dated 2018-08-30

Title: Tune Random Forest of the 'ranger' Package
Description: Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
Author: Philipp Probst [aut, cre], Simon Klau [ctb]
Maintainer: Philipp Probst <philipp_probst@gmx.de>

Diff between tuneRanger versions 0.3 dated 2018-08-30 and 0.4 dated 2019-01-22

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Package vegtable updated to version 0.1.4 with previous version 0.1.3 dated 2018-06-29

Title: Handling Vegetation Data Sets
Description: Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>). Also import/export routines for exchange of data with 'Juice' (<http://www.sci.muni.cz/botany/juice>) are implemented.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>)
Maintainer: Miguel Alvarez <kamapu78@gmail.com>

Diff between vegtable versions 0.1.3 dated 2018-06-29 and 0.1.4 dated 2019-01-22

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Package panelvar updated to version 0.5.2 with previous version 0.5.1 dated 2018-04-03

Title: Panel Vector Autoregression
Description: We extend two general methods of moment estimators to panel vector autoregression models (PVAR) with p lags of endogenous variables, predetermined and strictly exogenous variables. This general PVAR model contains the first difference GMM estimator by Holtz-Eakin et al. (1988) <doi:10.2307/1913103>, Arellano and Bond (1991) <doi:10.2307/2297968> and the system GMM estimator by Blundell and Bond (1998) <doi:10.1016/S0304-4076(98)00009-8>. We also provide specification tests (Hansen overidentification test, lag selection criterion and stability test of the PVAR polynomial) and classical structural analysis for PVAR models such as orthogonal and generalized impulse response functions, bootstrapped confidence intervals for impulse response analysis and forecast error variance decompositions.
Author: Michael Sigmund [aut], Robert Ferstl [aut, cre]
Maintainer: Robert Ferstl <robert.ferstl@ur.de>

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Package jomo updated to version 2.6-6 with previous version 2.6-5 dated 2018-11-09

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>

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Package IndexNumR updated to version 0.1.1 with previous version 0.1.0 dated 2018-01-26

Title: Index Number Calculation
Description: Computes bilateral and multilateral index numbers. It has support for several standard bilateral indices as well as the GEKS multilateral index number methods (see Ivancic, Diewert and Fox (2011) <doi:10.1016/j.jeconom.2010.09.003>) . It also supports updating of GEKS indexes using several splicing methods.
Author: Graham White
Maintainer: Graham White <g.white@unswalumni.com>

Diff between IndexNumR versions 0.1.0 dated 2018-01-26 and 0.1.1 dated 2019-01-22

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Package clusterlab updated to version 0.0.2.6 with previous version 0.0.2.5 dated 2018-10-05

Title: Flexible Gaussian Cluster Simulator
Description: Clustering is a central task in big data analyses and clusters are often Gaussian or near Gaussian. However, a flexible Gaussian cluster simulation tool with precise control over the size, variance, and spacing of the clusters in NXN dimensional space does not exist. This is why we created 'clusterlab'. The algorithm first creates X points equally spaced on the circumference of a circle in 2D space. These form the centers of each cluster to be simulated. Additional samples are added by adding Gaussian noise to each cluster center and concatenating the new sample co-ordinates. Then if the feature space is greater than 2D, the generated points are considered principal component scores and projected into N dimensional space using linear combinations using fixed eigenvectors. Through using vector rotations and scalar multiplication clusterlab can generate complex patterns of Gaussian clusters and outliers.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>

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Package simtimer updated to version 4.0.0 with previous version 3.0.0 dated 2017-12-21

Title: Datetimes as Integers for Discrete-Event Simulations
Description: Handles datetimes as integers for the usage inside Discrete-Event Simulations (DES). The conversion is made using the internally generic function as.numeric() of the base package. DES is described in Simulation Modeling and Analysis by Averill Law and David Kelton (1999) <doi:10.2307/2288169>.
Author: Adrian Staempfli, Christoph Strauss, Michael Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>

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Package mapdeck updated to version 0.2.1 with previous version 0.1.0 dated 2018-08-16

Title: Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Description: Provides a mechanism to plot an interactive map using 'Mapbox GL' (<https://www.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps, and 'Deck.gl' (<http://deck.gl/#/>), a javascript library which uses 'WebGL' for visualising large data sets.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between mapdeck versions 0.1.0 dated 2018-08-16 and 0.2.1 dated 2019-01-22

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Package kableExtra updated to version 1.0.1 with previous version 1.0.0 dated 2019-01-16

Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>

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Package eventstudies (with last version 1.2.1) was removed from CRAN

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

2019-01-21 1.2.1

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Package woeR (with last version 0.1.3) was removed from CRAN

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

2018-01-03 0.1.3

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Package mplot updated to version 1.0.2 with previous version 1.0.1 dated 2018-02-14

Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh (2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller (2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al. (2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre], Samuel Mueller [aut], Alan H Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>

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Package descriptr updated to version 0.5.0 with previous version 0.4.1 dated 2018-03-20

Title: Generate Descriptive Statistics
Description: Generate descriptive statistics such as measures of location, dispersion, frequency tables, cross tables, group summaries and multiple one/two way tables.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

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Package UCSCXenaTools updated to version 0.2.7 with previous version 0.2.6 dated 2018-12-09

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package MapGAM updated to version 1.2-4 with previous version 1.2 dated 2018-07-25

Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (submitted). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>

Diff between MapGAM versions 1.2 dated 2018-07-25 and 1.2-4 dated 2019-01-22

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Package CUFF updated to version 1.6 with previous version 1.5 dated 2018-05-28

