Thu, 06 Jan 2022

Package postcards updated to version 0.2.3 with previous version 0.2.2 dated 2021-07-31

Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>

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Package grantham updated to version 0.1.1 with previous version 0.1.0 dated 2021-12-20

Title: Calculate the 'Grantham' Distance
Description: A minimal set of routines to calculate the 'Grantham' distance <doi:10.1126/science.185.4154.862>. The 'Grantham' distance attempts to provide a proxy for the evolutionary distance between two amino acids based on three key chemical properties: composition, polarity and molecular volume. In turn, evolutionary distance is used as a proxy for the impact of missense mutations. The higher the distance, the more deleterious the substitution is expected to be.
Author: Ramiro Magno [aut, cre] (<https://orcid.org/0000-0001-5226-3441>), Isabel Duarte [aut] (<https://orcid.org/0000-0003-0060-2936>), Ana-Teresa Maia [aut] (<https://orcid.org/0000-0002-0454-9207>), CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>

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Package quarto updated to version 1.1 with previous version 1.0 dated 2021-08-06

Title: R Interface to 'Quarto' Markdown Publishing System
Description: Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.
Author: JJ Allaire [aut, cre] (<https://orcid.org/0000-0003-0174-9868>)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package datapackage.r (with last version 1.3.4) was removed from CRAN

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

2021-10-11 1.3.4

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Package SNPfiltR (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:

2021-10-28 0.1.0

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Package resevol updated to version 0.2.0.9 with previous version 0.2.0.8 dated 2021-10-05

Title: Simulate Agricultural Production and Evolution of Pesticide Resistance
Description: Simulates individual-based models of agricultural pest management and the evolution of pesticide resistance. Management occurs on a spatially explicit landscape that is divided into an arbitrary number of farms that can grow one of up to 10 crops and apply one of up to 10 pesticides. Pest genomes are modelled in a way that allows for any number of pest traits with an arbitrary covariance structure that is constructed using an evolutionary algorithm in the mine_gmatrix() function. Simulations are then run using the run_farm_sim() function. This package thereby allows for highly mechanistic social-ecological models of the evolution of pesticide resistance under different types of crop rotation and pesticide application regimes.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>), Rose McKeon [aut, ctr], Rosie Mangan [ctr], Luc Bussi&eacute;re [ctr], Matthew Tinsley [ctr]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

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Package effects updated to version 4.2-1 with previous version 4.2-0 dated 2020-08-11

Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Brad Price [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb], R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package bimets updated to version 2.0.1 with previous version 1.5.3 dated 2021-02-04

Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control.
Author: Andrea Luciani [aut, cre] (<https://orcid.org/0000-0002-7372-358X>), Roberto Stok [aut], Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>

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Package secr updated to version 4.5.0 with previous version 4.4.8 dated 2021-11-09

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Package NeuralNetTools updated to version 1.5.3 with previous version 1.5.2 dated 2018-07-26

Title: Visualization and Analysis Tools for Neural Networks
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>

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Package latrend updated to version 1.2.1 with previous version 1.1.2 dated 2021-04-14

Title: A Framework for Clustering Longitudinal Data
Description: A framework for clustering longitudinal datasets in a standardized way. Provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
Author: Niek Den Teuling [aut, cre] (<https://orcid.org/0000-0003-1026-5080>), Steffen Pauws [ctb], Edwin van den Heuvel [ctb], Copyright © 2021 Koninklijke Philips N.V. [cph]
Maintainer: Niek Den Teuling <niek.den.teuling@philips.com>

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Package cmprsk updated to version 2.2-11 with previous version 2.2-10 dated 2020-06-09

Title: Subdistribution Analysis of Competing Risks
Description: Estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154 <DOI:10.1214/aos/1176350951>, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509, <DOI:10.1080/01621459.1999.10474144>.
Author: Bob Gray <gray@jimmy.harvard.edu>
Maintainer: Bob Gray <gray@jimmy.harvard.edu>

Diff between cmprsk versions 2.2-10 dated 2020-06-09 and 2.2-11 dated 2022-01-06

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Package BIEN (with last version 1.2.4) was removed from CRAN

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2020-02-27 1.2.4
2018-05-09 1.2.3
2017-08-03 1.2.2
2017-07-31 1.2.1
2017-03-08 1.1.0
2017-01-12 1.0.0

