Package index • pharmhand

S7 Classes

Core S7 classes for clinical data structures and reporting objects.

ADaMData(): ADaMData Class
AnalysisMeta(): AnalysisMeta Class
AnalysisResults(): AnalysisResults Class
ClinicalPlot(): ClinicalPlot Class
ClinicalReport(): ClinicalReport Class
ClinicalTable(): ClinicalTable Class
ComparisonResult(): ComparisonResult Class
CompositeFormat(): CompositeFormat S7 Class
Endpoint(): Endpoint Class
EvidenceGrade(): EvidenceGrade Class
FormatSpec(): FormatSpec S7 Class
LayeredTable(): Layered Table Class
PerformanceReport(): PerformanceReport Class
ReportSection(): ReportSection Class
StatResult(): StatResult Class (Abstract Base)
StudyResult(): StudyResult Class

Configuration

Configuration classes and functions for managing clinical report settings, populations, subgroups, and SOC/PT configurations from YAML files or runtime.

ConfigurationRegistry(): ConfigurationRegistry Class
PTConfig(): PTConfig Class
PopulationConfig(): PopulationConfig Class
SOCConfig(): SOCConfig Class
SubgroupConfig(): SubgroupConfig Class
config_api: Configuration API for Clinical Reports
config_classes: S7 Configuration Classes for Clinical Reports
define_population_config(): Define or override a population configuration
define_subgroup_config(): Define or override a subgroup configuration
get_performance_setting(): Get performance setting
get_population_config(): Get population configuration
get_subgroup_config(): Get subgroup configuration
list_populations(): List available populations
list_subgroups(): List available subgroups
load_config(): Load configuration from YAML file
update_pt_config(): Update PT configuration
update_soc_config(): Update SOC configuration

Study Design Classes

Classes and methods for defining and analyzing clinical study designs. Supports single-arm, two-arm, and multi-arm study configurations.

SingleArmStudy(): SingleArmStudy Class
TwoArmStudy(): TwoArmStudy Class
MultiArmStudy(): MultiArmStudy Class
Study(): Study Class (Abstract Base)
StudySet(): StudySet Class
analyze_study(): Analyze Study (S7 Method)
analyze_study_SingleArmStudy(): Analyze SingleArmStudy
analyze_study_TwoArmStudy(): Analyze TwoArmStudy
analyze(): Analyze ADaM datasets
analyze_ADaMData(): Analyze ADaMData

HTA & Endpoint Classes

Health Technology Assessment (HTA) endpoint definitions and section classes for structured reporting.

HTAEndpoint(): HTAEndpoint Class
HTASection(): HTASection Class
PopulationSection(): PopulationSection Class
SOCPTSection(): SOCPTSection Class
SubgroupSection(): SubgroupSection Class

Efficacy Tables

Functions for creating efficacy analysis tables including time-to-event, responder, and subgroup analyses.

create_tte_summary_table(): Create Time-to-Event Summary Table
test_non_inferiority(): Non-Inferiority Test
create_responder_table(): Create Responder Summary Table
create_subgroup_table(): Create Subgroup Analysis Table
create_subgroup_analysis_table(): Create Subgroup Analysis Table
create_primary_endpoint_table(): Create Primary Endpoint Summary Table
create_cfb_summary_table(): Create Change from Baseline Summary Table
ancova_adjust_continuous(): ANCOVA Analysis for Continuous Endpoints

Safety Tables

Functions for adverse event and safety analysis tables including laboratory shifts and AE summaries.

create_ae_summary_table(): Create Adverse Event Summary Table
create_ae_comparison_table(): Create AE Comparison Table with Risk Differences
create_ae_exposure_table(): Create Exposure-Adjusted AE Table
create_ae_hierarchy_table(): Create AE Table with Full MedDRA Hierarchy
create_time_to_first_ae(): Create Time-to-First AE Analysis
create_lab_shift_table(): Create Laboratory Shift Table
create_lab_summary_table(): Create Laboratory Summary Table
create_conmeds_table(): Create Concomitant Medications Table
create_medical_history_table(): Create Medical History Table
create_vs_by_visit_table(): Create Vital Signs by Visit Table
analyze_soc_pt(): Analyze Adverse Events by SOC and PT
calculate_ae_tte_data(): Calculate AE TTE Data for a specific SOC
calculate_ae_risk_difference(): Calculate Risk Difference and Confidence Interval for AE
calculate_exposure_adjusted_rate(): Calculate Exposure-Adjusted Incidence Rate

