Package index • snp.slicer

All functions

calculate_allele_frequencies(): Calculate Allele Frequencies from MCMC Results
calculate_allele_frequencies_by_sets(): Calculate allele frequencies for multiple target sets
calculate_individual_coi(): Calculate estimated individual COI with uncertainty
clear_performance_log(): Clear performance log
effective_sample_size(): Calculate effective sample size for MCMC diagnostics
example_read0: Example Read Count Data - Reference Alleles
example_read1: Example Read Count Data - Alternate Alleles
example_snp_data: Example SNP Data
extract_allocations(): Extract allocation information from SNP-Slice results
extract_strains(): Extract strain information from SNP-Slice results
get_performance_summary(): Get performance summary
load_example_results(): Load Example Analysis Results
performance_env: Performance Logger for SNP-Slice
plot_convergence(): Plot convergence diagnostics
print(<ess_all_results>): Print comprehensive ESS results for all parameters
print(<ess_result>): Print effective sample size results
print(<snp_slice_results>): Print SNP-Slice results
print_performance_summary(): Print performance summary
snp_slice() snp_slice_categorical() snp_slice_poisson() snp_slice_binomial() snp_slice_negative_binomial(): Bayesian Nonparametric Resolution of Multi-Strain Infections
summary(<snp_slice_results>): Print summary of SNP-Slice results