R: Tidy Presentation of Clinical Reporting

# Tidy Presentation of Clinical Reporting

## Documentation for package ‘reportRmd’ version 0.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
boxcoxfitRx | fit box cox transformed linear model
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 labels
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
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
ctDNA | Tumour size change over time Longitudinal changes in tumour size since baseline for patients by changes in ctDNA status (clearance, decrease or increase) since baseline.
excelCol | Retrieve columns number from spreadsheet columns specified as unquoted letters
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 Document
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 (DEPRECATED)
geoR_boxcoxfit | Parameter Estimation for the Box-Cox Transformation
ggkmcif2 | Plot KM and CIF curves with ggplot
ggkmcif2Parameters | Additional parameters passed to ggkmcif2
ggkmcif2_2025 | Plot KM and CIF curves with ggplot
ggkmcif_paste | combine components of a call to ggkmci
hbld | Bold strings for HTML output
lpvalue2 | Format p-values for plot annotations
mvsum | Get multivariate summary dataframe
nestTable | Combine two table columns into a single column with levels of one nested within levels of the other.
outTable | Print tables to PDF/Latex HTML or Word
pembrolizumab | Survival data Survival status and ctDNA levels for patients receiving pembrolizumab
plotuv | Plot multiple bivariate relationships in a single plot
process_cif_medians | Process CIF Median Values
process_cif_timepoints | Process CIF Time-Specific Estimates
process_covariate | Process covariate variable (factor conversion, numeric cutoffs)
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 of differences
rm_survsum | Summarise survival data by group
rm_survtime | Display survival rates and events for specified times
rm_uvsum | Output several univariate models nicely in a single table
rm_uv_mv | Combine univariate and multivariable regression tables
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