Standard Tables

Demographics, disposition, baseline, and other standard clinical study tables.

create_demographics_table(): Create Demographics Table
create_disposition_table(): Create Subject Disposition Table
create_population_summary_table(): Create Analysis Populations Summary Table
create_region_table(): Create Enrollment by Region Table
create_clinical_table(): Create Clinical Table (Factory Function)
create_hta_table(): Create a flextable formatted for HTA/AMNOG submissions.
create_hta_module4_table(): Create Module 4 Table Template
calculate_baseline(): Calculate Baseline Characteristics

Plotting

Clinical visualization functions for Kaplan-Meier curves, forest plots, and other graphics.

create_km_plot(): Create Kaplan-Meier Plot
create_ae_cumulative_incidence_plot(): Create AE Cumulative Incidence Plot
create_forest_plot(): Create Subgroup Forest Plot
create_ae_km_plot_for_soc(): Create AE KM Plot for a specific SOC
create_loglog_plot(): Create Log-Log Survival Plot
create_mean_plot(): Create Mean Plot with Confidence Intervals Over Time
create_spider_plot(): Create Spider Plot for Individual Trajectories
save_plot_as(): Save ClinicalPlot to file
save_as_png(): Save ClinicalTable as PNG Saves a ClinicalTable's flextable to a PNG file.

Formatting

Number and content formatting utilities for data presentation. Includes format specifications and composite formatters.

format_number(): Format Number with Locale
format_percentage(): Format Percentage
format_pvalue(): Format P-Value (IQWiG-Compliant)
format_ci(): Format Confidence Interval (IQWiG-Compliant)
format_content(): Format clinical content to different output formats
format_spec(): Create Format Specification
fmt_n_pct() fmt_mean_sd() fmt_median_range() fmt_ci(): Common Clinical Format Presets
parse_format_pattern(): Parse a format pattern
composite_format(): Composite Format Specification
apply_format(): Apply a format specification to values
apply_composite(): Apply a composite format

Reporting Engine

Word document generation and report output using officer/flextable.

quick_demographics_report(): Quick Demographics Report
quick_safety_report(): Quick Safety Report
generate_word(): Generate a Word document from a ClinicalReport
write_docx(): Write clinical content to a Word document
write_docx_ClinicalReport(): Write ClinicalReport to Word (S7 Method)
to_word(): Convert clinical content to Word format
add_table() add_plot() add_section() add_content(): Add a table to a StudyResult
add_to_docx(): Add content to a Word document
create_study_report(): Create Report from Study
create_analysis_meta(): Create Analysis Metadata
apply_clinical_style(): Apply Clinical Table Styling
summarize_content(): Generate a summary of clinical content

Table Conversion

Convert clinical results to flextable or gt table formats for flexible output rendering.

as_flextable(): Convert analysis results to flextable
as_flextable_AnalysisResults(): Convert AnalysisResults to flextable (S7 Method)
as_gt(): Convert analysis results to gt
as_gt_AnalysisResults(): Convert AnalysisResults to gt (S7 Method)
clinical_table_from_results(): Clinical table from analysis results
layered_to_flextable(): Convert LayeredTable to flextable

Layers System

Layered table construction system for building complex tables with multiple summary statistics.

CountLayer(): Count Layer Class
DescriptiveLayer(): Descriptive Layer Class
ShiftLayer(): Shift Layer Class
add_layer(): Add a layer to a LayeredTable
build_layer(): Build a single layer
build_table(): Build a LayeredTable

Subgroup Analysis

Functions for subgroup and interaction analyses in clinical trials.

apply_subgroups(): Apply Subgroup Analysis
calculate_subgroup_effect(): Calculate Subgroup Effect (HR or OR)
calculate_subgroup_effect_table(): Calculate Subgroup Effect for Table (HR or OR)
calculate_interaction_pvalue(): Calculate Interaction P-value
calculate_interaction_pvalue_table(): Calculate Interaction P-value for Table
calculate_response_comparison(): Calculate Response Comparison (OR, RR, or RD)
assess_iceman(): Assess Subgroup Credibility Using ICEMAN Criteria

PRO Analysis

Patient-Reported Outcomes analysis functions including minimal clinically important difference (MCID) and time-to-deterioration.

