Tue, 28 Feb 2023

Package lamW updated to version 2.1.2 with previous version 2.1.1 dated 2022-01-18

Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function (Corless et al, 1996) <doi:10.1007/BF02124750> without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between lamW versions 2.1.1 dated 2022-01-18 and 2.1.2 dated 2023-02-28

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Package mdmb updated to version 1.8-7 with previous version 1.7-22 dated 2023-02-17

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>; Luedtke, Robitzsch, & West, 2020a, 2020b; <doi:10.1080/00273171.2019.1640104><doi:10.1037/met0000233>). The regression model can be nonlinear (e.g., interaction effects, quadratic effects or B-spline functions). Multilevel models with missing data in predictors are available for Bayesian estimation. Substantive-model compatible multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between mdmb versions 1.7-22 dated 2023-02-17 and 1.8-7 dated 2023-02-28

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Package COVID19 updated to version 3.0.3 with previous version 3.0.2 dated 2022-02-22

Title: R Interface to COVID-19 Data Hub
Description: Provides a daily summary of COVID-19 cases, deaths, recovered, tests, vaccinations, and hospitalizations for 230+ countries, 760+ regions, and 12000+ administrative divisions of lower level. Includes policy measures, mobility data, and geospatial identifiers. Data source: COVID-19 Data Hub <https://covid19datahub.io>.
Author: Emanuele Guidotti [aut, cre] , David Ardia [ctb]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>

Diff between COVID19 versions 3.0.2 dated 2022-02-22 and 3.0.3 dated 2023-02-28

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Package stream updated to version 2.0-1 with previous version 2.0-0 dated 2022-09-02

Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph] , Matthew Bolanos [ctb], John Forrest [ctb], Matthias Carnein [ctb], Dennis Assenmacher [ctb], Dalibor Krleža [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between stream versions 2.0-0 dated 2022-09-02 and 2.0-1 dated 2023-02-28

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Package automap updated to version 1.1-1 with previous version 1.0-16 dated 2022-04-05

Title: Automatic Interpolation Package
Description: Performs an automatic interpolation by automatically estimating the variogram and then calling gstat.
Author: Paul Hiemstra [aut], Jon Olav Skoien [aut, cre]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>

Diff between automap versions 1.0-16 dated 2022-04-05 and 1.1-1 dated 2023-02-28

 DESCRIPTION                    |   18 +-
 MD5                            |   48 ++---
 NAMESPACE                      |    7 
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 README                         |   40 ++--
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Package dtwclust updated to version 5.5.12 with previous version 5.5.11 dated 2022-09-24

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

Diff between dtwclust versions 5.5.11 dated 2022-09-24 and 5.5.12 dated 2023-02-28

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 11 files changed, 116 insertions(+), 119 deletions(-)

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Package comperes updated to version 0.2.7 with previous version 0.2.6 dated 2023-01-08

Title: Manage Competition Results
Description: Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

Diff between comperes versions 0.2.6 dated 2023-01-08 and 0.2.7 dated 2023-02-28

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 7 files changed, 364 insertions(+), 345 deletions(-)

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Package gimme updated to version 0.7-11 with previous version 0.7-10 dated 2022-12-15

Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl], Kathleen Gates [aut, cre, ccp], Zachary Fisher [aut], Cara Arizmendi [aut], Peter Molenaar [aut, ccp], Edgar Merkle [ctb], Michael Hallquist [ctb], Hallie Pike [ctb], Teague Henry [ctb], Kelly Duffy [ctb], Lan Luo [ctb], Ad [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>

Diff between gimme versions 0.7-10 dated 2022-12-15 and 0.7-11 dated 2023-02-28

 DESCRIPTION                  |   13 +
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New package parabar with initial version 0.10.1
Package: parabar
Title: Progress Bar for Parallel Tasks
Version: 0.10.1
Description: A simple interface in the form of R6 classes for executing tasks in parallel, tracking their progress, and displaying accurate progress bars.
License: MIT + file LICENSE
URL: https://parabar.mihaiconstantin.com
BugReports: https://github.com/mihaiconstantin/parabar/issues
Imports: R6, progress, parallel, callr, filelock, utils
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-02-27 19:08:51 UTC; mihai
Author: Mihai Constantin [aut, cre]
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Repository: CRAN
Date/Publication: 2023-02-28 17:12:30 UTC