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2021-04-30 0.1.1
2021-03-28 0.1.0
2021-02-26 0.0.13
2021-01-27 0.0.12
2021-01-13 0.0.11
2020-11-22 0.0.10
2020-11-07 0.0.9
2020-10-21 0.0.8
2020-09-14 0.0.7
2020-09-05 0.0.6
2020-08-28 0.0.5
2020-08-01 0.0.4
2020-02-13 0.0.3
2019-09-11 0.0.2
2019-06-18 0.0.1

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2021-11-09 0.4.2
2021-04-13 0.3.9
2021-03-23 0.3.7
2020-05-08 0.3.5
2020-03-16 0.3.2
2019-09-12 0.2-7
2019-08-07 0.2-6

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2021-12-15 0.3.2

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2021-12-08 0.1.0

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2020-05-12 0.1.1
2019-08-23 0.0.5
2015-03-10 0.0.3
2014-12-16 0.0.2
2014-08-04 0.0.1

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2021-06-27 0.0.2

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2021-07-22 0.1.0

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2021-12-13 1.0.0
2021-10-14 0.6.3
2021-02-23 0.6.2
2020-03-08 0.4.8
2019-08-20 0.4.6

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2021-09-30 1.2

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2021-12-17 0.99.14

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2020-05-22 0.1.7
2020-05-20 0.1.6
2020-02-28 0.1.0

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Package postGGIR updated to version 2.4.0.2 with previous version 2.4.0.1 dated 2021-10-15

Title: Data Processing after Running 'GGIR' for Accelerometer Data
Description: Generate all necessary R/Rmd/shell files for data processing after running 'GGIR' (v2.4.0) for accelerometer data. In part 1, all csv files in the GGIR output directory were read, transformed and then merged. In part 2, the GGIR output files were checked and summarized in one excel sheet. In part 3, the merged data was cleaned according to the number of valid hours on each night and the number of valid days for each subject. In part 4, the cleaned activity data was imputed by the average Euclidean norm minus one (ENMO) over all the valid days for each subject. Finally, a comprehensive report of data processing was created using Rmarkdown, and the report includes few exploratory plots and multiple commonly used features extracted from minute level actigraphy data.
Author: Wei Guo [aut, cre], Andrew Leroux [aut], Vadim Zipunnikov [aut], Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>

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Package file2meco updated to version 0.2.1 with previous version 0.2.0 dated 2021-11-16

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

Diff between file2meco versions 0.2.0 dated 2021-11-16 and 0.2.1 dated 2022-01-06

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Package qcr (with last version 1.3) was removed from CRAN

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2021-05-14 1.3

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2021-07-14 2.2.0
2018-01-12 2.1.0
2016-05-04 2.0.0
2014-10-08 1.4
2013-08-08 1.3
2013-01-16 1.2
2012-06-23 1.1
2011-05-12 1.0

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Package polyPK (with last version 3.1.0) was removed from CRAN

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2018-07-20 3.1.0

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2012-02-10 1.0.1

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2020-04-28 1.3.1

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Package PatternClass (with last version 2.0.1) was removed from CRAN

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2020-03-13 2.0.1
2020-01-23 2.0.0
2016-10-28 1.7.1
2013-07-23 1.5

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Package NetOrigin (with last version 1.1-2) was removed from CRAN

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

2021-04-01 1.1-2
2018-04-19 1.0-3
2016-07-07 1.0-2

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Package SoftRandomForest (with last version 0.1.0) was removed from CRAN

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2019-05-15 0.1.0

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2020-01-24 0.1.2
2018-03-09 0.1.1

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Package flightplanning (with last version 0.8.4) was removed from CRAN

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2021-02-24 0.8.4

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2021-07-08 0.1.1

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2021-12-16 2.0.0
2019-09-12 1.0.0
2019-02-11 0.0.1

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Package TIGERr updated to version 1.0.0 with previous version 0.1.0 dated 2021-09-02

Title: Technical Variation Elimination with Ensemble Learning Architecture
Description: The R implementation of TIGER. TIGER integrates random forest algorithm into an innovative ensemble learning architecture. Benefiting from this advanced architecture, TIGER is resilient to outliers, free from model tuning and less likely to be affected by specific hyperparameters. TIGER supports targeted and untargeted metabolomics data and is competent to perform both intra- and inter-batch technical variation removal. TIGER can also be used for cross-kit adjustment to ensure data obtained from different analytical assays can be effectively combined and compared. Reference: Han S. et al. (2022) <doi:10.1093/bib/bbab535>.
Author: Siyu Han [aut, cre], Jialing Huang [aut], Francesco Foppiano [aut], Cornelia Prehn [aut], Jerzy Adamski [aut], Karsten Suhre [aut], Ying Li [aut], Giuseppe Matullo [aut], Freimut Schliess [aut], Christian Gieger [aut], Annette Peters [aut], Rui Wang-Sattler [aut]
Maintainer: Siyu Han <siyu.han@helmholtz-muenchen.de>

