Fri, 06 May 2022

Package hdpGLM updated to version 1.0.2 with previous version 1.0.1 dated 2022-04-23

Title: Hierarchical Dirichlet Process Generalized Linear Models
Description: Implementation of MCMC algorithms to estimate the Hierarchical Dirichlet Process Generalized Linear Model (hdpGLM) presented in the paper Ferrari (2020) Modeling Context-Dependent Latent Heterogeneity, Political Analysis <DOI:10.1017/pan.2019.13>.
Author: Diogo Ferrari [aut, cre]
Maintainer: Diogo Ferrari <diogoferrari@gmail.com>

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Package prome updated to version 1.5.6.70 with previous version 0.0.0.8 dated 2022-02-24

Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>

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Package TidyDensity updated to version 1.1.0 with previous version 1.0.1 dated 2022-03-27

Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats distribution functions. All data is returned in a tidy and structured format making working with the data simple and straight forward. Given that the data is returned in a tidy 'tibble' it lends itself to working with the rest of the 'tidyverse'.
Author: Steven Sanderson [aut, cre], Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>

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Package plumbr updated to version 0.6.10 with previous version 0.6.9 dated 2014-02-22

Title: Mutable and Dynamic Data Models
Description: The base R data.frame, like any vector, is copied upon modification. This behavior is at odds with that of GUIs and interactive graphics. To rectify this, plumbr provides a mutable, dynamic tabular data model. Models may be chained together to form the complex plumbing necessary for sophisticated graphical interfaces. Also included is a general framework for linking datasets; an typical use case would be a linked brush.
Author: Michael Lawrence, Hadley Wickham
Maintainer: Michael Lawrence <michafla@gene.com>

Diff between plumbr versions 0.6.9 dated 2014-02-22 and 0.6.10 dated 2022-05-06

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Package onls (with last version 0.1-1) was removed from CRAN

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

2015-09-09 0.1-1
2015-01-17 0.1-0

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Package OptInterim (with last version 3.0.1) was removed from CRAN

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

2012-12-12 3.0.1

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Package frost (with last version 0.0.4) was removed from CRAN

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

2019-04-12 0.0.4

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Package sideChannelAttack (with last version 1.0-6) was removed from CRAN

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

2013-04-12 1.0-6
2012-12-28 1.0-5
2012-10-17 1.0-4
2012-07-21 1.0-3
2012-04-08 1.0-2
2011-08-08 1.0-1
2011-04-30 1.0

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Package hypothesestest (with last version 1.0) was removed from CRAN

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

2012-07-11 1.0

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Package PermAlgo updated to version 1.2 with previous version 1.1 dated 2015-04-01

Title: Permutational Algorithm to Simulate Survival Data
Description: This version of the permutational algorithm generates a dataset in which event and censoring times are conditional on an user-specified list of covariates, some or all of which are time-dependent.
Author: Marie-Pierre Sylvestre, Thad Edens, Todd MacKenzie, Michal Abrahamowicz
Maintainer: Marie-Pierre Sylvestre <marie-pierre.sylvestre@umontreal.ca>

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Package ff updated to version 4.0.7 with previous version 4.0.5 dated 2021-10-29

Title: Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
Description: The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.
Author: Daniel Adler [aut], Christian Glaeser [aut], Oleg Nenadic [aut], Jens Oehlschlaegel [aut, cre], Martijn Schuemie [aut], Walter Zucchini [aut]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>

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Package neatStats updated to version 1.11.0 with previous version 1.10.1 dated 2022-02-28

Title: Neat and Painless Statistical Reporting
Description: User-friendly, clear and simple statistics, primarily for publication in psychological science. The main functions are wrappers for other packages, but there are various additions as well. Every relevant step from data aggregation to reportable printed statistics is covered for basic experimental designs.
Author: Gaspar Lukacs [aut, cre] , Bennett Kleinberg [ctb] , Johnny van Doorn [ctb]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>

