Mon, 09 Aug 2021

Package tfestimators updated to version 1.9.2 with previous version 1.9.1 dated 2018-11-07

Title: Interface to 'TensorFlow' Estimators
Description: Interface to 'TensorFlow' Estimators <https://www.tensorflow.org/guide/estimator>, a high-level API that provides implementations of many different model types including linear models and deep neural networks.
Author: JJ Allaire [aut], Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>), Kevin Ushey [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), Tomasz Kalinowski [cre], Daniel Falbel [ctb, cph], RStudio [cph, fnd], Google Inc. [cph]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>

Diff between tfestimators versions 1.9.1 dated 2018-11-07 and 1.9.2 dated 2021-08-09

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Package nser updated to version 1.2.0 with previous version 1.1.0 dated 2021-08-03

Title: Bhavcopy and Live Market Data from National Stock Exchange(NSE) India of Equities and Derivatives(F&O)
Description: Download Historical Bhavcopy and get Live Market data from NSE of Equities and Derivatives(F&O) segment. Data source <https://www.nseindia.com/all-reports>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>

Diff between nser versions 1.1.0 dated 2021-08-03 and 1.2.0 dated 2021-08-09

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Package logbin updated to version 2.0.5 with previous version 2.0.4 dated 2018-08-31

Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre] (<https://orcid.org/0000-0003-0212-6443>), Ian C. Marschner [ths] (<https://orcid.org/0000-0002-6225-1572>), Alexandra C. Gillett [ctb] (wrote an initial version of the nplbin function, <https://orcid.org/0000-0002-5069-3197>)
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

Diff between logbin versions 2.0.4 dated 2018-08-31 and 2.0.5 dated 2021-08-09

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Package NMdata updated to version 0.0.9 with previous version 0.0.8 dated 2021-07-09

Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Helps with trivial but tedious tasks and tries to identify errors to save time on debugging. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>

Diff between NMdata versions 0.0.8 dated 2021-07-09 and 0.0.9 dated 2021-08-09

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Package nanotime updated to version 0.3.3 with previous version 0.3.2 dated 2020-09-04

Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package DynamicGP updated to version 1.1-7 with previous version 1.1-6 dated 2020-04-19

Title: Modelling and Analysis of Dynamic Computer Experiments
Description: Emulating and solving inverse problems for dynamic computer experiments. It contains two major functionalities: (1) localized GP model for large-scale dynamic computer experiments using the algorithm proposed by Zhang et al. (2018) <arXiv:1611.09488>; (2) solving inverse problems in dynamic computer experiments. The current version only supports 64-bit version of R.
Author: Ru Zhang [aut, cre], Chunfang Devon Lin [aut], Pritam Ranjan [aut], Robert B Gramacy [ctb], Nicolas Devillard [ctb], Jorge Nocedal [ctb], Jose Luis Morales [ctb], Ciyou Zhu [ctb], Richard Byrd [ctb], Peihuang Lu-Chen [ctb], Berend Hasselman [ctb], Jack Dongarra [ctb], Jeremy Du Croz [ctb], Sven Hammarling [ctb], Richard Hanson [ctb], University of Chicago [cph], University of California [cph]
Maintainer: Ru Zhang <heavenmarshal@gmail.com>

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Package domir updated to version 0.1.0 with previous version 0.0.1 dated 2021-03-29

Title: Tools to Support Relative Importance Analysis
Description: Provides tools that support relative importance analysis focusing on dominance analysis. Dominance analysis is a methodology for determining the relative importance of predictors/features/independent variables (Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>; Groemping, U. (2007) <doi:10.1198/000313007X188252>) as well as parameter estimates (Luchman, J. N, Lei, X., & Kaplan, S. (2020) <doi:10.47263/JASEM.4(2)02>). These tools are intended to extend relative importance analysis to, effectively, any statistical or machine learning function as defined or desired by the user-especially those where the user wants to use custom importance/fit statistic or modeling function.
Author: Joseph Luchman [aut, cre] (<https://orcid.org/0000-0002-8886-9717>)
Maintainer: Joseph Luchman <jluchman@gmail.com>

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Package simglm updated to version 0.8.8 with previous version 0.8.0 dated 2020-06-12

Title: Simulate Models Based on the Generalized Linear Model
Description: Simulates regression models, including both simple regression and generalized linear mixed models with up to three level of nesting. Power simulations that are flexible allowing the specification of missing data, unbalanced designs, and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>

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Package galah (with last version 1.3.0) was removed from CRAN

