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r-arpsdca
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Functions for Arps decline-curve analysis on oil and gas data. Includes exponential, hyperbolic, harmonic, and hyperbolic-to-exponential models as well as the preceding with initial curtailment or a period of linear rate buildup. Functions included for computing rate, cumulative production, instantaneous decline, EUR, time to economic limit, and performing least-squares best fits.
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2023-06-16 |
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r-arco
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Set of functions to analyse and estimate Artificial Counterfactual models from Carvalho, Masini and Medeiros (2016) <DOI:10.2139/ssrn.2823687>.
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2023-06-16 |
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r-ararredux
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Processes noble gas mass spectrometer data to determine the isotopic composition of argon (comprised of Ar36, Ar37, Ar38, Ar39 and Ar40) released from neutron-irradiated potassium-bearing minerals. Then uses these compositions to calculate precise and accurate geochronological ages for multiple samples as well as the covariances between them. Error propagation is done in matrix form, which jointly treats all samples and all isotopes simultaneously at every step of the data reduction process. Includes methods for regression of the time-resolved mass spectrometer signals to t=0 ('time zero') for both single- and multi-collector instruments, blank correction, mass fractionation correction, detector intercalibration, decay corrections, interference corrections, interpolation of the irradiation parameter between neutron fluence monitors, and (weighted mean) age calculation. All operations are performed on the logs of the ratios between the different argon isotopes so as to properly treat them as 'compositional data', sensu Aitchison [1986, The Statistics of Compositional Data, Chapman and Hall].
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2023-06-16 |
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r-arabicstemr
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Allows users to stem Arabic texts for text analysis.
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2023-06-16 |
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r-apsrtable
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Formats latex tables from one or more model objects side-by-side with standard errors below, not unlike tables found in such journals as the American Political Science Review.
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2023-06-16 |
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r-apc
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Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) <DOI:10.1093/biomet/asn026> is used. Thus, the analysis does not rely on ad hoc identification.
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2023-06-16 |
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r-adegraphics
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Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
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2023-06-16 |
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r-assa
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Functions to model and decompose time series into principal components using singular spectrum analysis (de Carvalho and Rua (2017) <doi:10.1016/j.ijforecast.2015.09.004>; de Carvalho et al (2012) <doi:10.1016/j.econlet.2011.09.007>).
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2023-06-16 |
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r-artp
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For calculating gene and pathway p-values using the Adaptive Rank Truncated Product test.
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2023-06-16 |
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r-apml0
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Fit linear, logistic and Cox models regularized with L0, lasso (L1), elastic-net (L1 and L2), or net (L1 and Laplacian) penalty, and their adaptive forms, such as adaptive lasso / elastic-net and net adjusting for signs of linked coefficients. It solves L0 penalty problem by simultaneously selecting regularization parameters and the number of non-zero coefficients. This augmented and penalized minimization method provides an approximation solution to the L0 penalty problem, but runs as fast as L1 regularization problem. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients. It could deal with very high dimensional data and has superior selection performance.
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2023-06-16 |
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r-batch
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Functions to allow you to easily pass command-line arguments into R, and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package.
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2023-06-16 |
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r-auc
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This package includes functions to compute the area under the curve of selected measures: The area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.
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2023-06-16 |
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r-astrolibr
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Several dozen low-level utilities and codes from the Interactive Data Language (IDL) Astronomy Users Library (http://idlastro.gsfc.nasa.gov) are implemented in R. They treat: time, coordinate and proper motion transformations; terrestrial precession and nutation, atmospheric refraction and aberration, barycentric corrections, and related effects; utilities for astrometry, photometry, and spectroscopy; and utilities for planetary, stellar, Galactic, and extragalactic science.
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2023-06-16 |
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r-antaresprocessing
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Process results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>. This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.
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2023-06-16 |
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r-arm
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Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.
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2023-06-16 |
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r-argonr
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R wrapper around the argon HTML library. More at <https://demos.creative-tim.com/argon-design-system/>.
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2023-06-16 |
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r-argo
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Augmented Regression with General Online data (ARGO) for accurate estimation of influenza epidemics in United States on both national level and regional level. It replicates the method introduced in paper Yang, S., Santillana, M. and Kou, S.C. (2015) <doi:10.1073/pnas.1515373112> and Ning, S., Yang, S. and Kou, S.C. (2019) <doi:10.1038/s41598-019-41559-6>.
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2023-06-16 |
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r-anoint
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The tools in this package are intended to help researchers assess multiple treatment-covariate interactions with data from a parallel-group randomized controlled clinical trial.
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2023-06-16 |
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r-annotlists
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Annotate multiple lists from a specific annotation file.
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2023-06-16 |
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r-assist
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A comprehensive package for fitting various non-parametric/semi-parametric linear/nonlinear fixed/mixed smoothing spline models.
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2023-06-16 |
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r-b6e6rl
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This package contains b6e6rl algorithm, adaptive differential evolution for global optimization.