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Package m61r updated to version 0.0.3 with previous version 0.0.2 dated 2021-04-15

Title: Package About Data Manipulation in Pure Base R
Description: Data manipulation in one package and in base R. Minimal. No dependencies. 'dplyr' and 'tidyr'-like in one place. Nothing else than base R to build the package.
Author: Jean-Marie Lepioufle [aut, cre]
Maintainer: Jean-Marie Lepioufle <pv71u98h1@gmail.com>

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Package liver updated to version 1.12 with previous version 1.11 dated 2022-03-03

Title: "Eating the Liver of Data Science"
Description: Provides a collection of helper functions that make various techniques from data science more user-friendly for non-experts. In this way, our aim is to allow non-experts to become familiar with the techniques with only a minimal level of coding knowledge. Indeed, following an ancient Persian idiom, we refer to this as "eating the liver of data science" which could be interpreted as "getting intimately close with data science". Examples of procedures we include are: data partitioning for out-of-sample testing, computing Mean Squared Error (MSE) for quantifying prediction accuracy, and data transformation (z-score and min-max). Besides such helper functions, the package also includes several interesting datasets that are useful for multivariate analysis.
Author: Reza Mohammadi [aut, cre] , Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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Package RProtoBuf updated to version 0.4.19 with previous version 0.4.18 dated 2021-12-16

Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of 'Protocol Buffers' library is required; currently version 3.3.0 from 2017 is the stated minimum.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package nephro updated to version 1.3 with previous version 1.2 dated 2017-05-10

Title: Utilities for Nephrology
Description: Set of functions to estimate kidney function and other phenotypes of interest in nephrology based on different biomechimal traits. MDRD, CKD-EPI, and Virga equations are compared in Pattaro (2013) <doi:10.1159/000351043>, where the respective references are given. In addition, the software includes Stevens (2008) <doi:10.1053/j.ajkd.2007.11.018> and Cockroft (1976) <doi:10.1159/000180580> formulas. The race-free CKD-EPI equations (2021) <doi:10.1056/NEJMoa2102953> are also implemented from ver.1.3.
Author: Cristian Pattaro, Ryosuke Fujii
Maintainer: Cristian Pattaro <cristian.pattaro@eurac.edu>

Diff between nephro versions 1.2 dated 2017-05-10 and 1.3 dated 2022-05-06

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Package JFE updated to version 2.5.3 with previous version 2.5.2 dated 2021-12-05

Title: Tools and GUI for Analyzing Time Series Data of Just Finance and Econometrics
Description: Support the analysis of financial and econometric time series, including data download.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

Diff between JFE versions 2.5.2 dated 2021-12-05 and 2.5.3 dated 2022-05-06

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Package GenericML updated to version 0.2.0 with previous version 0.1.1 dated 2021-12-07

Title: Generic Machine Learning Inference
Description: Generic Machine Learning Inference on heterogeneous treatment effects in randomized experiments as proposed in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802>. This package's workhorse is the 'mlr3' framework of Lang et al. (2019) <doi:10.21105/joss.01903>, which enables the specification of a wide variety of machine learners. The main functionality, GenericML(), runs Algorithm 1 in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802> for a suite of user-specified machine learners. All steps in the algorithm are customizable via setup functions. Methods for printing and plotting are available for objects returned by GenericML(). Parallel computing is supported.
Author: Max Welz [aut, cre] , Andreas Alfons [aut] , Mert Demirer [aut], Victor Chernozhukov [aut]
Maintainer: Max Welz <welz@ese.eur.nl>

Diff between GenericML versions 0.1.1 dated 2021-12-07 and 0.2.0 dated 2022-05-06

