Mon, 21 Nov 2022

Package future.tests updated to version 0.4.0 with previous version 0.3.0 dated 2021-10-10

Title: Test Suite for 'Future API' Backends
Description: Backends implementing the 'Future' API, as defined by the 'future' package, should use the tests provided by this package to validate that they meet the minimal requirements of the 'Future' API. The tests can be performed easily from within R or from outside of R from the command line making it easy to include them package tests and in Continuous Integration (CI) pipelines.
Author: Henrik Bengtsson [aut, cre, cph], The R Consortium [fnd] grant in 2017)
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future.tests versions 0.3.0 dated 2021-10-10 and 0.4.0 dated 2022-11-21

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Package dycdtools updated to version 0.4.3 with previous version 0.4.2 dated 2022-05-25

Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] , Christopher McBride [ctb], Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>

Diff between dycdtools versions 0.4.2 dated 2022-05-25 and 0.4.3 dated 2022-11-21

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Package parameters updated to version 0.20.0 with previous version 0.19.0 dated 2022-10-05

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Soeren Hoejsgaard [aut], Brenton M. Wiernik [aut] , Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] , Jeffrey Girard [ctb] , Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

Diff between parameters versions 0.19.0 dated 2022-10-05 and 0.20.0 dated 2022-11-21

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Package slgf updated to version 2.0.0 with previous version 0.1.0 dated 2021-02-17

Title: Bayesian Model Selection with Suspected Latent Grouping Factors
Description: Implements the Bayesian model selection method with suspected latent grouping factor methodology of Metzger and Franck (2020), <doi:10.1080/00401706.2020.1739561>. SLGF detects latent heteroscedasticity or group-based regression effects based on the levels of a user-specified categorical predictor.
Author: Thomas Metzger [aut, cre], Christopher Franck [aut]
Maintainer: Thomas Metzger <metzger.181@osu.edu>

Diff between slgf versions 0.1.0 dated 2021-02-17 and 2.0.0 dated 2022-11-21

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New package shapeR with initial version 1.0-1
Package: shapeR
Title: Collection and Analysis of Otolith Shape Data
Version: 1.0-1
Date: 2022-11-21
Maintainer: Lisa Anne Libungan <lisa.libungan@gmail.com>
Depends: R (>= 3.0.2)
Imports: plotrix, jpeg, pixmap, wavethresh, methods, vegan, MASS
Description: Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise described in Haines and Crampton (2000) <doi:10.1111/1475-4983.00148>, choose from conducting either a Fourier or wavelet see Gençay et al (2001) <doi:10.1016/S0378-4371(00)00463-5> transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional [...truncated...]
License: GPL (>= 2)
URL: https://github.com/lisalibungan/shapeR, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102
Packaged: 2022-11-21 18:54:49 UTC; lisa
Author: Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-11-21 22:30:04 UTC
Encoding: UTF-8

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Package maptiles updated to version 0.4.0 with previous version 0.3.0 dated 2021-09-24

Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and displays tiles from a large number of providers (e.g. 'OpenStreetMap', 'Stamen', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] , Diego Hernangomez [ctb] , Robert J. Hijmans [ctb] , Hugh A. Graham [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>

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Package shinylight updated to version 1.1.1 with previous version 1.1 dated 2022-11-18

Title: Web Interface to 'R' Functions
Description: Web front end for your 'R' functions producing plots or tables. If you have a function or set of related functions, you can make them available over the internet through a web browser. This is the same motivation as the 'shiny' package, but note that the development of 'shinylight' is not in any way linked to that of 'shiny' (beyond the use of the 'httpuv' package). You might prefer 'shinylight' to 'shiny' if you want a lighter weight deployment with easier horizontal scaling, or if you want to develop your front end yourself in JavaScript and HTML just using a lightweight remote procedure call interface to your R code on the server.
Author: Pieter Vermeesch [aut], Tim Band [aut, cre]
Maintainer: Tim Band <t.band@ucl.ac.uk>

Diff between shinylight versions 1.1 dated 2022-11-18 and 1.1.1 dated 2022-11-21

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Package rspm updated to version 0.2.3 with previous version 0.2.2 dated 2022-09-15

Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions. Provides access to 'RStudio' public repositories at <https://packagemanager.rstudio.com>, and transparent management of system requirements without administrative privileges. Currently supported distributions are 'CentOS' / 'RHEL' 7 and 8, and several 'RHEL' derivatives ('Rocky Linux' 8, 'AlmaLinux' 8, 'Oracle Linux' 7 and 8, 'Amazon Linux' 2), 'openSUSE' / 'SLES' 15.3, and 'Ubuntu' 18.04, 20.04 and 22.04.
Author: Inaki Ucar [aut, cph, cre] , R Core Team [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>

Diff between rspm versions 0.2.2 dated 2022-09-15 and 0.2.3 dated 2022-11-21

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Package RISCA updated to version 1.0.3 with previous version 1.0.1 dated 2022-05-02

Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.
Author: Yohann Foucher [aut, cre] , Florent Le Borgne [aut], Arthur Chatton [aut], Camille Sabathe [aut]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-poitiers.fr>

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Package prevR updated to version 4.0.1 with previous version 4.0.0 dated 2022-05-11

Title: Estimating Regional Trends of a Prevalence from a DHS and Similar Surveys
Description: Spatial estimation of a prevalence surface or a relative risks surface, using data from a Demographic and Health Survey (DHS) or an analog survey, see Larmarange et al. (2011) <doi:10.4000/cybergeo.24606>.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>

Diff between prevR versions 4.0.0 dated 2022-05-11 and 4.0.1 dated 2022-11-21

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New package multiness with initial version 1.0.1
Package: multiness
Title: MULTIplex NEtworks with Shared Structure
Version: 1.0.1
Description: Model fitting and simulation for Gaussian and logistic inner product MultiNeSS models for multiplex networks. The package implements a convex fitting algorithm with fully adaptive parameter tuning, including options for edge cross-validation. For more details see MacDonald et al. (2020).
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: glmnet (>= 4.0.2), Matrix (>= 1.1.0), RSpectra (>= 0.16.0),
Depends: R (>= 3.6.0)
URL: https://github.com/peterwmacd/multiness/
BugReports: https://github.com/peterwmacd/multiness/issues/
NeedsCompilation: no
Packaged: 2022-11-21 15:33:52 UTC; pwmacdon
Author: Peter W. MacDonald [aut, cre]
Maintainer: Peter W. MacDonald <pwmacdon@umich.edu>
Repository: CRAN
Date/Publication: 2022-11-21 22:00:10 UTC

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Package lazyNumbers updated to version 1.2.1 with previous version 1.2.0 dated 2022-11-21

Title: Exact Floating-Point Arithmetic
Description: Provides a new type of numbers called the lazy numbers. Arithmetic on lazy numbers is exact, contrary to ordinary floating-point arithmetic. The lazy numbers are implemented in 'C++' with the 'CGAL' library (<https://www.cgal.org/>).
Author: Stephane Laurent [aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>

Diff between lazyNumbers versions 1.2.0 dated 2022-11-21 and 1.2.1 dated 2022-11-21

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Package jpstat updated to version 0.3.0 with previous version 0.2.1 dated 2022-05-10

Title: Tools for Easy Use of 'e-Stat', 'RESAS' API, Etc
Description: Provides tools to use API such as 'e-Stat' (<https://www.e-stat.go.jp/>), the portal site for Japanese government statistics, and 'RESAS' (Regional Economy and Society Analyzing System, <https://resas.go.jp>).
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>

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Package globals updated to version 0.16.2 with previous version 0.16.1 dated 2022-08-28

Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions by code inspection using various strategies (ordered, liberal, or conservative). The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph], Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between globals versions 0.16.1 dated 2022-08-28 and 0.16.2 dated 2022-11-21

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Package pomp updated to version 4.4 with previous version 4.3 dated 2022-07-06

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Eamon B. O'Dea [c [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>

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Package mlflow updated to version 2.0.1 with previous version 1.30.0 dated 2022-10-27

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] , RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

Diff between mlflow versions 1.30.0 dated 2022-10-27 and 2.0.1 dated 2022-11-21

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Package scpi updated to version 2.0.1 with previous version 2.0.0 dated 2022-10-10

Title: Prediction Intervals for Synthetic Control Methods with Multiple Treated Units and Staggered Adoption
Description: Implementation of estimation and inference procedures for Synthetic Control methods using least square, lasso, ridge, or simplex-type constraints. Uncertainty is quantified with prediction intervals as developed in Cattaneo, Feng, and Titiunik (2021) <https://cattaneo.princeton.edu/papers/Cattaneo-Feng-Titiunik_2021_JASA.pdf>.
Author: Matias Cattaneo [aut], Yingjie Feng [aut], Filippo Palomba [aut, cre], Rocio Titiunik [aut]
Maintainer: Filippo Palomba <fpalomba@princeton.edu>

