Thu, 02 Aug 2018

Package dslabs updated to version 0.4.0 with previous version 0.3.3 dated 2017-11-06

Title: Data Science Labs
Description: Datasets and functions that facilitate data analysis labs in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>

Diff between dslabs versions 0.3.3 dated 2017-11-06 and 0.4.0 dated 2018-08-02

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New package pcgen with initial version 0.1.0.0
Package: pcgen
Type: Package
Title: Reconstruction of Causal Networks for Data with Random Genetic Effects
Version: 0.1.0.0
Author: Willem Kruijer, Pariya Behrouzi, Maria Xose Rodriguez-Alvarez
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Depends: R (>= 3.1.0)
Imports: pcalg, graph, Matrix, stats, MASS, utils, Hmisc, methods, lme4, sommer, ggm
Description: Implements the pcgen algorithm, which is a modified version of the standard pc-algorithm, with specific conditional independence tests and modified orientation rules.
License: GPL-3
Date: 2018-08-01
NeedsCompilation: no
Packaged: 2018-08-01 14:39:27 UTC; behro001
Repository: CRAN
Date/Publication: 2018-08-02 21:20:03 UTC

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Package seqminer updated to version 6.1 with previous version 6.0 dated 2017-05-05

Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph] (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.), Broad Institute / Massachusetts Institute of Technology [cph], Genome Research Ltd (GRL) [cph]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>

Diff between seqminer versions 6.0 dated 2017-05-05 and 6.1 dated 2018-08-02

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 19 files changed, 33 insertions(+), 33 deletions(-)

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Package FNN updated to version 1.1.2 with previous version 1.1 dated 2013-07-31

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

Diff between FNN versions 1.1 dated 2013-07-31 and 1.1.2 dated 2018-08-02

 ChangeLog                        |    8 ++++-
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 27 files changed, 221 insertions(+), 187 deletions(-)

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Package ADMMsigma updated to version 2.1 with previous version 2.0 dated 2018-05-31

Title: Penalized Precision Matrix Estimation via ADMM
Description: Estimates a penalized precision matrix via the alternating direction method of multipliers (ADMM) algorithm. It currently supports a general elastic-net penalty that allows for both ridge and lasso-type penalties as special cases. This package is an alternative to the 'glasso' package. See Boyd et al (2010) <doi:10.1561/2200000016> for details regarding the estimation method.
Author: Matt Galloway [aut, cre]
Maintainer: Matt Galloway <gall0441@umn.edu>

Diff between ADMMsigma versions 2.0 dated 2018-05-31 and 2.1 dated 2018-08-02

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 23 files changed, 324 insertions(+), 172 deletions(-)

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Package Rd2roxygen updated to version 1.7 with previous version 1.6.2 dated 2017-03-30

Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an Rd file to a list, create the 'roxygen' documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities that can help developers build packages using 'roxygen' more easily. The 'formatR' package can be used to reformat the R code in the examples sections so that the code will be more readable.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between Rd2roxygen versions 1.6.2 dated 2017-03-30 and 1.7 dated 2018-08-02

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New package ufs with initial version 0.0.1
Package: ufs
Type: Package
Title: Quantitative Analysis Made Accessible
Version: 0.0.1
Date: 2018-08-01
Authors@R: c(person("Gjalt-Jorn", "Peters", email = "gjalt-jorn@userfriendlyscience.com", role = c("aut", "cre", "ctb")))
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
License: GPL (>= 3)
Description: This is a new version of the 'userfriendlyscience' package, which has grown a bit unwieldy. This first submission contains a number of basic functions to easily format values, work with scales, and format vectors in a single character value. Over time, more functions presently in 'userfriendlyscience' will be migrated over to this package.
URL: https://userfriendlyscience.com
BugReports: https://github.com/matherion/userfriendlyscience/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-02 14:45:04 UTC; micro
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Repository: CRAN
Date/Publication: 2018-08-02 15:30:03 UTC

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New package rolocISCCNBS with initial version 0.1
Package: rolocISCCNBS
Type: Package
Title: A Colour List and Colour Metric Based on the ISCC-NBS System of Color Designation
Version: 0.1
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Description: A colour list and colour metric based on the ISCC-NBS System of Color Designation for use with the 'roloc' package for converting colour specifications to colour names.
License: GPL-2 | GPL-3
Depends: roloc
Imports: methods, colorspace
NeedsCompilation: no
Packaged: 2018-07-30 21:15:35 UTC; pmur002
Repository: CRAN
Date/Publication: 2018-08-02 15:30:06 UTC

