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r-iasd
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Calculate AIC's and AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of two normal distributions) which fit the distribution of indices of asymmetry (IAS), and plot their density, to help determine IAS distribution is unimodal or bimodal.
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2023-06-16 |
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r-iabin
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In randomized-controlled trials, interim analyses are often planned for possible early trial termination to claim superiority or futility of a new therapy. Blinded data also have information about the potential treatment difference between the groups. We developed a blinded data monitoring tool that enables investigators to predict whether they observe such an unblinded interim analysis results that supports early termination of the trial. Investigators may skip some of the planned interim analyses if an early termination is unlikely. This tool will provide reference information about N: Sample size at interim analysis, and T: Total number of responders at interim analysis for decision on performing an interim analysis.
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2023-06-16 |
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r-hwde
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Fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast terms are available that account for first order interactions between loci. Also implements, for a single locus in a single population, a conditional exact test for Hardy-Weinberg equilibrium.
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2023-06-16 |
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r-httprequest
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HTTP Request protocols. Implements the GET, POST and multipart POST request.
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2023-06-16 |
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r-htmltab
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HTML tables are a valuable data source but extracting and recasting these data into a useful format can be tedious. This package allows to collect structured information from HTML tables. It is similar to readHTMLTable() of the XML package but provides three major advantages. First, the function automatically expands row and column spans in the header and body cells. Second, users are given more control over the identification of header and body rows which will end up in the R table, including semantic header information that appear throughout the body. Third, the function preprocesses table code, corrects common types of malformations, removes unneeded parts and so helps to alleviate the need for tedious post-processing.
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2023-06-16 |
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r-hotelling
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A set of R functions which implements Hotelling's T^2 test and some variants of it. Functions are also included for Aitchison's additive log ratio and centred log ratio transformations.
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2023-06-16 |
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r-hnp
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Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
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2023-06-16 |
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r-hmr
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Statistical analysis of static chamber concentration data for trace gas flux estimation.
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2023-06-16 |
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r-hk80
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This is a collection of functions for converting coordinates between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems used in Hong Kong SAR, based on the algorithms described in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Mapping Office Lands Department, Hong Kong Government (1995).
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2023-06-16 |
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r-hindexcalculator
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H(x) is the h-index for the past x years. Here, the h(x) of a scientist/department/etc. can be calculated using the exported excel file from a Web of Science citation report of a search. Also calculated is the year of first publication, total number of publications, and sum of times cited for the specified period. Therefore, for h-10: the date of first publication, total number of publications, and sum of times cited in the past 10 years are calculated. Note: the excel file has to first be saved in a .csv format.
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2023-06-16 |
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r-hermite
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Probability functions and other utilities for the generalized Hermite distribution.
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2023-06-16 |
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r-hchinamap
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By binding R functions and the 'Highmaps' <https://www.highcharts.com.cn/products/highmaps> chart library, 'hchinamap' package provides a simple way to map China and its provinces. The map of China drawn by this package contains complete Chinese territory, especially the Nine-dotted line, South Tibet, Hong Kong, Macao and Taiwan.
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2023-06-16 |
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r-hcci
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This package calculates the interval estimates for the parameters of linear models heteroscedastic regression using bootstrap - (Wild Bootstrap) and double bootstrap-t (Wild Bootstrap). It is also possible to calculate confidence intervals using the percentile bootstrap and percentile bootstrap double. It is possible to calculate consistent estimates of the covariance matrix of the parameters of linear regression models with heteroskedasticity of unknown form. The package also provides function to calculate consistently the covariance matrix of the parameters of linear models with heteroskedasticity of unknown form.
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2023-06-16 |
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r-haplotyper
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Function to identify haplotypes within QTL (Quantitative Trait Loci). One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within the QTL. This function groups together all individuals of a population with the same haplotype. Each group contains individual with the same allele in each SNP, whether or not missing data. Thus, haplotyper groups individuals, that to be imputed, have a non-zero probability of having the same alleles in the entire sequence of SNP's. Moreover, haplotyper calculates such probability from relative frequencies.
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2023-06-16 |
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r-haplosim
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Simulate haplotypes through meioses. Allows specification of population parameters.