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Package maraca updated to version 0.4.0 with previous version 0.3.10 dated 2022-10-05

Title: The Maraca Plot: Visualization of Hierarchical Composite Endpoints in Clinical Trials
Description: Library that supports visual interpretation of hierarchical composite endpoints (HCEs). HCEs are complex constructs used as primary endpoints in clinical trials, combining outcomes of different types into ordinal endpoints, in which each patient contributes the most clinically important event (one and only one) to the analysis.
Author: Martin Karpefors [aut], Samvel B. Gasparyan [aut], Stefano Borini [ctb, cre]
Maintainer: Stefano Borini <stefano.borini@astrazeneca.com>

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Package epimdr2 updated to version 1.0-8 with previous version 1.0-7 dated 2022-09-14

Title: Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <https://link.springer.com/book/10.1007/978-3-319-97487-3>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the 'Coursera' Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package daiquiri updated to version 1.0.2 with previous version 1.0.1 dated 2022-11-11

Title: Data Quality Reporting for Temporal Datasets
Description: Generate reports that enable quick visual review of temporal shifts in record-level data. Time series plots showing aggregated values are automatically created for each data field (column) depending on its contents (e.g. min/max/mean values for numeric data, no. of distinct values for categorical data), as well as overviews for missing values, non-conformant values, and duplicated rows. The resulting reports are shareable and can contribute to forming a transparent record of the entire analysis process. It is designed with Electronic Health Records in mind, but can be used for any type of record-level temporal data (i.e. tabular data where each row represents a single "event", one column contains the "event date", and other columns contain any associated values for the event).
Author: T. Phuong Quan [aut, cre] , Jack Cregan [ctb], University of Oxford [cph], National Institute for Health Research [fnd], Brad Cannell [rev]
Maintainer: T. Phuong Quan <phuong.quan@ndm.ox.ac.uk>

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Package cpop updated to version 1.0.6 with previous version 1.0.4 dated 2022-11-11

Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope.
Author: Daniel Grose [aut, cre], Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>

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Package stars updated to version 0.6-0 with previous version 0.5-6 dated 2022-07-21

Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] , Michael Sumner [ctb] , Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package rsvg updated to version 2.4.0 with previous version 2.3.2 dated 2022-10-18

Title: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size bitmap arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg or webp format. In addition, the package can convert images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] , Salim Brueggemann [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package fundiversity updated to version 1.1.1 with previous version 1.0.0 dated 2022-08-25

Title: Easy Computation of Functional Diversity Indices
Description: Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (preprint: <doi:10.32942/osf.io/dg7hw>).
Author: Matthias Grenie [aut, cre] , Hugo Gruson [aut]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>

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Package edlibR updated to version 1.0.1 with previous version 1.0.0 dated 2022-01-12

Title: R Integration for Edlib, the C/C++ Library for Exact Pairwise Sequence Alignment using Edit (Levenshtein) Distance
Description: Bindings to edlib, a lightweight performant C/C++ library for exact pairwise sequence alignment using edit distance (Levenshtein distance). The algorithm computes the optimal alignment path, but also can be used to find only the start and/or end of the alignment path for convenience. Edlib was designed to be ultrafast and require little memory, with the capability to handle very large sequences. Three alignment methods are supported: global (Needleman-Wunsch), infix (Hybrid Wunsch), and prefix (Semi-Hybrid Wunsch). The original C/C++ library is described in "Edlib: a C/C++ library for fast, exact sequence alignment using edit distance", M. Šošić, M. Šikić, <doi:10.1093/bioinformatics/btw753>.
Author: Martin Sosić [aut], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Package survivalMPL updated to version 0.2-3 with previous version 0.2-2 dated 2022-11-20

Title: Penalised Maximum Likelihood for Survival Analysis Models
Description: Estimate the regression coefficients and the baseline hazard of proportional hazard Cox models with left, right or interval censored survival data using maximum penalised likelihood. A 'non-parametric' smooth estimate of the baseline hazard function is provided.
Author: Dominique-Laurent Couturier, Jun Ma, Stephane Heritier, Maurizio Manuguerra.
Maintainer: Dominique-Laurent Couturier <dominique-laurent.couturier@cruk.cam.ac.uk>

Diff between survivalMPL versions 0.2-2 dated 2022-11-20 and 0.2-3 dated 2022-11-21

