Sun, 16 Dec 2018

Package arulesCBA updated to version 1.1.4 with previous version 1.1.3-1 dated 2018-04-23

Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph], Michael Hahsler [aut, cph]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

Diff between arulesCBA versions 1.1.3-1 dated 2018-04-23 and 1.1.4 dated 2018-12-16

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Package spaero updated to version 0.4.0 with previous version 0.3.0 dated 2018-07-11

Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication of infectious diseases from surveillance time series. Also provides support for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>

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Package convexjlr updated to version 0.8.1 with previous version 0.7.0 dated 2018-04-28

Title: Disciplined Convex Programming in R using 'Convex.jl'
Description: Provides a simple high-level wrapper for 'Julia' package 'Convex.jl' (see <https://github.com/JuliaOpt/Convex.jl> for more information), which makes it easy to describe and solve convex optimization problems in R. The problems can be dealt with include: linear programs, second-order cone programs, semidefinite programs, exponential cone programs.
Author: Changcheng Li [aut, cre]
Maintainer: Changcheng Li <cxl508@psu.edu>

Diff between convexjlr versions 0.7.0 dated 2018-04-28 and 0.8.1 dated 2018-12-16

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Package rquery updated to version 1.2.1 with previous version 1.2.0 dated 2018-11-07

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

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Package mindr updated to version 1.1.9 with previous version 1.1.5 dated 2018-10-09

Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package netCoin updated to version 0.3.2 with previous version 0.3.0 dated 2018-07-25

Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>, David Barrios <metal@usal.es>, Carlos Prieto <cprietos@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

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Package wevid updated to version 0.5.2 with previous version 0.5.1 dated 2018-10-11

Title: Quantifying Performance of a Binary Classifier Through Weight of Evidence
Description: The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test (McKeigue (2018), <doi:10.1177/0962280218776989>). The package can be used with any test dataset on which you have observed case-control status and have computed prior and posterior probabilities of case status using a model learned on a training dataset. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Author: Paul McKeigue [aut] (<https://orcid.org/0000-0002-5217-1034>), Marco Colombo [ctb, cre] (<https://orcid.org/0000-0001-6672-0623>)
Maintainer: Marco Colombo <mar.colombo13@gmail.com>

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Package nestfs updated to version 0.9.1 with previous version 0.9 dated 2018-09-25

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 <mar.colombo13@gmail.com>

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Package cosa updated to version 1.2.1 with previous version 1.2.0 dated 2018-04-04

Title: Bound Constrained Optimal Sample Allocation
Description: Implements bound constrained optimization of sample sizes in power analysis of multilevel regression discontinuity studies (RDDs) and multilevel randomized controlled trials (RCTs) with continuous outcomes. Functions for statistical power and minimum detectable effect size calculations are also provided. Bulus, M. (2017). Design Considerations in Three-level Regression Discontinuity Studies (Doctoral dissertation). University of Missouri, Columbia, MO.
Author: Metin Bulus [aut, cre, cph], Nianbo Dong [aut, cph]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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 cosa-1.2.1/cosa/man/crd4r4.Rd               |    8 -
 cosa-1.2.1/cosa/man/ird1r1.Rd               |   15 --
 cosa-1.2.1/cosa/man/plot.Rd                 |    7 -
 cosa-1.2.1/cosa/vignettes/cosa_tutorial.Rmd |    2 
 39 files changed, 264 insertions(+), 347 deletions(-)

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Package bookdownplus updated to version 1.5.4 with previous version 1.5.2 dated 2018-10-16

Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

Diff between bookdownplus versions 1.5.2 dated 2018-10-16 and 1.5.4 dated 2018-12-16