Diff between TIGERr versions 0.1.0 dated 2021-09-02 and 1.0.0 dated 2022-01-06

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Package jsmodule updated to version 1.3.0 with previous version 1.2.0 dated 2021-10-11

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], Hyunki Lee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package fbst updated to version 1.6 with previous version 1.5 dated 2021-04-12

Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available. For details on the computation and theory of the FBST see <arXiv:2005.13181>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

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Package NAP updated to version 1.1 with previous version 1.0 dated 2021-11-04

Title: Non-Local Alternative Priors in Psychology
Description: Conducts Bayesian Hypothesis tests of a point null hypothesis against a two-sided alternative using Non-local Alternative Prior (NAP) for one- and two-sample z- and t-tests (Pramanik and Johnson, 2022). Under the alternative, the NAP is assumed on the standardized effects size in one-sample tests and on their differences in two-sample tests. The package considers two types of NAP densities: (1) the normal moment prior, and (2) the composite alternative. In fixed design tests, the functions calculate the Bayes factors and the expected weight of evidence for varied effect size and sample size. The package also provides a sequential testing framework using the Sequential Bayes Factor (SBF) design. The functions calculate the operating characteristics (OC) and the average sample number (ASN), and also conducts sequential tests for a sequentially observed data.
Author: Sandipan Pramanik [aut, cre], Valen E. Johnson [aut]
Maintainer: Sandipan Pramanik <sandy@stat.tamu.edu>

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Package MFSIS updated to version 0.1.2 with previous version 0.1.1 dated 2021-12-15

Title: Moder-Free Sure Independent Screening Procedures
Description: An implementation of popular screening methods that are commonly employed in ultra-high and high dimensional data. Through this publicly available package, we provide a unified framework to carry out model-free screening procedures including SIS (Fan and Lv (2008) <doi:10.1111/j.1467-9868.2008.00674.x>), SIRS(Zhu et al. (2011)<doi:10.1198/jasa.2011.tm10563>), DC-SIS (Li et al. (2012) <doi:10.1080/01621459.2012.695654>), MDC-SIS(Shao and Zhang (2014) <doi:10.1080/01621459.2014.887012>), Bcor-SIS (Pan et al. (2019) <doi:10.1080/01621459.2018.1462709>), PC-Screen (Liu et al. (2020) <doi:10.1080/01621459.2020.1783274>), WLS (Zhong et al.(2021) <doi:10.1080/01621459.2021.1918554>), Kfilter (Mai and Zou (2015) <doi:10.1214/14-AOS1303>), MVSIS (Cui et al. (2015) <doi:10.1080/01621459.2014.920256>) and CSIS.
Author: Xuewei Cheng [aut, cre], Hong Wang [aut], Liping Zhu [aut], Wei Zhong [aut], Hanpu Zhou [aut]
Maintainer: Xuewei Cheng <xwcheng@csu.edu.cn>

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Package BayesCACE updated to version 1.2 with previous version 1.1 dated 2022-01-05

Title: Bayesian Model for CACE Analysis
Description: Performs CACE (Complier Average Causal Effect analysis) on either a single study or meta-analysis of datasets with binary outcomes, using either complete or incomplete noncompliance information. Our package implements the Bayesian methods proposed in Zhou et al. (2019) <doi:10.1111/biom.13028>, which introduces a Bayesian hierarchical model for estimating CACE in meta-analysis of clinical trials with noncompliance, and Zhou et al. (2021) <doi:10.1080/01621459.2021.1900859>, with an application example on Epidural Analgesia.
Author: Jinhui Yang [aut, cre] (<https://orcid.org/0000-0001-8322-1121>), Jincheng Zhou [aut] (<https://orcid.org/0000-0003-2641-2495>), James Hodges [ctb], Haitao Chu [ctb] (<https://orcid.org/0000-0003-0932-598X>)
Maintainer: Jinhui Yang <james.yangjinhui@gmail.com>

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Package NeuralSens updated to version 0.2.3 with previous version 0.2.2 dated 2020-11-16

Title: Sensitivity Analysis of Neural Networks
Description: Analysis functions to quantify inputs importance in neural network models. Functions are available for calculating and plotting the inputs importance and obtaining the activation function of each neuron layer and its derivatives. The importance of a given input is defined as the distribution of the derivatives of the output with respect to that input in each training data point.
Author: José Portela González [aut], Antonio Muñoz San Roque [aut], Jaime Pizarroso Gonzalo [aut, ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>

