Package: reportRmd 0.1.4

Lisa Avery

reportRmd: Tidy Presentation of Clinical Reporting

Streamlined statistical reporting in 'Rmarkdown' environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.

Authors:Lisa Avery [cre, aut], Ryan Del Bel [aut], Osvaldo Espin-Garcia [aut], Katherine Lajkosz [aut], Clarina Ong [aut], Tyler Pittman [aut], Anna Santiago [aut], Yanning Wang [ctr], Jessica Weiss [aut], Wei Xu [aut]

reportRmd_0.1.4.tar.gz
reportRmd_0.1.4.zip(r-4.7-any)reportRmd_0.1.4.zip(r-4.6-any)reportRmd_0.1.4.zip(r-4.5-any)
reportRmd_0.1.4.tgz(r-4.6-any)reportRmd_0.1.4.tgz(r-4.5-any)
reportRmd_0.1.4.tar.gz(r-4.7-any)reportRmd_0.1.4.tar.gz(r-4.6-any)
reportRmd_0.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
reportRmd/json (API)

# Install 'reportRmd' in R:

install.packages('reportRmd', repos = c('https://biostatspmh.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biostatspmh/reportrmd/issues

Pkgdown/docs site:https://biostatspmh.github.io

Datasets:

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.
pembrolizumab - Survival data Survival status and ctDNA levels for patients receiving pembrolizumab

On CRAN:

7.21 score 6 stars 1 packages 35 scripts 399 downloads 41 exports 106 dependencies

Last updated from:b3cffd452e. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	357
source / vignettes	OK	565
linux-release	NOTE	382
macos-release	NOTE	276
macos-oldrel	NOTE	285
windows-devel	NOTE	185
windows-release	NOTE	223
windows-oldrel	NOTE	227
wasm-release	OK	187

Exports:autoreg clear_labels coeffSum crrRx delta_l delta_u excelCol excelColLetters extract_labels extract_package_details forestplot2 forestplotMV forestplotUV forestplotUVMV get_cluster_ids get_event_counts get_model_coef get_model_data ggkmcif ggkmcif2 ggkmcif2Parameters gp mterms nestTable outTable plotuv predsum replace_plot_labels rm_cifsum rm_compactsum rm_covsum rm_mvsum rm_survdiff rm_survsum rm_survtime rm_uv_mv rm_uvsum scrolling_table set_labels set_var_labels xvar_function

Dependencies:abind aod backports base64enc boot broom bslib cachem car carData cli cmprsk colorspace corrplot cowplot cpp11 Deriv digest doBy dplyr evaluate farver fastmap fontawesome forecast Formula fracdiff fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr htmltools isoband jquerylib jsonlite kableExtra knitr labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels memoise mgcv mime minqa modelr nlme nloptr nnet numDeriv pander pbkrtest pillar pkgconfig polynom purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown rstatix rstudioapi S7 sass scales SparseM stringi stringr survival svglite systemfonts textshaping tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun xml2 yaml zoo

reportRmd Package

Rendered fromreportRmd.Rmdusingknitr::rmarkdown

Last update: 2026-10-26
Started: 2022-07-13

Help page	Topics
Add censor marks to KM plot	add_censor_marks
Add CIF Hazard Ratios to Strata Labels	add_cif_hazard_ratios
Add confidence bands to plot	add_confidence_bands
Add hazard ratios to strata labels	add_km_hazard_ratios
Add median survival lines to plot	add_median_lines
Add median survival text to plot	add_median_text
Add survival at set time lines to plot	add_set_time_lines
Add survival at set time text to plot	add_set_time_text
Add statistical test results to plot	add_statistical_tests
Apply colour and linetype scales	apply_scales_and_guides
fit box cox transformed linear model	boxcoxfitRx
Calculate median survival times and add to labels	calculate_and_add_median_times
Calculate survival/CIF at specific time points and add to labels	calculate_and_add_time_specific_estimates
Calculate Median Time to Event for CIF	calculate_cif_median
Calculate CIF Estimates at Specific Time Points	calculate_cif_timepoints
Clear variable labels from a data frame	clear_labels
Get covariate summary dataframe	covsum
Create base ggplot for survival curves	create_base_plot
Create CIF Plotting Data Frame	create_cif_dataframe
Create Survival Fit for Risk Table in CIF	create_cif_risk_table_sfit
Create plotting dataframe for KM curves	create_km_dataframe
Create risk table for survival plot	create_risk_table
fit crr model	crrRx
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.	ctDNA
Retrieve columns number from spreadsheet columns specified as unquoted letters	excelCol
Retrieve spreadsheet column letter-names from columns indices	excelColLetters
Extract Gray's test results from CIF fit	extract_grays_test
Extract variable labels from labelled data frame	extract_labels
Extract Function and Package Information from Current Document	extract_package_details
Fit Competing Risks Model	fit_cif_model
Fit Kaplan-Meier survival curves	fit_km_model
Create a forest plot using ggplot2 (DEPRECATED)	forestplot2
Create a multivariable forest plot using ggplot2	forestplotMV
Create a univariable forest plot using ggplot2	forestplotUV
Combine univariable and multivariable forest plot (DEPRECATED)	forestplotUVMV
Parameter Estimation for the Box-Cox Transformation	geoR_boxcoxfit
combine components of a call to ggkmci	ggkmcif_paste
Plot KM and CIF curves with ggplot	ggkmcif2
Additional parameters passed to ggkmcif2	ggkmcif2Parameters
Bold strings for HTML output	hbld
Format p-values for plot annotations	lpvalue2
Get multivariate summary dataframe	mvsum
Combine two table columns into a single column with levels of one nested within levels of the other.	nestTable
Print tables to PDF/Latex HTML or Word	outTable
Survival data Survival status and ctDNA levels for patients receiving pembrolizumab	pembrolizumab
Plot multiple bivariate relationships in a single plot	plotuv
Summarise Performance of a Prediction Model	predsum
Process CIF Median Values	process_cif_medians
Process CIF Time-Specific Estimates	process_cif_timepoints
Process covariate variable (factor conversion, numeric cutoffs)	process_covariate
Replace variable names with labels in ggplot	replace_plot_labels
Summarize cumulative incidence by group	rm_cifsum
Output a compact summary table	rm_compactsum
Add header row to table Outputs a descriptive covariate table	rm_covsum
Format a regression model nicely for 'Rmarkdown'	rm_mvsum
Display event counts, expected event counts and logrank test of differences	rm_survdiff
Summarise survival data by group	rm_survsum
Display survival rates and events for specified times	rm_survtime
Combine univariate and multivariable regression tables	rm_uv_mv
Output several univariate models nicely in a single table	rm_uvsum
Output a scrollable table	scrolling_table
Set variable labels	set_labels
Set variable labels	set_var_labels
Validate and prepare input data	validate_and_prepare_data

Package: reportRmd 0.1.4

reportRmd: Tidy Presentation of Clinical Reporting

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