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r-rweblogo
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public |
RWebLogo is a wrapper for the WebLogo python package that allows generating of customised sequence logos. Sequence logos are graphical representations of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
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2025-03-25 |
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r-rwc
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public |
Code to facilitate simulation and inference when connectivity is defined by underlying random walks. Methods for spatially-correlated pairwise distance data are especially considered. This provides core code to conduct analyses similar to that in Hanks and Hooten (2013) <doi:10.1080/01621459.2012.724647>.
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2025-03-25 |
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r-rwars
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public |
Provides functions to retrieve and reformat data from the 'Star Wars' API (SWAPI) <https://swapi.co/>.
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2025-03-25 |
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r-rvtdt
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public |
Used to compute population controls weighted rare variants transmission distortion test
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2025-03-25 |
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r-rviewgraph
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public |
This is an 'R' interface to Alun Thomas's 'ViewGraph' 'Java' graph viewing program. It takes a graph specified as an incidence matrix, list of edges, or in 'igraph' format and runs a graphical user interface that shows an animation of a force directed algorithm positioning the vertices in two dimensions. It works well for graphs of various structure of up to a few thousand vertices. It's not fazed by graphs that comprise several components. The coordinates can be read as an 'igraph' style layout matrix at any time. The user can mess with the layout using a mouse, preferably one with 3 buttons, and some keyed commands. The 'Java' program 'ViewGraph' is contained in Alun Thomas's 'JPSGCS' collection of 'Java' programs for statistical genetics and computational statistics. The homepage for 'JPSGCS' is <http://www-genepi.med.utah.edu/~alun/software/index.html>. The documentation page for 'ViewGraph' is at <http://www-genepi.med.utah.edu/~alun/software/docs/ViewGraph.html>.
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2025-03-25 |
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r-rviennacl
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public |
'ViennaCL' is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports 'CUDA', 'OpenCL', and 'OpenMP' (including switches at runtime). I have placed these libraries in this package as a more efficient distribution system for CRAN. The idea is that you can write a package that depends on the 'ViennaCL' library and yet you do not need to distribute a copy of this code with your package.
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2025-03-25 |
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r-rvhpdt
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public |
To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.
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2025-03-25 |
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r-rvcheck
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public |
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
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2025-03-25 |
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r-rv
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public |
Implements a simulation-based random variable class and a suite of methods for extracting parts of random vectors, calculating extremes of random vectors, and generating random vectors under a variety of distributions following Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>.
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2025-03-25 |
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r-ruta
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public |
Implementation of several unsupervised neural networks, from building their architecture to their training and evaluation. Available networks are auto-encoders including their main variants: sparse, contractive, denoising, robust and variational, as described in Charte et al. (2018) <doi:10.1016/j.inffus.2017.12.007>.
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2025-03-25 |
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r-runstats
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public |
Provides methods for fast computation of running sample statistics for time series. These include: (1) mean, (2) standard deviation, and (3) variance over a fixed-length window of time-series, (4) correlation, (5) covariance, and (6) Euclidean distance (L2 norm) between short-time pattern and time-series. Implemented methods utilize Convolution Theorem to compute convolutions via Fast Fourier Transform (FFT).
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2025-03-25 |
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r-runiversal
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public |
This package contains some functions for converting R objects to Java style variables and XML. Generated Java code is interpretable by dynamic Java libraries such as Beanshell. Calling R externally and handling the Java or XML output is an other way to call R from other languages without native interfaces. For a Java implementation of this approach visit http://www.mhsatman.com/rcaller.php and http://stdioe.blogspot.com/search/label/rcaller
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2025-03-25 |
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r-runit
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public |
R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools.
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2025-03-25 |
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r-rtype
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public |
A strong type system for R which supports symbol declaration and assignment with type checking and condition checking.
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2025-03-25 |
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r-rtwalk
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public |
The 't-walk' is a general-purpose MCMC sampler for arbitrary continuous distributions that requires no tuning.