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

2021-08-06 1.3.0
2021-07-02 1.2.0
2021-05-05 1.1.0
2021-04-06 1.0.0

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Package fairml updated to version 0.6 with previous version 0.5 dated 2021-06-16

Title: Fair Models in Machine Learning
Description: Fair machine learning regression models which take sensitive attributes into account in model estimation. Currently implementing Komiyama et al. (2018) <http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al. (2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own approach that uses ridge regression to enforce fairness.
Author: Marco Scutari [aut, cre]
Maintainer: Marco Scutari <marco.scutari@gmail.com>

Diff between fairml versions 0.5 dated 2021-06-16 and 0.6 dated 2021-08-09

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Package rfishbase updated to version 3.1.9 with previous version 3.1.8 dated 2021-06-07

Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Duncan Temple Lang [aut], Peter Wainwright [aut], Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between rfishbase versions 3.1.8 dated 2021-06-07 and 3.1.9 dated 2021-08-09

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Package rbibutils updated to version 2.2.3 with previous version 2.2.2 dated 2021-07-31

Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between rbibutils versions 2.2.2 dated 2021-07-31 and 2.2.3 dated 2021-08-09

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New package NMproject with initial version 0.6.2
Package: NMproject
Title: Script Based 'NONMEM' Model Development
URL: https://tsahota.github.io/NMproject/, https://github.com/tsahota/NMproject
BugReports: https://github.com/tsahota/NMproject/issues
Version: 0.6.2
Maintainer: Tarj Sahota <t.sahota0@gmail.com>
Description: Industrialisation of 'NONMEM' <https://www.iconplc.com/innovation/nonmem/> via fully and rapidly reusable model development 'workflows' entirely within 'RStudio'. Quickly get started with new models by importing 'NONMEM' templates from the built-in code library. Manipulate 'NONMEM' code from within R either via the tracked 'manual edit' interface or 'programmatically' via convenience functions. Script 'workflows' by piping sequences of model building steps from control file creation, to execution, to post-processing and evaluation. Run caching makes 'workflows' R markdown friendly for easy documentation of thoughts and modelling decisions alongside executable code. Share, reuse and recycle 'workflows' for new problems.
License: GPL (>= 3)
Encoding: UTF-8
Imports: shiny, reshape2, dygraphs, DT, git2r (>= 0.18.0), dplyr (>= 0.7.2), methods, stringr (>= 1.3.1), rlang (>= 0.2.1), diffobj (>= 0.1.11), tidyr, miniUI (>= 0.1.1), rstudioapi (>= 0.7), crayon (>= 1.3.4), rprojroot, htmltools, rmarkdown, magrittr, usethis, lifecycle (>= 1.0.0)
Suggests: testthat, knitr, ggplot2, future, data.tree, xpose, lubridate, pmxTools, Hmisc, rsample, renv, desc, purrr, digest, covr, devtools, roxygen2
NeedsCompilation: no
Packaged: 2021-08-09 10:11:37 UTC; tsahota0
Author: Tarj Sahota [aut, cre, cph], AstraZeneca [cph], Nuria Buil Bruna [ctb], Stein Schalkwijk [ctb]
Repository: CRAN
Date/Publication: 2021-08-09 14:20:02 UTC

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New package nflreadr with initial version 1.0.0
Package: nflreadr
Title: Download 'nflverse' Data
Version: 1.0.0
Description: A low-level package for downloading data from 'GitHub' repositories of the 'nflverse' project.
License: MIT + file LICENSE
URL: https://nflreadr.nflverse.com, https://github.com/nflverse/nflreadr
BugReports: https://github.com/nflverse/nflreadr/issues
Depends: R (>= 3.5.0)
Imports: cachem (>= 1.0.0), dplyr (>= 1.0.0), curl (>= 4.3.2), memoise (>= 2.0.0), purrr (>= 0.3.0), qs (>= 0.24.0), rappdirs (>= 0.3.3)
Suggests: covr (>= 3.0.0), DT (>= 0.15.0), knitr (>= 1.0.0), progressr (>= 0.8.0), rmarkdown (>= 2.6.0), testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-08-09 13:27:56 UTC; Tan
Author: Tan Ho [aut, cre, cph] (<https://orcid.org/0000-0001-8388-5155>), Sebastian Carl [aut], John Edwards [ctb], Ben Baldwin [ctb], Thomas Mock [ctb], Lee Sharpe [ctb]
Maintainer: Tan Ho <tan@tanho.ca>
Repository: CRAN
Date/Publication: 2021-08-09 14:40:02 UTC