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Package rpact updated to version 3.2.1 with previous version 3.2.0 dated 2021-12-16

Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut], Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>

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 src/f_utilities.cpp                                 |   26 
 tests/testthat/test-f_simulation_enrichment_rates.R |    7 
 20 files changed, 3513 insertions(+), 3144 deletions(-)

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New package mccca with initial version 0.1.0
Package: mccca
Title: Visualizing Class Specific Heterogeneous Tendencies in Categorical Data
Version: 0.1.0
Author: Mariko Takagishi [aut, cre]
Maintainer: Mariko Takagishi <m.takagishi0728@gmail.com>
Description: Functions for performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result.
License: GPL (>= 2)
Depends: R (>= 4.1.0)
Imports: dummies, magic, parallel, stringr, ggplot2, wordcloud, RColorBrewer, methods, stats, utils, grDevices
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2022-01-05 13:11:02 UTC; takagishimariko
Repository: CRAN
Date/Publication: 2022-01-06 10:10:02 UTC

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New package FastJM with initial version 1.0.0
Package: FastJM
Title: Semi-Parametric Joint Modeling of Survival and Longitudinal Data
Version: 1.0.0
Date: 2022-01-04
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying one way scan algorithm, proposed by Li and colleagues (2021) <arXiv:2110.14822>. The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model is estimated using am Expectation Maximization algorithm.
License: GPL (>= 3)
NeedsCompilation: yes
Imports: Rcpp (>= 1.0.7), MASS, statmod, survival, dplyr, nlme, mvtnorm
LinkingTo: Rcpp, RcppEigen
Depends: R (>= 3.5.0)
LazyData: true
Packaged: 2022-01-05 14:13:11 UTC; shanpengli
Suggests: testthat (>= 3.0.0), spelling
Language: en-US
Author: Shanpeng Li [aut, cre], Ning Li [ctb], Hong Wang [ctb], Jin Zhou [ctb], Hua Zhou [ctb], Gang Li [ctb]
Repository: CRAN
Date/Publication: 2022-01-06 10:10:05 UTC

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Package DRomics updated to version 2.4-0 with previous version 2.3-0 dated 2021-10-04

Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Author: Marie-Laure Delignette-Muller [aut], Elise Billoir [aut], Floriane Larras [ctb], Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Diff between DRomics versions 2.3-0 dated 2021-10-04 and 2.4-0 dated 2022-01-06

 DESCRIPTION                                                 |    6 
 MD5                                                         |   91 +-
 R/RNAseqdata.R                                              |   15 
 R/bmdboot.R                                                 |  165 +--
 R/bmdcalc.R                                                 |   14 
 R/bmdplotwithgradient.R                                     |    2 
 R/continuousanchoringdata.R                                 |   13 
 R/curvesplot.R                                              |    2 
 R/drcfit.R                                                  |  538 ++++++++----
 R/itemselect.R                                              |    9 
 R/metabolomicdata.R                                         |   17 
 R/microarraydata.R                                          |   13 
 R/omicdata.R                                                |    4 
 R/targetplot.R                                              |    2 
 R/util-basicandfitfunc.R                                    |  180 ++--
 R/util-plotfunc.R                                           |    4 
 build/partial.rdb                                           |binary
 build/vignette.rds                                          |binary
 inst/DRomics-shiny/global.R                                 |    4 
 inst/DRomics-shiny/server.R                                 |  112 +-
 inst/DRomics-shiny/ui.R                                     |  424 +++++----
 inst/DRomics-shiny/www/informations_bmdcalc_results.txt     |    2 
 inst/DRomics-shiny/www/informations_modelling_procedure.txt |   27 
 inst/NEWS                                                   |   32 
 inst/doc/DRomics_vignette.R                                 |   11 
 inst/doc/DRomics_vignette.Rmd                               |   39 
 inst/doc/DRomics_vignette.html                              |  328 +++----
 inst/extdata/insitu_RNAseq_sample.txt                       |only
 man/RNAseqdata.Rd                                           |    5 
 man/Scenedesmus.Rd                                          |    4 
 man/bmdboot.Rd                                              |   23 
 man/bmdcalc.Rd                                              |   14 
 man/continuousanchoringdata.Rd                              |   11 
 man/drcfit.Rd                                               |   89 +
 man/itemselect.Rd                                           |    7 
 man/metabolomicdata.Rd                                      |    8 
 man/microarraydata.Rd                                       |    8 
 man/sensitivityplot.Rd                                      |    6 
 tests/examplewithNAvalues.R                                 |    4 
 tests/examplewithRNAseq.R                                   |   36 
 tests/examplewithanchoringdata.R                            |   11 
 tests/examplewithinsitudata.R                               |only
 tests/examplewithmetabolomic.R                              |   40 
 tests/examplewithmicroarray.R                               |   31 
 tests/examplewithnoreplicate.R                              |   16 
 tests/testAIC.R                                             |   57 +
 tests/testplotfit.R                                         |only
 vignettes/DRomics_vignette.Rmd                              |   39 
 48 files changed, 1662 insertions(+), 801 deletions(-)

