ungroup input data when loading long form #37
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m-murphy
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Oct 30, 2024
* implement logging of latent genotypes (#14) * Fix NA values in allele frequency vector (#20) The code now checks for NA values in the allele frequency vector and replaces them with 0. A warning message is displayed if NA values are detected, indicating a potential problem with the MCMC chain or loci with no diversity. * Add start_profiler and stop_profiler functions (#24) - Added start_profiler function to R/RcppExports.R - Added stop_profiler function to R/RcppExports.R - Modified src/Makevars to include ENABLE_PROFILER flag and link with -lprofiler - Added start_profiler and stop_profiler functions to src/RcppExports.cpp - Created new file src/profiler.cpp containing the implementation of start_profiler and stop_profiler functions * Refactor Chain class to include methods for calculating likelihood, prior, and posterior for a specific sample. (#33) - Add `get_llik(int sample)` method to calculate the likelihood for a specific sample. - Add `get_prior(int sample)` method to calculate the prior for a specific sample. - Add `get_posterior(int sample)` method to calculate the posterior for a specific sample. These changes allow for more granular calculations of likelihood, prior, and posterior values based on individual samples. * Implement maximum runtime (#34) * Implement maximum runtime * log chain runtime * add utility to detect if openmp is enabled * ungroup input data when loading long form (#37) * fix memory crash in prob_any_missing (#38) The code fix addresses a memory crash issue in the `prob_any_missing` function. The fix includes adding a condition to check if `maxNumEvents` is less than `totalEvents`. If true, it fills the `probVec` vector with 1.0 and returns it. This prevents the memory crash and ensures proper execution of the function. * restore accidentally removed openmp library to compilation * Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. (#27) Add new datasets namibia_data and regional_allele_frequencies. Update vignette with code to use the new datasets. - Added new datasets namibia_data and regional_allele_frequencies. - Updated vignette with code to use the new datasets. * update citation and manuscript
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