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New package ODRF with initial version 0.0.2
Package: ODRF
Title: Oblique Decision Random Forest for Classification and Regression
Version: 0.0.2
Author: Yu Liu [aut, cre, cph], Yingcun Xia [aut]
Maintainer: Yu Liu <liuyuchina123@gmail.com>
Description: The oblique decision tree (ODT) uses linear combinations of predictors as partitioning variables in a decision tree. Oblique Decision Random Forest (ODRF) is an ensemble of multiple ODTs generated by feature bagging. Both can be used for classification and regression as supplements to the classical CART of Breiman (1984) <https://imsarchives.nus.edu.sg/oldwww/Programs/014swclass/files/mark.pdf> and Random Forest of Breiman (2001) <DOI:10.1023/A:1010933404324> respectively.
License: GPL (>= 3)
URL: https://liuyu-star.github.io/ODRF/
BugReports: https://github.com/liuyu-star/ODRF/issues
Depends: partykit, R (>= 3.5.0)
Imports: doParallel, foreach, glue, graphics, grid, lifecycle, magrittr, nnet, parallel, Pursuit, Rcpp, rlang (>= 0.4.11), stats
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: yes
NeedsCompilation: yes
Packaged: 2023-02-27 17:01:12 UTC; Administrator
Repository: CRAN
Date/Publication: 2023-02-28 17:12:35 UTC

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New package MACP with initial version 0.1.0
Package: MACP
Title: Macromolecular Assemblies from Co-Elution Profile (MACP)
Version: 0.1.0
Description: The MACP employs machine learning algorithm for automated scoring of co-fractionation mass spectrometry (CF-MS) and then systematically map multi-protein complexes from these high-confidence protein-protein interactions (PPIs) using unsupervised learning (i.e., clustering).
Depends: R (>= 4.1)
Imports: stats, zoo, utils, dplyr, lsa, WGCNA, tidyr, tibble, Hmisc, igraph, PRROC, pROC, ggplot2, grDevices, fmsb, stringr, caret
Maintainer: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
URL: https://github.com/mrbakhsh/MACP
BugReports: https://github.com/mrbakhsh/MACP/issues
VignetteBuilder: knitr
Suggests: knitr, ptw, e1071, kernlab, ranger, proxy, infotheo, gridExtra, philentropy, randomForest, gprofiler2, purrr, minet, entropy, MCL, orthogene, protti, arules, rmarkdown, BiocStyle
NeedsCompilation: no
Packaged: 2023-02-27 17:42:22 UTC; Matine
Author: Matineh Rahmatbakhsh [aut, trl, cre], Mohan Babu [led]
Repository: CRAN
Date/Publication: 2023-02-28 17:32:30 UTC

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New package LorenzRegression with initial version 1.0.0
Package: LorenzRegression
Title: Lorenz and Penalized Lorenz Regressions
Version: 1.0.0
Description: Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.3.1)
LazyData: true
Imports: stats, ggplot2, parallel, doParallel, foreach, MASS, GA, locpol, Rearrangement, Rcpp (>= 0.11.0), knitr
Suggests: rmarkdown
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2023-02-28 14:30:05 UTC; jacquemain
Author: Alexandre Jacquemain [aut, cre] , Xingjie Shi [ctb]
Maintainer: Alexandre Jacquemain <aljacquemain@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-28 17:32:34 UTC

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Package haven updated to version 2.5.2 with previous version 2.5.1 dated 2022-08-22

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] , Danny Smith [aut], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between haven versions 2.5.1 dated 2022-08-22 and 2.5.2 dated 2023-02-28

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 NAMESPACE                                 |    1 
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Package cquad updated to version 2.3 with previous version 2.2 dated 2020-10-10

Title: Conditional Maximum Likelihood for Quadratic Exponential Models for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) <DOI:10.3982/ECTA7531> and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a [...truncated...]
Author: Francesco Bartolucci , Claudia Pigini , Francesco Valentini
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>