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2025-03-25 |
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r-rt.test
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public |
Performs one-sample t-test based on robustified statistics using median/MAD (TA) and Hodges-Lehmann/Shamos (TB). For more details, see Park and Wang (2018)<arXiv:1807.02215>. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
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2025-03-25 |
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r-rtsplot
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public |
A fast and elegant time series visualization package. In addition to the standard R plot types, this package supports candle sticks, open-high-low-close, and volume plots. Useful for visualizing any time series data, e.g., stock prices and technical indicators.
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2025-03-25 |
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r-rtson
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TSON, short for Typed JSON, is a binary-encoded serialization of JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
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2025-03-25 |
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r-rts
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public |
This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
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2025-03-25 |
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r-rtrim
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public |
The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.
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2025-03-25 |
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r-rtorch
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public |
'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible to perform calculations in CPUs as well as 'GPUs' to accelerate the process.
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2025-03-25 |
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r-rtnmin
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public |
Truncated Newton function minimization with bounds constraints based on the 'Matlab'/'Octave' codes of Stephen Nash.
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2025-03-25 |
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r-rtika
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public |
Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
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2025-03-25 |
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r-rticles
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public |
A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
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2025-03-25 |
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r-rtf
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public |
A set of R functions to output Rich Text Format (RTF) files with high resolution tables and graphics that may be edited with a standard word processor such as Microsoft Word.
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2025-03-25 |
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r-rtexturemetrics
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public |
This package contains several functions for calculation of texture metrics for Grey Level Co-occurrence matrices
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2025-03-25 |
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r-rtephra
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public |
Models and displays tephra transport through custom (windy, turbulent, heterogeneous) atmosphere over custom topography. Includes a Lagrangian (particle-tracking) tephra transport model and a function to save snapshots of model as png files.
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2025-03-25 |
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r-rtensor
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public |
A set of tools for creation, manipulation, and modeling of tensors with arbitrary number of modes. A tensor in the context of data analysis is a multidimensional array. rTensor does this by providing a S4 class 'Tensor' that wraps around the base 'array' class. rTensor provides common tensor operations as methods, including matrix unfolding, summing/averaging across modes, calculating the Frobenius norm, and taking the inner product between two tensors. Familiar array operations are overloaded, such as index subsetting via '[' and element-wise operations. rTensor also implements various tensor decomposition, including CP, GLRAM, MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some auxiliary functions include the Khatri-Rao product, Kronecker product, and the Hamadard product for a list of matrices.
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2025-03-25 |
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r-rtematres
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public |
Exploit controlled vocabularies organized on tematres servers.
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2025-03-25 |
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r-rtde
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public |
Robust tail dependence estimation for bivariate models. This package is based on two papers by the authors:'Robust and bias-corrected estimation of the coefficient of tail dependence' and 'Robust and bias-corrected estimation of probabilities of extreme failure sets'. This work was supported by a research grant (VKR023480) from VILLUM FONDEN and an international project for scientific cooperation (PICS-6416).
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2025-03-25 |
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r-rtconnect
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public |
Tools for analyzing sales report files of iTunes Connect.
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2025-03-25 |
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r-rtaxometrics
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public |
We provide functions to perform taxometric analyses. This package contains 44 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.
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2025-03-25 |
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r-rtauchen
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public |
Discretize AR(1) process following Tauchen (1986) <http://www.sciencedirect.com/science/article/pii/0165176586901680>. A discrete Markov chain that approximates in the sense of weak convergence a continuous-valued univariate Autoregressive process of first order is generated. It is a popular method used in economics and in finance.
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2025-03-25 |
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r-rtape
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public |
Storing huge data in RData format causes problems because of the necessity to load the whole file to the memory in order to access and manipulate objects inside such file; rtape is a simple solution to this problem. The package contains several wrappers of R built-in serialize/unserialize mechanism allowing user to quickly append objects to a tape-like file and later iterate over them requiring only one copy of each stored object to reside in memory a time.
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2025-03-25 |
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r-rt3
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public |
Play the classic game of tic-tac-toe (naughts and crosses).
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2025-03-25 |
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r-rsvd
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public |
Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence of large-scale data has severely challenged our computational ability to analyze big data. The concept of randomness has been demonstrated as an effective strategy to quickly produce approximate answers to familiar problems such as the singular value decomposition (SVD). The rsvd package provides several randomized matrix algorithms such as the randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided. The methods are discussed in detail by Erichson et al. (2016) <arXiv:1608.02148>.