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New package polyRAD with initial version 0.5-0
Package: polyRAD
Version: 0.5-0
Date: 2018-07-31
Title: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Authors@R: c(person("Lindsay V.", "Clark", email = "lvclark@illinois.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3881-9252")), person("U.S. National Science Foundation", role = "fnd"))
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>), U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Imports: fastmatch, pcaMethods, methods, Rcpp
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures
LinkingTo: Rcpp
VignetteBuilder: knitr, rmarkdown
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2018) <doi:10.1101/380899>.
License: GPL (>= 2)
URL: https://github.com/lvclark/polyRAD
NeedsCompilation: yes
Packaged: 2018-08-02 14:21:52 UTC; lvclark
Repository: CRAN
Date/Publication: 2018-08-02 15:30:10 UTC

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Package GPCMlasso updated to version 0.1-2 with previous version 0.1-1 dated 2018-02-12

Title: Differential Item Functioning in Generalized Partial Credit Models
Description: Provides a function to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>

Diff between GPCMlasso versions 0.1-1 dated 2018-02-12 and 0.1-2 dated 2018-08-02

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Package gestalt updated to version 0.1.4 with previous version 0.1.2 dated 2018-07-09

Title: Tools for Making and Combining Functions
Description: Provides a suite of function-building tools centered around a (forward) composition operator, %>>>%, which extends the semantics of the 'magrittr' %>% operator and supports 'tidyverse' quasiquotation. It enables you to construct composite functions that can be inspected and transformed as list-like objects. In conjunction with %>>>%, a compact function constructor, fn(), and a function that performs partial application, partial(), are also provided. Both support quasiquotation.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>

Diff between gestalt versions 0.1.2 dated 2018-07-09 and 0.1.4 dated 2018-08-02

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Package nestfs updated to version 0.8.5 with previous version 0.8.4 dated 2018-07-05

Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated linear and logistic regression.
Author: Marco Colombo [aut, cre] (<https://orcid.org/0000-0001-6672-0623>), Felix Agakov [ctb]
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>

Diff between nestfs versions 0.8.4 dated 2018-07-05 and 0.8.5 dated 2018-08-02

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Package gjam updated to version 2.2.5 with previous version 2.2.4 dated 2018-06-02

Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>

Diff between gjam versions 2.2.4 dated 2018-06-02 and 2.2.5 dated 2018-08-02

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New package tidybayes with initial version 1.0.1
Package: tidybayes
Title: Tidy Data and 'Geoms' for Bayesian Models
Version: 1.0.1
Date: 2018-07-30
Authors@R: c(person("Matthew", "Kay", role = c("aut", "cre"), email = "mjskay@umich.edu"))
Maintainer: Matthew Kay <mjskay@umich.edu>
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Depends: R (>= 2.10)
Imports: plyr, dplyr, tidyr, ggplot2 (>= 3.0.0), stringi, stringr, LaplacesDemon, coda, purrr (>= 0.2.3), tibble, MASS, rlang, ggstance, ggridges, grid, forcats, HDInterval, arrayhelpers, tidyselect, magrittr
Suggests: knitr, import, testthat, vdiffr, rstan (>= 2.17.0), runjags, rjags, jagsUI, rstanarm (>= 2.17.2), rstantools, emmeans, broom (>= 0.4.3), dotwhisker, MCMCglmm, bayesplot, modelr, brms (>= 2.4.0), cowplot, covr, gdtools, rmarkdown, bindrcpp
License: GPL (>= 3)
Language: en-US
BugReports: https://github.com/mjskay/tidybayes/issues/new
URL: http://mjskay.github.io/tidybayes, https://github.com/mjskay/tidybayes
VignetteBuilder: knitr
RoxygenNote: 6.1.0
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-08-02 12:27:13 UTC; matth
Author: Matthew Kay [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-02 13:10:03 UTC

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Package strip updated to version 0.1.7 with previous version 0.1.1 dated 2017-01-12

Title: Lighten your R Model Outputs
Description: The strip function deletes components of R model outputs that are useless for specific purposes, such as predict[ing], print[ing], summary[izing], etc.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between strip versions 0.1.1 dated 2017-01-12 and 0.1.7 dated 2018-08-02

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 13 files changed, 81 insertions(+), 32 deletions(-)

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Package heatwaveR updated to version 0.3.3 with previous version 0.3.0 dated 2018-06-22

