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r-powermediation
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Functions to calculate power and sample size for testing (1) mediation effects; (2) the slope in a simple linear regression; (3) odds ratio in a simple logistic regression; (4) mean change for longitudinal study with 2 time points; (5) interaction effect in 2-way ANOVA; and (6) the slope in a simple Poisson regression.
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2023-06-16 |
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r-poweranalysis
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Basic functions for power analysis and effect size calculation.
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2023-06-16 |
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r-poprange
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Runs a forward genetic simulator
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2023-06-16 |
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r-poolfstat
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Functions for the computation of F-statistics from Pool-Seq data in population genomics studies. The package also includes several utilities to manipulate Pool-Seq data stored in standard format ('vcf' or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software).
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2023-06-16 |
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r-polypatex
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Functions to perform paternity exclusion via allele matching, in autopolyploid species having ploidy 4, 6, or 8. The marker data used can be genotype data (copy numbers known) or 'allelic phenotype data' (copy numbers not known).
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2023-06-16 |
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r-plotwidgets
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Small self-contained plots for use in larger plots or to delegate plotting in other functions. Also contains a number of alternative color palettes and HSL color space based tools to modify colors or palettes.
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2023-06-16 |
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r-planets
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The goal of 'planets' is to provide of very simple and accessible data containing basic information from all known planets.
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2023-06-16 |
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r-pkconverter
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Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion. The pharmacokinetics model explains that how the drug concentration change as the drug moves through the different compartments of the body. For pharmacokinetic modeling and analysis, it is essential to understand the basic pharmacokinetic parameters. All parameters are considered, but only some of parameters are used in the model. Therefore, we need to convert the estimated parameters to the other parameters after fitting the specific pharmacokinetic model. This package is developed to help this converting work. For more detailed explanation of pharmacokinetic parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001"; "Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>; "Mould and Upton" (2012) <doi:10.1038/psp.2012.4>; "Mould and Upton" (2013) <doi:10.1038/psp.2013.14>.
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2023-06-16 |
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r-s20x
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A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
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2023-06-16 |
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r-rweblogo
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RWebLogo is a wrapper for the WebLogo python package that allows generating of customised sequence logos. Sequence logos are graphical representations of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
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2023-06-16 |
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r-ruta
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Implementation of several unsupervised neural networks, from building their architecture to their training and evaluation. Available networks are auto-encoders including their main variants: sparse, contractive, denoising, robust and variational, as described in Charte et al. (2018) <doi:10.1016/j.inffus.2017.12.007>.
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2023-06-16 |
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r-rt.test
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Performs one-sample t-test based on robustified statistics using median/MAD (TA) and Hodges-Lehmann/Shamos (TB). For more details, see Park and Wang (2018)<arXiv:1807.02215>. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
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2023-06-16 |
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r-rstack
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An extremely simple stack data type, implemented with 'R6' classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.
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2023-06-16 |
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r-rspc
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Implementation of Nelson rules for control charts in 'R'. The 'Rspc' implements some Statistical Process Control methods, namely Levey-Jennings type of I (individuals) chart, Shewhart C (count) chart and Nelson rules (as described in Montgomery, D. C. (2013) Introduction to statistical quality control. Hoboken, NJ: Wiley.). Typical workflow is taking the time series, specify the control limits, and list of Nelson rules you want to evaluate. There are several options how to modify the rules (one sided limits, numerical parameters of rules, etc.). Package is also capable of calculating the control limits from the data (so far only for i-chart and c-chart are implemented).
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2023-06-16 |
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r-rsocrata
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Provides easier interaction with 'Socrata' open data portals <http://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.
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2023-06-16 |
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r-rpivottable
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Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab) and dynamically slice & dice / drag 'n' drop your data. 'rpivotTable' is a wrapper of 'pivottable', a powerful open-source Pivot Table library implemented in 'JavaScript' by Nicolas Kruchten. Aligned to 'pivottable' v2.19.0.
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2023-06-16 |
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r-rpexe.rpext
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This reduced piecewise exponential survival software implements the likelihood ratio test and backward elimination procedure in Han, Schell, and Kim (2012 <doi:10.1080/19466315.2012.698945>, 2014 <doi:10.1002/sim.5915>), and Han et al. (2016 <doi:10.1111/biom.12590>). Inputs to the program can be either times when events/censoring occur or the vectors of total time on test and the number of events. Outputs of the programs are times and the corresponding p-values in the backward elimination. Details about the model and implementation are given in Han et al. 2014. This program can run in R version 3.2.2 and above.
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2023-06-16 |
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r-rpca
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Suppose we have a data matrix, which is the superposition of a low-rank component and a sparse component. Candes, E. J., Li, X., Ma, Y., & Wright, J. (2011). Robust principal component analysis?. Journal of the ACM (JACM), 58(3), 11. prove that we can recover each component individually under some suitable assumptions. It is possible to recover both the low-rank and the sparse components exactly by solving a very convenient convex program called Principal Component Pursuit; among all feasible decompositions, simply minimize a weighted combination of the nuclear norm and of the L1 norm. This package implements this decomposition algorithm resulting with Robust PCA approach.