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Package QRISK3 updated to version 0.4.0 with previous version 0.3.0 dated 2019-12-06

Title: 10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017)
Description: This function aims to calculate risk of developing cardiovascular disease of individual patients in next 10 years. The package was based on published risk prediction algorithm <https://qrisk.org/three/src.php>.
Author: Yan Li <bluefatterplaydota@gmail.com> [aut, cre, trl], Matthew Sperrin [aut, ctb], ClinRisk Ltd. [cph], Tjeerd Pieter van Staa [aut, ths]
Maintainer: Yan Li <bluefatterplaydota@gmail.com>

Diff between QRISK3 versions 0.3.0 dated 2019-12-06 and 0.4.0 dated 2022-11-21

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Package purgeR updated to version 1.6 with previous version 1.5 dated 2022-07-11

Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.
Author: Eugenio Lopez-Cortegano [aut, cre]
Maintainer: Eugenio Lopez-Cortegano <elcortegano@gmail.com>

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Package mlmts updated to version 1.1.0 with previous version 1.0.1 dated 2022-04-19

Title: Machine Learning Algorithms for Multivariate Time Series
Description: An implementation of several machine learning algorithms for multivariate time series. The package includes functions allowing the execution of clustering, classification or outlier detection methods, among others. It also incorporates a collection of multivariate time series datasets which can be used to analyse the performance of new proposed algorithms. Some of these datasets are stored in GitHub data packages 'ueadata1' to 'ueadata8'. To access these data packages, run 'install.packages(c('ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5', 'ueadata6', 'ueadata7', 'ueadata8'), repos='<https://anloor7.github.io/drat/>')'. The installation takes a couple of minutes but we strongly encourage the users to do it if they want to have available all datasets of mlmts. Practitioners from a broad variety of fields could benefit from the general framework provided by 'mlmts'.
Author: Angel Lopez-Oriona [aut, cre], Jose A. Vilar [aut]
Maintainer: Angel Lopez-Oriona <oriona38@hotmail.com>

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Package DIZtools updated to version 0.0.6 with previous version 0.0.5 dated 2022-05-18

Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Author: Jonathan M. Mang [aut, cre] , Lorenz A. Kapsner [aut] , MIRACUM - Medical Informatics in Research and Care in University Medicine [fnd], Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>

Diff between DIZtools versions 0.0.5 dated 2022-05-18 and 0.0.6 dated 2022-11-21

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Package asciicast updated to version 2.2.1 with previous version 2.2.0 dated 2022-10-26

Title: Create 'Ascii' Screen Casts from R Scripts
Description: Record 'asciicast' screen casts from R scripts. Convert them to animated SVG images, to be used in 'README' files, or blog posts. Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast' 'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
Author: Gabor Csardi [aut, cre], Romain Francois [aut], Mario Nebl [aut] , Marcin Kulik [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between asciicast versions 2.2.0 dated 2022-10-26 and 2.2.1 dated 2022-11-21

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New package SourceSet with initial version 0.1.5
Package: SourceSet
Title: A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways
Version: 0.1.5
Date: 2022-11-21
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>
Description: The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')'). More details in Salviato et al., (2020) <doi:10.1371/journal.pcbi.1007357> and Djordjilovic et al., (2022) <doi:10.1016/j.jmva.2022.104973> [...truncated...]
Depends: R (>= 2.10)
Imports: gRbase, progress, reshape2, graph, igraph, gtools, methods, plyr, scales
License: AGPL-3
Encoding: UTF-8
LazyData: true
Suggests: AnnotationDbi, networkD3, ggplot2, grDevices, Rgraphviz, knitr, rmarkdown, r2cytoscape, BiocStyle, Biobase, graphite, hgu95av2.db, ALL, mvtnorm, org.Hs.eg.db
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2022-11-21 10:07:19 UTC; esalviat
Author: Elisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Repository: CRAN
Date/Publication: 2022-11-21 11:30:02 UTC

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Package csvwr updated to version 0.1.7 with previous version 0.1.6 dated 2021-11-09

Title: Read and Write CSV on the Web (CSVW) Tables and Metadata
Description: Provide functions for reading and writing CSVW - i.e. CSV tables and JSON metadata. The metadata helps interpret CSV by setting the types and variable names.
Author: Robin Gower
Maintainer: Robin Gower <csvwr@infonomics.ltd.uk>