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New package ymd with initial version 0.0.1
Package: ymd
Title: Parse 'YMD' Format Number or String to Date
Version: 0.0.1
Maintainer: Xianying Tan <shrektan@126.com>
Description: Convert 'YMD' format number or string to Date efficiently, using Rust's standard library. It also provides helper functions to handle Date, e.g., quick finding the beginning or ending of the given period, adding months to Date, etc.
License: MIT + file LICENSE
URL: https://shrektan.github.io/ymd/, https://github.com/shrektan/ymd
BugReports: https://github.com/shrektan/ymd/issues
SystemRequirements: Cargo (rustc package manager)
Encoding: UTF-8
Biarch: true
Suggests: testthat (>= 3.0.0)
Config/ymd/windows_toolchain: stable-msvc
Config/ymd/crate_name: ymd
Config/ymd/github_repo: shrektan/ymd
Config/ymd/github_tag: v0.0.1
Config/ymd/binary_sha256sum: list( `aarch64-apple-darwin-libymd.a` = "e6f9a33396a8c97dcd6b0faf92b822f4efa1ae02cc9ddc10a7aea2a25b4e3293", `i686-pc-windows-gnu-libymd.a` = "dabad815be64e6134f8e4a453dcfca35229d19726c551c071f203fa636527f35", `ucrt-x86_64-pc-windows-gnu-libymd.a` = "063862240340b93ad5eb96138e42a5392c3f3c77241468f2d8e5bb39815cc2ee", `x86_64-apple-darwin-libymd.a` = "4e4bfa69b22c0611d212fd6e09f32c6066c3af61d2f8c16e29327782308b98d4", `x86_64-pc-windows-gnu-libymd.a` = "063862240340b93ad5eb96138e42a5392c3f3c77241468f2d8e5bb39815cc2ee" )
NeedsCompilation: yes
Packaged: 2022-01-04 17:01:56 UTC; shrektan
Author: Xianying Tan [aut, cre] (<https://orcid.org/0000-0002-6072-3521>), Hiroaki Yutani [ctb] (<https://orcid.org/0000-0002-3385-7233>, configure, configure.win, tools/configure.R)
Repository: CRAN
Date/Publication: 2022-01-06 09:10:02 UTC

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New package WebAnalytics with initial version 0.9.1
Package: WebAnalytics
Title: Web Server Log Analysis
Version: 0.9.1
Date: 2022-01-05
Author: Greg Hunt [aut, cre, cph]
Maintainer: Greg Hunt <greg@firmansyah.com>
Description: Provides Apache and IIS log analytics for transaction performance, client populations and workload definitions.
License: GPL-3
Depends: R (>= 4.0), xtable (>= 1.7-3), ggplot2, scales, utils, digest
Imports: brew, testthat, fs
Suggests: whoami
NeedsCompilation: no
Packaged: 2022-01-05 10:35:02 UTC; listiari
Repository: CRAN
Date/Publication: 2022-01-06 09:50:08 UTC

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New package WaveletSVR with initial version 0.1.0
Package: WaveletSVR
Title: Wavelet-SVR Hybrid Model for Time Series Forecasting
Version: 0.1.0
Author: Ranjit Kumar Paul [aut, cre], Md Yeasin [aut]
Maintainer: Ranjit Kumar Paul <ranjitstat@gmail.com>
Description: The main aim of this package is to combine the advantage of wavelet and support vector machine models for time series forecasting. This package also gives the accuracy measurements in terms of RMSE and MAPE. This package fits the hybrid Wavelet SVR model for time series forecasting The main aim of this package is to combine the advantage of wavelet and Support Vector Regression (SVR) models for time series forecasting. This package also gives the accuracy measurements in terms of Root Mean Square Error (RMSE) and Mean Absolute Prediction Error (MAPE). This package is based on the algorithm of Raimundo and Okamoto (2018) <DOI: 10.1109/INFOCT.2018.8356851>.
License: GPL-3
Encoding: UTF-8
Imports: stats, wavelets, fracdiff, forecast, e1071, tsutils
NeedsCompilation: no
Packaged: 2022-01-05 11:33:17 UTC; yeasi
Repository: CRAN
Date/Publication: 2022-01-06 10:00:08 UTC

