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r-knitrprogressbar
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Provides a progress bar similar to 'dplyr' that can write progress out to a variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown', and you still want to see progress of calculations in the terminal.
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2023-06-16 |
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r-kdensity
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Handles univariate non-parametric density estimation with parametric starts and asymmetric kernels in a simple and flexible way. Kernel density estimation with parametric starts involves fitting a parametric density to the data before making a correction with kernel density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>. Asymmetric kernels make kernel density estimation more efficient on bounded intervals such as (0, 1) and the positive half-line. Supported asymmetric kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>, the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>. User-supplied kernels, parametric starts, and bandwidths are supported.
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2023-06-16 |
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r-jvcoords
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Provides functions to standardize and whiten data, and to perform Principal Component Analysis (PCA). The main advantage of this package over alternatives like prcomp() is, that jvcoords makes it easy to convert (additional) data between the original and the transformed coordinates. The package also provides a class coords, which can represent affine coordinate transformations. This class forms the basis of the transformations provided by the package, but can also be used independently. The implementation has been optimized to be of comparable speed (and sometimes even faster) than existing alternatives.
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2023-06-16 |
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r-jtrans
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Transforming univariate non-normal data to normality using Johnson families of distributions. Johnson family is a comprehensive distribution family that accommodates many kinds of non-normal distributions. A bunch of distributions with various parameters will be fit and the corresponding p-values under a user-specified normality test will be given. The final transformation will be the one with the largest p-value under the given normality test.
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2023-06-16 |
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r-json64
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Encode/Decode 'base64', with support for JSON format, using two functions: j_encode() and j_decode(). 'Base64' is a group of similar binary-to-text encoding schemes that represent binary data in an ASCII string format by translating it into a radix-64 representation, used when there is a need to encode binary data that needs to be stored and transferred over media that are designed to deal with textual data, ensuring that the data will remain intact and without modification during transport. <https://developer.mozilla.org/en-US/docs/Web/API/WindowBase64/Base64_encoding_and_decoding> On the other side, JSON (JavaScript Object Notation) is a lightweight data-interchange format. Easy to read, write, parse and generate. It is based on a subset of the JavaScript Programming Language. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. JSON structure is built around name:value pairs and ordered list of values. <https://www.json.org> The first function, j_encode(), let you transform a data.frame or list to a 'base64' encoded JSON (or JSON string). The j_decode() function takes a 'base64' string (could be an encoded JSON) and transform it to a data.frame (or list, depending of the JSON structure).
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2023-06-16 |
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r-jaatha
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An estimation method that can use computer simulations to approximate maximum-likelihood estimates even when the likelihood function can not be evaluated directly. It can be applied whenever it is feasible to conduct many simulations, but works best when the data is approximately Poisson distributed. It was originally designed for demographic inference in evolutionary biology. It has optional support for conducting coalescent simulation using the 'coala' package.
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2023-06-16 |
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r-ioncopy
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Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.
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2023-06-16 |
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r-invctr
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Vector operations between grapes: An infix-only package! The 'invctr' functions perform common and less common operations on vectors, data frames matrices and list objects: - Extracting a value (range), or, finding the indices of a value (range). - Trimming, or padding a vector with a value of your choice. - Simple polynomial regression. - Set and membership operations. - General check & replace function for NAs, Inf and other values.
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2023-06-16 |
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r-interferenceci
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Computes large sample confidence intervals of Liu and Hudgens (2014), exact confidence intervals of Tchetgen Tchetgen and VanderWeele (2012), and exact confidence intervals of Rigdon and Hudgens (2014) for treatment effects on a binary outcome in two-stage randomized experiments with interference.
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2023-06-16 |
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r-infra
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Takes a data frame containing latitude and longitude coordinates and downloads images from map servers to determine their file size as a proxy of infrastructure
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2023-06-16 |
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r-indexnumr
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Computes bilateral and multilateral index numbers. It has support for several standard bilateral indices as well as the GEKS multilateral index number methods (see Ivancic, Diewert and Fox (2011) <doi:10.1016/j.jeconom.2010.09.003>) . It also supports updating of GEKS indexes using several splicing methods.