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New package INSPECTumours with initial version 0.1.0
Package: INSPECTumours
Title: IN-vivo reSPonsE Classification of Tumours
Version: 0.1.0
Maintainer: Bairu Zhang <bairu.zhang@astrazeneca.com>
Description: This is a shiny app used for the statistical classifying and analysing pre-clinical tumour responses.
License: Apache License (== 2)
Depends: R (>= 3.5.0)
Imports: brms, dplyr, DT, ggeffects, ggplot2, knitr, lme4, modelr, pander, plotly, purrr, readxl, rlang, rmarkdown, shiny, shinyalert, shinyFeedback, shinyjs, shinytoastr, shinyvalidate, tidybayes, tippy, tidyr, vroom, waiter
Suggests: spelling, lintr, testthat
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-05 09:35:58 UTC; kjrg087
Author: Bairu Zhang [cre, aut], Olga Muraeva [aut], Natasha Karp [aut]
Repository: CRAN
Date/Publication: 2022-05-06 12:10:02 UTC

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Package archive updated to version 1.1.5 with previous version 1.1.4 dated 2022-01-30

Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] , Gabor Csardi [aut, cre], Ondrej Holy [cph] , RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between archive versions 1.1.4 dated 2022-01-30 and 1.1.5 dated 2022-05-06

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Package smurf updated to version 1.1.3 with previous version 1.1.2 dated 2021-04-17

Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2021) <doi:10.1016/j.insmatheco.2020.11.010> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] , Sander Devriendt [aut], Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>

Diff between smurf versions 1.1.2 dated 2021-04-17 and 1.1.3 dated 2022-05-06

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New package tvmComp with initial version 1.0.2
Package: tvmComp
Title: Discounting and Compounding Calculations for Various Scenarios
Version: 1.0.2
Author: MaheshP Kumar [aut, cre], MaheshP Kumar [aut], MaheshP Kumar [ctb]
Maintainer: MaheshP Kumar <maheshparamjitkumar@gmail.com>
Imports: Rdpack
Description: Functions for compounding and discounting calculations included here serve as a complete reference for various scenarios of time value of money. Raymond M. Brooks (“Financial Management,” 2018, ISBN: 9780134730417). Sheridan Titman, Arthur J. Keown, John D. Martin (“Financial Management: Principles and Applications,” 2017, ISBN: 9780134417219). Jonathan Berk, Peter DeMarzo, David Stangeland, Andras Marosi (“Fundamentals of Corporate Finance,” 2019, ISBN: 9780134735313). S. A. Hummelbrunner, Kelly Halliday, Ali R. Hassanlou (“Contemporary Business Mathematics with Canadian Applications,” 2020, ISBN: 9780135285015).
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-04 19:06:05 UTC; mahes
Repository: CRAN
Date/Publication: 2022-05-06 11:00:02 UTC

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New package Robyn with initial version 3.6.3
Package: Robyn
Title: Semi-Automated Marketing Mix Modeling (MMM) from Meta Marketing Science
Version: 3.6.3
Maintainer: Bernardo Lares <bernardolares@fb.com>
Description: Semi-Automated Marketing Mix Modeling (MMM) aiming to reduce human bias by means of ridge regression and evolutionary algorithms, enables actionable decision making providing a budget allocation and diminishing returns curves and allows ground-truth calibration to account for causation.
Depends: R (>= 4.0.0)
Imports: data.table, doParallel, doRNG, dplyr, foreach, ggplot2, ggridges, glmnet, lares, lubridate, minpack.lm, nloptr, patchwork, prophet, reticulate, rPref, stringr, tidyr
Suggests: shiny
Config/reticulate: list( packages = list( list(package = "nevergrad", pip = TRUE) ) )
URL: https://github.com/facebookexperimental/Robyn, https://facebookexperimental.github.io/Robyn/
BugReports: https://github.com/facebookexperimental/Robyn/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-04 18:20:02 UTC; bernardolares
Author: Gufeng Zhou [aut], Leonel Sentana [aut], Igor Skokan [aut], Bernardo Lares [cre, aut], Meta Platforms, Inc. [cph, fnd]
Repository: CRAN
Date/Publication: 2022-05-06 10:50:02 UTC

