Mon, 09 Sep 2019

Package updog updated to version 1.1.1 with previous version 1.1.0 dated 2019-07-31

Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allelic bias, overdispersion, and sequencing error. The main function is flexdog(), which allows the specification of many different genotype distributions. An experimental function that takes into account varying levels of relatedness is implemented in mupdog(). Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2019) <doi:10.1101/751784> for details on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>

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Package seqgendiff updated to version 1.1.1 with previous version 1.1.0 dated 2019-08-05

Title: RNA-Seq Generation/Modification for Simulation
Description: Generates/modifies RNA-seq data for use in simulations. We provide a suite of functions that will add a known amount of signal to a real RNA-seq dataset. The advantage of using this approach over simulating under a theoretical distribution is that common/annoying aspects of the data are more preserved, giving a more realistic evaluation of your method. The main functions are select_counts(), thin_diff(), thin_lib(), thin_gene(), thin_2group(), thin_all(), and effective_cor(). See Gerard (2019) <doi:10.1101/758524> for details on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>

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Package provSummarizeR updated to version 1.2 with previous version 1.1 dated 2019-06-18

Title: Summarizes Provenance Related to Inputs and Outputs of a Script or Console Commands
Description: Reads the provenance collected by the 'rdt' or 'rdtLite' packages, or other tools providing compatible PROV JSON output created by the execution of a script, and provides a human-readable summary identifying the input and output files, the script used (if any), errors and warnings produced, and the environment in which it was executed. It can also optionally package all the files into a zip file. The exact format of the JSON created by 'rdt' and 'rdtLite' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about 'rdtLite' and associated tools is available at <https://github.com/End-to-end-provenance/> and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Barbara Lerner [cre], Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>

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Package widyr updated to version 0.1.2 with previous version 0.1.1 dated 2018-03-10

Title: Widen, Process, then Re-Tidy Data
Description: Encapsulates the pattern of untidying data into a wide matrix, performing some processing, then turning it back into a tidy form. This is useful for several operations such as co-occurrence counts, correlations, or clustering that are mathematically convenient on wide matrices.
Author: David Robinson [aut, cre], Kanishka Misra [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>

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Package huge updated to version 1.3.3 with previous version 1.3.2 dated 2019-04-08

Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline. In preprocessing stage, the nonparanormal(npn) transformation is applied to help relax the normality assumption. In the graph estimation stage, the graph structure is estimated by Meinshausen-Buhlmann graph estimation or the graphical lasso, and both methods can be further accelerated by the lossy screening rule preselecting the neighborhood of each variable by correlation thresholding. We target on high-dimensional data analysis usually d >> n, and the computation is memory-optimized using the sparse matrix output. We also provide a computationally efficient approach, correlation thresholding graph estimation. Three regularization/thresholding parameter selection methods are included in this package: (1)stability approach for regularization selection (2) rotation information criterion (3) extended Bayesian information criterion which is only available for the graphical lasso.
Author: Haoming Jiang, Xinyu Fei, Han Liu, Kathryn Roeder, John Lafferty, Larry Wasserman, Xingguo Li, and Tuo Zhao
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>

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Package heatwaveR updated to version 0.4.1 with previous version 0.4.0 dated 2019-07-11

Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb] (<https://orcid.org/0000-0002-0705-1287>), Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>

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Package languageserver updated to version 0.3.0 with previous version 0.2.9 dated 2019-03-28

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package fingertipsR updated to version 0.2.8 with previous version 0.2.7 dated 2019-07-18

Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre], Julian Flowers [aut, ctb], Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>), Duncan Gormansway [ctb], Carl Ganz [ctb], David Whiting [ctb], Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>

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Package fingertipscharts updated to version 0.0.9 with previous version 0.0.8 dated 2019-07-18

Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>

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Package mcca updated to version 0.6.0 with previous version 0.5.0 dated 2019-02-05

