Sat, 15 Jun 2019

Package castor updated to version 1.4.1 with previous version 1.4.0 dated 2019-06-14

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

Diff between castor versions 1.4.0 dated 2019-06-14 and 1.4.1 dated 2019-06-15

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More information about castor at CRAN
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Package statnetWeb updated to version 0.5.4 with previous version 0.5.0 dated 2018-07-21

Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet' software <https://github.com/statnet>.
Author: Martina Morris [cre, aut], Emily Beylerian [aut], Kirk Li [ctb], Samuel Jenness [ctb]
Maintainer: Martina Morris <morrism@uw.edu>

Diff between statnetWeb versions 0.5.0 dated 2018-07-21 and 0.5.4 dated 2019-06-15

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Package openCR updated to version 1.4.0 with previous version 1.3.5 dated 2019-03-10

Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between openCR versions 1.3.5 dated 2019-03-10 and 1.4.0 dated 2019-06-15

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More information about openCR at CRAN
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Package urlshorteneR updated to version 1.1.1 with previous version 0.9.2 dated 2016-02-14

Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening Services
Description: Allows using two URL shortening services, which also provide expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth2) and 'is.gd' (no API key).
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>

Diff between urlshorteneR versions 0.9.2 dated 2016-02-14 and 1.1.1 dated 2019-06-15

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More information about urlshorteneR at CRAN
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Package assist updated to version 3.1.5 with previous version 3.1.4 dated 2019-06-02

Title: A Suite of R Functions Implementing Spline Smoothing Techniques
Description: A comprehensive package for fitting various non-parametric/semi-parametric linear/nonlinear fixed/mixed smoothing spline models.
Author: Yuedong Wang <yuedong@pstat.ucsb.edu>, and Chunlei Ke <chunlei_ke@yahoo.com>.
Maintainer: Yuedong Wang <yuedong@pstat.ucsb.edu>

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More information about assist at CRAN
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Package edpclient (with last version 0.5.1) was removed from CRAN

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

2018-04-24 0.5.1
2018-03-05 0.3.1
2017-08-24 0.2.0
2017-05-30 0.1.0
2017-05-28 0.0.1

Permanent link
Package OutlierDetection updated to version 0.1.1 with previous version 0.1.0 dated 2019-02-07

Title: Outlier Detection
Description: To detect outliers using different methods namely model based outlier detection (Barnett, V. 1978 <https://www.jstor.org/stable/2347159>), distance based outlier detection (Hautamaki, V., Karkkainen, I., and Franti, P. 2004 <http://cs.uef.fi/~franti/papers.html>), dispersion based outlier detection (Jin, W., Tung, A., and Han, J. 2001 <https://link.springer.com/chapter/10.1007/0-387-25465-X_7>), depth based outlier detection (Johnson, T., Kwok, I., and Ng, R.T. 1998 <http://www.aaai.org/Library/KDD/1998/kdd98-038.php>) and density based outlier detection (Ester, M., Kriegel, H.-P., Sander, J., and Xu, X. 1996 <https://dl.acm.org/citation.cfm?id=3001507>). This package provides labelling of observations as outliers and outlierliness of each outlier. For univariate, bivariate and trivariate data, visualization is also provided.
Author: Vinay Tiwari, Akanksha Kashikar
Maintainer: Vinay Tiwari <vinaystiwari786@gmail.com>

Diff between OutlierDetection versions 0.1.0 dated 2019-02-07 and 0.1.1 dated 2019-06-15

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Package detrendr updated to version 0.6.2 with previous version 0.6.1 dated 2019-04-13

Title: Detrend Images
Description: Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between detrendr versions 0.6.1 dated 2019-04-13 and 0.6.2 dated 2019-06-15

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Package strex updated to version 1.1.0 with previous version 1.0.3 dated 2019-06-04

Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged: it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between strex versions 1.0.3 dated 2019-06-04 and 1.1.0 dated 2019-06-15

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Package photobiologyInOut updated to version 0.4.20 with previous version 0.4.19 dated 2018-12-13

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiologyInOut versions 0.4.19 dated 2018-12-13 and 0.4.20 dated 2019-06-15