Diff between csvwr versions 0.1.6 dated 2021-11-09 and 0.1.7 dated 2022-11-21

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New package vMF with initial version 0.0.1
Package: vMF
Title: Sampling from von Mises-Fisher Distribution
Version: 0.0.1
Date: 2022-11-20
Description: Provides fast sampling from von Mises-Fisher distribution using the method proposed by Andrew T.A Wood (1994) <doi:10.1080/03610919408813161>.
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/ahoundetoungan/vMF/issues
URL: https://github.com/ahoundetoungan/vMF
Depends: R (>= 3.5.0)
Imports: Rcpp
LinkingTo: Rcpp, RcppArmadillo, BH
Suggests: movMF, rbenchmark, knitr, rmarkdown, ggplot2, ddpcr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-11-19 17:56:11 UTC; haache
Author: Elysee Aristide Houndetoungan [cre, aut]
Maintainer: Elysee Aristide Houndetoungan <ariel92and@gmail.com>
Repository: CRAN
Date/Publication: 2022-11-21 10:50:02 UTC

More information about vMF at CRAN
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New package scistreer with initial version 1.0.0
Package: scistreer
Title: Maximum-Likelihood Perfect Phylogeny Inference at Scale
URL: https://github.com/kharchenkolab/scistreer, https://kharchenkolab.github.io/scistreer/
Version: 1.0.0
Description: Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1.0)
Imports: ape, dplyr, ggplot2, ggtree, igraph, parallelDist, patchwork, phangorn, Rcpp, reshape2, RcppParallel, stringr, tidygraph
Suggests: testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
NeedsCompilation: yes
SystemRequirements: C++11, GNU make
Author: Teng Gao [cre, aut], Evan Biederstedt [aut], Peter Kharchenko [aut], Yufeng Wu [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Packaged: 2022-11-19 17:56:13 UTC; teng
Repository: CRAN
Date/Publication: 2022-11-21 10:50:05 UTC

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New package PEIMAN2 with initial version 0.1.0
Package: PEIMAN2
Title: Post-Translational Modification Enrichment, Integration, and Matching Analysis
Version: 0.1.0
Description: Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2022) <bioRxiv:10.1101/2022.11.09.515610>.
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 2.10), tidyverse
Imports: ggplot2, dplyr, glue, lifecycle, purrr, rlang, stringr, graphics, forcats, stats, magrittr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
LazyData: true
NeedsCompilation: no
Packaged: 2022-11-19 02:31:43 UTC; payma
Author: Mohieddin Jafari [aut], Payman Nickchi [aut, cre]
Maintainer: Payman Nickchi <pnickchi@sfu.ca>
Repository: CRAN
Date/Publication: 2022-11-21 10:30:02 UTC

More information about PEIMAN2 at CRAN
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New package lazyNumbers with initial version 1.2.0
Package: lazyNumbers
Title: Exact Floating-Point Arithmetic
Version: 1.2.0
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Description: Provides a new type of numbers called the lazy numbers. Arithmetic on lazy numbers is exact, contrary to ordinary floating-point arithmetic. The lazy numbers are implemented in 'C++' with the 'CGAL' library (<https://www.cgal.org/>).
License: GPL-3
URL: https://github.com/stla/lazyNumbers
BugReports: https://github.com/stla/lazyNumbers/issues
Imports: methods, Rcpp (>= 1.0.9), stats
LinkingTo: BH, Rcpp, RcppCGAL, RcppEigen
Encoding: UTF-8
SystemRequirements: C++ 17, gmp, mpfr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2022-11-19 11:25:52 UTC; stla
Author: Stephane Laurent [aut, cre]
Repository: CRAN
Date/Publication: 2022-11-21 10:50:08 UTC

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New package changeRangeR with initial version 1.0.0
Package: changeRangeR
Title: Change Metrics for Species Geographic Ranges
Version: 1.0.0
Description: Facilitates workflows to reproducibly transform estimates of species’ distributions into metrics relevant for conservation. For example, combining predictions from species distribution models with other maps of environmental data to characterize the proportion of a species’ range that is under protection, calculating metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and calculating more general metrics such as taxonomic and phylogenetic diversity, as well as endemism. Also facilitates temporal comparisons among biodiversity metrics to inform efforts towards complementarity and consideration of future scenarios in conservation decisions. 'changeRangeR' also provides tools to determine the effects of modeling decisions through sensitivity tests.
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: phylobase, raster, dplyr, rangeModelMetadata, rgeos, sf, sp
Suggests: ape, rgdal, tidyverse, rmarkdown, testthat, tinytex, knitr, picante, wallace, R.utils, tools, dismo
NeedsCompilation: no
Packaged: 2022-11-19 22:42:10 UTC; kass1
Author: Peter J. Galante [aut], Samuel Chang [aut], Andrea Paz [aut], Jamie M. Kass [aut], Matthew Aiello-Lammens [aut], Beth Gerstner [aut], Bethany Johnson [aut], Cory Merow [aut], Elkin Noguera-Urbano [aut], Gonzalo E. Pinilla-Buitrago [aut], Dan Rosauer [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Repository: CRAN
Date/Publication: 2022-11-21 11:00:02 UTC

