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r-akmeans
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Adaptive K-means algorithm with various threshold settings. It support two distance metric: Euclidean distance, Cosine distance (1 - cosine similarity) In version 1.1, it contains one more threshold condition.
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2023-06-16 |
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r-acnr
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Provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.
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2023-06-16 |
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r-acd
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Categorical data analysis with complete or missing responses
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2023-06-16 |
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r-abc.rap
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It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.
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2023-06-16 |
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r-ambient
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Generation of natural looking noise has many application within simulation, procedural generation, and art, to name a few. The 'ambient' package provides an interface to the 'FastNoise' C++ library and allows for efficient generation of perlin, simplex, worley, cubic, value, and white noise with optional pertubation in either 2, 3, or 4 (in case of simplex and white noise) dimensions.
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2023-06-16 |
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r-adpss
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Provides the functions for planning and conducting a clinical trial with adaptive sample size determination. Maximal statistical efficiency will be exploited even when dramatic or multiple adaptations are made. Such a trial consists of adaptive determination of sample size at an interim analysis and implementation of frequentist statistical test at the interim and final analysis with a prefixed significance level. The required assumptions for the stage-wise test statistics are independent and stationary increments and normality. Predetermination of adaptation rule is not required.
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2023-06-16 |
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r-alphavantageclient
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Download data from the Alpha Vantage API (<https://www.alphavantage.co/>). Alpha Vantage is a RESTful API which provides various financial data, including stock prices and technical indicators. There is documentation for the underlying API available here: <https://www.alphavantage.co/documentation/>. To get access to this API, the user needs to first claim an API key: <https://www.alphavantage.co/support/>.
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2023-06-16 |
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r-algebraichaplopackage
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Two unordered pairs of data of two different snips positions is haplotyped by resolving a small number ob closed equations.
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2023-06-16 |
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r-agsemisc
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High-featured panel functions for bwplot and xyplot, some plot management helpers, various convenience functions
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2023-06-16 |
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r-activpalprocessing
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Performs estimation of physical activity and sedentary behavior variables from activPAL (PAL Technologies, Glasgow, Scotland) events files. See <http://paltechnologies.com> for more information on the activPAL.
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2023-06-16 |
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r-admit
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Provides functions to perform the fitting of an adaptive mixture of Student-t distributions to a target density through its kernel function as described in Ardia et al. (2009) <doi:10.18637/jss.v029.i03>. The mixture approximation can then be used as the importance density in importance sampling or as the candidate density in the Metropolis-Hastings algorithm to obtain quantities of interest for the target density itself.
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2023-06-16 |
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r-ade4
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Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
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2023-06-16 |
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r-adagio
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The R package 'adagio' will provide methods and algorithms for discrete optimization, e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and Hooke-Jeeves minimization, and some (evolutionary) global optimization functions.
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2023-06-16 |
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r-altmeta
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Provides alternative statistical methods for meta-analysis, including new heterogeneity tests and measures that are robust to outliers.
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2023-06-16 |
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r-alleleretain
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Simulate the effect of management or demography on allele retention and inbreeding accumulation in bottlenecked populations of animals with overlapping generations.
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2023-06-16 |
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r-agridat
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Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
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2023-06-16 |
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r-agreementinterval
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A tool for calculating agreement interval of two measurement methods (Jason Liao (2015) <DOI:10.1515/ijb-2014-0030>) and present results in plots with discordance rate and/or clinically meaningful limit to quantify agreement quality.
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2023-06-16 |
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r-adpf
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This function takes a vector or matrix of data and smooths the data with an improved Savitzky Golay transform. The Savitzky-Golay method for data smoothing and differentiation calculates convolution weights using Gram polynomials that exactly reproduce the results of least-squares polynomial regression. Use of the Savitzky-Golay method requires specification of both filter length and polynomial degree to calculate convolution weights. For maximum smoothing of statistical noise in data, polynomials with low degrees are desirable, while a high polynomial degree is necessary for accurate reproduction of peaks in the data. Extension of the least-squares regression formalism with statistical testing of additional terms of polynomial degree to a heuristically chosen minimum for each data window leads to an adaptive-degree polynomial filter (ADPF). Based on noise reduction for data that consist of pure noise and on signal reproduction for data that is purely signal, ADPF performed nearly as well as the optimally chosen fixed-degree Savitzky-Golay filter and outperformed sub-optimally chosen Savitzky-Golay filters. For synthetic data consisting of noise and signal, ADPF outperformed both optimally chosen and sub-optimally chosen fixed-degree Savitzky-Golay filters. See Barak, P. (1995) <doi:10.1021/ac00113a006> for more information.