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2023-06-16 |
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r-roughsetknowledgereduction
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Rough Sets were introduced by Zdzislaw Pawlak on his book "Rough Sets: Theoretical Aspects of Reasoning About Data". Rough Sets provide a formal method to approximate crisp sets when the set-element belonging relationship is either known or undetermined. This enables the use of Rough Sets for reasoning about incomplete or contradictory knowledge. A decision table is a prescription of the decisions to make given some conditions. Such decision tables can be reduced without losing prescription ability. This package provides the classes and methods for knowledge reduction from decision tables as presented in the chapter 7 of the aforementioned book. This package provides functions for calculating the both the discernibility matrix and the essential parts of decision tables.
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2023-06-16 |
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r-rocc
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Functions for a classification method based on receiver operating characteristics (ROC). Briefly, features are selected according to their ranked AUC value in the training set. The selected features are merged by the mean value to form a metagene. The samples are ranked by their metagene value and the metagene threshold that has the highest accuracy in splitting the training samples is determined. A new sample is classified by its metagene value relative to the threshold. In the first place, the package is aimed at two class problems in gene expression data, but might also apply to other problems.
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2023-06-16 |
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r-rnaturalearthdata
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Vector map data from <http://www.naturalearthdata.com/>. Access functions are provided in the accompanying package 'rnaturalearth'.
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2023-06-16 |
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r-rmthreshold
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An algorithm which can be used to determine an objective threshold for signal-noise separation in large random matrices (correlation matrices, mutual information matrices, network adjacency matrices) is provided. The package makes use of the results of Random Matrix Theory (RMT). The algorithm increments a suppositional threshold monotonically, thereby recording the eigenvalue spacing distribution of the matrix. According to RMT, that distribution undergoes a characteristic change when the threshold properly separates signal from noise. By using the algorithm, the modular structure of a matrix - or of the corresponding network - can be unraveled.
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2023-06-16 |
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r-rmsfact
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Display a randomly selected quote about Richard M. Stallman based on the collection in the 'GNU Octave' function 'fact()' which was aggregated by Jordi Gutiérrez Hermoso based on the (now defunct) site stallmanfacts.com (which is accessible only via <http://archive.org>).
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2023-06-16 |
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r-rleafmap
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Display spatial data with interactive maps powered by the open-source JavaScript library 'Leaflet' (see <http://leafletjs.com/>). Maps can be rendered in a web browser or displayed in the HTML viewer pane of 'RStudio'. This package is designed to be easy to use and can create complex maps with vector and raster data, web served map tiles and interface elements.
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2023-06-16 |
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r-rldcp
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Linguistic Descriptions of Complex Phenomena (LDCP) is an architecture and methodology that allows us to model complex phenomena, interpreting input data, and generating automatic text reports customized to the user needs (see <doi:10.1016/j.ins.2016.11.002> and <doi:10.1007/s00500-016-2430-5>). The proposed package contains a set of methods that facilitates the development of LDCP systems. It main goal is increasing the visibility and practical use of this research line.
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2023-06-16 |
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r-rjsplot
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Creates interactive graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.
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2023-06-16 |
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r-riverload
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Implements several of the most popular load estimation procedures, including averaging methods, ratio estimators and regression methods. The package provides an easy-to-use tool to rapidly calculate the load for various compounds and to compare different methods. The package also supplies additional functions to easily organize and analyze the data.
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2023-06-16 |
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r-riskportfolios
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Collection of functions designed to compute risk-based portfolios as described in Ardia et al. (2017) <doi:10.1007/s10479-017-2474-7> and Ardia et al. (2017) <doi:10.21105/joss.00171>.
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2023-06-16 |
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r-ri
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This package provides a set of tools for conducting exact or approximate randomization-based inference for experiments of arbitrary design. The primary functionality of the package is in the generation, manipulation and use of permutation matrices implied by given experimental designs. Among other features, the package facilitates estimation of average treatment effects, constant effects variance estimation, randomization inference for significance testing against sharp null hypotheses and visualization of data and results.
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2023-06-16 |
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r-rhpcbenchmark
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Microbenchmarks for determining the run time performance of aspects of the R programming environment and packages relevant to high-performance computation. The benchmarks are divided into three categories: dense matrix linear algebra kernels, sparse matrix linear algebra kernels, and machine learning functionality.
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2023-06-16 |
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r-rgabriel
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This package was created to analyze multi-level one-way experimental designs. It is designed to handle vectorized observation and factor data where there are unequal sample sizes and population variance homogeneity can not be assumed. To conduct the Gabriel test, create two vectors: one for your observations and one for the factor level of each observation. The function, rgabriel, conduct the test and save the output as a vector to input into the gabriel.plot function, which produces a confidence interval plot for Multiple Comparison.