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2023-06-16 |
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r-imap
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Zoom in and out of maps or any supplied lines or points, with control for color, poly fill, and aspect.
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2023-06-16 |
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r-ig.vancouver.2014.topcolour
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A dataset of the top colours of photos from Instagram taken in 2014 in the city of Vancouver, British Columbia, Canada. It consists of: top colour and counts data. This data was obtained using the Instagram API. Instagram is a web photo sharing service. It can be found at: <https://instagram.com>. The Instagram API is documented at: <https://instagram.com/developer/>.
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2023-06-16 |
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r-idbg
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An interactive R debugger
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2023-06-16 |
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r-hrw
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The book "Semiparametric Regression with R" by J. Harezlak, D. Ruppert & M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets and scripts to explain semiparametric regression concepts. Each of the book's scripts are contained in this package as well as datasets that are not within other R packages. Functions that aid semiparametric regression analysis are also included.
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2023-06-16 |
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r-housingdata
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Monthly median home listing, sale price per square foot, and number of units sold for 2984 counties in the contiguous United States From 2008 to January 2016. Additional data sets containing geographical information and links to Wikipedia are also included.
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2023-06-16 |
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r-hoardr
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Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.
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2023-06-16 |
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r-hmstimer
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Tracks elapsed clock time using a 'hms()' scalar (inherits from 'difftime()' with seconds as the unit).
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2023-06-16 |
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r-hgnchelper
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Contains functions for identifying and correcting HGNC human gene symbols and MGI mouse gene symbols which have been converted to date format by Excel, withdrawn, or aliased. Also contains functions for reversibly converting between HGNC symbols and valid R names.
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2023-06-16 |
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r-hexview
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Functions to view files in raw binary form like in a hex editor. Additional functions to specify and read arbitrary binary formats.
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2023-06-16 |
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r-helminthr
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Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently <http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.
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2023-06-16 |
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r-heatmap.plus
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Allows heatmap matrix to have non-identical X- and Y-dimensions. Allows multiple tracks of annotation for RowSideColors and ColSideColors.
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2023-06-16 |
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r-hdpca
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In high-dimensional settings: Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model. Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors. Adjust the shrinkage bias in the predicted PC scores.
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2023-06-16 |
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r-hcp
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Estimation of parameters in 3-segment (i.e. 2 change-point) regression models with heteroscedastic variances is provided based on both likelihood and hybrid Bayesian approaches, with and without continuity constraints at the change points.
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2023-06-16 |
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r-hapim
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The package provides a set of functions whose aim is to propose 4 methods of QTL detection. HAPimLD is an interval-mapping method designed for unrelated individuals with no family information that makes use of linkage disequilibrium. HAPimLDL is an interval-mapping method for design of half-sib families. It combines linkage analysis and linkage disequilibrium. HaploMax is based on an analysis of variance with a dose haplotype effect. HaploMaxHS is based on an analysis of variance with a sire effect and a dose haplotype effect in half-sib family design. Fundings for the package development were provided to the LDLmapQTL project by the ANR GENANIMAL program and APIS-GENE.
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2023-06-16 |
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r-handyplots
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Several handy plots for quickly looking at the relationship between two numeric vectors of equal length. Quickly visualize scatter plots, residual plots, qq-plots, box plots, confidence intervals, and prediction intervals.
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2023-06-16 |
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r-gwg
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Based on calculations of 758 women this package calculates positive predictive values (PPV) and negative predictive values (NPV) for inadequate and excessive gestational weight gain (GWG) for different prevalences for different BMI categories.
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2023-06-16 |
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r-gvlma
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Methods from the paper: Pena, EA and Slate, EH, "Global Validation of Linear Model Assumptions," J. American Statistical Association, 101(473):341-354, 2006.
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2023-06-16 |
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r-gtests
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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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2023-06-16 |
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r-gsafishercombined
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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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2023-06-16 |
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r-grouped
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Regression models for grouped and coarse data, under the Coarsened At Random assumption.