Title: Charles's Utility Function using Formula
Description: Utility functions that provides wrapper to descriptive base functions like cor, mean and table. It makes use of the formula interface to pass variables to functions. It also provides operators to concatenate (%+%), to repeat (%n%) and manage character vectors for nice display.
Author: Charles-Édouard Giguère
Maintainer: Charles-Édouard Giguère <ce.giguere@gmail.com>

Diff between CUFF versions 1.5 dated 2018-05-28 and 1.6 dated 2019-01-22

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Package BigVAR updated to version 1.0.4 with previous version 1.0.3 dated 2018-07-22

Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with structured Lasso Penalties.
Author: Will Nicholson [cre, aut], David Matteson [aut], Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>

Diff between BigVAR versions 1.0.3 dated 2018-07-22 and 1.0.4 dated 2019-01-22

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Package RcppBlaze (with last version 0.2.2) was removed from CRAN

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

2017-10-09 0.2.2
2017-02-22 0.1.1
2017-02-20 0.1.0

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Package OutbreakTools (with last version 0.1-16) was removed from CRAN

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

2017-10-05 0.1-16
2017-09-27 0.1-15
2015-12-25 0.1-14
2015-03-23 0.1-13
2015-02-06 0.1-12
2014-08-11 0.1-11
2014-08-06 0.1-1
2014-01-09 0.1-0

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Mon, 21 Jan 2019

Package tor updated to version 1.1.1 with previous version 1.0.1 dated 2019-01-11

Title: Import Multiple Files From a Single Directory at Once
Description: The goal of tor (to-R) is to help you to import multiple files from a single directory at once, and to do so as quickly, flexibly, and simply as possible.
Author: Mauro Lepore [aut, cre]
Maintainer: Mauro Lepore <maurolepore@gmail.com>

Diff between tor versions 1.0.1 dated 2019-01-11 and 1.1.1 dated 2019-01-21

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New package RcppHNSW with initial version 0.1.0
Package: RcppHNSW
Title: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
Version: 0.1.0
Authors@R: c(person("James", "Melville", email = "jlmelville@gmail.com", role = c("aut", "cre")), person("Aaron", "Lun", role = "ctb"))
Description: 'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R interface by relying on the 'Rcpp' package. See <https://github.com/nmslib/hnswlib> for more on 'hnswlib'. 'hnswlib' is released under Version 2.0 of the Apache License.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: methods, Rcpp (>= 0.11.3)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Suggests: testthat, covr
NeedsCompilation: yes
Packaged: 2019-01-15 03:34:10 UTC; jlmel
Author: James Melville [aut, cre], Aaron Lun [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Repository: CRAN
Date/Publication: 2019-01-21 23:30:06 UTC

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Package future updated to version 1.11.0 with previous version 1.10.0 dated 2018-10-17

Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future versions 1.10.0 dated 2018-10-17 and 1.11.0 dated 2019-01-21

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New package ensr with initial version 0.1.0
Package: ensr
Title: Elastic Net SearcheR
Version: 0.1.0
Authors@R: c( person("Peter", "DeWitt", , "peter.dewitt@ucdenver.edu", role = c("aut", "cre")), person("Tell", "Bennett", , "tell.bennett@ucdenver.edu", role = c("ctb")) )
Description: Elastic net regression models are controlled by two parameters, lambda, a measure of shrinkage, and alpha, a metric defining the model's location on the spectrum between ridge and lasso regression. glmnet provides tools for selecting lambda via cross validation but no automated methods for selection of alpha. Elastic Net SearcheR automates the simultaneous selection of both lambda and alpha. Developed, in part, with support by NICHD R03 HD094912.
License: GPL-2
Encoding: UTF-8
URL: https://github.com/dewittpe/ensr
LazyData: true
Depends: R (>= 3.5.0), glmnet
Imports: data.table, ggplot2
Suggests: digest, ggforce, gridExtra, knitr, magrittr, microbenchmark, qwraps2 (>= 0.4.0), R.rsp, rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2019-01-14 22:51:48 UTC; dewittp
Author: Peter DeWitt [aut, cre], Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@ucdenver.edu>
Repository: CRAN
Date/Publication: 2019-01-21 23:30:03 UTC

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Package pubchunks updated to version 0.2.0 with previous version 0.1.0 dated 2018-10-14

Title: Fetch Sections of XML Scholarly Articles
Description: Get chunks of XML scholarly articles without having to know how to work with XML. Custom mappers for each publisher and for each article section pull out the information you want. Works with outputs from package 'fulltext', 'xml2' package documents, and file paths to XML documents.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

Diff between pubchunks versions 0.1.0 dated 2018-10-14 and 0.2.0 dated 2019-01-21

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Package IsoSpecR updated to version 1.9.2 with previous version 1.9.1 dated 2018-11-18

Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most probable masses of a chemical compound given the frequencies of the composing isotopes and their masses. It finds the smallest set of isotopologues with a given probability. The probability is assumed to be that of the product of multinomial distributions, each corresponding to one particular element and parametrized by the frequencies of finding these elements in nature. These numbers are supplied by IUPAC - the International Union of Pure and Applied Chemistry.
Author: Mateusz Krzysztof Lacki and Michal Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>

Diff between IsoSpecR versions 1.9.1 dated 2018-11-18 and 1.9.2 dated 2019-01-21

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Package curveDepth updated to version 0.1.0.8 with previous version 0.1.0.7 dated 2019-01-08

Title: Tukey Curve Depth and Distance in the Space of Curves
Description: Data recorded as paths or trajectories may be suitably described by curves, which are independent of their parametrization. For the space of such curves, the package provides functionalities for reading curves, sampling points on curves, calculating distance between curves and for computing Tukey curve depth of a curve w.r.t. to a bundle of curves. For details see Lafaye De Micheaux, Mozharovskyi, and Vimond (2019) <arXiv:1901.00180>.
Author: Pavlo Mozharovskyi [aut, cre], Pierre Lafaye De Micheaux [aut], Myriam Vimond [aut]
Maintainer: Pavlo Mozharovskyi <pavlo.mozharovskyi@telecom-paristech.fr>

