accept_leftmost_improvement | Alternative acceptance function for multi-dimensional scores in which order (left to right, e.g. first to last) denotes relevance. |

assign_from_table | Distributes samples based on a sample sheet. |

assign_in_order | Distributes samples in order. |

assign_random | Assignment function which distributes samples randomly. |

BatchContainer | R6 Class representing a batch container. |

BatchContainerDimension | R6 Class representing a batch container dimension. |

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

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

complete_random_shuffling | Reshuffle sample indices completely randomly |

drop_order | Drop highest order interactions |

first_score_only | Aggregation of scores: take first (primary) score only |

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

generate_terms | Generate 'terms.object' (formula with attributes) |

get_order | Get highest order interaction |

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

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

L1_norm | Aggregation of scores: L1 norm |

L2s_norm | Aggregation of scores: L2 norm squared |

locations_table_from_dimensions | Create locations table from dimensions and exclude table |

longitudinal_subject_samples | Subject sample list with group and time plus controls |

mk_exponentially_weighted_acceptance_func | Alternative acceptance function for multi-dimensional scores with exponentially downweighted score improvements from left to right |

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

mk_simanneal_acceptance_func | Generate acceptance function for an optimization protocol based on simulated annealing |

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

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

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

multi_trt_day_samples | Unbalanced treatment and time sample list |

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

optimize_multi_plate_design | Convenience wrapper to optimize a typical multi-plate design |

osat_score | Compute OSAT score for sample assignment. |

osat_score_generator | Convenience wrapper for the OSAT score |

plate_effect_example | Example dataset with a plate effect |

plot_plate | Plot plate layouts |

shuffle_grouped_data | 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 |

shuffle_with_constraints | Shuffling proposal function with constraints. |

shuffle_with_subgroup_formation | Compose shuffling function based on already available subgrouping and allocation information |

sum_scores | Aggregation of scores: sum up all individual scores |

validate_samples | Validates sample data.frame. |

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