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New package dnapath with initial version 0.6.8
Package: dnapath
Title: Differential Network Analysis using Gene Pathways
Version: 0.6.8
Description: Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
Depends: R (>= 3.6)
License: GPL-2 | GPL-3
LazyData: true
Imports: Rcpp (>= 1.0.1), biomaRt, corpcor, igraph, ggplot2, SeqNet, Rdpack, dplyr, tibble, stats, methods, curl, graphics, grDevices, utils, xml2
RdMacros: Rdpack
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
SystemRequirements: C++11
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, readr, bc3net, DWLasso, huge, GENIE3, minet, reactome.db
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-08-05 12:48:10 UTC; Grimes
Author: Tyler Grimes [aut, cre], Somnath Datta [aut]
Maintainer: Tyler Grimes <tyler.grimes@unf.edu>
Repository: CRAN
Date/Publication: 2021-08-09 15:00:02 UTC

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New package ConformalSmallest with initial version 1.0
Package: ConformalSmallest
Title: Efficient Tuning-Free Conformal Prediction
Version: 1.0
Description: An implementation of efficiency first conformal prediction (EFCP) and validity first conformal prediction (VFCP) that demonstrates both validity (coverage guarantee) and efficiency (width guarantee). To learn how to use it, check the vignettes for a quick tutorial. The package is based on the work by Yang Y., Kuchibhotla A.,(2021) <arxiv:2104.13871>.
URL: https://github.com/Elsa-Yang98/ConformalSmallest
Imports: glmnet, mvtnorm, stats, MASS, quantregForest
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, ggplot2, repr
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-08-08 15:56:27 UTC; elsayang
Author: Yachong Yang [aut, cre]
Maintainer: Yachong Yang <yachong@wharton.upenn.edu>
Repository: CRAN
Date/Publication: 2021-08-09 14:10:06 UTC

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New package cloudos with initial version 0.2.0
Package: cloudos
Title: R Client Library for CloudOS
Version: 0.2.0
Description: The 'CloudOS' client library for R makes it easy to interact with CloudOS <https://cloudos.lifebit.ai/> in the R environment for analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, utils, methods, dplyr (>= 1.0.0), jsonlite, rappdirs, ggplot2, tibble
Suggests: httptest, kableExtra, knitr, lintr, rmarkdown, testthat
URL: https://github.com/lifebit-ai/cloudos
BugReports: https://github.com/lifebit-ai/cloudos/issues
NeedsCompilation: no
Packaged: 2021-08-09 11:20:37 UTC; ilya
Author: Sangram Keshari Sahu [aut, cre], Lifebit Biotech Ltd. [cph]
Maintainer: Sangram Keshari Sahu <sangram@lifebit.ai>
Repository: CRAN
Date/Publication: 2021-08-09 14:30:02 UTC

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Package causalCmprsk updated to version 1.0.3 with previous version 1.0.2 dated 2021-08-09

Title: Nonparametric and Cox-Based Estimation of ATE in Competing Risks
Description: Estimation of average treatment effects (ATE) of two static treatment regimes on time-to-event outcomes with K competing events (K can be 1). The method uses propensity scores weighting for emulation of baseline randomization.
Author: Bella Vakulenko-Lagun, Colin Magdamo, Marie-Laure Charpignon, Bang Zheng, Mark Albers, Sudeshna Das
Maintainer: Bella Vakulenko-Lagun <blagun@stat.haifa.ac.il>

Diff between causalCmprsk versions 1.0.2 dated 2021-08-09 and 1.0.3 dated 2021-08-09

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Package bigtime updated to version 0.2.1 with previous version 0.2.0 dated 2021-06-24

Title: Sparse Estimation of Large Time Series Models
Description: Estimation of large Vector AutoRegressive (VAR), Vector AutoRegressive with Exogenous Variables X (VARX) and Vector AutoRegressive Moving Average (VARMA) Models with Structured Lasso Penalties, see Nicholson, Wilms, Bien and Matteson (2020) <https://jmlr.org/papers/v21/19-777.html> and Wilms, Basu, Bien and Matteson (2021) <doi:10.1080/01621459.2021.1942013>.
Author: Ines Wilms [cre, aut], David S. Matteson [aut], Jacob Bien [aut], Sumanta Basu [aut], Will Nicholson [aut], Enrico Wegner [aut]
Maintainer: Ines Wilms <i.wilms@maastrichtuniversity.nl>

Diff between bigtime versions 0.2.0 dated 2021-06-24 and 0.2.1 dated 2021-08-09

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Package florestal (with last version 0.1.3) was removed from CRAN