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Package rim updated to version 0.5.1 with previous version 0.5.0 dated 2021-11-17

Title: R's Interface to Maxima, Bringing Symbolic Computation into R
Description: Provides an interface to the powerful and fairly complete computer algebra system maxima. It can be used to start and control 'Maxima' from within R by entering 'Maxima' commands. It facilitates outputting results from 'Maxima' in 'LaTeX' and 'MathML'. 2D and 3D plots can be displayed directly. This package also registers a 'knitr'-engine enabling 'Maxima' code chunks to be written in 'RMarkdown' documents.
Author: Eric Stemmler [aut, cre], Kseniia Shumelchyk [aut], Hans W. Borchers [aut]
Maintainer: Eric Stemmler <stemmler.eric@gmail.com>

Diff between rim versions 0.5.0 dated 2021-11-17 and 0.5.1 dated 2022-05-06

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New package PhilipsHue with initial version 1.0.0
Package: PhilipsHue
Title: R Interface to the Philips Hue API
Version: 1.0.0
Description: Control Philips Hue smart lighting. Use this package to connect to a Hue bridge on your local network (remote authentication not yet supported) and control your smart lights through the Philips Hue API. All API V1 endpoints are supported. See API documentation at <https://developers.meethue.com/>.
License: GPL (>= 3)
URL: https://fascinatingfingers.gitlab.io/philipshue, https://gitlab.com/fascinatingfingers/philipshue
BugReports: https://gitlab.com/fascinatingfingers/philipshue/-/issues
Depends: R (>= 4.1)
Imports: httr, methods, pkgload, purrr, utils, yaml
Suggests: covr, DT, fs, knitr, lubridate, mockery, rmarkdown, spelling, testthat, uuid, withr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-04 20:06:46 UTC; justi
Author: Justin Brantley [aut, cre]
Maintainer: Justin Brantley <fascinatingfingers@icloud.com>
Repository: CRAN
Date/Publication: 2022-05-06 11:00:05 UTC

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Package psychotree updated to version 0.16-0 with previous version 0.15-4 dated 2021-05-21

Title: Recursive Partitioning Based on Psychometric Models
Description: Recursive partitioning based on psychometric models, employing the general MOB algorithm (from package partykit) to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.
Author: Achim Zeileis [aut, cre] , Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Komboz [aut], Julia Kopf [aut], Lennart Schneider [aut] , David Dreifuss [aut], Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package melt updated to version 1.5.1 with previous version 1.5.0 dated 2022-05-03

Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests for regression analysis. Much of its functionality and syntax mimics the corresponding base R functions. The core computational routines are implemented using the 'Eigen' C++ library and 'RcppEigen' interface, with OpenMP for parallel computation. Additional functions are available for multiple testing for the analysis of experimental designs. Details of the testing procedures are given in Kim et al. (2021) <arxiv:2112.09206>.
Author: Eunseop Kim [aut, cre], Steven MacEachern [aut, ths], Mario Peruggia [aut, ths]
Maintainer: Eunseop Kim <kim.7302@osu.edu>

Diff between melt versions 1.5.0 dated 2022-05-03 and 1.5.1 dated 2022-05-06

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Package lessR updated to version 4.1.9 with previous version 4.1.8 dated 2022-04-23

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics, and comprehensive summary statistics via pivot tables. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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More information about lessR at CRAN
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Package file2meco updated to version 0.2.3 with previous version 0.2.2 dated 2022-03-25

Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>

Diff between file2meco versions 0.2.2 dated 2022-03-25 and 0.2.3 dated 2022-05-06