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New package BIS with initial version 0.3.1
Package: BIS
Title: Programmatic Access to Bank for International Settlements Data
Version: 0.3.1
Description: Provides an interface to data provided by the Bank for International Settlements <https://www.bis.org>, allowing for programmatic retrieval of a large quantity of (central) banking data.
License: CC0
URL: https://www.bis.org
BugReports: https://github.com/stefanangrick/BIS/issues
Suggests: knitr, rmarkdown, ggplot2, zoo
Imports: dplyr, readr, tidyr, tidyselect, rvest, xml2
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-11-20 06:11:49 UTC; qwerty
Author: Eric Persson [aut], Stefan Angrick [cre]
Maintainer: Stefan Angrick <contact@stefanangrick.net>
Repository: CRAN
Date/Publication: 2022-11-21 10:20:02 UTC

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Package RcppClassic updated to version 0.9.13 with previous version 0.9.12 dated 2019-12-09

Title: Deprecated 'classic' 'Rcpp' 'API'
Description: The 'RcppClassic' package provides a deprecated C++ library which facilitates the integration of R and C++. New projects should use the new 'Rcpp' 'API' in the 'Rcpp' package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss, and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppClassic versions 0.9.12 dated 2019-12-09 and 0.9.13 dated 2022-11-21

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New package prismjs with initial version 1.0.0
Package: prismjs
Title: Server-Side Syntax Highlighting
Version: 1.0.0
Description: 'Prism' <https://prismjs.com/> is a lightweight, extensible syntax highlighter, built with modern web standards in mind. This package provides server-side rendering in 'R' using 'V8' such that no 'JavaScript' library is required in the resulting 'HTML' documents. Over 400 languages are supported.
License: MIT + file LICENSE
URL: https://github.com/ropensci/prismjs, https://docs.ropensci.org/prismjs/
BugReports: https://github.com/ropensci/prismjs/issues
Encoding: UTF-8
Imports: V8, xml2
Language: en-US
NeedsCompilation: no
Packaged: 2022-11-18 16:32:41 UTC; jeroen
Author: Jeroen Ooms [aut, cre] , Lea Verou [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2022-11-21 10:00:02 UTC

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Package paradox updated to version 0.11.0 with previous version 0.10.0 dated 2022-08-05

Title: Define and Work with Parameter Spaces for Complex Algorithms
Description: Define parameter spaces, constraints and dependencies for arbitrary algorithms, to program on such spaces. Also includes statistical designs and random samplers. Objects are implemented as 'R6' classes.
Author: Michel Lang [cre, aut] , Bernd Bischl [aut] , Jakob Richter [aut] , Xudong Sun [aut] , Martin Binder [aut], Marc Becker [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between paradox versions 0.10.0 dated 2022-08-05 and 0.11.0 dated 2022-11-21

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New package histoslider with initial version 0.1
Package: histoslider
Title: A Histogram Slider Input for 'Shiny'
Version: 0.1
Description: A histogram slider input binding for use in 'Shiny'. Currently supports creating histograms from numeric, date, and 'date-time' vectors.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rlang, htmltools, reactR, shiny
Suggests: testthat, shinytest2, bslib
NeedsCompilation: no
Packaged: 2022-11-18 16:47:15 UTC; cpsievert
Author: Carson Sievert [cre, aut] , Samuel Hogg [ctb, cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Repository: CRAN
Date/Publication: 2022-11-21 10:00:05 UTC

