Package index • appendMCP

All functions

add_criteria_headers(): Function to add criteria headers (removes criteria and time columns)
add_hypothesis_headers(): Function to add hypothesis header rows (removes hypothesis column)
appendMCP-package appendMCP: Generate analysis documentation for graphical MCPs in group sequential trials
apply_hypothesis_tests(): Apply hypothesis tests to analyses
calculate_analysis_timing_cpp_wrapper(): Wrapper function to fix C++ list-column issue
calculate_z_bounds(): Calculate z bounds
check_allowed_columns(): Check allowed columns
check_analyses_dependencies(): Check analyses dependencies
check_analyses_structure(): Check analyses data.frame structure
check_bounded_double_column(): Check bounded double column
check_character_column(): Check character column
check_character_or_na_column(): Check character or NA column
check_character_vector_or_na_column(): Check character vector or NA column (list column)
check_column_all_or_none(): Check that column is present in all objects or none
check_column_all_or_none_mapped(): Check that mapped columns are present in all objects or none
check_column_presence(): Check that all objects have specified column
check_config_by_element(): Check if config is a valid list with required structure
check_config_column_consistency(): Check column consistency across config components
check_config_dependencies(): Check dependencies between config components
check_distribution_bin_structure(): Check distribution_bin data.frame structure
check_distribution_combinations(): Check distribution combinations exist
check_distribution_presence(): Check at least one distribution is present
check_distribution_tte_structure(): Check distribution_tte data.frame structure
check_double_or_null_column(): Check double or NULL column
check_enroll_rate_dependencies(): Check enroll_rate dependencies
check_enroll_rate_structure(): Check enroll_rate data.frame structure
check_graph_dependencies(): Check graph dependencies
check_graph_structure(): Check graph list structure
check_hypotheses_dependencies(): Check hypotheses dependencies
check_hypotheses_structure(): Check hypotheses data.frame structure
check_nonnegative_double_column(): Check non-negative double column
check_optional_character(): Check optional character field
check_optional_date(): Check optional date field
check_positive_double_column(): Check positive double column
check_positive_double_or_inf_column(): Check positive double or Inf column
check_positive_double_or_na_column(): Check positive double or NA column
check_positive_double_vector_or_null_column(): Check positive double vector or NULL column (list column)
check_positive_integer_or_na_column(): Check positive integer or NA column
check_positive_integer_vector_column(): Check positive integer vector column (list column)
check_required_dataframe(): Check required data.frame field
check_required_list(): Check required list field
check_required_numeric_bounded(): Check required numeric field with bounds
check_sf_sfpar(): Check sf and sfpar combination
create_study(): Create new study from config and template
create_summary_tables(): Create summary tables
example_study_config: Example Study Configuration List
exec_sims(): Execute simulations for marginal operating characteristics
expected_d_at_t(): Expected events at specific time
expected_n_at_t(): Expected sample size at specific time
expected_t_at_d(): Expected time for specific number of events
expected_t_at_n(): Expected time for specific sample size
extract_information_levels(): Extract information levels from analyses results
generate_report(): Generate GSD Report
get_boundaries(): Get boundary specifications for group sequential design
get_config_path(): Get path to config file from repository
get_cum_alpha_spend(): Extract nominal cum alpha-spending from OC object
get_description_effect_size(): Get description of effect size
get_description_max_info(): Get description of maximal information level
get_description_sf(): Get description of spending function
get_description_trigger_long(): Get long description of analysis trigger
get_description_trigger_short(): Get short description of analysis trigger
get_enroll_rate_combinations(): Get enroll_rate combinations (unnested)
get_hurdles(): Extract exit hurdles from OC object
get_hypothesis_combinations(): Get all hypothesis combinations
get_maurer_bretz(): Implement M/B - version for IPD simulations
get_maurer_bretz_z_raw(): Simplified Maurer-Bretz procedure with matrix-based rejection tracking
get_nominal_p(): Extract nominal p-value thresholds from OC object
get_p_thresholds(): Get p thresholds
get_pooled_rate(): Calculate pooled rate across strata
get_powers(): Extract cumulative powers from OC object
get_rmd_template_path(): Get path to Rmd template skeleton
get_treatment_colors(): Get consistent treatment colors
get_weights(): Get all possible weights for each endpoint in graphical testing procedure
list_config_repository(): Get available config repository entries
list_rmd_template_repository(): Get available Rmd template repository entries
load_config(): Load study configuration from file path
load_config_from_repository(): Load config from repository
load_rmd_template(): Load Rmd template from file path
load_rmd_template_from_repository(): Load Rmd template from repository
plot_distribution_bin(): Plot binary endpoint rates
plot_distribution_bin_rd(): Plot risk difference for binary endpoints
plot_distribution_tte(): Plot time-to-event survival curves
plot_distribution_tte_ahr(): Plot average hazard ratio over time by hypothesis
plot_distribution_tte_cumhaz(): Plot cumulative hazard
plot_distribution_tte_dropout(): Plot dropout rate over time
plot_distribution_tte_dropout_probability(): Plot dropout patterns
plot_distribution_tte_hazard(): Plot time-to-event hazard rates
plot_distribution_tte_hr(): Plot hazard ratio over time by hypothesis
plot_distribution_tte_median(): Plot median survival time
plot_distribution_tte_quantiles(): Plot quantiles
plot_distribution_tte_weighted(): Plot enrollment-weighted survival by hypothesis
plot_enroll_rate(): Plot enrollment rates over time
plot_enroll_rate_cumulative(): Plot cumulative enrollment over time
plot_graph(): Create multiplicity graph visualization
plot_information(): Plot information factor or fraction over time for each hypothesis
plot_spending_functions(): Plot alpha spending functions
process_analyses_1(): Process analyses with timing information
process_analyses_2(): Process analyses with hypothesis information
process_config(): Process configuration into complete GSD analysis
process_distribution(): Combine time-to-event and binary endpoint distributions
process_enroll_rate(): Process enroll_rate
process_hypotheses(): Process hypotheses with boundary specifications
process_rejection_rules(): Process rejection rules
resolve_config_source(): Resolve config source (name, path, or list)
resolve_rmd_template_source(): Resolve rmd_template source (name or path)
sim_dataset(): Dataset simulation
sim_outcomes(): Simulation with data.table optimization
table1_hux(): Table 1: Trial Design Summary
table2_hux(): Table 2: Summary by hypothesis (with header rows)
table3_hux(): Table 3: Summary by criteria for conduct
table4_hux(): Table 4: Summary of alpha allocation by hypothesis
table5_hux(): Table 5: Boundary specifications
table6a_hux(): Table 6a: Operating characteristics by analysis
table6b_hux(): Table 6b: Operating characteristics across analyses
update_graph(): Update graph
update_p_thresholds(): Update p thresholds
validate_config(): Validate study configuration