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r-sp23design
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public |
Provides methods for generating, exploring and executing seamless Phase II-III designs of Lai, Lavori and Shih using generalized likelihood ratio statistics. Includes pdf and source files that describe the entire R implementation with the relevant mathematical details.
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2024-01-16 |
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r-sortable
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public |
Enables drag-and-drop behaviour in Shiny apps, by exposing the functionality of the 'SortableJS' <https://sortablejs.github.io/Sortable/> JavaScript library as an 'htmlwidget'. You can use this in Shiny apps and widgets, 'learnr' tutorials as well as R Markdown. In addition, provides a custom 'learnr' question type - 'question_rank()' - that allows ranking questions with drag-and-drop.
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2024-01-16 |
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r-solitude
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public |
Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
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2024-01-16 |
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r-sotu
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public |
The President of the United States is constitutionally obligated to provide a report known as the 'State of the Union'. The report summarizes the current challenges facing the country and the president's upcoming legislative agenda. While historically the State of the Union was often a written document, in recent decades it has always taken the form of an oral address to a joint session of the United States Congress. This package provides the raw text from every such address with the intention of being used for meaningful examples of text analysis in R. The corpus is well suited to the task as it is historically important, includes material intended to be read and material intended to be spoken, and it falls in the public domain. As the corpus spans over two centuries it is also a good test of how well various methods hold up to the idiosyncrasies of historical texts. Associated data about each address, such as the year, president, party, and format, are also included.
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2024-01-16 |
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r-sound
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public |
Basic functions for dealing with wav files and sound samples.
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2024-01-16 |
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r-sotkanet
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public |
Access statistical information on welfare and health in Finland from the Sotkanet open data portal <https://sotkanet.fi/sotkanet/fi/index>.
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2024-01-16 |
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r-sos
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public |
Search contributed R packages, sort by package.
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2024-01-16 |
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r-sorptionanalysis
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public |
Provides tools to efficiently analyze and visualize laboratory data from aqueous static adsorption experiments. The package provides functions to plot Langmuir, Freundlich, and Temkin isotherms and functions to determine the statistical conformity of data points to the Langmuir, Freundlich, and Temkin adsorption models through statistical characterization of the isothermic least squares regressions lines. Scientific Reference: Dada, A.O, Olalekan, A., Olatunya, A. (2012) <doi:10.9790/5736-0313845>.
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2024-01-16 |
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r-sor
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public |
Estimation for longitudinal data following outcome dependent sampling using the sequential offsetted regression technique. Includes support for binary, count, and continuous data. The first regression is a logistic regression, which uses a known ratio (the probability of being sampled given that the subject/observation was referred divided by the probability of being sampled given that the subject/observation was no referred) as an offset to estimate the probability of being referred given outcome and covariates. The second regression uses this estimated probability to calculate the mean population response given covariates.
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2024-01-16 |
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r-sopie
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public |
Provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.
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2024-01-16 |
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r-soql
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public |
Used to construct the URLs and parameters of 'Socrata Open Data API' <https://dev.socrata.com> calls, using the API's 'SoQL' parameter format. Has method-chained and sensical syntax. Plays well with pipes.
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2024-01-16 |
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r-soniclength
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public |
Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
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2024-01-16 |
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r-sonar
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public |
Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.
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2024-01-16 |
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r-soildb
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public |
A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
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2024-01-16 |
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r-somemtp
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public |
It's a collection of functions for Multiplicity Correction and Multiple Testing.
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2024-01-16 |
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r-solvesaphe
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public |
Universal and robust algorithm for solving the total alkalinity-pH equation presented in G. Munhoven (2013) <doi:10.5194/gmd-6-1367-2013> and G. Munhoven (2021) <doi:10.5194/gmd-2020-447>. The total alkalinity-pH equation relates total alkalinity and pH for a given set of acid-base concentrations in a given water sample, among which carbonic acid. This package is particularly useful in marine chemistry involving dissolved inorganic carbon. Original package in Fortran can be found at <doi:10.5281/zenodo.4328965>.
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2024-01-16 |
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r-solrium
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public |
Provides a set of functions for querying and parsing data from 'Solr' (<https://solr.apache.org/>) 'endpoints' (local and remote), including search, 'faceting', 'highlighting', 'stats', and 'more like this'. In addition, some functionality is included for creating, deleting, and updating documents in a 'Solr' 'database'.
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2024-01-16 |
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r-solrad
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public |
For surface energy models and estimation of solar positions and components with varying topography, time and locations. The functions calculate solar top-of-atmosphere, open, diffuse and direct components, atmospheric transmittance and diffuse factors, day length, sunrise and sunset, solar azimuth, zenith, altitude, incidence, and hour angles, earth declination angle, equation of time, and solar constant. Details about the methods and equations are explained in Seyednasrollah, Bijan, Mukesh Kumar, and Timothy E. Link. 'On the role of vegetation density on net snow cover radiation at the forest floor.' Journal of Geophysical Research: Atmospheres 118.15 (2013): 8359-8374, <doi:10.1002/jgrd.50575>.
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2024-01-16 |
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r-solarpos
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public |
Calculation of solar zenith and azimuth angles.
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2024-01-16 |
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r-solartime
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public |
Provide utilities to work with solar time, i.e. where noon is exactly when sun culminates. Provides functions for computing sun position and times of sunrise and sunset.
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2024-01-16 |
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r-solar
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public |
Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
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2024-01-16 |
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r-sokoban
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public |
Interactively play a game of sokoban ,which has nine game levels.Sokoban is a type of transport puzzle, in which the player pushes boxes or crates around in a warehouse, trying to get them to storage locations.