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2023-06-16 |
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r-halfcircle
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There are growing concerns on flow data in diverse fields including trade, migration, knowledge diffusion, disease spread, and transportation. The package is an effective visual support to learn the pattern of flow which is called halfcircle diagram. The flow between two nodes placed on the center line of a circle is represented using a half circle drawn from the origin to the destination in a clockwise direction. Through changing the order of nodes, the halfcircle diagram enables users to examine the complex relationship between bidirectional flow and each potential determinants. Furthermore, the halfmeancenter function, which calculates (un) weighted mean center of half circles, makes the comparison easier.
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2023-06-16 |
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r-gtwas
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Quantitative trait loci mapping and genome wide association analysis are used to find candidate molecular marker or region associated with phenotype based on linkage analysis and linkage disequilibrium. Gene expression quantitative trait loci mapping is used to find candidate molecular marker or region associated with gene expression. In this package, we applied the method in Liu W. (2011) <doi:10.1007/s00122-011-1631-7> and Gusev A. (2016) <doi:10.1038/ng.3506> to genome and transcriptome wide association study, which is aimed at revealing the association relationship between phenotype and molecular markers, expression levels, molecular markers nested within different related expression effect and expression effect nested within different related molecular marker effect. F test based on full and reduced model are performed to obtain p value or likelihood ratio statistic. The best linear model can be obtained by stepwise regression analysis.
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2023-06-16 |
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r-grt
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Functions to generate and analyze data for psychology experiments based on the General Recognition Theory.
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2023-06-16 |
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r-grpss
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Contains the tools to screen grouped variables, and select screened grouped variables afterwards. The main function grpss() can perform the grouped variables screening as well as selection for ultra-high dimensional data with group structure. The screening step is primarily used to reduce the dimensions of data so that the selection procedure can easily handle the moderate or low dimensions instead of ultra-high dimensions.
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2023-06-16 |
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r-grpregoverlap
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Fit the regularization path of linear, logistic or Cox models with overlapping grouped covariates based on the latent group lasso approach. Latent group MCP/SCAD as well as bi-level selection methods, namely the group exponential lasso and the composite MCP are also available. This package serves as an extension of R package 'grpreg' (by Dr. Patrick Breheny <[email protected]>) for grouped variable selection involving overlaps between groups.
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2023-06-16 |
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r-glsme
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Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
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2023-06-16 |
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r-globalgsa
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Implementation of three different Gene set analysis (GSA) algorithms for combining the individual pvalues of a set of genetic variats (SNPs) in a gene level pvalue. The implementation includes the selection of the best inheritance model for each SNP.
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2023-06-16 |
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r-glm.predict
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Functions to calculate predicted values and the difference between the two cases with confidence interval for lm() [linear model], glm() [general linear model], glm.nb() [negative binomial model], polr() [ordinal logistic model] and multinom() [multinomial model] using Monte Carlo simulations. Reference: Bennet A. Zelner (2009) <doi:10.1002/smj.783>.
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2023-06-16 |
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r-glmc
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Fits generalized linear models where the parameters are subject to linear constraints. The model is specified by giving a symbolic description of the linear predictor, a description of the error distribution, and a matrix of constraints on the parameters.
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2023-06-16 |
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r-gifti
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Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.
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2023-06-16 |
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r-gfa
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Factor analysis implementation for multiple data sources, i.e., for groups of variables. The whole data analysis pipeline is provided, including functions and recommendations for data normalization and model definition, as well as missing value prediction and model visualization. The model group factor analysis (GFA) is inferred with Gibbs sampling, and it has been presented originally by Virtanen et al. (2012), and extended in Klami et al. (2015) <DOI:10.1109/TNNLS.2014.2376974> and Bunte et al. (2016) <DOI:10.1093/bioinformatics/btw207>; for details, see the citation info.
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2023-06-16 |
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r-geonames
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The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.
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2023-06-16 |
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r-generalhoslem
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Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models. Included are the Hosmer-Lemeshow tests (binary, multinomial and ordinal) and the Lipsitz and Pulkstenis-Robinson tests (ordinal).
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2023-06-16 |
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r-kfigr
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A streamlined cross-referencing system for R Markdown documents generated with 'knitr'. R Markdown is an authoring format for generating dynamic content from R. 'kfigr' provides a hook for anchoring code chunks and a function to cross-reference document elements generated from said chunks, e.g. figures and tables.
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2023-06-16 |
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r-jpen
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A Joint PENalty Estimation of Covariance and Inverse Covariance Matrices.