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 GENEAclassify updated to version 1.4.13 with previous version 1.4.12 dated 2018-07-07

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

Diff between GENEAclassify versions 1.4.12 dated 2018-07-07 and 1.4.13 dated 2018-08-02

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Package cxhull updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-31

Title: Convex Hull
Description: Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
Author: C. B. Barber [cph] (author of the Qhull library), The Geometry Center [cph], Stéphane Laurent [cph, aut, cre]
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>

Diff between cxhull versions 0.1.0 dated 2018-07-31 and 0.1.1 dated 2018-08-02

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New package SparseMDC with initial version 0.99.5
Package: SparseMDC
Type: Package
Title: Implementation of SparseMDC Algorithm
Version: 0.99.5
Authors@R: c( person("Martin", "Barron", email = "mbarron2@nd.edu",role = c("aut")), person("Jun", "Li", email = "jun.li@nd.edu",role = c("aut","cre")) )
Description: Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
License: GPL-3
Imports: stats, foreach, parallel, doParallel
Depends: R (>= 3.1.0), doRNG
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-01 16:44:39 UTC; Martin
Author: Martin Barron [aut], Jun Li [aut, cre]
Maintainer: Jun Li <jun.li@nd.edu>
Repository: CRAN
Date/Publication: 2018-08-02 12:40:16 UTC

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Package rmake updated to version 1.0.1 with previous version 1.0.0 dated 2018-03-22

Title: Makefile Generator for R Analytical Projects
Description: Creates and maintains a build process for complex analytic tasks in R. Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process by (in parallel) executing build commands in order to update results accordingly to given dependencies on changed data or updated source files.
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>

Diff between rmake versions 1.0.0 dated 2018-03-22 and 1.0.1 dated 2018-08-02

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New package omu with initial version 1.0.2
Package: omu
Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Version: 1.0.2
Authors@R: person("Connor", "Tiffany", email = "crtiffany@ucdavis.edu", role = c("aut", "cre"))
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data using the package 'KEGGREST' to access the 'KEGG' API.
Depends: R (>= 3.3.0)
biocViews:
Imports: plyr, dplyr, stringr, KEGGREST, reshape2, ggfortify, ggplot2, magrittr, tidyr
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/connor-reid-tiffany/Omu, https://www.kegg.jp/kegg/rest/keggapi.html
BugReports: https://github.com/connor-reid-tiffany/Omu/issues
NeedsCompilation: no
Packaged: 2018-08-02 02:18:17 UTC; connor
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>
Repository: CRAN
Date/Publication: 2018-08-02 12:40:03 UTC

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Package MultiFit updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-31

Title: Multivariate Multiscale Framework for Independence Tests
Description: Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky and Ma (2018) <arXiv:1806.06777>.
Author: S. Gorsky, L. Ma
Maintainer: S. Gorsky <s.gorsky@duke.edu>

Diff between MultiFit versions 0.1.0 dated 2018-07-31 and 0.1.1 dated 2018-08-02

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New package jsonstat with initial version 0.0.1
Package: jsonstat
Type: Package
Title: Interface to 'JSON-stat'
Version: 0.0.1
Author: Kim Seonghyun [aut, cre]
Maintainer: Kim Seonghyun <zedoul@gmail.com>
Authors@R: c( person("Kim", "Seonghyun", "", "zedoul@gmail.com", c("aut", "cre")) )
Description: Interface to 'JSON-stat' <https://json-stat.org/>, a simple lightweight 'JSON' format for data dissemination.
URL: https://github.com/zedoul/jsonstat
BugReports: https://github.com/zedoul/jsonstat/issues
Depends: R (>= 3.3.0)
Imports: cli, dplyr, jsonlite, rlang
Suggests: knitr, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-02 07:27:47 UTC; zedoul
Repository: CRAN
Date/Publication: 2018-08-02 12:40:06 UTC

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Package hipread updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-30

Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by many census data providers. Also allows for reading of data in chunks, and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut, cre], Derek Burk [ctb], Joe Grover [ctb], Mark Padgham [ctb], Hadley Wickham [ctb] (Code adapted from readr), Jim Hester [ctb] (Code adapted from readr), Romain Francois [ctb] (Code adapted from readr), R Core Team [ctb] (Code adapted from readr), RStudio [cph, fnd] (Code adapted from readr), Jukka Jylänki [ctb, cph] (Code adapted from readr), Mikkel Jørgensen [ctb, cph] (Code adapted from readr), University of Minnesota [cph]
Maintainer: Greg Freedman Ellis <gfellis@umn.edu>

