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r-glmbb
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Find all hierarchical models of specified generalized linear model with information criterion (AIC, BIC, or AICc) within specified cutoff of minimum value. Alternatively, find all such graphical models. Use branch and bound algorithm so we do not have to fit all models.
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2023-06-16 |
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r-gestalt
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Provides a suite of function-building tools centered around a (forward) composition operator, %>>>%, which extends the semantics of the 'magrittr' %>% operator and supports 'tidyverse' quasiquotation. It enables you to construct composite functions that can be inspected and transformed as list-like objects. In conjunction with %>>>%, a compact function constructor, fn(), and a function that performs partial application, partial(), are also provided. Both support quasiquotation.
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2023-06-16 |
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r-genomic.autocorr
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Local structure in genomic data often induces dependence between observations taken at different genomic locations. Ignoring this dependence leads to underestimation of the standard error of parameter estimates. This package uses block bootstrapping to estimate asymptotically correct standard errors of parameters from any standard generalised linear model that may be fit by the glm() function.
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2023-06-16 |
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r-genesignaturefinder
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A tool for finding an ensemble gene-signature by a steepest ascending algorithm partially supervised by survival time data.
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2023-06-16 |
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r-lambda.r
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A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
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2023-06-16 |
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r-knapsacksampling
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The sampl.mcmc() function creates samples of the feasible region of a knapsack problem with both equalities and inequalities constraints.
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2023-06-16 |
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r-klin
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The package implements efficient ways to evaluate and solve equations of the form Ax=b, where A is a kronecker product of matrices. Functions to solve least squares problems of this type are also included.
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2023-06-16 |
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r-johnson
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RE.Johnson performs the Johnson Transformation to increase the normality.
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2023-06-16 |
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r-jiebard
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jiebaR is a package for Chinese text segmentation, keyword extraction and speech tagging. This package provides the data files required by jiebaR.
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2023-06-16 |
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r-itunesr
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To enable 'iOS' App Developers to access iTunes App Store Ratings and Reviews using R to extract Basic App Information and Reviews submitted by their App users, Since Apple Store does not provide this straightforward.
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2023-06-16 |
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r-isat
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Reads the output of the 'PerkinElmer InForm' software <http://www.perkinelmer.com/product/inform-cell-analysis-one-seat-cls135781>. In addition to cell-density count, it can derive statistics of intercellular spatial distance for each cell-type.
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2023-06-16 |
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r-ippp
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Generates random numbers corresponding to the events on a Poisson point process with changing event rates. This includes the possibility to incorporate additional information such as the number of events occurring or the location of an already known event. It can also generate the probability density functions of specific events in the cases where additional information is available. Based on Hohmann (2019) <arXiv:1901.10754>.
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2023-06-16 |
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r-intrval
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Evaluating if values of vectors are within different open/closed intervals (`x %[]% c(a, b)`), or if two closed intervals overlap (`c(a1, b1) %[]o[]% c(a2, b2)`). Operators for negation and directional relations also implemented.
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2023-06-16 |
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r-interpol.t
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Hourly interpolation of daily minimum and maximum temperature series. Carries out interpolation on multiple series ad once. Requires some hourly series for calibration (alternatively can use default calibration table).
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2023-06-16 |
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r-interlinear
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Interlinearized glossed texts (IGT) are used in descriptive linguistics for representing a morphological analysis of a text through a morpheme-by-morpheme gloss. 'InterlineaR' provide a set of functions that targets several popular formats of IGT ('SIL Toolbox', 'EMELD XML') and that turns an IGT into a set of data frames following a relational model (the tables represent the different linguistic units: texts, sentences, word, morphems). The same pieces of software ('SIL FLEX', 'SIL Toolbox') typically produce dictionaries of the morphemes used in the glosses. 'InterlineaR' provide a function for turning the LIFT XML dictionary format into a set of data frames following a relational model in order to represent the dictionary entries, the sense(s) attached to the entries, the example(s) attached to senses, etc.
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2023-06-16 |
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r-infix
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Contains a number of infix binary operators that may be useful in day to day practices.
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2023-06-16 |
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r-idmining
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Contains techniques for mining large and high-dimensional data sets by using the concept of Intrinsic Dimension (ID). Here the ID is not necessarily an integer. It is extended to fractal dimensions. And the Morisita estimator is used for the ID estimation, but other tools are included as well.
