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r-plde
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public |
We present a penalized log-density estimation method using Legendre polynomials with lasso penalty to adjust estimate's smoothness. Re-expressing the logarithm of the density estimator via a linear combination of Legendre polynomials, we can estimate parameters by maximizing the penalized log-likelihood function. Besides, we proposed an implementation strategy that builds on the coordinate decent algorithm, together with the Bayesian information criterion (BIC).
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2024-01-16 |
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r-plantecophys
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public |
Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
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2024-01-16 |
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r-plaqr
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public |
Estimation, prediction, thresholding, transformation, and plotting for partially linear additive quantile regression. Intuitive functions for fitting and plotting partially linear additive quantile regression models. Uses and works with functions from the 'quantreg' package.
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2024-01-16 |
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r-pks
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public |
Fitting and testing probabilistic knowledge structures, especially the basic local independence model (BLIM, Doignon & Flamagne, 1999) and the simple learning model (SLM), using the minimum discrepancy maximum likelihood (MDML) method (Heller & Wickelmaier, 2013 <doi:10.1016/j.endm.2013.05.145>).
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2024-01-16 |
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r-pkgsearch
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public |
Search CRAN metadata about packages by keyword, popularity, recent activity, package name and more. Uses the 'R-hub' search server, see <https://r-pkg.org> and the CRAN metadata database, that contains information about CRAN packages. Note that this is _not_ a CRAN project.
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2024-01-16 |
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r-planets
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public |
The goal of 'planets' is to provide of very simple and accessible data containing basic information from all known planets.
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2024-01-16 |
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r-planesmuestra
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public |
Calculates an acceptance sampling plan, (sample size and acceptance number) based in MIL STD 105E, Dodge Romig and MIL STD 414 tables and procedures. The arguments for each function are related to lot size, inspection level and quality level. The specific plan operating curve (OC), is calculated by the binomial distribution.
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2024-01-16 |
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r-plan
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public |
Supports the creation of 'burndown' charts and 'gantt' diagrams.
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2024-01-16 |
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r-pksea
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public |
A tool for inferring kinase activity changes from phosphoproteomics data. 'pKSEA' uses kinase-substrate prediction scores to weight observed changes in phosphopeptide abundance to calculate a phosphopeptide-level contribution score, then sums up these contribution scores by kinase to obtain a phosphoproteome-level kinase activity change score (KAC score). 'pKSEA' then assesses the significance of changes in predicted substrate abundances for each kinase using permutation testing. This results in a permutation score (pKSEA significance score) reflecting the likelihood of a similarly high or low KAC from random chance, which can then be interpreted in an analogous manner to an empirically calculated p-value. 'pKSEA' contains default databases of kinase-substrate predictions from 'NetworKIN' (NetworKINPred_db) <http://networkin.info> Horn, et. al (2014) <doi:10.1038/nmeth.2968> and of known kinase-substrate links from 'PhosphoSitePlus' (KSEAdb) <https://www.phosphosite.org/> Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.
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2024-01-16 |
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r-pknca
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public |
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
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2024-01-16 |
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r-pkgnet
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public |
Tools from the domain of graph theory can be used to quantify the complexity and vulnerability to failure of a software package. That is the guiding philosophy of this package. 'pkgnet' provides tools to analyze the dependencies between functions in an R package and between its imported packages. See the pkgnet website for vignettes and other supplementary information.
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2024-01-16 |
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r-pkmon
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We implement two least-squares estimators under k-monotony constraint using a method based on the Support Reduction Algorithm from Groeneboom et al (2008) <DOI:10.1111/j.1467-9469.2007.00588.x>. The first one is a projection estimator on the set of k-monotone discrete functions. The second one is a projection on the set of k-monotone discrete probabilities. This package provides functions to generate samples from the spline basis from Lefevre and Loisel (2013) <DOI:10.1239/jap/1378401239>, and from mixtures of splines.
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2024-01-16 |
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r-pkgmaker
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None |
Provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like 'NMF', 'RcppOctave', 'doRNG', and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.