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2023-06-16 |
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r-rformatter
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The R Formatter formats R source code. It is very much based on formatR, but tries to improve it by heuristics. For example, spaces can be forced around the division operator "/".
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2023-06-16 |
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r-rfoaas
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R access to the 'FOAAS' (F... Off As A Service) web service is provided.
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2023-06-16 |
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r-rflights
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Query plane tickets, from several airlines, using the 'Kiwi' API (similar to 'Google Flights'). The API is documented at <https://docs.kiwi.com/>.
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2023-06-16 |
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r-renpow
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Supports calculations and visualization for renewable power systems and the environment. Analysis and graphical tools for DC and AC circuits and their use in electric power systems. Analysis and graphical tools for thermodynamic cycles and heat engines, supporting efficiency calculations in coal-fired power plants, gas-fired power plants. Calculations of carbon emissions and atmospheric CO2 dynamics. Analysis of power flow and demand for the grid, as well as power models for microgrids and off-grid systems. Provides resource and power generation for hydro power, wind power, and solar power.
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2023-06-16 |
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r-relen
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This function computes the relative entropy (H) as an index for qualitative variation of a factor.
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2023-06-16 |
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r-recoder
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Simple, easy to use, and flexible functionality for recoding variables. It allows for simple piecewise definition of transformations.
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2023-06-16 |
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r-readabf
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Loads Axon Binary Files (both 'ABF' and 'ABF2') created by Axon Instruments/Molecular Devices software such as 'pClamp'.
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2023-06-16 |
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r-rdnb
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A wrapper for the 'Deutsche Nationalbibliothek (German National Library) API', available at <http://www.dnb.de>. The German National Library is the German central archival library, collecting, archiving, bibliographically classifying all German and German-language publications, foreign publications about Germany, translations of German works, and the works of German-speaking emigrants published abroad between 1933 and 1945. A personal access token is required for usage.
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2023-06-16 |
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r-rdistance
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Distance-sampling is a popular method for estimating density and abundance of organisms in ecology. Rdistance contains routines that assist with analysis of distance-sampling data collected on point or line transects. Distance models are specified using regression-like formula (similar to lm, glm, etc.). Abundance routines perform automated bootstrapping and automated detection-function selection. Overall (study area) and site-level (transect or point) abundance estimates are available. A large suite of classical, parametric detection functions are included along with some uncommon parametric functions (e.g., Gamma, negative exponential) and non-parametric smoothed distance functions. Custom (user-defined) detection functions are easily implemented (see vignette). The help files and vignettes have been vetted by multiple authors and tested in workshop settings.
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2023-06-16 |
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r-rde
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Allows caching of raw data directly in R code. This allows R scripts and R Notebooks to be shared and re-run on a machine without access to the original data. Cached data is encoded into an ASCII string that can be pasted into R code. When the code is run, the data is automatically loaded from the cached version if the original data file is unavailable. Works best for small datasets (a few hundred observations).
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2023-06-16 |
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r-rclone
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R version of 'GenClone' (a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization, Arnaud-Haond & Belkhir 2007, <http://wwz.ifremer.fr/clonix/content/download/68205/903914/file/GenClone2.0.setup.zip>), this package allows clone handling as 'GenClone' does, plus the possibility to work with several populations, MultiLocus Lineages (MLL) custom definition and use, and p-value calculation for psex statistic (probability of originating from distinct sexual events) and psex_Fis statistic (taking account of Hardy-Weinberg equilibrium departure) as 'MLGsim'/'MLGsim2' (a program for detecting clones using a simulation approach, Stenberg et al. 2003).
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2023-06-16 |
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r-rastervis
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Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
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2023-06-16 |
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r-randomizebe
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Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
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2023-06-16 |
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r-r3port
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Create and combine HTML and PDF reports from within R. Possibility to design tables and listings for reporting and also include R plots.
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2023-06-16 |
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r-r1magic
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Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple sparse signal generator, mutual cumulative coherence between two matrices and examples, Lp complex norm, scaling back regression coefficients.
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2023-06-16 |
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r-qqvases
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Presents an explanatory animation of normal quantile-quantile plots based on a water-filling analogy. The animation presents a normal QQ plot as the parametric plot of the water levels in vases defined by two distributions. The distributions decorate the axes in the normal QQ plot and are optionally shown as vases adjacent to the plot. The package draws QQ plots for several distributions, either as samples or continuous functions.
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2023-06-16 |
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r-qiitr
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Qiita is a technical knowledge sharing and collaboration platform for programmers. See <https://qiita.com/api/v2/docs> for more information.
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2023-06-16 |
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r-qcgwas
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Tools for (automated and manual) quality control of the results of Genome Wide Association Studies
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2023-06-16 |
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r-pzfx
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Read and write 'GraphPad Prism' '.pzfx' files in R.
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2023-06-16 |
