All functions 


R6 Class representing a batch container. 

R6 Class representing a batch container dimension. 

Aggregation of scores: L1 norm 

Aggregation of scores: L2 norm squared 

Alternative acceptance function for multidimensional scores in which order (left to right, e.g. first to last) denotes relevance. 

Distributes samples based on a sample sheet. 

Distributes samples in order. 

Assignment function which distributes samples randomly. 

Creates a BatchContainer from a table (data.frame/tibble::tibble) containing sample and location information. 

Compile list of all possible ways to assign levels of the allocation variable to a given set of subgroups 

Reshuffle sample indices completely randomly 

Drop highest order interactions 

Aggregation of scores: take first (primary) score only 

Form groups and subgroups of 'homogeneous' samples as defined by certain variables and size constraints 

Generate 

Get highest order interaction 

A sample list from an in vivo experiment with multiple treatments and 2 strains 

A treatment list together with additional constraints on the strain and sex of animals 

Create locations table from dimensions and exclude table 

Subject sample list with group and time plus controls 

Alternative acceptance function for multidimensional scores with exponentially downweighted score improvements from left to right 

Create a list of scoring functions (one per plate) that quantify the spatially homogeneous distribution of conditions across the plate 

Generate acceptance function for an optimization protocol based on simulated annealing 

Create a temperature function that returns the annealing temperature at a given step (iteration) 

Created a shuffling function that permutes samples within certain subgroups of the container locations 

Create function to propose swaps of samples on each call, either with a constant number of swaps or following a user defined protocol 

Unbalanced treatment and time sample list 

Generic optimizer that can be customized by user provided functions for generating shuffles and progressing towards the minimal score 

Convenience wrapper to optimize a typical multiplate design 

Compute OSAT score for sample assignment. 

Convenience wrapper for the OSAT score 

Example dataset with a plate effect 

Plot plate layouts 

Generate in one go a shuffling function that produces permutations with specific constraints on multiple sample variables and group sizes fitting one specific allocation variable 

Shuffling proposal function with constraints. 

Compose shuffling function based on already available subgrouping and allocation information 

Aggregation of scores: sum up all individual scores 

Validates sample data.frame. 

Aggregation of scores: take the maximum (i.e. worst score only) 