 DESCRIPTION                   |   10 ++---
 MD5                           |   23 +++++++-----
 NAMESPACE                     |    3 +
 R/fun.R                       |   77 ++++++++++++++++++++++++++++++++++++------
 inst/templates/copernicus.zip |binary
 inst/templates/crc.zip        |binary
 inst/templates/demo_zh.zip    |binary
 inst/templates/mdpi.zip       |binary
 inst/templates/poem.zip       |binary
 man/bookdownplus.Rd           |    3 -
 man/get_template.Rd           |    4 +-
 man/mail_font.Rd              |only
 man/more_output.Rd            |only
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 14 files changed, 91 insertions(+), 29 deletions(-)

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New package geohashTools with initial version 0.2.0
Package: geohashTools
Version: 0.2.0
Title: Tools for Working with Geohashes
Author: Michael Chirico, Hiroaki Kawai
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Depends: R (>= 3.0.0)
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, ported to R from Hiroaki Kawai's 'Python' implementation and embellished to sit naturally in the R ecosystem.
URL: https://github.com/MichaelChirico/geohashTools
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.0)
Suggests: sf, sp, testthat, mockery
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-12-07 12:22:49 UTC; michael.chirico
Repository: CRAN
Date/Publication: 2018-12-16 16:10:03 UTC

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New package CornerstoneR with initial version 1.0.0
Package: CornerstoneR
Version: 1.0.0
Title: Collection for 'CornerstoneR' Interface
Description: Collection of scripts for interface between 'Cornerstone' and 'R'. 'Cornerstone' (<https://www.camline.com/>) as a software for engineering analytics supports an interface to 'R'. The scripts are designed to support an easy usage of this interface.
Authors@R: c( person("Dirk", "Surmann", NULL, "dirk.surmann@versuchsplanung.de" , role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0873-137X")) )
URL: https://gitlab.com/camLine/CornerstoneR
BugReports: https://gitlab.com/camLine/CornerstoneR/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.2.1)
Imports: checkmate (>= 1.5) , data.table (>= 1.10) , ranger , vcd
Suggests: knitr , rmarkdown , testthat
ByteCompile: yes
LazyData: yes
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-08 12:08:10 UTC; Dirk
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>
Repository: CRAN
Date/Publication: 2018-12-16 16:50:02 UTC

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New package tinter with initial version 0.0.1
Package: tinter
Title: Generate a Monochromatic Palette
Version: 0.0.1
Authors@R: c( person("Sebastian", "Dalgarno", role = c("aut", "cre"), email = "seb@poissonconsulting.ca"), person("Joe", "Thorley", role = "ctb", email = "joe@poissonconsulting.ca", comment = c(ORCID = "0000-0002-7683-4592")))
Description: Generate a palette of tints, shades or both from a single colour.
URL: https://github.com/poissonconsulting/tinter
BugReports: https://github.com/poissonconsulting/tinter/issues
Imports: checkr, grDevices
Suggests: graphics, covr, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2018-12-06 00:06:41 UTC; sebastiandalgarno
Author: Sebastian Dalgarno [aut, cre], Joe Thorley [ctb] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Sebastian Dalgarno <seb@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-12-16 15:10:03 UTC

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New package lmreg with initial version 1.0
Package: lmreg
Type: Package
Title: Data and Functions Used in Linear Models and Regression with R: An Integrated Approach
Version: 1.0
Date: 2018-11-13
Author: Debasis Sengupta <shairiksengupta@gmail.com>, S. Rao Jammalamadaka <rao@gmail.com>, Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Maintainer: Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Description: Data files and a few functions used in the book 'Linear Models and Regression with R: An Integrated Approach' by Debasis Sengupta and Sreenivas Rao Jammalamadaka (2019).
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Depends: MASS
Packaged: 2018-12-06 20:28:25 UTC; william
Date/Publication: 2018-12-16 16:00:02 UTC

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New package mined with initial version 1.0-1
Package: mined
Type: Package
Title: Minimum Energy Designs
Version: 1.0-1
Date: 2018-11-24
Author: Dianpeng Wang and V. Roshan Joseph
Maintainer: Dianpeng Wang <wdp@bit.edu.cn>
Description: This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2018). The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate.
License: LGPL-2.1
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2018-12-05 08:22:40 UTC; Administrator
Repository: CRAN
Date/Publication: 2018-12-16 14:40:02 UTC

