Transparent Analysis of Ordered Categorical Sequences

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Documentation for package ‘gp3sequences’ version 0.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

as_arules_sequences	Convert sequence data to cSPADE transaction input
as_grpstring_data	Create GrpString-compatible event and string inputs
as_igraph_transition_network	Convert a transition network to an igraph object
as_seqhmm_sequences	Convert sequence data to seqHMM observations
as_traminer_sequences	Convert sequence data to a TraMineR state-sequence object
audit_sequence_analysis	Audit a gp3sequences analysis object
audit_sequence_data	Audit Long-Format Sequence Data
bootstrap_sequence_clusters	Bootstrap sequence-cluster stability
bootstrap_sequence_group_difference	Bootstrap a sequence group difference
bootstrap_transition_network	Bootstrap transition-network edge weights
cluster_sequences	Cluster sequences from a distance object
compare_sequence_analysis_results	Compare two gp3sequences analysis results
compare_sequence_groups	Compare sequence groups descriptively
compare_sequence_hmms	Compare fitted sequence HMMs descriptively
compare_sequence_panel_changes	Compare within-panel sequence changes
compare_sequence_subsequences	Compare subsequence prevalence between groups
compute_sequence_distance	Compute pairwise sequence distances
create_consensus_sequence	Create an aligned-position consensus sequence
create_sequence_cluster_ensemble	Create a sequence-cluster ensemble
create_transition_network	Create a transition network from ordered sequences
declare_sequence_comparison_design	Declare a sequence group-comparison design
decode_covariate_sequence_states	Decode states from a covariate-dependent HMM
decode_multichannel_sequence_states	Decode latent states from a multichannel HMM
decode_sequence_states	Decode hidden states from a fitted HMM
detect_transition_communities	Detect descriptive transition communities
encode_sequence_data	Encode Ordered Sequence States
extract_representative_sequences	Extract representative sequences from clusters
extract_sequence_ngrams	Extract Contiguous Sequence N-Grams
extract_sequence_subsequences	Extract bounded non-contiguous sequence subsequences
filter_sequence_motifs	Filter Sequence Motif Summaries
filter_sequence_subsequences	Filter non-contiguous subsequence summaries
fit_covariate_sequence_hmm	Fit a covariate-dependent categorical hidden Markov model
fit_higher_order_transition_model	Fit a higher-order transition model
fit_multichannel_sequence_hmm	Fit a multichannel categorical hidden Markov model
fit_sequence_hmm	Fit a categorical hidden Markov model
fit_sequence_hmm_mixture	Fit a mixture of categorical hidden Markov models
fit_time_varying_sequence_model	Fit a time-varying sequence condition model
format_consensus_sequence	Format consensus sequences as paths
format_sequence_motifs	Format Sequence Motif Summaries
format_sequence_motif_positions	Format Sequence Motif Position Summaries
format_sequence_paths	Format Ordered Sequence Paths
plot_consensus_sequence	Plot a consensus sequence
plot_multichannel_sequence_hmm	Plot multichannel HMM emission profiles
plot_sequence_cluster_silhouette	Plot sequence-cluster silhouette values
plot_sequence_distance_heatmap	Plot a sequence-distance heatmap
plot_sequence_entropy	Plot position-wise state entropy
plot_sequence_group_comparison	Plot a descriptive sequence-group comparison
plot_sequence_group_inference	Plot sequence group inference
plot_sequence_index	Plot a sequence index heatmap
plot_sequence_motifs	Plot Sequence Motif Summaries
plot_sequence_motif_positions	Plot Sequence Motif Positions
plot_sequence_panel_changes	Plot longitudinal sequence changes
plot_sequence_state_distribution	Plot state distributions over aligned positions
plot_sequence_subsequences	Plot non-contiguous subsequence summaries
plot_time_varying_sequence_model	Plot predicted time-varying sequence probabilities
plot_transition_network	Plot a first-order transition network
predict_covariate_transition_probabilities	Predict covariate-dependent transition probabilities
predict_next_state	Predict the next state from a transition model
predict_time_varying_sequence_model	Predict a time-varying sequence model
prepare_gp3tools_sequences	Prepare common gp3tools-style sequence outputs
prepare_sequence_data	Prepare Long-Format Sequence Data
prepare_sequence_panel	Prepare longitudinal or panel sequence data
sequence_capabilities	Report gp3sequences capabilities and optional integrations
summarise_consensus_agreement	Summarise consensus agreement
summarise_covariate_sequence_hmm	Summarise a covariate-dependent HMM
summarise_multichannel_sequence_hmm	Summarise a multichannel sequence HMM
summarise_sequence_cluster_stability	Summarise sequence-cluster stability
summarise_sequence_distance	Summarise a sequence-distance object
summarise_sequence_group_inference	Summarise sequence group inference
summarise_sequence_hmm	Summarise a fitted sequence HMM
summarise_sequence_motifs	Summarise Contiguous Sequence Motifs
summarise_sequence_motif_positions	Summarise Sequence Motif Positions
summarise_sequence_panel	Summarise a sequence panel
summarise_sequence_states	Summarise Sequence States
summarise_sequence_subsequences	Summarise non-contiguous subsequences
summarise_sequence_transitions	Summarise Adjacent Sequence Transitions
summarise_time_varying_sequence_model	Summarise a time-varying sequence model
summarise_transition_centrality	Summarise transition-network centrality
test_sequence_group_difference	Test a sequence group difference
validate_sequence_clusters	Validate sequence clusters descriptively
validate_sequence_data	Validate Long-Format Sequence Data