Diff between cquad versions 2.2 dated 2020-10-10 and 2.3 dated 2023-02-28

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New package datetoiso with initial version 0.1.0
Package: datetoiso
Title: Modify Dates to ISO Standard ("International Organization for Standardization")
Version: 0.1.0
URL: https://github.com/andzoluk
Language: en-US
Description: Transfer any date type to ISO standard. Package recognizes dates in given data frame and transform to ISO format. Only one date format can be applied within one data frame column.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stringr, lubridate
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-02-28 08:15:27 UTC; Andrzejewski
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-28 17:22:30 UTC

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Package cohortBuilder updated to version 0.2.0 with previous version 0.1 dated 2022-06-01

Title: Data Source Agnostic Filtering Tools
Description: Common API for filtering data stored in different data models. Provides multiple filter types and reproducible R code. Works standalone or with 'shinyCohortBuilder' as the GUI for interactive Shiny apps.
Author: Krystian Igras [cre, aut], Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>

Diff between cohortBuilder versions 0.1 dated 2022-06-01 and 0.2.0 dated 2023-02-28

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Package windex updated to version 2.0.4 with previous version 2.0.3 dated 2021-10-21

Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>

Diff between windex versions 2.0.3 dated 2021-10-21 and 2.0.4 dated 2023-02-28

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Package rstpm2 updated to version 1.6.1 with previous version 1.5.9 dated 2023-01-06

Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Benjamin Christoffersen [aut], Paul Lambert [ctb], Lasse Hjort Jakobsen [ctb], Alessandro Gasparini [ctb], Gordon Smyth [cph], Patrick Alken [cph], Simon Wood [cph], Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>

Diff between rstpm2 versions 1.5.9 dated 2023-01-06 and 1.6.1 dated 2023-02-28

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Package webmockr updated to version 0.9.0 with previous version 0.8.2 dated 2022-08-28

Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.
Author: Scott Chamberlain [aut, cre] , Aaron Wolen [ctb] , rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

Diff between webmockr versions 0.8.2 dated 2022-08-28 and 0.9.0 dated 2023-02-28

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Package UCSCXenaShiny updated to version 1.1.10 with previous version 1.1.9 dated 2022-12-12

Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] , Yi Xiong [aut] , Longfei Zhao [aut] , Kai Gu [aut] , Yin Li [aut], Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between UCSCXenaShiny versions 1.1.9 dated 2022-12-12 and 1.1.10 dated 2023-02-28

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New package PSAWR with initial version 0.1.0
Package: PSAWR
Title: 'Pushshift' API Wrapper for 'Reddit' Submission and Comment Search
Version: 0.1.0
Description: Connects to the API of <https://pushshift.io/> to search for 'Reddit' comments and submissions.
URL: https://github.com/schochastics/PSAWR/
BugReports: https://github.com/schochastics/PSAWR/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: dplyr, httr, tibble
Suggests: covr, testthat (>= 3.0.0), vcr (>= 0.6.0)
NeedsCompilation: no
Packaged: 2023-02-27 19:40:49 UTC; david
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Repository: CRAN
Date/Publication: 2023-02-28 15:02:30 UTC

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Package partykit updated to version 1.2-17 with previous version 1.2-16 dated 2022-06-20

Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure. A description of this package was published by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] , Heidi Seibold [ctb] , Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between partykit versions 1.2-16 dated 2022-06-20 and 1.2-17 dated 2023-02-28

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Package party updated to version 1.3-12 with previous version 1.3-11 dated 2022-10-07

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available. The methods are described in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] , Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between party versions 1.3-11 dated 2022-10-07 and 1.3-12 dated 2023-02-28

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New package shinyChatR with initial version 1.0.0
Package: shinyChatR
Title: R Shiny Chat Module
Version: 1.0.0
Description: Provides an easy-to-use module for adding a chat to a Shiny app. Allows users to send messages and view messages from other users. Messages can be stored in a database or a .rds file.
License: GPL (>= 3)
Encoding: UTF-8
Imports: DBI, purrr, R6, shiny
VignetteBuilder: knitr
Suggests: covr, knitr, rmarkdown, RSQLite, testthat (>= 3.0.0)
URL: https://github.com/julianschmocker/shinyChatR
NeedsCompilation: no
Packaged: 2023-02-27 17:00:21 UTC; julianschmocker
Author: Julian Schmocker [aut, cre, cph]
Maintainer: Julian Schmocker <julian.schmocker@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-28 14:30:02 UTC