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New package epiGWAS with initial version 1.0.0
Package: epiGWAS
Title: Robust Methods for Epistasis Detection
Version: 1.0.0
Authors@R: c(person("Lotfi", "Slim", email = "lotfi.slim@mines-paristech.fr", role = c("aut", "cre")), person("Clément", "Chatelain", email = "clement.chatelain@sanofi.com", role = "ctb"), person("Chloé-Agathe", "Azencott", email = "chloe-agathe.azencott@mines-paristech.fr", role ="ctb"), person("Jean-Philippe", "Vert", email = "jpvert@google.com", role ="ctb"))
Description: Functions to perform robust epistasis detection in genome-wide association studies, as described in Slim et al. (2018) <doi:10.1101/442749>. The implemented methods identify pairwise interactions between a particular target variant and the rest of the genotype, using a propensity score approach. The propensity score models the linkage disequilibrium between the target and the rest of the genotype. All methods are penalized regression approaches, which differently incorporate the propensity score to only recover the synergistic effects between the target and the genotype.
Depends: R (>= 3.4.0)
Imports: matrixStats, DescTools, glmnet, SNPknock
Suggests: foreach, iterators, precrec, parallel, doParallel, bigmemory, biglasso, testthat, knitr, rmarkdown, kableExtra
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-04 20:00:21 UTC; lotfislim
Author: Lotfi Slim [aut, cre], Clément Chatelain [ctb], Chloé-Agathe Azencott [ctb], Jean-Philippe Vert [ctb]
Maintainer: Lotfi Slim <lotfi.slim@mines-paristech.fr>
Repository: CRAN
Date/Publication: 2018-12-16 14:10:03 UTC

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New package cliapp with initial version 0.1.0
Package: cliapp
Title: Create Rich Command Line Applications
Version: 0.1.0
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Description: Create rich command line applications, with colors, headings, lists, alerts, progress bars, etc. It uses CSS for custom themes.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/r-lib/cliapp#readme
BugReports: https://github.com/r-lib/cliapp/issues
RoxygenNote: 6.1.1
Imports: cli, crayon, fansi, glue (>= 1.3.0), prettycode, progress (>= 1.2.0), R6, selectr, utils, withr, xml2
Suggests: callr, covr, rstudioapi, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-05 09:41:39 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2018-12-16 14:40:05 UTC

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New package bfsl with initial version 0.1.0
Package: bfsl
Title: Best-Fit Straight Line
Version: 0.1.0
Authors@R: person("Patrick", "Sturm", email = "sturm@tofwerk.com", role = c("aut", "cre"))
Description: Provides the solution from York (1968) <doi:10.1016/S0012-821X(68)80059-7> for fitting a straight line to bivariate data with errors in both coordinates. It gives unbiased estimates of the intercept, slope and standard errors of the best-fit straight line to independent points with (possibly correlated) normally distributed errors in both x and y. Other commonly used errors-in-variables methods, such as orthogonal distance regression, geometric mean regression or Deming regression are special cases of York’s solution.
Depends: R (>= 3.5.0)
License: GPL-3
URL: https://github.com/pasturm/bfsl
BugReports: https://github.com/pasturm/bfsl/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-12-05 12:58:44 UTC; pst
Author: Patrick Sturm [aut, cre]
Maintainer: Patrick Sturm <sturm@tofwerk.com>
Repository: CRAN
Date/Publication: 2018-12-16 14:50:03 UTC

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Package texteffect updated to version 0.2 with previous version 0.1 dated 2017-11-27