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2023-06-16 |
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r-activityindex
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Read raw accelerometry from 'GT3X+' data and plain table data to calculate Activity Index from Bai et al. (2016) <doi:10.1371/journal.pone.0160644>.
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2023-06-16 |
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r-amap
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Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).
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2023-06-16 |
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r-admmnet
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Fit linear and cox models regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty, and their adaptive forms, such as adaptive lasso and net adjusting for signs of linked coefficients. In addition, it treats the number of non-zero coefficients as another tuning parameter and simultaneously selects with the regularization parameter. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
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2023-06-16 |
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r-albopictus
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Implements discrete time deterministic and stochastic age-structured population dynamics models described in Erguler and others (2016) <doi:10.1371/journal.pone.0149282> and Erguler and others (2017) <doi:10.1371/journal.pone.0174293>.
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2023-06-16 |
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r-aim
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R functions for adaptively constructing index models for continuous, binary and survival outcomes. Implementation requires loading R-pacakge "survival"
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2023-06-16 |
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r-adfexplorer
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Amiga Disk Files (ADF) are virtual representations of 3.5 inch floppy disks for the Commodore Amiga. Most disk drives from other systems (including modern drives) are not able to read these disks. To be able to emulate this system, the ADF format was created. This package enables you to read ADF files and import and export files from and to such virtual DOS-formatted disks.
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2023-06-16 |
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r-addhaz
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Functions to fit the binomial and multinomial additive hazard models and to estimate the contribution of diseases/conditions to the disability prevalence, as proposed by Nusselder and Looman (2004) and extended by Yokota et al (2017).
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2023-06-16 |
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r-adct
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Existing adaptive design methods in clinical trials. The package includes power, stopping boundaries (sample size) calculation functions for two-group group sequential designs, adaptive design with coprimary endpoints, biomarker-informed adaptive design, etc.
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2023-06-16 |
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r-accrued
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Package for visualizing data quality of partially accruing data.
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2023-06-16 |
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r-abcp2
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Tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.
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2023-06-16 |
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r-aghmatrix
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Computation of A (pedigree), G (genomic-base), and H (A corrected by G) relationship matrices for diploid and autopolyploid species. Several methods are implemented considering additive and non-additive models.
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2023-06-16 |
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r-amcp
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Accompanies "Designing experiments and analyzing data: A model comparison perspective" (3rd ed.) by Maxwell, Delaney, & Kelley (forthcoming from Routledge). Contains all of the data sets in the book's chapters and end-of-chapter exercises. Information about the book is available at <http://www.DesigningExperiments.com>.
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2023-06-16 |
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r-agrmt
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Calculate agreement or consensus in ordered rating scales. The package implements van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, which can be used to describe agreement, consensus, or polarization among respondents. It also implements measures of consensus (dispersion) by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, and Garcia-Montalvo and Reynal-Querol. Furthermore, an implementation of Galtungs AJUS-system is provided to classify distributions, as well as a function to identify the position of multiple modes.
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2023-06-16 |
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r-acm4r
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Fragment lengths or molecular weights from pairs of lanes are compared, and a number of matching bands are calculated using the Align-and-Count Method.
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2023-06-16 |
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r-allelic
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This is the implementation in R+C of a new association test described in "A fast, unbiased and exact allelic exact test for case-control association studies" (Submitted). It appears that in most cases the classical chi-square test used for testing for allelic association on genotype data is biased. Our test is unbiased, exact but fast throught careful optimization.
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2023-06-16 |
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r-ahaz
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Computationally efficient procedures for regularized estimation with the semiparametric additive hazards regression model.
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2023-06-16 |
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r-agop
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Tools supporting multi-criteria and group decision making, including variable number of criteria, by means of aggregation operators, spread measures, fuzzy logic connectives, fusion functions, and preordered sets. Possible applications include, but are not limited to, quality management, scientometrics, software engineering, etc.
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2023-06-16 |
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r-adaptivesparsity
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Implements Figueiredo EM algorithm for adaptive sparsity (Jeffreys prior) (see Figueiredo, M.A.T.; , "Adaptive sparseness for supervised learning," Pattern Analysis and Machine Intelligence, IEEE Transactions on , vol.25, no.9, pp. 1150- 1159, Sept. 2003) and Wong algorithm for adaptively sparse gaussian geometric models (see Wong, Eleanor, Suyash Awate, and P. Thomas Fletcher. "Adaptive Sparsity in Gaussian Graphical Models." In Proceedings of the 30th International Conference on Machine Learning (ICML-13), pp. 311-319. 2013.)
