# A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants

## Documentation for package ‘ViralEntropR’ version 0.6.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculate_entropy | Calculate Shannon Entropy
calculate_hellinger_matrix | Calculate Hellinger Distance Matrix
cluster_sites_by_entropy | Cluster a Univariate Numeric Vector by Gaussian Mixture Model
decode_aa_sequence | Decode Amino Acid Sequences
detect_changepoints_ecp | Detect Temporal Change Points (ECP)
detect_changepoints_hdcp | Detect Temporal Change Points (HDcpDetect)
encode_aa_sequence | Encode Amino Acid Sequences
extract_fasta_countries | Extract Countries from FASTA Sequence Names
extract_fasta_dates | Extract Dates from FASTA Sequence Names
fasta_to_char_matrix | Convert FASTA Object to Character Matrix
filter_ambiguous_sequences | Remove Sequences Containing Ambiguous Residues
partition_time_windows | Partition Data into Time Windows
plot_entropy_trajectories | Plot Shannon Entropy Trajectories
plot_site_class_trajectory | Plot GMM Entropy Class Trajectory for a Single Site
relabel_entropy_classes | Relabel Entropy Classes
sarscov2_sample | SARS-CoV-2 Surface Glycoprotein Sequences - NCBI Demo Sample
sarscov2_variants | SARS-CoV-2 VOC/VOI Curated Variant Metadata
simulate_variant_evolution | Simulate Viral Variant Evolution
tabulate_site_evolution | Tabulate Site Frequency Evolution