Maximal Biclique Enumeration in Bipartite Graphs

A tool for enumerating maximal complete bipartite graphs. The input should be a edge list file or a binary matrix file. The output are maximal complete bipartite graphs. Algorithms used can be found in this paper Y. Lu et al. BMC Res Notes 13, 88 (2020) .

Perform Forward and Backwards Chasing in Evidence Syntheses

In searching for research articles, we often want to obtain lists of references from across studies, and also obtain lists of articles that cite a particular study. In systematic reviews, this supplementary search technique is known as 'citation chasing': forward citation chasing looks for all records citing one or more articles of known relevance; backward citation chasing looks for all records referenced in one or more articles. Traditionally, this process would be done manually, and the resulting records would need to be checked one-by-one against included studies in a review to identify potentially relevant records that should be included in a review. This package contains functions to automate this process by making use of the Lens.org API. An input article list can be used to return a list of all referenced records, and/or all citing records in the Lens.org database (consisting of PubMed, PubMed Central, CrossRef, Microsoft Academic Graph and CORE; < https://www.lens.org>).

Process Accelerometer Data for Physical Activity Measurement

It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.

Segmentation and Classification of Accelerometer Data

Segmentation and classification procedures for data from the 'Activinsights GENEActiv' < https://activinsights.com/technology/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.

Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

CEU Mass Mediator RESTful API

CEU (CEU San Pablo University) Mass Mediator is an on-line tool for aiding researchers in performing metabolite annotation. 'cmmr' (CEU Mass Mediator RESTful API) allows for programmatic access in R: batch search, batch advanced search, MS/MS (tandem mass spectrometry) search, etc. For more information about the API Endpoint please go to < https://github.com/YaoxiangLi/cmmr>.

Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS Optimization

Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian. If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the 'Scilab' optimization documentation located at < https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.

Analytical Methods for Stream DAGs

Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) , and in the introductory package vignette.

Bayesian Inference of Binary, Count and Continuous Data in Toxicology

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of several type of toxicological data. 'binary' (e.g., survival, mobility), 'count' (e.g., reproduction) and 'continuous' (e.g., growth as length, weight). Estimation procedures can be used without a deep knowledge of their underlying probabilistic model or inference methods. Rather, they were designed to behave as well as possible without requiring a user to provide values for some obscure parameters. That said, models can also be used as a first step to tailor new models for more specific situations.

Wrangle Phylogenetic Distance Matrices and Other Utilities

Harriet was Charles Darwin's pet tortoise (possibly). 'harrietr' implements some function to manipulate distance matrices and phylogenetic trees to make it easier to plot with 'ggplot2' and to manipulate using 'tidyverse' tools.