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r-bayesm
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public |
Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).
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2023-06-16 |
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r-bayesbio
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public |
A hodgepodge of hopefully helpful functions. Two of these perform shrinkage estimation: one using a simple weighted method where the user can specify the degree of shrinkage required, and one using James-Stein shrinkage estimation for the case of unequal variances.
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2023-06-16 |
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r-barcodingr
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public |
To perform species identification using DNA barcodes.
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2023-06-16 |
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r-automl
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public |
Fits from simple regression to highly customizable deep neural networks either with gradient descent or metaheuristic, using automatic hyper parameters tuning and custom cost function. A mix inspired by the common tricks on Deep Learning and Particle Swarm Optimization.
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2023-06-16 |
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r-assocind
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Implements several new association indices that can control for various types of errors. Also includes existing association indices and functions for simulating the effects of different rates of error on estimates of association strength between individuals using each method.
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2023-06-16 |
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r-asdreader
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A simple driver that reads binary data created by the ASD Inc. portable spectrometer instruments, such as the FieldSpec (for more information, see <http://www.asdi.com/products/fieldspec-spectroradiometers>). Spectral data can be extracted from the ASD files as raw (DN), white reference, radiance, or reflectance. Additionally, the metadata information contained in the ASD file header can also be accessed.
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2023-06-16 |
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r-apsimbatch
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public |
Run APSIM in Batch mode
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2023-06-16 |
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r-apfr
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Implements a multiple testing approach to the choice of a threshold gamma on the p-values using the Average Power Function (APF) and Bayes False Discovery Rate (FDR) robust estimation. Function apf_fdr() estimates both quantities from either raw data or p-values. Function apf_plot() produces smooth graphs and tables of the relevant results. Details of the methods can be found in Quatto P, Margaritella N, et al. (2019) <doi:10.1177/0962280219844288>.
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2023-06-16 |
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r-analyz
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public |
Class with methods to read and execute R commands described as steps in a CSV file.
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2023-06-16 |
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r-atsd
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public |
Provides functions for retrieving time-series and related meta-data such as entities, metrics, and tags from the Axibase Time-Series Database (ATSD). ATSD is a non-relational clustered database used for storing performance measurements from IT infrastructure resources: servers, network devices, storage systems, and applications.
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2023-06-16 |
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r-ade4tkgui
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public |
A Tcl/Tk GUI for some basic functions in the 'ade4' package.
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2023-06-16 |
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r-bamp
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public |
Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov Chain Monte Carlo Methods. This is the R version of the previous BAMP software as described in Volker Schmid and Leonhard Held (2007) <DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and Prediction - BAMP, Journal of Statistical Software 21:8. This package includes checks of convergence using Gelman's R.
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2023-06-16 |
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r-astrofns
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public |
Miscellaneous astronomy functions, utilities, and data.
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2023-06-16 |
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r-ardec
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Package ArDec implements autoregressive-based decomposition of a time series based on the constructive approach in West (1997). Particular cases include the extraction of trend and seasonal components.
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2023-06-16 |
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r-approxmatch
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public |
Tools for constructing a matched design with multiple comparison groups. Further specifications of refined covariate balance restriction and exact match on covariate can be imposed. Matches are approximately optimal in the sense that the cost of the solution is at most twice the optimal cost, Crama and Spieksma (1992) <doi:10.1016/0377-2217(92)90078-N>.
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2023-06-16 |
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r-aplore3
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public |
An unofficial companion to "Applied Logistic Regression" by D.W. Hosmer, S. Lemeshow and R.X. Sturdivant (3rd ed., 2013) containing the dataset used in the book.
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2023-06-16 |
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r-apcanalysis
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public |
Analysis of data from unreplicated orthogonal experiments
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2023-06-16 |
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r-aoos
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Another implementation of object-orientation in R. It provides syntactic sugar for the S4 class system and two alternative new implementations. One is an experimental version built around S4 and the other one makes it more convenient to work with lists as objects.