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Permanent link

New package datarobot with initial version 2.18.2
Package: datarobot
Title: 'DataRobot' Predictive Modeling API
Version: 2.18.2
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Depends: R (>= 3.2), methods, stats
Imports: httr (>= 1.2.0), jsonlite (>= 1.0), yaml (>= 2.1.19)
License: MIT + file LICENSE
Encoding: UTF-8
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut], Chester Ismay [aut], AJ Alon [aut], Andrew Watson [aut], Gregory Williams [aut], Anastasiia [...truncated...]
Maintainer: AJ Alon <api-maintainer@datarobot.com>
Suggests: lubridate, knitr, testthat, lintr, stubthat, data.table, MASS, mlbench, beanplot, doBy, insuranceData, rmarkdown, ggplot2, modelwordcloud, withr, memoise
Additional_repositories: https://cran.microsoft.com/snapshot/2022-04-12/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-05 19:03:39 UTC; aj
Language: en-US
Repository: CRAN
Date/Publication: 2022-05-06 09:20:04 UTC

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New package spatsurv with initial version 1.8
Package: spatsurv
Title: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models
Version: 1.8
Date: 2022-05-05
Author: Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models. See Benjamin M. Taylor, Barry S. Rowlingson (2017) <doi:10.18637/jss.v077.i04>.
License: GPL-3
Imports: survival, sp, spatstat.core, spatstat.geom, spatstat.random, spatstat (>= 2.0-0), raster, iterators, fields, Matrix, stringr, rgeos, RColorBrewer, methods, lubridate
Suggests: rgdal, rgl, OpenStreetMap
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-05 09:09:17 UTC; taylorb7
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2022-05-06 09:00:02 UTC

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New package metaumbrella with initial version 1.0.3
Package: metaumbrella
Title: Umbrella Review Package for R
Version: 1.0.3
Author: Corentin J Gosling [aut, cre], Aleix Solanes [aut], Paolo Fusar-Poli [aut], Joaquim Radua [aut]
Maintainer: Corentin J Gosling <cgosling@parisnanterre.fr>
Description: A comprehensive range of facilities to perform umbrella reviews with stratification of the evidence in R. The package accomplishes this aim by building on three core functions that: (i) automatically perform all required calculations in an umbrella review (including but not limited to meta-analyses), (ii) stratify evidence according to various classification criteria, and (iii) generate a visual representation of the results. Note that if you are not familiar with R, the core features of this package are available from a web browser (<https://www.metaumbrella.org/>).
License: GPL-3
Imports: meta, powerSurvEpi, readxl, tcltk, withr, writexl, xtable
Encoding: UTF-8
LazyData: true
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), spelling, DT, epiR, esc, pwr, metafor
Depends: R (>= 2.10)
VignetteBuilder: knitr, rmarkdown
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-05 08:26:59 UTC; Corentin Gosling
Repository: CRAN
Date/Publication: 2022-05-06 09:00:08 UTC

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Package DanielBiostatistics10th updated to version 0.1.1 with previous version 0.1.0 dated 2022-05-03

Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>

Diff between DanielBiostatistics10th versions 0.1.0 dated 2022-05-03 and 0.1.1 dated 2022-05-06

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Package tfarima updated to version 0.3.1 with previous version 0.2.1 dated 2021-05-29

Title: Transfer Function and ARIMA Models
Description: Building customized transfer function and ARIMA models with multiple operators and parameter restrictions. Functions for model identification, model estimation (exact or conditional maximum likelihood), model diagnostic checking, automatic outlier detection, calendar effects, forecasting and seasonal adjustment. See Bell and Hillmer (1983) <doi:10.1080/01621459.1983.10478005>, Box, Jenkins, Reinsel and Ljung <ISBN:978-1-118-67502-1>, Box, Pierce and Newbold (1987) <doi:10.1080/01621459.1987.10478430>, Box and Tiao (1975) <doi:10.1080/01621459.1975.10480264>, Chen and Liu (1993) <doi:10.1080/01621459.1993.10594321>.
Author: Jose L. Gallego [aut, cre]
Maintainer: Jose L. Gallego <jose.gallego@unican.es>

