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r-sae
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public |
Functions for small area estimation.
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2025-03-25 |
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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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2025-03-25 |
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r-sacobra
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public |
Performs surrogate-assisted optimization for expensive black-box constrained problems.
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2025-03-25 |
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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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2025-03-25 |
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r-sabarsi
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public |
Implements a new approach 'SABARSI' described in Wang et al., "A Statistical Approach of Background Removal and Spectrum Identification for SERS Data" (Unpublished). Sabarsi forms a pipeline for SERS (surface-enhanced Raman scattering) data analysis including background removal, signal detection, signal integration, and cross-experiment comparison. The background removal algorithm, the very first step of SERS data analysis, takes into account the change of background shape.
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2025-03-25 |
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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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2025-03-25 |
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r-rzeit2
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public |
Interface to gather newspaper articles from 'DIE ZEIT' and 'ZEIT ONLINE', based on a multilevel query <http://developer.zeit.de/>. A personal API key is required for usage.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-ryoudaotranslate
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public |
You can use this package to translate thousands of words. The Youdao translation open API is applied in this package. But, it just translates less than 1000 English words into Chinese.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-rxnat
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public |
Allows communication with Extensible Neuroimaging Archive Toolkit <https://www.xnat.org>. 'Rxnat' is using the 'XNAT' REST API to perform data queries and download images.
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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r-rwinsteps
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public |
Facilitates communication between R and the Rasch modeling software Winsteps. Currently includes functions for reading and writing command files, sending them to Winsteps, reading and writing data according to command file specifications, reading output into R, and plotting various results.
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2025-03-25 |
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r-rwhois
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public |
Queries data from WHOIS servers.
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2025-03-25 |
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r-rwekajars
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public |
External jars required for package 'RWeka'.
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2025-03-25 |
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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 |
Provides 'Java' graphical user interfaces for viewing, manipulating and plotting graphs. Graphs may be directed or undirected.
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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-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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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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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' 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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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 Hadamard 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 |