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New package rpyANTs with initial version 0.0.1
Package: rpyANTs
Title: An Alternative Advanced Normalization Tools ('ANTs')
Version: 0.0.1
Description: Provides portable access from 'R' to biomedical image processing toolbox 'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless integration with the 'Python' implementation 'ANTsPy'. Allows biomedical images to be processed in 'Python' and analyzed in 'R', and vice versa via shared memory. See 'citation("rpyANTs")' for more reference information.
License: Apache License 2.0
Language: en-US
Encoding: UTF-8
Imports: grDevices, rpymat (>= 0.1.4), reticulate (>= 1.26)
Suggests: RNifti (>= 1.4.4), testthat (>= 3.0.0)
URL: http://dipterix.org/rpyANTs/
BugReports: https://github.com/dipterix/rpyANTs/issues
Copyright: For the rpyANTs package - Zhengjia Wang; For ANTs - ConsortiumOfANTS; For ANTsPy - ANTs Contributors.
NeedsCompilation: no
Packaged: 2023-02-27 18:27:42 UTC; dipterix
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-28 14:42:29 UTC

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New package NTSS with initial version 0.1.0
Package: NTSS
Title: Nonparametric Tests in Spatial Statistics
Version: 0.1.0
Description: Nonparametric test of independence between a pair of spatial objects (random fields, point processes) based on random shifts with torus or variance correction. See Mrkvička et al. (2021) <doi:10.1016/j.spasta.2020.100430>, Dvořák et al. (2022) <doi:10.1111/insr.12503>, Dvořák and Mrkvička (2022) <arxiv:2210.05424>.
Imports: stats, graphics, spatstat, spatstat.random, spatstat.geom, spatstat.model, spatstat.explore, ks
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-02-27 12:58:30 UTC; dvorak
Author: Jiri Dvorak [aut, cre] , Tomas Mrkvička [ctb]
Maintainer: Jiri Dvorak <dvorak@karlin.mff.cuni.cz>
Repository: CRAN
Date/Publication: 2023-02-28 14:32:37 UTC

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New package izmir with initial version 0.1.0
Package: izmir
Title: R Wrapper for Izmir Municipality Open Data Portal
Version: 0.1.0
Maintainer: Ozancan Ozdemir <ozancanozdemir@gmail.com>
Description: Call the data wrappers for Izmir Metropolitan Municipality's Open Data Portal. This will return all datasets formatted as Excel files (.csv or .xlsx), as well as datasets that require an API key.
License: MIT + file LICENSE
URL: https://github.com/ozancanozdemir/izmir
BugReports: https://github.com/ozancanozdemir/izmir/issues
Depends: R (>= 3.4)
Imports: dplyr, rvest, stringr, jsonlite, readr, openxlsx, utils, magrittr
Suggests: testthat (>= 3.0.0), devtools, roxygen2, covr, usethis
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-02-27 18:57:13 UTC; ozancan
Author: Ozancan Ozdemir [aut, cre]
Repository: CRAN
Date/Publication: 2023-02-28 14:42:33 UTC

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New package cbcTools with initial version 0.2.0
Package: cbcTools
Title: Design and Evaluate Choice-Based Conjoint Survey Experiments
Version: 0.2.0
Maintainer: John Helveston <john.helveston@gmail.com>
Description: Design and evaluate choice-based conjoint survey experiments in R. Generate survey designs, including randomized designs and Bayesian D-efficient designs as well as designs with "no choice" options and labeled designs. Conveniently inspect the design balance and overlap, and simulate choice data for a survey design either randomly or according to a multinomial or mixed logit utility model defined by user-provided prior parameters. Conduct power analyses on a survey design by estimating the same model multiple times using different subsets of the data to simulate different sample sizes. Choice simulation and model estimation are handled using the 'logitr' package, and Bayesian D-efficient designs are obtained using the 'idefix' package. For more details see Helveston (2023) <doi:10.18637/jss.v105.i10> and Traets et al (2020) <doi:10.18637/jss.v096.i03>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0)
Suggests: testthat, tibble
Imports: fastDummies, ggplot2, idefix, logitr (>= 1.0.1), MASS, parallel, randtoolbox, rlang, stats, utils
URL: https://github.com/jhelvy/cbcTools
BugReports: https://github.com/jhelvy/cbcTools/issues
NeedsCompilation: no
Packaged: 2023-02-27 11:12:00 UTC; jhelvy
Author: John Helveston [cre, aut, cph]
Repository: CRAN
Date/Publication: 2023-02-28 14:32:34 UTC

