Radmeth performance improvements#282
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andrewdavidsmith merged 12 commits intomasterfrom Aug 11, 2025
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…e and into the radmeth_model.chpp sources
…lgorithm to calculate the beta-binomial likelihood
…get the mapping from sample to group; also put some functions here that were previously in radmeth.cpp because they belong with the model structs
…mputing the beta-binomial likelihood and gradients. This algorithm accumulates mass without the use of unstable gamma functions but minimizes the number of summations by re-grouping terms. Doing this required a focus on groups rather than factors and samples, where a group is a set of factor level combinations
…for more optimization
…ecutive sites of extreme coverage can cause an imbalance in terms of work done by threads. Also using a decimal digit of precision in the progress reporting
…o cache some log1p calculations
…ting some log1p that can be reused across groups
…mputing the beta-binomial likelihood and gradients. This algorithm accumulates mass without the use of unstable gamma functions but minimizes the number of summations by re-grouping terms. Doing this required a focus on groups rather than factors and samples, where a group is a set of factor level combinations
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Implemented a novel algorithm for computing the likelihood and for computing the likelihood's gradient for the beta binomial with general design