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2023-06-16 |
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r-aods3
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Provides functions to analyse overdispersed counts or proportions. These functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM). aods3 is an S3 re-implementation of the deprecated S4 package aod.
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2023-06-16 |
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r-apple
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public |
Approximate Path for Penalized Likelihood Estimators for Generalized Linear Models penalized by LASSO or MCP
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2023-06-16 |
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r-barborgradient
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public |
Tool to find where a function has its lowest value(minimum). The functions can be any dimensions. Recommended use is with eps=10^-10, but can be run with 10^-20, although this depends on the function. Two more methods are in this package, simple gradient method (Gradmod) and Powell method (Powell). These are not recommended for use, their purpose are purely for comparison.
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2023-06-16 |
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r-b2z
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public |
This package fits the Bayesian two-Zone Models.
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2023-06-16 |
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r-automultinomial
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public |
Fits the autologistic model described in Besag's famous 1974 paper on auto- models <http://www.jstor.org/stable/2984812>. Fits a multicategory generalization of the autologistic model when there are more than 2 response categories. Provides support for both asymptotic and bootstrap confidence intervals. For full model descriptions and a guide to the use of this package, please see the vignette.
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2023-06-16 |
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r-assertive.reflection
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public |
A set of predicates and assertions for checking the state and capabilities of R, the operating system it is running on, and the IDE being used. 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-assertive.properties
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A set of predicates and assertions for checking the properties of variables, such as length, names and attributes. 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-banxicor
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Provides functions to scrape IQY calls to Bank of Mexico, downloading and ordering the data conveniently.
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2023-06-16 |
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r-bannercommenter
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public |
A convenience package for use while drafting code. It facilitates making stand-out comment lines decorated with bands of characters. The input text strings are converted into R comment lines, suitably formatted. These are then displayed in a console window and, if possible, automatically transferred to a clipboard ready for pasting into an R script. Designed to save time when drafting R scripts that will need to be navigated and maintained by other programmers.
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2023-06-16 |
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r-babar
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public |
Babar is designed to use nested sampling (a Bayesian analysis technique) to compare possible models for bacterial growth curves, as well as extracting parameters. It allows model evidence and parameter likelihood values to be extracted, and also contains helper functions for comparing distributions as well as direct access to the underlying nested sampling code.
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2023-06-16 |
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r-awr
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public |
Installs the compiled Java modules of the Amazon Web Services ('AWS') 'SDK' to be used in downstream R packages interacting with 'AWS'. See <https://aws.amazon.com/sdk-for-java> for more information on the 'AWS' 'SDK' for Java.
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2023-06-16 |
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r-autoencoder
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Implementation of the sparse autoencoder in R environment, following the notes of Andrew Ng (http://www.stanford.edu/class/archive/cs/cs294a/cs294a.1104/sparseAutoencoder.pdf). The features learned by the hidden layer of the autoencoder (through unsupervised learning of unlabeled data) can be used in constructing deep belief neural networks.
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2023-06-16 |
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r-atsa
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public |
Contains some tools for testing, analyzing time series data and fitting popular time series models such as ARIMA, Moving Average and Holt Winters, etc. Most functions also provide nice and clear outputs like SAS does, such as identify, estimate and forecast, which are the same statements in PROC ARIMA in SAS.
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2023-06-16 |
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r-asymld
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public |
Computes asymmetric LD measures (ALD) for multi-allelic genetic data. These measures are identical to the correlation measure (r) for bi-allelic data.
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2023-06-16 |
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r-asnipe
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public |
Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
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2023-06-16 |
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r-arsenal
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public |
An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.
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2023-06-16 |
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r-argumentcheck
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The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message.
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2023-06-16 |
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r-appnn
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Amyloid propensity prediction neural network (APPNN) is an amyloidogenicity propensity predictor based on a machine learning approach through recursive feature selection and feed-forward neural networks, taking advantage of newly published sequences with experimental, in vitro, evidence of amyloid formation.
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2023-06-16 |
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r-apng
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public |
Convert several png files into an animated png file. This package exports only a single function `apng'. Call the apng function with a vector of file names (which should be png files) to convert them to a single animated png file.