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Package visvow updated to version 1.3.6 with previous version 1.3.5 dated 2022-07-21

Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa [aut, cre], Hans Van de Velde [aut]
Maintainer: Wilbert Heeringa <wheeringa@fryske-akademy.nl>

Diff between visvow versions 1.3.5 dated 2022-07-21 and 1.3.6 dated 2023-02-28

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Package spdep updated to version 1.2-8 with previous version 1.2-7 dated 2022-10-01

Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord' (1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured join count statistics, 'APLE' ('Li 'et al.' ) <doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C' ('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and 'Getis/Ord' G ('Ord' and 'Getis' 1995) < [...truncated...]
Author: Roger Bivand [cre, aut] , Micah Altman [ctb], Luc Anselin [ctb], Renato Assuncao [ctb], Olaf Berke [ctb], F. Guillaume Blanchet [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stephane Dray [ctb], D [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package meta updated to version 6.2-1 with previous version 6.2-0 dated 2023-02-14

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis model; - generalised linear mixed model; - Hartung-Knapp method for random effects model; - Kenward-Roger method for random effects model; - prediction interval; - statistical tests for funnel plot asymmetry; - trim-and-fill method to evaluate bias in meta-analysis; - meta-regression; - cumulative meta-analysis and leave-one-out meta-analysis; - import data from 'RevMan 5'; - produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>

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Package metasens updated to version 1.5-2 with previous version 1.5-1 dated 2022-12-21

Title: Statistical Methods for Sensitivity Analysis in Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 'Small-Study Effects in Meta-Analysis': - Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>; - limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>; - upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>; - imputation methods for missing binary data by Gamble & Hollis (2005) <DOI:10.1016/j.jclinepi.2004.09.013> and Higgins et al. (2008) <DOI:10.1177/1740774508091600>; - LFK index test and Doi plot by Furuya-Kanamori et al. (2018) <DOI:10.1097/XEB.0000000000000141>.
Author: Guido Schwarzer [cre, aut] , James R. Carpenter [aut] , Gerta Ruecker [aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>

Diff between metasens versions 1.5-1 dated 2022-12-21 and 1.5-2 dated 2023-02-28

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Package forrel updated to version 1.5.0 with previous version 1.4.1 dated 2022-02-25

Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including likelihood ratios for relationship testing, general relatedness inference, marker simulation, and power analysis. General computation of exclusion powers is based on Egeland et al. (2014) <doi:10.1016/j.fsigen.2013.05.001>. Several functions deal specifically with family reunion cases, implementing and developing ideas from Kling et al. (2017) <doi:10.1016/j.fsigen.2017.08.006>. A novelty of 'forrel' is the ability to model background inbreeding in forensic pedigree computations. This can have significant impact in applications, as exemplified in Vigeland and Egeland (2019) <doi:10.1016/j.fsigss.2019.10.175>. 'forrel' is part of the ped suite, a collection of packages for pedigree analysis. In particular, 'forrel' imports 'pedtools' for creating and manipulating pedigrees and markers, 'pedprobr' for likelihood computations, and 'pedmut' for mutation modelling. Pedigree data may be created from scratch, or loaded [...truncated...]
Author: Magnus Dehli Vigeland [aut, cre] , Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

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Package ClimProjDiags updated to version 0.3.0 with previous version 0.2.1 dated 2022-12-02

Title: Set of Tools to Compute Various Climate Indices
Description: Set of tools to compute metrics and indices for climate analysis. The package provides functions to compute extreme indices, evaluate the agreement between models and combine theses models into an ensemble. Multi-model time series of climate indices can be computed either after averaging the 2-D fields from different models provided they share a common grid or by combining time series computed on the model native grid. Indices can be assigned weights and/or combined to construct new indices.
Author: BSC-CNS [aut, cph], Nuria Perez-Zanon [aut] , An-Chi Ho [cre, ctb], Nicolau Manubens [ctb], Alasdair Hunter [aut], Louis-Philippe Caron [ctb], Eva Rifa [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>