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New package spatstat.random with initial version 2.0-0
Package: spatstat.random
Version: 2.0-0
Date: 2022-01-05
Title: Random Generation Functionality for the 'spatstat' Family
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Depends: R (>= 3.5.0), spatstat.data (>= 2.1-0), spatstat.geom (>= 2.3-0), stats, utils, methods, grDevices
Imports: spatstat.utils (>= 2.2-0), spatstat.sparse (>= 2.0-0)
Suggests: spatial, RandomFields (>= 3.1.24.1), RandomFieldsUtils(>= 0.3.3.1), spatstat.linnet (>= 2.0-0), spatstat.core (>= 2.3-2), spatstat (>= 2.0-0)
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes (simple sequential inhibition, Matern inhibition models, Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes) and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.
License: GPL (>= 2)
URL: http://spatstat.org/
NeedsCompilation: yes
ByteCompile: true
BugReports: https://github.com/spatstat/spatstat.random/issues
Packaged: 2022-01-05 10:45:26 UTC; adrian
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut], Kasper Klitgaard Berthelsen [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb]
Repository: CRAN
Date/Publication: 2022-01-06 10:00:02 UTC

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New package SangerTools with initial version 1.0.1
Package: SangerTools
Title: Tools for Population Health Management Analytics
Version: 1.0.1
Maintainer: Asif Laldin <laldin.asif@gmail.com>
Description: Created for population health analytics and monitoring. The functions in this package work best when working with patient level Master Patient Index-like datasets . Built to be used by NHS bodies and other health service providers.
License: AGPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: ggplot2, dplyr, scales, janitor, readr, utils, ggthemes, magrittr, readxl, ggtext, DBI, odbc
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
Language: en-gb
NeedsCompilation: no
Packaged: 2022-01-04 17:22:18 UTC; ald04
Author: Asif Laldin [aut, cre], Gary Hutson [aut] (<https://orcid.org/0000-0003-3534-6143>)
Repository: CRAN
Date/Publication: 2022-01-06 09:10:05 UTC

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New package PermutationR with initial version 0.1.0
Package: PermutationR
Title: Conduct Permutation Analysis of Variance in R
Version: 0.1.0
Author: Osama Abdalla
Maintainer: Osama Abdalla <osama.abdalla@mail.utoronto.ca>
Description: Conduct permutation One-Way or Two-Way Analysis of Variance in R. Use different permutation types for two-way designs.
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-01-04 20:43:19 UTC; Osama
Repository: CRAN
Date/Publication: 2022-01-06 09:30:06 UTC

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New package lingglosses with initial version 0.0.2
Package: lingglosses
Title: Linguistic Examples and Abbreviation Lists Generation
Version: 0.0.2
Depends: R (>= 3.5.0)
Maintainer: George Moroz <agricolamz@gmail.com>
Description: Helps to render glossed linguistic examples in html 'rmarkdown' documents and then semi-automatically compiles the glosses list at the end of the document. It also provides a database of linguistic glosses.
Language: en-US
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://CRAN.R-project.org/package=phonfieldwork, https://agricolamz.github.io/lingglosses/
BugReports: https://github.com/agricolamz/lingglosses/issues
Imports: kableExtra, knitr, rmarkdown, utils
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-01-04 18:18:38 UTC; agricolamz
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>)
Repository: CRAN
Date/Publication: 2022-01-06 09:20:02 UTC

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New package limonaid with initial version 0.1.1
Package: limonaid
Title: Working with 'LimeSurvey' Surveys and Responses
Version: 0.1.1
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
License: GPL (>= 3)
Description: 'LimeSurvey' is Free/Libre Open Source Software for the development and administrations of online studies, using sophisticated tailoring capabilities to support multiple study designs (see <https://www.limesurvey.org>). This package supports programmatic creation of surveys that can then be imported into 'LimeSurvey', as well as user friendly import of responses from 'LimeSurvey' studies.
Encoding: UTF-8
URL: https://r-packages.gitlab.io/limonaid
BugReports: https://gitlab.com/r-packages/limonaid/-/issues
Imports: httr (>= 1.4), jsonlite (>= 1.7), R6 (>= 2.4)
Suggests: ggplot2, ggrepel, knitr, parallel, sticky, testthat
NeedsCompilation: no
Packaged: 2022-01-05 09:46:42 UTC; Gjalt-Jorn Peters
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>)
Repository: CRAN
Date/Publication: 2022-01-06 09:50:02 UTC

