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r-saltsampler
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public |
The SALTSampler package facilitates Monte Carlo Markov Chain (MCMC) sampling of random variables on a simplex. A Self-Adjusting Logit Transform (SALT) proposal is used so that sampling is still efficient even in difficult cases, such as those in high dimensions or with parameters that differ by orders of magnitude. Special care is also taken to maintain accuracy even when some coordinates approach 0 or 1 numerically. Diagnostic and graphic functions are included in the package, enabling easy assessment of the convergence and mixing of the chain within the constrained space.
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2024-01-16 |
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r-saic
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public |
Computes the Akaike information criterion for the generalized linear models (logistic regression, Poisson regression, and Gaussian graphical models) estimated by the lasso.
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2024-01-16 |
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r-saemix
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public |
The 'saemix' package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm (i) computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, (ii) provides standard errors for the maximum likelihood estimator (iii) estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm (see Comets et al. (2017) <doi:10.18637/jss.v080.i03>). Many applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. The full PDF documentation for the package including references about the algorithm and examples can be downloaded on the github of the IAME research institute for 'saemix': <https://github.com/iame-researchCenter/saemix/blob/7638e1b09ccb01cdff173068e01c266e906f76eb/docsaem.pdf>.
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2024-01-16 |
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r-safd
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public |
The aim of the package is to provide some basic functions for doing statistics with one dimensional Fuzzy Data (in the form of polygonal fuzzy numbers). In particular, the package contains functions for the basic operations on the class of fuzzy numbers (sum, scalar product, mean, median, Hukuhara difference) as well as for calculating (Bertoluzza) distance and sample variance. Moreover a function to simulate fuzzy random variables and bootstrap tests for the equality of means is included. Version 2.1 fixes some bugs of previous versions.
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2024-01-16 |
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r-rworldmap
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public |
Enables mapping of country level and gridded user datasets.
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2024-01-16 |
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r-sae
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public |
Functions for small area estimation.
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2024-01-16 |
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r-sadeg
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public |
We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequences. Besides, in a variety of different organisms unequal use of synonymous codons, or codon usage bias, occurs which also show variation among genes in the same genome. Seemingly, codon usage bias is affected by both selective constraints and mutation bias which allows and enables us to examine and detect changes in these two evolutionary forces between genomes or along one genome. Therefore, we determined the codon adaptation index (CAI), effective number of codons (ENC) and codon usage analysis with calculation of the relative synonymous codon usage (RSCU), and subsequently predicted the translation efficiency and accuracy through GC-rich codon usages. Furthermore, we estimated the relative stability of the DNA sequence following calculation of the average free energy (Delta G) and Dimer base-stacking energy level.
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2024-01-16 |
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r-sac
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public |
Semiparametric empirical likelihood ratio based tests of change-point with one-change or epidemic alternatives with data-based model diagnostic are contained.
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2024-01-16 |
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r-rweka
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public |
An R interface to Weka (Version 3.9.3). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package 'RWeka' contains the interface code, the Weka jar is in a separate package 'RWekajars'. For more information on Weka see <https://www.cs.waikato.ac.nz/ml/weka/>.
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2024-01-16 |
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r-s20x
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public |
A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
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2024-01-16 |
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r-rzabbix
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public |
R interface to the 'Zabbix API' data <https://www.zabbix.com/documentation/3.0/manual/api/reference>. Enables easy and direct communication with 'Zabbix API' from 'R'.
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2024-01-16 |
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r-ryoutheria
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public |
A programmatic interface to web-services of YouTheria. YouTheria is an online database of mammalian trait data <http://www.utheria.org/>.
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2024-01-16 |
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r-rym
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public |
Allows work with 'Management API' for load counters, segments, filters, user permissions and goals list from Yandex Metrica, 'Reporting API' allows you to get information about the statistics of site visits and other data without using the web interface, 'Logs API' allows to receive non-aggregated data and 'Compatible with Google Analytics Core Reporting API v3' allows receive information about site traffic and other data using field names from Google Analytics Core API. For more information see official documents <https://yandex.ru/dev/metrika/doc/api2/concept/about-docpage>.
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2024-01-16 |
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r-ryandextranslate
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public |
'Yandex Translate' (https://translate.yandex.com/) is a statistical machine translation system. The system translates separate words, complete texts, and webpages. This package can be used to detect language from text and to translate it to supported target language. For more info: https://tech.yandex.com/translate/doc/dg/concepts/About-docpage/ .