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2023-06-16 |
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r-grnn
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The program GRNN implements the algorithm proposed by Specht (1991).
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2023-06-16 |
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r-grex
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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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2023-06-16 |
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r-gmac
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Performs genomic mediation analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/078683>. It implements large scale mediation analysis and adaptively selects potential confounding variables to adjust for each mediation test from a pool of candidate confounders. The package is tailored for but not limited to genomic mediation analysis (e.g., cis-gene mediating trans-gene regulation pattern where an eQTL, its cis-linking gene transcript, and its trans-gene transcript play the roles as treatment, mediator and the outcome, respectively), restricting to scenarios with the presence of cis-association (i.e., treatment-mediator association) and random eQTL (i.e., treatment).
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2023-06-16 |
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r-glmdm
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This package contains functions to perform generalized linear mixed Dirichlet models using posterior simulation.
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2023-06-16 |
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r-glba
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Analyses response times and accuracies from psychological experiments with the linear ballistic accumulator (LBA) model from Brown and Heathcote (2008). The LBA model is optionally fitted with explanatory variables on the parameters such as the drift rate, the boundary and the starting point parameters. A log-link function on the linear predictors can be used to ensure that parameters remain positive when needed.
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2023-06-16 |
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r-ggm
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Functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.
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2023-06-16 |
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r-genoplotr
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Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.
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2023-06-16 |
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r-genalg
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R based genetic algorithm for binary and floating point chromosomes.
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2023-06-16 |
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r-gcd
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Contains the Global Charcoal database data. Data include charcoal series (age, depth, charcoal quantity, associated units and methods) and information on sedimentary sites (localisation, depositional environment, biome, etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
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2023-06-16 |
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r-larf
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Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
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2023-06-16 |
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r-labstats
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Contains data sets to accompany the book: Lazic SE (2016). "Experimental Design for Laboratory Biologists: Maximising Information and Improving Reproducibility". Cambridge University Press.
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2023-06-16 |
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r-l2boost
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Efficient implementation of Friedman's boosting algorithm with l2-loss function and coordinate direction (design matrix columns) basis functions.
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2023-06-16 |
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r-kulife
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Provides various functions and data sets from experiments at the Faculty of Life Sciences, University of Copenhagen. This package will be discontinued and archived, and the functions and datasets will be maintained and updated in the MESS package
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2023-06-16 |
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r-kirby21.base
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Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <https://www.nitrc.org/projects/multimodal/>, including functional and structural imaging.
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2023-06-16 |
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r-kidney.epi
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Contains kidney care oriented functions. Current version contains only function for calculation of Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors by Rao et al. (2009) <doi:10.1097/TP.0b013e3181ac620b>. Citation: Bikbov B. R open source programming code for calculation of the Kidney Donor Profile Index and Kidney Donor Risk Index. Kidney Diseases (2018) <doi:10.1159/000492427>.
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2023-06-16 |
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r-kernscr
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Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018) <doi: 10.1177/0962280216653427>.
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2023-06-16 |
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r-jmetrik
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The main purpose of this package is to make it easy for userR's to interact with 'jMetrik' an open source application for psychometric analysis. For example it allows useR's to write data frames to file in a format that can be used by 'jMetrik'. It also allows useR's to read *.jmetrik files (e.g. output from an analysis) for follow-up analysis in R. The *.jmetrik format is a flat file that includes a multiline header and the data as comma separated values. The header includes metadata about the file and one row per variable with the following information in each row: variable name, data type, item scoring, special data codes, and variable label.
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2023-06-16 |
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r-jenkins
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Manage jobs and builds on your Jenkins CI server <https://jenkins.io/>. Create and edit projects, schedule builds, manage the queue, download build logs, and much more.
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2023-06-16 |
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r-ivprobit
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Compute the instrumental variables probit model using the Amemiya's Generalized Least Squares estimators (Amemiya, Takeshi, (1978) <doi: 10.2307/1911443>).
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2023-06-16 |