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2023-06-16 |
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r-abcoptim
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An implementation of Karaboga (2005) Artificial Bee Colony Optimization algorithm <http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf>. This (working) version is a Work-in-progress, which is why it has been implemented using pure R code. This was developed upon the basic version programmed in C and distributed at the algorithm's official website.
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2023-06-16 |
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r-ameco
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Annual macro-economic database provided by the European Commission.
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2023-06-16 |
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r-alterryx
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A tool to access each of the 'Alteryx' Gallery 'API' endpoints. Users can queue jobs, poll job status, and retrieve application output as a data frame. You will need an 'Alteryx' Server license and have 'Alteryx' Gallery running to utilize this package. The 'API' is accessed through the 'URL' that you setup for the server running 'Alteryx' Gallery and more information on the endpoints can be found at <https://gallery.alteryx.com/api-docs/>.
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2023-06-16 |
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r-allehap
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Tools to simulate alphanumeric alleles, impute genetic missing data and reconstruct non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used with simulated datasets or real databases (previously loaded in .ped format). Haplotype reconstruction can be carried out even with missing data, since the program firstly imputes each family genotype (without a reference panel), to later reconstruct the corresponding haplotypes for each family member. All this considering that each individual (due to meiosis) should unequivocally have two alleles per marker (one inherited from each parent) and thus imputation and reconstruction results can be deterministically calculated.
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2023-06-16 |
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r-ald
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It provides the density, distribution function, quantile function, random number generator, likelihood function, moments and Maximum Likelihood estimators for a given sample, all this for the three parameter Asymmetric Laplace Distribution defined in Koenker and Machado (1999). This is a special case of the skewed family of distributions available in Galarza et.al. (2017) <doi:10.1002/sta4.140> useful for quantile regression.
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2023-06-16 |
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r-affluenceindex
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Computes the statistical indices of affluence (richness) and constructs bootstrap confidence intervals for these indices. Also computes the Wolfson polarization index.
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2023-06-16 |
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r-ada
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Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set. The package ada provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets.
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2023-06-16 |
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r-acss.data
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Data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or a large number of random samples of Turing machines (TM) with a given number of states (e.g., 5) and number of symbols corresponding to the number of symbols in the strings were simulated until they reached a halting state or failed to end. This package contains data on 4.5 million strings from length 1 to 12 simulated on TMs with 2, 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states of the TMs.
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2023-06-16 |
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r-abnormality
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Contains the functions to implement the methodology and considerations laid out by Marks et al. in the manuscript Measuring Abnormality in High Dimensional Spaces: Applications in Biomechanical Gait Analysis. As of 2/27/2018 this paper has been submitted and is under scientific review. Using high-dimensional datasets to measure a subject’s overall level of abnormality as compared to a reference population is often needed in outcomes research. Utilizing applications in instrumented gait analysis, that article demonstrates how using data that is inherently non-independent to measure overall abnormality may bias results. A methodology is introduced to address this bias to accurately measure overall abnormality in high dimensional spaces. While this methodology is in line with previous literature, it differs in two major ways. Advantageously, it can be applied to datasets in which the number of observations is less than the number of features/variables, and it can be abstracted to practically any number of domains or dimensions. After applying the proposed methodology to the original data, the researcher is left with a set of uncorrelated variables (i.e. principal components) with which overall abnormality can be measured without bias. Different considerations are discussed in that article in deciding the appropriate number of principal components to keep and the aggregate distance measure to utilize.
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2023-06-16 |
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r-airgr
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Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
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2023-06-16 |
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r-ahocorasicktrie
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Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.
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2023-06-16 |
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r-amctestmaker
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Generate code for use with the Optical Mark Recognition free software Auto Multiple Choice (AMC). More specifically, this package provides functions that use as input the question and answer texts, and output the LaTeX code for AMC.
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2023-06-16 |
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r-ake
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Continuous and discrete (count or categorical) estimation of density, probability mass function (p.m.f.) and regression functions are performed using associated kernels. The cross-validation technique and the local Bayesian procedure are also implemented for bandwidth selection.
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2023-06-16 |
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r-adeptdata
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Created to host raw accelerometry data sets and their derivatives which are used in the corresponding 'adept' package.
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2023-06-16 |