Diff between tfarima versions 0.2.1 dated 2021-05-29 and 0.3.1 dated 2022-05-06

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Package steepness updated to version 0.3-0 with previous version 0.2-2 dated 2014-10-01

Title: Testing Steepness of Dominance Hierarchies
Description: The steepness package computes steepness as a property of dominance hierarchies. Steepness is defined as the absolute slope of the straight line fitted to the normalized David's scores. The normalized David's scores can be obtained on the basis of dyadic dominance indices corrected for chance or by means of proportions of wins. Given an observed sociomatrix, it computes hierarchy's steepness and estimates statistical significance by means of a randomization test.
Author: David Leiva <dleivaur@ub.edu> & Han de Vries <J.deVries1@uu.nl>.
Maintainer: David Leiva <dleivaur@ub.edu>

Diff between steepness versions 0.2-2 dated 2014-10-01 and 0.3-0 dated 2022-05-06

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Package spatstat.utils updated to version 2.3-1 with previous version 2.3-0 dated 2021-12-12

Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] , Rolf Turner [aut] , Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.utils versions 2.3-0 dated 2021-12-12 and 2.3-1 dated 2022-05-06

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Package smacof updated to version 2.1-5 with previous version 2.1-3 dated 2021-07-20

Title: Multidimensional Scaling
Description: Implements the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): ratio/interval/ordinal/spline MDS on symmetric dissimilarity matrices, MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal), MDS with spherical restrictions, and ratio/interval/ordinal/spline unfolding (circular restrictions, row-conditional). Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Patrick J. F. Groenen [aut], Ingwer Borg [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

Diff between smacof versions 2.1-3 dated 2021-07-20 and 2.1-5 dated 2022-05-06

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New package iheiddown with initial version 0.9.2
Package: iheiddown
Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Date: 2022-05-03
Version: 0.9.2
URL: https://github.com/jhollway/iheiddown
BugReports: https://github.com/jhollway/iheiddown/issues
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Imports: bookdown, dplyr, ggplot2, rmarkdown, xaringan, crayon, pdftools, rlang, servr, readr, rstudioapi, tibble, tidytext, bib2df, stringr, fs, usethis, gender, pagedown
Encoding: UTF-8
Suggests: testthat, kableExtra, knitr, DT, leaflet, remotes, modelsummary, gt
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-03 04:10:50 UTC; hollway
Author: James Hollway [aut, cre, cph] , Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Repository: CRAN
Date/Publication: 2022-05-06 07:10:06 UTC

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New package fishflux with initial version 0.0.1.6
Package: fishflux
Title: Model Elemental Fluxes in Fishes
Version: 0.0.1.6
Description: Model fluxes of carbon, nitrogen, and phosphorus with the use of a coupled bioenergetics and stoichiometric model that incorporates flexible elemental limitation. Additional functions to help the user to find parameters are included. Finally, functions to extract and visualize results are available as well. For an introduction, see vignette. For more information on the theoretical background of this model, see Schiettekatte et al. (2020) <doi:10.1111/1365-2435.13618>.
URL: https://nschiett.github.io/fishflux/
BugReports: https://github.com/nschiett/fishflux/issues/
License: MIT + file LICENSE
Encoding: UTF-8
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.0.0), parallel, dplyr, fishualize, ggplot2, plyr, rfishbase (>= 3.1.9), tidybayes, tidyr, httr, curl
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown, testthat, covr
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.4.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
LazyData: true
VignetteBuilder: knitr
Biarch: true
NeedsCompilation: yes
Packaged: 2022-05-02 17:08:20 UTC; nina
Author: Nina M. D. Schiettekatte [aut, cre], Diego Barneche [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-06 07:10:09 UTC

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Package EpiLPS updated to version 1.0.5 with previous version 1.0.2 dated 2022-01-03