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

2020-10-24 0.1.3
2020-07-07 0.1.1
2020-07-06 0.1.0

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Package sysfonts updated to version 0.8.5 with previous version 0.8.4 dated 2021-07-26

Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

Diff between sysfonts versions 0.8.4 dated 2021-07-26 and 0.8.5 dated 2021-08-09

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Package string2path updated to version 0.0.2 with previous version 0.0.1 dated 2021-08-04

Title: Rendering Font into 'data.frame'
Description: Extract glyph information from a font file, and translate the outline curves to flattened paths or tessellated polygons. The converted data is returned as a 'data.frame' in easy-to-plot format.
Author: Hiroaki Yutani [aut, cre] (<https://orcid.org/0000-0002-3385-7233>)
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>

Diff between string2path versions 0.0.1 dated 2021-08-04 and 0.0.2 dated 2021-08-09

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Package FCVAR updated to version 0.1.1 with previous version 0.1.0 dated 2021-08-05

Title: Estimation and Inference for the Fractionally Cointegrated VAR
Description: Estimation and inference using the Fractionally Cointegrated Vector Autoregressive (VAR) model. It includes functions for model specification, including lag selection and cointegration rank selection, as well as a comprehensive set of options for hypothesis testing, including tests of hypotheses on the cointegrating relations, the adjustment coefficients and the fractional differencing parameters. An article describing the FCVAR model with examples is available on the Webpage <https://sites.google.com/view/mortennielsen/software>.
Author: Lealand Morin [aut, cre] (<https://orcid.org/0000-0001-8539-1386>), Morten Nielsen [aut] (<https://orcid.org/0000-0002-1337-9844>), Michal Popiel [aut]
Maintainer: Lealand Morin <lealand.morin@ucf.edu>

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Package edgebundle updated to version 0.2.1 with previous version 0.2.0 dated 2021-08-02

Title: Algorithms for Bundling Edges in Networks and Visualizing Flow and Metro Maps
Description: Implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.
Author: David Schoch [aut, cre] (<https://orcid.org/0000-0003-2952-4812>)
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

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Package AgroReg updated to version 1.1.0 with previous version 1.0.0 dated 2021-08-02

Title: Regression Analysis Linear and Nonlinear for Agriculture
Description: Linear and nonlinear regression analysis common in agricultural science papers (Archontoulis & Miguez (2015). <doi:10.2134/agronj2012.0506>). The package includes linear, quadratic, cubic, inverse quadratic, exponential, negative exponential, biexponential, Gaussian, three- or four-parameter logistic, four- or five-parameter Brain-Cousens logistic, four- or five-parameter Cedergreen-Ritz-Streibig logistic models. five parameters, Gompertz logistic, Michaelis-Menten, logarithmic, linear-linear segmented, linear-plate segmented, quadratic-plate segmented, nonparametric loess. The functions return the model coefficients and their respective p values, coefficient of determination, root mean square error, AIC, BIC, as well as graphs with the equations automatically.
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>

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Package reportfactory updated to version 0.4.0 with previous version 0.3.1 dated 2021-06-16

Title: Lightweight Infrastructure for Handling Multiple R Markdown Documents
Description: Provides an infrastructure for handling multiple R Markdown reports, including automated curation and time-stamping of outputs, parameterisation and provision of helper functions to manage dependencies.
Author: Thibaut Jombart [aut], Amy Gimma [ctb], Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package edgar updated to version 2.0.4 with previous version 2.0.3 dated 2020-05-22

Title: Tool for the U.S. SEC EDGAR Retrieval and Parsing of Corporate Filings
Description: In the USA, companies file different forms with the U.S. Securities and Exchange Commission (SEC) through EDGAR (Electronic Data Gathering, Analysis, and Retrieval system). The EDGAR database automated system collects all the different necessary filings and makes it publicly available. This package facilitates retrieving, storing, searching, and parsing of all the available filings on the EDGAR server. It downloads filings from SEC server in bulk with a single query. Additionally, it provides various useful functions: extracts 8-K triggering events, extract "Business (Item 1)" and "Management's Discussion and Analysis(Item 7)" sections of annual statements, searches filings for desired keywords, provides sentiment measures, parses filing header information, and provides HTML view of SEC filings.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>

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Package multigraph updated to version 0.95 with previous version 0.93 dated 2020-02-28

Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs, signed and valued graphs, bipartite graphs, multilevel graphs, and Cayley graphs with various layout options. Please note that this package still under a devel version.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>

