Identifies an optimal transformation of a surrogate marker such that the proportion of treatment effect explained can be inferred based on the transformation of the surrogate and nonparametrically estimates two model-free quantities of this proportion. Details are described in Wang et al (2020) <doi:10.1093/biomet/asz065>.

This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays.

Cucumber is a tool for running automated tests written in plain language. Because they're written in plain language, they can be read by anyone on your team. Because they can be read by anyone, you can use them to help improve communication, collaboration and trust on your team.

This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.

Uses locality sensitive hashing and creates a neighbourhood graph for a data set and calculates the adjusted rank index value for the same. It uses Gaussian random planes to decide the nature of a given point. Datar, Mayur, Nicole Immorlica, Piotr Indyk, and Vahab S. Mirrokni(2004) <doi:10.1145/997817.997857>.

This package provides a unique dataset of historical forest cover across all states in the United States, spanning from 1907 to 2017, along with 1630 as a reference year. This dataset is important for understanding environmental changes and land use trends over time. It includes functionality for easy access of the data.

Offers a comprehensive solution for managing empty states in Shiny applications. It provides tools to create both default and customizable components for scenarios where data is absent or doesn't match user-defined filters. The package prioritizes user experience, ensuring clarity and consistency even when data is not available to display.

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Supports the definition of sets of properties on objects. Observers can listen to changes on individual properties or the set as a whole. The properties are meant to be fully self-describing. In support of this, there is a framework for defining enumerated types, as well as other bounded types, as S4 classes.

Access open data from <https://www.threesixtygiving.org>, a database of charitable grant giving in the UK operated by 360Giving'. The package provides functions to search and retrieve data on charitable grant giving, and process that data into tidy formats. It relies on the 360Giving data standard, described at <https://standard.threesixtygiving.org/>.

Climate stability measures are not formalized in the literature and tools for generating stability metrics from existing data are nascent. This package provides tools for calculating climate stability from raster data encapsulating climate change as a series of time slices. The methods follow Owens and Guralnick <doi:10.17161/bi.v14i0.9786> Biodiversity Informatics.

Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>.

This is a package for saving matrices, arrays and similar objects into file artifacts, and loading them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

eval-in-repl provides a consistent ESS-like evaluation interface for various REPLs. In particular, it mimics ESS' C-RET binding, which sends a line or region to an appropriately configured shell. This package provides just the core of eval-in-repl---for the languages themselves, see their respective packages.

Adjust the Gamma regression models from a Bayesian perspective described by Cepeda and Urdinola (2012) <doi:10.1080/03610918.2011.600500>, modeling the parameters of mean and shape and using different link functions for the parameter associated to the mean. And calculates different adjustment statistics such as the Akaike information criterion and Bayesian information criterion.

Estimation of optimal portfolio weights as combination of simple portfolio strategies, like the tangency, global minimum variance (GMV) or naive (1/N) portfolio. It is based on a utility maximizing 8-fund rule. Popular special cases like the Kan-Zhou(2007) 2-fund and 3-fund rule or the Tu-Zhou(2011) estimator are nested.

This package provides a quasiquoter for raw string literals, i.e. string literals that don't recognise the standard escape sequences. Basically, they make your code more readable by freeing you from the responsibility to escape backslashes. They are useful when working with regular expressions, DOS/Windows paths and markup languages (such as XML).

This module exports a single hash (%RE) that stores or generates commonly needed regular expressions. Patterns currently provided include: balanced parentheses and brackets, delimited text (with escapes), integers and floating-point numbers in any base (up to 36), comments in 44 languages, offensive language, lists of any pattern, IPv4 addresses, URIs, and Zip codes.

This package provides a collection of functions to set up Google Public Data Explorer <https://www.google.com/publicdata/> data visualization tool with your own data, building automatically the corresponding DataSet Publishing Language file, or DSPL (XML), metadata file jointly with the CSV files. All zip-up and ready to be published in Public Data Explorer'.

Local structure in genomic data often induces dependence between observations taken at different genomic locations. Ignoring this dependence leads to underestimation of the standard error of parameter estimates. This package uses block bootstrapping to estimate asymptotically correct standard errors of parameters from any standard generalised linear model that may be fit by the glm() function.

Ensemble functions for outlier/anomaly detection. There is a new ensemble method proposed using Item Response Theory. Existing outlier ensemble methods from Schubert et al (2012) <doi:10.1137/1.9781611972825.90>, Chiang et al (2017) <doi:10.1016/j.jal.2016.12.002> and Aggarwal and Sathe (2015) <doi:10.1145/2830544.2830549> are also included.

Scraping content from archived web pages stored in the Internet Archive (<https://archive.org>) using a systematic workflow. Get an overview of the mementos available from the respective homepage, retrieve the Urls and links of the page and finally scrape the content. The final output is stored in tibbles, which can be then easily used for further analysis.

You can apply image processing effects that modifies the perceived material properties of objects in photos, such as gloss, smoothness, and blemishes. This is an implementation of the algorithm proposed by Boyadzhiev et al. (2015) "Band-Sifting Decomposition for Image Based Material Editing". Documentation and practical tips of the package is available at <https://github.com/tsuda16k/materialmodifier>.

Extract the signed backbones of intrinsically dense weighted networks based on the significance filter and vigor filter as described in the following paper. Please cite it if you find this software useful in your work. Furkan Gursoy and Bertan Badur. "Extracting the signed backbone of intrinsically dense weighted networks." Journal of Complex Networks. <arXiv:2012.05216>.