Diff between curveDepth versions 0.1.0.7 dated 2019-01-08 and 0.1.0.8 dated 2019-01-21

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Package ical updated to version 0.1.6 with previous version 0.1.5 dated 2018-12-03

Title: 'iCalendar' Parsing
Description: A simple wrapper around the 'ical.js' library executing 'Javascript' code via 'V8' (the 'Javascript' engine driving the 'Chrome' browser and 'Node.js' and accessible via the 'V8' R package). This package enables users to parse 'iCalendar' files ('.ics', '.ifb', '.iCal', '.iFBf') into lists and 'data.frames' to ultimately do statistics on events, meetings, schedules, birthdays, and the like.
Author: Peter Meissner [aut, cre], Philipp Kewisch [cph] (Ical.js file is is licences under MPL. Source: https://github.com/mozilla-comm/ical.js)
Maintainer: Peter Meissner <retep.meissner@gmail.com>

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Package bfp updated to version 0.0-40 with previous version 0.0-39.1 dated 2019-01-16

Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms, see Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre], Isaac Gravestock [aut], Robert Davies [cph], Stephen Moshier [cph]
Maintainer: ORPHANED

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Package markovchain updated to version 0.6.9.14 with previous version 0.6.9.12 dated 2018-08-23

Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut, cre] (<https://orcid.org/0000-0002-0315-8888>), Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb] (<https://orcid.org/0000-0001-7242-1873>), Deepak Yadav [aut], Ignacio Cordón [ctb], Vandit Jain [ctb], Toni Giorgino [ctb] (<https://orcid.org/0000-0001-6449-0596>)
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

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Package LexisNexisTools updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-10

Title: Working with Files from 'LexisNexis'
Description: My PhD supervisor once told me that everyone doing newspaper analysis starts by writing code to read in files from the 'LexisNexis' newspaper archive (retrieved e.g., from <http://www.nexis.com/> or any of the partner sites). However, while this is a nice exercise I do recommend, not everyone has the time. This package takes TXT files downloaded from the newspaper archive of 'LexisNexis', reads them into R and offers functions for further processing.
Author: Johannes Gruber [aut, cre]
Maintainer: Johannes Gruber <j.gruber.1@research.gla.ac.uk>

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Package BayesianTools updated to version 0.1.6 with previous version 0.1.5 dated 2018-07-16

Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre], Francesco Minunno [aut], Stefan Paul [aut], David Cameron [ctb], Tankred Ott [ctb], Maximilian Pichler [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

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Package stylo updated to version 0.6.9 with previous version 0.6.8 dated 2018-10-08

Title: Stylometric Multivariate Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html> You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont, Steffen Pielstroem
Maintainer: Maciej Eder <maciejeder@gmail.com>

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Package Spbsampling updated to version 1.1.0 with previous version 1.0.0 dated 2018-05-30

Title: Spatially Balanced Sampling
Description: Selection of spatially balanced samples. In particular, the implemented sampling designs allow to select probability samples spread over the population of interest, in any dimension and using any distance function (e.g. Euclidean distance, Manhattan distance). For more details, Benedetti R and Piersimoni F (2017) <doi:10.1002/bimj.201600194> and Benedetti R and Piersimoni F (2017) <arXiv:1710.09116>. The implementation has been done in C++ through the use of 'Rcpp' and 'RcppArmadillo'.
Author: Francesco Pantalone [aut, cre], Roberto Benedetti [aut], Federica Piersimoni [aut]
Maintainer: Francesco Pantalone <pantalone.fra@gmail.com>

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Package MCAvariants updated to version 2.2 with previous version 2.0 dated 2016-11-22

Title: Multiple Correspondence Analysis Variants
Description: Provides two variants of multiple correspondence analysis (ca): multiple ca and ordered multiple ca via orthogonal polynomials of Emerson.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unicampania.it>

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Package RcppXPtrUtils updated to version 0.1.1 with previous version 0.1.0 dated 2017-08-04

Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>

Diff between RcppXPtrUtils versions 0.1.0 dated 2017-08-04 and 0.1.1 dated 2019-01-21

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Package MHTcop updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-05

Title: Tests Controlling the FDR / FWER under Certain Copula Models
Description: Implements tests controlling the false discovery rate (FDR) / family-wise error rate (FWER) for some copula models.
Author: Jonathan von Schroeder [aut, cre], Taras Bodnar [aut], Jens Stange [aut]
Maintainer: Jonathan von Schroeder <jvs@uni-bremen.de>

Diff between MHTcop versions 0.1.0 dated 2018-04-05 and 0.1.1 dated 2019-01-21

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Package konfound updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-06

Title: Quantify the Robustness of Causal Inferences
Description: Statistical methods that quantify the conditions necessary to alter inferences, also known as sensitivity analysis, are becoming increasingly important to a variety of quantitative sciences. A series of recent works, including Frank (2000) <doi:10.1177/0049124100029002001> and Frank et al. (2013) <doi:10.3102/0162373713493129> extend previous sensitivity analyses by considering the characteristics of omitted variables or unobserved cases that would change an inference if such variables or cases were observed. These analyses generate statements such as "an omitted variable would have to be correlated at xx with the predictor of interest (e.g., treatment) and outcome to invalidate an inference of a treatment effect". Or "one would have to replace pp percent of the observed data with null hypothesis cases to invalidate the inference". We implement these recent developments of sensitivity analysis and provide modules to calculate these two robustness indices and generate such statements in R. In particular, the functions konfound(), pkonfound() and mkonfound() allow users to calculate the robustness of inferences for a user's own model, a single published study and multiple studies respectively.
Author: Joshua M Rosenberg [aut, cre], Ran Xu [ctb], Kenneth A Frank [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package island updated to version 0.2.2 with previous version 0.2.1 dated 2018-05-09