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New package IDSL.UFAx with initial version 1.0
Package: IDSL.UFAx
Title: Exhaustive Chemical Enumeration for Ultimate Formula Annotation
Version: 1.0
Depends: R (>= 4.0)
Imports: Rcpp, BiocManager, mzR, readxl, parallel, doSNOW, foreach, stringr, RcppAlgos, IDSL.IPA (>= 1.3), IDSL.UFA
Author: Sadjad Fakouri-Baygi [cre, aut] (<https://orcid.org/0000-0002-6864-6911>), Dinesh Barupal [aut] (<https://orcid.org/0000-0002-9954-8628>)
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using a exhaustive chemical enumeration-based approach.
License: MIT + file LICENSE
URL: https://ufa.idsl.me, https://github.com/idslme/idsl.ufa
BugReports: https://github.com/idslme/idsl.ufa/issues
Encoding: UTF-8
LazyData: true
Archs: i386, x64
NeedsCompilation: no
Packaged: 2022-01-04 17:30:40 UTC; sfbaygi
Repository: CRAN
Date/Publication: 2022-01-06 09:20:04 UTC

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New package ghclass with initial version 0.2.1
Package: ghclass
Title: Tools for Managing Classes on GitHub
Version: 0.2.1
Description: Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.
License: GPL-3
URL: https://github.com/rundel/ghclass
BugReports: https://github.com/rundel/ghclass/issues
Depends: R (>= 3.4.0)
Imports: base64enc, fs, gh, glue, httr, lubridate, purrr, rlang, tibble, whisker, withr, dplyr, cli (>= 3.0.0)
Suggests: here, knitr, rmarkdown, sodium, styler, usethis, gert, readr, gitcreds
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-01-04 21:19:13 UTC; rundel
Author: Colin Rundel [aut, cre], Mine Cetinkaya-Rundel [aut], Therese Anders [ctb]
Maintainer: Colin Rundel <rundel@gmail.com>
Repository: CRAN
Date/Publication: 2022-01-06 09:30:02 UTC

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New package geeasy with initial version 0.1.1
Package: geeasy
Title: Solve Generalized Estimating Equations for Clustered Data
Version: 0.1.1
Date: 2022-01-03
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Depends: geepack, stats
Imports: ggplot2, geeM, lme4, methods, Matrix, MESS
Suggests: testthat, MuMIn
Description: Estimation of generalized linear models with correlated/clustered observations by use of generalized estimating equations (GEE). See e.g. Halekoh and Højsgaard, (2005, <doi:10.18637/jss.v015.i02>), for details. Several types of clustering are supported, including exchangeable variance structures, AR1 structures, M-dependent, user-specified variance structures and more. The model fitting computations are performed using modified code from the 'geeM' package, while the interface and output objects have been written to resemble the 'geepack' package. The package also contains additional tools for working with and inspecting results from the 'geepack' package, e.g. a 'confint' method for 'geeglm' objects from 'geepack'.
License: GPL-3
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-01-05 09:41:28 UTC; sorenh
Author: Anne Helby Petersen [aut], Lee McDaniel [aut] (Author of geeM), Claus Ekstrøm [ctb] (Wrote code for drop1 methods), Søren Højsgaard [aut, cre] (Author of geepack)
Repository: CRAN
Date/Publication: 2022-01-06 09:50:05 UTC

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New package CGNM with initial version 0.1.0
Package: CGNM
Title: Cluster Gauss-Newton Method
Version: 0.1.0
Author: Yasunori Aoki
Maintainer: Yasunori Aoki <yaoki@uwaterloo.ca>
Description: Find multiple solutions of a nonlinear least squares problem. Cluster Gauss-Newton method does not assume uniqueness of the solution of the nonlinear least squares problem and compute approximate multiple minimizers. Please cite the following paper when this software is used in your research: Aoki et al. (2020) <doi:10.1007/s11081-020-09571-2>. Cluster Gauss–Newton method. Optimization and Engineering, 1-31.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, ggplot2
Suggests: knitr, rmarkdown, RxODE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-01-05 11:12:45 UTC; yaoki
Repository: CRAN
Date/Publication: 2022-01-06 10:00:11 UTC