Diff between multigraph versions 0.93 dated 2020-02-28 and 0.95 dated 2021-08-09

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New package insect with initial version 1.4.2
Package: insect
Title: Informatic Sequence Classification Trees
Version: 1.4.2
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Description: Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
License: GPL-3
LazyData: TRUE
URL: https://github.com/shaunpwilkinson/insect/
BugReports: https://github.com/shaunpwilkinson/insect/issues/
Encoding: UTF-8
Imports: ape (>= 3.0.0), aphid (>= 1.3.1), kmer (>= 1.1.0), openssl, phylogram (>= 2.0.0), RANN, seqinr, stats, utils, xml2
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-08-06 23:35:00 UTC; shaun
Repository: CRAN
Date/Publication: 2021-08-09 09:20:02 UTC

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Package precautionary updated to version 0.2.6 with previous version 0.2-1 dated 2021-01-12

Title: Safety Diagnostics for Dose-Escalation Trial Designs
Description: Enhances various R packages that support the design and simulation of phase 1 dose-escalation trials, adding diagnostics to examine the safety characteristics of these designs in light of expected inter-individual variation in pharmacokinetics and pharmacodynamics. See Norris (2020b), "Retrospective analysis of a fatal dose-finding trial" <arXiv:2004.12755> and (2020c) "What Were They Thinking? Pharmacologic priors implicit in a choice of 3+3 dose-escalation design" <arXiv:2012.05301>.
Author: David C. Norris [aut, cre, cph] (<https://orcid.org/0000-0001-9593-6343>), Markus Triska [ctb]
Maintainer: David C. Norris <david@precisionmethods.guru>

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New package PLFD with initial version 0.1.0
Package: PLFD
Title: Portmanteau Local Feature Discrimination for Matrix-Variate Data
Version: 0.1.0
Date: 2021-08-06
Maintainer: Zengchao Xu <zengc.xu@aliyun.com>
Description: The portmanteau local feature discriminant approach first identifies the local discriminant features and their differential structures, then constructs the discriminant rule by pooling the identified local features together. This method is applicable to high-dimensional matrix-variate data.
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 1.0.2), mathjaxr
LinkingTo: Rcpp (>= 1.0.2), RcppArmadillo (>= 0.9.800)
URL: https://gitee.com/xu-zc/PLFD
BugReports: https://gitee.com/xu-zc/PLFD/issues
License: GPL-3
Language: en-US
Encoding: UTF-8
Suggests: knitr, rmarkdown, markdown
RdMacros: mathjaxr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-08-08 04:54:12 UTC; zengc
Author: Zengchao Xu [aut, cre], Shan Luo [aut], Zehua Chen [aut]
Repository: CRAN
Date/Publication: 2021-08-09 07:40:12 UTC

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New package NonpModelCheck with initial version 4.0
Package: NonpModelCheck
Title: Model Checking and Variable Selection in Nonparametric Regression
Version: 4.0
Date: 2021-08-01
Imports: dr
Author: Adriano Zanin Zambom
Maintainer: Adriano Zanin Zambom <adriano.zambom@csun.edu>
Description: Provides tests of significance for covariates (or groups of covariates) in a fully nonparametric regression model and a variable (or group) selection procedure based on False Discovery Rate. In addition, it provides a function for local polynomial regression for any number of dimensions, using a bandwidth specified by the user or automatically chosen by cross validation or an adaptive procedure. Zambom and Akritas (2014) <doi:10.5705/ss.2013.112>, Zambom and Akritas (2015) <doi:10.1016/j.jmva.2014.08.014>, Zambom and Akritas (2017) <doi:10.18637/jss.v077.i10>.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2021-08-06 21:08:37 UTC; adrianozambom
Repository: CRAN
Date/Publication: 2021-08-09 07:10:02 UTC

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New package MFPCA with initial version 1.3-8
Package: MFPCA
Title: Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains
Version: 1.3-8
Date: 2021-08-04
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Description: Calculate a multivariate functional principal component analysis for data observed on different dimensional domains. The estimation algorithm relies on univariate basis expansions for each element of the multivariate functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are represented by S4 classes for this type of data implemented in the package 'funData'. For more details on the general concepts of both packages and a case study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
URL: https://github.com/ClaraHapp/MFPCA
License: GPL-2
Imports: abind, foreach, irlba, Matrix, methods, mgcv (>= 1.8-33), plyr, stats
Depends: R (>= 3.2.0), funData (>= 1.3-4)
Suggests: covr, fda, testthat (>= 2.0.0)
NeedsCompilation: yes
SystemRequirements: libfftw3 (>= 3.3.4)
Packaged: 2021-08-08 10:29:38 UTC; clara
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Repository: CRAN
Date/Publication: 2021-08-09 07:50:02 UTC

