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Blocking and Randomization for Experimental Design

Vignettes

- Package overview
- README.md
- Basic example
- designit: a flexible engine to generate experiment layouts
- In-vivo study design
- Nested dimension example
- Optimizer examples
- OSAT and scoring functions
- Plate layouts
- Shuffling with constraints
- Using custom shuffle schedule

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**accept_leftmost_improvement:**Alternative acceptance function for multi-dimensional scores...**accept_strict_improvement:**Default acceptance function. Accept current score if and only...**all_equal_df:**Compare two data.frames.**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...**compile_possible_subgroup_allocation:**Compile list of all possible ways to assign levels of the...**complete_random_shuffling:**Reshuffle sample indices completely randomly**designit-package:**designit: Blocking and Randomization for Experimental Design**dot-datatable.aware:**Show that the package is designed to rely on data.table...**drop_order:**Drop highest order interactions**extract_shuffle_params:**Extract relevant parameters from a generic shuffle function...**find_possible_block_allocations:**Internal function to generate possible subgroup combinations...**first_score_only:**Aggregation of scores: take first (primary) score only**form_homogeneous_subgroups:**Form groups and subgroups of 'homogeneous' samples as defined...**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...**invivo_study_treatments:**A treatment list together with additional constraints on the...**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**make_colnames:**Make matrix column names unique.**mk_autoscale_function:**Create a function that transforms a current...**mk_constant_swapping_function:**Create function to propose n pairwise swaps of samples on...**mk_dist_matrix:**Internal helper function to set up an (n m) x (n m) pairwise...**mk_exponentially_weighted_acceptance_func:**Alternative acceptance function for multi-dimensional scores...**mk_plate_scoring_functions:**Create a list of scoring functions (one per plate) that...**mk_simanneal_acceptance_func:**Generate acceptance function for an optimization protocol...**mk_simanneal_temp_func:**Create a temperature function that returns the annealing...**mk_subgroup_shuffling_function:**Created a shuffling function that permutes samples within...**mk_swapping_function:**Create function to propose swaps of samples on each call,...**multi_trt_day_samples:**Unbalanced treatment and time sample list**optimize_design:**Generic optimizer that can be customized by user provided...**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**pairwise_swapping:**Proposes pairwise swap of samples on each call.**plate_effect_example:**Example dataset with a plate effect**plot_plate:**Plot plate layouts**random_score_variances:**Estimate the variance of individual scores by a series of...**report_scores:**Helper function to print out one set of scores plus (if...**sample_random_scores:**Sample scores from a number of completely random sample...**shrink_mat:**Shrinks a matrix with scores and adds an iteration column.**shuffle_grouped_data:**Generate in one go a shuffling function that produces...**shuffle_with_constraints:**Shuffling proposal function with constraints.**Browse all...**

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