Package index • ViralEntropR

Package overview

ViralEntropR ViralEntropR-package: ViralEntropR: A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants

Preprocessing

Fully vectorised FASTA-to-feature-matrix preprocessing layer.

extract_fasta_dates(): Extract Dates from FASTA Sequence Names
extract_fasta_countries(): Extract Countries from FASTA Sequence Names
fasta_to_char_matrix(): Convert FASTA Object to Character Matrix
filter_ambiguous_sequences(): Remove Sequences Containing Ambiguous Residues
encode_aa_sequence(): Encode Amino Acid Sequences
decode_aa_sequence(): Decode Amino Acid Sequences

Site selection

Per-site Shannon entropy, Gaussian mixture model classification, and temporal partitioning into cumulative, sliding, or disjoint windows.

calculate_entropy(): Calculate Shannon Entropy
cluster_sites_by_entropy(): Cluster a Univariate Numeric Vector by Gaussian Mixture Model
relabel_entropy_classes(): Relabel Entropy Classes
partition_time_windows(): Partition Data into Time Windows

Distance and change-point detection

Pairwise Hellinger distances and non-parametric change-point detection (energy statistics; wild binary segmentation).

calculate_hellinger_matrix(): Calculate Hellinger Distance Matrix
detect_changepoints_ecp(): Detect Temporal Change Points (ECP)
detect_changepoints_hdcp(): Detect Temporal Change Points (HDcpDetect)

Visualisation and tabulation

Entropy trajectories, per-site class trajectories, and amino-acid frequency tables.

plot_entropy_trajectories(): Plot Shannon Entropy Trajectories
plot_site_class_trajectory(): Plot GMM Entropy Class Trajectory for a Single Site
tabulate_site_evolution(): Tabulate Site Frequency Evolution

Simulation

Multi-variant evolutionary simulator for benchmarking detection.

simulate_variant_evolution(): Simulate Viral Variant Evolution

Data

Bundled datasets and example sequences for runnable examples and reproducible analyses.

sarscov2_variants: SARS-CoV-2 VOC/VOI Curated Variant Metadata
sarscov2_sample: SARS-CoV-2 Surface Glycoprotein Sequences – NCBI Demo Sample