Title: Stochastic Island Biogeography Theory Made Easy
Description: Tools to develop stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <DOI:10.1023/A:1016393430551> and extensions. The package implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulate community assembly, and perform model selection.
Author: Vicente Jimenez [aut, cre], David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>

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Package Immigrate updated to version 0.0.2 with previous version 0.0.1 dated 2018-10-14

Title: Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection
Description: Based on large margin principle, this package performs feature selection methods: "IM4E"(Iterative Margin-Maximization under Max-Min Entropy Algorithm); "imIM4E"(imbalance Iterative Margin-Maximization under Max-Min Entropy Algorithm); "Immigrate"(Iterative Max-Min Entropy Margin-Maximization with Interaction Terms Algorithm); "BIM"(Boosted version of IMMIGRATE algorithm); "Simba"(Iterative Search Margin Based Algorithm); "LFE"(Local Feature Extraction Algorithm). This package also performs prediction for the above feature selection methods. See Zhao et al. (2018) <arXiv:1810.02658> for more details.
Author: Ruzhang Zhao, Pengyu Hong, Jun S. Liu
Maintainer: Ruzhang Zhao<zrz6787@gmail.com>

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Package taxlist updated to version 0.1.6 with previous version 0.1.5 dated 2018-06-29

Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>)
Maintainer: Miguel Alvarez <kamapu78@gmail.com>

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Package SSBtools updated to version 0.4.0 with previous version 0.3.0 dated 2018-08-22

Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included. The hierarchy specification functions are useful within statistical disclosure control.
Author: Øyvind Langsrud [aut, cre], Bjørn-Helge Mevik [cph]
Maintainer: Øyvind Langsrud <oyl@ssb.no>

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Package simode updated to version 1.1.2 with previous version 1.1.1 dated 2018-10-05

Title: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching
Description: Implements statistical inference for systems of ordinary differential equations, that uses the integral-matching criterion and takes advantage of the separability of parameters, in order to obtain initial parameter estimates for nonlinear least squares optimization. Dattner & Yaari (2018) <arXiv:1807.04202>. Dattner et al. (2017) <doi:10.1098/rsif.2016.0525>. Dattner & Klaassen (2015) <doi:10.1214/15-EJS1053>.
Author: Itai Dattner [aut], Rami Yaari [aut, cre]
Maintainer: Rami Yaari <ramiyaari@gmail.com>

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Package rprev updated to version 1.0.1 with previous version 1.0.0 dated 2018-06-07

Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date, using existing registry data extended with Monte Carlo simulations.
Author: Stuart Lacy [cre, aut], Simon Crouch [aut], Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>

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Package ranger updated to version 0.11.0 with previous version 0.10.1 dated 2018-06-04

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix') can be directly analyzed.
Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>

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Package BDgraph updated to version 2.54 with previous version 2.53 dated 2018-11-14

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides 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 antaresRead updated to version 2.2.2 with previous version 2.2.1 dated 2018-10-18

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 mixpack (with last version 0.3.6) was removed from CRAN

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

2017-01-27 0.3.6
2015-12-08 0.3.4

Permanent link
Package portalr (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:

2018-11-14 0.1.4

Permanent link
Package TH.data updated to version 1.0-10 with previous version 1.0-9 dated 2018-07-10

Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between TH.data versions 1.0-9 dated 2018-07-10 and 1.0-10 dated 2019-01-21

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Package RSmartlyIO updated to version 0.1.3 with previous version 0.1.2 dated 2017-06-08

Title: Loading Facebook and Instagram Advertising Data from 'Smartly.io'
Description: Aims at loading Facebook and Instagram advertising data from 'Smartly.io' into R. 'Smartly.io' is an online advertising service that enables advertisers to display commercial ads on social media networks (see <http://www.smartly.io/> for more information). The package offers an interface to query the 'Smartly.io' API and loads data directly into R for further data processing and data analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>

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Package ethnobotanyR updated to version 0.1.3 with previous version 0.1.2 dated 2019-01-19

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 e1071 updated to version 1.7-0.1 with previous version 1.7-0 dated 2018-07-28

Title: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...
Author: David Meyer [aut, cre], Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut], Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package ddsPLS updated to version 1.0.61 with previous version 1.0.53 dated 2019-01-08

Title: Data-Driven Sparse PLS Robust to Missing Samples for Mono and Multi-Block Data Sets
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre], Jerome Saracco [aut], Rodolphe Thiebaut [aut]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>

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Package outbreaks updated to version 1.5.0 with previous version 1.3.0 dated 2017-05-10

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

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Permanent link

Package hrbrthemes updated to version 0.6.0 with previous version 0.5.0.1 dated 2018-08-19

Title: Additional Themes, Theme Components and Utilities for 'ggplot2'
Description: A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/> is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type> and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts are also included to support their respective typography-oriented themes.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Patrick Kennedy [ctb], Philipp Reiner [ctb], Dan Wilson [ctb] (Secondary axis support), Xavier Adam [ctb], Google [cph] (Roboto Condensed & Titillium Web Fonts), IBM [cph] (Plex Sans Font), Jacob Barnett [ctb], Thomas J. Leeper [ctb] (<https://orcid.org/0000-0003-4097-6326>), Joris Meys [ctb]
Maintainer: Bob Rudis <bob@rud.is>