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New package unikn with initial version 0.1.0
Package: unikn
Type: Package
Title: Graphical Elements of the University of Konstanz's Corporate Design
Version: 0.1.0
Date: 2019-06-14
Authors@R: c(person("Hansjoerg", "Neth", role = c("aut", "cre"), email = "h.neth@uni.kn"), person("Nico", "Gradwohl", role = "aut"))
Author: Hansjoerg Neth [aut, cre], Nico Gradwohl [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other institutions and purposes.
Depends: R (>= 3.4.0)
Imports: utils
Suggests: knitr, rmarkdown, roxygen2, spelling
Collate: 'color_def_1.R' 'color_def_2.R' 'color_util.R' 'color_fun.R' 'plot_util.R' 'plot_box.R' 'plot_box_calls.R' 'plot_text.R' 'plot_text_calls.R' 'start_unikn.R'
Encoding: UTF-8
LazyData: true
License: CC BY-SA 4.0
URL: https://github.com/hneth/unikn
BugReports: https://github.com/hneth/unikn/issues
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2019-06-14 17:02:37 UTC; hneth
Repository: CRAN
Date/Publication: 2019-06-15 08:20:03 UTC

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New package NST with initial version 2.0.3
Package: NST
Type: Package
Title: Normalized Stochasticity Ratio
Version: 2.0.3
Date: 2019-6-14
Author: Daliang Ning
Maintainer: Daliang Ning <ningdaliang@ou.edu>
Imports: vegan,parallel,permute,ape
Depends: R (>= 3.1.0)
Description: To estimate ecological stochasticity in community assembly. Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. The new index, normalized stochasticity ratio (NST), is to estimate ecological stochasticity, i.e. relative importance of stochastic processes, in community assembly. With functions in this package, NST can be calculated based on different similarity metrics and/or different null model algorithms, as well as some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard Effect Size (SES), modified Raup-Crick metrics (RC). Functions for permutational test and bootstrapping analysis are also included. Previous ST is published by Zhou et al (2014) <doi:10.1073/pnas.1324044111>. NST is modified from ST by considering two alternative situations and normalizing the index to range from 0 to 1 which will be published soon (Ning et al 2019). A modified version, MST, is a special case of NST, used in some recent or upcoming publications, e.g. Liang et al (2019) <doi:10.1101/638908>. SES is calculated as described in Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as reported by Chase et al (2011) <doi:10.1890/es10-00117.1> and Stegen et al (2013) <doi:10.1038/ismej.2013.93>.
License: GPL-2
NeedsCompilation: no
Packaged: 2019-06-14 18:35:15 UTC; ndl81
Repository: CRAN
Date/Publication: 2019-06-15 08:30:03 UTC

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New package modelDown with initial version 1.0.1
Package: modelDown
Title: Make Static HTML Website for Predictive Models
Version: 1.0.1
Authors@R: c(person("Przemysław", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut")), person("Magda", "Tatarynowicz", email = "magda.tatarynowicz@gmail.com", role = c("aut")), person("Kamil", "Romaszko", email = "kamil.romaszko@gmail.com", role = c("aut", "cre")), person("Mateusz", "Urbański", email = "matiszak@gmail.com", role = c("aut")))
Description: Website generator with HTML summaries for predictive models. This package uses 'DALEX' explainers to describe global model behavior. We can see how well models behave (tabs: Model Performance, Auditor), how much each variable contributes to predictions (tabs: Variable Response) and which variables are the most important for a given model (tabs: Variable Importance). We can also compare Concept Drift for pairs of models (tabs: Drifter). Additionally, data available on the website can be easily recreated in current R session. Work on this package was financially supported by the NCN Opus grant 2017/27/B/ST6/01307 at Warsaw University of Technology, Faculty of Mathematics and Information Science.
Depends: R (>= 3.4.0)
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
Imports: DALEX (>= 0.2.8), auditor (>= 0.3.0), ggplot2 (>= 3.1.0), whisker (>= 0.3-2), DT (>= 0.4), kableExtra (>= 0.9.0), psych (>= 1.8.4), archivist (>= 2.1.0), svglite (>= 1.2.1), devtools (>= 2.0.1), breakDown (>= 0.1.6), drifter (>= 0.2.1)
Suggests: ranger, testthat, useful
RoxygenNote: 6.1.1
URL: https://github.com/MI2DataLab/modelDown
BugReports: https://github.com/MI2DataLab/modelDown/issues
NeedsCompilation: no
Packaged: 2019-06-14 22:09:40 UTC; Kamil
Author: Przemysław Biecek [aut], Magda Tatarynowicz [aut], Kamil Romaszko [aut, cre], Mateusz Urbański [aut]
Maintainer: Kamil Romaszko <kamil.romaszko@gmail.com>
Repository: CRAN
Date/Publication: 2019-06-15 08:50:02 UTC

