Resistance profile code cleanup and Updated Vignettes

[Nilanjana1606]

• profile_convex.R: new Pathway 1 pipeline — validate_profile_inputs,
  preprocess_for_profiles, validate_aggregate_inputs,
  compute_marginals_from_data, compute_pairwise_from_data (Pearson
  back-calc), estimate_profiles_convex (QP), enumerate_binary_profiles,
  build_constraint_matrix, check_profile_constraints,
  bootstrap_profiles_convex
  • daly_resistance_prevalence.R: export daly_filter_profiles_to_rr_classes
    and daly_calc_resistance_prevalence_fatal; fix prioritize_resistance to
    accept unnamed hierarchy vector; fix check.names=FALSE for class names
    with hyphens; store constraint_targets alongside constraint_residuals
  • Remove redundant RR mapping functions (daly_lookup_rr,
    daly_map_rr_pathogen, daly_map_rr_drug_class, get_rr_pathogen_map,
    get_class_rr_map); consolidate into daly_add_rr_mappings
• Vignettes: split getting-started into landing page + preprocessing
  pipeline + new daly-pipeline vignette

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