Diff between hrbrthemes versions 0.5.0.1 dated 2018-08-19 and 0.6.0 dated 2019-01-21

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Package hBayesDM updated to version 0.7.1 with previous version 0.7.0 dated 2018-12-13

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut], Harhim Park [ctb], Jaeyeong Yang [ctb], Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

Diff between hBayesDM versions 0.7.0 dated 2018-12-13 and 0.7.1 dated 2019-01-21

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New package eventstudies with initial version 1.2.1
Package: eventstudies
Version: 1.2.1
Date: 2019-01-08
Type: Package
Title: Event Study Analysis
Authors@R: c( person("Chirag", "Anand", role = c("aut", "cre"), email = "anand.chirag@gmail.com"), person("Vikram", "Bahure", role = "aut", email = "economics.vikram@gmail.com"), person("Vimal", "Balasubramaniam", role = "aut", email = "vimsaa@gmail.com"), person("Shekhar", "Harikumar", role = "ctb", email = "shekhar.harikumar@gmail.com"), person("Sargam", "Jain", role = "ctb", email = "sargamjain13@gmail.com"), person("Ajay", "Shah", role = "aut", email = "ajayshah@mayin.org") )
Maintainer: Chirag Anand <anand.chirag@gmail.com>
Depends: R (>= 3.1), zoo, xts
Description: A platform for conducting event studies (Fama, Fisher, Jensen, Roll (1969) <doi:10.2307/2525569>) and for methodological research on event studies. The package supports market model, augmented market model, and excess returns methods for data modelling along with Wilcox, classical t-test, and Bootstrap as inference procedures.
VignetteBuilder: knitr
Suggests: knitr
Imports: boot, graphics, methods, testthat, sandwich, stats, utils
License: GPL-2
URL: https://github.com/nipfpmf/eventstudies
BugReports: https://github.com/nipfpmf/eventstudies/issues
LazyLoad: yes
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2019-01-21 06:58:41.50401 UTC; chirag
Author: Chirag Anand [aut, cre], Vikram Bahure [aut], Vimal Balasubramaniam [aut], Shekhar Harikumar [ctb], Sargam Jain [ctb], Ajay Shah [aut]
Repository: CRAN
Date/Publication: 2019-01-21 09:10:15 UTC

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New package CluMix with initial version 2.3.1
Package: CluMix
Type: Package
Title: Clustering and Visualization of Mixed-Type Data
Version: 2.3.1
Date: 2019-01-20
Author: M. Hummel, D. Edelmann, A. Kopp-Schneider
Maintainer: Manuela Hummel <manuela.hummel@web.de>
Description: Provides utilities for clustering subjects and variables of mixed data types (Hummel, Edelmann, Kopp-Schneider (2017) <doi: 10.1371/journal.pone.0188274>). Similarities between subjects are measured by Gower's general similarity coefficient with an extension of Podani for ordinal variables. Similarities between variables can be assessed i) by combination of appropriate measures of association for different pairs of data types or ii) based on distance correlation. Alternatively, variables can also be clustered by the 'ClustOfVar' approach. The main feature of the package is the generation of a mixed-data heatmap. For visualizing similarities between either subjects or variables, a heatmap of the corresponding distance matrix can be drawn. Associations between variables can be explored by a 'confounder plot', which allows visual detection of possible confounding, collinear, or surrogate factors for some variables of primary interest. Distance matrices and dendrograms for subjects and variables can be derived and used for further visualizations and applications. This work was supported by BMBF grant 01ZX1609B, Germany.
License: GPL (>= 2)
Depends:
Imports: ClustOfVar, Hmisc, DescTools, extracat, marray, FD, gplots, Matrix, Biobase
Suggests:
NeedsCompilation: no
Packaged: 2019-01-20 22:01:33 UTC; Humpas
Repository: CRAN
Date/Publication: 2019-01-21 09:10:22 UTC

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Package WRSS updated to version 2.1 with previous version 2.0 dated 2018-11-05

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>

Diff between WRSS versions 2.0 dated 2018-11-05 and 2.1 dated 2019-01-21

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Package RcppEnsmallen updated to version 0.1.13.0.1 with previous version 0.1.12.0.1 dated 2019-01-04

Title: Header-Only C++ Mathematical Optimization Library for 'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library (by the 'MLPACK' team) that provides a simple set of abstractions for writing an objective function to optimize. Provided within are various standard and cutting-edge optimizers that include full-batch gradient descent techniques, small-batch techniques, gradient-free optimizers, and constrained optimization. The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library and pairs the appropriate header files from 'armadillo' through the 'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor 'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under 3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2, 'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under similar terms. Note that 'Ensmallen' requires a compiler that supports 'C++11' and 'Armadillo' 6.500 or later.
Author: James Joseph Balamuta [aut, cre, cph] (<https://orcid.org/0000-0003-2826-8458>), Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

Diff between RcppEnsmallen versions 0.1.12.0.1 dated 2019-01-04 and 0.1.13.0.1 dated 2019-01-21

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Package ParallelLogger updated to version 1.1.0 with previous version 1.0.1 dated 2018-10-25

Title: Support for Parallel Computation, Logging, and Function Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk, and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in parallel).
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between ParallelLogger versions 1.0.1 dated 2018-10-25 and 1.1.0 dated 2019-01-21

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Package AcceptanceSampling updated to version 1.0-6 with previous version 1.0-5 dated 2016-12-29

Title: Creation and Evaluation of Acceptance Sampling Plans
Description: Provides functionality for creating and evaluating acceptance sampling plans. Sampling plans can be single, double or multiple.
Author: Andreas Kiermeier [aut, cre], Peter Bloomfield [ctb]
Maintainer: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>