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2023-06-16 |
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r-autoshiny
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Static code compilation of a 'shiny' app given an R function (into 'ui.R' and 'server.R' files or into a 'shiny' app object). See examples at <https://github.com/alekrutkowski/autoshiny>.
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2023-06-16 |
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r-atus
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Abridged data from the American Time Use Survey (ATUS) for years 2003-2016. The ATUS is an annual survey conducted on a sample of individuals across the United States studying how individuals spent their time over the course of a day. Individual respondents were interviewed about what activities they did, during what times (rounded to 15 minute increments), at what locations, and in the presence of which individuals. The activities are subsequently encoded based on 3 separate tier codes for classification. This package includes data from the multi-year ATUS Activities, ATUS-CPS, and ATUS Respondents files were included. Columns were selected based on completeness of data as well as presence on the Frequently Used Variables list provided by the ATUS website. All activity codes (other than code '50' for 'Unable to Code') were included. Permission was obtained from the Bureau of Labor Statistics for inclusion in this package. The full data can be obtained from <http://www.bls.gov/tus/>.
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2023-06-16 |
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r-attempt
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Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.
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2023-06-16 |
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r-assertive.models
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A set of predicates and assertions for checking the properties of models. This is mainly for use by other package developers who want to include run-time testing features in their own packages. End-users will usually want to use assertive directly.
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2023-06-16 |
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r-bayesdccgarch
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Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635).
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2023-06-16 |
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r-basicspace
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Conducts Aldrich-McKelvey and Blackbox Scaling (Poole et al 2016) <doi:10.18637/jss.v069.i07> to recover latent dimensions of judgment.
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2023-06-16 |
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r-audio
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Interfaces to audio devices (mainly sample-based) from R to allow recording and playback of audio. Built-in devices include Windows MM, Mac OS X AudioUnits and PortAudio (the last one is very experimental).
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2023-06-16 |
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r-assortnet
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Functions to calculate the assortment of vertices in social networks. This can be measured on both weighted and binary networks, with discrete or continuous vertex values.
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2023-06-16 |
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r-artiva
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Reversible Jump MCMC (RJ-MCMC)sampling for approximating the posterior distribution of a time varying regulatory network, under the Auto Regressive TIme VArying (ARTIVA) model (for a detailed description of the algorithm, see Lebre et al. BMC Systems Biology, 2010). Starting from time-course gene expression measurements for a gene of interest (referred to as "target gene") and a set of genes (referred to as "parent genes") which may explain the expression of the target gene, the ARTIVA procedure identifies temporal segments for which a set of interactions occur between the "parent genes" and the "target gene". The time points that delimit the different temporal segments are referred to as changepoints (CP).
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2023-06-16 |
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r-arht
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Perform the Adaptable Regularized Hotelling's T^2 test (ARHT) proposed by Li et al., (2016) <arXiv:1609.08725>. Both one-sample and two-sample mean test are available with various probabilistic alternative prior models. It contains a function to consistently estimate higher order moments of the population covariance spectral distribution using the spectral of the sample covariance matrix (Bai et al. (2010) <doi:10.1111/j.1467-842X.2010.00590.x>). In addition, it contains a function to sample from 3-variate chi-squared random vectors approximately with a given correlation matrix when the degrees of freedom are large.
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2023-06-16 |
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r-apdesign
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An implementation of the additive polynomial (AP) design matrix. It constructs and appends an AP design matrix to a data frame for use with longitudinal data subject to seasonality.
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2023-06-16 |
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r-ampd
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A method for automatic detection of peaks in noisy periodic and quasi-periodic signals. This method, called automatic multiscale-based peak detection (AMPD), is based on the calculation and analysis of the local maxima scalogram, a matrix comprising the scale-dependent occurrences of local maxima. For further information see <doi:10.3390/a5040588>.
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2023-06-16 |
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r-aspbay
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This package allows to make inference on the properties of causal genetic variants in linkage disequilibrium with genotyped markers. In a first step, we select a subset of variants using a score statistic for affected sib-pairs. In a second step, on the selected subset, we make inference on causal genetic variants in the considered region.
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2023-06-16 |
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r-arrangements
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Fast generators and iterators for permutations, combinations and partitions. The iterators allow users to generate arrangements in a memory efficient manner and the generated arrangements are in lexicographical (dictionary) order. Permutations and combinations can be drawn with/without replacement and support multisets. It has been demonstrated that 'arrangements' outperforms most of the existing packages of similar kind. Some benchmarks could be found at <https://randy3k.github.io/arrangements/articles/benchmark.html>.
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2023-06-16 |
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r-bayesdistreg
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Implements Bayesian Distribution Regression methods. This package contains functions for three estimators (non-asymptotic, semi-asymptotic and asymptotic) and related routines for Bayesian Distribution Regression in Huang and Tsyawo (2018) <doi:10.2139/ssrn.3048658> which is also the recommended reference to cite for this package. The functions can be grouped into three (3) categories. The first computes the logit likelihood function and posterior densities under uniform and normal priors. The second contains Independence and Random Walk Metropolis-Hastings Markov Chain Monte Carlo (MCMC) algorithms as functions and the third category of functions are useful for semi-asymptotic and asymptotic Bayesian distribution regression inference.