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New package hellorust with initial version 1.0.0
Package: hellorust
Title: Minimal Example of Using 'Rust' Code in 'R'
Version: 1.0.0
Description: Template 'R' package that calls out to 'Rust' code in a way that complies with 'CRAN' policy. Includes simple examples of passing numbers and strings from 'Rust' to 'R' and using threads.
License: MIT + file LICENSE
URL: https://github.com/r-rust/hellorust
BugReports: https://github.com/r-rust/hellorust/issues
SystemRequirements: Cargo (rustc package manager)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-11-18 14:46:44 UTC; jeroen
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2022-11-21 09:50:02 UTC

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New package formatdown with initial version 0.1.1
Package: formatdown
Title: Formatting Tools for 'rmarkdown' Documents
Version: 0.1.1
Language: en-US
Description: Provides a small set of tools for formatting tasks when creating documents in 'rmarkdown' or 'quarto'. Convert the elements of a numerical vector to character strings in which the numbers are formatted using powers-of-ten notation in scientific or engineering form and delimited for rendering as inline equations.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
LazyDataCompression: bzip2
Imports: checkmate, data.table, wrapr
Suggests: covr, knitr, rmarkdown, tinytest
VignetteBuilder: knitr
URL: https://github.com/graphdr/formatdown/
BugReports: https://github.com/graphdr/formatdown/issues
NeedsCompilation: no
Packaged: 2022-11-18 14:41:17 UTC; layto
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>
Repository: CRAN
Date/Publication: 2022-11-21 09:50:05 UTC

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New package ActiSleep with initial version 0.2.1
Package: ActiSleep
Title: Sleep Duration Estimate Algorithm
Version: 0.2.1
Date: 2022-11-17
Description: Estimate sleep duration using a Pruned Dynamic Programming (PDP) algorithm that quickly and efficiently identifies changepoints. When applied to physical activity data it can identify transitions from wakefulness to sleep and vice versa. Baek, Jonggyu, Banker, Margaret, Jansen, Erica C., She, Xichen, Peterson, Karen E., Pitchford, E. Andrew, Song, Peter X. K. (2021) "An Efficient Segmentation Algorithm to Estimate Sleep Duration from Actigraphy Data" <doi:10.1007/s12561-021-09309-3>.
License: GPL (>= 2)
Imports: dplyr, stringr, lubridate, accelerometry, DBI, RSQLite, lazyeval, methods, utils, tibble
Depends: R (>= 3.5)
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2022-11-18 17:03:53 UTC; mk
Author: Margaret Banker [aut], Nathan Szeto [aut], Jonggyu Baek [aut], Alice Cleynen [aut], Guillem Rigaill [aut], Michel Koskas [aut], Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Repository: CRAN
Date/Publication: 2022-11-21 10:00:08 UTC

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Package rcarbon updated to version 1.5.0 with previous version 1.4.4 dated 2022-07-21

Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut] , Enrico Crema [aut, cre] , R. Kyle Bocinsky [ctb], Martin Hinz [ctb], Philip Riris [ctb], Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>

Diff between rcarbon versions 1.4.4 dated 2022-07-21 and 1.5.0 dated 2022-11-21

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Package idopNetwork updated to version 0.1.1 with previous version 0.1.0 dated 2022-11-09

Title: A Cartographic Tool to Chart Spatial Microbial Interaction Networks
Description: Most existing approaches for network reconstruction can only infer an overall network and, also, fail to capture a complete set of network properties. To address these issues, a new model has been developed, which converts static data into their 'dynamic' form. 'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic, omnidirectional and personalized networks. For more information on functional clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>, Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model, see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022) <doi:10.1080/19490976.2022.2106103>.
Author: Ang Dong
Maintainer: Ang Dong <fantasys05227@gmail.com>

Diff between idopNetwork versions 0.1.0 dated 2022-11-09 and 0.1.1 dated 2022-11-21

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Package geohashTools updated to version 0.3.2 with previous version 0.3.1 dated 2020-05-26

Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre], Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>

Diff between geohashTools versions 0.3.1 dated 2020-05-26 and 0.3.2 dated 2022-11-21

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Package shinyStorePlus updated to version 0.8 with previous version 0.7 dated 2022-11-03

Title: Secure in-Browser Storage for 'Shiny' Inputs and Variables
Description: Store persistent and synchronized data from 'Shiny' inputs within the browser in a secure format. Refresh 'Shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'Shiny' input or output values.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>

Diff between shinyStorePlus versions 0.7 dated 2022-11-03 and 0.8 dated 2022-11-21

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Package metevalue updated to version 0.1.13 with previous version 0.1.10 dated 2022-10-28

