Sat, 21 Aug 2021

Package mgcViz updated to version 0.1.8 with previous version 0.1.6 dated 2020-03-04

Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre], Raphael Nedellec [aut], Yannig Goude [ctb], Christian Capezza [ctb], Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

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Package soilDB updated to version 2.6.5 with previous version 2.6.3 dated 2021-07-23

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

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Package RSQLite updated to version 2.2.8 with previous version 2.2.7 dated 2021-04-22

Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The source for the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), Hadley Wickham [aut], David A. James [aut], Seth Falcon [aut], SQLite Authors [ctb] (for the included SQLite sources), Liam Healy [ctb] (for the included SQLite sources), R Consortium [fnd], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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

Title: Iterative Solvers for (Sparse) Linear System of Equations
Description: Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. We provide basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using 'Matrix' package along with 'RcppArmadillo'. For a more detailed description, see a book by Saad (2003) <doi:10.1137/1.9780898718003>.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>

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Package rgl updated to version 0.107.14 with previous version 0.107.10 dated 2021-07-22

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre], Daniel Adler [aut], Oleg Nenadic [ctb], Simon Urbanek [ctb], Ming Chen [ctb], Albrecht Gebhardt [ctb], Ben Bolker [ctb], Gabor Csardi [ctb], Adam Strzelecki [ctb], Alexander Senger [ctb], The R Core Team [ctb, cph], Dirk Eddelbuettel [ctb], The authors of Shiny [cph], The authors of knitr [cph], Jeroen Ooms [ctb], Yohann Demont [ctb], Joshua Ulrich [ctb], Xavier Fernandez i Marin [ctb], George Helffrich [ctb], Ivan Krylov [ctb], Michael Sumner [ctb]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

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Package matlib updated to version 0.9.5 with previous version 0.9.4 dated 2020-10-29

Title: Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. These functions are mainly for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre] (<https://orcid.org/0000-0002-3237-0941>), John Fox [aut], Phil Chalmers [aut], Georges Monette [ctb], Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package emayili updated to version 0.4.16 with previous version 0.4.15 dated 2021-07-30

Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre], Matt Dennis [ctb], Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>), Daniel Fahey [ctb], Johann R. Kleinbub [ctb], Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>

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Package RiemBase updated to version 0.2.5 with previous version 0.2.4 dated 2020-03-21

Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>

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Package NetworkDistance updated to version 0.3.4 with previous version 0.3.3 dated 2020-05-08

Title: Distance Measures for Networks
Description: Network is a prevalent form of data structure in many fields. As an object of analysis, many distance or metric measures have been proposed to define the concept of similarity between two networks. We provide a number of distance measures for networks. See Jurman et al (2011) <doi:10.3233/978-1-60750-692-8-227> for an overview on spectral class of inter-graph distance measures.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>

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Package filling updated to version 0.2.3 with previous version 0.2.2 dated 2020-07-02

Title: Matrix Completion, Imputation, and Inpainting Methods
Description: Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>

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Package DeclareDesign updated to version 0.28.0 with previous version 0.26.0 dated 2021-02-14

Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of research designs before implementation using `DeclareDesign`. Ex ante declaration and diagnosis of designs can help researchers clarify the strengths and limitations of their designs and to improve their properties, and can help readers evaluate a research strategy prior to implementation and without access to results. It can also make it easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] (<https://orcid.org/0000-0001-9164-2102>), Jasper Cooper [aut] (<https://orcid.org/0000-0002-8639-3188>), Alexander Coppock [aut] (<https://orcid.org/0000-0002-5733-2386>), Macartan Humphreys [aut] (<https://orcid.org/0000-0001-7029-2326>), Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

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Package dashboardthemes updated to version 1.1.5 with previous version 1.1.3 dated 2020-08-26

Title: Customise the Appearance of 'shinydashboard' Applications using Themes
Description: Allows manual creation of themes and logos to be used in applications created using the 'shinydashboard' package. Removes the need to change the underlying css code by wrapping it into a set of convenient R functions.
Author: Nik Lilovski [aut, cre]
Maintainer: Nik Lilovski <nik.lilovski@outlook.com>

Diff between dashboardthemes versions 1.1.3 dated 2020-08-26 and 1.1.5 dated 2021-08-21

