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r-extremefit
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public |
Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
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2023-06-16 |
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r-extratrees
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public |
Classification and regression based on an ensemble of decision trees. The package also provides extensions of ExtraTrees to multi-task learning and quantile regression. Uses Java implementation of the method.
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2023-06-16 |
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r-exactcidiff
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This is a package for exact Confidence Intervals for the difference between two independent or dependent proportions.
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2023-06-16 |
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r-ganpadata
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This is a dataset package for GANPA, which implements a network-based gene weighting approach to pathway analysis. This package includes data useful for GANPA, such as a functional association network, pathways, an expression dataset and multi-subunit proteins.
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2023-06-16 |
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r-gamlss.data
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public |
Data used as examples to demonstrate GAMLSS models.
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2023-06-16 |
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r-fuzzystattra
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public |
The aim of the package is to provide some basic functions for doing statistics with trapezoidal fuzzy numbers. In particular, the package contains several functions for simulating trapezoidal fuzzy numbers, as well as for calculating some central tendency measures (mean and two types of median), some scale measures (variance, ADD, MDD, Sn, Qn, Tn and some M-estimators) and one diversity index and one inequality index. Moreover, functions for calculating the 1-norm distance, the mid/spr distance and the (phi,theta)-wabl/ldev/rdev distance between fuzzy numbers are included, and a function to calculate the value phi-wabl given a sample of trapezoidal fuzzy numbers.
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2023-06-16 |
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r-fuzzyfdr
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public |
Exact calculation of fuzzy decision rules for multiple testing. Choose to control FDR (false discovery rate) using the Benjamini and Hochberg method, or FWER (family wise error rate) using the Bonferroni method. Kulinsakaya and Lewin (2007).
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2023-06-16 |
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r-freestats
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A collections of useful statistical functions used in Columbia course W4240/W4400.
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2023-06-16 |
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r-frailtyhl
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Implements the h-likelihood estimation procedures for general frailty models including competing-risk models and joint models.
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2023-06-16 |
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r-folderfun
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public |
If you find yourself working on multiple different projects in R, you'll want a series of folders pointing to raw data, processed data, plot results, intermediate table outputs, etc. This package makes it easier to do that by providing a quick and easy way to create and use functions for project-level directories.
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2023-06-16 |
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r-flowregenvcost
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An application to calculate the daily environmental costs of river flow regulation by dams based on GarcÃa de Jalon et al. 2017 <doi:10.1007/s11269-017-1663-0>.
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2023-06-16 |
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r-fitsio
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public |
Utilities to read and write files in the FITS (Flexible Image Transport System) format, a standard format in astronomy (see e.g. <https://en.wikipedia.org/wiki/FITS> for more information). Present low-level routines allow: reading, parsing, and modifying FITS headers; reading FITS images (multi-dimensional arrays); reading FITS binary and ASCII tables; and writing FITS images (multi-dimensional arrays). Higher-level functions allow: reading files composed of one or more headers and a single (perhaps multidimensional) image or single table; reading tables into data frames; generating vectors for image array axes; scaling and writing images as 16-bit integers. Known incompletenesses are reading random group extensions, as well as bit, complex, and array descriptor data types in binary tables.
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2023-06-16 |
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r-filenamer
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public |
Create descriptive file names with ease. New file names are automatically (but optionally) time stamped and placed in date stamped directories. Streamline your analysis pipeline with input and output file names that have informative tags and proper file extensions.
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2023-06-16 |
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r-extrabinomial
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This package tests for differences in minor allele frequency between groups and is based on an extra-binomial variation model for pooled sequencing data.
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2023-06-16 |
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r-eventinterval
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public |
Functions for analysis of rate changes in sequential events.
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2023-06-16 |
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r-forestplot
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public |
A forest plot that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. The aim is to extend the use of forest plots beyond meta-analyses. This is a more general version of the original 'rmeta' package's forestplot() function and relies heavily on the 'grid' package.
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2023-06-16 |
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r-fontcm
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Computer Modern font for use with extrafont package
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2023-06-16 |
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r-flury
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Contains data sets from Bernard Flury (1997) A First Course in Multivariate Statistics, Springer NY
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2023-06-16 |
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r-fluosurv
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public |
Use spectrophotometry measurements performed on insects as a way to infer pathogens virulence. Insect movements cause fluctuations in fluorescence signal, and functions are provided to estimate when the insect has died as the moment when variance in autofluorescence signal drops to zero. The package provides functions to obtain this estimate together with functions to import spectrophotometry data from a Biotek microplate reader. Details of the method are given in Parthuisot et al. (2018) <doi:10.1101/297929>.
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2023-06-16 |
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r-fivethirtyeight
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Datasets and code published by the data journalism website 'FiveThirtyEight' available at <https://github.com/fivethirtyeight/data>. Note that while we received guidance from editors at 'FiveThirtyEight', this package is not officially published by 'FiveThirtyEight'.
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2023-06-16 |
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r-finepop
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public |
Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
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2023-06-16 |
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r-fbonds
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It implements the Nelson-Siegel and the Nelson-Siegel-Svensson term structures.
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2023-06-16 |
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r-fbn
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public |
Normalizes the data from a file containing the raw values of the SNP probes of microarrray data by using the FISH probes and their corresponding CNs.
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2023-06-16 |
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r-fastpseudo
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Computes pseudo-observations for survival analysis on right-censored data based on restricted mean survival time.
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2023-06-16 |
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r-extrafontdb
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Package for holding the database for the extrafont package
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2023-06-16 |
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r-exrq
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Estimation for high conditional quantiles based on quantile regression.