Title: Multi-Category Classification Accuracy
Description: It contains six common multi-category classification accuracy evaluation measures. All of these measures could be found in Li and Ming (2019) <doi:10.1002/sim.8103>. Specifically, Hypervolume Under Manifold (HUM), described in Li and Fine (2008) <doi:10.1093/biostatistics/kxm050>. Correct Classification Percentage (CCP), Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), R-Squared Value (RSQ), described in Li, Jiang and Fine (2013) <doi:10.1093/biostatistics/kxs047>. Polytomous Discrimination Index (PDI), described in Van Calster et al. (2012) <doi:10.1007/s10654-012-9733-3>. Li et al. (2018) <doi:10.1177/0962280217692830>. We described all these above measures and our mcca package in Li, Gao and D'Agostino (2019) <doi:10.1002/sim.8103>.
Author: Ming Gao, Jialiang Li
Maintainer: Ming Gao <gaoming@umich.edu>

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Package NNS updated to version 0.4.5 with previous version 0.4.4 dated 2019-08-08

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

Diff between NNS versions 0.4.4 dated 2019-08-08 and 0.4.5 dated 2019-09-09

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Package MomTrunc updated to version 4.51 with previous version 3.19 dated 2019-07-19

Title: Moments of Folded and Doubly Truncated Multivariate Distributions
Description: It computes the raw moments for the truncated and folded multivariate normal, Skew-normal (SN), Extended skew normal (ESN) and Student's t-distribution. It also offers specific functions to compute the mean and variance-covariance matrix as well as the cumulative distribution function (cdf) for the folded normal, SN, ESN, and folded t-distribution. Density and random deviates are offered for the ESN (SN as particular case) distribution. Most algorithms are extensions based on Kan, R., & Robotti, C. (2017) <doi:10.1080/10618600.2017.1322092>.
Author: Christian E. Galarza, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

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Package activity updated to version 1.3 with previous version 1.2 dated 2019-01-16

Title: Animal Activity Statistics
Description: Provides functions to express clock time data relative to anchor points (typically solar); fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; evaluate variation in linear variables with time (or other circular variables).
Author: Marcus Rowcliffe
Maintainer: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>

Diff between activity versions 1.2 dated 2019-01-16 and 1.3 dated 2019-09-09

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Package GGIR updated to version 1.10-4 with previous version 1.10-3 dated 2019-09-08

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb], Joan Capdevila Pujol [ctb], Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

Diff between GGIR versions 1.10-3 dated 2019-09-08 and 1.10-4 dated 2019-09-09

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Package apollo updated to version 0.0.8 with previous version 0.0.7 dated 2019-05-08

Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds has developed flexible code for the estimation and application of choice models in R. Users are able to write their own model functions or use a mix of already available ones. Random heterogeneity, both continuous and discrete and at the level of individuals and choices, can be incorporated for all models. There is support for both standalone models and hybrid model structures. Both classical and Bayesian estimation is available, and multiple discrete continuous models are covered in addition to discrete choice. Multi-threading processing is supported for estimation and a large number of pre and post-estimation routines, including for computing posterior (individual-level) distributions are available. For examples, a manual, and a support forum, visit www.ApolloChoiceModelling.com. For more information on choice models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess, S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview of the field.
Author: Stephane Hess [aut], David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>

Diff between apollo versions 0.0.7 dated 2019-05-08 and 0.0.8 dated 2019-09-09

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Package qrng updated to version 0.0-7 with previous version 0.0-6 dated 2019-08-07

Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in high dimensions.
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between qrng versions 0.0-6 dated 2019-08-07 and 0.0-7 dated 2019-09-09

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Package jack updated to version 1.1.0 with previous version 1.0.0 dated 2019-08-25

Title: Jack, Zonal, and Schur Polynomials
Description: Symbolic calculation and evaluation of the Jack polynomials, zonal polynomials, and Schur polynomials. Mainly based on Demmel & Koev's paper (2006) <doi:10.1090/S0025-5718-05-01780-1>. Zonal polynomials and Schur polynomials are particular cases of Jack polynomials. Zonal polynomials appear in random matrix theory. Schur polynomials appear in the field of combinatorics.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

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Package EpiCurve updated to version 2.2-1 with previous version 2.1-1 dated 2018-04-24

Title: Plot an Epidemic Curve
Description: Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>

