Sat, 10 Aug 2019

Package overture updated to version 0.4-0 with previous version 0.2-0 dated 2019-03-15

Title: Tools for Writing MCMC
Description: Simplifies MCMC setup by automatically looping through sampling functions and saving the results. Reduces the memory footprint of running MCMC and saves samples to disk as the chain runs. Allows samples from the chain to be analyzed while the MCMC is still running. Provides functions for commonly performed operations such as calculating Metropolis acceptance ratios and creating adaptive Metropolis samplers. References: Roberts and Rosenthal (2009) <doi:10.1198/jcgs.2009.06134>.
Author: Kurtis Shuler [aut, cre]
Maintainer: Kurtis Shuler <>

Diff between overture versions 0.2-0 dated 2019-03-15 and 0.4-0 dated 2019-08-10

 overture-0.2-0/overture/man/AcceptProposal.Rd           |only
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 overture-0.4-0/overture/MD5                             |   20 +-
 overture-0.4-0/overture/NAMESPACE                       |    2 
 overture-0.4-0/overture/                         |    9 +
 overture-0.4-0/overture/R/mcmc.R                        |  106 +++++++++---
 overture-0.4-0/overture/R/utilities.R                   |   55 ++----
 overture-0.4-0/overture/build/partial.rdb               |binary
 overture-0.4-0/overture/man/Amwg.Rd                     |   46 ++++-
 overture-0.4-0/overture/man/Resume.Rd                   |only
 overture-0.4-0/overture/tests/testthat/test-mcmc.R      |  139 +++++++++++++++-
 overture-0.4-0/overture/tests/testthat/test-utilities.R |   32 +++
 12 files changed, 340 insertions(+), 75 deletions(-)

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Package oppr updated to version 0.0.4 with previous version 0.0.3 dated 2019-04-10

Title: Optimal Project Prioritization
Description: A decision support tool for prioritizing conservation projects. Prioritizations can be developed by maximizing expected feature richness, expected phylogenetic diversity, the number of features that meet persistence targets, or identifying a set of projects that meet persistence targets for minimal cost. Constraints (e.g. lock in specific actions) and feature weights can also be specified to further customize prioritizations. After defining a project prioritization problem, solutions can be obtained using exact algorithms, heuristic algorithms, or random processes. In particular, it is recommended to install the 'Gurobi' optimizer (available from <>) because it can identify optimal solutions very quickly. Finally, methods are provided for comparing different prioritizations and evaluating their benefits.
Author: Jeffrey O Hanson [aut, cre], Richard Schuster [aut], Matthew Strimas-Mackey [aut], Joseph Bennett [aut]
Maintainer: Jeffrey O Hanson <>

Diff between oppr versions 0.0.3 dated 2019-04-10 and 0.0.4 dated 2019-08-10

 DESCRIPTION                          |   10 
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 R/add_gurobi_solver.R                |    2 
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 build/vignette.rds                   |binary
 inst/CITATION                        |    2 
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 man/add_gurobi_solver.Rd             |    2 
 man/figures/README-readme-plot-1.png |binary
 man/oppr.Rd                          |    2 
 12 files changed, 679 insertions(+), 673 deletions(-)

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Package ggplot2 updated to version 3.2.1 with previous version 3.2.0 dated 2019-06-16

Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Author: Hadley Wickham [aut, cre], Winston Chang [aut], Lionel Henry [aut], Thomas Lin Pedersen [aut], Kohske Takahashi [aut], Claus Wilke [aut], Kara Woo [aut], Hiroaki Yutani [aut], RStudio [cph]
Maintainer: Hadley Wickham <>

Diff between ggplot2 versions 3.2.0 dated 2019-06-16 and 3.2.1 dated 2019-08-10

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 MD5                                  |   18 ++++++------                              |   12 ++++++++
 R/position-stack.r                   |    2 -
 R/quick-plot.r                       |    5 ++-
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 inst/doc/profiling.html              |    8 ++---
 tests/testthat/Rplots.pdf            |binary
 tests/testthat/test-coord_sf.R       |   52 ++++++++++++++++++++++-------------
 tests/testthat/test-position-stack.R |   10 +++---
 10 files changed, 72 insertions(+), 43 deletions(-)

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Package yarr updated to version 0.1.2 with previous version 0.1.1 dated 2019-05-17