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2024-01-16 |
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r-pkgkitten
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public |
Provides a function kitten() which creates cute little packages which pass R package checks. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative. Unit test support can be added via the 'tinytest' package (if present), and documentation-creation support can be added via 'roxygen2' (if present).
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2024-01-16 |
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r-pkgdown
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public |
Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
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2024-01-16 |
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r-pkgfilecache
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public |
Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).
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2024-01-16 |
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r-pkgdepends
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public |
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain a consistent set of packages to install. Download packages, and install them. It supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local package trees and files. It caches metadata and package files via the 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and installations in parallel. 'pkgdepends' is the workhorse of the 'pak' package.
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2024-01-16 |
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r-pkgconfig
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public |
Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.
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2024-01-16 |
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r-pivottabler
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public |
Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
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2024-01-16 |
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r-pkgcond
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public |
This provides utilities for creating classed error and warning conditions based on where the error originated.
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2024-01-16 |
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r-pixiedust
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public |
The introduction of the 'broom' package has made converting model objects into data frames as simple as a single function. While the 'broom' package focuses on providing tidy data frames that can be used in advanced analysis, it deliberately stops short of providing functionality for reporting models in publication-ready tables. 'pixiedust' provides this functionality with a programming interface intended to be similar to 'ggplot2's system of layers with fine tuned control over each cell of the table. Options for output include printing to the console and to the common markdown formats (markdown, HTML, and LaTeX). With a little 'pixiedust' (and happy thoughts) tables can really fly.
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2024-01-16 |
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r-pkgbuild
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public |
Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.
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2024-01-16 |
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r-pkconverter
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public |
Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion. The pharmacokinetics model explains that how the drug concentration change as the drug moves through the different compartments of the body. For pharmacokinetic modeling and analysis, it is essential to understand the basic pharmacokinetic parameters. All parameters are considered, but only some of parameters are used in the model. Therefore, we need to convert the estimated parameters to the other parameters after fitting the specific pharmacokinetic model. This package is developed to help this converting work. For more detailed explanation of pharmacokinetic parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001"; "Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>; "Mould and Upton" (2012) <DOI: 10.1038/psp.2012.4>; "Mould and Upton" (2013) <DOI: 10.1038/psp.2013.14>.
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2024-01-16 |
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r-pk
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public |
Estimation of pharmacokinetic parameters using non-compartmental theory.
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2024-01-16 |
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r-phytools
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public |
A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.
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2024-01-16 |
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r-pixmap
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public |
Functions for import, export, plotting and other manipulations of bitmapped images.
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2024-01-16 |
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r-piecewisesem
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public |
Implements piecewise structural equation modeling from a single list of structural equations, with new methods for non-linear, latent, and composite variables, standardized coefficients, query-based prediction and indirect effects. See <http://jslefche.github.io/piecewiseSEM/> for more.
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2024-01-16 |
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r-pixels
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public |
Provides tools to show and draw image pixels using 'HTML' widgets and 'Shiny' applications. It can be used to visualize the 'MNIST' dataset for handwritten digit recognition or to create new image recognition datasets.
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2024-01-16 |
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r-pivotaltrackr
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public |
'Pivotal Tracker' <https://www.pivotaltracker.com> is a project management software-as-a-service that provides a REST API. This package provides an R interface to that API, allowing you to query it and work with its responses.
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2024-01-16 |
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r-piper
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public |
Provides various styles of function chaining methods: Pipe operator, Pipe object, and pipeline function, each representing a distinct pipeline model yet sharing almost a common set of features: A value can be piped to the first unnamed argument of a function and to dot symbol in an enclosed expression. The syntax is designed to make the pipeline more readable and friendly to a wide range of operations.
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2024-01-16 |
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r-pipeliner
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public |
A framework for defining 'pipelines' of functions for applying data transformations, model estimation and inverse-transformations, resulting in predicted value generation (or model-scoring) functions that automatically apply the entire pipeline of functions required to go from input to predicted output.
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2024-01-16 |
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r-pipegs
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public |
Code for various permutation p-values estimation methods for gene set test. The description of corresponding methods can be found in the dissertation of Yu He(2016) "Efficient permutation P-value estimation for gene set tests" <https://searchworks.stanford.edu/view/11849351>. One of the methods also corresponds to the paper "Permutation p-value approximation via generalized Stolarsky invariance" <arXiv:1603.02757>.