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Package adiv updated to version 2.1 with previous version 2.0.1 dated 2020-08-26

Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>

Diff between adiv versions 2.0.1 dated 2020-08-26 and 2.1 dated 2021-08-21

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More information about adiv at CRAN
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Package shattering updated to version 1.0.7 with previous version 1.0.6 dated 2021-06-02

Title: Estimate the Shattering Coefficient for a Particular Dataset
Description: The Statistical Learning Theory (SLT) provides the theoretical background to ensure that a supervised algorithm generalizes the mapping f:X -> Y given f is selected from its search space bias F. This formal result depends on the Shattering coefficient function N(F,2n) to upper bound the empirical risk minimization principle, from which one can estimate the necessary training sample size to ensure the probabilistic learning convergence and, most importantly, the characterization of the capacity of F, including its under and overfitting abilities while addressing specific target problems. In this context, we propose a new approach to estimate the maximal number of hyperplanes required to shatter a given sample, i.e., to separate every pair of points from one another, based on the recent contributions by Har-Peled and Jones in the dataset partitioning scenario, and use such foundation to analytically compute the Shattering coefficient function for both binary and multi-class problems. As main contributions, one can use our approach to study the complexity of the search space bias F, estimate training sample sizes, and parametrize the number of hyperplanes a learning algorithm needs to address some supervised task, what is specially appealing to deep neural networks. Reference: de Mello, R.F. (2019) "On the Shattering Coefficient of Supervised Learning Algorithms" <arXiv:1911.05461>; de Mello, R.F., Ponti, M.A. (2018, ISBN: 978-3319949888) "Machine Learning: A Practical Approach on the Statistical Learning Theory".
Author: Rodrigo F. de Mello [aut, cre] (<https://orcid.org/0000-0002-0435-3992>)
Maintainer: Rodrigo F. de Mello <mellorf@gmail.com>

Diff between shattering versions 1.0.6 dated 2021-06-02 and 1.0.7 dated 2021-08-21

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Package RcppFastFloat updated to version 0.0.3 with previous version 0.0.2 dated 2021-02-13

Title: 'Rcpp' Bindings for the 'fast_float' Header-Only Library for Number Parsing
Description: Converting ascii text into (floating-point) numeric values is a very common problem. The 'fast_float' header-only C++ library by Daniel Lemire does it very well and very fast at up to or over to 1 gigabyte per second as described in more detail in <arXiv:2101.11408>. 'fast_float' is licensed under the Apache 2.0 license and provided here for use by other R packages via a simple 'LinkingTo:' statement.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppFastFloat versions 0.0.2 dated 2021-02-13 and 0.0.3 dated 2021-08-21

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Package pathfindR updated to version 1.6.2 with previous version 1.6.1 dated 2021-01-04

Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Author: Ege Ulgen [cre, cph] (<https://orcid.org/0000-0003-2090-3621>), Ozan Ozisik [aut] (<https://orcid.org/0000-0001-5980-8002>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>

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Package spatialTIME updated to version 1.1.0 with previous version 1.0.0 dated 2021-05-14

Title: Spatial Analysis of Vectra Immunoflourescent Data
Description: Visualization and analysis of Vectra Immunoflourescent data. Options for calculating both the univariate and bivariate Ripley's K are included. Calculations are performed using a permutation-based approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Author: Jordan Creed [aut], Ram Thapa [aut], Christopher Wilson [aut], Alex Soupir [aut], Brooke Fridley [cph], Fridley Lab [cre]
Maintainer: Fridley Lab <fridley.lab@moffitt.org>

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Package onlineforecast updated to version 0.10.0 with previous version 0.9.3 dated 2020-09-15

Title: Forecast Modelling for Online Applications
Description: A framework for fitting adaptive forecasting models. Provides a way to use forecasts as input to models, e.g. weather forecasts for energy related forecasting. The models can be fitted recursively and can easily be setup for updating parameters when new data arrives. See the included vignettes, the website <https://onlineforecasting.org> and the paper "Short-term heat load forecasting for single family houses" <doi:10.1016/j.enbuild.2013.04.022>.
Author: Peder Bacher [cre], Hjorleifur G Bergsteinsson [aut]
Maintainer: Peder Bacher <pbac@dtu.dk>