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New package LexFindR with initial version 1.0.0
Package: LexFindR
Title: Find Related Items and Lexical Dimensions in a Lexicon
Version: 1.0.0
Date: 2021-07-17
Description: Implements code to identify lexical competitors in a given list of words. We include many of the standard competitor types used in spoken word recognition research, such as functions to find cohorts, neighbors, and rhymes, amongst many others. The package includes documentation for using a variety of lexicon files, including those with form codes made up of multiple letters (i.e., phoneme codes) and also basic orthographies. Importantly, the code makes use of multiple CPU cores and vectorization when possible, making it extremely fast and able to handle large lexicons. Additionally, the package contains documentation for users to easily write new functions, allowing researchers to examine other relationships within a lexicon. Li, Z., Crinnion, A. M., & Magnuson, J. S. (2021) "LexFindR: A fast, simple, and extensible R package for finding similar words in a lexicon." <https://magnuson.psy.uconn.edu/wp-content/uploads/sites/1140/2021/02/lexfindr-brm-rev-2021-02-25.pdf>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: tidyverse, knitr, rmarkdown, testthat, future.apply, tictoc
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
URL: https://github.com/maglab-uconn/LexFindR
BugReports: https://github.com/maglab-uconn/LexFindR/issues
NeedsCompilation: no
Packaged: 2021-08-08 21:50:53 UTC; zhaobinli
Author: ZhaoBin Li [aut, cre], Anne Marie Crinnion [aut], James S. Magnuson [aut, cph]
Maintainer: ZhaoBin Li <bzilplj@gmail.com>
Repository: CRAN
Date/Publication: 2021-08-09 07:50:05 UTC

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Package joinet updated to version 0.0.10 with previous version 0.0.8 dated 2021-07-16

Title: Multivariate Elastic Net Regression
Description: Implements high-dimensional multivariate regression by stacked generalisation (Rauschenberger 2021 <doi:10.1093/bioinformatics/btab576>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement. If required, install MRCE or remMap from GitHub (<https://github.com/cran/MRCE>, <https://github.com/cran/remMap>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>

Diff between joinet versions 0.0.8 dated 2021-07-16 and 0.0.10 dated 2021-08-09

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New package IDSpatialStats with initial version 0.3.12
Package: IDSpatialStats
Version: 0.3.12
Date: 2021-08-07
Title: Estimate Global Clustering in Infectious Disease
Maintainer: Justin Lessler <jlessler@unc.edu>
License: GPL (>= 2)
Description: Implements various novel and standard clustering statistics and other analyses useful for understanding the spread of infectious disease.
Encoding: UTF-8
LazyData: true
Imports: igraph, spatstat.core, spatstat.geom
Depends: doParallel, foreach, parallel, R (>= 2.10)
Suggests: knitr, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2021-08-07 18:59:24 UTC; johngiles
Author: John Giles [aut, ctb], Henrik Salje [aut, ctb], Justin Lessler [aut, cre]
Repository: CRAN
Date/Publication: 2021-08-09 07:50:09 UTC

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New package ggrisk with initial version 1.3
Package: ggrisk
Title: Risk Score Plot for Cox Regression
Version: 1.3
Description: The risk plot may be one of the most commonly used figures in tumor genetic data analysis. We can conclude the following two points: Comparing the prediction results of the model with the real survival situation to see whether the survival rate of the high-risk group is lower than that of the low-level group, and whether the survival time of the high-risk group is shorter than that of the low-risk group. The other is to compare the heat map and scatter plot to see the correlation between the predictors and the outcome.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: ggplot2, survival, egg, do, set, cutoff, grid, rms, nomogramFormula, reshape2
URL: https://github.com/yikeshu0611/ggrisk
BugReports: https://github.com/yikeshu0611/ggrisk/issues
NeedsCompilation: no
Packaged: 2021-08-07 14:40:20 UTC; asus
Author: Jing Zhang [aut, cre], Zhi Jin [aut]
Maintainer: Jing Zhang <zj391120@163.com>
Repository: CRAN
Date/Publication: 2021-08-09 07:40:06 UTC