Diff between AcceptanceSampling versions 1.0-5 dated 2016-12-29 and 1.0-6 dated 2019-01-21

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Package tensorr updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-01

Title: Sparse Tensors in R
Description: Provides methods to manipulate and store sparse tensors. Tensors are multidimensional generalizations of matrices (two dimensional) and vectors (one dimensional).
Author: Robert Zamora [aut, cre]
Maintainer: Robert Zamora <zamora.rr@gmail.com>

Diff between tensorr versions 0.1.0 dated 2017-04-01 and 0.1.1 dated 2019-01-21

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Package groupedstats updated to version 0.0.5 with previous version 0.0.4 dated 2018-12-01

Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests across all levels of multiple grouping variables.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package elo updated to version 1.1.0 with previous version 1.0.1 dated 2017-12-14

Title: Elo Ratings
Description: A flexible framework for calculating Elo ratings and resulting rankings of any two-team-per-matchup system (chess, sports leagues, 'Go', etc.). This implementation is capable of evaluating a variety of matchups, Elo rating updates, and win probabilities, all based on the basic Elo rating system.
Author: Ethan Heinzen [aut, cre]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>

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Sun, 20 Jan 2019

Package SUMMER updated to version 0.2.2 with previous version 0.2.1 dated 2018-07-16

Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
Description: Provides methods for estimating, projecting, and plotting spatio-temporal under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>.
Author: Bryan D Martin [cre, aut], Zehang R Li [aut], Yuan Hsiao [aut], Jessica Godwin [aut], Jon Wakefield [aut], Samuel J Clark [aut]
Maintainer: Bryan D Martin <bmartin6@uw.edu>

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Package SemiCompRisks updated to version 3.2 with previous version 3.1 dated 2018-05-06

Title: Hierarchical Models for Parametric and Semi-Parametric Analyses of Semi-Competing Risks Data
Description: Hierarchical multistate models are considered to perform the analysis of independent/clustered semi-competing risks data. The package allows to choose the specification for model components from a range of options giving users substantial flexibility, including: accelerated failure time or proportional hazards regression models; parametric or non-parametric specifications for baseline survival functions and cluster-specific random effects distribution; a Markov or semi-Markov specification for terminal event following non-terminal event. While estimation is mainly performed within the Bayesian paradigm, the package also provides the maximum likelihood estimation approach for several parametric models. The package also includes functions for univariate survival analysis as complementary analysis tools.
Author: Kyu Ha Lee, Catherine Lee, Danilo Alvares, and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee15239@gmail.com>

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Package DescriptiveStats.OBeu updated to version 1.3.1 with previous version 1.3.0 dated 2018-05-08

Title: Descriptive Statistics 'OpenBudgets.eu'
Description: Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> datasets. Calculate descriptive statistical measures in budget data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring central tendency and dispersion of amount variables along with their distributions and correlations and the frequencies of categorical variables for a given dataset. Also, can be used generally to extract visualization parameters, convert them to 'JSON' format and use them as input in a different graphical interface.
Author: Kleanthis Koupidis [aut, cre], Aikaterini Chatzopoulou [aut], Charalampos Bratsas [aut]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>

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Package TimeSeries.OBeu updated to version 1.2.3 with previous version 1.2.2 dated 2018-01-22

Title: Time Series Analysis 'OpenBudgets.eu'
Description: Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> time series data. Calculate time series model and forecast parameters in budget time series data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring deterministic and stochastic trend of the input time series data with 'ACF', 'PACF', 'Phillips Perron' test, 'Augmented Dickey Fuller (ADF)' test, 'Kwiatkowski-Phillips-Schmidt-Shin (KPSS)' test, 'Mann Kendall' test for monotonic trend and 'Cox and Stuart' trend test, decomposing with local regression models or 'stl' decomposition, fitting the appropriate 'arima' model and provide forecasts for the input 'OpenBudgets.eu' time series fiscal data. Also, can be used generally to extract visualization parameters convert them to 'JSON' format and use them as input in a different graphical interface.
Author: Kleanthis Koupidis [aut, cre], Charalampos Bratsas [aut]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>

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Package geniusr updated to version 1.1.0 with previous version 1.0.0 dated 2017-12-06

Title: Tools for Working with the 'Genius' API
Description: Provides tools to interact nicely with the 'Genius' API <https://docs.genius.com/>. Search hosted content, extract different types of associated metadata and retrieve lyrics with ease.
Author: Ewen Henderson [aut, cre]
Maintainer: Ewen Henderson <ewenhenderson@gmail.com>

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Package HiClimR updated to version 2.1.4 with previous version 2.1.3 dated 2019-01-11

Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering. It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution, geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function with preliminary big data support, different clustering methods, hybrid hierarchical clustering, multivariate clustering (MVC), cluster validation, visualization of regionalization results, and exporting region map and mean timeseries into NetCDF-4 file.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>

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Package cdata updated to version 1.0.5 with previous version 1.0.4 dated 2019-01-07

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>

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Package Cluster.OBeu updated to version 1.2.2 with previous version 1.2.1 dated 2018-02-12

Title: Cluster Analysis 'OpenBudgets.eu'
Description: Estimate and return the needed parameters for visualisations designed for 'OpenBudgets' <http://openbudgets.eu/> data. Calculate cluster analysis measures in Budget data of municipalities across Europe, according to the 'OpenBudgets' data model. It involves a set of techniques and algorithms used to find and divide the data into groups of similar observations. Also, can be used generally to extract visualisation parameters convert them to 'JSON' format and use them as input in a different graphical interface.
Author: Kleanthis Koupidis [aut, cre], Charalampos Bratsas [aut], Jaroslav Kuchar [ctb]
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>