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New package vcmeta with initial version 1.0.0
Package: vcmeta
Title: Varying Coefficient Meta-Analysis
Version: 1.0.0
Description: Implements functions for varying coefficient meta-analysis methods. These methods do not assume effect size homogeneity. Subgroup effect size comparisons, general linear effect size contrasts, and linear models of effect sizes based on varying coefficient methods can be used to describe effect size heterogeneity. Varying coefficient meta-analysis methods do not require the unrealistic assumptions of the traditional fixed-effect and random-effects meta-analysis methods. For details, see: Bonett (2008) <doi:10.1037/a0012868>, Bonett (2009) <doi:10.1037/a0016619>, Bonett (2010) <doi:10.1037/a0020142>, Bonett & Price (2014) <doi:10.1111/bmsp.12024>, Bonett & Price (2015) <doi:10.1111/bmsp.12024>, Bonett (2020) <doi:10.1111/bmsp.12189>, Bonett (2021) <doi:10.1177/1094428120911088>.
URL: https://github.com/dgbonett/vcmeta
BugReports: https://github.com/dgbonett/vcmeta/issues
License: GPL-3
Encoding: UTF-8
Imports: stats, mathjaxr, Rdpack, ggplot2
RdMacros: Rdpack, mathjaxr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-08-19 18:38:57 UTC; rcali
Author: Douglas G. Bonett [aut, cre], Robert J. Calin-Jageman [ctb]
Maintainer: Douglas G. Bonett <dgbonett@ucsc.edu>
Repository: CRAN
Date/Publication: 2021-08-21 09:40:02 UTC

More information about vcmeta at CRAN
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New package roger with initial version 0.99-0
Package: roger
Title: Automated Grading of R Scripts
Version: 0.99-0
Date: 2021-08-20
Description: Tools for grading the coding style and documentation of R scripts. This is the R component of Roger the Omni Grader, an automated grading system for computer programming projects based on Unix shell scripts; see <https://gitlab.com/roger-project>. The package also provides an R interface to the shell scripts. Inspired by the lintr package.
Depends: R (>= 4.0.0)
Imports: utils
SystemRequirements: roger-base (for interface functions only)
License: GPL (>= 2)
URL: https://roger-project.gitlab.io
BugReports: https://gitlab.com/roger-project/roger-rpkg/-/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-08-20 03:53:23 UTC; vincent
Author: Vincent Goulet [aut, cre], Samuel Fréchette [aut], Jean-Christophe Langlois [aut], Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Repository: CRAN
Date/Publication: 2021-08-21 09:10:02 UTC

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New package onc.api with initial version 2.0.1.0
Package: onc.api
Title: Oceans 2.0 API Client Library
Description: Allows users to discover and retrieve Ocean Networks Canada's oceanographic data in raw, text, image, audio, video or any other format available. Provides a class that wraps web service calls and business logic so that users can download data with a single line of code.
Version: 2.0.1.0
URL: https://wiki.oceannetworks.ca/display/O2A/Oceans+2.0+API+Home
License: MIT + file LICENSE
Imports: anytime, httr, methods, humanize, lubridate, stringi, tictoc, crayon, utils, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-08-20 15:34:53 UTC; blm
Author: Dany Cabrera [aut], Allan Rempel [ctb], Ryan Ross [ctb], Bennit Mueller [ctb, cre]
Maintainer: Bennit Mueller <data@oceannetworks.ca>
Repository: CRAN
Date/Publication: 2021-08-21 09:40:07 UTC

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New package naturaList with initial version 0.4.1
Package: naturaList
Title: Classify Occurrences by Confidence Levels in the Species ID
Version: 0.4.1
Description: Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrence inside grid cells and to manually check for possibles errors with an interactive shiny application.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: shiny, shinyWidgets, dplyr, stringr, sp, raster, shinydashboard, leaflet, leaflet.extras, tidytext, magrittr, vegan, fasterize, sf, htmltools, methods, rlang
Suggests: knitr, rmarkdown, testthat, tm, rgeos, rgdal, rnaturalearth, lwgeom, shinyLP, maptools
VignetteBuilder: knitr
Depends: R (>= 2.10)
URL: https://github.com/avrodrigues/naturaList
BugReports: https://github.com/avrodrigues/naturaList/issues
NeedsCompilation: no
Packaged: 2021-08-20 12:15:47 UTC; avrodrigues
Author: Arthur Vinicius Rodrigues [cre], Gabriel Nakamura [aut], Leandro Duarte [aut]
Maintainer: Arthur Vinicius Rodrigues <rodrigues.arthur.v@gmail.com>
Repository: CRAN
Date/Publication: 2021-08-21 09:30:02 UTC