Diff between hipread versions 0.1.0 dated 2018-07-30 and 0.1.1 dated 2018-08-02

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New package HCT with initial version 0.1.0
Package: HCT
Type: Package
Title: Calculates Significance Criteria and Power for a Single Arm Trial
Version: 0.1.0
Author: David A. Schoenfeld
Maintainer: David A. Schoenfeld <dschoenfeld@mgh.harvard.edu>
Description: Given a database of previous treatment/placebo estimates, their standard errors and sample sizes, the program calculates a significance criteria and power estimate that takes into account the among trial variation.
Depends: R (>= 2.10), rstan
Suggests: testthat
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-01 14:37:03 UTC; das15
Repository: CRAN
Date/Publication: 2018-08-02 12:30:12 UTC

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New package GFE with initial version 0.1.0
Package: GFE
Type: Package
Title: Gross Flows Estimation under Complex Surveys
Version: 0.1.0
Author: Acero William <wfaceror@unal.edu.co>, Gutiérrez Andrés <andres.gutierrez@un.org>, Trujillo Leonardo <ltrujillo@unal.edu.co>
Maintainer: Acero William <wfaceror@unal.edu.co>
Description: The philosophy in the package is described in Stasny (1988) <doi:10.2307/1391558> and Gutiérrez, A., Trujillo, L. & Silva, N. (2014), <ISSN:1492-0921> to estimate the gross flows under complex surveys using a Markov chain approach with non response.
Depends: R (>= 3.3.1)
License: GPL (>= 2)
Encoding: latin1
LazyData: true
RoxygenNote: 6.0.1
Repository: CRAN
Imports: dplyr, data.table, TeachingSampling
NeedsCompilation: no
Packaged: 2018-08-01 14:29:18 UTC; wacero
Date/Publication: 2018-08-02 12:10:10 UTC

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New package fieldRS with initial version 0.1.0
Package: fieldRS
Type: Package
Title: Remote Sensing Field Work Tools
Version: 0.1.0
Date: 2018-08-01
Authors@R: person("Ruben", "Remelgado", role = c("aut", "cre"), email="ruben.remelgado@uni-wuerzburg.de")
URL: https://github.com/RRemelgado/fieldRS/
BugReports: https://github.com/RRemelgado/fieldRS/issues/
Maintainer: Ruben Remelgado <ruben.remelgado@uni-wuerzburg.de>
Description: In remote sensing, designing a field campaign to collect ground-truth data can be a challenging task. We need to collect representative samples while accounting for issues such as budget constraints and limited accessibility created by e.g. poor infrastructure. As suggested by Olofsson et al. (2014) <doi:10.1016/j.rse.2014.02.015>, this demands the establishment of best-practices to collect ground-truth data that avoid the waste of time and funds. 'fieldRS' addresses this issue by helping scientists and practitioners design field campaigns through the identification of priority sampling sites, the extraction of potential sampling plots and the conversion of plots into consistent training and validation samples that can be used in e.g. land cover classification.
LazyData: TRUE
Imports: raster, sp, caret, rgdal, ggplot2, grDevices, rsMove, spatialEco, rgeos, RStoolbox
RoxygenNote: 6.0.1
License: GPL (>= 3)
Suggests: knitr, rmarkdown, kableExtra, imager
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-01 15:22:53 UTC; rus14jh
Author: Ruben Remelgado [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-02 12:10:06 UTC

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Package dlnm updated to version 2.3.5 with previous version 2.3.4 dated 2017-12-06

Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre], Ben Armstrong [aut], Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>

Diff between dlnm versions 2.3.4 dated 2017-12-06 and 2.3.5 dated 2018-08-02

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Package disto updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-19

Title: Unified Interface to Distance, Dissimilarity, Similarity Matrices
Description: Provides a high level API to interface over sources storing distance, dissimilarity, similarity matrices with matrix style extraction, replacement and other utilities. Currently, in-memory dist object backend is supported.
Author: KS Srikanth [aut, cre]
Maintainer: KS Srikanth <sri.teach@gmail.com>