Diff between EpiCurve versions 2.1-1 dated 2018-04-24 and 2.2-1 dated 2019-09-09

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New package corporaexplorer with initial version 0.6.2
Package: corporaexplorer
Type: Package
Title: A 'Shiny' App for Exploration of Text Collections
Version: 0.6.2
Authors@R: person("Kristian Lundby", "Gjerde", email = "kristian.gjerde@gmail.com", role = c("aut", "cre"))
Description: Facilitates dynamic exploration of text collections through an intuitive graphical user interface. The package contains 1) a helper function to convert a data frame to a 'corporaexplorerobject', 2) a 'Shiny' app for fast and flexible exploration of a 'corporaexplorerobject', and 3) a 'Shiny' app for simple retrieval/extraction of documents from a 'corporaexplorerobject' in a reading-friendly format. The intended primary audience is qualitatively oriented researchers who rely on close reading of textual documents as part of their academic activity. Auto-scrolling is enabled by the 'jquery.scrollTo' plugin, see <https://github.com/flesler/jquery.scrollTo>. For 'shinytest' to work, 'PhantomJS' (<http://phantomjs.org/>) is required.
Depends: R (>= 3.0.0)
Imports: data.table, dplyr, forcats, ggplot2, lubridate, magrittr, padr, plyr, RColorBrewer, re2r, rlang, rmarkdown, scales, shiny, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, stringi, stringr, tibble, tidyr, zoo
Suggests: shinytest, testthat
License: GPL-3
Date/Publication: 2019-09-09 11:20:02 UTC
LazyData: true
RoxygenNote: 6.1.1
Encoding: UTF-8
URL: https://github.com/kgjerde/corporaexplorer
BugReports: https://github.com/kgjerde/corporaexplorer/issues
NeedsCompilation: no
Packaged: 2019-09-07 11:05:22 UTC; Kristian
Author: Kristian Lundby Gjerde [aut, cre]
Maintainer: Kristian Lundby Gjerde <kristian.gjerde@gmail.com>
Repository: CRAN

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New package leri with initial version 0.0.1
Package: leri
Title: Access Landscape Evaporative Response Index Raster Data
Version: 0.0.1
Authors@R: person(given = "Max", family = "Joseph", role = c("aut", "cre"), email = "maxwell.b.joseph@colorado.edu", comment = c(ORCID = "0000-0002-7745-9990"))
Description: Finds and downloads Landscape Evaporative Response Index (LERI) data, then reads the data into 'R' using the 'raster' package. The LERI product measures anomalies in actual evapotranspiration, to support drought monitoring and early warning systems. More info on LERI is available at <https://www.esrl.noaa.gov/psd/leri/>.
License: GPL-3
URL: https://github.com/earthlab/leri
BugReports: https://github.com/earthlab/leri/issues
Imports: ncdf4, raster
Suggests: covr, knitr, maptools, rmarkdown, sf, sp, testthat, viridis
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-09-06 17:42:28 UTC; max
Author: Max Joseph [aut, cre] (<https://orcid.org/0000-0002-7745-9990>)
Maintainer: Max Joseph <maxwell.b.joseph@colorado.edu>
Repository: CRAN
Date/Publication: 2019-09-09 11:00:02 UTC

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New package dwlm with initial version 0.1.0
Package: dwlm
Type: Package
Title: Doubly Weighted Linear Model
Version: 0.1.0
Date: 2019-09-01
Author: Hugo Gasca-Aragon [aut,cre]
Maintainer: Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>
Description: This linear model solution is useful when both predictor and response have associated uncertainty. The doubly weights linear model solution is invariant on which quantity is used as predictor or response. Based on the results by Reed(1989) <doi:10.1119/1.15963> and Ripley & Thompson(1987) <doi:10.1039/AN9871200377>.
Depends: stats (>= 3.4.0), R (>= 3.4.0)
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-09-06 11:18:30 UTC; hugo_
Repository: CRAN
Date/Publication: 2019-09-09 10:20:02 UTC

