Colony Formation Assay: Taking into Account Cellular Cooperation

Cellular cooperation compromises the plating efficiency-based analysis of clonogenic survival data. This tool provides functions that enable a robust analysis of colony formation assay (CFA) data in presence or absence of cellular cooperation. The implemented method has been described in Brix et al. (2020). (Brix, N., Samaga, D., Hennel, R. et al. "The clonogenic assay: robustness of plating efficiency-based analysis is strongly compromised by cellular cooperation." Radiat Oncol 15, 248 (2020). ) Power regression for parameter estimation, calculation of survival fractions, uncertainty analysis and plotting functions are provided.

Sequential Parameter Optimization Toolbox

A set of tools for model-based optimization and tuning of algorithms (hyperparameter tuning respectively hyperparameter optimization). It includes surrogate models, optimizers, and design of experiment approaches. The main interface is spot, which uses sequentially updated surrogate models for the purpose of efficient optimization. The main goal is to ease the burden of objective function evaluations, when a single evaluation requires a significant amount of resources.

Linear Programming / Optimization

Can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.

Interface to 'TensorFlow IO'

Interface to 'TensorFlow IO', Datasets and filesystem extensions maintained by `TensorFlow SIG-IO` < https://github.com/tensorflow/community/blob/master/sigs/io/CHARTER.md>.

'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

An extension of the 'AlphaSimR' package (< https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of individual bees that form a colony, which includes a queen, fathers (drones the queen mated with), virgin queens, workers, and drones. Multiple colony can be merged into a population of colonies, such as an apiary or a whole country of colonies. Functions enable operations on castes, colony, or colonies, to ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with respect to genomes and genetic and phenotype values is available and further extended for honeybees, including haplo-diploidy, complementary sex determiner locus, colony events (swarming, supersedure, etc.), and colony phenotype values.

Generate Attractive Random Colors

Simple methods to generate attractive random colors. The random colors are from a wrapper of 'randomColor.js' < https://github.com/davidmerfield/randomColor>. In addition, it also generates optimally distinct colors based on k-means (inspired by 'IWantHue' < https://github.com/medialab/iwanthue>).

Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Support Vector Regression with Metaheuristic Algorithms Optimization

Provides a hybrid modeling framework combining Support Vector Regression (SVR) with metaheuristic optimization algorithms, including the Archimedes Optimization Algorithm (AO) (Hashim et al. (2021) ), Coot Bird Optimization (CBO) (Naruei & Keynia (2021) ), and their hybrid (AOCBO), as well as several others such as Harris Hawks Optimization (HHO) (Heidari et al. (2019) ), Gray Wolf Optimizer (GWO) (Mirjalili et al. (2014) ), Ant Lion Optimization (ALO) (Mirjalili (2015) ), and Enhanced Harris Hawk Optimization with Coot Bird Optimization (EHHOCBO) (Cui et al. (2023) ). The package enables automatic tuning of SVR hyperparameters (cost, gamma, and epsilon) to enhance prediction performance. Suitable for regression tasks in domains such as renewable energy forecasting and hourly data prediction. For more details about implementation and parameter bounds see: Setiawan et al. (2021) and Liu et al. (2018) .

Rmetrics - Portfolio Selection and Optimization

A collection of functions to optimize portfolios and to analyze them from different points of view.

An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization

An R interface to version 0.3 of the 'ROPTLIB' optimization library (see < https://www.math.fsu.edu/~whuang2/> for more information). Optimize real- valued functions over manifolds such as Stiefel, Grassmann, and Symmetric Positive Definite matrices. For details see Martin et. al. (2020) . Note that the optional ldr package used in some of this package's examples can be obtained from either JSS < https://www.jstatsoft.org/index.php/jss/article/view/v061i03/2886> or from the CRAN archives < https://cran.r-project.org/src/contrib/Archive/ldr/ldr_1.3.3.tar.gz>.