MEchanistic Clustering - Treatment eXposure Framework

[Up] [Top]

Documentation for package ‘mectx’ version 1.1.1

Help Pages

cox_forest_plot_from_df Cox Proportional Hazards Forest Plot
dominant_exclusive Assign Mutually Exclusive Dominant Treatment Regimen Per Patient
get_focus_cohort Extract Focus Cohort Sample IDs
km_panel_from_df Kaplan-Meier Survival Panel with Optional Risk Table
plot_timeline_for_k Treatment Timeline Facet Plot by Cluster Assignment
prep_segs Recode and clip treatment segments to canonical types Validates a raw segments data frame, recodes free-text treatment type labels to the eight canonical MEC-TX types via regex, and clips segment start/end times to '[0, horizon_years]'. Zero-duration segments (after clipping) and rows with 'NA' in 'sample', 't0', or 't1' are dropped. Called upstream by 'plot_timeline_for_k()' and 'timeline_panel()' - not intended for direct use.
standardise_status Standardise Survival Status Column to 0/1 Integer
timeline_panel Treatment Timeline Panel for Selected Patients
treatment_shares Compute per-patient treatment type durations and shares Takes a clipped and recoded segments data frame (output of 'prep_segs') and computes per-patient treatment duration and share for each of the eight canonical treatment types. Returns a wide-format tibble with one row per patient. Called upstream by 'timeline_panel' and 'plot_timeline_for_k' - not intended for direct use.
tx_cluster_surv Cluster Treatment Timelines and Attach Survival Data
tx_compare_groups Flexible Survival Comparison by Grouping Variable or Custom Groups
tx_duration Treatment Duration Analysis by Grouping Variable
tx_focus_dt Digital Twin Focus Analysis for a Specific Treatment Type
tx_intervals Convert Normalised Treatment Timeline to Treatment Intervals
tx_lines Detect Lines of Therapy from Treatment Timelines
tx_normalize Normalise Raw Medication Data into a Grid-Based Treatment Timeline
tx_pooled_analysis Pooled Treatment Cohort Analysis