Title: Discovering Latent Treatments in Text Corpora and Estimating Their Causal Effects
Description: Implements the approach described in Fong and Grimmer (2016) <https://aclweb.org/anthology/P/P16/P16-1151.pdf> for automatically discovering latent treatments from a corpus and estimating the average marginal component effect (AMCE) of each treatment. The data is divided into a training and test set. The supervised Indian Buffet Process (sibp) is used to discover latent treatments in the training set. The fitted model is then applied to the test set to infer the values of the latent treatments in the test set. Finally, Y is regressed on the latent treatments in the test set to estimate the causal effect of each treatment.
Author: Christian Fong <christianfong@stanford.edu>
Maintainer: Christian Fong <christianfong@stanford.edu>

Diff between texteffect versions 0.1 dated 2017-11-27 and 0.2 dated 2018-12-16

 texteffect-0.1/texteffect/R/get_training_set.R     |only
 texteffect-0.1/texteffect/data/BioSample.tab.gz    |only
 texteffect-0.1/texteffect/man/get_training_set.Rd  |only
 texteffect-0.2/texteffect/ChangeLog                |    3 
 texteffect-0.2/texteffect/DESCRIPTION              |   10 +-
 texteffect-0.2/texteffect/MD5                      |   34 ++++------
 texteffect-0.2/texteffect/NAMESPACE                |    5 -
 texteffect-0.2/texteffect/R/sibp.R                 |   18 ++++-
 texteffect-0.2/texteffect/R/sibp_amce.R            |   71 +++++++++++----------
 texteffect-0.2/texteffect/R/sibp_exclusivity.R     |    3 
 texteffect-0.2/texteffect/R/sibp_infer_Z.R         |   12 ++-
 texteffect-0.2/texteffect/R/sibp_param_search.R    |    4 -
 texteffect-0.2/texteffect/R/sibp_updates.R         |   41 ++++++++----
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 texteffect-0.2/texteffect/man/infer_Z.Rd           |   13 +--
 texteffect-0.2/texteffect/man/sibp.Rd              |    7 +-
 texteffect-0.2/texteffect/man/sibp_amce.Rd         |   13 ++-
 texteffect-0.2/texteffect/man/sibp_exclusivity.Rd  |    3 
 texteffect-0.2/texteffect/man/sibp_param_search.Rd |    7 +-
 texteffect-0.2/texteffect/man/sibp_top_words.Rd    |    6 -
 20 files changed, 150 insertions(+), 100 deletions(-)

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Package LadR updated to version 1.0.5 with previous version 1.0.4 dated 2018-08-06

Title: Routines for Fit, Inference and Diagnostics in LAD Models
Description: LAD (Least Absolute Deviations) estimation for linear regression, confidence intervals, tests of hypotheses, methods for outliers detection, measures of leverage, methods of diagnostics for LAD regression, special diagnostics graphs and measures of leverage. The algorithms are based in Dielman (2005) <doi:10.1080/0094965042000223680>, Elian et al. (2000) <doi:10.1080/03610920008832518> and Dodge (1997) <doi:10.1006/jmva.1997.1666>. This package also has two datasets "houses" and "pollution", respectively, from Narula and Wellington (1977) <doi:10.2307/1268628> and Santos et al. (2016) <doi:10.1371/journal.pone.0163225>.
Author: Kévin Allan Sales Rodrigues <kevin.asr@outlook.com>
Maintainer: Kevin Allan Sales Rodrigues <kevin.asr@outlook.com>

Diff between LadR versions 1.0.4 dated 2018-08-06 and 1.0.5 dated 2018-12-16

 DESCRIPTION        |    6 +--
 MD5                |   16 ++++----
 R/detectOutliers.R |    4 ++
 R/ladreg.R         |  102 +++++++++++++++++++++--------------------------------
 R/likelihoodD.R    |    9 +++-
 R/likelihoodDC.R   |    8 ++--
 build/partial.rdb  |binary
 inst/CITATION      |   11 ++---
 man/ladreg.Rd      |   10 ++---
 9 files changed, 78 insertions(+), 88 deletions(-)

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