MCIDResult(): MCIDResult Class
calculate_mcid(): Calculate MCID (Combined Approach)
calculate_mcid_anchor(): Calculate MCID using Anchor-Based Method
calculate_mcid_distribution(): Calculate MCID using Distribution-Based Methods
create_ttd_analysis(): Create Time-to-Deterioration Analysis

Multiple Imputation

Functions for multiple imputation using mice package with Rubin’s rules for pooling results.

ImputationResult(): ImputationResult Class
perform_multiple_imputation(): Perform Multiple Imputation
pool_rubin(): Pool Results Using Rubin's Rules
analyze_with_imputation(): Analyze Data with Multiple Imputation
get_complete_data(): Get Completed Datasets from Imputation
summarize_missing(): Summarize Missing Data Patterns
imputation: Multiple Imputation Functions
create_imputation_report(): Create Imputation Diagnostic Report
plot_imputation_convergence(): Plot Imputation Convergence
plot_imputation_distributions(): Plot Imputation Distributions
plot_missing_pattern(): Plot Missing Data Pattern

Meta-Analysis

Functions for conducting meta-analyses including heterogeneity assessment, sensitivity analysis, and publication bias detection.

meta_analysis(): Perform Meta-Analysis
MetaResult(): MetaResult Class
calculate_heterogeneity(): Calculate Heterogeneity Statistics
leave_one_out(): Perform Leave-One-Out Sensitivity Analysis
create_meta_forest_plot(): Create Forest Plot for Meta-Analysis
create_funnel_plot(): Create Funnel Plot for Publication Bias Assessment
eggers_test(): Egger's Test for Funnel Plot Asymmetry
trim_and_fill(): Duval & Tweedie Trim-and-Fill Publication Bias Adjustment
bayesian_meta_analysis(): Bayesian Meta-Analysis
create_bayesian_forest_plot_iqwig(): Create IQWiG-Compliant Forest Plot for Bayesian Meta-Analysis
create_bayesian_trace_plots(): Create Trace Plots for Bayesian Meta-Analysis
format_bayesian_result_iqwig(): Format Bayesian Meta-Analysis Result for IQWiG Submission
prior_sensitivity_analysis(): Prior Sensitivity Analysis for Bayesian Meta-Analysis
bias_adjusted_meta(): Bias-Adjusted Meta-Analysis
rob_sensitivity_analysis(): Sensitivity Analysis Across Risk of Bias Scenarios
calculate_rob_weights(): Calculate Study Weights Based on Risk of Bias
summarize_bias_adjusted(): Summarize Bias-Adjusted Meta-Analysis Results
BayesianMetaFewResult(): BayesianMetaFewResult Class
bayesian_meta_analysis_few(): Bayesian Meta-Analysis for Few Studies
create_bayesian_few_table(): Create Bayesian Meta-Analysis Table for Few Studies
create_meta_analysis_priors(): Create Default Prior Set for Meta-Analysis
create_prior_specification(): Create Prior Specification
PriorSpecification(): PriorSpecification Class
validate_prior_parameters(): Validate Prior Parameters
get_default_prior(): Get Default Prior
create_prior_specification_set(): Create Prior Specification Set
summarize_prior_specification(): Summarize Prior Specification
summary_bayesian_few(): Summarize Bayesian Meta-Analysis for Few Studies
plot_bayesian_few(): Plot Bayesian Meta-Analysis Results for Few Studies
meta_bayesian_few: Bayesian Meta-Analysis for Few Studies
prior_specification: Prior Specification Interface

Competing Risks

Functions for competing risks analysis including cumulative incidence estimation and Gray’s test for comparing groups.

CompetingRiskResult(): CompetingRiskResult Class
competing_risks: Competing Risk Analysis
competing_risk_analysis(): Competing Risk Analysis
create_competing_risk_table(): Create Competing Risk Table
plot_cif(): Plot Cumulative Incidence Function

MMRM Analysis

Functions for Mixed-Effects Models for Repeated Measures (MMRM) analysis with robust variance estimation.

