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r-gsodr
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public |
Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
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2024-01-16 |
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r-gtests
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public |
Four graph-based tests are provided for testing whether two samples are from the same distribution. It works for both continuous data and discrete data.
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2024-01-16 |
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r-gtable
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None |
Tools to make it easier to work with "tables" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.
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2024-01-16 |
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r-gt4ireval
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public |
Provides tools to measure the reliability of an Information Retrieval test collection. It allows users to estimate reliability using Generalizability Theory and map those estimates onto well-known indicators such as Kendall tau correlation or sensitivity.
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2024-01-16 |
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r-gsubfn
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public |
The gsubfn function is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable. There is also a facility for returning multiple objects from functions and a version of transform that allows the RHS to refer to LHS used in the same transform.
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2024-01-16 |
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r-gstream
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public |
Uses an approach based on k-nearest neighbor information to sequentially detect change-points. Offers analytic approximations for false discovery control given user-specified average run length. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available. See references (1) Chen, H. (2019) Sequential change-point detection based on nearest neighbors. The Annals of Statistics, 47(3):1381-1407. (2) Chu, L. and Chen, H. (2018) Sequential change-point detection for high-dimensional and non-Euclidean data <arXiv:1810.05973>.
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2024-01-16 |
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r-gsloid
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public |
Contains published data sets for global benthic d18O data for 0-5.3 Myr <doi:10.1029/2004PA001071> and global sea levels based on marine sediment core data for 0-800 ka <doi:10.5194/cp-12-1-2016>.
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2024-01-16 |
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r-gsmx
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public |
Estimating trait heritability and handling overfitting. This package includes a collection of functions for (1) estimating genetic variance-covariances and calculate trait heritability; and (2) handling overfitting by calculating the variance components and the heritability through cross validation.
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2024-01-16 |
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r-groupdata2
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public |
Methods for dividing data into groups. Create balanced partitions and cross-validation folds. Perform time series windowing and general grouping and splitting of data. Balance existing groups with up- and downsampling or collapse them to fewer groups.
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2024-01-16 |
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r-gsm
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public |
Implementation of a Bayesian approach for estimating a mixture of gamma distributions in which the mixing occurs over the shape parameter. This family provides a flexible and novel approach for modeling heavy-tailed distributions, it is computationally efficient, and it only requires to specify a prior distribution for a single parameter.
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2024-01-16 |
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r-gsaq
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public |
Computation of Quantitative Trait Loci hits in the selected gene set. Performing gene set validation with Quantitative Trait Loci information. Performing gene set enrichment analysis with available Quantitative Trait Loci data and computation of statistical significance value from gene set analysis. Obtaining the list of Quantitative Trait Loci hit genes along with their overlapped Quantitative Trait Loci names.
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2024-01-16 |
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r-gsheet
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public |
Simple package to download Google Sheets using just the sharing link. Spreadsheets can be downloaded as a data frame, or as plain text to parse manually. Google Sheets is the new name for Google Docs Spreadsheets <https://www.google.com/sheets/about>.
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2024-01-16 |
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r-gseg
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public |
Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
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2024-01-16 |
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r-gsarima
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public |
Write SARIMA models in (finite) AR representation and simulate generalized multiplicative seasonal autoregressive moving average (time) series with Normal / Gaussian, Poisson or negative binomial distribution. The methodology of this method is described in Briet OJT, Amerasinghe PH, and Vounatsou P (2013) <doi:10.1371/journal.pone.0065761>.
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2024-01-16 |
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r-grt
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public |
Functions to generate and analyze data for psychology experiments based on the General Recognition Theory.
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2024-01-16 |
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r-gsalib
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public |
Provides utility functions used by the Genome Analysis Toolkit ('GATK') to load tables and plot data. The 'GATK' is a toolkit for variant discovery in high-throughput sequencing data.
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2024-01-16 |
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r-gsafishercombined
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public |
Provides the p-value for a joint test of association between a phenotype and a set of genetic variants (SNPs) by combining marginal p-values using the Fisher method. See Fisher, R.A. (1925,ISBN:0-05-002170-2) Statistical Methods for Research Workers.
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2024-01-16 |
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r-groundhog
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public |
Make R scripts reproducible, by ensuring that every time a given script is run, the same version of the used packages are loaded (instead of whichever version the user running the script happens to have installed). This is achieved by using the command groundhog.library() instead of the base command library(), and including a date in the call. The date is used to call on the same version of the package every time (the most recent version available at that date). Load packages from CRAN, GitHub, or Gitlab.
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2024-01-16 |
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r-gsa
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public |
Gene Set Analysis.
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2024-01-16 |
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r-grto
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public |
Offers functions for the comparison of Gutenberg-Richter b-values. Several functions in GRTo are helpful for the assessment of the quality of seismicity catalogs.
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2024-01-16 |
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r-grs.test
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public |
Computational resources for test proposed by Gibbons, Ross, Shanken (1989)<DOI:10.2307/1913625>. It also has the functions for the power analysis and the choice of the optimal level of significance. The optimal level is determined by minimizing the expected loss from hypothesis testing.
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2024-01-16 |
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r-grpstring
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public |
Methods include converting series of event names to strings, finding common patterns in a group of strings, discovering featured patterns when comparing two groups of strings as well as the number and starting position of each pattern in each string, obtaining transition matrix, computing transition entropy, statistically comparing the difference between two groups of strings, and clustering string groups. Event names can be any action names or labels such as events in log files or areas of interest (AOIs) in eye tracking research.
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2024-01-16 |
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r-grplasso
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public |
Fits user-specified (GLM-) models with group lasso penalty.
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2024-01-16 |
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r-growthrate
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public |
A nonparametric empirical Bayes method for recovering gradients (or growth velocities) from observations of smooth functions (e.g., growth curves) at isolated time points.
