Evaluates the Owen Q-function for an integer value of the degrees of freedom, by applying Owen's algorithm (1965) <doi:10.1093/biomet/52.3-4.437>. It is useful for the calculation of the power of equivalence tests.

Ordnance Survey ('OS') is the national mapping agency for Great Britain and produces a large variety of mapping and geospatial products. Much of OS's data is available via the OS Data Hub <https://osdatahub.os.uk/>, a platform that hosts both free and premium data products. osdatahub provides a user-friendly way to access, query, and download these data.

This package implements a tree-based method specifically designed for personalized medicine applications. By using genomic and mutational data, ODT efficiently identifies optimal drug recommendations tailored to individual patient profiles. The ODT algorithm constructs decision trees that bifurcate at each node, selecting the most relevant markers (discrete or continuous) and corresponding treatments, thus ensuring that recommendations are both personalized and statistically robust. This iterative approach enhances therapeutic decision-making by refining treatment suggestions until a predefined group size is achieved. Moreover, the simplicity and interpretability of the resulting trees make the method accessible to healthcare professionals. Includes functions for training the decision tree, making predictions on new samples or patients, and visualizing the resulting tree. For detailed insights into the methodology, please refer to Gimeno et al. (2023) <doi:10.1093/bib/bbad200>.

Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.

This package provides a derivative-based optimization framework that allows users to combine eight convergence criteria. Unlike standard optimization functions, this package includes a built-in mechanism to verify the positive definiteness of the Hessian matrix at the point of convergence. This additional check helps prevent the solver from falsely identifying non-optimal solutions, such as saddle points, as valid minima.

This package provides a database resource that is accessible through the Open Database Connectivity ('ODBC') API. This package uses the Resource model, with URL "resolver" and "client", to dynamically discover and make accessible tables stored in a MS SQL Server database. For more details see Marcon (2021) <doi:10.1371/journal.pcbi.1008880>.

This package provides details such as Morphine Equivalent Dose (MED), brand name and opioid content which are calculated of all oral opioids authorized for sale by Health Canada and the FDA based on their Drug Identification Number (DIN) or National Drug Code (NDC). MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI) and Von Korff et al (2008) and information obtained from Health Canada's Drug Product Database's monthly data dump or FDA Daily database for Canadian and US databases respectively. Please note in no way should output from this package be a substitute for medical advise. All medications should only be consumed on prescription from a licensed healthcare provider.

Computes confidence regions on the location of response surface optima. Response surface models can be up to cubic polynomial models in up to 5 controllable factors, or Thin Plate Spline models in 2 controllable factors.

We provide an R interface to OpenML.org which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.

Facilitates the automatic detection of acoustic signals, providing functions to diagnose and optimize the performance of detection routines. Detections from other software can also be explored and optimized. This package has been peer-reviewed by rOpenSci. Araya-Salas et al. (2022) <doi:10.1101/2022.12.13.520253>.

This package provides carefully chosen color palettes as used a.o. at OpenAnalytics <http://www.openanalytics.eu>.

Image analysis techniques for positron emission tomography (PET) that form part of the Rigorous Analytics bundle.

This package provides a novel method to implement cancer subtyping and subtype specific drug targets identification via non-negative matrix tri-factorization. To improve the interpretability, we introduce orthogonal constraint to the row coefficient matrix and column coefficient matrix. To meet the prior knowledge that each subtype should be strongly associated with few gene sets, we introduce sparsity constraint to the association sub-matrix. The average residue was introduced to evaluate the row and column cluster numbers. This is part of the work "Liver Cancer Analysis via Orthogonal Sparse Non-Negative Matrix Tri- Factorization" which will be submitted to BBRC.

Crawler for OJS pages and scraper for meta-data from articles. You can crawl OJS archives, issues, articles, galleys, and search results. You can scrape articles metadata from their head tag in html, or from Open Archives Initiative ('OAI') records. Most of these functions rely on OJS routing conventions (<https://docs.pkp.sfu.ca/dev/documentation/en/architecture-routes>).

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in noisy datasets with unknown number of clusters. Results on summarized genetic data of 1,200 patients are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>. A short video tutorial can be found at <https://www.youtube.com/watch?v=P2XAjqI5Lc4/>.

This package provides an interface to connect R with the <https://github.com/IDEMSInternational/open-app-builder> OpenAppBuilder platform, enabling users to retrieve and work with user and notification data for analysis and processing. It is designed for developers and analysts to seamlessly integrate data from OpenAppBuilder into R workflows via a Postgres database connection, allowing direct querying and import of app data into R.

Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package alabama', or by sequential quadratic programming using solver slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package cccp'.

Applies an objective Bayesian method to the Mb capture-recapture model to estimate the population size N. The Mb model is a class of capture-recapture methods used to account for variations in capture probability due to animal behavior. Under the Mb formulation, the initial capture of an animal may effect the probability of subsequent captures due to their becoming "trap happy" or "trap shy.".

Apache OpenNLP jars and basic English language models.

Calculates autoecological data (optima and tolerance ranges) of a biological species given an environmental matrix. The package calculates by weighted averaging, using the number of occurrences to adjust the tolerance assigned to each taxon to estimate optima and tolerance range in cases where taxa have unequal occurrences. See the detailed methodology by Birks et al. (1990) <doi:10.1098/rstb.1990.0062>, and a case example by Potapova and Charles (2003) <doi:10.1046/j.1365-2427.2003.01080.x>.

Predictive scores must be updated with care, because actions taken on the basis of existing risk scores causes bias in risk estimates from the updated score. A holdout set is a straightforward way to manage this problem: a proportion of the population is held-out from computation of the previous risk score. This package provides tools to estimate a size for this holdout set and associated errors. Comprehensive vignettes are included. Please see: Haidar-Wehbe S, Emerson SR, Aslett LJM, Liley J (2022) <doi:10.48550/arXiv.2202.06374> (to appear in Annals of Applied Statistics) for details of methods.

An implementation of optimal weight exchange algorithm Yang(2013) <doi:10.1080/01621459.2013.806268> for three models. They are Crossover model with subject dropout, crossover model with proportional first order residual effects and interference model. You can use it to find either A-opt or D-opt approximate designs. Exact designs can be automatically rounded from approximate designs and relative efficiency is provided as well.

This package provides a tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.

The client streamlines access to the services provided by <https://api.openrouteservice.org>. It allows you to painlessly query for directions, isochrones, time-distance matrices, geocoding, elevation, points of interest, and more.