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New package diyar with initial version 0.3.1
Package: diyar
Title: Record Linkage and Epidemiological Case Definitions in R
Date: 2021-08-07
Version: 0.3.1
URL: https://olisansonwu.github.io/diyar/index.html
BugReports: https://github.com/OlisaNsonwu/diyar/issues
Author: Olisaeloka Nsonwu
Maintainer: Olisaeloka Nsonwu <olisa.nsonwu@gmail.com>
Description: An R package for record linkage and implementing epidemiological case definitions in R. Record linkage is implemented either through a multistage deterministic approach or a probabilistic approach. Matching records are assigned to unique groups. There are mechanisms to address missing data and conflicting matches across linkage stages. Track and assign events (e.g. sample collection) and periods (e.g. hospital admission) to unique groups based on a case definition. The tracking process permits several options such as episode lengths and recurrence. Duplicate events or records can then be identified for removal or further analyses.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: methods, grDevices, graphics, utils, Rfast, ggplot2, rlang
Suggests: knitr, rmarkdown, testthat, covr, stringdist
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2021-08-07 19:11:40 UTC; Olisaeloka.Nsonwu
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-08-09 08:00:07 UTC

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New package causalCmprsk with initial version 1.0.2
Package: causalCmprsk
Title: Nonparametric and Cox-Based Estimation of ATE in Competing Risks
Version: 1.0.2
Author: Bella Vakulenko-Lagun, Colin Magdamo, Marie-Laure Charpignon, Bang Zheng, Mark Albers, Sudeshna Das
Maintainer: Bella Vakulenko-Lagun <blagun@stat.haifa.ac.il>
Description: Estimation of average treatment effects (ATE) of two static treatment regimes on time-to-event outcomes with K competing events (K can be 1). The method uses propensity scores weighting for emulation of baseline randomization.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.6)
Imports: survival, inline, doParallel, parallel, utils, foreach, data.table, purrr
Suggests: knitr, rmarkdown, bookdown, tidyverse, ggalt, cobalt, ggsci, modEvA, naniar, DT, Hmisc, hrbrthemes, summarytools, kableExtra
VignetteBuilder: knitr
URL: https://github.com/Bella2001/causalCmprsk
BugReports: https://github.com/Bella2001/causalCmprsk/issues
NeedsCompilation: no
Packaged: 2021-08-08 08:49:18 UTC; blagun
Repository: CRAN
Date/Publication: 2021-08-09 07:40:09 UTC

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New package GNRS with initial version 0.3.1
Package: GNRS
Title: Access the 'Geographic Name Resolution Service'
Version: 0.3.1
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: RCurl, jsonlite
Suggests: knitr, rmarkdown, testthat, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-08-06 17:10:26 UTC; Brian
Author: Brad Boyle [aut], Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Repository: CRAN
Date/Publication: 2021-08-09 06:50:02 UTC

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New package ggborderline with initial version 0.1.0
Package: ggborderline
URL: https://github.com/wurli/ggborderline, https://wurli.github.io/ggborderline/
Title: Line Plots that Pop
Version: 0.1.0
Author: Jacob Scott
Maintainer: Jacob Scott <jscott2718@gmail.com>
Description: A set of geometries to make line plots a little bit nicer. Use along with 'ggplot2' to: - Improve the clarity of line plots with many overlapping lines - Draw more realistic worms.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: ggplot2, scales
NeedsCompilation: no
Packaged: 2021-08-06 20:25:52 UTC; Jacob
Repository: CRAN
Date/Publication: 2021-08-09 07:00:02 UTC

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New package divseg with initial version 0.0.4
Package: divseg
Title: Calculate Diversity and Segregation Indices
Version: 0.0.4
Date: 2021-08-06
Description: Implements common measures of diversity and spatial segregation. This package has tools to compute the majority of measures are reviewed in Douglas and Massey (1988) <doi:10.2307/2579183>. Multiple common measures of within-geography diversity are implemented as well. All functions operate on data frames with a 'tidyselect' based workflow.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/christopherkenny/divseg/issues
URL: https://github.com/christopherkenny/divseg/, https://christopherkenny.github.io/divseg/
Suggests: roxygen2, testthat (>= 3.0.0)
Imports: sf (>= 1.0.0), rlang (>= 0.1.2), dplyr, magrittr, tidyselect, tibble, units
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-08-06 19:50:25 UTC; chris
Author: Christopher T. Kenny [aut, cre] (<https://orcid.org/0000-0002-9386-6860>)
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2021-08-09 07:00:05 UTC

More information about divseg at CRAN
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Package covid19jp (with last version 0.1.0) was removed from CRAN

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

2021-01-09 0.1.0

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Package nlgeocoder (with last version 0.1.3) was removed from CRAN

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

2018-10-08 0.1.3

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Package RSNNS updated to version 0.4-13 with previous version 0.4-12 dated 2019-09-17