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Package jose updated to version 1.0 with previous version 0.2 dated 2018-04-12

Title: JavaScript Object Signing and Encryption
Description: Read and write JSON Web Keys (JWK, rfc7517), generate and verify JSON Web Signatures (JWS, rfc7515) and encode/decode JSON Web Tokens (JWT, rfc7519). These standards provide modern signing and encryption formats that are the basis for services like OAuth 2.0 or LetsEncrypt and are natively supported by browsers via the JavaScript WebCryptoAPI.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package harrypotter updated to version 2.1.0 with previous version 2.0.0 dated 2018-12-13

Title: Palettes Generated from All "Harry Potter" Movies
Description: Implementation of the characteristic palette of the houses of Hogwarts School of magic, present in all Harry Potter movies.
Author: Alejandro Jimenez Rico [aut, cre], Alfredo Hernandez [ctb]
Maintainer: Alejandro Jimenez Rico <aljrico@gmail.com>

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New package bender with initial version 0.1.0
Package: bender
Type: Package
Title: Bender Client
Version: 0.1.0
Author: Dylan Heirstraeten
Maintainer: Valentin Thorey <valentin@dreem.com>
Description: R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: R6, jsonlite, httr
NeedsCompilation: no
Packaged: 2019-01-15 08:42:05 UTC; dylan
Repository: CRAN
Date/Publication: 2019-01-20 18:30:03 UTC

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New package RGCxGC with initial version 1.0.0
Package: RGCxGC
Type: Package
Title: Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Version: 1.0.0
Date: 2019-01-09
Authors@R: c( person("Cristian", "Quiroz-Moreno", email = "cristianquirozd1997@gmail.com", role = c("aut", "cre")), person("Guilherme", "L. Alexandrino", email = "Alexandrinogl@gmail.com", role = "aut"), person("Noroska", "G.S. Mogollón", email = "gaby867@gmail.com", role = "aut"))
Author: Cristian Quiroz-Moreno [aut, cre], Guilherme L. Alexandrino [aut], Noroska G.S. Mogollón [aut]
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>
Description: Implementation of chemometrics analysis for bidimensional gas chromatography data. This package can handle data for common scientific data format (netCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
License: MIT + file LICENSE
Imports: colorRamps (>= 2.3), Rdpack (>= 0.7), prettydoc (>= 0.2)
RdMacros: Rdpack
Depends: R (>= 3.5.0), stats, methods, graphics, RNetCDF (>= 1.9-1), ptw (>= 1.9-13)
LazyData: true
RoxygenNote: 6.1.1
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-01-12 22:56:13 UTC; cizquime
Repository: CRAN
Date/Publication: 2019-01-20 17:30:03 UTC

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New package abstractr with initial version 0.1.0
Package: abstractr
Type: Package
Title: An R-Shiny Application for Creating Visual Abstracts
Version: 0.1.0
Author: Matthew Kumar <mattkumar@gmail.com>
Maintainer: Matthew Kumar <mattkumar@gmail.com>
Description: An R-Shiny application to create visual abstracts for original research. A variety of user defined options and formatting are included.
URL: https://matt-kumar.shinyapps.io/portfolio
Imports: shiny (>= 1.2.0), ggplot2 (>= 3.0.0), gridExtra (>= 2.3.0), colourpicker, shinythemes, emojifont, rintrojs
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-01-14 22:41:00 UTC; Kumar
Repository: CRAN
Date/Publication: 2019-01-20 17:20:03 UTC

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New package trendchange with initial version 0.1.0
Package: trendchange
Type: Package
Title: Innovative Trend Analysis and Time-Series Change Point Analysis
Version: 0.1.0
Author: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>
Description: Innovative Trend Analysis is a graphical method to examine the trends in time series data. Sequential Mann-Kendall test uses the intersection of prograde and retrograde series to indicate the possible change point in time series data. Distribution free cumulative sum charts indicate location and significance of the change point in time series. Zekai, S. (2011). <doi:10.1061/(ASCE)HE.1943-5584.0000556>. Grayson, R. B. et al. (1996). Hydrological Recipes: Estimation Techniques in Australian Hydrology. Cooperative Research Centre for Catchment Hydrology, Australia, p. 125. Sneyers, S. (1990). On the statistical analysis of series of observations. Technical note no 5 143, WMO No 725 415. Secretariat of the World Meteorological Organization, Geneva, 192 pp.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown,covr
NeedsCompilation: no
Packaged: 2019-01-13 04:23:08 UTC; Deepu
Repository: CRAN
Date/Publication: 2019-01-20 16:10:03 UTC

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Package srvyr updated to version 0.3.4 with previous version 0.3.3 dated 2018-05-22

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre], Thomas Lumley [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 0.3.3 dated 2018-05-22 and 0.3.4 dated 2019-01-20

 DESCRIPTION                              |   10 ++--
 MD5                                      |   58 ++++++++++++++--------------
 NEWS.md                                  |    6 ++
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 R/rlang-compat-purrr.R                   |   29 +++++++++++++-
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 R/survey_statistics.r                    |    7 +--
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 R/utils.r                                |    3 +
 build/vignette.rds                       |binary
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 inst/doc/srvyr-database.html             |   40 +++----------------
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 man/srvyr.Rd                             |    6 +-
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 tests/testthat/test_as_survey.r          |    1 
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 tests/testthat/test_survey_proportion.R  |   20 +++++++++
 tests/testthat/test_survey_statistics.r  |   18 ++++++++
 vignettes/srvyr-vs-survey.Rmd            |    2 
 30 files changed, 223 insertions(+), 157 deletions(-)