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Package GGEBiplotGUI (with last version 1.0-9) was removed from CRAN

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

2016-02-17 1.0-9
2014-04-28 1.0-8
2013-12-29 1.0-7
2013-06-22 1.0-6
2013-05-01 1.0-5
2013-04-03 1.0-4
2012-07-23 1.0-3
2012-05-03 1.0-2
2012-04-11 1.0-1

Permanent link
Package GGEBiplots (with last version 0.1.2) was removed from CRAN

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

2021-12-20 0.1.2
2017-07-24 0.1.1

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Package geneticae (with last version 0.2.0) was removed from CRAN

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

2021-12-20 0.2.0
2021-09-16 0.1.0

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Package udunits2 updated to version 0.13.2 with previous version 0.13.1 dated 2021-11-05

Title: Udunits-2 Bindings for R
Description: Provides simple bindings to Unidata's udunits library.
Author: James Hiebert <hiebert@uvic.ca>
Maintainer: ORPHANED

Diff between udunits2 versions 0.13.1 dated 2021-11-05 and 0.13.2 dated 2022-01-06

 CHANGELOG                 |    5 +++++
 DESCRIPTION               |   10 ++++++----
 MD5                       |   21 +++++++++++----------
 configure                 |   45 +++++++++++++++++++++------------------------
 configure.ac              |   34 ++++++++++++++++++----------------
 man/ud.are.convertible.Rd |    4 ++--
 man/ud.convert.Rd         |    4 ++--
 man/ud.get.name.Rd        |    8 ++++----
 man/ud.is.parseable.Rd    |    4 ++--
 man/ud.set.encoding.Rd    |    2 +-
 man/udunits2-package.Rd   |    2 +-
 src/init.c                |only
 12 files changed, 73 insertions(+), 66 deletions(-)

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Package spam updated to version 2.8-0 with previous version 2.7-0 dated 2021-06-25

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre] (<https://orcid.org/0000-0002-6319-2332>), Florian Gerber [aut] (<https://orcid.org/0000-0001-8545-5263>), Roman Flury [aut] (<https://orcid.org/0000-0002-0349-8698>), Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam versions 2.7-0 dated 2021-06-25 and 2.8-0 dated 2022-01-06

 spam-2.7-0/spam/demo/article-jss-example1.R               |only
 spam-2.7-0/spam/demo/article-jss-example2.R               |only
 spam-2.7-0/spam/demo/article-jss.R                        |only
 spam-2.7-0/spam/demo/jss10-example2.R                     |only
 spam-2.7-0/spam/tests/demo_article-jss-example1.R         |only
 spam-2.7-0/spam/tests/demo_article-jss-example1.Rout.save |only
 spam-2.7-0/spam/tests/demo_article-jss-example2.R         |only
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 spam-2.7-0/spam/tests/demo_article-jss.R                  |only
 spam-2.7-0/spam/tests/demo_article-jss.Rout.save          |only
 spam-2.8-0/spam/DESCRIPTION                               |   11 
 spam-2.8-0/spam/MD5                                       |   88 +--
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Package FlexScan updated to version 0.2.2 with previous version 0.2.1 dated 2021-09-09

Title: Flexible Scan Statistics
Description: An easy way to conduct flexible scan. Monte-Carlo method is used to test the spatial clusters given the cases, population, and shapefile. A table with formal style and a map with clusters are included in the result report. The method can be referenced at: Toshiro Tango and Kunihiko Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du <dgdzc@hotmail.com>

Diff between FlexScan versions 0.2.1 dated 2021-09-09 and 0.2.2 dated 2022-01-06

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Package ivsacim updated to version 2.0.0 with previous version 1.3.1 dated 2021-08-07

Title: Structural Additive Cumulative Intensity Models with IV
Description: An instrumental variable estimator under structural cumulative additive intensity model is fitted, that leverages initial randomization as the IV. The estimator can be used to fit an additive hazards model under time to event data which handles treatment switching (treatment crossover) correctly. We also provide a consistent variance estimate.
Author: Andrew Ying
Maintainer: Andrew Ying <aying9339@gmail.com>

Diff between ivsacim versions 1.3.1 dated 2021-08-07 and 2.0.0 dated 2022-01-06

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Package BiodiversityR updated to version 2.14-1 with previous version 2.13-1 dated 2021-04-20

Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut] (<https://orcid.org/0000-0002-7672-0712>)
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>

Diff between BiodiversityR versions 2.13-1 dated 2021-04-20 and 2.14-1 dated 2022-01-06

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