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2023-06-16 |
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r-icluster
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Integrative clustering of multiple genomic data types using a joint latent variable model.
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2023-06-16 |
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r-icc
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Assist in the estimation of the Intraclass Correlation Coefficient (ICC) from variance components of a one-way analysis of variance and also estimate the number of individuals or groups necessary to obtain an ICC estimate with a desired confidence interval width.
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2023-06-16 |
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r-hybridhclust
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Hybrid hierarchical clustering via mutual clusters. A mutual cluster is a set of points closer to each other than to all other points. Mutual clusters are used to enrich top-down hierarchical clustering.
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2023-06-16 |
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r-httpcode
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Find and explain the meaning of 'HTTP' status codes. Functions included for searching for codes by full or partial number, by message, and get appropriate dog and cat images for many status codes.
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2023-06-16 |
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r-hssvd
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A data mining tool for discovering subgroups of patients and genes that simultaneously display unusual levels of variability compared to other genes and patients. Based on sparse singular value decomposition (SSVD), the method can detect both mean and variance biclusters in the presence of heterogeneous residual variance.
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2023-06-16 |
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r-hqmisc
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This package contains some miscellaneous convenience functions, to create a matrix of dummy columns from a factor, to determine whether x lies in range [a,b], to add a rectangular bracket to an existing plot, and to convert frequencies between Hz, semitones, mel and Bark. This package also contains an example data set of a stratified sample of 80 talkers of Dutch.
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2023-06-16 |
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r-horizon
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Calculates horizon elevation angle and sky view factor from a digital terrain model (Dozier and Frew, 1990).
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2023-06-16 |
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r-hmmcont
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The package includes the functions designed to analyse continuous observations processes with the Hidden Markov Model approach. They include Baum-Welch and Viterbi algorithms and additional visualisation functions. The observations are assumed to have Gaussian distribution and to be weakly stationary processes. The package was created for analyses of financial time series, but can also be applied to any continuous observations processes.
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2023-06-16 |
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r-histdata
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The 'HistData' package provides a collection of small data sets that are interesting and important in the history of statistics and data visualization. The goal of the package is to make these available, both for instructional use and for historical research. Some of these present interesting challenges for graphics or analysis in R.
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2023-06-16 |
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r-hiest
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Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hybrid classifications (parentals, F1, F2, backcrosses). Estimates genomic clines.
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2023-06-16 |
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r-het.test
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An implementation of White's Test for Heteroskedasticity as outlined in Doornik (1996).
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2023-06-16 |
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r-hash
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Implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.
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2023-06-16 |
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r-harvest.tree
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Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.
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2023-06-16 |
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r-gwidgets
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Provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project <http://scigraphica.sourceforge.net>.
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2023-06-16 |
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r-gweram
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This package provides functions to calculate the significance threshold for controlling the type I error rate in mixed-model association mapping analyses.
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2023-06-16 |
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r-gtheory
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Estimates variance components, generalizability coefficients, universe scores, and standard errors when observed scores contain variation from one or more measurement facets (e.g., items and raters).
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2023-06-16 |
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r-gprofiler
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This package has been deprecated and will not be updated. New users should use the package 'gprofiler2' (<https://CRAN.R-project.org/package=gprofiler2>) for up-to-date data and improved functionality. Functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the 'g:Profiler' toolkit (<https://biit.cs.ut.ee/gprofiler/>).
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2023-06-16 |
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r-gomms
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A zero-inflated quasi-Poisson factor model to display similarity between samples visually in a low (2 or 3) dimensional space.
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2023-06-16 |
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r-gmm
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It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), the iterated GMM and continuous updated estimator (Hansen, Eaton and Yaron 1996; <doi:10.2307/1392442>) and several methods that belong to the Generalized Empirical Likelihood family of estimators (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).
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2023-06-16 |
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r-gmfd
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Some methods for the inference and clustering of univariate and multivariate functional data, using a generalization of Mahalanobis distance, along with some functions useful for the analysis of functional data. For further details, see Martino A., Ghiglietti, A., Ieva, F. and Paganoni A. M. (2017) <arXiv:1708.00386>.
