This package provides data structures and functions for file input/output in the ribios software suite, supporting common bioinformatics and computational biology file formats, designed for fast loading and high performance with minimal dependencies.

Scelestial infers a lineage tree from single-cell DNA mutation matrix. It generates a tree with approximately maximum parsimony through a Steiner tree approximation algorithm.

Adds subtotal rows / sections (a la the SAS Proc Tabulate All option) to a Group By output by running a series of Group By functions with partial sets of the same variables and combining the results with the original. Can be used to add comprehensive information to a data report or to quickly aggregate Group By outputs used to gain a greater understanding of data.

An implementation of calls designed to collect and organize Mastodon data via its Application Program Interfaces (API), which can be found at the following URL: <https://docs.joinmastodon.org/>.

This package provides a set of tools for creation, manipulation, and modeling of tensors with arbitrary number of modes. A tensor in the context of data analysis is a multidimensional array. rTensor does this by providing a S4 class Tensor that wraps around the base array class. rTensor provides common tensor operations as methods, including matrix unfolding, summing/averaging across modes, calculating the Frobenius norm, and taking the inner product between two tensors. Familiar array operations are overloaded, such as index subsetting via [ and element-wise operations. rTensor also implements various tensor decomposition, including CP, GLRAM, MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some auxiliary functions include the Khatri-Rao product, Kronecker product, and the Hadamard product for a list of matrices.

Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).

This package implements the pseudo-R2D2 prior for ordinal regression from the paper "Pseudo-R2D2 prior for high-dimensional ordinal regression" by Yanchenko (2025) <doi:10.1007/s11222-025-10667-x>. In particular, it provides code to evaluate the probability distribution function for the cut-points, compute the log-likelihood, calculate the hyper-parameters for the global variance parameter, find the distribution of McFadden's coefficient-of-determination, and fit the model in rstan'. Please cite the paper if you use these codes.

The Refugee Population Statistics Database published by The Office of The United Nations High Commissioner for Refugees (UNHCR) contains information about forcibly displaced populations spanning more than 70 years of statistical activities. It covers displaced populations such as refugees, asylum-seekers and internally displaced people, including their demographics. Stateless people are also included, most of who have never been displaced. The database also reflects the different types of solutions for displaced populations such as repatriation or resettlement. More information on the data and methodology can be found on the UNHCR Refugee Data Finder <https://www.unhcr.org/refugee-statistics/>.

Compute an exact CI for the population mean under a random effects model. The routines implement the algorithm described in Michael, Thronton, Xie, and Tian (2017) <https://haben-michael.github.io/research/Exact_Inference_Meta.pdf>.

You can easily share url pages using React Router in shiny applications and Quarto documents. The package wraps the react-router-dom React library and provides access to hash routing to navigate on multiple url pages.

Extract the implied risk neutral density from options using various methods.

This package provides tools to perform random forest consensus clustering of different data types. The package is designed to accept a list of matrices from different assays, typically from high-throughput molecular profiling so that class discovery may be jointly performed. For references, please see Tao Shi & Steve Horvath (2006) <doi:10.1198/106186006X94072> & Monti et al (2003) <doi:10.1023/A:1023949509487> .

Mimic the style of traditional reporting macros for clinical trials. The purpose is to generate tables, listings and figures that support clinical research. This package is well suited for firms or individuals who wish to incorporate R without changing their ways of working as it follows a traditional clinical research workflow. Invoke functions (instead of macros) to summarize data and produce formatted reports. This package differs from others in that it includes tools (wrappers) for both analyzing and reporting data.

Aims at loading Facebook and Instagram advertising data from Smartly.io into R. Smartly.io is an online advertising service that enables advertisers to display commercial ads on social media networks (see <http://www.smartly.io/> for more information). The package offers an interface to query the Smartly.io API and loads data directly into R for further data processing and data analysis.

Univariate and multivariate versions of risk-based control charts. Univariate versions of control charts, such as the risk-based version of X-bar, Moving Average (MA), Exponentially Weighted Moving Average Control Charts (EWMA), and Cumulative Sum Control Charts (CUSUM) charts. The risk-based version of the multivariate T2 control chart. Plot and summary functions. Kosztyan et. al. (2016) <doi:10.1016/j.eswa.2016.06.019>.

This package provides a set of functions for receiver operating characteristic (ROC) curve estimation and area under the curve (AUC) calculation. All functions are designed to work with aggregated data; nevertheless, they can also handle raw samples. In ROCket', we distinguish two types of ROC curve representations: 1) parametric curves - the true positive rate (TPR) and the false positive rate (FPR) are functions of a parameter (the score), 2) functions - TPR is a function of FPR. There are several ROC curve estimation methods available. An introduction to the mathematical background of the implemented methods (and much more) can be found in de Zea Bermudez, Gonçalves, Oliveira & Subtil (2014) and Cai & Pepe (2004).

Quantitative Structure-Activity Relationship (QSAR) modeling is a valuable tool in computational chemistry and drug design, where it aims to predict the activity or property of chemical compounds based on their molecular structure. In this vignette, we present the rQSAR package, which provides functions for variable selection and QSAR modeling using Multiple Linear Regression (MLR), Partial Least Squares (PLS), and Random Forest algorithms.

Upload R data.frame to Arm Treasure Data, see <https://www.treasuredata.com/>. You can execute database or table handling for resources on Arm Treasure Data.

Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.

This package provides a high-performance interface for calculating string similarities and distances, leveraging the efficient library RapidFuzz <https://github.com/rapidfuzz/rapidfuzz-cpp>. This package integrates the C++ implementation, allowing R users to access cutting-edge algorithms for fuzzy matching and text analysis.

Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.

The rearrangement operator (Hardy, Littlewood, and Polya 1952) for univariate, bivariate, and trivariate point estimates of monotonic functions. The package additionally provides a function that creates simultaneous confidence intervals for univariate functions and applies the rearrangement operator to these confidence intervals.

Value-calibrated color ramps can be useful to emphasize patterns in data from complex distributions. Colors can be tied to specific values, and the association can be expanded into full color ramps that also include the relationship between colors and values. Such ramps can be used in a variety of cases when heatmap-type plots are necessary, including the visualization of vector and raster spatial data, such as topographies.

OpenWeatherMap (OWM) <http://openweathermap.org/api> is a service providing weather related data. This package can be used to access current weather data for one location or several locations. It can also be used to forecast weather for 5 days with data for every 3 hours.