MMRMResult(): MMRMResult Class
RMSTResult(): RMSTResult Class
create_mmrm_table(): Create MMRM Table
summary_mmrm(): Extract MMRM Model Summary
mmrm: Mixed Model Repeated Measures (MMRM)
mmrm_analysis(): MMRM Analysis
rmst: Restricted Mean Survival Time (RMST)
rmst_analysis(): RMST Analysis
create_rmst_table(): Create RMST Table
plot_rmst(): Plot RMST Results

MCMC Diagnostics

Functions for diagnosing Markov Chain Monte Carlo (MCMC) convergence and assessing mixing quality.

assess_mcmc_convergence(): Assess MCMC Convergence
calculate_effective_sample_size(): Calculate Effective Sample Size
calculate_gelman_rubin(): Calculate Gelman-Rubin Diagnostic
create_mcmc_diagnostics_report(): Create MCMC Diagnostics Report
mcmc_diagnostics: MCMC Diagnostics
plot_mcmc_trace(): Plot MCMC Trace
plot_mcmc_density(): Plot MCMC Density

Network Meta-Analysis

Indirect treatment comparison and network meta-analysis functions for comparing multiple treatments across studies.

NMAResult(): NMAResult Class
indirect_comparison(): Indirect Treatment Comparison (Bucher Method)
compare_direct_indirect(): Compare Direct and Indirect Evidence
network_meta(): Conducts network meta-analysis (NMA) to compare multiple treatments simultaneously using direct and indirect evidence.
create_network_plot(): Visualize Network Geometry
assess_transitivity(): Assess Transitivity for Indirect Comparisons
node_splitting(): Separates direct and indirect evidence for each comparison and tests for inconsistency between them.
calculate_sucra(): Calculates ranking probabilities and SUCRA (Surface Under Cumulative Ranking curve) or P-scores for treatments in network meta-analysis.
create_league_table(): Generates a league table showing all pairwise treatment comparisons from a network meta-analysis.

Bias Assessment

Functions for assessing risk of bias in clinical studies using standardized tools (RoB 2 for RCTs, ROBINS-I for observational studies).

RoB2Result(): RoB2Result S7 Class
assess_rob2(): Assess Risk of Bias using RoB 2
assess_rob2_batch(): Assess Multiple Studies with RoB 2
rob2_summary(): Create Summary Table of RoB 2 Assessments
ROBINSIResult(): ROBINSIResult S7 Class
assess_robins_i(): Assess Risk of Bias using ROBINS-I
assess_robins_i_batch(): Assess Multiple Studies with ROBINS-I
robins_i_summary(): Create Summary Table of ROBINS-I Assessments
robins_i_plot(): Create ROBINS-I Summary Plot
robins_i_to_df(): Export ROBINS-I Assessment to Data Frame
create_rob_traffic_light_plot(): Create Traffic Light Plot for Risk of Bias
create_rob_summary_plot(): Create Summary Plot for Risk of Bias
save_rob_plot(): Save Risk of Bias Plot
rob_data_to_tidy(): Export Risk of Bias Data to Tidy Format

Evidence Grading

IQWiG evidence grading functions for assessing certainty of evidence using Beleg/Hinweis/Anhaltspunkt system.

grade_evidence(): Grade Evidence According to IQWiG Criteria
assess_evidence_domains(): Assess Individual IQWiG Evidence Domains
format_evidence_grade(): Format Evidence Grade for Display
evidence_summary_table(): Create Evidence Summary Table
create_evidence_summary_table(): Create Evidence Summary Table
create_study_characteristics_table(): Create Study Characteristics Table
export_evidence_table(): Export Evidence Table
create_rob_summary_table(): Create Risk of Bias Summary Table
evidence_narrative: Evidence Narrative Generation
generate_evidence_narrative(): Generate Evidence Narrative
generate_endpoint_narrative(): Generate Endpoint-Specific Narrative
generate_batch_narratives(): Generate Batch Narratives
generate_full_evidence_report(): Generate Full Evidence Report
export_narrative(): Export Narrative to Text File
narrative_template(): Narrative Template

GBA/AMNOG Utilities

Functions for German Health Technology Assessment (G-BA/AMNOG) including standardized mean difference (SMD) calculation, baseline balance assessment, and multiplicity adjustment.