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Package prqlr updated to version 0.2.1 with previous version 0.2.0 dated 2023-02-18

Title: R Bindings for the 'prql-compiler' Rust Library
Description: Provides a function to convert 'PRQL' strings to 'SQL' strings. Combined with other R functions that take 'SQL' as an argument, 'PRQL' can be used on R.
Author: Tatsuya Shima [aut, cre]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>

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Package opalr updated to version 3.3.1 with previous version 3.3.0 dated 2023-02-03

Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Author: Yannick Marcon [aut, cre] , Amadou Gaye [ctb] , OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>

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Package politeness updated to version 0.8.9 with previous version 0.8.8 dated 2023-01-09

Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>

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Package classInt updated to version 0.4-9 with previous version 0.4-8 dated 2022-09-29

Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre] , Bill Denney [ctb] , Richard Dunlap [ctb], Diego Hernangomez [ctb] , Hisaji Ono [ctb], Josiah Parry [ctb] , Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between classInt versions 0.4-8 dated 2022-09-29 and 0.4-9 dated 2023-02-28

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Package hdme updated to version 0.5.1 with previous version 0.5.0 dated 2022-07-20

Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for measurement error problems (aka. errors-in-variables). The package contains a version of the lasso (L1-penalization) which corrects for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>). It also contains an implementation of the Generalized Matrix Uncertainty Selector, which is a version the (Generalized) Dantzig Selector for the case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen [aut, cre]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package BNSP updated to version 2.2.1 with previous version 2.2.0 dated 2022-11-26

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for: 1. single response multiple regression, see Papageorgiou, G. (2018) <doi: 10.32614/RJ-2018-069>, 2. multivariate response multiple regression, with nonparametric models for the means, the variances and the correlation matrix, with variable selection, see Papageorgiou, G. and Marshall, B. C. (2020) <doi: 10.1080/10618600.2020.1739534>, 3. joint mean-covariance models for multivariate responses, see Papageorgiou, G. (2022) <doi: 10.1002/sim.9376>, and 4.Dirichlet process mixtures, see Papageorgiou, G. (2019) <doi: 10.1111/anzs.12273>.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

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Package ast2ast updated to version 0.3.0 with previous version 0.2.1 dated 2022-10-19

Title: Translates an R Function to a C++ Function
Description: Enable translation of a tiny subset of R to C++. The user has to define a R function which gets translated. For a full list of possible functions check the documentation. After translation an R function is returned which is a shallow wrapper around the C++ code. Alternatively an external pointer to the C++ function is returned to the user. The intention of the package is to generate fast functions which can be used as ode-system or during optimization.
Author: Kraemer Konrad [aut, cre]
Maintainer: Kraemer Konrad <konrad_kraemer@yahoo.de>

Diff between ast2ast versions 0.2.1 dated 2022-10-19 and 0.3.0 dated 2023-02-28

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New package suddengains with initial version 0.7.2
Package: suddengains
Title: Identify Sudden Gains in Longitudinal Data
Date: 2023-02-27
Version: 0.7.2
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://milanwiedemann.github.io/suddengains/
BugReports: https://github.com/milanwiedemann/suddengains/issues
LazyData: true
Imports: dplyr (>= 0.8.0), tibble (>= 2.1.1), magrittr (>= 1.5), rlang (>= 0.3.4), stringr (>= 1.4.0), ggplot2 (>= 3.1.1), psych (>= 1.8.12), readr (>= 1.3.1), tidyr (>= 0.8.2), ggrepel (>= 0.8.0), patchwork (>= 1.0.0), forcats, naniar, scales, cli
Suggests: haven (>= 2.1.0), writexl (>= 1.1.0), knitr (>= 1.21), DT (>= 0.5), rmarkdown (>= 1.11), spelling (>= 2.1)
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2023-02-27 10:16:59 UTC; milanwiedemann
Author: Milan Wiedemann [aut, cre] , Graham M Thew [aut] , Richard Stott [ctb] , Anke Ehlers [ctb, ths] , Mental Health Research UK [fnd], Wellcome Trust [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-28 08:30:02 UTC