Title: A Bayesian Tool for Approximate Real-Time Estimation of the Reproduction Number
Description: Estimation of the instantaneous reproduction number with Laplacian-P-splines following the methodology of Gressani et al.(2021) <doi:10.1101/2021.12.02.21267189>. The negative Binomial distribution is used to model the time series of case counts. Two methods are available for inference : (1) a sampling-free approach based on a maximum a posteriori calibration of the hyperparameter vector and (2) a fully stochastic approach with a Metropolis-within-Gibbs algorithm and Langevin diffusions for efficient sampling of the posterior distribution.
Author: Oswaldo Gressani [aut, cre]
Maintainer: Oswaldo Gressani <oswaldo_gressani@hotmail.fr>

Diff between EpiLPS versions 1.0.2 dated 2022-01-03 and 1.0.5 dated 2022-05-06

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Package datamods updated to version 1.3.2 with previous version 1.3.0 dated 2022-04-25

Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], Zauad Shahreer Abeer [aut], Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between datamods versions 1.3.0 dated 2022-04-25 and 1.3.2 dated 2022-05-06

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New package aspect with initial version 1.0-6
Package: aspect
Title: A General Framework for Multivariate Analysis with Optimal Scaling
Version: 1.0-6
Date: 2022-05-05
Description: Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
Depends: R (>= 3.0.0)
Suggests: sem, polycor
Imports: stats, graphics, grDevices
License: GPL-2
URL: https://r-forge.r-project.org/projects/psychor/
LazyData: yes
LazyLoad: yes
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2022-05-05 21:36:16 UTC; patrick
Author: Patrick Mair [cre, aut], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-05-06 07:04:44 UTC

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Package spm updated to version 1.2.2 with previous version 1.2.1 dated 2021-09-06

Title: Spatial Predictive Modeling
Description: Introduction to some novel accurate hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. It contains two commonly used geostatistical methods, two machine learning methods, four hybrid methods and two averaging methods. For each method, two functions are provided. One function is for assessing the predictive errors and accuracy of the method based on cross-validation. The other one is for generating spatial predictions using the method. For details please see: Li, J., Potter, A., Huang, Z., Daniell, J. J. and Heap, A. (2010) <https:www.ga.gov.au/metadata-gateway/metadata/record/gcat_71407> Li, J., Heap, A. D., Potter, A., Huang, Z. and Daniell, J. (2011) <doi:10.1016/j.csr.2011.05.015> Li, J., Heap, A. D., Potter, A. and Daniell, J. (2011) <doi:10.1016/j.envsoft.2011.07.004> Li, J., Potter, A., Huang, Z. and Heap, A. (2012) <https:www.ga.gov.au/metadata-gateway/metadata/record/74030>.
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jinli68@gmail.com>

Diff between spm versions 1.2.1 dated 2021-09-06 and 1.2.2 dated 2022-05-06

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Package simMSM updated to version 1.1.42 with previous version 1.1.41 dated 2015-03-03

Title: Simulation of Event Histories for Multi-State Models
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen <hreulen@uni-goettingen.de>

Diff between simMSM versions 1.1.41 dated 2015-03-03 and 1.1.42 dated 2022-05-06

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Package shinyAce updated to version 0.4.2 with previous version 0.4.1 dated 2019-09-24

Title: Ace Editor Bindings for Shiny
Description: Ace editor bindings to enable a rich text editing environment within Shiny.
Author: Vincent Nijs [aut, cre], Forest Fang [aut], Trestle Technology, LLC [aut], Jeff Allen [aut], Institut de Radioprotection et de Surete Nucleaire [cph], Ajax.org B.V. [ctb, cph]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package SAMtool updated to version 1.3.1 with previous version 1.3.0 dated 2022-04-08

Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre], Tom Carruthers [aut], Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>