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2023-06-16 |
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r-jaggr
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All the data and functions used to produce the book. We do not expect most people to use the package for any other reason than to get simple access to the 'JAGS' model files, the data, and perhaps run some of the simple examples. The authors of the book are David Lucy (now sadly deceased) and James Curran. It is anticipated that a manuscript will be provided to Taylor and Francis around February 2020, with bibliographic details to follow at that point. Until such time, further information can be obtained by emailing James Curran.
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2023-06-16 |
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r-itsmr
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Provides functions for modeling and forecasting time series data. Forecasting is based on the innovations algorithm. A description of the innovations algorithm can be found in the textbook "Introduction to Time Series and Forecasting" by Peter J. Brockwell and Richard A. Davis. <http://www.springer.com/us/book/9781475777505>.
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2023-06-16 |
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r-iswr
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Data sets and scripts for text examples and exercises in P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
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2023-06-16 |
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r-isco08conversions
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Implementation of functions to assign corresponding common job prestige scores (SIOPS, ISEI), the official job or group title and the ISCO-88 code to given ISCO-08 codes. ISCO-08 is the latest version of the International Standard Classification of Occupations which is used to organise information on labour and jobs.
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2023-06-16 |
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r-ipec
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Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model.
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2023-06-16 |
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r-intubate
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Interface to popular R functions with formulas and data, such as 'lm', so they can be included painlessly in data science pipelines implemented by 'magrittr' with the operator %>%.
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2023-06-16 |
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r-insight
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A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.
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2023-06-16 |
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r-idiogramfish
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Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
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2023-06-16 |
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r-icebox
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Implements Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. ICE plots refine Friedman's partial dependence plot by graphing the functional relationship between the predicted response and a covariate of interest for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate of interest, suggesting where and to what extent they may exist.
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2023-06-16 |
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r-icaff
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Imperialist Competitive Algorithm (ICA) <http://en.wikipedia.org/wiki/Imperialist_competitive_algorithm> is a computational method that is used to solve optimization problems of different types and it is the mathematical model and the computer simulation of human social evolution. The package provides a minimum value for the cost function and the best value for the optimization variables by Imperialist Competitive Algorithm. Users can easily define their own objective function depending on the problem at hand. This version has been successfully applied to solve optimization problems, for continuous functions.
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2023-06-16 |
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r-ic2
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Lorenz and concentration curves; Atkinson, Generalized entropy and SGini indices (with decomposition)
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2023-06-16 |
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r-hyphy
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A Bay Area high level phylogenetic analysis package mostly using the birth-death process. Analysis of species tree branching times and simulation of species trees under a number of different time variable birth-death processes. Analysis of gene tree species tree reconciliations and simulations of gene trees in species trees.
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2023-06-16 |
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r-heatmapfit
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Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic described in Esarey and Pierce (2012) <DOI:10.1093/pan/mps026>.
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2023-06-16 |
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r-hdinterval
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A generic function and a set of methods to calculate highest density intervals for a variety of classes of objects which can specify a probability density distribution, including MCMC output, fitted density objects, and functions.
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2023-06-16 |
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r-hdfqlr
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Provides an interface to 'HDFql' <http://www.hdfql.com/> and helper functions for reading data from and writing data to 'HDF5' files. 'HDFql' provides a high-level language for managing 'HDF5' data that is platform independent. For more information, see the reference manual <http://www.hdfql.com/resources/HDFqlReferenceManual.pdf>.
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2023-06-16 |
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r-hda
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Functions to perform dimensionality reduction for classification if the covariance matrices of the classes are unequal.
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2023-06-16 |
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r-hbstm
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This package fits Hierarchical Bayesian space-Time models for Gaussian data. Furthermore, its functions have been implemented for analysing the fitting qualities of those models.
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2023-06-16 |
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r-hbm
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A package for building hierarchical block matrices from association matrices and for performing multi-scale analysis. It specifically targets chromatin contact maps, generated from high-throughput chromosome conformation capture data, such as 5C and Hi-C, and provides methods for detecting movements and for computing chain hierarchy and region communicability across scales.
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2023-06-16 |
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r-hartools
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The goal of 'HARtools' is to provide a simple set of functions to read/parse, write and visualise HTTP Archive ('HAR') files in R.
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2023-06-16 |
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r-hadoopstreaming
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Provides a framework for writing map/reduce scripts for use in Hadoop Streaming. Also facilitates operating on data in a streaming fashion, without Hadoop.
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2023-06-16 |