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New package KLexp with initial version 1.0.0
Package: KLexp
Title: Kernel_lasso Expansion
Version: 1.0.0
Maintainer: Zongrui Dai <dzr17723980497@gmail.com>
Description: Provides the function to calculate the kernel-lasso expansion, Z-score, and max-min-scale standardization.It can increase the dimension of existed dataset and remove abundant features by lasso. Z Dai, L Jiayi, T Gong, C Wang (2021) <doi:10.1088/1742-6596/1955/1/012047>.
License: GPL-2
URL: https://github.com/Zongrui-Dai/Kernel-lasso-feature-expansion
Encoding: UTF-8
Depends: glmnet (>= 4.1-2)
Imports: graphics, stats
NeedsCompilation: no
Packaged: 2021-08-20 12:30:59 UTC; 10979
Author: Zongrui Dai [aut, cre] (<https://orcid.org/0000-0002-7893-5004>)
Repository: CRAN
Date/Publication: 2021-08-21 09:30:08 UTC

More information about KLexp at CRAN
Permanent link

Package ggh4x updated to version 0.2.0 with previous version 0.1.2.1 dated 2021-02-11

Title: Hacks for 'ggplot2'
Description: A 'ggplot2' extension that does a variety of little helpful things. The package extends 'ggplot2' facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. Also allows multiple colour and fill scales per plot. Also hosts a smaller collection of stats, geoms and axis guides.
Author: Teun van den Brand [aut, cre] (<https://orcid.org/0000-0002-9335-7468>)
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>

Diff between ggh4x versions 0.1.2.1 dated 2021-02-11 and 0.2.0 dated 2021-08-21

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Permanent link

New package galah with initial version 1.3.1
Package: galah
Title: Atlas of Living Australia (ALA) Data and Resources in R
Version: 1.3.1
Description: The Atlas of Living Australia ('ALA') provides tools to enable users of biodiversity information to find, access, combine and visualise data on Australian plants and animals; these have been made available from <https://ala.org.au/>. 'galah' provides a subset of the tools to be directly used within R. It enables the R community to directly access data and resources hosted by the 'ALA'.
Depends: R (>= 4.0.0)
Imports: assertthat, crul, data.table, data.tree, digest, httr, jsonlite (>= 0.9.8), sf, sp, stringr (>= 1.0.0), utils, wellknown
Suggests: vcr (>= 0.6.0), collapsibleTree, covr, dplyr, ggplot2, knitr, magrittr, pkgdown, rmarkdown, taxize, testthat, treemapify, viridis
License: MPL-2.0
URL: https://github.com/AtlasOfLivingAustralia/galah
BugReports: https://github.com/AtlasOfLivingAustralia/galah/issues
Maintainer: Martin Westgate <martin.westgate@csiro.au>
LazyLoad: yes
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-08-19 03:07:12 UTC; wes186
Author: Martin Westgate [aut, cre], Matilda Stevenson [aut], Dax Kellie [aut], Peggy Newman [aut]
Repository: CRAN
Date/Publication: 2021-08-21 09:20:02 UTC

More information about galah at CRAN
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New package convertid with initial version 0.1.1
Package: convertid
Title: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Version: 0.1.1
Date: 2021-08-20
Author: Vidal Fey [aut, cre], Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa.
Depends: AnnotationDbi
Imports: org.Hs.eg.db, org.Mm.eg.db, plyr, stringr, biomaRt, stats, xml2
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-08-20 10:35:35 UTC; fsvife
Repository: CRAN
Date/Publication: 2021-08-21 09:30:06 UTC

