clinDataReview-templates {clinDataReview}

Rmarkdown templates for clinical data

Description

Template reports with standard visualizations/tables available in the package are described here.

Details

For each template, required parameters are indicated in bold.

Value

No return value, used for the documentation of the Rmarkdown template reports contained in the package.

Parameter type

Please note that the type mentioned below corresponds to the type in the config file (in YAML/JSON format).
The mapping to R data type is as followed:

• string: character vector of length 1

• integer: integer vector of length 1

• array: vector/list without names

• object: list with names

Clinical data template for a visualization of count data : countsVisualizationTemplate

This report compute counts of variable(s) of interest (with the inTextSummaryTable package) and visualize them with a treemap and/or sunburst.
The following parameters are available:

• template: string set to: 'countsVisualizationTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• dataFileName: string or array, name of the data file(s) of interest. If multiple files are specified, the data are combined by rows ('row bind'), with a column: 'DATASET' containing the name of the file (in upper case and without extension) the data originate from.

• dataProcessing: (optional) array, data processing parameters, passed to processData

• dataTotalFileName: (optional) string, filename of the total dataset

• dataTotalProcessing: (optional) array, data processing parameters for 'dataTotalFileName', passed to processData

• countVar: string, variable of data to count on

• parentVar: (optional) string or array, parent variable(s) of the counting variable, used for grouping

• colorVar: (optional) string or object, numeric variable(s) to consider for coloring, named by count/parent variable if different for each variable

• colorRange: (optional) array of number(s) of length: minimum 2, maximum 2, range of the color variable for the visualization

• loopingVar: (optional) array or string, data variable(s) to loop over. Each group of the variable(s) is displayed in a separated section of the report.

• loopingNMax: (optional) integer, maximum number of elements of loopingVar to include in the report

• loopingTotal: (optional) boolean, should the total also be computed by loopingVar (TRUE by default)?

• typePlot: (optional) array or string of string(s) among: 'sunburst', 'treemap'

• startup: (optional) array or string, R commands that should be run at the start of the report

Clinical data template to create a report division : divisionTemplate

This report includes a division, i.e. extra chapter, section of subsection in the report.
The following parameters are available:

• template: string set to: 'divisionTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• content: (optional) string, any content that should be included after the title

Clinical data template to create a listing : listingTemplate

This report displays a listing of the variables and data of interest, displayed in an interactive table. This table can contains comparison with a previous batch ('comparisonTable' parameters).
The following parameters are available:

• template: string set to: 'listingTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• dataFileName: string or array, name of the data file(s) of interest. If multiple files are specified, the data are combined by rows ('row bind'), with a column: 'DATASET' containing the name of the file (in upper case and without extension) the data originate from.

• dataProcessing: (optional) array, data processing parameters, passed to processData

• dataTotalFileName: (optional) string, filename of the total dataset

• dataTotalProcessing: (optional) array, data processing parameters for 'dataTotalFileName', passed to processData

• tableParams: (optional) object, parameters to create the table, passed to tableClinData

• comparisonTableType: (optional) string among: 'none', 'newData-diff-interactive', 'table-comparison-interactive' , output type of the comparison table

• comparisonTableParams: (optional) object, parameters for the comparison table, passed to compareTables

• loopingVar: (optional) array or string, data variable(s) to loop over. Each group of the variable(s) is displayed in a separated section of the report.

• loopingNMax: (optional) integer, maximum number of elements of loopingVar to include in the report

• listingDocx: (optional) boolean, export listing to Word

Clinical data template for the creation of patient profiles : patientProfilesTemplate

This report creates the specified patient profiles (with the patientProfilesVis package) by subject, and export them to a specified directory.
The following parameters are available:

• template: string set to: 'patientProfilesTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• createPatientProfiles: (optional) boolean, Should the patient profiles be created or only loaded from a previous execution?

• patientProfilesGeneralParams: (optional) object, set of parameters used for all patient profiles modules. These parameters are passed to all subjectProfile[]Plot functions.

• patientProfilesParams: array of object(s)
  The following parameters are available:

  • typePlot: string among: 'text', 'line', 'interval', 'event' , plot type, used to get the appropriate plot module function:

    • 'text': subjectProfileTextPlot

    • 'line': subjectProfileLinePlot

    • 'interval': subjectProfileIntervalPlot

    • 'event': subjectProfileEventPlot

  • dataFileName: string, name of the data file of interest

  • dataProcessing: (optional) array, data processing parameters, passed to processData

  • plotParams: object, parameters for the plotting function. Parameters depending on the dataset of interest can be specified as:
    [parameterName]: !r-lazy [dataI]

  , parameters for each patient profile module

• patientProfilesCreateReportParams: (optional) object, parameters for the creation of the patient profile report(s), passed to createSubjectProfileReport

• tableParams: (optional) object, parameters specifying a table containing data of interest and links to created patient profiles

• startup: (optional) array or string, R commands that should be run at the start of the report

Clinical data generic template for visualization : plotTemplate

This report visualizes input data with a function of the clinical data review package. The data can be compared to the data of a previous batch, in the table associated to the plot ('comparisonTable' parameters).Summary statistics can be computed optionally and included in the plot (see 'tableParams' parameter).
The following parameters are available:

• template: string set to: 'plotTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• dataFileName: string or array, name of the data file(s) of interest. If multiple files are specified, the data are combined by rows ('row bind'), with a column: 'DATASET' containing the name of the file (in upper case and without extension) the data originate from.