Title: E-Value in the Omics Data Association Studies
Description: In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Among those p-value correction methods, E-value is recently studied based on V. Vovk and R. Wang (2021) <doi:10.1214/20-AOS2020>. This package provides e-value calculation for several types of omics data association studies. Currently, four data formats are supported: BiSeq, MDRfinder, methylKit and metilene data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) <doi:10.18129/B9.bioc.BiSeq>; Altuna Akalin et.al (2012) <doi:10.18129/B9.bioc.methylKit>.
Author: Yifan Yang [aut, cre, cph], Xiaoqing Pan [aut], Haoyuan Liu [aut]
Maintainer: Yifan Yang <yfyang.86@hotmail.com>

Diff between metevalue versions 0.1.10 dated 2022-10-28 and 0.1.13 dated 2022-11-21

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Package ggfun updated to version 0.0.9 with previous version 0.0.8 dated 2022-11-07

Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggfun versions 0.0.8 dated 2022-11-07 and 0.0.9 dated 2022-11-21

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Package curvHDR updated to version 1.2-1.1 with previous version 1.2-1 dated 2019-01-09

Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of flow cytometry samples using the curvHDR method, which is described in Naumann, U., Luta, G. and Wand, M.P. (2010) <DOI:10.1186/1471-2105-11-44>.
Author: Matt Wand [aut, cre], George Luta [aut], Ulrike Naumann [aut], Mathew W. McLean [ctb], Dai Feng [ctb], Luke Tierney [ctb], Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>

Diff between curvHDR versions 1.2-1 dated 2019-01-09 and 1.2-1.1 dated 2022-11-21

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Package dblcens (with last version 1.1.7) was removed from CRAN

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

2012-12-17 1.1.7
2010-04-28 1.1.6
2010-04-27 1.1.5
2008-04-04 1.1.4
2005-08-07 1.1.3

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Package mgee2 (with last version 0.2) was removed from CRAN

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2021-05-01 0.2
2020-11-02 0.1

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Package paramGUI (with last version 2.1.4) was removed from CRAN

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2020-02-13 2.1.4
2018-03-15 2.1.3
2017-02-17 2.1.2
2017-02-09 2.1.1
2017-02-06 2.1
2016-06-16 2.0

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Package mudens (with last version 1.3.2) was removed from CRAN

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2018-10-30 1.3.2

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Package riot (with last version 1.0.0) was removed from CRAN

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2022-05-10 1.0.0
2022-05-05 0.0.1

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Package cgraph (with last version 6.0.1) was removed from CRAN

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2020-02-09 6.0.1
2020-02-04 6.0.0
2019-11-26 5.0.1
2019-11-21 5.0.0
2019-04-08 4.0.3
2019-04-06 4.0.2
2019-03-11 4.0.1
2019-03-08 4.0.0
2018-11-05 3.0.1
2018-11-01 3.0.0
2018-09-24 2.0.3
2018-08-19 2.0.2
2018-08-13 2.0.1
2018-08-05 2.0.0
2018-07-28 1.0.1

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Package SoDA (with last version 1.0-6.1) was removed from CRAN

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2020-10-28 1.0-6.1
2013-06-12 1.0-6
2012-12-16 1.0-5
2012-03-28 1.0-4
2008-10-19 1.0-3
2008-08-18 1.0-2
2008-07-14 1.0-1
2008-01-07 0.97-1
2007-11-23 0.96

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Package TIMP (with last version 1.13.2) was removed from CRAN

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2019-03-15 1.13.2
2019-01-28 1.13.1
2015-10-19 1.13.0
2014-12-11 1.12.1
2014-12-02 1.12.0
2014-01-25 1.11.0
2013-09-30 1.10.3

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Package EL (with last version 1.1) was removed from CRAN

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2022-05-10 1.1

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Package AdaptFitOS (with last version 0.69) was removed from CRAN

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2022-07-21 0.69
2022-02-25 0.68
2018-05-23 0.67
2017-09-22 0.65
2015-06-16 0.62
2014-07-22 0.54
2014-03-19 0.50
2012-12-14 0.45
2012-03-20 0.43

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Package catnet (with last version 1.16.1) was removed from CRAN

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2022-11-07 1.16.1
2020-03-10 1.15.7
2020-03-06 1.15.6

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Package ergmito (with last version 0.3-0) was removed from CRAN

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2020-08-10 0.3-0
2020-02-12 0.2-1
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Package metabolighteR (with last version 0.1.3) was removed from CRAN

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2022-02-09 0.1.3

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