Diff between disto versions 0.1.0 dated 2018-07-19 and 0.2.0 dated 2018-08-02

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New package cromwellDashboard with initial version 0.5.1
Package: cromwellDashboard
Type: Package
Title: A Dashboard to Visualize Scientific Workflows in 'Cromwell'
Version: 0.5.1
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Description: A dashboard supports the usage of 'cromwell'. 'Cromwell' is a scientific workflow engine for command line users. This package utilizes 'cromwell' REST APIs and provides these convenient functions: timing diagrams for running workflows, 'cromwell' engine status, a tabular workflow list. For more information about 'cromwell', visit <http://cromwell.readthedocs.io>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinydashboard, stringr, httr, dplyr, DT
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-02 05:42:05 UTC; xzhan9
Repository: CRAN
Date/Publication: 2018-08-02 12:40:13 UTC

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New package BivGeo with initial version 1.0.1
Package: BivGeo
Type: Package
Title: Basu-Dhar Bivariate Geometric Distribution
Version: 1.0.1
Author: Ricardo Puziol de Oliveira and Jorge Alberto Achcar
Maintainer: Ricardo Puziol de Oliveira <rpuziol.oliveira@gmail.com>
Description: Computes the joint probability mass function, the joint cumulative distribution, the correlation coefficient and generate random deviates from the Basu-Dhar bivariate geometric distribution. The package also computes the joint survival function in presence of cure fraction using the mixture model approach (For more details, see Achcar et. al (2016) <doi:10.1080/02664763.2015.1117589> and de Oliveira et. al (2018) <doi:10.1080/02664763.2018.1495701>).
Depends: R (>= 3.0.2)
Imports: stats
RoxygenNote: 6.0.1
Encoding: UTF-8
NeedsCompilation: no
LazyData: TRUE
License: GPL (>= 2)
Packaged: 2018-08-01 17:36:53 UTC; ricky
Repository: CRAN
Date/Publication: 2018-08-02 12:30:15 UTC

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Package bayesplot updated to version 1.6.0 with previous version 1.5.0 dated 2018-03-30

Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, model checking, and MCMC diagnostics. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre], Tristan Mahr [aut], Paul-Christian Bürkner [ctb], Martin Modrák [ctb], Malcolm Barrett [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between bayesplot versions 1.5.0 dated 2018-03-30 and 1.6.0 dated 2018-08-02

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Package tribe updated to version 0.1.7 with previous version 0.1.6 dated 2017-11-14

Title: Play with the Tribe of Attributes
Description: Functions to make manipulation of object attributes easier. It also contains a few functions that extend the 'dplyr' package for data manipulation, and it provides new pipe operators, including the pipe '%@>%' similar to the 'magrittr' '%>%', but with the additional functionality to enable attributes propagation.
Author: Paul Poncet [aut, cre], Stefan Milton Bache [aut] (for functions copied or modified from the 'magrittr' package), Hadley Wickham [aut] (for functions copied or modified from the 'magrittr' package)
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between tribe versions 0.1.6 dated 2017-11-14 and 0.1.7 dated 2018-08-02

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New package sparkbq with initial version 0.1.0
Package: sparkbq
Type: Package
Title: Google 'BigQuery' Support for 'sparklyr'
Version: 0.1.0
Date: 2018-07-31
Authors@R: c(person(family = "Mirai Solutions GmbH", role = "aut", email = "info@mirai-solutions.com"), person("Martin", "Studer", role = "cre", email = "martin.studer@mirai-solutions.com"), person("Nicola", "Lambiase", role = "ctb", email = "nicola.lambiase@mirai-solutions.com"), person("Omer", "Demirel", role = "ctb"))
URL: http://www.mirai-solutions.com, https://github.com/miraisolutions/sparkbq
BugReports: https://github.com/miraisolutions/sparkbq/issues
Description: A 'sparklyr' extension package providing an integration with Google 'BigQuery'. It supports direct import/export where records are directly streamed from/to 'BigQuery'. In addition, data may be imported/exported via intermediate data extracts on Google 'Cloud Storage'.
Depends: R (>= 3.3.2)
Imports: sparklyr (>= 0.7.0)
Suggests: dplyr
License: GPL-3 | file LICENSE
SystemRequirements: Spark (>= 2.2.x)
Encoding: UTF-8
LazyData: yes
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-31 16:17:56 UTC; mstuder
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], Nicola Lambiase [ctb], Omer Demirel [ctb]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Repository: CRAN
Date/Publication: 2018-08-02 11:40:02 UTC

