Utility functions are provided to create a standard clinical data review report. Please note that the examples in this section are only informative, and not evaluated in the vignette itself.
To create your clinical data review report, we advise to start from a skeleton of such report, via:
This report is based on an example dataset (subset of the CDISC Pilot 01 dataset), available in the clinUtils package.
The report is created via:
You can further tailor the report to your dataset(s) of interest and sections of interest.
See the next sections for further informations.
The input for the clinical data report consists of a set of Rmardown files and a config directory.
Rmd files
A set of Rmarkdown files in the working directory should be
index.Rmd file, containing the front page of the document.
This file should be formatted as a Rmarkdown report with YAML header, with output set to: clinDataReview::gitbook_clinDataReview_report
multiple Rmd files, one for each chapter (or template for multiple chapters). These files can be included in a R package.
Config files
There should be a config directory containing:
a general configuration file: config.yml with:
pathDataFolder: path to a directory containing input data in sas7bdat or xpt formatpatientProfilesPath(optional) : path to a directory that will contain patient profiles (if they are created with the patientProfilesTemplate.Rmd template report)study (optional): study nameversion (optional): data version, e.g. batchtemplate: filename of the Rmd file to consider for this chaptertemplatePackage: name of the R package where the Rmd should be extracted fromclinDataReview package, these include:
reportTitle: chapter title, used for section headerdataFileName: filename of the dataset of interest for this chapter, e.g.: ‘adae.sas7bdat’reportTitleLevel: integer with section level, e.g. 2params$Please see the ? clinDataReview-templates documentation for further information on the template reports available in the clinDataReview package, and their input parameters.
The clinical data report consists of a final report output and a set of intermediary results.
Final output
A final output folder (‘report’ by default) containing the:
extraDirs parameter)Intermediary results
A folder of intermediary results (‘interim’ by default) containing:
template/templatePackage combination of the config file(s))knit_meta object) and session information required for each report partA set of template reports are available in the clinDataReview package itself.
The full list of the reports and the corresponding input parameters is available at: ?clinDataReview-templates.
To use a template available in the package for one of your report, your config file should contain the corresponding name of the template via the template tag and the templatePackage set to ‘clinDataReview’.
For example, to include a division in the report, your YAML config file should be formatted as:
The function render_clinDataReviewReport renders a clinical data report for production.
The render_clinDataReviewReport creates several html files, one per section/subsection.
To open the full report, the user should open the introduction.html file.
In case a lot of different html chapters are created, a landing page can be created to guide the end-user to the opening of the report.
A convenient way to store all html files into one location, and have only one page to look for to open the report is the function
This function:
The default names of the folder and landing page are report_dependencies and report.html. The names can be changed by the user.
A dedicated functionality is available to zip the report and send it to colleagues within the team.
Once a report has been rendered, the user can call:
This function zips the report, so that the analyses can be easily put as attachement in a mail/uploaded to a shared drive.
If the folder is not unzipped before opening the reports, a message in the browser reminds to unzip the documents.
Metadata can be added in the landing page, containing information concerning the data set creation time, the path to the original data etc.
A metadata file should be in yaml format.
The metadata function can be directly called in a Rmd documents with
To facilitate the creation of the report, a few utility functions & dedicated parameters are available.
In case the creation of the entire report is time-consuming, and only part(s) of the report have been updated, it might be interesting to only re-run some parts of the report. Config files associated to the parts of the report that should be rerun can be specified via the configFiles parameter.
To convert all created Markdown files to HTML, the dedicated function convertMdToHtml can be used.
To debug a sub-report, it might be interesting to run only one specific R report in the current R session, with the parameters provided by the associated config file. This can be achieved as followed:
# get parameters from the general 'config.yml' and the specified config file
params <- getParamsFromConfig(configFile = "config-AE_timeprofile.yml")
# extract template from package if specified
if(params$templatePackage == "clinDataReview"){
pathTemplate <- clinDataReview::getPathTemplate(file = params$template)
file.copy(from = pathTemplate, to = ".")
}
# run a current chapter (without clinical data Js libraries)
# Note that Js library to have the functionality to download patient profiles is not imported
rmarkdown::render(input = params$template)
# preview a specific chapter (with clinical data Js libraries)
bookdown::render_book(input = params$template, preview = TRUE)
# include the index file:
bookdown::render_book(input = c("index.Rmd", params$template), preview = TRUE)R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=C, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: plyr(v.1.8.6), inTextSummaryTable(v.3.1.1), reshape2(v.1.4.4), plotly(v.4.10.0), ggplot2(v.3.3.5), clinUtils(v.0.1.1), clinDataReview(v.1.2.2), pander(v.0.6.4) and knitr(v.1.37)
loaded via a namespace (and not attached): ggrepel(v.0.9.1), Rcpp(v.1.0.8), tidyr(v.1.2.0), digest(v.0.6.29), utf8(v.1.2.2), R6(v.2.5.1), evaluate(v.0.15), httr(v.1.4.2), pillar(v.1.7.0), gdtools(v.0.2.4), rlang(v.1.0.1), lazyeval(v.0.2.2), uuid(v.1.0-3), data.table(v.1.14.2), DT(v.0.20), flextable(v.0.6.10), rmarkdown(v.2.11), labeling(v.0.4.2), stringr(v.1.4.0), htmlwidgets(v.1.5.4), munsell(v.0.5.0), compiler(v.4.1.2), xfun(v.0.29), pkgconfig(v.2.0.3), systemfonts(v.1.0.4), base64enc(v.0.1-3), htmltools(v.0.5.2), tidyselect(v.1.1.1), tibble(v.3.1.6), bookdown(v.0.24), jsonvalidate(v.1.3.2), fansi(v.1.0.2), viridisLite(v.0.4.0), crayon(v.1.5.0), dplyr(v.1.0.8), withr(v.2.4.3), grid(v.4.1.2), jsonlite(v.1.7.3), gtable(v.0.3.0), lifecycle(v.1.0.1), magrittr(v.2.0.2), scales(v.1.1.1), zip(v.2.2.0), cli(v.3.2.0), stringi(v.1.7.6), farver(v.2.1.0), xml2(v.1.3.3), ellipsis(v.0.3.2), generics(v.0.1.2), vctrs(v.0.3.8), cowplot(v.1.1.1), tools(v.4.1.2), forcats(v.0.5.1), glue(v.1.6.1), officer(v.0.4.1), purrr(v.0.3.4), hms(v.1.1.1), crosstalk(v.1.2.0), fastmap(v.1.1.0), yaml(v.2.3.5), colorspace(v.2.0-3) and haven(v.2.4.3)