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2024-01-16 |
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r-pipefittr
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public |
To take nested function calls and convert them to a more readable form using pipes from package 'magrittr'.
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2024-01-16 |
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r-pins
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public |
Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'RStudio' connect, Amazon S3, and more.
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2024-01-16 |
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r-pinp
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public |
A 'PNAS'-alike style for 'rmarkdown', derived from the 'Proceedings of the National Academy of Sciences of the United States of America' ('PNAS', see <https://www.pnas.org>) 'LaTeX' style, and adapted for use with 'markdown' and 'pandoc'.
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2024-01-16 |
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r-pinochet
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public |
Packages data about the victims of the Pinochet regime as compiled by the Chilean National Commission for Truth and Reconciliation Report (1991, ISBN:9780268016463).
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2024-01-16 |
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r-pinfsc50
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public |
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
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2024-01-16 |
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r-pillar
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public |
Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.
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2024-01-16 |
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r-piggyback
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public |
Because larger (> 50 MB) data files cannot easily be committed to git, a different approach is required to manage data associated with an analysis in a GitHub repository. This package provides a simple work-around by allowing larger (up to 2 GB) data files to piggyback on a repository as assets attached to individual GitHub releases. These files are not handled by git in any way, but instead are uploaded, downloaded, or edited directly by calls through the GitHub API. These data files can be versioned manually by creating different releases. This approach works equally well with public or private repositories. Data can be uploaded and downloaded programmatically from scripts. No authentication is required to download data from public repositories.
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2024-01-16 |
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r-physicalactivity
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public |
It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.
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2024-01-16 |
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r-phyreg
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public |
Provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and categorical and arbitrary interactions) for cross-species data. The method is, however, based on the nowadays rather uncommon situation in which uncertainty about a phylogeny is well represented by adopting a single polytomous tree. The theory is in A. Grafen (1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recognised phylogeny (closely related species tend to be similar) and unrecognised phylogeny (a polytomy usually indicates ignorance about the true sequence of binary splits).
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2024-01-16 |
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r-physactbedrest
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public |
Contains a function to categorize accelerometer readings collected in free-living (e.g., for 24 hours/day for 7 days), preprocessed and compressed as counts (unit-less value) in a specified time period termed epoch (e.g., 1 minute) as either bedrest (sleep) or active. The input is a matrix with a timestamp column and a column with number of counts per epoch. The output is the same dataframe with an additional column termed bedrest. In the bedrest column each line (epoch) contains a function-generated classification 'br' or 'a' denoting bedrest/sleep and activity, respectively. The package is designed to be used after wear/nonwear marking function in the 'PhysicalActivity' package. Version 1.1 adds preschool thresholds and corrects for possible errors in algorithm implementation.
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2024-01-16 |
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r-phosphoricons
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public |
Use 'Phosphor' icons in 'shiny' applications or 'rmarkdown' documents. Icons are available in 5 different weights and can be customized by setting color, size, orientation and more.
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2024-01-16 |
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r-phylotools
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public |
A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
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2024-01-16 |
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r-phylotate
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public |
Functions to read and write APE-compatible phylogenetic trees in NEXUS and Newick formats, while preserving annotations.
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2024-01-16 |
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r-phylometrics
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public |
Provides functions to estimate statistical errors of phylogenetic metrics particularly to detect binary trait influence on diversification, as well as a function to simulate trees with fixed number of sampled taxa and trait prevalence.
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2024-01-16 |
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r-phylogram
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public |
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
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2024-01-16 |
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r-phylogr
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public |
Manipulation and analysis of phylogenetically simulated data sets and phylogenetically based analyses using GLS.
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2024-01-16 |
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r-phyloclim
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public |
Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.
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2024-01-16 |
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r-phia
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public |
Analysis of terms in linear, generalized and mixed linear models, on the basis of multiple comparisons of factor contrasts. Specially suited for the analysis of interaction terms.
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2024-01-16 |