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New package simode with initial version 1.0.1
Package: simode
Type: Package
Title: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching
Version: 1.0.1
Authors@R: c( person("Itai", "Dattner", email = "idattner@stat.haifa.ac.il", role = c("aut", "cre")), person("Rami", "Yaari", email = "ramiyaari@gmail.com", role = "aut"))
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>.
Depends: R (>= 3.4.0)
Imports: deSolve, pracma, quadprog
Suggests: parallel, Rcgmin, Rvmmin, R.rsp
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2018-07-31 12:10:40 UTC; ramiy
Author: Itai Dattner [aut, cre], Rami Yaari [aut]
Maintainer: Itai Dattner <idattner@stat.haifa.ac.il>
Repository: CRAN
Date/Publication: 2018-08-02 12:00:03 UTC

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New package rmi with initial version 0.1.1
Package: rmi
Title: Mutual Information Estimators
Version: 0.1.1
Author: Isaac Michaud [cre, aut]
Maintainer: Isaac Michaud <ijmichau@ncsu.edu>
Description: Provides mutual information estimators based on k-nearest neighbor estimators by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138>, S. Gao, et al. (2015) <http://proceedings.mlr.press/v38/gao15.pdf> and local density estimators by W. Gao, et al. (2017) <doi:10.1109/ISIT.2017.8006749>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
LinkingTo: Rcpp, RcppArmadillo, BH
Imports: Rcpp, stats, graphics
Suggests: testthat, parallel, tgp
NeedsCompilation: yes
Packaged: 2018-07-31 17:15:50 UTC; isaacmichaud
Repository: CRAN
Date/Publication: 2018-08-02 11:40:06 UTC

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New package readmnist with initial version 1.0.6
Package: readmnist
Type: Package
Title: Read MNIST Dataset
Version: 1.0.6
Author: Jiang Junfeng
Maintainer: Jiang Junfeng <a412133593@gmail.com>
Description: You can use the function Read.mnist() to read data and arrange them properly from MNIST dataset (the open handwriting digit database <http://yann.lecun.com/exdb/mnist/>). With this package, you can conveniently get all of necessary informations and then immediately start to check whether your machine learning algorithm works well. It can automatically recognize the type of dataset and returns the informations in corresponding structure.
License: GPL
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-07-31 16:32:37 UTC; coldog
Repository: CRAN
Date/Publication: 2018-08-02 11:40:09 UTC

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Package FSelectorRcpp updated to version 0.2.1 with previous version 0.1.10 dated 2018-06-27

Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf> with a sparse matrix support. It is also equipped with a parallel backend.
Author: Zygmunt Zawadzki [aut, cre], Marcin Kosinski [aut], Krzysztof Slomczynski [ctb], Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between FSelectorRcpp versions 0.1.10 dated 2018-06-27 and 0.2.1 dated 2018-08-02

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Package reportROC updated to version 3.1 with previous version 3.0 dated 2017-10-30

Title: An Easy Way to Report ROC Analysis
Description: Provides an easy way to report the results of ROC analysis, including: 1. an ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (accuracy), SEN (sensitivity), SPE (specificity), PLR (positive likelihood ratio), NLR (negative likelihood ratio), PPV (positive predictive value), NPV (negative predictive value).
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

Diff between reportROC versions 3.0 dated 2017-10-30 and 3.1 dated 2018-08-02

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Package LncFinder updated to version 1.1.3 with previous version 1.0.0 dated 2017-02-06

Title: LncRNA Identification and Analysis Using Heterologous Features
Description: Long non-coding RNAs identification and analysis. Default models are trained with human, mouse and wheat datasets by employing SVM. Features are based on intrinsic composition of sequence, EIIP value (electron-ion interaction pseudopotential), and secondary structure. This package can also extract other classic features and build new classifiers. Reference: Han SY., Liang YC., Li Y., et al. (2018) <doi:10.1093/bib/bby065>.
Author: Siyu HAN [aut, cre], Ying LI [aut], Yanchun LIANG [aut]
Maintainer: Siyu HAN <hansy15@mails.jlu.edu.cn>

Diff between LncFinder versions 1.0.0 dated 2017-02-06 and 1.1.3 dated 2018-08-02

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Package princurve updated to version 2.1.2.1 with previous version 2.1.2 dated 2018-07-24

Title: Fits a Principal Curve in Arbitrary Dimension
Description: Fitting a principal curve to a data matrix in arbitrary dimensions.
Author: Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (HenrikBengtsson), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

Diff between princurve versions 2.1.2 dated 2018-07-24 and 2.1.2.1 dated 2018-08-02

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Package RMongo (with last version 0.0.25) was removed from CRAN

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

2013-09-08 0.0.25
2013-03-08 0.0.23
2011-10-09 0.0.21
2011-10-01 0.0.20

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