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2023-06-16 |
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r-globe
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Basic functions for plotting 2D and 3D views of a sphere, by default the Earth with its major coastline, and additional lines and points.
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2023-06-16 |
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r-geosed
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Find the smallest circle that contains all longitude and latitude input points. From the generated center and radius, variable side polygons can be created, navigation based on bearing and distance can be applied, and more. Based on a modified version of Welzl's algorithm for smallest circle. Distance calculations are based on the haversine formula. Calculations for distance, midpoint, bearing and more are derived from <https://www.movable-type.co.uk>.
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2023-06-16 |
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r-genelistpie
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"geneListPie" package is for mapping a gene list to function categories defined in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick view of the genes distribution of the gene list among the function categories. The gene list must contain a list of gene symbols. The package contains a set of pre-processed gene sets obtained from Gene Ontology and MSigDB including human, mouse, rat and yeast. To provide a high level concise view, only GO slim and kegg are provided. The gene sets are regulared updated. User can also use customized gene sets. User can use the R Pie() or Pie3D() function for plotting the pie chart. Users can also choose to output the gene function mapping results and use external software such as Excel(R) for ploting.
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2023-06-16 |
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r-kstmatrix
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Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework, which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kstMatrix' package provides basic functionalities to generate, handle, and manipulate knowledge structures and knowledge spaces. Opposed to the 'kst' package, 'kstMatrix' uses matrix representations for knowledge structures. Furthermore, 'kstMatrix' contains several knowledge spaces developed by the research group around Cornelia Dowling through querying experts.
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2023-06-16 |
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r-knotr
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Makes nice pictures of knots using Bezier curves and numerical optimization.
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2023-06-16 |
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r-kmda
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Compute p-values of metabolite differential expression analysis using the kernel-based approach.
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2023-06-16 |
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r-kgc
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Aids in identifying the Koeppen-Geiger (KG) climatic zone for a given location. The Koeppen-Geiger climate zones were first published in 1884, as a system to classify regions of the earth by their relative heat and humidity through the year, for the benefit of human health, plant and agriculture and other human activity [1]. This climate zone classification system, applicable to all of the earths surface, has continued to be developed by scientists up to the present day. Recently one of use (FZ) has published updated, higher accuracy KG climate zone definitions [2]. In this package we use these updated high-resolution maps as the data source [3]. We provide functions that return the KG climate zone for a given longitude and lattitude, or for a given United States zip code. In addition the CZUncertainty() function will check climate zones nearby to check if the given location is near a climate zone boundary. In addition an interactive shiny app is provided to define the KG climate zone for a given longitude and lattitude, or United States zip code. Digital data, as well as animated maps, showing the shift of the climate zones are provided on the following website <http://koeppen-geiger.vu-wien.ac.at>. This work was supported by the DOE-EERE SunShot award DE-EE-0007140. [1] W. Koeppen, (2011) <doi:10.1127/0941-2948/2011/105>. [2] F. Rubel and M. Kottek, (2010) <doi:10.1127/0941-2948/2010/0430>. [3] F. Rubel, K. Brugger, K. Haslinger, and I. Auer, (2016) <doi:10.1127/metz/2016/0816>.
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2023-06-16 |
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r-kedd
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Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
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2023-06-16 |
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r-jrich
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These functions calculate the taxonomic measures presented in Miranda-Esquivel (2016). The package introduces Jack-knife resampling in evolutionary distinctiveness prioritization analysis, as a way to evaluate the support of the ranking in area prioritization, and the persistence of a given area in a conservation analysis. The algorithm is described in: Miranda-Esquivel, D (2016) <DOI:10.1007/978-3-319-22461-9_11>.
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2023-06-16 |
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r-jetpack
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Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
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2023-06-16 |
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r-jacpop
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Uses the Jaccard similarity index to account for population structure in sequencing studies. This method was specifically designed to detect population stratification based on rare variants, hence it will be especially useful in rare variant analysis.
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2023-06-16 |
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r-isoplotr
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Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
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2023-06-16 |
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r-iptmnetr
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Provides an R interface to the 'iPTMnet' database REST API, which can be used to retrieve Post Translational Modification (PTM) data in systems biology context. This package handles all the aspects of communicating with the API, which involve sending the request, checking the error codes and parsing the response in a format that is ready to integrate into existing workflows.
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2023-06-16 |