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2024-01-16 |
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r-rxshrink
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public |
Functions are provided to calculate and display ridge TRACE Diagnostics for a variety of alternative Shrinkage Paths. While all methods focus on Maximum Likelihood estimation of unknown true effects under normal distribution-theory, some estimates are modified to be Unbiased or to have "Correct Range" when estimating either [1] the noncentrality of the F-ratio for testing that true Beta coefficients are Zeros or [2] the "relative" MSE Risk (i.e. MSE divided by true sigma-square, where the "relative" variance of OLS is known.) The eff.ridge() function implements the "Efficient Shrinkage Path" introduced in Obenchain (2022) <Open Statistics>. This "p-Parameter" Shrinkage-Path always passes through the vector of regression coefficient estimates Most-Likely to achieve the overall Optimal Variance-Bias Trade-Off and is the shortest Path with this property. Functions eff.aug() and eff.biv() augment the calculations made by eff.ridge() to provide plots of the bivariate confidence ellipses corresponding to any of the p*(p-1) possible ordered pairs of shrunken regression coefficients. Functions for plotting TRACE Diagnostics now have more options.
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2024-01-16 |
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r-rwa
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public |
Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes the total variance predicted in a regression model into weights that accurately reflect the proportional contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios, RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
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2024-01-16 |
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r-rxseq
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public |
Analysis of combined total and allele specific reads from the reciprocal cross study with RNA-seq data.
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2024-01-16 |
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r-rxkcd
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public |
Visualize your favorite XKCD comic strip directly from R. XKCD <https://xkcd.com> web comic content is provided under the Creative Commons Attribution-NonCommercial 2.5 License.
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2024-01-16 |
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r-rworldxtra
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public |
High resolution vector country boundaries derived from Natural Earth data, can be plotted in rworldmap.
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2024-01-16 |
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r-rvertnet
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public |
Retrieve, map and summarize data from the 'VertNet.org' archives (<http://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
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2024-01-16 |
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r-rwishart
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public |
An expansion of R's 'stats' random wishart matrix generation. This package allows the user to generate singular, Uhlig and Harald (1994) <doi:10.1214/aos/1176325375>, and pseudo wishart, Diaz-Garcia, et al.(1997) <doi:10.1006/jmva.1997.1689>, matrices. In addition the user can generate wishart matrices with fractional degrees of freedom, Adhikari (2008) <doi:10.1061/(ASCE)0733-9399(2008)134:12(1029)>, commonly used in volatility modeling. Users can also use this package to create random covariance matrices.
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2024-01-16 |
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r-rwhois
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public |
Queries data from WHOIS servers.
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2024-01-16 |
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r-rwekajars
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public |
External jars required for package 'RWeka'.
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2024-01-16 |
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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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2024-01-16 |
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r-runonce
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public |
Package 'runonce' helps automating the saving of long-running code to help running the same code multiple times. If you run some long-running code once, it saves the result in a file on disk. Then, if the result already exists, i.e. if the code has already been run and its output has already been saved, it just reads the result from the stored file instead of running the code again.
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2024-01-16 |
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r-rvenn
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public |
Set operations for many sets. The base functions for set operations in R can be used for only two sets. This package uses 'purr' to find the union, intersection and difference of three or more sets. This package also provides functions for pairwise set operations among several sets. Further, based on 'ggplot2' and 'ggforce', a Venn diagram can be drawn for two or three sets. For bigger data sets, a clustered heatmap showing presence/absence of the elements of the sets can be drawn based on the 'pheatmap' package. Finally, enrichment test can be applied to two sets whether an overlap is statistically significant or not.
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2024-01-16 |
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r-rviewgraph
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public |
Provides 'Java' graphical user interfaces for viewing, manipulating and plotting graphs. Graphs may be directed or undirected.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-rvest
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public |
Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.
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2024-01-16 |
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r-rversions
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None |
Query the main 'R' 'SVN' repository to find the versions 'r-release' and 'r-oldrel' refer to, and also all previous 'R' versions and their release dates.
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2024-01-16 |
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r-rucm
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public |
Unobserved Components Models (introduced in Harvey, A. (1989), Forecasting, structural time series models and the Kalman filter, Cambridge New York: Cambridge University Press) decomposes a time series into components such as trend, seasonal, cycle, and the regression effects due to predictor series which captures the salient features of the series to predict its behavior.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-rules
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public |
Bindings for additional models for use with the 'parsnip' package. Models include prediction rule ensembles (Friedman and Popescu, 2008) <doi:10.1214/07-AOAS148>, C5.0 rules (Quinlan, 1992 ISBN: 1558602380), and Cubist (Kuhn and Johnson, 2013) <doi:10.1007/978-1-4614-6849-3>.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-rtweet
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public |
An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
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2024-01-16 |
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r-rtoot
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public |
An implementation of calls designed to collect and organize Mastodon data via its Application Program Interfaces (API), which can be found at the following URL: <https://docs.joinmastodon.org/>.
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2024-01-16 |
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r-rtables
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public |
Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
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r-rtson
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public |
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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2024-01-16 |
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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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2024-01-16 |
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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' Python packages 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 in performing calculations in CPUs as well as 'GPUs' to accelerate tensor operations.
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2024-01-16 |
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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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2024-01-16 |
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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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2024-01-16 |