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2024-01-16 |
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r-soiltexture
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public |
"The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
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2024-01-16 |
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r-socialmixr
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public |
Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
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2024-01-16 |
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r-soilwater
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public |
It implements parametric formulas of soil water retention or conductivity curve. At the moment, only Van Genuchten (for soil water retention curve) and Mualem (for hydraulic conductivity) were implemented. See reference (<http://en.wikipedia.org/wiki/Water_retention_curve>).
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2024-01-16 |
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r-soilphysics
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public |
Basic and model-based soil physical analyses.
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2024-01-16 |
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r-socviz
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public |
Supporting materials for a course and book on data visualization. It contains utility functions for graphs and several sample data sets. See Healy (2019) <ISBN 978-0691181622>.
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2024-01-16 |
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r-soilhyp
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public |
Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
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2024-01-16 |
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r-softclustering
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public |
It contains soft clustering algorithms, in particular approaches derived from rough set theory: Lingras & West original rough k-means, Peters' refined rough k-means, and PI rough k-means. It also contains classic k-means and a corresponding illustrative demo.
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2024-01-16 |
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r-sofia
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public |
Software that leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. Circos is a novel software that addresses the challenges in visualizing genetic data by creating circular ideograms composed of tracks of heatmaps, scatter plots, line plots, histograms, links between common markers, glyphs, text, and etc. Please see <http://www.circos.ca>.
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2024-01-16 |
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r-sofa
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public |
Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
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2024-01-16 |
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r-snpassoc
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public |
Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
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2024-01-16 |
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r-sodavis
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public |
Variable and interaction selection are essential to classification in high-dimensional setting. In this package, we provide the implementation of SODA procedure, which is a forward-backward algorithm that selects both main and interaction effects under logistic regression and quadratic discriminant analysis. We also provide an extension, S-SODA, for dealing with the variable selection problem for semi-parametric models with continuous responses.
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2024-01-16 |
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r-snowfall
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public |
Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
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2024-01-16 |
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r-soar
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public |
Allows objects to be stored on disc and automatically recalled into memory, as required, by delayed assignment.
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2024-01-16 |
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r-sns
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public |
Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability density functions (PDFs) where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A Boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the PDF (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle. Numerical differentiation is available when analytical expressions for gradient and Hessian are not available. Facilities for validation and numerical differentiation of log-density are provided. Note: Formerly available versions of the MfUSampler can be obtained from the archive <https://cran.r-project.org/src/contrib/Archive/MfUSampler/>.
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2024-01-16 |
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r-smoothr
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public |
Tools for smoothing and tidying spatial features (i.e. lines and polygons) to make them more aesthetically pleasing. Smooth curves, fill holes, and remove small fragments from lines and polygons.
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2024-01-16 |
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r-smotefamily
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public |
A collection of various oversampling techniques developed from SMOTE is provided. SMOTE is a oversampling technique which synthesizes a new minority instance between a pair of one minority instance and one of its K nearest neighbor. (see <https://www.jair.org/media/953/live-953-2037-jair.pdf> for more information) Other techniques adopt this concept with other criteria in order to generate balanced dataset for class imbalance problem.
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2024-01-16 |
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r-snowflakes
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public |
The function generates and plots random snowflakes. Each snowflake is defined by a given diameter, width of the crystal, color, and random seed. Snowflakes are plotted in such way that they always remain round, no matter what the aspect ratio of the plot is. Snowflakes can be created using transparent colors, which creates a more interesting, somewhat realistic, image. Images of the snowflakes can be separately saved as svg files and used in websites as static or animated images.
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2024-01-16 |
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r-snn
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public |
Implement K-nearest neighbor classifier, weighted nearest neighbor classifier, bagged nearest neighbor classifier, optimal weighted nearest neighbor classifier and stabilized nearest neighbor classifier, and perform model selection via 5 fold cross-validation for them. This package also provides functions for computing the classification error and classification instability of a classification procedure.
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2024-01-16 |
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r-snow
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public |
Support for simple parallel computing in R.
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2024-01-16 |
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r-snapshot
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public |
Functions for reading and writing Gadget N-body snapshots. The Gadget code is popular in astronomy for running N-body / hydrodynamical cosmological and merger simulations. To find out more about Gadget see the main distribution page at www.mpa-garching.mpg.de/gadget/
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2024-01-16 |
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r-snem
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public |
Efficient estimation of multivariate skew-normal distribution in closed form.
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2024-01-16 |
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r-snakesandladdersanalysis
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public |
Plays the game of Snakes and Ladders and has tools for analyses. The tools included allow you to find the average moves to win, frequency of each square, importance of the snakes and the ladders, the most common square and the plotting of the game played.
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2024-01-16 |
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r-snakecase
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public |
A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.
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2024-01-16 |
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r-sn
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None |
Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t and the SUN families. For the skew-normal and the skew-t distributions, statistical methods are provided for data fitting and model diagnostics, in the univariate and the multivariate case.
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2024-01-16 |
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r-smvar
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public |
Implementation of the structural model for variances in order to detect differentially expressed genes from gene expression data.
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2024-01-16 |
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r-sms
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public |
Produce small area population estimates by fitting census data to survey data.
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2024-01-16 |
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r-smss
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public |
Datasets used in "Statistical Methods for the Social Sciences" (SMSS) by Alan Agresti and Barbara Finlay.
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2024-01-16 |
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r-smpracticals
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public |
Contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves can be found at <http://statwww.epfl.ch/davison/SM/>.
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2024-01-16 |