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2025-03-25 |
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r-rsurrogate
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public |
Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
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2025-03-25 |
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r-rsurfer
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public |
The software suite, 'Freesurfer', is a open-source software suite involving the segmentation of brain MRIs (see <http://freesurfer.net/> for more information). This package provides functionality to import the data generated by 'Freesurfer'; functions to easily manipulate the data; and provides brain specific normalisation commonly used when studying structural brain MRIs. This package has been designed using an installation of and data generated from 'Freesurfer' version 5.3.
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2025-03-25 |
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r-rsubgroup
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public |
A collection of efficient and effective tools and algorithms for subgroup discovery and analytics. The package integrates an R interface to the org.vikamine.kernel library of the VIKAMINE system (http://www.vikamine.org) implementing subgroup discovery, pattern mining and analytics in Java.
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2025-03-25 |
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r-rstripe
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public |
A convenience interface for communicating with the Stripe payment processor to accept payments online. See <https://stripe.com> for more information.
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2025-03-25 |
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r-rstorm
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public |
While streaming processing provides opportunities to deal with extremely large and ever growing data sets in (near) real time, the development of streaming algorithms for complex models is often cumbersome: the software packages that facilitate streaming processing in production environments do not provide statisticians with the simulation, estimation, and plotting tools they are used to. Developers of streaming algorithms would thus benefit from the flexibility of [R] to create, plot and compute data while developing streaming algorithms. Package RStorm implements a streaming architecture modeled on Storm for easy development and testing of streaming algorithms in [R]. RStorm is not intended as a production package, but rather a development tool for streaming algorithms.
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2025-03-25 |
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r-rstatscn
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public |
R interface for china national data <http://data.stats.gov.cn/>, some convenient functions for accessing the national data are provided.
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2025-03-25 |
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r-rstata
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public |
A simple R -> Stata interface allowing the user to execute Stata commands (both inline and from a .do file) from R.
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2025-03-25 |
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r-rstantools
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public |
Provides various tools for developers of R packages interfacing with 'Stan' <http://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and vignettes with recommendations for developers.
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2025-03-25 |
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r-rstackdeque
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public |
Provides fast, persistent (side-effect-free) stack, queue and deque (double-ended-queue) data structures. While deques include a superset of functionality provided by queues, in these implementations queues are more efficient in some specialized situations. See the documentation for rstack, rdeque, and rpqueue for details.
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2025-03-25 |
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r-rstack
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public |
An extremely simple stack data type, implemented with 'R6' classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.
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2025-03-25 |
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r-rssop
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public |
Reservoir Systems Standard Operation Policy. A system for simulation of supply reservoirs. It proposes functionalities for plotting and evaluation of supply reservoirs systems.
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2025-03-25 |
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r-rsq
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public |
Calculate generalized R-squared, partial R-squared, and partial correlation coefficients for generalized linear models (including quasi models with well defined variance functions).
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2025-03-25 |
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r-rsps
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public |
Provides functions for estimating power or sample size for RNA-Seq studies. Empirical approach is used and the data is assumed to be count in nature. The underlying distribution of data is assumed to be Poisson or negative binomial. The package contains 6 function; 4 functions provide estimates of sample size or power for Poisson and Negative Binomial distribution; 2 functions provide plots of power for given sample size or sample size for given power.
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2025-03-25 |
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r-rspincalc
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public |
Conversion between attitude representations: DCM, Euler angles, Quaternions, and Euler vectors. Plus conversion between 2 Euler angle set types (xyx, yzy, zxz, xzx, yxy, zyz, xyz, yzx, zxy, xzy, yxz, zyx). Fully vectorized code, with warnings/errors for Euler angles (singularity, out of range, invalid angle order), DCM (orthogonality, not proper, exceeded tolerance to unity determinant) and Euler vectors(not unity). Also quaternion and other useful functions. Based on SpinCalc by John Fuller and SpinConv by Paolo de Leva.
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2025-03-25 |