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New package ccostr with initial version 0.1.0
Package: ccostr
Type: Package
Title: Estimation of Mean Costs in Censored Data
Version: 0.1.0
Authors@R: c( person("Lars", "Boerty", email = "lars.borty@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3715-8528")), person("Rasmus", "Broendum", role = "aut", comment = c(ORCID = "0000-0001-5537-6767")), person("Martin", "Boegsted", role = "aut", comment = c(ORCID = "0000-0001-9192-1814")), person("Haematology Research Unit - Aalborg", role = "cph"))
Description: Implementation of estimators for inferring the mean of censored cost data. Including the estimators BT from Bang and Tsiatis (2000) <doi:10.1093/biomet/87.2.329> and ZT from Zhao and Tian (2001) <doi:10.1111/j.0006-341X.2001.01002.x>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: rmarkdown, parallel, testthat (>= 2.1.0)
VignetteBuilder: knitr
Imports: ggplot2, dplyr, tibble, knitr, msm, forcats, rlang, data.table, survival, Rdpack
Depends: R (>= 3.5.0)
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2019-09-06 10:34:08 UTC; larsn
Author: Lars Boerty [aut, cre] (<https://orcid.org/0000-0002-3715-8528>), Rasmus Broendum [aut] (<https://orcid.org/0000-0001-5537-6767>), Martin Boegsted [aut] (<https://orcid.org/0000-0001-9192-1814>), Haematology Research Unit - Aalborg [cph]
Maintainer: Lars Boerty <lars.borty@gmail.com>
Repository: CRAN
Date/Publication: 2019-09-09 10:10:02 UTC

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Package RcmdrPlugin.NMBU updated to version 1.8.11 with previous version 1.8.10 dated 2019-08-23

Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between RcmdrPlugin.NMBU versions 1.8.10 dated 2019-08-23 and 1.8.11 dated 2019-09-09

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Package Rborist updated to version 0.2-2 with previous version 0.2-1 dated 2019-09-05

Title: Extensible, Parallelizable Implementation of the Random Forest Algorithm
Description: Scalable implementation of classification and regression forests, as described by Breiman (2001), <DOI:10.1023/A:1010933404324>.
Author: Mark Seligman
Maintainer: Mark Seligman <mseligman@suiji.org>

Diff between Rborist versions 0.2-1 dated 2019-09-05 and 0.2-2 dated 2019-09-09

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Package googleAuthR updated to version 1.1.1 with previous version 1.1.0 dated 2019-09-07

Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Jennifer Bryan [ctb], Johann deBoer [ctb], Neal Richardson [ctb], David Kulp [ctb], Joe Cheng [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

Diff between googleAuthR versions 1.1.0 dated 2019-09-07 and 1.1.1 dated 2019-09-09

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 inst/doc/building.html                    |    4 ++--
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Package biglasso updated to version 1.3-7 with previous version 1.3-6 dated 2017-05-04

Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for ultrahigh-dimensional, multi-gigabyte data sets that cannot be loaded into memory. It's much more memory- and computation-efficient as compared to existing lasso-fitting packages like 'glmnet' and 'ncvreg', thus allowing for very powerful big data analysis even with an ordinary laptop.
Author: Yaohui Zeng [aut,cre], Patrick Breheny [ctb]
Maintainer: Yaohui Zeng <yaohui.zeng@gmail.com>

Diff between biglasso versions 1.3-6 dated 2017-05-04 and 1.3-7 dated 2019-09-09

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Package shadowtext updated to version 0.0.6 with previous version 0.0.5 dated 2019-05-29

Title: Shadow Text Grob and Layer
Description: Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between shadowtext versions 0.0.5 dated 2019-05-29 and 0.0.6 dated 2019-09-09

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 NAMESPACE                 |   46 +++--
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Package estimatr updated to version 0.20.0 with previous version 0.18.0 dated 2019-05-26

Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre], Jasper Cooper [aut], Alexander Coppock [aut], Macartan Humphreys [aut], Luke Sonnet [aut], Neal Fultz [ctb], Lily Medina [ctb], Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

Diff between estimatr versions 0.18.0 dated 2019-05-26 and 0.20.0 dated 2019-09-09

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 18 files changed, 218 insertions(+), 179 deletions(-)

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