Title: Yet Another 'ARFF' Reader
Description: A parser and a writer for 'WEKA' Attribute-Relation File Format <> in pure R, with no dependencies. As opposed to other R implementations, this package can read standard (dense) as well as sparse files, i.e. those where each row does only contain nonzero components. Unlike 'RWeka', 'yarr' does not require any 'Java' installation nor is dependent on external software. This implementation is generalized from those in packages 'mldr' and 'mldr.datasets'.
Author: David Charte [aut, cre] (<>), Francisco Charte [aut] (<>)
Maintainer: David Charte <>

Diff between yarr versions 0.1.1 dated 2019-05-17 and 0.1.2 dated 2019-08-10

 DESCRIPTION                           |    6 -
 MD5                                   |   22 ++--
 R/read.R                              |  156 ++++++++++++++++++++++------------
 R/utils.R                             |    2 
 R/write.R                             |   12 +-                             |   41 +++++---
 man/read.arff.Rd                      |    9 +
 man/utils.Rd                          |    2 
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 tests/testthat/test-idempotence.R     |   12 ++
 tests/testthat/test-relation.R        |only
 tests/testthat/test-sparse-defaults.R |    1 
 tests/testthat/test-values.R          |only
 13 files changed, 215 insertions(+), 98 deletions(-)

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New package xgxr with initial version 1.0.0
Package: xgxr
Title: Exploratory Graphics for Pharmacometrics
Version: 1.0.0
Authors@R: c(person(given = "Andrew", family = "Stein", role = c("aut", "cre"), email = ""), person(given = "Alison", family = "Margolskee", role = "aut"), person(given = "Fariba", family = "Khanshan", role = "aut"), person(given = "Konstantin", family = "Krismer", role = "aut", email = "", comment = c(ORCID = "0000-0001-8994-3416")), person(given = "Matthew", family = "Fidler", role = "ctb", email = "", comment = c(ORCID = "0000-0001-8538-6691")), person("Novartis Pharma AG", role = c("cph","fnd")))
Description: Supports a structured approach for exploring PKPD data <>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
Imports: assertthat, binom, dplyr, ggplot2, graphics, grDevices, labeling, magrittr, pander, png, scales, stats, tibble, utils
Suggests: caTools, gridExtra, knitr, rmarkdown, RxODE, stringr, testthat, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-09 16:35:29 UTC; steinanf
Author: Andrew Stein [aut, cre], Alison Margolskee [aut], Fariba Khanshan [aut], Konstantin Krismer [aut] (<>), Matthew Fidler [ctb] (<>), Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <>
Repository: CRAN
Date/Publication: 2019-08-10 09:30:02 UTC

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New package spiritR with initial version 0.1.0
Package: spiritR
Title: Template for Clinical Trial Protocol
Version: 0.1.0
Authors@R: person(given = "Aaron", family = "Conway", role = c("aut", "cre"), email = "", comment = c(ORCID = "0000-0002-9583-8636"))
Description: Contains an R Markdown template for a clinical trial protocol adhering to the SPIRIT statement. The SPIRIT (Standard Protocol Items for Interventional Trials) statement outlines recommendations for a minimum set of elements to be addressed in a clinical trial protocol. Also contains functions to create a xml document from the template and upload it to<> for trial registration.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: xml2, httr, magrittr, tibble
RoxygenNote: 6.1.1
Suggests: testthat, knitr, rmarkdown, pkgdown
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2019-08-09 18:10:55 UTC; aaronconway
Author: Aaron Conway [aut, cre] (<>)
Maintainer: Aaron Conway <>
Repository: CRAN
Date/Publication: 2019-08-10 09:30:07 UTC

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New package ds4psy with initial version 0.1.0
Package: ds4psy
Type: Package
Title: Data Science for Psychologists
Version: 0.1.0
Date: 2019-08-09
Authors@R: c(person("Hansjoerg", "Neth", role = c("aut", "cre"), email = ""))
Author: Hansjoerg Neth [aut, cre]
Maintainer: Hansjoerg Neth <>
Description: All data sets required for the examples and exercises in the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2019), freely available at <>. The book and course introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for graphics and text-manipulation that are used in the book and its exercises.
Depends: R (>= 3.4.0)
Imports: ggplot2, cowplot, here, readr, stringr, tibble, tidyr, tidyverse, unikn
Suggests: knitr, rmarkdown, spelling
Collate: 'data.R' 'color_fun.R' 'text_fun.R' 'data_fun.R' 'theme_fun.R' 'plot_fun.R' 'util_fun.R' 'start.R'
Encoding: UTF-8
LazyData: true
License: CC BY-SA 4.0
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2019-08-09 17:52:11 UTC; hneth
Repository: CRAN
Date/Publication: 2019-08-10 09:30:10 UTC

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