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2024-01-16 |
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r-gridpattern
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public |
Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
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2024-01-16 |
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r-growthmodels
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public |
A compilation of nonlinear growth models.
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2024-01-16 |
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r-grouptest
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public |
Contains functions for a two-stage multiple testing procedure for grouped hypothesis, aiming at controlling both the total posterior false discovery rate and within-group false discovery rate.
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2024-01-16 |
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r-groupseq
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public |
Computes probabilities related to group sequential designs for normally distributed test statistics. Enables to derive critical boundaries, power, drift, and confidence intervals of such designs. Supports the alpha spending approach by Lan-DeMets (1994) <doi:10.1002/sim.4780131308>.
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2024-01-16 |
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r-groupica
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public |
Contains an implementation of an independent component analysis (ICA) for grouped data. The main function groupICA() performs a blind source separation, by maximizing an independence across sources and allows to adjust for varying confounding for user-specified groups. Additionally, the package contains the function uwedge() which can be used to approximately jointly diagonalize a list of matrices. For more details see the project website <https://sweichwald.de/groupICA/>.
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2024-01-16 |
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r-grates
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public |
Provides a coherent interface and implementation for creating grouped date classes. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
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2024-01-16 |
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r-grnn
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public |
The program GRNN implements the algorithm proposed by Specht (1991).
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2024-01-16 |
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r-grimport2
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public |
Functions for importing external vector images and drawing them as part of 'R' plots. This package is different from the 'grImport' package because, where that package imports 'PostScript' format images, this package imports 'SVG' format images. Furthermore, this package imports a specific subset of 'SVG', so external images must be preprocessed using a package like 'rsvg' to produce 'SVG' that this package can import. 'SVG' features that are not supported by 'R' graphics, e.g., gradient fills, can be imported and then exported via the 'gridSVG' package.
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2024-01-16 |
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r-gratia
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public |
Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
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2024-01-16 |
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r-grimport
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public |
Functions for converting, importing, and drawing PostScript pictures in R plots.
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2024-01-16 |
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r-gridsvg
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public |
Functions to export graphics drawn with package grid to SVG format. Additional functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.
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2024-01-16 |
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r-gridextra
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None |
Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.
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2024-01-16 |
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r-gridgraphics
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public |
Functions to convert a page of plots drawn with the 'graphics' package into identical output drawn with the 'grid' package. The result looks like the original 'graphics'-based plot, but consists of 'grid' grobs and viewports that can then be manipulated with 'grid' functions (e.g., edit grobs and revisit viewports).
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2024-01-16 |
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r-gridbezier
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public |
Functions for rendering Bezier curves (Pomax, 2018) <https://pomax.github.io/bezierinfo/> in 'grid'. There is support for both quadratic and cubic Bezier curves. There are also functions for calculating points on curves, tangents to curves, and normals to curves.
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2024-01-16 |
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r-gridbase
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None |
Integration of base and grid graphics
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2024-01-16 |
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r-grex
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public |
Convert 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
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2024-01-16 |
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r-gremlins
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public |
We define generalized multipartite networks as the joint observation of several networks implying some common pre-specified groups of individuals. The aim is to fit an adapted version of the popular stochastic block model to multipartite networks, as described in Bar-hen, Barbillon and Donnet (2020) <arXiv:1807.10138>.
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2024-01-16 |
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r-greenclust
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public |
Implements a method of iteratively collapsing the rows of a contingency table, two at a time, by selecting the pair of categories whose combination yields a new table with the smallest loss of chi-squared, as described by Greenacre, M.J. (1988) <doi:10.1007/BF01901670>. The result is compatible with the class of object returned by the 'stats' package's hclust() function and can be used similarly (plotted as a dendrogram, cut, etc.). Additional functions are provided for automatic cutting and diagnostic plotting.
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2024-01-16 |
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r-greedyexperimentaldesignjars
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public |
These are GreedyExperimentalDesign Java dependency libraries. Note: this package has no functionality of its own and should not be installed as a standalone package without GreedyExperimentalDesign.
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2024-01-16 |
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r-grafify
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public |
Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify-vignettes.netlify.app/>. Citation: <doi:10.5281/zenodo.5136508>.
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2024-01-16 |
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r-grcdata
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public |
We implement two main functions. The first function uses a given grouped and/or right-censored grouping scheme and empirical data to infer parameters, and implements chi-square goodness-of-fit tests. The second function searches for the global optimal grouping scheme of grouped and/or right-censored count responses in surveys.
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2024-01-16 |
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r-grapher
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public |
A multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
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2024-01-16 |
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r-gramevol
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public |
A native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.
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2024-01-16 |
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r-grape
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public |
Gene-Ranking Analysis of Pathway Expression (GRAPE) is a tool for summarizing the consensus behavior of biological pathways in the form of a template, and for quantifying the extent to which individual samples deviate from the template. GRAPE templates are based only on the relative rankings of the genes within the pathway and can be used for classification of tissue types or disease subtypes. GRAPE can be used to represent gene-expression samples as vectors of pathway scores, where each pathway score indicates the departure from a given collection of reference samples. The resulting pathway- space representation can be used as the feature set for various applications, including survival analysis and drug-response prediction. Users of GRAPE should use the following citation: Klein MI, Stern DF, and Zhao H. GRAPE: A pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics, 18:317 (June 2017).
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2024-01-16 |
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r-grapes
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public |
Turn arbitrary functions into binary operators.
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2024-01-16 |
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r-grangers
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public |
Contains five functions performing the calculation of unconditional and conditional Granger-causality spectra, bootstrap inference on both, and inference on the difference between them via the bootstrap approach of Farne' and Montanari, 2018 <arXiv:1803.00374>.
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2024-01-16 |