• dataProcessing: (optional) array, data processing parameters, passed to processData

• plotFunction: string among: 'timeProfileIntervalPlot', 'scatterplotClinData', 'boxplotClinData' , plotting function of the package to consider

• plotParams: object, parameters for the plotting function. Parameters depending on the dataset of interest can be specified as:
  [parameterName]: !r-lazy [dataI]

• tableParams: (optional) object, parameters for a summary table, passed to computeSummaryStatisticsTable
  Summary statistics are computed and merged as extra columns available for the plot data.

• tableProcessing: (optional) array, data processing parameters for the summary table, passed to processData

• comparisonTableType: (optional) string among: 'none', 'newData-diff' , output type of the comparison table. If specified, an additional column: 'Comparison Type' is included in the table attached to the plot.

• comparisonTableParams: (optional) object, parameters for the comparison table, passed to compareTables. If referenceVars is not specified, all variables displayed in the plot are used.

• loopingVar: (optional) array or string, data variable(s) to loop over. Each group of the variable(s) is displayed in a separated section of the report.

• loopingNMax: (optional) integer, maximum number of elements of loopingVar to include in the report

• startup: (optional) array or string, R commands that should be run at the start of the report

Clinical data template for visualization of summarized data : summaryPlotTemplate

This report summarizes the data of interest (with the inTextSummaryTable package) and visualize it with any clinical data review plot function.
The following parameters are available:

• template: string set to: 'summaryPlotTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• dataFileName: string or array, name of the data file(s) of interest. If multiple files are specified, the data are combined by rows ('row bind'), with a column: 'DATASET' containing the name of the file (in upper case and without extension) the data originate from.

• dataProcessing: (optional) array, data processing parameters, passed to processData

• dataTotalFileName: (optional) string, filename of the total dataset

• dataTotalProcessing: (optional) array, data processing parameters for 'dataTotalFileName', passed to processData

• tableParams: object, parameters to summarize the data in a table, passed to computeSummaryStatisticsTable

• tableProcessing: (optional) array, data processing parameters for the summary table, passed to processData

• plotFunction: string among: 'timeProfileIntervalPlot', 'scatterplotClinData', 'sunburstClinData', 'treemapClinData', 'barplotClinData', 'errorbarClinData' , plotting function to visualize summary data

• plotParams: object, parameters for the plotting function

• loopingVar: (optional) array or string, data variable(s) to loop over. Each group of the variable(s) is displayed in a separated section of the report.

• loopingNMax: (optional) integer, maximum number of elements of loopingVar to include in the report

• loopingTotal: (optional) boolean, should the total also be computed by loopingVar (TRUE by default)?

• startup: (optional) array or string, R commands that should be run at the start of the report

Clinical data template for a summary table of the data : summaryTableTemplate

This report summarizes the data of interest (with the inTextSummaryTable package). This table is displayed with an interactive table in the report, and exported to a docx file. This table can be compared to a summary table of a previous batch ('comparisonTable' parameters).
The following parameters are available:

• template: string set to: 'summaryTableTemplate.Rmd', name of the template report

• templatePackage: string set to: 'clinDataReview', package from which the template should be extracted

• reportTitle: string, header title

• reportTitleLevel: (optional) integer, header level, 1 by default (1: 'chapter', '2': 'section', '3': subsection, ...)

• parallel: (optional) boolean, does this chapter use parallel execution? If the entire report is run in parallel, this ensures that this specific chapter is created outside of the report parallelization.

• split_by: (optional) integer of length: minimum 0, maximum 7 or string among: 'none', 'chapter', 'section' , split the chapter at the specified level: 1 (for 'chapter'), 2 (for 'section') until 7. This overwrites the 'split_by' parameter defined in the output format of the report.

• dataFileName: string or array, name of the data file(s) of interest. If multiple files are specified, the data are combined by rows ('row bind'), with a column: 'DATASET' containing the name of the file (in upper case and without extension) the data originate from.

• dataProcessing: (optional) array, data processing parameters, passed to processData

• dataTotalFileName: (optional) string, filename of the total dataset

• dataTotalProcessing: (optional) array, data processing parameters for 'dataTotalFileName', passed to processData

• tableParams: object, parameters to summarize the data in a table, passed to computeSummaryStatisticsTable .Parameters depending on the dataset of interest can be specified as:
  [parameterName]: !r-lazy [dataI].

• tableParamsDocx: (optional) object, parameters to format the table to the docx format, passed to exportSummaryStatisticsTable

• tableParamsDT: (optional) object, parameters to format the table to the DT interactive table included in the report, passed to exportSummaryStatisticsTable

• comparisonTableType: (optional) string among: 'none', 'table-comparison-interactive', 'newData-diff', 'table-combine' , output type of the comparison table:

  • 'table-comparison-interactive': the summary statistics are computed for the old and new batch separately, and the statistics are compared

  • 'newData-diff': the differences at a record level between the new and old batch are first identified, and then summarized

  • 'table-combine': the summary tables are computed for the old and new batch and displayed next to each other in a combined table

• comparisonTableParams: (optional) object, parameters for the comparison table, passed to compareTables. By default, statistics variables are compared across row and column elements.

• loopingVar: (optional) array or string, data variable(s) to loop over. Each group of the variable(s) is displayed in a separated section of the report.

• loopingNMax: (optional) integer, maximum number of elements of loopingVar to include in the report

• loopingTotal: (optional) boolean, should the total also be computed by loopingVar (TRUE by default)?