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Package robber updated to version 0.2.3 with previous version 0.2.2 dated 2021-09-20

Title: Using Block Model to Estimate the Robustness of Ecological Network
Description: Implementation of a variety of methods to compute the robustness of ecological interaction networks with binary interactions as described in <doi:10.1002/env.2709>. In particular, using the Stochastic Block Model and its bipartite counterpart, the Latent Block Model to put a parametric model on the network, allows the comparison of the robustness of networks differing in species richness and number of interactions. It also deals with networks that are partially sampled and/or with missing values.
Author: Saint-Clair Chabert-Liddell [aut, cre]
Maintainer: Saint-Clair Chabert-Liddell <academic@chabert-liddell.com>

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Package geometries updated to version 0.2.2 with previous version 0.2.1 dated 2023-02-23

Title: Convert Between R Objects and Geometric Structures
Description: Geometry shapes in 'R' are typically represented by matrices (points, lines), with more complex shapes being lists of matrices (polygons). 'Geometries' will convert various 'R' objects into these shapes. Conversion functions are available at both the 'R' level, and through 'Rcpp'.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <david.cooley.au@gmail.com>

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Package civis updated to version 3.1.1 with previous version 3.1.0 dated 2023-02-22

Title: R Client for the 'Civis Platform API'
Description: A convenient interface for making requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform/>. Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.
Author: Peter Cooman [cre, ctb], Patrick Miller [aut], Keith Ingersoll [aut], Bill Lattner [ctb], Anh Le [ctb], Michelangelo D'Agostino [ctb], Sam Weiss [ctb], Stephen Hoover [ctb], Danning Chen [ctb], Elizabeth Sander [ctb], Madison Hobbs [ctb], Anna Bladey [...truncated...]
Maintainer: Peter Cooman <pcooman@civisanalytics.com>

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Package MetChem updated to version 0.3 with previous version 0.2 dated 2023-02-02

Title: Chemical Structural Similarity Analysis
Description: A new pipeline to explore chemical structural similarity across metabolite. It allows to classify metabolites in structurally-related modules and identify common shared functional groups. KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Author: Ebtesam Abdel-Shafy [aut], Tadele Melak [aut], David A. MacIntyre [aut], Giorgia Zadra [aut], Luiz F. Zerbini [aut], Silvano Piazza [aut], Stefano Cacciatore [aut, cre]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>

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Package etwfe updated to version 0.3.1 with previous version 0.3.0 dated 2023-02-08

Title: Extended Two-Way Fixed Effects
Description: Convenience functions for implementing extended two-way fixed effect regressions a la Wooldridge (2021, 2022) <doi:10.2139/ssrn.3906345>, <doi:10.2139/ssrn.4183726>.
Author: Grant McDermott [aut, cre] , Frederic Kluser [ctb]
Maintainer: Grant McDermott <grantmcd@uoregon.edu>

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Package aRchi (with last version 2.1.3) was removed from CRAN

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

2022-09-03 2.1.3
2022-08-07 2.1.2
2022-04-12 2.1.0
2021-04-16 1.0.5
2021-04-09 1.0.3

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Package geneHapR (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:

2023-02-13 1.1.7
2022-12-08 1.1.6
2022-12-06 1.1.5
2022-09-19 1.1.1
2022-08-22 1.0.8

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Package ech (with last version 0.1.2.0) was removed from CRAN

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

2022-04-06 0.1.2.0

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Package moranajp updated to version 0.9.6 with previous version 0.9.5 dated 2022-07-11

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

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Package ForestFit updated to version 2.2.3 with previous version 1.2.3 dated 2021-10-16

Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. 1 ) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models. 2 ) Point estimation of the parameters of two - parameter Weibull distribution using twelve methods and three - parameter Weibull distribution using nine methods. 3 ) The Bayesian inference for the three - parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. 5 ) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve fitted to the height - diameter observation, 7 ) Estimating parameters, computing probability density function, cum [...truncated...]
Author: Mahdi Teimouri [aut, cre, cph, ctb]
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>

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