Title: Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the 'RSNNS' low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph], José M. Benítez [ths], Andreas Zell [ctb] (Part of original SNNS development team), Niels Mache [ctb] (Part of original SNNS development team), Günter Mamier [ctb] (Part of original SNNS development team), Michael Vogt [ctb] (Part of original SNNS development team), Sven Döring [ctb] (Part of original SNNS development team), Ralf Hübner [ctb] (Part of original SNNS development team), Kai-Uwe Herrmann [ctb] (Part of original SNNS development team), Tobias Soyez [ctb] (Part of original SNNS development team), Michael Schmalzl [ctb] (Part of original SNNS development team), Tilman Sommer [ctb] (Part of original SNNS development team), Artemis Hatzigeorgiou [ctb] (Part of original SNNS development team), Dietmar Posselt [ctb] (Part of original SNNS development team), Tobias Schreiner [ctb] (Part of original SNNS development team), Bernward Kett [ctb] (Part of original SNNS development team), Martin Reczko [ctb] (Part of original SNNS external contributors), Martin Riedmiller [ctb] (Part of original SNNS external contributors), Mark Seemann [ctb] (Part of original SNNS external contributors), Marcus Ritt [ctb] (Part of original SNNS external contributors), Jamie DeCoster [ctb] (Part of original SNNS external contributors), Jochen Biedermann [ctb] (Part of original SNNS external contributors), Joachim Danz [ctb] (Part of original SNNS development team), Christian Wehrfritz [ctb] (Part of original SNNS development team), Patrick Kursawe [ctb] (Contributors to SNNS Version 4.3), Andre El-Ama [ctb] (Contributors to SNNS Version 4.3)
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>

Diff between RSNNS versions 0.4-12 dated 2019-09-17 and 0.4-13 dated 2021-08-09

 ChangeLog                      |    7 ++++++
 DESCRIPTION                    |   10 ++++----
 MD5                            |   46 ++++++++++++++++++++---------------------
 R/RSNNS-package.R              |   10 ++++----
 inst/CITATION                  |    4 +--
 man/RSNNS-package.Rd           |   14 ++++++------
 man/SnnsR-class.Rd             |    2 -
 man/SnnsRObjectMethodCaller.Rd |    1 
 man/analyzeClassification.Rd   |    2 -
 man/art1.Rd                    |   24 +++++++++++++++------
 man/art2.Rd                    |   20 ++++++++++++-----
 man/artmap.Rd                  |   30 ++++++++++++++++++--------
 man/assoz.Rd                   |   19 ++++++++++++----
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 man/elman.Rd                   |   24 ++++++++++++++++-----
 man/jordan.Rd                  |   23 +++++++++++++++-----
 man/mlp.Rd                     |   29 ++++++++++++++++++-------
 man/rbf.Rd                     |   23 +++++++++++++++-----
 man/rbfDDA.Rd                  |   19 ++++++++++++----
 man/rsnnsObjectFactory.Rd      |   19 +++++++++++++---
 man/som.Rd                     |   22 ++++++++++++++-----
 man/train.Rd                   |   12 ++++++++--
 src/kr_io.cpp                  |   14 +++++++-----
 src/kr_pat_scan.cpp            |    2 +
 24 files changed, 266 insertions(+), 126 deletions(-)

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Package jsmodule updated to version 1.1.8 with previous version 1.1.7 dated 2021-03-13

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jsmodule versions 1.1.7 dated 2021-03-13 and 1.1.8 dated 2021-08-09

 DESCRIPTION            |   20 ++++++++-----------
 MD5                    |   44 +++++++++++++++++++++---------------------
 NAMESPACE              |   13 ++++++------
 NEWS.md                |    8 ++++++-
 R/coxph.R              |    2 -
 R/display2.R           |    4 +--
 R/gee.R                |    2 -
 R/ggpairs.R            |   42 ++++++++++++++++++++++++----------------
 R/jsBasicGadget.R      |    1 
 R/kaplan.R             |   19 ++++++++++--------
 R/regress.R            |    2 -
 R/roc.R                |   42 ++++++++++++++++++++--------------------
 R/scatter.R            |   18 ++++++++++-------
 R/tb1.R                |    6 ++---
 R/tb1simple.R          |   10 ++-------
 R/timeroc.R            |   51 ++++++++++++++++++++++++++-----------------------
 build/vignette.rds     |binary
 inst/doc/jsmodule.html |    4 +--
 man/rocModule.Rd       |    2 -
 man/rocModule2.Rd      |    2 -
 man/tb1module2.Rd      |    2 -
 man/tb1simple.Rd       |    1 
 man/tb1simple2.Rd      |    1 
 23 files changed, 153 insertions(+), 143 deletions(-)

More information about jsmodule at CRAN
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