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) |