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New package conmet with initial version 0.1.0
Package: conmet
Title: Construct Measurement Evaluation Tool
Version: 0.1.0
Description: With this package you can run 'ConMET' locally in R. 'ConMET' is an R-shiny application that facilitates performing and evaluating confirmatory factor analyses (CFAs) and is useful for running and reporting typical measurement models in applied psychology and management journals. 'ConMET' automatically creates, compares and summarizes CFA models. Most common fit indices (E.g., CFI and SRMR) are put in an overview table. ConMET also allows to test for common method variance. The application is particularly useful for teaching and instruction of measurement issues in survey research. The application uses the 'lavaan' package (Rosseel, 2012) to run CFAs.
Depends: R (>= 3.5.0), shiny, shinydashboard
Imports: foreign, waiter, shinyWidgets, purrr, lavaan, summarytools, stringr, dplyr, Hmisc, semTools, openxlsx, DT
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-08-20 13:40:18 UTC; 68883lde
Author: Leander De Schutter [aut, cre] (<https://orcid.org/0000-0001-9826-4896>)
Maintainer: Leander De Schutter <deschutter@rsm.nl>
Repository: CRAN
Date/Publication: 2021-08-21 09:40:09 UTC

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New package coffee with initial version 0.1.1
Package: coffee
Title: Chronological Ordering for Fossils and Environmental Events
Version: 0.1.1
Date: 2021-08-20
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Description: While individual calibrated radiocarbon dates can span several centuries, combining multiple dates together with any chronological constraints can make a chronology much more robust and precise. This package uses Bayesian methods to enforce the chronological ordering of radiocarbon and other dates, for example for trees with multiple radiocarbon dates spaced at exactly known intervals (e.g., 10 annual rings). For methods see Christen 2003 <doi:10.11141/ia.13.2>. Another example is sites where the relative chronological position of the dates is taken into account - the ages of dates further down a site must be older than those of dates further up (Buck, Kenworthy, Litton and Smith 1991 <doi:10.1017/S0003598X00080534>; Nicholls and Jones 2001 <doi:10.1111/1467-9876.00250>).
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Language: en-GB
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, utf8
Depends: IntCal (>= 0.2.2)
Packaged: 2021-08-20 13:33:32 UTC; maarten
Author: Maarten Blaauw [aut, cre] (<https://orcid.org/0000-0002-5680-1515>), J. Andres Christen [ctb, cph] (<https://orcid.org/0000-0002-5795-4345>)
Repository: CRAN
Date/Publication: 2021-08-21 09:40:12 UTC

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Package english updated to version 1.2-6 with previous version 1.2-5 dated 2020-01-26

Title: Translate Integers into English
Description: Allow numbers to be presented in an English language version, one, two, three, ... Ordinals are also available, first, second, third, ... and indefinite article choice, "a" or "an".
Author: John Fox, Bill Venables, Anthony Damico and Anne Pier Salverda
Maintainer: Bill Venables <Bill.Venables@gmail.com>

Diff between english versions 1.2-5 dated 2020-01-26 and 1.2-6 dated 2021-08-21

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Package metavcov updated to version 2.1 with previous version 1.1 dated 2017-03-29

Title: Variance-Covariance Matrix for Multivariate Meta-Analysis
Description: Compute variance-covariance matrix for multivariate meta-analysis. Effect sizes include correlation (r), mean difference (MD), standardized mean difference (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference (RD).
Author: Min Lu <m.lu6@umiami.edu>
Maintainer: Min Lu <m.lu6@umiami.edu>

Diff between metavcov versions 1.1 dated 2017-03-29 and 2.1 dated 2021-08-21

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Package tablet updated to version 0.4.0 with previous version 0.3.2 dated 2021-07-18

Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics for factor and numeric columns in a data frame. Displays these by groups, if any. Highly customizable, with support for 'html' and 'pdf' provided by 'kableExtra'. Respects original column order, column labels, and factor level order. See ?tablet.data.frame and vignettes.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

Diff between tablet versions 0.3.2 dated 2021-07-18 and 0.4.0 dated 2021-08-21

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Package Sequential updated to version 3.3.3 with previous version 3.3.2 dated 2021-08-18

Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>

Diff between Sequential versions 3.3.2 dated 2021-08-18 and 3.3.3 dated 2021-08-21

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Package poismf updated to version 0.3.1-1 with previous version 0.3.1 dated 2021-07-13