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2023-06-16 |
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r-aster2
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Aster models are exponential family regression models for life history analysis. They are like generalized linear models except that elements of the response vector can have different families (e. g., some Bernoulli, some Poisson, some zero-truncated Poisson, some normal) and can be dependent, the dependence indicated by a graphical structure. Discrete time survival analysis, zero-inflated Poisson regression, and generalized linear models that are exponential family (e. g., logistic regression and Poisson regression with log link) are special cases. Main use is for data in which there is survival over discrete time periods and there is additional data about what happens conditional on survival (e. g., number of offspring). Uses the exponential family canonical parameterization (aster transform of usual parameterization). Unlike the aster package, this package does dependence groups (nodes of the graph need not be conditionally independent given their predecessor node), including multinomial and two-parameter normal as families. Thus this package also generalizes mark-capture-recapture analysis.
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2023-06-16 |
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r-aspect
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public |
Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
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2023-06-16 |
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r-artp2
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public |
Pathway and gene level association test using raw data or summary statistics.
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2023-06-16 |
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r-arrapply
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public |
High performance variant of apply() for a fixed set of functions. Considerable speedup is a trade-off for universality, user defined functions cannot be used with this package. However, 21 most currently employed functions are available for usage. They can be divided in three types: reducing functions (like mean(), sum() etc., giving a scalar when applied to a vector), mapping function (like normalise(), cumsum() etc., giving a vector of the same length as the input vector) and finally, vector reducing function (like diff() which produces result vector of a length different from the length of input vector). Optional or mandatory additional arguments required by some functions (e.g. norm type for norm() or normalise() functions) can be passed as named arguments in '...'.
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2023-06-16 |
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r-armspp
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An efficient 'Rcpp' implementation of the Adaptive Rejection Metropolis Sampling (ARMS) algorithm proposed by Gilks, W. R., Best, N. G. and Tan, K. K. C. (1995) <doi:10.2307/2986138>. This allows for sampling from a univariate target probability distribution specified by its (potentially unnormalised) log density.
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2023-06-16 |
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r-anmc
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public |
Computationally efficient method to estimate orthant probabilities of high-dimensional Gaussian vectors. Further implements a function to compute conservative estimates of excursion sets under Gaussian random field priors.
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2023-06-16 |
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r-barcode
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public |
This package includes the function \code{barcode()}, which produces a histogram-like plot of a distribution that shows granularity in the data.
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2023-06-16 |
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r-badgecreatr
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public |
Tired of copy and pasting almost identical markdown for badges in every new R-package that you create, on Github or other code-sharing sites? This package allows you to easily paste badges. If you want to, it will also search your DESCRIPTION file and extract the package name, license, R-version, and current projectversion and transform that into badges. It will also search for a ".travis.yml" file and create a "Travis"" badge, if you use "Codecov.io" to check your code coverage after a "Travis" build this package will also build a "Codecov.io"-badge. All the badges can be placed individually or can be placed below the top "YAML"" content of your "RMarkdown file" (Readme.Rmd) or "README.md" file. Currently creates badges for Projectstatus ("Repostatus.org"), license Travis Build Status, Codecov, Minimal R version, CRAN status, CRAN downloads, Github stars and forks, Package rank, rdocumentation, current version of your package and last change of "README.Rmd".
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2023-06-16 |
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r-bacprior
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The BACprior package provides an approximate sensitivity analysis of the Bayesian Adjustment for Confounding (BAC) algorithm (Wang et al., 2012) with regards to the hyperparameter omega. The package also provides functions to guide the user in their choice of an appropriate omega value. The method is based on Lefebvre, Atherton and Talbot (2014).
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2023-06-16 |
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r-audit
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public |
Two Bayesian methods for Accounting Populations
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2023-06-16 |
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r-asypow
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public |
A set of routines written in the S language that calculate power and related quantities utilizing asymptotic likelihood ratio methods.
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2023-06-16 |
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r-bart
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public |
Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
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2023-06-16 |
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r-arulessequences
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Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
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2023-06-16 |