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New package rdiversity with initial version 2.2.0
Package: rdiversity
Title: Measurement and Partitioning of Similarity-Sensitive Biodiversity
Version: 2.2.0
Date: 2022-04-29
Maintainer: Richard Reeve <richard.reeve@glasgow.ac.uk>
URL: https://github.com/boydorr/rdiversity
BugReports: https://github.com/boydorr/rdiversity/issues
Description: Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) <arXiv:1404.6520v3>.
License: GPL-3
Depends: R (>= 2.10)
Imports: methods, reshape2, stats, stringdist, utils
Suggests: ape, testthat, knitr, markdown, rmarkdown, covr
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-05 23:28:39 UTC; richardr
Author: Sonia Mitchell [aut] , Richard Reeve [cre, aut, ths] , Tom White [ctb] , Daniel Doerrhoefer [ctb], Aaron Rudkin [ctb]
Repository: CRAN
Date/Publication: 2022-05-06 07:00:02 UTC

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Package pandocfilters updated to version 0.1-5 with previous version 0.1-4 dated 2019-11-26

Title: Pandoc Filters for R
Description: The document converter 'pandoc' <https://pandoc.org/> is widely used in the R community. One feature of 'pandoc' is that it can produce and consume JSON-formatted abstract syntax trees (AST). This allows to transform a given source document into JSON-formatted AST, alter it by so called filters and pass the altered JSON-formatted AST back to 'pandoc'. This package provides functions which allow to write such filters in native R code. Although this package is inspired by the Python package 'pandocfilters' <https://github.com/jgm/pandocfilters/>, it provides additional convenience functions which make it simple to use the 'pandocfilters' package as a report generator. Since 'pandocfilters' inherits most of it's functionality from 'pandoc' it can create documents in many formats (for more information see <https://pandoc.org/>) but is also bound to the same limitations as 'pandoc'.
Author: Florian Schwendinger [aut, cre], Kurt Hornik [aut], Andrie de Vries [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>

Diff between pandocfilters versions 0.1-4 dated 2019-11-26 and 0.1-5 dated 2022-05-06

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Package moranajp updated to version 0.9.4 with previous version 0.9.3 dated 2022-03-30

Title: Morphological Analysis for Japanese
Description: Supports morphological analysis for Japanese by using 'MeCab'. Can input data.frame and obtain all results of 'MeCab' and row number of original data.frame as a text id.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>

Diff between moranajp versions 0.9.3 dated 2022-03-30 and 0.9.4 dated 2022-05-06

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New package mvMonitoring with initial version 0.2.0
Package: mvMonitoring
Title: Multi-State Adaptive Dynamic Principal Component Analysis for Multivariate Process Monitoring
Version: 0.2.0
Maintainer: Gabriel Odom <gabriel.odom@fiu.edu>
Description: Use multi-state splitting to apply Adaptive-Dynamic PCA (ADPCA) to data generated from a continuous-time multivariate industrial or natural process. Employ PCA-based dimension reduction to extract linear combinations of relevant features, reducing computational burdens. For a description of ADPCA, see <doi:10.1007/s00477-016-1246-2>, the 2016 paper from Kazor et al. The multi-state application of ADPCA is from a manuscript under current revision entitled "Multi-State Multivariate Statistical Process Control" by Odom, Newhart, Cath, and Hering, and is expected to appear in Q1 of 2018.
License: GPL-2
Depends: R (>= 2.10)
Imports: dplyr, lazyeval, plyr, rlang, utils, xts, zoo, robustbase, graphics
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/gabrielodom/mvMonitoring
NeedsCompilation: no
Packaged: 2022-05-02 16:13:20 UTC; grantinnerst
Author: Melissa Innerst [aut], Gabriel Odom [aut, cre], Ben Barnard [aut], Karen Kazor [aut], Amanda Hering [aut]
Repository: CRAN
Date/Publication: 2022-05-06 07:00:07 UTC

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Package gamboostMSM updated to version 1.1.88 with previous version 1.1.87 dated 2014-12-02

Title: Boosting Multistate Models
Description: Contains infrastructure for using mboost::gamboost() in order to estimate multistate models.
Author: Holger Reulen
Maintainer: Holger Reulen <hreulen@uni-goettingen.de>

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