Title: Factorization of Sparse Counts Matrices Through Poisson Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>). Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph], Jean-Sebastien Roy [cph] (Copyright holder of included tnc library), Stephen Nash [cph] (Copyright holder of included tnc library)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package PDFEstimator updated to version 3.0 with previous version 2.2 dated 2021-03-21

Title: Nonparametric Probability Density Estimator
Description: Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>

Diff between PDFEstimator versions 2.2 dated 2021-03-21 and 3.0 dated 2021-08-21

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Package LexFindR updated to version 1.0.1 with previous version 1.0.0 dated 2021-08-09

Title: Find Related Items and Lexical Dimensions in a Lexicon
Description: Implements code to identify lexical competitors in a given list of words. We include many of the standard competitor types used in spoken word recognition research, such as functions to find cohorts, neighbors, and rhymes, amongst many others. The package includes documentation for using a variety of lexicon files, including those with form codes made up of multiple letters (i.e., phoneme codes) and also basic orthographies. Importantly, the code makes use of multiple CPU cores and vectorization when possible, making it extremely fast and able to handle large lexicons. Additionally, the package contains documentation for users to easily write new functions, allowing researchers to examine other relationships within a lexicon. <https://psyarxiv.com/8dyru/>.
Author: ZhaoBin Li [aut, cre], Anne Marie Crinnion [aut], James S. Magnuson [aut, cph]
Maintainer: ZhaoBin Li <bzilplj@gmail.com>

Diff between LexFindR versions 1.0.0 dated 2021-08-09 and 1.0.1 dated 2021-08-21

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 LexFindR-1.0.1/LexFindR/DESCRIPTION                                                                         |   13 +----
 LexFindR-1.0.1/LexFindR/MD5                                                                                 |   14 ++---
 LexFindR-1.0.1/LexFindR/NEWS.md                                                                             |    4 +
 LexFindR-1.0.1/LexFindR/README.md                                                                           |    8 ---
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Package keras updated to version 2.6.0 with previous version 2.4.0 dated 2021-03-29

Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre], Daniel Falbel [ctb, cph], JJ Allaire [aut, cph], François Chollet [aut, cph], RStudio [ctb, cph, fnd], Google [ctb, cph, fnd], Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>), Wouter Van Der Bijl [ctb, cph], Martin Studer [ctb, cph], Sigrid Keydana [ctb]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>

Diff between keras versions 2.4.0 dated 2021-03-29 and 2.6.0 dated 2021-08-21

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More information about keras at CRAN
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Package echor updated to version 0.1.6 with previous version 0.1.5 dated 2020-08-05

Title: Access EPA 'ECHO' Data
Description: An R interface to United States Environmental Protection Agency (EPA) Environmental Compliance History Online ('ECHO') Application Program Interface (API). 'ECHO' provides information about EPA permitted facilities, discharges, and other reporting info associated with permitted entities. Data are obtained from <https://echo.epa.gov/>.
Author: Michael Schramm [aut, cre, cph]
Maintainer: Michael Schramm <michael.schramm@ag.tamu.edu>

Diff between echor versions 0.1.5 dated 2020-08-05 and 0.1.6 dated 2021-08-21

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 echor-0.1.6/echor/vignettes/int/0/cwa_rest_services.get_download-3c337b.csv               |only
 echor-0.1.6/echor/vignettes/int/0/cwa_rest_services.get_facility_info-29a83a.json         |21755 +++++-----
 echor-0.1.6/echor/vignettes/int/0/cwa_rest_services.get_facility_info-760dfb.json         |10043 ++--
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 echor-0.1.6/echor/vignettes/int/0/eff_rest_services.download_effluent_chart-1ca27d.csv    |  160 
 echor-0.1.6/echor/vignettes/int/0/eff_rest_services.download_effluent_chart-79e012.csv    | 1781 
 echor-0.1.6/echor/vignettes/int/0/eff_rest_services.download_effluent_chart-d48281.csv    | 3561 -
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 echor-0.1.6/echor/vignettes/int/0/rest_lookups.cwa_parameters-e1774c.json                 |   54 
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 94 files changed, 32377 insertions(+), 27037 deletions(-)

More information about echor at CRAN
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