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Package DHARMa updated to version 0.2.2 with previous version 0.2.1 dated 2019-01-17

Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are (generalized) linear mixed models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (Theoretical Ecology, University of Regensburg, Regensburg, Germany)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

Diff between DHARMa versions 0.2.1 dated 2019-01-17 and 0.2.2 dated 2019-01-20

 DESCRIPTION          |    8 
 MD5                  |   10 
 NEWS                 |    7 
 inst/doc/DHARMa.Rmd  |    4 
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 6 files changed, 732 insertions(+), 893 deletions(-)

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New package dapr with initial version 0.0.2
Package: dapr
Title: 'purrr'-Like Apply Functions Over Input Elements
Version: 0.0.2
Authors@R: person(given = "Michael W.", family = "Kearney", role = c("aut", "cre"), email = "kearneymw@missouri.edu", comment = c(ORCID = "0000-0002-0730-4694"))
Description: An easy-to-use, dependency-free set of functions for iterating over elements of various input objects. Functions are wrappers around base apply()/lapply()/vapply() functions but designed to have similar functionality to the mapping functions in the 'purrr' package <https://purrr.tidyverse.org/>. Specifically, function names more explicitly communicate the expected class of the output and functions also allow for the convenient shortcut of '~ .x' instead of the more verbose 'function(.x) .x'.
License: GPL-3
Encoding: UTF-8
Language: en
LazyData: true
RoxygenNote: 6.1.1
URL: https://github.com/mkearney/dapr
BugReports: https://github.com/mkearney/dapr/issues
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2019-01-13 20:48:34 UTC; mwk
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>
Repository: CRAN
Date/Publication: 2019-01-20 16:20:03 UTC

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New package cmenet with initial version 0.1.0
Package: cmenet
Type: Package
Title: Bi-Level Selection of Conditional Main Effects
Version: 0.1.0
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Description: Provides functions for implementing cmenet - a bi-level variable selection method for conditional main effects (see Mak and Wu (2018) <doi:10.1080/01621459.2018.1448828>). CMEs are reparametrized interaction effects which capture the conditional impact of a factor at a fixed level of another factor. Compared to traditional two-factor interactions, CMEs quantify more interpretable interaction effects in many problems of interest (e.g., genomics, molecular engineering, personalized medicine). The current implementation performs variable selection on only binary CMEs, but we are working on an extension for the continuous setting. This work was supported by USARO grant W911NF-14-1-0024.
License: GPL (>= 2)
LazyData: FALSE
Imports: Rcpp (>= 0.12.4), MASS, glmnet, hierNet
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2019-01-13 03:13:15 UTC; smak6
Repository: CRAN
Date/Publication: 2019-01-20 16:10:06 UTC

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New package Bayesrel with initial version 0.1.0
Package: Bayesrel
Type: Package
Title: Bayesian Reliability Estimation
Version: 0.1.0
Author: Julius Pfadt and Don van den Bergh
Maintainer: Julius Pfadt <julius.pfadt@gmail.com>
Description: So far, it provides the most common single test reliability estimates, being: Coefficient Alpha, Guttman's lambda-2/-4/-6, greatest lower bound and Mcdonald's Omega. The Bayesian estimates are provided with credible intervals. The method for the Bayesian estimates, except for omega, is sampling from the posterior inverse Wishart for the covariance matrix based measures. See Murphy (2007) <https://www.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>. Gibbs Sampling from the joint conditional distributions of a single factor model in the case of omega. See Lee (2007, ISBN:978-0-470-02424-9). Methods for the glb are from Moltner and Revelle (2018) <https://www.rdocumentation.org/packages/psych/versions/1.8.10/topics/glb.algebraic>; lambda-4 is from Benton (2015) <doi:10.1007/978-3-319-07503-7_19>; the principal factor analysis is from Schlegel (2017) <https://www.r-bloggers.com/iterated-principal-factor-method-of-factor-analysis-with-r/>; and the analytic alpha interval is from Bonnett and Wright (2014) <doi:10.1002/job.1960>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: LaplacesDemon, Rcsdp, MASS, ggplot2, ggridges, lavaan, plotrix, coda, methods, stats, graphics, Rdpack
RdMacros: Rdpack
RoxygenNote: 6.1.0
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2019-01-14 13:09:08 UTC; julius
Repository: CRAN
Date/Publication: 2019-01-20 16:40:02 UTC

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New package odds.n.ends with initial version 0.1.0
Package: odds.n.ends
Title: Odds Ratios, Contingency Table, and Model Significance from a Generalized Linear Model Object
Version: 0.1.0
Date: 2019-01-07
Author: Jenine Harris <harrisj@wustl.edu>
Maintainer: Jenine Harris <harrisj@wustl.edu>
Description: Computes odds ratios and 95% confidence intervals from a generalized linear model object. It also computes model significance with the chi-squared statistic and p-value and it computes model fit using a contingency table to determine the percent of observations for which the model correctly predicts the value of the outcome. Calculates model sensitivity and specificity.
License: CC0
Encoding: UTF-8
LazyData: true
Imports: MASS
NeedsCompilation: no
Packaged: 2019-01-11 23:33:15 UTC; jenine
Repository: CRAN
Date/Publication: 2019-01-20 15:40:03 UTC

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Package rotl updated to version 3.0.6 with previous version 3.0.5 dated 2018-09-29

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>

Diff between rotl versions 3.0.5 dated 2018-09-29 and 3.0.6 dated 2019-01-20

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 rotl-3.0.6/rotl/inst/doc/meta-analysis.R      |   20 +
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 13 files changed, 1088 insertions(+), 368 deletions(-)

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