BalanceAssessment(): BalanceAssessment S7 Class
assess_baseline_balance(): Assess Baseline Balance Between Treatment Groups
check_gba_compliance(): Check G-BA Compliance for Tables
add_smd_to_table(): Add SMD Column to Demographics/Baseline Table
create_love_plot(): Create Love Plot for SMD Visualization
calculate_smd(): Calculate Standardized Mean Difference for Continuous Variables
calculate_smd_binary(): Calculate Standardized Mean Difference for Binary Variables
calculate_smd_from_data(): Calculate SMD Directly from Data
adjust_pvalues(): Adjust P-values for Multiple Comparisons
calculate_nnt(): Calculate Number Needed to Treat (NNT) / Number Needed to Harm (NNH)
theme_gba(): G-BA Module 4 Theme for Flextable
theme_iqwig(): IQWiG Theme for Flextable
to_gba_template(): Convert Clinical Content to G-BA Template

Localization

Internationalization and localization functions for translating table headers and content.

set_locale(): Set the Current Locale
get_locale(): Get the Current Locale
tr(): Translate a Key to the Current Locale
tr_col(): Translate Column Names
get_translations(): Get All Translations for a Locale
add_translation(): Add Custom Translation
list_translation_keys(): List Available Translation Keys
reset_custom_translations(): Reset Custom Translations

Utilities

Helper functions for data filtering, treatment information, statistical diagnostics, and other common operations.

assert_non_negative(): Assert Non-Negative
get_filtered_data(): Get Filtered Data
get_subject_n(): Get Total Subject Count
get_subject_var(): Get Subject Variable Name
get_summary_label(): Get Summary Label
get_trt_n(): Get Treatment Group Counts
get_trt_var(): Get Treatment Variable Name
calculate_proportion_ci(): Calculate Proportion Confidence Interval
detect_floor_ceiling(): Detect Floor and Ceiling Effects
test_ph_assumption(): Test Proportional Hazards Assumption

Internal

Internal package documentation for architecture and modules.

S7_classes: S7 Classes for Clinical Study Reports
S7_generics: S7 Generics and Methods for Clinical Reports
S7_registration: S7 Method Registration and Package Initialization
adam_core: ADaM Analysis Core
formatting: Format String Grammar
layers: Layer System
reporting_engine: Reporting Engine
study_logic: Study Logic
efficacy_primary: Primary Endpoint Tables
efficacy_cfb: Change from Baseline Tables
efficacy_lab: Lab Summary Tables
efficacy_tte: Time-to-Event Tables
efficacy_responder: Responder Analysis Tables
efficacy_subgroup: Subgroup Analysis Tables
safety_summary: Adverse Event Summary Tables
safety_tte: Adverse Event Time-to-Event Analysis
safety_comparison: Adverse Event Comparison Tables
safety_exposure: Exposure-Adjusted AE Analysis
safety_hierarchy: Adverse Event Hierarchy Tables
standard_tables: Standard Clinical Tables
gba_utils: GBA/AMNOG Utilities for Health Technology Assessment
localization: Internationalization and Localization Support
plotting_common: Plotting Common Utilities
plotting_survival: Survival Analysis Plots
plotting_efficacy: Efficacy Visualization Plots
plotting_forest: Forest Plots for Subgroup Analysis
meta_core: Meta-Analysis Core Functions
meta_plots: Meta-Analysis Visualization Functions
meta_indirect: Indirect Comparison Functions
meta_network: Network Meta-Analysis Functions
meta_bayesian: Bayesian Meta-Analysis Functions
bias_rob2: Risk of Bias 2 (RoB 2) Assessment for RCTs
bias_robins_i: ROBINS-I (Risk Of Bias In Non-randomized Studies - of Interventions)
bias_plots: Risk of Bias Visualization Functions
meta_bias: Publication Bias Assessment Functions
meta_bias_adjusted: Bias-Adjusted Meta-Analysis Functions
pro_analysis: PRO Analysis Functions
evidence_grading: IQWiG Evidence Grading Implementation
evidence_summary_tables: Evidence Summary Tables
imputation: Multiple Imputation Functions
imputation_diagnostics: Imputation Diagnostic Plots