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2023-06-16 |
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r-excessmass
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Implementation of a function which calculates the empirical excess mass for given \eqn{\lambda} and given maximal number of modes (excessm()). Offering powerful plot features to visualize empirical excess mass (exmplot()). This includes the possibility of drawing several plots (with different maximal number of modes / cut off values) in a single graph.
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2023-06-16 |
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r-excerptr
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This is an R interface to the python package 'excerpts' (<https://pypi.python.org/pypi/excerpts>).
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2023-06-16 |
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r-fusionclust
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Provides the Big Merge Tracker and COSCI algorithms for convex clustering and feature screening using L1 fusion penalty. See Radchenko, P. and Mukherjee, G. (2017) <doi:10.1111/rssb.12226> and T.Banerjee et al. (2017) <doi:10.1016/j.jmva.2017.08.001> for more details.
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2023-06-16 |
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r-frm
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Estimation and specification analysis of one- and two-part fractional regression models and calculation of partial effects.
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2023-06-16 |
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r-fragman
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Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
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2023-06-16 |
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r-fractaldim
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Implements various methods for estimating fractal dimension of time series and 2-dimensional data.
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2023-06-16 |
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r-foto
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The Fourier Transform Textural Ordination method uses a principal component analysis on radially averaged two dimensional Fourier spectra to characterize image texture.
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2023-06-16 |
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r-fmsmsnreg
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Fit linear regression models where the random errors follow a finite mixture of of Skew Heavy-Tailed Errors.
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2023-06-16 |
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r-fluxweb
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Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.
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2023-06-16 |
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r-flux
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Functions for the calculation of greenhouse gas flux rates from closed chamber concentration measurements. The package follows a modular concept: Fluxes can be calculated in just two simple steps or in several steps if more control in details is wanted. Additionally plot and preparation functions as well as functions for modelling gpp and reco are provided.
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2023-06-16 |
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r-fit.models
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The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to compare robustly and classically fitted model objects. The aim of the fit.models package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.
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2023-06-16 |
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r-fishtree
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An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.
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2023-06-16 |
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r-findr
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Scans all directories and subdirectories of a path for code snippets, R scripts, R Markdown, PDF or text files containing a specific pattern. Files found can be copied to a new folder.
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2023-06-16 |
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r-fhidata
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Provides structural data for Norway. Datasets relating to maps, population in municipalities, vaccination coverage for childhood vaccines, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2019.
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2023-06-16 |
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r-ffmanova
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General linear modeling with multiple responses (MANCOVA). An overall p-value for each model term is calculated by the 50-50 MANOVA method by Langsrud (2002) <doi:10.1111/1467-9884.00320>, which handles collinear responses. Rotation testing, described by Langsrud (2005) <doi:10.1007/s11222-005-4789-5>, is used to compute adjusted single response p-values according to familywise error rates and false discovery rates (FDR). The approach to FDR is described in the appendix of Moen et al. (2005) <doi:10.1128/AEM.71.4.2086-2094.2005>. Unbalanced designs are handled by Type II sums of squares as argued in Langsrud (2003) <doi:10.1023/A:1023260610025>. Furthermore, the Type II philosophy is extended to continuous design variables as described in Langsrud et al. (2007) <doi:10.1080/02664760701594246>. This means that the method is invariant to scale changes and that common pitfalls are avoided.
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2023-06-16 |
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r-fastimputation
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TrainFastImputation() uses training data to describe a multivariate normal distribution that the data approximates or can be transformed into approximating and stores this information as an object of class 'FastImputationPatterns'. FastImputation() function uses this 'FastImputationPatterns' object to impute (make a good guess at) missing data in a single line or a whole data frame of data. This approximates the process used by 'Amelia' <http://gking.harvard.edu/amelia/> but is much faster when filling in values for a single line of data.
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2023-06-16 |
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r-factorplot
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Methods to calculate, print, summarize and plot pairwise differences from GLMs, GLHT or Multinomial Logit models.
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2023-06-16 |
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r-exprep
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Allows to calculate the probabilities of occurrences of an event in a great number of repetitions of Bernoulli experiment, through the application of the local and the integral theorem of De Moivre Laplace, and the theorem of Poisson. Gives the possibility to show the results graphically and analytically, and to compare the results obtained by the application of the above theorems with those calculated by the direct application of the Binomial formula. Is basically useful for educational purposes.
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2023-06-16 |
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r-gad
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This package analyses complex ANOVA models with any combination of orthogonal/nested and fixed/random factors, as described by Underwood (1997). There are two restrictions: (i) data must be balanced; (ii) fixed nested factors are not allowed. Homogeneity of variances is checked using Cochran's C test and 'a posteriori' comparisons of means are done using Student-Newman-Keuls (SNK) procedure.
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2023-06-16 |
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r-fuzzysim
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Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.
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2023-06-16 |
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r-funr
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A small utility which wraps Rscript and provides access to all R functions from the shell.
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2023-06-16 |
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r-fticrms
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This package was developed partially with funding from the NIH Training Program in Biomolecular Technology (2-T32-GM08799).
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2023-06-16 |
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r-fsthet
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A program to generate smoothed quantiles for the Fst-heterozygosity distribution. Designed for use with large numbers of loci (e.g., genome-wide SNPs). The best case for analyzing the Fst-heterozygosity distribution is when many populations (>10) have been sampled. See Flanagan & Jones (2017) <doi:10.1093/jhered/esx048>.
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2023-06-16 |
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r-freegroup
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Provides functionality for manipulating elements of the free group (juxtaposition is represented by a plus) including inversion, multiplication by a scalar, group-theoretic power operation, and Tietze forms. The package is fully vectorized.
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2023-06-16 |
