Package index • gp3sequences

Sequence data contract

sequence_capabilities(): Report gp3sequences capabilities and optional integrations
audit_sequence_analysis(): Audit a gp3sequences analysis object
compare_sequence_analysis_results(): Compare two gp3sequences analysis results

extract_sequence_ngrams(): Extract Contiguous Sequence N-Grams
summarise_sequence_motifs(): Summarise Contiguous Sequence Motifs
filter_sequence_motifs(): Filter Sequence Motif Summaries
format_sequence_motifs(): Format Sequence Motif Summaries
summarise_sequence_motif_positions(): Summarise Sequence Motif Positions
format_sequence_motif_positions(): Format Sequence Motif Position Summaries
plot_sequence_motifs(): Plot Sequence Motif Summaries
plot_sequence_motif_positions(): Plot Sequence Motif Positions

create_consensus_sequence(): Create an aligned-position consensus sequence
summarise_consensus_agreement(): Summarise consensus agreement
format_consensus_sequence(): Format consensus sequences as paths
plot_consensus_sequence(): Plot a consensus sequence
compare_sequence_groups(): Compare sequence groups descriptively
plot_sequence_group_comparison(): Plot a descriptive sequence-group comparison

compute_sequence_distance(): Compute pairwise sequence distances
summarise_sequence_distance(): Summarise a sequence-distance object
cluster_sequences(): Cluster sequences from a distance object
validate_sequence_clusters(): Validate sequence clusters descriptively
extract_representative_sequences(): Extract representative sequences from clusters
create_sequence_cluster_ensemble(): Create a sequence-cluster ensemble
bootstrap_sequence_clusters(): Bootstrap sequence-cluster stability
summarise_sequence_cluster_stability(): Summarise sequence-cluster stability

create_transition_network(): Create a transition network from ordered sequences
summarise_transition_centrality(): Summarise transition-network centrality
detect_transition_communities(): Detect descriptive transition communities
fit_higher_order_transition_model(): Fit a higher-order transition model
predict_next_state(): Predict the next state from a transition model
bootstrap_transition_network(): Bootstrap transition-network edge weights

fit_sequence_hmm(): Fit a categorical hidden Markov model
fit_sequence_hmm_mixture(): Fit a mixture of categorical hidden Markov models
decode_sequence_states(): Decode hidden states from a fitted HMM
summarise_sequence_hmm(): Summarise a fitted sequence HMM
compare_sequence_hmms(): Compare fitted sequence HMMs descriptively

as_traminer_sequences(): Convert sequence data to a TraMineR state-sequence object
as_arules_sequences(): Convert sequence data to cSPADE transaction input
as_grpstring_data(): Create GrpString-compatible event and string inputs
as_seqhmm_sequences(): Convert sequence data to seqHMM observations
as_igraph_transition_network(): Convert a transition network to an igraph object
prepare_gp3tools_sequences(): Prepare common gp3tools-style sequence outputs

prepare_sequence_panel(): Prepare longitudinal or panel sequence data
summarise_sequence_panel(): Summarise a sequence panel
compare_sequence_panel_changes(): Compare within-panel sequence changes
plot_sequence_panel_changes(): Plot longitudinal sequence changes
fit_time_varying_sequence_model(): Fit a time-varying sequence condition model
predict_time_varying_sequence_model(): Predict a time-varying sequence model
summarise_time_varying_sequence_model(): Summarise a time-varying sequence model
plot_time_varying_sequence_model(): Plot predicted time-varying sequence probabilities

extract_sequence_subsequences(): Extract bounded non-contiguous sequence subsequences
summarise_sequence_subsequences(): Summarise non-contiguous subsequences
filter_sequence_subsequences(): Filter non-contiguous subsequence summaries
compare_sequence_subsequences(): Compare subsequence prevalence between groups
plot_sequence_subsequences(): Plot non-contiguous subsequence summaries

fit_multichannel_sequence_hmm(): Fit a multichannel categorical hidden Markov model
decode_multichannel_sequence_states(): Decode latent states from a multichannel HMM
summarise_multichannel_sequence_hmm(): Summarise a multichannel sequence HMM
plot_multichannel_sequence_hmm(): Plot multichannel HMM emission profiles
fit_covariate_sequence_hmm(): Fit a covariate-dependent categorical hidden Markov model
predict_covariate_transition_probabilities(): Predict covariate-dependent transition probabilities
decode_covariate_sequence_states(): Decode states from a covariate-dependent HMM
summarise_covariate_sequence_hmm(): Summarise a covariate-dependent HMM

declare_sequence_comparison_design(): Declare a sequence group-comparison design
test_sequence_group_difference(): Test a sequence group difference
bootstrap_sequence_group_difference(): Bootstrap a sequence group difference
summarise_sequence_group_inference(): Summarise sequence group inference
plot_sequence_group_inference(): Plot sequence group inference

plot_sequence_index(): Plot a sequence index heatmap
plot_sequence_state_distribution(): Plot state distributions over aligned positions
plot_sequence_entropy(): Plot position-wise state entropy
plot_sequence_distance_heatmap(): Plot a sequence-distance heatmap
plot_transition_network(): Plot a first-order transition network
plot_sequence_cluster_silhouette(): Plot sequence-cluster silhouette values