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2023-06-16 |
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r-assertive.sets
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A set of predicates and assertions for checking the properties of sets. This is mainly for use by other package developers who want to include run-time testing features in their own packages. End-users will usually want to use assertive directly.
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2023-06-16 |
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r-bayesianetas
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The Epidemic Type Aftershock Sequence (ETAS) model is one of the best-performing methods for modeling and forecasting earthquake occurrences. This package implements Bayesian estimation routines to draw samples from the full posterior distribution of the model parameters, given an earthquake catalog. The paper on which this package is based is Gordon J. Ross - Bayesian Estimation of the ETAS Model for Earthquake Occurrences (2016), available from the below URL.
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2023-06-16 |
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r-awsmethods
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Defines the method extract and provides 'openMP' support as needed in several packages.
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2023-06-16 |
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r-aspi
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Tools for the analysis and visualization of bilateral asymmetry in parasitic infections.
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2023-06-16 |
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r-asgs.foyer
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The Australian Statistical Geography Standard ('ASGS') is a set of shapefiles by the Australian Bureau of Statistics. This package provides an interface to those shapefiles, as well as methods for converting coordinates to shapefiles.
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2023-06-16 |
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r-archdata
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The archdata package provides several types of data that are typically used in archaeological research. It provides all of the data sets used in "Quantitative Methods in Archaeology Using R" by David L Carlson, one of the Cambridge Manuals in Archaeology.
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2023-06-16 |
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r-basetheme
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Functions to create and select graphical themes for the base plotting system. Contains: 1) several custom pre-made themes 2) mechanism for creating new themes by making persistent changes to the graphical parameters of base plots.
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2023-06-16 |
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r-atlas
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Stanford 'ATLAS' (Advanced Temporal Search Engine) is a powerful tool that allows constructing cohorts of patients extremely quickly and efficiently. This package is designed to interface directly with an instance of 'ATLAS' search engine and facilitates API queries and data dumps. Prerequisite is a good knowledge of the temporal language to be able to efficiently construct a query. More information available at <https://shahlab.stanford.edu/start>.
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2023-06-16 |
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r-ate
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Nonparametric estimation and inference for average treatment effects based on covariate balancing.
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2023-06-16 |
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r-bain
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Computes approximated adjusted fractional Bayes factors for equality, inequality, and about equality constrained hypotheses. S3 methods are available for specific types of lm() models, namely ANOVA, ANCOVA, and multiple regression, and for the t_test(). The statistical underpinnings are described in Hoijtink, Mulder, van Lissa, and Gu, (2018) <doi:10.31234/osf.io/v3shc>, Gu, Mulder, and Hoijtink, (2018) <doi:10.1111/bmsp.12110>, Hoijtink, Gu, and Mulder, (2018) <doi:10.1111/bmsp.12145>, and Hoijtink, Gu, Mulder, and Rosseel, (2018) <doi:10.1037/met0000187>.
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2023-06-16 |
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r-av
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Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generate high quality videos files by capturing images from the R graphics device combined with custom audio stream. This package interfaces directly to the C API and does not require any command line utilities.
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2023-06-16 |
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r-aod
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Provides a set of functions to analyse overdispersed counts or proportions. Most of the methods are already available elsewhere but are scattered in different packages. The proposed functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM).
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2023-06-16 |
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r-amen
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Analysis of dyadic network and relational data using additive and multiplicative effects (AME) models. The basic model includes regression terms, the covariance structure of the social relations model (Warner, Kenny and Stoto (1979) <DOI:10.1037/0022-3514.37.10.1742>, Wong (1982) <DOI:10.2307/2287296>), and multiplicative factor models (Hoff(2009) <DOI:10.1007/s10588-008-9040-4>). Four different link functions accommodate different relational data structures, including binary/network data (bin), normal relational data (nrm), ordinal relational data (ord) and data from fixed-rank nomination schemes (frn). Several of these link functions are discussed in Hoff, Fosdick, Volfovsky and Stovel (2013) <DOI:10.1017/nws.2013.17>. Development of this software was supported in part by NIH grant R01HD067509.
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2023-06-16 |
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r-argon2
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Utilities for secure password hashing via the argon2 algorithm. It is a relatively new hashing algorithm and is believed to be very secure. The 'argon2' implementation included in the package is the reference implementation. The package also includes some utilities that should be useful for digest authentication, including a wrapper of 'blake2b'. For similar R packages, see sodium and 'bcrypt'. See <https://en.wikipedia.org/wiki/Argon2> or <https://eprint.iacr.org/2015/430.pdf> for more information.
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2023-06-16 |
