Man pages for reportRmd
Tidy Presentation of Clinical Reporting
| add_censor_marks | Add censor marks to KM plot |
| add_cif_hazard_ratios | Add CIF Hazard Ratios to Strata Labels |
| add_confidence_bands | Add confidence bands to plot |
| add_km_hazard_ratios | Add hazard ratios to strata labels |
| add_median_lines | Add median survival lines to plot |
| add_median_text | Add median survival text to plot |
| add_set_time_lines | Add survival at set time lines to plot |
| add_set_time_text | Add survival at set time text to plot |
| add_statistical_tests | Add statistical test results to plot |
| apply_scales_and_guides | Apply colour and linetype scales |
| autoreg | Fit a regression model based on response type |
| boxcoxfitRx | fit box cox transformed linear model |
| break_function | Standard break function using pretty() |
| break_function_custom | Custom break function for axis scaling |
| build_arrow_segments | Build arrow segments for CIs extending beyond xlim |
| build_forest_ggplot | Build a forest plot from prepared data |
| build_log_scale | Build log scale for forest plot x-axis |
| build_secondary_axis | Build secondary axis specification |
| calculate_and_add_median_times | Calculate median survival times and add to labels |
| calculate_and_add_time_specific_estimates | Calculate survival/CIF at specific time points and add to... |
| calculate_cif_median | Calculate Median Time to Event for CIF |
| calculate_cif_timepoints | Calculate CIF Estimates at Specific Time Points |
| clear_labels | Clear variable labels from a data frame |
| coeffSum | Extract model coefficient summary |
| covnm | Match coefficient names to covariate names |
| covsum | Get covariate summary dataframe |
| create_base_plot | Create base ggplot for survival curves |
| create_cif_dataframe | Create CIF Plotting Data Frame |
| create_cif_risk_table_sfit | Create Survival Fit for Risk Table in CIF |
| create_km_dataframe | Create plotting dataframe for KM curves |
| create_risk_table | Create risk table for survival plot |
| crrRx | fit crr model |
| csep | Column separator for paste operations |
| ctDNA | Tumour size change over time Longitudinal changes in tumour... |
| deduplicate_refs | Remove duplicate reference level rows |
| delta_l | Lower bound of non-centrality parameter confidence interval |
| delta_u | Upper bound of non-centrality parameter confidence interval |
| excelCol | Retrieve columns number from spreadsheet columns specified as... |
| excelColLetters | Retrieve spreadsheet column letter-names from columns indices |
| extract_grays_test | Extract Gray's test results from CIF fit |
| extract_labels | Extract variable labels from labelled data frame |
| extract_package_details | Extract Function and Package Information from Current... |
| fillNAs | Forward fill NA values (vectorized implementation) |
| fit_cif_model | Fit Competing Risks Model |
| fit_km_model | Fit Kaplan-Meier survival curves |
| forestplot2 | Create a forest plot using ggplot2 (DEPRECATED) |
| forestplotMV | Create a multivariable forest plot using ggplot2 |
| forestplotUV | Create a univariable forest plot using ggplot2 |
| forestplotUVMV | Combine univariable and multivariable forest plot... |
| geoR_boxcoxfit | Parameter Estimation for the Box-Cox Transformation |
| get_beta_label | Get beta label for model type |
| get_cluster_ids | Extract cluster IDs from a fitted model |
| get_event_counts | Extract event counts from a fitted model |
| get_model_class | Get model class from model specifications |
| get_model_coef | Extract model coefficients |
| get_model_data | Extract data from a fitted model |
| ggkmcif | Create Kaplan-Meier or cumulative incidence plots |
| ggkmcif2 | Plot KM and CIF curves with ggplot |
| ggkmcif2_2025 | Plot KM and CIF curves with ggplot |
| ggkmcif2Parameters | Additional parameters passed to ggkmcif2 |
| ggkmcif2Parameters_2025 | Additional parameters passed to ggkmcif2 |
| ggkmcif_paste | combine components of a call to ggkmci |
| gp | Calculate global p-values for categorical variables |
| GVIF | Compute Generalized Variance Inflation Factor (GVIF) |
| hbld | Bold strings for HTML output |
| lpvalue2 | Format p-values for plot annotations |
| matchcovariate | Match coefficient names to covariate indices |
| matchdata | Extract data frame name from model call argument |
| modelmatrix | Create model matrix from formula |
| m_summary | Output a table for multivariate or univariate regression... |
| mterms | Extract model term names |
| mvsum | Get multivariate summary dataframe |
| nestTable | Combine two table columns into a single column with levels of... |
| nicecall | Format model call as clean string |
| order_forest_data | Order forest plot data by risk and factor levels |
| outTable | Print tables to PDF/Latex HTML or Word |
| pembrolizumab | Survival data Survival status and ctDNA levels for patients... |
| plotuv | Plot multiple bivariate relationships in a single plot |
| prepare_forest_data | Extract and prepare forest plot data from m_summary output |
| process_cif_medians | Process CIF Median Values |
| process_cif_timepoints | Process CIF Time-Specific Estimates |
| process_covariate | Process covariate variable (factor conversion, numeric... |
| psthr | Round and paste with parentheses (smart formatting) |
| pstprn | Paste vector elements with parentheses |
| removedollar | Remove dollar sign prefix from column names |
| replace_plot_labels | Replace variable names with labels in ggplot |
| rm_cifsum | Summarize cumulative incidence by group |
| rm_compactsum | Output a compact summary table |
| rm_covsum | Add header row to table Outputs a descriptive covariate table |
| rm_mvsum | Format a regression model nicely for 'Rmarkdown' |
| rm_survdiff | Display event counts, expected event counts and logrank test... |
| rm_survsum | Summarise survival data by group |
| rm_survtime | Display survival rates and events for specified times |
| rm_uv_mv | Combine univariate and multivariable regression tables |
| rm_uvsum | Output several univariate models nicely in a single table |
| round_sprintf | Round with sprintf formatting |
| scrolling_table | Output a scrollable table |
| set_labels | Set variable labels |
| set_var_labels | Set variable labels |
| validate_and_prepare_data | Validate and prepare input data |
| xvar_function | Create a summary table for an individual covariate |