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New package uplifteval with initial version 0.1.0
Package: uplifteval
Type: Package
Title: Uplift Model Evaluation with Plots and Metrics
Version: 0.1.0
Author: Roland Stevenson
Maintainer: Roland Stevenson <roland@rmg-services.com>
Description: Provides a variety of plots and metrics to evaluate uplift models including the 'R uplift' package's Qini metric and Qini plot, a port of the 'python pylift' module's plotting function, and an alternative plot (in beta) useful for continuous outcomes. Background: Radcliffe (2007) <https://pdfs.semanticscholar.org/147b/32f3d56566c8654a9999c5477dded233328e.pdf>.
License: GPL-3
URL: https://github.com/ras44/uplifteval
BugReports: https://github.com/ras44/uplifteval/issues
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown, grf, tweedie, qpdf
Depends: R (>= 3.0.0),
Imports: ggplot2, whisker, gridExtra, dplyr
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-06-14 16:37:51 UTC; rstevenson
Repository: CRAN
Date/Publication: 2019-06-15 07:50:03 UTC

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New package tsibbledata with initial version 0.1.0
Package: tsibbledata
Version: 0.1.0
Title: Diverse Datasets for 'tsibble'
Description: Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted.
Authors@R: c( person("Mitchell", "O'Hara-Wild", email = "mail@mitchelloharawild.com", role = c("aut", "cre")), person("Rob", "Hyndman", role = "aut"), person("Earo", "Wang", role = "aut") )
Depends: R (>= 3.1.3)
Imports: tsibble (>= 0.8.0)
Suggests: ggplot2
ByteCompile: true
License: GPL-3
URL: http://tsibbledata.tidyverts.org/
BugReports: https://github.com/tidyverts/tsibbledata/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-06-14 09:31:58 UTC; mitchell
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Repository: CRAN
Date/Publication: 2019-06-15 07:30:03 UTC

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New package rjwsacruncher with initial version 0.1.0
Package: rjwsacruncher
Title: Interface to the 'JWSACruncher' of 'JDemetra+'
Version: 0.1.0
Authors@R: c(person("Alain", "Quartier-la-Tente", role = c("aut", "cre"), email = "alain.quartier@yahoo.fr"))
Description: 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>) is the seasonal adjustment software officially recommended to the members of the European Statistical System and the European System of Central Banks. Seasonal adjustment models performed with 'JDemetra+' can be stored into workspaces. 'JWSACruncher' (<https://github.com/jdemetra/jwsacruncher/releases>) is a console tool that re-estimates all the multi-processing defined in a workspace and to export the result. 'rjwsacruncher' allows to launch easily the 'JWSACruncher'.
URL: https://github.com/AQLT/rjwsacruncher
BugReports: https://github.com/AQLT/rjwsacruncher/issues
Imports: XML
Suggests: knitr, rmarkdown
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-06-11 19:09:51 UTC; alainquartierlatente
Author: Alain Quartier-la-Tente [aut, cre]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Repository: CRAN
Date/Publication: 2019-06-15 07:30:11 UTC

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New package DDPNA with initial version 0.2.1
Package: DDPNA
Type: Package
Title: Disease-Related Differential Proteins and Co-Expression Network Analysis
Version: 0.2.1
Date: 2019-6-5
Authors@R: c(person("Kefu","Liu",email="liukefu19@163.com",role=c("aut","cre")))
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>
URL: http://github.com/liukf10/DDPNA
BugReports: https://github.com/liukf10/DDPNA/issues
Description: Functions designed to connect disease-related differential proteins and co-expression network. It provides the basic statics analysis included t test, ANOVA analysis. The network construction is not offered by the package, you can used 'WGCNA' package which you can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and hub analysis.
Imports: stats, ggplot2, ggalt, MEGENA, igraph, Hmisc, utils, grDevices, plyr, scales, grid, VennDiagram
Suggests: WGCNA, Biostrings, impute, ggfortify
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.5)
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-06-14 15:07:20 UTC; lkf
Repository: CRAN
Date/Publication: 2019-06-15 07:40:03 UTC

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Package climwin updated to version 1.2.2 with previous version 1.2.1 dated 2019-06-02

Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response. Please see van de Pol et al. (2016) <doi:10.1111/2041-210X.12590> and Bailey and van de Pol (2016) <doi:10.1371/journal.pone.0167980> for details.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@liamdbailey.com>

Diff between climwin versions 1.2.1 dated 2019-06-02 and 1.2.2 dated 2019-06-15

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Package deldir updated to version 0.1-21 with previous version 0.1-16 dated 2019-01-04

Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

Diff between deldir versions 0.1-16 dated 2019-01-04 and 0.1-21 dated 2019-06-15

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